TEST BANK for Lehninger Principles of Biochemistry 8th Edition. by David L. Nelson & Michael M. Cox. by digitaldownload87

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Chap 01_8e Indicate the answer choice that best completes the statement or answers the question. 1. Hereditary information (with the exception of some viruses) is preserved in: a. deoxyribonucleic acid. b. membrane structures. c. nuclei. d. polysaccharides. e. ribonucleic acid. 2. Accurate folding of a protein does NOT depend on: a. proper pH. b. correct ionic strength. c. correct temperature. d. correct metal ion concentration. e. binding to DNA. 3. What is the correct name for the configuration of the molecule shown?

a. orthogonal b. trans c. cis d. zis e. chiros 4. Which statement is NOT true about the formation of early organisms? a. The first organisms were anaerobic because the atmosphere was devoid of oxygen. b. The original electron donor for photosynthetic processes was probably H2S. c. Oxygen, a powerful oxidant, was probably welcomed by anaerobic organisms as a preferable choice for metabolic reactions. d. The transfer of electrons to O2 releases more energy than transferring electrons to SO42–. e. Cyanobacteria are modern descendants of early photosynthetic oxygen-producers.

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Chap 01_8e 5. Enzymes are biological catalysts that enhance the rate of a reaction by: a. decreasing the activation energy. b. decreasing the amount of free energy released. c. increasing the activation energy. d. increasing the amount of free energy released. e. increasing the energy of the transition state. 6. Which ranking correctly describes the rigidity of the red bond (the central bond) shown in the figure?

a. 2 = most rigid, 3 = least rigid b. 1 = most rigid, 5 = least rigid c. 4 = most rigid, 3 = least rigid d. 2 = most rigid, 1 = least rigid e. 4 = most rigid, 1 = least rigid 7. When Stanley Miller, in Harold Urey's laboratory, subjected a gaseous mixture mimicking the prebiotic atmosphere on Earth to electrical sparks, he found that _____ were formed. a. amino acids b. aldehydes c. ribonucleotides d. both amino acids and aldehydes e. amino acids, aldehydes, and ribonucleotides

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Chap 01_8e 8. In the theory for the origin of life that was tested by Miller and Urey, the prebiotic atmosphere was presumed to: a. already contain some primitive RNA molecules. b. basically be very similar to the atmosphere of today. c. contain many amino acids. d. have an abundance of methane, ammonia, hydrogen, and water. e. be rich in oxygen. 9. An increase in the entropy of a system can be described as an increase in the total amount of _____ of a system. a. kinetic energy b. potential energy c. oxidative energy d. disorder e. heat energy 10. Which statement about living systems is NOT true? a. Living organisms can be described as an open system. b. Living organisms maintain a more or less constant composition at maturity. c. Living systems are in equilibrium with their surroundings. d. Living systems exist in a dynamic steady state. e. Living systems have efficient mechanisms to convert chemical energy from one form into another. 11. The _____ of homologous proteins or genes can be used to estimate the degree of evolutionary relatedness. a. three-dimensional structure b. expression profiles c. sequence similarity d. endosymbiotic nature e. chromosomes 12. The typical three-dimensional structure of a protein in a cell, or _____ conformation, is critical to a protein's function. a. native b. molecular c. chaperone d. macromolecular e. high-affinity

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Chap 01_8e 13. The sum of all the proteins functioning in a cell is the: a. metabolome. b. proteasome. c. lysosome. d. proteome. e. genome. 14. Which discipline uses an approach that tries to understand complex interactions among intermediates and pathways in quantitative terms? a. metabolomics b. genomics c. systems biology d. proteomics e. lipidomics 15. The enzyme fumarase catalyzes the reversible hydration of fumaric acid to L-malate, but it will not catalyze the hydration of maleic acid, which is the cis isomer of fumaric acid. This is an example of: a. biological activity. b. chiral activity. c. racemization. d. stereoisomerization. e. stereospecificity. 16. If a scientist wanted to know whether a particular hydrocarbon was in use in a cell's plasma membrane, they could search the organism's: a. metabolome. b. lipidome. c. glycome. d. proteome. e. genome. 17. If an organism is a facultative anaerobe, which statement is true? a. The organism requires sulfur to live. b. The organism will die if exposed to oxygen. c. The organism requires oxygen to live. d. The organism does not require oxygen to live but will not die if exposed to oxygen. e. The organism requires methane to live.

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Chap 01_8e 18. Which is NOT found in both animal and plant cells? a. ribosome b. Golgi complex c. endoplasmic reticulum d. vacuole e. mitochondrion 19. Which statement is true about genetic mutations? a. Mutations may arise from an unrepaired mistake in DNA replication. b. Mutations may arise from incorrectly repaired damage to one of the DNA strands. c. Mutations in reproductive cells can be passed to offspring. d. Mutations may better equip an organism or cell to survive in its environment. e. All of the statements are true. 20. Which list has the cellular components arranged in order of increasing size? a. nucleotide < DNA < nucleus < chromatin b. nucleotide < DNA < chromatin < nucleus c. nucleotide < chromatin < DNA < nucleus d. DNA < nucleotide < nucleus < chromatin e. DNA < chromatin < nucleus < nucleotide 21. Which element is NOT among the four most abundant in living organisms? a. carbon b. hydrogen c. nitrogen d. oxygen e. phosphorus 22. Which is NOT a property of living organisms? a. precise self-replication b. in a dynamic steady state with the environment c. evolution over time d. composed of cells e. conversion of energy into matter

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Chap 01_8e 23. Which is the major feature that distinguishes eukaryotes from Bacteria and Archaea? a. DNA b. photosynthetic capability c. plasma membranes d. ribosomes e. the nucleus 24. Reaction 1 has a ΔG° of –12.3 kJ/mol, and reaction 2 has a ΔG° of –23.4 kJ/mol. Which statement is true of these two reactions? a. Reaction 1 occurs faster. b. Reaction 2 occurs faster. c. Both reactions occur at the same rate. d. Reaction 2 will not occur. e. It is impossible to know which reaction occurs faster with this information. 25. Which organelle probably originated as an endosymbiotic engulfing of an aerobic bacterium by a eukaryotic cell? a. ribosome b. mitochondrion c. Golgi body d. nucleus e. endoplasmic reticulum 26. In a bacterial cell, the DNA is in the: a. cell envelope. b. cell membrane. c. nucleoid. d. nucleus. e. ribosomes. 27. _____ pathways _____ large molecules, _____ energy. a. Catabolic; break down; releasing b. Anabolic; break down; releasing c. Catabolic; break down; storing d. Anabolic; break down; storing e. Anabolic; build up; releasing

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Chap 01_8e 28. Which statement correctly describes the molecules shown?

a. A and D are enantiomers, and B and C are enantiomers. b. A and D are diastereomers, and B and C are enantiomers. c. A and C are enantiomers, and B and D are diastereomers. d. A and C are diastereomers, and B and D are enantiomers. e. All are diastereomers to each other. 29. Which method is the MOST versatile for separating subcellular components of tissue into fractions containing things ranging from large (e.g., whole cells) to small (e.g., ribosomes)? a. centrifugation b. precipitation c. chromatography d. restriction digest e. peroxidation 30. When two genes share detectable sequence similarity, those genes or their gene products, are said to be: a. homologs. b. symbiologs. c. complimentary sequences. d. co-genes. e. housekeeping genes. 31. Which statement is NOT true regarding the plasma membrane? a. It is a physical barrier separating the inside of the cell from its surroundings. b. It is flexible, with a hydrophobic internal structure. c. The individual lipids and proteins of the plasma membrane are covalently linked. d. The plasma membrane incorporates newly made lipid and protein components as a cell grows. e. Cell division occurs without loss of the membrane integrity. Copyright Macmillan Learning. Powered by Cognero.

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Chap 01_8e 32. Which factor can be changed without breaking covalent bonds? a. conformation b. configuration c. chirality d. stereochemistry e. None of the answers is correct. 33. Stereoisomers that are nonsuperimposable mirror images of each other are known as: a. anomers. b. cis-trans isomers. c. diastereoisomers. d. enantiomers. e. geometric isomers. 34. Which statement is true when Keq >> 1? a. ΔG° is large and negative b. ΔG° is large and positive c. ΔG° is small and negative d. ΔG° is small and positive e. the value of ΔG° is independent of Keq 35. Which is true about a racemic mixture? a. The components are not separable by any means. b. It has no optical rotation. c. It is a mixture of diastereomers. d. It contains both polar and nonpolar substances. e. It can be separated into its components by differential centrifugation. 36. Which group of single-celled microorganisms has many members found growing in extreme environments? a. bacteria b. archaea c. eukaryotes d. heterotrophs e. None of the answers is correct.

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Chap 01_8e 37. The joining of two amino acids via a peptide bond (the process of protein synthesis) has a positive ΔG value. What does this imply? a. Forming a peptide bond is endergonic and must be coupled to another reaction. b. Forming a peptide bond is exergonic and must be coupled to another reaction. c. Forming a peptide bond is spontaneous and does not need to be coupled to another reaction. d. Forming a peptide bond is spontaneous and can sometimes be coupled to another reaction. e. Forming a peptide bond increases the entropy of a system. 38. Which reason is MOST probable for why carbon is the main element used in living organisms? a. Carbon has the simplest isotopic distribution, with no radioactive isotopes. b. Carbon's bonds to other elements are easily formed and broken. c. Carbon has the most valence electrons for its size. d. Carbon has a great capacity to make substances of widely different sizes, shapes, and composition. e. Carbon forms primarily aliphatic compounds. 39. Organisms that derive energy from the oxidation of chemical fuels and require organic compounds as sources of carbon are classified as: a. chemoautotrophs. b. chemoheterotrophs. c. lithotrophs. d. photoautotrophs. e. photoheterotrophs. 40. Which choice correctly lists the molecular masses from smallest to largest? a. 18 kDa < 15,000 Da < 15,100 amu < 1.8 MDa < 1.8 mDa b. 1.8 mDa < 15,000 Da < 15,100 amu < 18 kDa < 1.8 MDa c. 1.8 MDa < 15,000 Da < 15,100 amu < 18 kDa < 1.8 mDa d. 1.8 mDa < 15,100 amu < 15,000 Da < 18 kDa < 1.8 MDa e. 1.8 MDa < 18 kDa < 15,100 amu < 1.8 mDa < 15,000 Da

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Chap 01_8e 41. What functional groups are present on this molecule?

a. ether and aldehyde b. hydroxyl and aldehyde c. hydroxyl and carboxylic acid d. hydroxyl and ester e. hydroxyl and ketone 42. The macromolecules that serve in the storage and transmission of genetic information are: a. carbohydrates. b. lipids. c. membranes. d. nucleic acids. e. proteins. 43. Which statement is true regarding energy sources used by organisms? a. Phototrophs can use carbon dioxide as a carbon source. b. Phototrophs can use carbon dioxide as an energy source. c. All phototrophs are autotrophs. d. All chemotrophs are heterotrophs. e. All phototrophs are autotrophs that can use carbon dioxide as a carbon source. 44. In double-stranded DNA, the two polynucleotide strands are held together by _____ bonds. a. covalent b. ionic c. polypeptide d. hydrogen e. phosphodiester

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Chap 01_8e 45. In supramolecular complexes, macromolecules are held primarily through noncovalent interactions. Which one is NOT considered a noncovalent interaction? a. carbon–carbon bonds b. hydrogen bonds c. hydrophobic interactions d. ionic interactions e. van der Waals interactions 46. When energy is used by a system, can it be "used up"? a. Yes, it is used up when the energy source is depleted. b. Yes, it is used up when all energy is converted into chemical energy. c. No, all energy is converted into potential energy. d. No, all energy is converted into kinetic energy. e. No, energy can be converted into kinetic and potential energy. 47. The four covalent bonds in methane (CH4) are arranged around carbon to give which geometry? a. linear b. tetrahedral c. trigonal bipyramidal d. trigonal planar e. trigonal pyramidal 48. Which does NOT contain a double membrane? a. mitochondrion b. ribosome c. chloroplast d. endoplasmic reticulum e. Golgi body 49. Which present-day observable piece of evidence supports the RNA world hypothesis? a. RNA molecules participate in biologically significant reactions. b. RNA can serve as an information-carrying molecule. c. RNA nucleotides catalyze peptide bond formation. d. RNA molecules participate in biologically significant reactions, and RNA nucleotides catalyze peptide bond formation. e. RNA molecules participate in biologically significant reactions, RNA can serve as an informationcarrying molecule, and RNA nucleotides catalyze peptide bond formation.

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Chap 01_8e 50. In eukaryotes, the nucleus is enclosed by a double membrane called the: a. cell membrane. b. nuclear envelope. c. nucleolus. d. nucleoplasm. e. nucleosome. 51. Jacques Monod wrote, "What is true of E. coli is true of the elephant." What did he mean? a. Bacterial cells are identical to animal cells. b. Bacterial cells can synthesize ivory under certain conditions. c. Bacterial cells have protein repair mechanisms similar to animal cells. d. Bacterial cells contain enzymes similar to those found in animal cells. e. Bacterial cells contain molecules with complexity similar to molecules found in the "mineral world." 52. The similarities of gene sequences and metabolic pathways across the three domains of life are evidence that: a. all modern organisms are derived from a common evolutionary progenitor. b. multiple evolutionary progenitors converged to a single evolutionary model. c. cross-species genetic transfer happens with ease. d. evolution ceases when an organism is successful in its niche. e. All of the above. 53. Which answer choice represents the largest percentage, by weight, of an E. coli cell? a. RNA b. DNA c. protein d. lipids e. water 54. Which is a list of organelles? a. mitochondria, chromatin, endoplasmic reticulum b. peroxisomes, lysosomes, plasma membrane c. proteasomes, peroxisomes, lysosomes d. mitochondria, endoplasmic reticulum, peroxisomes e. All of the answers are correct.

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Chap 01_8e 55. If the free-energy change ΔG for a reaction is –46.11 kJ/mol, the reaction is: a. at equilibrium. b. endergonic. c. endothermic. d. exergonic. e. exothermic. 56. Fructose-1-phosphate can be hydrolyzed into fructose and inorganic phosphate (Pi) with a ΔG° of –16.0 kJ/mol. If ATP can be hydrolyzed into ADP and Pi with a ΔG° of –30.5 kJ/mol, what is the free-energy change for the reaction shown? fructose + ATP → fructose-1-phosphate + ADP a. –46.5 kJ/mol b. –14.5 kJ/mol c. 46.5 kJ/mol d. 14.5 kJ/mol e. –1.45 kJ/mol 57. Energy-requiring metabolic pathways that yield complex molecules from simpler precursors are: a. amphibolic. b. anabolic. c. autotrophic. d. catabolic. e. heterotrophic. 58. _____ are typically expressed under all conditions and are not subject to regulation. a. Housekeeping genes b. Homologous genes c. Bacterial genomes d. Eukaryotic genomes e. Endosymbiotic genes 59. The three-dimensional structure of a protein is determined primarily by: a. electrostatic guidance from nucleic acid structure. b. how many amino acids are in the protein. c. hydrophobic interaction with lipids that provide a folding framework. d. modification during interactions with ribosomes. e. the sequence of amino acids in the protein.

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Chap 01_8e 60. In an oxidation-reduction reaction, the reactant that is oxidized _____, and the reactant that is reduced _____. a. is energized; is de-energized b. is de-energized; is energized c. loses electrons; gains electrons d. gains electrons; loses electrons e. maintains the same number of electrons; loses electrons 61. Which statement is NOT a distinguishing feature of living organisms? a. There exists a high degree of organizational complexity. b. The structure of components influences their function. c. Organisms can reproduce themselves. d. Organisms can exist without interacting with their environment. e. Organisms change over time. 62. Which list of descriptive terms for biological molecules is placed in correct order from smallest to largest? a. monomer, oligomer, polymer b. monomer, multimer, macromer c. oligomer, monomer, polymer d. polymer, oligomer, monomer e. metamer, oligomer, polymer 63. Humans maintain a nearly constant level of hemoglobin by continually synthesizing and degrading it. This is an example of a(n): a. dynamic steady state. b. equilibrium state. c. exergonic change. d. free-energy change. e. waste of energy. 64. Which substance is NOT a secondary metabolite in plants? a. adenine b. morphine c. quinine d. nicotine e. caffeine

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Chap 01_8e 65. Which are the four MOST abundant elements in living organisms? a. carbon, hydrogen, oxygen, iron b. carbon, hydrogen, nitrogen, oxygen c. carbon, hydrogen, phosphorous, oxygen d. carbon, nitrogen, phosphorous, oxygen e. carbon, hydrogen, sulfur, oxygen 66. The major difference between prokaryotes and eukaryotes is that: a. prokaryotes have a nucleus, while eukaryotes do not. b. eukaryotes have a nucleus, while prokaryotes do not. c. eukaryotes have double-stranded DNA, while prokaryotes have single-stranded DNA. d. prokaryotes have double-stranded DNA, while eukaryotes have single-stranded DNA. e. prokaryotes do not have ribosomes. 67. The diagram is a generic example of what process?

a. systems biology b. feedback inhibition c. positive feedback d. equilibrium e. catabolism 68. The breakage of a phosphoanhydride bond in which molecule is a major source of chemical energy to drive cellular reactions? a. acetyl triphosphate b. adenosine monophosphate c. adenosine triphosphate d. cytosine tetraphosphate e. uridine diphosphate

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Chap 01_8e 69. Which types of molecules can serve as informational macromolecules in cells? a. proteins b. nucleic acids c. oligosaccharides d. both proteins and nucleic acids e. proteins, nucleic acids, and oligosaccharides 70. When a region of DNA must be repaired by removing and replacing some of the nucleotides, what ensures that the new nucleotides are in the correct sequence? a. DNA cannot be repaired and this explains why mutations occur. b. Specific enzymes bind the correct nucleotides. c. The new nucleotides base-pair accurately with those on the complementary strand. d. The repair enzyme recognizes the removed nucleotide and brings in an identical one to replace it. e. The three-dimensional structure determines the order of nucleotides. 71. Living cells produce only one chiral form of a biomolecule because: a. biomolecules, by definition, can exist as only one chiral form. b. living cells can only create L isomers. c. living cells choose to express only the correct isomer. d. living cells have enzymes that are also chiral. e. living cells can produce the opposite chiral form only under certain metabolic conditions. 72. Which is the range of typical diameters of animal and plant cells? a. 0.1 μmto 10 μm b. 0.3 μm to 30 μm c. 5 μm to 100 μm d. 10 nm to 300 nm e. 1 μm to 300 μm 73. A chemist working in a pharmaceutical lab synthesized a new drug as a racemic mixture. Why is it important that the chemist separate the two enantiomers and test each for its biological activity?

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Chap 01_8e 74. List and explain the factors that limit the dimensions of living cells on both the lower and upper limits.

75. Describe the RNA world hypothesis.

76. The free-energy change for the formation of a protein from the individual amino acids is positive and is thus an endergonic reaction. How, then, do cells accomplish this process?

77. Describe how the rise of O2-producing bacteria might have led to the eventual predominance of aerobic organisms on Earth.

78. How is chirality generated by an asymmetric carbon atom and why is this important in the study of biochemistry?

79. What is the difference, if any, between cytosol and cytoplasm?

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Chap 01_8e 80. Briefly, compare and contrast the three domains of life.

81. What is meant by the term "in vitro"? What are the challenges and benefits to studying enzymes in vitro?

82. (a) What is the diagram? (b) Describe what it illustrates about the relationship between animals, halophiles, slime mold positive bacteria. (c) Explain the evidence used in construction of this diagram.

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Chap 01_8e 83. Most cells of higher plants have a cell wall outside the plasma membrane. What is the function of the cell wall?

84. Discuss how a mutation in DNA could be harmful or beneficial to an organism.

85. Describe the relationship between a living organism and its surroundings in terms of both matter and energy.

86. What six characteristics distinguish living organisms from inanimate objects?

87. Describe Stanley Miller's experiment (1953) and its relevance.

88. Proteins are constantly being synthesized in a living cell. Why doesn't the number of protein molecules become too great for the cell to contain, leading to cell destruction?

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Chap 01_8e 89. (a) What is optical activity? (b) How did Louis Pasteur arrive at an explanation for the phenomenon of optical activity?

90. Explain the difference, if any, between a proteome and a proteasome.

91. What is the underlying, organizing biochemical principle that results in the chemical similarity of virtually all living things? Given this biochemical similarity, how is the structural and functional diversity of living things possible?

92. Hereditary transmission of genetic information can be viewed as a balance between stability and change. Explain.

93. What is meant by feedback inhibition and why is it important in a living organism?

94. Draw the structures of the functional groups in their nonionized forms for (a) hydroxyl, (b) carboxyl, (c) amino, (d) phosphoryl.

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Chap 01_8e 95. Explain why living organisms are able to produce particular chiral forms of different biomolecules while laboratory chemical synthesis usually produces a racemic mixture.

96. E. coli is known as a gram-negative bacterial species. (a) How is this determined? (b) How do gramnegative bacteria differ structurally from gram-positive bacteria?

97. Differentiate between configuration and conformation.

98. Instant cold packs get cold when the contents, usually solid urea and liquid water, are mixed, producing an aqueous solution of urea. Although this process is clearly spontaneous, the products are colder than the reactants. Explain how this is possible in terms of the difference between ΔG and ΔH.

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Chap 01_8e 99. (a) On the reaction coordinate diagram, label the transition state and the overall free-energy change (ΔG) for the uncatalyzed reaction A→B. (b) Is this an exergonic or endergonic reaction? (c) Draw a second curve showing the energetics of the reaction if it were enzyme-catalyzed.

100. Provide a brief explanation for the observation that macromolecules diffuse at a slower rate in the cytosol than they do in dilute solution.

101. How is the genetic information encoded in DNA, and how is a new copy of DNA synthesized?

102. What is meant by endosymbiotic association? How can this concept explain the evolution of eukaryotic cells that are capable of carrying out photosynthesis and/or aerobic metabolism?

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Chap 01_8e 103. All cells are surrounded by a plasma membrane composed of lipid and protein molecules. What is the function of the plasma membrane?

104. Name two functions of (a) proteins, (b) nucleic acids, (c) polysaccharides, (d) lipids.

105. (a) List the types of noncovalent interactions that are important in providing stability to the three-dimensional structures of macromolecules. (b) Why is it important that these interactions be noncovalent, rather than covalent, bonds?

106. Why is the use of the expression Mr = 18,000 daltons incorrect?

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Chap 01_8e Answer Key 1. a 2. e 3. c 4. c 5. a 6. c 7. d 8. d 9. d 10. c 11. c 12. a 13. d 14. c 15. e 16. b 17. d 18. d 19. e 20. b 21. e 22. e 23. e 24. e 25. b 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 01_8e 27. a 28. a 29. a 30. a 31. c 32. a 33. d 34. a 35. b 36. b 37. a 38. d 39. b 40. b 41. b 42. d 43. a 44. d 45. a 46. e 47. b 48. b 49. e 50. b 51. d 52. a 53. e 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 01_8e 55. d 56. b 57. b 58. a 59. e 60. c 61. d 62. a 63. a 64. a 65. b 66. b 67. b 68. c 69. e 70. c 71. d 72. c 73. Biomolecules such as receptors for drugs are stereospecific, so each of the two enantiomers of the drug may have very different effects on an organism. One may be beneficial, the other toxic; or one enantiomer may be ineffective and its presence could reduce the efficacy of the other enantiomer. 74. On the lower end, cell dimensions are limited by the minimum number of biomolecules necessary for function. On the upper end, cells are limited by the rate of diffusion of solutes such as oxygen. 75. Initially, RNA molecules were both genes and catalysts. Self-replication of these molecules over long periods of time produced variants that were able to catalyze polymerization of amino acids to form peptides that assumed the function of catalysts. Eventually, genomic RNA was copied into DNA, which assumed the function of genetic information storage. 76. The endergonic (thermodynamically unfavorable) reaction is coupled to an exergonic (thermodynamically favorable) reaction through a shared intermediate, so that the overall free-energy change of the coupled reactions is negative (the overall reaction is exergonic).

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Chap 01_8e 77. The rise of O2-producing bacteria would result in an increase in the levels of O2 in Earth's atmosphere. This would give a selective advantage to aerobic organisms (which utilized O2 as electron acceptor) over anaerobic organisms for which O2 was toxic. 78. An asymmetric carbon has four different substituents attached, and cannot be superimposed on its mirror image, just as a right hand cannot fit into a left glove. Thus, a molecule with one asymmetric (chiral) carbon will have two stereoisomers, which may be distinguishable from one another in a biological system. 79. The cytoplasm is the internal volume enclosed by the plasma membrane; the cytosol is the aqueous portion of the cytoplasm. 80. Bacteria and Archaea consist of unicellular organisms, while Eukarya contains both single- and multicellular organisms. Bacteria and Archaea have been found in all kinds of environments. Archaea historically were characterized from extreme environments. Neither bacteria nor archaea have chromosomes separated from the cytoplasm by a nuclear membrane, but eukaryotes have chromosomes inside a membrane-bounded nucleus. 81. "In vitro" means "in glass"—in the test tube. Challenges include that the experiment may not include all of the molecules that influence an enzyme's activity, the rate of reaction may differ from in vivo due to concentration and crowding/diffusion effects. Benefits include that the enzyme activity is isolated from interfering components, and that the reaction takes place in a thoroughly stirred solution. 82. (a) This diagram is a phylogenetic tree. (b) It illustrates the evolutionary distance between different organisms in the three domains of life. Of the organisms listed, animals are most closely related to slime molds, next closest to halophilic archaea. Archaea and Eukarya are more similar to each other than either is to Bacteria, making grampositive bacteria the most distant relative to all of the organisms listed in this question. (c) The distances between the branches of the tree are calculated by comparing sequence similarity between homologous proteins in different organisms. 83. The cell wall provides a rigid, protective shell for the cell. It is porous, allowing water and small molecules to pass readily, but it is rigid enough to resist the swelling of the cell caused by the accumulation of water (see Fig. 1-8). 84. Some mutations lead to the synthesis of an inactive or defective enzyme or other protein that can no longer carry out its proper function, which is thus harmful to the organism. However, other mutations may lead to a more stable enzyme or to a protein that is better able to carry out its function in a particular environment, making it beneficial to the organism. 85. Living organisms are open systems and exchange both matter and energy with their surroundings. They are not at equilibrium with their surroundings; that is, the exchange of matter and energy with the surroundings is not constant and equal in both directions. To maintain this situation, the organism must acquire energy from its surroundings, either in the form of chemical energy or directly from sunlight. 86. Living organisms (1) are chemically complex and highly organized; (2) extract, transform, and use energy from their environment; (3) have the capacity to precisely self-replicate and self-assemble; (4) exploit a chemical interplay with their environment; (5) possess programmatically defined functions; and (6) evolve to new forms over many generations.

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Chap 01_8e 87. Miller subjected a gaseous mixture of ammonia, methane, water vapor, and hydrogen to electrical sparks for periods of a week or more. When he analyzed the contents of the closed reaction vessel, the gas phase contained CO and CO2, as well as unreacted starting materials. The water phase contained a variety of organic compounds, including some amino acids, hydroxy acids, aldehydes, and hydrogen cyanide. This experiment established the possibility of abiotic production of biomolecules in relatively short times under relatively mild conditions. 88. The proteins in a cell are continuously being synthesized and degraded. The cell maintains a dynamic steady state in which the amount of each protein remains fairly constant at the level required under given conditions. 89. (a) Optical activity is the capacity of a substance to rotate the plane of plane-polarized light. (b) Using fine forceps, he was able to separate the two types of crystals found in tartaric acid (racemic acid) that are identical in shape, but mirror images of each other. One sample rotated polarized light to the left; the mirror image crystals rotated polarized light to the right. 90. A proteome is the list of all proteins that function in a given cell. A proteasome is a molecular machine or supramolecular structure responsible for protein degradation in a cell. 91. Living things are composed primarily of macromolecules, polymers of simple compounds of just a few different types. The properties of these polymers are determined by their sequence of monomers and these can be combined in many different ways. Diversity is thus achieved through the nearly limitless variety of sequences that can exist when amino acids are linked to form proteins, nucleotides are linked to form nucleic acids, and monosaccharides are linked to form polysaccharides. Branching in the latter can contribute additional heterogeneity. Each type of organism constructs a unique set of macromolecules from these monomeric units, resulting in the structural and functional diversity among species. 92. Hereditary transmission of genetic information occurs via replication of DNA, the information-containing molecule. This process is very accurate and thus results in relatively few changes in genetic information. This stability is important to maintain individual and species characteristics over long periods of time. On the other hand, regular changes in genetic information (mutations) do occur, primarily as a result of infrequent errors in replication. These mutations are essential for generating genetic diversity, which allows for adaptation of species. 93. feedback inhibition is the regulation of a biochemical pathway in which a reaction product inhibits an earlier (usually the first) step in the pathway. It is an important type of regulation because it ensures that energy is not wasted by an organism producing molecules it does not need.

94. 95. Laboratory syntheses usually use achiral reagents and thus produce racemic mixtures of products. In contrast, because all enzymes are made of chiral precursors, all enzymes are inherently chiral catalysts. Thus, they will show strong stereoselectivity in reactants and mechanisms, leading to the production of chiral products. Copyright Macmillan Learning. Powered by Cognero.

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Chap 01_8e 96. (a) Gram-negative bacteria have little affinity for the dye gentian violet used in Gram's stain, but gram-positive bacteria retain Gram's stain. (b) Gram-negative bacteria have an outer membrane and a peptidoglycan layer; gram-positive bacteria lack an outer membrane and the peptidoglycan layer is much thicker. 97. Configuration denotes the spatial arrangement of the atoms of a molecule that is conferred by the presence of either double bonds or rings, around which there is no freedom of rotation, or chiral centers, which give rise to stereoisomers. Configurational isomers can only be interconverted by temporarily breaking covalent bonds. Conformation refers to the spatial arrangement of substituent groups that, without breaking any bonds, are free to assume different positions in space because of the freedom of bond rotation. 98. Since the dissolution reaction is spontaneous, the ΔG must be negative. Since the reaction absorbs heat, the ΔH must be positive. Given ΔG = ΔH – TΔS, this is possible if the ΔS is very large and positive, as one would expect for a solid dissolving. 99. (a) and (c) see Fig. 1-28 (b) exergonic reaction 100. The cytosol is very crowded and gel-like. The diffusion of macromolecules is slowed by collisions with other large molecules and structures. 101. The genetic information is encoded in the linear sequence (order) of the four different deoxyribonucleotides in the DNA. When a new copy of DNA is needed, the two strands of the DNA unwind and each strand serves as a template on which a new strand is synthesized. 102. An endosymbiotic association is the envelopment of one organism by another to form a relationship that is beneficial to both organisms. It is believed that primitive eukaryotic cells, which were incapable of photosynthesis or aerobic metabolism, formed endosymbiotic associations with photosynthetic and/or aerobic bacteria. The aerobic bacteria then evolved into the mitochondria found in modern eukaryotic cells, and the photosynthetic bacteria evolved into the chloroplasts found in plant cells (see Fig. 1-37). 103. The plasma membrane acts as a barrier to the free passage of inorganic ions and most other charged or polar compounds into or out of the cell. It contains proteins that can transport specific ions or molecules. Other membrane proteins act as receptors that transmit signals from the outside to the inside of the cell. 104. Many answers are possible including: (a) proteins function as enzymes, structural elements, signal carriers, transporters; (b) nucleic acids store and transmit genetic information and act as both structural and catalytic elements; (c) polysaccharides serve as energy-yielding fuel stores and cellular and extracellular structural and recognition elements; (d) lipids function as membrane components, fuel stores, and cellular signals. 105. (a) Noncovalent interactions include hydrogen bonds, ionic interactions between charged groups, van der Waals interactions, and hydrophobic interactions. (b) Because noncovalent interactions are weak, they can form, break, and re-form more rapidly and with less energy input than can covalent bonds. This is important to maintain the flexibility needed in macromolecules. 106. Mr is a ratio and therefore dimensionless. Daltons are only used when describing molecular mass, not molecular weight or relative molecular mass.

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Chap 02_8e Indicate the answer choice that best completes the statement or answers the question. 1. The hydrophobic effect makes important energetic contributions to: a. binding of a hormone to its receptor protein. b. enzyme-substrate interactions. c. membrane structure. d. three-dimensional folding of a polypeptide chain. e. All of the answers are correct. 2. Which statement is true about the hydrophobic effect? a. It is the driving force in the formation of micelles of amphipathic compounds in water. b. It does not contribute significantly to maintaining the native conformation of water-soluble proteins. c. Hydrophobic effect interactions have bonding energies of approximately 20 to 40 kJ/mol. d. The hydrophobic effect involves interaction with water to denature proteins. e. The hydrophobic effect primarily determines the solubility of polar solutes. 3. A compound is known to have two ionizable groups: a free amino group with a pKa of 8.8, and another group with a pKa between 5 and 7. A mixture of 100 mL of a 0.2 M solution of this compound at pH 8.2 and 40 mL of 0.2 M hydrochloric acid has a final pH of 6.2. What is the pKa of the second ionizable group? a. The pH cannot be determined from this information. b. 5.4 c. 5.6 d. 6.0 e. 6.2 4. Which would have the greatest effect on osmotic pressure? a. 1 M NaCl (molecular weight = 58 g/mol) b. 1 M CaCl2 (molecular weight = 111 g/mol) c. 1 M glucose (molecular weight = 180 g/mol) d. 1 M sucrose (molecular weight = 342 g/mol) e. All of the answer choices would have the same effect. 5. When two atoms are joined together covalently, the van der Waals radius of the atoms in the covalent bond are _____ than the radius of the atoms alone because the joined atoms are _____. a. shorter; pulled together by the shared electron pair b. shorter; pulled together by the attraction of the nucleus to the bonded atom c. shorter; pulled together by hydrogen bonding d. longer; repelled due to the shared electron pair e. longer; repelled due to the nuclear repulsion between bonded atoms Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 6. What is the pH of a 0.1 M NaOH solution? a. 0.1 b. 1.0 c. 12.8 d. 13 e. 14 7. Distilled white vinegar has a pH of 2.4. What is the [H+] of distilled white vinegar? a. 2.4 M b. 2.5 × 10–12 M c. 2.5 × 10–3 M d. 3.98 × 10–3 M e. 3.98 × 10–6 M 8. The pH of a sample of blood is 7.4, while gastric juice is pH 1.4. The blood sample has _____ [H+] than the gastric juice. a. 0.189 times the b. 5.29 times lower c. 6 times lower d. 6,000 times lower e. one million times lower 9. When water is found bound in the internal structure of a biomolecule, which statement is false? a. The properties of the bound water molecules are different from those of the "bulk" water of the solvent. b. The bound water molecules may provide a path for proton hopping. c. The bound water molecules may form an essential part of the protein's ligand-binding site. d. The orientation of bound water molecules is precise. e. None of the above; all of the statements are true. 10. Which statement does NOT describe a strategy used by multicellular animals to maintain osmotic balance with their surroundings? a. Cells have a contractile vacuole, an organelle that pumps water out of the cell. b. Animals have a high concentration of albumin and other proteins in blood plasma. c. Cells actively pump out Na+ and other ions. d. Cells store fuel as a polysaccharide instead of as simple sugars. e. All of the statements describe a strategy to maintain osmotic balance.

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Chap 02_8e 11. If a person is suffering from mild acidosis, which treatment/action would help counteract the acidosis the most? a. intravenous administration glucose b. deep breathing c. breathing into a paper bag d. vigorous exercise e. All of these treatments/actions could be used to counteract acidosis. 12. Which diagram correctly illustrates the clustering of lipids in the formation of a micelle?

a. A b. B c. both A and B d. neither A nor B 13. Which is the conjugate base of H2PO41–? a. H3PO4 b. H2PO42– c. HPO42– d. HPO43– e. PO43– 14. If the pH of a solution is 5.5, what is the pOH? a. 8.5 b. –5.5 c. –8.5 d. 14 e. 6.5

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Chap 02_8e 15. Which force plays the greatest role in stabilizing biological membranes? a. hydrogen bonding because it a strong noncovalent bond b. hydrophobic interactions that increase solvent entropy c. covalent interactions because they are very stable interactions d. electrostatic interactions between oppositely charged ions e. van der Waals interactions because of the attraction between transient dipoles 16. According to the titration curve shown, acid A is _____ because the pH _____.

a. weak; resists change when 50% titrated b. strong; resists change when 50% titrated c. weak; changes dramatically when 50% titrated d. strong; changes dramatically when 50% titrated e. It cannot be determined from the information given.

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Chap 02_8e 17. A 1.0 M solution of a compound with two ionizable groups (pKa values = 6.2 and 9.5; 100 mL total) has an initial pH of 6.8. If a biochemist adds 60 mL of 1.0 M HCl to this solution, what is the final pH? a. 5.60 b. 8.90 c. 9.13 d. 9.32 e. The pH cannot be determined from this information. 18. List the acids in increasing order of strength (weakest to strongest): nitrous acid (Ka = 4.0 × 10–4), carbonic acid (Ka = 4.4 × 10–7), acetic acid (Ka = 1.7 × 10–5), phosphoric acid (Ka = 7.3 × 10–3). a. acetic acid, carbonic acid, nitrous acid, phosphoric acid b. carbonic acid, acetic acid, nitrous acid, phosphoric acid c. acetic acid, nitrous acid, carbonic acid, phosphoric acid d. phosphoric acid, nitrous acid, acetic acid, carbonic acid e. carbonic acid, phosphoric acid, nitrous acid, acetic acid 19. Three buffers are made by combining a 1 M solution of acetic acid with a 1 M solution of sodium acetate in the ratios shown. 1 M acetic acid 1 M sodium acetate Buffer 1: 10 mL 90 mL Buffer 2: 50 mL 50 mL Buffer 3: 90 mL 10 mL Which statement is true of the resulting buffers? a. pH of buffer 1 < pH of buffer 2 < pH of buffer 3 b. pH of buffer 1 = pH of buffer 2 = pH of buffer 3 c. pH of buffer 1 > pH of buffer 2 > pH of buffer 3 d. The problem cannot be solved without knowing the value of pKa. e. None of the statements is true. 20. According to the Henderson-Hasselbalch equation, when is the pH equal to the pKa? a. when the concentration of acid is close to zero b. when the pH approaches 7 c. when the concentration of the conjugate base is equal to the ionization constant for water d. when the concentration of the conjugate base is equal to the concentration of the acid e. None of the answers is correct.

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Chap 02_8e 21. Which statement correctly describes the situation of the cell in the diagram? The black dots represent solute molecules.

a. The cell is in a hypotonic solution; water will move into the cell and cause it to swell. b. The cell is in a hypotonic solution; solute will move into the cell and cause it to swell. c. The cell is in a hypotonic solution; water will move out of the cell and cause it to shrink. d. The cell is in a hypertonic solution; solute will move into the cell and cause it to swell. e. The cell is in a hypertonic solution; water will move out of the cell and cause it to shrink.

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Chap 02_8e 22. Ibuprofen is a weak acid with a pKa of 4.9 (structure is shown with the ionizable hydrogen marked with a star). Ibuprofen is absorbed through the stomach and the small intestine. In these tissues, absorption is a function of polarity. Charged and very polar molecules are absorbed slowly; neutral hydrophobic molecules absorb quickly. If the stomach pH is about 1.5 and the small intestine pH is about 6, where (and why) will more ibuprofen be absorbed into the bloodstream?

a. More ibuprofen will be absorbed in the small intestine because it will be uncharged due to the pH being greater than the pKa. b. More ibuprofen will be absorbed in the stomach because it will be uncharged due to the pH being lower than the pKa. c. More ibuprofen will be absorbed in the small intestine because it will be charged due to the pH being greater than the pKa. d. More ibuprofen will be absorbed in the stomach because it will be charged due to the pH being lower than the pKa. e. Ibuprofen will be absorbed equally well in both the stomach and small intestine. 23. Which list correctly shows bond/interaction strength in decreasing order (strongest to weakest)? a. covalent bond > hydrogen bond > ionic bond > van der Waals interaction b. covalent bond > ionic bond > hydrogen bond > van der Waals interaction c. ionic bond > covalent bond > hydrogen bond > van der Waals interaction d. covalent bond > van der Waals interaction > ionic bond > hydrogen bond e. hydrogen bond > ionic bond > van der Waals interaction > covalent bond

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Chap 02_8e 24. What is the pH of a 1 M HCl solution? a. 0 b. 0.1 c. 1 d. 10 e. –1 25. A hydronium ion is: a. H3O+. b. immediately formed when hydrogen ions are released in water. c. a hydrated proton. d. formed by the dissociation of water. e. All of the answers are correct. 26. Formic acid is in the venom of some ant species. What is the pH of a 0.2 M solution of formic acid (Ka = 1.78 × 10–4 M)? a. 8.90 b. 4.45 c. 3.75 d. 2.2 e. 1.72 27. The OH– concentration of a solution is 4.3 × 10–10 M. What is the pH? a. –9.37 b. 9.37 c. –4.63 d. 4.63 e. 13.4

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Chap 02_8e 28. According to the titration curve shown, what is a good buffering range for acid A?

a. 0.3 M to 0.8 M OH– b. 0.9 M to 1.0 M OH– c. pH 3.5 to pH 4.2 d. pH 2.8 to pH 3.8 e. pH 2.8 to pH 4.8 29. An example of osmosis is movement of a _____ molecule across a membrane. a. charged solute b. gas c. nonpolar solute d. polar solute e. water 30. Which statement about hydrogen bonds is false? a. Hydrogen bonds are highly directional. b. Hydrogen bonds are capable of holding molecules in a specific geometric arrangement. c. Hydrogen bonds are strongest when the three atoms in the bond are in a straight line. d. Hydrogen bonds are strongest when the oxygen atom is perpendicular to the hydrogen donor. e. Hydrogen bonds place a hydrogen with a partial positive charge directly between two atoms with partial negative charges. Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 31. Which correctly represent hydrogen bonding?

a. A and D b. A and C c. B and C d. C and D e. B and D 32. Which statement correctly describes the forces that drive the formation of micelles by amphipathic molecules, such as fatty acids, dissolved in water? a. Head groups of the molecules are sequestered in the interior of the micelle, maximizing hydrogen bonding of the hydrophobic tail with surrounding solvent molecules. b. Head groups of the molecules are exposed on the outer surface of the micelle, maximizing hydrogen bonding between hydrophobic tails. c. Head groups of the molecules are exposed on the outer surface of the micelle, minimizing the order of the surrounding water molecules. d. Hydrophilic tails are exposed on the outer surface of the micelle, maximizing hydrogen bonding between the tails and surrounding water molecules. e. Hydrophobic tails are exposed on the outer surface of the micelle, maximizing hydrogen bonding between head groups. 33. Adding a solute to water lowers the freezing point of water. The solute changes this colligative property of water by _____ the water. a. lowering the concentration of b. increasing hydrogen bonding in c. altering the ionic bonding within d. changing the pH of e. changing the temperature of

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Chap 02_8e 34. If the Ka of an acid is 1.38 × 10–7, what is the pKa? a. 6.86 b. 7.14 c. 4.37 d. 10.7 e. 1.38 35. Which statement about buffers is true? a. A buffer composed of a weak acid of pKa = 5 has greater buffering capacity at pH 4 than at pH 6. b. At pH values lower than the pKa, the conjugate base concentration is higher than that of the conjugate acid. c. The pH of a buffered solution remains constant no matter how much acid or base is added to the solution. d. The best buffers are those composed of strong acids and strong bases. e. When pH = pKa, the weak acid and conjugate base concentrations in a buffer are equal. 36. Milk of magnesia has a pH of 10.2. What is the [OH– ] of milk of magnesia? a. 6.31 × 10–11 M b. 1.58 × 10–4 M c. 1.58 × 10–5 M d. 1.02 × 10–3 M e. 6.31 × 10–4 M 37. Phosphoric acid is tribasic, with three pKa values: 2.14, 6.86, and 12.4. Which ionic form predominates at pH 4.5? a. H3PO4 b. H2PO4– c. HPO42– d. PO43– e. None of the answers is correct.

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Chap 02_8e 38. "Proton hopping" essentially means that: a. an individual proton jumps from one electronegative group to the next. b. a free proton moves from one hydroxyl group of ionized water to the next. c. several protons move between hydrogen-bonded water molecules causing the net movement of a proton over a long distance in a short time. d. individual protons are freer to move among and between water molecules in solution. e. hydronium ions are freer to move among and between water molecules in solution. 39. Which statement about hydrogen bonds is NOT true? a. Hydrogen bonds account for the high boiling point of water compared to molecules of similar size. b. In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules. c. Individual hydrogen bonds are much weaker than covalent bonds. d. Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes. e. The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. 40. Which process would NOT disrupt the weak interactions between two biomolecules in solution? a. heating the solution b. cooling the solution c. lowering the pH of the solution d. increasing the ionic strength of the solution e. All of the answer choices would disrupt interactions between biomolecules. 41. The aqueous solution with the highest pH is: a. 1 M HCl. b. 1 M NH3 (pKa = 9.25). c. 0.5 M NaHCO3 (pKa = 3.77). d. 0.1 M NaOH. e. 0.001 M NaOH.

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Chap 02_8e 42. Which diagram illustrates an amphipathic molecule?

a. A b. B c. C d. D 43. When a nonpolar solute is dispersed in water, which will occur? a. the entropy of the water decreases b. the entropy of the water increases c. the enthalpy of solution is negative d. the system reaches equilibrium quickly e. All of the answers are correct.

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Chap 02_8e 44. Polar molecules cannot easily pass through the cell membrane, but hydrophobic molecules can easily pass through the membrane. Both molecules shown can raise blood pressure. Compare the molecules and select the statement that is true.

a. Ephedrine can more easily pass through the cell membrane than epinephrine. b. Epinephrine can more easily pass through the cell membrane than ephedrine. c. Both epinephrine and ephedrine can pass through the cell membrane equally well. d. Neither epinephrine nor ephedrine can pass through the cell membrane. e. None of the statements is true. 45. Which statement regarding long-chain fatty acids in aqueous solution is NOT true? a. Fatty acids in small concentrations are surrounded by highly ordered water molecules in a cagelike structure. b. Fatty acids will cluster together to minimize the lipid surface area. c. Fatty acids will form micelles to sequester hydrophobic groups from water. d. The driving force of solubilizing fatty acids is increasing entropy of the fatty acid. e. All of the statements are true. 46. A 0.6 M solution of a weak acid had a pH of 5.8. What is the pKa of the weak acid? a. 11.3 b. 10.5 c. 8.2 d. 5.7 e. 2.9

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Chap 02_8e 47. The objective is to maintain pH = 7.0 for an enzyme-catalyzed reaction that will produce hydrogen ions along with the desired product. At equal concentrations, which weak acid, if any, will serve as the better buffer for the reaction: acid A with pKa = 6.5, or acid B with pKa = 7.5? a. acid A b. Water is as good as either of the acids available. c. acid B d. Both are equally effective. 48. Which statement is true about the properties of aqueous solutions? a. A pH change from 5.0 to 6.0 reflects an increase in the hydroxide ion concentration, [OH– ], of 20%. b. A pH change from 8.0 to 6.0 reflects a decrease in the proton concentration, [H+], by a factor of 100. c. Charged molecules are generally insoluble in water. d. Hydrogen bonds form readily in aqueous solutions. e. The pH can be calculated by adding 7 to the value of the pOH. 49. Which answer choice is involved in important biological buffering systems? a. histidine b. bicarbonate c. phosphate d. bicarbonate and phosphate e. histidine, bicarbonate, and phosphate 50. Ice is _____ dense than water because _____. a. less; frozen water maintains more hydrogen bonds than liquid water b. less; liquid water maintains more hydrogen bonds than frozen water c. more; frozen water maintains more hydrogen bonds than liquid water d. more; liquid water maintains more hydrogen bonds than frozen water e. more; frozen water cannot hydrogen bond 51. Which contributes to water's unusual properties? a. the geometry of water molecules b. the polarity of water c. the ability of water molecules to hydrogen bond d. the electronegativity of the oxygen in water e. All of the answers are correct.

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Chap 02_8e 52. Substance X has a pKa of 7.4. What is the pH of the final solution formed by mixing 100 mL of a 1.0 M solution of X that is initially at pH 8.0 and 30 mL of 1.0 M hydrochloric acid? a. 6.5 b. 6.8 c. 7.2 d. 7.4 e. 7.5 53. Which compound is a diprotic acid? a. CH3COOH b. NH4+ c. H2CO3 d. H3PO4 e. CH3CH2OH 54. The H+ concentration of a solution is 5.6 × 10–5 M. What is the pH? a. –4.25 b. 4.25 c. 5.65 d. –9.75 e. 9.75 55. The aqueous solution with the lowest pH is: a. 0.01 M HCl. b. 0.1 M acetic acid (pKa = 4.86). c. 0.1 M formic acid (pKa = 3.75). d. 0.1 M HCl. e. 10–12 M NaOH. 56. Oxygen and carbon dioxide are both biologically important gases. Which statement about these gases is true? a. O2 and CO2 are both nonpolar and are very soluble in water. b. O2 and CO2 are both polar and are very soluble in water. c. O2 and CO2 are both nonpolar and are poorly soluble in water. d. CO2 contains polar bonds and is very soluble in water, but O2 is nonpolar and is poorly soluble in water. e. O2 contains polar bonds and is very soluble in water, but CO2 is nonpolar and is poorly soluble in water. Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 57. Of the seven the steps listed, which four (in the correct order) are needed to prepare 1 L of a 0.02 M Tris buffer solution at pH 7.6? A lab station has a 0.1 M solution of Tris in its protonated form, 0.1 M solution of HCl and NaOH, and plentiful distilled water. The Ka of Tris is 8.32 × 10–9. 1. Calculate the volume of 0.1 M Tris to use (C1V1 = C2V2). 2. Calculate the volume of 0.1 M HCl to use (C1V1 = C2V2). 3. Calculate the volume of 0.1 M NaOH to use (C1V1 = C2V2). 4. Use the Henderson-Hasselbalch equation to calculate the ratio of Tris base to protonated Tris. 5. Adjust the pH to 7.6 by adding 0.1 M NaOH. 6. Adjust the pH to 7.6 by adding 0.1 M HCl. 7. Fill to 1 L with distilled water. a. 1, 4, 6, 7 b. 1, 4, 5, 7 c. 1, 2, 4, 7 d. 1, 3, 4, 7 e. 1, 7, 4, 6 58. In water, which substance would most force surrounding water molecules to become highly ordered? a. CH2O b. CH4 c. NH3 d. CH3CH2OH e. None of the answers is correct.

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Chap 02_8e 59. According to the titration curve shown, what is the approximate pKa of acid A?

a. 0.2 b. 0.5 c. 3.2 d. 3.8 e. 4.8 60. Which factor causes water to have a bent geometry rather than a linear geometry? a. the net dipole of a water molecule b. the unshared electron pairs (nonbonding orbitals) on the oxygen atom c. the electronegativity difference between hydrogen and oxygen d. the unequal electron sharing between hydrogen and oxygen e. All of the answers are correct. 61. Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the: a. pH remains constant. b. pH rises more than if the same amount of NaOH is added to an acetate buffer initially at pH 6.76. c. pH rises more than if the same amount of NaOH is added to unbuffered water at pH 4.76. d. ratio of acetic acid to acetate ion in the buffer decreases. e. sodium acetate formed precipitates because it is less soluble than acetic acid. Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 62. The Henderson-Hasselbalch equation: a. allows the graphic determination of the molecular weight of a weak acid from its pH alone. b. does not explain the behavior of di- or tribasic weak acids. c. employs the same value for pKa for all weak acids. d. is equally useful with solutions of acetic acid and of hydrochloric acid. e. relates the pH of a solution to the pKa and the concentrations of acid and conjugate base. 63. Draw a titration curve for a monoprotic weak acid and indicate the region in which the buffering capacity of the system is greatest.

64. If ice were denser than water, how would that affect life on Earth?

65. In proteins, the amino acid histidine (His) plays an important role in many biological reactions. The pKa for the protonation of His to form HisH+ = 6.0. When pH = 7.0, what is the fraction of total histidine that will be in the HisH+ form?

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Chap 02_8e 66. Phosphoric acid (H3PO4) has three dissociable protons with the pKa values shown. Which form of phosphoric acid predominates in a solution at pH 4? Explain. Acid pKa H3PO4 2.14 H2PO4–

6.86

HPO42–

12.4

67. Define pKa for a weak acid in two ways: (1) in relation to its acid dissociation constant, Ka, and (2) by reference to a titration curve for the weak acid.

68. For a weak acid with a pKa of 6.0, show how to calculate the ratio of acid to base at pH 5.

69. Explain with an appropriate diagram why amphipathic molecules tend to form micelles in water. What force drives micelle formation?

70. A weak acid HA, has a pKa of 5.0. If 1.0 mol of this acid and 0.1 mol of NaOH were dissolved in one liter of water, what is the final pH?

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Chap 02_8e 71. (a) In terms of osmolarity, briefly define isotonic, hypotonic, and hypertonic solutions. (b) Describe what happens when a cell is placed in each of these types of solutions.

72. Recall the equilibria: H+ + HCO3– ⇋ H2CO3 ⇋ CO2 + H2O Severe diarrhea is accompanied by a loss of HCO3– . If untreated, will the condition result in acidosis or alkalosis? Use the bicarbonate buffer system given in the scheme above and Le Chatelier's principle to explain your answer.

73. Name and briefly define five types of noncovalent interactions that occur between biological molecules.

74. What is the pH of a solution containing 0.2 M acetic acid (pKa = 4.7) and 0.1 M sodium acetate?

75. Explain the fact that ethanol (CH3CH2OH) is more soluble in water than is ethane (CH3CH3).

76. A solution is made by combining 50 mL of a 0.1 M sodium acetate solution with 150 mL of 1 M acetic acid (pKa = 4.7). What is the pH of the resulting solution?

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Chap 02_8e 77. After adding 100 mL of a solution containing 0.5 mol of acetic acid per liter to 400 mL of 0.5 M NaOH, what is the final pH? (The pKa of acetic acid is 4.7.)

78. Speculate why weak forces, not strong forces, are the basis for molecular recognition among biomolecules.

79. For each pair, circle the conjugate base. RCOOH RCOO– RNH2

RNH3+

H2PO4–

H3PO4

H2CO3

HCO3–

80. Explain the fact that triethylammonium chloride ((CH3CH2)3N-HCl) is more soluble in water than is triethylamine ((CH3CH2)3N).

81. As two atoms get nearer to each other, do van der Waals attractive forces always increase?

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Chap 02_8e Answer Key 1. e 2. a 3. c 4. b 5. a 6. d 7. d 8. e 9. e 10. a 11. b 12. b 13. c 14. a 15. b 16. a 17. a 18. b 19. c 20. d 21. e 22. b 23. b 24. a 25. e 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 27. d 28. e 29. e 30. d 31. c 32. c 33. a 34. a 35. e 36. b 37. b 38. c 39. d 40. b 41. d 42. d 43. a 44. a 45. d 46. a 47. a 48. d 49. e 50. a 51. e 52. d 53. c 54. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e 55. d 56. c 57. b 58. b 59. d 60. b 61. d 62. e 63. The inflection point, which occurs when the weak acid has been exactly one-half titrated with NaOH, occurs at a pH equal to the pKa of the weak acid. The region of greatest buffering capacity (where the titration curve is flattest) occurs at pH values of pKa ± 1 (see Fig. 2-17). 64. Ice that formed at the surface of bodies of water would sink; hence, streams, ponds, lakes, and so on would freeze from the bottom up. With a reservoir of ice at the bottom, they would be perpetually cold, and in the limit they would freeze solid, precluding life as we know it. 65. Use the Henderson-Hasselbalch equation to determine the ratio of [His] to [HisH+]. pH = pKa + log ([His]/[HisH+]) 7.0 = 6.0 + log ([His]/[HisH+]) 1.0 = log ([His]/[HisH+]) [His]/[HisH+] = antilog (1) = 10 To determine the fraction of the total in the HisH+ form, [His]total = [His] + [HisH+], fraction = [HisH+]/[His]total = [HisH+]/([His] + [HisH+]) substitute from ratio calculated above = [HisH+]/(10[HisH+] + [HisH+]) = 1/11, or 0.09 66. At pH 4, the first dissociable proton (pKa = 2.14) has been titrated nearly completely, and the second (pKa = 6.86) has just started to be titrated. The dominant form at pH 4 is therefore H2PO4– , the form with one dissociated proton (see Fig. 2-15). 67. (1) pKa = –log Ka. (2) See Fig. 2-17; pKa is the value of pH at the inflection point in a plot of pH versus extent of titration of the weak acid. At the pKa, the concentration of ionized acid equals the concentration of nonionized acid. Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_8e

68.

69. Micelle formation minimizes the surface area of the hydrophobic part of amphipathic molecules that contacts the polar solvent, water. Hydrophobic interactions between hydrophobic moieties are the driving force for micelle formation. When amphipathic molecules form micelles in water, the entropy decrease, due to the formation of ordered arrays of water molecules around the hydrophobic moieties, is minimized (see Fig. 2-7). 70. Combining 1 mol of weak acid with 0.1 mol of NaOH yields 0.9 mol of weak acid and 0.1 mol of salt.

71. (a) An isotonic solution has the same osmolarity as the solution to which it is being compared. A hypotonic solution has a lower osmolarity than the solution to which it is being compared. A hypertonic solution has a higher osmolarity than the solution to which it is being compared. (b) Higher osmolarity results in osmotic pressure, which generally leads to movement of water across a membrane. In an isotonic solution, in which the osmolarity of the solution is the same as the cell cytoplasm, there will be no net water movement. In a hypotonic solution, water will move into the cell causing the cell to swell and possibly burst. In a hypertonic solution, water will move out of the cell and it will shrink. 72. Acidosis. The removal of HCO3– will pull the equilibria in the direction of HCO3– , which will produce H+, thereby lowering the pH. 73. (1) Hydrogen bonds: weak electrostatic attractions between one electronegative atom (such as oxygen or nitrogen) and a hydrogen atom covalently linked to a second electronegative atom; (2) electrostatic interactions: relatively weak charge-charge interactions (attractions of opposite charges, repulsions of like charges) between two ionized groups; (3) hydrophobic interactions: the forces that tend to bring two hydrophobic groups together, reducing the total area of the two groups that is exposed to surrounding molecules of the polar solvent (water); (4) van der Waals interactions: weak interactions between the electric dipoles that two close-spaced atoms induce in each other; (5) tightly bound water molecules can form as an essential part of the binding site in a protein for its ligand. 74.

75. Ethanol can form hydrogen bonds with water molecules, but ethane cannot. When ethanol dissolves, there is some decrease in the system's entropy from formation of clathrate around the alkyl portion, but this is more than compensated for by the favorable interactions (hydrogen bonds) of the hydroxyl group of ethanol with water molecules. Ethane cannot form such hydrogen bonds and is therefore insoluble in water.

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Chap 02_8e 76.

77. Addition of 200 mM of NaOH (400 mL×0.5 M) to 50 mM of acetic acid (100 mL×0.5 mM) completely titrates the acid so that it can no longer act as a buffer and leaves 150 mM of NaOH dissolved in 500 mL, an [OH– ] of 0.3 M. Given [OH– ], [H+] can be calculated from the equilibrium constant for the dissociation of water (the ion product of water): [H+][OH– ] = 10–14 [H+] = 10–14 M2/0.3 M pH is, by definition, log (1/[H+]) pH = log (0.3 M/10–14 M2) = 12.48 78. Weak forces make the biological interactions reversible within physiological constraints. The cumulative effects of many weak interactions can be very significant. Strong forces would require large amounts of energy to reverse any interaction. 79. RCOO– , RNH2, H2PO4– , HCO3– 80. Triethylammonium chloride is an ionic substance. The positive charge of the triethylammonium ion makes it hydrophilic. This leads to stronger favorable interactions with water, leading to increased solubility. Triethylamine is uncharged. 81. No, the attractive forces created by the transient dipole-induced dipole interaction increases until the van der Waals radius is reached, where the net attraction is maximal. At this point, the electron clouds begin to repel each other.

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Chap 03_8e Indicate the answer choice that best completes the statement or answers the question. 1. When the ribosome forms a peptide bond, which two atoms form a covalent bond? a. the α carbon and the amino nitrogen b. the amino nitrogen and carboxylic acid carbon c. the α carbon and the carboxylic acid carbon d. the amino nitrogen and the β carbon e. It depends on the amino acids being joined. 2. How are sequential reactions controlled in the Edman degradation procedure? a. A high salt step is followed by a low salt step. b. A low salt step is followed by a high salt step. c. A high pH step is followed by a low pH step. d. A low pH step is followed by a high pH step. e. None of the answers is correct. 3. Which of the lanes in the gel would represent an "uninduced" sample?

a. 1 b. 2 c. 3 d. 4 e. 5

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Chap 03_8e 4. Selective precipitation of a protein from a crude extract is MOST effective by which molecule? a. ammonium sulfate b. urea c. sodium dodecyl sulfate d. EDTA (ethylenediaminetetraacetic acid) e. All of the answers are correct. 5. By convention, polypeptides are read in which order? a. N to C terminus b. C to N terminus c. 5′ to 3′ d. 3′ to 5′ e. smallest to largest amino acid by molecular weight 6. In an SDS-PAGE experiment two markers of molecular weight, 11,000 g/mol and 3,000 g/mol, traveled 5 cm and 9 cm, respectively. Approximately, how far will a fragment of size 7,945 g/mol travel? a. 6 cm b. 5 cm c. 8 cm d. 7 cm e. The answer cannot be determined from the information given. 7. In a conjugated protein, a prosthetic group is: a. a fibrous region of a globular protein. b. a nonidentical subunit of a protein with many identical subunits. c. a part of the protein that is not composed of amino acids. d. a subunit of an oligomeric protein. e. synonymous with "protomer." 8. Which reagent and application are mismatched? a. dithiothreitol, reduction of disulfide bonds b. dansyl chloride, modify the C-terminal amino acid c. iodoacetate, carboxymethylation to prevent disulfide formation d. anhydrous trifluoroacetic acid, removal of N-terminal amino acid e. Fmoc, protecting group

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Chap 03_8e 9. Which statement is true about the pKa values for ionizable R groups of amino acids within a polypeptide? a. The pKa values for R groups do not change from free amino acids. b. The pKa values for R groups are 1 pH unit higher than free amino acids. c. The pKa values for R groups are 1 pH unit lower than free amino acids. d. The pKa values for R groups vary depending on the local environment of the side chain. e. The pKa values for R groups depend on how close the R group is to the N or C terminus of the polypeptide. 10. Two amino acids of the standard 20 contain sulfur atoms. They are: a. cysteine and serine. b. cysteine and threonine. c. methionine and cysteine. d. methionine and serine. e. threonine and serine. 11. The chirality of an amino acid results from the fact that its α carbon: a. has no net charge. b. is a carboxylic acid. c. is bonded to four different chemical groups. d. is in the L absolute configuration in naturally occurring proteins. e. is symmetric. 12. The functional differences, as well as differences in three-dimensional structures, between two different enzymes from E. coli result directly from their different: a. affinities for ATP. b. amino acid sequences. c. roles in DNA metabolism. d. roles in the metabolism of E. coli. e. secondary structures. 13. Identify the pair of peptides that are NOT distinguished by tandem mass spectrometry. a. VTSPLYANEGK and VTCPLYANEGK b. VTSPLYANEGK and VTSPLYADEGK c. VTSPLYANEGK and VTSPIYANEGK d. VTSPLYANEGK and VSTPLYANEGK e. All of the answer choices are correct.

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Chap 03_8e 14. According to the diagram, what is the average net charge of this amino acid at pH = 2?

a. +1 b. +0.5 c. 0 d. –0.5 e. –1 15. The pKa of lysine's carboxyl group, amino group, and side chain are 2.2, 9.0, and 10.5, respectively. If lysine is in a pH 13 solution, what is its net charge? a. –2 b. –1 c. 0 d. +1 e. +2

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Chap 03_8e 16. Which statement is correct with respect to the amino acid composition of proteins? a. Larger proteins have a more uniform distribution of amino acids than smaller proteins. b. Proteins contain at least one each of the 20 different standard amino acids. c. Proteins with different functions usually differ significantly in their amino acid composition. d. Proteins with the same molecular weight have the same amino acid composition. e. The average molecular weight of an amino acid in a protein increases with the size of the protein. 17. The "signature sequence" shown represents a portion of a protein from four different organisms. The proteins can be classified as:

a. homologs. b. orthologs. c. paralogs. d. both homologs and orthologs. e. both homologs and paralogs. 18. In a highly basic solution, pH = 13, which is the dominant form of glycine? a. NH2—CH2—COOH b. NH2—CH2—COO– c. NH2—CH3+—COO– d. NH3+—CH2—COOH e. NH3+—CH2—COO– 19. At pH 7.0, converting a proline to hydroxyproline, will have what effect on the overall charge of the protein containing it? a. It will become more negative. b. It will become more positive. c. It will stay the same. d. There is not enough information to answer the question. e. The answer depends on the salt concentration.

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Chap 03_8e 20. At pH 7.0, converting a glutamic acid to γ-carboxyglutamate, will have what effect on the overall charge of the protein containing it? a. It will become more negative. b. It will become more positive. c. It will stay the same. d. There is not enough information to answer the question. e. The answer depends on the salt concentration. 21. The amino acid proline is unique because the R group: a. has a phosphate attached. b. is cyclical. c. is attached to the carboxylic acid carbon. d. is positively charged. e. None of the answers is correct. 22. R. Bruce Merrifield provided an innovation to synthesize peptides. Which statement does NOT describe part of his technology? a. One end of the peptide is attached to a solid support. b. At each step in the cycle, protective chemical groups block unwanted reactions. c. The peptide product must be purified between each step of the cycle. d. The support for the peptides is similar to a chromatography column. e. All of the statements describe part of Merrifield's technology. 23. The term "specific activity" differs from the term "activity" in that specific activity: a. is measured only under optimal conditions. b. is the activity (enzyme units) in a milligram of protein. c. is the activity (enzyme units) of a specific protein. d. refers only to a purified protein. e. refers to proteins other than enzymes. 24. In a mixture of the five proteins listed, which should elute second in size-exclusion (gel-filtration) chromatography? a. cytochrome c, Mr = 13,000 b. immunoglobulin G, Mr = 145,000 c. ribonuclease A, Mr = 13,700 d. RNA polymerase, Mr = 450,000 e. serum albumin, Mr = 68,500

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Chap 03_8e 25. The first step in two-dimensional gel electrophoresis generates a series of protein bands by isoelectric focusing. In a second step, a strip of this gel is turned 90 degrees, placed on another gel containing SDS, and electric current is again applied. In this second step: a. proteins with similar isoelectric points become further separated according to their molecular weights. b. the individual bands become stained so that the isoelectric focus pattern can be visualized. c. the individual bands become visualized by interacting with protein-specific antibodies in the second gel. d. the individual bands undergo a second, more intense isoelectric focusing. e. the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current. 26. Which type of structure describes the overall three-dimensional folding of a polypeptide? a. primary structure b. secondary structure c. tertiary structure d. quaternary structure e. None of the answers is correct. 27. Why can only some amino acids be used to measure protein concentration based on absorption of UV light? a. Only some amino acids are aromatic. b. Only some amino acids are positively charged. c. Only some amino acids are strongly hydrophobic. d. Only some amino acids are strongly hydrophilic. e. Only some amino acids are negatively charged. 28. The peptide alanylglutamylglycylalanylleucine has: a. a disulfide bridge. b. five peptide bonds. c. four peptide bonds. d. no free carboxyl group. e. two free amino groups.

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Chap 03_8e 29. A nonapeptide was determined to have the amino acid composition (Lys)2, (Gly)2, (Phe)2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4-dinitrobenzene (FDNB) and then hydrolyzed; 2,4dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys)2, Phe, and Gly. What is the native sequence determined to be? a. Gly–Phe–Lys–Lys–Gly–Leu–Met–Phe–His b. His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met c. His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly d. His–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly e. Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His 30. The uncommon amino acid selenocysteine has an R group with the structure —CH2—SeH (pKa ≈ 5). In an aqueous solution, pH = 7.0, the R group of selenocysteine would be: a. deprotonated. b. uncharged. c. protonated. d. dimerized. e. aromatic. 31. The structure is a molecule used in the sweeteners Equal and NutraSweet. When heated, the peptide bond will hydrolyze into methanol and which two amino acids?

a. asparagine and tyrosine b. aspartic acid and phenylalanine c. glutamic acid and phenylalanine d. aspartic acid and tryptophan e. glutamic acid and histidine

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Chap 03_8e 32. An octapeptide composed of four repeating glycylalanyl units has: a. one free amino group on an alanyl residue. b. one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue. c. one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. d. two free amino and two free carboxyl groups. e. two free carboxyl groups, both on glycyl residues. 33. Which two amino acids differ from each other by only one atom? a. Ser and Thr b. Leu and Ile c. Ala and Ser d. Asp and Asn e. Ser and Cys 34. According to the table, ion-exchange chromatography would be the LEAST effective method to separate which protein mixture? Protein Molecular weight pI A 12,500 3.2 B 13,200 5.7 C 13,500 10.5 D 36,900 5.8 E 78,400 6.1 a. proteins A, B, and C b. proteins A, C, and D c. proteins B, D, and E d. proteins B, C, and D e. All of the answers are correct.

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Chap 03_8e 35. Compare the sequences taken from four different proteins, and select the answer that BEST characterizes their relationships. A

1 DVEKGKKIDIMKCS

HTVEKGGKHKTGPNLH

GLFGRKTGQAPGYSYT

2 DVQRALKIDNNLGQ

HTVEKGAKHKTAPNVH

GLADRIAYQAKATNEE

3 LVTRPLYIFPNEGQ

HTLEKAAKHKTGPNLH

ALKSSKDLMFTVINDD

4 FFMNEDALVARSSN

HQFAASSIHKNAPQFH

NLKDSKTYLKPVISET

a. Based only on sequences in column B, protein 4 reveals the greatest evolutionary divergence. b. Comparing proteins 1 and 2 in column A reveals that these two proteins have diverged the most throughout evolution. c. Protein 4 is the protein that shows the greatest overall homology to protein 1. d. Proteins 2 and 3 show a greater evolutionary distance than proteins 1 and 4. e. The portions of amino acid sequence shown suggest that these proteins are completely unrelated.

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Chap 03_8e 36. According to the diagram, what is the average net charge of this amino acid at pH = 1?

a. +1 b. +0.5 c. 0 d. –0.5 e. –1 37. All of the 20 common amino acids contain an R group that is attached to the: a. carboxyl group. b. amino group. c. α carbon. d. β carbon. e. It depends on the amino acid.

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Chap 03_8e 38. For the study of a protein in detail, an effort is usually made to first: a. conjugate the protein to a known molecule. b. determine its amino acid composition. c. determine its amino acid sequence. d. determine its molecular weight. e. purify the protein. 39. According to the diagram, which is the BEST estimate of this amino acid's isoelectric point?

a. 0.5 b. 1 c. 1.5 d. 6 e. 11

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Chap 03_8e 40. Which type of structure refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? a. primary structure b. secondary structure c. tertiary structure d. quaternary structure e. None of the answers is correct. 41. All of the amino acids that are found in proteins, except for proline, contain a(n) _____ group. a. amino b. carbonyl c. carboxyl d. ester e. thiol 42. One method used to prevent disulfide bond interference with protein sequencing procedures is: a. cleaving proteins with proteases that specifically recognize disulfide bonds. b. protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups. c. reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups. d. removing cystines from protein sequences by proteolytic cleavage. e. sequencing proteins that do not contain cysteinyl residues. 43. A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which problem? a. Macromolecules were insoluble in the solvents used in mass spectrometry. b. Mass spectrometric analyses of macromolecules were too complex to interpret. c. Mass spectrometric analysis involved molecules in the gas phase. d. Most macromolecules could not be purified to the degree required for mass spectrometric analysis. e. The specialized instruments required were prohibitively expensive. 44. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have: a. a net negative charge. b. a net positive charge. c. no charged groups. d. no net charge. e. positive and negative charges in equal concentration.

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Chap 03_8e 45. What is the approximate charge difference between glutamic acid and α-ketoglutarate at pH 9.5? a. 0 b. c. 1 d. 1 e. 2 46. Iodoacetamides, maleimides, benzyl halides, and bromomethyl ketones can all be used to modify the _____ group on _____ residues. a. amino; basic b. phenyl; Tyr and Trp c. carboxyl; acidic d. sulfhydryl; Cys e. hydroxyl; Ser and Tyr 47. The average molecular weight of the 20 standard amino acids is 138, but biochemists use 110 when estimating the number of amino acids in a protein of known molecular weight. Why? a. The number 110 is based on the fact that the average molecular weight of a protein is 110,000 with an average of 1,000 amino acids. b. The number 110 reflects the higher proportion of small amino acids in proteins, as well as the loss of water when the peptide bond forms. c. The number 110 reflects the number of amino acids found in the typical small protein, and only small proteins have their molecular weight estimated this way. d. The number 110 takes into account the relatively small size of nonstandard amino acids. e. The number 138 represents the molecular weight of conjugated amino acids. 48. Amino acids are ampholytes because they can function as either a(n): a. acid or a base. b. neutral molecule or an ion. c. polar or a nonpolar molecule. d. standard or a nonstandard monomer in proteins. e. transparent or a light-absorbing compound.

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Chap 03_8e 49. To determine the isoelectric point of a protein, first establish that a gel: a. contains a denaturing detergent that can distribute uniform negative charges over the protein's surface. b. exhibits a stable pH gradient when ampholytes become distributed in an electric field. c. is washed with an antibody specific to the protein of interest. d. neutralizes all ionic groups on a protein by titrating them with strong bases. e. relates the unknown protein to a series of protein markers with known molecular weights, Mr. 50. According to the diagram, which pH range offers the greatest buffering power for this amino acid?

a. 0.5–1.5 b. 0–1 c. 1–2 d. 2–3 e. 1–3

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Chap 03_8e 51. According to the diagram, how many titratable groups does this amino acid have?

a. 0 b. 1 c. 2 d. 3 e. It cannot be determined by this diagram. 52. The MOST useful way to classify amino acids is by: a. molecular weight. b. pKa. c. polarity. d. propensity in proteins. e. alphabetical order.

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Chap 03_8e 53. A protein with a high percentage of lysine and arginine residues would be BEST purified and concentrated with which type of column? a. cation exchange b. anion exchange c. size-exclusion chromatography d. affinity chromatography e. reverse-phase chromatography 54. Which pair of amino acids can be used to measure the concentration of proteins based on absorption of UV light? a. proline and valine b. serine and threonine c. aspartate and glutamate d. lysine and histidine e. tyrosine and tryptophan 55. The pKa's of arginine's a-carboxyl group, a-amino group, and side chain are 1.8, 9.0, and 12.5, respectively. What is arginine's pI? a. 7.8 b. 7.2 c. 10.8 d. 5.4 e. 12.5 56. Which correctly matches the amino acid name with its one-letter abbreviation? a. tyrosine, T b. lysine, L c. phenylalanine, P d. aspartic acid, D e. proline, R 57. Which compound is a side product of a peptide bond formation? a. water b. phosphate c. ammonium d. carboxylic acid e. None of the answers is correct.

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Chap 03_8e 58. According to the table, size-exclusion (gel-filtration) chromatography could NOT be used to separate which protein mixture? Protein Molecular weight pI A 12,500 3.2 B 13,200 5.7 C 13,500 10.5 D 36,900 5.8 E 78,400 6.1 a. proteins A, D, and F b. proteins C, E, and F c. proteins B, E, and F d. proteins A, B, and C e. All of the answers are correct. 59. Prosthetic groups in the class of proteins known as glycoproteins are composed of: a. carbohydrates. b. flavin nucleotides. c. lipids. d. metals. e. phosphates. 60. Which item is NOT a biochemical use or function of peptides of small molecular weight? a. artificial sweetener b. hormone c. poison d. antibiotics e. All of the answer choices are correct. 61. A protein with a high percentage of aspartate and glutamate residues would be BEST purified and concentrated with which type of column? a. cation exchange b. anion exchange c. size-exclusion chromatography d. affinity chromatography e. reverse-phase chromatography

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Chap 03_8e 62. The protein bovine serum albumin (BSA), has a molecular weight of about 66,400. Using the Lambert-Beer Law, calculate the concentration of a sample of BSA with an absorbance of 1.3 at 280 nm, assuming the molar extinction coefficient at 280 nm is 43,824 M–1 cm–1. a. 0.51 mg/mL b. 0.86 mg/mL c. 1.97 mg/mL d. 2.56 mg/mL e. 3.78 mg/mL 63. Which statement about aromatic amino acids is correct? a. All are strongly hydrophilic. b. Histidine's ring structure results in its being categorized as aromatic or basic, depending on pH. c. On a molar basis, tryptophan absorbs more ultraviolet light than tyrosine. d. The major contribution to the characteristic absorption of light at 280 nm by proteins is the phenylalanine R group. e. The presence of a ring structure in its R group determines whether or not an amino acid is aromatic.

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Chap 03_8e 64. The gel illustrates the purification of the RecA protein from E. coli. This gel was loaded from the top. Which statement BEST describes how proteins "run" in an SDS gel?

a. The proteins are separated primarily by molecular weight—the largest molecular weight proteins are on the bottom, and the smallest are on the top. b. The proteins are separated primarily by molecular weight—the smallest molecular weight proteins are on the bottom, and the largest are on the top. c. The proteins are separated primarily by charge—the protein with the smallest pI is on the top, and the protein with the largest pI is on the bottom. d. The proteins are separated primarily by charge—the protein with the largest pI is on the top, and the protein with the smallest pI is on the bottom. e. The proteins are separated primarily by their propensity to precipitate—as electrophoresis progresses, the heat generated by the current denatures proteins faster or slower. The slowest to denature is on the bottom, and the fastest to denature is on the top. 65. The term "proteome" has been used to describe: a. regions (domains) within proteins. b. regularities in protein structures. c. the complement of proteins expressed by an organism's genome. d. the structure of a protein-synthesizing ribosome. e. the tertiary structure of a protein.

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Chap 03_8e 66. Which statement about cystine is correct? a. Cystine forms when the —CH2—SH R group is oxidized to form a —CH2—S—S—CH2— disulfide bridge between two cysteines. b. Cystine is an example of a nonstandard amino acid, derived by linking two standard amino acids. c. Cystine is formed by the oxidation of the carboxylic acid group on cysteine. d. Cystine is formed through a peptide linkage between two cysteines. e. Two cystines are released when a —CH2—S—S—CH2— disulfide bridge is reduced to —CH2— SH. 67. Even when a gene is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine: a. molecular weight of the protein. b. the amino-terminal amino acid. c. the location of disulfide bonds. d. the number of amino acids in the protein. e. whether the protein has the amino acid methionine in its sequence. 68. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to: a. determine a protein's isoelectric point. b. determine an enzyme's specific activity. c. determine the amino acid composition of the protein. d. preserve a protein's native structure and biological activity. e. separate proteins exclusively on the basis of molecular weight. 69. On the molecule, the arrow is pointing to the _____ carbon.

a. amino b. α c. β d. γ e. carboxylic acid

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Chap 03_8e 70. According to the diagram, at which pH will this amino acid have a net charge of 0?

a. 11 b. 6 c. 1.5 d. 1 e. 0.5 71. Of the 20 standard amino acids, only _____ is not optically active. The reason is that its side chain _____. a. alanine; is a simple methyl group b. glycine; is a hydrogen atom c. glycine; is unbranched d. lysine; contains only nitrogen e. proline; forms a covalent bond with the amino group

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Chap 03_8e 72. Titration of valine by a strong base, for example NaOH, reveals two pK's. Which is the titration reaction occurring at pK2 (pK2 = 9.62)? a. —COOH + OH– → —COO– + H2O b. —COOH + —NH2 → —COO– + —NH2+ c. —COO– + —NH2+ → —COOH + —NH2 d. —NH3+ + OH– → —NH2 + H2O e. —NH2 + OH– → —NH– + H2O 73. The formation of a peptide bond between two amino acids is an example of a(n) _____ reaction. a. cleavage b. condensation c. group transfer d. isomerization e. oxidation reduction 74. What are the name and abbreviations of the amino acid shown?

a. aspartate; asp; D b. asparagine; asp; N c. asparagine; asn; N d. alanine; ala; A e. arginine; arg; R

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Chap 03_8e 75. If protein A has a pI of 3.1, protein B has a pI of 6.8, and protein C has a pI of 8.9, which protein would elute first from a cation exchange column at pH 7? a. protein A b. protein B c. protein C d. All three proteins would elute at the same time from the column. e. Not enough information about the proteins is given in the problem. 76. According to the diagram, does this amino acid have a titratable R group?

a. yes, as evidenced by the steep center of the curve b. yes, as evidenced by the two relatively flat parts of the curve c. no, as evidenced by only two relatively flat parts of the curve d. no, as evidenced by the steepness of the center of the curve e. It cannot be determined from this graph.

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Chap 03_8e 77. Amino acids without ionizable R groups can act as a zwitterion in a(n) _____ solution. a. nonpolar b. boiling c. acidic d. basic e. neutral 78. What does the molecule SDS do to proteins? a. It neutralizes any charged residues on the protein. b. It denatures large portions of proteins. c. It distributes a large negative charge throughout the protein. d. It neutralizes any charged residues on the protein and denatures large portions of proteins. e. It distributes a large negative charge throughout the protein after it has been denatured. 79. How many units of enzyme activity are there in a sample that uses 4,000 mmol of substrate in 30 seconds? a. 8,000 b. 4,000 c. 120,000 d. 133 e. 4,030 80. At the isoelectric pH of a tetrapeptide: a. only the amino and carboxyl termini contribute charge. b. the amino and carboxyl termini are not charged. c. the total net charge is zero. d. there are four ionic charges. e. two internal amino acids of the tetrapeptide cannot have ionizable R groups. 81. A polypeptide is hydrolyzed, and it is determined that there are 3 Lys residues and 2 Arg residues (as well as other residues). How many peptide fragments can be expected when the native polypeptide is incubated with the proteolytic enzyme trypsin?

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Chap 03_8e 82. These reagents are often used in protein chemistry. Match the reagent with the purpose for which it is best suited. Some answers may be used more than once or not at all; more than one reagent may be suitable for a given purpose. (a) CNBr (cyanogen bromide)

(e) performic acid

(b) Edman reagent (phenylisothiocyanate)

(f) chymotrypsin

(g) trypsin

(d) reducing agent (dithiothreitol) (h) iodoacetamide ___ hydrolysis of peptide bonds on the carboxyl side of Lys and Arg ___ cleavage of peptide bonds on the carboxyl side of Met ___ breakage of disulfide (—S—S—) bonds ___ modification of sulfhydryl groups of Cys ___ determination of the amino acid sequence of a peptide ___ determining the amino-terminal amino acid in a polypeptide

83. If the average molecular weight of the 20 standard amino acids is 138, why do biochemists divide a protein's molecular weight by 110 to estimate its number of amino acid residues?

84. Why do amino acids, when dissolved in water, become zwitterions?

85. How can a polypeptide have only one free amino group and one free carboxyl group?

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Chap 03_8e 86. Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a sizeexclusion (gel-filtration) column?

87. What is the pI, and how is it determined for amino acids that have nonionizable R groups?

88. You are given a solution containing an enzyme that converts B into A. Describe what you would do to determine the specific activity of this enzyme solution.

89. The "signature sequence" shown represents a portion of a protein from four different organisms.

(a) (b) (c) (d)

At which position(s) are amino acid residues invariant? At which position(s) are amino acids limited to positively charged residues? At which position(s) are amino acids limited to negatively charged residues? At which position(s) are amino acids limited to nonpolar residues?

90. Define the primary structure of a protein.

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Chap 03_8e 91. A biochemist wishes to determine the sequence of a protein that contains 123 amino acid residues. After breaking all of the disulfide bonds, the protein is treated with cyanogen bromide (CNBr), and it is determined that this treatment breaks up the protein into seven conveniently sized peptides, which are separated from each other. It is your turn to take over. Outline the steps you would take to determine, unambiguously, the sequence of amino acid residues in the original protein.

92. Describe two major differences between chemical synthesis of polypeptides and synthesis of polypeptides in the living cell.

93. As more OH– equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5?

94. Describe the structures of the amino acids phenylalanine and aspartate in the ionization state expected at pH 7.0. Why is aspartate very soluble in water, whereas phenylalanine is much less soluble?

95. Name two uncommon amino acids that occur in proteins. By what route do they get into proteins?

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Chap 03_8e 96. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins have the properties: pI (isoelectric point)

Size

Bind to DNA?

Protein A

7.4

82,000

yes

3.8

21,500

yes

7.9

23,000

7.8

22,000

yes

What type of protein separation techniques might the biochemist use to separate: (a) protein X from protein A? (b) protein X from protein B? (c) protein X from protein C?

97. You are trying to determine the sequence of a protein that you know is pure. Give the most likely explanation for each of the experimental observations. You may use a simple diagram for your answer. (a) The Sanger reagent (FDNB, fluorodinitrobenzene) identifies Ala and Leu as amino-terminal residues, in roughly equal amounts. (b) The protein has an apparent Mr of 80,000, as determined by SDS-polyacrylamide gel electrophoresis. After treatment of the protein with performic acid, the same technique reveals two proteins of Mr 35,000 and 45,000. (c) Size-exclusion (gel-filtration) chromatography experiments indicate the native protein has an apparent Mr of 160,000.

98. How can isoelectric focusing be used in conjunction with SDS gel electrophoresis?

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Chap 03_8e 99. Lys residues make up 10.5% of the weight of ribonuclease. The ribonuclease molecule contains 10 Lys residues. Calculate the molecular weight of ribonuclease.

100. As a protein is purified, both the amount of total protein and the activity of the purified protein decrease. Why, then, does the specific activity of the purified protein increase?

101. What are the structural characteristics common to all amino acids found in naturally occurring proteins?

102. In the amino acid glycine, what effect does the positively charged —NH3+ group have on the pKa of an amino acid's —COOH group?

103. How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK's?

104. Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide bonds quite stable?

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Chap 03_8e 105. A

Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe Which of the tripeptides: ____ (a) is most negatively charged at pH 7? ____ (b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid? ____ (c) contains the largest number of nonpolar R groups? ____ (d) contains sulfur? ____ (e) will have the greatest light absorbance at 280 nm?

106. The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2, respectively. (a) Which pKa corresponds to the histidine side chain? (b) In a solution at pH 5.4, what percentage of the histidine side chains will carry a positive charge?

107. Briefly describe the five major groupings of amino acids.

108. Only one of the common amino acids has no free α-amino group. Name this amino acid.

109. What ionic form of Gly–Ala–Glu predominates at pH 7? Explain in terms of the structural component of the tripeptide.

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Chap 03_8e 110. The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work.

111. What is the uniquely important acid-base characteristic of the histidine R group?

112. Provide a brief definition for a polymorphic protein.

113. Distinguish between homologs, paralogs, and orthologs as classes of related proteins.

114. Conjugated proteins contain chemical substituents in addition to amino acids. List three classes of conjugated proteins and identify the type of prosthetic group associated with each one.

115. In one or two sentences, describe the usefulness of each of these reagents or reactions in the analysis of protein structure: (a) Edman reagent (phenylisothiocyanate) (b) protease (c) reducing agent (dithiothreitol or β-mercaptoethanol)

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Chap 03_8e 116. What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of sodium dodecyl sulfate (SDS)?

117. For each of these methods of separating proteins, describe the principle of the method, and tell what property of proteins allows their separation by this technique. (a) ion-exchange chromatography (b) size-exclusion (gel-filtration) chromatography (c) affinity chromatography

118. How are "signature sequences" useful in analyzing groups of functionally related proteins?

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Chap 03_8e Answer Key 1. b 2. c 3. b 4. a 5. a 6. a 7. c 8. b 9. d 10. c 11. c 12. b 13. c 14. b 15. b 16. c 17. d 18. b 19. c 20. a 21. b 22. c 23. b 24. b 25. a 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_8e 27. a 28. c 29. c 30. a 31. b 32. c 33. e 34. c 35. a 36. a 37. c 38. e 39. d 40. b 41. a 42. c 43. c 44. b 45. b 46. d 47. b 48. a 49. b 50. e 51. c 52. c 53. a 54. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_8e 55. c 56. d 57. a 58. d 59. a 60. e 61. b 62. c 63. c 64. b 65. c 66. a 67. c 68. e 69. c 70. b 71. b 72. d 73. b 74. c 75. a 76. c 77. e 78. e 79. a 80. c 81. Six fragments would be expected, unless the carboxyl-terminal residue is Lys or Arg; in which case there would be five. Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_8e 82. g; a; d and e; h; b; c 83. For each peptide bond formed, a molecule of water is lost, bringing the average molecular weight down to 120. To reflect the preponderance of low molecular weight amino acids, the average molecular weight is lowered further to 110. 84. Near pH = 7, the carboxylic acid group (—COOH) will dissociate to become a negatively charged —COO– group, and the —NH2 amino group will attract a proton to become a positively charged —NH3+ group. 85. This is possible only if the peptide has no side chains with carboxyl or amino groups. Then, with the exception of the single amino-terminal amino acid and the single carboxyl-terminal amino acid, all the other α-amino and carboxyl groups are covalently condensed into peptide bonds. 86. The column matrix is composed of cross-linked polymers with pores of selected sizes. Smaller molecules can enter pores in the polymer beads from which larger molecules would be excluded. Smaller molecules therefore have a larger three-dimensional space in which to diffuse, making their path through the column longer. Larger molecules migrate faster because they pass directly through the column, unhindered by the bead pores. 87. The pI is the isoelectric point. It occurs at a characteristic pH when a molecule has an equal number of positive and negative charges, or no net charge. For amino acids with nonionizable R groups, pI is the arithmetic mean of a molecule's two pKa values: pI =

(pK1 + pK2)

88. First, add a known volume of the enzyme solution (say, 0.01 mL) to a solution of its substrate B and measure the initial rate at which product A is formed, expressed as μmol/mL of enzyme solution/min. Then measure the total protein concentration, expressed as mg/mL. Finally, divide the enzyme activity (μmol/min/mL) by the protein concentration (mg/mL); the quotient is the specific activity. 89. (a) position 3 (G) and position 8 (C) (b) position 5 (c) position 7 (d) position 2, position 3, position 4, and position 10 90. The primary structure of a protein is its unique sequence of amino acids and any disulfide bridges present in the native structure, that is, its covalent bond structure. 91. (1) Use Edman degradation to determine the sequence of each peptide. (2) Create a second set of peptides by treatment of the protein with a specific protease (e.g., trypsin), and determine the sequence of each of these. (3) Place the peptides in order by their overlaps. (4) Finally, by a similar analysis of the original protein without first breaking disulfide bonds, determine the number and location of —S—S— bridges. 92. There are many such differences; here are a few. Chemical synthesis proceeds from carboxyl terminus to amino terminus; in the living cell, the process starts at the amino terminus and ends at the carboxyl terminus. In the living cell, synthesis occurs under physiological conditions; chemical synthesis does not. Chemical synthesis is only capable of synthesizing short polypeptides; cells can produce proteins of several thousand amino acids. Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_8e 93. Around pH = 9.5, the —NH3+ group will be titrated according to the reaction —NH3+ + OH– → —NH2 + H2O. 94. Aspartate has a polar (hydrophilic) side chain, which forms hydrogen bonds with water. In contrast, phenylalanine has a nonpolar (hydrophobic) side chain. (See Fig. 3-5.) 95. Some examples are 4-hydroxyproline, 5-hydroxylysine, g-carboxyglutamate, N-methyllysine, desmosine, and selenocysteine. Uncommon amino acids in proteins (other than selenocysteine) usually result from chemical modifications of standard amino acid R groups after a protein has been synthesized. 96. (a) Size-exclusion (gel-filtration) chromatography to separate on the basis of size; (b) ion-exchange chromatography or isoelectric focusing to separate on the basis of charge; (c) specific affinity chromatography, using immobilized DNA. 97. (a) The protein has some multiple of two subunits, with Ala and Leu as the amino-terminal residues. (b) The protein has two subunits (Mr 35,000 and 45,000), joined by one or more disulfide bonds. (c) The native protein (Mr 160,000) has two Mr 35,000 subunits and two Mr 40,000 subunits. 98. Isoelectric focusing can separate proteins of the same molecular weight on the basis of differing isoelectric points. SDS gel electrophoresis can then separate proteins with the same isoelectric points on the basis of differing molecular weights. When combined in two-dimensional electrophoresis, a great resolution of large numbers of proteins can be achieved. 99. From the structure of lysine, we can calculate its molecular weight (146); when it condenses (loses H2O, Mr = 18) to form a peptide bond, the resulting residue contributes 146 – 18 = 128 to the protein's molecular weight. If 10 Lys residues contribute 10.5% of the protein's molecular weight, each Lys residue is 1.05%. To calculate the total molecular weight, divide 128 by 1.05% (0.0105); the result is 12,190. (The actual value is 13,700.) 100. Specific activity is the units of enzyme activity (μmol of product/min) divided by the amount of protein (mg). As the protein is purified, some of it is lost in each step, resulting in a drop in activity. However, other contaminating proteins are lost to a much greater extent. Therefore, with each purification step, the purified protein constitutes a greater proportion of the total, resulting in an increase in specific activity. (See also Table 3-5.) 101. All amino acids found in naturally occurring proteins have an α carbon to which are attached a carboxylic acid, an amine, a hydrogen, and a variable side chain. All the amino acids are also in the L configuration. 102. The positively charged amino group stabilizes the negatively charged ionized form of the carboxyl group, — COO– , and repels the departing H+ thereby promoting deprotonation. The effect is to lower the pKa of the carboxyl group. (See Fig. 3-11.) 103. In a certain range around the pKa's of an amino acid, the titration curve levels off. This indicates that for a solution with pH ≈ pK, any given addition of base or acid equivalents will result in the smallest change in pH, which is the definition of a buffer. 104. Peptide bonds are stable because hydrolysis of peptide (or amide) bonds has a high activation energy and as a result occurs very slowly. 105. (a) D; (b) A; (c) E; (d) A; (e) C Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_8e 106. (a) 6.0; (b) 80%. (See the previous problem for an expanded solution to this problem.) 107. Amino acids may be categorized by the chemistry of their R groups: (1) nonpolar aliphatics; (2) polar, uncharged; (3) aromatic; (4) positively charged; (5) negatively charged. (See Fig. 3-5.) 108. The amino acid L-proline has no free α-amino group, but rather has an imino group formed by cyclization of the Rgroup aliphatic chain with the amino group (see Fig. 3-5). 109. The peptide must have an amino-terminal Gly residue, a carboxyl-terminal Glu residue, and ionized amino and carboxyl groups. 110. pH = pKa + log pKa – pH = log antilog (pKa – pH) = antilog (6.0 – 5.4) = 4 = [acid]/[conjugate base], or 4[conjugate base] = [acid] Therefore, at pH 5.4, four-fifths (80%) of the histidine will be in the protonated form. 111. Only the imidazole ring of the histidine R group has a pKa near physiological pH (pKa = 6.0), which suggests that histidine may provide buffering power in intercellular and intracellular fluids. 112. A polymorphic protein is one whose amino acid sequence varies among the human population. The variants have little or no differences in the function or activity of the protein. 113. Homologs are any members of a particular protein family, paralogs are two homologs present in the same species, and orthologs are two homologs present in different species. 114. Any of these are acceptable answers: Lipoproteins, with lipid groups Glycoproteins, with carbohydrate groups Phosphoproteins, with phosphoryl groups Hemoproteins, with heme groups Flavoproteins, with flavin nucleotide groups Metalloproteins, with metal ions (zinc, iron, calcium, etc.) 115. (a) Used in determination of the amino acid sequence of a peptide, starting at its amino terminus; (b) used to produce specific peptide fragments from a polypeptide; (c) used to break disulfide bonds or "bridges" or to keep them from forming and to keep Cys residues in their reduced form. 116. Without SDS, protein migration through a gel would be influenced by the protein's intrinsic net charge—which could be positive or negative—and its unique three-dimensional shape, in addition to its molecular weight. Thus, it would be difficult to ascertain the difference between proteins based upon a comparison of their mobilities in gel electrophoresis.

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Chap 03_8e 117. (a) Ion-exchange chromatography separates proteins on the basis of their charges. (b) Size-exclusion or gelfiltration chromatography separates on the basis of size. (c) Affinity chromatography separates proteins with specific, high affinity for some ligand (attached to an inert support) from other proteins with no such affinity. (See Fig. 3-17.) 118. Such sequences are often present in one taxonomic group or shared by closely related taxonomic groups but are absent in evolutionarily more distant groups. They thus aid in constructing more elaborate evolutionary trees based on protein sequences.

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Chap 04_8e Indicate the answer choice that best completes the statement or answers the question. 1. The structural classification of proteins (based on motifs) is based primarily on their: a. amino acid sequence. b. evolutionary relationships. c. function. d. secondary structure content and arrangement. e. subunit content and arrangement. 2. A lack of ascorbic acid (vitamin C) will result in reduced stability of: a. keratin. b. collagen. c. fibroin. d. myoglobin. e. None of the answers is correct. 3. Which factor is NOT known to be involved in the process of assisted folding of proteins? a. chaperonins b. disulfide interchange c. heat shock proteins d. peptide bond condensation e. peptide bond isomerization 4. A sequence of amino acids in a certain protein is found to be –Ser–Gly–Pro–Gly–. The sequence is most probably part of a(n): a. antiparallel β sheet. b. parallel β sheet. c. α helix. d. α sheet. e. β turn.

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Chap 04_8e 5. Using the Ramachandran plot, identify the secondary structure adopted by an amino acid with phi and psi angles of –90 and 60°, respectively.

a. right-handed α helix b. left-handed α helix c. β sheet d. twisted β sheets e. Amino acids will not adopt this conformation. 6. Which statement concerning protein domains is true? a. They are a form of secondary structure. b. They are examples of structural motifs. c. They consist of separate polypeptide chains (subunits). d. They have been found only in prokaryotic proteins. e. They may retain their correct shape even when separated from the rest of the protein. 7. In an α helix, the R groups on the amino acid residues: a. alternate between the outside and the inside of the helix. b. are found on the outside of the helix spiral. c. cause only right-handed helices to form. d. generate the hydrogen bonds that stabilize the helix. e. stack within the interior of the helix.

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Chap 04_8e 8. The α-keratin chains indicated by the diagram have undergone one chemical step. What subsequent steps are required to alter the shape of the α-keratin chains, such as in hair waving?

a. chemical oxidation and then shape remodeling b. chemical reduction and then chemical oxidation c. chemical reduction and then shape remodeling d. shape remodeling and then chemical oxidation e. shape remodeling and then chemical reduction 9. Which image shows that there are folding intermediates with substantial stability along nearly every folding pathway?

a. I b. II c. III d. IV e. None of the answers is correct.

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Chap 04_8e 10. The MOST important contribution to the stability of a protein's conformation appears to be the: a. entropy increase from the decrease of ordered water molecules forming a solvent shell around it. b. maximum entropy increase from ionic interactions between the ionized amino acids in a protein. c. sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein. d. sum of free energies of formation of many weak interactions between its polar amino acids and surrounding water. e. stabilizing effect of hydrogen bonding between the carbonyl group of one peptide bond and the amino group of another. 11. Which statement is false? a. Collagen is a protein in which the polypeptides are mainly in the α-helical conformation. b. Disulfide linkages are important for keratin structure. c. Gly residues are particularly abundant in collagen. d. Silk fibroin is a protein in which the polypeptide is almost entirely in the β conformation. e. α-Keratin is a protein in which the polypeptides are mainly in the α-helical conformation. 12. Which residues are MOST likely to be enriched in an intrinsically disordered protein that is soluble in water? a. Y, K, W b. E, C, F c. V, I, L d. R, K, A e. H, F, W 13. Which peptide could form an amphipathic α helix? a. Nterm-RIFHKVAE-Cterm b. Nterm-RIHFKMEA-Cterm c. Nterm-RHKEMVAI-Cterm d. Nterm-ALIWSQDK-Cterm e. None of the answers is correct. 14. A protein is highly unlikely to have both f and y angles equal to 0° due to: a. steric hindrance between the side chain and the peptide backbone. b. polarity differences between adjacent side chains. c. hydrophobic interactions between adjacent side chains. d. steric hindrance between adjacent side chains. e. too few van der Waals contacts for proper folding.

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Chap 04_8e 15. In an aqueous solution, protein conformation is determined by two major factors. One is the formation of the maximum number of hydrogen bonds. The other is the: a. formation of the maximum number of hydrophilic interactions. b. maximization of ionic interactions. c. minimization of entropy by the formation of a water solvent shell around the protein. d. placement of hydrophobic amino acid residues within the interior of the protein. e. placement of polar amino acid residues around the exterior of the protein. 16. Which statement about oligomeric proteins is false? a. A subunit may be similar to other proteins. b. All subunits must be identical. c. Many have regulatory roles. d. Some oligomeric proteins can further associate to form large fibers. e. Some subunits may have nonprotein prosthetic groups. 17. Proteins in their functional, folded conformation are called _____ proteins. a. native b. unique c. intrinsic d. inherent e. natural 18. In the α helix, the hydrogen bonds: a. are roughly parallel to the axis of the helix. b. are roughly perpendicular to the axis of the helix. c. occur mainly between electronegative atoms of the R groups. d. occur only between some of the amino acids of the helix. e. occur only near the amino and carboxyl termini of the helix.

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Chap 04_8e 19. Using the Ramachandran plot, identify the secondary structure adopted by an amino acid with phi and psi angles of –90 and –180°, respectively.

a. right-handed α helix b. left-handed α helix c. β sheet d. twisted β sheets e. Amino acids will not adopt this conformation. 20. An ideal α helix has a length per turn of 0.54 nm and a rise along the helix axis for each amino acid residue of 0.15 nm. About how many turns are there for a segment of an ideal α helix that contains 54 amino acids? a. 15 b. 8 c. 100 d. 29 e. less than 1 21. An average protein will NOT be denatured by: a. a detergent such as sodium dodecyl sulfate. b. heating to 90 °C. c. iodoacetic acid. d. pH 10. e. urea.

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Chap 04_8e 22. Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease have shown that: a. folding of denatured ribonuclease into the native, active conformation, requires the input of energy in the form of heat. b. native ribonuclease does not have a unique secondary and tertiary structure. c. the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active. d. the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in ribonuclease. e. the primary sequence of ribonuclease is sufficient to determine its specific secondary and tertiary structure. 23. Which factor is LEAST likely to result in protein denaturation? a. altering net charge by changing pH b. changing the salt concentration c. disruption of weak interactions by boiling d. exposure to detergents e. mixing with organic solvents such as acetone 24. Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a _____ for protein S. a. proteasome b. molecular chaperone c. protein precursor d. structural motif e. supersecondary structural unit 25. Which disease is NOT one characterized by or associated with an unfolded protein aggregate? a. Alzheimer disease b. diabetes c. Parkinson disease d. scurvy e. All of these diseases are linked to unfolded protein aggregates.

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Chap 04_8e 26. Roughly how many amino acids are there in one turn of an α helix? a. 1 b. 2.8 c. 3.6 d. 4.2 e. 10 27. Long-range interactions between residues on a single polypeptide chain could BEST be classified as _____ structure. a. primary b. secondary c. tertiary d. quaternary e. globular 28. Which statement about intrinsically disordered proteins is true? a. They contain small hydrophobic cores. b. They represent misfolded conformations of cellular proteins. c. They have no stable three-dimensional structure and therefore have no cellular function. d. They are responsible for proteostasis. e. They can interact with multiple protein-binding partners and are central to protein interaction networks. 29. Which statement concerning the process of spontaneous folding of proteins is false? a. It may be an essentially random process. b. It may be defective in some human diseases. c. It may involve a gradually decreasing range of conformational species. d. It may involve initial formation of a highly compact state. e. It may involve initial formation of local secondary structure. 30. The _____ secondary structure is formed more readily than other types of secondary structures, most likely due to _____. a. β-turn; hydrogen bonds with solvent molecules b. β-sheet; R-group contacts c. β-sheet; internal hydrogen bonds d. α-helical; R-group contacts e. α-helical; internal hydrogen helical bonds

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Chap 04_8e 31. Which feature tends to prevent the formation of an α helix? a. aromatic residues spaced three or four residues apart b. a sequence with no Gly residues c. a positively charged Lys residue at the carboxyl terminal of a helix d. the presence of a Pro residue e. two Ala residues side by side 32. Which of the images depict a protein-folding pathway with no stable folding intermediates?

a. I b. III c. IV d. I and III e. II and IV 33. Which method would NOT increase the strength of a fibrous protein? a. increasing the number of coiled coils in the supercomplex b. increasing the number of Pro residues in the polypeptide c. increasing the number of Cys residues in the polypeptide d. placing the protein in an oxidizing environment e. All of these methods could increase the strength of a fibrous protein.

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Chap 04_8e 34. This image plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement?

a. The addition of GdnHCl has little effect on protein secondary structure. b. Increasing temperature causes the protein to become unfolded. c. Unfolding of this protein is a cooperative process. d. Ribonuclease A is a heat-stable protein. e. The peptide bonds of the protein are broken around 3.4 M GdnHCl. 35. Intrinsically disordered proteins may: a. wrap around their targets. b. have multiple interaction partners. c. function as molecular "scavengers." d. lack a hydrophobic core. e. All of the answers are correct. 36. The dimensions of an α helix from a fibrous protein such as keratin differ slightly from an a helix from a globular protein. What is the reason for this difference in helical dimensions? a. An α helix from a fibrous protein is left-handed, not right-handed. b. An α helix from a fibrous protein contains mainly hydrophobic residues, elongating the helix. c. An α helix from a fibrous protein contains mainly polar residues, elongating the helix. d. An α helix from a fibrous protein forms a coiled coil, distorting the helix. e. An α helix from a fibrous protein contains mainly Gly residues for more efficient packing.

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Chap 04_8e 37. Pauling and Corey's studies of the peptide bond showed that: a. at pH 7, many different peptide bond conformations are equally probable. b. peptide bonds are essentially planar, with no rotation about the C—N axis. c. peptide bonds in proteins are unusual, and unlike those in small model compounds. d. peptide bond structure is extraordinarily complex. e. primary structure of all proteins is similar, although the secondary and tertiary structure may differ greatly. 38. The difference between the stretching ability of silk and wool fibers, low and high ability to stretch, respectively, is due to their protein components. Which statement correctly attributes the secondary structure contributions to this stretch ability? a. Both silk and wool fibers have roughly equal distributions of a helices and β sheets, but they are arranged in different conformations. b. Silk is mainly β sheets; wool is mainly α helices. c. Silk is mainly α helices; wool is mainly β sheets. d. Silk contains mainly β barrels; wool contains mainly coiled coil α helices. e. Silk contains coiled coil α helices; wool contains mainly β barrels. 39. This secondary structure is an example of a(n):

a. parallel β sheet. b. antiparallel β sheet. c. right-handed α helix. d. left-handed α helix. e. β turn.

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Chap 04_8e 40. Which group of amino acids would be MOST likely to be found in the core of a protein that is folded into a three-dimensional structure and soluble in water? a. N, Y, and K b. I, M, and V c. V, T, and R d. M, S, and Y e. F, Y, and Q 41. Which method would be MOST useful to solve the structure of a small, soluble protein that does not easily form a repeating structure? a. NMR b. x-ray crystallography c. mass spectrometry d. circular dichroism e. electron microscopy 42. Which pairs of bonds within a peptide backbone show free rotation around both bonds? a. Cα—C and N—Cα b. C=O and N—C c. C=O and N—Cα d. N—C and Cα—C e. N—Cα and N—C 43. Which statement does NOT describe a feature of the E. coli GroEL/GroES chaperonin system? a. The conformational changes in GroEL/GroES do not require external energy input. b. An unfolded protein binds to the hydrophobic surface of the GroEL chamber. c. Constraining a protein inside the GroEL chamber restricts the conformational space a protein can explore while folding. d. Constraining a protein inside the GroEL chamber prevents protein aggregation. e. All of these function in the process of the GroEL/GroES chaperonin. 44. Proteins often have regions that can fold and function as an independent entity from the whole protein. These regions are called: a. domains. b. oligomers. c. peptides. d. sites. e. subunits. Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 45. Which backbone arrangement BEST represents that of two peptide bonds? a. Cα—N—Cα—C—Cα—N—Cα—C b. Cα—N—C—C—N—Cα c. C—N—Cα—Cα—C—N d. Cα—C—N—Cα—C—N e. Cα—Cα—C—N—Cα—Cα—C 46. Proteostasis is the cellular process by which protein(s): a. are synthesized. b. are folded. c. are modified. d. are degraded. e. levels are maintained. 47. Kendrew and colleague's studies of the globular myoglobin structure demonstrated that: a. "corners" between α-helical regions invariably lacked proline residue. b. highly polar or charged amino acid residues tended to be located interiorally. c. as expected, myoglobin was completely different from hemoglobin. d. the structure was very compact, with virtually no internal space available for water. e. the α helix predicted by Pauling and Corey was not found in myoglobin. 48. An α helix would be destabilized MOST by: a. an electric dipole spanning several peptide bonds throughout the α helix. b. interactions between neighboring Asp and Arg residues. c. interactions between two adjacent hydrophobic Val residues. d. the presence of an Arg residue near the carboxyl terminus of the α helix. e. the presence of two Lys residues near the amino terminus of the α helix. 49. Which statement is NOT an appropriate description for van der Waals interactions? a. They involve dipole-dipole interactions. b. Their strength depends on the distance between the two interacting atoms. c. They are highly specific. d. An individual van der Waals interaction does not contribute significantly to the stability of a protein. e. They can involve hydrophobic amino acids.

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Chap 04_8e 50. In the diagram, the plane drawn behind the peptide bond indicates the:

a. absence of rotation around the C—N bond because of its partial double-bond character. b. plane of rotation around the Cα—N bond. c. region of steric hindrance determined by the large C=O group. d. region of the peptide bond that contributes to a Ramachandran plot. e. theoretical space between –180 and +180° that can be occupied by the f and y angles in the peptide bond. 51. Which statement about protein folding is NOT true? a. Burial of hydrophobic residues requires at least two layers of secondary structure. b. Generally, α helices and β sheets are found in different layers of a protein structure. c. Residues close together in tertiary structure are always close together in primary structure. d. The β conformation is most stable in a right-handed twist. e. The backbone of a β sheet cannot readily hydrogen-bond to an adjacent α helix. 52. Which interactions are NOT considered to be weak in proteins? a. hydrogen bonds b. hydrophobic interactions c. ionic bonds d. peptide bonds e. van der Waals forces 53. The major reason that antiparallel β-stranded protein structures are more stable than parallel β-stranded structures is that the latter: a. are in a slightly less extended configuration than antiparallel strands. b. do not have as many disulfide cross-links between adjacent strands. c. do not stack in sheets as well as antiparallel strands. d. have fewer lateral hydrogen bonds than antiparallel strands. e. have weaker hydrogen bonds laterally between adjacent strands. Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 54. A repeating structural unit in a multimeric protein is known as a(n): a. domain. b. motif. c. oligomer. d. protomer. e. subunit. 55. If a protein is not folded correctly or becomes partially unfolded, what could NOT be a consequence? a. The protein may form an inactive aggregate that leads to disease. b. The protein may be remodeled by a chaperone. c. The protein may be degraded by the proteasome. d. The protein may be refolded. e. All of these consequences are possible. 56. Which bond has freedom of rotation? I. N—Cα II. Cα—C III. C—N IV. R—Cα a. All of them. b. II, III, and IV c. I, II, and IV d. I, II, and III e. I and IV 57. A _____ protein will often have properties that allow it to be both strong and flexible. a. macromolecular b. fibrous c. globular d. helical e. membrane 58. Amino acid residues commonly found in the middle of β turns are: a. Ala and Gly. b. hydrophobic. c. Pro and Gly. d. those with ionized R groups. e. two Cys.

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Chap 04_8e 59. Which method would be BEST to use to monitor protein secondary structure during the titration of a denaturing agent? a. x-ray crystallography b. electron microscopy c. circular dichroism d. mass spectrometry e. liquid chromatography 60. Interactions between residues on separate polypeptide chains could be BEST classified as _____ structure. a. primary b. secondary c. tertiary d. quaternary e. global 61. Disulfide bonds are more likely to be formed _____ of the cell, due to the _____ environment there. a. inside; oxidizing b. inside; reducing c. outside; oxidizing d. outside; reducing e. inside; hydrophobic 62. Proline residues are infrequently found in _____ due to their _____. a. α helices; decreased ability to serve as hydrogen-bond donors b. α helices; large positive charge that disrupts the repeating structure c. β sheets; decreased ability to serve as hydrogen-bond donors d. β sheets; large positive charge that disrupts the repeating structure e. β turns; decreased flexibility as an amino acid 63. Which amino acid is MOST likely to be found outside of the highlighted/shaded regions on a Ramachandran plot? a. Met b. Cys c. Ala d. Gly e. His

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Chap 04_8e 64. As humans age, their connective tissue, rich in collagen, becomes more rigid and brittle. What is the molecular cause of this change? a. Collagen fibrils change their degree of supercoiling over time. b. Many older adults have vitamin C deficiencies that result in collagen oxidation. c. As cells age, a variant of collagen is expressed. d. Cross-links between collagen fibrils accumulate over time. e. UV damage to collagen accumulates over time. 65. Proteins are classified within families or superfamilies based on similarities in: a. evolutionary origin. b. physicochemical properties. c. structure and/or function. d. subcellular location. e. subunit structure. 66. Which method would be MOST useful to solve the atomic resolution structure of a protein that happens to easily form a repeating structure? a. NMR b. x-ray crystallography c. mass spectrometry d. circular dichroism e. electron microscopy 67. The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are: a. always side by side. b. generally near each other in sequence. c. invariably restricted to about 7 of the 20 standard amino acids. d. often on different polypeptide strands. e. usually near the polypeptide chain's amino terminus or carboxyl terminus.

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Chap 04_8e 68. This secondary structure is an example of a(n):

a. parallel β sheet. b. antiparallel β sheet. c. right-handed α helix. d. left-handed α helix. e. β turn. 69. Which statement is false about salt bridges? a. They can be either stabilizing or destabilizing. b. Their strength increases in environments of lower dielectric constant. c. In the interior of a water-soluble protein, they can provide significant stabilization. d. Most salt bridges occur on the outer surface of water-soluble proteins. e. Thermophilic organisms tend to have a high occurrence of salt bridges.

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Chap 04_8e 70. What is the correct way to classify this protein according to its secondary structural elements?

a. all β b. α + β c. α / β d. β / α / β e. α / β / α 71. Which mutation would be MOST likely to result in amyloid formation? a. Lys→Arg b. Gln→Glu c. Lys→Phe d. Tyr→His e. Trp→Ile 72. Glu residues tend to disrupt an α helix when they occur next to each other in a protein at pH 7.0 because: a. Glu is highly hydrophobic, which destabilizes the helix. b. covalent interactions may occur between the Glu side chains. c. electrostatic repulsion occurs between the Glu side chains. d. Glu adds too much conformational flexibility for helix formation. e. the R groups of Glu can form a hydrogen bond with each other. 73. Describe a reservation about the use of x-ray crystallography in determining the three-dimensional structures of biological molecules.

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Chap 04_8e 74. Describe three of the important features of a β-sheet polypeptide structure. Provide one or two sentences for each feature.

75. What is the rationale for many large proteins containing multiple copies of a polypeptide subunit?

76. Explain how circular dichroism (CD) spectroscopy could be used to measure the denaturation of a protein.

77. Describe the resonance structure of a peptide bond, and explain why there is no rotation around the C—N bond.

78. In a β - α - β loop, describe what is found in the interior of the loop.

79. What are two mechanisms by which "chaperone" proteins assist in the correct folding of polypeptides?

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Chap 04_8e 80. In superhelical proteins, such as collagen, several polypeptide helices are intertwined. What is the function of this superhelical twisting?

81. What important concepts regarding protein thermal denaturation can be inferred from the egg white of a boiled egg?

82. Pauling and Corey showed that in small peptides, six atoms associated with the peptide bond all lie in a plane. On a dipeptide of two amino acids in trans linkage (side chains can be shown as —R), which six atoms are part of the planar structure of the peptide bond?

83. Explain what is meant by motifs in protein structure.

84. Describe the quaternary structure of hemoglobin.

85. Why are glycine and proline often found within a β turn?

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Chap 04_8e 86. What is typically found in the interior of a water-soluble globular protein?

87. Identify and quantify the secondary structures present in this protein.

88. Two proteins, X and Y, have similar tertiary structures. The quaternary structures of the proteins are indicated by the diagram. What differences can be expected in the surfaces of the polypeptides X and Y?

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Chap 04_8e 89. When a polypeptide is in its native conformation, there are weak interactions between its R groups. However, when it is denatured there are similar interactions between the protein groups and water. What then accounts for the greater stability of the native conformation?

