Test Bank for Fundamentals of Biochemistry Life at the Molecular Level, 5th Edition by Donald Voet, by ACADEMIAMILL

Chapter 1: Introduction to the Chemistry of Life Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N

phylogenetic negative H2 O DH° H – TS halobacteria open entropy flux polymers DG°¢ thermophiles nitrogen positive

1. The most abundant molecule in the human body is _____. Ans: C Level of Difficulty: Easy Section: 1.1.A Learning objective: The Origin of Life 2. During chemical evolution, small organic molecules condense to form more complex molecules called ______. Ans: J Level of Difficulty: Easy Section: 1.1.B Learning objective: The Origin of Life 3. Evolutionary relationships can be visualized using a ______ tree. Ans: A Level of Difficulty: Easy Section: 1.2.C Learning objective: Cellular Architecture

4. The organisms most likely to be found in a brine environment would be ______. Ans: F Level of Difficulty: Easy Section: 1.2.C Learning objective: Cellular Architecture 5. The organisms most likely to be found in high temperature environments would be ______. Ans: L Level of Difficulty: Easy Section: 1.2.C Learning objective: Cellular Architecture 6. The term used to indicate the degree of randomness within a system is ______. Ans: H Level of Difficulty: Easy Section: 1.3.B Learning objective: Thermodynamics 7. Spontaneous processes are characterized by a change in Gibbs free energy that is ______. Ans: B Level of Difficulty: Easy Section: 1.3.B Learning objective: Thermodynamics 8. Gibbs free energy is defined as G = ______. Ans: E Level of Difficulty: Easy Section: 1.3.C Learning objective: Thermodynamics 9. The symbol for free energy under standard biochemical conditions is ______. Ans: K Level of Difficulty: Easy Section: 1.3.C Learning objective: Thermodynamics

10. Living creatures can be described thermodynamically as ______ systems. Ans: G Level of Difficulty: Easy Section: 1.3.E Learning objective: Thermodynamics

Multiple Choice 11. What are the four most abundant elements in a human body? A) C, N, O, H B) C, N, O, P C) C, S, O, H D) C, Na, O, H E) none of the above Ans: A Level of Difficulty: Moderate Section: 1.1.A Learning objective: The Origin of Life 12. The atmosphere of prebiotic earth probably contained the following molecules: A) H2O, CO2, N2 , CH4, and NH3. B) H2O, CO2, CH4, C6H12O6, and NH3. C) H2O, CO2, CH4, C6H12O6, and COO-CH2NH+3. D) H2O, CO2, CH4, COOHCH2NH3, and NH3. E) none of the above Ans: A Level of Difficulty: Easy Section: 1.1.A Learning objective: The Origin of Life

13. In 1953, Urey and Miller carried out an experiment in which they subjected a mixture of H2O, CH4, NH3, and H2 to electrical discharges. Which of the following were among the products? A) proteins B) amino acids C) nucleic acids D) ribosomes E) all of the above Ans: B Level of Difficulty: Easy Section: 1.1.A Learning objective: The Origin of Life 14. Which of the following statements about hydrothermal vents is true? A) The vents have temperatures as high as 800°C and emit H2S and metal sulfides. B) The vents have temperatures as high as 600°C and emit H2S and metal nitrates. C) The vents have temperatures as high as 400°C and emit H2S and metal sulfides. D) none of the above E) all of the above Ans: C Level of Difficulty: Moderate Section: 1.1.A Learning objective: The Origin of Life

For questions 15-18, consider the structure of the coenzyme NADP

O NH 2

O O

H O

NH2

O N

O H

E O

15. Which arrow points at a phosphate ester bond? A) A B) B C) C D) D E) E Ans: E Level of Difficulty: Easy Section: 1.1.B Learning objective: The Origin of Life

16. Which arrow points at an amide bond? A) A B) B C) C D) D E) E Ans: B Level of Difficulty: Easy Section: 1.1.B Learning objective: The Origin of Life 17. Which arrow points at an anhydride bond? A) A B) B C) C D) D E) E Ans: A Level of Difficulty: Moderate Section: 1.1.B Learning objective: The Origin of Life 18. Which arrow points at a glycosidic bond? A) A B) B C) C D) D E) E Ans: D Level of Difficulty: Moderate Section: 1.1.B Learning objective: The Origin of Life

19. Which of the following developed during the evolution of eukaryotic cells from prokaryotic cells? A) DNA B) the cell membrane C) nuclear membranes D) ribosomes E) proteins Ans: C Level of Difficulty: Easy Section: 1.2.C Learning objective: Cellular Architecture 20. Using phylogeny all living organisms can be divided into the following domains: A) bacteria, eukarya, and vertebrate B) archaea and eukarya C) bacteria, eukarya, and archaea D) eukarya and bacteria E) none of the above Ans: C Level of Difficulty: Moderate Section: 1.2.C Learning objective: Cellular Architecture 21. The theory of evolution includes which of the following principles? A) Evolution is not directed toward a specific goal. B) Evolution is ongoing, and is constrained by its past. C) Evolution requires some sloppiness for adaptation to changes. D) A and B E) A, B, and C Ans: E Level of Difficulty: Easy Section: 1.2.D Learning objective: Cellular Architecture

22. Which three cellular components are present in both prokaryotes and eukaryotes? A) ribosomes, chloroplasts, mitochondria B) nucleus, ribosomes, RNA C) RNA, DNA, ribosomes D) endoplasmic reticulum, DNA, RNA E) mitochondria, DNA, RNA Ans: C Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 23. The bulk of aerobic metabolism in eukaryotic cells takes place in A) the endoplasmic reticulum. B) the nucleus. C) the mitochondria. D) peroxisomes. E) the Golgi apparatus. Ans: C Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 24. Which cellular compartment or organelle is involved in the synthesis of proteins and lipids? A) endoplasmic reticulum B) lysosomes C) peroxisomes D) vacuoles E) all of the above Ans: A Level of Difficulty: Moderate Section: 1.2.C Learning objective: Cellular Architecture

25. Which of the following is a similarity between all prokaryotes and all eukaryotes? A) Both contain DNA in a nucleus. B) Both contain some of the same membrane bound cell organelles (like mitochondria, Golgi complexes, etc). C) Both have a cytoskeleton. D) All of the above are similarities between prokaryotes and eukaryotes. E) None of the above is a similarity between prokaryotes and eukaryotes. Ans: E Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 26. Which of the following statements concerning prokaryotes is false? A) Prokaryotes are made up of two major groupings: the eubacteria and the archaea, which are as different from each other as from the eukaryotes. B) Prokaryotes are generally much smaller than the eukaryotic cells. C) Prokaryotes are one branch of the newer, more accurate phylogenic tree made up of prokarya, archaea and eukarya. D) Prokaryotes do not have organelles. E) None of the above is false. Ans: C Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 27. Which of the following statements about eukaryotes is not true? A) They contain organelles like mitochondria, chloroplasts, the endoplasmic reticulum and the nucleus. B) They are usually 10 to 100 microns in diameter. C) They can be either unicellular or multicellular. D) They are also called archaea. E) All of the above are true of eukaryotes. Ans: D Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture

28. Which of the following statements about the theories of (bio)chemical evolution is not true? A) During chemical evolution, simple organic molecules (monomers) condensed to form more complex molecules (polymers) which then began to replicate based upon complementarity. B) Margulis suggested that mitochondria and chloroplasts evolved from the symbiotic relationship between primordial prokaryotic and eukaryotic cells. C) The first cells were probably formed when self-replicating systems were enveloped in membranous vesicles. D) Oparin and Haldane demonstrated that by passing an electrical discharge through a vessel containing H2O, CO2, N2, CH4 and NH3 some basic biological building blocks (like simple amino acids) could have formed abiotically in the earth’s early atmosphere. E) The RNA world hypothesis as proposed by Woese, Crick and Orgel states that RNA, instead of protein, was the first self replicating biochemical molecule that evolved because RNA could have stored genetic information and performed the catalytic roles necessary for primitive selfreplication. Ans: D Level of Difficulty: Moderate Section: 1.2.C Learning objective: Cellular Architecture 29. Which of the following statement(s) is (are) not true? A) Margulis proposed the endosymbiotic theory to explain the evolution of mitochondria and chloroplasts. B) Woese proposed the “new” phylogenic tree that divides living organisms into the 3 domains of bacteria, archaea and eukarya based upon genetic relationships rather than obvious morphological similarities. C) Urey and Miller conducted an experiment that involved sparking a mixture of NH3, CH4, H2O and H2 gases to yield amino acids, some of the fundamental building blocks of life. D) All of the above are false. E) All of the above are true. Ans: E Level of Difficulty: Easy Section: 1.2.C Learning objective: Cellular Architecture

30. Halophiles and thermophiles are A) early versions of eukaryotic cells. B) highly evolved organisms that thrive in their specific environments. C) relatively inefficient and unevolved organisms. D) more complex than eukaryotes. E) extremely slow growing. Ans: B Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 31. Which of the statements about viruses is not true? A) Viruses are much simpler than cells. B) Viruses are the simplest living organisms. C) Viruses lack the necessary metabolic apparatus to reproduce. D) Viruses are dependent on host cells. E) All the statements are true. Ans: B Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 32. Lynn Margulis’ Theory of Endosymbiosis is an explanation for the origin of A) the endoplasmic reticulum. B) the nucleus. C) the mitochondria. D) peroxisomes. E) the Golgi apparatus. Ans: C Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture

33. Phylogeny is A) the science of biological classification based on gross morphology. B) the science of biological classification based on the evolutionary relationships between organisms. C) the science of biological classification based on reproductive strategies. D) the branch of science that studies phyllopods. E) none of the above Ans: B Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 34. Taxonomy is A) the science of biological classification based on gross morphology. B) the science of biological classification based on the evolutionary relationships between organisms. C) the science of biological classification based on reproductive strategies. D) the branch of science that studies taxidermy. E) none of the above Ans: A Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture 35. Which group of organisms is not prokaryotic? A) Fungi B) Archaea C) Purple bacteria D) Cyanobacteria E) Methanococcus Ans: A Level of Difficulty: Easy Section: 1.2.B Learning objective: Cellular Architecture

36. The term molecular weight is a term used by biochemists that refers to A) the density of a particle. B) a dimensionless quantity that is defined as the ratio of the mass of the particle to 1/12 the mass of a 12C atom. C) Daltons divided by the mass of a hydrogen atom. D) all of the above E) none of the above Ans: B Level of Difficulty: Moderate Section: 1.3.A Learning objective: Thermodynamics 37. The second law of thermodynamics states: A) that spontaneous processes are characterized by the overall conversion of order to disorder. B) that spontaneous processes are characterized by the conversion of work to force. C) that nonspontaneous processes are characterized by the conversion of order to disorder. D) that spontaneous processes are characterized by the conversion heat to pressure. E) none of the above Ans: A Level of Difficulty: Easy Section: 1.3.B Learning objective: Thermodynamics 38. Change in enthalpy (DH) is best defined as A) the sum of heat absorbed and work done. B) the heat transferred at constant pressure. C) the pressure change at constant temperature. D) the measure of disorder in a system. E) none of the above Ans: B Level of Difficulty: Easy Section: 1.3.B Learning objective: Thermodynamics

39. If gas molecules in an enclosed chamber are allowed to enter a second chamber, the resulting redistribution of gas molecules represents an increase in A) enthalpy. B) entropy. C) force. D) chemical potential. E) all of the above Ans: B Level of Difficulty: Easy Section: 1.3.B Learning objective: Thermodynamics 40. Consider the reaction A + B « C + D. After reaching equilibrium at 25°C, the following concentrations of reactants and products were measured: [A] = 10 µM, [B] = 15 µM, [C] = 10 µM, [D] = 10 µM. Calculate DG°¢ for this reaction. A) 1000 J/mol B) 10 kJ/mol C) 1 J/mol D) insufficient data to determine answer E) none of the above Ans: A Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics 41. A reaction with a ______ DH and a ______ DS, will never be spontaneous. A) positive, positive B) positive, negative C) negative, positive D) negative, negative E) none of the above Ans: B Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics

42. An endergonic reaction with a ______ DH and a ______ DS can be changed into an exergonic reaction by decreasing the temperature. A) positive, positive B) positive, negative C) negative, positive D) negative, negative Ans: D Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics 43. The DG° for the conversion of glucose 6-phosphate (G6P) to fructose 6-phosphate (F6P) is +1.7 kJ/mole. In a particular human cell the concentration G6P is 8.0 µM and the concentration F6P is 1.0 µM. Calculate the DG of the reaction as it occurs in this cell at 37°C? A) −37 kJ/mol B) −3.7 kJ/mol C) 0 kJ/mol D) +7.1 kJ/mol E) −0.6 kJ/mol Ans: B Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics 44. For a reaction with DH = 23 kJ/mol and DS =22 J/K•mol, at 2°C, the reaction is: A) spontaneous B) nonspontaneous C) at equilibrium D) impossible to determine reactivity E) none of the above Ans: B Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics

45. Calculate the DG for a reaction with DH = 20. kJ/mol and DS =20. J/K•mol, that is carried out at 27°C. A) 14 J/mol B) 140 J/mol C) 1400 J/mol D) 14,000 J/mol E) none of the above Ans: D Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics 46. A spontaneous process A) occurs without the addition of free energy. B) has a DG<0. C) is exergonic. D) is all of the above E) is none of the above Ans: D Level of Difficulty: Easy Section: 1.3.C Learning objective: Thermodynamics 47. An increase in disorder in the system A) is required for a process to be spontaneous. B) results in a decrease in entropy. C) is characteristic of a system increasing in enthalpy. D) results in the factor TDS being positive . E) is found in every exergonic process. Ans: D Level of Difficulty: Moderate Section: 1.3.B Learning objective: Thermodynamics

48. Living organisms A) are closed systems. B) maintain a steady state. C) exist outside the laws of thermodynamics. D) are all of the above E) are none of the above Ans: B Level of Difficulty: Easy Section: 1.3.E Learning objective: Thermodynamics 49. Enzymes accelerate biochemical reactions by A) decreasing the DG for the reactions. B) increasing the DG for the reactions. C) establishing a ‘closed system’ for each reaction. D) promoting reaction pathways associated with a positive DG. E) providing a more favorable pathway for the reactions. Ans: E Level of Difficulty: Moderate Section: 1.3.E Learning objective: Thermodynamics 50. A van’t Hoff plot A) plots ln Keq versus T B) plots DK versus –TDS. C) plots Keq versus 1/T. D) is a good method to determine DH° and DS°. E) determines Keq by plotting DH° versus 1/T. Ans: D Level of Difficulty: Moderate Section: 1.3.D Learning objective: Thermodynamics

51 Keq can be determined from the change in standard free energy using the equation A) Keq = e−DG°/RT B) Keq = ln e−DG°/TDS C) Keq = e−DH/RT D) Keq = e−DG°/TDS E) Keq = log e−DG°/RT Ans: A Level of Difficulty: Easy Section: 1.3.D Learning objective: Thermodynamics 52. Living organisms are classified thermodynamically as: A) open systems. B) closed systems. C) isolated systems. D) thermally isolated. E) none of the above Ans: A Level of Difficulty: Easy Section: 1.3.D Learning objective: Thermodynamics

Short answer 53. Carbohydrates, proteins, nucleotides, and nucleic acids are important groups of molecules found in living organisms. Which 6 elements do living organisms need to build these molecules? Ans: C, H, O, N, S, P Level of Difficulty: Moderate Section 1.1.A Learning objective: The Origin of Life

54. Explain in one or two sentences why scientists believe that all living organisms are related (that they have all evolved from a common ancestor)? Ans: Biochemically, all living organisms are very similar. Level of Difficulty: Moderate Section 1.2.C Learning objective: Cellular Architecture 55. Consider a reaction in which DH = -20. kJ/mol and DS = 10. J/mol · K. a. Calculate the DG for this reaction at 25°C. b. Is the reaction spontaneous (explain your answer)? Ans: a. DG = DH − TDS Þ DG = -20,000 J/mol -(298 × 10 J/mol) = −23,000 J/mol b. The reaction is spontaneous because the DG is negative. Level of Difficulty: Moderate Section 1.3.C Learning objective: Thermodynamics 56. Consider the isomerization reaction R D P, in which R is converted to P. The DG°’ for this reaction is −10. kJ/mol. Calculate the [P]/[R] at equilibrium at 25°C. At equilibrium [P]/[R] = Keq = e−DG°/RT Þ [P]/[R] = e− -(−-10000 J/mol)/8.3145 ·x 298 J/mol = e10000/8.3145 ×x 298 = 57 Level of Difficulty: Moderate Section 1.3.D Learning objective: Thermodynamics 57. Phosphoglucomutase catalyses the reaction in which a phosphate group is transferred from the 1 carbon of glucose to the 6 carbon of glucose (G1P D G6P). A student at SDSU incubates a 0.2 M solution of glucose-1-phosphate overnight with a small amount of the enzyme. At equilibrium the concentration of glucose 1-phosphate is 9.0 × 10−3 M and the concentration of glucose 6-phosphate is 19.1 × 10−2 M. Calculate the equilibrium constant (Keq) and the standard state free energy (∆G°’) for this reaction at 25°C. Ans: The equilibrium constant Keq = [G6P]eq/[G1P]eq = 19.1 × 10−2 M/ 9.0 × 10−3 M = 21. DG°ꞌ = −RTlnKeq = −8.3145 × 298 J/mol × ln 21.2 = −7,600 J/mol. Level of Difficulty: Difficult Section 1.3.D Learning objective: Thermodynamics