90. Describe three of the important features of the α-helical polypeptide structure predicted by Pauling and Corey. Provide one or two sentences for each feature.

91. Where are the hydrogen bonding typically found between two residues in an a helix?

92. How can changes in pH alter the conformation of a protein?

93. Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: The primary sequence of a protein determines its three-dimensional shape and thus its function.

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Chap 04_8e 94. Each of these reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure. (a) urea (b) high temperature (c) detergent (d) low pH

95. Briefly describe the process by which a protein aggregate is degraded by autophagy.

96. Provide a brief explanation for this statement: Soluble globular proteins can be distinguished from soluble intrinsically disordered proteins on the basis of their amino acid content.

97. Why is silk fibroin so strong, but at the same time so soft and flexible?

98. How does one determine the three-dimensional structure of a protein? Your answer should be more than the name of a technique.

99. Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation?

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Chap 04_8e 100. In a classic experiment by Christian Anfinsen in the 1950s, it was shown that ribonuclease A could be denatured and then refolded into a catalytically active protein. What control experiment demonstrated that ribonuclease A did not need a chaperone to become properly folded?

101. Name four factors (bonds or other forces) that contribute to stabilizing the native structure of a protein, and describe one condition or reagent that interferes with each type of stabilizing force.

102. Any given protein is characterized by a unique amino acid sequence (primary structure) and threedimensional (tertiary) structure. How are these related?

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Chap 04_8e Answer Key 1. d 2. b 3. d 4. e 5. c 6. e 7. b 8. d 9. d 10. a 11. a 12. d 13. a 14. a 15. d 16. b 17. a 18. a 19. c 20. a 21. c 22. e 23. b 24. b 25. d 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 27. c 28. e 29. a 30. e 31. d 32. d 33. b 34. c 35. e 36. d 37. b 38. b 39. c 40. b 41. a 42. a 43. a 44. a 45. d 46. e 47. d 48. e 49. c 50. a 51. c 52. d 53. e 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 55. e 56. c 57. b 58. c 59. c 60. d 61. c 62. a 63. d 64. d 65. c 66. b 67. b 68. b 69. d 70. c 71. c 72. c 73. To obtain an x-ray picture of a biomolecule, the molecule must be purified and crystallized under laboratory conditions far different from those encountered by the native molecule. Biomolecules in the cell also have more flexibility and freedom of motion than can be accommodated in a rigid crystal structure. Therefore, the static picture obtained from an x-ray analysis of a crystal may not provide a complete or accurate representation of the biomolecule in vivo. 74. In the β-sheet structure, several extended polypeptides, or two regions of the same polypeptide, lie side by side and are stabilized by hydrogen bonding between adjacent chains. Adjacent chains may be either parallel (with a repeat distance of about 6.5 Å) or antiparallel (7 Å repeat). The R groups are often small and alternately protrude from opposite faces of the β sheet. 75. Each different polypeptide requires a separate gene that must be replicated and transcribed. It is therefore more efficient to have fewer genes, encoding shorter polypeptides that can be used to construct many large proteins.

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Chap 04_8e 76. CD spectroscopy measures the amount of α helix in a given protein. As the protein denatures, the amount of α helix should decrease as the protein chain becomes disordered; this change would be detectable using CD spectroscopy. 77. The intermediate resonance structure imparts a partial double-bond characteristic to the C—N bond, thereby prohibiting rotation. (See Fig. 4-2.) 78. Hydrophobic amino acid residues are usually found in the interior of the loop; these help stabilize the arrangement through hydrophobic interactions. (See Fig. 4-20.) 79. Chaperones protect unfolded polypeptides from aggregation by binding to hydrophobic regions. They can also provide a microenvironment that promotes correct folding. 80. The superhelical twisting of multiple polypeptide helices makes the overall structure more compact and increases its overall strength. 81. Denatured proteins often precipitate and/or aggregate. Denaturation is often not a reversible process. 82. The N and H of the amino and the C and O of the carbonyl are all in the same plane with the two Cα atoms, which are diagonally opposite relative to the C—N bond. (See Fig. 4-2.) 83. Motifs are particularly stable arrangements of elements of secondary structure (e.g., α helix and β conformation), including the connections between them, which are found in a variety of proteins. 84. Each protein molecule is composed of two copies each of two different subunits α and β. The two αβ protomers are arranged with C2 symmetry. 85. A β turn results in a tight 180° reversal in the direction of the polypeptide chain. Glycine is the smallest and thus most flexible amino acid, and proline can readily assume the cis configuration, which facilitates a tight turn. 86. Hydrophobic amino acid residues cluster away from the surface in globular proteins, so much of the protein's interior is a tightly packed combination of hydrocarbon and aromatic ring R groups with very few water molecules. 87. This peptide contains four α helices and two β sheets. 88. Protein X could be expected to have polar or charged amino acids on its surface, as it is soluble as a monomer. Protein Y could be expected to have hydrophobic residues on its surface, which could contribute to a dimerization interface between two monomeric subunits. 89. In the unfolded polypeptide, there are ordered solvation shells of water around the protein groups. The number of water molecules involved in such ordered shells is reduced when the protein folds, resulting in higher entropy. Hence, the lower free energy of the native conformation. 90. The α-helical structure of a polypeptide is tightly wound around a long central axis; each turn of the right-handed helix contains 3.6 residues and stretches 5.4 Å along the axis. The peptide NH is hydrogen-bonded to the carbonyl oxygen of the fourth amino acid along the sequence toward the amino terminus. The R groups of the amino acid residues protrude outward from the helical backbone. Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 91. Hydrogen bonds occur between every carbonyl oxygen in the polypeptide backbone and the peptide —NH of the fourth amino acid residue toward the amino terminus of the chain. (See Fig. 4-2.) 92. Changes in pH can influence the extent to which certain amino acid side chains (or the amino and carboxyl termini) are protonated. The result is a change in net charge on the protein, which can lead to electrostatic attractions or repulsions between different regions of the protein. The final effect is a change in the protein's three-dimensional shape or even complete denaturation. 93. Anfinsen showed that a completely denatured enzyme (ribonuclease) could fold spontaneously into its native, enzymatically active form with only the primary sequence to guide it. 94. (a) Urea acts primarily by disrupting hydrophobic interactions. (b) High temperature provides thermal energy greater than the strength of the weak interactions (hydrogen bonds, electrostatic interactions, hydrophobic interactions, and van der Waals forces), breaking these interactions. (c) Detergents bind to hydrophobic regions of the protein, preventing hydrophobic interactions among several hydrophobic patches on the native protein. (d) Low pH causes protonation of the side chains of Asp, Glu, and His, preventing electrostatic interactions. 95. A protein aggregate is first encapsulated in a membrane, and the contents of the resulting vesicle are degraded after docking with a cytosolic lysosome. 96. Soluble globular proteins contain significant percentages of hydrophobic amino acids that are usually clustered to facilitate packing into the core of the structure. Intrinsically disordered proteins are enriched in charged amino acids and small amino acids such as Gly and Ala. 97. Unlike collagen and keratin, silk fibroin has no covalent cross-links between adjacent strands, or between its stacked sheets, making it very flexible. Fibroin's unusual tensile strength derives from the fact that the peptide backbone of antiparallel β strands is fully extended, and that the R groups in the stacked pleated sheets interdigitate, preventing any longitudinal sliding of the sheets across one another. 98. The protein is crystallized, and the crystal structure is determined by x-ray diffraction. The pattern of diffracted xrays yields, by Fourier transformation, the three-dimensional distribution of electron density. By matching electron density with the known sequence of amino acids in the protein, each region of electron density is identified as a single atom. Sometimes, the three-dimensional structure of a small protein or peptide can be determined in solution by sophisticated analysis of the NMR spectrum of the polypeptide. This technique can also reveal dynamic aspects of protein structure such as conformational changes. Computer analysis of multidimensional NMR spectra can be used to generate a picture of the three-dimensional structure of a protein. A threedimensional structure can also be determined by cryo-electron microscopy. 99. Because a protein may be denatured through the disruption of hydrogen bonds and hydrophobic interactions by salts or organic solvents, removal of those conditions will reestablish the original aqueous environment, often permitting the protein to fold once again into its native conformation. If the protein does not renature, it may be because the denaturing treatment removed a required prosthetic group, or because the normal folding pathway requires the presence of a polypeptide chain binding protein or molecular chaperone. The normal folding pathway could also be mediated by a larger polypeptide, which is then cleaved (e.g., insulin). Denatured insulin would not refold easily. Copyright Macmillan Learning. Powered by Cognero.

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Chap 04_8e 100. A chemically synthesized ribonuclease A was shown to be catalytically active. This control demonstrated that a minor contaminant in Anfinsen's experiment did not contribute to the renaturation of the enzyme. 101. Any of the following forces stabilize native protein structures and are disrupted by the listed conditions or reagents: (a) disulfide bonds by reducing conditions or mercaptoethanol or dithiothreitol, (b) hydrogen bonds by pH extremes, (c) hydrophobic interactions by detergents or urea or guanidine hydrochloride, (d) ionic interactions by changes in pH or ionic strength, and (e) van der Waals interactions by any unfolding condition. 102. The three-dimensional structure is determined by the amino acid sequence. This means that the amino acid sequence contains all of the information that is required for the polypeptide chain to fold up into a discrete threedimensional shape.

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Chap 05_8e Indicate the answer choice that best completes the statement or answers the question. 1. When oxygen binds to a heme-containing protein, the two open coordination bonds of Fe2+ are occupied by: a. one O atom and one amino acid atom. b. one O2 molecule and one amino acid atom. c. one O2 molecule and one heme atom. d. two O atoms. e. two O2 molecules. 2. If myosin head groups were able to bind but not hydrolyze ATP due to an alteration in the protein structure, but could still bind and release ADP and inorganic phosphate (Pi), which step in the actin-myosin cycle would NOT take place? a. dissociation of the myosin head group from the actin filament b. repositioning of the myosin head group on the actin filament c. attachment of the myosin head group to the actin filament d. the "power stroke" conformational change in the myosin head group e. the conformational change in the myosin head group in the presence of Ca2+ 3. The coordinated nitrogen atoms in the heme prosthetic group have _____ character, which prevents conversion of the heme iron from the _____ state to the _____ state. a. electron-donating; Fe2+; Fe3+ b. electron-donating; Fe3+; Fe2+ c. electron-accepting; Fe2+; Fe3+ d. electron-accepting; Fe3+; Fe2+ e. electron-accepting; Fe+; Fe0 4. The interactions of ligands with proteins: a. are relatively nonspecific. b. are relatively rare in biological systems. c. are usually irreversible. d. are usually transient. e. usually result in the inactivation of the proteins.

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Chap 05_8e 5. Muscle fibers are made up of which protein? a. myosin b. actin c. calcitonin d. both myosin and actin e. both myosin and calcitonin 6. The change in hemoglobin-binding affinity for oxygen due to changing pH and CO2 concentration in the blood is known as the: a. Hill hypothesis. b. Messelson theory. c. Bohr effect. d. Higgs observation. e. Boyle hypothesis. 7. Antigens typically bind to antibodies via which type of interactions? a. covalent bonding b. hydrophobic interactions c. hydrogen bonding d. both covalent bonding and hydrophobic interactions e. both hydrophobic interactions and hydrogen bonding 8. During muscle contraction, hydrolysis of ATP results in a change in the: a. conformation of actin. b. conformation of myosin. c. structure of the myofibrils. d. structure of the sarcoplasmic reticulum. e. structure of the Z disk. 9. A significant contribution to the change in hemoglobin affinity for oxygen from pH 7.2 to pH 7.6 is due to a change in the protonation state of which amino acid side chain? a. Cys b. His c. Ser d. Asp e. Lys

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Chap 05_8e 10. If a developing fetus made beta hemoglobin subunits instead of gamma hemoglobin subunits, what would be MOST likely to occur? a. The fetus would extract O2 from its mother's blood more effectively. b. The fetal hemoglobin would have a higher affinity for 2,3-bisphosphoglycerate. c. The fetal hemoglobin would have a lower affinity for CO. d. The fetus would not be able to extract O2 from its mother's blood as effectively. e. The fetus would be less susceptible to sickle cell anemia. 11. Carbon monoxide (CO) is toxic to humans because it: a. binds to myoglobin and causes it to denature. b. is rapidly converted to toxic CO2. c. binds to the globin portion of hemoglobin and prevents the binding of O2. d. binds to the Fe in hemoglobin and prevents the binding of O2. e. binds to the heme portion of hemoglobin and causes heme to unbind from hemoglobin. 12. Which statement is NOT correct concerning 2,3-bisphosphoglycerate (BPG)? a. It binds at a distance from the heme groups of hemoglobin. b. It binds with lower affinity to fetal hemoglobin than to adult hemoglobin. c. It increases the affinity of hemoglobin for oxygen. d. It is an allosteric modulator. e. It is normally found associated with the hemoglobin extracted from red blood cells. 13. Individual contractile units in muscle fibers are called: a. Z disks. b. sarcomeres. c. myofibrils. d. myomeres. e. porphyrins. 14. Which generalization concerning motor proteins is correct? a. They convert chemical energy into kinetic energy. b. They convert chemical energy into potential energy. c. They convert kinetic energy into chemical energy. d. They convert kinetic energy into rotational energy. e. They convert potential energy into chemical energy.

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Chap 05_8e 15. Which antibody is secreted as a cross-linked pentamer? a. IgA b. IgD c. IgE d. IgG e. IgM 16. What is the biological advantage to the sigmoidal binding curve of hemoglobin for oxygen? a. It ensures that hemoglobin has a high affinity for oxygen. b. It allows hemoglobin to bind oxygen irreversibly. c. It ensures that hemoglobin can bind oxygen only weakly. d. It allows hemoglobin to shift between low and high affinities for oxygen. e. It allows hemoglobin to bind oxygen at varying pH. 17. Which statement about antigen-antibody interactions is correct? a. Antigens bind to antibodies cooperatively. b. Antigens bind to antibodies through induced fit. c. Antigens bind to antibodies at both the Fab and Fc parts of the antibody. d. Molecules with molecular weights of less than 5,000 daltons are exceptionally antigenic and bind to antibodies extremely well. e. Antigens bind only to antibodies that have a preformed binding site that is perfectly complementary to the antigen. 18. A person who is HIV positive has reduced immune system function. A deficiency of which cells that are targets of HIV viral infections would be the MOST likely reason? a. B cells b. neutrophils c. cytotoxic T cells d. helper T cells e. erythrocytes 19. The amino acid substitution of Val for Glu in hemoglobin S results in aggregation of the protein because of _____ interactions between molecules. a. covalent b. disulfide c. hydrogen-bonding d. hydrophobic e. ionic

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Chap 05_8e 20. You are examining the effects of a mutation in the proximal histidine of a heme-containing protein. This mutation has changed the histidine into an alanine. Based on your knowledge of the role of heme in hemoglobin and how it is coordinated in the protein, what is the MOST likely effect of the mutation? a. Heme will no longer be bound in the protein. b. The iron in heme will be fully coordinated. c. The iron in heme will have two uncoordinated bonds. d. The heme will be able to bind to O2 more effectively than it will to CO. e. There will be no effect on the protein due to this mutation. 21. Two proteins bind to the same ligand, and protein A has half of its binding sites occupied when the ligand concentration is 0.5 mM, while protein B has half of its binding sites occupied when the ligand concentration is at 0.3 mM. Which protein binds the ligand more strongly, and what is the dissociation constant for that protein-ligand interaction? a. Protein A binds more strongly, and Kd = 0.3 mM. b. Protein A binds more strongly, and Kd = 0.5 mM. c. Protein B binds more strongly, and Kd = 0.3 mM. d. Protein B binds more strongly, and Kd = 0.5 mM. e. Both proteins bind the ligand with the same affinity, and Kd = 0.4 mM. 22. In the binding of oxygen to myoglobin, the relationship between the concentration of oxygen and the fraction of binding sites occupied can BEST be described as: a. hyperbolic. b. linear with a negative slope. c. linear with a positive slope. d. random. e. sigmoidal.

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Chap 05_8e 23. Examine the binding curves for two proteins (A and B) that bind the same ligand. Which statement applies?

a. The dissociation constant for A is less than that of B. b. B has more than one type of ligand that can bind. c. B has a stronger affinity for the ligand than protein A does. d. Protein A is oligomeric. e. Protein A has multiple binding sites for the ligand. 24. Macrophages bind to the _____ region of IgG antibodies, thereby triggering phagocytosis of antibodyantigen complexes. a. Fab b. Fc c. epitope d. hinge e. antigen 25. Which amino acid in hemoglobin is involved in coordinating iron in addition to the heme prosthetic group? a. Tyr b. Glu c. His d. Val e. Cys

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Chap 05_8e 26. A Hill coefficient (nH) of 2 indicates that there: a. is positive cooperativity in ligand binding. b. are two ligand-binding sites. c. is negative cooperativity in ligand binding. d. is positive cooperativity in ligand binding and there are two ligand-binding sites. e. is negative cooperativity in ligand binding and there are two ligand-binding sites. 27. Calculate the fraction of binding sites occupied by a ligand if the equilibrium concentrations of protein-ligand complex and free protein are 8 mM and 12 mM, respectively. a. 0.667 b. 0.400 c. 0.600 d. 0.750 e. 0.500 28. Which statement about CO binding to hemoglobin is NOT correct? a. CO binds to hemoglobin better than O2 does. b. CO binding to hemoglobin is reversible. c. The binding of one CO molecule to hemoglobin makes the binding of other CO molecules more efficient. d. A histidine residue in hemoglobin reduces the affinity of CO binding to heme. e. The binding of one CO molecule to hemoglobin makes the binding of O2 molecules more efficient. 29. Which type of antibody interacts with basophils and plays a role in the allergic response? a. IgA b. IgD c. IgE d. IgG e. IgM 30. Which statement about protein-ligand binding is correct? a. The Ka is equal to the concentration of ligand when all of the binding sites are occupied. b. The Ka is independent of such conditions as salt concentration and pH. c. The larger the Ka (association constant), the weaker the affinity. d. The larger the Ka, the faster is the binding. e. The larger the Ka, the smaller the Kd (dissociation constant).

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Chap 05_8e 31. Which statement about antibodies is incorrect? a. Antibodies bind to antigens via induced fit. b. Antibodies typically bind to antigens more strongly than enzymes bind to substrates. c. Antibodies can be both soluble and membrane-bound. d. Antibodies never release antigens once they are bound together. e. More than 100 million different antibodies can be produced in humans. 32. An individual molecular structure within an antigen to which an individual antibody binds is a(n): a. antigen. b. epitope. c. Fab region. d. Fc region e. MHC site. 33. You want to purify a specific soluble protein from a solution of lysed cells so that you can conduct biochemical tests of the protein's function. To best achieve this, which type of antibody would be MOST effective to use in your affinity purification? a. monoclonal IgE b. polyclonal IgE c. monoclonal IgG d. polyclonal IgG e. monoclonal IgM 34. Which immune system cells are responsible for producing antibodies? a. macrophages b. B cells c. helper T cells d. cytotoxic T cells e. erythrocytes 35. Tropomyosin and troponin prevent muscle contractions in the absence of Ca2+ because they: a. block the myosin head binding sites on actin filaments. b. prevent the hydrolysis of ATP by myosin. c. degrade the actin filaments. d. increase the release of Pi by myosin. e. block the "power stroke" conformational change of actin filaments.

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Chap 05_8e 36. Which molecule binds MOST strongly to the heme iron? a. N2 b. O2 c. CO2 d. CO e. H2O 37. Consider a protein-ligand equilibrium where P + L ⇌ PL. What happens to the ratio of protein-ligand complex to free protein if the equilibrium concentration of free ligand is doubled? Note: P = protein; L = ligand; PL = protein-ligand complex. a. The ratio decreases by a factor of four. b. The ratio is constant. c. The ratio is doubled. d. The ratio is halved. e. There is no effect on the ratio. 38. In hemoglobin, the transition from T state to R state (low to high affinity) is triggered by: a. Fe2+ binding. b. heme binding. c. oxygen binding. d. subunit association. e. subunit dissociation. 39. Which statement comparing hemoglobin and myoglobin is NOT correct? a. Hemoglobin binds to O2 cooperatively, while myoglobin does not. b. Hemoglobin is a multisubunit protein, while myoglobin is not. c. Hemoglobin and myoglobin are both primarily composed of α helices. d. Hemoglobin has a stronger binding affinity for O2 than myoglobin does. e. Hemoglobin and myoglobin both contain the heme prosthetic group. 40. The fundamental cause of sickle-cell disease is a change in the structure of: a. blood. b. capillaries. c. hemoglobin. d. red cells. e. the heart.

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Chap 05_8e 41. Myoglobin and the subunits of hemoglobin have: a. no obvious structural relationship. b. very different primary and tertiary structures. c. very similar primary and tertiary structures. d. very similar primary structures, but different tertiary structures. e. very similar tertiary structures, but different primary structures. 42. Antibodies against a specific antigen can be injected into a person to provide passive immunity. For which reason is this NOT as effective as the process of vaccination with that antigen? a. Injection of antibodies does not provide long-lasting immunity. b. Vaccination with antigens triggers a clonal selection of B cells and cytotoxic T cells. c. Injection of antibodies may cause allergic reactions, while vaccination never causes allergic reactions. d. Injection of antibodies does not provide long-lasting immunity, and vaccination with antigens triggers a clonal selection of B cells and cytotoxic T cells. e. Injection of antibodies does not provide long-lasting immunity and may cause allergic reactions, while vaccination never causes allergic reactions. 43. The predominant structural feature in myosin molecules is: a. a β structure. b. an α helix. c. the Fab domain. d. the light chain. e. the meromyosin domain. 44. Which event triggers a "power stroke" in myosin? a. hydrolysis of ATP b. binding of ATP c. release of ADP d. release of Pi e. degradation of actin 45. During muscle contraction, the _____ of myofibrils contract and the _____ move closer together due to the movement of myosin thick filaments along actin thin filaments. a. Z disks; A bands b. A bands; M lines c. I bands; Z disks d. I bands; M lines e. M lines; I bands

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Chap 05_8e 46. Sickle cell anemia is often lethal in childhood, yet the gene for sickle cell hemoglobin persists in the human population. Which statement BEST describes why this is the case? a. Individuals with sickle cell anemia are healthier than are individuals with normal hemoglobin. b. Individuals with sickle cell trait can carry more oxygen in their blood than do individuals with normal hemoglobin. c. Individuals with normal hemoglobin have malaria infections less often than do individuals with sickle cell trait. d. Individuals with sickle cell trait are protected from malaria infection, while individuals with normal hemoglobin are not. e. Individuals with sickle cell anemia have more hemoglobin in their blood than do individuals with normal hemoglobin. 47. The covalent bonds that hold antibody structures together are formed from which amino acid side chains? a. His b. Thr c. Cys d. Met e. Ser 48. Myosin obtains its high tensile strength due to its composition of: a. α helices supercoiled around each other in a left-handed coiled coil. b. β strands layered on top of each other. c. α helices supercoiled around each other in a right-handed coiled coil. d. β strands coiled around each other in a β-barrel conformation. e. β helices supercoiled around each other in a right-handed coiled coil. 49. Which types of covalent bonds hold antibody structures together? a. hydrogen bonds b. disulfide bonds c. van der Waals interactions d. London forces e. ionic bonds 50. Which statement is NOT correct concerning cooperative binding of a ligand to a protein? a. It is usually a form of allosteric interaction. b. It is usually associated with proteins with multiple subunits. c. It rarely occurs in enzymes. d. It results in a nonlinear Hill plot. e. It results in a sigmoidal binding curve. Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_8e 51. A test where antibodies are used to quantitatively detect the presence of antiviral antibodies in human blood samples is referred to as: a. Western blot. b. ELISA. c. Northern blot. d. FRET. e. PCR. 52. Which part of the IgG molecule is NOT involved in binding to an antigen? a. Fab b. Fc c. heavy chain d. light chain e. variable domain 53. Which antibody is principally found in saliva, tears, and breast milk? a. IgA b. IgD c. IgE d. IgG e. IgM 54. IgG antibodies have _____ binding site(s) that is/are made up of the _____ regions of the light and heavy chains. a. one; variable b. one; constant c. two; variable d. two; constant e. one; diversity 55. Myosin moves relative to actin filaments by using energy derived from the hydrolysis of which molecule? a. GTP b. ATP c. NADH d. coenzyme A e. ADP

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Chap 05_8e 56. Nerve impulses control muscle contractions by releasing which ion? a. H+ b. Mg2+ c. Na+ d. Ca2+ e. Fe2+ 57. Small molecules attached to larger protein structures that elicit an immune response are referred to as: a. antibodies. b. globins. c. allergens. d. haptens. e. hemes. 58. An allosteric interaction between a ligand and a protein is one in which: a. binding of a molecule to a binding site affects binding of additional molecules to the same site. b. binding of a molecule to a binding site affects binding properties of another site on the protein. c. binding of the ligand to the protein is covalent. d. multiple molecules of the same ligand can bind to the same binding site. e. two different ligands can bind to the same binding site. 59. The immunoglobulin fold motif in antibodies is composed primarily of which type(s) of secondary structure? a. α helices b. β strands c. random coils d. double helices e. δ sheets 60. You are working as a scientist in an antibody-design group at a biologics company. Based on your knowledge of antibodies, which region(s) on which antibody type should you target for your design efforts to develop new antigen-binding capabilities in soluble antibodies? a. IgG antibodies, variable light and variable heavy chain regions b. IgE antibodies, constant light and variable heavy chain regions c. IgG antibodies, only variable heavy chain regions d. IgD antibodies, variable light and variable heavy chain regions e. IgA antibodies, constant light and constant heavy chain regions

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Chap 05_8e 61. Sickle cell anemia is caused by a single mutation in the hemoglobin protein from a Glu to a Val, which results in which alteration in the hemoglobin subunits? a. more neutral charges and formation of a nucleophilic contact point b. fewer negative charges and formation of a hydrophobic contact point c. fewer positive charges and formation of a hydrophobic contact point d. more negative charges and formation of a hydrophilic contact point e. more positive charges and formation of a hydrophilic contact point 62. A monoclonal antibody differs from a polyclonal antibody in that monoclonal antibodies: a. are labeled with chemicals that can be visualized. b. are produced by cells from the same organism that produced the antigen. c. are synthesized by a population of identical, or "cloned," cells. d. are synthesized only in living organisms. e. have only a single polypeptide chain that can recognize an antigen. 63. Conversion of CO2 in the blood into the more soluble form of HCO3– is catalyzed by which enzyme? a. hemoglobinase b. carbonic anhydrase c. bicarbonase d. carbondioxidease e. carbon hydratase 64. The binding of oxygen to hemoglobin stabilizes the _____ state of the protein due to interactions between _____ residues in the center of the multisubunit complex. a. R; Thr b. R; Glu c. R; His d. T; Glu e. T; His 65. The energy that is released by the hydrolysis of ATP by actin is used for: a. actin filament assembly. b. actin filament disassembly. c. actin-myosin assembly. d. actin-myosin disassembly. e. muscle contraction.

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Chap 05_8e 66. Which protein undergoes a conformational change upon interacting with Ca2+, leading to stimulation of muscle contraction? a. actin b. myosin c. troponin d. hemoglobin e. immunoglobin 67. The binding site of a protein is complementary to a specific ligand due to which characteristic of the binding site? a. its size b. its shape c. its charge d. its hydrophobicity e. All of the answers are correct. 68. Patients with chronic hypoxia (low O2 levels) due to decreased lung function may adapt by increasing their circulating BPG levels. Predict which outcome will be true for such a patient. a. p50 for O2 will be decreased. b. p50 for O2 will be increased. c. The R state of hemoglobin will be favored. d. O2 binding to hemoglobin will be hyperbolic. e. None of the answers is correct. 69. The Fab regions of an antibody are made of which protein chain? a. a light chain containing variable and constant regions b. a heavy chain containing variable and constant regions c. a heavy chain containing only constant regions d. both a light chain and a heavy chain containing variable and constant regions e. both a light chain containing variable and constant regions and a heavy chain containing only constant regions 70. A prosthetic group of a protein is a nonprotein structure that is _____ the protein. a. a ligand of b. a part of the secondary structure of c. a substrate of d. permanently associated with e. transiently bound to Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_8e 71. CO binds more strongly to the heme iron than O2 does due to which reason? a. CO binds to the heme iron perpendicular to the porphyrin ring, allowing maximum electron orbital overlap between CO and Fe2+. b. CO weighs less than O2, therefore binding to the heme iron more easily. c. CO binds to the heme iron covalently, while O2 binds via ionic interactions. d. All of the answers are correct. e. None of the answers is correct. 72. Hemoglobin is involved in the transport of which ion and/or molecule through the blood? a. CO2 b. O2 c. H+ d. both CO2 and O2 e. CO2, O2, and H+ 73. Describe briefly the structure of myosin.

74. What fraction of ligand binding sites are occupied (θ) when [ligand] = Kd ? Show your work.

75. What is the chemical basis for the specificity of binding of an immunoglobulin antibody to a particular antigen?

76. Describe the concept of induced fit in protein-ligand binding.

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Chap 05_8e 77. Explain why the structure of myoglobin makes it function well as an oxygen-storage protein, whereas the structure of hemoglobin makes it function well as an oxygen-transport protein.

78. Why is carbon monoxide (CO) toxic to aerobic organisms?

79. What is the concept of induced fit as it applies to antigen-antibody binding?

80. (a) What is the effect of pH on the binding of oxygen to hemoglobin (the Bohr effect)? (b) Briefly describe the mechanism of this effect.

81. What is the role of ATP and ATP hydrolysis in the cycle of actin-myosin association and dissociation that leads to muscle contraction?

82. Describe how you would determine the Ka (association constant) for a ligand and a protein.

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Chap 05_8e 83. What properties of antibodies make them useful biochemical reagents? Describe one biochemical application of antibodies (with more than just the name of the technique).

84. Explain why most multicellular organisms use an iron-containing protein for oxygen binding rather than free Fe2+. Your answer should include an explanation of (a) the role of heme and (b) the role of the protein itself.

85. Describe the process of using ELISA to detect the presence of anti-HIV protease IgG antibodies in human blood samples. Include how the assay would be prepared, the order of reagent addition, and how differing levels of anti-HIV protease antibodies could be detected by the assay.

86. Imagine that you are an athlete competing in an international event that will take place at sea level. Without taking any performance-enhancing drugs or blood doping, what could you do in your training to enhance oxygen transport in your body? Describe what will chemically change in your blood as a result of your training and how this will enhance oxygen transport.

87. Explain briefly why the relative affinity of heme for oxygen and carbon monoxide is changed by the presence of the myoglobin protein.

88. What is the relationship between G-actin and F-actin?

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Chap 05_8e 89. Describe the cycle of actin-myosin association and dissociation that leads to muscle contraction.

90. How does BPG binding to hemoglobin decrease its affinity for oxygen?

91. Describe briefly the two principal models for the cooperative binding of ligands to proteins with multiple binding sites.

92. For the binding of a ligand to a protein, what is the relationship between the Ka (association constant), the Kd (dissociation constant), and the affinity of the protein for the ligand?

93. Explain how the effects of sickle cell disease demonstrate that hemoglobin undergoes a conformational change upon releasing oxygen.

94. Describe how immunoaffinity chromatography is performed.

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Chap 05_8e 95. Describe in detail the cycle of myosin movement along actin filaments, including the role of ATP and its hydrolysis products in generating the "power stroke."

96. Although the myosin molecule "walks" along actin in discrete steps, you are able to make smooth motions using your muscles. Explain how this is possible.

97. Describe briefly the basic structure of an IgG protein molecule.

98. Fetal hemoglobin binds BPG with lower affinity than adult hemoglobin. How does this property facilitate the transfer of O2 from mother to fetus?

99. Describe how cooperativity of oxygen binding in hemoglobin is advantageous for the transport of oxygen from the lungs to the tissues and why myoglobin would not be a good protein to use for oxygen transport.

100. Describe how calcium ions are involved in stimulating muscle contraction. Include the involvement of troponin and tropomyosin in your description.

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Chap 05_8e Answer Key 1. b 2. b 3. a 4. d 5. d 6. c 7. e 8. b 9. b 10. d 11. d 12. c 13. b 14. a 15. e 16. d 17. b 18. d 19. d 20. c 21. c 22. a 23. a 24. b 25. c 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_8e 27. b 28. d 29. c 30. e 31. d 32. b 33. c 34. b 35. a 36. d 37. e 38. c 39. d 40. c 41. e 42. d 43. b 44. d 45. c 46. d 47. c 48. a 49. b 50. c 51. b 52. b 53. a 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_8e 55. b 56. d 57. d 58. b 59. b 60. a 61. b 62. c 63. b 64. c 65. a 66. c 67. e 68. b 69. d 70. d 71. a 72. e 73. Myosin contains two copies of a large polypeptide (heavy chain) and four copies of a small polypeptide (light chain). The α helix contributes significantly to the structure of the heavy chains. At their carboxyl termini, the heavy chains are wrapped around each other in a fibrous left-handed coil. At their amino termini, they each have a globular domain with which the light chains are associated. 74. Half of the ligand binding sites are occupied when [ligand] = Kd . 75. Specific binding results from complementarity between the chemical properties (such as size, charge, and hydrophobicity) of the antigen and the antigen-binding site of the antibody. 76. Induced fit refers to the structural adaptations that occur when a ligand binds to a protein. This often involves a conformational change in the protein that alters the binding site to make it more complementary to the ligand.

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Chap 05_8e 77. The hyperbolic binding of oxygen to the single binding site of myoglobin results in a high affinity even at the relatively low partial pressures of O2 that occur in tissues. In contrast, the cooperative (sigmoidal) binding of O2 to the multiple binding sites of hemoglobin results in high affinity at high partial pressures such as occur in the lungs, but lower affinity in the tissues. This permits hemoglobin to bind O2 in the lungs and release it in the tissues. 78. It binds to heme with a higher affinity than oxygen, and thus prevents oxygen from binding to hemoglobin. 79. The conformations of the antigen and antigen-binding site of the antibody are influenced by each other and change as binding occurs. These conformational changes increase the chemical complementarity of the sites and result in tighter binding. 80. (a) The affinity decreases with decreasing pH. (b) At lower pH (i.e., higher H+ concentration), there is increasing protonation of protein residues such as histidine, which stabilizes the low-affinity conformation of the protein subunits. 81. ATP binding to myosin results in a conformational change that causes dissociation of actin from the myosin. ATP hydrolysis results in a change of orientation of the myosin relative to the actin filament, which allows movement to the next actin subunit. This is followed initially by release of the phosphate hydrolysis product and weak binding of the myosin to this actin subunit, and, subsequently, by tight binding and release of the ADP hydrolysis product. 82. An experiment would be carried out in which a fixed amount of the protein is incubated with varying amounts of ligand (long enough to reach equilibrium). The fraction of protein molecules that have a molecule of ligand bound is then determined. A plot of this fraction (θ) versus ligand concentration [L] should yield a hyperbola. The value of [L] when θ= 0.5 is equal to 1/Ka. 83. The important properties are the high specificity of protein recognition, and the high affinity of the antibody-antigen association. These make possible immunoaffinity chromatography, immunocytochemistry, enzyme-linked immunosorbent assay (ELISA), and immunoblotting. 84. (a) Binding of free Fe2+ to oxygen would result in the formation of reactive oxygen species that can damage biological structures. Heme-bound iron is less reactive in this regard. (b) Binding of oxygen to free heme can result in irreversible oxidation of the Fe2+ to Fe3+ that does not bind oxygen. The environment of the heme group in proteins helps to prevent this from occurring. 85. First, the assay must be prepared by adhering HIV protease to a surface, then the remaining sites on the surface must be blocked by adhering other non-HIV proteins. Samples of human blood could then be applied to the surface and washed off. Any antibodies in the blood samples that can bind to the HIV protease should then remain. Secondary antibodies that recognize human IgG antibodies should then be applied to the surface. These secondary antibodies should have an enzyme or fluorescent molecule attached to them. After applying the secondary antibodies, the surface should again be washed. If the human blood contained anti-HIV protease IgG antibodies, then their presence should be detected by either fluorescence of the secondary antibodies or by enzymatic reactions catalyzed by the enzymes on the secondary antibodies. The higher the fluorescence or enzyme activity, the more anti-HIV protease antibodies were present in the human blood sample.

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Chap 05_8e 86. You could train at high elevations to increase the level of 2,3-bisphosphoglycerate (BPG) in your blood. This increased BPG will result in a decreased affinity of your hemoglobin for oxygen. At high elevations, this will result in your hemoglobin binding less oxygen in the lungs but releasing more oxygen in the tissues, allowing for optimal cellular respiration. At sea level, the increased BPG will also decrease the binding affinity of your hemoglobin for oxygen, but the pressure of oxygen in your lungs at sea level will be much higher. Due to the high BPG levels, however, you will still release more oxygen to the tissues since hemoglobin won't bind it as tightly due to the elevated BPG. Overall, this will increase oxygen transport from your lungs to your tissues while your BPG level in your blood remains higher due to your prior training at high elevations. 87. The geometry of binding O2 and CO to heme is slightly different. In myoglobin, there is a histidine residue that does not interact with the heme iron but can interact with a ligand that is bound to the heme. It does not affect O2 binding, but because of steric hindrance, it may prevent CO binding. As a result, the relative affinity of proteinbound heme for CO and O2 is only 200, compared with 20,000 for free heme. 88. G-actin is a monomeric protein that can polymerize to form a long polymeric filament known as F-actin. 89. First, ATP binds to myosin and a cleft in the myosin molecule opens, disrupting the actin-myosin interaction so that the bound actin is released. Second, ATP is hydrolyzed, causing a conformational change in the protein to a "highenergy" state that moves the myosin head and changes its orientation in relation to the actin thin filament. Myosin then binds weakly to an F-actin subunit closer to the Z disk than the one just released. Third, as the phosphate product of ATP hydrolysis is released from myosin, another conformational change occurs in which the myosin cleft closes, strengthening the myosin-actin binding. Fourth, this is followed quickly by a "power stroke" during which the conformation of the myosin head returns to the original resting state, its orientation relative to the bound actin changing so as to pull the tail of the myosin toward the Z disk. ADP is then released to complete the cycle. (See Fig. 5-31.) 90. BPG binds to a cavity between the β subunits. It binds preferentially to molecules in the low-affinity T state, thereby stabilizing that conformation. 91. In the concerted model, binding of a ligand to one site on one subunit results in an allosteric effect that converts all of the remaining subunits to the high-affinity conformation. As a result, all of the subunits are either in the low- or high-affinity conformation. In the sequential model, each subunit is changed individually to the high-affinity conformation. As a result, there are many possible combinations of low- and high-affinity subunits. 92. Ka = 1/Kd . The larger the Ka (and hence the smaller the Kd ), the higher the affinity of the protein for the ligand. 93. In hemoglobin S, the wild-type glutamate at residue 6 of the B-chain is replaced by valine. When oxygen is bound, both hemoglobin A and hemoglobin S are soluble, but in the deoxy form. Hemoglobin S (but not hemoglobin A) becomes very insoluble due to exposure of the hydrophobic valine residue. This exposed "patch" causes aggregation of deoxyhemoglobin S into long insoluble fibrous aggregates, resulting in distorted shapes of the red blood cells (and leading to the symptoms of the disease). (Fig. 5-20.) 94. The specific antibody is covalently attached to an inert supporting material, which is then packed into a chromatography column. The protein solution is passed through the column slowly; most proteins pass directly through, but those for which the antibody has specific affinity are adsorbed. They can subsequently be eluted by a buffer of low pH, a salt solution, or some other agent that breaks the antibody-antigen association. Copyright Macmillan Learning. Powered by Cognero.

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Chap 05_8e 95. At the start of the actin-myosin cycle, myosin head groups are bound to the actin filaments. When ATP binds to the myosin head groups, this causes them to dissociate from the actin filaments. Hydrolysis of ATP then triggers a conformational change in the myosin head group, which moves it relative to the actin filament. The hydrolysis products of ADP and inorganic phosphate (Pi) remain bound to the myosin. The myosin head group will then interact with the actin filament in a different position from where it was at the start of the actin-myosin cycle. Upon binding to the actin filament, the Pi is released from the myosin head group. The release of Pi triggers another conformational change in the myosin head group, which is referred to as the "power stroke" and causes the actin filament to be moved relative to the myosin. During this "power stroke" process, the ADP is released from the myosin head group, leaving it available to bind another ATP molecule and start the cycle again. 96. A given muscle consists of many bundled muscle fibers, each of which contains many myofibrils, each of which contains many thick and thin filaments. Furthermore, when a muscle contracts, the myosin molecules move asynchronously. Thus, the individual steps of individual myosin molecules are masked by the millions of other myosin molecules taking steps at different times. 97. An IgG protein contains two copies of a large polypeptide (heavy chain) and two copies of a small polypeptide (light chain). β structure contributes significantly to the tertiary structure of domains of both chains. Disulfide bonds link the heavy chains to one another and to the light chains. The chains are arranged in a Y-shaped structure where the two arms are linked to the base by a protease sensitive ("hinge") region. 98. Lower affinity for BPG means that fetal hemoglobin will have less BPG bound than the mother's hemoglobin. This shifts the fetus's fractional O2 saturation curve to the left (i.e., lower p50) of the mother's. At low pO2, O2 will dissociate from the maternal hemoglobin and can be bound by the fetal hemoglobin. 99. Cooperativity of oxygen binding in hemoglobin means that, when there is not much oxygen bound to the hemoglobin protein, binding of additional oxygen will not be enhanced. This is the case in the tissues, where there are low oxygen levels. In the lungs, however, oxygen levels are high, and the binding of some oxygen to hemoglobin will enhance binding of additional oxygen molecules. In this way, at high oxygen concentrations, such as in the lungs, hemoglobin will bind several oxygen molecules. When in the tissues, however, hemoglobin will release oxygen since it is at a lower concentration and by releasing oxygen, the affinity of hemoglobin for the other oxygens that are bound will decrease, leading to more effective release of oxygen in the tissues. A protein like myoglobin, which does not exhibit cooperativity in oxygen binding, will bind oxygen very well in the lungs but will not release oxygen in the tissues, thus being a poor protein to use for oxygen transport. 100. Release of calcium ions from the sarcoplasmic reticulum triggers a conformational change in troponin, which is a calcium-binding protein that is bound to the actin thin filaments along with tropomyosin, thereby blocking the myosin binding sites on those filaments. When the conformational change in troponin occurs, it alters the positioning of itself and tropomyosin along the actin filaments, exposing the myosin binding sites. Myosin can then bind to the actin filaments and contract the muscles.

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Chap 06_8e Indicate the answer choice that best completes the statement or answers the question. 1. How is trypsinogen converted to trypsin? a. A protein kinase-catalyzed phosphorylation converts trypsinogen to trypsin. b. An increase in Ca2+ concentration promotes the conversion. c. Proteolysis of trypsinogen forms trypsin. d. Trypsinogen dimers bind an allosteric modulator, cAMP, causing dissociation into active trypsin monomers. e. Two inactive trypsinogen dimers pair to form an active trypsin tetramer. 2. The combination of amoxicillin and clavulanic acid into the drug known as Augmentin is widely used as an antibacterial agent. The purpose of amoxicillin in this drug is to target _____, which catalyzes cross-linking of peptidoglycan, and the purpose of clavulanic acid in this drug is to target _____, which normally would inactivate the amoxicillin. Both of these compounds act as _____ inhibitors of enzyme function. a. transpeptidase; hexokinase; competitive b. peptidoglycanase; β-lactamase; uncompetitive c. transpeptidase; β-lactamase; suicide d. glycanprotease; penicillinase; competitive e. β-lactamase; lysozyme; suicide 3. A small molecule that decreases the activity of an enzyme by binding to a site other than the catalytic site is called a(n): a. allosteric inhibitor. b. alternative inhibitor. c. competitive inhibitor. d. stereospecific agent. e. transition-state analog. 4. An enzyme-catalyzed reaction was carried out with the substrate concentration initially a thousand times greater than the Km for that substrate. After 9 minutes, 1% of the substrate had been converted to product, and the amount of product formed in the reaction mixture was 12 μmol. If, in a separate experiment, onethird as much enzyme and twice as much substrate had been combined, how long would it take for the same amount (12 μmol) of product to be formed? a. 1.5 min b. 13.5 min c. 27 min d. 3 min e. 6 min

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Chap 06_8e 5. The number of substrate molecules converted to product in a given unit of time by a single enzyme molecule at saturation is referred to as the: a. dissociation constant. b. half-saturation constant. c. maximum velocity. d. Michaelis-Menten number. e. turnover number. 6. These data were obtained in a study of an enzyme known to follow Michaelis-Menten kinetics. V0 Substrate added (μmol/min) (mmol/L) 217 325 433 488 647

0.8 2 4 6 1,000

The Km for this enzyme is approximately: a. 1 mM. b. 1,000 mM. c. 2 mM. d. 4 mM. e. 6 mM. 7. In what way does an uncompetitive inhibitor bind to an enzyme? a. It reversibly binds to the enzyme active site. b. It irreversibly binds to the enzyme active site. c. It reversibly binds to the enzyme-substrate complex but does not bind to the free enzyme. d. It reversibly binds to both the free enzyme and the enzyme-substrate complex. e. It irreversibly binds to an enzyme allosteric site. 8. Which statement BEST describes why niacin is required in the mammalian diet? a. Niacin is a precursor of nicotinamide adenine dinucleotide, which is a coenzyme required by many oxidoreductase enzymes. b. Niacin is a precursor of flavin adenine dinucleotide, which is a coenzyme required by many ligases. c. Niacin is a precursor of thiamine pyrophosphate, which is a coenzyme required by many transferases. d. Niacin is a component of coenzyme A, which is involved in many transferase reactions. e. Niacin is not actually required in the mammalian diet. Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_8e 9. In competitive inhibition, an inhibitor: a. binds at several different sites on an enzyme. b. binds covalently to the enzyme. c. binds only to the ES complex. d. binds reversibly at the active site. e. lowers the characteristic Vmax of the enzyme. 10. Phenyl-methane-sulfonyl-fluoride inactivates serine proteases by binding covalently to the catalytic serine residue at the active site; this enzyme-inhibitor bond is NOT cleaved by the enzyme. This is an example of what kind of inhibition? a. irreversible b. competitive c. noncompetitive d. mixed e. pH inhibition 11. The double-reciprocal transformation of the Michaelis-Menten equation, also called the Lineweaver-Burk plot, is given by 1/V0 = Km/(Vmax[S]) + 1/Vmax To determine Km from a double-reciprocal plot: a. multiply the reciprocal intercept on the x axis by –1. b. multiply the reciprocal intercept on the y axis by –1. c. take the reciprocal intercept on the x axis. d. take the reciprocal intercept on the y axis. e. take the intercept on the x axis, where V0 = 1/2Vmax. 12. Which enzymes are NOT among the seven internationally accepted classes of enzymes? a. hydrolases b. ligases c. oxidoreductases d. polymerases e. transferases 13. Allosteric enzymes: a. are regulated primarily by covalent modification. b. usually catalyze several different reactions within a metabolic pathway. c. usually have more than one polypeptide chain. d. usually have only one active site. e. usually show strict Michaelis-Menten kinetics. Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_8e 14. Binding energy between an enzyme and a substrate contributes to catalysis in which way? a. Binding energy provides the enzyme specificity for the substrate. b. Binding energy contributions allow for entropy reduction in the substrate-enzyme complex. c. Binding energy compensates for energy changes as a result of desolvation of the substrate. d. Binding energy contributes to the process of induced fit between the substrate and the enzyme. e. All of the answers are correct. 15. The concept of induced fit refers to the fact that: a. enzyme specificity is induced by enzyme-substrate binding. b. enzyme-substrate binding induces an increase in the reaction entropy, thereby catalyzing the reaction. c. enzyme-substrate binding induces movement along the reaction coordinate to the transition state. d. substrate binding may induce a conformational change in the enzyme, which then brings catalytic groups into proper orientation. e. when a substrate binds to an enzyme, the enzyme induces a loss of water (desolvation) from the substrate. 16. Which factor has NOT been shown to play a role in determining the specificity of protein kinases? a. disulfide bonds near the phosphorylation site b. primary sequence at phosphorylation site c. protein quaternary structure d. protein tertiary structure e. residues near the phosphorylation site 17. Which statement is true of enzyme catalysts? a. Their catalytic activity is independent of pH. b. They are generally equally active on D and L isomers of a given substrate. c. They can increase the equilibrium constant for a given reaction by a 1,000-fold or more. d. They can increase the reaction rate for a given reaction by many orders of magnitude. e. To be effective, they must be present at the same concentration as their substrate.

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Chap 06_8e 18. For enzymes in which the slowest (rate-limiting) step is the reaction

Km becomes equivalent to: a. k cat. b. the [S], where V0 = Vmax. c. the dissociation constant, Kd , for the ES complex. d. the maximal velocity. e. the turnover number. 19. Which enzyme uses general acid-base catalysis and/or covalent catalysis mechanisms to hydrolyze peptidoglycan? a. enolase b. lysozyme c. chymotrypsin d. pepsin e. β-lactamase 20. In a plot of l/V against 1/[S] for an enzyme-catalyzed reaction, the presence of a competitive inhibitor will alter the: a. curvature of the plot. b. intercept on the l/[S] axis. c. intercept on the l/V axis. d. pK of the plot. e. Vmax. 21. Which statement regarding enzyme activity is correct? a. Enzymes bind their substrates better than the transition state. b. Enzymes bind the products better than the reaction intermediates. c. Enzymes increase the activation energy required for the reaction to take place. d. Enzymes bind their substrates better than the transition state and the transition state better than the reaction products. e. Enzymes bind the transition state better than the reaction products and reduce the activation energy required for the reaction to take place.

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Chap 06_8e 22. Which statement is false? a. A reaction may not occur at a detectable rate even though it has a favorable equilibrium. b. After a reaction, the enzyme involved becomes available to catalyze the reaction again. c. For S→P, a catalyst shifts the reaction equilibrium to the right. d. Lowering the temperature of a reaction usually lowers the reaction rate. e. Substrate binds to an enzyme's active site. 23. Both water and glucose include an —OH that can serve as a substrate for a reaction with the terminal phosphate of ATP catalyzed by hexokinase. Glucose, however, is about a million times more reactive as a substrate than water. The BEST explanation is that: a. glucose has more —OH groups per molecule than does water. b. glucose induces a conformational change in hexokinase that brings active-site amino acids into position for catalysis. c. the —OH group of water is attached to an inhibitory H atom, while the glucose —OH group is attached to C. d. water and the second substrate, ATP, compete for the active site resulting in a competitive inhibition of the enzyme. e. water normally will not reach the active site because it is hydrophobic. 24. Which statement about a plot of V0 versus [S] for an enzyme that follows Michaelis-Menten kinetics is false? a. As [S] increases, the initial velocity of reaction V0 also increases. b. At very high [S], the velocity curve becomes a horizontal line that intersects the y axis at Km. c. Km is the [S] at which V0 = 1/2Vmax. d. The shape of the curve is a hyperbola. e. The y axis is a rate term with units such as mmol/min. 25. A transition-state analog: a. is less stable when binding to an enzyme than the normal substrate. b. resembles the active site of general acid-base enzymes. c. resembles the transition-state structure of the normal enzyme-substrate complex. d. stabilizes the transition state for the normal enzyme-substrate complex. e. typically reacts more rapidly with an enzyme than the normal substrate. 26. Why are the Mg2+ metal ions involved in the enolase reaction mechanism required? a. They form covalent bonds with a porphyrin ring to coordinate the substrate. b. They enhance the electron-withdrawing potential of the carbonyl group of 2-phosphoglycerate. c. They stabilize the phosphate group of 2-phosphoglycerate. d. They allow a Lys in the active site to donate a proton to the 2-phosphoglycerate substrate. e. They prevent the reverse catalysis of 3-phosphoglycerate to 2-phosphoglycerate from taking place. Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_8e 27. Michaelis and Menten assumed that the overall reaction for an enzyme-catalyzed reaction could be written as

Using this reaction, the rate of breakdown of the enzyme-substrate complex can be described by the expression: a. k 1([Et] – [ES]). b. k 1([Et] – [ES])[S]. c. k 2[ES]. d. k –1[ES] + k 2[ES]. e. k –1[ES]. 28. Enzyme X exhibits maximum activity at pH = 6.9. X shows a fairly sharp decrease in its activity when the pH goes much lower than 6.4. One likely interpretation of this pH activity is that: a. a Glu residue on the enzyme is involved in the reaction. b. a His residue on the enzyme is involved in the reaction. c. the enzyme has a metallic cofactor. d. the enzyme is found in gastric secretions. e. the reaction relies on specific acid-base catalysis. 29. Chymotrypsin catalyzes the cleavage of proteins at peptide bonds adjacent to aromatic amino acid residues by using which catalytic mechanism? a. general acid-base catalysis b. metal ion catalysis c. covalent catalysis d. both general acid-base catalysis and metal ion catalysis e. both general acid-base catalysis and covalent catalysis 30. A double-reciprocal plot of 1/V0 versus 1/[S] for an enzyme in the presence of increasing concentrations of an uncompetitive inhibitor will have lines corresponding to the different inhibitor concentrations that are BEST described by which statement? a. The lines will intersect at the x axis to the left of the y axis with the same y intercept. b. The lines will cross the y axis and will be parallel to each other. c. The lines will intersect to the left of the y axis but above the x axis. d. The lines will intersect below the x axis, to the right of the y axis. e. The lines will be parallel to each other but will not cross the y axis.

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Chap 06_8e 31. Which statement is false about enzyme catalysts? a. They sometimes bind covalently to substrates or intermediates during catalysis. b. They increase the equilibrium constant for a reaction, thus favoring product formation. c. They increase the stability of the transition state. d. They have a high level of specificity for their substrates. e. They can be effective, even at a concentration much lower than that of their substrate. 32. Treatment of methanol poisoning by using ethanol is an example of what type of enzyme inhibition? a. mixed b. uncompetitive c. competitive d. noncompetitive e. suicide 33. In this diagram of the first step in the reaction catalyzed by the protease chymotrypsin, the process of general base catalysis is illustrated by the number _____, and the process of covalent catalysis is illustrated by the number _____.

a. 1; 2 b. 1; 3 c. 2; 3 d. 2; 3 e. 3; 2

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Chap 06_8e 34. A reaction that has a ΔG'º of 25 kJ/mol is likely to have which property? a. a large equilibrium constant b. a small equilibrium constant c. a slow reaction rate d. both a large equilibrium constant and a slow reaction rate e. both a small equilibrium constant and a slow reaction rate 35. The steady state assumption, as applied to enzyme kinetics, implies: a. Km = Ks . b. the enzyme is regulated. c. the ES complex is formed and broken down at equivalent rates. d. the Km is equivalent to the cellular substrate concentration. e. the maximum velocity occurs when the enzyme is saturated. 36. The HIV protease enzyme uses a general acid-base catalysis mechanism to cleave viral polypeptides but does not use a covalent catalysis. This enzyme functions optimally in the pH range of 4 to 6. Due to the specific amino acids involved in this catalysis, HIV protease is a member of which subclass of proteases? a. metalloproteases b. serine proteases c. aspartyl proteases d. cysteine proteases e. lysine proteases 37. Which protein polymerizes into a gel-like matrix after it is activated to assist in blood clotting? a. trypsinogen b. fibrinogen c. prothrombin d. thrombin e. warfarin 38. Which statement about allosteric control of enzymatic activity is false? a. Allosteric effectors give rise to sigmoidal V0 versus [S] kinetic plots. b. Allosteric proteins are generally composed of several subunits. c. An effector may either inhibit or activate an enzyme. d. Binding of the effector changes the conformation of the enzyme molecule. e. Heterotropic allosteric effectors compete with substrate for binding sites.

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Chap 06_8e 39. Which molecule would NOT be effective to administer as an anticoagulant? a. aspirin b. warfarin c. heparin d. vitamin K e. antithrombin 40. A good transition-state analog: a. binds covalently to the enzyme. b. binds to the enzyme more tightly than the substrate. c. binds very weakly to the enzyme. d. is too unstable to isolate. e. must be almost identical to the substrate. 41. Which statement is true of the binding energy derived from enzyme-substrate interactions? a. It cannot provide enough energy to explain the large rate accelerations brought about by enzymes. b. It is sometimes used to hold two substrates in the optimal orientation for reaction. c. It is the result of covalent bonds formed between enzyme and substrate. d. Most of it is derived from covalent bonds between enzyme and substrate. e. Most of it is used up simply binding the substrate to the enzyme. 42. The Lineweaver-Burk plot is used to: a. determine the equilibrium constant for an enzymatic reaction. b. determine how much the activation energy is lowered by the presence of the enzyme. c. illustrate the effect of temperature on an enzymatic reaction. d. solve, graphically, for the rate of an enzymatic reaction at infinite substrate concentration. e. solve, graphically, for the ratio of products to reactants for any starting substrate concentration. 43. If chemical reactions will eventually reach an equilibrium state, what is the purpose of enzymes in a biological system? a. Enzymes are consumed to speed up chemical reactions. b. Enzymes speed up chemical reactions without being used up in the process. c. Enzymes slow down chemical reactions. d. Enzymes alter the equilibrium state between reactants and products. e. Enzymes prevent the formation of unstable reaction intermediates.

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Chap 06_8e 44. The role of the metal ion (Mg2+) in catalysis by enolase is to: a. act as a general acid catalyst. b. act as a general base catalyst. c. stabilize an intermediate during general acid catalysis. d. stabilize an intermediate during general base catalysis. e. stabilize protein conformation. 45. To calculate the turnover number of an enzyme, one needs to know: a. the enzyme concentration. b. the initial velocity of the catalyzed reaction at [S] >> Km. c. the initial velocity of the catalyzed reaction at low [S]. d. the Km for the substrate. e. both the enzyme concentration and the initial velocity of the catalyzed reaction at [S] >> Km. 46. A complex organic molecule that is necessary for enzyme function but is NOT permanently associated with the enzyme is a: a. prosthetic group. b. cofactor. c. holofactor. d. coenzyme. e. metal ion.

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Chap 06_8e 47. Compare the two reaction coordinate diagrams and select the answer that correctly describes their relationship. In each case, the single intermediate is the ES complex.

a. Diagram (a) describes a strict lock and key model, whereas (b) describes a transition-state complementarity model. b. The activation energy for the catalyzed reaction is arrow 5 in (a) and is arrow 7 in (b). c. The activation energy for the uncatalyzed reaction is given by the sum of arrows 5 and 6 in (a) and by the sum of arrows 7 and 8 in (b). d. The contribution of binding energy is given by arrow 5 in (a) and by arrow 7 in (b). e. The ES complex is given by point 2 in (a) and point 3 in (b). 48. An enzyme's specificity constant (k cat/Km) has a maximum upper limit due to: a. substrate concentration. b. enzyme concentration. c. the enzyme turnover number. d. diffusion of the enzyme and substrate together. e. the Michaelis constant. 49. Which amino acid is NOT capable of using its side chain (R group) to participate in general acid-base catalysis? a. Asp b. His c. Ser d. Val e. Lys

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Chap 06_8e 50. The enzyme pepsin is produced in the stomach lining initially as a _____, which requires _____ for activation in the stomach. a. kinase; phosphorylation b. zymogen; irreversible proteolytic cleavage c. proprotein; reversible proteolytic cleavage d. zymogen; ubiquitination e. phosphorylase; irreversible proteolytic cleavage 51. An enzyme that can convert glucose into fructose is a member of which class of enzymes? a. oxidoreductases b. transferases c. hydrolases d. lyases e. isomerases 52. Enzymes are potent catalysts because they: a. are consumed in the reactions they catalyze. b. are very specific and can prevent the conversion of products back to substrates. c. drive reactions to completion while other catalysts drive reactions to equilibrium. d. increase the equilibrium constants for the reactions they catalyze. e. lower the activation energy for the reactions they catalyze. 53. Enzymes differ from other catalysts in that only enzymes: a. are not consumed in the reaction. b. display specificity toward a single reactant. c. fail to influence the equilibrium point of the reaction. d. form an activated complex with the reactants. e. lower the activation energy of the reaction catalyzed. 54. Vmax for an enzyme-catalyzed reaction: a. generally increases when pH increases. b. increases in the presence of a competitive inhibitor. c. is limited only by the amount of substrate supplied. d. is twice the rate observed when the concentration of substrate is equal to the Km. e. is unchanged in the presence of an uncompetitive inhibitor.

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Chap 06_8e 55. The allosteric enzyme ATCase is regulated by CTP, which binds to the T state of ATCase. CTP is a: a. positive regulator. b. negative regulator. c. cofactor. d. competitive inhibitor. e. coenzyme. 56. Penicillin and related drugs inhibit the enzyme _____; this enzyme is produced by _____. a. β-lactamase; bacteria b. transpeptidase; human cells c. transpeptidase; bacteria d. lysozyme; human cells e. aldolase; bacteria 57. For the simplified representation of an enzyme-catalyzed reaction shown, the statement "ES is in steadystate" means that:

a. k 2 is very slow. b. k 1 = k 2. c. k 1 = k –1. d. k 1[E][S] = k –1[ES] + k 2[ES]. e. k 1[E][S] = k –1[ES]. 58. Which statement about enzyme-catalyzed reactions is false? a. At saturating levels of substrate, the rate of an enzyme-catalyzed reaction is proportional to the enzyme concentration. b. If enough substrate is added, the normal Vmax of a reaction can be attained even in the presence of a competitive inhibitor. c. The rate of a reaction decreases steadily with time as substrate is depleted. d. The activation energy for the catalyzed reaction is the same as for the uncatalyzed reaction, but the equilibrium constant is more favorable in the enzyme-catalyzed reaction. e. The Michaelis-Menten constant Km equals the [S] at which V = 1/2Vmax.

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Chap 06_8e 59. The role of an enzyme in an enzyme-catalyzed reaction is to: a. bind a reaction intermediate and prevent it from converting back to substrate. b. ensure that all of the substrate is converted to product. c. ensure that the product is more stable than the substrate. d. increase the rate at which substrate is converted into product. e. make the free-energy change for the reaction more favorable. 60. If one were attempting to design a new drug for the treatment of a disease by interfering with enzyme activity in the disease-causing organism, which type of inhibitor would likely be the MOST effective? a. a transition-state analog that is an irreversible inhibitor b. a substrate analog that is a competitive inhibitor c. a transition-state analog that is a competitive inhibitor d. a product analog that is an uncompetitive inhibitor e. a substrate analog that is a mixed inhibitor 61. Enzymes that cleave carbon–carbon bonds without the use of water in the chemical reaction are members of which class of enzymes? a. oxidoreductases b. transferases c. hydrolases d. lyases e. isomerases 62. The benefit of measuring the initial rate of a reaction V0 is that at the beginning of a reaction: a. [ES] can be measured accurately. b. changes in [S] are negligible, so [S] can be treated as a constant. c. changes in Km are negligible, so Km can be treated as a constant. d. V0 = Vmax. e. varying [S] has no effect on V0. 63. Blood coagulation involves: a. a kinase cascade. b. zymogen activation. c. serine proteases. d. both a kinase cascade and zymogen activation. e. both zymogen activation and serine proteases.

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Chap 06_8e 64. Which type of enzyme is responsible for attaching phosphate groups to specific amino acids? a. a protein phosphatase b. a ribosylase c. a protein kinase d. a protein glycosylase e. an ATPase 65. Which amino acid is NOT one that may be targeted for phosphorylation to modulate the activity of an enzyme? a. Tyr b. His c. Ser d. Ala e. Thr 66. One of the enzymes involved in glycolysis, aldolase, requires Zn2+ for catalysis. When the enzyme lacks zinc, it is referred to as the: a. apoenzyme. b. coenzyme. c. holoenzyme. d. prosthetic group. e. substrate. 67. Describe why the Michaelis constant (Km) and the dissociation constant (Kd ) should not be considered to be the same. Use the rate constant definitions of these terms in the explanation, and also indicate in what case Km and Kd can be considered to be the same.

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Chap 06_8e 68. The enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK value for the carboxyl side chains of these two residues are 5.9 and 4.5, respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these two amino acid residues explain the pH-activity profile of lysozyme?

69. When 10 μg of an enzyme of Mr 50,000 is added to a solution containing its substrate at a concentration one hundred times the Km, it catalyzes the conversion of 75 μmol of substrate into product in 3 minutes. What is the enzyme's turnover number?

70. For a reaction that can take place with or without catalysis by an enzyme, what would be the effect of the enzyme on the: (a) standard free-energy change of the reaction? (b) activation energy of the reaction? (c) initial velocity of the reaction? (d) equilibrium constant of the reaction?

71. Write out the equation that describes the mechanism for enzyme action used as a model by Michaelis and Menten. List the important assumptions used by Michaelis and Menten to derive a rate equation for this reaction.

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Chap 06_8e 72. Chymotrypsin belongs to a group of proteolytic enzymes called the serine proteases, many of which have an Asp, His, and Ser residue that are crucial to the catalytic mechanism. The serine hydroxyl functions as a nucleophile. What do the other two amino acids do to support this nucleophilic reaction?

73. Give the Michaelis-Menten equation and define each term in it. Does this equation apply to all enzymes? If not, to which kind does it not apply?

74. How does the total enzyme concentration affect turnover number and Vmax?

75. Enzymes with a k cat /Km ratio of about 108 M–1s–1 are considered to show optimal catalytic efficiency. Fumarase, which catalyzes the reversible-dehydration reaction fumarate + H2O ⇌ malate has a ratio of turnover number to the Michaelis-Menten constant, (k cat/Km) of 1.6×108 for the substrate fumarate and 3.6×107 for the substrate malate. Because the turnover number for both substrates is nearly identical, what factors might be involved that explain the different ratio for the two substrates?

76. Penicillin and related antibiotics contain a four-membered β-lactam ring. Explain why this feature is important to the mechanism of action of these drugs.

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Chap 06_8e 77. Sometimes the difference in (standard) free-energy content, ΔG'º, between a substrate S and a product P is very large, yet the rate of chemical conversion, S→P, is quite slow. Why?

78. What is a zymogen (proenzyme)? Explain briefly with an example.

79. The difference in (standard) free-energy content, ΔG'º, between substrate S and product P may vary considerably among different reactions. What is the significance of these differences?

80. Explain how a biochemist might discover that a certain enzyme is allosterically regulated.

81. Draw and label a reaction coordinate diagram for an uncatalyzed reaction, S→P, and the same reaction catalyzed by an enzyme, E.

82. Leucine biosynthesis occurs in a multistep pathway starting from 2-oxovalerate, and the final product of the pathway (leucine) inhibits the first enzyme involved in the biosynthetic pathway through a process called feedback inhibition. This enzyme inhibition occurs regardless of whether or not the 2-oxovalerate substrate is bound in the active site of the enzyme. Describe what type of inhibitor leucine is and justify the response.

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Chap 06_8e 83. In a reaction catalyzed by the enzyme hexokinase, ATP reacts with glucose to produce glucose 6-phosphate and ADP at a rate five orders of magnitude faster than ATP reacts with H2O to form phosphate and ADP. The intrinsic chemical reactivity of the —OH group in water is about the same as that of the glucose molecule, and water can certainly fit into the active site. Explain this rate differential in two sentences or less.

84. Define the term "suicide inhibitor."

85. An enzyme catalyzes a reaction at a velocity of 20 μmol/min when the concentration of substrate (S) is 0.01 M. The Km for this substrate is 10–5 M. Assuming that Michaelis-Menten kinetics are followed, what will the reaction velocity be when the concentration of S is (a) 10–5 M and (b) 10–6 M?

86. An enzyme can catalyze a reaction with either of two substrates, S1 or S2. The Km for S1 was found to be 2.0 mM, and the Km for S2 was found to be 20 mM. A student determined that the Vmax was the same for the two substrates. Unfortunately, he lost the page of his notebook and needed to know the value of Vmax. He carried out two reactions: one with 0.1 mM S1, the other with 0.1 mM S2. Unfortunately, he forgot to label which reaction tube contained which substrate. Determine the value of Vmax from the results he obtained. Tube number Rate of formation of product 1 0.5 2 4.8

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Chap 06_8e 87. Methanol (wood alcohol) is highly toxic because it is converted to formaldehyde in a reaction catalyzed by the enzyme alcohol dehydrogenase NAD+ + methanol → NADH + H+ + formaldehyde Part of the medical treatment for methanol poisoning is to administer ethanol (ethyl alcohol) in amounts large enough to cause intoxication under normal circumstances. Explain this in terms of examples of enzymatic reactions.

88. Two different enzymes are able to catalyze the same reaction, A→B. They both have the same Vmax, but differ in their Km values. For enzyme 1, the Km is 1.0 mM; for enzyme 2, the Km is 10 mM. When enzyme 1 was incubated with 0.1 mM A, it was observed that B was produced at a rate of 0.0020 mmol/min. (a) What is the value of the Vmax of the enzymes? (b) What will be the rate of production of B when enzyme 2 is incubated with 0.1 mM A? (c) What will be the rate of production of B when enzyme 1 is incubated with 1 M (i.e., 1,000 mM) A?

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Chap 06_8e 89. The initial rate of an enzyme reaction is measured as a function of substrate concentration in the presence and absence of an inhibitor. The data obtained: V0

[S] 0.0001 0.0002 0.0005 0.001 0.002 0.005 0.01 0.02 0.05 0.1 0.2

–Inhibitor 33 50 71 83 91 96 98 99 100 100 100

+Inhibitor 17 29 50 67 80 91 95 98 99 100 100

(a) What is the Vmax in the absence of inhibitor? (b) What is the Km in the absence of inhibitor? (c) When [S] = 0.0004, what will V0 be in the absence of inhibitor? (d) When [S] = 0.0004, what will V0 be in the presence of inhibitor? (e) What kind of inhibitor is it likely to be?

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Chap 06_8e 90. A biochemist obtains this set of data for an enzyme that is known to follow Michaelis-Menten kinetics. Substrate concentration (μm) 1 2 8 50 100 1,000 5,000

Initial velocity (μmol/min) 49 96 349 621 676 698 699

(a) Vmax for the enzyme is _____. Explain in one sentence how to determine Vmax. (b) Km for the enzyme is _____. Explain in one sentence how to determine Km.

91. For the reaction E + S→ES→P the Michaelis-Menten constant, Km, is actually a combination of three terms. What are they? How is Km determined graphically?

92. Define the terms "cofactor" and "coenzyme."

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Chap 06_8e 93. Cells can develop a resistance to drugs by increasing the cellular concentration of the enzyme that drug inhibits. If a cell increases its concentration of a given enzyme to 10 times the normal amount, which parameters will be increased 10-fold? Km kI [S] Vmax V0 when [S] = Km k cat catalytic efficiency

94. An enzyme follows Michaelis-Menten kinetics. Indicate (with an X) which of the kinetic parameters at the left would be altered by the factors. Give only one answer for each.

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Chap 06_8e 95. The turnover number for an enzyme is known to be 5,000 min–1. From the set of data, calculate the Km and the total amount of enzyme present in these experiments. Substrate concentration (mm) 1 2 4 6 100 1,000

Initial velocity (μmol/min) 167 250 334 376 498 499

(a) Km = _____; (b) Total enzyme = _____ μmol

96. Write an equilibrium expression for the reaction S→P and briefly explain the relationship between the value of the equilibrium constant and free energy.

97. Why does pH affect the activity of an enzyme?

98. For serine to work effectively as a nucleophile in covalent catalysis in chymotrypsin a nearby amino acid, histidine, must serve as general base catalyst. Briefly describe, in words, how these two amino acids work together.

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Chap 06_8e 99. Michaelis-Menten kinetics is sometimes referred to as "saturation" kinetics. Why would this be an appropriate term?

100. Why is the Lineweaver-Burk (double reciprocal) plot (see Box 6-1) more useful than the standard V versus [S] plot in determining kinetic constants for an enzyme? (The answer should probably show typical plots.)

101. Fifteen μg of an enzyme of Mr 30,000 working at Vmax catalyzes the conversion of 60 μmol of substrate into product in 3 minutes. What is the enzyme's turnover number?

102. Why is a transition-state analog not necessarily the same as a competitive inhibitor?

103. What is the difference between general acid-base catalysis and specific acid-base catalysis? (Assume that the solvent is water.)

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Chap 06_8e 104. An enzyme catalyzes the reaction A→B. The initial rate of the reaction was measured as a function of the concentration of A. The data obtained: [A], micromolar 0.05 0.1 0.5 1 5 10 50 100 500 1,000 5,000 10,000 20,000

V0, nmol/min 0.08 0.16 0.79 1.6 7.3 13 40 53 73 76 79 80 80

(a) What is the Km of the enzyme for the substrate A? (b) What is the value of V0 when [A] = 43 micromolar? The data were plotted as 1/V0 versus 1/[A], and a straight line was obtained. (c) What is the value of the y intercept of the line? (d) What is the value of the x intercept of the line?

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Chap 06_8e Answer Key 1. c 2. c 3. a 4. c 5. e 6. c 7. c 8. a 9. d 10. a 11. a 12. d 13. c 14. e 15. d 16. a 17. d 18. c 19. b 20. b 21. e 22. c 23. b 24. b 25. c 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_8e 27. d 28. b 29. e 30. b 31. b 32. c 33. a 34. b 35. c 36. c 37. b 38. e 39. d 40. b 41. b 42. d 43. b 44. d 45. e 46. d 47. a 48. d 49. d 50. b 51. e 52. e 53. b 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 06_8e 55. b 56. c 57. d 58. d 59. d 60. a 61. d 62. b 63. e 64. c 65. d 66. a 67. The Km refers to the rate of product formation plus the rate of enzyme and substrate dissociation with the sum divided by the rate of substrate and enzyme association, or (k 2 + k –1)/k 1. This is not the same as the Kd , which is defined just as the ratio between enzyme and substrate dissociation and enzyme and substrate association, or k – 1/k 1. Since the Km includes k 2 as an additional term, it should not be considered to be the same as the Kd . However, in the limited case where k 2 is rate-limiting and is much less than k –1, then k 2 can be approximated as zero, which reduces the Km term to (0 + k –1)/k 1. This then makes the Km and Kd terms equal, and then they can be considered the same, although this case does not apply for most enzymes. 68. For the enzyme to be active, it is likely that Asp52 is unprotonated and Glu35 is protonated. When the pH is below 4.5, Asp52 becomes protonated, and when it is above 5.9, Glu35 is deprotonated, either of which decreases the activity of the enzyme. 69. Because the velocity measured occurs far above Km, it represents Vmax. Ten μg of the enzyme represents 10×10–6 g/(5×104 g/mol), or 2×10–10 mol of enzyme. In 3 minutes, this amount of enzyme produced 75 μmol of product, equivalent to 25×10–6 mol of product per minute. The turnover number is therefore (25×10–6 mol/min)/(2×10–10 mol) = 12.5×104 min–1. 70. (a) no change; (b) decrease; (c) increase; (d) no change

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Chap 06_8e 71. The two equations are

One assumption is that [P] = 0 so that the rate of the reaction depends exclusively on the breakdown of ES and is not influenced by the reverse reaction; that is, k –2 can be ignored and V0 = k 2[ES]. This condition is possible only if early reaction times are measured; the velocity, therefore, is an initial velocity. A second assumption is that the rate of ES formation equals the rate of ES breakdown; in other words, the reaction is at a steady state. A third assumption is [S] >> [Et], so that total [S], which equals free substrate and enzyme-bound substrate, is essentially equal to [S]. 72. In chymotrypsin, histidine functions as a general base, accepting a proton from the serine hydroxyl, thereby increasing serine's reactivity as a nucleophile. The negatively charged Asp stabilizes the positive charge that develops on the His. 73. The Michaelis-Menten equation is V0 = Vmax [S]/(Km + [S]), in which V0 is the initial velocity at any given concentration of S, Vmax is the velocity when all enzyme molecules are saturated with S, [S] is the concentration of S, and Km is a constant characteristic for the enzyme. This equation does not apply to enzymes that display sigmoidal V0 versus [S] curves, but only to those giving hyperbolic kinetic plots. 74. The turnover number, k cat, is the number of substrate molecules converted to product in a given time by a single enzyme molecule, so turnover number is not affected by the total enzyme concentration, [Et]. For any given reaction, however, Vmax can change because Vmax is the product of turnover number × the total enzyme concentration, or Vmax = k cat [Et]. 75. If the turnover number is nearly identical for both substrates, then the Km for malate must be much larger than for fumarate. Similar turnover numbers suggest no significant differences in rate of conversion of substrate to product, but the different Km values could possibly be explained by a stronger binding affinity of the enzyme for fumarate than for malate or some other aspect of the reaction mechanism that affects Km. 76. The strained four-membered ring is easily opened (ΔG<< 0); this energy drives the reaction that covalently inactivates the transpeptidase. 77. The rate of conversion from substrate to product (or the reverse reaction, from product to substrate) does not depend on the free-energy difference between them. The rate of the reaction depends on the activation energy of the reaction ΔG'º, which is the difference between the free-energy content of S (or P) and the reaction transition state. 78. A zymogen is an inactive form of an enzyme that is activated by one or more proteolytic cleavages in its sequence. Chymotrypsinogen, trypsinogen, and proelastase are all zymogens, becoming chymotrypsin, trypsin, and elastase, respectively, after proper cleavage.

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Chap 06_8e 79. The difference in free-energy content between substrate (or reactant) and product for each reaction reflects the relative amounts of each compound present at equilibrium. The greater the difference in free energy, the greater the difference in amounts of each compound at equilibrium. 80. The enzyme would show kinetics that do not fit the Michaelis-Menten equation; the plot of V versus [S] would be sigmoidal, not hyperbolic. The enzyme kinetics would be affected by molecules other than the substrate(s). 81. See Figure 6-3. 82. Leucine is a mixed inhibitor in this case. Since enzyme inhibition occurs even if 2-oxovalerate is bound to the active site of the enzyme, inhibition must occur through leucine binding to a site other than the active site. This is consistent with both mixed inhibition and uncompetitive inhibition. However, since enzyme inhibition also occurs in the absence of 2-oxovalerate binding to the active site, uncompetitive inhibition can be ruled out because that form of inhibition only takes place when the inhibitor binds to the enzyme-substrate complex. Therefore, leucine is acting as a mixed inhibitor of enzyme activity. 83. The binding of glucose to hexokinase induces a conformation change that brings the amino acid residues that facilitate the phosphoryl transfer into position in the active site. Binding of water alone does not induce this conformational change. 84. A suicide inhibitor is a molecule that is unreactive until it binds to the active site of an enzyme. In the active site, it undergoes the first chemical steps of the normal enzymatic reaction and is converted into a highly reactive species that combines irreversibly with the enzyme's active site, rendering the enzyme inactive toward substrate. 85. The velocity of 20 μmol/min is essentially Vmax because it is measured at [S] >> Km. (a) When [S] = 10–5 M = Km, V = 1/2Vmax, or 10 μmol/min. (b) When [S] is 10–6 M, velocity can be calculated from the Michaelis-Menten equation V0 = Vmax [S]/(Km + [S]) = (20 μmol/min)(10–6 M)/(10–5 + 10–6) = 1.8 μmol/min 86. Vmax = 101 87. Ethanol is a structural analog of methanol, and competes with methanol for the binding site of alcohol dehydrogenase, slowing the conversion of methanol to formaldehyde, and allowing its clearance by the kidneys. The effect of ethanol is that of a competitive inhibitor. 88. (a) 0.022 mmol/min; (b) 0.00022 mmol/min; (c) 0.022 mmol/min 89. (a) 100; (b) 0.0002; (c) 66.7; (d) 40; (e) competitive 90. (a) Vmax is about 700 μmol/min. In a plot of V versus [S], the asymptote is Vmax. Simple inspection of the data shows the approach to Vmax, the rate increases by only 1 unit when [S] increases fivefold. (b) Km is about 8 μM, the [S] at which the velocity is half-maximal. Because Vmax is about 700 μmol/min, 1/2Vmax is about 350 μmol/min. The [S] at that rate is about 8 μM.

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Chap 06_8e 91. Km = (k 2 + k –1)/k 1, where k –1 and k 1 are the rate constants for the breakdown and association, respectively, of the ES complex and k 2 is the rate constant for the breakdown of ES to form E + P. Km can be determined graphically on a plot of V0 versus [S] by finding the [S] at which V0 = 1/2Vmax. More conveniently, on a doublereciprocal plot, the intercept on the x axis equals –1/Km. 92. A cofactor is any chemical component required for enzyme activity; it includes both organic molecules, called coenzymes, and inorganic ions. 93. Only Vmax and V0 are linearly dependent on [E]. 94. (a) Km; (b) Km and Vmax; (c) Km and Vmax; (d) neither 95. Km = about 2 mM (the concentration of S needed to achieve one-half Vmax, which is about 500 μmol/min). The total enzyme present is producing about 500 μmol of product per minute. Because the turnover number is 5,000/min, the amount of enzyme present must be 0.1 μmol; 1 μmol of enzyme would produce 5,000 μmol product/min. 96. Keq' = [P]/[S]. The value of Keq' reflects the difference between the free-energy content of S and P. Free energy and equilibrium constant are related by the expression ΔG'º = –RT lnKeq' For each change in Keq' by one order of magnitude, ΔG'º changes by 5.7 kJ/mol. 97. The state of ionization of several amino acid side chains is affected by pH, and the activity of many enzymes requires that certain of the amino acid residue side chains be in a specific ionization state. 98. The serine is a polar hydroxyl with the oxygen functioning as an electronegative nucleophile. A nearby histidine residue with pKa ≈ 6.0, however, functions as a base to abstract the proton from the serine hydroxyl group. The result is to substantially increase the electronegativity of the serine oxygen, making it a much stronger nucleophile. This, in turn, lowers the activation energy of the covalent catalysis between serine and the carbonyl carbon of the substrate peptide bond. 99. According to the Michaelis-Menten model of enzyme-substrate interaction, when [S] becomes very high, an enzyme molecule's active site will become occupied with a new substrate molecule as soon as it releases a product. Therefore, at very high [S], V0 does not increase with additional substrate, and the enzyme is said to be "saturated" with substrate. 100. The plot of V versus [S] is hyperbolic; maximum velocity is never achieved experimentally because it is impossible to do experiments at infinitely high [S]. The Lineweaver-Burk transformation of the Michaelis-Menten equation produces a linear plot that can be extrapolated to infinite [S] (where 1/[S] becomes zero), allowing a determination of Vmax. 101. The amount of enzyme present is 15×10–6 g, which is (15×10–6 g)/(3×104 g/mol) = 5×10–10 mol of enzyme. The rate of product formation is 60×10–6 mol/3 min, or 20×10–6 mol of product per minute. The turnover number is therefore (20×10–6 mol/min)/(5×10–10 mol of enzyme), or 4×10–4 min–1.

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Chap 06_8e 102. The structure of a competitive inhibitor may be similar to the structure of the free substrate. Similar structure will mean that the competitive inhibitor can associate with the enzyme at the active site, effectively blocking the normal substrate from binding. A transition-state analog, however, is similar in structure to the transition-state of the reaction catalyzed by the enzyme. Often, a transition-state analog will bind tightly to an enzyme, and it is not easily replaced by substrate. 103. Specific acid-base catalysis refers to catalysis by the constituents of water; that is, the donation of a proton by the hydronium ion, H3O+ or the acceptance of a proton by the hydroxyl ion OH– . General acid-base catalysis refers to the donation or acceptance of a proton by weak acids and bases other than water. 104. (a) 50 micromolar; (b) 37 nmol/min; (c) 0.0125 (nmol/min)–1; (d) –0.02 micromolar–1

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Chap 07_8e Indicate the answer choice that best completes the statement or answers the question. 1. The antiviral drugs oseltamivir (Tamiflu) and zanamivir (Relenza) do NOT work by: a. inhibiting the viral enzyme that trims the host cell's oligosaccharides. b. causing the viral particles to aggregate. c. competing with the host cell's oligosaccharides for binding. d. preventing the release of viruses from the infected cell. e. All of the answers are correct. 2. A glycoconjugate may include a carbohydrate as well as a(n): a. amino acid. b. lipid. c. saccharide. d. protein or lipid. e. amino acid, a lipid, or a saccharide. 3. Which pair is anomeric? a. D-glucose and D-fructose b. D-glucose and L-fructose c. D-glucose and L-glucose d. α-D-glucopyranose and β-D-glucopyranose e. α-D-glucopyranose and β-L-glucopyranose 4. The reference compound for naming D and L isomers of sugars is: a. fructose. b. glucose. c. glyceraldehyde. d. ribose. e. sucrose. 5. Assuming 20 common amino acids and 20 different monosaccharide subunits that are available for construction of polypeptides and oligosaccharides, respectively, compare the possible variations of these macromolecules using a hypothetical hexameric oligomer. a. 206 possible variations for both polypeptides and oligosaccharides b. 620 variations for both polypeptide and oligosaccharides c. 206 variations for polypeptides and orders of magnitude greater for oligosaccharides d. 206 variations for oligosaccharides and orders of magnitude greater for polypeptides e. It cannot be determined from the information given.

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Chap 07_8e 6. Which is the MOST plausible reason why most hexoses of living organisms are D isomers? a. D isomers are more energetically favorable. b. D isomers are also used by amino acids. c. Sugars must be opposite isomers from amino acids. d. Evolving enzymes were made to remain with an initial preference. e. Evolving enzymes switch preference often to find the best isomer. 7. Following complete hydrolysis of a sample of glycogen and a sample of cellulose, which statement must be true? a. The glycogen sample is more soluble than the cellulose sample. b. The cellulose sample is more soluble than the glycogen sample. c. Both samples consist of a mixture of α-D-glucose and β-D-glucose. d. The glycogen sample has a higher ratio of α-D-glucose than the cellulose sample. e. The cellulose sample contains only β-D-glucose. 8. When two carbohydrates are epimers: a. one is a pyranose, the other a furanose. b. one is an aldose, the other a ketose. c. they differ in length by one carbon. d. they differ only in the configuration around one carbon atom. e. they rotate plane-polarized light in the same direction. 9. Which pair is epimeric? a. D-glucose and D-glucosamine b. D-glucose and D-mannose c. D-glucose and L-glucose d. D-lactose and D-sucrose e. L-mannose and L-fructose 10. In amylose, the MOST stable structure is a _____, which is stabilized by _____. a. coiled helix; interchain hydrogen bonds b. coiled helix; interchain covalent branching c. coiled helix; hydrogen bonds to surrounding water molecules d. straight, extended chain; interchain hydrogen bonds e. straight, extended chain; hydrogen bonds to surrounding water molecules

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Chap 07_8e 11. The hydrogen bonding in cellulose has what effect? a. Extensive intrachain and interchain hydrogen bonding yields a low water content in cellulose. b. The hydrogen bonding yields cellulose chains that make straight, stable supramolecular fibers. c. Hydrogen bonding gives cellulose a high tensile strength. d. Hydrogen bonding enables cellulose to perform well as plant cell walls. e. All of the answers are correct. 12. Under what circumstance might an organism's patterns of glycosylation NOT be altered? a. development b. genetic diseases c. cancer d. cell differentiation e. All of the answers are correct. 13. What is the correct linkage designation for the glycosidic bond between the two monosaccharide rings?

a. (α1→4) b. (β1→4) c. (1→4) d. (α1→β4) e. (α1→α4)

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Chap 07_8e 14. Based on the form of the cyclic sugar in a Haworth projection, which Fischer projection formula could have formed this structure?

a. A b. B c. C d. D e. E 15. When the linear form of glucose cyclizes, the product is a(n): a. anhydride. b. glycoside. c. hemiacetal. d. lactone. e. oligosaccharide.

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Chap 07_8e 16. Which answer choice is the BEST description of the mechanisms used by cells to overcome the modest affinity between an oligosaccharide and an individual carbohydrate binding domain (CBD) of a lectin? a. lectin multivalency b. expressing multiple lectin receptors c. placing multiple CBDs on a single lectin molecule d. both lectin multivalency and placing multiple CBDs on a single lectin molecule e. lectin multivalency, expressing multiple lectin receptors, and placing multiple CBDs on a single lectin molecule 17. Which compound is NOT a reducing sugar? a. fructose b. glucose c. glyceraldehyde d. ribose e. sucrose 18. From the abbreviated name of the compound Gal(β1 → 4)Glc, we know that: a. C-4 of glucose is joined to C-1 of galactose by a glycosidic bond. b. the compound is a D-enantiomer. c. the galactose residue is at the reducing end. d. the glucose is in its pyranose form. e. the glucose residue is the β anomer. 19. Which pair are NOT digestible by vertebrates? a. cellulose and amylose b. amylose and glycogen c. cellulose and chitin d. chitin and amylopectin e. amylose and amylopectin 20. Which statement about cellulose is true? a. Cellulose is the main storage polysaccharide of animal cells. b. Cellulose is a highly branched polysaccharide. c. Cellulose is a homopolysaccharide. d. Cellulose glucose residues contain the same configuration as amylose glucose residues. e. Cellulose cannot be broken down by invertebrate animals.

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Chap 07_8e 21. Which modification cannot be made to a sugar molecule by an organism? a. oxidation of the carbonyl carbon b. replacing a hydroxyl group with an amino group c. oxidizing a carbon atom to a carboxyl group d. replacing a hydroxyl group with a hydrogen atom e. All of the answer choices are possible sugar derivatives. 22. In a(n) _____, the carbonyl group is at the end of the carbon chain, but in a(n) _____, the carbonyl group can be at any other position. a. aldose; ketose b. ketose; aldose c. hexose; heptose d. aldose; hexose e. ketose; tetrose 23. Which statement concerning sialic acid residues on glycoproteins is true? a. Sialic residues on erythrocytes are recognized by lectins, leading to removal of the erythrocytes. b. Sialic residues on ceruloplasmin are recognized by lectins, leading to removal of ceruloplasmin. c. Sialic residues are removed by neuraminidases. d. The antiviral drug oseltamivir (Tamiflu) accelerates the removal of sialic acid residues. e. All of the statements are true. 24. Which statement accurately describes the interactions between the molecules thrombin, antithrombin, and heparan sulfate? a. In the absence of heparan sulfate, antithrombin binds tightly to thrombin, inhibiting blood coagulation. b. In the absence of heparan sulfate, antithrombin cannot bind to thrombin, inhibiting blood coagulation. c. In the presence of heparan sulfate, antithrombin binds tightly to thrombin, inhibiting blood coagulation. d. In the presence of heparan sulfate, antithrombin cannot bind to thrombin, enabling blood coagulation. e. In the presence of heparan sulfate, antithrombin binds tightly to thrombin, enabling blood coagulation. 25. Hemoglobin glycation is a process where _____ is _____ attached to hemoglobin. a. glycerol; covalently b. glucose; enzymatically c. glucose; nonenzymatically d. N-acetyl-galactosamine; enzymatically e. galactose; nonenzymatically

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Chap 07_8e 26. It is useful to analyze hemoglobin glycation to determine a(n): a. single-time measurement of blood glucose levels. b. single-time measurement of blood glycogen levels. c. average blood glucose level over days or weeks. d. average blood glycogen level over days or weeks. e. None of the answers is correct. 27. Which disaccharide has an anomeric carbon available for oxidation? a. Glc(α1↔1α)Glc b. Glc(α1↔2β)Fru c. Fru(β2↔1α)Glc d. both Glc(α1↔2β)Fru and Fru(β2↔1α)Glc e. None of the answers is correct. 28. Oligosaccharides differ from nucleic acids and proteins in that oligosaccharides are commonly: a. branched. b. polymeric. c. acidic. d. basic. e. None of the answers is correct. 29. Which is a heteropolysaccharide? a. cellulose b. chitin c. glycogen d. glycosaminoglycan e. starch 30. Which monosaccharide is NOT a hexose? a. fructose b. ribose c. mannose d. glucose e. galactose

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Chap 07_8e 31. Which statement is NOT true regarding phosphorylated sugar? a. It is trapped inside the cell. b. It is relatively stable at neutral pH. c. It is activated for subsequent chemical transformation. d. It can be a component of a nucleotide. e. All of the statements are true. 32. Which polysaccharide is NOT a homopolysaccharide? a. glycogen b. chitin c. amylose d. hyaluronan e. dextran 33. Which statement about dextrans is false? a. Dextrans are bacterial extracellular adhesives. b. Dextrans can be branched. c. Dextrans can have (α1→3) and (α1→6) linkages. d. Dextrans are heteropolysaccharides. e. All of the statements are true. 34. During which process are chemical bonds NOT broken? a. mutarotation b. interconverting between two configurations c. interconverting between two conformations d. interconverting between two anomers e. None of the answers is correct: all involve breaking a chemical bond. 35. Which monosaccharide is NOT a carboxylic acid? a. 6-phospho-gluconate b. gluconate c. glucose d. glucuronate e. muramic acid

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Chap 07_8e 36. Which technique is NOT commonly used to study oligosaccharide structures? a. x-ray crystallography b. mass spectroscopy c. nuclear magnetic resonance d. affinity chromatography e. chemical synthesis 37. Which statement is false regarding proteoglycans? a. Both syndecans and glypicans can be shed into the extracellular space. b. Proteoglycan shedding is unregulated in cells. c. A protease or phospholipase is responsible for releasing proteoglycans. d. Proteoglycan shedding is activated in cancerous cells. e. Cell features such as proteoglycans can be changed quickly. 38. What is the purpose of glycosidase treatment of glycoproteins and glycolipids? a. to release oligosaccharides from the protein or lipid portion b. to hydrolyze all glycosidic bonds c. to release terminal monosaccharides as part of sequencing d. to remove branches from the main carbohydrate chains of branched glycoconjugates e. All of the answers are correct. 39. The basic structure of a proteoglycan consists of a core protein and a: a. glycolipid. b. glycosaminoglycan. c. lectin. d. lipopolysaccharide. e. peptidoglycan. 40. In most cases, in order for an informational carbohydrate to become a biologically active molecule it must: a. be an asymmetric molecule. b. contain a reducing sugar. c. contain an O-glycosidic bond. d. be covalently joined to a protein or lipid. e. be present in the extracellular matrix.

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Chap 07_8e 41. Several types of human joint and skeletal defects are a result of a defect in a biosynthetic enzyme responsible for synthesis of: a. glycosaminoglycans. b. glycoproteins. c. glycolipids. d. lipopolysaccharides. e. glycosphingolipids. 42. Which glycosaminoglycan is found in the synovial fluid of joints? a. chondroitin sulfate b. dermatan sulfate c. hyaluronan d. keratin sulfate e. heparan sulfate 43. About what percentage of mammalian proteins are glycosylated? a. 5% b. 15% c. 50% d. 90% e. 95% 44. _____ is the systematic characterization of all carbohydrate components of a given cell or tissue. a. Genomics b. Proteomics c. Glycomics d. Metabolomics e. Lipidomics 45. Which compound(s) is a dominant feature of the outer membrane of the cell wall of gram-negative bacteria? a. amylose b. cellulose c. glycoproteins d. lipopolysaccharides e. lipoproteins

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Chap 07_8e 46. Which statement about starch and glycogen is false? a. Amylose is unbranched; amylopectin and glycogen contain many (α1 → 6) branches. b. Both are homopolymers of glucose. c. Both serve primarily as structural elements in cell walls. d. Both starch and glycogen are stored intracellularly as insoluble granules. e. Glycogen is more extensively branched than starch. 47. To possess optical activity, a compound must be: a. a carbohydrate. b. a hexose. c. asymmetric. d. colored. e. D-glucose. 48. Which arrow correctly identifies the atom that will become the anomeric carbon?

a. A b. B c. C d. D e. E 49. The biochemical property of lectins that is the basis for most of their biological effects is their ability to bind to: a. amphipathic molecules. b. hydrophobic molecules. c. specific lipids. d. specific oligosaccharides. e. specific peptides.

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Chap 07_8e 50. In glycoproteins, the carbohydrate moiety is always attached through the amino acid residues: a. asparagine, serine, or threonine. b. aspartate or glutamate. c. glutamine or arginine. d. glycine, alanine, or aspartate. e. tryptophan, aspartate, or cysteine. 51. Which of these monosaccharides is NOT an aldose? a. erythrose b. fructose c. glucose d. glyceraldehyde e. ribose 52. Which type of protein interaction is NOT one with the NS domains of heparan sulfate? a. conformational activation b. cell-surface localization/concentration c. enhanced protein-protein interaction d. binding extracellular signaling molecules e. All of the answer choices are types of protein interaction with heparan sulfate. 53. Which pair is interconverted in the process of mutarotation? a. D-glucose and D-fructose b. D-glucose and D-galactose c. D-glucose and D-glucosamine d. D-glucose and L-glucose e. α-D-glucopyranose and β-D-glucopyranose 54. Polysaccharides cannot be used by cells: a. as fuel storage molecules. b. for structural elements in cell walls. c. for structural elements in animal exoskeletons. d. for the extracellular matrix in animal cells. e. All of the answers are correct.

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Chap 07_8e 55. Which answer choice is the BEST description of the benefits that are provided by the extended conformation that the heteropolysaccharide glycosaminoglycans assume in solution? a. The repulsive forces of densely packed negative charges are minimized. b. The hydrophobic portions of the molecules may pack closely together to maximize van der Waals forces. c. The patterns of sulfated and nonsulfated sugar residues are more easily recognized by their respective ligands. d. The repulsive forces of densely packed negative charges are minimized, and the hydrophobic portions of the molecules may pack closely together to maximize van der Waals forces. e. The repulsive forces of densely packed negative charges are minimized, and the patterns of sulfated and nonsulfated sugar residues are more easily recognized by their respective ligands. 56. Starch and glycogen are both polymers of: a. fructose. b. glucose-1-phosphate. c. sucrose. d. α-D-glucose. e. β-D-glucose. 57. Which sequence is the correct one for leukocyte extravasation in the inflammatory response? a. integrin binding→selectin binding→adhesion→arrest→extravasation b. adhesion→integrin binding→selectin binding→arrest→extravasation c. selectin binding→integrin binding→arrest→adhesion→extravasation d. integrin binding→adhesion→selectin binding→arrest→extravasation e. selectin binding→adhesion→integrin binding→arrest→extravasation 58. Which statement about hydrogen bonding in glycogen and cellulose is true? a. Glycogen forms more internal hydrogen bonds than cellulose. b. Extensive internal hydrogen bonding makes cellulose more water soluble than glycogen. c. Extensive hydrogen bonding with water makes cellulose more soluble than glycogen. d. Glycogen is stabilized by interchain hydrogen bonds. e. The hydrogen bonding in cellulose favors a helical conformation.

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Chap 07_8e 59. These two monosaccharides could BEST be described as:

a. ketoses. b. anomers. c. rotamers. d. epimers. e. enantiomers. 60. _____ could be used to determine human blood group type. a. Lipopolysaccharides b. Gangliosides c. Glycoproteins d. Lipoproteins e. Mucins 61. Which statement about heparan sulfate is NOT true? a. Sulfation of heparan sulfate to form NS domains is important for its role as an anticoagulant. b. Heparan sulfate can promote protein-protein interactions via the NS domains. c. The secondary structure of heparan sulfate is completely random. d. The NA domains of heparan sulfate contain no sulfation. e. The core repeating structure of heparan sulfate is made up of alternating GlcNAc and GlcA. 62. _____ are secreted or membrane proteins that contain large numbers of O-linked oligosaccharide chains. a. Gangliosides b. Mucins c. Glycins d. Aminoglycans e. Immunoglobulins

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Chap 07_8e 63. D-Glucose is called a reducing sugar because it undergoes an oxidation-reduction reaction at the anomeric carbon. One of the products of this reaction is: a. D-galactose. b. D-gluconate. c. D-glucuronate. d. D-ribose. e. muramic acid. 64. Which description of a ganglioside is MOST accurate? a. the dominant surface feature of gram-negative bacteria b. the dominant surface feature of gram-positive bacteria c. an oligosaccharide chain attached to a newly synthesized protein in the ER d. a membrane lipid in which the polar head group is a complex oligosaccharide containing at least one sialic acid e. a membrane lipid in which the oligosaccharide is attached to a mucin 65. The polysaccharide chitin is MOST chemically similar to: a. cellulose. b. dextran. c. glycogen. d. starch. e. amylose. 66. When drawing a Haworth perspective formula from a Fisher projection, which statement is true regarding anomers? a. It is α if the hydroxyl group on the anomeric carbon is up. b. It is α if the hydroxyl group on the anomeric carbon is down. c. It is α if the hydroxyl group on the anomeric carbon is on the same side of the ring as the C-6. d. It is α if the hydroxyl group on the anomeric carbon is on the opposite side of the ring as the C-6. e. None of the answers is correct. 67. Which statement is NOT a reason that it is difficult to study oligosaccharide composition from biological systems? a. Oligosaccharides are often branched. b. Oligosaccharides often have a high charge density. c. Oligosaccharides have a variety of linkages (e.g., α1→6 or β1→4). d. Glycosaminoglycan oligosaccharides have extremely stable sulfate esters. e. There are no specific glycosidase enzymes that can be used to selectively digest oligosaccharides.

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Chap 07_8e 68. Why is it surprising that the side chains of tryptophan residues in lectins can interact with sugars? a. The side chain of tryptophan is hydrophilic and sugars are hydrophobic. b. The side chain of tryptophan is negatively charged and sugars are generally positively charged or neutral. c. The side chain of tryptophan can make hydrogen bonds and sugars cannot. d. The side chain of tryptophan is hydrophobic and sugars are generally hydrophilic. e. None of the answers is correct. 69. Why is methyl iodide used in the classical method of exhaustive methylation to determine the positions of glycosidic bonds in a linear polysaccharide? a. All free hydroxyls become unstable, allowing hydrolysis of only glycosidic bonds to occur in acid. b. All free hydroxyls become stable, allowing hydrolysis of only glycosidic bonds to occur in acid. c. All glycosidic bonds react with methyl iodide. d. All glycosidic bonds become stable for treatment with acid. e. All glycosidic bonds are hydrolyzed with methyl iodide. 70. Which factor is NOT a part of determining the complete structure of an oligosaccharide or polysaccharide? a. determination of linear sequence b. determination of lectin partners c. determination of branching positions d. determination of glycosidic linkages e. determination of monosaccharide configuration 71. When forming the disaccharide maltose from two glucose monosaccharides: a. water is eliminated. b. a hemiacetal is converted to an acetal. c. the resulting disaccharide is no longer a reducing sugar. d. water is eliminated and a hemiacetal is converted to an acetal. e. None of the answers is correct. 72. Why does the cyclization of sugars create an additional chiral center in that molecule? What is the nomenclature of the stereoisomer produced by this reaction?

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Chap 07_8e 73. Describe one biological advantage of storing glucose units in branched polymers (glycogen, amylopectin) rather than in linear polymers.

74. Categorize each of these as an aldose, a ketose, or neither.

75. Explain how it is possible that a polysaccharide molecule, such as glycogen, may have only one reducing end, and yet have many nonreducing ends.

76. Describe the differences between a proteoglycan and a glycoprotein.

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Chap 07_8e 77. Describe the principal components of a typical proteoglycan, including their relationships and connections to one another.

78. Describe the structure of a proteoglycan aggregate such as is found in the extracellular matrix.

79. The compound L-glyceraldehyde is shown. Describe a stereochemically correct representation of C-1 and C2 of D-glucose.

80. In the structure, (a) how many of the monosaccharide units are furanoses and how many are pyranoses? (b) What is the linkage between the two monosaccharide units? (c) Is this a reducing sugar? Explain.

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Chap 07_8e 81. Briefly explain how the drugs Tamiflu and Relenza work to prevent the flu.

82. The glycosaminoglycans are negatively charged at neutral pH. What components of these polymers confer the negative charge?

83. Identify all the epimeric pairs in the structures, taking into account the possibility of mutarotation in solution.

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Chap 07_8e 84. Describe the structure of the repeating basic unit of (a) amylose and (b) cellulose.

85. What are lectins? What are some biological processes that involve lectins?

86. Define each of these in 20 words or fewer. (a) anomeric carbon (b) enantiomers (c) furanose (d) pyranose (e) glycoside (f) epimers (g) aldose (h) ketose

87. In measuring long-term glucose levels in the bloodstream, glycated hemoglobin must be separated from unmodified hemoglobin to determine the percentage of glycated hemoglobin. Suggest a simple chromatographic method by which this separation can be performed.

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Chap 07_8e 88. Match these molecules with their biological roles. (a) glycogen (b) starch (c) trehalose (d) chitin (e) cellulose (f) peptidoglycan (g) hyaluronate (h) proteoglycan

_____ viscosity, lubrication of extracellular secretions _____ carbohydrate storage in plants _____ transport/storage in insects _____ exoskeleton of insects _____ structural component of bacterial cell wall _____ structural component of plant cell walls _____ extracellular matrix of animal tissues _____ carbohydrate storage in animal liver

89. Describe the process by which old serum glycoproteins are removed from the mammalian circulatory system.

90. (a) In the pyranose ring form structure, how many asymmetric carbons (chiral centers) does each of the anomers of glucose have? (b) How many stereoisomers of the glucose are theoretically possible?

91. Of the 16 possible aldohexoses, 8 are D forms and 8 are L forms. However, most of the hexoses of living organisms are D isomers. Speculate in a few sentences the possible reason for this preference.

92. The primary amino group of hemoglobin can react with glucose to form products that, downstream, generate advanced glycation end products (AGE). Briefly explain why these AGE are a problem in people with diabetes.

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Chap 07_8e 93. Explain why all monosaccharides and disaccharides are soluble in water.

94. What is the biological advantage to an organism that stores its carbohydrate reserves as starch or glycogen rather than as an equivalent amount of free glucose?

95. The number of structurally different polysaccharides that can be made with 20 different monosaccharides is far greater than the number of different polypeptides that can be made with 20 different amino acids if both polymers contain an equal number (say 100) of total residues. Explain why.

96. (a) Define "reducing sugar." (b) Show the reaction product of glucose after it is used as a reducing sugar. (c) Explain why fructose is also considered a reducing sugar. (Hint: It must first undergo a chemical conversion.) (d) Sucrose is a disaccharide composed of glucose and fructose (Glc(α1→2)Fru). Explain why sucrose is not a reducing sugar, even though both glucose and fructose are.

97. How do oligosaccharide portions of glycoproteins change the properties of the proteins?

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Chap 07_8e Answer Key 1. e 2. d 3. d 4. c 5. c 6. d 7. c 8. d 9. b 10. a 11. e 12. e 13. b 14. a 15. c 16. e 17. e 18. a 19. c 20. c 21. e 22. a 23. c 24. c 25. c 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 07_8e 27. e 28. a 29. d 30. b 31. e 32. d 33. d 34. c 35. c 36. a 37. b 38. a 39. b 40. d 41. a 42. c 43. c 44. c 45. d 46. c 47. c 48. a 49. d 50. a 51. b 52. e 53. e 54. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 07_8e 55. e 56. d 57. c 58. d 59. d 60. b 61. c 62. b 63. b 64. d 65. a 66. d 67. d 68. d 69. b 70. b 71. d 72. The alcohol can add in either of two ways, attacking the "front" or the "back" of the carbonyl carbon, producing either an alpha or beta stereoisomer. 73. The enzymes that act on these polymers to mobilize glucose for metabolism act only on their nonreducing ends. With extensive branching, there are more such ends for enzymatic attack than would be present in the same quantity of glucose stored in a linear polymer. In effect, branched polymers increase the substrate concentration for these enzymes. 74. Molecules (b) and (d) are aldoses; (a) is a ketose; (c) and (e) are neither. 75. The molecule is branched with each branch ending in a nonreducing end. 76. Both are made up of proteins and polysaccharides. In proteoglycans, the carbohydrate moiety dominates, constituting 95% or more of the mass of the complex. In glycoproteins, the protein constitutes a larger fraction, generally 50% or more of the total mass.

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Chap 07_8e 77. A typical proteoglycan consists of a core protein with covalently attached glycosaminoglycan polysaccharides, such as chondroitin sulfate and keratin sulfate. The polysaccharides generally attach to a serine residue in the protein via a trisaccharide (Gal–Gal–Xyl). (See Fig. 7-21.) 78. A proteoglycan aggregate is a supramolecular assembly of proteoglycan monomers. Each monomer consists of a core protein with multiple, covalently linked polysaccharide chains. Hundreds of these monomers can bind noncovalently to a single extended molecule of hyaluronic acid to form large structures. 79. In D-glucose, the positions of the —H and —OH on C-2 are the reverse of those for C-2 of L-glyceraldehyde. (See Fig. 7-2.) 80. (a) 2 pyranoses; (b) β1→4; (c) yes; There is a free anomeric carbon on one of the monosaccharide units that can undergo oxidation upon ring opening. 81. A newly formed flu virus needs to get out of its host cell in order to infect new cells and make more virus. As the new virus buds off the host cell, it initially binds (via lectins) to cell surface receptors located in the membrane that are specific for sialic acid residues. The release from these receptors is facilitated by a viral sialidase that cleaves the sialic acid from the oligosaccharides displayed on the surface of the host cell. After these sialic residues are removed, the virus can depart and find a new host for replication. Both Tamiflu and Relenza are inhibitors of the viral neuraminidase, thus blocking the release of new flu viruses. 82. Uronic acids, such as glucuronic acid, and sulfated hydroxyl groups confer negative charges. See Figure 7-19. 83. Epimeric pairs should have one carbon of altered stereochemistry compared to each other, as long as that carbon is not the anomeric carbon, because of the easy mutarotation to the opposite anomer. Therefore, C and D are anomers of each other, but are both epimers of A. Likewise, E and F are anomers of each other, but both are epimers of B. 84. (a) For the structure of amylose, see Figure 7-13a. The repeating unit is -D-glucose linked to α-D-glucose; the glycosidic bond is therefore (α1→4). (b) Cellulose has the same structure as amylose, except that the repeating units are β-D-glucose and the glycosidic bond is (β1→4). (See Fig. 7-14.) 85. Lectins are proteins that bind to specific oligosaccharides. They interact with specific cell surface glycoproteins thus mediating cell-cell recognition and adhesion. Several microbial toxins and viral capsid proteins, which interact with cell surface receptors, are lectins. 86. (a) The anomeric carbon is the carbonyl carbon atom of a sugar, which is involved in ring formation. Once the anomeric carbon is involved in a glycosidic bond it is the only carbon with more than one oxygen. (b) Enantiomers are stereoisomers that are nonsuperimposable mirror images of each other. (c) Furanose is a sugar with a fivemembered ring. (d) Pyranose is a sugar with a six-membered ring. (e) A glycoside is an acetal formed between a sugar anomeric carbon hemiacetal and an alcohol, which may be part of a second sugar. (f) Epimers are stereoisomers differing in configuration at only one asymmetric carbon. (g) An aldose is a sugar with an aldehyde carbonyl group. (h) A ketose is a sugar with a ketone carbonyl group.

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Chap 07_8e 87. Free hemoglobin has more positively charged residues (both lysine side chains and free amino ends) than glycated hemoglobin, where these amines have been converted to uncharged Schiff bases (see Box 7-2). Therefore, free hemoglobin is more positively charged than glycated hemoglobin and ion-exchange chromatography could be used. (Whether one uses anion- or cation-exchange chromatography depends on the pI of hemoglobin (6.9) and the pH of the buffer; see Chapter 3.) 88. g; b; c; d; f; e; h; a 89. Newly synthesized serum glycoproteins bear oligosaccharide chains that end in sialic acid. With time, the sialic acid is removed. Glycoproteins that lack the terminal sialic acid are recognized by asialoglycoprotein receptors in the liver, internalized, and destroyed. 90. (a) The number of chiral centers is 5; all the carbons except C-6. (b) The number of possible stereoisomers for a compound with n chiral centers is 2n ; in this case, 25, or 32 possible isomers. 91. The basis for the initial preference during evolution is unknown; however, once one isomer was selected, it was likely that evolving enzymes would retain their preference for that stereoisomer. 92. Due to the high levels of blood glucose in patients with diabetes, AGE may accumulate to relatively high concentrations. These AGE can cross-link critical proteins, causing damage to the kidneys, retinas, and cardiovascular system. 93. These compounds have many hydroxyl groups, each of which can hydrogen bond with water. 94. The polymers are essentially insoluble and contribute little to the osmolarity of the cell, thereby avoiding the influx of water that would occur with the glucose in solution. They also make the uptake of glucose energetically more feasible than it would be with free glucose in the cell. 95. Because virtually all peptides are linear (i.e., are formed with peptide bonds between the α-carboxyl and α-amino groups), the variability of peptides is limited by the number of different subunits. Polysaccharides can be linear or branched, can be α- or β-linked, and can be joined 1→4, 1→3, 1→6, and so on. The number of different ways to arrange 20 different sugars in a branched oligosaccharide is therefore much larger than the number of different ways a peptide could be made with an equal number of residues. 96. (a) A reducing sugar is one with a free carbonyl carbon (aldehyde) that can be oxidized to the carboxylic acid by Cu2+ or Fe3+. (b) The reaction should convert the aldehyde carbon of linear glucose to a carboxylic acid. (c) Fructose is a ketose, which cannot be readily oxidized; that is, it does not act as a reducing agent in its unaltered form. Fructose can tautomerize to an aldehyde, a reaction that is readily catalyzed by acidic or basic conditions. (d) The carbonyl carbons of sucrose are C-1 of glucose and C-2 of fructose. When the carbonyl carbons are involved in glycosidic linkages, they are no longer accessible to oxidizing agents. In sucrose (Glc(α1→2)Fru), both oxidizable carbons are involved in the glycosidic linkage. 97. Hydrophilic carbohydrates can alter the polarity and solubility of the proteins. Steric and charge interactions may influence the conformation of regions of the polypeptide and protect it from proteolysis. Carbohydrates attached to proteins can provide binding sites for lectins.

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Chap 08_8e Indicate the answer choice that best completes the statement or answers the question. 1. In the Watson-Crick model of DNA structure: a. both strands run in the same direction, 3'→5'; they are parallel. b. phosphate groups project toward the middle of the helix, where they are protected from interaction with water. c. T can form three hydrogen bonds with either G or C in the opposite strand. d. the distance between the sugar backbone of the two strands is just large enough to accommodate either two purines or two pyrimidines. e. the vertical distance between two adjacent bases in one strand is about 3.4 Å. 2. The 5'→3' orientation of a DNA or RNA chain refers to the: a. linkage of the phosphodiester bonds between the nucleotides. b. location of the attachment of the nitrogenous base on the pentose sugar. c. positions of the chain that do not have a nucleotide attached. d. positions of the chain that do not have a phosphate group attached. e. respective net charges found at each end of the chain. 3. Chargaff's rules state that in typical DNA: a. A = G. b. A = C. c. A = U. d. A + T = G + C. e. A + G = T + C.

4. According to the sequence (note that the DNA is written in the 5'→3' direction, and the gene of interest is underlined)

a. (5')ATTGAATCCTTGGCT GGTGA(3'). b. (5')ATTGAATCCTTGGCT GGTGA(5'). c. (5')TCACCAGCCAAGGAATTCAAT(3'). d. (3')TCACCAGCCAAGGA TTCAAT(5'). e. (3')GGTGAGTCGG TTCAATTCGT(5').

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Chap 08_8e 5. In the Watson-Crick model of DNA structure (B-form DNA): a. a purine in one strand always hydrogen bonds with a purine in the other strand. b. A=T pairs share three hydrogen bonds. c. G≡C pairs share two hydrogen bonds. d. the 5' ends of both strands are at one end of the helix. e. the bases occupy the interior of the helix. 6. Which molecule contains the greatest amount of stored chemical energy? a. dGTP b. GDP c. dGDP d. GMP e. cGMP 7. In the chemical synthesis of DNA the: a. dimethoxytrityl group catalyzes formation of the phosphodiester bond. b. direction of synthesis is 5' to 3'. c. maximum length of oligonucleotide that can be synthesized is 8 to 10 nucleotides. d. nucleotide initially attached to the silica gel support will become the 3' end of the finished product. e. protecting cyanoethyl groups are removed after each step. 8. The alkaline hydrolysis of RNA does NOT produce: a. 2'-AMP. b. 2',3'-cGMP. c. 2'-CMP. d. 3',5'-cAMP. e. 3'-UMP. 9. A tetraplex of DNA is MOST likely to form with which residue? a. adenosine b. thymidine c. guanosine d. cytidine e. A tetraplex is equally likely with all bases.

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Chap 08_8e 10. In DNA sequencing by the Sanger (dideoxy) method: a. radioactive dideoxy ATP is included in each of four reaction mixtures before enzymatic synthesis of complementary strands. b. specific enzymes are used to cut the newly synthesized DNA into small pieces, which are then separated by electrophoresis. c. the dideoxynucleotides must be present at high levels to obtain long stretches of DNA sequence. d. the role of the dideoxy CTP is to occasionally terminate enzymatic synthesis of DNA where a G occurs in the template strands. e. the template DNA strand is radioactive. 11. The sequence of one strand of double-stranded DNA is shown in the 5' → 3' direction. Which sequence is palindromic? a. AGGTCC b. CCTTCC c. GAATCC d. GGATCC e. GTATCC 12. These structures would MOST likely be formed by:

a. W: RNA; X: RNA; Y: DNA b. W: RNA; X: DNA; Y: DNA c. W: DNA; X: DNA; Y: RNA d. W: DNA; X: RNA; Y: RNA e. W: RNA; X: RNA; Y: RNA

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Chap 08_8e 13. Which statement about the polymerase chain reaction (PCR) is false? a. DNA amplified by PCR can be cloned. b. DNA amplification is linear in magnitude. c. Newly synthesized DNA must be heat denatured before the next round of DNA synthesis begins. d. The boundaries of the amplified DNA segment are determined by the synthetic oligonucleotides used to prime DNA synthesis. e. The technique is sufficiently sensitive that DNA sequences can be amplified from a single animal or human hair. 14. Incubation of DNA at low pH is MOST likely to cause: a. depurination. b. depyrimidination. c. mutation of cytosine to uracil. d. hydrolysis of the phosphodiester bond. e. deamination of adenine and guanine. 15. Which part of the nucleotide structure enables quantification of concentration via UV absorbance? a. phosphate group(s) b. pentose sugar c. nitrogenous base d. hydroxyl group(s) on the pentose sugar e. None of the answers is correct. 16. The experiment by Avery, MacLeod, and McCarty in which nonvirulent bacteria were made virulent by transformation was significant because it showed that: a. bacteria can undergo transformation. b. genes are composed of only DNA. c. mice are more susceptible to pneumonia than are humans. d. pneumonia can be cured by transformation. e. virulence is determined genetically. 17. What is the MOST likely length of an mRNA that will code for a polypeptide with 150 amino acids? a. 50 nucleotides b. 150 nucleotides c. 450 nucleotides d. >450 nucleotides e. All of these lengths are possible depending on the organism in which the mRNA is found.

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Chap 08_8e 18. In a nucleoside, the pentose sugar is in its _____ form, and the ring is _____. a. α-furanose; planar b. α-pyranose; puckered c. β-furanose; planar d. β-furanose; puckered e. β-pyranose; planar 19. Which statement concerning the tautomeric forms of bases such as uracil is correct? a. The double-lactim form contains a ketone group. b. The lactam form contains an alcohol group. c. The lactam form predominates at neutral pH. d. Formation of the lactim from the lactam is irreversible. e. The lactim and double-lactim forms are stabilized at high pH. 20. DNA is _____ chemically stable than RNA due to the _____-hydroxyl groups on _____. a. more; 2'; RNA b. more; 2'; DNA c. more; 3'; RNA d. less; 2'; RNA e. less; 2'; DNA 21. An example of a next-generation method of DNA sequencing is _____ sequencing. a. capillary array b. reverse Sanger c. tandem PCR d. reversible terminator e. MALDI-MS 22. Which type of damage to DNA structure is MOST likely to be caused by UV light? a. deamination b. pyrimidine dimers c. depurination d. depyrimidination e. hydrolysis of the phosphodiester bond

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Chap 08_8e 23. The difference between thymine and uracil is one _____ group on the _____ ring. a. methylene; pyrimidine b. methyl; pyrimidine c. hydroxyl; ribose d. amine; pyrimidine e. methyl; purine 24. In nucleotides and nucleic acids, syn and anti conformations relate to: a. base stereoisomers. b. rotation around the phosphodiester bond. c. rotation around the sugar-base bond. d. sugar pucker. e. sugar stereoisomers. 25. The energy carrier ATP is an example of a: a. deoxyribonucleoside triphosphate. b. dinucleotide. c. peptide. d. ribonucleotide. e. ribonucleoside triphosphate. 26. The compound that consists of ribose linked by an N-glycosidic bond to N-9 of adenine is: a. a deoxyribonucleoside. b. a purine nucleotide. c. a pyrimidine nucleotide. d. adenosine monophosphate. e. adenosine. 27. The chemical difference between a nucleotide and a nucleoside is that: a. a different nitrogenous base is added to each. b. nucleotides do not contain phosphate groups. c. nucleosides do not contain phosphate groups. d. nucleotides do not contain pentose sugars. e. nucleosides do not contain pentose sugars.

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Chap 08_8e 28. Triple-helical DNA structures can result from Hoogsteen (non-Watson-Crick) interactions. These interactions are primarily: a. covalent bonds involving deoxyribose. b. covalent bonds involving the bases. c. hydrogen bonds involving deoxyribose. d. hydrogen bonds involving the bases. e. hydrophobic interactions involving the bases. 29. Which statement is false about base stacking when nucleic acids are in a double-stranded conformation? a. Stacking interactions occur when two or more bases are positioned with their rings parallel to each other. b. Stacking interactions are hydrophilic in nature. c. Stacking involves a combination of van der Waals and dipole-dipole interactions between bases. d. Base stacking helps to minimize contact of the bases with water. e. Base stacking interactions are important in stabilizing the three-dimensional structure of nucleic acids. 30. The difference between a ribonucleotide and a deoxyribonucleotide is a: a. deoxyribonucleotide has an —H instead of an —OH at C-2. b. deoxyribonucleotide has an —H instead of an —OH at C-3. c. ribonucleotide has an extra —OH at C-4. d. ribonucleotide has more structural flexibility than deoxyribonucleotide. e. ribonucleotide is a pyranose, deoxyribonucleotide is a furanose.

31. According to the sequence (note that the DNA is written in the 5'→3' direction, and the gene of interest is underlined)

a. (5')GGTTTGAATCAAATGGCTGA(3'). b. (5')ATGACTGATACATCATCCTC(3'). c. (3')ATGACTGATACATCATCCTC(5'). d. (5')GAGGATGATGTATCAGTCAT(3'). e. (3')GAGGATGATGTATCAGTCA(5').

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Chap 08_8e 32. The image shows a DNA sequencing gel using the Sanger method. Migration during electrophoresis was from the top to the bottom. Which band represents the shortest and longest fragments of DNA?

a. shortest = Z, longest = W b. shortest = X, longest = Z c. shortest = W, longest = Y d. shortest = Y, longest = X e. shortest = W, longest = Z 33. Which single-stranded nucleic acid could form a hairpin structure? a. (5')TTTGCGATACTCATCGCATT(3') b. (5')TTTGCGATACTCACGCTATT(3') c. (5')TTTGCGATACTCTGCGATTT(3') d. All of the answers are correct. e. None of the answers is correct. 34. When double-stranded DNA is heated at neutral pH, which change does NOT occur? a. the absorption of UV light increases (260 nm) b. the covalent N-glycosidic bond between the base and the pentose breaks c. the helical structure unwinds d. the hydrogen bonds between A and T break e. the viscosity of the solution decreases

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Chap 08_8e 35. The covalent backbone of DNA and RNA consists of alternating: a. phosphate groups and nitrogenous bases. b. phosphate groups and pentose residues. c. pentose residues and nitrogenous bases. d. pentose residues and cyclic nucleosides. e. None of the answers is correct. 36. The DNA oligonucleotide abbreviated pATCGAC: a. has seven phosphate groups. b. has a hydroxyl at its 3' end. c. has a phosphate on its 3' end. d. has an A at its 3' end. e. violates Chargaff's rules. 37. The scientists who used x-ray crystallography to shed light on the three-dimensional structure of DNA were: a. Erwin Chargaff and colleagues. b. Alfred D. Hershey and Martha Chase. c. James Watson and Francis Crick. d. Rosalind Franklin and Maurice Wilkins. e. Oswald T. Avery, Colin MacLeod, and Maclyn McCarty. 38. Which of these would have the highest melting temperature? a. 20 mer double-stranded DNA-DNA duplex b. 20 mer double-stranded RNA-RNA duplex c. 40 mer double-stranded DNA-DNA duplex d. 40 mer double-stranded DNA-RNA duplex e. 40 mer double-stranded RNA-RNA duplex 39. In comparison with DNA-DNA double helices, the stability of DNA-RNA and RNA-RNA helices is: a. DNA-DNA > DNA-RNA > RNA-RNA. b. DNA-DNA > RNA-RNA > DNA-RNA. c. RNA-DNA > RNA-RNA > DNA-DNA. d. RNA-RNA > DNA-DNA > DNA-RNA. e. RNA-RNA > DNA-RNA > DNA-DNA.

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Chap 08_8e 40. The image shows a DNA sequencing gel using the Sanger method. Migration during electrophoresis was from the top to the bottom. What is the sequence of the template DNA?

a. (5')ACTAGTGACCGT(3') b. (5')TGCCAGTGATCA(3') c. (5')ACGGTCACTAGT(3') d. (5')TGATCACTGGCA(3') e. It cannot be determined from this information. 41. What would happen if blocking tags were NOT used in reversible terminator sequencing, a next-generation method of DNA sequencing? a. The DNA fragments to sequence/read would be too large. b. More than one dNTP could be incorporated to the same growing nucleotide chain during a single cycle. c. The flow cell could not immobilize DNA fragments. d. Multiple fluorescent colors could be observed across the flow cell at the same time. e. Luciferase would not react in the presence of ATP. 42. Double-stranded regions of RNA: a. are less stable than double-stranded regions of DNA. b. can be observed in the laboratory, but probably have no biological relevance. c. can form between two self-complementary regions of the same single strand of RNA. d. do not occur. e. have the two strands arranged in parallel (unlike those of DNA, which are antiparallel).

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Chap 08_8e 43. The polymerase chain reaction mixture does NOT include: a. all four deoxynucleoside triphosphates. b. DNA containing the sequence to be amplified. c. DNA ligase. d. heat-stable DNA polymerase. e. oligonucleotide primers. 44. The phosphodiester bond that joins adjacent nucleotides in DNA: a. associates ionically with metal ions, polyamines, and proteins. b. is positively charged. c. is susceptible to alkaline hydrolysis. d. links C-2 of one base to C-3 of the next. e. links C-3 of deoxyribose to N-1 of thymine or cytosine. 45. The phosphodiester bonds that link adjacent nucleotides in both RNA and DNA: a. always link A with T and G with C. b. are susceptible to alkaline hydrolysis. c. are uncharged at neutral pH. d. form between the planar rings of adjacent bases. e. join the 3' hydroxyl of one nucleotide to the 5' hydroxyl of the next.

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Chap 08_8e 46. The image shows a Sanger DNA sequencing gel where one ingredient was left out of all sequencing reactions. Migration during electrophoresis was from the top to the bottom. Other than the one missing ingredient, the gel ran correctly. What is the MOST likely missing ingredient?

a. dNTPs b. ddNTPs c. radioactive DNA primer d. DNA polymerase e. template DNA 47. Which base compositions for single-stranded RNA are possible? a. 5%A, 45%G, 45%C, 0%T, 5%U b. 25%A, 25%G, 25%C, 0%T, 25%U c. 35%A, 10%G, 30%C, 0%T, 25%U d. All of these answers are correct. e. None of these answers are correct. 48. In the laboratory, several factors are known to cause alteration of the chemical structure of DNA. The factor(s) likely to be important in a living cell is/are: a. heat. b. low pH. c. reactive oxygen species. d. UV light. e. both reactive oxygen species and UV light. Copyright Macmillan Learning. Powered by Cognero.

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Chap 08_8e 49. A major component of RNA but not of DNA is: a. adenine. b. cytosine. c. guanine. d. thymine. e. uracil. 50. The correct name for the molecule is:

a. 5-methylcytidine. b. C5-methylcytidine. c. 5-methyluridine. d. C5-methylthymidine. e. 5-methylthymidine. 51. Double-stranded DNA was isolated from a cryophilic bacterium that grow at very low temperatures. Which choice is MOST likely to represent a possible composition of its bases? a. 30% A:T, 70% G:C b. 50% A:T, 50% G:C c. 70% A:T, 30% G:C d. Any of these choices is a likely composition. e. None of these choices is a likely composition. 52. In the Watson-Crick model for the DNA double helix (B form) the A=T and G≡C base pairs share which property? a. The distance between the two glycosidic (base-sugar) bonds is the same in both base pairs, within a few tenths of an angstrom. b. The molecular weights of the two base pairs are identical. c. The number of hydrogen bonds formed between the two bases of the base pair is the same. d. The plane of neither base pair is perpendicular to the axis of the helix. e. The proton-binding groups in both base pairs are in their charged or ionized form.

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Chap 08_8e 53. Which deoxyoligonucleotide is complementary to the DNA sequence (5')AGACTGGTC(3')? a. (5')CTCATTGAG(3') b. (5')GACCAGTCT(3') c. (5')GAGTCAACT(3') d. (5')TCTGACCAG(3') e. (5')TCTGGATCT(3') 54. Hoogsteen base-pairing occurs when a third strand of DNA binds along the _____ of a double helix of DNA. a. minor groove b. major groove c. free 5' end d. free 3' end e. Any of these parts of a DNA double helix could participate in a Hoogsteen interaction. 55. The nucleic acid bases: a. absorb UV light maximally at 280 nm. b. are all about the same size. c. are relatively hydrophilic. d. are roughly planar. e. can all stably base-pair with one another. 56. In living cells, nucleotides and their derivatives can serve as: a. carriers of metabolic energy. b. enzyme cofactors. c. intracellular signals. d. precursors for nucleic acid synthesis. e. All of the answers are correct. 57. For the helix in double-stranded B-form DNA, the majority of the stability can be attributed to: a. base-pairing interactions via hydrogen bonds. b. hydration of the phosphate backbone. c. metal cations interacting with the phosphate backbone and base-stacking interactions. d. covalent bonds between adjacent bases in one strand. e. the presence of a dipole along each strand.

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Chap 08_8e 58. Which statement describes a function of the addition of methyl groups to DNA? a. Methylation is used by E. coli as part of a defense mechanism to distinguish its DNA from foreign DNA. b. Methylation distinguishes newly synthesized DNA from older DNA. c. Enzymatic methylation is involved in the regulation of gene expression. d. All of the statements describe a function of DNA methylation. e. None of the statements describes a function of DNA methylation. 59. The double helix of DNA in the B form is stabilized by: a. covalent bonds between the 3' end of one strand and the 5' end of the other. b. hydrogen bonding between the phosphate groups of two side-by-side strands. c. hydrogen bonds between the riboses of each strand. d. nonspecific base-stacking interaction between two adjacent bases in the same strand. e. ribose interactions with the planar base pairs. 60. When performing a polymerase chain reaction (PCR), what is the advantage of using a DNA polymerase isolated from a thermophilic organism? a. The PCR does not need to be cooled below the denaturation step. b. The PCR does not need primers to proceed. c. The PCR does not need to have fresh enzyme added after each cycle. d. The PCR does not need to have fresh dNTPs added after each cycle. e. The PCR does not need to have fresh template DNA added after each cycle. 61. The ribonucleotide polymer (5')GUGAUCAAGC(3') could only form a double-stranded structure with: a. (5')CACUAGUUCG(3'). b. (5')CACUAGUUCG(3'). c. (5')CACUUUCGCCC(3'). d. (5')GCUUGAUCAC(3'). e. (5')GCCUAGUUUG(3'). 62. For the oligoribonucleotide pACGUAC, the nucleotide at the: a. 3' end has a phosphate at its 3' hydroxyl. b. 3' end is a purine. c. 5' end has a 5' hydroxyl. d. 5' end has a phosphate on its 5' hydroxyl. e. 5' end is a pyrimidine.

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Chap 08_8e 63. The MOST striking difference between A-, B-, and Z-form DNA is that: a. A form does not contain a major and minor groove. b. B form has the smallest helical diameter. c. Z form is left-handed. d. B form has the greatest number of base pairs per helical turn. e. A form maximizes base-stacking interactions. 64. Which conformation is NOT permitted due to steric interference? a. purine in syn conformation b. purine in anti conformation c. pyrimidine in syn conformation d. pyrimidine in anti conformation e. All of these conformations are permitted. 65. B-form DNA in vivo is a _____-handed helix, _____ Å in diameter with a rise of _____ Å per base pair. a. left; 20; 3.9 b. right; 18; 3.4 c. right; 18; 3.6 d. right; 20; 3.4 e. right; 23; 2.6 66. Compounds that generate nitrous acid (such as nitrites, nitrates, and nitrosamines) change DNA molecules by: a. breakage of phosphodiester bonds. b. deamination of bases. c. depurination. d. formation of thymine dimers. e. transformation of A→T. 67. A pyrimidine is joined covalently to the pentose sugar through the _____ of the base to the _____ carbon of the pentose. a. N-1; 1' b. N-9; 1' c. N-1; 5' d. N-9; 5' e. None of the answers is correct.

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Chap 08_8e 68. Which statement is NOT true of all naturally occurring DNA? a. Deoxyribose units are connected by 3',5'-phosphodiester bonds. b. The amount of A always equals the amount of T. c. The ratio A+T/G+C is constant for all natural DNAs. d. The two complementary strands are antiparallel. e. Two hydrogen bonds form between A and T. 69. Double-stranded regions of RNA typically take on a(n) _____-handed helix. a. A-form left b. A-form right c. B-form left d. B-form right e. Z-form left 70. Purines have ____ ring(s), with each ring containing _____ nitrogen(s); pyrimidines have one ring, with each ring containing _____ nitrogens. a. one; one; one b. one; two; two c. two; one; two d. two; two; one e. two; two; two 71. One of the MOST common regulatory second messengers in cells is: a. FAD. b. NAD+. c. coenzyme A. d. ATP. e. cAMP. 72. Which DNA primer would have the highest melting temperature? a. GCATCGGC b. AATCGGAT c. ATACAGATCGGC d. ACCGGCAGGTCGGC e. ATACGCAGATCGGC

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Chap 08_8e 73. Based on Chargaff's rules, which base compositions for double-stranded DNA are possible? a. 5%A, 45%G, 45%C, 5%T, 0%U b. 20%A, 20%G, 20%C, 20%T, 20%U c. 35%A, 15%G, 35%C, 15%T, 0%U d. All of the answers are correct. e. None of the answers are correct. 74. In the Watson-Crick model for the DNA double helix, which statement is NOT true? a. The two strands run antiparallel to one another. b. The base-pairing occurs on the inside of the double helix. c. The double helix is right-handed. d. There are two equally sized grooves that run up the sides of the helix. e. The two strands have complementary sequences. 75. In a double-stranded nucleic acid, cytosine typically base-pairs with: a. adenosine. b. guanine. c. inosine. d. thymine. e. uracil. 76. How did the addition of different-colored fluorescent tags on each ddNTP improve the Sanger DNA sequencing method? a. Scientists did not need to use a heat-stable DNA polymerase. b. A DNA primer was no longer needed. c. All four ddNTPs could be incorporated into a single reaction. d. Scientists could now use short tandem repeats to assist their sequencing. e. The template DNA could now be double stranded. 77. Which statement is true of the pentoses found in nucleic acids? a. C-5 and C-1 of the pentose are joined to phosphate groups. b. The pentoses are in a planar configuration. c. The bond that joins nitrogenous bases to pentoses is an O-glycosidic bond. d. The pentoses are always in the β-furanose form. e. The straight-chain and ring forms undergo constant interconversion.

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Chap 08_8e 78. In the Watson-Crick structure of B-form DNA, the: a. planes of the bases are nearly perpendicular to the helical axis. b. adenine content of one strand must equal the thymine content of the same strand. c. nucleotides are arranged in the A form. d. purine content (fraction of bases that are purines) must be the same in both strands. e. two strands are parallel. 79. What is the approximate length of a DNA molecule (in the B form) containing 10,000 base pairs?

80. A solution of DNA is heated slowly until the t m is reached. What is the likely structure of the DNA molecules at this temperature?

81. Briefly describe the experimental evidence of Avery, MacLeod, and McCarty that DNA is the genetic material.

82. In one sentence, identify the most obvious structural difference between A-form (Watson-Crick) DNA and Z-form DNA.

83. What is the principal effect of UV radiation on DNA?

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Chap 08_8e 84. Mouse DNA hybridizes more extensively with human DNA than with yeast DNA. Explain by describing the factor or factors that determine extent of hybridization.

85. What happens in automated Sanger DNA sequencing reaction if one forgets to add (a) all fluorescent ddNTPs? (b) fluorescent ddGTP? (c) all dNTPs? (d) dGTP?

86. Match the type of bond with its role. (a) phosphodiester _____ links base to pentose in nucleotide (b) N-glycosidic _____ joins adjacent nucleotides in one strand (c) phosphate ester _____ joins complementary nucleotides in two strands (d) hydrogen _____ difference between a nucleoside and a nucleotide

87. Explain how nucleoside triphosphates (such as ATP) act as carriers of chemical energy.

88. Describe briefly what is meant by saying that two DNA strands are complementary.

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Chap 08_8e 89. (a) Explain the similarities and differences between monocistronic and polycistronic mRNAs. (b) State the domains (Bacteria, Archaea, Eukarya) in which these types of mRNAs may be found.

90. Describe briefly how noncovalent interactions contribute to the three-dimensional shapes of RNA molecules.

91. Speculate why adenosine, rather than another large molecule, is used often as a cofactor in a nucleotidebinding fold of different enzymes.

92. (a) Compounds that contain a nitrogenous base, a sugar, and a phosphate group are called _____. (b) Two purines found in DNA are _____ and _____. (c) A pyrimidine found in all DNA but in only some RNA is _____. (d) In DNA, the base pair _____ is held together by three hydrogen bonds; (e) the base pair _____ has only two such bonds.

93. (a) List and explain the function of the ingredients required for a polymerase chain reaction (PCR). (b) Describe the steps of each cycle of PCR.

94. Discuss the similarities and differences between the structures of nucleosides and nucleotides.

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Chap 08_8e 95. Describe qualitatively how the t m for a double-stranded DNA depends on its nucleotide composition.

96. Define short tandem repeat (STR) and explain briefly how an STR locus can be used to convict or acquit criminal suspects or provide paternity information.

97. Write a double-stranded DNA sequence containing a six-nucleotide palindrome.

98. Why does lowering the ionic strength of a solution of double-stranded DNA permit the DNA to denature more readily (e.g., to denature at a lower temperature than at a higher ionic strength)?

99. Based on the spontaneous deamination of cytosine, explain why it is advantageous for DNA to contain thymine, not uracil.

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Chap 08_8e 100. The composition (mole fraction) of one of the strands of a double-helical DNA is [A] = 0.3, and [G] = 0.24. Calculate the composition, if possible. If impossible, write I. For the same strand: (a) [T] = ____ (b) [C] = ____ (c) [T] + [C] = ____ For the other strand: (d) [A] = ____ (e) [T] = ____ (f) [A] + [T] = ____ (g) [G] = ____ (h) [C] = ____ (i) [G] + [C] = ____

101. What happens in polymerase chain reaction using DNA polymerase derived from E. coli instead of from a thermostable source?

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Chap 08_8e Answer Key 1. e 2. c 3. e 4. a 5. e 6. a 7. d 8. d 9. c 10. d 11. d 12. a 13. b 14. a 15. c 16. b 17. d 18. d 19. c 20. a 21. d 22. b 23. b 24. c 25. e 26. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 08_8e 27. c 28. d 29. b 30. a 31. b 32. a 33. a 34. b 35. b 36. b 37. d 38. e 39. e 40. d 41. b 42. c 43. c 44. a 45. e 46. b 47. d 48. e 49. e 50. a 51. c 52. a 53. b 54. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 08_8e 55. d 56. e 57. c 58. d 59. d 60. c 61. d 62. d 63. c 64. c 65. d 66. b 67. a 68. c 69. b 70. e 71. e 72. d 73. a 74. d 75. b 76. c 77. d 78. a 79. 3.4 μm × 10,000 = 34,000 μm= 3.4 μm. 80. The DNA molecules are partially denatured; in each molecule approximately 50% of the DNA is single-stranded and 50% is double-helical. The single-stranded regions, which appear as bubbles within the molecules, are those that denatured at lower temperatures because of their higher content of A=T base pairs. Copyright Macmillan Learning. Powered by Cognero.

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Chap 08_8e 81. Avery and colleagues showed that DNA isolated from a virulent (disease-causing) bacterium (Streptococcus pneumoniae), when mixed with living cells of a nonvirulent strain of this bacterium, provided the genetic instructions for transforming the nonvirulent strain to a virulent strain. 82. A-form DNA is a right-handed helix; Z-form DNA is a left-handed helix. (See Fig. 8-17.) 83. UV radiation causes the formation of a dimer between adjacent thymine bases on the same DNA strand. This results in a kink in the double helix at that site. 84. In general, the more similar the sequences in two DNA molecules are the more readily they will hybridize. Because the evolutionary distance between mouse and yeast is greater than that between mouse and human, mouse and human DNA sequences are more similar than those of mouse and yeast. 85. (a) The polymerase will synthesize the whole strand without any breaks, but there will not be any detectable product at all because there are no short fragments and there is no detectable molecule. (b) The polymerase will never stop at a complementary C when incorporating a G. All other bases will work normally. Thus, it will be interpreted that the sequence does not contain any C. However, on carefully inspection, there should be an extra space (gap) in the sequence, where a normal nontermination dGTP was incorporated. (c) Essentially, no reaction will occur, with the exception of incorporating the first ddNTP. Thus, nothing will be seen. (d) The polymerase reaction will proceed up to the first complementary C in the sequence and then terminate. Thus, at best a very short strand of DNA sequence will be seen. 86. b; a; d; c 87. In these molecules, there is a phosphoric anhydride linkage between the phosphates. Hydrolysis of this linkage (i.e., of ATP to ADP and phosphate) is a highly exergonic reaction that results in the release of a large amount of free energy. Conversely, the input of a large amount of free energy is required for the synthesis of the linkage; that is, for the phosphorylation of ADP to form ATP. Thus, synthesis of ATP results in the storage of energy that can be released upon hydrolysis. 88. The nucleotide sequences of complementary strands are such that, wherever an A occurs in one strand, there is a T in the other strand with which it can form a hydrogen-bonded base pair. Wherever a C occurs in one strand, a G occurs in the other. A is the base complementary to T, and C is the base complementary to G. 89. (a) Monocistronic mRNAs code for only one polypeptide, polycistronic mRNAs code for two or more polypeptide chains. Both contain noncoding regions that regulate protein synthesis. (b) Eukarya contains monocistronic mRNAs; Bacteria and Archaea contain both mono- and polycistronic mRNAs. 90. Hydrogen bonding in regions of complementarity within an RNA chain can result in regions of double helix that are stabilized by base stacking. Breaks in complementary regions can result in loops and bulges that, together with the helical regions, can generate a precise three-dimensional structure. 91. Although adenosine does not contribute more than other nucleotides in binding energy, once ATP was selected through evolution as a source of chemical energy, its abundance made it a logical choice for incorporation into enzymes. Additionally, a single protein domain could be used in multiple enzymes to bind adenosine.

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Chap 08_8e 92. (a) nucleotides; (b) adenine; guanine; (c) thymidine; (d) G≡C; (e) A=T 93. (a) PCR reactions need a template DNA molecule containing a region to be amplified, synthetic DNA oligonucleotide primers to serve as the starting point for DNA polymerase to extend the template, dNTPs that serve as the raw materials to be added to the growing nucleotide chains and the energy for the reaction, and a thermostable DNA polymerase to catalyze 5' to 3' DNA synthesis. (b) Step 1: Template denaturation is done at a high temperature; Step 2: the temperature of the reaction is lowered for primers to anneal to the template DNA; Step 3: the temperature is raised to the optimum temperature for the Taq (or other thermostable) DNA polymerase to catalyze DNA synthesis. 94. Both have a nitrogenous base and a pentose; nucleotides also have a phosphate group, which nucleosides lack. 95. In general, the higher the proportion of G and C, the higher the melting temperature, t m. More thermal energy is required to break the three hydrogen bonds holding G≡C pairs than to break the two hydrogen bonds holding A=T pairs. Also, G≡C pairs stack better than A=T pairs, thereby stabilizing the double helix better. 96. A short tandem repeat is a location on a chromosome where a short (usually 4 bp) DNA sequence is repeated many times. The precise number of times the locus is repeated varies in the human population. The length of the STR can be determined using PCR, followed by capillary gel electrophoresis. Analysis of multiple STR loci can yield a profile unique to an individual, providing evidence for a criminal case or paternity test. 97. Any double-stranded sequence that has the form: 1-2-3-4-5-6-6'-5'-4'-3'-2'-1' 1'-2'-3'-4'-5'-6'-6-5-4-3-2-1 where each number and its prime represent correctly paired bases (A with T, C with G) all along the doublestranded molecule. 98. Lower ionic strength reduces the screening of the negative charges on the phosphate groups by positive ions in the medium. The result is stronger charge-charge repulsion between the phosphate, which favors strand separation. 99. Cytosine undergoes spontaneous deamination to form uracil. If uracil were normally present in DNA, a deamination event could not be recognized as damaged goods. Thus, C→U changes would not be repaired by normal cellular processes and these new U's would end up pairing with A, leading to a point mutation. The extra methyl group in thymine is sufficient for differentiating U and T. 100. (a) I; (b) I; (c) 0.46; (d) I; (e) 0.3; (f) I; (g) I; (h) 0.24; (i) I 101. In the very first denaturation step, the DNA polymerase from E. coli will also denature and it will not refold. Therefore, there will be no reaction products at all.

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Chap 09_8e Indicate the answer choice that best completes the statement or answers the question. 1. To express two different genes on different plasmids in a bacterial host, which procedure will NOT be successful? a. using plasmids that have the same promoter sequence b. using EcoRI and BamHI restriction endonucleases to clone the genes into their respective plasmids c. placing different fusion tags on each of the genes when cloning them d. using plasmids with the same origin of replication e. using plasmids that have different selectable markers 2. Which statement does NOT apply to the construction or use of a DNA library? a. Determining the location of a particular DNA sequence in a DNA library requires a suitable hybridization probe. b. Genomic libraries are better for expressing gene products than cDNA libraries. c. Many segments of DNA from a cellular genome are cloned. d. Specialized DNA libraries can be made by cloning DNA copies of mRNAs. e. The DNA copies of mRNA found in a cDNA library are made by reverse transcriptase. 3. _____ is NOT a commonly used tag for affinity purification of cloned proteins. a. Glutathione-S-transferase b. Maltose binding protein c. Nickel d. Protein A e. Chitin-binding domain 4. Which method is NOT used in linkage analysis? a. comparing densely spaced polymorphisms b. collecting DNA from a family affected by the disease of interest c. sequencing selected parts of the genome d. introducing retroviruses at the mutated locus e. looking for SNP variants 5. Which tag is NOT used to study protein function? a. green fluorescent protein b. synteny tag c. tandem affinity purification d. Gal4p DNA-binding domain e. Gal4p activation domain

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Chap 09_8e 6. Which restriction endonuclease cuts DNA in a way that leaves blunt ends? a. EcoRI b. HindIII c. BamHI d. EcoRV e. PstI 7. Which statement regarding plasmid-cloning vectors is correct? a. Circular plasmids do not require an origin of replication to be propagated in E. coli. b. Foreign DNA fragments up to 45,000 base pairs can be cloned into a typical plasmid. c. Plasmids do not need to contain genes that confer resistance to antibiotics. d. Plasmid vectors must carry promoters for inserted gene fragments. e. The copy number of plasmids may vary from a few to several hundred. 8. Which amino acid when repeated six to ten times at the N- or C-terminal ends of a protein allows that protein to bind to Ni2+ ions? a. Glu b. His c. Ala d. Tyr e. Asp 9. The E. coli recombinant plasmid pBR322 has been widely utilized in genetic engineering experiments. Which feature does pBR322 NOT have? a. a number of conveniently located recognition sites for restriction enzymes b. a number of palindromic sequences near the EcoRI site, which permit the plasmid to assume a conformation that protects newly inserted DNA from nuclease degradation c. a replication origin, which permits it to replicate autonomously d. resistance to two different antibiotics, which permits rapid screening for recombinant plasmids containing foreign DNA e. small overall size, which facilitates entry of the plasmid into host cells 10. The sequence of one strand of dsDNA is shown in the 5'→3' direction. Which sequence is a palindrome? a. AATGCC b. GGATCC c. GATATG d. CCCGCG e. AGTAGT

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Chap 09_8e 11. Which refers to a method of transformation when the DNA used includes viral sequences and leads to viral replication? a. transformation b. transfection c. transduction d. electroporation e. ligation 12. Common problems with expression of eukaryotic proteins in bacteria may include proteins: a. aggregating into inclusion bodies. b. not folding correctly. c. not undergoing posttranslational modification. d. All of the answers are correct. e. None of the answers is correct. 13. Conserved gene order observed on the chromosomes of closely related organisms is called: a. synteny. b. tandem homology. c. paralogy. d. sequential orthology. e. gene linkage. 14. The precise biochemical activity of a protein, such as reaction details involved in enzymatic activity, is called its _____ function. a. phenotypic b. genotypic c. cellular d. molecular e. organismal 15. Due primarily to single-nucleotide polymorphisms, each human differs from every other human, on average, by what percentage of the human genome? a. 6% b. 15% c. 0.1% d. 98% e. 1.5%

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Chap 09_8e 16. The DNA sequences of several species with a shared evolutionary ancestry is being compared. Species 1 has a sequence of ATGCCA, species 2 has a sequence of ATACCA, species 3 has a sequence of ATACTA, species 4 has a sequence of ACACTG, and species 5 has a sequence of ATGCCA. Which species is an outgroup compared with all the others? a. species 1 b. species 2 c. species 3 d. species 4 e. species 5 17. Certain restriction enzymes produce cohesive (sticky) ends. This means that they: a. cut both DNA strands at the same base pair. b. cut in regions of high G≡C content, leaving ends that can form more hydrogen bonds than ends of high A=T content. c. make a staggered double-strand cut, leaving ends with a few nucleotides of single-stranded DNA protruding. d. make ends that can anneal to cohesive ends generated by any other restriction enzyme. e. stick tightly to the ends of the DNA they have cut. 18. Which repeating sequences in the human genome are the targets of technologies used in forensic DNA analysis? a. simple-sequence repeats b. single-nucleotide polymorphisms c. introns d. short tandem repeats e. long repetitive sequences 19. In the laboratory, recombinant plasmids are commonly introduced into bacterial cells by: a. electrophoresis—a gentle low-voltage gradient draws the DNA into the cell. b. infection with a bacteriophage that carries the plasmid. c. microinjection. d. mixing plasmids with an extract of broken cells. e. transformation—heat shock of the cells incubated with plasmid DNA in the presence of CaCl2.

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Chap 09_8e 20. Which technique can be used to estimate the relative copy numbers of particular DNA sequences in a sample? a. reverse transcriptase PCR b. quantitative PCR c. some gel-based analysis d. normal PCR e. in vitro transcription 21. Which protein forms a complex with a guide RNA to target DNA for cleavage and destruction? a. RecA b. Cas9 c. EcoRI d. Gal4p e. GST 22. To determine which proteins might be interacting in a cell, which technique would be used to examine the interaction in a living cell? a. yeast two-hybrid analysis b. immunoprecipitation c. CRISPR/Cas9 d. immunofluorescence e. comparative genomics 23. The fluorophore in green fluorescent protein is derived from oxidation of three _____ in the interior of the protein. a. coenzymes b. amino acids c. prosthetic groups d. metal ions e. nucleotides 24. What type of insert is referred to as a linker? a. type of cloning vector b. DNA fragment with multiple recognition sequences for restriction endonucleases c. type of expression vector d. enzyme that joins DNA molecules together e. method of getting DNA into a cell

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Chap 09_8e 25. Compensatory mutations in genes for noncoding RNAs indicate that: a. these genes are not important for the function of the organism. b. the secondary structure of the noncoding RNA is important for its function. c. the noncoding RNA is not undergoing accelerated evolution. d. All of the answers are correct. e. None of the answers is correct. 26. Which method of visualizing a protein's location should be used to determine its location in a living cell? a. a GFP fusion tag b. immunofluorescence c. qPCR d. Gram's stain e. affinity purification 27. Common features found in a cloning plasmid used for protein do NOT include: a. a multiple cloning site insert. b. an origin of replication. c. an antibiotic-resistance marker. d. a ribosome-binding site. e. telomeric ends. 28. The gene for green fluorescent protein was originally isolated from which species? a. panda b. firefly c. mushroom d. jellyfish e. glowworm 29. Which type of organism is NOT expected to functionally express green fluorescent protein? a. obligate aerobe b. multicellular eukaryotic organism c. facultative anaerobe d. obligate anaerobe e. unicellular eukaryotic organism

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Chap 09_8e 30. Which statement regarding type I and type II restriction endonucleases is NOT accurate? a. Type I endonucleases may have methylase activity. b. Type II endonucleases recognize small (4 to 6 bp) palindromic sequences. c. Type II endonucleases always make staggered cuts in DNA strands. d. Type I endonucleases require ATP. e. Type I endonucleases are generally large, multisubunit complexes. 31. Suppose a researcher wants to clone a gene by using E. coli and then transfer that cloned gene into yeast to express the protein the gene encodes. What type of self-replicating DNA should be used for the cloning process? a. bacmid b. plasmid c. yeast artificial chromosome d. shuttle vector e. bacterial artificial chromosome 32. To clone a large fragment of DNA into a unicellular eukaryotic host, what would be used? a. bacmid b. plasmid c. bacterial artificial chromosome d. yeast artificial chromosome e. virus 33. To make a DNA copy of an RNA sequence, a researcher will need the reverse transcriptase enzyme and an oligonucleotide primer made of which nucleotide? a. deoxyadenosine b. deoxythymine c. deoxycytosine d. deoxyuridine e. deoxyguanosine 34. Which statement about transposons is NOT correct? a. They are a form of molecular parasite. b. They have played a major role in human evolution. c. All transposons are active and move around the human genome. d. Some transposons move to another genomic location via an RNA intermediate. e. They often contain genes that encode proteins that catalyze transposon movement.

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Chap 09_8e 35. Restriction enzymes: a. act at the membrane to restrict the passage of certain molecules into the cell. b. are highly specialized ribonucleases that degrade mRNA soon after its synthesis. c. are sequence-specific DNA endonucleases. d. are proteases that cleave peptides only at recognized sequences. e. catalyze the addition of a certain amino acid to a specific tRNA. 36. The process of linkage analysis does NOT rely on which technique to determine the genetic causes of diseases? a. analysis of family pedigrees b. identification of SNPs that are most often inherited with the disease-causing gene c. the sequence of the entire chromosome where the disease-causing gene is located to directly identify it d. comparing the DNA of people who have the disease with the DNA of people who don't have the disease e. obtaining many sequences of a region of the chromosome that is associated with the disease 37. When cloning a gene into a plasmid, which enzyme would be used to covalently attach the gene to the plasmid DNA? a. DNA polymerase b. exonuclease III c. DNA ligase d. alkaline phosphatase e. restriction endonuclease 38. A good cloning vector should NOT have: a. an origin of replication. b. an antibiotic resistance gene. c. several unique restriction sites. d. a small size. e. genes allowing its insertion into the host chromosome. 39. The technique known as two-hybrid analysis for detecting interacting gene products depends on: a. activation of DNA polymerase by the nearby binding of hybridizing protein complexes. b. direct binding of a Gal4p activation domain to a DNA sequence in the promoter region. c. having a promoter that responds directly to one of the two proteins whose interactions is being measured. d. hybridization of DNA segments corresponding to the two genes being examined. e. stimulation of transcription by interaction of two Gal4p domains via fused protein sequences.

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Chap 09_8e 40. A restriction endonuclease that has a recognition sequence of 8 bp in length would be expected to cut dsDNA on average once in how many base pairs? a. 256 b. 1,024 c. 4,096 d. 65,536 e. 1,048,576 41. Current estimates indicate that _____ of the human genome is translated into protein. a. less than 0.5% b. roughly 1.5% c. roughly 10% d. roughly 25% e. more than 50% 42. Yeast two-hybrid analysis functions due to which reason? a. The DNA-binding domain and transcriptional activation domain of a separated transcription factor are only brought into close proximity when the two proteins of interest interact with each other. b. The DNA-binding domain and the transcriptional activation domain of a separated transcription factor may remain stable independent of each other. c. Yeast can be grown as either a haploid or a diploid cell. d. All of the answers are correct. e. None of the answers is correct. 43. Which type of DNA sequence is NOT found in the human genome? a. long repetitive repeats b. introns c. retropalindromes d. simple-sequence repeats e. transposons 44. During their multiple migrations from Africa to the rest of the world, gene flow likely occurred between which populations of early humanoids? a. between Neanderthals and modern humans b. between Denisovans and modern humans c. between Neanderthals and Denisovans d. All of the answers are correct. e. None of the answers is correct.

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Chap 09_8e 45. What common protein tertiary structure does green fluorescent protein contain? a. α helix b. β barrel c. coiled coil d. Greek key e. four-helix bundle 46. A convenient cloning vector with which to introduce foreign DNA into E. coli is a(n): a. E. coli chromosome. b. messenger RNA. c. plasmid. d. yeast "ARS" sequence. e. yeast transposable element. 47. Which component or components are required to accurately determine the relative amount of gene expression of two or more genes in an organism using qPCR? a. a "no template" control b. an oligonucleotide probe labeled with a fluorophore and a quenching molecule at its ends c. use of reverse transcriptase to copy the RNA products into DNA d. All of the answers are correct. 48. A good expression vector for protein expression in E. coli should have which feature(s)? a. an origin of replication b. a selectable marker c. a promoter, operator, and ribosome-binding site d. All of the answers are correct. e. None of the answers is correct. 49. Which statement is NOT correct? a. Humans and chimpanzees share a common ancestor. b. Orangutans are an outgroup when compared with humans and chimpanzees. c. Humans and chimpanzees differ over approximately 4% of their genomes. d. Humans evolved from chimpanzees. e. Humans have 23 pairs of chromosomes, while chimpanzees have 24 pairs of chromosomes.

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Chap 09_8e 50. Which technique is NOT used to make a cDNA library? a. extraction of DNA from the organism being studied b. extraction of mRNA from the organism being studied c. use of reverse transcriptase to copy RNA into DNA d. ligation of DNA into a cloning vector e. insertion of a cloning vector into cells 51. The biological role of restriction enzymes is to: a. aid recombinant DNA research. b. degrade foreign DNA that enters a bacterium. c. make bacteria resistant to antibiotics. d. restrict the damage to DNA by UV light. e. restrict the size of DNA in certain bacteria. 52. Which statement about type II restriction enzymes is false? a. Many make staggered (off-center) cuts within their recognition sequences. b. Some cut DNA to generate blunt ends. c. They are part of a bacterial defense system in which foreign DNA is cleaved. d. They cleave and ligate DNA. e. They cleave DNA only at recognition sequences specific to a given restriction enzyme. 53. Mutations in which genetic sequences are MOST likely to have a phenotypic effect? a. introns b. exons c. interspersed nuclear elements d. transposons e. None of the answers is correct. 54. Genes that have sequence and functional relationships to each other within a single species are called: a. orthologs. b. paralogs. c. analogs. d. homologs. e. lincolnlogs.

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Chap 09_8e 55. A(n) _____ would NOT be used as a heterologous host for the expression of recombinant proteins. a. retrovirus b. bacterium such as E. coli c. eukaryote such as S. cerevisiae d. insect cell e. mammalian cell 56. A method of determining if proteins are interacting in vivo that makes use of a transcription factor involved in regulating galactose metabolism genes is: a. a DNA microarray. b. yeast two-hybrid analysis. c. tandem affinity purification. d. immunofluorescence. e. quantitative PCR. 57. Groups of single-nucleotide polymorphisms that are usually inherited together from one parent are called: a. genotypes. b. haplotypes. c. phenotypes. d. karyotypes. e. cytotypes. 58. Which list ranks the organisms in order from smallest genome (number of base pairs of DNA) to largest genome? a. human, fruit fly, E. coli bacterium b. E. coli bacterium, human, fruit fly c. E. coli bacterium, fruit fly, human d. fruit fly, E. coli bacterium, human e. fruit fly, human, E. coli bacterium 59. Which compound is NOT needed to build a cDNA library? a. genomic DNA b. mRNA c. reverse transcriptase d. dNTPs e. DNA polymerase

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Chap 09_8e 60. To create specific DNA sequence changes to a plasmid in the coding sequence for a protein, without any suitably located restriction sites nearby, which technique would be used? a. error-prone PCR b. site-directed mutagenesis c. oligonucleotide-directed mutagenesis d. exposing the plasmid DNA to UV light e. exposing the cells containing the plasmid DNA to chemical mutagens 61. The size of the DNA region specifically recognized by type II restriction enzymes is typically: a. 4 to 6 base pairs. b. 10 to 15 base pairs. c. 50 to 60 base pairs. d. 200 to 300 base pairs. e. about the size of an average gene. 62. Which makes up the largest portion of human DNA sequence types (25.9%)? a. introns b. exons c. transposons d. SINEs e. simple-sequence repeats 63. Overall, chimpanzees and humans differ by approximately what percent across their entire genomic sequences? a. 1.5% b. 4% c. 95% d. 10% e. 0.1% 64. For what reason are the mitochondrial genome and the Y chromosome the easiest portions of human DNA to use to trace human evolutionary lineages? a. All human cells have mitochondria and Y chromosomes. b. Mitochondrial DNA and the Y chromosome do not undergo significant meiotic recombination. c. The size of the mitochondrial genome and the Y chromosome is small. d. Mitochondrial DNA and the Y chromosome exhibit very unstable haplotypes. e. Mitochondrial DNA is inherited along both the male and female human evolutionary lineages.

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Chap 09_8e 65. Current estimates indicate that humans have about _____ protein-coding genes. a. 2,000 b. 10,000 c. 20,000 d. 100,000 e. 200,000 66. What is a significant problem with regard to making cDNA libraries to analyze overall gene function in a eukaryotic organism? a. A cDNA library will only contain genes that are actively transcribed in the organism. b. Reverse transcriptase cannot be used to make cDNA libraries. c. cDNA cannot be amplified by polymerase chain reaction. d. cDNA libraries do not contain intron sequences. e. cDNA libraries may contain several alternatively spliced forms of the same gene. 67. To study the effects of inactivating a specific gene on the development of a mouse, which technique or system would be used to inactivate that gene? a. transfection b. CRISPR/Cas9 c. tandem affinity purification d. yeast two-hybrid analysis e. oligonucleotide-directed mutagenesis 68. To determine what other proteins might be interacting with the protein being studied, what type of fusion tag would be added to the protein to aid in purification of both the protein being studied and the proteins interacting with it? a. green fluorescent protein fusion tag b. tandem affinity purification tag c. maltose-binding protein tag d. epitope tag e. β-galactosidase tag 69. To compare the sequence of a gene isolated in the laboratory with a database of other genetic sequences, which tool would be used? a. linkage analysis b. BLAST c. forensic DNA analysis d. haplotype identification e. quantitative PCR Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_8e 70. Especially stable haplotypes exist in which portions of the human genome due to their relative lack of meiotic recombination? a. the Y chromosome b. the X chromosome c. the mitochondrial genome d. both the Y chromosome and the mitochondrial genome e. both the X chromosome and the mitochondrial genome 71. As the cost of sequencing personal human genome rapidly declines, consider the benefits and risks of having every fetus's DNA sequenced before birth.

72. A scientist wishes to produce a mammalian protein in E. coli. The protein is a glycoprotein with a molecular weight of 40,000. Approximately 20% of its mass is polysaccharide. The isolated protein is usually phosphorylated and contains three disulfide bonds. The cloned gene contains no introns. (a) What sequences or sites will be required in the vector to get this gene regulated, transcribed, and translated in E. coli? (b) List two problems that might arise in producing a protein identical to that isolated from mammalian cells and describe each problem in no more than two sentences.

73. Name one enzyme that is always used to make a cDNA library but is generally not used to make a genomic DNA library. Describe its function briefly.

74. Describe the difference between selectable markers and screenable markers and their use in cloning experiments.

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Chap 09_8e 75. When bacterial artificial chromosomes (BACs) are used as cloning vectors, what size of DNA fragment can be cloned?

76. What sequences are required in an expression vector (for use with E. coli) that are NOT essential in a cloning plasmid?

77. List three different heterologous expression systems and include one advantage and one disadvantage for each.

78. What is the essential difference between a genomic library and a cDNA library?

79. Describe how the CRISPR/Cas9 system is used to inactivate a gene during the process of genomic engineering.

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Chap 09_8e 80. Match each feature of the plasmid pBR322 (at left) with one appropriate description presented (at right). Descriptions may be used more than once.

_____ ampR _____ ori _____ tetR _____ BamHI _____ PstI

(a) Permits selection of bacteria containing the plasmid. (b) A sequence required for packaging recombinant plasmids into bacteriophage. (c) Origin of replication. (d) Cleavage of the plasmid here does not affect antibiotic sequence-resistance genes. (e) Insertion of foreign DNA here permits identification of bacteria-containing recombinant plasmids.

81. Explain how each of these is used in cloning in a plasmid: (a) antibiotic-resistance genes; (b) origin of replication; (c) multiple cloning site (MCS) linkers.

82. Distinguish between protein function at the molecular, cellular, and phenotypic level.

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Chap 09_8e 83. Which would be expected to be larger, the percentage of the human genome that is translated into protein or the percentage of the genome of a bacterium that is translated into protein? Why?

84. How does a bacterial artificial chromosome (BAC) differ from a plasmid?

85. Name two different methods by which protein-protein interactions can be discovered and probed.

86. Explain the importance of outgroups for understanding genomic lineages.

87. Explain briefly the properties of the plasmid pBR322 that make it so convenient as a vector for cloning fragments of foreign DNA.

88. What is the distinguishing feature(s) of a shuttle vector?

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Chap 09_8e 89. A plasmid that encodes resistance to ampicillin and tetracycline is digested with the restriction enzyme PstI, which cuts the plasmid at a single site in the ampicillin-resistance gene. The DNA is then annealed with a PstI digest of human DNA, ligated, and used to transform E. coli cells. (a) What antibiotic would be put in an agar plate to ensure that the cells of a bacterial colony contain the plasmid? (b) What antibiotic-resistance phenotypes will be found on the plate? (c) Which phenotype will indicate the presence of plasmids that contain human DNA fragments?

90. Diagram a phylogenetic tree to show the relationship between several sequences from the same gene in different organisms. The sequences are GAACTA, GGATTA, AGATCA, GGACTA, and AGATTA.

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Chap 09_8e Answer Key 1. d 2. b 3. c 4. d 5. b 6. d 7. e 8. b 9. b 10. b 11. b 12. d 13. a 14. d 15. c 16. d 17. c 18. d 19. e 20. b 21. b 22. a 23. b 24. b 25. b 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_8e 27. e 28. d 29. d 30. c 31. d 32. d 33. b 34. c 35. c 36. c 37. c 38. e 39. e 40. d 41. b 42. d 43. c 44. d 45. b 46. c 47. d 48. d 49. d 50. a 51. b 52. d 53. b 54. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 09_8e 55. a 56. b 57. b 58. c 59. a 60. c 61. a 62. a 63. b 64. b 65. c 66. a 67. b 68. b 69. b 70. d 71. Answers are expected to vary, but key points that should be brought up include: (1) identification of treatable diseases before they become a problem; (2) identification of untreatable diseases that lead to questions like abortion; (3) identification of trending mutations that may or may not be causative for some diseases; (4) too much data (remember the human genome has 3 billion bp) without sufficient understanding of what it means regarding individual human health. 72. (a) The cloned gene must be preceded by a good E. coli promoter and its associated operator and by a ribosomebinding sequence. The other end of the gene should have a transcription-termination sequence. (b) Examples of potential problems are that (1) E. coli enzymes may not glycosylate the protein, which may affect its folding and activity, and (2) the protein kinases that phosphorylate the protein in mammalian cells are probably absent in E. coli; therefore, the engineered protein will not be phosphorylated. 73. Reverse transcriptase is used to first make a single-stranded DNA complementary to mRNA, then a doublestranded DNA.

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Chap 09_8e 74. Selectable markers are used to either permit the growth of a cell that contains a plasmid with those markers or to kill a cell that contains those markers. This is typically accomplished by providing the cell with antibiotic resistance or the enzymes necessary to use certain metabolites for growth. In some cases, though, a selectable marker will be a toxic protein and, only by disrupting that marker with a gene insertion, will the cell be able to grow. Screenable markers do not provide growth advantages or disadvantages but instead allow visualization of cells that contain the plasmid DNA where those markers are encoded. Inserting genes that disrupt screenable markers provides an easy way to determine if cells contain plasmids with those genes or just plasmids with the selectable marker intact. 75. 100,000 to 300,000 base pairs 76. Regulated expression of the cloned gene requires: (1) a bacterial promoter and (2) its associated operator, (3) a transcription-termination sequence, and (4) a ribosome-binding site. (See Fig. 9-7.) 77. Expression system E. coli

Insect cells

Mammalian cells

Advantage Inexpensive Easy to cultivate High levels of protein expression High levels of protein expression Proper posttranslational modification for eukaryotic proteins Proper posttranslational modification for eukaryotic proteins

Disadvantage No or improper posttranslational modifications for eukaryotic proteins Relatively difficult to cultivate

Very difficult to cultivate in large quantities

78. A genomic library contains (in principle) all of the sequences present in the chromosome(s), including DNA sequences that are not transcribed. Because a cDNA library is made as a DNA copy of mRNA, it contains only those DNA sequences that are expressed in the cell. 79. First, a plasmid with the CRISPR/Cas9 system is inserted into a target cell. This plasmid encodes both the Cas9 protein and the CRISPR single guide RNA (sgRNA) that is used to target a region of genomic DNA for cleavage. The sgRNA forms a complex with Cas9, and due to specific base pairing between the sgRNA and the genomic DNA target, the Cas9 protein is bound to the DNA target. The nuclease domains of the Cas9 protein can then cleave both of the DNA strands in the target gene, resulting in a double-strand break. This double-strand break is typically repaired by nonhomologous end joining, which often deletes or alters base pairs when the break is repaired. The alteration or deletion of base pairs may then inactivate the target gene on the cell's genome. 80. a; c; a; e; e 81. (a) Antibiotic resistance allows a researcher to select for a bacterial cell clone that carries the plasmid; loss of an antibiotic marker in a strain known to contain the plasmid can be used to infer the presence of a cloned DNA segment that interrupts the antibiotic-resistance gene. (b) An origin of replication assures that the plasmid will replicate autonomously in the bacterium. (c) MCS linkers have cut sites for a variety of restriction enzymes, allowing insertion of DNA fragments produced with any of them.

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Chap 09_8e 82. Molecular function describes the precise biochemical activity of the protein (such as enzymatic reaction or ligand binding), cellular function depends on the network of interactions engaged in by the protein within a cell, and phenotypic function refers to the effects of the protein on the entire organism. 83. Because bacteria do not have introns, the percentage of their genome that is translated into protein would be larger than that of humans, who do have introns. 84. A BAC is a plasmid that has a very stable origin of replication and is present in a small copy number in the bacterial cell. This allows it to carry a larger fragment of cloned DNA than a regular plasmid. Also, BACs contain par genes that code for proteins that ensure reliable distribution of the BACs to daughter cells at cell division. 85. (1) purification of protein complexes by immunoprecipitation or tandem affinity purification (TAP) tags, for example; (2) yeast two-hybrid analysis 86. This question is best answered by considering an example. If compared, the sequence of the progesterone receptor from chimpanzees and humans, certain amino acid differences are seen. Some of these differences may have arisen as chimpanzees diverged from the common ancestor; others may have arisen as humans diverged from the common ancestor. That is, it is not known in which lineage these differences arose. Therefore, an outgroup is needed, like an orangutan. If the amino acid of interest is identical between chimps and orangutans, then it was probably present in the common ancestor, and it is distinctly human to have that changed amino acid. On the other hand, if the amino acid is identical between orangutans and humans, then the difference is a chimp-specific change. 87. pBR322 has two antibiotic-resistance markers, so that its presence in a bacterium can be detected, bacteria that carry it can be selected, and insertion of cloned DNA into one of the resistance markers can be detected by loss of antibiotic resistance. The plasmid also has an origin of replication so that it replicates autonomously in E. coli. Several convenient restriction sites allow easy insertion of restricted DNA fragments. Its small size facilitates its entry into E. coli by standard transformation protocols. 88. Shuttle vectors contain multiple sequences (such as replication origins) that allow their autonomous replication in two or more hosts, such as E. coli and yeast. 89. (a) tetracycline; (b) resistant to both antibiotics and resistant to only tetracycline; (c) The resistance to only tetracycline phenotype indicates that the gene for ampicillin resistance has been interrupted by the insertion of a human DNA fragment.

90.

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Chap 10_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which statement is false? a. Phospholipase A1 hydrolyzes the fatty acid from the 1-position on the glycerol backbone. b. Phospholipase B1 hydrolyzes the fatty acid from the 2-position on the glycerol backbone. c. Phospholipase C hydrolyzes the complete phospho-head group from the glycerol backbone. d. Phospholipase D hydrolyzes just the head group from the phospho-glycerol backbone. 2. Which types of lipids would NOT have their fatty acids completely hydrolyzed by treatment with acid or alkali? a. triacylglycerols b. galactolipids c. sphingomyelins d. prostaglandins e. phosphatidylcholines 3. In high-performance liquid chromatography of lipid mixtures using a column packed with a silica gel, which types of lipids will elute in the first chloroform wash? a. positively charged lipids b. neutral lipids c. negatively charged lipids d. polar lipids e. the smallest molecular weight lipids 4. When a tissue sample is homogenized and extracted with a mixture of chloroform, methanol, and water, followed by addition of more water to separate the liquid phases, which molecules will remain in the methanol/water phase? a. lipids b. proteins c. sugars d. both lipids and proteins e. both proteins and sugars 5. Which types of membrane lipids make up 70% to 80% of the total membrane lipids in a vascular plant? a. phosphatidylserines b. glycosphingolipids c. galactolipids d. plasmalogens e. sphingomyelins Copyright Macmillan Learning. Powered by Cognero.

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Chap 10_8e 6. Which statement BEST describes how the volatility of lipids is increased for analysis by gas chromatography? a. The lipids are transesterified to convert fatty acids into fatty acid methyl esters. b. The lipids are cleaved with phospholipase enzymes. c. The lipids are degraded by treatment with mild acid or base. d. The lipids are dissolved in chloroform. e. The lipids are desaturated by reaction with a platinum catalyst. 7. Which technique is NOT commonly used to analyze lipid composition? a. selective extraction using organic solvents b. adsorption chromatography c. x-ray crystallography d. gas chromatography e. mass spectroscopy 8. Which statement about sterols is true? a. Sterols have four fused rings in their structure. b. Sterols are found in the membranes of all living cells. c. Sterols are soluble in water, but less so in organic solvents such as chloroform. d. Cholesterol is the principal sterol in fungi. e. The principal sterol of animal cells is ergosterol. 9. Which compound is NOT a type of membrane lipid? a. sphingolipid b. glycerophospholipid c. sulfolipid d. sterol e. triacylglycerol 10. Which statement BEST describes why lipids typically float on water? a. Lipids are nonpolar, while water is polar. b. Lipids have lower specific gravities than water does. c. Lipids have higher melting temperature than water does. d. Lipids store more energy than water does. e. Lipids contain carbon, while water does not.

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Chap 10_8e 11. The study and classification of the complete set of lipids produced in an organism is called: a. proteomics. b. lipidomics. c. genomics. d. lipidification. e. fatification. 12. Tay-Sachs disease is the result of a genetic defect in the metabolism of: a. gangliosides. b. phosphatidyl ethanolamine. c. sterols. d. triacylglycerols. e. vitamin D. 13. _____ is NOT a biological use of waxes. a. Energy storage b. Lubrication c. Structure d. Insulation e. Waterproofing 14. In neutral fats, three fatty acids are generally linked to a _____ backbone. a. glycogen b. glycerol c. sphingosine d. glucose e. phosphoglycerol 15. Which method can be used to visualize lipids that have been separated by thin-layer chromatography by reversibly reacting with double bonds in fatty acids? a. ethanol b. iodine fumes c. low-wavelength UV light d. rhodamine e. ethidium bromide

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Chap 10_8e 16. The steroid hormones testosterone and beta-estradiol are derived from which lipid molecule? a. phosphatidylcholine b. cholesterol c. lipoxin A d. arachidonic acid e. geraniol 17. Which vitamin is derived from 7-dehydrocholesterol? a. vitamin A b. vitamin B12 c. vitamin D d. vitamin E e. vitamin K 18. Which is/are derived from sterols? a. arachidonic acid b. gangliosides c. phosphatidylglycerol d. prostaglandins e. cortisol 19. Which phospholipid head group is positively charged at pH 7? a. serine b. ethanolamine c. choline d. both serine and ethanolamine e. both ethanolamine and choline 20. Which technique would be LEAST (or not) useful for the separation and/or analysis of lipids in a laboratory? a. gel electrophoresis b. thin-layer chromatography c. adsorption chromatography d. mass spectrometry e. high-performance liquid chromatography

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Chap 10_8e 21. Which statement is true of lipids? a. Many contain fatty acids involved in ester or amide linkages. b. Most are classified as polymers. c. Testosterone is an important sphingolipid found in myelin. d. They are more soluble in water than in chloroform. e. They play only passive roles as energy-storage molecules. 22. Which gives the advantages to using triacylglycerols, rather than polysaccharides, to store energy? a. The carbon–carbon bonds triacylglycerols are stronger and release more energy when broken. b. Triacylglycerols contain more oxygen than polysaccharides and therefore are more efficient to oxidize. c. In mammals, triacylglycerols can be transported via the blood to high-energy demand sites more easily than polysaccharides. d. The carbon atoms of triacylglycerols are more reduced, and since triacylglycerols are hydrophobic, excess water does not need to be stored along with them. e. Triacylglycerols are more suitable for long-term energy storage because they are not ionizable, are more stable over a larger pH range, and are less susceptible to degradation than polysaccharides. 23. Fatty acids are a component of: a. carotenes. b. cerebrosides. c. sterols. d. vitamin D. e. vitamin K. 24. To analyze membrane lipids from a biological sample, which solvent would MOST effectively extract those lipids? a. benzene b. methanol c. water d. chloroform e. ethyl ether 25. An example of a glycerophospholipid that is involved in cell signaling is: a. arachidonic acid. b. ceramide. c. phosphatidylinositol. d. testosterone. e. vitamin A (retinol).

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Chap 10_8e 26. Which membrane lipid serves as a reservoir of messenger molecules for signal transduction? a. taurocholic acid b. phosphatidylserine c. phosphatidylinositol 4,5-bisphosphate d. thromboxane A2 e. sphingomyelin 27. What is the abbreviated nomenclature for a 14-carbon omega-3 fatty acid that contains no other double bonds? a. 14:1 (Δ11) b. 17:1 (Δ14) c. 14:1 (Δ3) d. 13:1 (Δ11) e. 14:0 (Δ11) 28. Which enzyme catalyzes the breakdown of triacylglycerols in human adipocytes? a. glycerase b. lipase c. fatase d. esterase e. triacylase 29. Which statement is true about fatty acids? a. Fatty acids with longer chains have lower melting points. b. Fatty acids with longer chains have higher solubility in water. c. Fatty acids with more double bonds have higher melting points. d. Fatty acids with longer chains have higher melting points and lower solubility in water. e. None of the statements is true. 30. What feature do Tay-Sachs disease, Fabry disease, and Niemann-Pick disease have in common? a. defects in enzymes responsible for synthesizing membrane lipids b. defects in enzymes responsible for breaking down membrane lipids in the lysosomes c. hyperactive membrane lipid degradation enzymes d. defects in enzymes responsible for cholesterol synthesis e. All of the answers are correct.

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Chap 10_8e 31. Commercial vegetable oils can be converted from liquid forms to solid forms and have their shelf lives increased due to which process? a. partial desaturation b. unsaturation c. partial hydrogenation d. hydrolysis e. complete esterification 32. Biological waxes are all: a. triesters of glycerol and palmitic acid. b. esters of single fatty acids with long-chain alcohols. c. triesters of glycerol and three long-chain saturated fatty acids. d. sphingolipids. e. None of the answers is correct. 33. Humans make which omega-3 polyunsaturated fatty acid from alpha-linolenic acid? a. only eicosapentaenoic acid b. only arachidonic acid c. only docosahexaenoic acid d. both eicosapentaenoic acid and arachidonic acid e. both eicosapentaenoic acid and docosahexaenoic acid 34. Bile acids are derived from which lipid? a. cholesterol b. sphingomyelin c. ceramide d. digalactosyldiacylglycerol e. phosphatidylcholine 35. Which compound can be cleaved in half to generate a molecule important in vision? a. calcitriol b. beta-carotene c. arachidonic acid d. tocopherol e. isoprene

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Chap 10_8e 36. _____ contain(s) an ether-linked alkyl group. a. Cerebrosides b. Gangliosides c. Phosphatidyl serine d. Platelet-activating factor e. Sphingomyelin 37. Sphingosine is NOT a component of: a. cardiolipin. b. ceramide. c. cerebrosides. d. gangliosides. e. sphingomyelin. 38. A patient appears to be deficient in vitamin D. The patient was previously prescribed vitamin D supplements, but they do not appear to be working. Which organs and/or tissues should be checked to make sure that the enzymes they produce are functioning appropriately? a. the liver b. the kidneys c. the pancreas d. both the liver and the kidneys e. the liver, the kidneys, and the pancreas 39. Which statement is true? a. Glycerophospholipids are found only in the membranes of plant cells. b. Glycerophospholipids contain fatty acids linked to glycerol through amide bonds. c. Phosphatidylcholine is a sphingolipid. d. Some sphingolipids include oligosaccharides in their structure. e. Triacylglycerols are the principal components of erythrocyte membranes. 40. Which compound is NOT a glycerophospholipid? a. phosphatidylcholine b. phosphatidylethanolamine c. phosphatidylserine d. cardiolipin e. ceramide

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Chap 10_8e 41. Which statement describes a distinct difference between membrane lipids in archaea and membrane lipids in eukaryotes? a. Archaeal membrane lipids have alkyl acids that are ether-linked to glycerol at both ends. b. Eukaryotic membrane lipids consist of glycerol that is ester-linked to three fatty acids. c. Only eukaryotic membrane lipids are amphipathic. d. Archaeal membrane lipids always contain sphingosine. e. Eukaryotic membrane lipids always have a phosphate group attached to glycerol. 42. Overproduction of which types of signaling lipids causes asthmatic attacks? a. prostaglandins b. thromboxanes c. arachidonates d. lipoxins e. leukotrienes 43. A patient has asthmatic attacks due to the overproduction of leukotrienes, which drug should be prescribed to help treat that condition? a. testosterone b. ibuprofen c. aspirin d. prednisone e. warfarin 44. Waxes are BEST described as: a. esters of glycerol and three fatty acids. b. esters of one long-chain fatty acid and one long-chain alcohol. c. polyunsaturated long-chain fatty acids. d. esters of two long-chain fatty acids. e. ethers of glycerol and short-chain alcohols. 45. Which statement is false about sterols? a. Cholesterol is a sterol that is commonly found in mammals. b. Sterols are commonly found in bacterial membranes. c. Sterols are more common in plasma membranes than in intracellular membranes (mitochondria, lysosomes, etc.). d. Sterols are precursors of steroid hormones. e. Sterols have a structure that includes four fused rings.

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Chap 10_8e 46. Which statement concerning fatty acids is true? a. Lipases release fatty acids from storage so they can be used as fuel. b. Cholesterol is a common fatty acid. c. Fatty acids all contain one or more double bonds. d. Fatty acids are a constituent of sterols. e. Fatty acids are strongly hydrophilic. 47. A compound containing N-acetylneuraminic acid (sialic acid) is: a. cardiolipin. b. ganglioside GM2. c. phosphatidylcholine. d. platelet-activating factor. e. sphingomyelin. 48. Which type of chemical linkage is used to join fatty acids to glycerol? a. ether linkage b. peptide bond c. ester linkage d. double bond e. peroxide bond 49. Which eicosanoids contains a five-carbon ring as part of its structure? a. thromboxanes b. prostaglandins c. lipoxins d. leukotrienes e. arachidonates 50. Which types of signaling lipids are produced by platelets to aid in the formation of blood clots? a. prostaglandins b. thromboxanes c. arachidonates d. lipoxins e. leukotrienes

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Chap 10_8e 51. Which factor is NOT a consequence of partial hydrogenation of vegetable oils? a. longer shelf life b. lower melting temperature c. reduction of carbon–carbon double bonds to single bonds d. conversion of some cis double bonds to trans double bonds e. increased risk of cardiovascular disease upon consumption by humans 52. Which feature allows certain lipid molecules to be used as colorful pigments in plants and animals? a. Their high oxygen content helps electrons circulate, which allows absorption of visible light. b. Their conjugated bond structures allow absorption of visible light. c. Their four fused ring structure allows visible light reflection. d. Their hydrophobicity bends light around them. e. Their low specific gravities cause light to reflect from their surfaces. 53. Which glycerophospholipid has a net charge of zero at pH 7? a. phosphatidylserine b. phosphatidic acid c. phosphatidylcholine d. phosphatidylglycerol e. phosphatidylinositol 4,5-bisphosphate 54. Nonsteroidal anti-inflammatory drugs (NSAIDs) like aspirin and ibuprofen act by blocking production of: a. adrenaline. b. prostaglandins. c. sphingolipids. d. vitamin D. e. tocopherols. 55. Which vitamin is fat soluble? a. vitamin A b. vitamin K c. vitamin D d. vitamin E e. All of the answers are correct.

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Chap 10_8e 56. Which solvent is NOT used alone to dissolve lipids? a. ethyl ether b. water c. benzene d. methanol e. chloroform 57. Platelet-activating factor is much more water soluble than most other glycerophospholipids due to which feature? a. its ether-linked alkyl chain at the C-1 of glycerol b. its ester-linked acetic acid at the C-2 of glycerol c. its ethanolamine head group d. its lack of any long alkyl chains linked to glycerol e. the presence of sphingosine, rather than glycerol, as a lipid backbone 58. Phospholipase C hydrolyzes phosphatidylinositol 4,5-bisphosphate to form which signaling molecule that triggers Ca2+ release from the endoplasmic reticulum? a. diacylglycerolphosphate b. inositol 5-monophosphate c. diacylglycerol d. inositol 1,4,5-triphosphate e. inositol 4,5-bisphosphate 59. Which lipid compound is NOT at least partially made from the condensation of isoprene units? a. sterols b. limonene c. beta-carotene d. vitamin E e. phosphatidylinositol 60. What is the abbreviated nomenclature for octadecenoic acid with two double bonds? a. 16:1 b. 14:2 c. 18:2 d. 18:0 e. 18:1

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Chap 10_8e 61. Which types of membrane lipids are modified to determine blood type in humans? a. phosphatidylserines b. glycosphingolipids c. galactolipids d. plasmalogens e. sphingomyelins 62. Researchers working in a laboratory are trying to design a drug that specifically binds to the surface of certain cells. To which membrane lipid constituents should the drug bind in order to achieve this specificity? a. sphingomyelins b. phosphatidylcholines c. gangliosides d. triacylglycerols e. sterols 63. Which technique separates lipids based on their affinity for a silica gel material? a. thin-layer chromatography b. adsorption chromatography c. mass spectrometry d. both thin-layer and absorption chromatography e. both thin-layer chromatography and mass spectrometry 64. Triacylglycerols are composed of: a. a glycerol backbone with ether-linked fatty acids. b. three fatty acids joined by a glucose unit. c. amide linkages between the fatty acids and a glycerol unit. d. a glycerol backbone with ester links to three fatty acids. e. a glycerol backbone, three fatty acids, and amide linkages between the fatty acids and the glycerol. 65. Specific hydrolysis of phosphatidylcholine can be achieved by which technique? a. treatment of the lipid with phospholipase C b. treatment of the lipid with mild acid c. dissolving the lipid in chloroform d. treatment of the lipid with both phospholipase C and mild acid e. both treatment of the lipid with phospholipase C and dissolving the lipid in chloroform

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Chap 10_8e 66. Which health effect is NOT associated with consumption of trans fats? a. lowering of HDL cholesterol b. increased inflammatory response in the body c. raising of LDL cholesterol d. increased joint flexibility due to additional membrane fluidity e. increased risk of heart disease 67. Which statement is true of sphingolipids? a. Cerebrosides and gangliosides are sphingolipids. b. Phosphatidylcholine is a typical sphingolipid. c. They always contain glycerol and fatty acids. d. They contain two esterified fatty acids. e. They may be charged, but are never amphipathic. 68. Which molecules or substances contain, or are derived from, fatty acids? a. beeswax b. galactolipids c. sphingolipids d. triacylglycerols e. All of these contain or are derived from fatty acids. 69. Which solvent is commonly used to extract all the lipids from homogenized tissue samples and subsequent separation of the lipids from the proteins and sugars present in those samples? a. ethanol b. benzene c. a mixture of chloroform, methanol, and water d. water e. a mixture of chloroform and benzene 70. Which term BEST describes the polarity of membrane lipids? a. ambidextrous b. completely nonpolar c. amphipathic d. completely polar e. amphibolic

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Chap 10_8e 71. Which term BEST describes the cholesterol molecule? a. amphipathic b. nonpolar, charged c. nonpolar, uncharged d. polar, charged e. polar, uncharged 72. Fatty acids are attached to sphingosine by what type of chemical linkage? a. ether b. amide c. ester d. peroxide e. alkyl 73. Which drug is NOT lipid based? a. prednisone b. warfarin c. erythromycin d. aspirin e. lovastatin 74. Explain the cause of the hereditary diseases of sphingolipid metabolism, Tay-Sachs and Niemann-Pick diseases.

75. A researcher working in a lab is studying a bacterial organism, but is continually having problems with contamination from fungal growth. What might the researcher add to the growth media to address this contamination issue and why?

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Chap 10_8e 76. Draw the structure of phosphatidylcholine. Circle the part of the molecule that is polar and draw an arrow to the part that is nonpolar.

77. Describe two functions of triacylglycerols in mammals and one function in higher plants.

78. What chemical features distinguish a plasmalogen from a common glycerophospholipid?

79. Match each of these vitamins with its biological role: A, D, E, K. _____ blood clotting _____ vision _____ Ca2+ and phosphate metabolism _____ prevention of oxidative damage

80. Describe the process of column chromatography of lipid extract mixtures, including which types of lipids elute first and how lipids of progressively higher polarity can be eluted from the silica gel column.

81. Describe why saturated fatty acids have higher melting points than do unsaturated fatty acids of the same chain length.

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Chap 10_8e 82. The venom of some rattlesnakes contains phospholipase A2. (a) Explain why a snake bite causes rapid pain and inflammation. (b) Based on a biochemical understanding of the mechanism of the pain, suggest a possible treatment. (c) If too much phospholipase A2 enters the bloodstream, the significant accumulation of one of the products of the reaction acts as a powerful detergent, causing the lysis of red blood cells and potential death. What is this dangerous product and what makes it such a good detergent?

83. In cells, fatty acids are stored as triacylglycerols for energy reserves. (a) What is the molecule to which fatty acids are esterified to form triacylglycerols? (b) What benefits are there to cells storing fatty acids in an esterified form?

84. Explain why extraction of lipids from tissues requires organic solvents.

85. Match the compounds on the left with the important roles they play listed on the right. (Answers are used only once.) (a) prostaglandins _____ blood clotting (b) vitamin E _____ intratissue messengers (c) sphingolipids _____ necessary for sight (d) thromboxanes _____ mediates pain and inflammation (e) vitamin A _____ important component of myelin membranes (f) steroids _____ reducing agent

86. Draw the structure of phosphatidylserine in the ionic form it would have at pH 7.

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Chap 10_8e 87. What is the most significant chemical difference between triacylglycerols and glycerophospholipids that leads to their different functions?

88. Describe how vitamin A1 (all-trans-retinol) is altered to produce the visual pigment used in rhodopsin to absorb visible light. Include in the description what is structurally altered in this visual pigment upon light absorption.

89. Circle the fatty acid in each pair that has the higher melting temperature. (a) 18:1 (Δ9) 18:2 (Δ9,12) (b) 18:0 18:1 (Δ9) (c) 18:0 16:0

90. Describe the differences between the glycosphingolipids corresponding to the A, B, and O human blood group antigens.

91. What do all these compounds have in common: vitamin A, vitamin K, ubiquinone, and dolichol?

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Chap 10_8e 92. Describe the trends of the melting points fatty acids upon (a) chain length and (b) unsaturation; (c) explain these trends in molecular terms.

93. What chemical features distinguish a cerebroside from a ganglioside?

94. Draw the structure of isoprene; explain what is meant by isoprenoid compounds and give an example.

95. Give the structure of phosphatidylethanolamine containing one palmitate and one oleate. Show the ionic form expected at pH 7. How many ester bonds are there in this compound?

96. A food chemist would like to modify lard, an animal fat that is normally a semisolid at room temperature, so that it can be marketed as a product that is a liquid at room temperature. What modification could the food chemist make in terms of carbon–carbon bonds in the lard to achieve the desired result?

97. Draw the structure of sphingosine and describe the relationship between sphingosine and ceramide.

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Chap 10_8e 98. Draw and describe the basic structure shared by all glycerophospholipids.

99. If beeswax, cholesterol, and phosphatidylglycerol are dissolved in chloroform, then subjected to thin-layer chromatography on silica gel using a mixture of chloroform/methanol/water as the developing solvent, which would move fastest?

100. What are the chemical components of a biological wax, and what is their general structure?

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Chap 10_8e Answer Key 1. b 2. d 3. b 4. e 5. c 6. a 7. c 8. a 9. e 10. b 11. b 12. a 13. d 14. b 15. b 16. b 17. c 18. e 19. e 20. a 21. a 22. d 23. b 24. b 25. c 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 10_8e 27. a 28. b 29. d 30. b 31. c 32. b 33. e 34. a 35. b 36. d 37. a 38. d 39. d 40. e 41. a 42. e 43. d 44. b 45. b 46. a 47. b 48. c 49. b 50. b 51. b 52. b 53. c 54. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 10_8e 55. e 56. b 57. b 58. d 59. e 60. c 61. b 62. c 63. d 64. d 65. d 66. d 67. a 68. e 69. c 70. c 71. a 72. b 73. d 74. These diseases are the result of mutations in the genes that code for enzymes of sphingolipid breakdown. The mutant enzyme is defective and unable to catalyze its reaction in the metabolic pathway; this results in the accumulation of the metabolic intermediate that is the substrate for the enzyme. (See Box 10-1.) 75. If one is available, an inhibitor of sterol synthesis could be added. This would have the effect of inhibiting a necessary metabolic function in eukaryotic organisms, but since bacteria do not synthesize sterols, they would not be targeted by the inhibitor. Therefore, the fungal contaminants should be prevented without necessarily impacting bacterial growth. 76. The head group and general glycerophospholipid structures are shown in Figure 10-8. At neutral pH, there is a negative charge on the phosphate group, and the quaternary amino group of choline carries a fixed positive charge; this entire phosphorylcholine moiety is polar. The acyl chains attached to glycerol are the nonpolar part of the molecule.

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Chap 10_8e 77. Triacylglycerols provide mammals with (1) stored fuel and (2) insulation. In plants, oxidation of the triacylglycerols stored in seeds provides the energy and precursors for biosynthetic processes during germination, before photosynthetic mechanisms become functional. Note: Some students may know that in animals, such as camels and desert rats, the oxidation of stored lipids provides water. 78. (1) The long-chain acyl group attached to C-1 of glycerol is ether-linked in a plasmalogen but is an ester-linked fatty acyl group in typical glycerophospholipids. (2) There is a double bond between C-1 and C-2 of this fatty acyl chain in plasmalogens, but not in other phospholipids. (See Fig. 10-9.) 79. K; A; D; E 80. First, the lipid extract that is dissolved in chloroform is applied to the silica gel column. Polar lipids will bind to the silicic acid of the column, while neutral lipids will elute immediately with the chloroform solvent. The polar lipids that are bound to the column can then be eluted by washing with acetone to remove uncharged polar lipids, then by washing with methanol to elute charged or very polar lipids. 81. Saturated fatty acids contain no double bonds and are therefore very flexible in their orientation. However, the fully extended conformation is the most energetically favorable, and many saturated fatty acids can pack together tightly when they are all in the extended conformation. This tight packing leads to significant hydrophobic interactions, which increases the overall melting point of the saturated fatty acids. Unsaturated fatty acids contain one or more double bonds, which form kinks in the fatty acid structure that makes them less flexible. Those kinks also interfere with the tight packing together of the fatty acids, leading to less stable aggregates of these fatty acids, with fewer hydrophobic interactions, and therefore lower melting points than saturated fatty acids that have the same chain length. (See Fig. 10-1 for images.) 82. (a) Phospholipase A2 cleaves the C-2 position of the phospholipids. The C-2 position often contains arachidonic acid, which is converted to prostaglandins via the action of cyclooxygenase (COX). Increased prostaglandins yield pain and inflammation. (b) Blocking the activity of COX using NSAIDs such as ibuprofen or aspirin might be useful. (c) The other product of phospholipase A2 is a lysophospholipid (a lipid with a head group and only one fatty acid tail). These look a lot like detergents (i.e., SDS) and they are really good at solubilizing things such as membrane vesicles. 83. (a) Three fatty acids are esterified to glycerol. (b) Triacylglycerols are uncharged and insoluble in water; they do not require any water of hydration, unlike polysaccharides. 84. Lipids are either strongly hydrophobic or amphipathic. Because the solvent in tissues is water, lipids are mainly present in aggregates. This aggregation does not occur in organic solvents; as a result, the lipids are more soluble and thus extractable from the tissues. 85. d; f; e; a; c; b 86. The head group and general glycerophospholipid structures are shown in Figure 10-8. At neutral pH, there is a charge on the phosphate group, and serine is in the zwitterionic form; it has a protonated amino group and an ionized carboxyl group.

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Chap 10_8e 87. Triacylglycerols are nonpolar hydrophobic molecules that can be stored in specialized nonaqueous cellular compartments. Glycerophospholipids are amphipathic molecules that can serve as structural components of membranes, which have hydrophilic and hydrophobic regions. 88. Vitamin A1 is first oxidized from retinol to a retinal form. During this process, the all-trans organization of carbon– carbon double bonds in the molecular structure is reorganized to generate a cis bond in the middle of the molecule, making 11-cis-retinal. This is the visual pigment used in rhodopsin. When light is absorbed by this pigment, it excites the conjugated electrons of the molecule, leading to conversion of the 11-cis-retinal to an alltrans-retinal state. This structural conversion leads to a nerve signal that will stimulate vision centers in the brain. (See Fig. 10-20 for structures of these compounds.) 89. (a) 18:1 (Δ9); (b) 18:0; (c) 18:0 90. The type O structure is found in all three glycosphingolipids. In both type A and type B, there is an added sugar; this sugar differs between type A and B. (See Fig. 10-13.) 91. They are all lipids with potent biological activities derived from isoprenoid precursors. 92. All other things being equal, (a) the longer the acyl chain, the higher the melting temperature; and (b) the more unsaturation, the lower the melting temperature. (c) The melting temperature is a measure of the thermal energy needed to break the intermolecular interactions that stabilize the solid form of a lipid, which depends on how well the lipid molecules pack together. The longer the carbon chains are, the greater the surface area, which means more collective van der Waals attractions between neighboring chains. Saturated lipids can adopt a nearly straight conformation that packs easily. In unsaturated chains a cis double bond introduces a kink into the acyl chain so that it does not pack as easily as saturated lipids. 93. A cerebroside has a single sugar residue joined to ceramide; a ganglioside has an oligosaccharide joined to ceramide. (See Fig. 10-11.) 94. The structure is shown in section 10-3. Isoprenoid compounds contain chains that consist of multiple isoprene units. (See Fig. 10-22 for examples.) 95. See Figure 10-8 for the phospholipid structure, and Table 10-1 for the structures of the fatty acids. There are two carboxylate esters and two phosphate esters (one phosphodiester) in the molecule. 96. The food chemist could dehydrogenate the lard. This adds carbon–carbon double bonds, creating rigid bends (kinks) in the hydrocarbon chains. This lowers the melting point of the fat. Controlling the extent of dehydrogenation controls the melting point to achieve the desired result. 97. The structure of sphingosine is shown in Figure 10-11, which also shows that the attachment of a fatty acyl group to sphingosine in amide linkage converts it to ceramide. 98. The general glycerophospholipid structure is shown in Figure 10-8. All glycerophospholipids have two fatty acids in ester linkage with C-1 and C-2 of glycerol; often, the fatty acid at C-1 is saturated and that at C-2 is unsaturated. C-3 of glycerol is joined to an alcohol-containing head group through a phosphodiester linkage, which is negatively charged at neutral pH. (See Fig. 10-8.)

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Chap 10_8e 99. In this chromatography, the least polar compound (beeswax) moves fastest and the most polar (phosphatidylglycerol, which has a negative charge on its head group) moves the slowest. (See Fig. 10-25.) 100. A wax consists of a long-chain fatty acid in an ester linkage with a long-chain fatty alcohol. (See Fig. 10-5a.)

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Chap 11_8e Indicate the answer choice that best completes the statement or answers the question. 1. A ligand-gated ion channel (such as the nicotinic acetylcholine receptor): a. is a charged lipid in the membrane bilayer that allows ions to pass through. b. is a membrane protein that permits a ligand to pass through the membrane only when opened by the appropriate ion. c. is a membrane protein that permits an ion to pass through the membrane only when opened by the appropriate ligand. d. is a molecule that binds to the membrane thereby allowing ions to pass through. e. always requires a second ligand to close the channel once it is opened. 2. Glucose transport into erythrocytes is an example of: a. active transport. b. antiport. c. electrogenic uniport. d. passive transport. e. symport. 3. If a monovalent cation is being imported into a cell in the absence of a concentration gradient (i.e., the concentration for the transported cation is equal on both sides of the membrane), what could be predicted about ΔGt? Assume the transmembrane potential is 50 mV (inside negative). a. The value of ΔGt will have a positive sign. b. The value of ΔGt will have a negative sign. c. The value of ΔGt will likely be close to zero. d. It is impossible to predict anything about the value of ΔGt. 4. The fluidity of the lipid side chains in the interior of a bilayer is generally increased by: a. a decrease in temperature. b. an increase in fatty acyl chain length. c. an increase in the number of double bonds in fatty acids. d. an increase in the percentage of phosphatidylethanolamine. e. the binding of water to the fatty acyl side chains. 5. Which are choline-containing lipids typically found in the outer leaflet of plasma membranes? a. cardiolipin b. phosphatidylinositol c. sphingomyelin d. phosphatidylcholine e. both sphingomyelin and phosphatidylcholine Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 6. In humans, the fatty acid composition of membrane lipids in skin cells is different from the fatty acid composition of membrane lipids in the internal organs because the internal organs function at a slightly higher temperature. Which difference in fatty acid composition is MOST likely to be observed? a. Skin cells show lower levels of 18:0 relative to 18:1 and higher levels of 16:0 relative to 18:0. b. Skin cells show higher levels of 20:0 relative to 18:0 and higher levels of 18:2 relative to 18:0. c. Skin cells show lower levels of 20:0 relative to 18:0 and lower levels of 18:0 relative to 18:2. d. Skin cells show higher levels of 18:2 relative to 18:0 and lower levels of 16:0 relative to 18:0. e. Both answers A and C are true. 7. Which process does NOT involve the fusion of two membranes or two regions of the same membrane? a. endocytosis b. entry of enveloped viruses into cells c. entry of glucose into cells d. exocytosis e. fusion of egg and sperm 8. Which transporter will move lipids from the outer leaflet to the cytosolic leaflet of a plasma membrane? a. a flippase b. a floppase c. a scramblase d. both a flippase and a floppase e. both a flippase and a scramblase 9. Which type of membrane transport uses ion gradients as the energy source (driving force) for transport? a. facilitated diffusion b. passive transport c. primary active transport d. secondary active transport e. simple diffusion 10. Consider the transport of K+ from the blood (where its concentration is about 4 mM) into an erythrocyte that contains 150 mM K+. The transmembrane potential is about 60 mV, inside negative relative to outside. What is the free-energy change for this transport process? (These values may be of use: R = 8.315 J/mol·K; T = 298 K; F (Faraday constant) = 96,480 J/V·mol; N = 6.022 × 1023/mol.) a. about 5 J/mol b. about 15 J/mol c. about 5 kJ/mol d. about 15 kJ/mol e. It is impossible to calculate with the information given. Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 11. The inner (plasma) membrane of E. coli is about 75% lipid and 25% protein by weight. How many molecules of membrane lipid are there for each molecule of protein? (Assume that the average protein is Mr 50,000 and the average lipid is 750.) a. 1 b. 50 c. 200 d. 10,000 e. 50,000 12. Which statement describes a general feature of the lipid bilayer in all biological membranes? a. Individual lipid molecules are free to diffuse laterally on the surface of the bilayer. b. Individual lipid molecules in one face (monolayer) of the bilayer readily diffuse (flip-flop) to the other monolayer. c. Polar, but uncharged, compounds readily diffuse across the bilayer. d. The bilayer is stabilized by covalent bonds between neighboring phospholipid molecules. e. The polar head groups face inward toward the inside of the bilayer. 13. Which statement about membranes is true? a. Most plasma membranes contain more than 70% proteins. b. Sterol lipids are common in bacterial plasma membranes. c. Sterol lipids are common in human cell plasma membranes. d. Sterol lipids are common in plant cell plasma membranes. e. The plasma membranes of all cell types within a particular organism have basically the same lipid and protein composition. 14. Bacterial cells change the fluidity of their lipid membranes to adapt to growth at lower temperatures by increasing the synthesis of: a. cholesterol. b. long-chain fatty acids and increasing the saturation of their membrane lipids. c. both long- and short-chain fatty acids. d. long-chain fatty acids and decreasing the saturation of their membrane lipids. e. short-chain fatty acids and decreasing the saturation of their membrane lipids.

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Chap 11_8e 15. Consider the transport of glucose into an erythrocyte by facilitated diffusion. What is the free-energy change for glucose uptake into the cell when the glucose concentrations are 5 mM on the outside and 0.1 mM on the inside? (These values may be of use: R = 8.315 J/mol·K; T = 298 K; F (Faraday constant) = 96,480 J/V·mol; N = 6.022 × 1023/mol.) a. less than 2 kJ/mol b. about –10 kJ/mol c. about 30 kJ/mol d. about –30 kJ/mol e. It is impossible to calculate without knowledge of the membrane potential. 16. FRAP experiments are generally used in membrane studies to examine: a. transverse diffusion rates. b. active transport rates. c. lateral diffusion rates. d. both transverse diffusion rates and active transport rates. e. both transverse diffusion rates and lateral diffusion rates. 17. Which step is NOT involved in neurotransmitter release at a synapse? a. creation of a fusion pore b. hemifusion induced by zipping and lateral tension on the bilayers c. v-SNARE binding to t-SNARE d. pore widening and release of neurotransmitter e. flippase-mediated movement of phosphatidylserine from the inner to the outer leaflet 18. The shortest α helix segment in a protein that will span a membrane bilayer has about _____ amino acid residues. a. 5 b. 20 c. 50 d. 100 e. 200 19. Which statement is true regarding the SERCA pump? a. The E1 conformation has a higher affinity for Ca2+ than the E2 conformation. b. The P domain contains a serine that is phosphorylated to drive the reaction. c. Three calcium ions are moved in each cycle of the transporter. d. This protein can be classified as an antiport. e. None of the statements is true.

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Chap 11_8e 20. Integrins are: a. membrane proteins that are involved in ion transport. b. membrane proteins that are involved in sugar transport. c. membrane proteins that mediate cell adhesion. d. proteins of the extracellular matrix that bind to cell surface proteins. e. proteins that are found at the membrane-cytoplasm interface. 21. Which phrase BEST describes the term "amphitropic" protein? a. cytosolic lipid-linked proteins b. GPI-linked proteins c. proteins that are reversibly membrane-associated or cytosolic d. proteins that are either integral or lipid-linked e. proteins that can be on either leaflet of the bilayer 22. A protein is discovered that transports Ca2+ up a concentration gradient from the cytoplasm into the endoplasmic reticulum. No other ions move during this transport. What type of transport protein does this appear to be? a. Ca2+ channel b. Ca2+ ion porin c. primary active uniporter d. secondary active uniporter e. ionophore 23. What is meant by the term "positive-inside rule"? a. The typical transmembrane potential for plasma membranes is positive on the inside. b. Integral plasma membrane proteins commonly have positively charged amino acids on the cytosolic side. c. Concentrations of cations are usually higher inside than outside of cells. d. All of the answers are correct. e. None of the answers is correct. 24. For the process of solute transport, the constant Kt is: a. analogous to Ka for ionization of a weak acid. b. analogous to Km for an enzyme-catalyzed reaction. c. analogous to Vmax for an enzyme reaction. d. proportional to the number of molecules of glucose transporter per cell. e. the maximum rate of glucose transport.

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Chap 11_8e 25. Which statement about facilitated diffusion across a membrane is true? a. A specific membrane protein lowers the activation energy for movement of the solute through the membrane. b. It can increase the transmembrane concentration gradient of the diffusing solute. c. It is impeded by the solubility of the transported solute in the nonpolar interior of the lipid bilayer. d. It is responsible for the transport of gases such as O2, N2, and CH4 across biological membranes. e. The rate is not saturable by the transported substrate. 26. Facilitated diffusion through a biological membrane is: a. driven by a difference of solute concentration across the membrane. b. driven by energy supplied ATP. c. an endergonic process. d. generally irreversible. e. not specific with respect to the substrate. 27. Which statement is generally true of integral membrane proteins? a. The secondary structure in the transmembrane region consists solely of α helices or β sheets. b. The domains that protrude on the cytoplasmic face of the plasma membrane nearly always have covalently attached oligosaccharides. c. They are unusually susceptible to degradation by trypsin. d. They can be removed from the membrane with high salt or mild denaturing agents. e. They undergo constant rotational motion that moves a given domain from the outer face of a membrane to the inner face and then back to the outer. 28. Which transporters can be classified as active transporters? a. flippases b. floppases c. scramblases d. both flippases and floppases e. both flippases and scramblases 29. Which statement does NOT describe a characteristic of the fluid mosaic model of membranes? a. Hydrophobic interactions predominate between lipids in the membrane. b. Proteins and lipids are able to move laterally at different rates. c. Protein structures are able to move easily from one leaflet to another. d. Noncovalent forces predominate in intermolecular interactions. e. Proteins may traverse a membrane or be associated with one side or the other of the membrane.

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Chap 11_8e 30. Membrane proteins: a. are sometimes covalently attached to lipid moieties. b. are sometimes covalently attached to carbohydrate moieties. c. are composed of the same 20 amino acids found in soluble proteins. d. diffuse laterally in the membrane unless they are anchored. e. All of the answers are correct. 31. The fluidity of a lipid bilayer will be increased by: a. decreasing the number of unsaturated fatty acids. b. decreasing the temperature. c. increasing the length of the alkyl chains. d. increasing the temperature. e. substituting 18:0 (stearic acid) in place of 18:2 (linoleic acid). 32. Which statement is true for passive transport across a biological membrane? a. Passive transport is driven by a solute electrochemical gradient. b. Passive transport is driven by ATP. c. Passive transport is irreversible. d. Passive transport is driven by both a solute electrochemical gradient and ATP. e. Passive transport is driven by a solute electrochemical gradient and is irreversible. 33. Which structure describes an integral membrane protein containing a β barrel? a. maltoporin b. aquaporin c. outer membrane phospholipase A d. both maltoporin and outer membrane phospholipase A e. both maltoporin and aquaporin 34. When a bacterium such as E. coli is shifted from a warmer growth temperature to a cooler growth temperature, it may compensate by: a. increasing its metabolic rate to generate more heat. b. putting longer-chain fatty acids into its membranes. c. putting more unsaturated fatty acids into its membranes. d. shifting from aerobic to anaerobic metabolism. e. synthesizing thicker membranes to insulate the cell.

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Chap 11_8e 35. Movement of water across membranes is facilitated by proteins called: a. annexins. b. aquaporins. c. hydropermeases. d. selectins. e. transportins. 36. Which statement is true about aquaporins? a. The activation energy for transport of water is high and must have energy provided by ATP. b. Aquaporins primarily are used to store water in connective tissues. c. The transport channel is hydrophilic. d. They allow the passage of water as hydronium ion, H3O+. e. They are present only in plant roots for the uptake of water. 37. Membrane fusion leading to neurotransmitter release requires the action of: a. cadherins. b. selectins. c. flippases. d. tSNARE and vSNARE. e. None of the answers is correct. 38. In one catalytic cycle, the Na+/K+ ATPase transporter transports _____, and converts one _____. a. two Na+ out, three K+ in; ATP to ADP + Pi b. three Na+ out, two K+ in; ATP to ADP + Pi c. three Na+ in, two K+ out; ATP to ADP + Pi d. one Na+ out, one K+ in; ATP to ADP + Pi e. two Na+ out, three K+ in; ADP + Pi to ATP 39. What kind of bond can link a myristoyl anchor to a polypeptide? a. an ester bond to an internal serine b. an amide bond to a glycine c. a thioester to a cysteine d. an ester bond to the C terminus e. a thioether bond to a cysteine side chain

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Chap 11_8e 40. Which factor MOST significantly determines the direction in which an ion moves through an ion channel in a membrane? a. the electrochemical gradient across the membrane b. the size and shape of the channel c. the ion selectivity of the channel d. both the electrochemical gradient across the membrane and the size and shape of the channel e. both the size and shape of the channel and the ion selectivity of the channel 41. Peripheral membrane proteins: a. are generally noncovalently bound to membrane lipids. b. are usually denatured when released from membranes. c. can be released from membranes only by treatment with detergent(s). d. may have functional units on both sides of the membrane. e. penetrate deeply into the lipid bilayer. 42. Which process does NOT require a protein facilitator? a. simple diffusion b. ionophore-mediated diffusion c. a primary active uniport d. a passive antiporter e. both simple diffusion and ionophore-mediated diffusion 43. Which statement about the composition of biological membranes is false? a. In a given eukaryotic cell type (e.g., a hepatocyte), all intracellular membranes have essentially the same complement of lipids and proteins. b. Carbohydrate is found in membranes as part of either a glycolipid or glycoprotein. c. The plasma membranes of the cells of vertebrate animals contain more cholesterol than the mitochondrial membranes. d. The ratio of lipid to protein varies widely among cell types in a single organism. e. Triacylglycerols are not commonly found in membranes. 44. For membrane proteins the hydropathy plot can be used to: a. determine the carbohydrates attached to a protein. b. deduce the quaternary structure of a membrane protein. c. determine the percent of water embedded in the protein structure. d. extrapolate for the true molecular weight of a membrane protein. e. predict whether a given protein sequence contains membrane-spanning segments.

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Chap 11_8e 45. An integral membrane protein can be extracted with: a. a buffer of alkaline or acid pH. b. a chelating agent that removes divalent cations. c. a solution containing detergent. d. a solution of high ionic strength. e. hot water. 46. What kind of bond can link a palmitoyl anchor to a polypeptide? a. an ether bond to an internal threonine b. an amide bond to a glycine c. a thioester to a cysteine d. an ester bond to the C terminus 47. ABC transporters are known to facilitate the transport of: a. cancer drugs out of cancer cells. b. antibiotics out of bacteria. c. membrane lipids from the inner leaflet to the outer leaflet. d. chloride ions in the lung. e. All of the answers are correct. 48. As the temperature for a membrane lipid preparation is raised, what would be the order of states that would be adopted? a. liquid-ordered, gel phase, liquid-disordered b. liquid-disordered, liquid-ordered, gel phase c. liquid-disordered, gel phase, liquid-ordered d. gel phase, liquid-disordered, liquid-ordered e. gel phase, liquid-ordered, liquid-disordered 49. The specificity of the potassium channel for K+ over Na+ is mainly the result of the: a. more favorable interaction of K+ with the selectivity filter protein. b. hydrophobicity of the channel. c. phospholipid composition of the channel. d. presence of carbohydrates in the channel. e. presence of cholesterol in the channel.

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Chap 11_8e 50. An electrogenic Na+ transporter: a. catalyzes facilitated diffusion of Na+ from a region of high Na+ concentration to one of lower Na+ concentration. b. must catalyze an electron transfer (oxidation-reduction) reaction simultaneously with Na+ transport. c. must transport both Na+ and a counterion (Cl– , for example). d. transports Na+ against its concentration gradient. e. transports Na+ without concurrent transport of a counterion. 51. Which statement about the composition of membranes is true? a. All biological membranes contain cholesterol. b. Free fatty acids are major components of all membranes. c. The inner and outer membranes of mitochondria have different protein compositions. d. The lipid composition of all membranes of eukaryotic cells is essentially the same. e. The lipid:protein ratio is similar in most membranes. 52. Which statement is true about GLUT1? a. GLUT1 transports glucose into erythrocytes against a concentration gradient. b. In the blood GLUT1 is normally half-saturated with glucose and operates at close to

Vmax.

c. GLUT1 can transport galactose with close to the same rate at the same concentration. d. GLUT1 is a lipid-anchored protein. e. GLUT1 increases the transport of glucose into erythrocytes at about 10 times the rate expected in the absence of a transporter. 53. Lipid rafts are often enriched in all of these types of molecules EXCEPT: a. sphingolipids. b. cholesterol. c. GPI-linked proteins. d. glycerophospholipids. e. long-chain saturated fatty acids. 54. Which enzymes are NOT involved in moving phospholipids from one leaflet to another? a. flippases that move phosphatidylethanolamine and phosphatidylserine b. floppases that move phospholipids from the cytosolic leaflet to the extracellular leaflet c. flip-floppases that allow phospholipids to move back and forth between the inner and outer leaflets d. scramblases that allow phospholipids to move down their concentration gradient e. phosphatidylinositol transfer proteins that play a role in lipid signaling

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Chap 11_8e 55. Which statement about caveolin is false? a. Caveolin is an integral membrane protein. b. Caveolin induces outward membrane curvature. c. Caveolin is palmitoylated. d. Caveolin associates with cholesterol-rich regions. e. Caveolin is involved in membrane trafficking and cellular signaling. 56. Which statement is true concerning the chloride-bicarbonate exchanger? a. This transporter is electrogenic. b. The exchanger is a passive symporter. c. This protein decreases the carbon dioxide–carrying capacity of the bloodstream. d. The exchanger is a passive antiporter, and it increases the carbon dioxide–carrying capacity of the bloodstream. e. This transporter is electrogenic, and the exchanger is a passive antiporter. 57. The zipping of SNARE proteins causes the _____ during membrane fusion. a. first attachment of a vesicle to the plasma membrane b. formation of the fusion pore c. formation of the hemifusion state d. expansion of the fusion pore 58. Which statement is false about the chloride-bicarbonate exchanger? a. The chloride-bicarbonate exchange protein increases the rate of bicarbonate transport across the membrane. b. The chloride-bicarbonate exchange protein uses ATP as an energy source to drive bicarbonate transport. c. The chloride-bicarbonate exchange protein transports chloride ions across the membrane. d. The chloride-bicarbonate exchange protein is classified as an antiporter. e. The chloride-bicarbonate exchange protein spans the membrane many times. 59. F-type ATPase transporters can be classified as what type of enzymes? a. oxidoreductases b. transferases c. hydrolases d. synthases e. transferases

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Chap 11_8e 60. Which transporter will move lipids from the cytosolic leaflet to the outer leaflet of a plasma membrane? a. a flippase b. a floppase c. a scramblase d. both a flippase and a floppase e. both a floppase and a scramblase 61. Which statement does NOT apply to valinomycin? a. This can act as an antibiotic. b. This molecule is a small cyclic peptide. c. This compound preferentially transports potassium ions over sodium ions. d. This substance is an ionophore. e. It shuttles ions against a concentration gradient. 62. Which factor contributes to the selectivity of the potassium channel from S. lividans? a. cotransport of water which binds to the potassium ions b. positively charged amino acids near the channel opening c. the N-terminal ends of four α helices d. backbone carbonyl groups in the selectivity filter e. aspartate residues lining the cone of the channel 63. (a) When relatively high concentrations of fatty acids are suspended in water, they form structures known as _____. (b) When relatively high concentrations of membrane phospholipids are dissolved in water, they form structures known as _____. (c) Why are the structures listed in the answers to (a) and (b) energetically favored?

64. Calculate the free-energy change associated with pumping protons out of a cell if the pH inside is 7 while the pH outside is 6. Assume 37 ºC (310 K) and a 50 mV membrane potential (inside negative). (R = 8.315 J/mol·K; F (Faraday constant) = 96,480 J/V·mol)

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Chap 11_8e 65. The plasma membrane of an animal cell consists of 45% by weight of phospholipid and 55% protein. What is the mole ratio (moles of lipid/moles of protein) if the average molecular weight of phospholipids is 750 and the average molecular weight of membrane proteins is 50,000?

66. In the context of the fluid mosaic model, indicate the positions and orientations of phospholipids, cholesterol, integral and peripheral membrane proteins, and the carbohydrate moieties of glycoproteins and glycolipids.

67. What are the similarities and differences between integrins, cadherins, and selectins?

68. Sketch a hydropathy plot for a hypothetical integral membrane protein with 3 transmembrane segments and containing 190 amino acids.

69. Compare the structure and activity of a membrane transport protein that transports a polar substance across a membrane with a typical soluble enzyme. How are transporter and enzyme similar? How are they different?

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Chap 11_8e 70. Glycosphingolipids and cholesterol cluster together in membrane regions known as _____.These microdomains are more _____ than the surrounding phospholipid-rich membrane due to a high content of _____ fatty acids. These regions are rich in proteins that are anchored to the membrane by covalently attached _____ and _____ groups and also those anchored by GPI linkage. Proteins aggregated in this fashion are often functionally related. Examples are (1) _____ proteins and (2) _____ proteins.

71. What are the principle features of the fluid mosaic model of membranes?

72. What are three differences between ion channels and ion transporters?

73. The bacterium E. coli can grow at 20 ºC or at 40 ºC. At which growth temperature would the membrane phospholipids have a higher ratio of saturated to unsaturated fatty acids, and why?

74. A plant breeder has developed a new frost-resistant variety of tomato that contains higher levels of unsaturated fatty acids in membrane lipids than those found in standard tomato varieties. However, when temperatures climb above 95 ºF, this frost-resistant variety dies, whereas the standard variety continues to grow. Provide a likely explanation of the biochemical basis of increased tolerance to cold and increased susceptibility to heat of this new tomato variety.

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Chap 11_8e 75. This sequence is taken from an integral membrane protein.

Which part of this sequence most likely corresponds to a transmembrane helix?

76. Transport of histidine into a bacterial cell was measured at several different histidine concentrations. Is it possible using only these data to distinguish if histidine uptake operates by passive or facilitated transport? Explain. Histidine (μM) 2.5 7 16 31 72

Transport (μM/min) 42.5 119 240 490 1,000

77. (a) Explain why glycerophospholipids are capable of spontaneously assembling into the bilayer structure found in biological membranes but triacylglycerols are not. (b) What are the forces that drive bilayer formation?

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Chap 11_8e 78. A researcher is trying to isolate an enzyme that catalyzes the conversion of A→ B, and has a sensitive assay for this enzyme. After lysing the cells, it is found that the activity is associated with the membrane fraction, not the soluble fraction (which is thrown away). The researcher then follows the procedure shown. Explain the sudden reoccurrence of activity at the end of the protocol.

79. Reagents A and B both react covalently with primary amino groups such as those of phosphatidylethanolamine. Reagent A permeates erythrocytes, but reagent B does not. Both A and B are available in radioisotopically labeled form. Describe a simple experiment to determine whether the phosphatidylethanolamine of erythrocyte membranes is located in the outer leaflet of the lipid bilayer, the inner leaflet, or in both. Assume that phosphatidylethanolamine is equally distributed on both sides of the bilayer if it is present in both leaflets.

80. What is an amphipathic compound? Explain how such compounds contribute to the structure of biological membranes.

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Chap 11_8e 81. Distinguish between simple diffusion, facilitated diffusion, and active transport across a membrane for these questions. (More than one may be true.) (a) Which processes are energy dependent? (b) Which processes need some kind of carrier protein(s)? (c) Which processes can be saturated by substrate? (d) Which processes can establish a concentration gradient? (e) How much energy does it take to transport an uncharged substrate in, if its starting inside concentration is 10-fold greater than outside?

82. Explain why nonpolar compounds are generally able to diffuse across biological membranes without the aid of a specific transport system.

83. If the hydrophobic interior of a membrane were about 3 nm thick, what would be the minimum number of amino acids in a stretch of transmembrane α helix?

84. Describe two different ways a plant can adjust the components of its cell membranes to keep them as fluid as possible on a cold winter morning.

85. A protein is found to extend all the way through the membrane of a cell. Describe this protein in terms of the location of particular types of amino acid side chains in its structure and its ability to move within the membrane.

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Chap 11_8e 86. In a chloride channel, an α helix is found to be part of the specificity filter. Which end of the helix is interacting with the chloride anions and why?

87. Explain the differences between integral and peripheral membrane proteins.

88. (a) List three different major components of eukaryotic membranes. (b) When a preparation of mitochondrial membranes was treated with high salt (0.5 M NaCl), it was observed that 40% of the total protein in this preparation was solubilized. What kind of membrane proteins are in this soluble extract, and what forces normally hold them to the membrane? (c) What kind of proteins constitute the insoluble 60%, and what forces hold these proteins in the membrane?

89. Compare and contrast symport and antiport. Which term best describes the transport system mediated by the Na+K+ ATPase?

90. (a) What kinds of forces or bonds anchor an integral membrane protein in a biological membrane? (b) What forces hold a peripheral membrane protein to the membrane? (c) What might one do to solubilize each of the two types of membrane proteins?

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Chap 11_8e Answer Key 1. c 2. d 3. b 4. c 5. e 6. e 7. c 8. e 9. d 10. d 11. c 12. a 13. c 14. e 15. b 16. c 17. e 18. b 19. a 20. c 21. c 22. c 23. b 24. b 25. a 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 27. a 28. d 29. c 30. e 31. d 32. a 33. d 34. c 35. b 36. c 37. d 38. b 39. b 40. a 41. a 42. e 43. a 44. e 45. c 46. c 47. e 48. e 49. a 50. e 51. c 52. b 53. d 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 55. b 56. d 57. c 58. b 59. c 60. e 61. e 62. d 63. (a) micelles; (b) bilayers or vesicles; (c) Micelles are favored when the polar head group has a greater crosssectional area than the nonpolar acyl chain, making the molecule wedge-shaped; bilayers and vesicles are favored when the cross-sectional area of head group and acyl chain(s) are about the same, so that the molecule is cylindrical. (See Fig. 11-1.) 64. 10.7 kJ/mol = (8.315 J/mol·K)(310 K) ln (10) + (1)(96,480 J/V·mol)(0.050 V) (See Eqn 11-4.) There is a 10fold difference in the concentration of protons between pH 7 and pH 6 (pH 6 is 10×higher). 65. The ratio of moles lipid/moles protein is about 55. In 100 g of membrane, there are 45 g/750 g·mol–1 = 0.06 mol phospholipid, and 55 g/50,000 g·mol–1 = 1.1 × 10–3 mol protein. So lipid/protein = 0.06/0.0011 = 55. 66. Phospholipids and sterols are found in both faces of the lipid bilayer. Integral membrane proteins penetrate or span the lipid bilayer, but peripheral membrane proteins associate at the membrane surface with lipid head groups or integral membrane proteins. The carbohydrate moieties of glycolipids and glycoproteins are invariably on the outside face of the plasma membrane. (See Fig. 11-3.) 67. All three are families of integral membrane proteins that are involved in cell adhesion. Integrins mediate cell adhesion to proteins of the extracellular matrix. Cadherins and selectins mediate cell-cell adhesion, the former by interaction with cadherins on the surface of other cells, the latter by interaction with polysaccharides on the surface of other cells. 68. The plot should have a y axis that is labeled "hydropathy index" and an x axis that is labeled "residue number" or "position in the protein." The y axis should have values from +3 to –3; the x axis should have an integral number that has a range of zero to several hundred. The plot should show three distinct peaks corresponding to the 3 transmembrane segments. 69. Both proteins have domains that specifically recognize and bind to their substrates via weak interactions; they both therefore mediate processes that are stereospecific and saturable. The membrane transporter usually spans the membrane, having one or several hydrophobic domains that interact with the hydrophobic acyl chains of fatty acids in the interior of the lipid bilayer. Soluble enzymes tend to have their hydrophobic residues buried within their interiors, and their hydrophilic residues on the surface, where they interact with water. 70. rafts; ordered; saturated; myristoyl; palmitoyl; receptor; signaling Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 71. The principle features of the fluid mosaic model of membranes include: (1) a lipid bilayer in which individual lipids are free to move laterally but not across the bilayer; (2) integral membrane proteins, which penetrate or span the bilayer, associating with lipid acyl chains by hydrophobic interactions and exhibiting lateral mobility; (3) peripheral membrane proteins, which associate noncovalently with the lipid head groups and protruding domains of integral membrane proteins, and which are sometimes tethered to the membrane by a covalent lipid anchor. 72. (1) The rate of ion movement through channels is much greater; (2) ion transporters exhibit saturation, whereas ion channels do not; (3) ion channels open and close in response to external stimuli or events such as ligand-binding or changes in electrical potential across the membrane. 73. At 40 ºC, the membranes of E. coli will contain more saturated fatty acids than at 20 ºC. The cell regulates fatty acid composition to achieve the same fluidity in its membranes, regardless of growth temperature. Saturated fatty acids counterbalance the fluidizing effect of high temperature. 74. More unsaturated fatty acids will cause an increase in membrane fluidity because unsaturated fatty acids contain kinks and cannot pack as tightly as saturated fatty acids. At cold temperatures, the fluidity increase from the extra unsaturated fatty acids counterbalances the tendency of lipids to solidify at low temperature. At high temperatures, the fluidizing effects of the extra unsaturated fatty acids add to the fluidizing effect of higher temperature, and the membrane of the new plant loses its integrity. 75. The sequence corresponding to (excluding the single threonine) and contains no prolines.

is a stretch of –20 hydrophobic amino acids

76. At first glance, the mechanism appears to be passive transport: twice the substrate concentration exhibits twice the rate of uptake, with no observable saturation. However, from the data provided, it cannot be determined whether the mechanism is passive or facilitated. Why? Because it is possible that the experiment was performed at concentrations significantly below the Kt for the transporter where the data will vary linearly with substrate concentration. One might need to use much higher concentrations of histidine to observe saturation. 77. (a) Triacylglycerols have three fatty acyl groups in ester linkage with glycerol; they are very hydrophobic because the carboxyl groups, which are involved in the ester linkages, cannot ionize. Glycerophospholipids have a polar region at their head group, where a phosphate in a phosphodiester linkage bears a full negative charge. The head group itself (serine, ethanolamine, choline, etc.) may also be charged and is polar in any case. Thus, the phospholipid is amphipathic, having both polar and nonpolar regions, and it forms lipid bilayers spontaneously in water. (b) These lipid bilayers are stabilized by the energy gained from burying hydrophobic groups out of contact with water. A hydrophobic chain in water forces the formation of a cage of low-entropy water molecules around it. When several hydrophobic regions cluster in a bilayer, the surface area exposed to water decreases, and the water molecules in the cage are released, accompanied by a gain in entropy that drives the formation of the bilayer. 78. The activity of interest is membrane-bound. In the first mild rinse at pH 6, the researcher "lost" the activity due to a mild rinse, presumably losing a required peripheral membrane protein to the soluble fraction. In the next treatment with mild detergent, the researcher presumably lost a protein with a lipid anchor to the soluble fraction. When combining the peripheral membrane protein lost in the pH 6 wash with the lipid-anchor protein lost in the mild detergent, activity recovered. Therefore, the enzyme requires two components to be active: the peripheral part and the lipid-anchor part. This is not uncommon. Copyright Macmillan Learning. Powered by Cognero.