58. The reaction pyruvate + ATP D PEP + ADP is catalyzed by the enzyme pyruvate kinase. The DG°ꞌ for this reaction is 31.4 kJ/mol. Use this information to answer the following questions. a. Does this reaction move forward (from left to right) or backward under standard state conditions? Explain you answer in one sentence. b. Calculate the Keq for this reaction at 25°C. c. After the reaction has reached equilibrium at 25°C [ATP] = 5 mM, [ADP] = 0.5 mM, [pyruvate] = 0.2 mM. Calculate the concentration PEP. Ans: a. The reaction goes backward (from right to left) because DG°ꞌ for the forward reaction is positive. b. Keq = e−DG°ꞌ/RT = e−31400/8.3145 × 298 = 3.13 × 10−6 c. Keq = [ADP]eq × [PEP]eq/[ATP]eq × [Pyruvate]eq Þ 3.1 × 10−6 = 0.5 mM × [PEP]eq/0.2 mM × 5 mM Þ [PEP]eq = (3.1 × 10−6 × 0.2 mM × 5 mM)/0.5 mM = 6.2 × 10−6 mM (6.2 × 10−9 M) Level of Difficulty: Difficult Section 1.3.D Learning objective: Thermodynamics

Chapter 2: Water Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N)

hydrogen bond rotational H3PO4 H2PO4– HPO4 2– disordered positive entropy negative entropy higher electronegativity insoluble tetrahedral arrangement acid base only partially ionized

1. Translational and ______ thermal motion causes liquid water molecules to reorient approximately every 10–12 seconds. Ans: B Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 2. The 104.5° bond angle in the water molecule is the result of the ______ of electron orbitals around oxygen. Ans: K Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 3. The polarity of the O–H bond is caused by the ______ of oxygen relative to that of hydrogen. Ans: I Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

4. For the ______ represented by D–H××××A, the donor D is weakly acidic and the acceptor A is weakly basic. Ans: A Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 5. Octane molecules dispersed in water tend to aggregate because that allows water molecules to be more ______. Ans: F Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water 6. The insolubility of nonpolar molecules in water is due to the large ______, which is the result of water molecules forming an ordered network surrounding nonpolar molecules. Ans: H Level of Difficulty: Moderate Section: 2.1.C Learning objective: Physical Properties of Water 7. A strong acid is completely ionized in water, whereas a weak acid is ______. Ans: N Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water 8. Phosphate (pK1 = 2.15, pK2 = 6.82, and pK3 = 12.38) will be mostly in the HPO42– form at pH 7.2. At pH 5.82 it is mostly in the ______ form. Ans: D Level of Difficulty: Moderate Section: 2.2.C Learning objective: Chemical Properties of Water

9. A solution containing a weak acid (pK = 7.5) and its conjugate base at pH of 8.5 has a good capacity to buffer the addition of ______. Ans: L Level of Difficulty: Moderate Section: 2.2.C Learning objective: Chemical Properties of Water 10. A phosphate buffer solution at pH = pK1 = 2.15 would have equal amounts of phosphate in the ______ form and the H2PO4– form. Ans: C Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water

Multiple Choice 11. Rank the following interactions in order of increasing strength (start with the weakest interaction). A) ionic interactions, hydrogen bonds, London dispersion forces, covalent bonds B) London dispersion forces, hydrogen bonds, ionic interactions, covalent bonds C) London dispersion forces, ionic interactions, hydrogen bonds, covalent bonds D) covalent bonds, London dispersion forces, ionic interactions, hydrogen bonds E) hydrogen bonds, London dispersion forces, ionic interactions, covalent bonds Ans: B Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 12. The strongest noncovalent interactions are A) ionic interactions. B) hydrogen bonds. C) dipole-dipole interactions. D) London dispersion forces. E) van der Waals forces. Ans: A Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

13. Hydrogen bonds within liquid water A) are attractions between protons and oxygen nuclei. B) are attractions between two hydrogen atoms. C) are attractions between protons and hydroxide ions. D) are ion-induced dipole attractions. E) are dipole-dipole attractions. Ans: E Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 14. Urea is a water-soluble product of nitrogen metabolism. How many hydrogen bonds can one urea molecule donate to surrounding water molecules?

A) 2 B) 3 C) 4 D) 5 E) 6 Ans: C Level of Difficulty: Moderate Section: 2.1.A Learning objective: Physical Properties of Water

15. Methanol can act both as a H-bond donor and as a H-bond acceptor. What is the maximal number of H-bonds a single molecule of methanol can form with surrounding water molecules. A) 1 B) 2 C) 3 D) 4 E) 5 Ans: C Level of Difficulty: Moderate Section: 2.1.A Learning objective: Physical Properties of Water 16. In a hydrogen bond between a water molecule and another biomolecule A) a hydrogen ion on the water molecule forms an ionic bond with a hydride ion on the other molecule. B) the partial charge on a hydrogen of the water molecule interacts with the partial charge on a hydrogen of the other molecule. C) the hydrogen bond will typically form between a hydrogen atom of the water molecule and either a nitrogen, sulfur, or oxygen atom of the other molecule. D) a hydrogen on the water molecule forms a covalent bond with a hydrogen atom on the other molecule. E) the hydrogen atom is located between an oxygen atom of the water and a carbon atom of the other molecule. Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 17. Which of the following statements about water is not true? A) It has a high dielectric constant. B) It dissolves salts and polar substances. C) It can form two hydrogen bonds per water molecule. D) It packs in a hexagonal (honeycomb) shaped lattice when the temperature falls below 0°C. E) In the liquid state it is only 15% less hydrogen bonded than in the solid state at 0°C. Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

18. Which of the following statements about water is not true? A) The electron-rich oxygen atom of one water molecule can interact with the electron-poor proton on another water molecule to form a hydrogen bond. B) Liquid water is only 15% less hydrogen bonded than ice. C) Water is a nonpolar molecule that with a bent molecular geometry. D) Water can form highly ordered, cage-like, structures around nonpolar molecules. E) Water is a key player in the energetics of hydrophobic interactions. Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 19. Which of the following statements about water is incorrect? A) Water is an excellent solvent for polar molecules. B) Pure water has a concentration of approximately 55.5 M. C) Cations are solvated by shells of water molecules oriented with their hydrogen atoms pointed toward the ions. D) Nonpolar molecules do not dissolve in water, but form a separate phase. E) Amphiphilic detergents often form micelles with the polar groups on the outside exposed to water (solvent) and the nonpolar groups sequestered in the interior. Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 20. Which of the following statements about water is incorrect? A) It is a small, polar molecule with a low dielectric constant. B) It has a marked dipole moment. C) It is largely hydrogen bonded, although any single H-bond exists only for a very short period of time (~10-12 s ). D) Acid-base reactions are very fast due to the mobility of hydronium ions in water which is a consequence of the ability of individual protons to “jump” from one water molecule to another. E) It has a bent geometry with each O─H bond approximately 0.958 Å long and with an O─H bond energy of approximately 460 kJ/mol. Ans: A Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

21. Ice A) is a crystal of water molecules packed in an open structure stabilized by hydrogen bonds. B) is less dense than liquid water. C) contains 17% more hydrogen bonds then water. D) All of the statements above are true. E) None of the statements above are true. Ans: D Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 22. Covalent C─C and C─H bonds have bond strengths that are approximately ____ times higher than those of H-bonds. A) 2 B) 5 C) 10 D) 20 E) 100 Ans: D Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 23. The boiling point of water is 264°C higher than the boiling point of methane because A) the molecular mass of methane is much lower than that of water. B) methane molecules tend to avoid contact with each other. C) water molecules are connected to each other by H-bonds. D) methane molecules do not undergo London dispersion forces. E) all of the above Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

24. _____ is exceptionally soluble in water due to the formation of hydrogen bonds. A) NaCl B) Benzene C) Sodium palmitate D) Ethanol E) Oxygen Ans: D Level of Difficulty: Easy Section: 2.1.B Learning objective: Physical Properties of Water 25. Molecules such as methanol and ethanol are very soluble in water because A) they tend to avoid contact with each other. B) they contain C─H groups that donate H-bonds to water. C) they contain C─H groups that accept H-bonds from water D) they contain O─H groups that can form multiple H-bonds with water. E) they do not form intermolecular H-bonds Ans: D Level of Difficulty: Easy Section: 2.1.B Learning objective: Physical Properties of Water 26. Hydrophobic interactions between nonpolar molecules A) result from the tendency of water to maximize contact with nonpolar molecules. B) are the result of strong attractions between nonpolar molecules. C) are the result of strong repulsion between water and nonpolar molecules. D) depend on strong permanent dipoles in the nonpolar molecules. E) require the presence of surrounding water molecules. Ans: E Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water

27. Fatty acids such as palmitate and oleate are usually characterized as A) hydrophobic. B) hydrophilic. C) polar. D) water soluble. E) amphiphilic. Ans: E Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water 28. Amphiphilic molecules A) have both oxidizing and reducing groups. B) are micelles. C) have chromophores in two different wavelength regions. D) have both acidic and basic groups. E) have both hydrophilic and hydrophobic groups. Ans: E Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water 29. Which of the following statements about hydrophobic interactions is not true? A) They are caused by hydrophobic molecules interacting strongly with each other. B) They are the driving force for micelle formation. C) When nonpolar molecules come in contact with water, a highly-ordered shell of water molecules forms at the interface between the nonpolar molecules and water. A hydrophobic interaction is caused by the desire of water molecules to regain the entropy lost during this organization around the nonpolar substance by excluding the substance from interaction with water molecules. D) They are entropy driven. E) They are the main driving force for protein folding into three dimensional structures. Ans: A Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water

30. Which of the following is the best explanation for the hydrophobic effect? A) It is caused by an affinity of hydrophobic groups for each other. B) It is caused by the affinity of water for hydrophobic groups. C) It is an entropic effect, caused by the desire of water molecules to increase their entropy by forming highly ordered structures around the hydrophobic groups. D) It is an entropic effect, caused by the desire of water molecules to increase their entropy by excluding hydrophobic groups, which they must otherwise surround with highly ordered structures. E) It is an entropic effect caused by the desire of hydrophobic groups to increase their entropy by associating with other hydrophobic groups. Ans: D Level of Difficulty: Difficult Section: 2.1.C Learning objective: Physical Properties of Water 31. In the energetics of transferring hydrocarbons from water to nonpolar solvents, the factor TDS is commonly A) negative. B) positive. C) unmeasurable. D) unimportant. E) assumed to be zero. Ans: B Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water 32. Globules of up to several thousand amphiphilic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center that form in water are called A) micelles. B) liposomes. C) vacuoles. D) bilayer membranes. E) none of the above Ans: A Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water

33. Sheets composed of two layers of amphipathic molecules arranged with the hydrophilic groups on the surface and the hydrophobic groups buried in the center that form in water are called A) micelles. B) liposomes. C) vacuoles. D) bilayer membranes. E) none of the above Ans: D Level of Difficulty: Easy Section: 2.1.C Learning objective: Physical Properties of Water 34. Physical properties that depend on the amounts of various species, rather than the identities of those species, are called A) osmotic properties. B) hydrophobic properties. C) London dispersion forces. D) aggregate properties. E) colligative properties. Ans: E Level of Difficulty: Easy Section: 2.1.B Learning objective: Physical Properties of Water 35. Osmotic pressure is a function of A) humidity. B) solute size. C) solute concentration. D) van der Waals forces. E) solute vapor pressure. Ans: C Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water

36. Kw, the ionization constant of water, is _____ at _____. A) 10-7; 25°C B) 107; 25K C) 1014; 25°C D) 10–14; 25°C E) 10–14; 0°C Ans: D Level of Difficulty: Easy Section: 2.1.A Learning objective: Physical Properties of Water 37. Weak acids A) are only partially ionized in an aqueous solution. B) give solutions with a high pH. C) do not provide hydronium ions. D) are almost insoluble in water. E) are of no value in a buffering system. Ans: A Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water 38. A solution is made by mixing 0.05 mL of 1.0 M HCl with 999.95 mL of pure water. Calculate the pH of the resulting solution (assume the total volume is 1.0 L). A) 2.7 B) 4.3 C) 9.7 D) 7.0 E) 5.0 Ans: B Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water

39. The pH of coffee is 5.6. The pH of grapefruit juice is 2.6. This means that the proton concentration in coffee is A) a thousand times higher than in grapefruit juice. B) a thousand times lower than in grapefruit juice. C) 3000 times lower than in grapefruit juice. D) 3 times the proton concentration of grapefruit juice. E) 3000 times higher than in grapefruit juice. Ans: B Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water 40. A solution is made by mixing 1.0 mL of 1.0 M acetic acid (pK = 4.76, Ka = 1.74 x 10–5 ) with one 999 mL of pure water. Calculate the pH of the resulting solution (assume the total volume is 1.0 L). A) 10.1 B) 3.0 C) 1.0 D) 3.9 E) 1.32 Ans: D Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water 41. You mix 999 mL pure water and 1 mL of 2.0 M NaOH. Calculate the pH of the resulting solution. (assume the total volume is 1.0 L). A) 0.3 B) 0.7 C) 2.7 D) 11.3 E) 13.7 Ans: D Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water

42. The pH of a 0.1 M solution of sodium acetate would be A) basic, because of the acetate ion reacts with water to form acetic acid and OH–. B) acidic, because the acetate ion is acidic. C) acidic, because the acetate ion forms acetic acid. D) neutral, because salts are neither acidic nor basic. E) basic, because the Na+ ionizes and combines with OH–. Ans: A Level of Difficulty: Easy Section: 2.2.B Learning objective: Chemical Properties of Water 43. Phosphoric acid is a polyprotic acid, with pK values of 2.14, 6.86, and 12.38. Which ionic form predominates at pH 9.3? A) H3PO4 B) H2PO41− C) HPO42− D) PO43− E) none of the above Ans: C Level of Difficulty: Moderate Section: 2.2.B Learning objective: Chemical Properties of Water 44. To make a phosphate buffer at pH 6.82 starting with one liter of 10 mM phosphoric acid (pKs are 2.15, 6.82, and 12.38), you could add A) 5 millimoles of HCl. B) 20 millimoles of K+. C) 25 millimoles of HCl. D) 15 millimoles of KOH. E) You can't make a buffer by adding HCl or KOH. Ans: E Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water

45. You mix equal volumes of 0.05 M NaH2PO4 and 0.05 M Na2HPO4 (pK's for phosphoric acid are 2.15, 6.82 and 12.38). Which of the following best describes the resulting solution? A) pH 2.15 and poorly buffered B) pH 2.15 and well buffered C) pH 6.82 and well buffered D) pH 12.38 and well buffered E) pH 6.82 and poorly buffered Ans: C Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water 46. To make an acetate buffer at pH 4.76 starting with 500 mL of 0.1 M sodium acetate (pK acetic acid = 4.76), you could add A) 0.1 mol of NaOH. B) 0.2 mol of HCl. C) 0.025 mol of HCl. D) 0.1 mol of HCl. E) You can't make a buffer by adding HCl or NaOH. Ans: C Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water 47. The pK1 of citric acid is 3.09. What is the citric acid : monosodium citrate ratio in a 1.0 M citric acid solution with a pH of 2.09? A) 10:1 B) 1:1 C) 1:10 D) 10:11 E) 1:11 Ans: A Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water

48. The pKs of succinic acid are 4.21 and 5.64. How many grams of monosodium succinate (FW = 140 g/mol) and disodium succinate (FW = 162 g/mol) must be added to 1 L of water to produce a solution with a pH 5.28 and a total solute concentration of 100 mM? (Assume the total volume remains 1 liter, answer in grams monosodium succinate, grams disodium succinate, respectively.) A) 11.3 g, 4.2 g B) 9.7 g, 4.9 g C) 4.9 g, 9.7 g D) 14.9 g, 1.1 g E) 1.1 g, 14.9 g Ans: B Level of Difficulty: Moderate Section: 2.2.C Learning objective: Chemical Properties of Water 49. What is the approximate pKa of a weak acid HA if a solution 0.1 M HA and 0.3 M A– has a pH of 6.5? A) 5.8 B) 6.0 C) 6.2 D) 6.4 E) 6.6 Ans: B Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water 50. A graduate student at SDSU wants to measure the activity of a particular enzyme at pH 4.0. To buffer her reaction, she will use a buffer system based on one of the acids listed below, which acid is most appropriate for the experiment? A) Formic acid (Ka 1.78 × 10−4) B) MES (Ka 8.13 × 10−7) C) PIPES (Ka 1.74 × 10−7) D) Tris (Ka 8.32 × 10−9) E) Piperidine (Ka 7.58 × 10−12) Ans: A Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water

51. The pH at the midpoint in the titration of an acid with a base is A) equal to the pK of the corresponding acid. B) equal to the pK of the corresponding base. C) equal to 14 minus the pK of the corresponding acid. D) equal to 14 plus the pK of the corresponding base. E) none of the above Ans: A Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water 52. The capacity of a buffer to resist changes in pH upon addition of protons or hydroxide ions depends on A) the pKa of the weak acid in the buffer. B) the pH of the buffer. C) the total concentration of the weak acid and its conjugate base in the buffer. D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water 53. The pH of blood is affected by A) the reaction of CO2 with H2O to form carbonic acid. B) the ionization of aqueous carbonic acid to hydronium ions and the bicarbonate anions. C) the decrease of the blood pH due to the production of hydronium ions. D) the excretion of bicarbonate and ammonium ions from the kidneys. E) all of the above Ans: E Level of Difficulty: Easy Section: 2.2.C Learning objective: Chemical Properties of Water