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Chap 11_8e 79. Reagent A will label phosphatidylethanolamine head groups in both the outer and the inner monolayer of the membrane; reagent B will label only the phosphatidylethanolamine molecules on the outer face. If phosphatidylethanolamine is equally distributed on both sides of the bilayer, twice as much labeling of phosphatidylethanolamine should be observed with reagent A as with reagent B. Deviations from this ratio indicate asymmetry in the distribution of phosphatidylethanolamine. 80. An amphipathic compound has one region or domain that is hydrophilic and another that is hydrophobic. When added to water, amphipathic compounds tend to arrange in a way that exposes their hydrophilic regions to the solvent and hides their hydrophobic domains. One structure that accomplishes this is the lipid bilayer, which forms spontaneously with phospholipids in water. (See Fig. 11-1.) 81. (a) only active transport; (b) facilitated diffusion and active transport; (c) facilitated diffusion and active transport; (d) only active transport; (e) 5.7 kJ/mol 82. A nonpolar compound is more soluble in nonpolar solutes, such as benzene or chloroform, than in polar solvents, such as water. They generally pass through biological membranes unaided because it is energetically favorable for them to move from the aqueous solvent into the nonpolar region of the bilayer interior. 83. The dimensions of an α helix are about 0.54 nm/turn, and there are 3.6 residues/turn, so each residue extends the helix by about 0.15 nm. To span 3 nm of lipid bilayer will therefore require a minimum of 20 residues. 84. To compensate for the solidifying effect of low temperature on membrane lipids, it can synthesize and place in the membrane (1) a greater proportion of unsaturated fatty acids and (2) shorter-chain fatty acids. Both increase the fluidity of the lipid bilayer. 85. This integral membrane protein associates with the lipid bilayer through hydrophobic interactions between domains containing many hydrophobic amino acids and the fatty acyl chains of membrane lipids. Polar and charged residues are located on portions of the protein that protrude out of either face of the membrane. The protein is free to diffuse laterally in the plane of the membrane, but cannot move across the lipid bilayer. 86. The N-terminal end of the helix will form part of the channel, as the helix dipole will mean that the N-terminal end is carrying a partial positive charge, which would be complementary to the negative charge on the anion. 87. Integral membrane proteins are very firmly associated with the membrane; their hydrophobic domains are associated with the fatty acyl groups in the interior in hydrophobic interactions. Peripheral membrane proteins are more loosely associated and usually do not penetrate the hydrophobic interior of the bilayer. Conditions that reduce ionic interactions and hydrogen bonds commonly release them. 88. (a) phospholipids, sterols, proteins (integral and peripheral); (b) peripheral membrane proteins, which are associated with the membrane through ionic and hydrogen bonds between their charged and polar side chains and the charged head groups of phospholipids; (c) integral membrane proteins (which are held to the membrane by hydrophobic interactions between their nonpolar side chains and the hydrophobic fatty acyl chains of phospholipids), and those peripheral membrane proteins that are held to the membrane by a covalent lipid anchor

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Chap 11_8e 89. Symport and antiport are both types of cotransport systems in which two solutes move through the membrane simultaneously. In symport, both move in the same direction; in antiport, one solute goes in one direction, the other in the opposite direction. The Na+K+ ATPase of the plasma membrane is an antiport system. It moves K+ in and Na+ out in a ratio of two K+ per three Na+. Neither of the two ions can be transported unless the other is present, which is characteristic of cotransport systems. (See Figs 11-35 and 11-37.) 90. (a) The forces that hold integral membrane proteins in the membrane are hydrophobic interactions between hydrophobic domains of the protein and the fatty acyl chains of the bilayer interior. (b) Peripheral membrane proteins associate with membranes primarily through ionic interactions and hydrogen bonds between charged and polar side chains of the protein and polar head groups of membrane lipids. Some peripheral membrane proteins contain a covalently bound lipid that anchors them to the bilayer. (c) To remove integral membrane proteins, it is generally necessary to use detergents, which convert membranes into soluble micelles. Peripheral membrane proteins can often be released by extraction with buffers of high or low salt concentration, high or low pH, or low concentrations of divalent cations.

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Chap 12_8e Indicate the answer choice that best completes the statement or answers the question. 1. Steroid hormones are carried on specific carrier proteins because the hormones: a. are too unstable to survive in the blood on their own. b. cannot dissolve readily in the blood because they are too hydrophobic. c. cannot find their target cells without them. d. need them in order to pass through the plasma membrane. e. require subsequent binding to specific receptor proteins in the nucleus. 2. Which statement BEST describes the concept of amplification in biosignaling? a. Higher concentrations of signal molecules lead to stronger cellular responses. b. In response to the presence of a signal molecule, more signal molecules are synthesized. c. Small amounts of extracellular signal will trigger multiple intracellular effects via enzyme cascades. d. All of the statements describe this concept. e. None of the statements describes this concept. 3. Salbutamol is an epinephrine agonist for the β-adrenergic receptor. What effects would be seen if a hepatocyte is treated with salbutamol? a. inactivation of adenylyl cyclase b. activation of the triacylglyceride synthesis c. activation of glycogen synthesis d. glucose export from cells e. both activation of the breakdown of glycogen and glucose export from cells 4. Steroid hormone response elements are _____, which, when bound to a(n) _____, alter gene expression at the level of _____. a. intron sequences; activated hormone receptor; translation b. nuclear proteins; hormone; transcription c. plasma membrane proteins; hormone; transcription d. sequences in DNA; receptor-hormone complex; replication e. sequences in DNA; receptor-hormone complex; transcription 5. The G protein involved in visual signal transduction is: a. a leukotriene. b. transducin. c. arrestin. d. rhodopsin. e. a GTP receptor.

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Chap 12_8e 6. Cholera toxins: a. block the activity of Gs . b. bind to gangliosides. c. are heterodimeric proteins. d. associate with a G protein. e. All of the answers are correct. 7. Protein kinase C is allosterically regulated by which second messengers? a. inositol triphosphate b. diacylglycerol c. calcium d. both diacylglycerol and calcium e. both inositol triphosphate and diacylglycerol 8. What is the correct order for the members (MEK, ERK, Raf, and RTK) of the MAP kinase cascade? a. RTK, ERK, Raf, MEK b. ERK, MEK, Raf, RTK c. RTK, Raf, MEK, ERK d. RTK, MEK, ERK, Raf e. RTK, Raf, ERK, MEK 9. Which characteristic is NOT one attributed to a second messenger? a. intracellular signaling molecules b. molecules that can easily pass across membrane bilayers c. molecules that can act as allosteric effectors for signaling proteins d. molecules that can be rapidly converted between active and inactive forms e. molecules that are synthesized in response to receptor/signal interactions 10. After membrane depolarization in neurons, export of potassium: a. makes the value of Vm more negative. b. decreases the concentration gradient for potassium. c. is energetically favorable. d. All of the answers are correct.

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Chap 12_8e 11. Cyclin-dependent protein kinases can regulate the progression of cells through the cell cycle by phosphorylation of proteins such as: a. insulin. b. myoglobin. c. myosin. d. retinal rod and cone proteins. e. All of the answers are correct. 12. Which statement is true regarding the Na+ voltage-gated channel in neurons? a. Similar to the potassium ion channel, it exists as a tetramer in the membrane. b. Positive membrane potentials on the extracellular side will close the channel. c. Aspartate residues are part of the voltage-sensing helices. d. Ion specificity comes from the voltage-sensing helices. 13. Phosphorylation of a tyrosine in the cyclin-dependent kinases (CDK) inactivates the protein by: a. inhibiting the binding of cyclin. b. inhibiting the binding of ATP. c. inhibiting the binding of the T loop. d. preventing dissociation of the cyclin-CDK complex. 14. Which compound(s) is involved in desensitization of the β-adrenergic receptor? a. β-adrenergic receptor kinase b. arrestin c. GTPase activating proteins d. both β-adrenergic receptor kinase and arrestin e. β-adrenergic receptor kinase, arrestin, and GTPase activating proteins 15. Autophosphorylation of receptor tyrosine kinases depends on: a. dimerization of the receptor. b. phosphorylation of multiple Tyr residues. c. ligand binding. d. transmission of conformational changes through the membrane. e. All of the answers are correct.

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Chap 12_8e 16. Which statement is true of gated ion channels? a. Each channel can allow 10 million ions per second through the membrane. b. The gating mechanism involves pistonlike movement of the transmembrane helices. c. Each channel lets both positive and negative ions flow through the pore. d. Closing of the gate requires phosphorylation of the channel protein. e. Gated channels only respond to intracellular ligands. 17. Which statement concerning cyclin-dependent protein kinases (CDKs) is NOT correct? a. Animal cell CDKs contain one of two types of cyclins (alpha and beta). b. Their activity fluctuates during the cell cycle. c. Their activity is regulated by changes in gene expression, protein phosphorylation, and proteolysis. d. Their activity is regulated by cyclins. e. They can alter the activity of proteins involved in the progression of cells through the cell cycle. 18. Which statement concerning signal transduction by the insulin receptor is correct? a. Activation of the receptor protein kinase activity results in the activation of additional protein glycosylases. b. Binding of insulin to the receptor activates a protein kinase. c. Binding of insulin to the receptor results in a change in its primary structure. d. The receptor protein kinase activity is specific for tryptophan residues on the substrate proteins. e. The substrates of the receptor protein kinase activity are mainly proteins that regulate transcription. 19. How do G proteins become activated? a. GDP binds to the α subunit. b. GTP is converted to cGMP. c. ATP is converted to cAMP in the active site. d. GDP is exchanged for GTP. e. All of the answers are correct. 20. Gustducin is: a. a trimeric G protein involved in taste. b. a gene element encoding the enzyme gustducase. c. the most important secondary messenger in taste sensory neurons. d. an ion channel involved in olfaction. e. a hormone that initiates a response in vision.

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Chap 12_8e 21. _____ is NOT involved in signal transduction by the β-adrenergic receptor pathway. a. ATP b. Cyclic AMP c. Cyclic GMP d. GTP e. All of these are involved. 22. If a FRET experiment was carried out with blue fluorescent protein attached to the α subunit of a stimulatory G protein and a green fluorescent protein attached to the β subunit, the presence of a strong FRET signal would be associated with: a. interaction of a G protein–coupled receptor with an antagonist. b. hydrolysis of GTP in the α subunit. c. increased concentrations of cAMP. d. both interaction of a G protein–coupled receptor with an antagonist and hydrolysis of GTP in the α subunit. e. both hydrolysis of GTP in the α subunit and increased concentrations of cAMP. 23. Which is true about estrogen transiting to its target tissue via the blood? a. Carrier proteins are necessary. b. Estrogen is freely dissolved in the blood plasma. c. Estrogen is carried via a covalent link to hemoglobin. d. Estrogen is transported via the lymphatic system, not via blood. 24. In signal transduction by the β-adrenergic receptor pathway, _____ catalyzes the synthesis of cyclic AMP. a. cAMP synthetase b. tyrosine kinase c. epinephrine d. Gsα e. adenylyl cyclase 25. Which statement concerning cyclins is NOT correct? a. They are activated and degraded during the cell cycle. b. They are regulatory subunits for enzymes that catalyze the phosphorylation of proteins. c. They can become linked to ubiquitin. d. When bound, they inhibit kinase activity. e. They contain specific amino acid sequences that target them for proteolysis.

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Chap 12_8e 26. Calmodulin is a(n): a. allosteric activator of calcium-dependent enzymes. b. allosteric inhibitor of calcium-dependent enzymes. c. calcium-dependent enzyme. d. cell surface calcium receptor. e. regulatory subunit of calcium-dependent enzymes. 27. Oncogenes that encode _____ are known. a. cytoplasmic G proteins and protein kinases b. transmembrane protein receptors c. growth factors d. secreted proteins e. All of the answers are correct. 28. The specificity of signaling pathways does NOT include: a. flippase-catalyzed movement of phospholipids from the inner to the outer leaflet. b. migration of signal proteins into membrane rafts. c. phosphorylation of target proteins at Ser, Thr, or Tyr residues. d. the ability to be switched off instantly by hydrolysis of a single phosphate-ester bond. e. the assembly of large multiprotein complexes. 29. The main effect of acetylcholine on the postsynaptic cell is: a. cyclic nucleotide synthesis. b. protein cleavage (proteolysis). c. opening of a cation channel. d. polarization of the cell. e. opening of a Cl– specific channel 30. Cholera toxin leads to the activation of the α subunit of G proteins through what kind of covalent modification? a. phosphorylation b. adenylation c. acetylation d. palmitoylation e. ADP-ribosylation

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Chap 12_8e 31. Guanylyl cyclase receptor enzymes: a. cleave phosphates from guanosyl units. b. are examples of ligand-gated ion channels. c. convert GTP to cGMP. d. catalyze synthesis of cyclic GDP and GTP. e. require hydrolysis of ATP in addition to GTP. 32. Which feature of signal transduction comes from precise molecular complementarity between a signal molecule and its receptor? a. specificity b. cooperativity c. amplification d. desensitization e. integration 33. During the cell cycle the depolymerization of _____ in the nuclear envelope is caused by a cyclin-dependent protein kinase. a. actin b. collagen c. adenylyl cyclase d. DNA e. lamin 34. Protein kinase A is: a. activated by covalent binding of cyclic AMP. b. affected by cyclic AMP only under unusual circumstances. c. allosterically activated by cyclic AMP. d. competitively inhibited by cyclic AMP. e. noncompetitively inhibited by cyclic AMP. 35. Which is a common cause for the production of oncogenes? a. defective ion channel proteins b. defects in DNA polymerase c. viral infection d. dephosphorylation of cyclin-dependent protein kinases e. exposure to infrared radiation

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Chap 12_8e 36. Which factor is NOT a shared feature of signaling by mammalian vision and gustatory receptor pathways? a. transmembrane receptors b. GDP-GTP exchange c. heterotrimeric G proteins d. opening and closing of ion channels e. All of the answers are shared. 37. In the insulin-receptor-dependent activation of the protein ERK (extracellular regulated kinase), what protein is responsible for phosphorylating ERK? a. the insulin receptor (INSR) b. insulin receptor substrate-1 (IRS-1) c. Raf-1 kinase d. MEK e. Ras 38. Which protein(s) is phosphorylated in response to an insulin/insulin-receptor interaction? a. IRS-1 b. phosphatidylinositol-4,5-bisphosphate c. GDP d. both IRS-1 and phosphatidylinositol-4,5-bisphosphate e. both phosphatidylinositol-4,5-bisphosphate and GDP 39. Which factor is NOT a feature of signal transduction? a. one stimulus can activate more than one pathway b. signal amplification c. covalent binding between the ligand and the receptor d. desensitization or adaptation of the receptor e. variable affinity for different signaling components 40. Which item is NOT one of the general types of signaling mechanisms found in multicellular organisms? a. gated ion channels b. receptor enzymes c. G protein–coupled receptors d. receptor cAMP cyclases e. nuclear receptors

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Chap 12_8e 41. In kidneys, what is the response when the atrial natriuretic factor binds to its receptor? a. increased cAMP concentration in the cytosol b. both increased cAMP concentration in the cytosol and activation of protein kinase G c. stimulation of water and sodium excretion d. both increased cAMP concentration in the cytosol and stimulation of water and sodium excretion 42. Which item does NOT use a cAMP-dependent signaling pathway? a. insulin b. epinephrine c. glucagon d. odorants e. serotonin 43. Which gated ion channel is associated with membrane repolarization in neurons? a. Na+ channel b. K+ channel c. Ca2+ channel d. acetylcholine receptor ion channel e. both Na+ and Ca2+ channels 44. The breast cancer treatment drug tamoxifen is a(n): a. antagonist of estrogen. b. agonist of estrogen. c. antagonist of estradiol. d. agonist of estradiol. e. All of the answers are correct. 45. Mutated versions of genes encoding signaling proteins involved in cell cycle regulation are called: a. mutagens. b. transposons. c. anti-alleles. d. oncogenes. e. cancer-promoting elements.

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Chap 12_8e 46. Which process acts through a G protein–coupled receptor? a. β-adrenergic response b. light detection by rhodopsin c. insulin-dependent activation of protein kinase B d. both β-adrenergic response and light detection by rhodopsin e. both light detection by rhodopsin and insulin-dependent activation of protein kinase B 47. Acetylcholine: a. is a neurotransmitter. b. triggers active transport of sodium and calcium into neurons. c. leads to membrane depolarization through potassium ion import. d. All of the answers are correct. e. None of the answers is correct. 48. Which statement concerning receptor enzymes is correct? a. They are not usually membrane-associated proteins. b. They contain an enzyme activity that acts on a cytosolic substrate. c. They contain an enzyme activity that acts on the extracellular ligand. d. They have a ligand-binding site on the cytosolic side of the membrane. e. They have an active site on the extracellular side of the membrane. 49. Which statement does NOT describe a step in the response to photon absorption by rhodopsin? a. Rhodopsin catalyzes GDP-GTP exchange on transducin. b. Rhodopsin is phosphorylated by rhodopsin kinase. c. Arrestin binds to the phosphorylated end of rhodopsin. d. Light absorption converts all-trans-retinal to 11-cis-retinal. e. Cation channels are kept open by cGMP. 50. _____ do bind to heterotrimeric G proteins. a. GTP-GDP exchange factors b. GTPase activating proteins c. G protein–coupled receptors d. Guanosine diphosphates e. All of the answers are correct.

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Chap 12_8e 51. Hormone-activated phospholipase C can convert phosphatidylinositol 4,5-bisphosphate to: a. diacylglycerol + IP3. b. diacylglycerol + inositol + inorganic phosphate. c. glycerol + inositol + inorganic phosphate. d. glycerol + phosphoserine. e. phosphatidyl glycerol + IP2. 52. Which statement is NOT true for G protein–coupled receptors (GPCRs)? a. Agonists mimic the effect of the natural ligand. b. Antagonists block the normal effect of the natural ligand. c. GPCRs interact with heterodimeric G proteins. d. GPCRs have seven transmembrane helices. e. There exist >100 orphan GPCRs in the human genome with no known ligand. 53. What is expected to happen when epinephrine binds to its receptor in a myocyte? a. Intracellular cAMP levels will rise. b. Glycogen synthase will become active. c. Glycogen phosphorylase will be phosphorylated. d. Intracellular cAMP levels will rise, and glycogen phosphorylase will be phosphorylated. e. Glycogen synthase will become active, and glycogen phosphorylase will be phosphorylated. 54. Ubiquitin is a: a. structural protein in the nuclear envelope. b. hormone receptor. c. protein kinase. d. calcium ion channel protein. e. protein that tags another protein for proteolysis. 55. G protein–coupled activation of phospholipase C directly generates which second messenger? a. diacylglycerol b. inositol triphosphate c. calcium d. both diacylglycerol and inositol triphosphate e. both inositol-1,4,5-trisphosphate and calcium

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Chap 12_8e 56. Programmed cell death is called: a. metastasis. b. apoptosis. c. mitotic termination. d. oncogenic transformation. e. ubiquitination. 57. The primary force that drives an ion through a membrane channel depends on the: a. charge on the membrane. b. difference in electrical potential across the membrane. c. size of the channel. d. size of the ion. e. size of the membrane. 58. Phosphorylation of a threonine in the T loop of cyclin-dependent kinases (CDK) causes the charge on threonine to be stabilized by what event? a. the T loop is rearranged and cyclin binds b. association with ADP c. donation of Ca2+ from calmodulin CDK d. three arginine residues form ionic interactions with the threonine e. dimerization of phosphorylated threonines. 59. Most transduction systems for hormones and sensory stimuli that involve trimeric G proteins do NOT have _____ in common. a. cyclic nucleotides b. nuclear receptors c. receptors that interact with a G protein d. receptors with multiple transmembrane segments e. self-inactivation 60. Which type of structures are involved in the binding of Ca2+ ions to calmodulin? a. EF hand, a helix-loop-helix motif b. beta barrel c. heme group d. an internal pocket lined with aspartate residues e. interstitial spaces between layered parallel beta sheets

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Chap 12_8e 61. Which factor is NOT involved in the specificity of signal transduction? a. interactions between receptor and signal molecules b. location of receptor molecules c. structure of receptor molecules d. structure of signal molecules e. transmembrane transport of signal molecules by receptor molecules 62. SH2 domains bind sequences containing: a. phosphoserine. b. phosphothreonine. c. phosphotyrosine. d. multiple phosphorylations. e. either phosphoserine or phosphothreonine. 63. The ion channel that opens to allow Na+ and Ca2+ to pass in response to acetylcholine is an example of a _____ signal transduction system. a. G-protein b. ligand-gated c. receptor-enzyme d. serpentine receptor e. voltage-gated 64. Match the signal input with the result. Input (a) Light (b) Odorant (c) Sweet molecule (d) Epinephrine

Result (1) Sensory cell depolarizes (2) Sensory cell hyperpolarizes (3) No effect on sensory cell membrane potential

65. Cholera is caused by a toxin produced by Vibrio cholerae. Describe the molecular basis for its toxic effects.

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Chap 12_8e 66. Briefly describe the key features of the proposed mechanism of the IP3-gated Ca2+ channel.

67. Briefly explain the difference between nitric oxide (NO)–dependent cGMP synthesis and atrial natriuretic factor (ANF)–dependent cGMP synthesis.

68. Explain how an increase in cytosolic Ca2+ concentration from 10–8 M to 10–6 M activates a Ca2+ and calmodulin-dependent enzyme.

69. How do ligand-gated ion channels play a role in sensory transduction in the eye?

70. Briefly describe the two types of guanylyl cyclases that participate in signal transduction.

71. What is meant by multivalent adaptor proteins in signaling pathways?

72. What is the mechanism of action of the drug tamoxifen in the treatment of breast cancer?

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Chap 12_8e 73. Explain why mutations in oncogenes are generally dominant while those in tumor suppressor genes are recessive.

74. Explain the importance of membrane rafts in cell signaling pathways.

75. Describe the sequence of biochemical events between the release of epinephrine into the bloodstream and the activation of the enzyme glycogen phosphorylase.

76. Explain how amplification occurs in signal transductions with examples from the β-adrenergic receptor and the insulin receptor.

77. These sequences are all phosphorylated by the insulin receptor tyrosine kinase. 1. HTDDGYMPMSPGVA 2. RKGNGDGYMPMSPKSV 3. RVDPNGYMMMSPSGS 4. LPCTGDYMNMSPVGD 5. GSEEYMNMDLGPGR 6. SRGDYMTMQIG (a) Comparing all these sequences, derive an apparent consensus/target specificity? (b) Changing the methionine immediately after the tyrosine in sequence 6 to isoleucine decreases the rate of phosphorylation of the substrate, while changing it to the unbranched amino acid norleucine (a linear isomer of leucine and isoleucine) does not. What does this reveal about the requirements for this amino acid position?

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Chap 12_8e 78. Explain two different approaches to targeting the activity of aberrant protein kinases for treating cancer. Give examples of each.

79. Compare and contrast ligand-gated and voltage-gated ion channels; give an example of each.

80. Describe the role of G proteins in olfactory sensory transduction.

81. Signals carried by hormones must eventually be terminated; the response continues for a limited time. Discuss important mechanisms for signal termination, using specific systems as examples.

82. GTP-binding proteins play critical roles in many signal transductions. Describe two cases in which such proteins act, and compare the role of the G proteins in each case.

83. Explain how amplification of a hormonal signal takes place; illustrate with a specific example.

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Chap 12_8e 84. Explain how mutations in these proteins might result in either loss of responsiveness to a given hormone or production of a continuous signal even in the absence of the hormone: (a) a mutation in the regulatory (R) subunit of cAMP-dependent protein kinase, making R incapable of binding to the catalytic (C) subunit; (b) a mutation in a growth factor receptor with protein kinase activity; (c) a defect in a G protein that renders the GTPase activity inactive.

85. Describe three factors that contribute to the high degree of sensitivity of signal transduction systems.

86. Compare and contrast the modes of action of epinephrine, acting through the β-adrenergic receptor, and of insulin, acting through the insulin receptor.

87. What type of receptor is the acetylcholine receptor, and what happens when acetylcholine is bound?

88. Describe the relationship between a proto-oncogene and an oncogene, and explain how one arises from the other.

89. What are cyclins? What is their role in the regulation of the cell cycle?

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Chap 12_8e Answer Key 1. b 2. c 3. e 4. e 5. b 6. e 7. d 8. c 9. b 10. d 11. c 12. b 13. b 14. d 15. e 16. a 17. a 18. b 19. d 20. a 21. c 22. d 23. a 24. e 25. d 26. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_8e 27. e 28. a 29. c 30. e 31. c 32. a 33. e 34. c 35. c 36. e 37. d 38. d 39. c 40. d 41. c 42. a 43. b 44. a 45. d 46. d 47. a 48. b 49. d 50. e 51. a 52. c 53. d 54. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_8e 55. d 56. b 57. b 58. d 59. b 60. a 61. e 62. c 63. b 64. (a)–(2); (b)–(1); (c)–(1); (d)–(3) 65. The toxin is an enzyme that catalyzes the ADP-ribosylation of G proteins that act in signal transduction. Attachment of the ADP-ribose moiety prevents the G proteins from cycling between their GDP-bound and GTP-bound forms, interfering with normal signal transductions and with metabolic events dependent on the signaling systems. 66. The IP3 receptor is a tetramer with 24 transmembrane helices that surround a central pore. The central pore is the channel for Ca2+ movement, which does not conduct Ca2+ in the absence of IP3. In the proposed model, IP3 binds near the amino-terminal end of each subunit which causes a major rearrangement of the α helix at the carboxyl-terminal end, opening the Ca2+ channel. (See Fig. 12-16.) 67. NO-dependent cGMP synthesis occurs in muscle (including cardiac) cells, while ANF-dependent cGMP synthesis occurs in kidney cells. NO can pass across membranes and interact with a soluble, cytosolic guanylyl cyclase, whereas ANF interacts with a membrane-bound receptor that also contains the guanylyl cyclase activity. (See Box 12-2.) 68. The higher Ca2+ concentration allows Ca2+ binding to the four binding sites on the protein calmodulin. As a consequence of Ca2+ binding, calmodulin undergoes a conformational change that allows it to interact productively with the enzyme that it activates; the Ca2+-calmodulin enzyme association activates the enzyme. Also, calmodulin is a subunit of a Ca2+/calmodulin-dependent protein kinase. The Ca2+-induced conformational change activates the kinase that in turn regulates the activity of a number of enzymes. 69. Rod and cone cells in the retina contain rhodopsin with a light-absorbing pigment. Absorbed photons cause a change in conformation that ultimately results in a decrease in the concentration of cyclic GMP, which causes Na+and Ca2+-gated ion channels to close. This leads to hyperpolarization of the cell membrane and initiates an electrical signal that travels to the brain. 70. One type is membrane-spanning cyclases that are homodimers with an extracellular ligand-binding domain and an intracellular guanylyl cyclase domain. The other type is a soluble cytosolic guanylyl cyclase enzyme containing a heme and is activated by nitrogen oxide (NO). (See Box 12-2.) Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_8e 71. The reversible phosphorylation (at Ser, Thr, or Tyr) of some signaling proteins creates docking sites for other proteins, and in many cases, the interactions between several different such proteins creates multiprotein signaling complexes. 72. Tamoxifen is an antagonist of estrogen, and competes with it for binding to the estrogen receptor. Unlike the situation with estrogen, the tamoxifen-receptor complex, though stable, cannot elicit significant changes in gene expression, thus slowing the growth of hormone-dependent cancerous cells. 73. With oncogenes, the abnormal protein product directly interferes with normal regulation of cell growth, overriding these functions. By contrast, tumor suppressor proteins normally restrain cell division, and both chromosomal copies have to be inactivated for growth to become unregulated, thus a mutation in only one copy does not exhibit the cancerous phenotype. 74. Rafts are membrane regions enriched in sphingolipids and sterols, which can sequester certain signaling proteins (usually ones from the same pathway), increasing the probability of productive interactions between them. 75. Epinephrine binds to its specific receptor on the cell surface. The occupied receptor causes GTP to be exchanged for GDP on a GTP-binding protein (Gs ); Gs then activates adenylate cyclase of the plasma membrane, which catalyzes production of 3',5'-cyclic AMP (cAMP). The cAMP-dependent protein kinase (protein kinase A) is activated by the resulting rise in cAMP, and it phosphorylates the enzyme phosphorylase kinase, activating it. Active phosphorylase kinase phosphorylates glycogen phosphorylase, activating it and stimulating glycogen breakdown. (See Fig. 12-7.) 76. In the β-adrenergic system, amplification is achieved (as is described in Fig. 12-7) when a single hormone molecule binds to a single adrenergic receptor that activates a number of Gs molecules, each of which activates an enzyme (adenylate cyclase) that catalyzes the formation of many second messenger molecules (cAMP). In the insulin receptor system, a single molecule of insulin binds to a receptor, activating its protein tyrosine kinase activity, which acts catalytically to alter the activity of many target proteins by phosphorylation (see Fig. 12-22). In short, amplification occurs when a single molecule of signal activates a cascade of catalysts. 77. (a) Aligning the tyrosines yields an apparent consensus sequence of YMXM at the point of phosphorylation (where X is variable). There is also a preference for at least one acidic amino acid upstream of the tyrosine (shown in bold in the sequences below). 1. HTDDGYMPMSPGVA 2. RKGNGDGYMPMSPKSV 3. RVDPNGYMMMSPSGS 4. LPCTGDYMNMSPVGD 5. GSEEYMNMDLGPGR 6. SRGDYMTMQIG (b) Norleucine, with its linear side chain (—CH2—CH2—CH2—CH3), is structurally similar to methionine and can adopt a similar conformation that allows the tyrosine to bind properly in the active site.

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Chap 12_8e 78. One approach is to design small molecule inhibitors that compete with the ATP-binding site such as imatinib (Gleevec), erlotinib (Tarceva), and sunitinib (Sutent). Despite the similarity in these binding sites, inhibitors that are specific toward different protein kinases can be found. Another approach is to raise antibodies that target these protein kinases such as Herceptin, Erbitux, and Avastin. (See Box 12-4.) 79. Ion channels are protein-based passages in the plasma membrane through which ions can pass. Gated channels open or close in response to external signals, either specific molecules (ligand-gated) or changes in transmembrane electrical potential (voltage-gated). An example of a ligand-gated channel is the acetylcholine receptor; the sodium and potassium channels are examples of voltage-gated channels. 80. When a sensory stimulant interacts with its receptor, it triggers a conformational change that results in displacement of bound GDP by GTP on a G protein. This activated G protein then activates either adenylyl cyclase or phospholipase C, which in turn increases the level of ligands that open ion channels. 81. Hormonal responses may be terminated by removal of the second messenger (e.g., degradation of cAMP); by dephosphorylation of the target protein (by phosphoprotein phosphatases); or by self-inactivation of G proteins (by hydrolysis of bound GTP to GDP). If the hormonal stimulus is present for extended periods, desensitization of the hormone receptor (e.g., by phosphorylation) makes the system unresponsive to the hormone. 82. GTP-binding proteins are self-inactivating switches; when a hormonal or other signal activates the G protein, GTP replaces bound GDP, changing the activity of the G protein. These active G proteins then act on the next element in the signaling cascade. In the case of the β-adrenergic receptor, Gs activates adenylate cyclase; in the IP3 pathways, Gp activates the phospholipase that generates the second messenger's diacylglycerol and IP3. (See Figs 12-4 and 12-11.) 83. Amplification occurs when one molecule of signal (epinephrine, for example) elicits the formation of many molecules of some enzyme (e.g., protein kinase A). This occurs when a single hormone molecule binds to its specific receptor in the plasma membrane and causes the activation of several molecules of Gs , each of which activates an enzyme (adenylate cyclase) that, acting catalytically, produces many molecules of cAMP for every active molecule of enzyme. Each of these many molecules of cAMP can activate protein kinase A that, acting catalytically, phosphorylates many molecules of target protein (e.g., glycogen synthase). (See Fig. 12-7.) 84. (a) When a mutation in the R subunit of cAMP-dependent protein kinase prevents R-C interaction, the inhibitory effect of R is lost, and the catalytic subunit continues to phosphorylate target proteins regardless of cAMP concentration. (b) A mutation in a receptor that acts via tyrosine kinase (the EGF receptor, for example) may lead to production of a receptor molecule in which tyrosine kinase is always active, even in the absence of the growth factor. (c) When a mutation in a G protein destroys its GTPase activity, it can no longer inactivate itself by converting bound GTP to GDP. Once activated, the mutant G protein continues to send its unregulated signal. 85. The sensitivity of signal transduction results from (a) the high affinity of receptors for signal molecules; (b) cooperative binding of signal molecules to receptors; (c) signal amplification by enzyme cascades. 86. (The mechanisms of epinephrine and insulin action are summarized in Figs 12-4 and 12-22.) The adrenergic receptor indirectly activates a catalyst (adenylate cyclase), which produces a second messenger (cAMP). The insulin receptor is itself a catalyst when occupied with insulin; its tyrosine kinase activity phosphorylates and activates another protein kinase, which initiates a cascade of phosphorylations of other proteins. Copyright Macmillan Learning. Powered by Cognero.

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Chap 12_8e 87. The acetylcholine receptor is an ionotropic receptor, which means that it is an ion channel in addition to being a receptor (as opposed to receptors that generate second messengers). It is a cation channel that opens when acetylcholine is bound allowing the passage of Ca2+, Na+, and K+. 88. A proto-oncogene is a gene that encodes a normal cellular protein that is involved in some regulatory process. Mutation in the normal gene creates an oncogene that encodes a defective regulatory protein. The result is defective regulation of such processes as DNA replication and cell division, which is characteristic of tumor cells. 89. Cyclins are regulatory subunits of protein kinases. The presence of the cyclin subunits is essential for activation of the protein kinase activity. The levels of cyclins fluctuate during the cell cycle and in response to cellular and extracellular signals. These changes result in changes in the activities of the cyclin-dependent protein kinases that in turn regulate and control the cell cycle.

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Chap 13_8e Indicate the answer choice that best completes the statement or answers the question. 1. Under cellular conditions (37°C), what is the actual free energy for the reaction shown when the ratio of glucose-6-phosphate to fructose-6-phosphate is 0.8:0.2? (R = 8.315 J/mol · K) glucose-6-phosphate → fructose-6-phosphate ΔG'° = 1.7 kJ/mol a. 1,730 kJ/mol b. 1,870 kJ/mol c. 1.73 kJ/mol d. –1.73 kJ/mol e. –1.87 kJ/mol 2. Which statement is false regarding biological oxidations? a. The redox potential is the affinity of a substance to accept electrons. b. Oxidation can occur by addition of oxygen to a molecule. c. Electrons are transferred from substances with a high reduction potential to substances with a lower reduction potential. d. Oxidases, oxygenases, and dehydrogenases are all enzymes that catalyze biological oxidation-reduction reactions. e. NAD+ is a cosubstrate of certain dehydrogenases and always accepts electrons in the form of hydride ions. 3. Which nucleotide forms are used in the cellular reactions for DNA replication? a. 3' triphosphates b. 5' triphosphates c. 2' diphosphates d. 5' monophosphates e. 3' monophosphates 4. Hydrolysis of 1 M glucose 6-phosphate catalyzed by glucose 6-phosphatase is 99% complete at equilibrium (i.e., only 1% of the substrate remains). Which statement is MOST nearly correct? (R = 8.315 J/mol · K; T = 298 K) a. ΔG'° is –11 kJ/mol. b. ΔG'° is –5 kJ/mol. c. ΔG'° is 0 kJ/mol. d. ΔG'° is +11 kJ/mol. e. ΔG'° cannot be determined from the information given.

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Chap 13_8e 5. Which compound is expected to have the MOST favorable (most negative) standard free energy of hydrolysis? a. 1,3-bisphosphoglycerate b. glucose 6-phosphate c. ADP d. phosphoenolpyruvate e. thioesters (e.g., acetyl-CoA) 6. What symbol represents the standard transformed free energy used by biochemists? a. ΔG b. ΔG' c. ΔG'° d. ΔG° 7. Which compound is classified as high energy? a. phosphocreatine b. ATP c. phosphoenolpyruvate d. acetyl-CoA e. All of the answers are correct. 8. Muscle contraction involves the conversion of _____ energy to _____energy. a. chemical; kinetic b. chemical; potential c. kinetic; chemical d. potential; chemical e. potential; kinetic 9. Biological oxidation-reduction reactions always involve: a. direct participation of oxygen. b. formation of water. c. mitochondria. d. transfer of electrons. e. transfer of hydrogens.

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Chap 13_8e 10. When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase (which catalyzes the interconversion of these two compounds) until equilibrium is reached, the final mixture contains twice as much glucose 6-phosphate as fructose 6-phosphate. Which statement is BEST applied to this reaction? (R = 8.315 J/mol · K; T = 298 K) glucose 6-phosphate → fructose 6-phosphate a. ΔG'° is incalculably large and negative. b. ΔG'° is –1.72 kJ/mol. c. ΔG'° is zero. d. ΔG'° is +1.72 kJ/mol. e. ΔG'° is incalculably large and positive. 11. Which statement is false regarding carbonyl groups? a. The carbon atom in a carbonyl group is more oxidized than the carbon atom in carbon dioxide. b. The carbon atom of a carbonyl group is an electrophile. c. Electron delocalization by a carbonyl group stabilizes an adjoining carbanion, thus facilitating its formation. d. Positively charged metal ions may enhance the ability of a carbonyl group to act as an electron sink. e. The functional group of aldehydes and ketones is a carbonyl group. 12. Which statement is true regarding actual free-energy change of a reaction? a. If the actual free-energy change is negative, the reaction is spontaneous. b. If the actual free energy is zero, the rate of the forward and reverse reactions are equal. c. The actual free energy becomes less negative as the reaction proceeds spontaneously. d. All of the statements are true. e. None of the statements is true. 13. Which statement is true for the reaction A + B → C + D if its Keq for the reaction is 104? a. When the reaction has reached equilibrium, there will be significantly more A and B than C and D in the solution. b. The formation of A and B will proceed at a high rate. c. The value of ΔG'° will be large and positive. d. All of the statements are true. e. None of the statements is true.

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Chap 13_8e 14. Which atom is a possible nucleophile? a. oxygen atom in a hydroxide ion b. oxygen atom of a carboxylate group c. nitrogen atom of a deprotonated amine d. All of the answers are correct. e. None of the answers is correct. 15. Which atom is a common electrophile? a. hydrogen atom b. oxygen atom of a carbonyl group c. oxygen atom of a phosphate group d. oxygen atom of a hydroxide group e. phosphorus of a phosphate group 16. For the reaction, ΔG'° = +29.7 kJ/mol L-malate + NAD+ → oxaloacetate + NADH + H+ The reaction as written: a. can never occur in a cell. b. can occur in a cell only if it is coupled to another reaction for which ΔG'° is positive. c. can occur only in a cell in which NADH is converted to NAD+ by electron transport. d. cannot occur because of its large activation energy. e. may occur in cells at some concentrations of substrate and product. 17. The reaction A + B → C has a ΔG'° of –20 kJ/mol at 25°C. Starting under standard conditions, one can predict that: a. at equilibrium, the concentration of B will exceed the concentration of A. b. at equilibrium, the concentration of C will be less than the concentration of A. c. at equilibrium, the concentration of C will be much greater than the concentration of A or B. d. C will rapidly break down to A + B. e. when A and B are mixed, the reaction will proceed rapidly toward formation of C. 18. Which enzyme catalyzes phosphate transfer reactions between nucleotides? a. nucleoside diphosphate kinase b. creatine kinase c. adenylate kinase d. both nucleoside diphosphate kinase and adenylate kinase e. both creatine kinase and adenylate kinase

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Chap 13_8e 19. What is the correct order of substances in terms of electronegativity, greatest to least? a. H > C > N > S > O b. H > C > S > O > N c. O > S > N > C > H d. N > O > S > H > C e. O > N > S > C > H 20. In this reaction, which molecules are oxidants (oxidizing agents)? 1,3-bisphosphoglycerate + NADH + H+ → glyceraldehyde-3-phosphate + Pi + NAD+ a. 1,3-bisphosphoglycerate b. NADH c. H+ d. glyceraldehyde-3-phosphate e. NAD+ and H+ 21. Which statement is true? a. The rate of a reaction that generates NAD+ can be determined by measuring the rate of increase in absorbance at 340 nm. b. NADH and NADPH are classified as pyrimidine nucleotides due to the presence of the nicotinamide ring which resembles pyrimidine. c. NAD+ has a net charge of +1. d. In many cells, the ratio of NADP+ to NADPH is high, favoring the reduction of biomolecules. e. A phosphoanhydride bond links the two nucleotides in nicotinamide dinucleotides. 22. Biological oxidation-reduction reactions never involve: a. transfer of e– from one molecule to another. b. formation of free e– . c. transfer of H+ (or H3O+) from one molecule to another. d. formation of free H3O+. e. None of the answers is correct.

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Chap 13_8e 23. Which statement regarding redox reactions is true? a. NADH and FADH2 are major electron acceptors in the oxidation of fuel molecules. b. In biological redox reactions, the reduction always involves the loss of hydrogen. c. Biological redox reactions rarely need an enzyme catalyst. d. A redox reaction is spontaneous when the sum of the half-reaction potentials is negative. e. The Nernst equation relates the standard reduction potential of a redox pair to its actual reduction potential at any concentration of either the oxidized or reduced form of the species. 24. Which statement is true with respect to the change in free energy for a given reaction? a. ΔG is linearly proportional to the rate of the reaction. b. ΔG is a logarithmic function of the equilibrium constant. c. ΔG provides no information about the rate of the reaction. d. All of the statements are true. e. None of the statements is true. 25. Which phosphorylated amino acid is used by invertebrates in a similar manner that vertebrates use phosphocreatine? a. phosphocysteine b. phosphoarginine c. phosphohistidine d. phosphoaspartate e. phosphotyrosine 26. Which statement is false for the nicotinamide cofactors? a. The oxidized form is positively charged. b. The reduced form has a large extinction coefficient at 340 nm. c. The cellular concentrations of NAD+/NADH are usually near 1 picomolar. d. Oxidation-reduction reactions with nicotinamides usually involve hydride transfer. e. Enzymes transfer hydrides stereospecifically to one or the other side of the nicotinamide ring. 27. Which statement about Gibbs free energy is false? a. At equilibrium, the actual free energy is zero and ΔG'° = –RT ln K'eq. b. When the reactants are in excess of their equilibrium concentrations, the conversion of product to reactant is more likely to occur. c. The standard free energy of a redox reaction can be determined if the standard reduction potentials of both the products and reactants are known. d. The actual free energy depends on temperature; the standard free energy is a constant. e. None of the statements is false. Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 28. The ΔG'° values for the two reactions are given. oxaloacetate + acetyl-CoA + H2O → citrate + CoASH citrate synthase oxaloacetate + acetate → citrate citrate lyase What is the ΔG'° for the hydrolysis of acetyl-CoA?

ΔG'° = –32.2 kJ/mol

ΔG'° = –1.9 kJ/mol

acetyl-CoA + H2O → acetate + CoASH + H+ a. –34.1 kJ/mol b. –32.2 kJ/mol c. –30.3 kJ/mol d. +61.9 kJ/mol e. +34.1 kJ/mol 29. Which is different in the biochemist's thermodynamic conventions compared to the conventions used in chemistry or physics? a. The standard temperature is 25°C. b. The standard [H+] is 10–7 M; pH = 7.0. c. The value for ΔG'° is a constant. d. The initial concentration of each component is 1.0 M (components other than H+). e. The standard pressure is 1 atm. 30. Which is the MOST oxidized carbon atom in a ketohexose sugar? a. C-1 b. C-2 c. C-3 d. C-5 e. C-6

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Chap 13_8e 31. For the reaction A → B, ΔG'° = –60 kJ/mol. The reaction is started with 10 mM A; no B is initially present. After 24 hours, analysis reveals the presence of 2 mM of B, 8 mM of A. Which statement is the MOST likely explanation? a. A and B have reached equilibrium concentrations. b. An enzyme has shifted the equilibrium toward A. c. B formation is kinetically slow; equilibrium has not been reached in 24 hours. d. Formation of B is thermodynamically unfavorable. e. The result described is impossible, given the fact that ΔG'° is –60 kJ/mol. 32. In this reaction, which molecule is the reductant (reducing agent)? 1,3-bisphosphoglycerate + NADH + H+ → glyceraldehyde-3-phosphate + Pi + NAD+ a. 1,3-bisphosphoglycerate b. NADH and NAD+ c. H+ d. Pi e. NADH 33. During glycolysis, glucose 1-phosphate is converted to fructose 6-phosphate in two successive reactions: glucose 1-phosphate → glucose 6-phosphate glucose 6-phosphate → fructose 6-phosphate

ΔG'° = –7.1 kJ/mol ΔG'° = +1.7 kJ/mol

ΔG'° for the overall reaction is: a. –8.8 kJ/mol. b. –7.1 kJ/mol. c. –5.4 kJ/mol. d. +5.4 kJ/mol. e. +8.8 kJ/mol. 34. Which statement is true about biochemical oxidation-reduction reactions? a. They usually proceed through homolytic cleavage. b. During oxidation a compound gains electrons. c. Dehydrogenases typically remove two electrons and two hydrides. d. There are two commonly accessed oxidation states of carbon. e. Every oxidation must be accompanied by a reduction.

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Chap 13_8e 35. Which carbon atom is in the MOST reduced state? a. carbon in an alkyl group b. carbon in an aldehyde group c. carbon in a ketone group d. carbon in a carboxylic acid group e. carbon in an alcohol group 36. When a mixture of 3-phosphoglycerate and 2-phosphoglycerate is incubated at 25°C with phosphoglycerate mutase until equilibrium is reached, the final mixture contains six times as much 2-phosphoglycerate as 3phosphoglycerate. Which statement is MOST nearly correct, when applied to the reaction shown? (R = 8.315 J/mol · K; T = 298 K) 3-phosphoglycerate → 2-phosphoglycerate a. ΔG'° is –4.44 kJ/mol. b. ΔG'° is zero. c. ΔG'° is +12.7 kJ/mol. d. ΔG'° is incalculably large and positive. e. ΔG'° cannot be calculated from the information given. 37. The hydrolysis of ATP has a large negative ΔG'°; nevertheless it is stable in solution due to: a. entropy stabilization. b. ionization of the phosphates. c. resonance stabilization. d. the hydrolysis reaction being endergonic. e. the hydrolysis reaction having a large activation energy. 38. Under standard conditions, is the oxidation of free FADH2 by ubiquinone sufficiently exergonic to drive the synthesis of ATP? (F = 96.5 kJ/V · mol) ubiquinone + 2H++ 2e– → ubiquinol FAD + 2H++ 2e– → FADH2

E'° = 0.045 V E'° = –0.219 V

a. no, as oxidation of FADH2 by ubiquinone generates 33.6 kJ/mol b. no, as oxidation of FADH2 by ubiquinone generates 50.9 kJ/mol c. no, as oxidation of FADH2 by ubiquinone generates –25.5 kJ/mol d. yes, as oxidation of FADH2 by ubiquinone generates –33.6 kJ/mol e. yes, as oxidation of FADH2 by ubiquinone generates –50.9 kJ/mol Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 39. Which carbon atom is in the MOST oxidized state? a. carbon in an alkyl group b. carbon in a ketone group c. carbon in carbon dioxide d. carbon in a carboxylic acid group e. carbon in an alcohol group 40. ΔG'° for the hydrolysis of ATP is –30.5 kJ/mol. What effect will doubling ATP concentration have on the value of ΔG'° for ATP hydrolysis? a. It will make the value of ΔG'° more negative. b. It will make the value of ΔG'° less negative. c. There will be no change in the value of ΔG'°. d. It will make the value of ΔG'° more positive. e. It will make the value of ΔG'° less positive. 41. Which biochemical reaction is NOT used in the process of activating a biological molecule? a. Phosphoryl group transfer from ATP forming a new phosphoester linkage. b. Formation of a thioester bond by linking a molecule to coenzyme A. c. Pyrophosphoryl group transfer from ATP forming a new phosphodiester linkage. d. Adenylyl transfer from ATP by forming a new phosphodiester linkage. e. All these reactions may be involved. 42. The structure of NAD+ does NOT include: a. a flavin nucleotide. b. a phosphoanhydride bond. c. an adenine nucleotide. d. nicotinamide. e. two ribose residues. 43. The reaction ATP → ADP + Pi is an example of a(n) _____ reaction. a. homolytic cleavage b. internal rearrangement c. free radical d. group transfer e. oxidation-reduction

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Chap 13_8e 44. Which redox reaction(s) will NOT proceed as written if the initial concentrations of reactants and products are equal? I. pyruvate + NADH → lactate + NAD+ II. FADH2 + NAD+ → FAD + NADH + H+ III. succinate + NAD+ → fumarate + NADH + H+ IV. NADH + H+ + ubiquinone → NAD+ + ubiquinol V. cytochrome c-Fe3+ + cytochrome b-Fe2+ → cytochrome c-Fe2+ + cytochrome b-Fe3+ a. I and IV b. I, IV, and V c. II d. II and III e. IV and V 45. What is the ΔG'° for this reaction if the concentrations of glucose-6-phosphate and glucose-1-phosphate at equilibrium are 19 mM and 1 mM, respectively? (R = 8.315 J/ mol · K; T = 298 K) glucose-6-phosphate → glucose-1-phosphate a. 7.3 kJ/mol b. 7.6 kJ/mol c. –7.3 kJ/mol d. –7.6 kJ/mol e. ΔG'° cannot be determined from the information given. 46. Under standard conditions, is the oxidation of NADH by free FAD sufficiently exergonic to drive the synthesis of ATP? (F = 96.5 kJ/V · mol) NAD++ H++ 2e– → NADH FAD + 2H++ 2e– → FADH2

E'° = –0.320 V E'° = –0.219 V

a. no, as oxidation of NADH by FAD only generates –9.7 kJ/mol b. no, as oxidation of NADH by FAD only generates –19.5 kJ/mol c. no, as oxidation of NADH by FAD only generates 9.7 kJ/mol d. no, as oxidation of NADH by FAD only generates 19.5 kJ/mol e. yes, as oxidation of NADH by FAD generates –104.2 kJ/mol

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Chap 13_8e 47. Which molecule is NOT considered a universal electron carrier? a. NAD b. NADP c. FMN d. FAD e. AMP 48. Which atom is the MOST electronegative? a. C b. N c. P d. O e. S 49. For the reaction A → B, the Keq' is 104. If a reaction mixture originally is 1 mM in A and contains no B, which statement must be true? a. At equilibrium, there will be far more B than A. b. The rate of the reaction is very slow. c. The reaction requires coupling to an exergonic reaction in order to proceed. d. The reaction will proceed toward B at a very high rate. e. ΔG'° for the reaction will be large and positive. 50. In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change (ΔG'°) of 23.8 kJ/mol. Under what conditions encountered in a normal cell will the free-energy change (ΔG) be negative, enabling the reaction to proceed spontaneously to the right? a. In a cell the concentrations of products and reactants yield a low value of the mass-action ratio Q. b. The reaction will not go to the right spontaneously under any conditions because the ΔG'° is positive. c. The reaction will proceed spontaneously to the right if there is a high concentration of products relative to the concentration of fructose 1,6-bisphosphate. d. The reaction will proceed spontaneously to the right if there is a high concentration of enzyme to catalyze the reaction. e. None of these conditions is sufficient. 51. Which item is NOT electrophilic? a. proton b. sulfhydryl c. protonated imine d. carbonyl group e. phosphoryl group Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 52. Which statement is true for the equilibrium constant? a. The equilibrium constant is independent of the initial concentrations of reactants and products. b. When the equilibrium constant is greater than one, the standard free-energy change for the reaction favors production of reactants. c. The equilibrium constant does not vary with changes in pH. d. The equilibrium constant does not vary with changes in temperature. e. A relatively small change in the equilibrium constant is associated with a large change in the standard free-energy change. 53. If the equilibrium constant for the dissociation of lactic acid is 1.38 × 10–4, what is the ΔG'° for this reaction? (R = 8.315 J/mol · K; T = 298 K) a. 16.3 kJ/mol b. –16.3 kJ/mol c. 16.96 kJ/mol d. +22.0 kJ/mol e. –22.0 kJ/mol 54. Which statement is NOT true? a. The carbon adjacent to a carbonyl can be resonance stabilized to form a carbanion. b. A carbonyl carbon can be made more electrophilic by a nearby metal ion. c. The carbon adjacent to an imine can be resonance stabilized to form a carbanion. d. Decarboxylation of an α-keto acid goes through a carbocation intermediate. e. A Claisen ester condensation reaction goes through a carbanion intermediate. 55. The hydrolysis of phosphoenolpyruvate proceeds with a ΔG'° of about –62 kJ/mol. The greatest contributing factors to this reaction are the destabilization of the reactants by electrostatic repulsion and stabilization of the product pyruvate by: a. electrostatic attraction. b. ionization. c. polarization. d. resonance. e. tautomerization.

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Chap 13_8e 56. The standard free-energy changes for the reactions are given. phosphocreatine → creatine + Pi ATP → ADP + Pi

ΔG'° = –43.0 kJ/mol ΔG'° = –30.5 kJ/mol

What is the overall ΔG'° for this reaction? phosphocreatine + ADP → creatine + ATP a. –73.5 kJ/mol b. –12.5 kJ/mol c. +12.5 kJ/mol d. +73.5 kJ/mol e. ΔG'° cannot be calculated without Keq'. 57. Which statement is true regarding the actual free-energy change for a reaction? a. The actual free-energy change varies depending on the pathway by which the reaction occurs. b. When the standard free energy is large and positive, the reaction will never occur. c. The actual free energy varies depending on the standard free energy and the concentration of reactants and products. d. The actual free energy depends on the rate of the reaction and the presence of catalysts. e. None of the statements is true. 58. Which item is NOT nucleophilic? a. proton b. carbanion c. imidazole d. hydroxide e. carboxylic acid 59. Which amino acid residue's side chain is a nucleophile at pH 7? a. Pro b. Phe c. Lys d. Asp e. Val

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Chap 13_8e 60. Which conjugate redox pair is involved in biological oxidations? a. Fe2+ and Fe3+ b. NADP+ and NAD+ c. FMN and FADH2 d. succinate and fumarate e. both Fe2+ and Fe3+ and succinate and fumarate 61. Which compound has the largest negative value for the standard free-energy change (ΔG'°) upon hydrolysis? a. acetic anhydride b. glucose 6-phosphate c. glutamine d. glycerol 3-phosphate e. lactose 62. What is the equilibrium constant for a reaction with a standard free-energy change of +25 kJ/mol? (R = 8.315 J/mol · K; T = 298 K) a. –1.1 b. –10.1 c. 4.1 × 10–5 d. 10.1 e. 2.4 × 104 63. If the ΔG'° of the reaction A → B is –40 kJ/mol, under standard conditions the reaction: a. is at equilibrium. b. will never reach equilibrium. c. will not occur spontaneously. d. will proceed at a rapid rate. e. will proceed spontaneously from A to B. 64. Which atom is the LEAST electronegative? a. C b. N c. H d. O e. S

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Chap 13_8e 65. Under standard conditions, ATP can be used in phosphate-transfer reactions to generate which molecule? a. phosphocreatine b. glycerol-3-phosphate c. phosphoenolpyruvate d. 1,3-bisphosphoglycerate e. All of the answers are correct. 66. For the reaction A → B, the Keq' is 10–6. If a reaction mixture originally is 1 mM in both A and B, which statement must be true? a. At equilibrium, there will still be equal levels of A and B. b. The rate of the reaction is very slow. c. At equilibrium, the amount of A will greatly exceed the amount of B. d. The reaction will proceed toward B at a very high rate. e. ΔG'° for the reaction will be large and negative. 67. Given that the ΔG'° values for the hydrolysis of glucose 1-phosphate and glucose 6-phosphate are approximately –21 kJ/mol and –14 kJ/mol, respectively, which statement is true regarding the isomerization shown? glucose 1-phosphate → glucose 6-phosphate a. Under cellular conditions the direction of the reaction depends on the concentrations of glucose 1phosphate and glucose 6-phosphate. b. The overall rate of this reaction is relatively slow. c. An increase in entropy drives this reaction. d. The value of ΔG'° for this isomerization reaction is small and positive. e. All the statements are true for the isomerization reaction shown. 68. Acyl phosphates, phosphoesters, and phosphoanhydrides are compounds of significantly different phosphoryl group transfer potentials. Which choice correctly ranks these phosphorylated intermediates with respect to their phosphoryl group transfer potential from highest to lowest? a. 1,3-bisphosphoglycerate > adenosine triphosphate > glucose 1-phosphate b. glucose 1-phosphate > adenosine triphosphate > 1,3-bisphosphoglycerate c. adenosine triphosphate > 1,3-bisphosphoglycerate > glucose 1-phosphate d. adenosine triphosphate > glucose 1-phosphate > 1,3-bisphosphoglycerate e. 1,3-bisphosphoglycerate > glucose 1-phosphate > adenosine triphosphate

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Chap 13_8e 69. Which statement is false regarding the biochemical standard state? a. The [H+] is 10–7 M. b. The temperature is 28°C. c. All reactants and products are present at 1 M concentrations. d. The pressure is 1 atm. e. The concentration of water is essentially constant at 55.5 M. 70. Which statement is true regarding coupled reactions? a. The standard free-energy changes of the coupled reactions are additive, and their equilibrium constants are multiplicative. b. The coupled reactions must share a common intermediate. c. The free energy of the endergonic reaction must be greater in magnitude than the free energy of the exergonic reaction. d. The standard free-energy changes of the coupled reactions are additive, their equilibrium constants are multiplicative, and the coupled reactions must share a common intermediate. e. None of the statements is true. 71. Which factor does NOT contribute to the large, negative, free-energy change upon hydrolysis of high-energy compounds? a. electrostatic repulsion in the reactant b. low activation energy of forward reaction c. stabilization of products by extra resonance forms d. stabilization of products by ionization e. stabilization of products by solvation 72. The standard reduction potentials (E'°) for the half-reactions are given. E'° = +0.031 V fumarate + 2H+ + 2e– → succinate FAD + 2H+ + 2e– → FADH2

E'° = –0.219 V

If mixed together, succinate, fumarate, FAD, and FADH2, all at l M concentrations and in the presence of succinate dehydrogenase, what would happen initially? a. Fumarate and succinate would become oxidized; FAD and FADH2 would become reduced. b. Fumarate would become reduced; FADH2 would become oxidized. c. No reaction would occur because all reactants and products are already at their standard concentrations. d. Succinate would become oxidized; FAD would become reduced. e. Succinate would become oxidized; FADH2 would be unchanged because it is a cofactor.

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Chap 13_8e 73. The free energy of hydrolysis of phosphoenolpyruvate is –61.9 kJ/mol. Rationalize this large, negative value for ΔG'° in chemical terms.

74. Why is the actual free energy (ΔG) of hydrolysis of ATP in the cell different from the standard free energy (ΔG'°)?

75. Explain what is meant by the statement: "Standard free-energy changes are additive." Give an example of the usefulness of this additive property in understanding how cells carry out thermodynamically unfavorable chemical reactions.

76. If ΔE'° for an oxidation-reduction reaction is positive, will ΔG'° be positive or negative? What is the equation that relates ΔG'° and ΔE'°?

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Chap 13_8e 77. Alcohol dehydrogenase catalyzes this reversible reaction acetaldehyde + NADH + H+ → ethanol + NAD+ Use the information to answer the questions. E'° = –0.20 V acetaldehyde + 2H+ + 2e– → ethanol E'° = –0.32 V NAD+ + H+ + 2e– → NADH The Faraday constant, F, is 96.48 kJ/V · mol. (a) Calculate ΔG'° for the reaction as written. Show the worked equations. (b) Given the answer to (a), what is the ΔG'° for the reaction occurring in the reverse direction? (c) Which reaction (forward or reverse) will tend to occur spontaneously under standard conditions? (d) In the cell, the reaction actually proceeds in the direction that has a positive ΔG'°. Explain how this could be possible.

78. For each pair of ions or compounds, indicate which is the more highly reduced species. (a) Co2+/Co+ (b) glucose/CO2 (c) Fe3+/Fe2+ (d) acetate/CO2 (e) ethanol/acetic acid (f) acetic acid/acetaldehyde

79. Explain why each of these statements is false. (a) In a reaction under standard conditions, only the initial concentration of reactants are fixed at 1 M. (b) When ΔG'° is positive, Keq'> 1. (c) ΔG and ΔG'° mean the same thing. (d) When ΔG'° = 1.0 kJ/mol, Keq' = 1.

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Chap 13_8e 80. The standard free-energy change (ΔG'°) for ATP hydrolysis is –30.5 kJ/mol. ATP, ADP, and Pi are mixed together at initial concentrations of 1 M of each, then left alone until the reaction ADP + Pi → ATP has come to equilibrium. For each species (i.e., ATP, ADP, and Pi), indicate whether the equilibrium concentration will be equal to 1 M, less than 1 M, or greater than 1 M.

81. Consider the reaction A + B → C + D. If the equilibrium constant for this reaction is a large number (say, 10,000), what is known about the standard free-energy change (ΔG'°) for the reaction? Describe the relationship between Keq'and ΔG'°.

82. The expression ΔG = ΔG'° + RT ln Keq' for the actual free-energy change for the reaction A + B → C + D is incorrect. Why is it wrong, and what is the correct expression for the real free-energy change of this reaction?

83. What is the difference between ΔG and ΔG'° of a chemical reaction? Describe, quantitatively, the relationship between them.

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Chap 13_8e 84. Classify each of the starred * atoms as an electrophile or a nucleophile.

85. Glycerol 3-phosphate dehydrogenase catalyzes this reversible reaction glycerol 3-phosphate + NAD+ → NADH + H+ + dihydroxyacetone phosphate Given the standard reduction potentials below, calculate ΔG'° for the glycerol 3-phosphate dehydrogenase reaction, proceeding from left to right as shown. Show the worked equations. (The Faraday constant, F, is 96.48 kJ/V · mol.) E'° = –0.29 V dihydroxyacetone phosphate + 2e– + 2H+ → glycerol 3-phosphate E° = –0.32 V NAD+ + H+ + 2e– → NADH

86. The value of ΔG'° for the hydrolysis of a phosphoanhydride in ATP bonds becomes a larger magnitude negative number with increasing pH above 7.0. Explain why this occurs.

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Chap 13_8e 87. Explain in quantitative terms the circumstances under which this reaction can proceed. citrate → isocitrate ΔG'° = +13.3 kJ/mol

88. Explain the relationships among changes in the degree of order, the entropy, and the free energy that occur during a chemical reaction.

89. If a 0.1 M solution of glucose 1-phosphate is incubated with a catalytic amount of phosphoglucomutase, the glucose 1-phosphate is transformed to glucose 6-phosphate until equilibrium is reached. At equilibrium, the concentration of glucose 1-phosphate is 4.5 × 10–3 M and that of glucose 6-phosphate is 8.6 × 10–2 M. Set up the expressions for the calculation of Keq' and ΔG'° for this reaction (in the direction of glucose 6phosphate formation). (R = 8.315 J/mol · K; T = 298 K)

90. Given ΔG'° for each of these reactions 1. ATP → ADP + Pi ΔG'° = –30.5 kJ/mol 2. glucose 6-phosphate → glucose + Pi ΔG'° = –13.8 kJ/mol show how to calculate the standard free-energy change (ΔG'°) for the reaction 3. ATP + glucose → glucose 6-phosphate + ADP

91. In general, when ATP hydrolysis is coupled to an energy-requiring reaction, the actual reaction often consists of the transfer of a phosphate group from ATP to another substrate, rather than an actual hydrolysis of the ATP. Explain.

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Chap 13_8e 92. In glycolysis, the enzyme pyruvate kinase catalyzes this reaction phosphoenolpyruvate + ADP → pyruvate + ATP Given the information below, show how to calculate the equilibrium constant for this reaction. (R = 8.315 J/mol · K; T = 298 K) Reaction 1: ATP → ADP + Pi ΔG'° = –30.5 kJ/mol Reaction 2: phosphoenolpyruvate → pyruvate + Pi ΔG'° = –61.9 kJ/mol

93. The first law of thermodynamics states that the amount of energy in the universe is constant, but that the various forms of energy can be interconverted. Describe four different types of such energy transduction that occur in living organisms and provide one example for each.

94. What is oxidation? What is reduction? Can oxidation occur without a simultaneous reduction? Why or why not?

95. Lactate dehydrogenase catalyzes the reversible reaction pyruvate + NADH + H+ → lactate + NAD+ Given these facts (a) tell in which direction the reaction will tend to go if NAD+, NADH, pyruvate, and lactate were mixed, all at 1 M concentrations, in the presence of lactate dehydrogenase at pH 7; (b) calculate ΔG'° for this reaction. (The Faraday constant, F, is 96.48 kJ/V · mol.) Show the worked equations. E'° = –0.32 V NAD+ + H+ + 2e– →NADH E'° = –0.19 V pyruvate + 2H+ + 2e– → lactate

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Chap 13_8e 96. During transfer of two electrons through the mitochondrial respiratory chain, the overall reaction is NADH + 1/2 O2 + H+ → NAD+ + H2O For this reaction, the difference in reduction potentials for the two half-reactions (ΔE'°) is +1.14 V. Show how to calculate the standard free-energy change, ΔG'°, for the reaction. (The Faraday constant, F, is 96.48 kJ/V · mol.)

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Chap 13_8e Answer Key 1. e 2. c 3. b 4. a 5. d 6. c 7. e 8. a 9. d 10. d 11. a 12. d 13. e 14. d 15. e 16. e 17. c 18. d 19. e 20. a 21. e 22. b 23. e 24. c 25. b 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 27. b 28. c 29. b 30. b 31. c 32. e 33. c 34. e 35. a 36. a 37. e 38. e 39. c 40. c 41. c 42. a 43. d 44. d 45. a 46. b 47. e 48. d 49. a 50. a 51. b 52. a 53. d 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 55. e 56. b 57. c 58. a 59. d 60. e 61. a 62. c 63. e 64. c 65. b 66. c 67. a 68. a 69. b 70. d 71. b 72. b 73. The product of hydrolysis is enol pyruvate, which quickly tautomerizes to pyruvate. This keto-enol tautomerization stabilizes the products of hydrolysis relative to phosphoenolpyruvate, which cannot tautomerize. 74. The concentrations of the reactant (ATP) and the products (ADP and Pi) are not all equal to 1 M. The pH is not exactly equal to 7.0 (the standard pH) and the temperature is usually higher than the standard temperature of 25 ∘ C. 75. When two chemical reactions can be summed to give a third reaction, the standard free-energy change for the third reaction is the arithmetic sum of the standard free-energy changes of the other two reactions. Many possible examples may be given. 76. For a positive ΔE'°, the ΔG'° is negative; ΔG'° = –nF ΔE'°.

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Chap 13_8e 77. (a) ΔG'° = E'° (acceptor) – E'°(donor) = –0.20 V – (–0.32 V) = +0.12 V ΔG'° = –nFΔE'° = (–2)(96.48kJ/V ∙ mol)(0.12 V) = –23.2 kJ/mol (b) For the reverse reaction, ΔG'° = +23.2 kJ/mol. (c) The forward reaction will occur spontaneously. (d) A reaction for which ΔG'° is positive can occur if ΔG'° is negative. From the relationship

it is clear that if the concentration of product is kept very low (by its removal in a subsequent metabolic step), the logarithm term becomes negative and ΔG can have a negative value. 78. (a) Co+; (b) glucose; (c) Fe2+; (d) acetate; (e) ethanol; (f) acetaldehyde 79. (a) Both reactants and products are fixed at 1 M. (b) ΔG'° = –RT ln Keq' , so when ΔG'° < 0, the term –RT ln Keq' has a negative value and Keq' > 1. (c) ΔG'° is the difference in free energies of the products and reactants at standard conditions, and is a constant, characteristic of each chemical reaction. ΔG is the actual free-energy change and is a variable that depends on ΔG'°, the temperature, and the concentrations of all reactants and products.

(d) ΔG'° = –RT ln Keq' . When ΔG'° = 1, Keq' < 1. 80. At equilibrium, ATP < 1 M; ADP > 1 M; Pi > 1 M. 81. ΔG'° = –RT ln Keq'. If Keq' is a large (positive) number, the term –RT ln Keq' (and therefore ΔG'°) has a relatively large, negative value. 82. The correct expression is

Substitution of Keq' for the concentration term is valid only for the special case in which these concentrations represent the equilibrium concentrations. In this situation, ΔG = 0. 83. ΔG'° is the difference in free energies of the products and reactants at standard conditions. Thus, it is a physical constant, characteristic of each chemical reaction. ΔG is actual free-energy change for a system. It is a variable that depends on ΔG'°, the temperature, and the concentrations of all reactants and products

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Chap 13_8e 84. (a) Nucleophile (b) Electrophile (c) Electrophile (d) Nucleophile (e) Nucleophile 85. E'° ΔG'° ΔG'°

= E'° (electron acceptor) – E'°(electron donor) = –nFΔE'° = (–2)(96.48 kJ/V · mol)(–0.03 V) = +5.8 kJ/mol

86. There is increased electrostatic repulsion in the terminal phosphate group of ATP due to increased deprotonation as the pH increases and this is also an increase in the resonance stabilization of the inorganic phosphate product due to an increase in the deprotonation state. Furthermore, there is an increase in the entropy upon hydrolysis due to the release of a proton into a more basic solution. 87. A reaction for which ΔG'° is positive can proceed under conditions in which ΔG is negative. From the relationship

it is clear that if the concentration of product is kept very low (by its subsequent metabolic removal, for instance), the logarithmic term becomes negative and ΔG can then have a negative value. Note: Students may also explain that an endergonic reaction can proceed if it is coupled to another reaction that is exergonic, as such the net freeenergy change of the coupled reactions is negative. 88. Entropy is a measure of disorder. Thus, if there is an increase in order there is a decrease in entropy. The greater the entropy of a system, the smaller its free energy (assuming enthalpy is constant). Thus, an increase in entropy during a reaction will result in a decrease in free energy. 89. Keq' = [glucose 6-phosphate] [glucose 1-phosphate]

= 0.086 M = 19 0.0045 M

ΔG'° = –RT ln Keq' = –(8.315 J/mol · K)(298 K)(ln 19) = –7.3 kJ/mol 90. Reaction 3 is the sum of reaction 1 and the reversal of reaction 2. Because of the additivity of free-energy changes, the overall ΔG'° for reaction 3 is the sum of the free-energy changes for reaction 1 and the reversal of reaction 2: 1. ATP → ADP + Pi ΔG1 '° = –30.5 kJ/mol 2. glucose + Pi → glucose 6-phosphate ΔG2 '∘ = +13.8 kJ/mol 3. ATP + glucose → ADP + glucose 6-phosphate ΔG3 '° = ΔG1 '° + ΔG2 '∘ = (–30.5 + 13.8) kJ/mol = –16.7 kJ/mol 91. Hydrolysis of the ATP would result in the loss of most of the free energy as heat. In a transfer reaction, the gamma (third) phosphate of ATP is transferred to the reaction substrate to produce a high-energy phosphorylated intermediate, which can then form the product in an exergonic reaction. Copyright Macmillan Learning. Powered by Cognero.

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Chap 13_8e 92. The reaction is the sum of reaction 2 and the reverse of reaction 1. Therefore, ΔG'° = –31.4 kJ/mol. ΔG'° = –RT ln Keq' ln Keq' = –ΔG'°/RT ln Keq' = 31.4 kJ/mol/[(8.315 J/mol · K)(298 K)] ln Keq' = 12.672 Keq' = 3.19 × 105 93. Conversion of: - chemical to osmotic energy (ATP-driven active transport across a membrane) - electromagnetic to electrical energy (light-induced electron flow in chloroplasts) - chemical to electromagnetic energy (ATP-dependent photon emission in fireflies) - chemical to mechanical energy (ATP-driven muscle contraction) Other answers are possible. Note that this activity requires students to draw upon past knowledge as well as the current chapter. 94. Oxidation is the loss of electrons; reduction is the gain of electrons. Free electrons are unstable (do not occur), so whenever an electron is released by oxidation of some species, an electron must be accepted by reduction of another species. 95. ΔG'° = E'° (acceptor) – E'° (donor) = –0.19 V – (–0.32 V) = +0.13 V ΔG'° = –nFΔE'°= (–2)(96.48 kJ/V · mol)(0.13 V) ΔG'° = –25.1 kJ/mol 96. ΔG'° = –nF ΔE'° For reactions involving NADH, two electrons are transferred (n = 2). So ΔG'° = (–2)(96.48 kJ/V · mol)(1.14 V) = –220 kJ/mol.

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Chap 14_8e Indicate the answer choice that best completes the statement or answers the question. 1. In humans, gluconeogenesis: a. can result in the conversion of protein into blood glucose. b. helps to reduce blood glucose after a carbohydrate-rich meal. c. is activated by the hormone insulin. d. is essential in the conversion of fatty acids to glucose. e. requires the enzyme hexokinase. 2. When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase, the final mixture contains twice as much glucose 6-phosphate as fructose 6phosphate. Which statement is MOST nearly correct, when applied to the reaction shown (R = 8.315 J/mol · K and T = 298 K)? glucose 6-phosphate ⇋ fructose 6-phosphate a. ΔG'° is +1.7 kJ/mol. b. ΔG'° is –1.7 kJ/mol. c. ΔG'°is incalculably large and negative. d. ΔG'°is incalculably large and positive. e. ΔG'°is zero. 3. There is reciprocal regulation of glycolytic and gluconeogenic reactions interconverting fructose-6-phosphate and fructose-1,6-bisphosphate. Which statement about this regulation is NOT correct? a. Fructose-2,6-bisphosphate activates phosphofructokinase-1. b. Fructose-2,6-bisphosphate inhibits fructose-1,6-bisphosphatase. c. The fructose-1,6-bisphosphatase reaction is exergonic. d. The phosphofructokinase-1 reaction is endergonic. e. This regulation allows control of the direction of net metabolite flow through the pathway. 4. Which statement regarding glycolysis is true? a. Both substrate-level phosphorylation reactions in glycolysis are irreversible. b. The oxidation reaction in glycolysis produces two high-energy molecules. c. There are four isomerization reactions in glycolysis. d. One inorganic phosphate is consumed as a substrate for each glucose molecule metabolized via glycolysis. e. All of the statements are true.

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Chap 14_8e 5. What role(s) does ATP have with respect to PFK-1? a. only substrate b. substrate and allosteric activator c. only allosteric inhibitor d. substrate and allosteric inhibitor e. only allosteric activator 6. What is the net yield of ATP produced by the anaerobic fermentation of one molecule of sucrose in myocytes? a. two b. three c. four d. six e. eight 7. Which statement is false concerning glycolysis? a. It is activated by high [AMP]. b. It results in a net synthesis of ATP. c. It results in the synthesis of NAD+. d. Its rate is slowed by a high [NADH]/[NAD+] ratio. 8. Which enzyme acts in the pentose phosphate pathway? a. 6-phosphogluconate dehydrogenase b. aldolase c. glycogen phosphorylase d. phosphofructokinase-1 e. pyruvate kinase 9. The steps of glycolysis between glyceraldehyde 3-phosphate and 3-phosphoglycerate do NOT involve: a. ATP synthesis. b. catalysis by phosphoglycerate kinase. c. oxidation of NADH to NAD+. d. the formation of 1,3-bisphosphoglycerate. e. utilization of Pi.

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Chap 14_8e 10. What is the net yield of ATP produced by the anaerobic fermentation of one molecule of galactose to two molecules of lactate in myocytes? a. two b. three c. four d. six e. None of the answers is correct. 11. During strenuous exercise, the NADH formed in the glyceraldehyde 3-phosphate dehydrogenase reaction in skeletal muscle must be reoxidized to NAD+ if glycolysis is to continue. The MOST important reaction involved in the reoxidation of NADH is: a. dihydroxyacetone phosphate → glycerol 3-phosphate. b. glucose 6-phosphate → fructose 6-phosphate. c. isocitrate → α-ketoglutarate. d. oxaloacetate → malate. e. pyruvate → lactate. 12. Which method directly regulates PFK-1? a. feedback inhibition by fructose 2,6-bisphosphate b. feed forward activation by phosphoenolpyruvate c. allosteric activation by AMP d. its phosphorylation in response to glucagon signaling e. allosteric activation by citrate 13. Cellular isozymes of pyruvate kinase are allosterically inhibited by _____ concentrations of _____. a. high; AMP b. high; ATP c. high; citrate d. low; acetyl-CoA e. low; ATP 14. Which substrate cannot contribute to net gluconeogenesis in mammalian liver? a. alanine b. glutamate c. palmitate d. pyruvate e. α-ketoglutarate

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Chap 14_8e 15. In comparison with the resting state, actively contracting human muscle tissue has a: a. higher concentration of ATP. b. higher rate of lactate formation. c. lower consumption of glucose. d. lower rate of consumption of oxygen e. lower ratio of NADH to NAD+. 16. Which statement about gluconeogenesis in animal cells is true? a. A rise in the cellular level of fructose 2,6-bisphosphate stimulates the rate of gluconeogenesis. b. An animal fed a large excess of fat in the diet will convert any fat not needed for energy production into glycogen to be stored for later use. c. The conversion of fructose 1,6-bisphosphate to fructose 6-phosphate is not catalyzed by phosphofructokinase-1, the enzyme involved in glycolysis. d. The conversion of glucose 6-phosphate to glucose is catalyzed by hexokinase, the same enzyme involved in glycolysis. e. The conversion of phosphoenolpyruvate to 2-phosphoglycerate occurs in two steps, including a carboxylation. 17. Which statement about gluconeogenesis is false? a. For starting materials, it can use carbon skeletons derived from certain amino acids. b. It consists entirely of the reactions of glycolysis, operating in the reverse direction. c. It employs the enzyme glucose 6-phosphatase. d. It is one of the ways that mammals maintain normal blood glucose levels between meals. e. It requires metabolic energy (ATP or GTP). 18. The first reaction in glycolysis that results in the formation of an energy-rich compound is catalyzed by: a. glyceraldehyde 3-phosphate dehydrogenase. b. hexokinase. c. phosphofructokinase-1. d. phosphoglycerate kinase. e. triose phosphate isomerase. 19. The metabolic function of the pentose phosphate pathway is to: a. act as a source of ADP biosynthesis. b. generate NADPH and pentoses for the biosynthesis of fatty acids and nucleic acids. c. participate in oxidation-reduction reactions during the formation of H2O. d. provide intermediates for the citric acid cycle. e. synthesize phosphorus pentoxide.

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Chap 14_8e 20. The compound [18F]2-fluoro-2-deoxyglucose is a(n): a. intermediate in glycolysis. b. positive regulator of glycolysis. c. potent anticancer agent. d. antibiotic. e. imaging agent used to detect tumors. 21. Which statement about the pentose phosphate pathway is correct? a. It generates 36 molecules of ATP per molecule of glucose consumed. b. It generates 6 molecules of CO2 for each molecule of glucose consumed. c. It is a reductive pathway; it consumes NADH. d. It is present in plants, but not in animals. e. It provides precursors for the synthesis of nucleotides. 22. The anaerobic conversion of one molecule of glucose to two molecules of lactate by fermentation is accompanied by a net gain of: a. one molecule of ATP. b. one molecule of NADH. c. two molecules of ATP. d. two molecules of NADH. e. None of the answers is correct. 23. Which amount of ATP and NADH identifies net production when one molecule of DHAP is converted to one molecule of pyruvate? a. two molecules of ATP and two molecules of NADH b. two molecules of ATP and one molecule of NADH c. two molecules of ATP and zero molecules of NADH d. one molecule of ATP and two molecules of NADH e. one molecule of ATP and zero molecules of NADH

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Chap 14_8e 24. Which statement does NOT describe a general function of the pentose phosphate pathway? a. The pentose phosphate pathway is used to produce NADPH for reductive biosynthesis in adipocytes. b. The pentose phosphate pathway is used to facilitate the elimination of dangerous peroxides in erythrocytes. c. The pentose phosphate pathway allows for the entry of dietary pentose intermediates into the glycolytic pathway. d. The pentose phosphate pathway allows for the conversion of hexoses into pentoses that may be used as precursors in the synthesis of nucleosides. e. The pentose phosphate pathway produces reduced molecules whose electrons may be shuttled to the mitochondria for oxidative phosphorylation. 25. The conversion of one molecule of fructose 1,6-bisphosphate to two molecules of pyruvate by the glycolytic pathway results in a net formation of _____ molecule(s) of _____ and _____ molecule(s) of ATP. a. one; NAD+; two b. one; NADH; one c. two; NAD+; four d. two; NADH; two e. two; NADH; four 26. In the alcoholic fermentation of glucose by yeast, thiamine pyrophosphate is a coenzyme required by: a. aldolase. b. hexokinase. c. lactate dehydrogenase. d. pyruvate decarboxylase. e. transaldolase. 27. What is the general name for an enzyme that catalyzes an intramolecular phosphoryl shift? a. phosphatase b. mutase c. kinase d. phosphorylase e. phosphate translocase 28. An enzyme used in both glycolysis and gluconeogenesis is: a. 3-phosphoglycerate kinase. b. glucose 6-phosphatase. c. hexokinase. d. phosphofructokinase-1. e. pyruvate kinase. Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_8e 29. Which products of glycolysis serve to store energy? a. fructose 1,6-bisphosphate b. ATP and NADH c. 1,3-bisphosphoglycerate and phosphoenolpyruvate d. fructose 1,6-bisphosphate, 1,3-bisphosphoglycerate, and phosphoenolpyruvate e. ATP, NADH, 1,3-bisphosphoglycerate, and phosphoenolpyruvate 30. Which reaction does NOT convert gluconeogenic precursors to the next step in gluconeogenesis? a. Glycerol is converted to dihydroxyacetone phosphate using the enzymes glycerol kinase and glycerol 3-phosphate dehydrogenase. b. Lactate is converted to alanine using lactate dehydrogenase. c. Alanine is converted to pyruvate using alanine aminotransferase. d. Glutamate is converted to α-ketoglutarate using either glutamate dehydrogenase or an aminotransferase. e. Pyruvate is carboxylated using bicarbonate and pyruvate carboxylase. 31. In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change (ΔG'°) of 23.8 kJ/mol. Under what conditions (encountered in a normal cell) will the free-energy change (ΔG) be negative, enabling the reaction to proceed to the right? a. If the concentrations of the two products are high relative to that of fructose 1,6-bisphosphate. b. The reaction will not go to the right spontaneously under any conditions because the ΔG'° is positive. c. Under standard conditions, enough energy is released to drive the reaction to the right. d. When there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of products. e. When there is a high concentration of products relative to the concentration of fructose 1,6bisphosphate. 32. Which statement is true for glycolysis? a. Pyruvate kinase phosphorylates pyruvate during glycolysis. b. Hexokinase catalyzes an unregulated step in glycolysis. c. A dehydration reaction generates a high-energy molecule. d. NADH is generated in an isomerization reaction. e. None of the statements is true.

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Chap 14_8e 33. Why is an anaerobic fate of pyruvate necessary in skeletal muscle? a. It is required to maintain the reducing environment of the cytosol. b. It allows for the reoxidation of NADH to NAD+, as NAD+ is in limited supply during anaerobic conditions. c. It decreases the pH of the skeletal muscle cell, thereby increasing release of oxygen from myoglobin. d. The anaerobic process directly generates additional ATP for working muscle tissue. e. None of the answers is correct. 34. If glucose, radioactively labeled in the C-2 position with 14C, is used as a substrate in a yeast extract maintained under strictly anaerobic conditions, what is the location of 14C in the product ethanol? a. 14CH3—CH2—OH b. CH3—14CH2—OH c. CH3—CHOH—14COO– d. It is released as 14CO2 by pyruvate decarboxylase and never becomes part of ethanol. e. It is released as 14CO2 by alcohol dehydrogenase and never becomes part of ethanol. 35. Hexokinase _____ predominates in the liver, and it requires a much _____ concentration of glucose to reach half-saturation as compared to hexokinases in myocytes (muscle cells). a. III; lower b. II; higher c. IV; higher d. I; lower e. V; higher 36. In humans, the Cori cycle shifts part of the metabolic burden of active muscle to the liver. Which two metabolic pathways are involved in this cycle? a. glycolysis and gluconeogenesis b. pentose phosphate pathway and gluconeogenesis c. glycolysis and the pentose phosphate pathway d. gluconeogenesis and the Calvin cycle e. None of the answers is correct.

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Chap 14_8e 37. Which statement is NOT true concerning glycolysis in anaerobic muscle? a. Fructose 1,6-bisphosphatase is one of the enzymes of the pathway. b. It is an endergonic process. c. It results in net synthesis of ATP. d. It results in synthesis of NADH. e. Its rate is slowed by a high [ATP]/[ADP] ratio. 38. In a tissue that metabolizes glucose via the pentose phosphate pathway, C-1 of glucose would be expected to end up principally in: a. carbon dioxide. b. glycogen. c. phosphoglycerate. d. pyruvate. e. ribulose 5-phosphate. 39. Which process is NOT involved in the steps of glycolysis between glyceraldehyde 3-phosphate and 3phosphoglycerate? a. a substrate-level phosphorylation reaction b. catalysis by an isomerase enzyme c. reduction of NAD+ to NADH d. the formation of a mixed anhydride intermediate e. the indirect coupling of reactions catalyzed by a kinase and a dehydrogenase enzyme 40. Gluconeogenesis must use "bypass reactions" to circumvent three reactions in the glycolytic pathway that are highly exergonic and essentially irreversible. Reactions carried out by which three of the enzymes listed must be bypassed in the gluconeogenic pathway? 1) Hexokinase 2) Phosphoglycerate kinase 3) Phosphofructokinase-1 4) Pyruvate kinase 5) Triosephosphate isomerase a. 1, 2, 3 b. 1, 2, 4 c. 1, 4, 5 d. 1, 3, 4 e. 2, 3, 4

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Chap 14_8e 41. The pentose phosphate pathway is multifunctional with metabolic flexibility. Which statement is false with respect to this pathway? a. All the enzymes in this pathway are located in the cytosol. b. All intermediates in this pathway are phosphorylated. c. The activities of transaldolases and transketolases link this pathway to gluconeogenesis. d. It generates NADH for reductive biosynthesis. e. In erythrocytes, this pathway is required to maintain glutathione in a reduced state. 42. If glucose labeled with 14C at C-2 were metabolized in the liver, the first radioactive pyruvate formed would be labeled in _____ carbon(s). a. all three b. both its carbonyl and carboxyl c. its carbonyl d. its carboxyl e. its methyl 43. Glycogen is converted to monosaccharide units by: a. glucokinase. b. glucose 6-phosphatase. c. glycogen phosphorylase. d. glycogen synthase. e. glycogenase. 44. In an anaerobic muscle preparation, lactate formed from glucose labeled in C-2 would be labeled in: a. all three carbon atoms. b. only the carbon atom carrying the OH. c. only the carboxyl carbon atom. d. only the methyl carbon atom. e. the methyl and carboxyl carbon atoms. 45. Which is a transcription factor that is involved in regulating the transcription of glycolytic or gluconeogenic enzymes? a. phosphofructokinase-2 b. carbohydrate response element binding protein c. sterol response element binding protein d. mRNA binding protein e. acetyl-CoA binding element

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Chap 14_8e 46. Which reaction in glycolysis is a ketose to aldose isomerization? a. hexokinase b. phosphoglycerate mutase c. enolase d. aldolase e. triose phosphate isomerase 47. Which enzyme or enzymes catalyze an energy-conserving reaction in glycolysis? a. hexokinase b. pyruvate kinase c. glyceraldehyde 3-phosphate dehydrogenase d. pyruvate kinase and glyceraldehyde 3-phosphate dehydrogenase e. hexokinase, pyruvate kinase, and glyceraldehyde 3-phosphate dehydrogenase 48. Inorganic fluoride inhibits enolase. In an anaerobic system that is metabolizing glucose as a substrate, which compound would be expected to increase in concentration following the addition of fluoride? a. 2-phosphoglycerate b. glucose c. glyoxylate d. phosphoenolpyruvate e. pyruvate 49. Which cofactor participates directly in MOST of the oxidation-reduction reactions in the fermentation of glucose to lactate? a. ADP b. ATP c. FAD/FADH2 d. glyceraldehyde 3-phosphate e. NAD+/NADH 50. Which item is a cofactor in the reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase? a. ATP b. Cu2+ c. heme d. NAD+ e. NADP+

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Chap 14_8e 51. Glucokinase (hexokinase IV) differs from hexokinase (hexokinase I): a. by having a higher affinity for glucose and not being inhibited by high levels of glucose. b. by requiring larger concentrations of glucose before reaching maximal activity. c. to allow the liver to export free glucose to the bloodstream when blood sugar levels drop. d. so that the liver does not compete with other tissues for glucose when glucose levels are high. e. to allow the pancreas to trigger insulin release when blood sugar levels are low. 52. Which reaction in glycolysis utilizes a covalent enzyme intermediate? a. phosphofructokinase-1 b. hexokinase c. phosphohexose isomerase d. aldolase e. triose phosphate isomerase 53. Which statement about the pentose phosphate pathway is NOT correct? a. It generates CO2 from C-1 of glucose. b. It involves the conversion of an aldohexose to an aldopentose. c. It is prominent in the lactating mammary gland. d. It is principally directed toward the generation of NADPH. e. It requires the participation of molecular oxygen. 54. In the phosphoglycerate mutase reaction, the side chain of which amino acid in the enzyme is transiently phosphorylated as part of the reaction? a. serine b. threonine c. tyrosine d. histidine e. arginine 55. The oxidation of three molecules of glucose by the pentose phosphate pathway may result in the production of _____ molecules of pentose, _____ molecules of NADPH, and _____ molecules of CO2. a. two; four; eight b. three; four; three c. three; six; three d. four; three; three e. four; six; six

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Chap 14_8e 56. Which process is NOT considered a general function of the pentose phosphate pathway? a. the production of NADPH for reductive biosynthesis in adipose cells b. the production of NADPH to help prevent oxidative stress in erythrocytes c. the production of pentoses necessary for nucleotide synthesis d. the production of erythrose 4-phosphate for synthesis of aromatic amino acids e. the transfer of electrons to NADP+ for eventual entry into the electron transport chain 57. Which statement is NOT correct? a. Aerobically, oxidative decarboxylation of pyruvate forms acetate (acetyl-CoA) that enters the citric acid cycle. b. In anaerobic muscle, pyruvate is converted to lactate. c. In yeast growing anaerobically, pyruvate is converted to ethanol. d. Reduction of pyruvate to lactate regenerates a cofactor essential for glycolysis. e. Under anaerobic conditions pyruvate does not form because glycolysis does not occur. 58. Which compound cannot serve as the starting material for the synthesis of glucose via gluconeogenesis? a. acetate b. glycerol c. lactate d. oxaloacetate e. α-ketoglutarate 59. Which reaction in glycolysis produces ATP as a product? a. hexokinase b. glyceraldehyde 3-phosphate dehydrogenase c. pyruvate kinase d. aldolase e. phosphofructokinase-1 60. Glucose breakdown in certain mammalian and bacterial cells can occur by mechanisms other than classic glycolysis. In MOST of these, glucose 6-phosphate is oxidized to 6-phosphogluconate, which is then further metabolized by: a. a type of aldolase split to form glyceric acid and glyceraldehyde 3-phosphate. b. a type of aldolase split to form glycolic acid and erythrose 4-phosphate. c. conversion to 1,6-bisphosphogluconate. d. decarboxylation to produce keto- and aldopentoses. e. oxidation to a six-carbon dicarboxylic acid.

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Chap 14_8e 61. Glucose labeled with 14C in C-1 and C-6 gives rise in glycolysis to pyruvate labeled in _____ carbon(s). a. both its carbonyl and carboxyl b. all three c. its carbonyl d. its carboxyl e. its methyl 62. Glycolysis is the name given to a metabolic pathway occurring in many different cell types. It consists of 11 enzymatic steps that convert glucose to lactic acid. Glycolysis is an example of: a. aerobic metabolism. b. anabolic metabolism. c. a net reductive process. d. fermentation. e. oxidative phosphorylation. 63. Which enzyme that is involved in the flow of carbon from glucose to lactate (glycolysis) is NOT also involved in the reversal of this flow (gluconeogenesis)? a. 3-phosphoglycerate kinase b. aldolase c. enolase d. phosphofructokinase-1 e. phosphoglucose isomerase 64. Which statement is true regarding the glycolytic pathway? a. It includes reactions catalyzed by three isomerase enzymes. b. It includes five phosphate transfer reactions. c. It includes three enzymes that are regulated by product inhibition. d. All of the statements are true. e. None of the statements is true. 65. Which reaction in glycolysis utilizes a covalent enzyme intermediate? a. phosphofructokinase-1 b. glyceraldehyde 3-phosphate dehydrogenase c. phosphohexose isomerase d. enolase e. triose phosphate isomerase

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Chap 14_8e 66. Which reaction in glycolysis requires ATP as a substrate? a. hexokinase b. glyceraldehyde 3-phosphate dehydrogenase c. pyruvate kinase d. aldolase e. phosphoglycerate kinase 67. Ethanol is produced by yeast under anaerobic conditions. This is accomplished by 2 reactions beyond the 10 reactions of glycolysis. What is the purpose served by these 2 reactions in the metabolism of yeast cells? a. They are required to reoxidize NADH. b. They are required to ensure a net oxidation of glucose. c. They are required to sustain gluconeogenesis. d. They are required to produce NADPH. 68. An increase in which compound leads to the dephosphorylation and activation of phosphofructokinase-2? a. glucagon b. xylulose 5-phosphate c. pyruvate d. citrate e. ADP 69. Which enzyme is used in both glycolysis and gluconeogenesis? a. 3-phosphoglycerate kinase b. hexokinase c. glucose 6-phosphatase d. phosphofructokinase-2 e. pyruvate kinase 70. Which compound links glycolysis and nucleotide synthesis? a. acetyl-CoA b. oxaloacetate c. citrate d. glucose 6-phosphate e. glucose 3-phosphate

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Chap 14_8e 71. In an anaerobic muscle preparation, lactate formed from glucose labeled in C-3 and C-4 would be labeled in: a. all three carbon atoms. b. only the carbon atom carrying the OH. c. only the carboxyl carbon atom. d. only the methyl carbon atom. e. the methyl and carboxyl carbon atoms. 72. The enzyme 2,3-BPG mutase produces 1,3-BPG in red blood cells through an isomerization (rearrangement) reaction. What amino acid(s) would you predict to be important in substrate binding? a. Asp b. Glu c. Lys d. Leu e. both Asp and Glu 73. Galactosemia is a genetic error of metabolism associated with: a. deficiency of galactokinase. b. deficiency of glucose 1-phosphatase. c. deficiency of UDP-glucose:galactose 1-phosphate uridylyltransferase. d. excessive ingestion of galactose. e. inability to digest lactose. 74. When six molecules of ribulose 5-phosphate are converted to pyruvate, how many molecules of ATP and NADH are produced? a. 4 molecules of ATP and 2 molecules of NADH b. 5 molecules of ATP and 3 molecules of NADH c. 8 molecules of ATP and 5 molecules of NADH d. 10 molecules of ATP and 5 molecules of NADH e. 10 molecules of ATP and 6 molecules of NADH 75. Which process does NOT occur in the steps of glycolysis between glyceraldehyde 3-phosphate and phosphoenolpyruvate? a. ATP synthesis b. an isomerization c. a hydration reaction d. phosphoryl transfer e. oxidation

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Chap 14_8e 76. _____ is a product (fate) of pyruvate in erythrocytes. a. CO2 + H2O b. Ethanol + CO2 c. Glucose d. Erythrose 4-phosphate e. Lactate 77. Which reaction in glycolysis is an aldose to ketose isomerization? a. enolase b. phosphoglycerate mutase c. phosphohexose isomerase d. aldolase e. glyceraldehyde 3-phosphate dehydrogenase 78. Glucose, labeled with 14C in different carbon atoms, is added to a crude extract of a tissue rich in the enzymes of the pentose phosphate pathway. The MOST rapid production of 14CO2 will occur when the glucose is labeled in: a. C-1. b. C-3. c. C-4. d. C-5. e. C-6. 79. Which compound(s) is a high-energy intermediate in glycolysis? a. fructose 1,6-bisphosphate b. NADH c. 1,3-bisphosphoglycerate and phosphoenolpyruvate d. fructose 1,6-bisphosphate, 1,3-bisphosphoglycerate, and phosphoenolpyruvate e. NADH, 1,3-bisphosphoglycerate, and phosphoenolpyruvate 80. When a muscle is stimulated to contract aerobically, less lactic acid is formed than when it contracts anaerobically because: a. glycolysis does not occur to a significant extent under aerobic conditions. b. muscle is metabolically less active under aerobic than anaerobic conditions. c. the lactic acid generated is rapidly incorporated into lipids under aerobic conditions. d. under aerobic conditions in muscle, the major energy-yielding pathway is the pentose phosphate pathway, which does not produce lactate. e. under aerobic conditions most of the pyruvate generated as a result of glycolysis is oxidized by the citric acid cycle rather than reduced to lactate. Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_8e 81. Which carbon atom in one of the glycolytic intermediates would have to be radiolabeled with 14C in order to ensure all the radioactivity would be released as 14CO2 during alcoholic fermentation? a. C-6 of glucose 6-phosphate b. C-3 of fructose 1,6-bisphosphate c. C-2 of pyruvate d. C-2 of glyceraldehyde 3-phosphate e. C-5 of fructose 6-phosphate 82. If glucose labeled with 14C in C-1 were fed to yeast carrying out the ethanol fermentation, where would the 14C label be in the products? a. in C-1 of ethanol and CO2 b. only in C-1 of ethanol c. only in C-2 (methyl group) of ethanol d. in C-2 of ethanol and CO2 e. only in CO2 83. The ultimate electron acceptor in the fermentation of glucose to ethanol is: a. acetaldehyde. b. acetate. c. ethanol. d. NAD+. e. pyruvate.

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Chap 14_8e 84. An extract of adipose (fat) tissue can metabolize glucose to CO2. When glucose labeled with 14C in either C-1 or C-6 was added to the extract, 14CO2 was released with the time courses shown. What is the major path of glucose oxidation in this extract? Explain how this conclusion is reached.

85. Briefly outline the pathway by which glucose activates the synthesis of pyruvate kinase.

86. Define "fermentation" and explain, by describing relevant reactions, how it differs from glycolysis. Include in the explanation a discussion of the role of NADH in the reaction(s).

87. There are a variety of fairly common human genetic diseases in which enzymes required for the breakdown of fructose, lactose, or sucrose are defective. However, there are very few cases of people having a genetic disease in which one of the enzymes of glycolysis is severely affected. Why are such mutations seen so rarely?

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Chap 14_8e 88. The yeast used in brewing the alcoholic beverage beer can break down glucose either aerobically or anaerobically using alcoholic fermentation. Explain why beer is brewed under anaerobic conditions.

89. The conversion of glyceraldehyde 3-phosphate to dihydroxyacetone phosphate is catalyzed by triose phosphate isomerase. The standard free-energy change (ΔG'°) for this reaction is –7.5 kJ/mol. Define the equilibrium constant for the reaction and calculate it using only the data given here (R = 8.315 J/mol · K; T = 298 K).

90. Briefly describe the possible metabolic fates of pyruvate produced by glycolysis in humans, and explain the circumstances that favor each.

91. In glycolysis there are two reactions that require one ATP each and two reactions that produce one ATP each. This being the case, how can fermentation of glucose to lactate lead to the net production of two ATP molecules per glucose?

92. At which point in glycolysis do C-3 and C-4 of glucose become chemically equivalent?

93. Does the regulation of PFK-1 affect the activity of hexokinase I in muscle tissue? Explain.

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Chap 14_8e 94. Explain with words, diagrams, or structures why lactate accumulates in the blood during bursts of very vigorous exercise (such as a 100-meter dash).

95. If you incubate 14C—CO2 with liver extracts capable of performing gluconeogenesis, where does the radioactive label end up?

96. Glyceraldehyde 3-phosphate that is labeled with 14C in a single carbon atom was added to a yeast cytoplasmic extract. After a short period of time, fructose 1,6-bisphosphate was produced that was labeled at C-3 and C-4. (a) What was the location of the radiolabeled carbon in the glyceraldehyde 3-phosphate molecule? (b) Where did the second 14C label of fructose 1,6-bisphosphate come from?

97. All of the intermediates in the glycolytic pathway are phosphorylated. Give two plausible reasons why this might be advantageous to the cell.

98. Under what circumstances does the bifunctional protein phosphofructokinase-2/fructose 2,6-bisphosphatase (PFK-2/FBPase-2) become phosphorylated, and what are the consequences of its phosphorylation to the glycolytic and gluconeogenic pathways?

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Chap 14_8e 99. When glucose is oxidized via glycolysis, the carbon atom that bears the phosphate in the 3-phosphoglycerate formed may have originally been either C-1 or C-6 of the original glucose. Describe this pathway in just enough detail to explain this fact.

100. What are the two reactions in glycolysis in which aldose to ketose isomerization is catalyzed by an enzyme? For both reactions the ΔG'° is positive. Briefly explain how the reactions are able to proceed without the input of additional energy.

101. Glucose is frequently administered to patients as a source of energy. Given that transformation of glucose to glucose 6-phosphate consumes energy in the form of ATP, why not administer glucose 6-phosphate?

102. Explain why Pi (inorganic phosphate) is absolutely required for glycolysis to proceed.

103. What would be the products of the reaction, if aldolase used glucose 6-phosphate instead of fructose 1,6bisphosphate? Based on the answer, suggest a possible rationale for why nature chose to include two extra steps prior to the aldolase step?

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Chap 14_8e 104. Rat liver is able to metabolize glucose by both the glycolytic and the pentose phosphate pathways. Indicate in the blanks if the properties are of the glycolytic pathway (G), pentose phosphate pathway (P), both (G + P), or neither (0). _____ NAD+ is involved. _____ CO2 is liberated. _____ Phosphate esters are intermediates. _____ Glyceraldehyde 3-phosphate is an intermediate. _____ Fructose 6-phosphate is an intermediate.

105. What is gluconeogenesis, and what useful purposes does it serve in people?

106. In the Cori cycle, actively contracting muscle cells convert pyruvate to lactate. The lactate is transported in the blood to the liver, where it is "recycled" by gluconeogenesis to glucose, which is transported back to the muscle for additional ATP production. Why do active muscle cells simply not export pyruvate, which can also be converted in the liver to glucose?

107. Describe the fate of pyruvate, formed by glycolysis in animal skeletal muscle, under two conditions: (a) at rest and (b) during an all-out sprint. Show enough detail in the answer to explain why pyruvate metabolism is different in these two cases.

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Chap 14_8e 108. If brewer's yeast is mixed with pure glucose in the absence of inorganic phosphate (Pi), no ethanol is produced. With the addition of a little Pi, ethanol production soon begins. Explain this observation in 25 words or less.

109. Describe the glycolytic pathway from glyceraldehyde 3-phosphate to pyruvate, showing structures of intermediates and names of enzymes. Indicate where any cofactors participate.

110. In the conversion of glucose to pyruvate via glycolysis, all of the enzymes listed participate. Indicate the order in which they function by numbering them. _____ hexokinase _____ triose phosphate isomerase _____ phosphohexose isomerase _____ enolase _____ glyceraldehyde 3-phosphate dehydrogenase _____ pyruvate kinase _____ phosphofructokinase-1 Which of the enzymes represents the most important regulation point in glycolysis? Which catalyzes a reaction in which ATP is produced? Which catalyzes a reaction in which NADH is produced?

111. In gluconeogenesis, how do animals convert pyruvate to phosphoenolpyruvate? Show structures, enzymes, and cofactors.

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Chap 14_8e 112. Describe the glycolytic pathway from glucose to glyceraldehyde 3-phosphate. Show structures of intermediates, enzyme names, and indicate where any cofactors participate.

113. During strenuous activity, muscle tissue demands large quantities of ATP, compared with resting muscle. In white skeletal muscle (in contrast with red muscle), ATP is produced almost exclusively by fermentation of glucose to lactate. If a person had white muscle tissue devoid of the enzyme lactate dehydrogenase, how would this affect the person's metabolism at rest and during strenuous exercise?

114. Explain why the phosphorolysis of glycogen is more efficient than the hydrolysis of glycogen in mobilizing glucose for the glycolytic pathway.

115. The bacterium E. coli can grow in a medium in which the only carbon source is glucose. How does this organism obtain ribose 5-phosphate for the synthesis of ATP? (Do not describe ATP synthesis, just the origin of ribose 5-phosphate.) Show structures and indicate where cofactors participate.

116. Explain the biochemical basis of the human metabolic disorder called lactose intolerance.

117. Two reactions in glycolysis produce ATP. For each of these, show the name and structure of reactant and product, indicate which cofactors participate, and name the enzymes involved.

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Chap 14_8e 118. What are the biological functions of the pentose phosphate pathway?

119. Show how NADH is recycled to NAD+ under aerobic conditions and under anaerobic conditions. Why is it important to recycle NADH produced during glycolysis to NAD+?

120. Both hexokinase IV and hexokinase I phosphorylate glucose at C-6. What properties of hexokinase IV make it important for maintaining stable blood sugar levels?

121. The conversion of glucose into glucose 6-phosphate, which must occur in the breakdown of glucose, is thermodynamically unfavorable (endergonic). How do cells overcome this problem?

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Chap 14_8e 122. Yeast can metabolize D-mannose to ethanol and CO2. In addition to the glycolytic enzymes, the only other enzyme needed is phosphomannose isomerase, which converts mannose 6-phosphate to fructose 6phosphate. If mannose is converted to ethanol and CO2 by the most direct pathway, which of the compounds and cofactors in this list are involved? A. Lactate B. Acetaldehyde C. Acetyl-CoA D. FAD E. Glucose 6-phosphate F. Fructose 1-phosphate G. Pyruvate H. Lipoic acid I. Thiamine pyrophosphate J. Dihydroxyacetone phosphate

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Chap 14_8e Answer Key 1. a 2. a 3. d 4. b 5. d 6. c 7. c 8. a 9. c 10. a 11. e 12. c 13. b 14. c 15. b 16. c 17. b 18. a 19. b 20. e 21. e 22. c 23. b 24. e 25. e 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_8e 27. b 28. a 29. b 30. b 31. d 32. c 33. b 34. b 35. c 36. a 37. b 38. a 39. b 40. d 41. d 42. c 43. c 44. b 45. b 46. e 47. d 48. a 49. e 50. d 51. b 52. d 53. e 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_8e 55. c 56. e 57. e 58. a 59. c 60. d 61. e 62. d 63. d 64. a 65. b 66. a 67. a 68. b 69. a 70. d 71. c 72. c 73. c 74. c 75. c 76. e 77. c 78. a 79. c 80. e 81. b 82. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 14_8e 83. a 84. The tissue must be oxidizing glucose primarily by the pentose phosphate pathway in which C-1 is released (as CO2) earlier than C-6. During glycolysis, C-1 and C-6 become equivalent at the level of glyceraldehyde 3-phosphate, and C-1 and C-6 are thus released simultaneously (during passage of acetate through the citric acid cycle). 85. Glucose is taken up by the cell and converted to xylulose 5-phosphate, which in turn activates protein phosphatase 2A (PP2A). PP2A dephosphorylates carbohydrate response element binding protein (ChREBP) in the cytosol. ChREBP is then taken up into the nucleus where it is further dephosphorylated by PP2A. ChREBP then forms a complex with Mlx to upregulate the transcription of the gene encoding pyruvate kinase. 86. Fermentation is the operation of the glycolytic pathway under anaerobic conditions. Under aerobic conditions, the pyruvate produced by glycolysis is oxidized to acetyl-CoA, which passes through the citric acid cycle. NADH produced in the oxidations passes electrons to O2, and is thus recycled to NAD+ allowing the continuation of the glycolytic reactions. When no O2 is available to reoxidize the NADH produced by the glyceraldehyde 3phosphate dehydrogenase reaction, electrons from NADH must be passed to one of the products of glycolysis, such as pyruvate or acetaldehyde, forming lactate or ethanol. 87. The glycolytic pathway is so central to all of cellular metabolism that mutations in glycolytic enzymes are lethal; embryos with such mutations would not survive. 88. Since aerobic breakdown of glucose yields more energy than fermentation, in the presence of oxygen, yeast cells would not carry out fermentation and no alcohol would be produced. Under anaerobic conditions, the yeast ferment the glucose to carbon dioxide and ethanol, both of which are key ingredients in beer.

89.

(See also Chapter 13.) 90. Under aerobic conditions, pyruvate is oxidized to acetyl-CoA and passes through the citric acid cycle. Under anaerobic conditions, pyruvate is reduced to lactate to recycle NADH to NAD+, allowing the continuation of glycolysis.

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Chap 14_8e 91. The two reactions that produce ATP in glycolysis (those catalyzed by phosphoglycerate kinase and pyruvate kinase) involve three-carbon compounds, whereas the two reactions that consume ATP occur at the level of hexoses. In glycolysis, each hexose yields two trioses, each of which undergoes the reactions that yield ATP. The ATP yield for triose reactions therefore must be doubled for stoichiometric comparison with the ATPs consumed in hexose phosphorylation. Two ATP molecules are consumed and four are produced for each glucose that passes through the pathway, resulting in a net yield of two ATP per glucose. 92. When dihydroxyacetone phosphate is converted into glyceraldehyde 3-phosphate by triose phosphate isomerase, C-3 and C-4 of glucose become equivalent; they are both C-1 of glyceraldehyde 3-phosphate. (See Fig. 14-6.) 93. Yes. Inhibition of PFK-1 will lead to a buildup of glucose 6-phosphate. Hexokinase I, which is found in skeletal muscle, is inhibited by glucose 6-phosphate. 94. During vigorous exercise, the cardiovascular system cannot deliver O2 to the muscle tissue fast enough to maintain aerobic conditions. As glycolysis proceeds under anaerobic conditions, NAD+ is converted to NADH (during the glyceraldehyde 3-phosphate dehydrogenase reaction), but the muscle tissue has no O2 to which NADH can pass electrons. To recycle NADH to NAD+, which is essential for continuing glycolysis, electrons from NADH are used to reduce pyruvate to lactate. 95. It ends up in CO2 again. After being attached to pyruvate, to form oxaloacetate, the label is released as CO2 again in the formation of PEP. 96. (a) C-1 of the glyceraldehyde 3-phosphate molecule. (b) C-1 of a dihydroxyacetone phosphate molecule that was formed by the isomerization of the glyceraldehyde 3-phosphate molecule. 97. There are at least three reasons: (1) so they will not cross the plasma membrane and be lost; (2) the resulting highenergy phosphoryl groups can be transferred directly to ADP to make ATP; and (3) the high binding energy of the ionic interactions between the (–) charged phosphoryl groups and (+) charged enzyme side chains helps to stabilize the enzyme-substrate interaction. 98. Glucagon, signaling low blood sugar, stimulates cAMP synthesis, which activates protein kinase A to phosphorylate PFK-2/FBPase-2 (among other proteins). This phosphorylation enhances FBPase-2 activity and inhibits PFK-2 activity of the enzyme, resulting in lower levels of fructose 2,6-bisphosphate (F26BP). In the absence of F26BP as an allosteric effector, the activity of PFK-1 is reduced (inhibiting glycolysis) and the activity of FBPase-1 is enhanced (stimulating gluconeogenesis), thus enabling the liver to replenish blood glucose. See Figures 14-22 and 14-23. 99. The 3-phosphoglycerate derived from glucose by glycolysis is formed from glyceraldehyde 3-phosphate. The action of aldolase on fructose 1,6-bisphosphate produces dihydroxyacetone phosphate (derived from C-1, C-2, and C3 of glucose) and glyceraldehyde 3-phosphate (derived from C-4, C-5, and C-6 of glucose). When triose phosphate isomerase then converts dihydroxyacetone phosphate to glyceraldehyde 3-phosphate, C-3 of glyceraldehyde 3-phosphate will contain both C-1 and C-6 from glucose. (See Fig. 14-6.)

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Chap 14_8e 100. The two reactions are those catalyzed by phosphohexose isomerase and triose phosphate isomerase: glucose 6-phosphate (aldose) ⇋ fructcose 6-phosphate (ketose) dihydroxyacetone phosphate (ketose) ⇋ glyceraldehyde 3-phosphate (aldose) Although both of these reactions have standard free-energy changes (ΔG'°) that are positive, they can occur within cells because the products are immediately removed by the subsequent steps in the pathway. The result is a very low steady-state concentration of the products, making the actual free-energy changes (ΔG) negative: ΔG = ΔG'° + RT ln ([products]/[substrates]) 101. There are no transporters for glucose 6-phosphate in the plasma membrane, hence the glucose 6-phosphate would not be taken up by cells. 102. Pi is an essential substrate in the reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase. 103. Based on the chemical requirements of an aldol cleavage, you must cleave such that the "carbanion" ends up added to the C = O, which would now be the aldehyde instead of the ketone. Therefore, the products would be asymmetrical (two different products; one with two carbons, one with four carbons) if isomerization to and phosphorylation of F-6-P did not occur. You might then need twice as many enzymes to break down the two different "halves" instead of having one common pathway. Also, the two-carbon unit would not have a phosphate attached, and therefore be prone to diffusion out of the cell.

104. G, P, G + P, G, G 105. Gluconeogenesis is the biosynthesis of glucose from simpler, noncarbohydrate precursors such as oxaloacetate or pyruvate. During periods of fasting, when carbohydrate reserves have been exhausted, gluconeogenesis provides glucose for metabolism in tissues (brain, erythrocytes) that derive their energy primarily from glucose metabolism. 106. Muscle contracting anaerobically must retain pyruvate so that it can be reduced to lactate and regenerate NAD+, which is required for continued glycolysis, and the production of ATP during low oxygen conditions.

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Chap 14_8e 107. (a) At rest, plenty of O2 is being delivered to the muscle, and pyruvate formed during glycolysis is oxidized to acetyl-CoA by the pyruvate dehydrogenase complex. Acetyl groups then enter the citric acid cycle and are oxidized to CO2. (b) Under the conditions of all-out exertion, skeletal muscle cannot be supplied with enough O2 to keep metabolism completely aerobic; under these conditions, muscle tissue must function anaerobically. Pyruvate is reduced to lactate to recycle NADH, formed by glycolysis, to NAD+ so that glycolysis can continue. 108. The reaction catalyzed by glyceraldehyde 3-phosphate dehydrogenase requires Pi as a substrate. Without Pi, glycolysis ceases, and no ethanol is produced. 109. The answer should show the reactions catalyzed by glyceraldehyde 3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, and pyruvate kinase. (See Fig. 14-2.) 110. 1, 4, 2, 6, 5, 7, 3; phosphofructokinase-1; pyruvate kinase; glyceraldehyde 3-phosphate dehydrogenase 111. Pyruvate is converted into phosphoenolpyruvate in two steps: (1) Pyruvate + HCO-3 + ATP → oxaloacetate + ADP + Pi (2) Oxaloacetate + GTP ⇋ CO2 +GDP + phosphoenolpyruvate The first reaction is catalyzed by pyruvate carboxylase, which requires biotin as a cofactor; the second, by phosphoenolpyruvate carboxykinase. (See Figs 14-17 and 14-18.) 112. This part of the pathway involves the reactions catalyzed by hexokinase, phosphohexose isomerase, phosphofructokinase-1, aldolase, and triose phosphate isomerase. (See Fig. 14-2.) 113. Lactate dehydrogenase allows cells to pass electrons from NADH to pyruvate, thus regenerating NAD+ for continued glycolysis under anaerobic conditions. The lack of this enzyme would cause no significant problems at rest because aerobic red muscle tissue would function well. During strenuous exercise, however, the absence of lactate dehydrogenase would severely reduce the ability of muscle to perform anaerobically. 114. Phosphorolysis yields glucose 1-phosphate, which can be converted into glucose 6-phosphate without the investment of energy from ATP. Hydrolysis of glycogen yields free glucose, which must be converted into glucose 6-phosphate (at the expense of ATP) before it can enter glycolysis. 115. Ribose 5-phosphate is produced from glucose by the reactions of the pentose phosphate pathway. (See Fig. 1429.) 116. In lactose intolerance, the enzyme lactase, found in the surface of intestinal epithelial cells in children, has been lost in adulthood. Without this enzyme, the individual cannot hydrolyze lactose in the small intestine and take up the resulting monosaccharides; instead, lactose passes into the large intestine, where it is metabolized by bacteria, producing gastric distress. 117. The two reactions are those catalyzed by phosphoglycerate kinase and pyruvate kinase. 118. The pentose phosphate pathway produces pentose phosphates (for nucleotide synthesis) and NADPH (reducing agent for biosynthetic processes).

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Chap 14_8e 119. Cells contain a limited supply of NAD+ and NADH. The oxidation of glyceraldehyde 3-phosphate requires NAD+ as an electron acceptor—it converts NAD+ to NADH. Unless this NADH is recycled to NAD+, oxidative metabolism in this cell will cease for lack of an electron acceptor. Under aerobic conditions, NADH passes electrons to O2; under anaerobic conditions, NADH reduces pyruvate to lactate, and is thereby recycled to NAD+. 120. Hexokinase IV has a high Km (low affinity) for glucose. When blood glucose levels rise, GLUT2 transporters will transport glucose into hepatocytes, where hexokinase IV will catalyze the phosphorylation of glucose to glucose 6-phosphate. This has the effect of keeping cellular glucose levels low, allowing for continued cellular uptake and a concomitant reduction in blood glucose levels. As hexokinase IV has a low affinity for glucose, it prevents the liver from using large amounts of glucose when blood sugar levels are low and in short supply, ensuring glucose is available for tissues that depend on glucose. Furthermore, hexokinase IV is not inhibited by its product; therefore, the higher the concentration of glucose, the faster hexokinase IV phosphorylates it. This allows the hepatocyte to keep its glucose concentrations relatively low, permitting continued transport by GLUT2 transporters when blood glucose levels are high. Hexokinase IV in beta pancreatic cells is used to sense high blood glucose levels. This enzyme plays a critical role in the release of insulin by the pancreas in response to high blood glucose levels. 121. Cells often drive a thermodynamically unfavorable reaction in the forward direction by coupling it to a highly exergonic reaction through a common intermediate. In this example, to make glucose 6-phosphate formation thermodynamically favorable, cells transfer phosphoryl groups from ATP to glucose. ATP "hydrolysis" is highly exergonic, making the overall reaction exergonic. (Numerical solution shown is not required.) glucose + Pi ⇋ flucose 6-phosphate + H2O ΔG'° = +13.8 kJ/mol ATP + H2O ⇋ ADP + Pi ΔG'° = –30 kJ/mol Sum: ATP + H2O ⇋ ADP + Pi ΔG'° = –16.7 kJ/mol (See also Chapter 13.) 122. B, G, I, J

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Chap 15_8e Indicate the answer choice that best completes the statement or answers the question. 1. Starting from glucose, what is the net number of nucleotide triphosphate molecules used in the synthesis of glycogen? a. zero b. one c. two d. three e. four 2. Which statement describes possible fates for glucose 1-phosphate in skeletal muscle? a. Glucose 1-phosphate can enter glycolysis or replenish blood glucose. b. Glucose 1-phosphate can be the substrate for UDP-glucose pyrophosphorylase to make substrate for glycogen synthase. c. The phosphate of glucose 1-phosphate can be used to phosphorylate glycogen phosphorylase. d. Glucose 1-phosphate can be used to add a glucosyl unit to UMP to produce UDP-glucose. 3. Which statement is true of glycogen phosphorylase? a. Glycogen phosphorylase is encoded by a single gene for both liver and muscle enzymes. b. Glucagon initiates a cascade that inhibits phosphorylase b kinase. c. Phosphorylation to activate the enzyme occurs at a threonine residue. d. The phosphorylated active (a) form is produced by covalent modification. e. In muscle tissue, AMP inhibits the activity of glycogen phosphorylase. 4. Protein kinase A (PKA) stimulates glycogen breakdown. Which molecular signal activates PKA? a. decrease in [AMP] b. increase in [insulin] c. increase in [cAMP] d. high blood glucose e. low [UDP] 5. Which enzyme does NOT play a role in glycogen metabolism? a. glucose 6-phosphatase b. fructose 1,6-bisphosphatase c. glycosyl (4 → 6) transferase d. protein phosphatase 1 e. phosphoglucomutase

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Chap 15_8e 6. Glycogen storage disease type 1a is associated with mutations in: a. glucose 6-phosphatase. b. phosphoglucomutase. c. pyruvate kinase. d. glycogen phosphorylase. 7. After ingestion of a carbohydrate-rich meal, the increased concentration of glucose in the blood is associated with many changes in the metabolism of humans. Which change would NOT be expected? a. a decrease in the secretion of glucagon from the pancreas b. an increase in glycogen phosphorolysis c. an increase in the levels of fructose 2,6-bisphosphate d. activation of phosphorylase b kinase e. All of these changes would be expected. 8. Which organ cannot use fatty acids as fuels for metabolic energy, and relies on a steady glucose supply for fuel? a. liver b. pancreas c. brain d. kidney e. There is no organ that cannot use fatty acids as fuels. 9. An altered version of glycogen synthase is produced in the laboratory with one of its amino acid residues substituted for another. Unlike normal glycogen synthase, the activity of the mutant protein is unaffected by glycogen synthase kinase 3. Which mutation is MOST likely to produce this effect? a. Cys→Ser b. Ile→Thr c. Ser→Ala d. Cys→Met e. Thr→Ser 10. Which statement is true of glycogen synthesis and breakdown? a. Phosphorylation activates the enzyme responsible for breakdown, and inactivates the enzyme responsible for synthesis. b. Synthesis is catalyzed by the same enzyme that catalyzes breakdown. c. The glycogen molecule "grows" at its reducing end. d. The immediate product of glycogen breakdown is free glucose. e. Under normal circumstances, glycogen synthesis and glycogen breakdown occur simultaneously and at high rates. Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_8e 11. The breakdown of glycogen to glucose 1-phosphate is called: a. neoglycogenesis. b. deglycogenization. c. glycogen anabolism. d. glycogenolysis. 12. In glycogen _____ glycosidic bonds occur at branch points, while all others are _____ glycosidic bonds. a. (β1 → 4); (α1 → 4) b. (α1 → 6); (α1 → 4) c. (α1 → 4); (α1 → 6) d. (β1 → 6); (α1 → 4) e. All glycosidic bonds in glycogen are (α1 → 4). 13. Is glycogen phosphorylase activated, inhibited, or unaffected in response to an insulin signal in skeletal muscle? a. activated b. inhibited c. unaffected 14. Glycogen phosphorylase a can be inhibited at an allosteric site by: a. AMP. b. calcium. c. GDP. d. glucagon. e. glucose. 15. In terms of the reaction mechanism, to which enzyme in glycolysis is phosphoglucomutase MOST similar? a. phosphohexose isomerase b. triosphosphate isomerase c. phosphoglycerate mutase d. enolase e. phosphoglycerate kinase 16. Mutating which protein(s) is likely to result in type Ia glycogen storage disease? a. glucose 6-phosphatase or T1 b. phosphorylase b kinase c. glycogen phosphorylase d. glycogenin e. protein kinase A

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Chap 15_8e 17. Glycogenin: a. catalyzes the conversion of starch into glycogen. b. is the enzyme responsible for forming branches in glycogen. c. is the gene that encodes glycogen synthase. d. is the primer on which new glycogen chains are initiated. e. regulates the synthesis of glycogen. 18. Which statement about mammalian glycogen synthase is NOT correct? a. It is especially predominant in liver and muscle. b. The donor molecule is a sugar nucleotide. c. The phosphorylated form of this enzyme is inactive. d. This enzyme adds glucose units to the nonreducing end of glycogen branches. e. This enzyme adds the initial glucose unit to a tyrosine residue in glycogenin. 19. The enzyme glycogen phosphorylase: a. catalyzes a cleavage of (β1 → 4) bonds. b. catalyzes a cleavage of (α1 → 4) bonds. c. is a substrate for a kinase. d. uses glucose 6-phosphate as a substrate. e. uses glucose as a substrate. 20. Which substance activates glycogen synthase b in liver? a. glucagon b. insulin c. glucose 6-phosphate d. both insulin and glucose 6-phosphate e. both glucagon and glucose 6-phosphate 21. Which statement is true for glycogen phosphorylase b? a. It catalyzes a phosphorolytic cleavage of (α1 → 6) glycosidic bonds. b. It catalyzes a hydrolytic cleavage of (α1 → 4) glycosidic bonds. c. It is regulated both allosterically and via covalent modification. d. It uses UDP-glucose as a substrate. e. It is an important blood glucose sensor in myocytes.

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Chap 15_8e 22. Epinephrine binding to β-adrenergic receptors on hepatocytes causes the eventual activation of protein kinase A (PKA). Which enzyme is a substrate for phosphorylation by PKA? a. phosphorylase a b. phosphorylase b kinase c. glycogen synthase b d. phosphoprotein phosphatase I e. pyruvate kinase 23. Which statement is true of the glycogen branching enzyme? a. It catalyzes glycogen degradation by removing glucose from the branch points. b. It catalyzes the lengthening of branches during glycogen synthesis. c. It catalyzes the addition of a glucose molecule to glycogenin. d. It is allosterically regulated by fructose 2,6-bisphosphate. e. It catalyzes the formation of an (α1 → 6) linkages during glycogen synthesis. 24. Glycogen is converted to monosaccharide units by: a. glucokinase. b. glucose 6-phosphatase c. glycogen phosphorylase. d. glycogen synthase. e. glycogenase. 25. Which enzyme phosphorylates three serines of glycogen synthase a to convert it to glycogen synthase b? a. AMP-activated protein kinase b. phosphoprotein phosphorylase 1 c. casein kinase II d. glycogen synthase kinase 3 e. insulin 26. What is the predominant source of glucose circulating in the bloodstream of a normal individual who is asleep at 3 AM? a. catabolism of even-chained fatty acids b. gluconeogenesis in the liver c. phosphorolysis of muscle glycogen d. glycogenolysis in the liver e. dietary carbohydrates

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Chap 15_8e 27. Which statement is NOT associated with controlling the rate of glycogen synthesis in muscle cells? a. Insulin stimulates the translocation of GLUT4 transporters to the plasma membrane. b. Insulin induces the synthesis of hexokinase I. c. Glucagon inhibits the activity of glycogen synthase via covalent modification. d. Epinephrine activates protein kinase A, resulting in an activation of glycogen phosphorylase kinase. e. Insulin inhibits the activity of glycogen synthase kinase 3. 28. Which is true about the core of glycogen granules in the liver? a. The core contains a glycogenin dimer. b. The core is composed of tightly wound glycogen helical structures. c. The single nonreducing end of glycogen is at the core. d. The core is the same as the rest of the granule; it is completely glycogen. 29. Is glycogen phosphorylase activated, inhibited, or unaffected in response to a glucagon signal in skeletal muscle? a. activated b. inhibited c. unaffected 30. The _____ tissues do NOT contribute glucose to the blood because they lack the enzyme _____. a. muscle and adipose; glucose 6-phosphatase b. kidney and adipose; glucose 6-phosphatase c. muscle and adipose; glycogen phosphorylase b d. muscle and liver; glycogen phosphorylase b 31. Which statement is true of glycogen synthase? a. It is activated by at least 11 different protein kinases. b. It is activated by Ca2+ ions in skeletal muscle. c. It catalyzes formation of (α1 → 4) glycosidic bonds. d. It uses glucose 1-phosphate as a substrate. e. All of the statements are true. 32. Animals store a great deal more energy in fats than in glycogen. Fats also store more energy per gram than glycogen. Which is a reason for having some energy stored in glycogen, rather than using fats alone? a. Glucose can be released very quickly from glycogen to provide energy. b. Glycogen is for longer-term energy storage for cases such as prolonged starvation. c. Glycogen can be transported in the blood more easily than fats. d. Energy released from glycogen is highly targeted for use in particular tissues associated with the lymphatic system. Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_8e 33. Glycogen phosphorylase removes glucose (as glucose 1-phosphate) from the _____ ends of glycogen chains until it is _____ a branch point. a. reducing; four glucose units from b. nonreducing; at c. nonreducing; four glucose units from d. reducing; at e. nonreducing; one glucose unit from 34. After a meal rich in carbohydrates, which change would NOT be expected in a normal human? a. increased secretion of the pancreatic hormone insulin b. increased activity of the liver enzyme hexokinase IV (glucokinase) c. increased glucose uptake in myocytes via GLUT4 transporters d. decreased activity of glycogen synthase kinase 3 in both myocytes and hepatocytes e. increased activity of glucose 6-phosphatase in hepatocytes 35. Muscle contraction is associated with elevated levels of cytosolic calcium. Which statement describes a consequence of this increase in calcium? a. Calcium is a divalent cation, which binds to ATP and reduces electrostatic repulsion between the phosphates. Glycogen is broken down to compensate for the decreased energy available from ATP hydrolysis. b. An increased level of calcium is associated with an increase in glycogen breakdown, as calcium is an allosteric activator of glycogen phosphorylase. c. Calcium activates phosphoprotein phosphatase 1, which in turn will stimulate glycogen synthesis by dephosphorylating phosphorylase b. d. An increased level of calcium is associated with an increase in glycogen breakdown, as calcium is an allosteric activator of phosphorylase b kinase. 36. In addition to phosphorylation, phosphorylase b kinase is activated by: a. insulin. b. increased ATP. c. calmodulin. d. cAMP. e. Ca2+.

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Chap 15_8e 37. Which metabolic effect is associated with AMP-activated protein kinase (AMPK)? a. When activated, AMPK stimulates insulin release from the pancreas. b. When activated, AMPK activates fructose 2,6-bisphosphatase. c. When activated, AMPK phosphorylates glycogen synthase, inhibiting glycogen synthesis during periods of metabolic stress d. When activated, AMPK both activates fructose 2,6-bisphosphatase and stimulates glucose uptake in cardiac and skeletal muscle. e. None of the answers is correct. 38. The action of which three enzymes are needed to release glucose from the outer branches of glycogen so that it may be used in glycolysis? a. protein kinase A; glycogen debranching enzyme; phosphoglucomutase b. protein kinase A; phosphoglucomutase; phosphoprotein phosphatase 1 c. glycogen phosphorylase; glycogen synthase; hexokinase IV d. glycogen synthase; glycogen synthase kinase 3; glycogen debranching enzyme e. glycogen phosphorylase; glycogen debranching enzyme; phosphoglucomutase 39. Which statement describes a characteristic of phosphoprotein phosphorylase 1 (PP1)? a. PP1 is inactivated when phosphorylated by protein kinase A. b. PP1 can phosphorylate glycogen phosphorylase. c. Insulin stimulates glycogen breakdown by activating PP1. d. PP1 is activated by activated glycogen phosphorylase. e. PP1 is phosphorylated by glycogen synthase kinase 3. 40. Which statement is true of muscle glycogen phosphorylase? a. It catalyzes cleavage of the (α1 → 6) bonds at the branch points of glycogen. b. It catalyzes the degradation of glycogen by hydrolysis of glycosidic bonds. c. It degrades glycogen to form glucose 6-phosphate. d. It removes glucose residues from the nonreducing ends of glycogen chains by phosphorolysis. e. It adds glucose residues to the reducing ends of a growing glycogen chain. 41. Is glycogen phosphorylase activated, inhibited, or unaffected in response to a glucagon signal in liver tissue? a. activated b. inhibited c. unaffected

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Chap 15_8e 42. The glycogen-branching enzyme catalyzes: a. degradation of (α1 → 4) linkages in glycogen. b. formation of (α1 → 4) linkages in glycogen. c. formation of (α1 → 6) linkages during glycogen synthesis. d. glycogen degradation in tree branches. e. removal of unneeded glucose residues at the ends of branches. 43. Which statement is true of glycogen synthase? a. Activation of the enzyme involves a phosphorylation. b. It catalyzes addition of glucose residues to the nonreducing end of a glycogen chain by formation of (α1 → 4) bonds. c. It uses glucose 6-phosphate as donor of glucose units. d. It catalyzes addition of glucose residues at branch points by formation of (α1 → 6) bonds. e. The enzyme has measurable activity only in the liver. 44. Which statement is NOT associated with controlling the rate of glycogen synthesis in the liver? a. Insulin activates glycogen synthase kinase 3. b. Insulin induces the synthesis of hexokinase IV. c. Glucagon inhibits the activity of glycogen synthase. d. Insulin activates phosphoprotein phosphatase 1. 45. Which statement is true for glycogen granules in liver cells? a. Liver glycogen granules account for up to 10% of the weight of the liver. b. Each particle may contain up to 55,000 glucose molecules. c. Glycogen is stored in the cytosol as granules. d. All of the statements are true. 46. Which statement is true about β-granules? a. The granules in liver are essentially absent after a 24-hour fast. b. Muscle and liver granules release glucose at similar rates. c. In the liver, granules cluster together in groups of several thousand. d. Granules are generally found in cellular liposomes or embedded in the endoplasmic reticulum. e. The outermost granular tiers consist mainly of highly branched B-chains.

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Chap 15_8e 47. During exercise, glycogen in both liver and muscle cells can be converted to glucose metabolites for ATP generation in skeletal muscle. Do liver glycogen and muscle glycogen supply the same amount of ATP to skeletal muscles? Explain.

48. What is the biological advantage of synthesizing glycogen with many branches?

49. Order the steps leading to glycogen breakdown resulting from the stimulation of liver cells by glucagon. 1) Activation of protein kinase A 2) cAMP levels rise 3) Phosphorylation of phosphorylase b 4) Phosphorylation of phosphorylase b kinase 5) Stimulation of adenyl cyclase

50. Describe the process of glycogen breakdown in muscle. Include a description of the structure of glycogen, the nature of the breakdown reaction and the breakdown product, and the required enzyme(s).

51. In mammalian liver, glucose 1-phosphate, the product of glycogen phosphorylase, can enter glycolysis or replenish blood glucose. Describe the first reaction necessary by which these two fates may proceed.

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Chap 15_8e 52. How are the relative concentrations of ATP and AMP correlated to the synthesis and breakdown of glycogen?

53. Describe the reaction catalyzed by glycogen synthase.

54. Although most of the glycogen stored in a human body is found in skeletal muscle, this tissue does not play a role in maintaining blood sugar levels between meals. How are muscle cells (myocytes) precluded from doing so?

55. Explain the role of glycogenin.

56. Order the steps leading to glycogen synthesis resulting from the stimulation of liver cells by glucose. 1) Glucose 1-phosphate is formed by phosphoglucomutase 2) Glucose is phosphorylated to glucose 6-phosphate 3) Glycogen synthase elongates a growing glycogen chain 4) UDP-glucose is formed

57. Sugar nucleotides are substrates or key intermediates in a number of important reactions in the biosynthesis of glycogen. Describe the properties of sugar nucleotides that make them suitable for their many roles.

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Chap 15_8e 58. Glycogen synthesis and glycogen breakdown are catalyzed by separate enzymes. Contrast the reactions in terms of substrate, cofactors (if any), and regulation.

59. Diagram the pathway from glucose to glycogen; show the participation of cofactors and name the enzymes involved.

60. Glycogen synthase kinase 3 (GSK3) inhibitors are being tested for their usefulness in the treatment of type 2 diabetes. Predict the role that these inhibitors could play in the treatment of this disease.

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Chap 15_8e Answer Key 1. c 2. b 3. d 4. c 5. b 6. a 7. b 8. c 9. c 10. a 11. d 12. b 13. b 14. e 15. c 16. a 17. d 18. e 19. b 20. d 21. c 22. b 23. e 24. c 25. d 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_8e 27. c 28. a 29. c 30. a 31. c 32. a 33. c 34. e 35. d 36. e 37. c 38. e 39. a 40. d 41. a 42. c 43. b 44. a 45. d 46. a 47. No, there is one fewer ATP produced from the glucose stored in liver glycogen compared with the glucose stored in muscle glycogen. The glycogen in the liver releases glucose, which must be phosphorylated to glucose 6-phosphate in skeletal muscle; this uses an ATP molecule. Muscle glycogen uses Pi to release glucose as glucose 1-phosphate; this step bypasses the hexokinase reaction and saves using an ATP in the activation of glucose from muscle glycogen. 48. Both glycogen synthase and glycogen phosphorylase act at the nonreducing ends of glycogen chains. Branched glycogen has far more ends for these enzymes to work on than would the equivalent amount of linear glycogen chains. Having more ends effectively increases the concentration of substrate for the enzymes, thereby increasing the rate of glycogen synthesis and breakdown. 49. The correct temporal order is 5, 2, 1, 4, 3. Copyright Macmillan Learning. Powered by Cognero.

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Chap 15_8e 50. Muscle glycogen consists of linear polymers of (α1 → 4)-linked D-glucose with many branches formed by (α1 → 6) glycosidic linkages to D-glucose. Glycogen phosphorylase in muscle catalyzes phosphorolytic cleavage of the terminal residue at the nonreducing ends, producing glucose 1-phosphate. When phosphorylase approaches (α1 → 6) branch points, a second enzyme (the "debranching enzyme") removes the four glucose residues nearest the branch point and reattaches them in (α1 → 4) linkage at a nonreducing end. Now phosphorylase can continue to degrade the molecule. 51. To enter glycolysis, glucose 1-phosphate must undergo isomerization to glucose 6-phosphate by phosphoglucomutase. To replenish glucose in the bloodstream, glucose 1-phosphate must be hydrolyzed to free glucose by glucose 1-phosphatase. 52. High [ATP] and low [AMP] will favor glycogen synthesis. During metabolic stress the reverse is true with high [AMP] and low [ATP]. Under these conditions, glycogen synthesis will be inhibited and the breakdown of glycogen to produce more energy will be favored. 53. The reaction is the addition of a glucose moiety from UDP-glucose to the nonreducing end of a glycogen chain; the linkage formed is (α1 → 4). 54. Myocytes do not have glucagon receptors that would allow them to respond to low blood sugar levels. Secondly, as they do not express glucose 6-phosphatase, they cannot catalyze the hydrolysis of glucose 6-phosphate released from glycogen stores to glucose. 55. Glycogenin is a protein that acts as the "primer" for the initiation of new glycogen molecules. It catalyzes the transfer of a glucose residue from UDP-glucose to a tyrosine hydroxyl group in glycogenin, then forms a complex with glycogen synthase. As more glucose residues are added, this first glucose residue, still attached to glycogenin, becomes the reducing end of the growing glycogen chain. 56. The correct temporal order is 2, 1, 4, 3. 57. 1. Since their formation is metabolically irreversible, they help keep the pathways in which they are involved also irreversible. 2. During a catalyzed reaction binding energy contributions may be made by noncovalent interactions from the nucleotide portion of the sugar nucleotide. 3. The nucleotidyl group makes a good leaving group in reactions. 4. The nucleotidyl portions can serve as "tags" to target molecules for a particular cellular use. 58. Glycogen synthesis is catalyzed by glycogen synthase and employs UDP-glucose as the activated precursor: UDP-glucose + glycogen (glucose)n → UDP + glycogen (glucose)n+1 Glycogen synthase is inactivated by phosphorylation, catalyzed by cAMP-dependent protein kinase; it is activated by dephosphorylation, catalyzed by phosphoprotein phosphatase. Glycogen breakdown is catalyzed by glycogen phosphorylase, which employs pyridoxal phosphate as a cofactor. The reaction is a phosphorolysis; the glycosidic bond is broken by the attack of Pi: Glycogen (glucose)n + Pi → glycogen (glucose)n+1 + glucose 1-phosphate. Glycogen phosphorylase is activated by phosphorylation, catalyzed by phosphorylase kinase, and it is inactivated by dephosphorylation, catalyzed by phosphorylase a phosphatase.

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Chap 15_8e 59. (1) Glucose + ATP → glucose 6-phosphate + ADP Hexokinase (2) Glucose 6-phosphate → glucose 1-phosphate phosphoglucomutase (3) Glucose 1-phosphate + UTP → UDP-glocose + PPi UDP-glucose pyrophosphorylase (4) UDP-glucose → glycogen + UDP glycogen synthase 60. GSK3 inhibitors are expected to increase the activity of glycogen synthase as GSK3 phosphorylates and decreases the activity of glycogen synthase. An increase in the activity of glycogen synthase should decrease blood glucose levels and lead to an improvement in the symptoms of type 2 diabetes.

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Chap 16_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which vitamin is NOT a precursor for a cofactor in the pyruvate dehydrogenase complex? a. thiamine for TPP b. riboflavin for FAD c. biotin for lipoate d. niacin for NAD+ e. pantothenate for CoA 2. The oxidative decarboxylation of α-ketoglutarate proceeds by means of multistep reactions. Which cofactor is NOT required? a. ATP b. coenzyme A c. lipoic acid d. NAD+ e. thiamine pyrophosphate 3. Which reaction in the citric acid cycle will NOT proceed in the absence of inorganic phosphate ions? a. the reaction catalyzed by α-ketoglutarate dehydrogenase b. the reaction catalyzed by succinate dehydrogenase c. the reaction catalyzed by succinyl-CoA synthetase d. the reaction catalyzed by aconitase e. the reaction catalyzed by fumarase 4. Which statement about the oxidative decarboxylation of pyruvate in animal cells is correct? a. One of the products of this reaction is a molecule containing a thioether bond. b. It only occurs under aerobic conditions. c. The process occurs in the glyoxysome compartment of the cell. d. It is often considered the first step in the glyoxylate cycle, as it generates acetyl-CoA, which is required by this pathway. e. It is the most important anaplerotic reaction in hepatocytes. 5. Which reaction of the citric acid cycle requires a water molecule? a. formation of citrate b. succinyl-CoA to succinate c. fumarate to malate d. All of the answers are correct.

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Chap 16_8e 6. Which compound is NOT an intermediate of the citric acid cycle? a. acetyl-CoA b. citrate c. oxaloacetate d. succinyl-CoA e. α-ketoglutarate 7. Which statement is false regarding the reaction catalyzed by the α-ketoglutarate dehydrogenase complex? a. A long lipoyllysine arm transfers intermediates from one active site to another within the complex. b. This reaction would be expected to be abnormally low in a person suffering from beriberi, a dietary deficiency of thiamine. c. Two different coenzymes containing sulfhydryl groups participate in the overall reaction. d. Both this complex and the pyruvate dehydrogenase complex contain a common subunit. e. The proximity of the catalytic enzymes allows for side reactions to take place in the cluster. 8. The reaction of the citric acid cycle that is MOST similar to the pyruvate dehydrogenase complex-catalyzed conversion of pyruvate to acetyl-CoA is the conversion of: a. citrate to isocitrate. b. fumarate to malate. c. malate to oxaloacetate. d. succinyl-CoA to succinate. e. α-ketoglutarateto succinyl-CoA. 9. Which enzyme catalyzes a hydration reaction? a. malate dehydrogenase b. fumarase c. citrate synthase d. pyruvate dehydrogenase complex e. succinyl-CoA synthetase 10. The glyoxylate pathway is important in bacteria, plants, fungi, and protists because it enables them to: a. carry out the net synthesis of carbohydrate from acetyl-CoA. b. form acetyl-CoA from malate. c. get rid of isocitrate formed from the aconitase reaction. d. obtain glyoxylate for cholesterol biosynthesis. e. obtain glyoxylate for pyrimidine synthesis.

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Chap 16_8e 11. Which enzyme does NOT have water as a substrate in the reaction it catalyzes? a. succinyl-CoA synthetase b. aconitase c. fumarase d. citrate synthase 12. The citric acid cycle has an important anabolic function by: a. allowing for the conversion of certain carbon atoms from even-chain fatty acids into glucose. b. producing lactate for gluconeogenesis. c. providing metabolites for the synthesis of cholesterol, amino acids, and glucose. d. completing the oxidation of acetyl-CoA and storing electrons in the form of NADH. 13. Which molecule(s) is an α-ketoacid? a. oxaloacetate b. citrate c. α-ketoglutarate d. oxaloacetate and α-ketoglutarate e. citrate and α-ketoglutarate 14. Malonate is a competitive inhibitor of succinate dehydrogenase. If malonate is added to a mitochondrial preparation that is oxidizing pyruvate as a substrate, which compound would be expected to decrease in concentration? a. citrate b. fumarate c. isocitrate d. pyruvate e. succinate 15. Which cofactors associated with the pyruvate dehydrogenase complex stay bound to the complex and can be classified as prosthetic groups? 1. TPP 2. lipoate 3. CoA-SH 4. NAD+ 5. FAD a. 1 and 5 b. 1, 2, and 4 c. 1, 2, and 5 d. 3 and 4 e. 4 and 5

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Chap 16_8e 16. In which pair is the second compound produced by a reduction of the first compound? a. fumarate and succinate b. oxaloacetate and citrate c. fumarate and malate d. malate and oxaloacetate e. isocitrate andα-ketoglutarate 17. Which cofactor is required for the conversion of fumarate to succinate? a. FAD b. GDP c. CoA d. FADH2 e. both GDP and CoA 18. The standard reduction potentials (E'°) for the half reactions are given Fumarate + 2H++ 2e– → succinate

E'° = +0.031 V

FAD + 2H+ + 2e– → FADH2

E'° = –0.219 V

If succinate, fumarate, FAD, and FADH2, all at l m concentrations, were mixed together in the presence of succinate dehydrogenase, what would happen initially? a. Fumarate and succinate would become oxidized; FAD and FADH2 would become reduced. b. Fumarate would become reduced; FADH2 would become oxidized. c. No reaction would occur because all reactants and products are already at their standard concentrations. d. Succinate would become oxidized; FAD would become reduced. e. Succinate would become oxidized; FADH2 would be unchanged because it is a cofactor, not a substrate. 19. Which compound is NOT required for the oxidative decarboxylation of α-ketoglutarate? a. FAD b. lipoic acid c. NAD+ d. ATP e. CoA-SH

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Chap 16_8e 20. The pyruvate dehydrogenase complex and the α-ketoglutarate dehydrogenase complex are homologous enzyme assemblies that require several different coenzymes to carry out their reactions. Which compound does NOT participate directly in the function of these complexes? a. flavin mononucleotide b. coenzyme A c. lipoic acid d. thiamine pyrophosphate e. nicotinamide adenine dinucleotide 21. How much carbon dioxide is produced from the complete aerobic catabolism of one molecule of 2phosphoglycerate via catabolic pathways? a. 2 CO2 b. 3 CO2 c. 4 CO2 d. 5 CO2 e. 6 CO2 22. Oxaloacetate uniformly labeled with 14C (i.e., with equal amounts of 14C in each of its carbon atoms) is condensed with unlabeled acetyl-CoA. After a single pass through the citric acid cycle back to oxaloacetate, what fraction of the original radioactivity will be found in the oxaloacetate? a. all b. one-half c. one-third d. one-fourth e. three-fourths 23. For the reaction, ΔG'° = 29.7 kJ/mol. + + L-Malate + NAD → oxaloacetate + NADH + H The reaction as written: a. can never occur in a cell. b. can only occur in a cell if it is coupled to another reaction for which ΔG'° is positive. c. can only occur in a cell in which NADH is converted to NAD+ by electron transport. d. occurs in cells because of the continual removal of oxaloacetate by citrate synthase. e. always proceeds at a very slow rate.

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Chap 16_8e 24. Which enzymes catalyze oxidation reactions in the citric acid cycle? 1. succinate dehydrogenase 2. pyruvate dehydrogenase 3. isocitrate dehydrogenase 4. α-ketoglutarate dehydrogenase a. 1 and 4 b. 1, 2, and 4 c. 1, 3, and 4 d. 2 and 3 e. All of the listed enzymes catalyze oxidation reactions in the citric acid cycle. 25. Which statement about NAD+ and NADH is true? a. NADH inhibits the pyruvate dehydrogenase complex. b. NAD+ is oxidized to NADH by the α-ketoglutarate dehydrogenase complex. c. NAD+ is a coenzyme for two of the enzymes in the pyruvate dehydrogenase complex. d. NAD+ is oxidized to NADH by isocitrate dehydrogenase. 26. Which high-energy bond is associated with the succinyl-CoA synthetase reaction? a. acyl phosphate b. thioester c. phosphohistidine d. phosphoanhydride e. All of the answers are correct. 27. Which are possible sources for acetyl-CoA that enters the citric acid cycle? 1. oxidative decarboxylation of pyruvate 2. β oxidation of fatty acids 3. catabolism of certain amino acids 4. citrate 5. carboxylation of pyruvate a. 1, 2, and 3 b. 1, 2, and 4 c. 1, 2, and 5 d. 1, 4, and 4 e. 2, 4, and 5

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Chap 16_8e 28. Entry of acetyl-CoA into the citric acid cycle is decreased when: a. [AMP] is high. b. NADH is rapidly oxidized through the respiratory chain. c. the ratio of [ATP]/[ADP] is low d. the ratio of [ATP]/[ADP] is high. e. the ratio of [NAD+]/[NADH] is high. 29. The conversion of one molecule of pyruvate to three molecules of CO2 via pyruvate dehydrogenase and the citric acid cycle also yields _____ molecules of NADH, _____ molecule(s) of FADH2, and _____ molecule(s) of ATP (or GTP). a. two; two; two b. three; one; one c. three; two; zero d. four; one; one e. four; two; one 30. Intermediates in the citric acid cycle are used as precursors in the biosynthesis of: a. amino acids. b. nucleotides. c. fatty acids. d. sterols. e. All of the answers are correct. 31. Arsenic inhibits the pyruvate dehydrogenase complex by inactivating the dihydrolipoamide component of dihydrolipoyl transacetylase. Which enzyme is also MOST likely to be inhibited by arsenic? a. GAP dehydrogenase b. isocitrate dehydrogenase c. succinyl-CoA synthetase d. malate dehydrogenase e. α-ketoglutarate dehydrogenase 32. Glucose labeled with 14C in C-3 and C-4 is completely converted to acetyl-CoA via glycolysis and the pyruvate dehydrogenase complex. What percentage of the acetyl-CoA molecules formed will be labeled with 14C, and in which position of the acetyl moiety will the 14C label be found? a. One hundred percent of the acetyl-CoA will be labeled at C-1 (carboxyl). b. One hundred percent of the acetyl-CoA will be labeled at C-2. c. Fifty percent of the acetyl-CoA will be labeled at C-2 (methyl). d. No label will be found in the acetyl-CoA molecules. e. Not enough information is given to answer this question.

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Chap 16_8e 33. In mammals, what process does NOT occur during the citric acid cycle? a. formation of α-ketoglutarate b. generation of NADH and FADH2 c. metabolism of acetate to carbon dioxide and water d. net synthesis of oxaloacetate from acetyl-CoA e. oxidation of acetyl-CoA 34. Which enzyme in the citric acid cycle has a standard free energy that is large and positive? a. malate dehydrogenase b. citrate synthase c. succinyl-CoA synthetase d. fumarase e. No enzyme in the citric acid cycle has a positiveΔG'°. 35. Which statement is NOT true of the reaction catalyzed by the pyruvate dehydrogenase complex? a. Biotin participates in the decarboxylation. b. Both NAD+ and a flavin nucleotide act as electron carriers. c. The reaction occurs in the mitochondrial matrix. d. The substrate is held by the lipoyllysine "swinging arm." e. Two different cofactors containing —SH groups participate. 36. Which process is NOT a metabolic fate for pyruvate in liver tissue? a. reduction to lactate b. oxidative decarboxylation to acetyl-CoA c. transamination to alanine d. phosphorylation to phosphoenolpyruvate e. carboxylation to oxaloacetate 37. Which statement is false regarding the citric acid cycle? a. Succinate dehydrogenase is a flavoprotein associated with the electron-transport chain. b. The rate of the citric acid cycle increases when the NAD+/NADH ratio is high. c. In eukaryotes, the citric acid cycle occurs in the mitochondrial matrix. d. Acetyl-CoA inhibits theα-ketoglutaratedehydrogenase complex.

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Chap 16_8e 38. Which factor is NOT associated with the oxidation of substrates by the citric acid cycle? a. CO2 production b. flavin reduction c. the presence of lipoic acid in some of the enzyme systems d. pyridine nucleotide oxidation e. All of these factors are associated with the oxidation of substrates by the citric acid cycle. 39. The two molecules of CO2 produced in the first turn of the citric acid cycle have their origin in the: a. carboxyl and methylene carbons of oxaloacetate b. carboxyl group of acetate and a carboxyl group of oxaloacetate. c. carboxyl group of acetate and the keto group of oxaloacetate. d. two carbon atoms of acetate. e. two carboxyl groups derived from oxaloacetate. 40. Which type of reaction is found in the citric acid cycle? a. isomerization b. hydration c. condensation d. redox e. All of the answers are correct. 41. Which citric acid cycle intermediate is chiral? a. citrate b. α-ketoglutarate c. fumarate d. succinate e. malate 42. Pyruvate dehydrogenase complex is regulated by: a. allosteric regulation. b. covalent modification. c. proteolytic cleavage. d. allosteric regulation and covalent modification. e. allosteric regulation, covalent modification, and proteolytic cleavage.

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Chap 16_8e 43. When is the consumption of acetyl-CoA by the citric acid cycle decreased? a. when the concentration of NAD+ is high b. when the concentration of oxaloacetate is high c. when NADH is rapidly reoxidized via the electron transport chain d. when the demand for ATP is low e. when the concentrations of NAD+ and oxaloacetate are both high 44. Anaplerotic reactions: a. produce oxaloacetate and malate to maintain constant levels of citric acid cycle intermediates. b. produce biotin needed by pyruvate carboxylase. c. recycle pantothenate used to make CoA. d. produce pyruvate and citrate to maintain constant levels of citric acid cycle intermediates. e. All of the answers are correct. 45. Which combination of cofactors is involved in the conversion of pyruvate to acetyl-CoA? a. biotin, FAD, and TPP b. biotin, NAD+, and FAD c. NAD+, biotin, and TPP d. pyridoxal phosphate, FAD, and lipoate e. TPP, lipoate, and NAD+ 46. In the citric acid cycle, a flavin coenzyme is required for: a. condensation of acetyl-CoA and oxaloacetate. b. oxidation of fumarate. c. oxidation of isocitrate. d. oxidation of malate. e. oxidation of succinate. 47. Citrate synthase and the NAD+-specific isocitrate dehydrogenase are two key regulatory enzymes of the citric acid cycle. These enzymes are inhibited by: a. acetyl-CoA and fructose 6-phosphate. b. AMP and/or NAD+. c. AMP and/or NADH. d. ATP and/or NAD+. e. ATP and/or NADH.

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Chap 16_8e 48. The reaction of the citric acid cycle that produces an ATP equivalent (in the form of GTP) by substrate level phosphorylation is the conversion of: a. citrate to isocitrate. b. fumarate to malate. c. malate to oxaloacetate. d. succinate to fumarate. e. succinyl-CoA to succinate. 49. Why is the citric acid cycle considered to be part of aerobic metabolism, even though oxygen is NOT a substrate in any reaction? a. because it takes place in the mitochondrion b. because it contains oxidation reactions c. because it produces NADH and FADH2, which ultimately transfer their electrons to oxygen d. because it produces carbon dioxide 50. Which compound is required for the oxidative decarboxylation of the carbon skeleton of isoleucine? a. FAD b. thiamine pyrophosphate c. NAD+ d. CoA-SH e. All of these compounds are required. 51. During the reaction of pyruvate carboxylase, CO2 is NOT covalently attached to: a. phosphate. b. biotin. c. pyruvate. d. lysine. 52. How many ATP equivalents are made from the aerobic conversion of pyruvate to oxaloacetate (through one turn of the citric acid cycle)? a. 9 ATP b. 10 ATP c. 11 ATP d. 11.5 ATP e. 12.5 ATP

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Chap 16_8e 53. Each molecule of acetyl-CoA oxidized by the citric acid results in the net production of _____ molecule(s) of _____. a. one; citrate b. one; FADH2 c. one; NADH d. one; oxaloacetate e. seven; ATP 54. Which cofactor is required for the conversion of succinate to fumarate in the citric acid cycle? a. ATP b. biotin c. FAD d. NAD+ e. NADP+ 55. Which statement is false of the citric acid cycle? a. All enzymes of the cycle are located in the cytoplasm, except succinate dehydrogenase, which is bound to the inner mitochondrial membrane. b. In the presence of malonate, one would expect succinate to accumulate. c. Oxaloacetate is used as a substrate but is not consumed in the cycle. d. Succinate dehydrogenase channels electrons directly into the electron transfer chain. 56. Which step is NOT catalyzed by the pyruvate dehydrogenase complex? a. E1 catalyzes the decarboxylation of pyruvate. b. E1 catalyzes the oxidation of a hydroxyethyl group to an acetyl group. c. E2 catalyzes the transfer of an acetyl group to CoA-SH. d. E3 catalyzes the reduction of oxidized lipoate. e. E3 catalyzes the transfer of electrons from FADH2 to NAD+. 57. The reaction catalyzed by which enzyme is NOT linked to the reduction of NAD+? a. isocitrate dehydrogenase b. malate dehydrogenase c. pyruvate dehydrogenase d. succinate dehydrogenase e. the α-ketoglutarate dehydrogenase complex

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Chap 16_8e 58. Which compound is NOT required for the oxidative decarboxylation of pyruvate to form acetyl-CoA? a. ATP b. CoA-SH c. FAD d. lipoate e. NAD+ 59. Which intermediate of the citric acid cycle is prochiral? a. citrate b. isocitrate c. malate d. oxaloacetate e. succinate 60. Which statement is false with respect to the pyruvate dehydrogenase complex? a. It is located in the mitochondrial matrix. b. Its activity is increased in the presence of Ca2+ ions in skeletal muscle. c. Its activity is increased in the presence of coenzyme A and ADP. d. The proximity of the catalytic enzymes in the cluster slows down the overall rate. 61. Why is flux through the citric acid cycle low in the resting state? a. Flux through the cycle is low due to a drop in serum adrenaline levels. b. Flux through the cycle is low due to allosteric inhibition of pyruvate carboxylase. c. Flux through the cycle is low due to complete oxidation of NADH because oxygen is readily available. d. Flux through the cycle is low due to low local concentrations of NAD+ because of a diminished rate of oxidative phosphorylation. e. Flux through the cycle is low due to product inhibition of the pyruvate dehydrogenase complex by ATP. 62. Which enzyme catalyzes a reversible reaction under normal cellular conditions? a. α-ketoglutarate dehydrogenase b. isocitrate dehydrogenase c. succinate dehydrogenase d. pyruvate dehydrogenase e. None of the answers is correct.

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Chap 16_8e 63. Thyroxine is a competitive inhibitor of malate dehydrogenase. If thyroxine is added to a mitochondrial preparation that is oxidizing pyruvate as a substrate, which compound would be expected to decrease in concentration first? a. citrate b. fumarate c. oxaloacetate d. pyruvate e. malate 64. Which enzymatic activity would be decreased by thiamine deficiency? a. fumarase b. isocitrate dehydrogenase c. malate dehydrogenase d. succinate dehydrogenase e. α-ketoglutaratedehydrogenase complex 65. Which statement about the oxidative decarboxylation of pyruvate in aerobic conditions in animal cells is correct? a. One of the products of the reactions of the pyruvate dehydrogenase complex is a thioester of acetate. b. The methyl (—CH3) group is eliminated as CO2. c. The process occurs in the cytosolic compartment of the cell. d. The pyruvate dehydrogenase complex uses cofactors: NAD+, lipoic acid, pyridoxal phosphate, and FAD. 66. Which reaction of the citric acid cycle produces a net of one water molecule? a. citrate to isocitrate b. fumarate to malate c. succinyl-CoA to succinate d. succinate to succinyl-CoA e. None of the answers is correct. 67. Which does NOT inhibit the activity of the pyruvate dehydrogenase (PDH) complex? a. dichloroacetate (DCA) b. NAD+ c. ATP d. acetyl-CoA e. phosphorylation of PDH

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Chap 16_8e 68. Show the steps of the citric acid cycle from only succinyl-CoA to oxaloacetate. For each step, show structures of substrate and product, name the enzyme responsible, and show where cofactors participate.

69. Show the steps of the citric acid cycle in which a six-carbon compound is converted into the first four-carbon intermediate in the path. For each step, show structures of substrate and product, name the enzyme responsible, and show where cofactors participate.

70. At what point in the citric acid cycle do the methyl carbon from acetyl-CoA and the carbonyl carbon from oxaloacetate become chemically equivalent?

71. The human disease beriberi is caused by a deficiency of thiamine in the diet. People with severe beriberi have higher than normal levels of pyruvate in their blood and urine. Explain this observation in terms of specific enzymatic reaction(s).

72. Degradation of leucine yields acetyl-CoA. Can degradation of this amino acid replenish the pool of citric acid cycle intermediates? Explain.

73. Show the three reactions in the citric acid cycle in which NADH is produced, including the structures. None of these reactions involves molecular oxygen (O2), but all three reactions are strongly inhibited by anaerobic conditions; explain why.

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Chap 16_8e 74. Acetyl-CoA is a positive allosteric modulator of pyruvate carboxylase. Explain why this makes metabolic sense.

75. The disease beriberi is caused by a deficiency of thiamine in the diet. Why is this disease often associated with metabolic acidosis and neurological disorders?

76. Which part of the citric acid cycle from only isocitrate to fumarate are the high-energy phosphate compounds or reduced electron carriers produced or consumed, and name the enzyme that catalyzes each step.

77. Preparation of an extract of muscle results in a dramatic decrease in the concentration of citric acid cycle intermediates compared to their concentrations in the tissue. However, in 1935, Szent-Gyorgi showed that the production of CO2 by the extract increased when succinate was added. In fact, for every molecule of succinate added, many extra molecules of CO2 were produced. Explain this effect in terms of the known catabolic pathways.

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Chap 16_8e 78. Match the cofactors with their roles in the pyruvate dehydrogenase complex reaction. Cofactors: A. Coenzyme A (CoA-SH) B. NAD+ C. Thiamine pyrophosphate (TPP) D. FAD E. Lipoic acid in oxidized form Roles: _____ Attacks and attaches to the central carbon in pyruvate _____ Oxidizes FADH2 _____ Accepts the acetyl group from reduced lipoic acid _____ Oxidizes the reduced form of lipoic acid _____ Initial electron acceptor in oxidation of pyruvate.

79. A researcher is in charge of genetically engineering a new bacterium that will derive all of its ATP from sunlight by photosynthesis. Will the researcher put the enzymes of the citric acid cycle in this organism? Briefly explain why or why not.

80. The citric acid cycle is frequently described as the major pathway of aerobic catabolism, which means that it is an oxygen-dependent degradative process. However, none of the reactions of the cycle directly involves oxygen as a reactant. Why is the pathway described as being oxygen dependent?

81. Show the structures of the reactants and products for two of the four redox reactions in the citric acid cycle. Indicate where any cofactors participate, and label the reactants, products, and cofactors as oxidants or reductants in the reaction.

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Chap 16_8e 82. Explain in quantitative terms the circumstances under which the reaction shown can proceed. L-Malate + NAD+ → oxaloacetate + NADH + H+ ΔG'º = +29.7 kJ/mol

83. Show the reactions by which α-ketoglutarateis converted to malate in the citric acid cycle.

84. The citric acid cycle begins with the condensation of acetyl-CoA with oxaloacetate. Describe three possible sources for the acetyl-CoA.

85. There are few, if any, humans with defects in the enzymes of the citric acid cycle. Explain this observation in terms of the role of the citric acid cycle.

86. Succinate can be synthesized from pyruvate via two distinct pathways that have no enzyme in common. What are the energy conditions of each pathway?

87. What is the function of FAD in the pyruvate dehydrogenase complex? How is it regenerated?

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Chap 16_8e 88. The pyruvate dehydrogenase complex catalyzes the oxidative decarboxylation of pyruvate. Two of the steps catalyzed by this complex do not involve any of the carbons of pyruvate. Briefly describe these reaction steps.

89. Explain why fluorocitrate, a potent inhibitor of the enzyme aconitase, is a deadly poison.

90. Briefly describe the relationship of the pyruvate dehydrogenase complex reaction to glycolysis and the citric acid cycle.

91. Describe the enzymes, cofactors, intermediates, and products of the pyruvate dehydrogenase complex.

92. In the citric acid cycle, a five-carbon compound is decarboxylated to yield an activated four-carbon compound. Show the substrate and product in this step, and indicate where any cofactor(s) participates.

93. Two of the steps in the oxidative decarboxylation of pyruvate to acetyl-CoA do not involve the three carbons of pyruvate, yet are essential to the operation of the pyruvate dehydrogenase complex. Explain.

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Chap 16_8e 94. Match the cofactor with its function in the citric acid cycle. A given function may be used more than once or not at all. Cofactor Function 1. carries O2 (a) NAD+/NADH (b) FAD/FADH2 2. carries small carbon-containing molecules (c) CoA 3. carries e– (d) thiamine 4. carries small nitrogen-containing molecules (e) biotin

95. There is an overly high level of pyruvate in a patient's blood and urine. One possible cause is a genetic defect in the enzyme pyruvate dehydrogenase, but another plausible cause is a specific vitamin deficiency. Explain what vitamin might be deficient in the diet, and why that would account for high levels of pyruvate to be excreted in the urine. How would the correct explanation be determined?

96. Although ADP is not directly involved in the isocitrate dehydrogenase reaction, the activity of this enzyme is dependent on the concentration of ADP in the matrix. Briefly explain how.

97. In which reaction of the citric acid cycle does substrate-level phosphorylation occur?

98. Carbon dioxide is produced in two reactions in the citric acid cycle. For each of these reactions, name and show the structures of reactant and product, name the enzyme, and show how any cofactors participate.

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Chap 16_8e Answer Key 1. c 2. a 3. c 4. b 5. d 6. a 7. e 8. e 9. b 10. a 11. a 12. c 13. d 14. b 15. c 16. a 17. d 18. b 19. d 20. a 21. b 22. b 23. d 24. e 25. a 26. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 16_8e 27. a 28. d 29. d 30. e 31. e 32. d 33. d 34. a 35. a 36. d 37. d 38. d 39. e 40. e 41. e 42. d 43. d 44. a 45. e 46. e 47. e 48. e 49. c 50. e 51. d 52. e 53. b 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 16_8e 55. a 56. d 57. d 58. a 59. a 60. d 61. d 62. c 63. c 64. e 65. a 66. e 67. b 68. These are the steps catalyzed by succinyl-CoA synthetase, succinate dehydrogenase, fumarase, and malate dehydrogenase. (See Fig. 16-7.)

69. The reactions are those catalyzed by isocitrate dehydrogenase, theα-ketoglutaratedehydrogenase complex, and succinyl-CoA synthetase. (See Fig. 16-7.)

70. This happens with the formation of succinate. 71. Thiamine is essential for the synthesis of the cofactor thiamine pyrophosphate. Without this cofactor the pyruvate dehydrogenase complex cannot convert pyruvate into acetyl-CoA, so the pyruvate produced by glycolysis accumulates.

72. No, the two carbons from the acetate in acetyl-CoA are lost as CO2 in the oxidative decarboxylation reactions of the citric acid cycle.

73. NADH is produced in the reactions catalyzed by isocitrate dehydrogenase, the α-ketoglutarate dehydrogenase complex, and malate dehydrogenase. These reactions are indirectly dependent on the presence of O2 because the NADH produced in the reactions is normally recycled to NAD+ by passage of electrons from NADH through the respiratory chain to O2. (See also Fig. 16-7.) 74. During starvation, there is an increase in the production of acetyl-CoA from oxidation of fatty acids. This acetyl-CoA activates pyruvate carboxylase, which catalyzes the conversion of pyruvate to oxaloacetate. Oxaloacetate is used in gluconeogenesis. During periods of heavy aerobic activity, there is also an increase in the production of acetyl-CoA from oxidation of fatty acids. To oxidize this acetyl-CoA via the citric acid cycle, an increase in the concentrations of oxaloacetate is required. The acetyl-CoA produced from the oxidation of fatty acids activates pyruvate carboxylase, which catalyzes the conversion of pyruvate to oxaloacetate. Copyright Macmillan Learning. Powered by Cognero.

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Chap 16_8e 75. Thiamine pyrophosphate (TPP) is a coenzyme necessary for the conversion of pyruvate to acetyl-CoA via the pyruvate dehydrogenase complex. A deficiency in TPP reduces the activity of this complex leading to an increase in the conversion of pyruvate to lactate. The transport of excessive lactate from skeletal muscle to the bloodstream is associated with metabolic acidosis. Tissues such as the brain are particularly susceptible in beriberi, as they have a very strong reliance on glucose (and the pyruvate dehydrogenase complex) for their energy needs.

76. This part of the citric acid cycle includes the reactions catalyzed by isocitrate dehydrogenase, theα-ketoglutaratedehydrogenase complex, succinyl-CoA synthetase, and succinate dehydrogenase. GTP, NADH, and FADH2 are produced. (See Fig. 16-7.)

77. Succinate is an intermediate in the citric acid cycle that is not consumed but is regenerated by the operation of the cycle. By adding succinate to an extract that is depleted in citric acid cycle intermediates, these intermediates are replenished and the cycle can resume operating, oxidizing acetyl-CoA to CO2 .

78. C, B, A, D, E 79. Yes; even though the citric acid cycle is not needed for catabolic reactions in this organism, the enzymes of the cycle are still essential. They produce precursors of amino acids (such asα-ketoglutarateand oxaloacetate), of heme (succinyl-CoA), and of a variety of other essential products.

80. The citric acid cycle produces NADH, which normally is recycled by passage of electrons from NADH to O2 via the respiratory chain. With no O2 to accept electrons from NADH, the accumulation of NADH effectively stops the citric acid cycle.

81. The four oxidation-reduction reactions are those catalyzed by isocitrate dehydrogenase, theαketoglutaratedehydrogenase complex, succinate dehydrogenase, and malate dehydrogenase. (See Fig. 16-7.) For isocitrate dehydrogenase, isocitrate is the reductant (i.e., it becomes oxidized), NAD+ is the oxidant (i.e., it becomes reduced), and a divalent metal is required for this reaction. For the α-ketoglutarate dehydrogenase complex, α-ketoglutarateis the reductant, NAD+ is the oxidant, and the enzyme requires the same menagerie of cofactors as does pyruvate dehydrogenase (TPP, lipoyllysine, FAD). For malate dehydrogenase, malate is the reductant, NAD+ is the oxidant, and no cofactors are required.

82. A reaction for which ΔG'º is positive can proceed under conditions in which the actual ΔG is negative. From the relationship

it is clear that if the concentration of product is kept very low (e.g., by its removal in a subsequent metabolic step), the logarithmic term becomes negative and the actual ΔG can then have a negative value. (See also Chapter 13.) 83. The reactions are those catalyzed by the α-ketoglutarate dehydrogenase complex, succinyl-CoA synthetase, succinate dehydrogenase, and fumarase. (See Fig. 16-7.) 84. Acetyl-CoA is produced by (1) the pyruvate dehydrogenase complex, (2) β oxidation of fatty acids, or (3) degradation of certain amino acids.

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Chap 16_8e 85. The citric acid cycle is central to all aerobic energy-yielding metabolisms and also plays a critical role in biosynthetic reactions by providing precursors. Mutations in the enzymes of the citric acid cycle are likely to be lethal during fetal development.

86. Pathway 1: Pyruvate is oxidized to acetyl-CoA and acetyl-CoA enters the citric acid cycle by condensation with oxaloacetate to form citrate. Citrate is converted to succinate via the next four steps in the cycle. In this pathway, the thioester bonds in acetylCoA and succinyl-CoA are hydrolyzed. The energy in the thioester bond in succinyl-CoA is saved as a phosphoanhydride bonds in GTP. There are two oxidation reactions, each generating a NADH molecule.

Pathway 2: Pyruvate is converted directly to oxaloacetate via a carboxylation reaction. A buildup of oxaloacetate may allow it to be reduced to malate; malate may be dehydrated to form fumarate, which may eventually be reduced to succinate. This pathway is very energy intensive, requiring an ATP for the carboxylation of pyruvate and a NADH and a FADH2 for the two reduction reactions. 87. FAD serves as the electron acceptor in the reoxidation of the cofactor dihydrolipoate. It is converted to FADH2 by this reaction and is regenerated by the passage of electrons to NAD+.

88. Step 4: Dihydrolipoamide is reoxidized by dihydrolipoyl dehydrogenase (E3) Step 5: The FADH2 prosthetic group of E3 is reoxidized by NAD+.

89. By inhibiting aconitase, fluorocitrate prevents the citric acid cycle from operating. This prevents the oxidation of acetyl-CoA and dramatically reduces the yield of ATP from carbohydrate and lipid catabolism. The resulting drop in ATP levels is lethal.

90. The pyruvate dehydrogenase complex converts pyruvate, the product of glycolysis, into acetyl-CoA, the starting material for the citric acid cycle.

91. The pyruvate dehydrogenase complex consists of multiple copies of each of three enzymes. The first enzyme to act is pyruvate dehydrogenase (E1 ), which converts pyruvate to CO2 and the hydroxyethyl derivative of thiamine pyrophosphate (TPP). The same enzyme then oxidizes the hydroxyethyl group to an acetyl group attached to enzyme-bound lipoate through a thioester linkage. The second enzyme, dihydrolipoyl transacetylase (E2 ), transfers the acetyl group to coenzyme A, forming acetyl-CoA. The third enzyme, dihydrolipoyl dehydrogenase (E3 ), oxidizes the dihydrolipoate to its disulfide form, passing the electrons through FAD to NAD+. (See Fig. 16-6.)

92. The oxidation ofα-ketoglutarateto succinyl-CoA involves five cofactors: lipoate, thiamine pyrophosphate, FAD, NAD+, and CoASH.

93. The two steps catalyzed by dihydrolipoyl dehydrogenase (E3 ) are required to regenerate the oxidized form of lipoate, bound to dihydrolipoyl transacetylase, from the dihydrolipoyl (reduced) form produced in the oxidation of pyruvate. First, FAD is reduced to FADH2 to reoxidize the dihydrolipoate, then NAD+ is reduced to NADH to reoxidize the FADH2 to complete the reaction.

94. (a) 3; (b) 3; (c) 2; (d) 2; (e) 2

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Chap 16_8e 95. The most likely explanation is that the patient has a deficiency of thiamine, without which the cell cannot make thiamine pyrophosphate, the cofactor for pyruvate dehydrogenase. The inability to oxidize pyruvate produced by glycolysis to acetylCoA would lead to accumulation of pyruvate in blood and urine. The most direct test for this deficiency is to feed a diet supplemented with thiamine and determine whether urinary pyruvate levels fall.

96. ADP is an allosteric activator of isocitrate dehydrogenase. Furthermore, when ADP levels are high in the matrix, ATP synthase and the electron transport chain are active. Enhanced activity of the electron transport chain leads to increased levels of NAD+ in the matrix. The availability of NAD+ enhances the activity of isocitrate dehydrogenase.

97. Substrate-level phosphorylation of GDP to GTP occurs in the succinyl-CoA synthetase reaction in which succinyl-CoA is converted to succinate during the citric acid cycle.

98. See the isocitrate dehydrogenase and α-ketoglutarate dehydrogenase reactions. (See also Fig. 16-7.)

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Chap 17_8e Indicate the answer choice that best completes the statement or answers the question. 1. The role of hormone-sensitive triacylglycerol lipase is to: a. hydrolyze lipids stored in the liver. b. hydrolyze membrane phospholipids in hormone-producing cells. c. hydrolyze triacylglycerols stored in adipose tissue. d. synthesize lipids in adipose tissue. e. synthesize triacylglycerols in the liver. 2. Which statements are true of the β oxidation of long-chain fatty acids? 1. The enzyme complex that catalyzes the reaction contains biotin. 2. FADH2 serves as an electron carrier. 3. NADH serves as an electron carrier. 4. Oxidation of an 18-carbon fatty acid produces six molecules of propionyl-CoA. 5. Oxidation of a 15-carbon fatty acid produces at least one propionyl-CoA. a. 1, 2, and 3 b. 1, 2, and 5 c. 2, 3, and 4 d. 2, 3, and 5 e. only 3 and 5 3. When comparing the β-oxidation and α-oxidation pathways, which statement is correct? a. β oxidation and α oxidation occur in the cytoplasm. b. β oxidation occurs at the carboxyl end of the fatty acid, whereas α oxidation occurs at the methyl end. c. β oxidation occurs at the methyl end of the fatty acid, whereas α oxidation occurs at the carboxyl end. d. β oxidation occurs mainly in the cytoplasm, whereas α oxidation occurs mainly in the mitochondria. e. β oxidation occurs mainly in the mitochondria, whereas α oxidation occurs mainly in the cytoplasm. 4. Which pathway is likely to be affected by a deficiency in carnitine? a. α oxidation b. β oxidation c. uptake of fatty acids from the bloodstream d. All of the answers are correct. 5. Which is NOT a symptom of ketosis? a. lower blood pH b. high levels of malonyl-CoA c. presence of ketone bodies in the urine d. smell of acetone in the breath

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Chap 17_8e 6. Which enzyme is involved in activation of fatty acids in the cytosol? a. acyl-CoA synthetase b. inorganic pyrophosphatase c. carnitine acyltransferase 1 d. both acyl-CoA synthetase and inorganic pyrophosphatase e. both inorganic pyrophosphatase and carnitine acyltransferase 1 7. In hepatocytes (liver cells), what is a possible fate of acetyl-CoA produced from the oxidation of a fatty acid? a. oxidation via the citric acid cycle b. use in the synthesis of ketone bodies c. use in gluconeogenesis d. both oxidation via the citric acid cycle and use in the synthesis of ketone bodies e. both oxidation via the citric acid cycle and use in gluconeogenesis 8. If the fatty acid 14:1(Δ7) is completely catabolized to CO2 and H2O, what would be the net yield of ATP? a. 90.5 b. 92 c. 92.5 d. 94 e. 94.5 9. If the 16-carbon saturated fatty acid palmitate is oxidized completely to carbon dioxide and water (via the βoxidation pathway and the citric acid cycle), and all of the energy-conserving products are used to drive ATP synthesis in the mitochondrion, the net yield of ATP per molecule of palmitate is: a. 3. b. 10. c. 25. d. 106. e. 1,000. 10. In β oxidation, which cofactor is required for the conversion of a trans-Δ2-enoyl-CoA to a β-hydroxyacylCoA? a. NAD+ b. FAD c. H2O d. CoA-SH 11. In the equation, which substance is being reduced?

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Chap 17_8e

a. β-ketoacyl-CoA b. l-β-hydroxyacyl-CoA c. NADH d. NAD+ e. H+ Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_8e 12. In β oxidation, which cofactor is required for the conversion of a β-ketoacyl-CoA to an acyl-CoA and an acetyl-CoA molecule? a. NAD+ b. FAD c. H2O d. CoA-SH 13. Why is oxidation necessary for phytanic acid? a. It has a double bond between the first two carbons to be removed by oxidation. b. It is a very-long-chain fatty acid. c. It contains many trans double bonds which must be removed for oxidation to occur. d. It has a methyl group on its β carbon. 14. What is the extra product resulting from the β oxidation of a saturated fatty acid with 19 carbons as compared to that of a fatty acid with 18 carbons? a. acetoacetyl-CoA b. succinyl-CoA c. acetyl-CoA d. malonyl-CoA e. propionyl-CoA 15. Ketone bodies are formed in the liver and transported to the extrahepatic tissues mainly as: a. acetoacetyl-CoA. b. acetone. c. β-hydroxybutyric acid. d. β-hydroxybutyryl-CoA. e. lactic acid. 16. Which statement is false regarding ketone bodies? a. During prolonged starvation, the brain adapts to using ketone bodies as a fuel. b. Excess acetone production during ketoacidosis is exhaled through the lungs. c. Ketone bodies can be used as a carbon source for fatty acid synthesis. d. Ketone bodies can be converted to glucose during ketosis. e. Ketone bodies are formed when the glucagon/insulin ratio is high. 17. The consumption of palmitoyl-CoA by β oxidation is decreased under which condition? a. the concentration of NAD+ being high in the matrix b. the concentration of ADP being high in the matrix c. the mitochondrial ATP synthase being inactive d. NADH being rapidly reoxidized via the electron-transport chain Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_8e 18. Complete oxidation of one molecule of which fatty acid would yield the MOST ATP? a. 16-carbon saturated fatty acid b. 18-carbon monounsaturated fatty acid c. 16-carbon monounsaturated fatty acid d. 16-carbon polyunsaturated fatty acid e. 14-carbon saturated fatty acid 19. The balanced equation for the degradation of CH3(CH2)10COOH via the β-oxidation pathway is: a. CH3(CH2)10COOH + 5FAD + 5NAD+ + 6CoA-SH + 5H2O + ATP → 6 Acetyl-CoA + 5FADH2 + 5NADH + 5H+ + AMP + PPi b. CH3(CH2)10COOH + 5FAD + 5NAD+ + 6CoA-SH + 5H2O → 6 Acetyl-CoA + 5FADH2 + 5NADH + 5H+ c. CH3(CH2)10COOH + 6FAD + 6NAD+ + 6CoA-SH + 6H2O + ATP → 6 Acetyl-CoA + 6FADH2 + 6NADH + 6H+ + AMP + PPi d. CH3(CH2)10COOH + 6FAD + 6NAD+ + 6CoA-SH + 6H2O → 6 Acetyl-CoA + 6FADH2 + 6NADH + 6H+ 20. Which compound is NOT considered a ketone body? a. acetoacetate b. 3-hydroxybutyrate c. acetone d. dihydroxyacetone e. β-hydroxybutyrate 21. Which statement regarding ketone bodies is false? a. The production of excess ketone bodies can cause a condition known as ketosis, which is associated with acidosis. b. In hepatocytes, the production of ketone bodies is an anaplerotic process because the products of βhydroxybutyrate oxidation can enter the citric acid cycle. c. Ketone bodies are produced by the liver during starvation or in cases when insulin production is insufficient. d. The production of ketone bodies increases when blood glucagon levels are elevated.

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Chap 17_8e 22. Which statement is false regarding β oxidation in peroxisomes? a. The peroxisomal system prefers very-long-chain fatty acids. b. The NADH generated by β-hydroxyacyl-CoA dehydrogenase must be exported for reoxidation. c. Acyl-CoA dehydrogenase passes its electrons directly to oxygen. d. The acetyl-CoA produced by β oxidation in peroxisomes is exported for further oxidation. e. The peroxisomal system can oxidize branched-chain fatty acids. 23. Which form of a fatty acid is NOT found in the blood? a. acyl-CoA b. free fatty acid bound to albumin c. a component of a chylomicron d. a component of a triacylglycerol 24. Which statement is NOT true about vitamin B12? a. Vitamin B12 contains a porphyrin ring. b. Vitamin B12 contains a carbon–cobalt bond. c. Vitamin B12 readily undergoes homolytic bond cleavage. d. Deficiency of vitamin B12 causes pernicious anemia. e. Vitamin B12 catalyzes hydrogen atom exchange with solvent H2O. 25. Some athletes believe that dietary carnitine supplements will enhance their ability to perform aerobic exercise. Which statement BEST describes the scientific basis of this belief? a. Carnitine is required in the transport of medium- and long-chain fatty acids into the mitochondrial matrix, and so increasing the amount of carnitine will increase the rate of transport. b. Carnitine activates carnitine acyltransferase 1 thereby increasing the rate of transport of fatty acids into the mitochondrial matrix. c. Carnitine levels in the cytoplasm are reduced when large amounts of fatty acyl–carnitine are transported into the mitochondrial matrix. d. Carnitine enhances the activation of fatty acids to fatty acyl–CoA, thereby increasing the rate of their transport into the mitochondrial matrix. e. Carnitine is an allosteric activator of carnitine acyltransferase 2. 26. Which tissue cannot use ketone bodies as a fuel? a. liver b. heart c. skeletal muscle d. brain

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Chap 17_8e 27. During β oxidation of fatty acids, _____ is produced in peroxisomes but not in mitochondria. a. acetyl-CoA b. FADH2 c. H2O d. H2O2 e. NADH 28. What is the symbol for the fatty acid shown in the figure?

a. 17:2(Δ8,11) b. 17:2(Δ8,10) c. 18:2(Δ9,11) d. 18:2(Δ9,12) e. 19:2(Δ10,13) 29. Palmitate (16:0) enters fatty acid oxidation as palmitoyl-CoA. How many molecules of water are produced by the complete oxidation of one molecule of palmitoyl-CoA to CO2 and water? a. 14 H2O b. 27 H2O c. 23 H2O d. 41 H2O e. 46 H2O 30. Carnitine is: a. a 15-carbon fatty acid. b. an essential cofactor for the citric acid cycle. c. essential for intracellular transport of fatty acids. d. one of the amino acids commonly found in protein. e. present only in carnivorous animals.

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Chap 17_8e 31. Various irreversible reactions drive processes bioenergetically. What is one such driving force leading to the formation of an acyl-CoA molecule? a. pyrophosphate hydrolysis b. thioester deacylation c. phosphoanhydride coupling d. enol to keto tautomerization e. concomitant decarboxylation 32. Which statement concerning the β oxidation of fatty acids is true? a. About 1,200 ATP molecules are ultimately produced per 20-carbon fatty acid oxidized. b. One FADH2 and two NADH are produced for each acetyl-CoA. c. The free fatty acid must be carboxylated in the β position by a biotin-dependent reaction before the process of β oxidation commences. d. The free fatty acid must be converted to a thioester before the process of β oxidation commences. e. Two NADH are produced for each acetyl-CoA. 33. In the liver, which enzyme is NOT required in the catabolism of glycerol? a. glycerol kinase b. triose phosphate isomerase c. hexokinase d. pyruvate kinase e. citrate synthase 34. Which statement(s) is true of the oxidation of one molecule of palmitate (a 16-carbon saturated fatty acid; 16:0) by the β-oxidation pathway, beginning with the free fatty acid in the cytoplasm? 1. Activation of the free fatty acid requires the equivalent of two ATPs. 2. Inorganic pyrophosphate is produced. 3. Carnitine functions as an electron acceptor. 4. Eight molecules of FADH2 are formed. 5. Eight molecules of acetyl-CoA are formed. 6. There is no direct involvement of NAD+. a. only 1 and 5 b. 1, 2, and 5 c. 1, 2, and 6 d. 1, 3, and 5 e. only 5

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Chap 17_8e 35. Which statement is true about perilipins? a. They are proteins on the surface of lipid droplets that help prevent untimely lipid mobilization. b. They are proteins in the interior of lipid droplets that stabilize the pH. c. They are proteins that aid in the transport of lipids in the bloodstream. d. They are modulators of hormone-sensitive lipase. 36. If an aerobic organism (e.g., the bacterium E. coli) were fed either alanine, glucose, or palmitate (16:0) as a source of energy, the energy yield from these molecules would be in the order: a. alanine, glucose, palmitate. b. glucose, alanine, palmitate. c. glucose, palmitate, alanine. d. palmitate, alanine, glucose. e. palmitate, glucose, alanine. 37. Which statement(s) about acetoacetate and β-hydroxybutyrate is false? 1. They can be used as a fuel by skeletal muscle. 2. They are synthesized in the liver. 3. They give rise to acetone. 4. They require acetoacetyl-CoA for their synthesis. 5. They may be regarded as water-soluble, transportable forms of citrate in the blood. a. 1 and 2 b. only 3 c. 1 and 4 d. 4 and 5 e. only 5 38. What are the two major sites in animals for fatty acid catabolism? a. the liver and the kidneys b. the liver and the brain c. skeletal muscle and the liver d. adipose tissue and the liver e. adipose tissue and skeletal muscle 39. Free fatty acids in the bloodstream are: a. bound to hemoglobin. b. carried by the protein serum albumin. c. freely soluble in the aqueous phase of the blood. d. nonexistent; the blood does not contain free fatty acids.

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Chap 17_8e 40. What is the MOST common human dietary source of phytanic acid? a. legumes b. citrus fruits c. meats d. dairy products 41. Which compound is required by an enzyme in the β-oxidation pathway in peroxisomes but not in the equivalent pathway in mitochondria? a. NAD+ b. CoA-SH c. O2 d. FAD e. H2O 42. Which compound is an intermediate of the β oxidation of fatty acids? a. CH3—(CH2)20—CO—COOH b. CH3—CH2—CO—CH2—CO— c. CH3—CH2—CO—CH2—OH d. CH3—CH2—CO—CO—S-CoA e. CH3—CO—CH2—CO—S-CoA 43. The fatty acid 14CH3(CH2)9COOH, in which the indicated carbon is labeled with 14C, is fed to an animal. 14CH (CH ) COOH 3 29

After allowing 30 minutes for fatty acid oxidation, in which would the label MOST likely be recovered? a. acetyl-CoA b. β-hydroxybutyryl-CoA c. both acetyl-CoA and propionyl-CoA d. palmitoyl-CoA e. propionyl-CoA 44. The carbon atoms from a fatty acid with an odd number of carbons will enter the citric acid cycle as acetylCoA and: a. butyrate. b. citrate. c. malate. d. succinyl-CoA. e. α-ketoglutarate.

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Chap 17_8e 45. Lipoprotein lipase acts in: a. hydrolysis of triacylglycerols of plasma lipoproteins to supply fatty acids to various tissues. b. intestinal uptake of dietary fat. c. intracellular lipid breakdown of lipoproteins. d. lipoprotein breakdown to supply needed amino acids. 46. Where is the major site of ketone body synthesis in mammals? a. the brain b. the liver c. adipose tissue d. skeletal muscle e. both the liver and adipose tissue 47. Which statement is true regarding the entry of long-chained fatty acids into the mitochondrial matrix? a. It is a rate-limiting step in the oxidation of these fatty acids. b. It is regulated by the concentration of chylomicrons. c. Entry is mediated by perilipin. d. Once these fatty acyl molecules enter the matrix, they may either be transported back out of the mitochondrion or proceed to β oxidation. 48. The conversion of palmitoyl-CoA (16:0) to myristoyl-CoA (14:0) and one molecule of acetyl-CoA by the βoxidation pathway results in the net formation of: a. one FADH2 and one NADH. b. one FADH2 and one NADPH. c. one FADH2, one NADH, and one ATP. d. two FADH2 and two NADH. e. two FADH2, two NADH, and one ATP. 49. Which statement is true regarding the regulation of β oxidation? a. AMPK activates acetyl-CoA carboxylase, which leads to the inhibition of β oxidation. b. A buildup in the levels of acetyl-CoA inhibits the thiolysis reaction in β oxidation. c. High levels of NADP+ activate β-hydroxyacyl-CoA dehydrogenase. d. Malonyl-CoA inhibits carnitine acyltransferase 2, which leads to the inhibition of β oxidation. e. β oxidation is enhanced in erythrocytes during starvation.

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Chap 17_8e 50. Which statement applies to the β oxidation of fatty acids? a. The process takes place in the cytosol of mammalian cells. b. Carbon atoms are removed from the acyl chain one at a time. c. Before oxidation, fatty acids must be converted to their CoA derivatives. d. NADP+ is the electron acceptor. 51. Which enzyme is the major regulatory control point for β-oxidation? a. pyruvate carboxylase b. carnitine acyltransferase 1 c. acetyl-CoA dehydrogenase d. enoyl-CoA isomerase e. methylmalonyl-CoA mutase 52. Refsum disease involves a genetic defect leading to a high blood concentration of: a. phytanic acid. b. ketone bodies. c. glucose. d. octanoic acid. 53. In solution at pH 6.5, palmitate has an overall negative charge. This means that the pKa of palmitate is: a. < 6.5. b. > 6.5. c. 6.5. 54. What is the major site of the formation of β-hydroxybutyrate from fatty acids? a. intestinal mucosa b. kidney c. liver d. adipose tissue e. skeletal muscle 55. What is the correct order of function of the enzymes of β oxidation? 1. β-hydroxyacyl-CoA dehydrogenase 2. thiolase 3. enoyl-CoA hydratase 4. acyl-CoA dehydrogenase a. 1, 2, 3, 4 b. 3, 1, 4, 2 c. 4, 3, 1, 2 d. 1, 4, 3, 2

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Chap 17_8e 56. Fatty acids are activated to acyl-CoAs and the acyl group is further transferred to carnitine because: a. acyl-carnitines readily cross the mitochondrial inner membrane, but acyl-CoAs do not. b. acyl-CoAs easily cross the mitochondrial membrane, but the fatty acids themselves will not. c. carnitine is required to oxidize NAD+ to NADH. d. fatty acids cannot be oxidized by FAD unless they are in the acyl-carnitine form. 57. In β oxidation, which cofactor is required for the conversion of a β-hydroxyacyl-CoA to a β-ketoacyl-CoA? a. NAD+ b. FAD c. H2O d. CoA-SH 58. Which statement(s) about lipases is true? 1. Intestinal lipases break down lipids in micelles found in the intestine. 2. Hormone-sensitive lipase is located primarily in hepatocytes. 3. Lipoprotein lipase is activated in capillaries by apoC-II. 4. Lipoprotein lipase delivers free fatty acids to peripheral tissues. a. 1 and 2 b. only 2 c. 1 and 4 d. 1, 3, and 4 e. only 4 59. In myocytes (muscle cells), what is a possible fate of acetyl-CoA produced from the oxidation of a fatty acid? a. oxidation via the citric acid cycle b. use in the synthesis of ketone bodies c. use in gluconeogenesis d. both oxidation via the citric acid cycle and use in the synthesis of ketone bodies e. both oxidation via the citric acid cycle and use in gluconeogenesis 60. The glycerol produced from the hydrolysis of triacylglycerols enters glycolysis as: a. glucose. b. glucose-6-phosphate. c. d-glyceraldehyde 3-phosphate. d. pyruvate. e. glyceryl-CoA.

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Chap 17_8e 61. Which statement is false regarding the catabolic oxidation of one molecule of palmitate (16:0)? a. Eight molecules of acetyl-CoA are formed. b. AMP and two Pi are formed in the cytosol. c. The oxidation reactions occur in the mitochondria. d. Eight molecules of H2O are required. e. Carnitine is required for the transport of fatty acids into the mitochondrial matrix. 62. How many ATP equivalents are produced for each round of β oxidation that removes two carbons from a fatty acid? Do not consider further oxidation of acetyl-CoA. a. 7.5 ATP b. 2 ATP c. 106 ATP d. 17.5 ATP e. 4 ATP 63. Which statement is true regarding fatty acids in adipocytes? a. They are primarily bound to albumin and stored in lipid droplets. b. They cannot be oxidized for energy in this tissue. c. In adipocytes, fatty acids from the bloodstream are assembled into triglycerides by esterifying them to glycerol. d. There is constant movement of fatty acids in and out of adipose tissues that is independent of hormone signals. 64. Transport of fatty acids from the cytoplasm to the mitochondrial matrix requires: a. ATP, carnitine, and coenzyme A. b. ATP, carnitine, and pyruvate dehydrogenase. c. ATP, coenzyme A, and hexokinase. d. ATP, coenzyme A, and pyruvate dehydrogenase. 65. The metabolite that regulates the activity of carnitine acyltransferase 1 is: a. acetyl-CoA. b. carnitine-CoA. c. malonyl-CoA. d. NADH. e. CoA.

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Chap 17_8e 66. Apolipoprotein B-48 is the main component of: a. ketone bodies. b. chylomicrons. c. lipoprotein lipase complex. d. lipid droplets. 67. What products from the oxidation of odd-numbered fatty acids enter the citric acid cycle? a. acetyl-CoA and citrate b. acetyl-CoA and malonyl-CoA c. acetyl-CoA and propionyl-CoA d. acetyl-CoA and succinyl-CoA e. succinyl-CoA and propionyl-CoA 68. Saturated fatty acids are degraded by the stepwise reactions of β oxidation, producing acetyl-CoA. Under aerobic conditions, how many ATP molecules would be produced as a consequence of removal of each acetyl-CoA? a. two b. three c. four d. five e. six 69. The major site of formation of acetoacetate from fatty acids is the: a. adipose tissue. b. intestinal mucosa. c. kidney. d. liver. e. muscle. 70. If the fatty acid 16:0 is catabolized completely, to carbon dioxide and water, the net yield of ATP per molecule of fatty acid is _____ ATP. a. 90.5 b. 97.5 c. 88.5 d. 106 e. 108

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Chap 17_8e 71. How much carbon dioxide is produced from the complete aerobic catabolism of one molecule of linoleate (18:2(Δ9,12)) via catabolic pathways? a. 18 CO2 b. 17 CO2 c. 16 CO2 d. 15 CO2 e. 8 CO2 72. In which cellular compartment are ketone bodies synthesized? a. the cytosol b. the mitochondrial matrix c. the mitochondrial intermembrane space d. the endoplasmic reticulum e. peroxisomes 73. What role does serum albumin play in fat metabolism? a. It is a component of the chylomicron lipoprotein. b. It acts as a carrier for free fatty acids in the bloodstream. c. It binds hormone-sensitive lipase that is responsible for the release of triglycerides from adipocytes. d. It is involved in the transport of short-chain fatty acids across the plasma membrane. e. It is important in the transport of ketone bodies from the liver to the brain. 74. In the disease sprue, vitamin B12 (cobalamin) is poorly absorbed in the intestine, resulting in B12 deficiency. If each of these fatty acids were in the diet, for which one would the process of fatty acid oxidation be MOST affected in a patient with sprue? a. CH3(CH2)10COOH b. CH3(CH2)11COOH c. CH3(CH2)12COOH d. CH3(CH2)14COOH e. CH3(CH2)18COOH 75. What is the role of lipoprotein lipase? a. It hydrolyzes triacylglycerols of plasma lipoproteins to supply fatty acids to various tissues. b. It aids intestinal uptake of dietary fat. c. It initiates intracellular lipid breakdown of lipoproteins. d. It degrades lipoproteins in order to supply needed amino acids to various tissues. e. It acts to regenerate lipoprotein particles in hepatocytes.

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Chap 17_8e 76. Which statement is NOT true regarding the oxidation of one molecule of palmitate (16:0) by the βoxidation pathway? a. One molecule of ATP is needed. b. Eight molecules of acetyl-CoA are formed. c. Eight molecules of FADH2 are formed. d. AMP and PPi are formed. e. The reactions occur in the mitochondria. 77. Which compound is able to cross the inner mitochondrial membrane? a. acetyl-CoA b. fatty acyl–carnitine c. fatty acyl–CoA d. malonyl-CoA 78. In which cellular compartment is oxidation carried out? a. the cytosol b. the mitochondrial matrix c. the mitochondrial intermembrane space d. the endoplasmic reticulum e. peroxisomes 79. Describe the steps in the metabolic pathway in which cells oxidize a four-carbon, straight-chain, saturated fatty acid (butyrate; 4:0) to the fragments that enter the citric acid cycle. Show the structures of intermediates and products, and indicate where any cofactors participate.

80. One of the steps in fatty acid oxidation in mitochondria involves the addition of water across a double bond. What is the next step in the process? Show structures and indicate where any cofactor(s) participates.

81. What are the two major differences between the β-oxidation pathway in mitochondria and the βoxidation pathway in peroxisomes?

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Chap 17_8e 82. Describe the steps in the metabolic pathway in which cells oxidize a five-carbon, straight-chain, saturated fatty acid (valerate; 5:0) to the fragments that enter the citric acid cycle. Show the structures of intermediates and products, and indicate where any cofactors participate.

83. Write a balanced equation for the complete oxidation (to acetyl-CoA and any other products that might be formed) of pelargonic acid, CH3(CH2)7COOH.

84. In the citric acid cycle, a double bond is introduced into a four-carbon compound containing the —CH2— CH2— group, producing fumarate. Show a similar reaction that occurs in the β-oxidation pathway.

85. Explain the chemical reason why the addition of water across the double bond in the second step of β oxidation occurs with the OH adding at the β carbon, not the α carbon. Also, how does addition at the β carbon aid in the subsequent steps of β oxidation?

86. An experimenter studying the oxidation of fatty acids in extracts of liver found that when palmitate (16:0) was provided as substrate, it was completely oxidized to CO2. However, when undecanoic acid (11:0) was added as substrate, incomplete oxidation occurred unless the experimenter bubbled CO2 through the reaction mixture. The addition of the protein avidin, which binds tightly to biotin, prevented the complete oxidation of undecanoic acid even in the presence of CO2, although it had no effect on palmitate oxidation. Explain these observations in light of what is known of fatty acid oxidation reactions.

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Chap 17_8e 87. Write a balanced equation for the β oxidation of palmitoyl-CoA, a 16-carbon, fully saturated fatty acid, and indicate how much of each product is formed.

88. Why is it more efficient to store energy as lipid, rather than as glycogen?

89. Describe the third and fourth steps in the β oxidation of a saturated fatty acid. Name the enzymes involved and indicate where any cofactors participate.

90. Briefly explain the basic concept of oxidation

91. A laboratory report shows the presence of a high concentration of ketone bodies in the urine of a patient, what disease would be suspected? Why do ketone bodies accumulate in such patients?

92. For each two carbon increase in the length of a saturated fatty acid chain, how many additional molecules of ATP can be formed upon complete oxidation of one molecule of the fatty acid to CO2 and H2O?

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Chap 17_8e 93. In the first step of fatty acid oxidation, the fatty acid (R—COOH) is converted to its coenzyme A derivative in the reaction: R—COOH + ATP + CoA-SH → R—CO—S-CoA + AMP + PPi The standard free-energy change (ΔG'º) for this reaction is –15 kJ/mol. What will tend to make the reaction even more favorable when it takes place within a cell?

94. Two vitamins, biotin and vitamin B12, play crucial roles in the metabolism of propionic acid (propionate). Explain this by showing the steps in which each is essential in propionate metabolism.

95. Explain why lipases are required in both the intestine and in the bloodstream.

96. Indicate whether the statement is likely true or false. Explain. After a breakfast rich in fat and very low in carbohydrates, acetyl-CoA levels rise and ketone body synthesis decreases.

97. The total degradation of a fatty acid with an odd number of carbons yields acetyl-CoA and another compound, X. Show the structure of X and describe the pathway by which it is converted into a citric acid cycle intermediate, including where any cofactors participate.

98. Adding carnitine to a culture of isolated, intact mitochondria stimulates the oxidation of acetyl-CoA. Why?

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Chap 17_8e 99. Describe the first two steps of β oxidation of saturated fatty acids. Indicate where any cofactors participate.

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Chap 17_8e Answer Key 1. c 2. d 3. b 4. b 5. b 6. d 7. d 8. a 9. d 10. c 11. d 12. d 13. d 14. e 15. c 16. d 17. c 18. b 19. a 20. d 21. b 22. c 23. a 24. e 25. a 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_8e 27. d 28. d 29. c 30. c 31. a 32. d 33. c 34. b 35. a 36. e 37. e 38. c 39. b 40. d 41. c 42. e 43. e 44. d 45. a 46. b 47. a 48. a 49. b 50. c 51. b 52. a 53. a 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_8e 55. c 56. a 57. a 58. d 59. a 60. c 61. d 62. e 63. c 64. a 65. c 66. b 67. d 68. c 69. d 70. d 71. a 72. b 73. b 74. b 75. a 76. c 77. b 78. e 79. Butyrate is first activated: Butyrate + ATP + CoA-SH → butyryl-CoA + AMP + PPi Then, the butyryl group is transferred to carnitine and transported into the mitochondrial matrix, where it is reconverted to the butyryl-CoA derivative. This passes through the four steps of β oxidation. (See Fig. 17-8a.)

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Chap 17_8e 80. The reaction is that catalyzed by β-hydoxyacyl-CoA dehydrogenase, for which NAD+ is cofactor. (See Fig. 178a.) 81. The first major difference lies in the detailed chemistry of the first of the four steps of β oxidation. In the mitochondria, the reduced flavin that is a product of the first step is reoxidized via the electron transport chain. In the peroxisomes, the reduced flavin is reoxidized by O2, thus producing H2O2. The second major difference is that the peroxisomal enzymes are much more active on longer (i.e., 26 carbons) fatty acids than the mitochondrial enzymes. 82. Valerate is first activated: Valerate + ATP + CoA-SH valeryl-CoA + AMP + PPi Then, the valeryl group is transferred to carnitine and transported into the mitochondrial matrix, where it is reconverted to the valeryl-CoA derivative. This passes through the four steps of β oxidation producing acetyl-CoA and propionyl-CoA. (See Fig. 17-8a.) Propionyl-CoA would be converted to succinyl-CoA by the reaction sequence in Figure 17-12. 83. The odd-chain fatty acid is first activated to the CoA derivative, then oxidized to three acetyl-CoAs and one propionyl-CoA by β oxidation. The propionyl-CoA is converted to succinyl-CoA through the sequence of reactions shown in Figure 17-12. The overall reaction is therefore: Pelargonic acid + HCO3– + ATP + 4CoA-SH + 3FAD + 3NAD+ → 3 acetyl-CoA + succinyl-CoA + 3FADH2 + 3NADH + AMP + PPi 84. This is the reaction catalyzed by acyl-CoA dehydrogenase. (See Fig. 17-8a.) 85. Recall that the carbon that is α to a carbonyl is readily able to become a carbanion; that is, it is not a good electrophilic center for nucleophilic addition of a hydroxide (see Chapter 13). The β carbon, by contrast, is a good electrophilic center as can be readily shown by "pushing" the electrons from the C C double bond onto the carbonyl oxygen. Addition of the OH in the β position is useful for later steps since after oxidation of the OH to a carbonyl, the α carbon is even more susceptible to becoming a carbanion, as is needed for the reverse Claisen condensation catalyzed by thiolase. 86. Oxidation of odd-chain fatty acid yields acetyl-CoA + propionyl-CoA. The reaction CO2 + propionylCoA → methylmalonyl-CoA is catalyzed by propionyl-CoA carboxylase, a biotin-containing enzyme, which is therefore inhibited by avidin. 87. The overall reaction is: Palmitoyl-CoA + 7CoA-SH + 7FAD + 7NAD+ + 7H2O → 8 acetyl-CoA + 7FADH2 + 7NADH + 7H+ 88. First, the energy yield per gram of lipid (about 38 kJ/g) is more than twice that for carbohydrate (about 17 kJ/g). Second, lipid is stored as anhydrous lipid droplets, but carbohydrates such as glycogen and starch are stored hydrated, and the water of hydration roughly triples the effective weight of the carbohydrate, reducing the energy yield to about 6 kJ/g.

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Chap 17_8e 89. The reactions are those catalyzed by β-hydoxyl-CoA dehydrogenase and thiolase. Note the formation of NADH for the third step and the cleavage of the carbon–carbon bond in a reverse Claisen condensation for the fourth step. (See Fig. 17-8a.) 90. Relatively short-chain fatty acids (i.e., 10–12 carbons) are oxidized on the α end (in three steps) to form a second carboxyl group. The "double-ended" fatty acid is then taken into the mitochondria and subjected to normal β oxidation, except that the last product is not acetyl-CoA, but rather succinate or adipate. 91. The patient is probably an untreated diabetic, but the condition might also result from fasting. In either case, the unavailability of glucose from the blood stimulates gluconeogenesis in the liver. As the substrate for glucose formation, oxaloacetate is withdrawn from the citric acid cycle, bringing that cycle to a near halt. The fatty acids being oxidized in the liver yield acetyl-CoA, which now cannot be oxidized via the citric acid cycle. Reversal of the thiolase reaction produces acetoacetyl-CoA, which is then converted into ketone bodies and exported from the liver. (See Fig. 17-18.) 92. Each —CH2—CH2— unit yields 14 extra ATP molecules. The two oxidations of the β-oxidation pathway produce 1 FADH2 and 1 NADH, which yield 1.5 and 2.5 ATP, respectively, by oxidative phosphorylation. The extra acetyl-CoA, when oxidized via the citric acid cycle, yields another 10 ATP equivalents: 3 NADH, 1 FADH2, and 1 ATP or GTP. 93. The hydrolysis of PPi by inorganic pyrophosphatase, for which ΔG'º is –19 kJ/mol, makes the overall ΔG'º more negative. 94. Biotin and vitamin B12 act as cofactors for propionyl-CoA carboxylase and methylmalonyl-CoA mutase, respectively; see Figure 17-12 for the complete sequence of reactions. 95. Fats ingested in the diet are mostly found as triacylglycerols. In order to be taken up through the intestinal mucosa these triacylglycerols must be converted to free fatty acids by the intestinal lipases. Once in the bloodstream, the free fatty acids are again converted to triacylglycerols for transport in chylomicrons. For absorption into remote tissues from the bloodstream, the triacylglycerols must again be converted to free fatty acids, this time by lipases found in the bloodstream. 96. This statement is likely false. Following an overnight fast, the glycogen stores in the liver are likely significantly reduced. Therefore, if one has a breakfast very low in carbohydrates, the gluconeogenic pathway will likely be activated to maintain blood glucose levels. If an individual is catabolizing fatty acids in the presence of gluconeogenic conditions, the excess acetyl-CoA that cannot be oxidized by the citric acid cycle will be converted to ketones. Therefore, after a breakfast rich in fat and very low in carbohydrates, acetyl-CoA levels rise and ketone body synthesis likely increases. 97. X is propionyl-CoA, and its conversion into succinyl-CoA is accomplished by the reactions in Figure 17-12. 98. Carnitine is essential in the transport of fatty acyl groups into the mitochondrial matrix, where fatty acid oxidation occurs. 99. The reactions are those catalyzed by fatty acyl–CoA dehydrogenase and enoyl hydratase. Note the formation of FADH2 for the first step and the addition of water across the double bond in the second step. (See Fig. 17-8a.) Copyright Macmillan Learning. Powered by Cognero.

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Chap 17_8e

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Chap 18_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which substance directly donates a nitrogen atom for the formation of urea during the urea cycle? a. adenine b. aspartate c. creatine d. glutamate e. ornithine 2. In mammals, which are possible compounds excreted for the elimination of nitrogen? a. ammonia b. urea c. pyrimidine d. both ammonia and urea e. both urea and pyrimidine 3. The conversion of glutamate to an α-keto acid and

a. does not require any cofactors. b. is a reductive deamination. c. is accompanied by ATP hydrolysis catalyzed by the same enzyme. d. is catalyzed by glutamate dehydrogenase. e. requires ATP. 4. In amino acid catabolism, the first reaction for many amino acids is a(n): a. decarboxylation requiring thiamine pyrophosphate. b. hydroxylation requiring NADPH and O2. c. oxidative deamination requiring NAD+. d. reduction requiring pyridoxal phosphate. e. transamination requiring pyridoxal phosphate. 5. Which amino acid can be directly converted into a citric acid cycle intermediate by transamination? a. glutamate b. serine c. threonine d. tyrosine e. proline

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Chap 18_8e 6. Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to: a. oxaloacetate. b. propionate. c. pyruvate. d. succinate. e. succinyl-CoA. 7. Catabolism of which substance can enter the citric acid cycle as succinyl-CoA? a. threonine b. proline c. histidine d. tyrosine 8. Which reaction associated with the urea cycle occurs in the cytosol? a. the synthesis of carbamoyl phosphate b. the synthesis of citrulline c. the synthesis of arginosuccinate d. transamination between glutamate and oxaloacetate to yield aspartate 9. Under which circumstances are amino acids NOT metabolized via oxidative degradation? a. starvation b. plants growing in nutrient-rich soils c. normal protein turnover d. uncontrolled diabetes 10. In maple syrup urine disease, the metabolic defect involves: a. a deficiency of the vitamin niacin. b. oxidative decarboxylation. c. synthesis of branched-chain amino acids. d. transamination of an amino acid. e. uptake of branched-chain amino acids into liver. 11. Which cofactor is NOT required for the conversion of serine into glycine? a. tetrahydrofolate b. pyridoxal phosphate c. NADH d. FMN

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Chap 18_8e 12. Which statement is true regarding glutamine synthetase? a. This enzyme is classified as a transferase. b. This enzyme is classified as a ligase and catalyzes a transamination reaction. c. This enzyme catalyzes a hydrolysis reaction. d. This enzyme converts glutamate to glutamine. 13. Which amino acid is not catabolized to acetyl-CoA? a. tryptophan b. lysine c. tyrosine d. valine e. leucine 14. Urea synthesis in mammals takes place primarily in tissues of the: a. brain. b. kidney. c. liver. d. skeletal muscle. e. small intestine. 15. Which two amino acids are exclusively ketogenic? a. leucine and lysine b. isoleucine and leucine c. alanine and glutamine d. proline and leucine e. lysine and arginine 16. Which statement is false regarding pepsin? a. This enzyme is activated by irreversible covalent modification. b. This enzyme is classified as a hydrolase. c. This enzyme is highly active at neutral pH. d. This enzyme is secreted in response to protein ingestion. e. This enzyme has a specificity for cleavage at aromatic amino acids. 17. Conversion of ammonia to carbamoyl phosphate in mitochondria consumes how many ATP equivalents? a. none b. one c. two d. three

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Chap 18_8e 18. Which amino acid can be catabolized to either acetyl-CoA or succinyl-CoA? a. asparagine b. serine c. alanine d. isoleucine e. leucine 19. Conversion of ornithine to citrulline is a step in the synthesis of: a. aspartate. b. carnitine. c. pyruvate. d. tyrosine. e. urea. 20. The coenzyme involved in a transaminase reaction is: a. biotin phosphate. b. lipoic acid. c. NADP+. d. pyridoxal phosphate. e. thiamine pyrophosphate. 21. If 15N-labeled glutamate is introduced into liver cells, what compounds in the urea cycle will NOT be rapidly labeled with the nitrogen? a. ornithine b. aspartate c. arginine d. urea e. both ornithine and aspartate 22. Phenylketonuria is associated with disorders in the catabolism of which amino acid? a. phenylalanine b. tyrosine c. tryptophan d. histidine 23. Which hormone is triggered by the entry of acidic stomach content into the intestine? a. gastrin b. insulin c. cholecystokinin d. secretin Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_8e 24. Which amino acid is used to transport amino groups from muscle to the liver in a nontoxic form? a. arginine b. asparagine c. threonine d. glutamate e. alanine 25. Which amino acids are converted to succinyl-CoA? 1. isoleucine 2. valine 3. methionine 4. arginine 5. threonine a. 2 and 4 b. 2, 3, and 4 c. 2, 4, and 5 d. 1 and 5 e. 1, 2, 3, and 5 26. Which amino acid enters the citric acid cycle as α-ketoglutarate during their catabolism? a. proline b. threonine c. aspartate d. leucine e. tyrosine 27. In the urea cycle, ornithine transcarbamoylase catalyzes: a. cleavage of urea to ammonia. b. formation of citrulline from ornithine and another reactant. c. formation of ornithine from citrulline and another reactant. d. formation of urea from arginine. e. transamination of arginine. 28. Which statement is true regarding tyrosine catabolism? a. The first step in catabolism of tyrosine is reduction to phenylalanine. b. Tyrosine can be considered solely glucogenic. c. Atoms from tyrosine's side chain enter the citric acid cycle as fumarate. d. All of the statements are true.

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Chap 18_8e 29. Which statement is true for uric acid? a. This compound is a precursor to urea. b. This compound is the major means of nitrogen elimination in uricotelic species, like birds. c. This compound is a pyrimidine base. d. The carbon atoms in uric acid are highly reduced. 30. In the digestion of protein that occurs in the small intestine, which enzyme is critical in the activation of zymogens? a. enteropeptidase b. hexokinase c. papain d. pepsin e. secretin 31. Methionine synthase uses what substrates to synthesize methionine? a. cysteine b. S-adenosylmethionine c. ATP d. homocysteine 32. The coenzyme required for all transaminations is derived from: a. niacin. b. pyridoxine (vitamin B6). c. riboflavin. d. thiamin. e. vitamin B12. 33. Which compound can be described as glucogenic and ketogenic? a. leucine b. phenylalanine c. lysine d. aspartate e. glutamine 34. Which substance is NOT involved in the production of urea from

via the urea cycle?

a. aspartate b. ATP c. carbamoyl phosphate d. malate e. ornithine Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_8e 35. Which cofactor is typically required in transamination reactions? a. pyridoxal phosphate b. coenzyme Q c. biotin d. thiamine pyrophosphate e. nicotinamide adenine dinucleotide 36. Which amino acid can be considered to be both glucogenic and ketogenic? a. threonine b. aspartate c. leucine d. serine 37. Carbamoyl phosphate synthetase I is allosterically activated by what molecule? a. glutamate b. arginine c. N-acetylglutamate d. carbamoyl phosphate e. acetyl-CoA 38. Which statement is false regarding ketogenic and glucogenic amino acids? a. Glucogenic amino acids cannot be used to make ketone bodies. b. Ketogenic amino acids can be used to synthesize fatty acids. c. Leucine and isoleucine are both exclusively ketogenic amino acids. d. Both valine and threonine catabolism produce succinyl-CoA. 39. Which compound is a zymogen that when converted to its active proteolytic enzyme form can activate more of its own zymogen? a. chymotrypsinogen b. pepsin c. pepsinogen d. trypsin e. trypsinogen 40. Which hormone is triggered by the entry of protein into the stomach? a. gastrin b. insulin c. cholecystokinin d. secretin

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Chap 18_8e 41. Which statement is NOT true of the reaction catalyzed by glutamate dehydrogenase? a. It is similar to transamination in that it involves the coenzyme pyridoxal phosphate. b. is produced. c. The enzyme can use either NAD+ or NADP+ as a cofactor. d. The enzyme is glutamate-specific, but the reaction is involved in oxidizing other amino acids. e. α-ketoglutarate is produced from an amino acid. 42. Which amino acid is essential for humans? a. alanine b. aspartic acid c. asparagine d. serine e. threonine 43. Which amino acid(s) can be transported into mitochondria from the cytosol in conjunction with the urea cycle? a. glutamine b. glutamate c. ornithine d. All of the answers are correct. 44. In which pair of compounds is the second molecule produced by the deamination of the first molecule? a. aspartic acid and oxaloacetate b. glutamine and glutamate c. alanine and pyruvate d. All of the answers are correct. 45. Which amino acids are converted to α-ketoglutarate? 1. glycine 2. glutamate 3. histidine 4. arginine 5. proline a. 1, 3, and 5 b. 2, 3, and 4 c. 2, 3, and 5 d. 2, 3, 4, and 5 e. 3, 4, and 5

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Chap 18_8e 46. Which amino acids are both ketogenic and glucogenic? 1. isoleucine 2. valine 3. histidine 4. arginine 5. tyrosine a. 1 and 5 b. 1, 3, and 5 c. 2 and 4 d. 2, 3, and 4 e. 2, 4, and 5 47. If a patient's urine contains unusually high concentrations of urea, which diet has the person probably been eating recently? a. high carbohydrate, low protein b. high carbohydrate, no protein, no fat c. high fat, high carbohydrate, no protein d. high fat, low protein e. low carbohydrate, high protein 48. Which product is created during the conversion of threonine into glycine during amino acid catabolism? a. acetyl-CoA b. water c. NADH d. both acetyl-CoA and NADH e. both water and NADH 49. Which is the most reduced state of tetrahydrofolate? a. N10-formyltetrahydrofolate b. N5,N10-methylenetetrahydrofolate c. N5-methyltetrahydrofolate d. N5-formyltetrahydrofolate 50. Glutamate is metabolically converted to α-ketoglutarate and

by a process described as:

a. deamination. b. hydrolysis. c. oxidative deamination. d. reductive deamination. e. transamination.

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Chap 18_8e 51. Alanine and pyruvate are interconverted by which enzyme? a. alanine-pyruvate hydrotase b. pyruvate transferase c. pyruvate kinase d. alanine racemase e. alanine aminotransferase 52. What enzyme converts arginine into urea and ornithine? a. arginase b. urease c. ornithine synthase d. argininosuccinase 53. Which compound is NOT a protease that acts in the small intestine? a. chymotrypsin b. elastase c. enteropeptidase d. secretin e. trypsin 54. What defines an essential amino acid? a. It is strictly glucogenic. b. It is ketogenic and glucogenic. c. It is strictly ketogenic. d. It is synthesized by the body. e. It must be obtained in the diet. 55. Which statement is true regarding lysine? a. This is a nonessential amino acid. b. Catabolism of lysine shares multiple steps with that of tryptophan. c. Carbons of lysine catabolism enter the citric acid cycle at succinyl-CoA. d. Lysine is both a glucogenic and ketogenic enzyme. 56. Deamination of MOST amino acids in the liver is accompanied by the conversion of: a. pyruvate into alanine. b. glutamate into glutamine. c. α-ketoglutarate to glutamate. d. nitrogen into urea. e. oxaloacetate into aspartate.

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Chap 18_8e 57. Serotonin is produced from the metabolism of which amino acid? a. valine b. serine c. cysteine d. tyrosine e. tryptophan 58. Which statement is true regarding the branched-chain α-keto acid dehydrogenase complex? a. This enzyme is activated by phosphorylation. b. This enzyme catalyzes a reaction homologous to succinate dehydrogenase. c. This enzyme catalyzes an oxidative decarboxylation. d. Defects in this complex are a cause of phenylketonuria. 59. Transamination from alanine to α-ketoglutarate requires the coenzyme: a. biotin. b. NADH. c. thiamine pyrophosphate. d. pyridoxal phosphate. e. No coenzyme is involved. 60. Classify the reaction type for the conversion of arginine into urea and ornithine by arginase. a. hydrolysis b. condensation c. transamination d. proteolytic cleavage 61. Which statement is false in reference to the mammalian synthesis of urea? a. Krebs was a major contributor to the elucidation of the pathway involved. b. The amino acid arginine is the immediate precursor to urea. c. The carbon atom of urea is derived from mitochondrial . d. The precursor to one of the nitrogens of urea is aspartate. e. The process of urea production is an energy-yielding series of reactions. 62. The amino acids serine, alanine, and cysteine can be catabolized to yield: a. fumarate. b. pyruvate. c. succinate. d. α-ketoglutarate.

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Chap 18_8e 63. Pyridoxal phosphate participates in a variety of reactions in amino acid metabolism, EXCEPT for: a. hydrolysis. b. decarboxylation. c. racemization. d. transamination. 64. Which statement is true regarding the conversion of arginine to ornithine in the urea cycle? a. The enzyme catalyzing this reaction is a hydrolase. b. This enzyme-catalyzed reaction occurs in the matrix. c. One of the products of this reaction is fumarate. d. The enzyme catalyzing this reaction is a ligase. e. The enzyme catalyzing this reaction is a hydrolase, and the reaction occurs in a matrix. 65. Which amino acid is catabolized to succinyl-CoA, but not acetyl-CoA? a. threonine b. isoleucine c. proline d. valine 66. Which statement is true regarding pyridoxal phosphate? a. This prosthetic group is critical in transamination reactions. b. It is necessary for the conversion of glycine to serine. c. Pyridoxal phosphate activates the α carbon of amino acids at critical stages of reactions. d. It helps catalyze elimination of water in the serine dehydratase reaction. e. All of the statements are true. 67. Which compound is NOT transported across the inner mitochondrial membrane as part of either the urea cycle and aspartate-argininosuccinate shunt? a. fumarate b. aspartate c. ornithine d. citrulline 68. Tetrahydrofolate and its derivatives shuttle _____ between different substrates. a. electrons b. H+ c. acyl groups d. one-carbon units e. NH2 groups

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Chap 18_8e 69. What processes are associated with the glucose-alanine cycle? a. formation of pyruvate b. formation of glutamate c. conversion of alanine to α-ketoglutarate d. All of the answers are correct. 70. Which amino acids are converted to oxaloacetate (not via pyruvate)? 1. asparagine 2. glutamine 3. serine 4. arginine 5. aspartate a. 2 and 4 b. 2, 3, and 4 c. 2, 4, and 5 d. 1 and 5 e. 1, 3, and 5 71. The human genetic disease phenylketonuria can result from: a. deficiency of protein in the diet. b. inability to catabolize ketone bodies. c. inability to convert phenylalanine to tyrosine. d. inability to synthesize phenylalanine. e. production of enzymes containing no phenylalanine. 72. The E3 subunit of pyruvate dehydrogenase, α-ketoglutarate dehydrogenase, and the branched-chain αketo acid dehydrogenase complex is identical in each multienzyme complex. What reaction is catalyzed by this subunit, and why does it make sense that it is common while E1 and E2 are not?

73. Why does a mammal go to all of the trouble of making urea from ammonia rather than simply excreting ammonia as many bacteria do?

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Chap 18_8e 74. Name one amino acid whose oxidation proceeds via the intermediate shown: (a) pyruvate, (b) oxaloacetate, (c) α-ketoglutarate, (d) succinyl-CoA, (e) fumarate.

75. Describe the three different forms of nitrogen by which different organisms dispose of excess nitrogen obtained in the diet. Give examples of organisms that produce these different forms.

76. Name four amino acids that can be converted directly (in one step) into pyruvate or a citric acid cycle intermediate, and name the intermediate formed from each.

77. Describe the roles of glutamine synthetase and glutaminase in the metabolism of amino groups in mammals.

78. Define zymogen and describe the role of one zymogen in protein digestion.

79. Explain why a doctor might provide high concentrations of the amino acid Arg to patients who have a deficiency in one of the first three enzymes of the urea cycle.

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Chap 18_8e 80. Diagram the degradative pathway from proline to an intermediate of either glycolysis or the citric acid cycle. Show structures of intermediates and indicate where cofactors are involved.

81. Give the name of the α-keto acid resulting when these amino acids undergo transamination with αketoglutarate: (a) glutamate, (b) aspartate, (c) alanine.

82. Describe (a) the fundamental nutritional problem faced by individuals with genetic defects in enzymes involved in urea formation and (b) two approaches to treatment of these diseases.

83. Amino acid catabolism involves the breakdown of 20 amino acids all of which contain nitrogen but have different carbon skeletons. What overall strategy is used to deal with this problem? Illustrate the strategy with two examples.

84. There are bacteria for which alanine can serve as the chief energy source; they oxidize the carbon skeleton of this amino acid, thereby generating ATP. Describe the first step in alanine degradation; show any cofactors that participate.

85. Briefly describe the role of (a) gastrin, (b) pepsinogen, (c) cholecystokinin, and (d) enteropeptidase in protein digestion.

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Chap 18_8e 86. Describe the reactions and the role of the glucose-alanine cycle.

87. Transamination reactions are catalyzed by a family of enzymes, all of which require _____ as a coenzyme. In the first step of a transamination, the coenzyme in the aldehyde form condenses with the _____ group of an amino acid to form a(n) _____.

88. The amino acids leucine, valine, and isoleucine are preferentially catabolized in muscle tissue, while other amino acids are catabolized primarily in the liver. Given the characteristics of these amino acids, why might this be advantageous? Where in the cell would they be catabolized?

89. In the treatment of diabetes, insulin is given intravenously. Why can't this hormone, a small protein, be taken orally?

90. During starvation, more urea production occurs. Explain this observation.

91. Show the reaction in which ammonia is formed from glutamate, include any required cofactors and/or intermediates.

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Chap 18_8e 92. Both glutamine and alanine transport nitrogen in the bloodstream. Why might it be considered an advantage to transport glutamine instead of alanine?

93. Describe, by showing the chemical intermediates, the role of pyridoxal phosphate in the transamination of an amino acid.

94. Outline two paths by which 14N-labeled glutamate can lead to labeled products in the urea cycle.

95. A nutritionist is responsible for formulating the diet for a 4-year-old boy with phenylketonuria. How will the nutritionist decide what kind and amount of protein to include in the diet?

96. A laboratory report shows the presence of a high concentration of phenylalanine and its metabolites in the urine of a patient. What disease would be suspected? What defect(s) in metabolism accounts for the accumulation of phenylalanine in such patients?

97. Degradation of amino acids yields compounds that are common intermediates in the major metabolic pathways. Explain the distinction between glucogenic and ketogenic amino acids in terms of their metabolic fates.

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Chap 18_8e Answer Key 1. b 2. d 3. d 4. e 5. a 6. c 7. a 8. c 9. b 10. b 11. d 12. d 13. d 14. c 15. a 16. c 17. c 18. d 19. e 20. d 21. a 22. a 23. d 24. e 25. e 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_8e 27. b 28. c 29. b 30. a 31. d 32. b 33. b 34. d 35. a 36. a 37. c 38. c 39. e 40. a 41. a 42. e 43. d 44. d 45. d 46. a 47. e 48. d 49. c 50. c 51. e 52. a 53. d 54. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_8e 55. b 56. c 57. e 58. c 59. d 60. a 61. e 62. b 63. a 64. a 65. d 66. e 67. a 68. d 69. d 70. d 71. c 72. E3 is responsible for the reduction of NAD+ to NADH with the associated reoxidations of the lipoamide swinging arm. This reaction is the same in all the different complexes. E1 and E2 have different substrates (depending on the specific complex) so they are not shared.

73. When bacteria release ammonia into the surrounding medium, it is diluted to nontoxic levels. The ammonia produced by amino acid catabolism in mammals cannot be sufficiently diluted in the tissues and the blood to avoid accumulating at toxic levels. Urea is much less toxic than ammonia.

74. Possible answers: (a) alanine, tryptophan, glycine, serine, cysteine; (b) aspartate, asparagine; (c) glutamate, glutamine, arginine, histidine, proline; (d) isoleucine, threonine, methionine, valine; (e) phenylalanine, tyrosine. 75. (1) ammonotelic: release into the surrounding medium as NH4 + (bacteria and many marine organisms); (2) uricotelic: production of uric acid (birds and reptiles); (3) ureotelic: production and excretion of urea (land-dwelling animals)

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Chap 18_8e 76. (1) aspartate, oxaloacetate; (2) glutamate, α-ketoglutarate; (3) alanine, pyruvate; (4) serine, pyruvate. (Order is not important.)

77. In tissues that are metabolizing the carbon skeletons of amino acids, the amino groups are transferred by transamination to glutamate, then released as ammonia. Ammonia, which is toxic, is then combined with glutamate to form glutamine; the reaction is catalyzed by glutamine synthetase and requires ATP. Glutamine is moved from the extrahepatic tissues to the liver and kidneys, where the amino group is released from glutamine by glutaminase; the products are glutamate and ammonia. The ammonia delivered in this way to the liver is converted to urea, then excreted.

78. A zymogen is an inactive form of an enzyme that can be activated by proteolytic cleavage. The pancreatic enzymes pepsinogen, chymotrypsinogen, trypsinogen, and procarboxypeptidases A and B are all inactive forms of proteases, which are activated by proteolytic cleavage after their release into the small intestine.

79. The Arg is converted efficiently to urea and ornithine since the last enzyme of the urea cycle is still functioning normally. Thus, one produces higher than normal concentrations of ornithine, which is required for the rest of the cycle to work. That is, increase the flux through the pathway by providing higher concentrations of the intermediates.

80. The shortest pathway is from proline to Δ1-pyrroline-5-carboxylate, glutamate semialdehyde, glutamate, and αketoglutarate. See Figure 18-26. 81. (a) α-ketoglutarate, (b) oxaloacetate, (c) pyruvate; see Figure 18-4

82. (a) A defect in urea synthesis can result in the formation of toxic blood levels of ammonia from the breakdown of ingested proteins. Thus, it is desirable to limit the intake of amino acids. However, some amino acids are essential for humans (i.e., not biosynthesized) and hence must be ingested in adequate amounts. (b) One approach is to administer compounds that deplete the supply of glycine and glutamine. The replenishment of these amino acids removes ammonia from the blood. Another approach is to administer compounds that allow the liver to bypass the enzyme that is defective in the individual.

83. Nitrogen is removed by transamination to glutamate. This converts the amino acid to an α-keto acid that either is an intermediate in carbohydrate catabolism or is converted to one. (See Fig. 18-2.) Specific examples are shown in section 18.3. 84. The first step is removal of the amino group by transamination, in which pyridoxal phosphate (PLP) serves as an essential cofactor and α-ketoglutarate is the usual amino group acceptor: Alanine + α-ketoglutarate

pyruvate + glutamate

85. (a) The hormone gastrin stimulates secretion of HCl and pepsinogen into the stomach; (b) pepsinogen, after its conversion to pepsin, begins protein degradation in the stomach; (c) the hormone cholecystokinin stimulates the secretion of the pancreatic zymogens chymotrypsinogen, trypsinogen, and procarboxypeptidase into the small intestine; (d) enteropeptidase is a proteolytic enzyme that activates trypsinogen in the small intestine. Trypsin in turn activates chymotrypsinogen, procarboxypeptidases, proelastase, and trypsinogen itself. Copyright Macmillan Learning. Powered by Cognero.

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Chap 18_8e 86. Toxic ammonia formed by amino acid catabolism in muscle is transported to the liver as alanine, which is nontoxic. Alanine is formed in muscle by transamination of pyruvate (formed by glycolysis); glutamate formed by glutamate dehydrogenase is the amino donor. In the liver, alanine is reconverted to pyruvate by transamination. Its amino group is eventually converted to urea, and the pyruvate is converted to glucose by gluconeogenesis in the liver, then exported to muscle.

87. pyridoxal phosphate (PLP); α-amino; Schiff base (or imine or aldimine) 88. The side chains of these amino acids are all saturated hydrocarbon chains, and their catabolism shares features of fatty acid catabolism and has the potential to yield reduced cofactors. Similar to fatty acid catabolism, this process takes place in the mitochondrial matrix.

89. First, the biological activity of insulin would be destroyed by the low pH of the gastric juice and the proteases that act in the small intestine. Furthermore, even if insulin escaped degradation in the intestine, it would not enter the bloodstream from the intestine; the transport systems in the cells that line the intestinal lumen transport free amino acids, not intact proteins.

90. During starvation, cellular proteins are degraded and their carbon skeletons are oxidized for energy. The first step in amino acid catabolism is removal of the amino groups, which are ultimately excreted as urea.

91. This is the reaction catalyzed by glutamate dehydrogenase; see Figure 18-7. 92. Glutamine contains two nitrogens, so it can transport twice as much nitrogen per molecule compared with alanine. 93. See the top line of Figure 18-6. 94. Via either deamination with subsequent incorporation of

into carbamoyl phosphate or via transamination to

form 14N-labeled aspartate (label at α-amino). 95. A growing child needs a certain amount of phenylalanine and tyrosine for the synthesis of new proteins. Because an excess of phenylalanine and tyrosine is toxic in phenylketonurics, the diet should include just enough of these amino acids in protein to supply these needs, but not enough so that phenylketones begin to accumulate in the blood and urine. If the defect causing phenylketonuria lies in the enzyme that regenerates tetrahydrobiopterin, 1-3,4-dihydroxyphenylalanine and 5-hydroxytryptophan must also be supplied in the diet. Adding tetrahydrobiopterin to the diet will not help because the compound is unstable and cannot cross the blood-brain barrier.

96. Phenylketonuria, the disease that results from a defect in either phenylalanine hydroxylase or the enzyme that catalyzes regeneration of tetrahydrobiopterin.

97. The glucogenic amino acids are those that are catabolized to intermediates that can serve as substrates for gluconeogenesis: pyruvate and any of the four- or five-carbon intermediates of the citric acid cycle. Ketogenic amino acids are catabolized to yield acetyl-CoA or acetoacetyl-CoA, the precursors for ketone body formation.