Short answer 54. Biological processes can be best understood in the context of water. a. What effect does water have on the noncovalent interactions between either charged or polar groups/molecules? b. Why is this effect important with respect to biochemical processes? Ans: a. Water reduces the strength of those interactions. b. Water reduces the strength of polar and ionic interactions. This makes those interactions reversible and life is based on reversible interaction between biomolecules. Level of Difficulty: Difficult Section 2.1.B Learning objective: Physical Properties of Water 55. The hydrophobic effect is an important driving force for protein folding and for the assembly of molecules into cellular structures. a. Give the definition of the hydrophobic effect b. What are amphiphilic (amphipathic) molecules? c. Which cellular structures are composed of many amphipathic molecules that are driven together under the influence of the hydrophobic effect? Ans: a. It is defined as the tendency of water to minimize contact with hydrophobic substances. b. Molecules with both polar and nonpolar regions c. Cellular membranes meet these criteria. Level of Difficulty: Moderate Section 2.1.C Learning objective: Physical Properties of Water

56. Intracellular fluids and the fluids surrounding cells in multicellular organisms are full of dissolved substances, including nucleotides, amino acids, proteins and ions. The total concentration of substances determines the colligative properties of a fluid. Osmosis is one of several such colligative properties. a. Give the definition of osmosis. b. Eukaryotic cells are aqueous solutions surrounded by semipermeable membranes. Consequently, incubation of a cell in a solution of lower osmotic pressure would cause the cell to swell up and burst. Discuss two solutions that have developed during evolution to solve this problem. Ans: a. Osmosis is the movement of solvent (water) through a semipermeable membrane from a region of high concentration to a region of low concentration (with concentration referring to the concentration of water). b. Plant cells are surrounded by a rigid cell wall that prevents the cell from expanding and therefore water from flowing into the cell. Animals surround their cells with a solution that has the same osmotic pressure as is found inside their cells. As a consequence there is no flow of water into or out of these cells. Level of Difficulty: Difficult Section 2.1.D Learning objective: Physical Properties of Water 57. Solutions that contain a mixture of a weak acid and its conjugate base are known to resist changes in pH. a. Calculate the pH of 1.0 L of an aqueous solution containing 75 mmol of MES (pKa = 6.09) and 25 mmol of its conjugate base. b. How much of a 5.0 M NaOH solution do you need to add to raise the pH to 6.09? Ans: a. pH = pKa + log [A−]/[HA] Þ pH = 6.09 + log 25 mM/75 mM = 6.09 – 0.48 = 5.61 b. pH = pKa + log [A−]/[HA] At pH = 6.09, 6.09 = 6.09 + log [A−]/[HA] Þ log [A−]/[HA] = 0 Þ [A−]/[HA] = 1 Þ [A−] = [HA] You know that [A−] + [HA] = 100 mM, substitute [A-] = [HA] in this equation Þ 2 × [A−] = 100 mM Þ [A−] = [HA] = 50 mM. You start with 1.0 L of a buffer containing 25 mmol A− and 75 mM HA. To change the pH to 6.09, 25 mmol of HA has to be converted to A−. This is done by adding 25 mmol of NaOH. The NaOH solution is 5.0 M Þ 25 × 10−3 mol/5.0 mol × 1.0 L−1 = 5.0 × 10−3 L or 5.0 mL Level of Difficulty: Difficult Section 2.2.B Learning objective: Chemical Properties of Water

58. A buffer contains 0.010 mol of lactic acid (pKa = 3.86) and 0.050 mol sodium lactate per liter of aqueous solution. a. Calculate the pH of this buffer. b. Calculate the pH after 5.0 mL of 0.50 M HCl is added to 1 liter of the buffer (assume the total volume will be 1005 mL). Ans: a. pH = pKa + log [A−]/[HA] Þ pH = 3.86 + log 50 mM/10 mM = 3.86 + 0.70 = 4.56 b. Add 5.0 × 10−3 L × 0.50 mol/L HCl = 2.5 x 10−3 mol or 2.5 mmol HCl added 50 mmol lactate + 2.5 mmol H+ = 47.5 mmol lactate + 2.5 mmol lactic acid Þ after adding 2.5 mmol HCl there is 47.5 mmol of lactate and 12.5 mmol of lactic acid Þ pH = 3.86 + log 47.5 mmol × (1005 mL)-1/12.5 mmol × (1005 mL) −1 = 3.86 + log 47.5/12.5 = 3.86 + 0.58 = 4.44 Level of Difficulty: Difficult Section 2.2.B Learning objective: Chemical Properties of Water 59. The pKa of carbonic acid is 6.35. A solution is made by combining 50 mL 1.0 M carbonic acid, 2.0 mL 5.0 M KOH and 448 mL pure water (assume the total volume is 500 mL). Calculate the pH of the resulting solution. Ans: 50 × 10−3 L × 1.0 mol/L carbonic acid = 50 × 10−3 mol or 50 mmol carbonic acid. 2 × 10−3 × 5.0 mol/L KOH = 10 × 10−3 mol or 10 mmol KOH. 50 mmol carbonic acid + 10 mmol OH− = 40 mmol carbonic acid and 10 mmol bicarbonate (and 10 mmol water). pH = pKa + log [A−]/[HA] = 6.35 + log 10 mmol × (500 mL) −1/40 mmol × (500 mL) −1 = 6.35 + log 10/40 = 6.35 – 0.60 = 5.75 Level of Difficulty: Difficult Section 2.2.B Learning objective: Chemical Properties of Water 60. You prepare a solution by mixing 50 mL 0.10 M sodium acetate and 150 mL 1.0 M acetic acid (pKa 4.76). a. Calculate the pH of this solution. b. Can this solution be used effectively as a buffer (explain your answer)? Ans: a. 50 × 10−3 L × 0.10 mol/L acetate = 5.0 × 10−3 mol or 5.0 mmol acetate 150 × 10−3 × 1.0 mol/L acetic acid = 150. × 10−3 mol or 150 mmol acetic acid. The total volume equals 200 mL (assuming additive volumes). pH = pKa + log [A−]/[HA] = 4.76 + log 5 mmol × (200 mL) −1/150 mmol × (200 mL) −1 = 4.76 + log 5/150 = 4.76−1.48 = 3.28 b. No, because the pH (3.28) is more than 1 unit from the pKa (4.76). Level of Difficulty: Difficult Section 2.2.B Learning objective: Chemical Properties of Water

Chapter 3: Nucleotides, Nucleic Acids, and Genetic Information Matching A) B) C) D) E) F) G) H) I) J) K) L) M)

diploid phosphodiester probe pyrimidine introns cloning transformed exons ampicillin autoradiography chain-terminator purine ester

1. Cytosine, uracil, and thymine are derivatives of ______. Ans: D Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 2. Nucleic acids are composed of nucleotides that are linked by ______ linkages. Ans: B Section 3.2.A Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure 3. Organisms composed of cells with two sets of chromosomes are called ______ organisms. Ans: A Section 3.3.A Difficulty: Easy Learning Objective: Overview of Nucleic Acid Function 4. Eukaryotic genes often contain regions that are transcribed and later excised from the RNA, called ______. Ans: E Section 3.5.D Difficulty: Moderate Learning Objective: Overview of Nucleic Acid Function

5. Experiments by Avery and colleagues proved that DNA was the substance that _____ a nonpathogenic pneumococcus strain into a virulent strain. Ans: G Section 3.3.A Difficulty: Moderate Learning Objective: Overview of Nucleic Acid Function 6. The method that Sanger developed for DNA sequencing using dideoxy nucleotides is called the ______ method. Ans: K Section 3.4.C Difficulty: Easy Learning Objective: Nucleic Acid Sequencing 7. Plasmids are small, circular DNA molecules that are used in ______. Ans: F Section 3.5.A Difficulty: Easy Learning Objective: Manipulating DNA 8. Certain plasmids contain genes that confer resistance to ______. Ans: I Section 3.5.A Difficulty: Easy Learning Objective: Manipulating DNA 9. A small fragment of labeled DNA or RNA used in a hybridization experiment is called a ______. Ans: C Section 3.5.B Difficulty: Easy Learning Objective: Manipulating DNA 10. After hybridization, the fragment of interest can be detected by ______. Ans: J Section 3.5.B Difficulty: Easy Learning Objective: Manipulating DNA

Multiple Choice 11. Nucleotides play a central role in living organisms because A) they mediate transport of energy within the cell. B) they are involved in oxidation-reduction reactions. C) they are involved in intracellular signaling. D) they function as building blocks for nucleic acids. E) all of the above Ans: E Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 12. Which of the following statements about nucleotides is false? A) Nucleotides mediate transport of energy within the cell. B) Nucleotides are involved in oxidation-reduction reactions. C) Nucleotides store genetic information. D) Nucleotides are involved in biosynthetic reactions. E) none of the above Ans: C Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 13. What group is attached to the pyrimidine ring in thymine and is not present in uracil? A) ribose B) —CH3 C) —NH2 D) deoxyribose E) none of the above Ans: B Section 3.1 Difficulty: Moderate Learning Objective: Nucleotides

14. The molecule shown in the diagram is a

A) purine. B) dinucleotide. C) nucleoside. D) nucleotide. E) none of the above Ans: E Section 3.1 Difficulty: Easy Learning Objective: Nucleotides

15. What is the name of the molecule shown in the diagram?

A) adenosine B) cytosine C) cytidine D) cytidine monophosphate E) uridine Ans: C Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 16. Nucleotides contain one or more phosphate groups that are usually attached to the: A) C3¢ or C5¢ atoms B) C3 or C3¢ atoms C) C5 or N3 atoms D) C1¢ or N3 atoms E) none of the above Ans: A Section 3.1 Difficulty: Moderate Learning Objective: Nucleotides

17. ‘AMP’ is used to refer to A) adenosine. B) adenylic acid. C) adenomethyl purine. D) adenine. E) all of the above Answer: B Section 3.1 Difficulty: Difficult Learning Objective: Nucleotides 18. Inside our cells, free nucleotides are almost always associated with ______. A) proteins B) cholesterol C) Cl− counterions D) fatty acids E) Mg2+ counterions Answer: E Section 3.1 Difficulty: Moderate Learning Objective: Nucleotides 19. Humans typically recycle approximately _____ of ATP each day. A) 50 kg B) 50 mg C) 50 g D) 50 µg E) 500 kg Answer: A Section 3.1 Difficulty: Easy Learning Objective: Nucleotides

20. Nucleoside triphosphates are useful for energy transfer because the phosphoanhydride bonds are relatively ______. A) stable B) high energy C) biocompatible D) large E) low energy Answer: B Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 21. Nucleoside triphosphates carry energy in the form of A) glycosidic bonds B) phosphoester bonds C) phosphoanhydride bonds D) hydrogen bonds E) amide linkages Answer: C Section 3.1 Difficulty: Moderate Learning Objective: Nucleotides 22. The major carrier of energy in the cell is: A) adenosine monophosphate B) adenosine diphosphate C) adenosine triphosphate D) adenosine tetraphosphate E) flavin adenine dinucleotide Answer: C Section 3.1 Difficulty: Easy Learning Objective: Nucleotides

23. Which of the following nucleotides contain energy rich bonds? A) ATP B) TTP C) GTP D) CTP E) all of the above Answer: E Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 24. Which of the following molecules does not contain an energy rich phosphoanhydride bond? A) ADP B) GDP C) AMP D) CDP E) all of the above Answer: C Section 3.1 Difficulty: Easy Learning Objective: Nucleotides 25. By convention, the sequence of nucleotide residues in a nucleic acid is written ___________ starting with the ____ end. A) left to right; 3¢ B) right to left; 3¢ C) left to right; 5¢ D) right to left; 3¢ E) top to bottom; 3¢ Answer: C Section 3.2.A Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure

26. Chargaff’s rules state that: A) The amount of guanine plus cytosine in mammalian genomes varies from about 39 to 46%. B) DNA is always double stranded and RNA is always single stranded. C) DNA contains two grooves, a major groove and a minor groove. D) In DNA the number of adenine residues is identical to the number of thymine residues and the number of guanine residues is identical to the number of cytosine residues. E) DNA contains two strands that run in opposite directions. Answer: D Section 3.2.B Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure 27. Which of the following bases pairs with guanine?

Answer: E Section 3.2.B Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure

28. The Watson and Crick model of a double-helical structure for DNA was based, in part, on evidence from A) NMR (nuclear magnetic resonance) spectroscopy. B) IR (infrared) spectroscopy. C) atomic force microscopy. D) electron microscopy. E) X-ray diffraction . Answer: E Section 3.2.B Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure 29. Knowledge about the tautomeric forms of the bases of nucleic acids is needed A) to understand H-bonding between the complementary bases B) to understand how the bases are linked to ribose. C) to understand how bases are linked to deoxyribose. D) to understand the ability of nucleotides to act as energy carriers. E) to distinguish the 5’-end of a DNA strand from the 3’-end. Answer: A Section 3.2.B Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure 30. Nucleotides in a DNA molecule are linked together through A) glycosidic bonds. B) amide linkages. C) hydrogen bonds. D) phosphoanhydride bonds. E) phosphodiester bonds. Answer: E Section 3.2.B Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure

31. A double stranded DNA fragment contains 12% adenine residues. Calculate the percentage cytosine residues. A) 12% B) 24% C) 38% D) 50% E) 78% Answer: C Section 3.2.B Difficulty: Moderate Learning Objective: Introduction to Nucleic Acid Structure 32. Which of the following bases is not present in RNA?

Answer: D Section 3.2.C Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure

33. RNA occurs primarily as single stranded molecules that can give rise to _______ structures. A) diploid B) stem-loop C) parallel D) tautomeric E) haploid Answer: B Section 3.2.C Difficulty: Easy Learning Objective: Introduction to Nucleic Acid Structure 34. In 1944 Avery, MacLeod, and McCarty did experiments with Diplococcus pneumoniae that proved that A) DNA is double stranded. B) DNA contains deoxyribose. C) DNA can be transcribed into RNA. D) DNA can permanently transform a non-pathogenic strain into a pathogenic strain. E) The structure of DNA provides a mechanism for reliable replication. Answer: D Section 3.3.A Difficulty: Easy Learning Objective: Overview of Nucleic Acid Function 35. In living organisms, genetic information is most often stored in the form of A) ribonucleic acid. B) deoxyribonucleic acid. C) proteins. D) enzymes. E) deoxynucleotides. Answer: B Section 3.3.A Difficulty: Easy Learning Objective: Overview of Nucleic Acid Function

36. It is impossible for RNA to store genetic information, because A) RNA does not base pair and therefore cannot be replicated. B) enzymes cannot process genetic information in the form of RNA. C) RNA forms complex folded structures. D) RNA is very unstable. E) None of the above answers is correct; RNA can store genetic information. Answer: E Section 3.3.A Difficulty: Difficult Learning Objective: Overview of Nucleic Acid Function 37. Genomic DNA is ______, resulting in the production of _________. A) transcribed; mRNA B) translated; tRNA C) transcribed; protein D) translated; protein E) translated; rRNA Answer: A Section 3.3.B Difficulty: Moderate Learning Objective: Overview of Nucleic Acid Function 38. Which of the following nucleic acids provides the key to decoding genetic information? A) tRNA B) rRNA C) mRNA D) DNA E) None of the above Answer: A Section 3.3.B Difficulty: Difficult Learning Objective: Overview of Nucleic Acid Function

39. Which diagram depicts correctly a ribosome engaged in translation?

A.) a B.) b C.) c D.) d Answer: A Section 3.3.B Difficulty: Difficult Learning Objective: Overview of Nucleic Acid Function 40. Transfer RNA molecules are involved in A) transcription. B) translation. C) replication. D) reverse transcription. E) posttranslational processing. Answer: B Section 3.3.B Difficulty: Easy Learning Objective: Overview of Nucleic Acid Function

41. Which of the following DNA sequences is considered palindromic? A) AAGCTT B) GAACTT C) GAACAA D) AAGCAA E) AAGTTC Ans: A Section 3.4.A Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 42. Which of the following DNA sequences (in which N is any nucleic acid residue) is palindromic? A) ANAGCTT B) AANGCTT C) AAGNCTT D) AAGCNTT E) AAGCTNT Ans: C Section 3.4.A Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 43. Double stranded DNA molecules can be cleaved at specific recognition sites by A) RNA polymerase. B) DNA ligase. C) DNA polymerase. D) reverse transcriptase. E) Type II restriction endonucleases. Answer: E Section 3.4.A Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing

44. Which of the restriction enzymes listed in the table below produces blunt-end fragments? Enzyme

Cleavage site

AluI HindIII BamHI EcoRI BglII

AG$CT A$AGCTT G$GATCC G$AATTC A$GATCA

A) AluI B) BamHI C) BglII D) EcoRI E) HindIII Answer: A Section 3.4.A Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 45. Which of the enzymes listed in the table below produce identical sticky ends? Enzyme

Cleavage site

AluI HindIII BamHI EcoRI BglII

AG$CT A$AGCTT G$GATCC G$AATTC A$GATCA

A) AluI and HindIII B) AluI and BamHI C) HindIII and EcoRI D) HindIII and BglII E) BamHI and BglII Answer: E Section 3.4.A Difficulty: Difficult Learning Objective: Nucleic Acid Sequencing