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Chap 19_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which statement about energy conservation in the mitochondrion is false? a. Drugs that inhibit the ATP synthase will also inhibit the flow of electrons down the chain of carriers. b. For oxidative phosphorylation to occur, it is essential to have a closed membranous structure with an inside and an outside. c. The yield of ATP per molecule of oxidizable substrate depends on the substrate. d. Uncouplers (such as dinitrophenol) have exactly the same effect on electron transfer as inhibitors such as cyanide; both block further electron transfer to oxygen. e. Uncouplers "short circuit" the proton gradient, thereby dissipating the proton-motive force as heat. 2. Which list shows the proteins in the correct order from highest to lowest reduction potential? a. acyl-CoA dehydrogenase → ETF:Q oxidoreductase → ETF b. ETF → ETF:Q oxidoreductase → acyl-CoA dehydrogenase c. ETF:Q oxidoreductase → acyl-CoA dehydrogenase → ETF d. ETF:Q oxidoreductase → ETF → acyl-CoA dehydrogenase e. ETF → acyl-CoA dehydrogenase → ETF:Q oxidoreductase 3. Which statement is correct concerning the mitochondrial ATP synthase? a. It can synthesize ATP after it is extracted from broken mitochondria. b. It catalyzes the formation of ATP even though the reaction has a large positive ΔG'º. c. It consists of Fo and F1 subunits, which are transmembrane (integral) polypeptides. d. It is actually an ATPase and only catalyzes the hydrolysis of ATP. e. When it catalyzes the ATP synthesis reaction, the ΔG'º is actually close to zero. 4. Which statement about the chemiosmotic theory is false? a. Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane. b. Energy is conserved as a transmembrane pH gradient. c. Oxidative phosphorylation cannot occur in membrane-free preparations. d. The effect of uncoupling reagents is a consequence of their ability to carry protons through membranes. e. The membrane ATPase has no significant role in the chemiosmotic theory. 5. Which statement is NOT true of electron transfer? a. The mobile electron carrier coenzyme A is located in the inner mitochondrial membrane. b. Electrons flow from redox centers with a lower reduction potential to redox centers with a higher reduction potential. c. The electron-transfer chain oxidizes reduced cofactors. d. Cytochrome c has a higher reduction potential than FADH2.

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Chap 19_8e 6. Which has the transport proteins and type of transport correctly matched? a. adenine nucleotide translocase (symport); phosphate translocase (antiport) b. adenine nucleotide translocase (symport); phosphate translocase (symport) c. adenine nucleotide translocase (antiport); phosphate translocase (antiport) d. adenine nucleotide translocase (antiport); phosphate translocase (symport) 7. The ratio of ATP formed per pair of electrons passing through the respiratory chain is called the: a. P/O ratio. b. ATP/e ratio. c. ATP flux ratio. d. ATP current. 8. Which statement is NOT true of the proton-motive force? a. One component of the proton-motive force is the chemical gradient of protons. b. One component of the proton-motive force is the charge gradient of protons. c. Generation of the proton-motive force in mitochondria requires succinate. d. The proton-motive force is generated by the electron-transfer chain in mitochondria. e. The proton-motive force drives ATP synthesis in mitochondria. 9. The oxidation of a particular hydroxy substrate to a keto product by mitochondria has a P/O ratio of less than 2. The initial oxidation step is very likely directly coupled to the: a. oxidation of a flavoprotein. b. oxidation of a pyridine nucleotide. c. reduction of a flavoprotein. d. reduction of a pyridine nucleotide. e. reduction of cytochrome a3. 10. When the ΔG'º of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it is found to be close to zero. This is thought to be due to: a. a very low energy of activation. b. enzyme-induced oxygen exchange. c. an offset of the enthalpy of the reaction by the entropy change. d. stabilization of ATP relative to ADP by enzyme binding. 11. In normal mitochondria, the rate of NADH consumption (oxidation) will: a. be increased in active muscle, decreased in inactive muscle. b. be very low if the ATP synthase is inhibited, but increase when an uncoupler is added. c. decrease if mitochondrial ADP is depleted. d. decrease when cyanide is used to prevent electron transfer through the cytochrome a + a3 complex. e. All of the answers are correct. Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_8e 12. Reduced QH2 is NOT formed by: a. Complex I and NADH. b. Complex II and succinate. c. Complex III and cytochrome c. d. fatty acid oxidation. e. oxidation of glycerol 3-phosphate. 13. Which component of the electron-transfer chain is NOT an integral membrane protein? a. NADH dehydrogenase b. cytochrome c c. cytochrome oxidase d. ubiquinone:cytochrome c oxidoreductase e. succinate dehydrogenase 14. Cyanide, oligomycin, and 2,4-dinitrophenol (DNP) are inhibitors of mitochondrial aerobic phosphorylation. Which statement correctly describes the mode of action of the three inhibitors? a. Cyanide and DNP inhibit the respiratory chain, and oligomycin inhibits the synthesis of ATP. b. Cyanide inhibits the respiratory chain, whereas oligomycin and DNP inhibit the synthesis of ATP. c. Cyanide, oligomycin, and DNP compete with O2 for cytochrome oxidase (Complex IV). d. Oligomycin and cyanide inhibit synthesis of ATP; DNP inhibits the respiratory chain. e. Oligomycin inhibits the respiratory chain, whereas cyanide and DNP prevent the synthesis of ATP. 15. Which protein is NOT encoded in human mitochondrial DNA? a. Complex I (NADH dehydrogenase) b. Complex II (succinate dehydrogenase) c. Complex III (ubiquinone:cytochrome c oxidoreductase) d. cytochrome c e. Complex IV (cytochrome oxidase) 16. What factor makes the outer mitochondrial membrane permeable to protons? a. proton symports b. proton antiports c. porins d. the presence of proton ionophores e. the presence of negatively charged lipids

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Chap 19_8e 17. Which characteristic describes heme a but not heme c? a. contains an isoprenoid structure b. contains methyl substituents on the porphyrin ring c. contains propionate substituents on the porphyrin ring d. contains a Cys substituent on the porphyrin ring 18. What will NOT occur when 2,4-dinitrophenol (an uncoupler of oxidative phosphorylation) is added to actively respiring mitochondria? a. The P/O ratio will increase. b. The rate of NADH reoxidation at Complex I will increase. c. The rate of oxidation of intermediates in the citric acid cycle will increase. d. Proton export from the matrix will occur. e. Heat will be released. 19. Mammals produce heat by using which endogenous uncoupling agent? a. the small molecule 2,4-dinitrophenol synthesized by the cell b. uncoupling protein 1 c. the protein thioredoxin d. the protein cytochrome c e. a modified form of the Fo F1 ATPase 20. The electron-transfer chain and ATP synthase are effectively coupled. Which statement BEST describes how this occurs? a. The electron-transfer chain reoxidizes reduced cofactors. b. The electron-transfer chain generates an electrochemical gradient that provides energy for the production of ATP. c. ATP synthase utilizes oxidized cofactors. d. Through a series of conformational changes, ATP synthase generates ATP. 21. During the operation of the malate-aspartate shuttle, what process does NOT occur? a. net movement of reducing potential from the cytosol to the matrix b. transfer of amino groups from glutamate to oxaloacetate in the cytosol c. transport of two different transport proteins d. reduction of oxaloacetate to malate in the cytosol 22. Mutations in mitochondrial genes do NOT play a role in: a. adult-onset diabetes. b. cystic fibrosis. c. hypertrophic cardiomyopathy. d. Leber's hereditary optic neuropathy. e. myoclonic epilepsy. Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_8e 23. During oxidative phosphorylation, the proton-motive force (electrochemical gradient) that is generated by electron transfer is used to: a. create a pore in the inner mitochondrial membrane. b. generate the substrates (ADP and Pi) for ATP synthase. c. drive transport processes essential to oxidative phosphorylation. d. reduce NAD+ to NADH. e. reduce O2 to H2O. 24. Cytochrome c can be reduced directly by small molecules such as ascorbate (vitamin C). If ascorbate is added to an oxygenated solution containing purified cytochrome c and cytochrome oxidase, what would be predicted to occur? a. ATP synthesis would occur. b. Cytochrome c would become reduced and remain reduced. c. Oxygen would be reduced to water. d. Ascorbate would become more reduced. e. No apparent change would be observed. 25. The rate of oxidative phosphorylation in mitochondria is controlled primarily by: a. feedback inhibition by CO2. b. the availability of NADH from the TCA cycle. c. the concentration of citrate or the glycerol 3-phosphate shuttle. d. the mass-action ratio of the ATP-ADP system. e. the presence of uncoupling protein 1. 26. Complex III contains which cofactor as a prosthetic group? a. iron-sulfur clusters (centers) b. FAD c. FMN d. coenzyme Q e. copper 27. Which statement regarding oxidative phosphorylation is true? a. The rate of electron transfer is independent of the magnitude of the proton electrochemical gradient. b. ATP synthase utilizes oxidized cofactors. c. Proton transfer through the Fo subunit of ATP synthase is required in order for ATP synthesis to occur. d. The addition of an uncoupler decreases the rate of reoxidation of NADH and FADH2, therefore decreases the rate of the citric acid cycle.

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Chap 19_8e 28. Which statement explains why the [ATP]/[ADP][Pi] ratio is relatively stable in a cell? a. [ATP] is always relatively low. b. ATP consumption is balanced by ATP synthase activity. c. ATP is used to regulate protein kinases. d. ATPases ensure that ATP concentration does not become too large. e. Energy consumption is minimized to ensure ATP is not consumed. 29. Which statement is false concerning Complex III and the Q cycle? a. Both Q and QH2 are substrates for Complex III. b. Four protons are released on the p side of the membrane for every two electrons transferred to cytochrome c. c. This protein contains both iron-sulfur clusters and heme as prosthetic groups. d. Two protons from the matrix side are used to generate QH2 from the semiquinone radical. e. Overall, in each cycle one cytochrome c is reduced for every QH2 oxidized (net). 30. Antimycin A blocks electron transfer between cytochromes b and c1. If intact mitochondria were incubated with antimycin A, excess NADH, and an adequate supply of O2, which compound would be found in the oxidized state? a. coenzyme Q b. cytochrome a3 c. cytochrome b d. cytochrome e e. cytochrome f 31. Which statement is false regarding 2,4-dinitrophenol? a. It is a proton carrier ionophore. b. It may be either neutral or negatively charged. c. It is soluble in the lipid core of membranes. d. It requires a specific transporter to enter mitochondria. e. It decreases ATP synthesis while increasing oxygen consumption. 32. Which phrase BEST describes the role of mitochondria in apoptosis? a. degradation of cytochrome c inside the mitochondrion b. increased rate of fatty acid β oxidation c. a decrease in permeability of outer membrane d. uncoupling of oxidative phosphorylation e. an increase in permeability of outer membrane that allows escape of cytochrome c into the cytoplasm

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Chap 19_8e 33. Which statement is false regarding ATP synthase? a. The active site contains multiple positive charges that interact with the substrates. b. The energy difference between bound substrate and bound product is close to zero. c. As an enzyme, ATP synthase is classified as a hydrolase. d. ATP synthase can be classified as a primary active transporter. e. ADP binds more tightly to the active site than ATP. 34. Which molecule can reduce the proton gradient in mitochondria? a. Pi-H+ symporter b. ATP synthase c. phosphate translocase d. All of the answers are correct. 35. Uncoupling of mitochondrial oxidative phosphorylation: a. allows continued mitochondrial ATP formation but halts O2 consumption. b. halts all mitochondrial metabolism. c. halts mitochondrial ATP formation but allows continued O2 consumption. d. slows down the citric acid cycle. e. slows the conversion of glucose to pyruvate by glycolysis. 36. During oxidative phosphorylation, the proton-motive force that is generated by electron transfer is used to: a. create a pore in the inner mitochondrial membrane. b. generate the substrates (ADP and Pi) for the ATP synthase. c. induce a conformational change in the ATP synthase. d. oxidize NADH to NAD+. e. reduce O2 to H2O. 37. Which statement is true regarding the gamma ( ) subunit of ATP synthase? a. It contains mostly α-helical regular secondary structure. b. It exists as a dimer in the F1 portion of ATP synthase. c. It prevents the F1 portion from rotating relative to the Fo portion. d. It interacts with the a and b subunits of the Fo portion. e. It binds protons as part of the proton-transfer process.

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Chap 19_8e 38. What mechanism accounts for mitochondrial inheritance in sexual reproduction in animals? a. Male gametes do not contain mitochondria. b. Mitochondria from male gametes do not enter the ovum. c. Female mitochondria are able to outcompete male mitochondria. d. Male mitochondria are degraded after fertilization. e. Male and female mitochondria merge after fertilization to form hybrids. 39. Which statement is NOT a feature of Complex IV? a. Cytochrome c is a one-electron donor. b. Oxygen is a substrate. c. Copper is an essential metal for the reaction. d. For every electron passed to Complex IV, two protons are consumed from the matrix (n side). e. In order to generate two water molecules, Complex IV must go through the catalytic cycle two times. 40. What is the role of cytochrome c in apoptosis? a. It acts as an allosteric effector for caspase-3. b. It transports electrons from mitochondria to the cytosol. c. It acts as a protease to activate various zymogens. d. It forms a complex with other proteins to generate an apoptosome. e. It activates pores in the outer mitochondrial membrane. 41. Which electron carrier is NOT able to transfer one electron at a time? a. NADH b. FMN c. FAD d. ubiquinone e. heme 42. What compound is a product of the reaction involving the superoxide free radical catalyzed by superoxide dismutase? a. water b. hydrogen peroxide c. reduced glutathione d. oxidized glutathione e. NADPH

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Chap 19_8e 43. If a drug that specifically prevented the interaction of cytochrome c with other proteins was added to respiring mitochondria in a test tube, what effects would be observed? a. ATP synthesis would immediately stop. b. Oxygen consumption would increase. c. Reduced cofactors (NADH/FADH2) would accumulate. d. Coenzyme Q would become oxidized. e. Proton export from the matrix would increase. 44. In the reoxidation of QH2 by purified ubiquinone:cytochrome c oxidoreductase (Complex III) from heart muscle, the overall stoichiometry of the reaction requires two molecules of cytochrome c per molecule of QH2 because: a. cytochrome c is a one-electron acceptor, whereas QH2 is a two-electron donor. b. cytochrome c is a two-electron acceptor, whereas QH2 is a one-electron donor. c. cytochrome c is water soluble and operates between the inner and outer mitochondrial membranes. d. heart muscle has a high rate of oxidative metabolism, and therefore requires twice as much cytochrome c as QH2 for electron transfer to proceed normally. e. two molecules of cytochrome c must first combine physically before they are catalytically active. 45. Which statement does NOT describe characteristics of the protein inhibitor IF1? a. This protein is relatively small (< 100 amino acids). b. This protein has very little ordered structure at pH 7.0. c. This protein will bind to the Fo portion of ATP synthase. d. This protein functions as a dimer when it is inhibiting ATP synthesis. e. This protein inhibits ATP hydrolysis by ATP synthase. 46. Most dehydrogenases that act in catabolism are specific for which cofactor as an electron carrier? a. NAD+ b. FAD c. NADPH d. NADH e. coenzyme Q

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Chap 19_8e 47. Which statement about the chemiosmotic theory is correct? a. Electron transfer in mitochondria is accompanied by an asymmetric release of protons on one side of the inner mitochondrial membrane. b. It predicts that oxidative phosphorylation can occur, even in the absence of an intact inner mitochondrial membrane. c. The effect of uncoupling reagents is a consequence of their ability to carry electrons through membranes. d. The membrane ATP synthase has no significant role in the chemiosmotic theory. 48. Which step is NOT part of the proton-transfer process in ATP synthase? a. A negatively charged amino acid in each c subunit becomes neutral upon proton binding. b. A positively charged amino acid in the a subunit forms an ion pair with a charged amino acid in a c subunit. c. Deprotonated c subunits are able to interact only with the a subunit. d. An arginine in the a subunit is reversibly protonated and deprotonated in each proton-binding event. e. Proton direction is determined by the relative concentrations of protons on either side of the membrane. 49. In some organisms, an alternative oxidase will accept electrons from ubiquinol and reduce oxygen to water with no associated proton translocation. What would be a consequence of having this oxidase active? a. decreased rate of NADH reoxidation b. decreased P/O ratio c. decreased rate of oxygen consumption d. inhibition of oxidative pathways like the citric acid cycle e. increased sensitivity to cyanide poisoning 50. Which statement does NOT describe a difference between the inner and outer mitochondrial membranes? a. The outer mitochondrial membrane contains porins, whereas the inner mitochondrial membrane does not. b. The outer mitochondrial membrane is permeable to large proteins (Mr> 10,000), whereas the inner mitochondrial membrane is not. c. A pH gradient exists across the inner mitochondrial membrane but not the outer mitochondrial membrane. d. The inner mitochondrial membrane contains a smaller percentage of lipid relative to protein compared with the outer mitochondrial membrane. e. The outer mitochondrial membrane has a smaller surface area than the inner mitochondrial membrane.

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Chap 19_8e 51. Which statement is true regarding the reduction potential of mitochondrial glycerol 3-phosphate dehydrogenase? a. It will be higher than the reduction potentials of both NADH and Complex III. b. It will be lower than the reduction potentials of both NADH and Complex III. c. It will be higher than that of NADH but lower than that of Complex III. d. It will be lower than that of NADH but higher than that of Complex III. 52. Cytochrome P-450 gets its name from what characteristic? a. It is a protein that is 450 amino acids long. b. It fluoresces at 450 nm. c. It absorbs light at 450 nm. d. It has a reduction potential of –450 mV. e. It contains a 450 dalton prosthetic group. 53. The consumption of acetyl-CoA by the citric acid cycle is decreased under which condition? a. high concentration of NAD+ b. high concentration of oxaloacetate c. NADH being rapidly reoxidized via the electron-transfer chain d. the mitochondrial ATP synthase being inactive e. high concentrations of both NAD+ and oxaloacetate 54. Which protein associated with electron transfer is NOT a flavoprotein? a. NADH dehydrogenase b. mitochondrial glycerol 3-phosphate dehydrogenase c. cytochrome oxidase d. succinate dehydrogenase e. acyl-CoA dehydrogenase 55. Which statement is false regarding flavoproteins? a. They may contain either a bound FMN or FAD. b. The reduction potential of the flavin will depend on the amino acids in the polypeptide chain. c. They will need at least two substrates in order to function as enzymes. d. They are always integral membrane proteins. e. Most flavoproteins in electron transfer have a lower reduction potential than coenzyme Q.

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Chap 19_8e 56. How many molecules of water are produced by the electron-transfer chain during the complete aerobic oxidation of one molecule of pyruvate? a. 3 H2O b. 4 H2O c. 5 H2O d. 8 H2O e. 10 H2O 57. Which complex in the electron-transfer chain contains copper ions? a. Complex I b. Complex II c. Complex III d. Complex IV e. None of these complexes contains copper ions. 58. Which factor is NOT controlled by hypoxia-inducible factor? a. glucose transport b. glycolysis c. citric acid cycle d. Complex I of the respiratory chain e. Complex IV of the respiratory chain 59. Upon the addition of 2,4-dinitrophenol to a suspension of mitochondria carrying out oxidative phosphorylation linked to the oxidation of malate, what does NOT occur? a. Oxygen consumption decreases. b. Oxygen consumption increases. c. The P/O ratio drops from a value of approximately 2.5 to 0. d. The proton gradient dissipates. e. The rate of transport of electrons from NADH to O2 becomes maximal. 60. Almost all of the oxygen one consumes in breathing is converted to: a. acetyl-CoA. b. carbon dioxide. c. carbon monoxide and then to carbon dioxide. d. water. e. None of the answers is correct.

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Chap 19_8e 61. How many cytochrome c need to be reoxidized for every oxygen molecule (O2) converted to water in the electron-transfer chain? a. one b. two c. three d. four e. eight 62. What effect will increasing the number of c subunits in ATP synthase have on the P/O ratio? a. It will increase for both NADH and FADH2. b. It will increase for NADH and decrease for FADH2. c. It will decrease for NADH and increase for FADH2. d. It will decrease for both NADH and FADH2. e. It will remain unchanged for both NADH and FADH2. 63. 2,4-Dinitrophenol (DNP) and oligomycin inhibit mitochondrial oxidative phosphorylation. DNP is an uncoupling agent; oligomycin blocks the ATP synthesis reaction itself. Therefore, DNP will: a. allow electron transfer in the presence of oligomycin. b. allow oxidative phosphorylation in the presence of oligomycin. c. block electron transfer in the presence of oligomycin. d. diminish O2 consumption in the presence of oligomycin. 64. If electron transfer in tightly coupled mitochondria is blocked (with antimycin A) between cytochrome b and cytochrome c1, then: a. all ATP synthesis will stop. b. ATP synthesis will continue, but the P/O ratio will drop to one. c. electron transfer from NADH will cease, but O2 uptake will continue. d. electron transfer from succinate to O2 will continue unabated. e. energy diverted from the cytochromes will be used to make ATP, and the P/O ratio will rise. 65. Which statement is true for mitochondria where an uncoupler for oxidative phosphorylation is present? a. The rate of NADH reoxidation will decrease relative to when no uncoupler is present. b. The citric acid cycle will be inhibited relative to when no uncoupler is present. c. The P/O ratio for FADH2 will increase relative to when no uncoupler is present. d. The amount of ATP generated from FADH2 will be less than the amount of ATP generated from NADH.

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Chap 19_8e 66. A new compound isolated from mitochondria is claimed to represent a previously unrecognized carrier in the electron-transfer chain. It is given the name coenzyme Z. Which line of evidence is the LEAST conclusive in assigning this compound a position in the electron-transfer chain? a. Alternate oxidation and reduction of the mitochondrion-bound coenzyme Z can be readily demonstrated. b. Removal of coenzyme Z from the mitochondria results in a decreased rate of oxygen consumption. c. The rate of oxidation and reduction of mitochondrion-bound coenzyme is of the same order of magnitude as the overall rate of electron transfer in mitochondria as measured by oxygen consumption. d. The reduction potential of Z is between that of two compounds known to participate in the electrontransfer chain. e. When added to a mitochondrial suspension, coenzyme Z is taken up very rapidly and specifically by the mitochondria. 67. The relative concentrations of ATP and ADP control the cellular rates of: a. glycolysis. b. oxidative phosphorylation. c. pyruvate oxidation. d. the citric acid cycle. e. All of the answers are correct. 68. Coenzyme Q is a prosthetic group for which complex in the electron-transfer chain? a. Complex I b. Complex II c. Complex III d. None of the above; Q is in the lipid bilayer of the inner mitochondrial membrane. 69. Which statement about human mitochondria is true? a. About 900 mitochondrial proteins are encoded by nuclear genes. b. Mitochondrial genes are inherited from both maternal and paternal sources. c. rRNA and tRNA are imported from the cytoplasm and used in mitochondrial protein synthesis. d. The mitochondrial genome codes for all proteins found in mitochondria. e. The mitochondrial genome is not subject to mutations.

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Chap 19_8e 70. In his studies of alcoholic fermentation by yeast, Louis Pasteur noted that the sudden addition of oxygen (O2) to a previously anaerobic culture of fermenting grape juice resulted in a dramatic decrease in the rate of glucose consumption. This Pasteur effect can be counteracted by the addition of 2,4-dinitrophenol (DNP), an uncoupler of oxidative phosphorylation. (a) Why would the yeast cells consume less glucose in the presence of oxygen? Estimate how much less glucose they would use. (b) Why would DNP counteract or prevent the Pasteur effect?

71. The compound 2,4-dinitrophenol (DNP), an uncoupler, was briefly used as a weight-loss drug. Some of its effects in people who took the drug included weight loss and higher than normal body temperature. Some people even died. Explain the first two effects of the compound in biochemical terms.

72. During electron transfer through the mitochondrial respiratory chain, the overall reaction is NADH +

O2 +

H+ NAD+ + H2O. The difference in reduction potentials for the two half-reactions (ΔE'∘ ) is +1.14 V. Show how to calculate the standard free-energy change, ΔG'∘ , for the reaction as written above. (The Faraday constant, F, is 96.48 kJ/V • mol.)

73. Diagram the path of electron flow from NADH to the final electron acceptor during electron transfer in mitochondria. For each electron carrier, indicate whether only electrons, or both electrons and protons, are accepted/donated by that carrier. Also, indicate where electrons from succinate oxidation enter the chain of carriers.

74. Describe and explain the two different ratios that affect the rate of respiration in mitochondria. What is accomplished by these control mechanisms?

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Chap 19_8e 75. The skunk cabbage (Symphocarpus foetidus) can maintain a temperature of 10 to 25 ºC higher than the temperature of the surrounding air. Suggest a mechanism for this.

76. Cyanide ion (CN– ) blocks electron transfer in mitochondria at the level of cytochrome a + a3. 2,4Dinitrophenol (DNP) is an uncoupler of mitochondrial oxidative phosphorylation. Draw graphs (ATP synthesized vs. time and O2 consumed vs. time) with labeled curves to show the effects of adding each of these compounds separately to a suspension of mitochondria supplied with O2, succinate, ADP, and Pi. Use an arrow to indicate the time of drug addition.

77. For the items listed, explain whether they are transported into or out of the mitochondrion and comment briefly on the mechanism for each. (a) NADH (b) Inorganic phosphate (c) ADP

78. When the F1 portion of the ATP synthetase complex is removed from the mitochondrial membrane and studied in solution, it functions as an ATPase. Why does it not function as an ATP synthetase?

79. Cytochrome c interacts with multiple different proteins (e.g., Complex III, Complex IV, Apaf-1, sulfite oxidase, etc.). It is a small protein (∼110 amino acids) and has a very low rate of mutation. Are these two aspects consistent with each other? Why or why not?

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Chap 19_8e 80. Under standard conditions, NADH reoxidation by the electron-transfer chain has a free-energy change equal to –220 kJ/mol. With 100% efficiency, how many ATP could be synthesized under standard conditions? What is the "actual" efficiency given these numbers?

81. Bovine ATP synthase contains 8 c subunits while yeast ATP synthase contains 10 c subunits. How many protons would be needed for each ATP in these two synthases, and how would it impact the P/O ratio?

82. Explain briefly the current model for how the proton-motive force that is generated by electron transfer is used to drive the ATP synthesis reaction.

83. When the ΔG'º of the ATP synthesis reaction is measured on the surface of the ATP synthase enzyme, it was found to be close to zero. Describe briefly why this is so.

84. Discuss three lines of evidence that support the theory that mitochondria evolved from endosymbiotic bacteria.

85. The standard reduction potential for ubiquinone (Q or coenzyme Q) is 0.045 V, and the standard reduction potential (ΔE'∘ ) for FAD is –0.219 V. Using these values, show that the oxidation of FADH2 by ubiquinone theoretically liberates enough energy to drive the synthesis of ATP. The Faraday constant, F, is 96.48 kJ/V • mol. ΔG'∘ for ATP synthesis is +30.5 kJ/mol.

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Chap 19_8e 86. Describe the role of cytochrome c in apoptosis.

87. Compound X is an inhibitor of mitochondrial ATP synthesis. It was observed that when compound X was added to cells, the NAD+/NADH ratio decreased. Would X be expected to be an uncoupling agent or an inhibitor of respiratory electron transfer? Explain.

88. Describe the role of hypoxia-inducible factor (HIF-1) in reducing reactive oxygen species (ROS).

89. As readers read and answer this question, they are (presumably) consuming oxygen. What single reaction accounts for most of their oxygen consumption?

90. Describe, in simple diagrams and a few words, the chemiosmotic theory for coupling oxidation to phosphorylation in mitochondria.

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Chap 19_8e 91. A recently discovered bacterium carries out ATP synthesis coupled to the flow of electrons through a chain of carriers to some electron acceptor. The components of its electron-transfer chain differ from those found in mitochondria; they are listed in the table with their standard reduction potentials.

(a) Place the electron carriers in the order in which they are most likely to act in carrying electrons. (b) Is it likely that O2 (for which E'º = 0.82 V) is the final electron acceptor in this organism? Why or why not? (c) Determine how to calculate the maximum number of ATP molecules that could theoretically be synthesized, under standard conditions, per pair of electrons transferred through this chain of carriers. (The Faraday constant, F, is 96.48 kJ/V · mol.) ΔG'º for ATP synthesis is +30.5 kJ/mol.

92. Give an example of (a) an uncoupler of oxidative phosphorylation, and (b) an inhibitor of respiration. (c) Describe the difference in the effects of such uncouplers and inhibitors on mitochondrial function.

93. Although molecular oxygen (O2) does not participate directly in any of the reactions of the citric acid cycle, the cycle operates only when O2 is present. Explain this observation.

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Chap 19_8e 94. Show the path of electrons from ubiquinone (Q or coenzyme Q) to oxygen in the mitochondrial respiratory chain. One of the two substances (Q and O2) has a standard reduction potential (E'º) of 0.82 V, and the other, 0.045 V. Which value belongs to each substance? How can this be deduced?

95. Mitochondria carrying out oxidative phosphorylation consume oxygen. Explain what happens to this oxygen, and describe the effect of an uncoupling agent such as 2,4-dinitrophenol (DNP) on the rate of oxygen consumption. Assume there is a sufficient supply of oxidizable substrate, ADP, and Pi.

96. How do the cytosolic and mitochondrial isozymes of glycerol 3-phosphate dehydrogenase differ from each other?

97. Consider a liver cell carrying out the oxidation of glucose under aerobic conditions. Suppose a very potent and specific inhibitor of the mitochondrial ATP synthase was added, completely inhibiting this enzyme. Each of the statements about the effect of this inhibitor is false. Explain in a sentence or two why each is false. a. ATP production in the cell will quickly drop to zero. b. The rate of glucose consumption by this cell will decrease sharply. c. The rate of oxygen consumption will increase. d. The citric acid cycle will speed up to compensate. e. The cell will switch to fatty acid oxidation as an alternative to glucose oxidation, and the inhibitor will therefore have no effect on ATP production.

98. Mutations in mitochondrial genes frequently produce diseases that affect the brain and skeletal muscle (mitochondrial encephalomyopathies). Why are these two tissues particularly sensitive to mitochondrial mutations?

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Chap 19_8e Answer Key 1. d 2. d 3. e 4. e 5. a 6. d 7. a 8. c 9. c 10. d 11. e 12. c 13. b 14. b 15. d 16. c 17. a 18. a 19. b 20. b 21. b 22. b 23. c 24. c 25. d 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_8e 27. c 28. b 29. e 30. b 31. d 32. e 33. e 34. d 35. c 36. c 37. a 38. d 39. e 40. d 41. a 42. b 43. c 44. a 45. c 46. a 47. a 48. d 49. b 50. b 51. c 52. c 53. d 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_8e 55. d 56. c 57. d 58. d 59. a 60. d 61. d 62. d 63. a 64. a 65. d 66. e 67. e 68. d 69. a 70. (a) During aerobic oxidation of glucose, the yield of ATP is about 38 molecules per molecule of glucose. Under anaerobic conditions, only 2 ATP are produced per glucose. Thus, to get the same amount of ATP, a cell needs to use 19 times more glucose anaerobically. (b) Because DNP blocks the principal path of aerobic ATP production, aerobic cells in the presence of DNP need about the same amount of glucose as anaerobic cells. 71. The uncoupler allows continuous oxidation of fuels (like fatty acids from adipose tissue). Because little or no ATP synthesis occurs, the respiratory control that normally limits fuel oxidation when ATP levels are high does not operate. The energy of fuel oxidation is dissipated as heat, accounting for the elevated body temperature. 72. ΔG'∘ = –nFΔE'∘ = (–2)(96.48 kJ/V · mol)(1.14 V) = –220 kJ/mol 73. NADH (both) → FP (both) → Q (both) → cyt b (only e– ) → cyt c1 (only e– ) → cyt c (only e– ) → cyt (a + a3) (only e– ) → O2 (both) Electrons from succinate enter at Q. 74. The acceptor control ratio describes how much respiration takes place in the presence of ADP versus the absence of ADP. (The availability of ADP to form ATP limits respiration.) The mass-action ratio relates the relative concentration of ATP to ADP. For both ratios, high ADP levels lead to increased O2 consumption. The overall effect is to keep the level of ATP nearly constant and to prevent oxidation of fuels when the demand for ATP is low.

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Chap 19_8e 75. One possible heat-generating mechanism is partially uncoupled mitochondria in which some of the energy of electron flow is dissipated as heat. This is most easily achieved using bypasses of some of the mitochondrial complexes that normally capture favorable electron flow toward making a proton gradient that then drives ATP synthesis. If some of these complexes are omitted, then larger downhill steps by electrons that do not drive proton flow will instead generate heat. (See Box 19-1.)

76. 77. (a) NADH produced by glycolysis is indirectly transferred into the mitochondrion via the aspartate-malate shuttle. (Only NADH equivalents are moved in, not the actual NADH molecule itself.) (b) Inorganic phosphate is moved into the mitochondrion via phosphate translocase, which is accompanied by antiport of a proton and is driven by the proton-motive force. (c) ADP is transported into the mitochondrion by the adenine nucleotide translocase that simultaneously moves an ATP out of the mitochondrion and is driven by the proton-motive force. 78. Like all enzymes, the F1 subunit of the ATP synthase catalyzes a reaction in both directions: ADP + Pi ⇌ ATP + H2O The standard free-energy change (ΔG'º) for ATP hydrolysis is –30.5 kJ/mol. With no proton-motive force to drive the reaction toward ATP synthesis, the hydrolysis (ATPase activity) occurs spontaneously. 79. Yes, they are consistent. If a protein interacts with multiple other proteins, each of those interactions must be maintained if that function is to be conserved. In a small protein like cytochrome c, changes in any amino acid may affect either interactions with one of the partners or the reduction potential (which would be critical in electrontransfer roles).

80. If the standard free energy for ATP hydrolysis is assumed to be –30.5 kJ/mol, then the maximum number of ATP that can possibly be synthesized is 220 kJ/mol ÷ 30.5 kJ/mol = 7.21 ATP. Compared with 2.5 ATP (assuming the P/O ratio is 2.5 for NADH), the actual efficiency is approximately 34%. 81. Bovine: 2.67; yeast: 3.33. In one turn of the Fo portion, three ATP are synthesized in the F1 portion, and the number of protons required for one turn will be equal to the number of subunits. This means (on this basis alone) that the P/O ratio will be slightly higher in the bovine system than in that of yeast.

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Chap 19_8e 82. The enzyme binds ATP more tightly than ADP thus stabilizing the former, making the ΔG'º of the synthetic reaction more favorable. Once the reaction has occurred, the ATP product must be released from the enzyme (which is unfavorable). The proton-motive force causes protons to move across the inner mitochondrial membrane through the pore in the Fo complex. This movement leads to conformational changes that decrease the affinity of the F1 portion of the synthase for ATP, resulting in its release from the enzyme. 83. The enzyme binds ATP more tightly than ADP thus stabilizing the former (i.e., the product of the synthesis reaction) relative to the latter (i.e., the reactant in the synthesis reaction). 84. (1) Modern prokaryotes have respiratory chains very similar to those in mitochondria. (2) Bacteria translate protons outward across their plasma membrane and use this proton gradient to drive ATP synthesis and other energyrequiring processes such as flagellar motion. (3) Unlike most other organelles, mitochondria in eukaryotic cells retain their own genome. 85. ΔE'∘ = ΔE'∘ (oxidant) – ΔE'∘ (reductant) = 0.045 – (–0.219 V) = +0.264 V ΔG'∘ = –nFΔE'∘ = (–2)(96.48 kJ/V · mol)(0.264 V) = –51.0 kJ/mol Passage of two electrons from FADH2 to Q can, in principle, provide sufficient energy for synthesizing 1 ATP. 86. Upon receiving one or more of a variety of signals to trigger apoptosis, the permeability of the outer membranes of mitochondria increase, allowing the escape of cytochrome c from the intermembrane space. Cytochrome c then associates with Apaf-1 to form an apoptosome. The apoptosome provides the scaffold for the caspases that initiate a cascade of proteolytic activations, ultimately leading to cell death. 87. It is an inhibitor of electron transfer; its addition lowers the NAD+/NADH ratio because NADH produced by oxidative reactions in mitochondria can no longer be reoxidized by electron flow to O2. If it had been an uncoupling agent, the NADH could be reoxidized, the ratio of NAD+/NADH would be unchanged, but there would be no buildup of a proton gradient (i.e., no synthesis of ATP). 88. Under conditions of low oxygen, the electron-transfer chain may accidentally generate ROS because of the low levels of the final electron acceptor (oxygen). Therefore, HIF-1 is induced and serves as a transcription factor to increase glycolysis (i.e., anaerobic consumption of glucose). Some of the proteins whose transcription are turned on to yield this response are the glucose transporter, glycolytic enzymes, and lactate dehydrogenase. Additionally, the activity of pyruvate dehydrogenase is reduced (via phosphorylation) to slow the citric acid cycle and the flux of electrons into the electron-transfer chain. 89. O2 is converted to H2O by electrons from the respiratory chain. The final step is the one catalyzed by cytochrome oxidase (Complex IV). 90. There are two central elements in the chemiosmotic model: (1) Energetically favorable electron flow through asymmetrically arranged membrane-bound carriers causes transmembrane flow of H+, creating a proton gradient (a proton-motive force). (2) The energy released by "downhill" movement of protons is captured when ADP and Pi are condensed by ATP synthase (Fo F1).

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Chap 19_8e 91. (a) FPb → NAD+ → cyt c → FPa → Fe-S (b) No; Fe-S has a larger E'º, so will probably be the terminal acceptor. (c) First, calculate ΔG'º for e– flow from FPb to Fe-S: ΔE'º = E'º (oxidant) – E'º (reductant) = +0.89 V – (–0.62 V) = +1.51 V ΔG'º = –nFΔE'º = (–2)(96.48 kJ/V · mol)(1.51 V) = –291 kJ/2e– Theoretically, the flow of two electrons from FPb to Fe-S could drive the synthesis of 291 kJ ÷ 30.5 kJ/mol = 9.5 molecules of ATP. Because only whole numbers of molecules can be made, the correct answer is 9 molecules of ATP per electron pair. 92. (a) Uncouplers include DNP, valinomycin, and FCCP. (b) Respiration inhibitors include antimycin A, piericidin A, CN– , rotenone, and amytal. (c) Uncouplers stop formation of ATP while allowing electron transfer to continue. Inhibitors of respiration block both electron transfer and phosphorylation. (See Table 19-4.) 93. The citric acid cycle produces NADH, which is normally reoxidized to NAD+ by the passage of electrons through the respiratory chain to O2. With no O2 to accept electrons, NADH accumulates, NAD+ is depleted, and the citric acid cycle slows for lack of NAD+. 94. QH2 →cyt b→cyt c1→cyt c→cyt (a + a3) →O2 E'º for O2 must be the larger positive value (+0.82 V) because electron flow occurs spontaneously to the electron acceptor with the more positiveE'º. 95. O2 is reduced to H2O by electrons passed through the respiratory chain. Addition of DNP, which uncouples phosphorylation (ATP synthesis) from electron flow, actually stimulates O2 consumption slightly by removing the "drag" of ATP synthesis. 96. The cytosolic isozyme uses NADH as a cosubstrate to reduce dihydroxyacetone phosphate to glycerol 3phosphate, and it is a soluble enzyme. The mitochondrial isozyme is associated with the inner mitochondrial membrane and has FADH2 as a prosthetic group. Reduction of FAD to FADH2 is associated with oxidation of glycerol 3-phosphate to dihydroxyacetone phosphate, and subsequent reoxidation of FADH2 is associated with reduction of ubiquinone to ubiquinol. 97. (a) Mitochondrial ATP synthesis will cease, but to compensate, cells will accelerate the production of ATP by glycolysis, preventing ATP levels from dropping to zero. (b) The acceleration of glycolysis noted above will actually increase the rate of glucose consumption. (c) Because electron transfer through the respiratory chain is tightly coupled to ATP synthesis, blocking ATP synthase blocks electron flow and oxygen consumption. (d) The citric acid cycle is an oxidative pathway, producing NADH. When electron flow from NADH to O2 is blocked, NADH accumulates, NAD+ is depleted, and the citric acid cycle slows for lack of an electron acceptor (NAD+). (e) Oxidation of fats produces NADH, FADH2, and acetyl-CoA, which is further oxidized via the citric acid cycle. For the reasons noted above, blocking electron flow through the respiratory chain prevents ATP synthesis with energy from fatty acid oxidation. Copyright Macmillan Learning. Powered by Cognero.

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Chap 19_8e 98. Both the brain and skeletal muscles are heavily dependent on an abundant supply of ATP for normal functioning.

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Chap 20_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which cofactor in photosynthesis contains metal ions? a. chlorophyll a b. β-carotene c. pheophytin a d. lutein e. both chlorophyll a and β-carotene 2. Which factor is NOT required to activate rubisco? a. ATP hydrolysis b. carbamoylation of the active site lysine by rubisco activase c. release of ribulose 1,5-bisphosphate from the active site d. binding of Mg2+ 3. Ferredoxin and plastocyanin are both: a. integral membrane proteins. b. found on the lumen side of thylakoid membranes. c. proteins that interact with photosystem I. d. light-harvesting pigments. 4. Which statement is true regarding the conversion of malate to pyruvate by malic enzyme in C4 plants? a. This is an oxidative decarboxylation reaction. b. The process generates NADH as a product. c. This process requires ATP consumption. d. This reaction increases rubisco-associated photorespiration. e. This process occurs predominantly in plant mitochondria. 5. The known mechanisms of activation of rubisco or of other enzymes of the Calvin cycle during illumination do NOT include: a. increased stromal pH. b. light-driven entry of Mg2+ into the stroma. c. phosphorylation by cAMP-dependent protein kinase. d. phosphorylation of phosphoenolpyruvate carboxylase. e. reduction of a disulfide bridge by thioredoxin.

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Chap 20_8e 6. The experimental determination of the effectiveness of light of different colors in promoting photosynthesis is called the _____ spectrum. a. absorption b. action c. difference d. reflectance e. refraction 7. Which statement is true about PQA and PQB? a. PQA is more tightly bound to protein than PQB. b. PQA is associated with photosystem I, and PQB is associated with photosystem II. c. Both PQA and PQB are light-harvesting pigments in photosystem I. d. PQA will only accept single electrons, while PQB will accept two electrons. 8. Which statement is true about PEP carboxylase in mesophyll cells? a. It can fix CO2 more efficiently than rubisco. b. Like rubisco, it used O2 as an alternative substrate. c. PEP carboxylase fixes CO2 in the form of fumarate. d. PEP carboxylase is activated by binding of a Mg2+ ion. 9. Which statement about photophosphorylation is false? a. It can be uncoupled from electron flow by agents that dissipate the proton gradient. b. The difference in pH between the luminal and stromal side of the thylakoid membrane is three pH units. c. The luminal side of the thylakoid membrane has a higher pH than the stromal side. d. The number of ATPs formed per oxygen molecule is about three. e. The reaction centers, electron carriers, and ATP-forming enzymes are located in the thylakoid membrane. 10. CO2 fixation specifically refers to the: a. specific reaction that incorporates CO2 into 3-phosphoglycerate. b. specific reactions for the synthesis of glucose and other carbohydrates in plants. c. transport of CO2 into plant cells. d. reactions catalyzed by transketolase for the interconversions of triose phosphates and pentose phosphates.

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Chap 20_8e 11. The final product that is formed by the enzyme rubisco is: a. 3-phosphoglycerate. b. ATP. c. ribulose 1,5-bisphosphate. d. glyceraldehyde 3-phosphate. e. CO2. 12. The synthesis of starch in plants uses _____ as the substrate, rather than _____, which is used in the synthesis of glycogen in animal cells. a. ADP-fructose; UDP-glucose b. ADP-glucose; UDP-glucose c. fructose 1-phosphate; glucose 1-phosphate d. glucose 1-phosphate; glucose 6-phosphate e. UDP-glucose; ADP-glucose 13. Which statement about the reactions in photosynthetic plants is false? a. A membrane-bound ATPase couples ATP synthesis to electron transfer. b. CO2 is fixed in the light-dependent reactions. c. The ultimate electron acceptor in photosynthesis is O2. d. The ultimate source of electrons for the photosynthetic process is H2O. e. There are two distinct photosystems, linked together by an electron-transfer chain. 14. The assimilation of CO2 into organic compounds (triose phosphates) in green plants: a. involves condensation of the two-carbon compound acetate with CO2 to form 3-phosphoglycerate. b. requires NADPH. c. results in the production of ATP. d. takes place at equal rates in light and darkness. e. takes place in the cytosol. 15. Which statement is true? a. Linear and cyclic electron transfer produce NADPH and ATP. b. Linear electron transfer produces only ATP, and cyclic electron transfer produces only NADPH. c. Linear electron transfer produces only NADPH, and cyclic electron transfer produces only ATP. d. Linear electron transfer produces NADPH and ATP, and cyclic electron transfer produces only ATP.

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Chap 20_8e 16. Place the electron carriers into the correct order as found in plant chloroplasts. 1. cytochrome b6f complex 2. P680 3. P700 4. Plastocyanin 5. NADPH a. 2, 1, 3, 4, 5 b. 2, 4, 3, 1, 5 c. 3, 1, 4, 2, 5 d. 2, 1, 4, 3, 5 e. 3, 4, 2, 1, 5 17. Which pair of enzymes is activated in the absence of photosynthesis (i.e., in the dark) in plants? a. fructose 1,6-bisphosphatase and fructose 2,6-bisphosphatase b. fructose 1,6-bisphosphatase and PPi-dependent phosphofructokinase c. PPi-dependent phosphofructokinase and fructose 2,6-bisphosphatase d. phosphofructokinase-2 and fructose 2,6-bisphosphatase e. phosphofructokinase-2 and PPi-dependent phosphofructokinase 18. Which statement is false regarding ribulose 1,5-bisphosphate? a. This molecule is a phosphorylated ketopentose. b. This molecule contains a phosphoester and an acyl-phosphate. c. This molecule is one of the substrates of rubisco. d. C-2 in this molecule is the position where CO2 is added during carbon fixation. e. This molecule is an inhibitor of rubisco activation. 19. Which enzyme is inhibited by fructose 2,6-bisphosphate in plants? a. fructose 1,6-bisphosphatase b. sucrose 6-phosphate synthase c. sucrose 6-phosphate phosphatase d. PPi-dependent phosphofructokinase 20. Which statement is NOT true of the Pi–triose phosphate antiporter? a. The antiporter can move phosphate in or out of the chloroplast. b. When Pi is moved into the chloroplast it supports synthesis of ATP. c. When triose phosphates are moved out of the chloroplast, they become incorporated into sucrose. d. ATP and reducing equivalents are moved into the chloroplast by the antiporter. e. The antiporter is found in the inner membrane of chloroplasts.

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Chap 20_8e 21. The glycine decarboxylase complex in the leaves of pea or spinach plants is localized mainly in the: a. chloroplast. b. endoplasmic reticulum. c. mitochondrion. d. cell membrane. e. peroxisome. 22. The major regulator of sucrose biosynthesis in plants is: a. fructose 2,6-bisphosphate. b. fructose 1,6-bisphosphate. c. sucrose. d. glucose and fructose. e. glucose 6-phosphate. 23. Which process is NOT a mechanism of regulation for sucrose 6-phosphate synthase? a. allosteric inhibition by phosphate b. inhibition by phosphorylation c. allosteric activation by fructose 6-phosphate d. allosteric regulation by glucose 6-phosphate e. inhibition of sucrose phosphate synthase kinase by glucose 6-phosphate 24. Which statement is NOT true about the biosynthesis of cellulose? a. UDP-glucose is used as a substrate. b. Glucose is transported across the membrane via a lipid-linked oligosaccharide intermediate. c. The extracellular form of cellulose synthase adds up to 15,000 glucose units to one chain. d. Cellulose polymers line up in an antiparallel fashion. e. The reaction catalyzed by cellulose synthase proceeds via inversion of configuration. 25. The light-dependent reactions in photosynthetic higher plants: a. do not require chlorophyll. b. produce ATP and consume NADH. c. require the action of a single reaction center. d. result in the splitting of H2O, yielding O2. 26. Which compound is produced by sucrose synthase and used by cellulose synthase to make cellulose? a. fructose 6-phosphate b. glucose 6-phosphate c. UDP-glucose d. sucrose 6-phosphate e. glucose 1-phosphate Copyright Macmillan Learning. Powered by Cognero.

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Chap 20_8e 27. When transketolase acts on fructose 6-phosphate and glyceraldehyde 3-phosphate, the products are: a. 3-phosphoglycerate and glyceraldehyde 3-phosphate. b. 3-phosphoglycerate and two molecules of glyceraldehyde 3-phosphate. c. dihydroxyacetone phosphate and glucose 6-phosphate. d. xylulose 5-phosphate and erythrose 4-phosphate. e. xylulose 5-phosphate and ribose 5-phosphate. 28. Photophosphorylation and oxidative phosphorylation appear to be generally similar processes, both consisting of ATP synthesis coupled to the transfer of electrons along an electron carrier chain. Which statement is NOT true of both processes? a. Both contain cytochromes and flavins in their electron carrier chains. b. Both processes are associated with membranous elements of the cell. c. Both use oxygen as a terminal electron acceptor. d. Each represents the major route of ATP synthesis in those cells in which it is found. e. Protons are pumped from the inside to the outside of both mitochondria and chloroplast membranes. 29. The three subcellular organelles involved in the phosphoglycolate salvage pathway are: a. endoplasmic reticulum, chloroplast, and mitochondrion. b. nucleus, endoplasmic reticulum, and chloroplast. c. Golgi apparatus, chloroplast, and mitochondrion. d. mitochondrion, peroxisome, and chloroplast. e. peroxisome, endoplasmic reticulum, and chloroplast. 30. The synthesis of glycogen, starch, and sucrose all: a. involve addition of a sugar residue at the reducing end of the growing polymer. b. take place in liver and muscle of mammals. c. use a sugar nucleotide as substrate. d. use glucose 1-phosphate as the only substrate. e. use glucose 6-phosphate as substrate. 31. Which statement is false concerning xylulose 5-phosphate and ribose 5-phosphate? a. These molecules are isomers of each other. b. These molecules are both ketopentoses. c. These molecules can both be generated from ribulose 5-phosphate in a single reaction. d. In the Calvin cycle, both of these are d enantiomers.

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Chap 20_8e 32. The compound that condenses with CO2 in the first reaction of carbon dioxide assimilation is: a. 3-phosphoglycerate. b. ribose 1,5-bisphosphate. c. ribulose 1,5-bisphosphate. d. ribulose 5-phosphate. e. rubisco. 33. In the photolytic cleavage of water by the oxygen-evolving complex (2H2O→4H+ + 4e– + O2), how many photons of light at a wavelength of 680 nm are required? a. one b. two c. four d. six e. eight 34. In C4 plants of tropical origin, the first intermediate into which 14CO2 is fixed is: a. aspartate. b. phosphoenolpyruvate. c. oxaloacetate. d. malate. e. 3-phosphoglycerate. 35. During carbon fixation in C4 plants, which reaction type or process does NOT occur between the conversion of phosphoenolpyruvate to pyruvate? a. movement of metabolites through plasmodesmata b. oxidation of metabolites c. ATP consumption d. carboxylation 36. Which statement is NOT true of photorespiration? a. It is driven by light. b. It oxidizes substrates to CO2. c. It produces O2. d. It results from a lack of specificity of the enzyme rubisco. e. It results in no fixation of carbon.

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Chap 20_8e 37. The precursors for sucrose biosynthesis are: a. glucose and fructose. b. UDP-glucose and fructose 6-phosphate. c. UDP-fructose and glucose 6-phosphate. d. UDP-glucose and fructose. e. UDP-glucose and UDP-fructose. 38. Which statement is NOT true about chloroplasts? a. Chloroplasts contain their own DNA. b. Chloroplasts have both an inner and an outer membrane. c. Chloroplasts are self-replicating. d. Chloroplast proteins are encoded by both chloroplast and nuclear DNA. e. The inner membrane of chloroplasts is free permeable to small molecules and ions. 39. Which statement is NOT true about cyclic electron flow? a. Cyclic electron flow produces more NADPH per photon than noncyclic electron flow. b. Cyclic electron flow involves PSI but not PSII. c. Plastocyanin is required for cyclic electron flow. d. Cyclic electron flow leads to the buildup of a proton gradient. e. Cyclic electron flow does not produce O2. 40. The carbon assimilation (dark reactions) of photosynthetic plants: a. are driven ultimately by the energy of sunlight. b. yield ATP, which is required for the light reactions. c. cannot occur in the light. d. yield (reduced) NADH. 41. In what order do the five steps occur in the photochemical reaction centers? 1. excitation of the chlorophyll a molecule at the reaction center 2. replacement of the electron in the reaction center chlorophyll 3. light excitation of antenna chlorophyll molecule 4. passage of excited electron to electron-transfer chain 5. exciton transfer to neighboring chlorophyll a. 1, 2, 3, 4, 5 b. 3, 2, 5, 4, 1 c. 3, 5, 1, 4, 2 d. 4, 2, 3, 5, 1 e. 5, 4, 3, 2, 1

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Chap 20_8e 42. Which statement is true regarding ATP synthase in chloroplasts? a. The CF1 portion of the complex is located on the lumen side of thylakoid membranes. b. This complex is homologous to the complex located in mitochondria. c. This complex will act as an ATPase in membrane-free preparations. d. The CF1 portion of the complex is located on the lumen side of thylakoid membranes, and this complex is homologous to the complex located in mitochondria. e. This complex is both homologous to the complex located in mitochondria and will act as an ATPase in membrane-free preparations. 43. In photophosphorylation, absorption of light energy in chloroplast "light reactions" leads to: a. absorption of CO2 and release of O2. b. absorption of O2 and release of CO2. c. hydrolysis of ATP and reduction of NADP+. d. synthesis of ATP and oxidation of NADPH. e. use of iron-sulfur proteins. 44. Which of the reactions of the Calvin cycle is reversible? a. the conversion of fructose 1,6-bisphosphate to fructose 6-phosphate b. the conversion of ribulose 5-phosphate to ribulose 1,5-bisphosphate c. the conversion of ribose 5-phosphate to ribulose 5-phosphate d. the conversion of sedoheptulose 1,7-bisphosphate into sedoheptulose 7-phosphate 45. Reactions from which pathway are NOT specifically needed to synthesize carbohydrate from fatty acids in plants? a. gluconeogenesis b. glyoxylate pathway c. citric acid cycle d. glycolate pathway e. All of these pathways are necessary to synthesize carbohydrates from fatty acids. 46. Which sugar phosphate is NOT part of one of the three common metabolite pools in plant cells? a. dihydroxyacetone phosphate b. fructose 2,6-bisphosphate c. glucose 1-phosphate d. glyceraldehyde 3-phosphate e. xylulose 5-phosphate

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Chap 20_8e 47. Which statement is true about reaction centers? a. Cyanobacteria and plants have two reaction centers arranged in tandem. b. Cyanobacteria contain a single reaction center of the Fe-S type. c. Green sulfur bacteria have two reaction centers arranged in tandem. d. Plant photosystems have a single reaction center of the pheophytin-quinone type. e. Purple bacteria contain a single reaction center of the Fe-S type. 48. In the carbon assimilation, dark reactions of photosynthesis, the biosynthesis of 1 molecule of hexose from 6 molecules of carbon dioxide requires _____ molecules of NADPH and _____ molecules of ATP. a. 12; 12 b. 12; 18 c. 18; 12 d. 18; 18 e. no; 12 49. Cyclic electron flow in chloroplasts produces _____ but not _____. a. ATP and O2; NADPH b. ATP; NADPH or O2 c. NADPH and ATP; O2 d. NADPH; ATP or O2 e. O2; ATP or NADPH 50. Which enzyme is NOT part of the Calvin cycle? a. aldolase b. glyceraldehyde 3-phosphate dehydrogenase c. phosphofructokinase-1 d. ribulose 5-phosphate kinase e. transketolase 51. What is the purpose of the glyoxylate cycle in germinating seeds? a. To convert fatty acids to carbohydrate fuel. b. To fix CO2 in seeds before photosynthesis has begun. c. To synthesize cellulose as the seed cells grow and divide. d. To recycle unused proteins in the seeds.

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Chap 20_8e 52. Which cellular organelle is NOT unique to plant cells? a. amyloplasts b. chloroplasts c. glyoxysomes d. mitochondria e. vacuoles 53. Which compound is NOT directly involved in the Calvin cycle? a. erythrose 4-phosphate b. glyceraldehyde 3-phosphate c. mannose 6-phosphate d. ribulose 5-phosphate e. sedoheptulose 7-phosphate 54. Which process occurs in photosynthesis? a. Carbon atoms in CO2 become reduced. b. Oxygen atoms in water become oxidized. c. NADP is reduced to NADPH by electron-transfer processes. d. All of the answers are correct. 55. Which reaction is unique to the glyoxylate cycle? a. citrate → isocitrate b. isocitrate → succinate and glyoxylate c. malate → oxaloacetate d. acetyl-CoA → glyoxylate and malate 56. How is the enzyme ADP-glucose pyrophosphorylase regulated in plants? a. It is activated by both inorganic phosphate and 3-phosphoglycerate. b. It is activated by inorganic phosphate and unaffected by 3-phosphoglycerate. c. It is activated by inorganic phosphate and inhibited by 3-phosphoglycerate. d. It is inhibited by both inorganic phosphate and 3-phosphoglycerate. e. It is inhibited by inorganic phosphate and activated by 3-phosphoglycerate. 57. Sucrose phosphate synthase is regulated by: a. allosteric modulation by ATP. b. phosphorylation/dephosphorylation. c. proteolytic cleavage. d. methylation/demethylation.

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Chap 20_8e 58. Which statement describes shared characteristics of both oxidative phosphorylation and photophosphorylation? a. During electron transfer, protons are exported across the outer membrane. b. ATP synthesis occurs in conjunction with proton translocation. c. Electron transfer proceeds from compounds with lower reduction potentials to those with higher reduction potentials. d. ATP synthesis occurs in conjunction with proton translocation, and electron transfer proceeds from compounds with lower reduction potentials to those with higher reduction potentials. e. None of these statements describes shared characteristics of both oxidative phosphorylation and photophosphorylation. 59. Oxidative phosphorylation and photophosphorylation do NOT share: a. chlorophyll. b. involvement of cytochromes. c. participation of quinones. d. proton pumping across a membrane to create electrochemical potential. e. use of iron-sulfur proteins. 60. Which reaction, cycle, or pathway is NOT found in plant systems? a. Calvin cycle b. gluconeogenesis pathway c. glyoxylate cycle d. rubisco reaction e. urea cycle 61. Which amino acid is NOT involved in coordinating magnesium in the active site of rubisco? a. Asp b. Glu c. His d. Lys 62. Which chloroplast enzyme catalyzes a reaction that consumes ATP? a. fructose 1,6-bisphosphatase b. glyceraldehyde 3-phosphate dehydrogenase c. ribulose 5-phosphate kinase d. sedoheptulose 1,7-bisphosphatase

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Chap 20_8e 63. Given that about eight photons are required to produce one molecule of O2, roughly how many photons are required to produce one molecule of glucose.

64. The processes of oxidative phosphorylation coupled with electron transfer (in mitochondria) and photophosphorylation (in chloroplasts) resemble each other in certain respects. Describe five ways in which the two processes are similar, and describe three significant differences between the two processes.

65. How does glyceraldehyde 3-phosphate formed in the chloroplast stroma by the Calvin cycle reactions enter the cytosol?

66. Outline the similarities and differences in the locations of photosystems I and II in chloroplasts.

67. Describe how thioredoxin participates in the regulation of several chloroplast enzymes by light.

68. DCMU is an herbicide that acts by blocking photosynthetic electron flow from photosystem II (PSII) to the cytochrome b6f complex. Predict the effect of DCMU on O2 production and on ATP synthesis in the chloroplasts of plants sensitive to DCMU.

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Chap 20_8e 69. Describe what happens at photosystem I from the point where an antenna chlorophyll molecule absorbs a photon of light to the passage of an electron to NADP+.

70. Describe the electron flow that begins when a photon is absorbed by photosystem II (PSII). List all participants in the passage of electrons and end the description of electron flow at plastoquinone.

71. Explain why photorespiration occurs in plant cells carrying out photosynthesis.

72. Electrons in the special pair of chlorophyll will be transferred to plastoquinone from the excited state but not from the ground state. Explain this in terms of reduction potentials.

73. Describe the reaction sequence by which 2-phosphoglycolate (produced when O2 replaces CO2 as substrate for rubisco) is converted to serine. Name each enzyme and any cofactors required and indicate the subcellular compartment in which the reaction takes place.

74. Explain the utility to plants in using sucrose as the transport form of carbon.

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Chap 20_8e 75. Why is changing the wavelength of incident light to higher energy NOT as effective as changing the intensity of incident light with respect to photosynthesis?

76. What is an action spectrum, and what do peaks in an action spectrum signify? Show a typical action spectrum plot for photosynthesis.

77. Describe briefly how the allosteric effector fructose 2,6-bisphosphate (F26BP) regulates starch and sucrose synthesis.

78. Diagram the reaction catalyzed by transketolase when fructose 6-phosphate and glyceraldehyde 3-phosphate are the substrates.

79. Show the reaction catalyzed by ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco).

80. CAM plants, such as cactus and pineapple, are native to very hot and dry environments. Briefly describe the biochemical events that allow CAM plants to minimize water loss by closing their stroma during daylight hours.

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Chap 20_8e 81. Describe how plants and some microorganisms can, unlike animals, convert acetyl-CoA derived from fatty acids into glucose or sucrose.

82. During photophosphorylation in plants, electrons flow through a series of carriers in the chloroplast. What is the ultimate donor of electrons, and what is the ultimate acceptor? What provides the energy to move those electrons?

83. Describe the interconversions between the triose-, pentose-, and hexose-phosphate metabolic pools in the plant cell.

84. Diagram the pathway by which sucrose is synthesized from glucose 6-phosphate; indicate how any required cofactors are involved.

85. Describe the role of fructose 2,6-bisphosphate (F26BP) in the regulation of sucrose biosynthesis in plant cells.

86. Show the path of electrons from photosystem II (PSII) to NADPH in the chloroplast. What is the source of the energy that moves electrons through this path? Show where oxygen is involved in this pathway.

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Chap 20_8e 87. Describe the oxygenase activity of ribulose 1,5-bisphosphate carboxylase/oxygenase (rubisco) and explain why this reaction is undesirable from the point of view of a plant.

88. Give five general classes of electron carriers that function in both mitochondrial electron transfer to O2 and photosynthetic electron transfer.

89. Show the reaction in which 3-phosphoglycerate is converted into glyceraldehyde 3-phosphate. Show all required cofactors, and circle the carbon atom(s) in glyceraldehyde 3-phosphate that is derived from CO2 during the photosynthetic fixation of CO2.

90. Plants carrying out photosynthesis produce O2. Describe the source of this O2, and explain, with chemical equations or schematic diagrams, why O2 production occurs only during daylight hours.

91. Write out the net balanced chemical reaction catalyzed by rubisco.

92. In the synthesis of cellulose, UDP-glucose in the α configuration is used as a substrate to synthesize (β1→4) linkages in cellulose. Why does this imply a single-displacement mechanism?

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Chap 20_8e 93. Carbon dioxide has two important roles in the rubisco active site. What are these roles, and how do they differ from each other?

94. Explain why both ATP and NADPH are required for the operation of the Calvin cycle, and why these two reactants are required in different amounts.

95. Name one similarity and one difference between the biosynthesis of glycogen and the biosynthesis of cellulose.

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Chap 20_8e Answer Key 1. a 2. a 3. c 4. a 5. c 6. b 7. a 8. a 9. c 10. a 11. a 12. b 13. b 14. b 15. d 16. d 17. e 18. b 19. a 20. d 21. c 22. a 23. c 24. d 25. d 26. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 20_8e 27. d 28. c 29. d 30. c 31. b 32. c 33. c 34. c 35. c 36. c 37. b 38. e 39. a 40. a 41. c 42. e 43. a 44. c 45. d 46. b 47. a 48. b 49. b 50. c 51. a 52. d 53. c 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 20_8e 55. b 56. e 57. b 58. d 59. a 60. e 61. c 62. c 63. Since the overall reaction of photosynthesis is 6CO2 + 6H2O → C6H12O6 + 6O2, six molecules of O2 must be produced, requiring 6 ´ 8, or roughly 48 photons. 64. Similarities include: both contain a chain of membrane-bound electron carriers; electron transfer leads to establishment of a proton gradient; an ATPase/ATP synthase is a coupling factor; ATP synthesis is sensitive to uncouplers; both require a system of intact membranes to separate electrons inside and outside. Differences include: source of reducing power (NADH vs. light), product (ATP in respiration; NADPH in photosynthesis); source of oxidizing power (O2 in mitochondria; light in photosynthesis).

65. It is converted to dihydroxyacetone phosphate or to 3-phosphoglycerate and carried into the cytosol by the Pi–triose phosphate antiporter, a specific transporter in the inner chloroplast membrane. (See Fig. 20-34.)

66. Both photosystems are found as integral membrane proteins in the thylakoid membranes. Photosystem I tends to be located in nonappressed stromal lamellae, while photosystem II tends to be located in the appressed membranes within the grana.

67. Thioredoxin is an electron-carrying protein that is reduced by electrons from ferredoxin during illumination. Electrons from thioredoxin reduce critical disulfide bonds in key enzymes of the Calvin cycle, activating those enzymes. (See Fig. 20-37.)

68. DCMU blocks electron flow from PSII to PSI, preventing generation of O2 from H2 O. ATP synthesis will be inhibited, but not completely; cyclic photophosphorylation can continue in the presence of DCMU.

69. The antenna chlorophyll molecule passes the energy of the photon, via exciton transfer, to neighboring chlorophyll molecules and ultimately to reaction center chlorophyll molecules. This excites P700 to P700*, which donates an electron to A0. From A0, electrons pass to phylloquinone (A1), through an Fe-S protein, to ferredoxin, then through a flavoprotein to NADP+. P700* → A → A → Fe-S → NADP+ (See Figs. 20-11 and 20-12.) 70. Absorption of a photon by PSII excites P680 to P680*, which passes an electron to pheophytin, which passes the electron to plastoquinone. P680, now lacking an electron, takes one away from a water-splitting complex of PSII, which in turn takes one from H2 O.

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Chap 20_8e 71. Because rubisco is not particularly specific, it sometimes reacts with O2 , which is much more abundant than the proper substrate CO2 . This results in the production of 2-phosphoglycolate, which is salvaged by the glycolate pathway, wherein O2 is consumed and CO2 is formed.

72. The reduction potential for the ground state of chlorophyll is higher than that of plastoquinones, so electron transfer will not occur (unfavorable free energy). Upon excitation, electrons are bound more weakly to chlorophyll, lowering their reduction potential so that the reduction potential of plastoquinone is now higher and electron transfer can occur.

73. 2-Phosphoglycolate is converted to glycolate by a phosphatase in the chloroplast. Glycolate is transported to the peroxisome and converted to glyoxylate by glycolate oxidase. The glyoxylate is then converted in the peroxisome to glycine by a transaminase that requires pyridoxal phosphate. Finally, two molecules of glycine are converted to serine + NH3 + CO2 by the enzyme glycine decarboxylase, which is located in the mitochondrion.

74. Sucrose is a nonreducing disaccharide with its glycosidic linkage between the anomeric carbons of glucose and fructose. The unavailability of these normally reactive carbons prevents sucrose from reacting nonenzymatically with amino acids or proteins, and this unusual bond is not hydrolyzed by amylases or other common carbohydrate-cleaving enzymes.

75. Light absorption is associated with an excitation of electrons to higher-energy states, and this absorption is only achieved when specific wavelengths of light are absorbed. Higher-energy light (shorter wavelengths) will not be absorbed and will not lead to excitation. Higher intensity, in contrast, means that a larger number of photons will increase the number of excitation events.

76. An action spectrum is a plot of the effectiveness of a process (such as photosynthesis) versus wavelength of incident light. Its peaks signify the presence of a chromophore that absorbs light at that wavelength. See Figures 20-6 and 20-7.

77. In vascular plants, the concentration of F26BP varies inversely with the rate of photosynthesis. At high levels of photosynthesis, the high levels of dihydroxyacetone phosphate that are formed inhibit phosphofructokinase-2. Thus, less F26BP is formed, which then leads to a greater flux of triose phosphate into fructose 6-phosphate formation and sucrose synthesis.

78. Fructose 6-phosphate + glyceraldehyde 3-phosphate → xylulose 5-phosphate + erythrose 4-phosphate (See Fig. 20-30.)

79. Ribulose 1,5-bisphosphate + CO2 → 2 (3-phosphoglycerate) (For the details of the reaction, see Fig. 20-29.) 80. CAM plants fix CO2 into malate in the dark when the stroma are open. The resulting malate is stored in vacuoles. During daylight hours, the CO2 is released from malate by the action of the NADP-linked malic enzyme, and the CO2 serves as substrate for rubisco.

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Chap 20_8e 81. The integration of reaction sequences in three subcellular compartments is required for the production of fructose 6phosphate or sucrose from stored lipids. Some of the essential enzymes are sequestered in glyoxysomes, where glyoxysome-specific isozymes of β oxidation break down fatty acids to acetyl-CoA. The physical separation of the glyoxylate cycle and β-oxidation enzymes from the mitochondrial citric acid cycle enzymes prevents further oxidation of acetyl-CoA to CO2. Instead, the acetyl-CoA is converted to succinate in the glyoxylate cycle, which passes into the mitochondrial matrix, where it is converted by citric acid cycle enzymes to oxaloacetate, which moves into the cytosol. Cytosolic oxaloacetate is converted by gluconeogenesis to fructose 6-phosphate, a precursor for glucose or sucrose. 82. The ultimate donor is H2 O, and the acceptor is NADP+. The energy that drives this electron flow is from light. 83. Compounds in each pool are readily interconverted by enzymatic reactions with small standard free-energy changes. Thus, a temporary imbalance is rapidly corrected to achieve a new equilibrium state. Specific interconversions are depicted in Figure 2048.

84. (See Fig. 20-41.) Glucose 6-phosphate is converted into glucose 1-phosphate by phosphoglucomutase, and into fructose 6-phosphate by phosphohexose isomerase. Then, Glucose 1-phosphate + UTP → UDP-glucose + PPi UDP-glucose + fructose 6-phosphate → sucrose 6-phosphate + UDP Sucrose 6-phosphate → sucrose + Pi 85. In conditions of intense light, 3-phosphoglycerate and dihydroxyacetone phosphate produced by the Calvin cycle inhibit PFK-2, slowing the conversion of fructose 6-phosphate to F26BP. The fructose 6-phosphate is then used to synthesize sucrose. In the dark, the F26BP level rises. Elevated levels of F26BP inhibit fructose 1,6-bisphosphatase (FBPase-1) and activate PFK-1, which results in an increase in the level of FBPase-1 and hence increased glycolysis. (See Fig. 20-42.)

86. H2O → P680 °→ pheophytin → PQA → PQB → cyt b6f complex → plastocyanin → P700→ A0 → A1 → Fe-S → ferredoxin → ferredoxin:NADP+ oxidoreductase → NADP+ The energy that drives the electron flow is from light. O2 is generated from H2O when H2O donates electrons to PSII.

87. The condensation of molecular oxygen with ribulose 1,5-bisphosphate yields 3-phosphoglycerate and the two-carbon compound 2-phosphoglycolate. 2-Phosphoglycolate has no known metabolic role; its carbon is salvaged by a series of reactions that consume O2 and produce CO2 —the photorespiration process. The salvage pathway requires energy, and therefore the oxygenase reaction of rubisco represents a net energy cost to the plant cell in which it occurs.

88. Any five of these: pyridine nucleotides (NADH, NADPH); flavin nucleotides (FADH2 , FMNH2 ); quinones (ubiquinone, plastoquinone); cytochromes; Fe-S proteins; flavoproteins.

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Chap 20_8e 89. (1) 3-Phosphoglycerate + ATP → 1,3-bisphosphoglycerate + ADP (2) 1,3-Bisphosphoglycerate + NADPH + H+ → glyceraldehyde 3-phosphate + NADP+ + Pi The carbon atom at C-1 of glyceraldehyde 3-phosphate is derived from CO2.

90. O2 is generated by the splitting and oxidation of H2 O, driven by the absorption of a photon by PSII (which occurs only in daylight).

91. CO2 + ribulose 1,5-bisphosphate + H2O → 2 3-phosphoglycerate + 2H+ See Figure 20-29. 92. With the oxygen at position 4 on the nonreducing end of the cellulose acting as a nucleophile, UDP displacement as the leaving group means that the O is attacking the anomeric carbon from the other side (the "top" in a Haworth projection). This results in an inversion of the anomeric carbon configuration. 93. Chemical modification of lysine and as a substrate. CO2 acts to chemically modify a lysine residue side chain, converting it into a carbamoylated structure (which now carries a net negative charge) capable of coordinating magnesium, a necessary cofactor, in the active site. It is also a substrate in the reaction to convert ribulose 1,5-bisphosphate into two molecules of 3phosphoglycerate.

94. ATP is required in two reactions of the Calvin cycle: the formation of 1,3-bisphosphoglycerate from 3-phosphoglycerate (two ATP per CO2 fixed) and the conversion of ribulose 5-phosphate into ribulose 1,5-bisphosphate (one ATP per CO2 fixed). NADPH is required in the reduction of 1,3-bisphosphoglycerate to glyceraldehyde 3-phosphate (two NADPH per CO2 fixed). Thus the operation of the cycle consumes three ATP and two NADPH per CO2 fixed.

95. Similarities include the use of UDP-glucose as a precursor and a final composition containing only glucose. Differences are much more numerous and include a complex export and extracellular deposition mechanism for cellulose, lipid-linked intermediates, and the lack of branching in cellulose.

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Chap 21_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which compound is NOT an intermediate in the synthesis of lanosterol from acetyl-CoA? a. isopentenyl pyrophosphate b. malonyl-CoA c. mevalonate d. squalene 2. Which statement is true of sphingolipid synthesis? a. All of the carbon atoms of palmitate and serine are incorporated into sphingosine. b. CDP-sphingosine is the activated intermediate. c. CO2 is produced during the synthesis of ceramide from palmitate and serine. d. Glucose 6-phosphate is the direct precursor of the glucose in cerebrosides. e. Phosphatidic acid is a key intermediate in the pathway. 3. Which statement does NOT describe a difference between fatty acid synthase I (FAS I) and fatty acid synthase II (FAS II)? a. FAS I is found in fungi, while FAS II is found in plants. b. FAS I in fungi has no quaternary structure, while FAS II does. c. Intermediates are not released in FAS I catalysis but are released in FAS II catalysis. d. A single lipid product is produced from FAS I while multiple products may be produced by FAS II. 4. In yeast, the synthesis of phosphatidylethanolamine directly involves: a. acyl carrier protein. b. biotin. c. CDP-choline. d. phosphatidylglycerol. e. serine. 5. Which statement is true regarding the formation of phosphatidylserine involving CDP-diacylglycerol in yeast? a. It leads to the synthesis of phosphatidylcholine. b. It involves a deamination reaction with the CDP-diacylglycerol. c. Phosphatidylserine is not formed in yeast. d. Phosphatidylserine is formed as a byproduct of fatty acid synthesis. e. Loss of a phosphoanhydride makes this reaction energetically unfavorable. 6. Which contains the highest percentage of cholesteryl esters? a. chylomicrons b. VLDL c. LDL d. HDL Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_8e 7. The rate-limiting step in fatty acid synthesis is: a. condensation of acetyl-CoA and malonyl-CoA. b. formation of acetyl-CoA from acetate. c. formation of malonyl-CoA from malonate and coenzyme A. d. the reaction catalyzed by acetyl-CoA carboxylase. e. the reduction of the acetoacetyl group to a D-β-hydroxybutyryl group. 8. Which statement is false regarding acyl carrier protein (ACP)? a. ACP is transiently attached to malonyl-CoA during fatty acid elongation. b. ACP contains a pantothenate-derived prosthetic group. c. ACP carries reaction intermediates from one active site to the next in fatty acid synthesis. d. ACP associates as a separate polypeptide with fatty acid synthase I in vertebrates. 9. Which statement is false regarding the conversion of dihydroxyacetone phosphate (DHAP) to glycerol 3phosphate in the cytosol of adipose cells? a. The reaction reduces C-1 of DHAP. b. This reaction creates a new chiral center. c. This reaction requires the cofactor NADH. d. This reaction is catalyzed by glycerol 3-phosphate dehydrogenase. 10. Cholesterol is synthesized from: a. acetyl-CoA. b. choline. c. lipoic acid. d. malate. e. oxalate. 11. Which lipoproteins do NOT originate from the liver? a. chylomicrons and VLDL b. VLDL and HDL c. LDL and HDL d. chylomicrons e. VLDL and LDL 12. After four rounds of fatty acid synthase activity, what size is the fatty acyl intermediate? a. 4 carbons long b. 5 carbons long c. 8 carbons long d. 9 carbons long e. 10 carbons long Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_8e 13. Synthesis of malonyl-CoA from acetyl-CoA is MOST similar to what other reaction? a. conversion of malate into fumarate b. conversion of pyruvate into acetyl-CoA c. conversion of phosphoenolpyruvate into 2-phosphoglycerate d. conversion of glutamate into α-ketoglutarate e. conversion of pyruvate into oxaloacetate 14. Which is another name for lipin? a. acyl-CoA synthetase b. acyl transferase c. PEP carboxykinase d. phosphatidic acid phosphatase e. CDP-diacylglycerol 15. The enzyme system for adding double bonds to saturated fatty acids does NOT require: a. a mixed-function oxidase. b. ATP. c. cytochrome b5. d. molecular oxygen (O2). e. NADPH. 16. Which apolipoprotein is found in chylomicrons but not in other lipoproteins? a. ApoB-48 b. ApoB-100 c. ApoC-II d. ApoC-III e. ApoE 17. Which statement is NOT true of the fatty acid synthase and the fatty acid β-oxidation systems? a. A derivative of the vitamin pantothenic acid is involved. b. Acyl-CoA derivatives are intermediates. c. Double bonds are oxidized or reduced by pyridine nucleotide coenzymes. d. The processes occur in different cellular compartments. e. The processes occur in the mitochondrial matrix.

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Chap 21_8e 18. What is the source of the polar head group in the formation of sphingomyelin? a. CDP-choline b. phosphocholine c. cardiolipin d. phosphoserine e. phosphatidylcholine 19. If malonyl-CoA is synthesized from 14CO2 and unlabeled acetyl-CoA, and the labeled malonate is then used for fatty acid synthesis, the final product (fatty acid) will have radioactive carbon in: a. every C. b. every even-numbered C atom. c. every odd-numbered C atom. d. no part of the molecule. e. only the omega-carbon atom (farthest carbon from C-1). 20. Which hormones stimulate the mobilization/release of fatty acids from adipose tissue to meet energy demands? a. insulin and epinephrine b. glucagon and epinephrine c. insulin and glucagon d. cortisol and insulin 21. Which statement is false concerning bile salts? a. They are more amphipathic than cholesterol. b. They are secreted in response to fat ingestion. c. They are synthesized in the gallbladder. d. They are sterol derivatives. e. They typically carry a negative charge. 22. All glycerol-containing phospholipids are synthesized from: a. cardiolipin. b. ceramide. c. gangliosides. d. mevalonate. e. phosphatidic acid.

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Chap 21_8e 23. Which is the precursor for the synthesis of both glycerophospholipids and triacylglycerols? a. CDP-choline b. CDP-diacylglycerol c. phosphatidate phosphatase d. phosphatidic acid e. phosphoethanolamine 24. Lipoprotein particles in human blood do NOT contain: a. an apolipoprotein B isoform. b. cholesterol. c. cholesteryl esters. d. phosphatidylcholine. e. triglycerides. 25. What type of inhibitor is acetylsalicylic acid (aspirin) for COX-2? a. competitive inhibitor b. noncompetitive inhibitor c. uncompetitive inhibitor d. mixed inhibitor e. irreversible inactivator 26. Which compound can be synthesized by plants but NOT by humans? a. linoleate (18:2(Δ9,12)) b. palmitate (16:0) c. phosphatidylcholine d. pyruvate e. stearate (18:0) 27. Conversion of saturated fatty acyl chains to unsaturated fatty acyl chains by fatty acyl-CoA desaturase is accompanied by what other net change? a. reduction of NAD+ to NADH b. reduction of NADP+ to NADPH c. reduction of O2 to H2O d. reduction of oxaloacetate to malate e. reduction of FAD to FADH2

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Chap 21_8e 28. Which statement applies to synthesis of malonyl-CoA? a. It is synthesized from acetyl-CoA and bicarbonate. b. The reaction is catalyzed by acetyl-CoA carboxylase. c. The three-step synthesis is irreversible. d. In animal cells the synthesis takes place in the cytoplasm. e. All of the statements apply to the synthesis of malonyl-CoA. 29. Synthesis of a triglyceride from three fatty acids and glycerol costs how many ATP equivalents? a. three b. four c. five d. six e. seven 30. Which list correctly ranks the polarity, from most polar to least polar, for the listed substances? a. cholesteryl ester > bile salts > cholesterol b. cholesterol > bile salts > cholesteryl esters c. bile salts > cholesteryl esters > cholesterol d. cholesteryl esters > cholesterol > bile salts e. bile salts > cholesterol > cholesteryl esters 31. Biosynthesis of mammalian membrane phospholipids takes place in what cellular locations? a. lysosomal membrane and the plasma membrane b. plasma membrane and the smooth endoplasmic reticulum c. inner mitochondrial membrane and the plasma membrane d. smooth endoplasmic reticulum and the inner mitochondrial membrane e. inner mitochondrial membrane and the lysosomal membrane 32. Which substance that can condense with CDP-diacylglycerol and the resulting phospholipid product are mismatched? a. phosphatidylglycerol → cardiolipin b. inositol → phosphatidylinositol c. serine → phosphatidylserine d. S-adenosylmethionine → phosphatidylcholine

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Chap 21_8e 33. Conversion of phosphatidylserine into phosphatidylethanolamine requires what chemical process? a. dehydration b. methylation c. dehydrogenation d. reduction e. decarboxylation 34. Which compound is NOT synthesized by a pathway that includes isoprene precursors? a. natural rubber b. plastoquinone c. vitamin A d. vitamin B12 e. vitamin K 35. Which statement is NOT true of the fatty acid elongation system of vertebrate cells? a. It involves the same four-step sequence seen in the fatty acid synthase complex. b. It is located in the smooth endoplasmic reticulum. c. It produces stearoyl-CoA by the extension of palmitoyl-CoA. d. It uses malonyl-CoA as a substrate. e. The immediate precursor of the added carbons is acetyl-CoA. 36. Which statement is NOT true of the reaction producing malonyl-CoA during fatty acid synthesis? a. It is stimulated by citrate. b. It requires acyl carrier protein (AC. c. It requires CO2 (or bicarbonate). d. One molecule of ATP is converted to ADP + Pi for each malonyl-CoA synthesized. e. The cofactor is biotin. 37. Conversion of VLDL into LDL is associated with what changes? a. depletion of cholesteryl esters b. an increase in particle diameter c. an increase in the protein-lipid ratio d. ApoE-mediated receptor interactions

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Chap 21_8e 38. Palmitoyl-CoA is a precursor of: a. cholesterol. b. malonyl-CoA. c. mevalonate. d. sphingomyelin. e. squalene. 39. Synthesis of phosphatidylcholine from choline and diacylglycerol in mammals requires which nucleotides as other substrates? a. ATP and UTP b. CTP and UTP c. ATP and CTP d. only CTP e. ATP, UTP, and CTP 40. Which statement is false concerning acetyl-CoA carboxylase? a. It catalyzes the rate-limiting step in fatty acid synthesis. b. This enzyme is inhibited by palmitate in mammals. c. This enzyme is allosterically activated by citrate in mammals. d. In mammals, this enzyme is inactivated under conditions when glycolysis is active. 41. In one cycle of acetyl transfer from mitochondria to the cytosol via citrate, what other net change occurs? a. net conversion of NADH to NADPH in the cytosol b. net export of coenzyme A from mitochondria c. net import of NADH from the cytosol into mitochondria d. net consumption of one ATP e. overall conversion of oxaloacetate into pyruvate 42. Which apolipoprotein binds to the LDL receptor? a. ApoB-100 b. ApoC-I c. ApoC-II d. ApoD e. ApoE

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Chap 21_8e 43. Synthesis of cardiolipin from phosphatidate, CDP-diacylglycerol, and glycerol 3-phosphate in E. coli consumes how many phosphoanhydride bonds? a. zero b. one c. two d. three e. four 44. In comparing fatty acid biosynthesis with β oxidation of fatty acids, which statement is incorrect? a. A thioester derivative of crotonic acid (trans-2-butenoic acid) is an intermediate in the synthetic path, and in the degradative path. b. A thioester derivative of D-β-hydroxybutyrate is an intermediate in the synthetic path, not in the degradative path. c. Fatty acid biosynthesis uses NADPH exclusively, whereas β oxidation uses NAD+ exclusively. d. Fatty acid degradation is catalyzed by cytosolic enzymes; fatty acid synthesis by mitochondrial enzymes. 45. CDP-diacylglycerol is NOT involved in the biosynthesis of: a. phosphatidylcholine. b. phosphatidylethanolamine. c. phosphatidylglycerol. d. phosphatidylserine. e. sphingomyelin. 46. Chylomicrons carry _____ in the _____. a. triacylglycerols; cell b. triacylglycerols; blood c. cholesterols; blood d. fatty acids; blood e. fatty acids; cell 47. Which statement about the regulation of cholesterol synthesis is NOT true? a. Cholesterol acquired in the diet has essentially no effect on the synthesis of cholesterol in the liver. b. Failure to regulate cholesterol synthesis predisposes humans to atherosclerosis. c. High intracellular cholesterol stimulates formation of cholesteryl esters. d. Insulin stimulates HMG-CoA reductase. e. Some metabolite or derivative of cholesterol inhibits HMG-CoA reductase.

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Chap 21_8e 48. How many phosphoanhydride bonds (net) are consumed in the conversion of mevalonate into the activated isoprene compound dimethylallyl pyrophosphate? a. zero b. one c. two d. three e. four 49. What cofactor is required for acetyl-CoA carboxylase activity? a. NADPH b. thiamine pyrophosphate c. lipoamide d. biotin 50. What statement is false regarding the differences between chylomicrons and VLDL? a. These two lipoproteins originate in different tissues. b. Chylomicrons have a lower density than VLDL. c. Chylomicrons contain ApoB-48 while VLDL contains ApoB-100. d. Chylomicrons contain a lower percentage of protein compared to VLDL. e. Chylomicrons contain an overall lower triacylglycerol percentage than VLDL. 51. Which protein is NOT typically found in HDL? a. ApoA-1 b. ApoE c. ApoH d. ApoC-I e. ApoD 52. Which compound is NOT an intermediate in transfer of acetyl groups from mitochondria to the cytosol? a. citrate b. malate c. oxaloacetate d. fumarate e. pyruvate

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Chap 21_8e 53. During fatty acid synthesis, malonyl-CoA becomes covalently attached to acyl carrier protein via _____ formation to a _____. a. ester-bond; serine b. thioester-bond; cysteine c. amide-bond; lysine d. ether-bond; serine e. thioester-bond; prosthetic group 54. Which statement about cholesterol synthesis is true? a. Cholesterol is the only known natural product whose biosynthesis involves isoprene units. b. Only half of the carbon atoms of cholesterol are derived from acetate. c. Squalene synthesis from farnesyl pyrophosphate results in the release of two molecules of PPi for each molecule of squalene formed. d. The activated intermediates in the pathway are CDP-derivatives. e. The condensation of two five-carbon units to yield geranyl pyrophosphate occurs in a "head-to-head" fashion. 55. Synthesis of β-ketosphinganine from palmitoyl-CoA and serine requires which enzymatic class? a. transferase b. oxidoreductase c. hydrolase d. ligase 56. Which statement is true about precursors required for fatty acid synthesis in animal cells? a. NADPH is produced in the cytosol by the pentose phosphate pathway. b. NADPH is produced in the nucleus by malic enzyme. c. Acetyl-CoA is transported out of the mitochondrion via the aspartate shuttle. d. CoA is transported across the mitochondrial membrane. e. Malonyl-CoA is formed in the mitochondrion. 57. Which types of groups are important carriers of fatty acid intermediates for both FAS I and FAS II? a. phosphate groups b. methyl groups c. —SH groups d. keto groups e. palmitate groups

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Chap 21_8e 58. Which compound(s) is derived from a sterol? a. bile salts b. gangliosides c. geraniol d. phosphatidylglycerol e. prostaglandins 59. Which statement is a step in the uptake of cholesterol from the bloodstream into cells? a. LDL containing ApoB-100 is recognized by the LDL receptor. b. LDL bound to the LDL receptor leads to endocytosis of the complex. c. The cholesteryl esters in the LDL are hydrolyzed to release free cholesterol. d. The ApoB-100 protein is degraded. e. All of the above are steps in the uptake of cholesterol. 60. A 30-carbon precursor of the steroid nucleus is: a. farnesyl pyrophosphate. b. geranyl pyrophosphate. c. isopentenyl pyrophosphate. d. lysolecithin. e. squalene. 61. What effect will the presence of citrate have on the activity of acetyl-CoA carboxylase in mammals? a. no effect b. decreased K0.5 c. increased K0.5 d. decreased Vmax e. increased Vmax 62. Which statement about triacylglycerol synthesis is correct? a. Humans can store more energy in glycogen than in triacylglycerols. b. Insulin stimulates conversion of dietary carbohydrate into triacylglycerols. c. It is not a hormone-sensitive process. d. Mammals are unable to convert carbohydrates into triacylglycerols. e. Phosphatidate is not on the pathway of triacylglycerol synthesis.

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Chap 21_8e 63. What statement is false regarding the regulation of HMG-CoA reductase? a. HMG-CoA reductase is inhibited by phosphorylation. b. Elevated levels of ATP will inhibit HMG-CoA reductase. c. Elevated blood glucose will increase the activity of HMG-CoA reductase. d. Statins act as competitive inhibitors for this enzyme. e. Low cellular concentrations of cholesterol will increase expression of this enzyme and the LDL receptor. 64. Which statement about eicosanoid synthesis is true? a. An early step in the path to thromboxanes is blocked by ibuprofen. b. Arachidonate is derived mainly by hydrolysis of triacylglycerols. c. Aspirin acts by blocking the synthesis of arachidonate. d. Plants can synthesize leukotrienes, but humans cannot. e. Thromboxanes are produced from arachidonate via the "linear" path. 65. In the synthesis of phosphatidylcholine from phosphatidylethanolamine, the methyl group donor is: a. a tetrahydrofolate derivative. b. choline. c. methanol. d. S-adenosylmethionine. e. serine. 66. Which factor does NOT contribute to lowering the risk of atherosclerosis? a. statin drugs b. HDL c. reverse cholesterol transport d. ApoA-I e. foam cells 67. Which compound is NOT required in the synthesis of fatty acids? a. acetyl-CoA b. biotin c. −(CO2) d. malonyl-CoA e. NADH

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Chap 21_8e 68. Reverse cholesterol transport is primarily associated with which lipoprotein? a. chylomicrons b. VLDL c. IDL d. LDL e. HDL 69. What is the net cost, in terms of high energy molecules, in the synthesis of squalene from acetyl-CoA? a. 2 NADPH and 3 ATP b. 6 NADPH and 9 ATP c. 6 NAPDH and 18 ATP d. 12 NADPH and 18 ATP e. 13 NADPH and 18 ATP 70. Which list ranks the compounds in order from the fewest to the greatest number of carbon atoms? a. acetate, cholesterol, mevalonate, squalene b. acetate, mevalonate, squalene, cholesterol c. mevalonate, cholesterol, squalene, acetate d. acetate, squalene, mevalonate, cholesterol e. acetate, mevalonate, cholesterol, squalene 71. Which phospholipase is critical for eicosanoid synthesis and why?

72. What are plasma lipoproteins? What is their general role in mammalian metabolism?

73. Show the two different biosynthetic pathways from phosphatidic acid to phosphatidylcholine. Use shorthand notation for phosphatidic acid, but name any cofactors required in the path and show where they are involved.

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Chap 21_8e 74. A molecule of squalene is shown, it is composed of six isoprene units. Draw lines to indicate the junctions between the six isoprene units.

75. Reduction of the gluconeogenesis intermediates dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate can generate glycerol 3-phosphate as a product. Why does it make sense to use DHAP instead of glyceraldehyde 3-phosphate in glycerol 3-phosphate formation?

76. Show the pathway from acetyl-CoA to mevalonate, indicating the roles of any cofactors.

77. Describe briefly the four stages in the pathway from acetyl-CoA to lanosterol.

78. Explain the triacylglycerol cycle and how drugs such as rosiglitazone (Avandia) promote this cycle and help lower fatty acid levels in the bloodstream.

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Chap 21_8e 79. Describe (briefly) two classes of genetic defects in humans that could produce an elevated blood serum cholesterol level.

80. Show the structure of Δ3-isopentenyl pyrophosphate and of dimethylallyl pyrophosphate. Connect with a dotted line the two carbon atoms that will be joined when these two molecules condense to form the 10carbon intermediate in cholesterol biosynthesis.

81. Sketch the pathway from arachidonate to thromboxanes and explain how aspirin blocks the synthesis of thromboxanes.

82. Show the pathway from mevalonate to dimethylallyl pyrophosphate, indicating where any cofactors participate.

83. Fatty acid synthesis and fatty acid breakdown occur by similar pathways. Describe, very briefly, four ways in which the synthetic and breakdown pathways differ.

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Chap 21_8e 84. The synthesis of fatty acids and their breakdown by β oxidation occur by separate pathways. Compare the two paths by filling in the blanks. (Some blanks may require more than one answer.) Synthesis β oxidation Activating group _______________ ______________ Electron carrier coenzyme(s) _______________ ______________ Basic units added or removed _______________ ______________ Cellular location of process _______________ ______________

85. Describe the process by which cholesterol esters in the bloodstream enter cells.

86. When a 10-carbon unit and a 5-carbon unit condense to a 15-carbon intermediate in the pathway to cholesterol, the mechanism of condensation is basically different from that of the condensation of two 15carbon units to the 30-carbon compound squalene. Describe the two condensations in enough chemical detail to illustrate the difference between them. (Show relevant structures.)

87. Describe two basic strategies for activating precursors in the biosynthesis of phospholipids.

88. Show the reaction that limits the rate of cholesterol synthesis from acetate, indicating the role of any cofactors that participate.

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Chap 21_8e 89. The reaction sequence that leads to fatty acid synthesis includes (1) condensation, (2) first reduction reaction, (3) dehydration, and (4) second reduction. Show the first reduction reaction, with any required cofactors.

90. What is the "cost" of synthesizing palmitate from acetyl-CoA in the cytosol in terms of high-energy molecules consumed?

91. What is the primary genetic defect that leads to familial hypercholesterolemia, and how does it lead to elevated blood cholesterol levels?

92. Describe the mechanism for moving acetyl-CoA produced in the mitochondrial matrix into the cytosol for fatty acid synthesis.

93. Show the structure of each intermediate in the conversion of β-hydroxybutyryl-ACPto butyryl-ACP by the fatty acid synthetase complex. Show where cofactors participate. In the first intermediate, circle the carbon atoms that are derived from malonyl-CoA.

94. The synthetic compound mevinolinic acid, also called lovastatin, is a potent competitive inhibitor of HMGCoA reductase (hydroxymethylglutaryl-CoA reductase). Predict and explain the effect of this drug on serum cholesterol levels in humans.

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Chap 21_8e 95. How does the energy cost of each round of fatty acid synthesis compare to each round of energy output fromβoxidation?

96. The synthesis of cholesterol begins with the condensation of a four-carbon unit from _____ with the two carbons of acetyl-CoA to form a six-carbon derivative. Give its structure, and circle the atoms that originated in the acetyl-CoA.

97. Describe the formation of farnesyl pyrophosphate from activated isoprenyl units.

98. If performing fatty acid biosynthesis with CO2 labeled with 14C, where does the label end up in a fatty acid?

99. Explain briefly why people require fats in their diets.

100. If starting with acetyl-CoA labeled with 14C in the methyl carbon, where does the label end up in malonylCoA?

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Chap 21_8e Answer Key 1. b 2. c 3. b 4. e 5. a 6. c 7. d 8. d 9. a 10. a 11. d 12. e 13. e 14. d 15. b 16. a 17. e 18. e 19. d 20. b 21. c 22. e 23. d 24. d 25. e 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_8e 27. c 28. e 29. e 30. e 31. d 32. d 33. e 34. d 35. e 36. b 37. c 38. d 39. c 40. d 41. a 42. a 43. e 44. d 45. e 46. b 47. a 48. d 49. d 50. e 51. c 52. d 53. e 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_8e 55. d 56. a 57. c 58. a 59. e 60. e 61. e 62. b 63. b 64. a 65. d 66. e 67. e 68. e 69. e 70. e 71. Phospholipase A2 is used to release arachidonate from membrane glycerophospholipids because unsaturated fatty acids (like arachidonate) are typically found attached to C-2 (as opposed to C-1).

72. Plasma lipoproteins are protein-lipid aggregates that circulate in the blood, carrying phospholipids, triacylglycerols, cholesterol, and cholesteryl esters from their points of synthesis or absorption to the tissues in which they will be used. The lipid-protein ratio, and therefore the density, of plasma lipoproteins varies, giving rise to particles separable by ultracentrifugation: HDL, LDL, VLDL, and chylomicrons, for example.

73. Phosphatidic acid condenses with CTP to form CDP-diacylglycerol; then serine displaces CMP, yielding phosphatidylserine. Decarboxylation of phosphatidylserine yields phosphatidylethanolamine, and methylation of the amino group of phosphatidylethanolamine with three methyl groups, each donated by S-adenosylmethionine, yields phosphatidylcholine. In an alternative path, phosphocholine condenses with CTP, forming CDP-choline; phosphatidic acid is dephosphorylated to yield diacylglycerol; and diacylglycerol displaces CMP from CDP-choline, forming phosphatidylcholine. (See Figs 21-25 and 21-26.)

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Chap 21_8e

74.

75. In gluconeogenesis, glyceraldehyde 3-phosphate has the D configuration, so reduction of this molecule would generate D -glycerol 3-phosphate instead of L -glycerol 3-phosphate and an extra step (racemization) would be required. Reduction of DHAP, which has no chirality for C-2, to glycerol 3-phosphate can directly generate glycerol 3-phosphate as the L enantiomer.

76. See Figure 21-34. 77. (1) Synthesis of mevalonate from acetate; (2) conversion of mevalonate to two activated isoprenes (isopentenyl pyrophosphate and dimethylallyl pyrophosphate); (3) condensation of six activated isoprene units to form squalene; (4) cyclization of squalene to form the steroid nucleus of lanosterol. (See Fig. 21-37.)

78. The triacylglycerol cycle is the constant cycling of fatty acids from adipose tissue to the liver and back again. It begins with hydrolysis of fatty acids in adipose tissue followed by transport of the free fatty acids through the bloodstream for re-esterification in the liver. Once in the liver, the process is reversed and the fatty acids end up in adipose tissue again. (See Fig. 21-20.) The constant attaching/detaching of fatty acids requires a relatively high concentration of glycerol 3-phosphate, which is synthesized from pyruvate in a "truncated" gluconeogenic pathway. (See Fig. 21-21.) Drugs such as rosiglitazone promote higher levels of PEP carboxykinase, thus raising the concentration of glycerol 3-phosphate available for re-esterification of free fatty acids in adipose tissue. 79. (1) Mutations in the LDL receptor result in the failure of cells to take up by receptor-mediated endocytosis the cholesterol in LDL; the resulting high level of LDL in the blood is characteristic of familial hypercholesterolemia. (2) Mutations in the ABC1 protein result in a failure of the HDL to take up cholesterol and remove it from the blood.

80. The "tail" of Δ3-isopentenyl pyrophosphate (its methylene carbon) displaces pyrophosphate from the "head" of dimethylallyl pyrophosphate, forming geranyl pyrophosphate. (See Fig. 21-36.) 81. (See Fig. 21-15.) Aspirin blocks the activity of cyclooxygenase (COX). 82. See Figure 21-35. Copyright Macmillan Learning. Powered by Cognero.

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Chap 21_8e 83. Fatty acid synthesis (in any order) (1) employs NADPH as reducing agent; (2) involves an acyl group bound to a protein, ACP; (3) takes place in the cytosol of animals; (4) involves the condensation of malonyl and acetyl groups; (5) involves the formation of the D-β-hydroxyacyl derivative. Fatty acid breakdown (1) employs NAD+ as electron acceptor; (2) involves acyl groups bound to coenzyme A; (3) occurs in the mitochondrial matrix; (4) does not involve malonyl derivatives; (5) involves the L stereoisomer of the β-hydroxyacyl derivative. 84. Activating group Electron carrier coenzyme(s) Basic units added or removed Cellular location of process

Synthesis acyl carrier protein NADPH malonyl and acetyl cytosol in animals, chloroplast in plants

β oxidation CoA-SH NAD+ acetyl mitochondrial matrix

85. The process is receptor-mediated endocytosis (described in Fig. 21-42). LDL particles containing cholesterol esters interact via apoB-100 with specific LDL receptors in the cell surface, initiating endocytosis that brings the LDL into the cell within endosomes. Endosomes fuse with lysosomes, and lysosomal enzymes degrade the apoproteins; cholesterol esters are released into the cytosol, and LDL receptors recirculate, reappearing on the cell surface.

86. The condensation of the 10-carbon geranyl pyrophosphate with the 5-carbon Δ3-isopentenyl pyrophosphate is a head-to-tail condensation; the methylene carbon (tail) of Δ3-isopentenyl pyrophosphate attacks and is joined to the "head" (the carbon that bears the pyrophosphate group) of geranyl pyrophosphate. The condensation of two molecules of farnesyl pyrophosphate is head to head; both pyrophosphate groups are eliminated, and the carbons to which they were attached are joined, forming squalene. (See Fig. 21-36.) 87. (1) Activate the head group by attachment to CDP, as in CDP-choline, then displace CMP with the hydroxyl group of glycerol in diacylglycerol. (2) Activate diacylglycerol by the attachment of CDP, then displace CMP with the hydroxyl group of the head group.

88. This is the reaction catalyzed by HMG-CoA reductase. NADPH is the cofactor. (See Fig. 21-34.) 89. β-Ketoacyl-ACP + NADPH + H+ → β-hydroxyacyl-ACP + NADP+ (See Fig. 21-2.) 90. 7 ATP and 14 NADPH. Malonyl-CoA synthesis consumes one ATP equivalent, and each round of elongation consumes two NADPH. Seven malonyl-CoA in seven rounds are needed to synthesize palmitate from eight acetyl-CoA. 91. Defective LDL receptors prevent receptor-mediated endocytosis of LDL by the liver and peripheral tissues, which leads to elevated levels of this lipoprotein (often referred to as "bad" cholesterol) in the bloodstream.

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Chap 21_8e 92. Acetyl-CoA in the mitochondrial matrix condenses with oxaloacetate to form citrate in a reaction catalyzed by citrate synthase. Citrate moves out of the matrix via the citrate transporter. Citrate in the cytosol is cleaved by citrate lyase, yielding acetyl-CoA and oxaloacetate. To complete the cycle, oxaloacetate in the cytosol is reduced to malate, which moves into the mitochondrial matrix on the malate–α-ketoglutarate transporter, and is converted to oxaloacetate in the matrix. 93. β-Hydroxybutyryl-ACPis first dehydrated, yielding trans-Δ2-butenoyl-ACP, which is then reduced to butyryl-ACP, with NADPH as the reducing agent. (See Fig. 21-6.) The carbon atoms coming from malonyl-CoA are those closer to the ACP. 94. HMG-CoA reductase catalyzes the rate-limiting step in cholesterol biosynthesis. By inhibiting this step, lovastatin reduces the endogenous production of cholesterol and lowers the level of cholesterol in the blood.

95. Each round of fatty acid synthesis consumes one ATP (malonyl-CoA synthesis) and two NADPH, while each round of β oxidation generates one NADH and one FADH2. More energy is required to proceed through one round of synthesis than would be released in each round of oxidation. 96. Acetoacetyl-CoA. The six-carbon product is β-hydroxy-β-methylglutaryl-CoA (HMG-CoA). (The structure and carbons originating in acetyl-CoA are shown in Fig. 21-34.) 97. This is the reaction in which dimethylallyl pyrophosphate condenses head to tail with isopentenyl pyrophosphate with the elimination of PPi. (See Fig. 21-36.)

98. There will not be any radioactivity in any fatty acid because the carboxyl group that is added to form malonyl-CoA is lost in the first condensation reaction.

99. Dietary fats provide the linoleate and linolenate that people need (for eicosanoid synthesis) but cannot synthesize. 100. Malonyl-CoA would be labeled in C-2 (C-1 is the acyl carbon).

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Chap 22_8e Indicate the answer choice that best completes the statement or answers the question. 1. Bile pigments are: a. formed in the degradation of heme. b. generated by oxidation of sterols. c. responsible for light reception in the vertebrate eye. d. secreted from the pancreas. e. the products of purine degradation. 2. Which statement is NOT true about glutamine amidotransferases? a. These enzymes proceed via a covalent intermediate. b. Ammonia is released into a channel. c. Glutamate is a product of the reaction. d. ATP is needed to activate the glutamine. e. A Cys at the active site is critical for the activity of these enzymes. 3. Which kind of reversible covalent modification is used to regulate glutamine synthetase? a. ADP-ribosylation b. adenylylation c. phosphorylation d. acetylation 4. Which amino acid is NOT considered to originate from α-ketoglutarate? a. arginine b. glutamate c. glutamine d. histidine e. proline 5. Which molecule is NOT a high-energy molecule involved in the synthesis of arginine from glutamate? a. acetyl-CoA b. ATP c. NADH/NADPH d. FADH2 e. All of these molecules are involved in this pathway.

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Chap 22_8e 6. An amino acid that does NOT derive its carbon skeleton, at least in part, from oxaloacetate is: a. aspartate. b. lysine. c. methionine. d. alanine e. threonine. 7. An important intermediate in the biosynthetic pathway to aromatic amino acids is: a. benzoic acid. b. lactate. c. orotate. d. shikimate. e. α-ketoglutarate. 8. Which statement does NOT accurately describe siroheme found in nitrite reductase? a. Siroheme contains carboxyl groups which may donate protons. b. Siroheme's iron ion has four coordinate bonds to nitrogens. c. Siroheme is involved in a six-electron transfer process. d. Siroheme contains four propionate groups. e. Siroheme contains Fe3+ 9. Which statement is false regarding the proposed mechanism for glutamine amidotransferases? a. Part of the mechanism includes the formation of a thioester to a cysteine. b. A hydrolysis reaction releases glutamine from the active site. c. Ammonia is released from one substrate before reacting with the second substrate. d. Phosphorylation is often used to activate the substrate accepting the amino group. e. Two portions of the enzymes are connected by an "ammonia channel." 10. Phosphocreatine is derived from which amino acid? a. alanine b. arginine c. cysteine d. serine e. lysine

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Chap 22_8e 11. Which drug is NOT chemotherapeutic? a. aminopterin b. allopurinol c. fluorouracil d. methotrexate e. trimethoprim 12. In the biosynthesis of tryptophan, the phenyl ring for the side chain is derived from: a. adenine. b. chorismate. c. cholesterol. d. shikimate. e. glucose. 13. Which statement is NOT true about the anammox reaction? a. Anammox converts ammonia to nitrogen. b. Anammox is performed by symbiotic bacteria of leguminous plants. c. Anammox generates the highly reactive molecule hydrazine that is a component of rocket fuel. d. Anammox occurs anaerobically. e. The ultimate electron acceptor in anammox is nitrite. 14. Which cofactor or functional group within the context of the nitrate reductase electron-transfer chain has the highest reduction potential? a. cysteine b. NAD+ c. FAD d. molybdenum cofactor e. cyt b557 15. Which statement is false regarding aspartate transcarbamoylase (ATCase) in prokaryotes? a. This enzyme catalyzes the rate-limiting step in cytidine biosynthesis. b. This enzyme catalyzes the first committed step of pyrimidine biosynthesis. c. The substrate for this enzyme is aspartate. d. CTP is a heterotropic inhibitor for ATCase. e. ATCase is regulated by product inhibition.

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Chap 22_8e 16. An amino acid that does NOT derive its carbon skeleton, at least in part, from α-ketoglutarate is: a. arginine. b. glutamate. c. glutamine. d. proline. e. valine. 17. What high-energy structure is found as part of the major intermediate in the glutamine synthetase reaction? a. phosphoanhydride bond b. phosphoester c. acyl phosphate d. enol e. thioester 18. De novo purine biosynthesis is distinguished from de novo pyrimidine biosynthesis by: a. condensation of the completed purine ring with ribose phosphate. b. incorporation of CO2. c. participation of PRPP (phosphoribosyl pyrophosphate). d. participation of aspartate. 19. One amino acid directly involved in the purine biosynthetic pathway is: a. alanine. b. glycine. c. glutamate. d. leucine. e. tryptophan 20. CMP, UMP, and TMP all have _____ as a common precursor. a. adenosine b. aspartate c. glutamine d. inosine e. S-adenosylmethionine

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Chap 22_8e 21. Which molecule does NOT require 5-phosphoribosyl-1-pyrophosphate (PRPP) as a substrate for biosynthesis? a. adenosine monophosphate b. cytidine monophosphate c. guanosine monophosphate d. histidine e. All of these molecules require PRPP for biosynthetic pathways. 22. Parkinson disease is associated with an underproduction of: a. dopamine. b. ATP. c. epinephrine. d. insulin. e. bile salts. 23. Which list correctly arranges nitrogen-containing species from most to least oxidized? a. > > > N2 b.

> N2 >

d. N2 > e.

> >

> N2 >

24. In purine biosynthesis, which contributes two of the ring nitrogens? a. urea b. formate c. aspartate d. glycine e. glutamine 25. If glucose labeled with 14C at C-1 were the starting material for amino acid biosynthesis, the product that would be readily formed is: a. serine labeled at the carboxyl carbon. b. serine labeled at alpha carbon. c. serine labeled at the R-group carbon. d. serine labeled at no carbons.

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Chap 22_8e 26. If a cell were unable to synthesize or obtain tetrahydrofolate, it would probably be deficient in the biosynthesis of: a. isoleucine. b. leucine. c. lysine. d. methionine. e. serine. 27. A cell that is unable to synthesize or obtain tetrahydrofolate (H4 folate) would probably be deficient in the biosynthesis of: a. CMP. b. GMP. c. orotate. d. thymidylate (TM. e. UMP. 28. The hormones epinephrine and norepinephrine are derived biosynthetically from: a. arginine. b. histidine. c. isoleucine. d. tryptophan. e. tyrosine. 29. The MOST direct precursors of the nitrogens of UMP are: a. aspartate and carbamoyl phosphate. b. glutamate and aspartate. c. glutamate and carbamoyl phosphate. d. glutamine and aspartate. e. glutamine and carbamoyl phosphate. 30. Glutathione is a(n): a. enzyme essential in the synthesis of glutamate. b. isomer of oxidized glutamic acid. c. methyl-group donor in many biosynthetic pathways. d. product of glutamate and methionine. e. tripeptide of glycine, glutamate, and cysteine.

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Chap 22_8e 31. The synthesis of methionine originates from which compound? a. α-ketoglutarate b. 3-phosphoglycerate c. oxaloacetate d. pyruvate e. ribose 5-phosphate 32. The ribosyl phosphate moiety needed for the synthesis of orotidylate, inosinate, and guanylate is provided by: a. 5-phosphoribosyl-1-pyrophosphate. b. cytosine 5'-phosphate. c. guanosine 5'-phosphate. d. ribose 5-phosphate. e. ribulose 5-phosphate. 33. Which statement correctly describes the biosynthetic pathway for purine nucleotides? a. Purine deoxynucleotides are made by the same path as ribonucleotides, followed by reduction of the ribose moiety. b. The first enzyme in the path is aspartate transcarbamoylase (ATCase). c. The nitrogen in the purine base that is bonded to ribose in the nucleotide is derived originally from glycine. d. The pathway occurs only in plants and bacteria, not in animals. e. The purine rings are first synthesized, then condensed with ribose phosphate. 34. Degradation of purines in primates leads to the formation of what major excreted product? a. allantoin b. ammonia c. hypoxanthine d. urea e. uric acid 35. Which statement is true regarding the regulation of nitrogen fixation? a. High concentrations of ADP will activate nitrogen fixation enzymes. b. Elevated concentrations of ammonia will reduce expression of genes associated with nitrogen fixation. c. ATP acts as a negative allosteric effector for nitrogenase. d. Nitrogenase is regulated via adenylylation. e. Oxygen acts as an allosteric effector for the nitrogenase complex.

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Chap 22_8e 36. Which is the immediate precursor of thymidylate (dTMP)? a. dGMP b. dCTP c. UTP d. dATP e. dUMP 37. The nitrogen atom in the indole ring of tryptophan is derived from which amino acid? a. aspartic acid b. glutamic acid c. glutamine d. asparagine e. arginine 38. Which statement is true about gout? a. Gout is caused by excessive breakdown of pyrimidine nucleotides. b. Gout can be treated by administration of fluorouracil. c. Gout is particularly prevalent in patients lacking xanthine oxidase. d. Gout leads to deposition of sodium urate crystals in the joints. e. Eating more liver is an effective way to treat the symptoms of gout. 39. Which statement is NOT a similarity in the synthesis of isoleucine, valine, and leucine? a. Pyruvate is the starting compound for synthesis of all these amino acids. b. Pyridoxal phosphate is a required cofactor in the synthesis of all these amino acids. c. These are all essential amino acids in humans. d. An α-keto acid is the immediate precursor for all three synthetic pathways. e. Acetyl-CoA is required as a substrate in all three synthetic pathways. 40. Which is the product of purine degradation in humans? a. glutamate b. NH4+ c. succinate d. urea e. uric acid

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Chap 22_8e 41. In the synthesis of serine from 3-phosphoglycerate, which answer lists the correct order and type of reactions? a. reduction, hydrolysis, transamination b. oxidation, transamination, hydrolysis c. reduction, transamination, hydrolysis d. oxidation, hydrolysis, transamination e. hydrolysis, transamination, reduction 42. Which enzyme is NOT involved in the assimilation of inorganic nitrogen into an organic molecule? a. dinitrogenase reductase b. nitrate reductase c. nitrite reductase d. nitrile reductase e. dinitrogenase 43. Which statement is false regarding glutamine synthetase? a. It is found in all organisms. b. Histidine, glycine, and alanine are all negative effectors for this enzyme. c. It is regulated by multiple feedback inhibitors and covalent modification. d. ATP is an inhibitor for this enzyme. e. In mammals it converts to glutamine. 44. Glutamine is a nitrogen donor in the synthesis of: a. CTP. b. dTTP. c. inosinic acid (IM. d. orotate. e. UMP. 45. Precursors for the biosynthesis of the pyrimidine ring system include: a. carbamoyl phosphate and aspartate. b. glutamate, NH3, and CO2. c. glycine and succinyl-CoA. d. glycine, glutamine, CO2, and aspartate. e. inosine and aspartate.

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Chap 22_8e 46. In which group are all the amino acids closely interrelated metabolically? a. arginine, hydroxyproline, and histidine b. arginine, tyrosine, and glutamate c. glycine, valine, glutamine, and aspartate d. ornithine, alanine, glycine, and valine e. ornithine, proline, arginine, and glutamate 47. Which statement is true regarding class I ribonucleotide reductase? a. The β subunit contains the regulatory sites for the enzyme. b. The α subunit contains the active site cysteines. c. The α subunit contains the binuclear iron center. d. This enzyme catalyzes a hydrolysis reaction. e. ATP is an inhibitor for most isoforms of this enzyme. 48. Erythrose 4-phosphate is a precursor of: a. aspartate. b. cysteine. c. phenylalanine. d. serine. e. threonine. 49. Which statement is false regarding the synthesis of glycine from 3-phosphoglycerate? a. Oxidation of 3-phosphoglycerate creates an α-keto acid. b. Pyridoxal phosphate is a required cofactor for this process. c. The uncommon amino acid phosphoserine is an intermediate in the process. d. A dehydration reaction produces glycine from serine. e. A phosphatase catalyzes one of the reaction steps. 50. Which statement is false regarding ladderanes? a. Ladderanes are classified as phospholipids. b. Ladderanes are associated with anammoxosomes. c. Ladderanes are amphipathic membrane components. d. Ladderanes have less conformational flexibility than equivalent fatty acids.