46. Gel electrophoresis generally separates nucleic acids on the basis of A) shape. B) sequence. C) size. D) charge-density. E) none of the above Ans: C Section 3.4.B Difficulty: Easy Learning Objective: Nucleic Acid Sequencing 47. DNA sequencing using the Sanger method requires A) template, primer, DNA polymerase, mRNA, dNTPs, ddNTPs. B) template, primer, DNA polymerase, dNTPs, ddNTPs. C) template, primer, DNA polymerase, rRNA, dNTPs, ddNTPs. D) template, primer, DNA polymerase, mRNA, dNTPs. E) none of the above Ans: B Section 3.4.C Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 48. In Sanger dideoxy DNA sequencing, DNA polymerase I is used to add nucleotides to the ___ end of the growing polynucleotide chain. A) sticky B) blunt C) 3¢ D) 5¢ E) dideoxy nucleotide containing Answer: C Section 3.4.C Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing

49. DNA sequencing by the chain-termination method utilizes DNA polymerase I to make a complementary copy of the target or template DNA molecule. A reaction with a 20 bp template and dideoxyadenosine nucleotides as terminators results in the production of a 5 bp fragment. Based on this result, we can conclude that the template contains A) a cytosine at position 5. B) a thymine at position 5. C) a cytosine at position 16. D) a thymine at position 16. E) a uracil at position 5. Answer: D Section 3.4.C Difficulty: Difficult Learning Objective: Nucleic Acid Sequencing 50. DNA fragments are usually inserted into a plasmid vector and cloned before they are analyzed by chain termination sequencing because A) DNA fragments need to be pure in order to obtain an unambiguous sequence. B) a large number of identical fragments is needed in a sequencing reaction in order to generate detectable amounts of products. C) plasmid vectors have known sequences that can be used for design and annealing of the primer oligonucleotides, which are used to initiate the sequencing reaction. D) all of the above E) none of the above Answer: D Section 3.4.C Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 51. Which of the following conclusions about the human genome is (are) true? A) Only about 80% of the human genome is transcribed to RNA. B) Only about 1-2% of the human genome codes for proteins. C) Most of the proteins found in humans are also found in many other animals. D) Nearly half of the human genome consists of repetitive DNA sequences. E) All of the above. Ans: E Section 3.4.D Difficulty: Difficult Learning Objective: Nucleic Acid Sequencing

52. Which of the following conclusions about the human genome is false? A) Only about 80% of the genome is transcribed to RNA. B) Most of the proteins found in humans are unique to vertebrates. C) Nearly half of the human genome consists of repetitive DNA sequences. D) The genomes of any two people are likely to be 99.9% identical E) None of the above Ans: B Section 3.4.D Difficulty: Difficult Learning Objective: Nucleic Acid Sequencing 53. Alterations in genetic information can be caused by A) mistakes made during replication. B) faulty recombination. C) transposition of genes. D) damage caused by chemicals or radiation. E) all of the above Ans: E Section 3.4.E Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing 54. Alterations in genetic information cannot be caused by A) mistakes made during replication B) faulty recombination. C) transposition of genes. D) mistakes made during translation. E) all of the above Ans: D Section 3.4.E Difficulty: Moderate Learning Objective: Nucleic Acid Sequencing

55. Mutations leading to changes that can be inherited by the next generation have to be introduced into at the _______ level. A) DNA B) rRNA C) protein D) mRNA E) tRNA Answer: A Section 3.4.E Difficulty: Easy Learning Objective: Nucleic Acid Sequencing 56. The production of multiple identical organisms from a single ancestor is called ________. A) DNA ligation B) phenotyping C) cloning D) transcription E) sequencing Answer: C Section 3.5.A Difficulty: Easy Learning Objective: Manipulating DNA 57. Small circular DNA molecules used to carry foreign DNA fragments are called ________. A) mRNAs B) bacteriophage C) clones D) plasmids E) nucleotides Answer: D Section 3.5.A Difficulty: Easy Learning Objective: Manipulating DNA

58. In molecular cloning, transformed organisms must be identified. One common method for accomplishing this involves the inclusion of ________ in the plasmid. A) a restriction site B) a nuclease gene C) a deletion D) an origin of replication E) an antibiotic resistance gene Answer: E Section 3.5.A Difficulty: Moderate Learning Objective: Manipulating DNA 59. A genomic library A) is a collection of protein structures from a specific organism. B) is a collection of cloned DNA fragments representing all of an organism’s DNA. C) contains only protein-coding DNA sequences. D) is best constructed from very short DNA fragments. E) is built from mRNA by reverse transcription. Answer: B Section 3.5.B Difficulty: Moderate Learning Objective: Manipulating DNA 60. Radioactively labeled, single-stranded oligonucleotides are often used in in situ hybridization. Which of the probes listed below would work best, when probing for a RNA molecule containing the sequence 5¢-AGCTAACGGG-3¢? A) 5¢-AGCTAACGGG-3¢ B) 5¢-GGGCAATCGA-3¢ C) 5¢-CCCGTTAGCT-3¢ D) 5¢-TCGATTGCCC-3¢ E) all of the above Answer: C Section 3.5.B Difficulty: Moderate Learning Objective: Manipulating DNA

61. In order to perform PCR, which of the following describes the reagents that must be included in the reaction mixture? A) DNA fragment, primers flanking the region of interest, dNTPs, DNA polymerase B) DNA fragment, primers flanking the region of interest, dNTPs, ddNTPS, DNA polymerase C) DNA fragment, one primer, dNTPs, DNA polymerase, DNA ligase D) DNA fragment, primers flanking the region of interest, dNTPs, DNA Ligase E) none of the above Ans: A Section 3.5.C Difficulty: Moderate Learning Objective: Manipulating DNA 62. Which of the following statements about PCR is (are) true? A) Small amounts of DNA can be easily amplified to millions of copies. B) PCR is often used in forensics laboratories. C) PCR reaction products can be used in molecular cloning. D) PCR is used in clinical laboratories. E) All of the above. Ans: E Section 3.5.C Difficulty: Difficult Learning Objective: Manipulating DNA 63. DNA polymerase from Thermus aquaticus is used in PCR because A) it is a soluble protein. B) the genes from Thermus aquaticus are readily distinguished from those of ‘normal’ organisms. C) the enzyme is readily deactivated by heat, effectively halting the reaction. D) it is stable at high temperatures. E) it is not infectious. Answer: D Section 3.5.C Difficulty: Easy Learning Objective: Manipulating DNA

64. A gene knockout is A) a gene that has been inactivated or removed from an organism. B) a dominant gene that knocks-out expression of other genes. C) a gene inserted in place of another gene. D) a gene present on a YAC. E) none of the above Ans: A Section 3.5.D Difficulty: Moderate Learning Objective: Manipulating DNA 65. Recombinant DNA technology can be used for A) constructing mutant proteins. B) the industrial production of useful proteins. C) producing transgenic organisms. D) correcting genetic defects. E) all of the above Answer: E Section 3.5.D Difficulty: Easy Learning Objective: Manipulating DNA

Short Answer 66. This is the structure of adenine.

a. Is adenine a purine or a pyrimidine? b. Which base does adenine base-pair (H-bond) with in DNA? c. What is the name of the molecule that is composed of adenine linked to the C1’ of ribose? d. Indicate on the drawing through which atom adenine is connected to ribose or deoxyribose. e. Indicate on the drawing which groups on adenine are involved in base-pairing or H-bonding with its complementary base. Ans: a. purine b. thymine c. adenosine d. see diagram e. see diagram Level of Difficulty: Difficult Section 3.2 Learning objective: Introduction to Nucleic Acid Structure

67. This is the structure of cytosine.

a. What are the names of the other three bases that are found in DNA. b. Is cytosine a purine or a pyrimidine? c. Give the name and the one letter abbreviation of the base cytosine base-pairs (H-bonds) with in DNA? d. Indicate on the drawing through which atom cytosine is connected to ribose or deoxyribose. e. What is the name of the molecule composed of cytosine linked to ribose? f. Indicate on the drawing which groups on cytosine are involved in base-pairing (H-bonding) with its complementary base. Ans: a. adenine, guanine, and thymine b. pyrimidine c. guanine, G d. cytidine e. see diagram f. see diagram Level of Difficulty: Difficult Section 3.2 Learning objective: Introduction to Nucleic Acid Structure

68. Describe the structure of a DNA molecule by listing 6 characteristics. Ans:

1. DNA forms a double helix 2. the two strands run anti-parallel 3. the sugar is deoxyribose 4. the sugar-phosphate groups are on the outside of the helix 5. the bases are in the center of the helix 6. the bases are planar and their plane is orientated perpendicular to the axis of the helix 6. there are four bases: Adenine, Guanine, Cytosine and Thymine 7. The strands are held together by H-bonding between complementary bases: AdenineThymine and Guanine-Cytosine 8. The helix has a minor and a major groove on its surface. Level of Difficulty: Difficult Section 3.2 Learning objective: Introduction to Nucleic Acid Structure 69. Describe the central dogma of molecular biology (to do this draw a diagram of the central dogma and describe all the arrows). Ans: Level of Difficulty: Difficult Section 3.3B Learning objective: Overview of Nucleic Acid Function

70. There are three types of RNA that are directly involved in translation. a. Name these three types of RNA b. Briefly describe the function of each of these types of RNA. Ans: a. mRNA, tRNA, rRNA. b. mRNA moves genetic information from the nucleus to the ribosomes in the cytoplasm. tRNA decodes the genetic message, it matches sequences of three nucleotides to amino acids. rRNA is involved in the catalysis of amide bond formation. Level of Difficulty: Difficult Section 3.3B Learning objective: Overview of Nucleic Acid Function

Chapter 4: Amino Acids Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N) O) P)

glutamate uncharged deprotonated three amino group two C-terminus lysine racemic mixture cysteine zero protonated isoleucine tryptophan phenylalanine N-terminus

1. The net charge of the zwitterion form of Gly is ______. Ans: K Section: 4.1.A Level of Difficulty: Easy Learning objective: Amino Acid Structure 2. When a peptide bond is formed, an ______ reacts with a carboxylate group. Ans: E Section: 4.1.B Level of Difficulty: Easy Learning objective: Amino Acid Structure 3. At a pH above its pKa, the phenol group of tyrosine is ______. Ans: C Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure

4. In the tripeptide Lys─Pro─Ile, there are ______ charged groups at pH 7. Ans: D Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 5. At a pH below its pKa, the e-amino group of lysine is ______. Ans: L Section: 4.1.D Level of Difficulty: Easy Learning objective: Amino Acid Structure 6. At a pH below its pKa, the b-carboxylate group of Asp is ______. Ans: B or L Section: 4.1.D Level of Difficulty: Easy Learning objective: Amino Acid Structure 7. In the peptide Trp─Ser─Val, valine is at the ______. Ans: G Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure 8. In the tripeptide Trp─Val─Phe, the N-terminal residue is ______. Ans: N Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure 9. In the tripeptide Lys─Pro─Ile, the C-terminal residue is _________. Ans: M Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure

10. Biological systems usually produce a single enantiomer, whereas chemical synthesis produces a ______. Ans: I Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry 11. GABA is a neurotransmitter derived from ______. Ans: A Section: 4.3.B Level of Difficulty: Easy Learning objective: Amino Acid Derivatives 12. Glutathione is a tripeptide containing a central ______ residue. Ans: J Section: 4.3.B Level of Difficulty: Easy Learning objective: Amino Acid Derivatives

Multiple Choice 13. In the early 1930’s William Rose fed laboratory rats a mixture of all 19 amino acids known to be present in proteins. He observed that his rats lost weight. This observation led to the discovery of ______ as the 20th amino acid found in proteins. A) Gly B) Ala C) Tyr D) Asn E) Thr Ans: E Section: 4.1 Level of Difficulty: Easy Learning objective: Amino Acid Structure 14. What percentage of the 20 amino acids is considered to be nutritionally essential to lab animals? A) 0% B) 25% C) 50% D) 75% E) 100% Ans: C Section: 4.1 Level of Difficulty: Easy Learning objective: Amino Acid Structure 15. About half of the 20 amino acids are called essential because A) they are essential for the synthesis of pyrimidines. B) they are essential for the synthesis of purines. C) they are essential for nitrogen metabolism. D) our bodies need them for protein synthesis. E) our bodies cannot synthesize them and therefore they need to be present in our diet. Ans: E Section: 4.1 Level of Difficulty: Easy Learning objective: Amino Acid Structure

16. Which amino acid does not have a primary a-amino group? A) glutamine B) arginine C) lysine D) proline E) glutamate Ans: D Section: 4.1 Level of Difficulty: Easy Learning objective: Amino Acid Structure 17. Which of the following statements is true? A) Amino acids can be derived from purines. B) Purines and pyrimidines can be derived from amino acids. C) Corn contains all 20 standard amino acids. D) Amino acids can be derived from pyrimidines. E) none of the above Ans: B Section: 4.1 Level of Difficulty: Easy Learning objective: Amino Acid Structure 18. Which of the following amino acids is the least abundant in proteins? A) V B) W C) G D) F E) A Ans: B Section: 4.1 Level of Difficulty: Difficult Learning objective: Amino Acid Structure

19. Zwitterions are A) amino acids. B) ionic molecules that are racemic. C) ions that bear both negatively and positively charged groups. D) side chain carboxylate anions. E) delocalized ions. Ans: C Section: 4.1.A Level of Difficulty: Easy Learning objective: Amino Acid Structure 20. The formation of a dipeptide from two amino acids involves A) side-chain complementarity. B) loss of water. C) oxidation of the a-carbon. D) reduction of the a-carbon. E) base catalysis. Ans: B Section: 4.1.B Level of Difficulty: Easy Learning objective: Amino Acid Structure

21. The diagram below shows

A) an amino acid. B) a dipeptide. C) a tripeptide. D) a tetrapeptide. E) a polypeptide. Ans: D Section: 4.1.B Level of Difficulty: Easy Learning objective: Amino Acid Structure 22. Which of the following amino acids has a charged polar side chain at pH 7.0? A) Leu B) Ala C) Met D) Trp E) Glu Ans: E Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure

23. Which of the following tripeptides carries a net positive charge at pH 7.0? A) Ala─Thr─Asn B) Gln─Val─Ser C) Arg─Glu─Met D) Pro─Ile─Leu E) Leu─Lys─Gly Ans: E Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure 24. Which of the following amino acids has a sulfur atom in its side chain? A) Asn B) Ser C) Phe D) Met E) Tyr Ans: D Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 25. Which of the following amino acids does not have an ionizable side chain? A) Asp B) Cys C) Lys D) His E) Asn Ans: E Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure

26. Which of the following amino acids has an uncharged polar side chain at pH 7.0? A) Arg B) Thr C) Glu D) Pro E) Ile Ans: B Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure For questions 27 and 28 refer to the diagram below

27. What is the three-letter symbol for the amino acid shown above? A) Ala B) Asn C) Gln D) Asp E) Glu Ans: B Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure

28. The ionization of amino acids depends on the pH and the pKas of the ionizable groups. The pK1 and pK2 for the amino acid shown above are 2.1 and 8.8, respectively. At what pH is the amino acid ionized predominantly as shown? A) pH 1.0 B) pH 2.1 C) pH 5.5 D) pH 8.8 E) pH 10.0 Ans: A Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 29. The pK1, pK2, and pKR for the amino acid arginine are 1.8, 9.0, and 12.5, respectively. At pH 7.0 arginine would be charged predominantly as follows: A) a-carboxylate 0, a-amino 0, guanidino +1, net charge +1 B) a-carboxylate +1, a-amino 0, guanidino -1, net charge 0 C) a-carboxylate +1, a-amino −1, guanidino −1, net charge −1 D) a-carboxylate −1, a-amino +1, guanidino +1, net charge +1 E) a-carboxylate −1, a-amino 0, guanidino +1, net charge 0 Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure 30. The pK1, pK2, and pKR for the amino acid aspartic acid are 2.0, 9.9, and 3.9, respectively. At pH 7.0, aspartic acid would be charged predominantly as follows: A) a-carboxylate 0, a-amino +1, b-carboxylate 0, net charge +1 B) a-carboxylate −1, a-amino +1, b-carboxylate −1, net charge −1 C) a-carboxylate 0, a-amino −1, b-carboxylate 0, net charge −1 D) a-carboxylate +1, a-amino −1, b-carboxylate +1, net charge +1 E) a-carboxylate +1, a-amino +1, b-carboxylate +1, net charge +3 Ans: B Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

31. The pK1, pK2, and pKR for the amino acid glutamate are 2.1, 9.5, and 4.1, respectively. At pH 11.0, glutamate would be charged predominantly as follows: A) a-carboxylate +1, a-amino 0, g-carboxylate +1, net charge +2 B) a-carboxylate −1, a-amino +1, g-carboxylate −1, net charge −1 C) a-carboxylate 0, a-amino 0, g-carboxylate 0, net charge 0 D) a-carboxylate +1, a-amino −1, g-carboxylate +1, net charge +1 E) a-carboxylate −1, a-amino 0, g-carboxylate −1, net charge −2 Ans: E Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure 32. The pK1, pK2, and pKR for the amino acid histidine are 1.8, 9.3, and 6.0, respectively. At pH 4.0 would be charged predominantly as follows: A) a-carboxylate +1, a-amino 0, imidazole −1, net charge 0 B) a-carboxylate −1, a-amino +1, imidazole 0, net charge 0 C) a-carboxylate +1, a-amino +1, imidazole −1, net charge +1 D) a-carboxylate −1, a-amino +1, imidazole +1, net charge +1 E) a-carboxylate 0, a-amino +1, imidazole +1, net charge +2 Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure 33. The pK1, pK2, and pKR for the amino acid cysteine are 1.9, 10.7, and 8.4, respectively. At pH 5.0, cysteine would be charged predominantly as follows: A) a-carboxylate 0, a-amino 0, sulfhydryl 0, net charge 0 B) a-carboxylate +1, a-amino −1, sulfhydryl −1, net charge −1 C) a-carboxylate −1, a-amino +1, sulfhydryl +1, net charge +1 D) a-carboxylate −1, a-amino +1, sulfhydryl 0, net charge 0 E) a-carboxylate +1, a-amino −1, sulfhydryl 0, net charge 0 Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

34. The pK1, pK2, and pKR for the amino acid lysine are 2.2, 9.1, and 10.5, respectively. At pH 1.0, lysine would be charged predominantly as follows: A) a-carboxylate 0, a-amino −1, e-amino −1, net charge −2 B) a-carboxylate −1, a-amino +1, e-amino +1, net charge +1 C) a-carboxylate +1, a-amino +2, e-amino +2, net charge +5 D) a-carboxylate 0, a-amino +1, e-amino +1, net charge +2 E) a-carboxylate +2, a-amino +1, e-amino +1, net charge +4 Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure Questions 35-37 are based on the diagram shown below.