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Chap 22_8e 51. Which statement about the fixation of atmospheric nitrogen (N2) into NH3 by living cells is false? a. It involves the transfer of eight electrons per molecule of N2. b. It occurs in certain microorganisms, but not in humans. c. It requires a source of electrons, which can be ferredoxin. d. It requires one ATP per molecule of fixed N2. e. It requires two key protein components, each containing iron. 52. The amino acid that gives rise to the biological messenger NO is: a. glutamine. b. arginine. c. proline. d. lysine. e. histidine. 53. Which statement is true of the biosynthetic pathway for purine nucleotides? a. CO2 does not participate in any of the steps in this pathway. b. Deoxyribonucleotides are formed from 5-phosphodeoxyribosyl 1-pyrophosphate. c. Inosinate is the purine nucleotide that is the precursor of both adenylate and guanylate. d. Orotic acid is an essential precursor for purine nucleotides. e. The amino acid valine is one of the precursors contributing to purine nucleotides. 54. Which amino acid derives its side chain nitrogen from a purine ring? a. histidine b. lysine c. arginine d. glutamine e. tryptophan 55. The bacteria A. vinelandii uncouples oxidative phosphorylation during nitrogen fixation for what reason? a. It increases the temperature so that the enzymes will function at maximum efficiency. b. It ensures that the citric acid cycle is fully active and providing substrates for nitrogen fixation. c. It ensures that ATP is not present to inhibit nitrogen fixation. d. It maintains a low level of reduced cofactors. e. It ensures that oxygen concentrations are kept low to prevent interference with enzymes.

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Chap 22_8e 56. Homoserine is: a. a precursor of both methionine and threonine. b. a precursor of serine. c. derived from homocysteine. d. derived from serine. e. derived from threonine. 57. L-Dopa is an intermediate in the conversion of: a. phenylalanine to homogentisic acid. b. phenylalanine to tyrosine. c. tyrosine to epinephrine. d. tyrosine to phenylalanine. e. tyrosine to phenylpyruvate. 58. Which enzyme is NOT involved in the assimilation of inorganic nitrogen into an organic molecule? a. arginase b. glutamate dehydrogenase c. glutamate synthase d. glutamine synthetase e. dinitrogenase 59. The synthesis of purine and pyrimidine nucleotides differ in that: a. ATP is required in the synthesis of purines but not in the synthesis of pyrimidines. b. purine biosynthesis starts with the formation of PRPP, whereas pyrimidines incorporate the PRPP near the end of the pathway. c. purine formation requires a THF derivative, whereas pyrimidine formation does not. d. pyrimidine biosynthesis is tightly regulated in the cell, whereas purine biosynthesis is not. e. pyrimidines go through many steps, adding a single carbon or nitrogen each time, whereas the basic skeleton for purines is formed by two main precursors. 60. The amino acid _____ is an intermediate in the biosynthesis of _____. a. histidine; purines b. glycine; heme c. serine; heme d. serine; sphingosine e. glutamine; glutathione

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Chap 22_8e 61. Which reaction step in the synthesis of proline is nonenzymatic? a. phosphorylation of the side chain b. reaction that generates an aldehyde product c. cyclization step d. reaction that releases inorganic phosphate as a product e. reaction that converts a double bond to a single bond 62. Glutamine, arginine, and proline: a. do not have a common precursor. b. may all be derived from a citric acid cycle intermediate. c. may all be derived from a Cori cycle intermediate. d. may all be derived from a glycolytic intermediate. e. may all be derived from a urea cycle intermediate. 63. Nonessential amino acids: a. are amino acids other than those required for protein synthesis. b. are not utilized in mammalian proteins. c. are synthesized by plants and bacteria, but not by humans. d. can be synthesized in humans as well as in bacteria. e. may be substituted with other amino acids in proteins. 64. 5-Phosphoribosyl-1-pyrophosphate (PRPP) is NOT a synthetic precursor for: a. AMP. b. arginine. c. histidine. d. tryptophan. e. UMP. 65. The enzymatic machinery to fix atmospheric N2 into

is:

a. a means of producing ATP when excess N2 is available. b. composed of two key proteins, each containing iron. c. relatively stable when exposed to O2. d. specific to plant cells. e. unaffected by the supply of electrons.

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Chap 22_8e 66. Which statement is NOT true of the reaction catalyzed by ribonucleotide reductase? a. Glutathione is part of the path of electron transfer. b. It acts on nucleoside diphosphates. c. Its mechanism involves formation of a free radical. d. There is a separate enzyme for each nucleotide (ADP, CDP, GDP, UDP). e. Thioredoxin acts as an essential electron carrier. 67. The plant hormone indole-3-acetate (auxin) is formed from: a. arginine. b. histidine. c. phenylalanine. d. threonine. e. tryptophan. 68. Which statement is true regarding the conversion of UTP into CTP by cytidylate synthetase? a. Glutamate is also a substrate for this reaction. b. This reaction consumes one phosphoanhydride bond. c. This enzyme is an isomerase. d. Ammonia is a substrate for the overall reaction. e. Folate is a required cofactor for the reaction. 69. Glutamine synthetase converts _____ to glutamine, whereas glutamate synthase converts _____ to glutamate. a. formate; ammonia b. asparagine; α-ketoglutarate c. α-ketoglutarate; oxaloacetic acid d. α-ketoglutarate; α-ketoglutarate e. glutamate; α-ketoglutarate 70. Describe and contrast with diagrams concerted (cumulative) feedback regulation and sequential feedback inhibition.

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Chap 22_8e 71. If acetyl-CoA containing radiolabeled carbons in the acetyl group was used to synthesize leucine, where would the radioactive carbons be found?

72. Describe two types of regulation of the enzyme glutamine synthetase and explain why the regulation of this enzyme is so complex.

73. In bacteria, the listed amino acids can be derived directly or indirectly from serine, alanine, aspartate, glutamate, or chorismate. Indicate which of these "parent" compounds provide the carbon skeleton for each amino acid. Parent Compound Asparagine __________________ Tryptophan __________________ Glycine __________________ Methionine __________________ Threonine __________________ Cysteine __________________ Proline __________________ Isoleucine __________________ Phenylalanine __________________

74. Show the biosynthetic pathway for the conversion of a citric acid cycle intermediate into proline. Indicate where any cofactors participate.

75. Show the reaction catalyzed by glycine synthase, indicating the role of any cofactors that participate.

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Chap 22_8e 76. Give the name and structure of the glycolytic or citric acid cycle intermediate that has the same carbon skeleton as (a) alanine, (b) glutamate, (c) aspartate.

77. Explain how lack of adenosine deaminase leads to a 100-fold increase in dATP, yet also causes a deficiency in dNTPs required for replication of T lymphocytes and B lymphocytes required for a functioning immune system.

78. Show how to form δ-aminolevulinate from either glycine and succinyl-CoA or from glutamate.

79. Show the reaction catalyzed by thymidylate synthase and explain with a simple diagram how the chemotherapeutic agents fluorouracil and methotrexate inhibit the synthesis of dTMP.

80. Match the signaling molecule with its amino acid precursor (a given precursor may be used more than once or not at all). Signal Molecule Amino Acid Precursor (a) auxin 1. histidine (b) epinephrine 2. glutamic acid 3. tyrosine (c) g-amino butyrate (d) histamine 4. tryptophan (e) serotonin 5. arginine (f) NO

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Chap 22_8e 81. Draw the structure of 5'-GMP. Indicate with an arrow the atom(s) derived from glutamine's amide group.

82. Give the equations for the two-step reaction sequence catalyzed by glutamine synthetase.

83. Show the two-step reaction catalyzed by tryptophan synthase.

84. Draw the structure of 5'-AMP. What is the first "committed" step in the biosynthetic sequence that leads to 5'-AMP? How is this step regulated?

85. Show the steps by which an intermediate of glycolysis can be converted into serine.

86. Azaserine is a structural analog of glutamine. It is a competitive inhibitor of many enzymes that use glutamine as substrates. Name three biosynthetic products whose synthesis would be inhibited by azaserine. Would eating azaserine be immediately fatal? Why or why not?

87. If acetyl-CoA containing radiolabeled carbons in the acetyl group was used to synthesize arginine, where would the radioactive carbons be found?

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Chap 22_8e 88. Give the overall reaction that results from the combined action of glutamate synthase and glutamine synthetase.

89. Describe the pathway by which GMP is converted into GTP; show the cosubstrates that are involved and name the enzymes.

90. Draw the structure of deoxythymidylic acid (dTMP). Indicate the source of each N and each C in the thymine ring, including its substituents.

91. What is the role of leghemoglobin in root nodules of legumes with respect to nitrogen fixation?

92. An animal cell is capable of converting alanine into serine. What is the shortest pathway using known enzymes by which this conversion could be accomplished? Show intermediates and cofactors; no enzyme names are required. (Hint: The first step is removal of the nitrogen by transamination.)

93. Draw the structure of 5'-UMP (uridylic acid). Circle those carbon atoms donated by atoms derived from aspartate.

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Chap 22_8e 94. Diagram the biosynthetic pathway from UMP to dTTP. Use abbreviations (e.g., UMP), not complete structures, and indicate where any cosubstrates participate.

95. Carbamoyl phosphate synthetase II is activated by ATP and PRPP but inhibited by UMP. How does this make metabolic sense? How does it compare to the regulation of ATCase?

96. Cytidylate synthetase (CTP synthetase) is allosterically regulated by both ATP and UTP. Predict how they will affect the activity of this enzyme.

97. Why is it necessary to have protein in human diets?

98. Draw the structure of 5'-IMP. Indicate with arrows those carbon atoms donated by derivatives of tetrahydrofolate and circle the atoms derived from glycine.

99. Reduction of nitrogen (N2) to ammonia (NH3) is energetically favorable. Why do nitrogen-fixing bacteria require a substantial amount of ATP to make this process proceed?

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Chap 22_8e 100. Trace the path of nitrogen from atmospheric N2 into glutamate. Name the intermediates (no structures necessary) and enzymes, and show any coenzymes involved.

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Chap 22_8e Answer Key 1. a 2. d 3. b 4. d 5. d 6. d 7. d 8. e 9. b 10. b 11. b 12. b 13. b 14. d 15. e 16. e 17. c 18. b 19. b 20. b 21. e 22. a 23. b 24. e 25. c 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 22_8e 27. d 28. e 29. a 30. e 31. c 32. a 33. a 34. e 35. b 36. e 37. c 38. d 39. e 40. e 41. b 42. d 43. d 44. c 45. a 46. e 47. b 48. c 49. d 50. a 51. d 52. b 53. c 54. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 22_8e 55. e 56. a 57. c 58. a 59. b 60. b 61. c 62. b 63. d 64. b 65. b 66. d 67. e 68. b 69. e 70. Both are allosteric mechanisms to reduce the flux through a pathway when the end product(s) is present in sufficient quantities. In concerted feedback regulation, each of several end products partially inhibits the first enzyme in the pathway. Glutamine synthetase exhibits this kind of regulation (Fig. 22-8). Sequential feedback inhibition occurs in a branched pathway; the product of each branch inhibits the first step in that branch. When both end products are present, the last intermediate before the branch accumulates, and it feeds back on (inhibits) the first enzyme in the main path. The synthesis of AMP and GMP (Fig. 22-37) exemplifies this mechanism. Sequential feedback inhibition is also seen in pathways where there is enzyme multiplicity, thus preventing one biosynthetic end product from shutting down key steps in the pathway when other end products might still be needed. The synthesis and control of lysine, methionine, threonine, and isoleucine exemplifies this mechanism (Fig. 22-24). 71. The acetyl group is introduced in the reaction with carbon 2 of α-ketoisovalerate. The carbons introduced here ultimately end up as carbons 1 (the α-carboxylate) and 2 (the α carbon). 72. (1) The enzyme is subject to cumulative allosteric inhibition by six compounds: AMP, tryptophan, carbamoyl phosphate, CTP, histidine, and glucosamine 6-phosphate, all of which are end products of pathways in which glutamine is a key precursor. Alanine and glycine are also allosteric inhibitors of the enzyme. (2) The enzyme is also subject to regulation by covalent alteration: adenylylation and deadenylylation. Adenylylation, which inhibits the enzyme, is indirectly stimulated by glutamine and Pi and inhibited by α-ketoglutarate and ATP. The complexity of the regulation reflects the fact that glutamine is involved in many synthetic pathways, and its level must be responsive to the concentrations of end products and precursors of each pathway. Copyright Macmillan Learning. Powered by Cognero.

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Chap 22_8e 73. Aspartate (asparagine); chorismate (tryptophan); serine (glycine); aspartate (methionine); aspartate (threonine); serine (cysteine); glutamate (proline); alanine via pyruvate (isoleucine); chorismate (phenylalanine) 74. α-Ketoglutarate → glutamate → γ-glutamyl phosphate → glutamate γ-semialdehyde → Δ1-pyrroline-5carboxylate → proline For enzymes and cofactors, see Figure 22-12. 75. CO2 + NH4+ + NADH + H+ + N5,N10-methylenetetrahydrofolate → glycine + NAD+ + tetrahydrofolate 76. (a) Pyruvate CH3—CO—COO– (b) α-Ketoglutarate – OOC—CH2—CH2—CO—COO– (c) Oxaloacetate – OOC—CH2—CO—COO– 77. Adenosine deaminase is a critical enzyme in the degradation of purines. A deficiency in this enzyme leads to extremely high concentrations of dATP. Instead of promoting DNA synthesis, these high concentrations of dATP actually shut down ribonucleotide reductase (see Fig. 22-44), thus preventing the formation of dCTP, dTTP, and dGTP. Therefore, there are no dNTPs available for DNA biosynthesis. 78. In most animals, glycine and succinyl-CoA condense to form α-amino-β-ketoadipate that is decarboxylated to form δ-aminolevulinate (Fig. 22-25a). In bacteria and plants, glutamate forms a glutamyl-tRNA that is subsequently reduced and cleaved from the tRNA. Finally, an amidotransferase moves the nitrogen to form δ-aminolevulinate (Fig. 22-25b). 79. The reaction mechanism catalyzed by thymidylate synthase is shown in Figure 22-52; dUMP is methylated on the pyrimidine ring, with N5,N10-methylenetetrahydrofolate as methyl donor, and dihydrofolate as the other product. The two key events of this mechanism are the nucleophilic attack at C-6 of the pyrimidine ring and the removal of the proton on C-5 of the pyrimidine ring. The modes of action of fluorouracil and methotrexate are shown in Figure 22-51. Fluorouracil is a suicide substrate of thymidylate synthase: The reaction begins as for the real substrate, but the enzyme gets stuck when trying to remove the —F instead of an —H+. Methotrexate, on the other hand, is a potent competitive inhibitor of dihydrofolate reductase, thus preventing the regeneration of tetrahydrofolate. 80. (a) 4; (b) 3; (c) 2; (d) 1; (e) 4; (f) 5 81. The structure of 5'-GMP is shown in Figure 22-36. The atoms derived from glutamine's amide group are the two "bottom" ring nitrogens (see Fig. 22-25) and the external ring nitrogen (see Fig. 22-36). 82. (1) Glutamate + ATP → γ-glutamyl phosphate + ADP (2) → γ-glutamyl phosphate + NH4+ → glutamine + Pi + H+ 83. (1) Indole-3-glycerol phosphate → indole + glyceraldehyde 3-phosphate (2) Indole + serine → tryptophan + H2O (See details in Fig. 22-20.)

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Chap 22_8e 84. The structure of AMP is in Figure 22-36. The first committed step in the pathway to AMP is the formation of 5phospho-β- D-ribosylamine from PRPP. (See Fig. 22-35.) This step is regulated by feedback inhibition; accumulated AMP, IMP, and GMP allosterically inhibit the first enzyme in the path, as shown in Figure 22-37. 85. Serine is derived from 3-phosphoglycerate by the pathway shown in Figure 22-14. Phosphoglycerate is oxidized by transamination from glutamate, yielding 3-phosphoserine. Removal of the phosphate yields serine. 86. Azaserine inhibits enzymes involved in the transfer of the amido nitrogen of glutamine in many biosynthetic pathways, including those leading to CTP, AMP, GMP, and tryptophan. Glutamine amidotransferases are in Figure 22-10. Eating azaserine would not be immediately fatal because it would take some time for the deficiencies of CTP, AMP, GMP, tryptophan, and so on to become severe enough to cause death. 87. The acetyl group, introduced in the initial reaction to synthesize N-acetylglutamate, is released as acetate to yield the amino acid ornithine (from N-acetylornithine). No carbon atoms in arginine are labeled as a result. 88. α-Ketoglutarate + NH4+ + NADPH + ATP → glutamate + NADP+ + ADP + Pi 89. GMP + ATP → GDP + ADP (nucleoside monophosphate kinase) GDP + ATP → GTP + ADP (nucleoside diphosphate kinase) 90. The structure of dTMP is shown in Figure 22-47. The methyl substituent on the ring is derived from N5,N10methylenetetrahydrofolate. The other atoms in the ring are derived from carbamoyl phosphate and aspartate, as seen in Figure 22-38. 91. Leghemoglobin serves to bind oxygen, maintaining a functionally anaerobic environment for the bacteria in the nodules to allow for nitrogenase activity. Oxygen will disrupt this enzyme, so its concentration must be kept low to allow for efficient conversion of nitrogen into ammonia. 92. (1) Alanine → pyruvate (2) Pyruvate + + ATP → oxaloacetate + ADP + Pi (3) Oxaloacetate + GTP → phosphoenolpyruvate + CO2 + GDP (4) Phosphoenolpyruvate → 2-phosphoglycerate → 3-phosphoglycerate; 3-phosphoglycerate + NAD+ → 3-phosphohydroxypyruvate + NADH (5) 3-Phosphohydroxypyruvate + glutamate → 3-phosphoserine + α-ketoglutarate (6) 3-Phosphoserine → serine + Pi (See Fig. 22-14.) 93. The structure of UMP is shown in Figure 22-38, which also shows the atoms contributed by aspartate in the first step of the pathway to UMP; all but the terminal —NH2 and the attached carbon in N-carbamoylaspartate come from aspartate.

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Chap 22_8e 94. UMP + ATP → UDP + ADP (nucleoside monophosphate kinase) UDP + NADPH → dUDP + NADP+ (ribonucleotide reductase and thioredoxin) dUDP + ATP → dUTP + ADP (nucleoside diphosphate kinase) dUTP → dUMP + PPi (dUTPase) dUMP + N5,N10-methylenetetrahydrofolate → dTMP + dihydrofolate (thymidylate synthase) dTMP + ATP → dTDP + ADP (nucleoside monophosphate kinase) dTDP + ATP → dTTP + ADP (nucleoside diphosphate kinase) (See Fig. 22-46.) 95. ATP is a signal that energy levels are high and synthesis of other nucleotides increases when adequate energy is available to ensure comparable amounts of different nucleotides. UMP is one of the end products of the pyrimidine synthesis pathways, where carbamoyl phosphate is an initial substrate (in the ATCase reaction), so it is acting as a feedback inhibitor. PRPP is also a substrate in the pyrimidine synthesis pathway, so it acting as an inhibitor makes sense when it is in excess. This is analogous to ATCase regulation, where ATP is an activator and CTP acts as an inhibitor. 96. CTP synthetase catalyzes the ATP-dependent conversion of UTP into CTP. Both ATP and UTP act as activators (and substrates) for the enzyme, maintaining a balance of the two pyrimidine nucleotides. 97. Protein provides the 10 essential amino acids that humans cannot synthesize. Humans need these amino acids for protein synthesis and for the production of a variety of products, such as histamine and serotonin, derived from the essential amino acids.

98. The structure of 5'-IMP with the origin of each atom is shown in Figures 22-34 and 22-35. 99. Even though the thermodynamics of nitrogen reduction are favorable, the kinetics are not owing to the stability of the N≡N triple bond. ATP hydrolysis is used, in part, to overcome the activation energy barrier in carrying out the reduction. 100. First, molecular nitrogen (N2) is reduced to ammonia in the reaction catalyzed by the nitrogenase complex, which is present in certain prokaryotes, including some that live symbiotically with legumes: N2 + 10H+ + 8e– + 16ATP → + 16ADP + 16Pi + H2 Then ammonia is incorporated into glutamine in the reaction catalyzed by glutamine synthetase: Glutamate + + ATP → glutamine + ADP + Pi + H+ Finally, glutamate synthase catalyzes formation of glutamate from glutamine: α-Ketoglutarate + glutamine + NAD(P)H + H+ → 2 glutamate + NAD(P)+ An alternative minor route from ammonia to glutamate involves the reaction catalyzed by glutamate dehydrogenase: α-Ketoglutarate + NH4+ + NADPH → glutamate + NADP+ + H2O

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Chap 23_8e Indicate the answer choice that best completes the statement or answers the question. 1. When blood glucose is abnormally low, the pancreas releases: a. epinephrine. b. glucagon. c. glucose. d. insulin. e. trypsin. 2. Which enzyme is likely to be activated by epinephrine? a. hormone-sensitive lipase b. acetyl-CoA carboxylase c. glycogen synthase d. HMG-CoA reductase e. fructose 1,6-bisphosphatase in skeletal muscle 3. Which is a normal blood glucose range? a. 40–65 mg/100 mL whole blood b. 50–150 mg/100 mL whole blood c. 100–120 mg/100 mL whole blood d. 120–125 mg/100 mL whole blood e. 60–90 mg/100 mL whole blood 4. PPARγ, PPARα, and PPARδ are examples of: a. transcription factors that respond to changes in dietary lipids. b. protein hormones that activate and deactivate AMPK. c. thyroid hormones that regulate growth. d. steroids that cause responses in the hypothalamus. e. subunits of the mTORC1 complex. 5. _____ is a peptide hormone produced in muscle as a result of exercise; it acts to convert white adipose tissue into beige adipose tissue. a. Leptin b. Irisin c. Neuropeptide Y d. Ghrelin e. Cortisol

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Chap 23_8e 6. Epinephrine is an example of a(n) _____ hormone. a. catecholamine b. eicosanoid c. paracrine d. peptide e. steroid 7. Which statement about metabolism in the mammalian liver is false? a. Most plasma lipoproteins are synthesized in the liver. b. The enzymatic complement of liver tissue changes in response to changes in the diet. c. The liver synthesizes most of the urea produced in the body. d. The presence of glucose 6-phosphatase makes liver uniquely able to release glucose into the bloodstream. e. Under certain conditions, most of the functions of the liver can be performed by other organs. 8. Elevated epinephrine levels do NOT normally stimulate: a. fatty acid mobilization in adipose tissue. b. gluconeogenesis in liver. c. glycogen breakdown in muscle. d. glycogen synthesis in liver. e. glycolysis in muscle. 9. Which complication is likely as a result of a condition known as metabolic syndrome? a. developing resistance to insulin b. developing type 1 diabetes c. developing cardiovascular disease d. developing both cardiovascular disease and resistance to insulin e. developing both type 1 diabetes and cardiovascular disease 10. Which factor is NOT associated with exercise? a. activation of AMP-activated protein kinase b. decreased release of insulin from the pancreas c. activation of acetyl-CoA carboxylase d. activation of the kinase activity of PFK-2 in skeletal muscle e. inhibition of glycogen synthase

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Chap 23_8e 11. In anaerobic skeletal muscle, breakdown of glycogen yields _____ ATP per glucose equivalent. a. 1 b. 2 c. 3 d. 4 e. 32 12. In an attempt to control type 2 diabetes, some people follow a high-fat, low-carbohydrate diet. Which substance(s) would NOT have an increased concentration in the blood after two weeks on this diet? a. fatty acids b. glucagon c. acetone d. glucose e. amino acids 13. The Cori cycle is the: a. conversion of lactate to pyruvate in skeletal muscle to drive glycogen synthesis. b. interconversion between glycogen and glucose 1-phosphate. c. production of lactate from glucose in peripheral tissues with the resynthesis of glucose from lactate in liver. d. synthesis of alanine from pyruvate in skeletal muscle and the synthesis of pyruvate from alanine in liver. e. synthesis of urea in liver and degradation of urea to carbon dioxide and ammonia by bacteria in the gut. 14. Insulin is an example of a(n) _____ hormone. a. catecholamine b. eicosanoid c. paracrine d. peptide e. steroid 15. Which statement does NOT describe a fate of amino acids in the liver? a. Amino acids are incorporated into new proteins. b. Nitrogen equivalents from amino acids are converted to urea. c. Carbon equivalents from amino acids are converted to glucose. d. Amino acids are stored for later use. e. Amino acids serve as precursors to nucleotide biosynthesis.

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Chap 23_8e 16. Which is NOT an activity of AMPK? a. phosphorylation and inactivation of acetyl-CoA carboxylase b. inhibition of cholesterol synthesis c. inactivation of HMG-CoA reductase d. activation of triacylglycerol synthesis e. interaction with protein kinase mTOR 17. Which statement is true regarding the late stages of starvation? a. The brain has decreased its need for glucose by switching to lactate as a major energy source. b. High levels of acetyl-CoA derived from lipid catabolism lead to the production of acetoacetate. c. Ketone bodies are produced from amino acids liberated from noncritical proteins. d. Gluconeogenesis is extremely active in the liver because of the large amounts of lactate exported from the muscle. e. Catabolism of triacylglycerols provides the major source of a gluconeogenic metabolite in the form of glycerol. 18. The mTORC1 complex associates with the _____ surface of _____, and is _____ by fasting. a. cytoplasmic; peroxisomes; activated b. cytoplasmic; lysosomes; inactivated c. interior membrane; lysosomes; activated d. interior membrane; peroxisomes; activated 19. In a cell, the relative concentrations of ATP and ADP in the matrix ultimately control the rate of: a. glycolysis. b. oxidative phosphorylation. c. pyruvate oxidation. d. both oxidative phosphorylation and pyruvate oxidation. e. All of the answers are correct. 20. One distinction between peptide and steroid hormones is that peptide hormones: a. act through nonspecific receptors, whereas steroid hormones act through specific receptors. b. are generally water insoluble, whereas steroid hormones are water soluble. c. are more stable than steroid hormones. d. bind to cell surface receptors, whereas steroid hormones bind to nuclear receptors. e. bind to their receptors with high affinity, whereas steroid hormones bind with low affinity.

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Chap 23_8e 21. Which effect is NOT mediated by the protein leptin? a. increased synthesis of uncoupler protein thermogenin b. decreased activity of the enzyme AMP-activated protein kinase (AMP c. increased activity of the sympathetic nervous system d. increasedβoxidation e. decreased desire to eat 22. Which protein is likely to be activated by cortisol? a. GLUT4 translocation to plasma membrane in myocytes b. phosphoenolpyruvate carboxykinase (PEP carboxykinase) c. glycogen synthase in hepatocytes d. All of the answers are correct. 23. In its role in the hormonal hierarchy, the hypothalamus produces and releases: a. epinephrine. b. insulin. c. progesterone. d. releasing factors. e. thyroxine. 24. _____ hormones are released into the blood and carried to target cells throughout the body, while _____ hormones are released into the extracellular space and diffuse to neighboring target cells. a. Endocrine; paracrine b. Paracrine; endocrine c. Peptide; steroid d. Steroid; peptide e. Autocrine; paracrine 25. Covalent modification via phosphorylation/dephosphorylation of specific key enzymes modifies their catalytic activity, and thus the flux through pathways. Which pathway is NOT regulated by this strategy? a. cholesterol synthesis in the liver b. lipolysis in adipocytes c. glycogen degradation in skeletal muscle d. fatty acid synthesis in the liver e. esterification to form triacylglycerols in the liver

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Chap 23_8e 26. Cortisol is released by the: a. hypothalamus. b. liver. c. pancreas. d. adrenal gland. 27. The hormone leptin _____ appetite; insulin _____ appetite. a. increases; increases b. increases; decreases c. decreases; increases d. decreases; decreases e. has no effect on; has no effect on 28. In uncontrolled insulin-dependent diabetes, which occurs? a. overproduction of β-hydroxybutyrate and acetoacetate b. underproduction of β-hydroxybutyrate and acetoacetate c. overproduction of β-hydroxybutyrate and underproduction of acetoacetate d. underproduction of β-hydroxybutyrate and overproduction of acetoacetate 29. Which describes ionotropic hormonal activity? a. Ion channels are opened or closed to change a membrane potential. b. Salt bridges are formed between a receptor and the hormone. c. The hormone is activated by protonation/deprotonation. d. The hormone must pass through an ion channel to reach its target receptor. 30. The normal sequence of action of these components of the hormonal hierarchy is: a. adrenal cortex → hypothalamus → anterior pituitary. b. anterior pituitary → adrenal cortex → hypothalamus. c. anterior pituitary → hypothalamus → adrenal cortex. d. hypothalamus → adrenal cortex → anterior pituitary. e. hypothalamus → anterior pituitary → adrenal cortex. 31. Which enzyme is NOT activated by insulin? a. acetyl-CoA carboxylase b. glycogen synthase c. kinase activity of PFK-2 d. hormone sensitive lipase

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Chap 23_8e 32. Which hormone triggers the release of α-melanocyte–stimulating hormone from anorexigenic neurons? a. leptin b. insulin c. ghrelin d. both leptin and insulin e. both leptin and ghrelin 33. Which signal is required for mTORC1 activation? a. branched-chain amino acids b. nutrient availability c. energy resources d. certain growth factors e. All of the answers are correct. 34. When blood glucose is abnormally high, the pancreas releases: a. epinephrine. b. glucagon. c. glucose. d. insulin. e. trypsin. 35. Brown adipose tissue (BAT) is a specialized fatty tissue present in some hibernating and cold-adapted animals. The mitochondria of BAT contain an additional protein called thermogenin, which spans the inner mitochondrial membrane. What occurs when this protein is active? a. decrease in the overall consumption of oxygen b. increase in the storage of triglycerides in brown adipocytes c. significant increase in heat production d. decrease in the flux of β oxidation in the matrix e. no change in the amount of ATP produced per fatty acid catabolized 36. Which statement is true regarding the islet cells of the pancreas? a. α cells secrete glucagon to stimulate glycogenolysis in skeletal muscle. b. α cells secrete glucagon to stimulate glycolysis in the liver. c. β cells secrete glucagon to stimulate glycogenolysis in the liver. d. β cells secrete insulin to stimulate glucose uptake by skeletal muscle, the liver, and adipose tissue. e. α cells secrete insulin to stimulate glycolysis in skeletal muscle.

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Chap 23_8e 37. In skeletal muscle, phosphocreatine functions as a(n): a. reservoir of Pi for mitochondria. b. reservoir of high energy for phosphate to replenish ATP. c. reservoir of amino acids for protein synthesis. d. electron acceptor under anaerobic conditions. e. None of the answers is correct. 38. Which compound is NOT a peptide hormone? a. ghrelin b. insulin c. adiponectin d. PPARγ e. PYY3–36 39. Which is the correct order of the leptin signal transduction pathway? 1. Binding of leptin to extracellular domain of the leptin receptor. 2. Increased production of α-MSH. 3. Increased synthesis of POMC. 4. Dimerization and phosphorylation of leptin receptor domains. 5. Brain receives signal "stop eating!" a. 1, 4, 3, 2, 5 b. 1, 4, 2, 3, 5 c. 4, 1, 3, 2, 5 d. 4, 1, 2, 3, 5 40. The largest energy store in a well-nourished human is: a. ATP in all tissues. b. blood glucose. c. liver glycogen. d. muscle glycogen. e. triacylglycerols in adipose tissue. 41. Long-term maintenance of body weight is regulated by the hormone: a. adiposin. b. hypothalmin. c. leptin. d. obesin. e. testosterone.

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Chap 23_8e 42. Which hormone acts on orexigenic neurons in the arcuate nucleus to produce hunger before a meal? a. leptin b. insulin c. ghrelin d. cortisol e. PPARd 43. Which factor is NOT involved in triggering insulin from β cells' release in response to glucose? a. reduced efflux through ATP-gated K+ channels b. increased concentrations of ATP c. cAMP-dependent phosphorylation of lipase d. phosphorylation of glucose to glucose 6-phosphate e. increased Ca2+ levels 44. A major difference between white adipose tissue and brown adipose tissue is that only _____ adipose tissue _____. a. white; stores fatty acids as triacylglycerols b. brown; degrades fatty acids via the citric acid cycle c. brown; contains thermogenin d. white; contains adipocytes e. white; responds to hormone signals 45. Which statement is true regarding diabetes mellitus? a. Diabetes mellitus is characterized by the abnormal depletion of blood glucose by the liver. b. Diabetes mellitus is characterized by reduced levels of gluconeogenesis in the liver. c. Diabetes mellitus is characterized by the destruction of glucagon-secreting cells of the pancreas. d. Diabetes mellitus is characterized by the secretion of glucagon in the urine leading to "sweet urine." e. Diabetes mellitus is characterized by ketonemia, metabolic acidosis, and ketonuria. 46. Which statement is false regarding the protein ghrelin? a. Levels of ghrelin are lowest in the blood just before a meal and highest just after a meal. b. Ghrelin is a peptide hormone produced by endocrine cells lining the gastrointestinal tract. c. The receptors for ghrelin are found in the same location as the receptors for leptin. d. Regulation of gastric ghrelin secretion may be influenced by specific microbes in the gut. e. Ghrelin causes the release of orexigenic peptides from arcuate neurons in the pituitary gland.

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Chap 23_8e 47. The peptide hormone adiponectin, produced in adipose tissue, circulates in the blood and: a. enhances fatty acid synthesis in liver cells. b. increases the rate of β oxidation of fatty acids in muscle cells. c. inhibits glucose uptake and catabolism in muscle and liver cells. d. reduces the transport of fatty acids into muscle cells. e. stimulates gluconeogenesis in liver cells. 48. An example of an eicosanoid hormone is: a. epinephrine. b. retinoic acid. c. testosterone. d. prostaglandin E2. e. thyroxine. 49. Which statement is true regarding the protein leptin? a. Leptin is a hormone made primarily by hepatocytes that functions to regulate energy balance by curtailing appetite. b. Leptin is an adipokine released when adipose cells are well-filled with triacylglycerols. c. Leptin is involved in regulating the sympathetic nervous system, resulting in a decrease in blood pressure, heart rate, and thermogenesis. d. The amount of leptin released by adipose tissue is independent of the number and size of adipocytes; rather, it is strictly correlated with ingestion of food. 50. Which process is NOT a mechanism for treating diabetes? a. increasing TAG by weight loss b. activating AMPK through exercise c. activating AMPK by taking metformin d. activating PPARγ through rosiglitazone e. stimulating insulin secretion by taking sulfonylureas 51. Which hormone stimulates appetite? a. ghrelin b. insulin c. adiponectin d. both ghrelin and insulin e. both ghrelin and adiponectin

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Chap 23_8e 52. Which statement does NOT describe a fate for fatty acids in the liver? a. They are oxidized to yield acetyl-CoA and NADPH. b. They are released into the bloodstream as a component of lipoproteins. c. They are oxidized and converted into ketone bodies. d. They are released as free fatty acids into the bloodstream. e. They are oxidized and used in the synthesis of cholesterol. 53. What would likely be the consequence of a biochemical defect in which glucagon was secreted in excess? a. muscular fatigue due to lactic acidosis b. inhibited glycolysis in the liver with depleted glycogen stores c. lowered concentrations of ketone bodies circulating in the bloodstream d. depressed rate of urea excretion e. excessive accumulation of triacylglycerols in adipocytes 54. Each enzyme listed catalyzes a reaction in the skeletal muscles of an Olympic sprinter. However, the role of which one would be considered LEAST significant during the running of a 100 meter sprint? a. adenylate kinase b. creatine kinase c. pyruvate dehydrogenase d. lactate dehydrogenase e. glycogen phosphorylase 55. Epinephrine triggers an increased rate of glycolysis in muscle by: a. activation of hexokinase. b. activation of phosphofructokinase-1. c. conversion of glycogen phosphorylase a to glycogen phosphorylase b. d. inhibition of the Cori cycle. e. the Pasteur effect. 56. Which statement does NOT describe a fate of fatty acids in the liver? a. Fatty acids are oxidized to generate ATP. b. Fatty acids are converted to ketone bodies. c. Fatty acids can be converted to cholesterol. d. Fatty acids are stored for later use. e. Fatty acids are converted to glucose.

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Chap 23_8e 57. Which condition is NOT typically associated with metabolic syndrome? a. hypotension b. elevated fasting plasma glucose c. elevated serum levels of LDL d. abdominal obesity e. reduced serum levels of HDL 58. After a meal rich in carbohydrates, which condition would NOT be expected? a. adenylate cyclase deactivation b. increased activity of glucokinase c. glycogen phosphorolysis d. decreased secretion of glucagon e. decreased production of β-hydroxybutyrate 59. Under conditions of prolonged starvation, which fuel is MOST catabolized by the brain in humans? a. ketone bodies b. glucose c. amino acids d. odd-chain fatty acids e. glycerol 60. Which protein is inhibited by insulin? a. glucokinase b. GLUT4 c. acetyl-CoA carboxylase d. pyruvate dehydrogenase e. glycogen phosphorylase 61. Which enzyme, found primarily in the liver, dictates that the gluconeogenic pathway of the Cori cycle occurs in the liver? a. glucose 6-phosphatase b. glucokinase c. glucose 6-phosphate dehydrogenase d. glyceraldehyde 3-phosphate dehydrogenase e. phosphoglucomutase

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Chap 23_8e 62. What would likely be the consequence of a biochemical defect in which insulin was secreted in excess? a. muscular fatigue due to lactic acidosis b. inhibited glycolysis in the liver resulting in enhanced glycogen stores c. lowered concentrations of glucose circulating in the bloodstream d. depressed rate of fatty acid synthesis in the liver e. enhanced rate of gluconeogenesis in hepatocytes 63. The maturation of insulin from its precursor (preproinsulin) involves: a. acetylation. b. oxidation. c. phosphorylation. d. proteolysis. e. reduction. 64. Which statement is true? a. The brain prefers glucose as an energy source, but can use ketone bodies. b. Muscle cannot use fatty acids as an energy source. c. In a well-fed human, about equal amounts of energy are stored as glycogen and as triacylglycerol. d. Fatty acids cannot be used as an energy source in humans because humans lack the enzymes of the glyoxylate cycle. e. Amino acids are a preferable energy source over fatty acids. 65. Hormones that bind to cell surface hormone receptors that activate or inhibit an enzyme downstream from the receptor are classified as being: a. ionotropic. b. allotropic. c. cascade initiators. d. metabotropic. e. modulatory. 66. A hyperventilating patient is admitted to the hospital after experiencing for some time excessive thirst, frequent urination, weight loss, and fatigue. Analysis of the blood reveals below normal pH and above normal glucose levels. What is the primary cause of this low blood pH? a. ketoacidosis resulting from starvation b. water loss due to frequent urination c. excessive amounts of lactate produced by anaerobic metabolism d. ketoacidosis resulting from untreated type 1 diabetes e. excessive amounts of lactate produced by chronic alcohol use

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Chap 23_8e 67. Which condition is associated with elevated insulin levels in the blood? a. acetyl-CoA levels rise and ketone body synthesis increases b. oxaloacetate levels are high and citrate synthesis increases c. gluconeogenesis is activated and glycolysis is inhibited d. the production of mevalonate decreases e. liver glycogen phosphorylase is activated 68. Glucokinase: a. acts in the conversion of liver glycogen to glucose 1-phosphate. b. converts fructose 6-phosphate to glucose 6-phosphate c. converts glucose 6-phosphate to fructose 6-phosphate. d. is a hexokinase isozyme found in liver hepatocytes. e. is found in all mammalian tissues. 69. An elevated insulin level in the blood: a. inhibits glucose uptake by the liver. b. inhibits glycogen synthesis in the liver and muscle. c. results from a below normal blood glucose level. d. stimulates glycogen breakdown in liver. e. stimulates synthesis of fatty acids and triacylglycerols in the liver. 70. Overeating may result in excess deposition of TAGs, insulin insensitivity, and type 2 diabetes due to: a. overproduction of leptin. b. stimulation of PPARγ. c. chronic activation of mTORC1. d. overproduction of epinephrine. e. All of the answers are correct. 71. Which two hormones play a crucial role in regulating short-term eating behavior? a. leptin and ghrelin b. cortisol and leptin c. ghrelin and PYY3–36 d. insulin and glucagon e. adiponectin and PYY3–36

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Chap 23_8e 72. Which statement describes one of the roles of mTORC1? a. mTORC1 activates AMP-activated protein kinase (AMP, resulting in energy production for cell growth. b. mTORC1 activates translation of proteins involved in lipid synthesis and mitochondrial metabolism. c. mTORC1 acts through AMPK to increase sensitivity of hepatocytes and myocytes to insulin. d. mTORC1 reduces the uptake of glucose by hepatocytes, ensuring the brain has an adequate glucose supply. 73. An example of a steroid hormone is: a. epinephrine. b. retinoic acid. c. testosterone. d. thromboxane. e. thyroxine. 74. In skeletal muscle: a. amino acids are an essential fuel. b. at rest, fatty acids are the preferred fuel. c. large quantities of triacylglycerol are stored as fuel. d. phosphocreatine can substitute for ATP as the direct source of energy for muscle contraction. e. stored muscle glycogen can be converted to glucose and released to replenish blood glucose. 75. Describe five possible fates for glucose 6-phosphate in the liver.

76. Compare in general terms the effects of epinephrine, glucagon, and insulin on glucose metabolism.

77. Which class(es) of hormone acts via nuclear receptors? Give an example of this type of hormone and briefly describe its mode of action.

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Chap 23_8e 78. Explain why peroxisome proliferator-activated receptor gamma (PPAR-γ) knockout mice fail to develop adipose tissue when fed a high-fat diet.

79. Describe the signaling cascade initiated by leptin binding to its receptor.

80. Briefly explain the role of phosphocreatine in muscle.

81. What explains the relative resistance to hypoglycemic coma in people who are starving compared with a normal person?

82. Describe five possible fates for fatty acids in the liver.

83. Describe five possible fates of amino acids arriving in the liver after intestinal uptake.

84. Provide three distinguishing characteristics between white adipose tissue (WAT) and brown adipose tissue (BAT).

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Chap 23_8e 85. Some hormones trigger very rapid responses, whereas for others the response takes much longer to develop. What generalization about the mechanisms of action of these two types of hormones can explain the differences in response times?

86. Describe the differences between eicosanoids and epinephrine. Specifically discuss their point of synthesis versus point of action, and the timing of production relative to demand.

87. What is leptin? How does it function in the long-term maintenance of body mass?

88. Explain the signaling pathway by which an increase in blood glucose causes the release of insulin from pancreatic β cells.

89. Briefly describe a hypothesis that explains the development of type 2 diabetes.

90. Agonists of peroxisome proliferator-activated receptor delta (PPAR-δ) have been used by professional athletes as performance-enhancing drugs; such drugs have been added in 2009 to list of drugs prohibited by the World Anti-Doping Agency. Explain the rational for their use as a performance-enhancing drug.

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Chap 23_8e 91. Briefly describe the effects of the hormone adiponectin.

92. How do hormonal cascades result in large amplification of the original signal?

93. Explain the response and the consequences of prolonged fasting on fuel metabolism by the liver.

94. Briefly explain the Cori cycle.

95. Brown adipose tissue has been described as the "the fat that makes you thin." Explain why brown fat is being investigated as a key to weight control.

96. Name five general classes of hormones and give an example of each.

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Chap 23_8e Answer Key 1. b 2. a 3. e 4. a 5. b 6. a 7. e 8. d 9. d 10. c 11. c 12. d 13. c 14. d 15. d 16. d 17. b 18. b 19. e 20. d 21. b 22. b 23. d 24. a 25. e 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 23_8e 27. d 28. a 29. a 30. e 31. d 32. d 33. e 34. d 35. c 36. d 37. b 38. d 39. a 40. e 41. c 42. c 43. c 44. c 45. e 46. a 47. b 48. d 49. b 50. a 51. e 52. a 53. b 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 23_8e 55. b 56. e 57. a 58. c 59. a 60. e 61. a 62. c 63. d 64. a 65. d 66. d 67. b 68. d 69. e 70. c 71. c 72. b 73. c 74. b 75. Possible answers include: (1) conversion to liver glycogen; (2) dephosphorylation and release of glucose into bloodstream; (3) oxidation via the pentose phosphate pathway; (4) oxidation via glycolysis and the citric acid cycle; (5) oxidation to acetyl-CoA, which then serves as precursor for synthesis of triacylglycerols, phospholipids, and cholesterol. (See Fig. 23-10.)

76. Epinephrine and glucagon cause an increase in the blood glucose level. Epinephrine acts when a higher than normal level of glucose is required; glucagon acts when the level is unusually low. Both stimulate gluconeogenesis and glycogen breakdown and decrease glycolysis and glycogen synthesis. Insulin causes a decrease in blood glucose levels; it acts by increasing glycogen synthesis, glycolysis, and glucose uptake by cells as well as by decreasing glycogen breakdown.

77. Steroid, vitamin D, retinoid, and thyroid hormones act via nuclear receptors. Examples are the sex hormones testosterone and estradiol. They pass through the plasma membrane and interact with receptor proteins in the nucleus. The hormone-receptor complex interacts with DNA and alters the expression of specific genes.

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Chap 23_8e 78. PPAR-γ is expressed primarily in liver and adipocytes. Ligand-bound PPAR-γ is a transcription factor involved in turning on genes required for the differentiation of fibroblasts into adipocytes and genes required for the synthesis of lipids and their storage in adipocytes. Hence, PPAR-γ knockout mice fed a high-fat diet did not display significant weight gain. 79. Leptin binds to two extracellular domains of the receptor. Binding of leptin to its receptor in the hypothalamus causes the receptor to dimerize and several Tyr residues are phosphorylated. A chain of events leads to activation of transcription of the gene for POMC, from which the α-melanocyte–stimulating hormone (α-MSH) is produced. The signal that α-MSH conveys to the brain is to "stop eating!" 80. During maximal muscle activity, muscle cells are in danger of depleting their ATP levels. Oxygen cannot be provided rapidly enough to support the electron-transfer chain, fermentation is not nearly as efficient as aerobic metabolism, and the decrease in pH caused by lactate accumulation is also detrimental to the efficiency of the muscles. Phosphocreatine provides an additional source of energy that can convert ADP back to ATP via the creatine kinase reaction to help maintain muscle activity.

81. During starvation, the brain switches from using glucose as its sole energy source to using ketones as the primary energy source. After a few days of starvation, the brain adapts to decrease glucose availability by producing enzymes required for metabolizing ketones for energy production. If a normal person is exposed to a sudden drop in blood glucose, they will experience an energy deficit in the brain, as they do not have the enzymes necessary to metabolize ketones. However, an individual who has been exposed to prolonged starvation conditions has switched to obtaining 70% of their energy from ketones and thus they are better able to deal with hypoglycemic conditions.

82. Possible answers include: (1) conversion to triacylglycerol or cholesterol esters for export in plasma lipoproteins; (2) conversion into hepatocyte phospholipids; (3) oxidation and conversion to ketone bodies for export to other tissues; (4) β oxidation to acetyl-CoA, and further oxidation via citric acid cycle for ATP production; (5) β oxidation to acetyl-CoA, followed by synthesis of cholesterol from acetyl-CoA; (6) binding to serum albumin for transport to heart and skeleton. (See Fig. 23-12.) 83. Possible answers include: (1) synthesis of nucleotides; (2) synthesis of hormones; (3) synthesis of other nitrogenous products such as porphyrins; (4) deamination, followed by oxidation of carbon skeleton for energy; (5) synthesis of proteins for export to plasma; (6) synthesis of proteins for liver; (7) export of free amino acids to other tissues. (See Fig. 23-11.)

84. Possible answers include: (1) WAT is more abundant than BAT. (2) The adipocytes of WAT are large and completely filled with a single droplet of triacylglycerols. The adipocytes of BAT are smaller and store triacylglycerols in many smaller droplets. (3) In WAT, burning of triacylglycerols leads to ATP formation, whereas in BAT, much of that energy is converted to heat instead. (4) BAT cells have more mitochondria than WAT. (5) BAT has a richer supply of capillaries than WAT.

85. Fast-acting hormones affect the activity of preexisting cellular enzymes. Slow-acting hormones alter gene expression thereby changing the levels of active cellular components.

86. Eicosanoids are paracrine hormones derived from fatty acids: They generally do not move long distances between their points of release and their points of action. Also, eicosanoids are not synthesized in advance but rather are produced as needed. Epinephrine is a member of the catecholamine hormones and is water soluble. Epinephrine is synthesized in advance, stored in vesicles, and when released, circulates through the bloodstream to remote tissues.

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Chap 23_8e 87. Leptin is a small polypeptide that is produced in adipocytes and is carried by the blood to the brain. It is produced when there are adequate stores of lipid in the adipocytes and interacts with a receptor in the hypothalamus. This interaction produces a cascade of effects that tend to suppress appetite and increase energy expenditure.

88. Glucose in the blood is transported into pancreatic β cells via the GLUT2 transporter, where it is phosphorylated and then metabolized via glycolysis and the citric acid cycle, ultimately leading to higher ATP concentrations via oxidative phosphorylation. Higher ATP levels close the ATP-gated K+ channels, depolarizing the membrane, which leads to the opening of the voltage-gated Ca2+ channels, an increase in intracellular Ca2+ concentrations, and the subsequent release of insulin via exocytosis. 89. Excessive caloric intake by obese individuals causes adipocytes to become completely filled with triacyclglycerols, unable to take up and store any additional fatty acids. These lipid-filled adipocytes release signals that attract macrophages that invade the fat tissue and trigger an inflammatory response. The inflammatory response further impairs uptake of fatty acids and leads to even higher levels of free fatty acids in the bloodstream. The excess free fatty acids are taken up by the liver and muscle cells. The fatty acids are then converted to triacylglycerols and stored as lipid droplets. These lipid droplets are toxic to these cells, leading to eventual insulin resistance through a variety of mechanisms.

90. Activation of peroxisome proliferator-activated receptor delta (PPAR-δ) enhances fatty acid metabolism. Receptors in this subtype of PPARs are found primarily in the liver and skeletal muscle. When activated by an agonist, they act as transcription factors for genes encoding proteins for β oxidation. Presumably, synthetic agonists of PPARδ improve physical performance by enhancing fuel utilization. 91. Adiponectin is a peptide hormone produced by adipose tissues that triggers increased uptake and oxidation of fatty acids in liver and muscle cells. It also blocks gluconeogenesis and fatty acid biosynthesis in the liver, and sensitizes the liver to insulin.

92. At each level, a small quantity of the signal molecule activates a larger number of molecules at the next level. When this occurs over several levels, this multiplicative effect can result in a several millionfold amplification of the original signal. (See Fig. 23-6.)

93. Under conditions of prolonged fasting (i.e., absence of glucose in the diet), the liver is responsible for providing energy, primarily to the brain. Fatty acids from adipocytes are broken down and converted to ketone bodies, which can be used as an alternative fuel source by the brain. Proteins from muscle cells are broken down to provide an alternative route to glucose via citric acid cycle intermediates and gluconeogenesis. The consequences include muscle wastage, loss of weight, acidic blood, and excess ketone bodies and urea in the urine.

94. The Cori cycle allows for lactate produced by anaerobic muscles to be transported to the liver where it is converted back to glucose. The glucose is then transported back to the muscle to complete the cycle.

95. Brown fat or brown adipose tissue contains a mitochondrial protein known as thermogenin. This protein provides an alternative route to ATP synthase for protons pumped during electron transport to re-enter the mitochondria. Energy from the movement of protons back to the matrix is not stored as ATP; rather, it is dissipated as heat. As less ATP is generated by oxidation of fatty acids in brown adipose tissue, metabolism and utilization of fatty acids in this tissue is accelerated compared with that in white adipose tissue. 96. (1) Peptide (e.g., insulin, glucagon); (2) catecholamine (e.g., epinephrine); (3) steroid (e.g., testosterone, progesterone); (4) eicosanoids (e.g., prostaglandins); (5) vitamin D (e.g., calcitriol); (6) retinoid (e.g., retinoic acid); (7) thyroid (e.g., triiodothyronine); (8) nitric oxide (e.g., nitric oxide). (See Table 23-1.) Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_8e Indicate the answer choice that best completes the statement or answers the question. 1. Which statement is true about type I topoisomerases? a. They can change the linking number in increments of 1 or 2. b. The mechanism of their reaction requires energy from ATP. c. They use a mechanism involving a covalent enzyme-substrate intermediate. d. All of the answers are correct. 2. In which cell-cycle step are cohesins loaded onto the chromosomes? a. G1/S b. S/G2 c. during prophase d. during anaphase e. during telophase 3. If a plasmid has 11,025 base pairs and a superhelical density of –0.06, what is the linking number? Assume the structure is B-DNA (10.5 bases/turn). a. 389 b. 661 c. 987 d. 1,050 e. 1,113 4. Which protein carries out ATP hydrolysis? a. histone H2A b. histone H1 c. E. coli topoisomerase I d. histone H3 e. E. coli topoisomerase IV 5. Two forms of DNA that differ only in linking number are classified as: a. plectonemic forms. b. anomers. c. heteroforms. d. catenanes. e. topoisomers.

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Chap 24_8e 6. If the structure of a fully relaxed, closed-circular DNA molecule is changed so that the specific linking difference is –0.05, the number of: a. bases is decreased by 5%. b. bases is increased by 5%. c. helical turns is decreased by 5%. d. helical turns is increased by 5%. e. helical turns is unchanged. 7. Which statement about nucleic acids is false? a. Mitochondria and chloroplasts contain DNA. b. Plasmids are genes that encode plasma proteins in mammals. c. The chromosome of E. coli is a closed-circular, double-helical DNA. d. The DNA of viruses is usually much longer than the viral particle itself. e. The genome of many plant viruses is RNA. 8. What are the minimal components of a virus? a. DNA and a lipid membrane b. genome (DNA or RNA), a lipid membrane, and a protein coat c. genome (DNA or RNA) and a protein coat d. protein genome and a lipid membrane 9. Nucleosomes: a. are important features of chromosome organization in eukaryotes and bacteria. b. are composed of proteins rich in acidic amino acids, such as Asp and Glu. c. are composed of protein and RNA. d. bind DNA and alter its supercoiling. e. occur in chromatin at irregular intervals along the DNA molecule. 10. It is correct to say that DNA supercoiling cannot: a. be induced by strand separation. b. be induced by underwinding of the double helix. c. form if there is Z-DNA structure present. d. occur if a closed-circular, double-stranded DNA molecule has a permanent nick. e. result in compaction of the DNA structure.

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Chap 24_8e 11. An average base pair in DNA is 650 daltons (Da). Histone masses are shown in the table. What is the approximate mass of a nucleosome bead (histone core wrapped with DNA) in kilodaltons (kDa)? Histone Mass (Da) H1 21,130 H2A 13,960 H2B 13,774 H3 15,273 H4 11,236 a. ~55 kDa b. ~75 kDa c. ~170 kDa d. ~205 kDa e. ~230 kDa 12. Samples of a purified plasmid often contain relaxed and supercoiled forms. What might be expected if such a sample is electrophoresed by agarose gel electrophoresis? a. Only one DNA band appears because both forms have the same molecular weight. b. The supercoiled form is more compact and will electrophorese faster through the gel pores. c. The relaxed form is more flexible and will electrophorese faster through the gel pores. d. The supercoiled form will be more highly charged and electrophorese faster. e. The relaxed form will be more highly charged and electrophorese faster. 13. Which statement is false regarding supercoils in nucleic acids? a. Supercoils allow DNA to become more compact. b. Supercoiling occurs in overwound DNA, but not in underwound DNA. c. Supercoiling requires DNA that is either circular or has constrained ends. d. Positive solenoidal supercoils have the opposite handedness to positive plectonemic supercoils. 14. Acetylation of lysine residues in histones has what effect? a. It increases the positive charge on the protein and increases compaction. b. It increases the positive charge on the protein and decreases compaction. c. It decreases the positive charge on the protein and increases compaction. d. It decreases the positive charge on the protein and decreases compaction. 15. The genome of organism A is 4.6 million base pairs long, while that of organism B is 12.1 million base pairs long. Given this information, what can be stated regarding these two organisms? a. Organism B will contain approximately three times the number of genes as organism A. b. Organism B will contain approximately 7.5 million more base pairs in introns compared with organism A. c. Organism B will contain three times as many chromosomes as organism A. d. The genome of each has its own unique number of genes. Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_8e 16. Which list ranks the organisms in order of increasing number of genes? a. S. cerevisiae, humans, rice b. S. cerevisiae, rice, humans c. rice, humans, S. cerevisiae d. rice, S. cerevisiae, humans e. humans, S. cerevisiae, rice 17. Which protein binds to the linker DNA between nucleosomes? a. histone H1 b. histone H2A c. histone H2B d. histone H3 e. histone H4 18. Which statement is true for histones? a. They vary in size from 200 to 400 amino acids in length. b. They form covalent complexes with DNA. c. They form both protein-DNA and protein-protein interactions. d. They contain large amounts of Asp residues. e. DNA wraps around them in a right-handed helical structure. 19. Plectonemic supercoils in a negatively supercoiled DNA molecule: a. are always left-handed. b. are always right-handed. c. are balanced by solenoidal supercoils. d. can be either right- or left-handed. e. never occur. 20. Which description is NOT accurate regarding telomeres? a. They are sequences found at the ends of linear DNA chromosomes. b. They are portions of DNA that contain stretches of small, repetitive DNA sequences. c. They are sequences involved in DNA replication. d. They are sequences involved in the initiation of replication in eukaryotes. e. They are sequences that do not contain genes.

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Chap 24_8e 21. Which statement is true about the replicative form of DNA for bacteriophage φX174 as compared to DNA in the viral particle? a. In both the viral particle and the replicative form the DNA is single-stranded. b. In both the viral particle and the replicative form the DNA is double-stranded. c. In the viral particle it is double-stranded; the replicative form is single-stranded. d. In the viral particle it is single-stranded; the replicative form is double-stranded. 22. DNA in a closed-circular, double-stranded molecule with no net bending of the DNA axis on itself is: a. a left-handed helix. b. a mixed right- and left-handed helix. c. relaxed. d. supercoiled. e. underwound. 23. The fundamental repeating unit of organization in a eukaryotic chromosome is the: a. centrosome. b. lysosome. c. microsome. d. nucleosome. e. polysome. 24. Heterochromatin is comprised of: a. linked chromatin between two or more chromosomes. b. DNA at the centromere. c. DNA-protein regions that are transcriptionally active. d. DNA-RNA hybrid regions that form during transcription. e. highly condensed transcriptionally inactive regions of DNA. 25. Which DNA structures are NOT generally circular? a. plasmids b. yeast chromosomes c. bacterial chromosomes d. mitochondrial DNA e. chloroplast DNA

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Chap 24_8e 26. The gene for the hemoglobinβsubunit is 1,420 bp long and contains two introns that are 131 bp and 851 bp long. How long is the β-subunit polypeptide? a. 146 amino acids long b. 327 amino acids long c. 438 amino acids long d. 473 amino acids long e. 2,140 amino acids long 27. Which statement is false regarding histones? a. Overall, histones are positively charged proteins. b. Lys and Arg residues are abundant in histones relative to other proteins. c. Histone H1 is found in the nucleosome core. d. The nucleosome core contains eight histone proteins. 28. How do coumarin antibiotics work? a. They inhibit the formation of bacterial cell walls. b. They block the assembly of bacterial nucleosomes. c. They nick bacterial DNA and cause it to be completely relaxed. d. They inhibit the ATP binding of bacterial type II topoisomerases. e. They increase the linking number of the bacterial DNA to the point it can no longer replicate. 29. Bacterial chromosomes: a. are highly compacted into structures called nucleoids. b. are seen in electron microscopy as "beads on a string." c. are surrounded by a nuclear membrane. d. contain large numbers of nucleosomes. e. when fully extended are as long as the bacterial cell. 30. The DNA in the E. coli chromosome is BEST described as: a. a single circular double-helical molecule. b. a single linear double-helical molecule. c. a single linear single-stranded molecule. d. multiple linear double-helical molecules. e. multiple linear single-stranded molecules. 31. Which of the components are NOT known to be associated with condensed eukaryotic chromosomes? a. core histones H2A, H2B, H3, and H4 b. histone H1 c. SMC proteins d. topoisomerase I Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_8e 32. Which statement is false regarding DNA-binding proteins? a. DNA-binding proteins typically form covalent bonds to DNA. b. DNA-binding proteins are important in DNA compaction. c. DNA-binding proteins typically interact with DNA via electrostatic interactions. d. DNA binding by proteins is influenced by the sequence of the nucleic acid. e. DNA-binding proteins often contain Arg and Lys residues. 33. Of the side-chain modifications listed, which ones will decrease the positive charge on a histone? a. only lysine acetylation b. only serine phosphorylation c. only lysine methylation d. both lysine methylation and acetylation e. both lysine acetylation and serine phosphorylation 34. Which protein is NOT important in the compaction of eukaryotic DNA? a. histone H1 b. cohesins c. condensins d. topoisomerases e. satellite proteins 35. The MOST precise modern definition of a gene is a segment of genetic material that: a. codes for one polypeptide. b. codes for a final polypeptide or RNA product. c. determines one phenotype. d. determines one trait. e. codes for one protein. 36. Which factor contributes to the structure of nucleosomes? a. plectonemic supercoiled DNA b. relaxed closed-circular DNA c. solenoidal supercoiled DNA d. spacer DNA e. Z (left-handed) DNA

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Chap 24_8e 37. CAF1 protein (chromatin assembly factor 1) promotes deposition of H3-containing histone complexes on DNA after replication. CAF1 is classified as a: a. satellite protein. b. condensin. c. histone chaperone. d. cohesin. e. topoisomerase. 38. What kind of posttranslational modifications can occur in histones? a. only methylation b. only acetylation c. only phosphorylation d. methylation and acetylation e. methylation, acetylation, and phosphorylation 39. In which phase of the cell cycle is DNA MOST condensed? a. G1 b. S c. G2 d. prophase e. metaphase 40. Which histone is replaced in nucleosomes found in the vicinity of centromeres? a. H1 b. H2A c. H2B d. H3 e. H4 41. The eukaryotic SMC protein condensin contains which SMC subunits? a. SMC1 and SMC2 b. SMC1 and SMC3 c. SMC2 and SMC3 d. SMC2 and SMC4 e. SMC3 and SMC4

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Chap 24_8e 42. Circular DNAs that intertwine like links on a chain are called _____. They can be separated by type _____ topoisomerases. a. solenoids; II b. catenanes; II c. catenanes; IV d. solenoids; IV 43. Which statement is false? a. Histones are very conserved at the primary sequence level in eukaryotes. b. Histones H2A, H2B, and H1 all contain the histone-fold domain. c. CENPA is most closely related to histone H3. d. The amino terminal tail of histone H3 is the location of most of its covalent modifications. e. Amino terminal ends of core histones are involved in internucleosome interactions. 44. What is the role of long noncoding RNAs (lncRNAs)? a. X chromosome inactivation in some mammals b. provide a link that tethers distant parts of the chromosome together c. participate in nucleosome positioning with proteins that bind lncRNA d. provide a scaffold for protein that affect chromosome structure e. All of the above are roles for lncRNAs. 45. Introns: a. are frequently present in prokaryotic genes but are rare in eukaryotic genes. b. are spliced out before transcription. c. are translated but not transcribed. d. can occur many times within a single gene. e. encode unusual amino acids in proteins. 46. If negatively supercoiled plasmid DNA is mixed with human topoisomerase I and ATP, which effect would be observed? a. Rapid ATP hydrolysis would occur. b. The linking number for the plasmid would increase. c. The writhe on the plasmid would increase. d. The superhelical density would become more negative. e. None of these effects would be observed.

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Chap 24_8e 47. Nucleosome formation condenses DNA by approximately sevenfold and 30 nm fiber formation condenses DNA by a further 100-fold. How long will a 450,000 bp segment of linear DNA be after compaction to a 30 nm fiber? a. ~2 nm b. ~20 nm c. ~200 nm d. ~2,000 nm e. ~20,000 nm 48. Which statement is false for euchromatin? a. Euchromatin is a form of chromatin. b. Euchromatin has less H1 associated with it than heterochromatin. c. Euchromatin is being more actively transcribed than heterochromatin. d. Euchromatin is more densely packed than heterochromatin. e. None of these statements is false. 49. What kind of supercoils are formed around nucleosomes? a. positive plectonemic supercoils b. negative plectonemic supercoils c. positive solenoidal supercoils d. negative solenoidal supercoils e. a mixture of solenoidal and plectonemic supercoils 50. Approximately what fraction of the human genome is transposable elements? a. less than 1% b. about 2% c. about 25% d. about 50% e. more than 90% 51. Which statement is true about bacterial DNA organization? a. It is very similar to eukaryotic organization with beads-on-a-string nucleosomes formed. b. It is similar in nucleosome structure except only two types of histones are known. c. Bacterial DNA does not have nucleosomes, but forms extremely condense plectonemic structures. d. Nucleosomes in bacteria are about seven times larger than in eukaryotes, with cores containing up to 30 histone molecules. e. Bacterial DNA does not have the nucleosome structure of eukaryotes, although some proteins (e.g., H associate and dissociate with the DNA.

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Chap 24_8e 52. The SMC proteins (for structural maintenance of chromosomes) include cohesins and condensins and are NOT known to have: a. a complete ATP-binding site. b. a hinge region. c. topoisomerase activity to produce positive supercoils. d. the ability to condense DNA. e. two coiled-coil domains. 53. Which aspect does NOT distinguish bacterial SMC proteins from eukaryotic SMC proteins? a. formation of coiled-coil structures b. binding and hydrolysis of ATP c. formation of hinge domains d. formation of head domains e. formation of homodimers versus heterodimers 54. Approximately what percent of human DNA is "coding" or exon DNA? a. 30% b. 90% c. 0.045% d. 1.5% e. The percent of exons varies widely among the human population. 55. The linking number of a closed-circular, double-stranded DNA molecule is changed by: a. breaking a strand, then rejoining it. b. breaking a strand, unwinding or rewinding the DNA, then rejoining it. c. breaking all hydrogen bonds in the DNA. d. supercoiling without the breaking of any phosphodiester bonds. e. underwinding without the breaking of any phosphodiester bonds. 56. Starting with a 5,000 bp plasmid containing one positive supercoil, after one round of E. coli DNA gyrase action, what would be the supercoiling state of the plasmid? a. three positive supercoils b. two positive supercoils c. no supercoils d. one negative supercoil e. two negative supercoils

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Chap 24_8e 57. Which statement is false regarding the formation of nucleosomes? a. Histone core proteins occur as pairs in the nucleosome. b. The coiling of DNA around the nucleosome is plectonemic. c. The coiling of DNA around the nucleosome is left-handed. d. Electrostatic interactions between histones and DNA are critical in nucleosome formation. e. The sequence affects the ability of DNA to adopt the curvature in a nucleosome. 58. Histones are _____ that are usually associated with _____. a. acidic proteins; DNA b. acidic proteins; RNA c. basic proteins; DNA d. basic proteins; RNA e. coenzymes derived from histidine; enzymes 59. Which statement is false concerning human mitochondrial DNA (mtDNA)? a. Human mtDNA is circular. b. Human mtDNA is smaller than the E. coli genome. c. Human mtDNA encodes the majority of mitochondrial protein genes. d. Human mtDNA is typically found as multiple copies in mitochondria. e. Human mtDNA encodes both polypeptide and tRNA genes. 60. Bacterial plasmids: a. are always covalently joined to the bacterial chromosome. b. are composed of RNA. c. are never circular. d. cannot replicate when cells divide. e. often encode proteins not normally essential to the bacterium's survival. 61. Functional DNA is NOT found in: a. bacterial nucleoids. b. chloroplasts. c. lysosomes. d. mitochondria. e. nuclei.

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Chap 24_8e 62. The DNA in a eukaryotic chromosome is BEST described as: a. a single circular double-helical molecule. b. a single linear double-helical molecule. c. a single linear single-stranded molecule. d. multiple linear double-helical molecules. e. multiple linear single-stranded molecules. 63. Topoisomerases: a. can change the linking number in increments of 1 or 2. b. can act on single-stranded DNA circles. c. change the degree of supercoiling of a DNA molecule but not its linking number of DNA. d. occur in bacteria, but not in eukaryotes. e. always require energy from ATP. 64. Which elements are NOT necessary to make a stable yeast artificial chromosome (YAC)? a. centromeres b. replication origins c. satellite DNA sequences d. telomeres e. All of these are required to make a stable YAC. 65. The chromosomal region that is the point of attachment of the mitotic spindle is the: a. centromere. b. endomere. c. exon. d. intron. e. telomere. 66. The formation of cruciforms can more easily occur in: a. underwound palindromic sequences. b. overwound palindromic sequences. c. underwound short tandem repeat sequences. d. overwound short tandem repeat sequences.

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Chap 24_8e 67. Which statement does NOT accurately describe a difference between histone H1 and the other histone proteins? a. Histone H1 is larger than the other histone proteins. b. Histone H1 is not part of the nucleosome core. c. Histone H1 has a lower percentage of basic amino acids than the other histones. d. Histone H1 proteins occur at a lower frequency than other histones in 30 nm fibers. e. Histone H1 associates with linker DNA, while the other histones do not. 68. Topoisomerases can: a. change the linking number of a DNA molecule. b. change the number of base pairs in a DNA molecule. c. change the number of nucleotides in a DNA molecule. d. convert d isomers of nucleotides to l isomers. e. interconvert DNA and RNA. 69. Which statement does NOT apply to the topoisomerase IA mechanism? a. A covalent bond is formed from the protein to the 3' phosphate of a nucleotide. b. Two strands of the nucleic acid remains intact. c. The action of the enzyme changes the linking number by single increments. d. The action of the enzyme will decrease the magnitude of the superhelical density. e. Energy for the process comes from the supercoiling strain in the nucleic acid. 70. In which cell-cycle step does the enzyme separase remove cohesion links to chromatids? a. G1/S b. S/G2 c. during prophase d. during anaphase e. during telophase 71. Which protein does NOT contribute to the octameric histone core? a. H1 b. H2A c. H2B d. H3 e. H4

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Chap 24_8e 72. How many nucleosomes would be expected to be found in a 1,000 bp piece of linear DNA? a. zero to one b. two to three c. four to five d. six to seven e. eight to nine 73. Which is true about the base-pair composition of DNA in centromeres? a. They are rich in A⇌T pairs. b. They are rich in G⇌C pairs. c. They are equal in A⇌T and G=C pairs. d. There is no pattern to A⇌T and G⇌C composition. 74. For a closed-circular DNA molecule of 10,000 base pairs in the fully relaxed form, the linking number is about: a. 10,000. b. 950. c. 100. d. 9.5. e. 2. 75. How long is the linker DNA between nucleosomes in the 30 nm fiber? a. approximately 20 base pairs b. approximately 50 base pairs c. approximately 100 base pairs d. approximately 150 base pairs e. approximately 200 base pairs 76. Define specific linking difference, also called superhelical density (σ).

77. What are introns?

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Chap 24_8e 78. Describe a current hypothesis to explain the presence of functional DNA in mitochondria and chloroplasts.

79. The genome of the bacterium E. coli is 4,639,675 bp long and consists of 4,435 genes; the human genome is 3,070,128,600 bp long and consists of roughly 29,000 genes. Calculate the average gene size in each organism and provide an explanation for the difference.

80. Describe two functions of DNA supercoiling.

81. The overall compaction of a eukaryotic chromosome is greater than _____-fold. The first level is nucleosome formation, which compacts about _____-fold. Next is the 30 nm fiber, which compacts about _____-fold overall. Higher-order folding involves association of the DNA with a nuclear _____, which contains large amounts of _____ and _____.

82. What are histones and what is their principal role in chromatin structure?

83. Describe the structure and function of a typical bacterial plasmid.

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Chap 24_8e 84. When plasmid DNA is purified from E. coli and then subsequently analyzed by electrophoresis in the presence of ethidium bromide (EtBr), three separate bands are typically observed. Predict what would be the difference in each band, and how they would migrate relative to each other (i.e., slowest to fastest).

85. Describe the composition and structure of a nucleosome.

86. What is satellite DNA?

87. Define, in the context of DNA structure, topological bonds.

88. Define topoisomerase, and explain the difference between type I and type II topoisomerases.

89. Define, in the context of DNA structure, topoisomers.

90. Briefly describe the changes in eukaryotic chromosome structure during the cell cycle.

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Chap 24_8e 91. Explain how inhibitors of topoisomerases would inhibit the growth of tumors. Would these drugs be expected to inhibit the growth of normal cells as well?

92. Indicate whether the statements are true (T) or false (F). ___ The linking number of a closed-circular DNA molecule can be changed only by breaking one or both strands. ___ DNA of all organisms is overwound (i.e., positively supercoiled). ___ Topoisomerase I relaxes DNA that is highly negatively supercoiled.

93. The DNA of virtually every cell is underwound (i.e., negatively supercoiled) relative to B-form DNA. In bacteria, an enzyme called (a) _____ introduces negative supertwists into DNA using (b) _____ as a source of energy. This enzyme is classified as a (c) _____, which affects the linking number in increments of (d) _____. The usual substrate for this enzyme within an E. coli cell is the bacterial chromosome. This circular DNA molecule of 4,700,000 base pairs has a linking number of approximately (e) _____ when it is closed and relaxed. This enzyme would (f) _____ [decrease/increase/not change] this linking number when acting upon this DNA molecule in the presence of the above energy source.

94. S. cerevisiae chromosome XI is 666,448 base pairs long. Calculate the length of this molecule, assuming it takes the form of B-DNA.

95. When studying nucleosomes in vitro, researchers will often add the enzyme trypsin to degrade the nucleosomes. Why is trypsin a particularly useful choice for this role?

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Chap 24_8e 96. SMC proteins facilitate the structural maintenance of chromosomes; describe the roles of the two main classes in eukaryotes.

97. Explain the difference between plectonemic and solenoidal supercoiling of DNA; use diagrams to help explain.

98. When plasmids are mixed with histones, they will bind fewer histones than the equivalent length of linear DNA. Upon addition of a topoisomerase, more histones will be bound. Explain this observation.

99. Calculate values for the topological properties of a closed-circular DNA molecule containing 2,000 base pairs (for simplicity, assume there are 10 base pairs per turn in the relaxed DNA). (a) The linking number when the DNA is relaxed (b) The linking number when the DNA has been underwound by 10 enzymatic turnovers of DNA gyrase (+ATP) (c) The linking number when the DNA has been underwound by binding five nucleosomes followed by complete relaxation by a eukaryotic topoisomerase (d) The superhelical density of the DNA molecule in (b) (e) The superhelical density of the DNA molecule in (c)

100. A plasmid containing 16,700 base pairs has a superhelical density of –0.015. Assuming the duplex is all BDNA, calculate the number of rounds of a type II topoisomerase that would be required to relax this DNA (as close as possible to completely relaxed).

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Chap 24_8e Answer Key 1. c 2. a 3. c 4. e 5. e 6. c 7. b 8. c 9. d 10. d 11. d 12. b 13. b 14. d 15. d 16. a 17. a 18. c 19. b 20. d 21. d 22. c 23. d 24. e 25. b 26. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_8e 27. c 28. d 29. a 30. a 31. d 32. a 33. e 34. e 35. b 36. c 37. c 38. e 39. e 40. d 41. d 42. c 43. b 44. e 45. d 46. b 47. c 48. d 49. d 50. d 51. e 52. c 53. e 54. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 24_8e 55. b 56. d 57. b 58. c 59. c 60. e 61. c 62. b 63. a 64. c 65. a 66. a 67. c 68. a 69. b 70. d 71. a 72. c 73. a 74. b 75. b 76. The specific linking difference (σ) is a measure of the number of turns removed (ΔLk) relative to the linking number of the fully relaxed form (Lk0): σ = ΔLk / Lk0. 77. Introns are regions of genes (primarily eukaryotic) that in mRNA are transcribed but are not translated. They do not code for amino acid sequences within the protein that is coded by the gene. Thus, they interrupt the colinearity between the nucleotide sequence of the gene and the amino acid sequence of the encoded protein.

78. These organelles are thought to have originated from aerobic bacteria and photosynthetic bacteria, which took up endosymbiotic residence within primitive eukaryotic cells. The DNA molecules of the organelles are putative vestiges of the chromosomes of these bacteria.

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Chap 24_8e 79. The average E. coli gene is 1,046 bp long; in humans it is 106,000 bp. The difference is due to the presence of significantly more "junk DNA" (introns, transposons, etc.) in human cells; these elements are not found in bacterial genomes. 80. Supercoiling allows for the extreme compaction required for DNA to fit in a cell. Negative supercoiling also facilitates the unwinding of the strands of the double-helical DNA that is required for its transcription and replication.

81. 10,000; 7; 100; scaffold; histone H1; topoisomerase II (last two in either order) 82. Histones are small basic proteins that bind to DNA. There are five main types, four of which interact with each other to form the core of the nucleosome around which the DNA is wrapped. The fifth (H1) is involved in compaction of nucleosomes to form a higher-order structure.

83. Bacterial plasmids are generally closed-circular, double-stranded DNA molecules that are much smaller than the bacterial chromosome itself. They replicate autonomously and may encode proteins that, although not normally essential to bacterial survival, may confer resistance to antibiotics.

84. Plasmid DNA is circular and typically will be supercoiled (particularly in the presence of an intercalating agent like EtBr) and will run rapidly in a gel electrophoresis experiment. The other bands will typically be linear DNA and DNA containing a nick in one strand (open-circular DNA). Open-circular DNA, in the presence of EtBr, migrates very slowly, as it experiences significant friction, while linear DNA will migrate faster than open-circular but slower than closed-circular (supercoiled) DNA.

85. A nucleosome consists of 146 base pairs of double-stranded DNA wrapped in a solenoidal supercoil around a core of histones (small, basic proteins). This core contains two copies each of histones H2A, H2B, H3, and H4.

86. Satellite DNA (also known as highly repetitive or simple-sequence DNA) consists of regions of the eukaryotic genome that are different enough in base composition from the bulk of the chromosomal DNA that they can be separated from it by density gradient centrifugation. Satellite DNA is often associated with centromeres and telomeres and consists of short sequences (5 to 10 base pairs) that are repeated millions of times per cell.

87. Topological bonds are links between two molecules that are not joined by specific chemical bonds, but that cannot be physically separated because they cross over each other like links in a chain.

88. Topoisomerases are enzymes that change the linking number in a closed-circular, double-stranded DNA molecule by breaking one or two strands, adding or removing twists, and rejoining the strand(s). Type I topoisomerases break and rejoin only one strand, changing the linking number in increments of 1. Type II topoisomerases break and rejoin both strands, changing the linking number in increments of 2.

89. Topoisomers are different forms of a closed-circular DNA molecule that differ only in a topological property such as their linking number (Lk).

90. Starting with prophase, the DNA undergoes condensation (employing cohesins and condensins). During the subsequent metaphase, the condensed chromosomes line up along a plane halfway between the spindle poles (to which they are connected by microtubules). As the cell moves into anaphase, the sister chromatids separate, each drawn toward its respective spindle pole. After cell division is complete, the chromosomes decondense, and remain so during interphase. (See Fig. 24-33.)

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Chap 24_8e 91. Dividing cells must replicate their DNA; replication requires the action of topoisomerases to resolve the resulting DNA tangles. Thus, inhibiting topoisomerases would be expected to inhibit cell division. Since cancer is inappropriate cell division, these drugs would inhibit the growth of cancer. They would also be expected to inhibit the growth of normal cells, but to a lesser extent since cancer cells are dividing more rapidly than most normal cells.

92. T; F; T 93. (a) E. coli topoisomerase II or DNA gyrase; (b) ATP; (c) type II topoisomerase; (d) 2; (e) 450,000; (f) decrease 94. Assuming a rise of 3.4 Å per base pair, the total length is 666,448 bp × 3.4 Å/bp = 2.27 × 106 Å, or 2.27 μm. 95. Histones are enriched for positively charged residues (Arg/Lys/His), and trypsin has a specificity for cleaving peptide bonds after these residues (which are often located on the surface as well). 96. The cohesins help link sister chromatids together after replication and keep them together as they condense, which is essential for proper segregation. The condensins are essential for DNA condensation as the cell enters mitosis, and their binding is thought to create positive supercoiling. (See Fig. 24-32.)

97. In plectonemic supercoiling, the double helix is intertwined such that it crosses over itself. In solenoidal supercoiling, the double helix forms a spiral resembling the helix formed by each of the strands. (See Fig. 24-21.)

98. Histones binding will introduce supercoiling in plasmid DNA, unlike the linear DNA. Once the superhelical density is high enough, it will not be possible to bind more histones. Topoisomerases will relieve the superhelical density in the portions of the plasmid that are unbound, allowing for more histones to bind.

99. (a) 200; (b) 180; (c) 195 (d) –0.1; (e) –0.025 100. Assuming 10.5 base pairs/turn, the relaxed linking number would be 1,590. For a superhelical density of –0.015, this means underwinding by –0.015 × 1,590 = –23.8 (negative number of supercoils). This means it would take 12 rounds of activity by a type II topoisomerase to reduce the supercoils to approximately zero.

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Chap 25_8e Indicate the answer choice that best completes the statement or answers the question. 1. What is NOT made out of DNA? a. Ter b. telomeres c. DNA unwinding elements d. TUS e. All of these are made out of DNA. 2. In contrast to bacteria, eukaryotic chromosomes need multiple DNA replication origins because: a. eukaryotic chromosomes cannot usually replicate bidirectionally. b. eukaryotic genomes are not usually circular, like the bacterial chromosome is. c. the processivity of the eukaryotic DNA polymerase is much less than the bacterial enzyme. d. their replication rate is much slower, and it would take too long with only a single origin per chromosome. e. they have a variety of DNA polymerases for different purposes, and need a corresponding variety of replication origins. 3. Which statement about enzymes that interact with DNA is true? a. E. coli DNA polymerase I is unusual in that it possesses only a 5′→3′ exonucleolytic activity. b. Endonucleases degrade circular but not linear DNA molecules. c. Exonucleases degrade DNA at a free end. d. Many DNA polymerases have a proofreading 5′→3′ exonuclease. e. Primases synthesize a short stretch of DNA to prime further synthesis. 4. In homologous recombination in E. coli, the protein that assembles into long, helical filaments that coat a region of DNA is: a. DNA methylase. b. DNA polymerase. c. histone. d. RecA protein. e. RecBCD enzyme. 5. Which process or aspect is NOT associated with RecBCD? a. helicase activity b. ATP hydrolysis c. nuclease activity d. sequence-specific binding interactions e. generation of 5′ overhangs

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Chap 25_8e 6. Which factor is NOT responsible for the variations in IgG light-chain variations? a. variations in the V segment sequence b. variations in the J segment sequence c. variations in the C segment sequence d. variations in the V–J junction e. All of these contribute to the variation in light-chain variations. 7. In DNA replication in E. coli: a. the leading strand requires multiple primers. b. polymerization is mostly 3′→5′. c. the process always finishes at a conserved terminator sequence. d. the process proceeds bidirectionally. e. the action of topoisomerases is not required. 8. Which eukaryotic DNA polymerase synthesizes the lagging strand? a. DNA polymerase α b. DNA polymerase β c. DNA polymerase γ d. DNA polymerase δ e. DNA polymerase ε 9. Which mechanism is used to repair a chemically modified base in DNA? a. mismatch repair b. base-excision repair c. nucleotide-excision repair d. direct repair e. More than one mechanism is used for this type of lesion. 10. Which statement does NOT describe a feature of site-specific recombination? a. A specific recombinase enzyme is required. b. The energy of the phosphodiester bond is preserved in covalent enzyme-DNA linkage. c. Recombination sites have nonpalindromic sequences. d. Both types of site-specific recombination systems rely on Thr and Phe in the enzyme active sites. e. Insertions or deletions can result from site-specific recombination.

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Chap 25_8e 11. Which sequences are palindromic? a. DNA unwinding elements (DUE) b. terminator sequences (Ter) c. (5′)GATC sites d. both DUE and Ter e. None of these sequences is palindromic. 12. Which statement is false regarding the DNA ligase mechanism? a. The mechanism is an example of covalent catalysis. b. Either ATP or NAD+ may contribute an adenyl group to the reaction. c. Energy from a phosphate anhydride bond is used to make a phosphodiester bond. d. One of the products of the reaction is ADP. e. A lysine is found in the active site of the enzyme. 13. Which compound is NOT a protein that binds to the origin of replication of E. coli (oriC)? a. DnaA b. DnaB c. integration host factor (IHF) d. histone-like protein (HU) e. Tus 14. The entire complex of enzymes and proteins that carries out replication is called the: a. polymerase. b. replicatase. c. replisome. d. Okazaki complex. e. duplicasome. 15. What is the role of the chi sequence in recombination DNA repair? a. It directs RecBCD binding to DNA. b. It acts as a target for an endonuclease activity. c. It is a sequence that binds tightly to the RecC subunit. d. It triggers the activity of a DNA helicase. e. It acts as a signal for branch migration of double-stranded intermediates.

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Chap 25_8e 16. When bacterial DNA replication introduces a mismatch in double-stranded DNA, the methyl-directed repair system: a. cannot distinguish the template strand from the newly replicated strand. b. changes both the template strand and the newly replicated strand. c. corrects the DNA strand that is methylated. d. corrects the mismatch by changing the newly replicated strand. e. corrects the mismatch by changing the template strand. 17. DnaA binds to what sites in the E. coli origin? a. only R sites b. only I sites c. only DUE sites d. both R and I sites e. both R and DUE sites 18. Which compound is NOT required for initiation of DNA replication in E. coli? a. DnaB (helicase) b. DnaG (primase) c. Dam methylase d. DNA ligase e. DnaA (AAA+ ATPase) 19. In homologous genetic recombination, RecA protein is involved in: a. formation of Holliday intermediates and branch migration. b. introduction of negative supercoils into the recombination products. c. nicking the two duplex DNA molecules to initiate the reaction. d. pairing a DNA strand from one duplex DNA molecule with sequences in another duplex, regardless of complementarity. e. resolution of the Holliday intermediate. 20. Which statement is true regarding DnaA? a. DnaA is a DNA sequence that is part of oriC in E. coli. b. DnaA is a protein that recognizes the oriC in E. coli replication during initiation. c. DnaA affects the amount of methylation in oriC in E. coli. d. DnaA binds to single-stranded DNA

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Chap 25_8e 21. The proofreading function of DNA polymerase does NOT involve: a. a 3′→5′ exonuclease. b. base pairing. c. detection of mismatched base pairs. d. phosphodiester bond hydrolysis. e. reversal of the polymerization reaction. 22. Which statement is false? a. In vitro, the strand-exchange reaction can include formation of a Holliday intermediate. b. In vitro, the strand-exchange reaction is accompanied by ATP hydrolysis. c. In vitro, the strand-exchange reaction may involve transient formation of a three- or four-stranded DNA complex. d. In vitro, the strand-exchange reaction needs RecA protein. e. In vitro, the strand-exchange reaction requires DNA polymerase. 23. Which feature is NOT applicable to homologous recombination during meiosis? a. a double-strand break b. cleavage of two crossover events c. alignment of homologous chromosomes d. formation of a single Holliday intermediate e. exposed 3ʹ ends invade the intact duplex DNA of the homolog 24. The ABC excinuclease is essential in _____ repair. a. base-excision b. methyl-directed c. mismatch d. nucleotide-excision e. SOS 25. Which statement is false about transposition of DNA? a. The diversity of immunoglobins is in part due to DNA recombination by transposition. b. Transposition occurs in both prokaryotes and eukaryotes. c. Enzymes are not required for transposition. d. The first step of transposition can be single- or double-stranded DNA cleavage. e. Transposition can lead to simple movement of a DNA region or duplication of that region in a new location.

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Chap 25_8e 26. Why does DNA replication in E. coli have a leading and lagging strand? a. Because the replication is 5′→3′ on one strand and 3′→5′ on the other strand. b. Because of the difference in supercoiling between the two strands. c. Because the replication of each strand is at a different replication fork. d. Because the DNA strands are antiparallel. 27. In which type of repair is E. coli DNA polymerase III involved? a. direct repair b. base-excision repair c. mismatch repair d. both direct repair and mismatch repair e. both direct repair and nucleotide-excision repair 28. Which factor is NOT required for elongation during DNA replication in E. coli? a. DnaB (helicase) b. DNA polymerase III c. DnaC d. β-sliding clamp e. clamp loader 29. When a DNA molecule is described as replicating bidirectionally, that means that it has two: a. chains. b. polymerases that synthesize 3′→5′ and 5′→3′. c. origins. d. replication forks. e. termination points. 30. The 5′→3′ exonuclease activity of E. coli DNA polymerase I is involved in: a. formation of a nick at the DNA replication origin. b. formation of Okazaki fragments. c. proofreading of the replication process. d. removal of RNA primers by nick translation. e. sealing of nicks by ligase action. 31. Which enzyme is NOT directly involved in methyl-directed mismatch repair in E. coli? a. DNA glycosylase b. DNA helicase II c. DNA ligase d. DNA polymerase III e. exonuclease I Copyright Macmillan Learning. Powered by Cognero.

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Chap 25_8e 32. An alternative repair system by error-prone translesion DNA synthesis can result in a high mutation rate because: a. alternative modified nucleotides can be incorporated more readily. b. interference from the RecA and SSB proteins hinders the normal replication accuracy. c. replication proceeds much faster than normal, resulting in many more mistakes. d. the DNA polymerases involved cannot facilitate base pairing as well as DNA polymerase III. e. the DNA polymerases involved lack exonuclease proofreading activities. 33. The repair of cyclobutane pyrimidine dimers by bacterial DNA photolyase involves the cofactor: a. coenzyme A. b. coenzyme Q. c. FADH– . d. pyridoxal phosphate. e. thiamine pyrophosphate. 34. Which mechanism is used to repair a thymidine dimer in DNA? a. mismatch repair b. base-excision repair c. nucleotide-excision repair d. direct repair 35. Which statement is false regarding the E. coli DNA unwinding element (DUE)? a. The DUE contains a specific sequence repeated in tandem. b. The sequence is part of the origin of replication. c. This sequence binds to DnaA. d. This sequence is where the helicase binds during initiation of replication. e. This sequence will be hemimethylated after replication begins. 36. An Okazaki fragment is a: a. fragment of DNA resulting from endonuclease action. b. fragment of RNA that is a subunit of the 30S ribosome. c. piece of DNA that is synthesized in the 3′→5′ direction. d. segment of DNA that is an intermediate in the synthesis of the lagging strand. e. segment of mRNA synthesized by RNA polymerase.

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Chap 25_8e 37. The Meselson and Stahl established that: a. DNA polymerase has a crucial role in DNA synthesis. b. DNA synthesis in E. coli proceeds by a conservative mechanism. c. DNA synthesis in E. coli proceeds by a semiconservative mechanism. d. DNA synthesis requires dATP, dCTP, dGTP, and dTTP. e. newly synthesized DNA in E. coli has a different base composition than the preexisting DNA. 38. Meselson and Stahl grew E. coli for several generations in a medium containing 15N. The isotopic label was incorporated into the DNA nucleotides. Cells were transferred to a normal medium containing the common (lighter) isotope of nitrogen, 14N. After replication the possible resulting DNAs could contain only 14N (low density), only 15N (high density) or both isotopes (hybrid density). The different DNAs were distinguished by centrifugation. What ratio of DNAs would Meselson and Stahl have observed after completion of three rounds of replication? a. 1:1 high density to low density; no hybrid density b. 1:1 high density to hybrid density; no low density c. 1:2 high density to low density; no hybrid density d. 3:1 low density to hybrid density; no high density e. 1:3 high density to low density; no hybrid density 39. In base-excision repair, the first enzyme to act is: a. AP endonuclease. b. Dam methylase. c. DNA glycosylase. d. DNA ligase. e. DNA polymerase. 40. In the Ames test, the clear region of no growth near the center of the plate (where the compound of interest is placed) typically indicates that the compound is: a. not mutagenic. b. an antibiotic. c. an amino acid. d. lethal at high enough concentrations. e. not taken up by bacteria. 41. Which process or protein(s) is NOT generally required for homologous recombination to occur? a. helicase activity b. DNA-dependent DNA polymerases c. primases d. ligases e. nucleases Copyright Macmillan Learning. Powered by Cognero.

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Chap 25_8e 42. At replication forks in E. coli: a. DNA helicases make endonucleolytic cuts in DNA. b. DNA primers are degraded by exonucleases. c. DNA topoisomerases make endonucleolytic cuts in DNA. d. RNA primers are removed by primase. e. RNA primers are synthesized by primase. 43. E. coli DNA polymerase III: a. can initiate replication without a primer. b. is efficient at nick translation. c. is the principal DNA polymerase in chromosomal DNA replication. d. represents over 90% of the DNA polymerase activity in E. coli extracts. e. requires a free 5′-hydroxyl group as a primer. 44. What is NOT a process or characteristic associated with RecA? a. It binds to single-stranded DNA. b. It forms part of DNA polymerase V. c. It is involved in the homologous genetic recombination. d. It facilitates strand invasion in repair pathways. e. It forms a dimer with single-stranded DNA–binding protein and single-stranded DNA. 45. The function of the eukaryotic DNA replication factor PCNA (proliferating cell nuclear antigen) is similar to that of the β subunit of bacterial DNA polymerase III in that it: a. facilitates replication of telomeres. b. forms a circular sliding clamp to increase the processivity of replication. c. has a 3′→5′ proofreading activity. d. increases the speed but not the processivity of the replication complex. e. participates in DNA repair. 46. Suppose E. coli is grown for several generations in a medium containing 15N, which is incorporated into the DNA nucleotides. The cells are then transferred to a normal medium containing the common isotope of nitrogen, 14N, for replication. How many rounds of replication would result in a 1:1 distribution of hybriddensity (containing both 15N and 14N) to low-density (containing only 14N) DNA? a. one b. two c. three d. four e. five

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Chap 25_8e 47. In a mammalian cell, DNA repair systems: a. are extraordinarily efficient energetically. b. are generally absent except in egg and sperm cells. c. can repair deletions but not mismatches. d. can repair most types of lesions except those caused by UV light. e. normally repair more than 99% of the DNA lesions that occur. 48. Which statement does NOT accurately describe a difference between E. coli DNA polymerases Pol I and Pol III? a. Pol I has a 3′→5′ exonuclease, and DNA Pol III does not. b. Pol I has a slower polymerization rate than Pol III. c. Pol I is less processive than Pol III. d. Pol I is a single subunit, while Pol III is a multisubunit protein. e. Both polymerases synthesize in the 5′→3′ direction. 49. What concept does NOT generally apply to bacterial transposons? a. Transposons are sometimes referred to as "jumping genes." b. Transposons contain segments of repeating DNA at either end. c. Insertion of a transposon followed by excision results in damage to the sequence at the insertion site. d. Transposases are the enzymes involved in transposition. e. Transposition is a homologous recombination process. 50. Nonpolyposis colon cancer has been linked to what type of defect? a. defects in mismatch repair genes b. defects in DNA Pol III c. defects in Dam methylase d. defects in direct repair genes e. All of the answers are correct. 51. Which process does NOT require the 5′→3′ exonuclease activity of Pol I in E. coli? a. joining of Okazaki fragments b. nucleotide-excision repair c. base-excision repair d. nick translation e. All of these require the 5′→3′ exonuclease activity of Pol I.

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Chap 25_8e 52. The role of the Dam methylase is to: a. add a methyl group to uracil, converting it to thymine. b. modify the template strand for recognition by repair systems. c. remove a methyl group from thymine. d. remove a mismatched nucleotide from the template strand. e. replace a mismatched nucleotide with the correct one. 53. In humans, what repair mechanism is used to correct thymine dimers? a. base-excision repair b. nucleotide-excision repair c. mismatch repair d. photolyase e. both nucleotide-excision repair and photolyase 54. The recombination mechanism to join the V and J segments in immunoglobulin gene rearrangement that uses the RAG1 and RAG2 proteins involves: a. coordinated base hydrolysis. b. transamination. c. transesterification. d. methylation. e. acetylation. 55. What role does AP endonuclease have in the base-excision repair system? a. It removes the damaged base from the nucleic acid. b. It cleaves the phosphodiester backbone after base removal. c. It removes nucleotides from the broken strand of the nucleic acid. d. It adds new nucleotides to replace the excised ones. e. It creates a new phosphodiester bond to repair the backbone. 56. It is possible to mutate E. coli DNA Pol I so that it no longer has any exonuclease activity. What would be a potential result of this change? a. The enzyme would become more processive. b. The enzyme would be more error-prone. c. The enzyme would become more efficient in base-excision repair. d. The enzyme would become more processive and more error-prone. e. None of these is a potential outcome.

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Chap 25_8e 57. Which protein is NOT required for E. coli Pol III elongation? a. SSB protein b. DnaB c. DnaG d. DNA gyrase e. All of these are required for elongation. 58. The Ames test is used to: a. detect bacterial viruses. b. determine the rate of DNA replication. c. examine the potency of antibiotics. d. measure the mutagenic effects of various chemical compounds. e. quantify the damaging effects of UV light on DNA molecules. 59. Which recombination or repair mechanism does NOT generally conserve the original DNA sequence? a. recombinational DNA repair b. site-specific recombination c. nonhomologous end joining d. photolyase repair e. nucleotide-excision repair 60. Which statement regarding the regulation of initiation in E. coli is correct? a. DnaA binds its consensus sequence at oriC only when the sequence is fully acetylated. b. After replication, the DNA at oriC is hemiacetylated and in this state it cannot bind DnaA. c. After replication, the DNA at oriC is hemimethylated and in this state it binds DnaA with high affinity. d. The binding affinity of DnaA for its binding sites in oriC is dependent only on acetylation of DNA. e. DnaA binds its consensus sequence at oriC only when the sequence is fully methylated. 61. Which repair mechanism does NOT require an endonuclease? a. base-excision repair b. nucleotide-excision repair c. mismatch repair d. direct repair by photolyase e. All of these require an endonuclease.

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Chap 25_8e 62. Prokaryotic DNA polymerase III: a. contains a 5′→3′ proofreading activity to improve the fidelity of replication. b. does not require a primer molecule to initiate replication. c. has β subunits that act as a circular clamp to improve the processivity of DNA synthesis. d. synthesizes DNA in the 3′→5′ direction. e. synthesizes only the leading strand; DNA polymerase I synthesizes the lagging strand. 63. In homologous recombination in E. coli, the protein that moves along a double-stranded DNA, unwinding the strands ahead of it and degrading them, is: a. chi. b. DNA ligase. c. RecA protein. d. RecBCD enzyme. e. RuvC protein (resolvase). 64. Which statement is false regarding the repair of 1-methyladenine in DNA to adenine? a. This is an example of direct repair. b. This repair process requires iron atoms as cofactors. c. α-Ketoglutarate and oxygen are also substrates in this reaction. d. The protein responsible for carrying out this reaction can also repair 3-methylcytosine. e. The process involves carboxylation followed by hydrolysis. 65. List the four enzymes involved in base-excision repair, in order of their activity, and briefly outline their function.

66. Nucleotide polymerization appears to be a thermodynamically balanced reaction (because one phosphodiester bond is broken and one is formed). Nevertheless, the reaction proceeds efficiently both in a test tube and in the cell. Explain.

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Chap 25_8e 67. Bacteriophage λ integrates into the E. coli genome using site-specific recombination between a bacteriophage sequence, identified as attP, and a bacterial sequence, identified as attB. The attP and attB sequences are different sizes: The attP site is approximately 240 bp long, while attB is significantly shorter at approximately 25 bp. Why does it make sense that the attB site is smaller than the attP site?

68. The protein O6-methylguanine-DNA methyltransferase is involved in DNA repair. Outline the reaction that is carried out by this protein. Why is it incorrect to describe this protein as an enzyme?

69. Diagram the reaction catalyzed by DNA polymerase that occurs between deoxyribose at the end of a DNA chain and the 5′ phosphates of a deoxyribonucleoside triphosphate. Include the chemical structure of the phosphate group, indicate the locations of the sugar and base, and show the rearrangements of electrons that occur.

70. Briefly explain the difference between base-excision repair and nucleotide-excision repair.

71. All known DNA polymerases catalyze synthesis only in the 5′→3′ direction. Nevertheless, during semiconservative DNA replication in the cell, they are able to catalyze the synthesis of both daughter chains, which would appear to require synthesis in the 3′→5′ direction. Explain the process that occurs in the cell that allows for synthesis of both daughter chains by DNA polymerase.

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Chap 25_8e 72. In E. coli oriC, the portion of the sequence corresponds to one strand of the DUE-containing region. (Shown in groups of 10.) Which nucleotides in this sequence can be methylated by Dam methylase?

73. All known DNA polymerases can only elongate a preexisting DNA chain (i.e., require a template and a primer) but cannot initiate a new DNA chain. Nevertheless, during semiconservative DNA replication in the cell, entirely new daughter DNA chains are synthesized. Explain the process that occurs in the cell that allows for the synthesis of daughter chains by DNA polymerase.

74. Outline the key steps that occur during crossing over during meiosis in animal germ-line cells.

75. Outline the key steps that occur during meiosis in animal germ-line cells.

76. What distinguishes the simple (insertion) from the complex class of bacterial transposon?

77. What is an Okazaki fragment? What enzyme(s) is required for its formation in E. coli?

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Chap 25_8e 78. A suitable substrate for DNA polymerase is shown. Label the primer and template, and indicate which end of each strand must be 3′ or 5′.

To observe DNA synthesis on this substrate in vitro, what additional reaction components must be added?

79. The high fidelity of DNA replication is due primarily to immediate error correction by the 3′→5′ exonuclease (proofreading) activity of the DNA polymerase. Some incorrectly paired bases escape this proofreading, and further errors can arise from challenges to the chemical integrity of the DNA. List the four classes of repair mechanisms that the cell can use to help correct such errors.

80. The DNA shown is replicated from left to right. Label the templates for leading strand and lagging strand synthesis. (5′)ACTTCGGATCGTTAAGGCCGCTTTCTGT(3′) (3′)TGAAGCCTAGCAATTCCGGCGAAAGACA(5′)

81. Why does DNA damage that causes alkylation of nucleotides sometimes lead to transition mutations? Transition mutations are those where a purine is changed to a different purine, or a pyrimidine is changed to a different pyrimidine.

82. List three types of DNA damage that require repair.

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Chap 25_8e 83. Outline the four key features of the current model for homologous recombination during meiosis in a eukaryotic cell.

84. E. coli cells exposed to visible light following exposure to ultraviolet light have higher survivability rates than cells that are kept in the dark after exposure to ultraviolet light. Briefly explain this observation, indicating both the type of damage and any significant enzymes that may be involved.

85. Describe the process of nucleotide-excision repair of lesions like pyrimidine dimers in E. coli.

86. The RNA primase in the E. coli Pol III replisome is one of the most highly error-prone polymerases known. Explain why this does not affect the accuracy of DNA replication in E. coli.

87. Explain the role of DNA glycosylases in DNA repair.

88. Name the three possible outcomes or consequences (at the DNA level) of a site-specific recombination event. For each of these, explain concisely (in one sentence) how the relative location and orientation of the recombination sites determines the outcome of the recombination event. Do not describe specific examples of site-specific recombination systems.

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Chap 25_8e 89. Explain how inheriting mutations in genes encoding DNA repair enzymes could lead to increased cancer risk.

90. List two proteins or enzymes, other than DNA polymerase III, that are found at the replication fork in E. coli. Describe each of their functions with no more than one sentence.

91. Briefly describe the role of recombination in the generation of antibody (immunoglobin) diversity.

92. DNA replication in E. coli begins at a site in the DNA called the (a) _____. At the replication fork the (b) _____ strand is synthesized continuously while the (c) _____ strand is synthesized discontinuously. On the strand synthesized discontinuously, the short pieces are called (d) _____ fragments. An RNA primer for each of the fragments is synthesized by an enzyme called (e) _____, and this RNA primer is removed after the fragment is synthesized by the enzyme (f) _____, using its (g) _____ activity. The nicks left behind in this process are sealed by the enzyme (h) _____.

93. What distinguishes the two general pathways for transposition in bacteria, and what is a cointegrate?

94. In the bacterial cell, what are catenated chromosomes, when do they arise, and how does the cell resolve the problem posed by their structure?

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Chap 25_8e 95. Briefly describe the biochemical role of the enzymes in DNA replication in E. coli: (a) DNA helicase; (b) primase; (c) the 3′→5′ exonuclease activity of DNA polymerase; (d) DNA ligase; (e) topoisomerases; (f) the 5′→3′ exonuclease activity of DNA polymerase I.

96. Why is the drug acyclovir effective against the herpes simplex virus?

97. In E. coli replication, DNA gyrase does not require ATP hydrolysis to lower the linking number of its substrate. Why is this, and where does the energy come from?

98. Many bases in DNA are susceptible to spontaneous deamination. Which of the standard bases in DNA cannot spontaneously deaminate?

99. DNA synthesis on the lagging strand in E. coli is a complex process known to involve several proteins. Initiation of a new chain is catalyzed by the enzyme (a) _____, and elongation is catalyzed by the enzyme (b) _____. Synthesis is discontinuous, yielding short segments called (c) _____, which are eventually joined by the enzyme (d) _____, which requires the cofactor (e) _____.

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Chap 25_8e 100. Match the damage type or repair step on the left with a related enzyme on the right. Only one answer will be the most direct for each. ___ cytosine deamination (a) hypoxanthine-N-glycosylase ___ base loss (b) AP endonuclease ___ adenine deamination (c) mutH protein ___ binds to GATC sequences (d) DNA polymerase I ___ binds to mismatch in DNA (e) uracil N-glycosylase ___ DNA synthesis in gaps (f) mutS–mutL complex ___ seals nicks (g) ABC excinuclease 6 (h) DNA photolyase ___ O -methylguanine ___ direct chemical reversal (i) O6-methylguanine of pyrimidine dimer formation methyltransferase ___ double-strand break (j) DNA ligase ___ excision of a lesion(k) λ integrase containing oligonucleotide (l) RecA protein (m) restriction endonuclease

101. What does it mean to say that DNA replication is semiconservative?

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Chap 25_8e Answer Key 1. d 2. d 3. c 4. d 5. e 6. c 7. d 8. d 9. e 10. d 11. c 12. d 13. e 14. c 15. c 16. d 17. d 18. d 19. a 20. b 21. e 22. e 23. d 24. d 25. c 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 25_8e 27. c 28. c 29. d 30. d 31. a 32. e 33. c 34. d 35. c 36. d 37. c 38. d 39. c 40. d 41. c 42. e 43. c 44. e 45. b 46. b 47. e 48. a 49. e 50. a 51. c 52. b 53. b 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 25_8e 55. b 56. b 57. e 58. d 59. c 60. e 61. d 62. c 63. d 64. e 65. (1) DNA glycosylase to remove the damaged base; (2) AP endonuclease to cleave the phosphodiester backbone in the region of the excised base; (3) DNA polymerase I to replace the nucleotides on the damaged strand and remove the damaged portion of the strand; and (4) DNA ligase to form a phosphodiester bond (seal the backbone).

66. Base-stacking and base-pairing interactions in the polymerized DNA product stabilize it and tend to make the overall reaction more exergonic. In the cell, pyrophosphatase may make a contribution by coupling polymerization to the highly exergonic hydrolysis of the pyrophosphate product.

67. A shorter sequence in the bacterial genome is more likely to be retained (especially if it is subject to evolutionary selection). As long as the two sites share a common core sequence for the homologous replication process, both sites do not need to be the same size to interact with the necessary proteins for recombination. 68. The protein is involved in a transfer of the methyl group from the modified base (position O6 if a guanine) onto a cysteine residue. In the process, the protein is inactivated, and so it is consumed. Enzymes are catalysts, not substrates, and as the protein is consumed stoichiometrically, it is not truly an enzyme.

69. See Figure 25-3. 70. Base excision involves removing only the defective base from the DNA by cleavage of the N-glycosyl bond. This leaves an apurinic or apyrimidinic site. In a subsequent step, the abasic nucleotide is removed and the missing nucleotide is replaced by DNA polymerase I. Nucleotide excision involves removing the defective base together with its deoxyribose and phosphate (as well as some neighboring nucleotides) by cleavage of phosphodiester bonds in the DNA chain in the first step.

71. During DNA replication, one strand is synthesized continuously and the other is synthesized by a discontinuous mechanism. The daughter chain, which appears to be growing in the 3′→5′ direction (the lagging strand), is actually being synthesized by continual initiation of new chains and their elongation in the 5′→3′ direction. 72. Positions 3, 19, 34 will be methylated in the duplex (the A in GATC).

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Chap 25_8e 73. In the cell, initiation of DNA chains occurs via the synthesis of an RNA primer by an RNA polymerase type of enzyme (primase). This primer is elongated by DNA polymerase to produce the daughter DNA chain. The RNA is removed by 5' exonucleolytic hydrolysis before replication is completed.

74. A double-strand break is converted to a double-strand gap by exonucleases leading to 3' single-stranded extensions. The 3' single-stranded extensions then invades its complementary sequence in the intact homolog. The 3' end is extended by DNA polymerase using the intact homolog as a template. This generates a DNA molecule with two crossovers (Holliday intermediates). Further DNA replication replaces the DNA missing from the original DNA break. Cleavage of the Holliday intermediates generates one of two product sets. (See Fig. 25-34.) 75. The chromosomes of a diploid cell are duplicated so that each cell now contains four copies of DNA. Each tetrad exists as a pair of sister chromatids, and these are segregated into daughter cells during the first cell division. A second cell division then takes place to generate a total of four daughter cells, each with a haploid genome. (See Fig. 25-33.)

76. The simple class called insertion sequences contains only the information needed for transposition and the genes for proteins (transposases) that carry out the process. Those in the class of complex transposons carry additional genes, such as those for antibiotic resistance, a property they confer upon any host bacterium that harbors them.

77. An Okazaki fragment is an intermediate in DNA replication in E. coli. It is a short fragment of newly synthesized DNA, attached to the 3′ end of a short RNA primer. Such fragments are produced by the combined action of primase (part of the primosome) and DNA polymerase III during replication of the lagging strand. (See Fig. 2511.) 78. The top strand (the primer) has its 5′ end to the left; the bottom (template) strand has the opposite polarity. For DNA synthesis with this substrate in vitro, one would have to add DNA polymerase, the four deoxynucleoside triphosphates, Mg2+, and a suitable buffer. 79. The four classes are listed in Table 25-5 and consist of (1) mismatch repair, (2) base-excision repair, (3) nucleotideexcision repair, and (4) direct repair. 80. The polarity of the strands indicates that the top strand is the template for lagging strand synthesis, and the bottom strand is the template for leading strand synthesis. (See Fig. 25-2.) 81. When guanine is alkylated to O6-methylguanine, it can base pair better with thymine than with guanine's normal partner, cytosine. This results in G≡C to A=T mutations when this erroneous pairing is replicated into the daughter chromosomes. (See Fig. 25-26.) 82. The defects in DNA that require repair include (1) mismatches that occur during replication; (2) abnormal bases; (3) pyrimidine dimers produced by UV irradiation. Other answers are possible.

83. (1) Homologous chromosomes are aligned. (2) A double-strand break is enlarged by an exonuclease, leaving a single-strand extension with a free 3' hydroxyl end. (3) The exposed 3' ends invade the homologous intact duplex DNA, followed by branch migration to create Holliday intermediates. (4) Cleavage of the two crossover products creates the two recombinant products. (See Fig. 25-34.) 84. The photolyase involved in repair of pyrimidine dimers requires energy from absorbed light in order to reverse the effect.

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Chap 25_8e 85. DNA lesions such as pyrimidine dimers are repaired by the excision of a 12 or 13 nucleotide fragment of the defective strand. The ABC excinuclease makes single-strand cuts on both sides of the defect. The fragment between the cuts is removed by the UvrD helicase. This leaves a gap in the DNA, which is filled in by DNA polymerase I and sealed by DNA ligase. (See Fig. 25-24.)

86. The RNA primer that is synthesized is ultimately removed through the action of DNA Pol I, so errors that exist do not end up being retained in the final daughter strand that is synthesized.

87. When spontaneous deamination converts cytosine in DNA to uracil, or adenine to hypoxanthine, DNA glycosylase breaks the Nglycosyl bond to the defective base, creating an abasic or AP site. The region containing the AP site is then excised by AP endonuclease, and the resulting gap is closed by DNA polymerase I and sealed by DNA ligase. (See Fig. 25-23.) Other DNA glycosylases recognize other types of modified or damaged bases.

88. When two sites on a single DNA have the same orientation, a piece of DNA will be deleted by recombination. When two sites on a single DNA have opposite orientations, inversion results. When two separate DNAs (one or both circular) recombine, an insertion will occur. (See Fig. 25-38.)

89. Mutations in DNA repair genes would lead to increased mutation rate. Since cancers begin by mutations in oncogenes, an increased mutation rate would lead to an increased risk of cancer.

90. The proteins are listed in Table 25-4. They include (a) DNA polymerase I, which fills gaps and excises RNA primers; (b) primase (the DnaG protein), which synthesizes short RNA primers; (c) DNA ligase, which seals nicks; and (d) proteins that aid in DNA unwinding and supercoiling.

91. The genes for immunoglobin polypeptide chains are divided into segments, with multiple versions of each segment (which code for slightly different amino acid sequences). Recombination results in the joining of individual versions of each segment to generate a complete gene. Antibody diversity results from the very large number of different combinations that are possible. (See Fig. 25-42.)

92. (a) origin; (b) leading; (c) lagging; (d) Okazaki; (e) primase; (f) DNA Pol I; (g) 5′→3′ exonuclease; (h) DNA ligase 93. Direct transposition moves the transposon itself to a new location, leaving behind a double-strand break in the donor DNA (which must be repaired). The transposon is inserted into a staggered cut at the target site, and DNA replication fills in the remaining gaps. Replicative transposition moves a copy of the element to a new site, leaving a copy behind at the donor location; the cointegrate intermediate carries two complete copies of the transposon with the donor region covalently linked to DNA at the target site. (See Figs 25-40, 25-41.)

94. Catenanes are topologically interlinked circular chromosomes, which are the normal end result of DNA replication of the parental circular genome when the bidirectional replication forks meet. They are unlinked by the bacterial topoisomerase IV (a type II enzyme), and thus become free to segregate into daughter cells upon cell division. (See Fig. 25-17.)

95. (a) Helicase unwinds double-stranded DNA during replication. (b) Primase synthesizes short RNA primers during lagging strand replication. (c) The 3′→5′ exonuclease activity of DNA polymerase proofreads newly synthesized DNA, removing mismatched nucleotides. (d) DNA ligase seals nicks in the DNA at the boundaries between Okazaki fragments. (e) Topoisomerases relieves the topological stress produced by the unwinding of doublestranded DNA at the replication fork. (f) The 5′→3′ exonuclease activity of DNA polymerase I removes RNA primers.

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Chap 25_8e 96. Acyclovir is a guanine nucleoside with an incomplete ribose ring, which can be phosphorylated much more efficiently by the viral thymidine kinase than the host enzyme. Further conversion forms acyclo-GTP, which competitively inhibits the viral DNA polymerase more strongly than the host enzyme, and when incorporated into DNA is a chain terminator, because it lacks a 3′-hydroxyl group. 97. The unwinding of the replication fork generates positive supercoils, so DNA gyrase is relaxing the DNA—the energy ultimately comes from ATP hydrolysis by DnaB, the helicase that is unwinding the DNA.

98. Thymine is the only base in DNA that cannot spontaneously deaminate, as it lacks an NH2 substituent. 99. (a) primase; (b) DNA Pol III; (c) Okazaki fragments; (d) DNA ligase; (e) NAD+ 100. e; b; a; c; f; d; j; i; h; m; g 101. Semiconservative means that after replication, each double-stranded DNA contains one newly synthesized strand and one strand from the original template DNA. The template DNA was thus conserved (saved), but it only comprises half (semi) of a newly synthesized duplex DNA.

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Chap 26_8e Indicate the answer choice that best completes the statement or answers the question. 1. Differential RNA processing may result in: a. a shift in the ratio of mRNA produced from two adjacent genes. b. attachment of the poly(A) tail to the 5' end of an mRNA. c. inversion of certain introns in the final mRNA. d. the production of the same protein from two different genes. e. the production of two distinct proteins from a single gene. 2. Which statement is false regarding transcription at RNA polymerase II promoters? a. Transcription requires binding of TBP to the –10 promoter element. b. TFIIB binds TBP and recruits TFIIF that directs RNA polymerase II to the promoter. c. TFIIH unwinds the DNA and phosphorylates the CTD of RNA polymerase II. d. TFIIH subunits contribute to a nucleotide-excision repair process. e. During the elongation phase, elongation factors suppress RNA polymerase II pausing and coordinate protein-protein interactions. 3. Which groups act as nucleophiles in the splicing of introns? a. 2′ OH on an A residue for group II introns b. 2′ OH on an A residue for group I introns c. 5′ OH on a G residue for group II introns d. 2′ OH on a G residue for group I introns 4. Which statement about E. coli RNA polymerase (core enzyme) is false? a. In the absence of the σ subunit, core polymerase has little specificity for where initiation begins. b. The core enzyme contains several different subunits. c. The core enzyme has no polymerizing activity until the σ subunit is bound. d. The RNA chain grows in a 5′→3′ direction. e. The RNA product is complementary to the DNA template. 5. Reverse transcriptase: a. can utilize only RNA templates. b. has a 3′→5′ proofreading exonuclease but not a 5′→3′ exonuclease. c. is activated by AZT. d. is encoded by retroviruses. e. synthesizes DNA with the same fidelity as a typical DNA polymerase.