35. How many amino acid residues are present in the peptide shown above? A) 1 B) 2 C) 3 D) 4 E) 5 Ans: C Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure

36. What is the name of the N-terminal amino acid in the peptide shown above? A) cysteine B) methionine C) valine D) alanine E) tryptophan Ans: B Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 37. What is the three-letter symbol for the C-terminal amino acid in the peptide shown above? A) Gly B) Asp C) Tyr D) Met E) Phe Ans: E Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 38. While proteins are usually composed of linear chains of amino acids, branched chains of amino acids and internally cross-linked chains can be found in certain proteins. Polypeptide chains are most commonly linked to each other through A) hydrogen bonds. B) glycosidic bonds. C) peptide bonds. D) disulfide bonds. E) ester linkages. Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

39. The disulfide bond between two cysteine molecules A) is a peptide bond. B) is an ionic interaction that is stable at physiological pH. C) is a covalent bond formed by oxidation. D) is a hydrogen bond between the two sulfhydryl groups. E) is a dipole-dipole interaction. Ans: C Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 40. The two peptides shown in the diagram below are linked through

A) a hydrogen bond. B) a glycosidic bond. C) a peptide bond. D) a disulfide bond. E) an ester linkage. Ans: D Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

41. Which one of the representations describes the oligopeptide shown below?

A) Tyr-Ala-Thr B) Tyr-Gly-Cys C) Tyr-Ala-Ser D) Phe-Gly-Cys E) Phe-Ala-Thr Ans: C Section: 4.1.C Level of Difficulty: Easy Learning objective: Amino Acid Structure 42. The tripeptide glycylarginylglutamate contains four ionizable groups with pKas of 2.1, 4.1 9.8, and 12.5. Calculate the pI for this molecule. A) 3.1 B) 6.4 C) 7.0 D) 7.3 E) 8.3 Ans: C Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure

43. The tripeptide alanyllysylaspartate contains four ionizable groups with pKas of 2.0, 3.9, 9.9, and 10.5. Calculate the pI for this molecule. A) 3.0 B) 6.0 C) 6.2 D) 10.2 E) none of the above Ans: E Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure 44. The isoelectronic point of an amino acid is the point where A) the pKa of the a-carboxylic acid is the same as the pKa of the a-amino group. B) the a-carboxylic acid is protonated and the a-amino group is unprotonated. C) the solubility of the amino acid is maximized. D) the a-carboxylic acid and the a-amino group are both half protonated. E) the amino acid carries no net electrical charge. Ans: E Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure 45. The side-chains of amino acids have A) a positive charge in every situation. B) pKas that assure the solubility of every protein. C) constant pKas no matter what aqueous environment they are found in. D) different pKas in peptides as compared to the free amino acids E) polar functional groups. Ans: D Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure

46. Asx refers to A) a negatively charged aspartic acid. B) a positively charged asparagine. C) a dipeptide containing both aspartic acid and asparagine. D) either aspartic acid or asparagine. E) an unnatural amino acid formed during acid hydrolysis of peptide bonds. Ans: D Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure 47. The peptide AYDG has an N-terminal _________ residue. A) glycine B) glutamic acid C) glutamine D) aspartic acid E) alanine Ans: E Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure 48. Which of the following tripeptides would be expected to be the most hydrophobic? A) KYG B) KYA C) GYA D) DYA E) DYG Ans: C Section: 4.1.E Level of Difficulty: Moderate Learning objective: Amino Acid Structure

49. What is the three-letter abbreviation for the peptide valylarginylisoleucine? A) Val─Arg─Ile B) Val─Agn─Leu C) Vln─Arg─Ile D) Val─Agn─Isl E) Vln─Arg─Leu Ans: A Section: 4.1.E Level of Difficulty: Easy Learning objective: Amino Acid Structure 50. Ribosomes use L amino acids to synthesize proteins. These amino acids are called “L” because A) they are chiral. B) they turn polarized light to the left. C) they have a configuration of groups around the Ca that can be related to the configuration of groups around the asymmetric carbon in L-glyceraldehyde. D) they are all (S)-amino acids. E) they are all (R)-amino acids. Ans: C Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry 51. Ribosomes use L amino acids to synthesize proteins. These amino acids are called “L” because A) they are chiral. B) they turn polarized light to the left. C) they are all (S)-amino acids. D) they are all (R)-amino acids. E) none of the above Ans: E Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry

52. Which of the amino acids represented below has two chiral centers? A) Ala B) Leu C) Ile D) Pro E) Asn Ans: C Section: 4.2 Level of Difficulty: Difficult Learning objective: Stereochemistry 53. Which of the five amino acids shown below has 2 chiral centers?

Ans: C Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry

54. All the standard amino acids except ____ are optically active. A) Pro B) Arg C) Trp D) Gly E) Phe Ans: D Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry 55. The __________ character of most standard amino acids causes solutions of amino acids to rotate the plane of polarized light. A) chiral B) zwitterionic C) polar D) hydrophobic E) none of the above Ans: A Section: 4.2 Level of Difficulty: Easy Learning objective: Stereochemistry 56. All amino acids derived from proteins have the same stereochemical conformation as. A) L-glyceraldehyde. B) (R)-alanine. C) D-glucose. D) (S)-cysteine. E) glycine. Ans: A Section: 4.2 Level of Difficulty: Moderate Learning objective: Stereochemistry

57. Typically, modified amino acids, those with side chain modifications that are present in proteins A) are synthesized due to genetic mutations. B) are assembled by specialized bacterial enzymes. C) are formed by modification of standard side chain residues after the protein is synthesized. D) are toxic. E) are racemic. Ans: C Section: 4.3.A Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives 58. An amide bond between a side-chain carboxylate and an a-amino group is also called a(n) A) disulfide bond. B) anhydride bond. C) ester bond. D) isopeptide bond. E) glycosidic bond. Ans: D Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives

Questions 59-61 are based on the diagram below.

59. What is the name of this molecule? A) GABA B) thyroxine C) g-carboxyglutamate D) glutathione E) epinephrine Ans: D Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives 60. Residues 1 and 2 in the peptide shown above are connected through a A) hydrogen bond. B) an isopeptide bond. C) an ester linkage. D) disulfide bond. E) a glycosidic bond. Ans: B Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives

61. What is the three-letter symbol of the N-terminal amino acid in the structure shown above? A) Asp B) Asn C) Gln D) Glu E) Lys Ans: D Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives

Short Answer 62. Glutamine is an amino acid (pKas are 2.2, and 9.1). Draw the predominant structure of glutamine at pH 1.0.

Ans: Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure 63. Glutamic acid is an amino acid (pKas are 2.1, 4.1 and 9.5). Calculate the isoelectric point of glutamic acid. Ans: At pH 1.0 glutamic acid has an electric charge of +1, at pH 3.0 the electric charge equal 0, and at pH 5.0 the electric charge equals −1. Therefore the pKas of the carboxylic acid groups surround the neutral form. pI = (2.1 + 4.1)/2 = 3.1 Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure

64. Tryptophan is an amino acid (pKas are 2.5, and 9.4). a. How many different amino acids can be incorporated into proteins during translation? b. Give the three- and one-letter abbreviation for tryptophan. c. Draw the predominant structure of tryptophan at pH 7.0. d. Calculate the pI of Tryptophan. Ans: a. 20 b. Trp and W

c. d. pI = (2.5 + 9.4)/2 = 6.0 Section: 4.1.D Level of Difficulty: Moderate Learning objective: Amino Acid Structure

65. In general, amino acids are chiral molecules that act as building blocks for proteins. In addition, amino acids and amino acid derivative can act as extracellular messenger molecules such as hormones or neurotransmitters. a. How many different amino acids can be incorporated into proteins during translation? b. Do ribosomes use L or D amino acids for protein synthesis? c. Name one amino acid or amino acid derivative that can act as hormone or neurotransmitter. d. Draw the predominant structure of valine at pH 10 (pKas are 2.3 and 9.7). Ans: a. 20 b. L c. glycine, glutamate, g-aminobutyric acid (GABA), dopamine, or serotonin

d. Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

66. The figure below shows the predominant structure of an oligopeptide at pH 7.0.

a. How many amino acids are present in this peptide? b. Circle one peptide bond in this peptide. c. Draw a square around one alpha carbon in this peptide d. The pKas of the ionizable groups in this peptide are 2.0, 4.0, and 9.0. What is the ionic charge of this molecule at pH 1.0 e. What is the name of the N-terminal amino acid in this peptide? Ans: a. 5

b. c. d. The charge of this molecule at pH 1.0 is +1. At pH 1.0 all ionizable groups are protonated; the two carboxylic acid groups are neutral and the amino group is positively charged. e. aspartate (aspartic acid) Section: 4.1.C Level of Difficulty: Moderate Learning objective: Amino Acid Structure

67. The picture below shows the structure of g-amino-butyric acid (GABA).

a. From which amino acid is GABA derived (give the name of the amino acid closest in structure to GABA). b. What is the structural difference between GABA and this amino acid. c. What is the function of GABA. Ans: a. glutamate b. GABA is missing the a-carboxylic acid group c. GABA is a neurotransmitter (a chemical that mediates communication between neurons) Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives

68. The picture below shows the structure of serotonin.

a. From which amino acid is serotonin derived? b. What are the structural differences between serotonin and this amino acid? c. What is the function of serotonin? d. Which illness can be caused by reduced levels of serotonin in the brain? Ans: a. Tryptophan b. Serotonin has a hydroxyl group attached to the 6-membered ring and it misses the a-amino group. c. Serotonin is a neurotransmitter d. Depression Section: 4.3.B Level of Difficulty: Moderate Learning objective: Amino Acid Derivatives

Chapter 5: Proteins: Primary Structure Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N) O) P) Q

electrophoresis hydrophobic interaction enzyme-linked immunosorbent assay three-dimensional shape N-terminal amino acid negative charge nucleases chromophore foaming high level expression 2-mercaptoethanol positive charge cation exchange pI chymotrypsin C-terminal amino acid Sodium dodecyl sulfate

1. One of the reasons the primary structure is important for a protein is that it determines the ______ the molecule adopts in aqueous solutions. Ans: D Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity 2. If the cDNA for a protein has been cloned, it may be possible to obtain large quantities of the protein by _________________ in bacteria. Ans: J Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis

3. To help prevent denaturation of proteins in solution, steps are taken to avoid _________ and adsorption to surfaces. Ans: I Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 4. Molecules that contain a(n) ______ are capable of absorbing light. Ans: H Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis 5. If antibodies to the protein being assayed are available, a(n) ______ can be carried out. Ans: C Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 6. In general, proteins are least soluble in water when the pH is close to the ______. Ans: N Level of Difficulty: Moderate Section: 5.2.B Learning objective: Protein Purification and Analysis 7. ______ chromatography is a method of fractionating a protein mixture according to differences in polarity. Ans: B Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis

8. In order for DEAE to act as an anion exchanger, it must have a ______. Ans: L Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis 9. In ______ chromatography, a protein mixture must be applied to the column at a low pH so that the proteins will have a net positive charge and bind to the column. Ans: M Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis 10. In SDS-PAGE, disulfide-linked polypeptides can be separated after reacting the protein first with ______. Ans: K Level of Difficulty: Easy Section: 5.2.D Learning objective: Protein Purification and Analysis 11. Either dansyl chloride or Edman's reagent can be used to identify the ______ of a protein. Ans: E Level of Difficulty: Moderate Section: 5.3.A Learning objective: Protein Sequencing 12. The endoprotease ______ cleaves polypeptides on the C-terminal side of certain bulky hydrophobic amino acid residues. Ans: O Level of Difficulty: Moderate Section: 5.3.B Learning objective: Protein Sequencing

Multiple Choice 13. Proteins are synthesized in vivo by the translation of A) cDNA. B) tRNA. C) rRNA. D) exons. E) mRNA. Ans: E Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity 14. Since there are 20 standard amino acids, the number of possible linear polypeptides of length N can be expressed as: A) n × 20 B) 20n C) 20 × 10n D) n20 E) n × 1020 Ans: B Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity 15. Natural proteins most commonly contain linear polypeptides between 100 and 1000 residues in length. One of the reasons polypeptides outside this range may be disfavored is that A) larger polypeptides would likely be insoluble. B) smaller polypeptides do not form stable folded structures. C) smaller polypeptides typically assemble into prion-like aggregates. D) amide linkages are not strong enough to keep larger polypeptides intact. E) ribosomes are unable to synthesize larger polypeptides. Ans: B Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity

16. The vast majority of polypeptides contain between ______ amino acid residues. A) 10 and 50 B) 50 and 100 C) 100 and 1000 D) 1000 and 2000 E) 2000 and 34,000 Ans: C Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity 17. Which of the following has the most dramatic influence on the characteristics of an individual protein? A) the amino-acid sequence B) the amino-acid composition C) the location of its encoding gene within the genome D) the stereochemistry at the a-carbon E) the sequence of tRNA molecules involved in its translation Ans: A Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity 18. Which statement about insulin is correct? A) Insulin is composed of two polypeptides, the A chain and the B chain. B) Insulin contains an intrachain disulfide bond. C) Insulin contains interchain disulfide bonds. D) The A chain and the B chain of insulin are encoded by a single gene. E) All of the above are correct. Ans: E Level of Difficulty: Easy Section: 5.1 Learning objective: Polypeptide Diversity

19. A fast and common method for determining the protein concentration in column effluent is A) tandem mass spectrometry. B) salting in with ammonium sulfate. C) drying a portion and weighing the solid. D) measuring light absorption at 280 nm. E) Edman degradation. Ans: D Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis 20. The salting in of proteins can be explained by: A) salt counter-ions reducing electrostatic attractions between protein molecules. B) salt ions reducing the polarity of the solution. C) salt ions increasing the hydrophobic interactions. D) releasing hydrophobic proteins from nonpolar tissue environments. E) hydration of the salt ions reducing solubility of proteins. Ans: A Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 21. The quantitation of proteins due to their absorbance at ~280 nm (UV region) is due to the large absorbtivity of the ________ amino acids. A) anionic B) dansylated C) cleaved D) polar E) aromatic Ans: E Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis

22. Which of the following ‘assays’ would be most specific for a particular protein? A) Bradford assay B) UV absorptivity C) radioimmunoassay D) molar absorptivity E) amino acid analysis Ans: C Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 23. An enzyme-linked immunosorbent assay requires A) a radioactive substrate. B) a radioactive standard for binding to the antibody. C) aromatic amino acids. D) an antibody that binds the protein of interest. E) a catalytic antibody. Ans: D Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 24. ELISA is an example of a(n): A) enzyme assay. B) biological assay. C) binding assay. D) immunological assay. E) none of the above Ans: D Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis

25. You are purifying a nuclease by affinity chromatography. To determine which fractions contain the protein of interest, you test samples of all fractions for their ability to break down DNA. This is an example of A) a binding assay. B) a biological assay. C) an enzyme assay. D) an immunological assay. E) none of the above Ans: C Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis 26. A radioimmunoassay requires A) an enzyme-linked antibody. B) a coupled enzymatic reaction. C) a radiolabeled antibody. D) a catalytic antibody. E) a radiolabeled standard protein that is used to compete for binding to the antibody. Ans: E Level of Difficulty: Moderate Section: 5.2.A Learning objective: Protein Purification and Analysis 27. Five graduate students prepare extracts from 5 different tissues. Each student measures the total amount of alcohol dehydrogenase and the total amount of protein in his or her extract. Which extract has the highest specific activity? Total protein (mg) A B C D E

300 200 3000 5000 1000

Total alcohol dehydrogenase activity (units) 60,000 80,000 96,000 100,000 200,000

Ans: B Level of Difficulty: Easy Section: 5.2.A Learning objective: Protein Purification and Analysis

28. Which physical characteristic is not commonly used in protein separation? A) solubility B) stereochemistry C) size D) charge E) polarity Ans: B Level of Difficulty: Easy Section: 5.2.B Learning objective: Protein Purification and Analysis 29. Adding additional salt to a protein solution can cause: A) an increase in solubility called ‘salting in’. B) a decrease in solubility called ‘salting out’. C) protein precipitation from solution. D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section: 5.2.B Learning objective: Protein Purification and Analysis 30. A first step in purifying a protein that was initially associated with fatty substances would be A) Coomassie Brilliant Blue dye staining. B) analytical ultracentrifugation. C) ELISA. D) Western blotting. E) hydrophobic interaction chromatography. Ans: E Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis