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Chap 26_8e 6. After binding by E. coli RNA polymerase, the correct order of events for transcription initiation is: a. closed complex formation, open complex formation, promoter clearance, start of RNA synthesis. b. closed complex formation, open complex formation, start of RNA synthesis, promoter clearance. c. open complex formation, closed complex formation, start of RNA synthesis, promoter clearance. d. start of RNA synthesis, closed complex formation, open complex formation, promoter clearance. e. start of RNA synthesis, open complex formation, closed complex formation, promoter clearance. 7. Processing of a primary mRNA transcript in a eukaryotic cell does NOT normally involve: a. attachment of a long poly(A) sequence at the 3′ end. b. conversion of normal bases to modified bases, such as inosine and pseudouridine. c. excision of intervening sequences (introns). d. joining of exons. e. methylation of one or more guanine nucleotides at the 5′ end. 8. What acts as the nucleophile in the mechanism of nucleotide addition by RNA polymerase? a. 5′ phosphate of an incoming nucleotide b. water molecule c. 5′ hydroxyl of the template DNA d. 3′ hydroxyl from the RNA being extended e. aspartate in the active site 9. In addition to the primary transcript RNA, the excision (splicing) of many group I introns requires: a. a cytosine nucleoside or nucleotide and a protein enzyme. b. a guanine nucleoside or nucleotide cofactor. c. only a protein enzyme. d. a small nuclear RNA and a protein enzyme. e. ATP, NAD, and a protein enzyme. 10. AZT (3′-azido-2′,3′-dideoxythymidine), used to treat HIV infection, acts in HIV-infected cells by: a. blocking ATP production. b. blocking deoxynucleotide synthesis. c. inhibiting reverse transcriptase. d. inhibiting RNA polymerase II. e. inhibiting RNA processing.

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Chap 26_8e 11. Which statement about E. coli RNA polymerase (core enzyme) is false? a. During transcription, it generally keeps about 17 bp unwound. b. It has no catalytic activity unless the σ factor is bound. c. It uses nucleoside 5′-triphosphates as substrates. d. Its activity is blocked by rifampin. e. Its RNA product will hybridize with the DNA template. 12. Retroviral genomes tend to mutate at a very high rate. What statement BEST explains this observation? a. The RNA genome is highly susceptible to chemical damage. b. Specific enzymes in cells will modify the genome as a protection against infection. c. RNA phosphodiester bonds will tend to hydrolyze spontaneously. d. The virus changes the sequence to prevent antibody binding to the viral genome. e. Reverse transcriptase lacks a 3′ to 5′ exonuclease activity. 13. Which characteristic does NOT apply to the ρ terminator in E. coli? a. The ρ terminator has an ATP-dependent RNA-DNA helicase activity. b. The ρ terminator migrates in the 3′→5′ direction along RNA. c. The ρ terminator causes RNA polymerase release at a CA-rich sequence near the end of the transcript. d. ATP is hydrolyzed by the ρ terminator during the termination process. e. All of these characteristics apply to the ρ terminator. 14. Which property of the L-19 IVS ribozyme is shared with enzymes that are purely protein? a. It acts as a true catalyst. b. It can be competitively inhibited. c. It displays Michaelis-Menten kinetics. d. It makes use of covalent and metal ion catalysis. e. All of these are properties L-19 IVS ribozyme shares with enzymes. 15. Which statement is true regarding the RNA product synthesized by E. coli RNA polymerase? a. Its sequence is identical to that of the template strand. b. Its sequence is identical to that of the nontemplate strand. c. It is able to form a duplex with the template strand. d. It is able to form a duplex with the nontemplate strand e. None of the statements is true.

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Chap 26_8e 16. AZT is one drug used as an HIV inhibitor. How does its structure differ from thymidine? a. The aromatic ring in AZT is not methylated at the 5 position. b. An azido group is present at C-2′ in AZT. c. An azido group is present at C-3′ in AZT. d. The 5′ OH is methylated in AZT. e. The aromatic ring is amidated at the 4 position. 17. Which factor is NOT known to be involved in initiation by eukaryotic RNA polymerase II? a. DNA helicase activity b. DNA polymerase activity c. formation of an open complex d. protein binding to specific DNA sequences e. protein phosphorylation 18. Which statement is true regarding topoisomerases during synthesis of nucleic acids by E. coli RNA polymerase? a. DNA gyrase is required to relieve supercoils on the DNA exit side of the polymerase. b. Since no strand cleavage occurs, supercoiling is not a factor in the action of RNA polymerase. c. Positive supercoils are generated ahead of the transcription bubble. d. Both the DNA and the RNA product will be supercoiled. e. None of the statements is true. 19. Which statement about ρ-independent termination of RNA transcription in E. coli is true? a. The RNA transcript contains no self-complementary sequences. b. There are 12 conserved A residues in the template strand near the end of the transcript. c. There is a CA-rich sequence near the end of the transcript. d. The RNA transcript contains self-complementary sequences, and there are three conserved A residues in the template strand near the end of the transcript. 20. In eukaryotic splicing, U1 snRNP: a. is made entirely of RNA. b. is the only snRNP in the active spliceosome. c. is complementary to the 5′ splice site for the intron. d. becomes covalently attached to a lariat intermediate. e. dissociates from the spliceosomal complex after spliceosome assembly.

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Chap 26_8e 21. Which statement about mRNA stability is true? a. Degradation always proceeds in the 5′→3′ direction. b. Degradation by polynucleotide phosphorylase (PNPase) proceeds by an irreversible hydrolysis reaction. c. In general, bacterial mRNAs have longer half-lives than do eukaryotic mRNAs. d. Rates of mRNA degradation are always at least 10-fold slower than rates of mRNA synthesis. e. Secondary structure in mRNA (hairpins, for example) slows the rate of degradation. 22. Which statement is true regarding the TATA box in transcription? a. It is involved in binding the σ subunit in E. coli transcription. b. It is found at position –10 relative to the transcription start site. c. It is a site for assembly of the preinitiation complex. d. It is a site for binding of repressor proteins. e. All of the statements are true. 23. Which statement about RNA processing in humans is true? a. Pre-mRNA splicing by the spliceosome only occurs in the cytosol. b. During RNA processing exons are removed and are not part of mature mRNA. c. While some mRNAs need processing, most need no modification prior to translation. d. RNA processing includes addition of a 3′ cap. e. Most splicing occurs cotranscriptionally. 24. Eukaryotic nuclear pre-mRNA splicing by the spliceosome requires: a. a guanine nucleoside or nucleotide. b. endoribonucleases. c. polynucleotide phosphorylase. d. RNA polymerase II. e. small nuclear ribonucleoproteins (snRNPs). 25. Which activity is NOT associated with reverse transcriptases? a. RNA-dependent DNA synthesis b. synthesis of RNA primers c. RNA degradation d. DNA-dependent DNA synthesis e. All of these are associated with reverse transcriptase.

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Chap 26_8e 26. RNA replicase carries out what function? a. DNA-dependent DNA synthesis b. RNA-dependent DNA synthesis c. DNA-dependent RNA synthesis d. RNA-dependent RNA synthesis e. None of the answers is correct. 27. Footprinting, or DNase protection, is a technique used to identify: a. a region of DNA that has been damaged by mutation. b. E. coli cells that contain a desired, cloned piece of DNA. c. the position of a particular gene of a chromosome. d. the position of internally double-stranded regions in a single-stranded DNA molecule. e. the specific binding site of a repressor, polymerase, or other protein on the DNA. 28. Which statement is correct with respect to ρ-dependent termination of RNA synthesis? a. Self-complementary GC sequences act as signals for transcriptional termination. b. Formation of a hairpin structure disrupts DNA duplex formation and facilitates dissociation of the transcript. c. ATP is hydrolyzed as part of the termination process. d. The terminator contains a sequence of repeated A residues. e. An important component is a GT-rich sequence called rut. 29. Which statement is false regarding telomerase? a. This enzyme requires a DNA component as a cofactor. b. This enzyme is a DNA polymerase. c. This enzyme extends the 3′ end of a linear nucleic acid structure. d. This enzyme uses dGTP and dTTP as substrates. e. This enzyme synthesizes nucleic acids in a 5′ to 3′ direction. 30. Which statement about E. coli RNA polymerase is false? a. Elongation by RNA polymerase is primarily done by the σ factor. b. RNA polymerase holoenzyme has several subunits. c. RNA produced by this enzyme will be complementary to the DNA template. d. The enzyme adds nucleotides to the 3′ end of the growing RNA chain. e. The enzyme cannot synthesize RNA in the absence of DNA.

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Chap 26_8e 31. Which statement about the synthesis of rRNA and tRNA in E. coli is true? a. Both rRNA and some tRNAs are part of the same primary transcript. b. Each rRNA sequence (16S, 23S, 5S) is transcribed as a separate primary transcript. c. Primary tRNA transcripts undergo methylation, but rRNA sequences are not methylated. d. The tRNA sequences all lie at the 3′ end of the rRNA transcripts. e. There is a single copy of the rRNA genes. 32. Which polymerase does NOT require a template? a. RNA Pol I b. RNA Pol II c. reverse transcriptase d. polyadenylate polymerase e. RNA replicase 33. Which statement about the reverse transcriptases of retroviruses and the RNA replicases of other singlestranded RNA viruses, such as influenza virus, is correct? a. Both enzymes can synthesize either RNA or DNA from an RNA template strand. b. Both enzymes can utilize DNA in addition to RNA as a template strand. c. Both enzymes carry the specificity for the RNA of their own virus. d. Both enzymes have error rates similar to those of cellular RNA polymerases. e. Both enzymes require host-encoded subunits for their replication function. 34. In order for RNA polymerase II to create a transcript, what is NOT necessary? a. magnesium b. dNTPs c. topoisomerases d. phosphorylation of CTD e. All of these are necessary. 35. What do reverse transcriptases use to initiate DNA synthesis? a. They can synthesize DNA without a primer. b. They require the action of cellular primase. c. They contain a primase activity. d. They use a tRNA molecule as a primer. e. None of these is used by reverse transcriptases in initiation of DNA synthesis.

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Chap 26_8e 36. The σ factor of E. coli RNA polymerase: a. associates with the promoter before binding core enzyme. b. combines with the core enzyme to confer specific binding to a promoter. c. is inseparable from the core enzyme. d. is required for termination of an RNA chain. e. will catalyze synthesis of RNA from both DNA template strands in the absence of the core enzyme. 37. The 5'-terminal cap structure of eukaryotic mRNAs is a(n) _____ joined to the mRNA via a _____. a. 7-methylcytosine; 2′,3′-cyclic linkage b. 7-methylguanosine; 5′,3′-diphosphate linkage c. 7-methylguanosine; 5′,5′-triphosphate linkage d. N6-methyladenosine; 5′,5′-phosphodiester bond e. O6-methylguanosine; 5′,5′-triphosphate linkage 38. Which process is NOT part of the processing of the 30S pre-rRNA transcript? a. addition of a poly(A) tail b. methylation of bases c. conversion of uridine to pseudouridine d. conversion of uridine to dihydrouridine e. hydrolysis by RNase P 39. Synthesis and maturation of tRNA does NOT require which process? a. transcription of a gene b. RNase D cleavage c. RNase P cleavage d. addition of CCA to the 5′ end of the molecule e. methylation of specific bases 40. Which process is associated with the carboxyl-terminal domain (CTD) of RNA polymerase II in eukaryotes? a. formation of spliceosomes b. attachment of the 5¢ cap to mRNA c. polyadenylation of the 3¢ end of mRNA d. phosphorylation and dephosphorylation e. All of the answers are correct.

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Chap 26_8e 41. Which statement does NOT describe the cap structure of mRNA? a. The cap structure contains two phosphoanhydride bonds. b. The cap is added to an existing 5′-triphosphate nucleotide. c. The cap structure may include multiple methylations. d. The cap structure is added after addition of the poly(A) structure. e. The cap interacts with both the ribosome and the carboxyl-terminal domain of RNA Pol II. 42. RNA polymerase: a. binds tightly to a region of DNA thousands of base pairs away from the DNA to be transcribed. b. can synthesize RNA chains without a primer. c. has a λ subunit, which acts as a proofreading ribonuclease. d. separates DNA strands throughout a long region of DNA (up to thousands of base pairs), then copies one of them. e. synthesizes RNA chains in the 3′→5′ direction. 43. What statement is true regarding synthesis of nucleic acids by E. coli RNA polymerase? a. The RNA-DNA hybrid assumes a B-form DNA conformation. b. The RNA-DNA hybrid is antiparallel. c. The RNA-DNA hybrid is between 20 and 30 base pairs long. d. Unwinding the DNA duplex creates negative supercoils in the template DNA. e. None of the statements is true. 44. Which statement is false with respect to different σ subunits in bacterial RNA polymerase? a. Specific amino acids in σ subunits will interact with the polymerase. b. DNA sequences spanning approximately three turns of the helix will specifically interact with σ subunits. c. Both DNA and the RNA polymerase interact with σ subunits. d. Multiple σ subunits exist in a single E. coli RNA polymerase. e. The binding of NusA is competitive with the binding of σ subunits in E. coli. 45. Which statement does NOT indicate how retrotransposons and retroviruses are similar to each other? a. Both contain long terminal repeated sequences. b. Both are able to produce RNA products from their DNA. c. Both contain reverse transcriptase–coding regions. d. Both contain envelope protein-coding sequences. e. Both integrate into a host genome.

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Chap 26_8e 46. Which statement is false about eukaryotic mRNA and its processing? a. Exons are used for polypeptide synthesis. b. Introns are complementary to their adjacent exons and will form hybrids with them. c. The mature mRNA is substantially shorter than the corresponding region on the DNA. d. The mRNA is originally synthesized in the nucleus, but ends up in the cytoplasm. e. The splicing that yields a mature mRNA occurs at very specific sites in the RNA primary transcript. 47. Which statement is false regarding the TATA-binding protein (TBP)? a. It is a general transcription factor in eukaryotic transcription. b. This protein stays associated with the RNA polymerase during elongation. c. This protein interacts with TBP-associated factors in TFIID. d. TFIID and PIC position TBP on the promoter. 48. Which compound is part of miRNA formation? a. pri-miRNA b. pre-miRNA c. Dicer d. RISC e. All of these are part of miRNA formation. 49. What metal ion cofactors are required to bind nucleotide triphosphate substrates by E. coli RNA polymerase? a. Fe2+ b. Zn2+ c. Mg2+ d. Mn2+ e. None of these ions is required. 50. Which step is NOT a part of the synthesis of a 5′-mRNA cap? a. conversion of a 5′-triphosphate into a 5′-diphosphate b. formation of a 5′ to 5′ phosphodiester bond c. methylation of 2′-OH groups d. transfer of a GMP group onto a nucleic acid e. All of these steps are part of 5′-cap synthesis.

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Chap 26_8e 51. E. coli RNA polymerase has no 3′→5′ exonuclease activity. Which statement BEST explains why this is not a required activity for this enzyme? a. RNA polymerase makes fewer errors in NTP addition, so this activity is unnecessary. b. RNA polymerase does not need to degrade nucleic acids ahead of the transcription bubble. c. Errors in transcription will have no impact on the function of the RNA product. d. Multiple RNA products are created and turnover rapidly, so errors have less impact. e. None of the statements explains why this is not a required activity. 52. Which statement is false about telomerase? a. Telomerase is a reverse transcriptase. b. Telomerase utilizes a tRNA template. c. The primer for telomerase is the 3′ end of the DNA chromosomes. d. Telomerase synthesizes DNA in the 5′→3′ direction. e. Telomerase consists of both RNA and protein. 53. Which is a function of TFIIH? a. DNA helicase activity b. 3′→5′ exonuclease activity c. recognizes the TATA box d. termination of transcription e. RNA splicing 54. RNA aptamers are: a. double-stranded RNA products of nuclease action on hairpin RNAs. b. repeat sequence elements at the ends of transposons. c. small RNA molecules selected for tight binding to specific molecular targets. d. the RNA primers required for retroviral replication. e. the short tandem repeat units found in telomeres. 55. Which property does NOT apply to RNA polymerase from E. coli (core enzyme alone)? a. It can extend an RNA chain and initiate a new chain. b. It is required for the synthesis of mRNA, rRNA, and tRNA in E. coli. c. It produces an RNA polymer that begins with a 5′-triphosphate. d. It recognizes specific start signals in DNA. e. It requires all four ribonucleoside triphosphates and a DNA template.

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Chap 26_8e 56. Which eukaryotic transcription factor has helicase activity? a. TFIIA b. TFIIB c. TFIIF d. TFIIH e. TBP 57. What statement is false regarding reverse transcriptases? a. They require nucleic acid templates. b. They have proofreading functions. c. They use dNTPs as substrates for synthesis. d. They require metal cofactors. e. All of the statements are true. 58. Compared with DNA polymerase, reverse transcriptase: a. does not require a primer to initiate synthesis. b. introduces no errors into genetic material because it synthesizes RNA, not DNA. c. makes fewer errors in synthesizing a complementary polynucleotide. d. makes more errors because it lacks the 3′→5′ proofreading exonuclease activity. e. synthesizes complementary strands in the opposite direction from 3′→5′. 59. Which are the fundamental reactions for ribozyme activity? a. transamination and phosphodiester bond hydrolysis b. transesterification and transamination c. transesterification and phosphodiester bond hydrolysis d. transesterification and phosphodiester bond formation 60. A branched lariat structure is formed during: a. attachment of a 5′ cap to mRNA. b. attachment of poly(A) tails to mRNA. c. processing of pre-ribosomal RNA. d. splicing of all classes of introns. e. splicing of group II introns. 61. Which process is part of the original central dogma? a. RNA-dependent RNA synthesis b. the process catalyzed by RNA polymerase II c. RNA editing processes d. RNA-dependent DNA synthesis e. None of these is part of the original central dogma. Copyright Macmillan Learning. Powered by Cognero.

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Chap 26_8e 62. AZT is one drug used to treat HIV infection. How does it specifically treat HIV infection? a. AZT binds to the protein coat of the HIV virus. b. AZT acts as a competitive inhibitor of dTTP for reverse transcriptase. c. AZT hydrolyzes the viral RNA. d. AZT degrades the tRNA primer needed by reverse transcriptase. e. AZT inhibits viral assembly and packing. 63. In eukaryotes, RNA polymerase II is: a. a multisubunit protein with the largest subunit being homologous to E. coli β′ subunit. b. associated with transcription of mRNA and rRNA. c. found in chloroplasts and mitochondria. d. activated by the acetylation of the carboxyl-terminal domain. e. All of the answers are correct. 64. Which statement does NOT accurately describe a difference between RNA synthesis by polynucleotide phosphorylase (PNPase) and RNA polymerase? a. RNA polymerase is a bacterial enzyme, while PNPase is not. b. RNA polymerase requires a template, while PNPase does not. c. RNA polymerase produces a specific product, while PNPase does not. d. RNA polymerase synthesizes RNA, while PNPase can synthesize or degrade RNA. 65. Which item(s) can be described as a ribozyme? a. self-splicing group I introns b. RNase P c. group III introns d. both group I and group III introns, but not RNase P e. self-splicing group I introns and RNase P 66. Which is the MOST common nucleoside modification in eukaryotic rRNA? a. 4-thiouridine b. pseudouridine c. dihydrouridine d. ribouridine e. ribothymidine

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Chap 26_8e 67. Which is NOT involved in rRNA processing in eukaryotes? a. conversion of uridine to pseudouridine b. the nucleolus c. ρ factor d. snoRNAs e. snoRNPs 68. One process the reverse transcriptase of an animal RNA virus catalyzes is: a. degradation of the RNA strand in a DNA-RNA hybrid. b. insertion of the viral genome into a chromosome of the host (animal) cell. c. RNA formation in the 3′→5′ direction. d. RNA synthesis, but not DNA synthesis. e. synthesis of an antisense RNA transcript. 69. Transfer RNAs have several bases in addition to the normal four found in RNA. How are these rare bases incorporated into the tRNA molecule?

70. Describe the mechanistic difference that distinguishes the splicing of group I introns from that of group II introns.

71. Describe the function of polyadenylate polymerase and name two properties that distinguish it from normal cellular RNA polymerases.

72. In the synthesis of the 5′-cap of mRNA, what enzyme classes are used at each step?

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Chap 26_8e 73. Describe all of the known catalytic activities of reverse transcriptase.

74. Beginning with the primary transcript containing a tRNA sequence, describe the steps in the formation of a mature tRNA molecule in E. coli.

75. Why did the RNA world hypothesis have to await the discovery of ribozymes in order to become a widely attractive scenario?

76. Explain why spliceosomal introns likely evolved from group II introns and not group I introns.

77. Rifampin blocks RNA polymerase; why would this be lethal to a cell that was sensitive to this drug?

78. What is the utility of the SELEX protocol and how does it work?

79. Describe in words (not using structures) the important features of the structures present on the 5′ and 3′ ends of mature (processed) eukaryotic mRNAs.

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Chap 26_8e 80. In a ρ-independent terminator, there is a palindrome rich in G≡C base pairs, followed by 8 to 10 uridine residues. Explain how each of these changes might affect terminator function: (a) substitution of cytidines for the 8 to 10 uridines; (b) mutations in the palindrome that decrease its G≡C content; (c) elimination of half of the palindromic sequence.

81. For each statement, indicate with a P if the statement applies only to prokaryotes, an E if the statement applies only to eukaryotes, and an E and P if the statement applies to both eukaryotes and prokaryotes. ___ RNA synthesis is blocked by actinomycin D. ___ A single RNA polymerase transcribes genes that encode mRNAs, tRNAs, and rRNAs. ___ Transcription of mRNA is blocked by α-amanitin. ___ A σ subunit detaches from RNA polymerase shortly after transcription has initiated. ___ The 5′ end of the mature mRNA begins with a triphosphate. ___ The primary mRNA transcript is inactive. ___ Termination of transcription requires the protein ρ factor.

82. List two main functions of the 5′-cap structure.

83. Write the sequence of the messenger RNA molecule synthesized from a DNA template strand having the sequence (5′)ATCGTACCGTTA(3′).

84. Describe the sequence of events in the initiation of transcription by E. coli RNA polymerase.

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Chap 26_8e 85. What is a telomere? Describe the key features of its structure. What is unusual about the structure and/or mechanism of action of telomerase?

86. Define ribozymes and briefly describe the structure and function of two ribozymes.

87. The DNA molecule shown is believed to contain a binding site for protein X. It is labeled at the 5′end of the top strand (*), then subjected to a footprinting experiment. In the idealized gel, there is a band for every base of the labeled strand. On the DNA sequence, point out the binding site for protein X. * (5′)GGATTCTAATAAAGTAACGCGTTACGACTTGG CCTAAGATTATTTCATTGCGCAATGCTGAACC

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Chap 26_8e 88. In 1989, Sidney Altman won a Nobel Prize for his work on RNase P. In no more than three sentences, describe the function of RNase P, as well as the unusual characteristic of this enzyme that made Altman's work so important.

89. Compare reverse transcription and transcription in terms of the listed characteristics. a. Direction of polynucleotide synthesis b. Nature of template c. Nature of primer d. Incorporated nucleotides

90. Shown is an RNA molecule being transcribed from a strand of DNA. Indicate the 5′ and 3′ ends of the RNA molecule and of the strand of DNA that is complementary to the RNA molecule. In which direction is synthesis occurring?

91. Indicate whether each statement about eukaryotic cells is true (T) or false (F). ___ They have three distinct RNA polymerases. ___ Their mRNAs are generally synthesized by RNA polymerase I. ___ RNA polymerase III synthesizes only rRNAs. ___ The 5S rRNA is synthesized by RNA polymerase I. ___ Their RNA polymerases initiate transcription at specific promoter sites on the DNA.

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Chap 26_8e 92. Name four general types of posttranscriptional processing reactions that are observed in RNA. Briefly (one sentence or less) point out an example of each type. In the example, identify the type of RNA molecule involved (tRNA, mRNA, rRNA, etc.), the type of processing involved, and whether the example is characteristic of eukaryotes, prokaryotes, or both. Do not describe specific genes, sequences, complicated structures, or enzymes.

93. Compare and contrast ρ-dependent and ρ-independent termination of transcription in prokaryotes.

94. Briefly describe two instances where the carboxyl-terminal domain (CTD) of RNA polymerase II is involved in RNA synthesis or processing.

95. Describe briefly the process of initiation by eukaryotic RNA polymerase.

96. The specific sequences that E. coli RNA polymerase usually binds to in E. coli DNA before initiating transcription generally contain more A=T base pairs than G≡C base pairs. In no more than a few sentences, speculate on why this might be the case.

97. In the synthesis of cDNA libraries for eukaryotic genes, reverse transcriptase can be used with a primer containing poly(T). Why is this not useful for prokaryotic systems?

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Chap 26_8e 98. Consider the small hypothetical gene. The DNA base pairs corresponding to the first and last nucleotides transcribed are indicated by a + and an *, respectively. Give the sequence of the mRNA strand produced by this gene. Label the 5′ and 3′ends of the mRNA.

99. List one important property that distinguishes RNA polymerases from DNA polymerases, and list one important property they share.

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Chap 26_8e Answer Key 1. e 2. a 3. a 4. c 5. d 6. b 7. b 8. d 9. b 10. c 11. b 12. e 13. b 14. e 15. c 16. c 17. b 18. c 19. d 20. c 21. e 22. c 23. e 24. e 25. b 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 26_8e 27. e 28. c 29. a 30. a 31. a 32. d 33. d 34. b 35. d 36. b 37. c 38. a 39. d 40. e 41. d 42. b 43. b 44. d 45. d 46. b 47. b 48. e 49. c 50. e 51. d 52. b 53. a 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 26_8e 55. d 56. d 57. b 58. d 59. c 60. e 61. b 62. b 63. a 64. a 65. e 66. b 67. c 68. a 69. The unusual bases in tRNA are made by first incorporating the usual four bases into a tRNA precursor, then enzymatically modifying specific nucleotide residues in the pre-tRNA molecule. 70. In the group I introns, the initial break in the RNA chain occurs as the hydroxyl group of a guanine nucleoside or nucleotide makes a nucleophilic attack on the phosphodiester bond. In group II introns, the attacking species is the 2'-hydroxylgroup of an adenylate residue in the intron itself. 71. Poly(A) polymerase is required to add the long polyadenylate tail onto the 3' end of eukaryotic mRNAs. Although it uses the ribonucleoside triphosphate ATP, releases pyrophosphate, and proceeds in the 5'→3' direction, as do cellular RNA polymerases, unlike them it is not template directed and it does require a 3'-hydroxylend to prime synthesis. 72. The individual enzymes are (in order of action) phosphohydrolase (a hydrolase), guanylyltransferase (a transferase), and methyltransferases (also transferases). 73. Reverse transcriptase can (1) synthesize DNA complementary to an RNA template; (2) degrade the RNA strand of the resulting RNA-DNA hybrid; and (3) synthesize DNA complementary to the resulting single-stranded DNA. 74. Short sequences at the 5' and 3' ends of the primary transcript are removed by RNase P and D, respectively. A specific enzyme adds CCA at the 3' end. Several bases are modified (e.g., forming pseudouridine or methylguanosine). In some cases, an intron is spliced out.

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Chap 26_8e 75. The existence of ribozymes proved that small RNA molecules could carry out catalytic functions, and have the potential capacity for self-replication. Since ribonucleotides can arise from prebiotic chemistry, once they form short polymers, the conceptual link to biochemical catalysis, which is essential for life, is complete. The finding that the ribosome has catalytic RNA to carry out amino acid polymerization into peptides and proteins (see Chapter 27) strengthens the case for catalytic RNA molecules to have preceded catalytic proteins (i.e., enzymes) in evolution. 76. The mechanisms in both spliceosomal introns and group II introns are very similar, including an internal A residue acting as a nucleophile and the formation of a lariat structure as one of the reaction products. Group I introns use a free nucleotide as a nucleophile and release a linear product instead. 77. Without RNA synthesis, there could be no protein synthesis and the cell would be unable to replenish proteins that had been turned over or synthesize new proteins. Since both processes are necessary to life, the sensitive cell would stop growing and die.

78. SELEX is accelerated evolution in a test tube that involves searching in pools of random RNA polymers to purify those that can bind tightly to particular substrates. As described in Box 26-4, a concentrated pool of RNA carrying randomized RNA sequences up to about 25 nucleotides is passed through an affinity column carrying the desired substrate. Those that bind are eluted, amplified by reverse transcriptase, and copied by RNA polymerase to make a new pool that is enriched for molecules that were retained on the column. This pool is cycled through the column again for a dozen or more passes, obtaining incremental enrichment on each pass. The final set of molecules is cloned to obtain individual aptamers, which are then screened for the desired characteristics. In practice, this method has been employed to generate a wide variety of RNA molecules with the ability to bind particular organic molecules or catalyze specific chemical reactions. 79. At the 5' end, there is a cap consisting of a guanosine joined to the 5'-terminalnucleotide through a 5' to 5' triphosphate group. This guanine nucleotide is methylated on N-7. The next two nucleotides in the chain are also sometimes methylated on their 2'-OH groups. At the 3' end is the poly(A) tail consisting of a run of 80 to 250 A residues. 80. (a) This substitution would decrease terminator function by stabilizing the RNA-DNA hybrid duplex. (b) These mutations would decrease terminator function by destabilizing hairpin formation, and the RNA-DNA hybrid will be stabilized as a result. (c) Without half the palindrome, the hairpin will not form, and the RNA-DNA hybrid will not be destabilized enough for the terminator to function. 81. E and P; P; E; P; P; E; P 82. The 5' cap of mRNA prevents degradation of the transcript by ribonucleases, and it is also involved in binding of mRNA to the ribosome in the initiation of translation. 83. (3')UAGCAUGGCAAU(5'); also acceptable is (5')UAACGGUACGAU(3') 84. The core enzyme plus σ subunit, called holoenzyme, binds to the promoter region forming a closed complex (i.e., in which the DNA double helix is not unwound). This is converted to an open complex by the unwinding of a short region of the promoter. Synthesis of the RNA chain begins within the complex. The complex then moves along the DNA away from the promoter region and the σ subunit dissociates.

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Chap 26_8e 85. Telomeres are specialized structures at the ends of linear chromosomes. They consist of tandem repeats of variable length, usually of the form TxGy in one strand and CyAx in the other. The TG strand is often longer, resulting in a region of single-stranded DNA. Telomerase is an enzyme that consists of RNA and protein; the RNA portion is an internal template for RNA-dependent DNA synthesis in the telomere TG strand by the protein portion. This unusual structure and composition allows telomerase to catalyze replication at the ends of linear chromosomes without the loss of DNA. 86. Ribozymes are enzymes that consist in part or entirely of RNA. RNase P, which contains both protein and RNA, cleaves extra nucleotides from the 5' end of tRNA molecules. The enzymatic activity is contained entirely in the RNA portion. Group I introns are RNA sequences in primary transcripts that catalyze their own excision, without any involvement of catalytic proteins. Small RNAs associated with certain RNA viruses of plants also contain selfsplicing RNA sequences. The enzyme peptidyl transferase (see Chapter 27), which forms peptide bonds during protein synthesis on ribosomes, is a ribozyme in which the essential catalytic component is RNA.

87. 88. RNase P catalyzes the removal of a short piece of RNA at the 5' end of a maturing tRNA. The enzyme is a ribozyme—an enzyme in which RNA is the catalytic species. 89. (a) Direction of polynucleotide synthesis (b) Nature of template (c) Nature of primer (d) Incorporated nucleotides

Reverse Transcription 5'→3' RNA or DNA tRNA dNTPs

Transcription 5'→3' DNA none NTPs

90. 91. T; F; F; F; T 92. Posttranscriptional reactions on mRNA in eukaryotes include: (1) the removal of introns, (2) the addition of a 5' cap, and (3) addition of a poly(A) tail. In prokaryotes and eukaryotes, tRNAs have sequences that are (4) trimmed and (5) spliced, (6) bases already incorporated into tRNA are modified (yielding, for example, pseudouridine and inosine), and (7) a 3'-CCA sequence is sometimes added to the tRNA. Eukaryotic tRNA is also subject to intron splicing and posttranscriptional modification of some bases. In prokaryotes and eukaryotes, pre-ribosomal RNAs are (8) cleaved to form individual rRNAs. Copyright Macmillan Learning. Powered by Cognero.

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Chap 26_8e 93. In both, the transcription complex pauses at specific sequences in the DNA template. In ρ-independent termination, the formation of hairpin structures causes pausing, which leads to dissociation of the product RNA and the polymerase from the template DNA and hence to termination. In ρ-dependent termination, the features that cause pausing are unclear, and dissociation requires the presence of the ρ protein. 94. Some examples of possible answers: (1) Phosphorylation of CTD by TFIIH causes conformational change in the overall complex, initiating transcription. (2) Elongation factors bind to CTD to suppress pausing and they also coordinate some mRNA processing. (3) Four enzymes associated with 5'-cap formation associate with CTD until capping is complete. (5) Some components of the splicing apparatus are tethered to CTD during the splicing process. (6) A large complex binds to CTD during addition of the poly(A) tail to mRNA. 95. One transcription factor (TBP) binds specifically to the TATA region of the promoter. A second factor (TFIIB) binds to the first factor, and RNA polymerase binds to the TFIIB-TBP complex. Additional factors bind to produce the complete closed complex that is converted to the open complex by the action of DNA helicases. Phosphorylation of the polymerase results in a conformational change that results in the actual initiation of the RNA chain. (See Fig. 26-9.) 96. Because A=T base pairs are stabilized by only two hydrogen bonds (compared with three for G≡C pairs), doublestranded regions rich in A=T pairs are easier for RNA polymerase to bind and unwind in preparation for the transcription of one of the DNA strands. 97. A poly(T) primer will form a duplex with the poly(A) tail of eukaryotic mRNA, which can then be used by reverse transcriptase to synthesize a DNA product from the mRNA template. Prokaryotic mRNA does not contain poly(A) tails, so the primers would not form a duplex effectively and reverse transcriptase would not have a primer with which to begin synthesis. 98. (5')GCUAUGUACGUAGCUACGU(3') 99. Among the distinguishing characteristics: RNA polymerase does not require a primer, but DNA polymerase does; RNA polymerase lacks the 3'→5' proofreading exonuclease activity present in DNA polymerase. Among the shared properties: both enzymes use nucleoside triphosphates as substrates, require Mg2+ to produce an antiparallel complement to the template, and synthesize nucleic acids in the 5'→3' direction.

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Chap 27_8e Indicate the answer choice that best completes the statement or answers the question. 1. In bacteria, the elongation stage of protein synthesis does NOT involve: a. aminoacyl-tRNAs. b. EF-Tu. c. GTP. d. IF2. e. peptidyl transferase. 2. What does it mean to say that the genetic code is degenerate? a. There is more than one tRNA that can specify a given amino acid. b. The genetic code is universal throughout living organisms. c. There is more than one codon for most amino acids. d. Only the first two nucleotides in a codon are needed to specify the amino acid. e. The genetic code cannot be described as being degenerate. 3. Which statement does NOT describe a general aspect of signal sequences? a. They are often found at the N terminus of secreted proteins. b. They contain 10 to 15 hydrophobic amino acids. c. At least one-third of their amino acids are negatively charged residues. d. The carboxy terminus contains a site for proteolytic cleavage. e. All of these are general aspects of signal sequences. 4. On average approximately how many NTPs must be converted to NDPs to incorporate one amino acid into a protein? a. zero b. one c. two d. four e. twelve 5. Assuming that the average amino acid residue contributes 110 to the peptide molecular weight, what will be the approximate minimum length of the mRNA encoding a protein of molecular weight 50,000? a. 133 nucleotides b. 460 nucleotides c. 1,400 nucleotides d. 5,000 nucleotides e. A minimum length cannot be determined from the data given.

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Chap 27_8e 6. In the activation of an amino acid for protein synthesis: a. leucine can be attached to tRNAPhe, by the aminoacyl-tRNA synthetase specific for leucine. b. methionine is first formylated, then attached to a specific tRNA. c. the amino acid is attached to the 5′ end of the tRNA through a phosphodiester bond. d. there is at least one specific activating enzyme and one specific tRNA for each amino acid. e. two separate enzymes are required, one to form the aminoacyl adenylate, the other to attach the amino acid to the tRNA. 7. If the nucleotides C and G are mixed together in a 1:1 ratio with polynucleotide phosphorylase in the Ochoa and Nirenberg experiments, which amino acids would NOT be incorporated into polypeptides? 5′end ↓ U C A G U UUU Phe UCU Ser UAU Tyr UGU Cys UUC Phe UCC Ser UAC Tyr UGC Cys UUA Leu UCA Ser UAA Stop UGA Stop UUG Leu UCG Ser UAG Stop UGG Trp C CUU Leu CCU Pro CAU His CGU Arg CUC Leu CCC Pro CAC His CGC Arg CUA Leu CCA Pro CAA Gln CGA Arg CUG Leu CCG Pro CAG Gln CGG Arg A AUU Ile ACU Thr AAU Asn AGU Ser AUC Ile ACC Thr AAC Asn AGC Ser AUA Ile ACA Thr AAA Lys AGA Arg AUG Met ACG Thr AAG Lys AGG Arg G GUU Val GCU Ala GAU Asp GGU Gly GUC Val GCC Ala GAC Asp GGC Gly GUA Val GCA Ala GAA Glu GGA Gly GUG Val GCG Ala GAG Glu GGG Gly a. Ala b. Arg c. Glu d. Gly e. Pro 8. Posttranslational glycosylation of proteins is inhibited specifically by: a. chloramphenicol. b. cycloheximide. c. puromycin. d. streptomycin. e. tunicamycin. Copyright Macmillan Learning. Powered by Cognero.

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Chap 27_8e 9. Which statement is false concerning translation of the apoB gene? a. apoB is a single gene that is expressed in both liver and intestine. b. The liver produces a longer protein product than the intestine. c. In the intestine, cytidine deaminase converts C nucleotide into a U. d. Guide RNA molecules mostly complementary to RNA to be edited serve as a template. e. Edited mRNA for apoB creates a termination codon from one for glutamine. 10. Ile-tRNA synthetase can distinguish valine from isoleucine. The enzyme preferentially binds Ile by a factor of about 200-fold, yet only about 1 in 3,000 times is a Val erroneously incorporated into proteins. How does the synthetase achieve this level of accuracy? a. It has an acylation site that rejects amino acids that are smaller than the correct one. b. It has a hydrolytic site that destroys activated intermediates that are larger than the correct species. c. It has a proofreading site into which Val-AMP fits, but Ile-AMP does not. d. It is unable to incorporate valine or leucine into aminoacylated tRNA structures. e. It has a secondary active site that methylates Val-AMP to Ile-AMP. 11. Which statement is false concerning ubiquitin? a. It is a prokaryotic protein and is not present in eukaryotes. b. This protein is covalently added to proteins targeted for degradation. c. This protein is small (<100 amino acids). d. Its sequence is highly conserved among the organisms in which it occurs. e. It forms an amide bond to a target protein. 12. Aminoacyl-tRNA synthetases (amino acid activating enzymes): a. "recognize" specific tRNA molecules and specific amino acids. b. in conjunction with another enzyme attach the amino acid to the tRNA. c. interact directly with free ribosomes. d. occur in multiple forms for each amino acid. e. require GTP to activate the amino acid. 13. Which reaction in protein synthesis leads to formation of an ester bond in one of its products? a. tRNA charging with amino acids b. binding of aminoacyl-tRNA to the ribosome c. reaction of acylated tRNA in the A site with acylated tRNA in the P site d. the translocation step in protein synthesis e. release of the final peptide product

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Chap 27_8e 14. Which antibiotic functions by interfering with the translational process? a. chloramphenicol b. cycloheximide c. streptomycin d. puromycin e. All of these antibiotics interfere with translation. 15. Which statement about tRNA molecules is false? a. A, C, G, and U are the only bases present in the molecule. b. Although composed of a single strand of RNA, each molecule contains several short, double-helical regions. c. Any given tRNA will accept only one specific amino acid. d. The amino acid attachment is always to an A nucleotide at the 3′ end of the molecule. e. There is at least one tRNA for each of the 20 amino acids. 16. In E. coli, aminoacyl-tRNA synthetases: a. activate amino acids in 12 steps. b. are amino acid specific; there is at least one enzyme specific for each amino acid. c. fall into two classes, each of which attaches amino acids to different ends of the tRNA. d. have no proofreading activities. e. require a tRNA, an amino acid, and GTP as substrates. 17. Which bases are important in ensuring a tRNA is charged with the correct amino acid? a. bases that are highly conserved between different tRNAs b. bases that vary between different tRNAs c. any modified bases in the tRNA d. all bases found in the anticodon loop e. All of the bases are equally important. 18. Which statement about bacterial mRNA is true? a. A ribosome usually initiates translation near the end of the mRNA that is synthesized last. b. An mRNA is rarely degraded and is usually passed on to the daughter cells at cell division. c. During polypeptide synthesis, ribosomes move along the mRNA in the 5′→3′ direction. d. Ribosome subunits stay together without dissociation for the synthesis of hundreds of proteins. e. The codon signaling peptide termination is located in the mRNA near its 5′ end.

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Chap 27_8e 19. If fMet-tRNAfMet were bound by EF-Tu, it would be: a. delivered to the ribosomal A site. b. delivered to the ribosomal P site. c. delivered to the ribosomal E site. d. unable to bind to the ribosome at all. e. degraded. 20. If a glycosylated protein is purified from the ER, what would be true about this protein? a. The glycosyl groups will contain very little mannose. b. The glycosylation is likely to be N-linked. c. The protein will still contain a signal sequence. d. The protein will be targeted to lysosomes. e. The protein will be an integral membrane protein. 21. Which statement is true for protein synthesis in eukaryotes? a. All proteins are initially synthesized with methionine at their C terminus. b. All proteins are initially synthesized with methionine at their N terminus. c. All proteins are initially synthesized with tryptophan at their C terminus. d. All proteins are initially synthesized with a repeat of five amino acids at their carboxyl terminal. e. None of the statements is true. 22. If peptide synthesis were carried out using an mRNA that has repeating sequence of two nucleotides (XY)n , what are the possible results for the protein sequence? a. The protein is composed of only one type of amino acid (e.g., polylysine). b. The protein is composed of two types of amino acids in an alternating pattern (ABAB). c. Ribosomes will not synthesize protein from this type of sequence. d. The protein is composed of three or more types of amino acids in an unpredictable pattern. e. The protein is composed of three types of amino acids in a repeating pattern (ABCABC). 23. Which characteristic distinguishes class I aminoacyl-tRNA synthetases from class II aminoacyl-tRNA synthetases? a. Class I enzymes are ligases, while class II enzymes are lyases. b. Class I enzymes have proofreading function, while class II enzymes do not. c. Class I enzymes bind to specific nucleotides in tRNA substrates, while class II enzymes do not. d. Class I enzymes transfer amino acids to the 2′ OH, while class II enzymes transfer amino acids to the 3′ OH. e. None of the answers is correct.

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Chap 27_8e 24. Which is an extremely toxic protein that inactivates ribosomes by depurination of an adenosine? a. ricin b. cyanide c. chloramphenicol d. puromycin e. arsenic 25. Which statement about the elongation phase of protein synthesis is true? a. At least five high-energy phosphoryl groups are expended for each peptide bond formed. b. During elongation, incoming aminoacylated tRNAs are first bound in the P site. c. Elongation factor EF-Tu facilitates translocation. d. Peptidyl transferase catalyzes formation of the peptide bond by covalent catalysis. e. Peptidyl transferase is a ribozyme with catalytic activity in the rRNA. 26. Nuclear localization sequences (NLSs) that direct proteins to the nucleus: a. are always at the amino terminus of the targeted protein. b. are cleaved after the protein arrives in the nucleus. c. are glycosyl moieties containing mannose 6-phosphate residues. d. may be located almost anywhere along the primary sequence of the protein. e. are the same as those that direct certain proteins to lysosomes. 27. A large structure consisting of one mRNA molecule being translated by multiple ribosomes is called a: a. lysosome. b. polysome. c. proteosome. d. translatosome. e. synthosome. 28. The initiation codon 5′→3′ is _____ and it codes for the amino acid _____. a. AUG; Met b. UUA; Met c. CCG; Glu d. GAA; Glu e. GGG; Gly

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Chap 27_8e 29. Ubiquitin is added to proteins targeted for degradation by formation of a(n) _____ bond between _____ of ubiquitin and a _____ the target protein. a. ester; the C terminus; serine of b. thioester; the C terminus; cysteine of c. amide; the C terminus; lysine of d. ester; a glutamate; serine in e. thioester; a glutamate; cysteine in 30. Which statement is true regarding wobble pairs in translation? a. The wobble position is the first position in the anticodon. b. In the anticodon, A can pair with C or U. c. In the anticodon, C and G can each pair with two nucleotides. d. Inosine in the wobble position can pair with both purines. e. G and U pairs are never found in the wobble position. 31. Which statement describes a feature of the wobble hypothesis? a. A naturally occurring tRNA exists in yeast that can read both arginine and lysine codons. b. A tRNA can recognize only one codon. c. Some tRNAs can recognize codons that specify two different amino acids if both are nonpolar. d. The third base of the codon pairs loosely with the corresponding base of its anticodon. e. The middle position of an anticodon is not important to the amino acid specified. 32. The pathway for polypeptides exported from E. coli includes these steps, which occur in what order for correct export? 1. A chaperone, SecA, binds to the polypeptide. 2. A chaperone, SecB, binds to the polypeptide. 3. ATP is hydrolyzed by SecA. 4. SecA pushes 20 amino acids of the polypeptide into the translocation complex. a. 1, 2, 3, 4 b. 1, 2, 4, 3 c. 2, 1, 4, 3 d. 2, 3, 1, 4 e. 3, 1, 4, 2 33. Which process is involved in generating the different forms of the apoB gene product in the liver and intestines? a. only alternative 5′ splice site choice b. only alternative 3′ splice site choice c. deamination of cytosine d. deamination of adenine e. methylation of cytosine Copyright Macmillan Learning. Powered by Cognero.

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Chap 27_8e 34. What is an open reading frame (ORF)? a. DNA sequence that can be transcribed into five or more different mRNAs b. DNA sequence that contains no initiation codon c. stretch of at least 50 codons that does not contain a termination codon d. mRNA sequence that can be translated into more than one protein e. "junk" DNA that has no known function 35. Pyrophosphatase hydrolyzes pyrophosphate to phosphate. Which process is NOT accompanied by the activity of pyrophosphatase in E. coli? a. DNA replication b. transcription c. aminoacylation of tRNA d. All of these are accompanied by the activity of pyrophosphatase. 36. When inosine is in the first (wobble) position of an anticodon, how many different codons can be recognized? a. none b. one c. two d. three e. more than three 37. What happens in bacteria if an mRNA that has no stop codon is translated? a. A stop codon is not necessary; translation stops at the last codon and the mRNA and completed protein are released. b. The ribosome subunits dissociate and the mRNA and any partial protein synthesized are immediately degraded. c. Translation will not begin on an mRNA with no stop codon. d. A rescue system involving a tmRNA is employed to complete translation. 38. Which statement about aminoacyl-tRNA synthetases is false? a. Some of the enzymes have an editing/proofreading capability. b. The enzyme attaches an amino acid to the 3′ end of a tRNA. c. The enzyme splits ATP to AMP + PPi. d. The enzyme will use any tRNA species but is highly specific for a given amino acid. e. There is a different synthetase for every amino acid.

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Chap 27_8e 39. Nirenberg and Matthaei used synthetic mRNAs incubated with everything necessary for protein synthesis (ribosomes, GTP, ATP, amino acids, etc.). Poly(A) yielded polylysine, but poly(G) (polyguanylate) did not generate any polypeptide. Why was no protein generated with poly(G)? a. because GGG does not code for an amino acid b. because CCC is not a possible anticodon sequence c. because poly(G) forms tetraplexes that do not bind to the ribosome d. because ribosomes cannot bind to the sequence GGG e. None of these reasons explains why no peptide product is produced. 40. Which statement about the tRNA that normally accepts phenylalanine is false? (mRNA codons for phenylalanine are UUU and UUC.) a. It interacts specifically with the Phe synthetase. b. It will accept only the amino acid phenylalanine. c. The tRNA likely contains 73 to 93 nucleotides. d. Phenylalanine can be specifically attached to an —OH group at the 3′ end. e. The tRNA must contain the sequence UUU. 41. Which statement is false with respect to disruption of protein synthesis by puromycin? a. The antibiotic puromycin resembles the aminoacyl end of a charged tRNA. b. Puromycin binds to the ribosomal P site and causes premature dissociation of the peptide from the ribosome. c. Puromycin participates in peptide bond formation. d. Formation of peptidyl puromycin causes premature chain termination. e. Puromycin becomes covalently attached to the carboxyl-terminal end of the peptide being synthesized. 42. The enzyme that attaches an amino acid to a tRNA (aminoacyl-tRNA synthetase): a. always recognizes only one specific tRNA. b. attaches a specific amino acid to any available tRNA species. c. attaches the amino acid at the 5′ end of the tRNA. d. catalyzes formation of an ester bond. e. splits ATP to ADP + Pi. 43. Which statement is false regarding the EF-G in prokaryotic translation? a. EF-G can bind to the A site of the ribosome. b. EF-G is associated with the translocation step of translation. c. GTP is hydrolyzed while bound to EF-G. d. EF-G is structurally similar to the EF-Tu–tRNA complex. e. None of the statements is false.

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Chap 27_8e 44. Addition of O-linked glycosylation occurs predominantly in which cellular compartment? a. nucleus b. endoplasmic reticulum c. Golgi apparatus d. lysosomes e. endosomes 45. What signal is used to identify a protein for transport to the lysosome? a. phosphorylation of N-acetylglucosamine residues in the ER b. phosphorylation of glucose residues in the ER c. phosphorylation of mannose residues in the ER d. phosphorylation of glucose residues in the Golgi apparatus e. phosphorylation of mannose residues in the Golgi apparatus 46. Which statement is true about the genetic code? a. All codons recognized by a given tRNA encode different amino acids. b. There is wide variation in the genetic code among all organisms. c. Several different codons may encode the same amino acid. d. The base in the middle position of the tRNA anticodon sometimes permits wobble base pairing with two or three different codons. e. The first position of the tRNA anticodon is always adenosine. 47. During protein translocation to the ER: a. mRNA for ER-targeted protein is initially translated on ER-associated ribosomes. b. emergence of the carboxyl-terminal signal sequence is bound by the ribonucleoprotein, SRP. c. SRP binds to both the signal sequence and ribosome and halts translation. d. SRP binds to SRP receptor and tethers the mRNA-ribosome to the nucleus. e. the complex of SRP-SRP receptor/mRNA-ribosome migrates to the translocon, where signal peptidase cleavage facilitates SRP dissociation and translation continues. 48. Which statement is true about the sorting pathway for proteins destined for incorporation into lysosomes or the plasma membrane of eukaryotic cells? a. Binding of SRP to the signal sequence and the ribosome temporarily accelerates protein synthesis. b. The newly synthesized polypeptides include a signal sequence at their carboxyl termini. c. The signal sequence is cleaved off inside the mitochondria by signal peptidase. d. Sorting occurs primarily on the trans side of the Golgi complex. e. The signal sequence is added to the polypeptide in a posttranslational modification reaction.

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Chap 27_8e 49. Which statement is false about tRNA molecules? a. The 3′-terminal sequence is CCA. b. Their anticodons are complementary to the triplet codon in the mRNA. c. They contain more than four different bases. d. They contain several short regions of double helix. e. With the right enzyme, any given tRNA molecule will accept any of the 20 amino acids. 50. Bacterial ribosomes: a. bind tightly to specific regions of DNA, forming polysomes. b. contain at least one catalytic RNA molecule (ribozyme). c. contain three types of RNAs and five different proteins. d. have specific, different binding sites for each of the 20 tRNAs. e. require puromycin for normal function. 51. Ubiquitin-mediated protein degradation is a complex process, and many of the signals remain unknown. One known signal involves recognition of amino acids in a processed protein that are either stabilizing (Ala, Gly, Met, Ser, etc.) or destabilizing (Arg, Asp, Leu, Lys, Phe, etc.) and are located at _____ the protein. a. a helix-turn-helix motif in b. a lysine-containing target sequence in c. a zinc finger structure in d. the amino terminus of e. the carboxy terminus of 52. The Shine-Dalgarno sequence: a. is found to the 5′ side of the transcription initiation codon in mRNA. b. forms a parallel duplex with sequences in ribosomal RNA. c. is important in eukaryotic gene translation. d. is complementary to the initiator tRNA anticodon. e. is a nontranslated sequence after the stop codon in mRNA. 53. The process that attaches an amino acid to a tRNA: a. consumes the equivalent of at least two phosphate bonds. b. uses ATP to activate the carboxylate of the amino acid. c. has as a final product an ester linkage between an adenosine and the amino acid. d. All of the answers are correct.

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Chap 27_8e 54. Formation of the ribosomal initiation complex for bacterial protein synthesis does NOT require: a. EF-Tu. b. N-formylmethionyl-tRNAfMet. c. GTP. d. initiation factor 2 (IF2). e. mRNA. 55. It is possible to convert the Cys that is a part of Cys-tRNACys to Ala by a catalytic reduction. If the resulting Ala-tRNACys were added to a mixture of ribosomes, all the other tRNAs and amino acids, all of the cofactors and enzymes needed to make protein in vitro, and mRNA for hemoglobin, where in the newly synthesized hemoglobin would the Ala from Ala-tRNACys be incorporated? a. Nowhere; this is the equivalent of a nonsense mutation. b. Wherever Ala normally occurs. c. Wherever Cys normally occurs. d. Wherever either Ala or Cys normally occurs. e. Wherever the dipeptide Ala–Cys normally occurs. 56. Which statement does NOT accurately compare ER signal sequences and nuclear localization sequences? a. Nuclear localization sequences are not removed, while ER signal sequences usually are. b. Nuclear localization sequences may be located anywhere, while signal sequences are usually found at the amino terminus. c. Both nuclear localization sequences and signal sequences must contain multiple Asp and Glu residues. d. Nuclear localization sequences and ER signal sequences are both sites for protein-protein interactions. e. All these statements accurately describe these sequences. 57. Which enzyme, discovered by Stephen Ochoa, was used to make synthetic mRNAs that helped determine codon composition based on varying concentrations of nucleotides in experiments? a. RNA polymerase II b. reverse transcriptase c. RNA replicase d. polynucleotide phosphorylase e. DNA polymerase I

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Chap 27_8e 58. A certain bacterial mRNA is known to represent only one gene and to contain about 800 nucleotides. Assuming that the average amino acid residue contributes 110 Da to the peptide molecular weight, the largest polypeptide that this mRNA could code for would have a molecular weight (Da) of about: a. 800. b. 5,000. c. 30,000. d. 80,000. e. An upper limit cannot be determined from the data given. 59. Which amino acids are coded by a single codon? a. only methionine b. only isoleucine c. methionine and isoleucine d. methionine and tryptophan e. methionine, isoleucine, and tryptophan 60. Which statement is false about RNA editing? a. RNA editing occurs mostly in mitochondria and chloroplasts. b. RNA editing may use guide RNAs that have sequences complementary to the edited mRNA. c. Deamination of G is a common reaction in RNA editing. d. Deamination of A is common reaction in RNA editing. e. RNA editing allows for the synthesis of two different proteins from one gene. 61. Which step is NOT one of the five steps of protein synthesis? a. termination and complete proteolytic degradation of the ribosome b. elongation of the peptide chain c. initiation of peptide synthesis d. activation of the amino acids e. protein folding and posttranslational processing 62. Glycosylation of proteins inside the endoplasmic reticulum does NOT involve: a. translocation of a 50 residue core oligosaccharide into the lumen. b. an Asn residue on the protein. c. dolichol phosphate. d. retention of a pentasaccharide core. e. N-acetylglucosamine.

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Chap 27_8e 63. In eukaryotes, which molecule is covalently linked to proteins headed for degradation? a. mannose b. ubiquitin c. guanosine d. acetyl-CoA e. methionine 64. Which statement about ribosomes is true? a. The large subunit contains rRNA molecules; the small subunit does not. b. The RNA in ribosomes plays a structural, not catalytic, role. c. There are about 25 ribosomes in an E. coli cell. d. There are two major ribosomal subunits, each with multiple proteins and RNA. e. Ribosomes are relatively small, with molecular weights less than 10,000.

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Chap 27_8e 65. Beyond the start codon, a segment of the template strand of a double-stranded DNA contains the sequence (5′)-CTT TGA TAA GGA TAG CCC TTC-(3′). 5′ end ↓ U C A G U

UUU Phe UUC Phe UUA Leu UUG Leu CUU Leu CUC Leu CUA Leu CUG Leu AUU Ile AUC Ile AUA Ile AUG Met GUU Val GUC Val GUA Val GUG Val

UCU Ser UCC Ser UCA Ser UCG Ser CCU Pro CCC Pro CCA Pro CCG Pro ACU Thr ACC Thr ACA Thr ACG Thr GCU Ala GCC Ala GCA Ala GCG Ala

UAU Tyr UAC Tyr UAA Stop UAG Stop CAU His CAC His CAA Gln CAG Gln AAU Asn AAC Asn AAA Lys AAG Lys GAU Asp GAC Asp GAA Glu GAG Glu

UGU Cys UGC Cys UGA Stop UGG Trp CGU Arg CGC Arg CGA Arg CGG Arg AGU Ser AGC Ser AGA Arg AGG Arg GGU Gly GGC Gly GGA Gly GGG Gly

a. What is the base sequence of the mRNA that can be transcribed from this strand segment? b. What amino acid sequence could be coded by the mRNA base sequence in (a), using only the first reading frame starting at the 5′ end? c. Suppose the other (complementary) strand segment is used as a template for transcription. What is the amino acid sequence of the resulting peptide, again starting from the 5′ end and using only the first reading frame?

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Chap 27_8e 66. Indicate whether the statements are true (T) or false (F). ___ Assembly of a complete ribosome onto an mRNA requires ATP hydrolysis. ___ Aminoacylation, or "charging," of tRNA requires the formation of an aminoacyl-AMP intermediate. ___ Aminoacyl-tRNA binding to the A site of the ribosome requires the accessory factor EF-G and GTP hydrolysis. ___ Translocation of a growing polypeptide from the A to the P site on the ribosome requires EF-G and GTP hydrolysis. ___ Termination of translation requires release factors, but no NTP hydrolysis.

67. The codon for Trp is UGG, while UGA is a stop codon. Briefly explain why it would not be possible to have the reverse (UGG = stop, UGA = Trp).

68. The process of charging tRNAs with their proper amino acids involves multiple proofreading steps to increase the overall fidelity. Briefly describe these steps.

69. Regarding translation in eukaryotes versus that in prokaryotes (bacteria), indicate whether the statements are true (T) or false (F). ___ In eukaryotes, the 3′ end of the mRNA is associated with the 5′ end during initiation, whereas in prokaryotes it is not. ___ In prokaryotes, it is initiated at an AUG near a Shine-Dalgarno sequence in the mRNA, whereas in eukaryotes it is initiated at an AUG near the 3′ end of the mRNA. ___ In prokaryotes, it is initiated with Met, whereas in eukaryotes it is initiated with fMet. ___ In prokaryotes, translation and transcription are coupled, whereas in eukaryotes they are not.

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Chap 27_8e 70. When first synthesized, proinsulin has an additional leader or signal sequence at its amino terminus. This complete molecule is called preproinsulin and the signal sequence is cleaved off to give proinsulin. Briefly, what is the likely function of the signal sequence?

71. Val-tRNA synthetase will sometimes use threonine as a substrate to charge the tRNA but then rapidly remove the threonine. Propose a mechanism for this proofreading.

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Chap 27_8e 72. The sequence of four amino acids occurred in the structure of a polypeptide found in a wild-type organism: Leu–Ser–Ile–Arg. Several mutants were isolated, each of which carried a single base pair change in the region of DNA that coded for this amino acid sequence. Their corresponding amino acid sequences are: Mutant 1 Met–Ser–Ile–Arg 2 Leu–Trp–Ile–Arg 3 Leu–Ser–Arg–Arg 4 Leu–Ser–Ile–Pro 5 Leu–Ser–Ile–Trp What was the nucleotide sequence of the region of mRNA that coded for the amino acid sequence in the wildtype organism? 5′ end ↓ U C A G U UUU Phe UCU Ser UAU Tyr UGU Cys UUC Phe UCC Ser UAC Tyr UGC Cys UUA Leu UCA Ser UAA Stop UGA Stop UUG Leu UCG Ser UAG Stop UGG Trp C CUU Leu CCU Pro CAU His CGU Arg CUC Leu CCC Pro CAC His CGC Arg CUA Leu CCA Pro CAA Gln CGA Arg CUG Leu CCG Pro CAG Gln CGG Arg A AUU Ile ACU Thr AAU Asn AGU Ser AUC Ile ACC Thr AAC Asn AGC Ser AUA Ile ACA Thr AAA Lys AGA Arg AUG Met ACG Thr AAG Lys AGG Arg G GUU Val GCU Ala GAU Asp GGU Gly GUC Val GCC Ala GAC Asp GGC Gly GUA Val GCA Ala GAA Glu GGA Gly GUG Val GCG Ala GAG Glu GGG Gly

73. Describe the role of ubiquitin in mediating intracellular protein breakdown.

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Chap 27_8e 74. Following the synthesis of their polypeptide chain, many proteins require further posttranslational modifications before they attain their full biological activity or function. List and describe briefly at least four possible types of modification that can occur.

75. Consider the hypothetical short mRNA shown; where does translation begin, and what would be the sequence of the protein produced if this were translated in an E. coli cell? 5′-AUAGGAGGUUUGACCUAUGCCUCGUUUAUAGCC-3′ 5′ end ↓ U C A G U

UUU Phe UUC Phe UUA Leu UUG Leu CUU Leu CUC Leu CUA Leu CUG Leu AUU Ile AUC Ile AUA Ile AUG Met GUU Val GUC Val GUA Val GUG Val

UCU Ser UCC Ser UCA Ser UCG Ser CCU Pro CCC Pro CCA Pro CCG Pro ACU Thr ACC Thr ACA Thr ACG Thr GCU Ala GCC Ala GCA Ala GCG Ala

UAU Tyr UAC Tyr UAA Stop UAG Stop CAU His CAC His CAA Gln CAG Gln AAU Asn AAC Asn AAA Lys AAG Lys GAU Asp GAC Asp GAA Glu GAG Glu

UGU Cys UGC Cys UGA Stop UGG Trp CGU Arg CGC Arg CGA Arg CGG Arg AGU Ser AGC Ser AGA Arg AGG Arg GGU Gly GGC Gly GGA Gly GGG Gly

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Chap 27_8e 76. Indicate whether the statements are true (T) or false (F). ___ Bacterial mRNA is broken down within a few minutes of its formation in E. coli. ___ Bacterial mRNA consists only of the bases that code for amino acids. ___ Polysomes do not necessarily contain mRNA. ___ Bacterial mRNA normally occurs as a double-stranded structure, with one strand containing codons, the other containing anticodons. ___ Bacterial mRNA can be translated while it is still being synthesized.

77. What would be the consequence to the rate of polypeptide synthesis in bacteria if transcription of mRNA was in the 3′→5′ direction? What would happen if this occurred in eukaryotes?

78. A new antibiotic was recently discovered that inhibits prokaryotic protein synthesis. In the presence of the antibiotic, protein synthesis can be initiated, but only dipeptides that remain bound to the ribosome are formed. What specific step of protein synthesis is likely to be blocked by this antibiotic?

79. Describe the possible outcomes that could occur because of a single base change in an mRNA.

80. Describe the sequence of events between the transcription of an mRNA for a secreted protein and the arrival of that protein in the lumen of the endoplasmic reticulum.

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Chap 27_8e 81. What are the stages in targeting of nuclear proteins, and why are the targeting sequences not removed upon arrival of the protein in the nucleus?

82. Describe what would happen to bacterial protein synthesis if EF-Tu could recognize tRNAfMet.

83. Briefly describe the role of these components in bacterial protein synthesis. (a) initiation factor 2 (IF2) (b) 16S RNA (c) peptidyl transferase (d) release factors (e) elongation factor G (EF-G) (f) N10-formyltetrahydrofolate (g) ATP (h) tRNAfMet

84. Describe two ways in which synthetic polynucleotides were used in solving the genetic code (do not describe how the synthetic polynucleotides were made).

85. Explain how insertions and deletions were used to provide evidence that the genetic code was a triplet code.

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Chap 27_8e 86. In protein synthesis, 61 codons specify the 20 amino acids. Base pairing between the codon and the tRNA anticodon assures that the correct amino acid will be inserted into the nascent polypeptide chain. Why then does the cell require only 32 different tRNAs to recognize 61 different codons?

87. A given mRNA sequence might be translated in any of three reading frames. Describe how prokaryotes and eukaryotes determine the correct reading frame.

88. Match the factor or enzyme at the right with the stage(s) of protein synthesis at which it acts. If a factor or enzyme participates in two stages of protein synthesis, indicate both of them. ___ Amino acid activation (a) RF1 ___ Initiation (b) EF-Tu ___ Elongation (c) Aminoacyl-tRNA ___ Termination (d) Shine-Dalgarno sequence

89. Name three GTP binding factors that function in bacterial protein translation, and describe their function.

90. Isoleucine is coded by the triplets AUU, AUC, and AUA. If a single tRNA was used to code for isoleucine, what would be the sequence of the anticodon?

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Chap 27_8e 91. The ribosome does not have a comparable protease proofreading function like the exonuclease activity found in DNA polymerase. What aspects of protein synthesis at the ribosome present difficulties in accommodating a proofreading function?

92. Polypeptide chain elongation in E. coli occurs by the cyclical repetition of three steps. What are these steps and what cellular components are necessary for each of them to occur?

93. To carry out the Nirenberg and Ochoa experiments (mixing different nucleotide proportions with polynucleotide phosphorylase and using this RNA to synthesize peptides) using a 2:1 mixture of GTP and CTP, what would be found in terms of (a) amino acids incorporated and (b) their relative abundance? 5′ end ↓ U C A G U

UUU Phe UUC Phe UUA Leu UUG Leu CUU Leu CUC Leu CUA Leu CUG Leu AUU Ile AUC Ile AUA Ile AUG Met GUU Val GUC Val GUA Val GUG Val

UCU Ser UCC Ser UCA Ser UCG Ser CCU Pro CCC Pro CCA Pro CCG Pro ACU Thr ACC Thr ACA Thr ACG Thr GCU Ala GCC Ala GCA Ala GCG Ala

UAU Tyr UAC Tyr UAA Stop UAG Stop CAU His CAC His CAA Gln CAG Gln AAU Asn AAC Asn AAA Lys AAG Lys GAU Asp GAC Asp GAA Glu GAG Glu

UGU Cys UGC Cys UGA Stop UGG Trp CGU Arg CGC Arg CGA Arg CGG Arg AGU Ser AGC Ser AGA Arg AGG Arg GGU Gly GGC Gly GGA Gly GGG Gly

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Chap 27_8e 94. Indicate whether the statements are true (T) or false (F). ___ A ribosome is the complex within which protein synthesis occurs. ___ Ribosomes contain many separate proteins. ___ Ribosomes contain many different RNAs. ___ The three ribosomal RNAs in a bacterial ribosome are distributed in three separate, large ribosomal subunits. ___ The catalytic machinery of the ribosome is protein-based. ___ There are four binding sites for aminoacyl-tRNAs on a ribosome.

95. Number the steps in the proper order with regard to protein synthesis. ___ Aminoacyl-tRNA binds to the A site. ___ Deacylated tRNA is released from ribosome. ___ Peptide bond formation shifts the growing peptide from the P to the A site. ___ The 50S subunit binds to the initiation complex of the 30S subunit and mRNA.

96. The recognition of an amino acid by its cognate aminoacyl-tRNA synthetase is said to involve a second genetic code. What is meant by this?

97. A fragment of viral DNA is isolated that totally encodes at least two proteins, 120 and 80 amino acids long. The DNA fragment is 400 base pairs long. (a) Why might this be considered unusual? (b) After sequencing the two proteins, no sequence homology is found. Propose a model to account for these findings.

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Chap 27_8e Answer Key 1. d 2. c 3. c 4. d 5. c 6. d 7. c 8. e 9. d 10. c 11. a 12. a 13. a 14. e 15. a 16. b 17. b 18. c 19. a 20. b 21. b 22. b 23. d 24. a 25. e 26. d Copyright Macmillan Learning. Powered by Cognero.

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Chap 27_8e 27. b 28. a 29. c 30. a 31. d 32. d 33. c 34. c 35. d 36. d 37. d 38. d 39. c 40. e 41. b 42. d 43. e 44. c 45. e 46. c 47. c 48. d 49. e 50. b 51. d 52. a 53. d 54. a Copyright Macmillan Learning. Powered by Cognero.

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Chap 27_8e 55. c 56. c 57. d 58. c 59. d 60. c 61. a 62. a 63. b 64. d 65. (a) (5')GAA GGG CUA UCC UUA UCA AAG(3') (b) Glu–Gly–Leu–Ser–Leu–Ser–Lys (c) The codons translate to Leu–Stop–Stop. No peptide would be produced because of the stop codons. 66. F; T; F; T; T 67. In order to recognize the codon UGA, the anticodon for tRNATrp would have to be UCA, but the anticodon U is in a wobble position, so it would also recognize UGG (UGA recognizes UG (A/G)). Inosine in the first position of the anticodon (which could also recognize A in the third position of the codon) would recognize UG (A/U/C).

68. There are two main stages of selection: (1) The synthetase strongly favors activation of the correct amino acid to become aminoacyl-AMP (incorrect amino acids are very poorly activated), and (2) when the correct uncharged tRNA is bound to the enzyme, only the correct aminoacyl-AMP is tolerated in the proofreading active site (incorrect aminoacyl-AMPs, though they may become bound, are rapidly hydrolyzed). In addition, for most synthetases, if their tRNA does manage to become acylated by the wrong amino acid, that product is also rapidly hydrolyzed.

69. T; F; F; T 70. The leader peptide in proinsulin is a signal sequence directing it to the endoplasmic reticulum, from which it enters the Golgi complex and is packaged into a secretory vesicle for secretion by exocytosis.

71. Threonine and valine have the same size, but they differ in polarity (threonine has a hydroxyl group, valine is aliphatic). The addition of threonine means that the proofreading must select for the polarity of the threonine, through noncovalent hydrogenbonding interactions in the editing site that threonine will hydrogen bond but not valine. (As it turns out, it is an aspartate in the editing site that can form this interaction.)

72. (5')C or (5')U UG UCG AUA CGG

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Chap 27_8e 73. Ubiquitin, a protein found in all eukaryotic cells, is covalently joined to proteins targeted for degradation. The carboxyl-terminal residue of ubiquitin is first activated by the formation of a thioester with the first enzyme in the pathway in an ATP-dependent reaction. After displacement of the first enzyme by a second, also yielding a thioester link, ubiquitin is finally joined through its carboxyl terminus to a lysine e-amino group in the protein to be degraded. The presence of ubiquitin targets the protein for degradation by cellular proteases.

74. (1) Amino-terminal modification (N-acetylation or deacetylation), (2) removal of signal sequences used for targeting, (3) side-chain modification (phosphorylation, carboxylation, methylation, etc.), (4) attachment of N-linked (to Asn) or O-linked (to Ser or Thr) oligosaccharide moieties, (5) isoprenylation of Cys side chains, (6) incorporation of prosthetic groups (heme, biotin, etc.), (7) processing of proenzymes or zymogens, and (8) formation of disulfide crosslinks.

75. Begin translation at the start codon, AUG. Sequence: N–Met–Pro–Arg–Leu–C 76. T; F; F; F; T 77. Translation begins in prokaryotes before transcription is complete, so this would necessarily slow down translation, as it would be unable to initiate until after transcription was complete. In eukaryotes this would have less impact, as translation begins only after RNA processing and export of mRNA from the nucleus. 78. The antibiotic probably blocks translocation. 79. The most likely result is a single amino acid change in the encoded protein, when a codon is altered to one of another amino acid. However, some nucleotide changes will be "silent" and not change the protein if the altered codon still specifies the original amino acid. Conversion to a nonsense (stop) codon will result in a truncated polypeptide, while alteration of the normal stop codon to a "sense" codon will result in a lengthened protein. Alteration of the initiation codon may result in the total failure to translate, and result in no protein product. Changes in mRNA sequence outside the protein-coding region may affect translational efficiency, splicing, or mRNA turnover rates. 80. (1) The mRNA forms an initiation complex with a cytoplasmic ribosome and transcription begins. (2) The amino-terminal portion of the nascent chain, containing a signal sequence, binds to an SRP (signal recognition particle), interrupting polypeptide elongation. (3) The SRP-ribosome-nascent chain complex binds to the ribosome and SRP receptors on the cytosolic face of the ER; the SRP then dissociates. (4) Chain elongation continues, with the newly synthesized polypeptide crossing into the ER lumen as it grows. (5) The signal sequence is cleaved.

81. In the cytoplasm, where eukaryotic protein synthesis occurs, proteins carrying nuclear localization signal (NLS) sequences are bound by a complex of importin α and β, which is then bound to a nuclear pore. Ran GTPase mediates translocation of this complex into the nucleus, where importin β dissociates from importin α, and importin α releases the nuclear protein. Importin α and β are then exported from the nucleus, and available for another cycle of import. The nuclear envelope of higher eukaryotes breaks down at each cell division, distributing the nuclear contents throughout the cell. When the nuclear envelope is reestablished, NLS-carrying proteins can be reimported to fulfill their function. Thus, it is imperative that their targeting sequences are not removed. Also, unlike many other targeting sequences that are located at the N terminus of the protein, the NLS sequence can be found anywhere in the primary sequence of a protein.

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Chap 27_8e 82. Protein synthesis would be slowed; however, it would not form truncated proteins. When tRNAfMet is brought into the A site of the ribosome for an AUG codon, no peptide bond with the elongating protein chain could form because of the formyl group on the nitrogen of the Met. Thus, the "incorrect" EF-Tu–tRNAfMet complex would eventually dissociate and normal peptide elongation could continue. 83. (a) IF2 is a protein factor that, when bound to GTP, brings the fMet-tRNAfMet to the initiation complex. (b) 16S RNA is a component of the small (30S) subunit. It contains a sequence complementary to the Shine-Dalgarno sequence in the mRNA, and helps to line up the mRNA initiation AUG codon on the ribosome. (c) Peptidyl transferase is a ribozyme in the 50S ribosomal subunit. It catalyzes formation of each peptide bond as the ribosome moves along the mRNA. (d) Release factors are proteins that bring about the release of the finished polypeptide when the ribosome encounters a termination codon in the mRNA. (e) EF-G participates in the translocation of the ribosome down the mRNA by one codon after each peptide bond is formed. (f) N10formyltetrahydrofolate is the cofactor that donates a methyl group in the conversion of tRNA-bound Met to fMet. (g) ATP is the substrate for aminoacyl-tRNA synthetases; it donates an AMP residue in the formation of aminoacyl adenylate, which donates the aminoacyl group to tRNA. (h) tRNAfMet is the transfer RNA that initiates protein synthesis by inserting the first amino acid (fMet) in every prokaryotic protein.

84. (1) When synthetic polymers of only one nucleotide were used as mRNA in vitro, only one of the 20 amino acids was converted into protein. For example, poly(U) (containing only the codon UUU) directed the synthesis of polyphenylalanine, showing that UUU encodes Phe. (2) Trinucleotides of known sequence were used to stimulate aminoacyl-tRNA binding to ribosomes. Because only that aminoacyl-tRNA whose anticodon matched the trinucleotide "mRNA" was bound, the coding specificity of each sequence of three bases could be determined by determining which of the 20 aminoacyl-tRNAs bound. (3) Random polymers of RNA containing known ratios of nucleotides (e.g., 70% A and 30% T) generate only certain codons in predictable ratios. The identities and ratios of the amino acids specified by such polymers provided important clues that helped solve the genetic code. (4) Additional assignments were made possible using synthetic oligonucleotides containing repeats of specific two, three, or four base pair sequences. 85. When one or two nucleotides were added to or deleted from a gene, the resulting mRNA produced a protein with a different amino acid sequence after the deletion or insertion. When three nucleotides were added or deleted, the resulting protein had a normal sequence except for the insertion or deletion of a single amino acid residue.

86. Certain tRNAs have the unusual nucleotide inosinate in the first anticodon position. Because inosinate can base pair with A, U, or C, a tRNA containing inosinate can recognize three different codons. In each recognized codon, there is a standard anticodon-codon base pair with the first two bases of the codon; "wobble" in the third base pair allows one tRNA to read three different codons. Similarly, tRNAs with U or G in the first anticodon position also exhibit a wobble effect that permits pairing with two different codons. 87. In prokaryotes, the Shine-Dalgarno sequence in the mRNA base pairs with a complementary sequence in the 16S RNA of the ribosome; this positions the correct start codon (AUG) on the 30S ribosomal subunit. Thus, the initiating AUG is distinguished by its proximity to the Shine-Dalgarno sequence. In eukaryotes, the initiating AUG codon is the first AUG that the ribosome encounters as it scans the mRNA from its 5' end. In both cases, the initiating AUG also sets the correct reading frame.

88. c; d; b; a 89. IF2, an initiation factor that is involved in binding of the initiator tRNA; EF-Tu, the elongation factor associated with binding of aminoacyl-tRNA molecules into the A site; EF-G that is associated with translocation of the ribosome (and also termination). Copyright Macmillan Learning. Powered by Cognero.

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Chap 27_8e 90. The only possible anticodon sequence would be IAU, where inosine can wobble pair with U, C, and A. 91. There are several aspects one can consider. First, the addition of the "newest" amino acid connects the growing peptide chain to the tRNA bound in the P site. If hydrolyzed off this amino acid, the partial protein chain would release into solution. Second, the "energy" for peptide bond formation lies in the bond between the newest amino acid and the tRNA. If this is hydrolyzed, then formation of the next peptide bond is not energetically favored, even if the peptide chain did not dissociate. Finally, it is hard to imagine a proofreading mechanism for protein synthesis. There is no complementary strand to the newly synthesized peptide that can be used to compare whether the sequence is correct or incorrect. 92. The three steps: (1) An aminoacyl-tRNA is brought to the A site by EF-Tu with bound GTP; (2) peptidyl transferase (a ribozyme) catalyzes peptide bond formation; (3) the ribosome translocates three nucleotides down the mRNA, helped by EF-G (translocase). This shifts the peptidyl-tRNA to the A site and the deacylated tRNA to the E site, after which the tRNA is released.

93. Possible codons for G and C are outlined in the table with their relative abundance. Codon Amino acid Expected abundance (relative to Gly (GGG)) GGG Gly 100 GGC Gly 50 GCG Ala 50 CGG Arg 50 CCG Pro 25 CGC Arg 25 GCC Ala 25 CCC Pro 12.5 This means that overall the relative abundances of Gly–Ala–Arg–Pro would be 150–75–75–37.5 (or 4–2–2–1). 94. T; T; T; F; F; F 95. 2; 4; 3; 1 96. Each of the 20 amino acids has a unique synthetase, but many have multiple cognate tRNAs that must be charged (aminoacylated). The "second code" refers to features common to all tRNAs that carry the same amino acid, making them specifically recognizable by the correct synthetase. These features occur at different places in different tRNA classes, and may be as simple as a single G and U base pair, or require 10 or more specific nucleotides throughout the sequence. (See Fig. 27-21.) 97. (a) Two distinct proteins of these sizes should require mRNAs of 360 and 240 base pairs because each amino acid residue requires 3 base pairs to code for it. (b) No homology means that the smaller protein cannot be derived from the larger by proteolysis; if it were, there would be 80 amino acid residues of identical sequence in the two proteins. One possible explanation is that the two genes coding for these proteins overlap and are read in different reading frames.

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Chap 28_8e Indicate the answer choice that best completes the statement or answers the question. 1. The diagram represents a hypothetical operon in the bacterium E. coli. The operon consists of two structural genes (A and B), which code for the enzymes A-ase and B-ase, respectively, and also includes P (promoter) and O (operator) regions as shown. For this arrangement of an operon, which statement is true about mRNA synthesis? a. All four regions (A, B, O, and P) and will be transcribed into an mRNA that will then be translated into four different proteins. b. Gene B will never be transcribed from this operon. If B-ase is produced, it is from another site where B has its own promotor and operator. c. Gene B will be transcribed before gene A. d. An activator must bind to the O region before transcription can begin. e. When RNA polymerase makes mRNA from this operon, it begins RNA synthesis just to the left of gene A. 2. _____ is a DNA sequence. a. Coactivator b. Corepressor c. Enhancer d. Inducer e. Transactivator 3. An example of coordinate control is the downregulation of ribosomal RNA synthesis in response to amino acid starvation, which will cause synthesis of ribosomal proteins to be limited. What is the correct order of the events that participate in the signaling process? 1. Binding of stringent factor to the ribosome 2. Formation of the unusual nucleotide ppGpp 3. Formation of the unusual nucleotide pppGpp 4. Binding of uncharged tRNA in the ribosomal A site a. 1, 4, 2, 3 b. 1, 4, 3, 2 c. 4, 1, 2, 3 d. 4, 1, 3, 2 e. 4, 2, 1, 3

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Chap 28_8e 4. A regulon is a(n): a. group of related triplet codons. b. network of operons with a common regulator. c. operon that is subject to regulation. d. protein that regulates gene expression. e. ribosomal protein that regulates translation. 5. Promoters for heat-shock proteins in E. coli differ from the general consensus sequence. What is the effect of this difference? a. These genes are never transcribed at high levels. b. These genes are always transcribed at high levels. c. These genes are only expressed in high amounts when an appropriate σ subunit is present. d. These genes recognize multiple different σ subunits. e. These genes are always transcribed at high levels, and they also recognize multiple different σ subunits. 6. Which statement correctly describes promoters in E. coli? a. A promoter may be present on either side of a gene or in the middle of it. b. All promoters have the same sequence that is recognized by RNA polymerase holoenzyme. c. Every promoter has a different sequence, with little or no resemblance to other promoters. d. Many promoters are similar and resemble a consensus sequence, which has the highest affinity for RNA polymerase holoenzyme. e. Promoters are not essential for gene transcription, but can increase its rate by two- to threefold. 7. Which statement is true about the leader peptide in transcription attenuation for the trp operon? a. The leader peptide is translated, immediately after it is transcribed, by a ribosome that follows closely behind RNA polymerase as transcription proceeds. b. The leader peptide is an inducer for the trp operon. c. The leader peptide is transcribed from sequence 2 of the leader region of the operon. d. The leader peptide is over 100 amino acids long. e. All of these statements are true about the leader peptide. 8. The leader peptide shown is from an E. coli biosynthetic operon. Which amino acid is MOST likely associated with this operon? MKRISTTITTTITITTGNGAG a. tyrosine b. threonine c. glycine d. tryptophan e. None of the answers is correct.

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Chap 28_8e 9. Which term BEST describes the process of increasing mRNA production for a gene in response to a stimulus? a. feedforward activation b. transcriptional induction c. feedback inhibition d. attenuation e. constitutive gene expression 10. What is the functional complex that leads to proteolysis of LexA? a. RecA-dsDNA b. LexA-dsDNA c. RecA-ssDNA d. LexA-ssDNA e. LexA-RecA-ssDNA 11. Which class is expressed in the unfertilized egg and is involved in directing the spatial organization of the Drosophila embryo early in development? a. gap genes b. homeotic genes c. maternal genes d. segment polarity genes e. segmentation genes 12. What is the role of HMG proteins in eukaryotic gene regulation? a. They bind to promoter regions. b. They are architectural regulators. c. They bind to specific enhancer sites. d. They act as coactivators for RNA polymerase. e. They are one type of TATA-binding protein. 13. The binding of CRP (cAMP receptor protein of E. coli) to DNA in the lac operon: a. assists RNA polymerase binding to the lac promoter. b. is inhibited by a high level of cAMP. c. occurs in the lac repressor region. d. occurs only when glucose is present in the growth medium. e. prevents the repressor from binding to the lac operator.

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Chap 28_8e 14. Which statement about eukaryotic gene regulation is NOT correct? a. Access to eukaryotic promoters is restricted by the structure of chromatin. b. Most regulation is positive, involving activators rather than repressors. c. Larger and more multimeric proteins are involved in regulation of eukaryotic transcription. d. Transcription and translation are separated in both space and time. e. Strong promoters in eukaryotes are generally fully active in the absence of regulatory proteins. 15. Allolactose binding to the I gene product in the regulation of the lac operon is an example of: a. transcriptional activation by reducing repressor binding. b. transcriptional inhibition by increasing repressor binding. c. transcriptional activation by increasing activator binding. d. transcriptional inhibition by decreasing activator binding. e. architectural regulation. 16. What is the role of the FljA protein in S. typhimurium? a. It is a protein that is used to synthesize flagellin. b. It is involved in promoting recombination of flagellin genes. c. It is a protein that undergoes mutation in order to escape host immune response. d. It is a transcriptional repressor for the fliC gene. e. None of the answers is correct. 17. Allolactose is an important molecule in regulation of the lac operon. How does allolactose differ from lactose? a. Lactose contains galactose and glucose; allolactose contains two glucose units. b. Lactose is a reducing sugar, while allolactose is not. c. Lactose contains a β–glycosidic bond; allolactose contains an α–glycosidic bond. d. Lactose contains a 1→4 glycosidic bond; allolactose contains a 1→6 glycosidic bond. e. None of these statements describes differences between lactose and allolactose. 18. Which statement is true regarding the cAMP receptor protein (CRP)? a. This protein is only involved in activating transcription of the lac operon. b. A zinc finger structure on the protein binds to the DNA. c. This protein binds as a tetramer to its DNA. d. This protein bends and distorts the DNA structure when it binds. e. Binding of cAMP by CRP increases the value of Kd for the protein-DNA interaction.

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Chap 28_8e 19. Housekeeping genes in bacteria are commonly expressed constitutively, but not all of these genes are expressed at the same level (the same number of molecules per cell). The primary mechanism responsible for variations in the level of constitutive enzymes from different genes is that: a. all constitutive enzymes are synthesized at the same rate, but are not degraded equally. b. their promoters have different affinities for RNA polymerase holoenzyme. c. some constitutively expressed genes are more inducible than others. d. some constitutively expressed genes are more repressible than others. e. the same number of mRNA copies are made from each gene but are translated at different rates. 20. Which does NOT apply to the regulation of the GAL genes in S. cerevisiae? a. The promoters contain similar sequences and are regulated coordinately by a common set b. Many of the mRNA transcripts are polycistronic. c. Galactose binds to Gal3p which interacts with other elements to activate transcription of the GAL genes. d. When glucose is present, most of the GAL genes are repressed, even if galactose is present. e. All of these apply to the GAL gene system. 21. If binding of a small molecule to a regulatory protein lowers the Kd of the protein/operator-binding interaction, what can reasonably be stated? a. The small molecule activates transcription by decreasing inhibition by the protein. b. The small molecule inhibits transcription by increasing inhibition by the protein. c. The small molecule activates transcription by increasing activation by the protein. d. The small molecule inhibits transcription by decreasing activation by the protein. e. None of these statements is reasonable. 22. Which statement is false? a. Unipotent cells can develop into only one type of cell or tissue. b. Pluripotent cells can develop into a complete organism. c. Multipotent bone marrow cells can develop into different types of blood cells. d. Totipotent cells can develop into any kind of tissue. e. Totipotent, unipotent, multipotent, and pluripotent are all types of stem cells. 23. The three types of regulatory proteins that regulate transcription initiation by RNA polymerase are: a. effectors, specificity factors, and enhancers. b. activators, effectors, and repressors. c. effectors, enhancers, and repressors. d. specificity factors, repressors, and activators. e. enhancers, repressors, and activators.

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Chap 28_8e 24. Which effect is NOT expected from changing the sequence in the –10 region of an E. coli promoter for a protein-coding gene? a. decreased binding of σ subunits b. decreased transcription of the mRNA c. decreased binding of ribosomes to the mRNA d. lower concentrations of the protein product in the cell e. All of these effects would be expected. 25. What kinds of regulation exist for the lac operon in E. coli? a. negative regulation and transcription attenuation b. negative regulation and positive regulation c. positive regulation and transcription attenuation d. only negative regulation e. only transcription attenuation 26. Which statement is true about DNA binding by regulatory proteins? a. Regulatory and other DNA-binding proteins never bind to the minor groove. b. Palindromic DNA sequences are rarely sites for protein binding. c. Serine is the most common amino acid used by regulatory proteins to hydrogen bond to the base pairs of DNA. d. Regulatory proteins prefer to bind sections of DNA that are in the Z-DNA form. e. Currently it is not possible to predict the DNA sequence to which a protein will bind based on the protein structure. 27. GCN5 is a histone acetyltransferase from S. cerevisiae. Given this, what can reasonably be stated about GCN5? a. GCN5 functions as a monomer in vivo. b. GCN5 will convert euchromatin into heterochromatin. c. GCN5 will decrease the positive charges on histone substrates. d. GCN5 will have a single histone target. e. GCN5 could be described as a histone chaperone. 28. What is NOT a common feature found in steroid hormone receptors? a. DNA-binding region b. transcription activation region c. hormone-binding region d. zinc finger motifs e. leucine zipper motifs

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Chap 28_8e 29. Which mechanism is primarily used to regulate ribosomal protein operons? a. transcription attenuation b. translational feedback c. catabolite repression d. combinatorial control e. positive regulation 30. What is a role of the aptamer in riboswitches that regulate mRNA function in cis? a. to form tertiary RNA structures that bind to TPP b. to form a complex with the operator sequence c. to bind to the ribosome and inhibit its ribozyme activity d. to prevent ribosome binding to the Shine-Dalgarno sequence e. All of the answers are correct. 31. Which BEST describes the attenuator structure used in the trp operon attenuation mechanism in E. coli? a. A=T–rich cruciform structure b. G≡C–rich cruciform structure c. A=T–rich stem-and-loop structure d. G≡C–rich stem-and-loop structure e. None of the above describe the attenuator structure. 32. What statement is false regarding transcription attenuation of amino acid biosynthetic operons? a. The leader peptide will contain multiple instances of the amino acid produced by the operon. b. Transcription attenuation will always be accompanied by other positive or negative regulatory mechanisms. c. Transcription will be reduced under conditions where concentration of the amino acid produced by the operon is high. d. Synthesis of the leader peptide depends on the concentration of the aminoacylated tRNA, not the amino acid directly. e. All of these statements are true. 33. For the trp operon attenuation mechanism in E. coli, which pair of leader sequences comprise the attenuator and base pair with each other? a. sequences 1 and 2 b. sequences 2 and 3 c. sequences 3 and 4 d. sequences 1 and 3 e. sequences 2 and 4

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Chap 28_8e 34. In a zinc finger, to which four amino acids can the Zn2+ ion be coordinated? a. 2 His and 2 Met b. 4 His c. 2 Cys and 2 Met d. 1 Cys and 3 His e. 4 Cys 35. Which statement does NOT describe a reason why the major groove is more suited for sequence specificity interactions by DNA-binding proteins? a. The methyl group of T in the major groove can be recognized by a van der Waals pocket in a binding protein. b. The major groove is larger, allowing more space for protein side chains. c. The minor groove is negatively charged because of the crowding by phosphates. d. Hydrogen-bond donor and acceptor patterns are different in the major groove for different base pairs. e. Two major groove hydrogen-bonding patterns allow for better discrimination between base pairs compared to the minor groove. 36. Which do NOT interact with Mediator complex? a. high mobility group (HMP) proteins b. TATA-binding protein (TBP) c. CTD of RNA polymerase d. TFIIH e. modification and remodeling enzymes 37. Which is correct about operators and operons? a. An operator is a repressor binding site; an operon consists of the gene cluster, promotor, and regulatory sequences. b. An operator is a molecule that binds to an operon to facilitate binding of architectural regulators. c. An operon is a protein that binds to an operator sequence to repress transcription. d. An operon is a clustering of four or more operators. e. There is no difference; the terms are interchangeable (synonyms). 38. Which statement is false regarding the mediator protein in eukaryotic gene regulation? a. It contains multiple subunits. b. It is involved in the formation of complexes with multiple additional proteins. c. It forms protein-protein interactions with RNA polymerase II. d. It enhances dephosphorylation of the RNA polymerase carboxyl-terminal domain. e. It is required for transcription of multiple different mRNA species.

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Chap 28_8e 39. Which statement BEST describes the interaction of the helix-turn-helix motif with the DNA to which it binds? a. Only one of the helices contains amino acids that are positioned in or nearly in the major groove. b. Both helices wrap into the major groove to bind the DNA. c. The β turn contains the four amino acids that are responsible for binding the DNA. d. One helix binds tightly to the major groove and the second binds tightly to the minor groove. e. The helix-turn-helix motif only binds to A-DNA. 40. Which statement is true of the attenuation mechanism used to regulate the tryptophan biosynthetic operon in E. coli? a. Attenuation is the only mechanism used to regulate the trp operon. b. One of the enzymes in the Trp biosynthetic pathway binds to the mRNA and blocks translation when tryptophan levels are high. c. The leader peptide plays a direct role in causing RNA polymerase to attenuate transcription. d. Trp codons in the leader peptide gene allow the system to respond to tryptophan levels in the cell. e. When tryptophan levels are low, the trp operon transcripts are attenuated (halted) before the operon's structural genes are transcribed. 41. Protein amino acid side chains can hydrogen bond in the major groove of DNA and discriminate between each of the four possible base pairs. In which group of amino acids can all three members potentially be used in such DNA-protein recognition? a. Ala, Asn, Glu b. Arg, Gln, Leu c. Asn, Gln, Trp d. Asn, Glu, Lys e. Glu, Lys, Pro 42. Which statement about the transcription attenuation mechanism is true? a. In some operons (e.g., the his operon), attenuation may be the only regulatory mechanism. b. Sequences of the trp operon leader RNA resemble an operator. c. The leader peptide acts by a mechanism that is similar to that of a repressor protein. d. The leader peptide gene of the trp operon includes no Trp codons. e. The leader peptide is an enzyme that catalyzes transcription attenuation. 43. Which method is NOT a way of regulating the concentration of a protein in a cell? a. transcriptional regulation b. translational regulation c. degradation of proteins d. posttranslational modification of proteins e. All of these methods are ways of regulating protein concentrations.

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Chap 28_8e 44. Which type of eukaryotic regulatory proteins interacts with enhancers? a. basal transcription factors b. coactivators c. repressors d. TATA-binding proteins e. transcription activators 45. The DNA-binding motif for many prokaryotic regulatory proteins, such as the lac repressor, is: a. helix-turn-helix. b. homeobox. c. homeodomain. d. leucine zipper. e. zinc finger. 46. Which outcome will be true when E. coli is grown in the absence of glucose? a. The level of cyclic AMP will be low. b. The CRP (cAMP receptor protein) cannot bind to its target DNA. c. If lactose is present, synthesis of lac operon mRNA will occur at a high level. d. A repressor is activated by cyclic AMP and will prevent the binding of RNA polymerase to the lac operon promoter. e. None of the statements is true. 47. What is the primary conclusion of "domain-swapping" experiments with transcriptional regulatory proteins? a. Formation of homo- and heterodimers provide combinatorial control of gene expression. b. Multiple protein-protein interactions are required to make transcription occur. c. Enhancer elements are separate from the promoter site. d. Zinc fingers are separate domains involved in DNA binding. e. DNA-binding elements and protein-protein interaction regions are often found in separate parts of a protein. 48. Which statement is false regarding riboswitches? a. Small RNAs can disrupt local hairpins that prevent ribosome binding. b. Riboswitches are natural aptamers found in prokaryotes and some eukaryotes. c. Riboswitches are often found at the 5' end of an untranslated region of genes. d. Each riboswitch can bind an assortment of small metabolites. e. Riboswitches can affect either transcription or translation.

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Chap 28_8e 49. Which class of genes is involved in specifying the localization of organs in the Drosophila embryo? a. gap genes b. homeotic genes c. maternal genes d. segment polarity genes e. segmentation genes 50. What statement is false regarding the molecule ppGpp? a. This molecule is a bacterial second messenger. b. This molecule is produced in response to low concentrations of amino acids. c. This molecule acts as an inhibitor of RNA polymerase. d. This molecule is produced directly from GTP and ATP. e. This molecule will reduce the synthesis of rRNA. 51. Attenuation in the trp operon of E. coli: a. can adjust transcription of the structural genes upward when tryptophan is present. b. can fine-tune the transcription of the operon in response to small changes in Trp availability. c. is a mechanism for inhibiting translation of existing (complete) trp mRNAs. d. results from the binding of the Trp repressor to the operator. e. results from the presence of short leader peptides at the 5' end of each structural gene. 52. The diagram represents a hypothetical operon in the bacterium E. coli. The operon consists of two structural genes (A and B) that code for the enzymes A-ase and B-ase, respectively, and also includes P (promoter) and O (operator) regions as shown. When a certain compound (X) is added to the growth medium of E. coli, the separate enzymes A-ase and Base are both synthesized at a 50-fold higher rate than in the absence of X (which has a molecular weight of about 200). Which statement is true of such an operon? a. Adding X to the growth medium causes a repressor protein to be released from the O region. b. Adding X to the growth medium causes a repressor protein to bind tightly to the O region. c. Synthesis of the mRNA from this operon is not changed by the addition of compound X. d. X must be an activator that binds at the operator. e. Adding X causes an activator to be released from the promotor. 53. Which factor is NOT associated with translational regulation? a. attenuation in the trp operon b. ribosomal protein/mRNA interactions c. riboswitches d. OxyS interaction with rpoS e. All of these are examples of translational regulation. Copyright Macmillan Learning. Powered by Cognero.

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Chap 28_8e 54. Small signal molecules that regulate transcription are NOT known to _____ DNA sites. a. cause activator proteins to bind b. cause repressor proteins to bind c. directly bind to d. prevent activator proteins from binding to e. release repressor proteins from 55. Which statement about eukaryotic gene regulation is correct? a. Large polycistronic transcripts are common. b. Most regulation is positive, involving activators rather than repressors. c. Eukaryotic regulatory proteins are similar in complexity and size to prokaryotic ones. d. Transcription does not involve promoters. e. Transcription occurs without major changes in chromosomal organization. 56. RecA protein provides the functional link between DNA damage and the SOS response by displacing the LexA protein from its operator sites on the SOS genes. RecA does so by: a. associating with polymerase holoenzyme to help it remove LexA from operator. b. binding LexA operator DNA to force dissociation of LexA repressor. c. binding to LexA protein to weaken directly its affinity for operator sites. d. enabling the self-cleavage of LexA, thus inactivating its binding to operator. e. competitively binding to LexA operators and serving as an activator. 57. Which statement is false about the SOS response in bacteria? a. It involves nearly 60 genes that constitute the SOS regulon. b. RecA protein and the LexA repressor are the key regulatory proteins for the SOS response. c. There is a single inducer that binds to LexA and removes it from the many genes it represses. d. LexA inhibits transcription of all SOS response genes. e. After a successful SOS response, replenishment of LexA requires a considerable energy cost in terms of ATP and GTP. 58. What kinds of regulation exist for the trp operon in E. coli? a. negative regulation and transcription attenuation b. negative regulation and positive regulation c. positive regulation and transcription attenuation d. only negative regulation e. only transcription attenuation

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Chap 28_8e 59. Which does NOT contribute to the activation of transcription in eukaryotes? a. SWI/SNF chromatin remodeling proteins b. histone acetyltransferases c. histone methylases d. histone deacetylases e. subunit exchange to introduce histone variants 60. Gene silencing by RNA interference acts by _____ of the target gene. a. only inhibiting transcription b. only inhibiting translation c. only inhibiting splicing d. degradation of the mRNA or translation inhibition e. only inhibiting polyadenylation 61. Transcription of the lactose (lac) operon in E. coli is stimulated by: a. a mutation in the repressor gene that strengthens the affinity of the repressor for the operator. b. a mutation in the repressor gene that weakens the affinity of the repressor for the operator. c. a mutation in the repressor gene that weakens the affinity of the repressor for the inducer. d. binding of the repressor to the operator. e. the presence of glucose in the growth medium. 62. Which statement about regulation of the lac operon is true? a. Glucose in the growth medium decreases the inducibility by lactose. b. Glucose in the growth medium does not affect the inducibility by lactose. c. Glucose in the growth medium increases the inducibility by lactose. d. Its expression is regulated mainly at the level of translation. e. The lac operon is fully induced whenever lactose is present. 63. When tryptophan binds to the Trp repressor, what is the effect on the repressor-operator interaction? a. The Kd for the repressor-operator complex increases, lowering affinity. b. The Kd for the repressor-operator complex decreases, increasing affinity. c. The Kd for the repressor-operator complex increases, increasing affinity. d. The Kd for the repressor-operator complex decreases, lowering affinity. e. There is no change in Kd .

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Chap 28_8e 64. In a regulatory protein with a leucine zipper motif, which statement is false? a. They contain helices with a leucine at every seventh position. b. Two α helices form a coiled coil. c. Hydrophobic surfaces are in contact in the dimer. d. The leucine zipper region is the DNA-binding region. e. These proteins contain DNA-binding, connector, and leucine zipper regions. 65. In the development of the fly Drosophila, homeotic genes: a. are transcribed during egg production; their mRNAs lie dormant in the egg until it is fertilized. b. determine the number of body segments that will form. c. are expressed late and determine the detailed structure within each body segment. d. generally have no introns. e. are not translated into proteins. 66. Which factor is NOT involved in steroid hormone action? a. plasma membrane receptors b. hormone-receptor complexes c. hormone response elements (HREs) d. transcription activation and repression e. zinc fingers 67. Which normally binds to the operator region? a. attenuators b. inducers c. mRNAs d. repressors e. suppressor tRNAs 68. Consider the lac operon of E. coli. When there is neither glucose nor lactose in the growth medium: a. CRP protein binds to the lac operator. b. CRP protein displaces the Lac repressor from the lac promoter. c. the repressor is bound to the lac operator. d. RNA polymerase binds the lac promoter and transcribes the lac operon. e. the operon is fully induced.

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Chap 28_8e 69. The tryptophan operon of E. coli is repressed by tryptophan added to the growth medium. The tryptophan repressor probably: a. binds to RNA polymerase when tryptophan is present. b. binds to the trp operator in the absence of tryptophan. c. binds to the trp operator in the presence of tryptophan. d. is a DNA sequence. e. is an attenuator. 70. Describe briefly the process by which steroid hormones affect gene expression.

71. What are three mechanisms of translational repression that are known to exist in eukaryotes?

72. Northern blotting is a technique used to detect RNA content. When analyzing transcriptional regulation with Northern blots, the RNA of housekeeping genes is typically examined in parallel with the gene of interest. Why would this be important?

73. Describe briefly the general role of the protein products of each type of gene in the embryonic development of the Drosophila: (a) maternal genes; (b) segmentation genes; (c) homeotic genes.

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Chap 28_8e 74. Match each of the operons with the type(s) of regulation present in that operon. Note that a given type can be used more than once, or not at all; also, a given operon may have more than one type of regulation. Operon Type or Regulation a. lac 1. Activation b. trp 2. Repression c. SOS 3. Attenuation 4. DNA rearrangement

75. Define in one to two sentences (a) heterochromatin; (b) euchromatin; (c) chromatin remodeling.

76. Name and contrast the four different types of stem cells found in humans.

77. In some prokaryotes, some riboswitches act as transcriptional terminators, and they have similarities to ρ– independent termination. Predict what structural/sequence features would be found in these riboswitches.

78. Describe in one or two sentences the role of the proteins in the regulation of gene expression in eukaryotes: (a) basal transcription factors; (b) transcription activators; (c) coactivators.

79. "A protein with a gene that is actively being transcribed will be present in high concentrations." Why is this statement not accurate?

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Chap 28_8e 80. In E. coli, lactose (allolactose) and tryptophan both bind to repressor proteins as part of regulation of the lac and trp operons, respectively. Outline two differences between the behavior of these compounds and their associated repressor proteins, and describe their effect on the transcription of their associated operons. Why do these differences make physiological sense?

81. Draw a simple map of the lactose operon indicating the relative positions of promoter, operator, CRP-binding site, repressor gene (I), and the structural genes of the operon (A, Y, Z). Indicate where the CRP protein binds within this operon. When it is bound to this site, does the CRP protein have a positive or negative effect on gene expression in this system?

82. Define operon and polycistronic mRNA.

83. Briefly describe the main structural features in the DNA-binding and activation domains for Gal4p, Sp1, and CTF1.

84. Explain how synthesis of ribosomal proteins in E. coli is regulated at the level of translation.

85. Briefly explain (a) why there is a lag in cell growth when bacteria are switched from a medium containing glucose to one containing lactose. (b) When the growth medium contains both lactose and glucose, what proteins will be bound to the lac operon regulatory region? (c) If only lactose is in the growth medium, what proteins will be bound to the lac operon regulatory region?

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Chap 28_8e 86. Match the molecule with its role in the lac operon. Note that a given molecule may have more than one role. Molecule Function a. Galactose 1. Substrate of β–galactosidase enzyme b. Glucose 2. Product of β–galactosidase enzyme c. IPTG 3. Inducer of lac operon d. Lactose

87. The SOS response in E. coli is triggered by extensive damage to the cell's DNA and increases the capacity for repairing such DNA. What molecular events bring about expression of the SOS genes?

88. E. coli cells are placed in a growth medium containing lactose. Indicate how these circumstances would affect (increase/decrease/no change) the expression of the lactose operon. a. Addition of high levels of glucose b. A Lac repressor mutation that prevents dissociation of Lac repressor from the operator c. A mutation that inactivates β–galactosidase d. A mutation that inactivates galactoside permease e. A mutation that prevents binding of CRP to its binding site near the lac promoter

89. High mobility group (HMG) proteins are named because they migrate rapidly in electrophoresis experiments relative to other DNA-binding proteins (particularly histones). What does this reveal about their amino acid composition?

90. The operators in the lac operon include two 6 base-pair sequences that are palindromes separated by approximately nine residues. What is the significance of that in terms of binding of the repressor protein?

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Chap 28_8e 91. Large numbers of microRNAs (miRNAs), also known as small temporal RNAs (stRNAs), have now been discovered in higher eukaryotes. Describe their characteristics and general function.

92. Describe briefly the relationship between chromatin structure and transcription in eukaryotes.

93. Describe and contrast positive regulation and negative regulation of gene expression.

94. In prokaryotes such as E. coli, many operons that encode enzymes involved in amino acid biosynthesis begin with a sequence coding for a leader peptide. This peptide has no known enzymatic function and is rich in the amino acid that is synthesized by the enzymes encoded in the operon. What is the function of this leader peptide?

95. Describe three different mechanisms by which riboswitches can modulate mRNA.

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Chap 28_8e 96. Match the protein or structural feature on the left with one appropriate description on the right. ____ Activator (a) A positive regulator ____ Helix-turn-helix (b) A negative regulator ____ Leucine zipper (c) Facilitates transcription only when bound to a signal ____ Repressor molecule ____ Zinc finger (d) A DNA-binding structural motif found in many prokaryotic regulatory proteins (e) A structural feature involved in protein-protein interactions between some regulatory protein monomers (f) A protein that dissociates from DNA when bound to a signal molecule (g) A DNA-binding or RNA-binding structural motif found in many eukaryotic and some bacterial regulatory proteins

97. The lac operon includes the open reading frame for the permease (lacY) that is necessary for lactose import. How then does lactose get into the cell to activate transcription of the lac operon?

98. Usually, a mutation in the promoter region of an operon causes reduced levels of synthesis of the proteins encoded by that operon. Occasionally, a mutation in the promoter region actually causes increased levels of synthesis. Suggest a plausible explanation.

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Chap 28_8e Answer Key 1. e 2. c 3. d 4. b 5. c 6. d 7. a 8. b 9. b 10. e 11. c 12. b 13. a 14. e 15. a 16. d 17. d 18. d 19. b 20. b 21. b 22. b 23. d 24. c 25. b 26. e Copyright Macmillan Learning. Powered by Cognero.

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Chap 28_8e 27. c 28. e 29. b 30. a 31. d 32. b 33. c 34. e 35. c 36. a 37. a 38. d 39. a 40. d 41. d 42. a 43. e 44. e 45. a 46. c 47. e 48. d 49. b 50. d 51. b 52. a 53. a 54. c Copyright Macmillan Learning. Powered by Cognero.

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Chap 28_8e 55. b 56. d 57. c 58. a 59. d 60. d 61. b 62. a 63. b 64. d 65. c 66. a 67. d 68. c 69. c 70. Steroid hormones usually enter a cell by diffusion and then bind to a nuclear receptor protein. The binding changes the conformation of the receptor protein such that the hormone-receptor complex can bind to specific DNA sequences (hormone response elements). This binding can either activate or repress the expression of adjacent genes. 71. (a) Inactivation of initiation factors usually by phosphorylation; (b) binding of repressor proteins to the mRNA, thereby interfering with initiation factors or the ribosome; (c) interference with elongation by the binding of proteins to elongation factors; (d) RNA-mediated regulation of gene expression. 72. Since housekeeping genes are expressed constitutively, their RNA concentration should not vary. In this way, these genes act as internal controls for RNA content. 73. (a) A maternal gene in Drosophila is a gene that is expressed in the unfertilized egg (see Fig. 28-39). These genes are involved in directing the spatial organization of the Drosophila embryo early in development. (b) Segmentation genes direct the formation of the correct number of body segments, and include the gap genes, pair-rule genes, and segment polarity genes as subclasses. (c) Homeotic genes help specific localization of organs and appendages in the segments of the embryo. They regulate their target genes by highly conserved DNA-binding homeodomains, depicted in Figure 28-13. 74. (a) 1, 2; (b) 2, 3; (c) 2

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Chap 28_8e 75. (a) Heterochromatin is highly condensed chromatin that is transcriptionally inactive, often associated with structures such as centromeres. (b) Euchromatin is most of the chromatin, not nearly as highly condensed as heterochromatin, and able to be activated for transcription. (c) Chromatin remodeling reflects structural changes resulting from enzymes that covalently modify the core histone complex in nucleosomes (such as histone acetyltransferases) and those that move or displace nucleosomes using the energy of ATP hydrolysis. 76. Totipotent stem cells are present in the first few cell divisions after oocyte fertilization and they have the capacity to differentiate into any tissue or a complete organism. Pluripotent stem cells, found in developing embryo, can differentiate into many different types of tissue but can no longer generate a complete organism. Multipotent stem cells, found in the adult organism, have even more limited ability to differentiate into other cells or tissue types. Unipotent stem cells can develop only into one type of tissue. 77. The terminator form of these riboswitches will need to form a hairpin loop (complementary stretches of nucleotides) followed by a stretch of U residues in the transcript upstream of the coding region of the transcript. This form will only form when the aptamer is in the correct conformation (e.g., when a small molecule is bound), and this will trigger termination of transcription by RNA polymerase. (Also see Chapter 26.) 78. (a) Basal transcription factors interact with specific DNA sequences and/or each other and/or with RNA polymerase to form a complex at promoters. (b) Transcription activators interact with both target sites on DNA and with other regulatory proteins such as coactivators to activate transcription. (c) Coactivators interact with transcription activators and proteins at the promoters to activate transcription. 79. Protein concentration does not exclusively depend on the rate of transcription. It will also depend on the stability of the RNA, the rate of translation, the rate of protein processing (e.g., posttranslational modifications), and the rate of protein degradation. 80. The lactose repressor binds to its operator to reduce expression when allolactose is not bound. Binding of allolactose reduces the affinity of the repressor, which causes it to dissociate (leading to transcriptional activation). The Trp repressor does not bind to its operator when Trp is not bound; instead it binds to the operator when Trp concentration is high, suppressing transcription. Functionally, the difference is between one substance being a substrate for an enzyme (and acting as activator, analogous to feedforward activation) or the product of an enzyme (analogous to feedback inhibition). 81. Bound CRP stimulates (has a positive effect on) transcription of this operon. (See Figs 28-8, 28-18.) 82. An operon is several contiguous structural genes that are coordinately regulated by promoter and operator regions, as depicted in Figure 28-6. All of the genes in an operon are transcribed in a polycistronic mRNA. That is, a single mRNA molecule encoding more than one structural gene. Note: Operons are not found in eukaryotic organisms. 83. (1) Gal4p (in yeast) has a zinc fingerlike DNA-binding domain. The activation domain is rich in acidic amino acids, (2) Sp1 has three zinc fingers in its DNA-binding domain and has two activation domains comprised of about 25% glutamine, and (3) CTF1 has a DNA-binding region rich in basic amino acids and likely arranged in an α helix. CTF1 has a proline-rich (>20%) activation domain. 84. Ribosomal proteins are encoded in several operons. One protein encoded in each operon, when not part of an assembled ribosome, binds tightly to that operon's mRNA, preventing its translation. Thus, when an excess of that protein is present, it slows its own translation. (See Fig. 28-22.) Copyright Macmillan Learning. Powered by Cognero.

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Chap 28_8e 85. (a) The lag represents the time required for lactose to enter the cell, be converted into the inducer allolactose, and turn on the synthesis of the genes of the lac operon that are essential for growth on lactose. (b) When both glucose and lactose are present, neither Lac repressor nor CRP will be bound. (c) If only lactose is present, CRP will be bound. (See Fig. 28-18.) 86. (a) 2; (b) 2; (c) 3; (d) 1, 3 87. The SOS genes are located in several operons, all under the regulation of the LexA repressor, which normally represses these operons. When DNA is damaged extensively, RecA protein binds to single-stranded DNA at the damaged sites, and bound RecA activates specific proteolysis of the LexA protein, relieving the repression of the SOS operons. (See Fig. 28-21.) 88. (a) decrease; (b) decrease; (c) decrease (this enzyme converts lactose into allolactose, the inducer); (d) decrease (because external lactose would not enter the cell, and allolactose would not be present to induce the operon); (e) decrease 89. Positively charged amino acids are typically abundant in DNA-binding proteins like histones, and they will tend to slow down protein migration in electrophoresis experiments. HMG proteins are abundant in both positively and negatively charged amino acids, and they often have pI values in pH ranges below 7.0, making them migrate more rapidly. The positively charged amino acids are necessary for complementary protein-DNA ionic interactions. 90. The repressor protein binds as a dimer to each operator. This is often achieved through the binding to palindromes (both end up with a twofold symmetry), and the palindromic portions are part of the protein-DNA interaction. Separating each of these two binding sites by nine residues means that they will be found roughly on the same side of the DNA duplex to allow for both the protein-DNA and protein-protein interactions necessary for dimer binding. 91. Their primary transcripts are about 70 nucleotides, with self-complementary internal sequences that can form hairpin structures. These are cleaved into short duplexes of 20 to 25 nucleotides. One strand is transferred to and binds the target mRNA. This can then inhibit gene expression by blocking translation of the target mRNA or facilitating its degradation. 92. Heterochromatin is highly condensed and transcriptionally inert because the chromatin proteins make promoters inaccessible. The less condensed euchromatin has undergone alteration of its structure ("remodeling"), allowing some regions to be transcribed. These alterations include covalent modification (such as acetylation) of histones and displacement of nucleosomes, creating exposed regions of DNA (hypersensitive sites) that are probably binding sites for regulatory proteins. 93. Positive regulation involves an activator protein that, when bound in the vicinity of the regulated gene, facilitates the binding of RNA polymerase to its promoter. The affinity of the activator for the DNA may be either increased or decreased by a signal molecule. Negative regulation involves a repressor protein that, when bound near the regulated gene, hinders access of RNA polymerase to its promoter or inhibits its activity. Repressor affinity for its binding site (the operator) may be increased or decreased by a signal molecule. (See Fig. 28-4.)

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Chap 28_8e 94. The leader peptide is integral to the regulatory mechanism called transcription attenuation. In prokaryotes, transcription and translation are closely coupled. The ability to translate the leader peptide signals that the relevant amino acid is readily available in the cell and that transcription of the operon is undesirable at this time. Translation through the leader peptide (when the amino acid is abundant) allows the formation of a hairpin attenuator structure downstream in the nascent RNA chain. This attenuator acts as a transcription terminator, causing dissociation of the RNA polymerase. When the relevant amino acid is in short supply, the ribosome stalls trying to synthesize the leader peptide. A different secondary structure forms in the nascent RNA, preventing formation of the terminator and allowing continued transcription of the operon. (See Fig. 28-20.) 95. Upon binding an effector, riboswitches can (1) stabilize a terminator structure, (2) block the ribosomal binding site, or (3) regulate intron splicing. (See Fig. 28-25.) 96. a; d; e; b; g 97. The transcription of the lac operon is never completely eliminated, and some basal transcription occurs. This means that there is sufficient permease present to allow for the initial import of lactose, which can then trigger further synthesis of the permease (allowing for increased import). 98. It is possible for a mutation to result in a promoter with above normal affinity for RNA polymerase (i.e., a promoter that more closely matches the promoter consensus sequence), resulting in increased expression in the mutant of the genes in this operon.

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