31. The acronym HPLC stands for A) hydrophobic protein liquid chromatography. B) high performance liquid chromatography. C) hydrophilic partition liquid chromatography. D) high priced liquid chromatography. E) hydrostatic process liquid chromatography. Ans: B Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis 32. A technique that can be used to separate proteins based primarily on the presence of nonpolar residues on their surface is called A) ion-exchange chromatography. B) gel filtration chromatography. C) affinity chromatography. D) gel electrophoresis. E) hydrophobic interaction chromatography. Ans: E Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis 33. A technique that can be used to separate proteins based primarily on their pI is called A) ion-exchange chromatography. B) gel filtration chromatography. C) affinity chromatography. D) isoelectric focusing. E) hydrophobic interaction chromatography. Ans: D Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis

34. Which of the following amino acids would be last to elute at pH 8.0 from an anion-exchange column? A) lysine B) alanine C) glutamic acid D) asparagine E) glycine Ans: C Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis 35. Which of the following amino acids would be first to elute at pH 8.0 from an anionexchange column? A) lysine B) alanine C) glutamic acid D) asparagine E) glycine Ans: A Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis 36. The pK1, pK2, and pKR of the amino acid lysine are 2.2, 9.1, and 10.5, respectively. The pK1, pK2, and pKR of the amino acid arginine are 1.8, 9.0, and 12.5, respectively. A student at SDSU wants to use ion exchange chromatography to separate lysine from arginine. What pH is likely to work best for this separation? A) 1.5 B) 2.5 C) 5.5 D) 7.5 E) 10.5 Ans: E Level of Difficulty: Difficult Section: 5.2.C Learning objective: Protein Purification and Analysis

37. The pK1, pK2, and pKR of the amino acid histdine are 1.8, 9.3, and 6.0, respectively. The pK1, pK2, and pKR of the amino acid arginine are 1.8, 9.0, and 12.5, respectively. You have a mixture of histidine and arginine, how would you try to separate these two amino acids? A) anion exchange chromatography at pH 2 B) anion exchange chromatography at pH 4 C) cation exchange chromatography at pH 2 D) cation exchange chromatography at pH 4 E) cation exchange chromatography at pH 9 Ans: E Level of Difficulty: Difficult Section: 5.2.C Learning objective: Protein Purification and Analysis 38. What can be done to increase the rate at which a protein of interest moves down an ionexchange chromatography column? A) reduce the ion concentration in the eluant B) add a small amount of a non-ionic detergents to the eluant C) change the pH of the eluant D) add a protease inhibitor to the eluant E) reduce the temperature of the eluant Ans: C Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis 39. Hydrophobic interaction chromatography can be used to separate proteins based on differences in A) ionic charge. B) solubility. C) size. D) polarity. E) binding specificity. Ans: D Level of Difficulty: Easy Section: 5.2.C Learning objective: Protein Purification and Analysis

40. You are trying to separate five proteins, which are listed below, by gel filtration chromatography. Which of the proteins will elute first from the column? A) cytochrome c (12 kDa) B) RNA polymerase (99 kDa) C) glutamine synthetase (621 kDa) D) interferon-g (34 kDa) E) hemoglobin (62 kDa) Ans: C Level of Difficulty: Moderate Section: 5.2.C Learning objective: Protein Purification and Analysis 41. SDS-PAGE separates proteins primarily due to differences in A) isoelectric point. B) mass. C) polarity. D) solubility. E) amino acid sequence. Ans: B Level of Difficulty: Easy Section: 5.2.D Learning objective: Protein Purification and Analysis 42. Which of these techniques is used to separate proteins mainly based on mass? A) polyacrylamide gel electrophoresis (in the absence of SDS) B) SDS-PAGE C) isoelectric focusing D) immunoblotting E) Western blotting Ans: B Level of Difficulty: Easy Section: 5.2.D Learning objective: Protein Purification and Analysis

43. Which of these techniques uses antibodies to detect very small amounts of specific proteins following separation by SDS-PAGE. A) immunoblotting B) silverstaining C) Coomassie Brilliant Blue staining D) ELISA E) RIA Ans: A Level of Difficulty: Easy Section: 5.2.D Learning objective: Protein Purification and Analysis 44. Disulfide bonds can be cleaved using A) iodoacetate. B) dansyl chloride. C) 2-mercaptoethanol (b-ME). D) trypsin. E) phenylisothiocyanate. Ans: C Level of Difficulty: Easy Section: 5.3.A Learning objective: Protein Sequencing 45. Which of these reagents is commonly used to determine the number of polypeptides in a protein? A) iodoacetate B) dansyl chloride C) 2-mercaptoethanol (b-ME) D) cyanogen bromide E) DEAE Ans: B Level of Difficulty: Easy Section: 5.3.A Learning objective: Protein Sequencing

46. Enzymes that hydrolyze the internal peptide bonds (not the peptide bonds of the terminal amino acids) of a protein are classified as A) oxidoreductases. B) lyases. C) endopeptidases. D) nucleases. E) exopeptidases. Ans: C Level of Difficulty: Easy Section: 5.3.B Learning objective: Protein Sequencing 47. Which of the following substances cannot be used to cleave peptide bonds in polypeptides? A) trypsin B) cyanogen bromide C) endopeptidases D) 2-mercaptoethanol E) pepsin Ans: D Level of Difficulty: Moderate Section: 5.3.B Learning objective: Protein Sequencing 48. Which of these are commonly used to cleave peptide bonds in polypeptides? A) 2-mercaptoethanol (b-ME) B) dansyl chloride C) iodoacetate D) sodium dodecyl sulfate E) trypsin Ans: E Level of Difficulty: Moderate Section: 5.3.B Learning objective: Protein Sequencing

49. The peptide Leu─Cys─Arg─Ser─Gln─Met is subjected to Edman degradation. In the first cycle the peptide first reacts with phenylisothiocyanate under basic conditions. The product of this reaction is incubated with anhydrous trifluoroacetic acid and subsequently with an aqueous acid. What are the products generated in the first cycle. A) PTH─Leu, PTH─Cys, PTH─Arg, PTH─Ser, PTH─Gln, and PTH─Met B) PTH─Leu─Cys─Arg─Ser─Gln─Met C) PTH─Met and Leu─Cys─Arg─Ser─Gln─Met D) PTH─Leu─Cys and PTH─Arg─Ser─Gln─Met E) PTH─Leu and Cys─Arg─Ser─Gln─Met Ans: E Level of Difficulty: Moderate Section: 5.3.C Learning objective: Protein Sequencing 50. Edman degradation can be used to A) identify the N-terminal amino acid of a polypeptide. B) identify the C-terminal amino acid of a polypeptide. C) separate the subunits of a multi-subunit protein. D) cleave a protein at specific sites. E) cleave disulfide bonds within a protein so that the individual polypeptides can be separated. Ans: A Level of Difficulty: Easy Section: 5.3.C Learning objective: Protein Sequencing 51. Although a protein’s primary sequence can be inferred from the nucleotide sequence, modifications such as ______ can be determined most easily by tandem mass spectrometry followed by protein database searching. A) phosphorylation B) disulfide crosslinks C) glycosylation D) acetylation E) all of the above Ans: E Level of Difficulty: Easy Section: 5.3.D Learning objective: Protein Sequencing

52. The positive charge on proteins in electrospray ionization mass spectrometry is the result of A) protons fired at the gas-phase protein molecules. B) protonated side chains of Asp and Glu residues. C) protonated side chains of Arg and Lys residues. D) a high pH. E) electrons fired at the gas-phase protein molecules. Ans: C Level of Difficulty: Moderate Section: 5.3.D Learning objective: Protein Sequencing 53. ______________ has emerged as a technique for protein sequencing. A) NMR spectroscopy B) Mass spectrometry C) Gel electrophoresis D) Phylogenetic analysis E) Limited proteolysis Ans: B Level of Difficulty: Easy Section: 5.3.D Learning objective: Protein Sequencing 54. Protein sequences are customarily ‘reconstructed’ from sequenced fragments because A) protein purification invariably results in the fragmentation of the protein of interest. B) proteins are naturally and inevitably cleaved by proteolytic enzymes. C) proteins are composed of multiple subunits. D) large polypeptides cannot be directly sequenced. E) all of the above Ans: D Level of Difficulty: Easy Section: 5.3.E Learning objective: Protein Sequencing

55. You have purified a new peptide hormone. To determine its amino acid sequence you have digested the polypeptide with trypsin and in a separate reaction you have cleaved the polypeptide with cyanogen bromide. Cleavage with trypsin yielded 5 peptides that were sequenced by Edman degradation as shown in the following. 1. Ser─Leu 2. Asp─Val─Arg 3. Val─Met─Glu─Lys 4. Ser─Gln─Met─His─Lys 5. Ile─Phe─Met─Leu─Cys─Arg Cleavage with cyanogen bromide yielded 4 peptides that were sequenced by Edman degradation: 1. His─Lys─Ser─Leu 2. Asp─Val─Arg─Val─Met 3. Glu─Lys─Ile─Phe─Met 4. Leu─Cys─Arg─Ser─Gln─Met Determine the identity of the N-terminal amino acid after reconstructing the intact protein. A) Asp B) Ser C) His D) Glu E) Ile Ans: A Level of Difficulty: Difficult Section: 5.3.E Learning objective: Protein Sequencing 56. In two homologous proteins, which residue is most likely to replace a Glu residue as a conservative substitution? A) Asp B) Trp C) Met D) Ile E) Lys Ans: A Level of Difficulty: Easy Section: 5.4.A Learning objective: Protein Evolution

57. A phylogenetic tree depicts ___________ of proteins. A) folding patterns B) hypervariable residues C) invariable residues D) evolutionary relationships E) gene sequences Ans: D Level of Difficulty: Easy Section: 5.4.A Learning objective: Protein Evolution 58. A protein that has had few changes in its amino acid sequence over evolutionary history is labeled A) a fibrinopeptide. B) evolutionarily conserved. C) random. D) a product of pseudogenes. E) phylogenetic. Ans: B Level of Difficulty: Easy Section: 5.4.B Learning objective: Protein Evolution 59. Paralogous genes are A) genes that do not encode protein. B) genes of slowly evolving proteins. C) relics of genes that are not expressed. D) genes of rapidly evolving proteins. E) the results of gene duplication. Ans: E Level of Difficulty: Moderate Section: 5.4.B Learning objective: Protein Evolution

60. A fast way for nature to generate new proteins is: A) generation of pseudogenes. B) mutation by neutral drift. C) shuffling protein domains or motifs. D) hypervariable positions. E) liberal substitution. Ans: C Level of Difficulty: Easy Section: 5.4.B Learning objective: Protein Evolution 61. ___________ is an example of a very slowly evolving protein. A) Histone H4 B) Hemoglobin C) Cytochrome c D) Fibrinopeptides E) none of the above Ans: A Level of Difficulty: Moderate Section: 5.4.B Learning objective: Protein Evolution 62. Proteins are often constructed from multiple segments of 40-200 amino acid residues, commonly called A) pseudogenes. B) hypervariable residues. C) protolytic fragments. D) domains. E) subunits. Ans: D Level of Difficulty: Easy Section: 5.4.B Learning objective: Protein Evolution

SHORT ANSWER 63. Proteins can vary in size from approximately 40 to 34,000 amino acids. a. Why is there a lower limit to the size of proteins? b. Why is there an upper limit to the size of polypeptides? Ans: a. Polypeptides shorter than 40 residues are unable to maintain a stable fold (probably because there are not enough functional groups to help stabilize the folded structure). b. The longer the polypeptide, the longer the corresponding mRNA and gene, resulting in an increase in mistakes made during transcription and translation. Beyond a certain size every protein encoded for by a very large gene will include debilitating mistakes. Level of Difficulty: Moderate Section: 5.1 Learning objective: Polypeptide Diversity 64. We are able to purify proteins because they differ from each other in various physical or chemical properties. List 5 physicochemical properties of proteins that can be used as basis for their separation. Give a method of separation based on each of these properties (match the method with the property). Ans: 1. solubility — salting out; 2. ionic charge — ion exchange chromatography, electrophoresis (in the absence of SDS), or isoelectric focusing; 3. polarity — hydrophobic interaction chromatography; 4. size (mass) — gel filtration chromatography (size exclusion chromatography) or SDS-PAGE 5. ability to bind to specific molecules — affinity chromatography Level of Difficulty: Moderate Section: 5.2A Learning objective: Protein Purification and Analysis

65. One technique commonly used in protein purification is chromatography. a. Explain briefly the general principle of column chromatography b. Name four types of chromatography and indicate for each of these types the basis for separation (match types of chromatography with the properties that form the basis for separation). Ans: a. In chromatography there are two phases, the stationary phase and the mobile phase. The stationary phase is the column material and the mobile phase is the buffer that runs through the column. Proteins or molecules are separated based on their relative affinities for these two phases. A molecule with very high affinity for the stationary phase will spend most of its time associated with the column material and will move very slowly down the column. A molecule with high affinity for the mobile phase will spend most of its time suspended in the buffer and will move quickly through the column. Molecules with high affinity for the stationary phase will elute late from the column. Molecules with a high affinity for the mobile phase will elute early. b. 1. ion-exchange chromatography — ionic charge; 2. gel filtration chromatography — size (mass); 3. hydrophobic interaction chromatography — polarity; 4. affinity chromatography — ability to bind to specific molecules. Level of Difficulty: Moderate Section: 5.2C Learning objective: Protein Purification and Analysis 66. Ion exchange chromatography is a commonly used method for separation of biomolecules. a. What are the two types of ion exchange chromatography? b. In what order would Arg, Val, and Glu elute from a carboxymethyl column at pH 6.0. Carboxymethyl is negatively charged at pH 6.0. c. You are trying to purify a protein using ion exchange chromatography. Unfortunately, your protein remains bound to the ion exchange column or it is eluting very slowly. What are the two changes you can make, to try to elute your protein more quickly from this column? Ans: a. cation exchange chromatography and anion exchange chromatography. b. First Glu, then Val, followed last by Arg, because at pH 6.0 Glu is has an electric charge of 1, Val is neutral, and Arg has an electric charge of +1. c. To make your protein move more quickly through the column you need to reduce the interactions with the column material. This can be done by changing the pH (changing the charge on your protein) or by increasing the ion concentration in the eluant (ions will compete with your protein for binding to the column material). Level of Difficulty: Moderate Section: 5.2C Learning objective: Protein Purification and Analysis

67. A variety of chromatographic techniques are available for protein purification. a. Explain briefly the principle of hydrophobic interaction chromatography. b. Name three changes that can be made to the eluant that can be used to speed up elution of the protein of interest from a hydrophobic interaction chromatography column. Ans: a. The column material is substituted with nonpolar groups. Proteins with nonpolar regions on their surface will be driven to interact with the column material as a result of the hydrophobic affect. b. To weaken the interaction between the column material and the nonpolar regions on your protein you can include detergents (they will shield nonpolar regions on proteins from interacting with water or other nonpolar groups), change the pH (will change the polarity of your protein), or reduce the ion concentration of the eluant (this will make it less polar). Level of Difficulty: Moderate Section: 5.2C Learning objective: Protein Purification and Analysis 68. You are interested in receptor protein-tyrosine kinases and you are purifying a novel phosphotyrosine-binding protein (NPBP-1). In order to characterize this protein you need to separate it from three other proteins (X, Y, and Z) that are still present in your partially purified material. The proteins in your preparation have the following properties:

protein X protein Y protein Z NPBP-1

binds to phosphotyrosine yes yes no yes

Size (kDa)

85 29 31 28

7.2 2.9 7.4 7.5

a. What type of separation technique can be used to separate protein NPBP-1 from protein X? b. What type of separation technique can be used to separate protein NPBP-1 from protein Y? c. What type of separation technique can be used to separate protein NPBP-1 from protein Z? Ans: a. On a size (mass) basis: gel permeation chromatography, SDS-PAGE, or ultracentrifugation. b. On a charge basis: ion exchange chromatography or isoelectric focusing c. On a binding behavior basis: phosphotyrosine affinity chromatography Level of Difficulty: Moderate Section: 5.2C Learning objective: Protein Purification and Analysis

69. You have purified the receptor for a hormone by affinity chromatography. During gel filtration chromatography under native conditions the receptor elutes between pyruvate decarboxylase (250 kDa) and glutamine synthetase (620 kDa). During SDS-PAGE, in the absence of reducing agents, the receptor migrates as a single band of approximately 230 kDa. When SDS-PAGE is carried out in the presence of 2-mercaptoethanol the receptor migrates as two bands of approximately 95 and 135 kDa. Explain this result. Ans: The receptor is a heterotetramer composed of two a subunits of 95 kDa and two b subunits of 135 kDa. Heterodimers of one a subunit and one b subunit are stabilized by disulfide bonds. Two heterodimers are held together by hydrophobic interactions. In the absence of detergents during gel filtration all subunits stay together and we observe a 460 kDa protein. During SDSPAGE (in the absence of reducing agents) SDS interferes with the hydrophobic interactions that hold the two ab dimers together and we observe a 230 kDa protein. Finally, when we add 2mercaptoethanol during SDS-PAGE the disulfide bonds are broken and we observe 2 polypeptides of 135 and 95 kDa.

Level of Difficulty: Moderate Section: 5.2D Learning objective: Protein Purification and Analysis

Chapter 6: Proteins: Three-Dimensional Structure Matching For questions 1-10: A) tertiary structure B) keratin C) molecular chaperones D) hydropathy E) cis F) trans G) sterically forbidden conformation H) regular secondary structure I) collagen J) peptide bond K) ribonuclease A (RNase A) L) alpha 1. Repeating values of f and y make up predictable orientations of amino acid with a chain, this predictable orientation forms___________. Ans: H Level of Difficulty: Easy Section 6.1.B Learning objective: Secondary Structure 2. The strength of _______ comes from close packing of glycine residues and the characteristics of hydroxyproline allowing formation of a left- handed helical conformation which combines with two other left handed structures to form a right-handed triplet helix. Ans: I Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 3. The overall arrangement of the regular structural elements such as the α helix and the β sheet in the protein are considered the protein's ______. Ans: A Level of Difficulty: Easy Section 6.2.C Learning Objective: Tertiary Structure

4. A historical experiment exploring denaturation upon β- mercaptoethanol reduction of disulfide bonds and spontaneous renaturation upon dialysis to remove the β- mercaptoethanol was carried out using the protein ______. This experiment demonstrated the importance of disulfide bonds and amino acid sequence in folding of proteins. Ans: K Level of Difficulty: Easy Section 6.4.B Learning Objective: Protein Stability 5. A rigid, planar structure between at least two amino acids consisting of about 40% double bond character is characteristic of a ______. Ans: J Section 6.1.A Level of Difficulty: Easy Learning Objective: Primary Structure 6. The _____________ of an amino acid can be used to predict whether an amino acid side chain folds towards the inside or outside of a globular protein. Ans: D Level of Difficulty: Easy Section 6.2.B Learning Objective: Tertiary Structure 7. ________ is a fibrous protein that contains a hydrophobic amino acid approximately every 4 residues which forms an α helix with one hydrophobic side. Ans: B Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 8. In most peptide groups the ______ conformation is not sterically favored. Ans: EF Level of Difficulty: Easy Section 6.1.A Learning Objective: Secondary Structure

9. In vivo protein folding is often is assisted by ______. Ans: C Level of Difficulty: Easy Section 6.5.B Learning Objective: Protein Folding 10. In a ______, the f and y angles of the peptide backbone would orient atoms closer than their van der Waals distance. Ans: G Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure

Multiple Choice 11. In a Ramachandran diagram, a larger area represents sterically allowed torsion angles of f and y that are allowed in _____ rather than in ______ because there is greater opportunity for separation of amino acid side chains. A) secondary structure…tertiary structure B) α helix…β sheet C) β sheet…α helix D) tertiary structure…secondary structure E) none of the above Ans: C Level of Difficulty: Difficult Section 6.1.A and B Learning Objective: Secondary Structure 12. In a protein, the most conformationally restricted amino acid is ______; the least conformationally restricted is ______. A) Trp, Gly B) Met, Cys C) Pro, Gly D) Ile, Ala E) Ala, Pro Ans: C Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure

13. Which of the following has (have) both a favorable hydrogen bonding pattern and f and y values that fall within the allowed Ramachandran conformational regions? A) a helix B) collagen helix C) b sheet D) all of the above E) none of the above Ans: D Level of Difficulty: Moderate Section 6.1.A, B, and C Learning Objective: Secondary Structure 14. Which one of these characteristics is not true for the a helix? A) There are 3.6 amino acids per turn. B) There is a requirement for glycine every third amino acid residue. C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the NH group of the (n + 4)th amino acid residue. D) Proline is typically not found in the a helix. E) It is right-handed. Ans: B Level of Difficulty: Easy Section 6.1.B Learning Objective: Secondary Structure 15. Which of these characteristics does not describe the b sheet? A) Amino acid side chains are located both above and below the sheet. B) b sheets have a pleated edge-on appearance. C) They can exist in either parallel or antiparallel configurations. D) The sheets contain as few as two and as many as 22 polypeptide chains. E) Parallel b sheets containing fewer than five chains are the most common. Ans: E Level of Difficulty: Moderate Section 6.1.B Learning Objective: Secondary Structure

16. Which statement below does not describe fibrous proteins? A) Domains have a globular fold. B) These proteins usually contain only one type of secondary structure. C) These proteins usually exhibit structural or protective characteristics. D) These proteins have usually elongated hydrophilic surfaces. E) These proteins are usually insoluble in water. Ans: A Level of Difficulty: Moderate Section 6.1.C Learning Objective: Secondary Structure 17. Which of the following changes would not alter the functional characteristics of α keratin? A) Increasing the number of residues per turn to 4.1 while maintaining the same amino acid sequence. B) Substitution of a hydrophilic amino acid for a hydrophobic amino acid at position a and d of the 7-residue pseudorepeat. C) Decreasing the number of cysteine amino acids within each protofilament. D) Changing the environment surrounding the protein to one that is more reductive. E) All of the above would alter the functional characteristics of keratin. Ans: E Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 18. Which of the following statements is true regarding collagen? A) The inability to hydroxylate proline results in the inability to synthesize collagen. B) The α helical structure is ideal for intertwining 3 filaments. C) Hydrogen bonds between the ─OH groups of Hyp residues stabilize the helix. D) The requirement for glycine every 3rd amino acid is essential for the triplet helix formation. E) On average, there is one proline for every hydroxyproline. Ans: D Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure

19. Which of the following gives the best example of a nonrepetitive structure in a protein? A) a random sequence of 12 amino acids with high Pα values forming an α helix B) an amino acid sequence with the following pattern "…a-b-c-d-e-a-b-c-d-a-b-c-d…" C) a 13 residue α helix with a Gln at position n+12 which hydrogen bonds to a residue at position n+10 D) All of the above statements describe nonrepetitive protein structures. E) None of the above describe nonrepetitive protein structures. Ans: C Level of Difficulty: Difficult Section 6.1.D Learning Objective: Secondary Structure 20. Which of the following is true regarding crystalline proteins? A) Many crystallized enzyme proteins remain catalytically active. B) The diffractive pattern observed during X-ray exposure to the crystal can be used to calculate the electron density map of the crystalline protein. C) The larger region indicating electron density with in the electron density map, the more accurate the structure determination. D) A and B are true. E) A, B, and C are true. Ans: D Level of Difficulty: Moderate Section 6.2.A Learning Objective: Tertiary Structure 21. In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to hydroxyproline, resulting in: A) lathyrism B) prion diseases C) amyloid formation D) scurvy E) allysine Ans: D Level of Difficulty: Easy Section 6.5.C Learning Objective: Protein Folding

22. Of the following, which amino acid is most likely to be found in position 1 or 4 on α keratin? A) Phe B) Ala C) Lys D) Trp E) Pro Ans: B Level of Difficulty: Moderate Section 6.2.B and 6.1.C Learning Objective: Tertiary Structure and Secondary Structure 23. Which of the following amino acids combinations have side chains with groups that have the greatest ability to stabilize the tertiary structure of a protein? A) Lys and Arg B) Cys and Glu C) Glu and Lys D) Gln and Glu E) Pro and Asp Ans: C Level of Difficulty: Difficult Section 6.4.A Learning Objective: Protein Stability 24. The low pH found in the gut can enhance the digestibility of dietary protein by causing ___. A) amide hydrolysis B) protein denaturation C) disulfide reduction D) prion formation E) cysteine oxidation Ans: B Level of Difficulty: Moderate Section 6.4.B Learning Objective: Protein Stability

25. Which of the following occurs first when folding a disordered polypeptide chain into a stable protein formation? A) formation of a low energy state B) association of ordered subunits C) aggregation of hydrophobic regions in the protein D) tertiary structure refinement E) formation of a low entropy state Ans: C Level of Difficulty: Moderate Section 6.5.A Learning Objective: Protein Folding 26. Imagine that a researcher treated a protein with a high concentration of a chaotropic agent. Which of the following is the most likely result of the treatment? I. Nonpolar portions of the protein become more soluble. II. The protein begins to denature , III. The protein stability increases due to hydrophobic collapse, A) I, II, III B) I, II C) II, III D) I, III E) II Ans: B Level of Difficulty: Difficult Section 6.4.B and 6.5.A Learning Objective: Protein Folding 27. For b-sheets, the terms ‘parallel’ and ‘antiparalllel’ refer to ___________. A) the ‘direction’ of the associated peptide strands B) the orientation of the amide cross-links C) the quaternary structure of the protein D) the orientation of the hydrogen bonding D) the topology of the reverse turns Ans: A Level of Difficulty: Easy Section 6.1.B Learning Objective: Secondary Structure

28. In general molecular chaperone proteins function by A) mediating disulfide bond formation B) synthesizing new proteins when one is misfolded. C) preventing premature folding by binding hydrophobic regions of the protein. D) enhancing salt bridge formation. E) none of the above Ans: C Level of Difficulty: Moderate Section 6.5.B Learning Objective: Protein Folding 29. Conventional one dimensional NMR spectroscopy is not generally an effective tool for determination of protein structure because… I. Proteins (including small proteins) have a high number of hydrogen atoms. II. NMR requires a high quality protein crystal. III. The NMR spectra exhibit high peak overlap. A) I and II B) II and III C) I and III D) I, II, and III E) III only Ans: C Level of Difficulty: Moderate Section 6.2.A Learning Objective: Tertiary Structure 30. When comparing similarities among multiple protein structures, which of the following is false? A) Proteins with the same function from a different species are likely to have similar motifs. B) Proteins with the same function from different species are likely to be more similar in sequence than in structure. C) An effective protein motif isl likely be observed in multiple proteins. D) Proteins with the same motifs are likely to perform similar functions. E) None of the above statements are false. Ans: B Level of Difficulty: Difficult Section 6.2.C Learning Objective: Tertiary Structure

31. The structure and sequence of a protein of unknown function was examined. Which of the following provides the best prediction of the protein's function? A) the observation of several disordered α helical domains. B) the observation of multiple protein subunits. C) the observation of motif known as the Rossmann fold. D) the observation of a large number of random coil regions. E) All of the above offer excellent prediction of the protein's function. Ans: C Level of Difficulty: Difficult Section 6.2.C Learning Objective: Tertiary Structure 32. The Protein Data Bank (PDB) is a database provides structural information about proteins that may be useful for which of the following? I. A researcher studying the changes in protein fold associated with prions. II. A researcher classifying structural elements by function. III A researcher designing a compound to bind tightly to a particular region in the protein. A) I only B) II only C) III only D) I, II E) I, II, II Ans: E Level of Difficulty: Moderate Section 6.2.E Learning Objective: Tertiary Structure 33. Noncovalent forces that stabilize protein structure include all of the following except __________. A) the hydrophobic effect B) salt bridges C) electrostatic interactions with metal ions D) hydrogen bonding E) disulfide bridges Ans: E Level of Difficulty: Easy Section 6.4.A Learning Objective: Protein Stability

34. The classic experiment demonstrating that reduced and denatured RNase A could refold into the native form demonstrates that _______. A) 1° structure can determine 3° structure B) denaturation does not disrupt protein 2° structure C) disulfide bonds do not stabilize folded proteins D) All of the above. E) None of the above Ans: A Level of Difficulty: Moderate Section 6.4.B Learning Objective: Protein Stability 35. The first step in the folding of disordered polypeptides into ordered functional protein is the formation of ______. A) 1o structure B) 2° structure C) 3° structure D) 4° structure E) hydrogen bonds Ans: B Level of Difficulty: Easy Section 6.5.A Learning Objective: Protein Folding 36. Evolutionary processes have A) increased the stability of 4° structures. B) decreased the number of subunits. C) increased similarity amount 1° structures. D) enhanced efficient folding pathways. E) all of the above Ans: D Level of Difficulty: Moderate Section 6.5.A Learning Objective: Protein Folding

37. Chaperonins such as the GroEL/ES system A) function with thermophilic proteins only. B) are required at low pH. C) require ATP hydrolysis. D) in vitro only. E) function in a nonaqueous environment. Ans: C Level of Difficulty: Moderate Section 6.5.B Learning Objective: Protein Folding 38. Protein diseases can be caused by which of the following A) mutations affecting the 1° structure. B) mutations affecting the 3° structure. C) changes in the post-synthetic processing of proteins. D) All of the above are potential causes. E) None of the above are potential causes. Ans: D Level of Difficulty: Difficult Section 6.5.C Learning Objective: Protein Folding 39. Which of the following would be most stable based on the information you have learned about protein structure? A) a loop region with 8 amino acids B) a β sheet region made up of amino acids Val, Ile, Phe C) an α helix made up of Cys, Pro, and Phe D) a β hairpin with 12 amino acids E) All have equal stability. Ans: B Level of Difficulty: Difficult Section 6.1.D Learning Objective: Secondary Structure

40. The structure of hen egg white protein has been solved and the torsion angles j and y are shown for each residue in the table below. What structure motif most likely forms as a result of this protein sequence? Residue Number 31 32 33 34 35 Break 42 43 44 45 46

-61 -72 -66 -67 -81 Break -30 -142 -154 -91 -110

-44 -29 -65 -23 -51 Break 142 150 121 136 174

A) β strand connected to another β strand with a break (or loop/turn) in between B) α Helix connect to another α Helix with a break (or loop/turn) in between C) β strand connected to another β strand with a alpha helix in between D) α Helix connected to a β strand with a break (or loop/turn) in between E) None of the above are correct. Ans: D Level of Difficulty: Moderate Section 6.1.A Learning Objective: Secondary Structure 41. Hydrogen bonds and maximum separation of amino acid side chains make the _____very stable and energetically ______________. A) α helix and β sheet, favorable B) α helix, unfavorable C) β sheet, unfavorable D) α helix, favorable E) β sheet, favorable Ans: A Level of Difficulty: Moderate Section 6.1.B Learning Objective: Secondary Structure

42. A chaperonin A) helps fold some proteins in their lowest energy state. B) is required for all proteins to fold properly. C) mediates the unfolding of proteins. D) is required for protein denaturation. E) counteracts the laws of thermodynamics. Ans: A Level of Difficulty: Moderate Section 6.5.B Learning Objective: Protein Folding 43. A helix has hydrogen bonds between the carbonyl group from residue “n” and the amino group of residue “n+6,” which of the following is TRUE? A) It has 3.6 residues per turn. B) It is a random coil, not a helix. C) It is an α helix. D) It has more residues per turn than an α helix. E) It has fewer residues per turn than an α helix. Ans: D Level of Difficulty: Difficult Section 6.1.B Learning Objective: Secondary Structure 44. Which of the following contribute to the minimization of energy that occurs with protein folding? A) orientating amino acid groups to maximize hydrogen bonding B) folding hydrophobic groups towards the exterior of the protein C) burying polar groups towards the interior of the protein D) extensive cavity formation E) all of the above Ans: A Level of Difficulty: Moderate Section 6.5.A Learning Objective: Protein Folding

45. Which of the following best describes the cause of Creutzfeld-Jakob Disease (a disease which human can develop with symptoms similar to those of mad cow disease)? A) aggregation of a misfolded protein. B) aggregation of random coil regions on a protein. C) ingestion of ammonium salts. D) the serious side effects of experimental treatment with Quinacrine E) All are potential causes Creutzfeld-Jakob disease. Ans: A Level of Difficulty: Difficult Section 6.5.C Learning Objective: Protein Folding 46. Which of the following lines in the figure at right indicates a b hairpin structure? A) A, C, D B) B and C C) A only D) A, B, and D E) C only Ans: D Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 47. Proteins can denature due to a change in A) pH. B) temperature. C) ionic strength. D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section 6.4.A-C Learning Objective: Protein Stability

48. Examine the three sequences below for collagen-like proteins. If hydrogen bonding were the most important feature in determining strength in fibrous proteins, which of the following sequences likely has the highest melting temperature and why? (Note: Flp = fluoroproline; Hyp = hydroxyproline) I. Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly II. Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly III. Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr A) “1” because Hyp has OH groups B) “1” because the electronegativity of oxygen is greater C) “2” because the electronegativity of proline is greater D) “2” because the electronegativity of the –OH group increases hydrogen bond strength E) “3” because Thr is a small amino acid which allows close packing Ans: A Level of Difficulty: Difficult Section 6.1.C and 6.4.A-C Learning Objective: Protein Stability and Secondary Structure 49. Based on what you know about fibrous protein structure and sequence, what type of fibrous protein is this sequence most likely to from (You can assume that the protein is longer than what is shown and is repeating as shown, also note the polarity of each amino acid.)? Val – Cys – Lys – Val - Cys – Ala – Cys - Val – Cys – Lys – Val - Cys – Ala – Cys A) a keratin B) β keratin C) collagen D) pleated collagen E) This sequence cannot be from any of the structural proteins. Ans: A Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure

50. Which of the following structural proteins has the greatest elasticity? A) akeratin B) β ketatin C) collagen D) pleated collagen E) A and B are equal Ans: D Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 51. Noncovalent interactions account for the strength of which of the following structural proteins? A) a keratin B) collagen C) pleated collagen D) A and B E) B and C Ans: B Level of Difficulty: Moderate Section 6.1.C Learning Objective: Secondary Structure 52. Examine the three sequences below for collagen-like proteins and their melting temperatures (Tm). (Note: Flp = fluoroproline; Hyp = hydroxyproline) Based on this data, what is the most important feature in determining the strength of the collagen protein? 1) …-Pro-Hyp-Gly-Pro-Hyp-Gly-Pro-Hyp-Gly-… Tm=60oC 2) …-Pro-Flp-Gly-Pro-Flp-Gly-Pro-Flp-Gly-… Tm=78oC 3) …-Gly-Pro-Thr-Gly-Pro-Thr-Gly-Pro-Thr-… Tm=30oC A) hydrogen bonding B) inductive effect C) electrostatic effect D) electrostatic and Inductive effect are equal E) hydrogen bonding and inductive effect are equal Ans: B Level of Difficulty: Difficult Section 6.1.C, Chapter Supplement: Case 6 (Note to instructor: the text does not use the term inductive, the case does – if you have not assigned the case, you may want to consider whether your students should be expected to know the term inductive.)

Learning Objective: Secondary Structure; Chapter Supplement: Case 6 53. When considering fibrous proteins, which of the following statements is TRUE? A) Noncovalent interactions contribute to the strength of all of these proteins. B) All of them consist of a helix structure. C) All of them require vitamin C. D) Decrease in amounts of any of them cause scurvy. E) All of these are true of fibrous proteins. Ans: A Level of Difficulty: Easy Section 6.1.C Learning Objective: Secondary Structure 54. In a Ramachandran diagram the region representing the angles of f and y that correspond to those commonly made by an amino acid that favors a left-handed a helix are different from those angles commonly made by an amino acid that favors right-handed a helix formation. Which of the following statements provides a plausible explanation for this difference? A) Groups which would normally undergo high steric hindrance in the right-handed arrangement are separated maximally in the left-handed arrangement. B) Left-handed helices have smaller pitch than right-handed helices. C) The peptide backbone can coil tighter in the left-handed helices than in the right-handed helices. D) Left-handed helices exhibit cyclic symmetry, while righthanded helices are asymmetric. E) All of the above are plausible explanations. Ans: A Level of Difficulty: Difficult Section 6.1.A Learning Objective: Secondary Structure 55. Which of the characteristics of collagen structure listed below contrubute to the tensi le strength of collagen? I. Collagen is made up of a triplet helix where 3 left-handed helices twist together in a right handed sense. II. Collagen includes at repeating sequence of amino acids with glycine every 3 amino acids in a helix with about 3 amino acids per turn. III. The three left-handed helices are staggered to allow close packing between glycine residues and rigidity from the bulky and inflexible proline/hydroxyproline. A) I B) I and II C) I, II, and III

D) II and III E) I and III Ans: C Level of Difficulty: Difficult Section 6.1.C Learning Objective: Secondary Structure 56. Native protein purifications often require multiple reaction steps in order to purify the protein of interest from other proteins. One method used for protein separation in purification procedures is a change from water to an organic solvent. Which of the following would be accomplished by this solvent change? A) Proteins with hydrophobic groups on the interior would maintain their native state. B) Proteins with hydrophilic groups on the exterior would denature and likely precipitate. C) Proteins with exposed hydrophobic groups would maintain their structure and remain in solution. D) Both A and B would occur. E) Both B and C would occur. Ans: E Level of Difficulty: Difficult Section 6.4.A Learning Objective: Protein Stability

57. When solving a protein structure using X-ray crystallography, the crystallographer generates a 3-D grid called an electron density map based on the observed diffraction pattern. The higher the resolution, the more detailed the electron density map and therefore the easier it is to identify what atoms (and therefore what amino acids) are in a given position. Based on the three choices below, in which of the following groups could the two of amino acids be the easiest to differentiate regardless of resolution? I. Leucine vs. Isoleucine II. Phenylalanine vs. Alanine III. Glutamate vs. Glutamic acid A) Those in both groups I and II could be differentiated B) Those in both groups I and III could be differentiated C) Only those in group II could be differentiated D) Only those in group III could be differentiated E) Only those in groupI could be differentiated Ans: C Level of Difficulty: Difficult

Section 6.2.A Learning Objective: Tertiary Structure 58. Protein dynamics is a field of study that examines the movements with in a protein. Which type of protein structure determination would be most useful to study this type of change? A) X-ray crystallography B) Nuclear Magnetic Resonance (NMR) C) X-ray absorption spectroscopy D) A and B E) B and C Ans: B Level of Difficulty: Difficult Section 6.2.A Learning Objective: Tertiary Structure 59. What observation about protein refolding or renaturation helped to solidify the connection between primary amino acid sequence and 3-D structure? A) Spontaneous refolding of proteins into their native state under physiologic conditions. B) Assisted refolding of proteins into their native state under laboratory conditions. C) Identification of thermostable proteins than maintain their native state in adverse temperatures. D) A and B E) B and C Ans: A Level of Difficulty: Moderate Section 6.2.A Learning Objective: Protein Structure 60. Molecular chaperones bind to unfolded or partially folded polypeptide chains in order to accomplish which of the following? A) ensure that improper aggregation of hydrophobic segments does not occur B) engulf the protein in order to ensure that the protein is not damaged by heat denaturation C) facilitate native folding by exposing hydrophobic segments of the protein as it is synthesized D) facilitate aggregation of multiple subunits of a protein during synthesis E) All of the above are accomplished by molecular chaperones. Ans: A Level of Difficulty: Moderate Section 6.4.B

Learning Objective: Protein Folding

Chapter 7: Protein Function Part I: Myoglobin and Hemoglobin Matching A) B) C) D) E) F) G) H) I) J) K) L) M

positively cooperative cyanosis His E7 decrease R hydrogen bonds increase symmetry His F8 ion pairs T hemolytic anemia sequencial

1. When oxygen binds to heme, the oxygen forms a hydrogen bond with ______. Ans: C Level of Difficulty: Moderate Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 2. In the ______ state of hemoglobin, the iron ion is out of the plane of the porphyrin ring. Ans: K Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 3. The conversion of hemoglobin from the T to the R state requires breaking of ______ involving C-terminal residues. Ans: J Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

4. Hemoglobin's subunits bind oxygen in a ______ manner. Ans: A Level of Difficulty: Easy Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 5. An increase in pCO2 causes hemoglobin's affinity for oxygen to ______. Ans: D Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 6. The absence of 2,3-BPG causes hemoglobin's affinity for oxygen to______. Ans: G Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 7. The ______ model of allosterism requires subunits to change conformation simultaneously. Ans: H Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 8. Sickle cell hemoglobin does not form fibers in the ______ form. Ans: E Level of Difficulty: Easy Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

9. When unstable hemoglobin is degraded; degradation products often cause cell lysis, leading to a condition called ______. Ans: L Level of Difficulty: Moderate Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 10. Mutations that favor the oxidation of the heme iron(II) to iron(III) can cause ______. Ans: B Level of Difficulty: Moderate Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

Multiple Choice 11. Which of the following is not a ligand to the porphyrin ring Fe(II) ion in oxymyoglobin? A) His E7 B) His F8 C) Nitrogen atoms in the porphyrin ring D) Oxygen E) all are ligands Ans: A Level of Difficulty: Moderate Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 12. Which gas does not bind to the porphyrin ring Fe(II) ion in myoglobin? A) NO B) CO C) CO2 D) O2 E) H2S Ans: C Level of Difficulty: Easy Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 13. Which of the following statements does not apply to the K value in the equation for the oxygen binding curve of myoglobin? A) It is numerically equal to p50. B) It is defined as that oxygen partial pressure at which half of the oxygen binding sites are occupied. C) It is a measure of the affinity of myoglobin for oxygen. D) If Y > K, then myoglobin is less than 50% saturated with oxygen. E) It is the value of pO2 at which Y = 0.5. Ans: D Level of Difficulty: Easy Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

14. Myoglobin’s secondary structure is primarily composed of ______________. A) parallel b-sheets B) antiparallel b-sheets C) a-helices D) W-loops E) polyproline helices Ans: C Level of Difficulty: Easy Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 15. Myoglobin’s primary physiological role is to facilitate oxygen ________. A) storage B) metabolism C) binding D) reduction E) diffusion Ans: E Level of Difficulty: Easy Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 16. If the gene for myoglobin is "knocked out" in mice, the mice: A) have larger lungs. B) respire extremely rapidly. C) have dark brown muscle tissue. D) appear normal, with lighter colored muscle tissue. E) have their growth stunted. Ans: D Level of Difficulty: Moderate Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

17. Carbon monoxide binds to heme: A) with a higher affinity than oxygen. B) resulting in the oxidation of the Fe(II) to Fe(III) C) in a manner that displaces carbon dioxide, causing CO2 poisoning. D) from the side opposite oxygen, resulting in a brown colored heme. E) with a lower affinity than oxygen. Ans: A Level of Difficulty: Easy Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 18. Myoglobin and a single chain of hemoglobin have similar ______ structures. A) primary B) secondary C) tertiary D) quaternary E) none of the above Ans: C Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 19. The primary structure of mammalian hemoglobin, an a2b2 tetramer, is approximately _____ identical to myoglobin. A) 2% B) 18% C) 50% D) 78% E) 98% Ans: B Level of Difficulty: Moderate Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

20. Hemoglobin is a heterotetramer. How many protomers are present in hemoglobin? A) 0 B) 1 C) 2 D) 3 E) 4 Ans: C Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 21. What is the type of symmetry that relates the protomers in hemoglobin with respect to each other? A) C2 B) C4 C) D2 D) D4 E) Tetrahedral symmetry Ans: A Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 22. Hemerythrin and hemocyanin are: A) human mutant hemoglobins with decreased oxygen affinity. B) hemoglobin variants that are found in animals at high altitude. C) synthetic derivatives of hemoglobin’s heme group used in artificial blood substitutes. D) oxygen transport proteins found in invertebrates. E) tetrameric hemoglobin derivatives containing only a-chains (a4 tetramers). Ans: D Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

23. Max Perutz’s investigation of the structure of hemoglobin primarily utilized_____. A) X-ray crystallography B) NMR spectroscopy C) genomics D) mass spectrometry E) genetic engineering Ans: A Level of Difficulty: Easy Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 24. The oxygen binding by hemocyanins is mediated by A) an iron ion B) a pair of iron ions C) a heme group D) a copper atom E) a pair of copper atoms Ans: E Level of Difficulty: Difficult Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 25. When the partial pressure of O2 in venous blood is 30 torr, the saturation of myoglobin with O2 is ______ while the saturation of hemoglobin with O2 is ______. A) 0.55, 0.91 B) 0.91, 0.55 C) 2.8 torr, 26 torr D) 0.91, 0.97 E) none of the above Ans: B Level of Difficulty: Difficult Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

26. Hemoglobin's p50 value is about ______ as great as myoglobin's p50 value. A) one-tenth B) half C) twice D) ten times E) twenty times Ans: D Level of Difficulty: Moderate Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 27. The value of n, the Hill constant (coefficient), for hemoglobin is about ______ as great as the value for myoglobin. A) half B) twice C) three times D) five times E) ten times Ans: C Level of Difficulty: Moderate Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 28. Consider a hypothetical hemoglobin-like molecule with a Hill coefficient (constant) of 1 and the same p50 value as normal hemoglobin. Choose the statement below that best describes the two proteins. A) There is a cooperative interaction between oxygen-binding sites in both the hypothetical and normal hemoglobins. B) The hypothetical hemoglobin has a greater oxygen affinity than normal hemoglobin. C) The oxygen binding curve for the hypothetical hemoglobin is hyperbolic, and the curve for normal hemoglobin is sigmoidal. D) The two hemoglobins would be able to deliver about the same amount of oxygen to the tissues. E) At pO2 less than p50, normal hemoglobin has a greater YO2 value. Ans: C Level of Difficulty: Moderate Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

29. The Hill plot shows that the fourth oxygen binds to hemoglobin with a ______-fold greater affinity than the first. A) 2 B) 5 C) 10 D) 20 E) 100 Ans: E Level of Difficulty: Moderate Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 30. While the binding of O2 to myoglobin as a function of pO2 is described by a simple __________ curve, the binding to hemoglobin is described by a more complex ______ curve. A) sigmoidal; hyperbolic B) hyperbolic; sigmoidal C) exponential; hyperbolic D) sigmoidal; bell-shaped E) hyperbolic; concave Ans: B Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 31. The Bohr effect refers to A) the decrease in affinity of Hb for O2 when the pH goes down B) the decrease in affinity of Hb for O2 when the pH goes up C) the increase in the affinity of Hb for O2 when the O2 concentration goes up D) the decrease in affinity of Hb for O2 when the BPG concentration goes up E) the decrease in affinity of Hb for O2 when the BPG concentration goes down Ans: A Level of Difficulty: Easy Section: 7.1.C Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

32. Which of the following increases the affinity of hemoglobin for O2? A) an increase in BPG concentration B) the formation of N-terminal carbamates C) an increase in pH D) a decrease in pH E) an increase in CO2 concentration Ans: C Level of Difficulty: Moderate Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 33. The most rapid way that erythrocytes adapt to high altitudes is A) by producing genetically altered hemoglobins that have higher O2-binding affinities. B) by adopting the symmetry model of allosterism. C) by increasing the concentration of hemoglobin. D) by relying upon the simpler protein myoglobin. E) by increasing the intracellular concentration of BPG. Ans: E Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 34. The rearrangement of T state hemoglobin to the R state A) occurs in each protein subunit independently when its heme binds oxygen. B) requires the binding of at least three oxygen molecules. C) increases the ion pairing interactions of the C-terminal amino acids. D) involves the movement of the Fe(II) into the heme plane. E) opens a central cavity for BPG binding. Ans: D Level of Difficulty: Moderate Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

35. Which of the following statements about the symmetry model of allosterism is not true? A) the protein is an oligomer of symmetrically (or pseudosymmetrically) related subunits. B) the oligomer can exist in two conformational states, which are in equilibrium. C) the ligand can bind to a subunit in either conformation. D) the molecular symmetry of the protein is conserved during the conformational change. E) none of the above. Ans: E Level of Difficulty: Moderate Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 36. BPG stands for A) biphenylglycine. B) boronylphenylglutamate. C) bisphosphoglycerate. D) bisphenylglycerol. E) betapropylglutamine. Ans: C Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 37. Why is the decreased affinity of fetal hemoglobin for BPG advantageous? A) With fewer BPG molecules bound there are more heme residues available for O2 binding. B) Decreased BPG binding biases the fetal hemoglobin toward the R state. C) More free BPG is available to bind to adult hemoglobin, resulting in a shift to the R state. D) BPG is available to bind to fetal myoglobin, helping to release O2 in fetal muscle tissue. E) none of the above Ans: B Level of Difficulty: Difficult Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

38. The reaction of carbonic anhydrase catalyzes A) the formation of carbamates with the concomitant release of protons. B) the hydration of bicarbonate, resulting in the formation of carbonic acid. C) the reduction of carbon dioxide with the concomitant consumption of protons. D) the hydration of carbon dioxide, forming bicarbonate and protons. E) the hydrolysis of carbamates with the concomitant consumption of protons. Ans: D Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 39. During the T to R conformational shift, Fe(II) drags the F-helix via a bond to the side chain of ________. A) Leu F7 B) Leu F4 C) His F8 D) Leu FG3 E) Val FG5 Ans: C Level of Difficulty: Easy Section: 7.1.D Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 40. Some abnormal hemoglobins have Hill coefficients that are ______ that of normal hemoglobin, indicating that their ability to bind oxygen cooperatively has been compromised. A) less than B) greater than C) much greater than D) about equal to E) The correct answer cannot be determined from the information given. Ans: A Level of Difficulty: Moderate Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

41. In sickle-cell anemia, the negatively charged glutamic acid residue is replaced by the neutral amino acid ____________. A) tyrosine B) lysine C) valine D) adenosine E) glycine Ans: C Level of Difficulty: Moderate Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 42. Hemoglobin S, the variant responsible for the misshapen red blood cells characteristic of the disease sickle-cell anemia, is potentially advantageous to heterozygotes because it confers some level of resistance to the disease _________. A) rickets B) AIDS C) cyanosis D) polycythemia E) malaria Ans: E Level of Difficulty: Easy Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 43. ______of the world’s human population carries an inherited variant hemoglobin gene. A) 5% B) 25% C) 50% D) 75% E) 90% Ans: A Level of Difficulty: Easy Section: 7.1.E Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

44. The repeating functional unit in a myofibril is called A) the A band. B) the I band. C) the sarcomere. D) the H zone. E) the M disk. Ans: C Level of Difficulty: Easy Section: 7.2.A Learning objective: Muscle Contraction 45. Muscle contraction is directly caused by A) structural changes in actin. B) structural changes in myosin. C) structural changes in the A band. D) structural changes in the Z disk. E) None of the above is correct. Ans: E Level of Difficulty: Moderate Section: 7.2.A Learning objective: Muscle Contraction 46. Muscle contraction is directly caused by A) structural changes in actin. B) structural changes in myosin. C) thick and thin filaments sliding past each other. D) structural changes in the Z disk. E) None of the above is correct. Ans: C Level of Difficulty: Easy Section: 7.2.A Learning objective: Muscle Contraction

47. Which of the statements about muscle contraction is correct? A) During muscle contraction the sarcomere becomes shorter. B) During muscle contraction the I band becomes shorter. C) During muscle contraction the H zone becomes shorter. D) During muscle contraction the distance between the Z disk and the M disk becomes shorter. E) All of the answers above are correct. Ans: E Level of Difficulty: Moderate Section: 7.2.A Learning objective: Muscle Contraction 48. Which of the statements about muscle contraction is not true? A) During muscle contraction the sarcomere becomes shorter. B) During muscle contraction the I band becomes shorter. C) During muscle contraction the H zone becomes shorter. D) During muscle contraction the A band becomes shorter E) During muscle contraction the distance between the Z disk and the M disk becomes shorter. Ans: D Level of Difficulty: Moderate Section: 7.2.A Learning objective: Muscle Contraction 49. What are the main bonds or forces that stabilize the dimer formed by two myosin heavy chains? A) hydrophobic interactions B) hydrogen-bonds C) ionic interactions D) disulfide bonds E) isopeptide bonds Ans: A Level of Difficulty: Easy Section: 7.2.A Learning objective: Muscle Contraction

50. During muscle contraction A) myosin pulls actin filaments toward the M disk. B) myosin pushes actin filaments toward the Z disk. C) actin pulls myosin toward the Z disk. D) actin pushes myosin toward the M disk. E) All of the answers above are correct. Ans: A Level of Difficulty: Easy Section: 7.2.A Learning objective: Muscle Contraction 51. Which statement about myosin is not true? A) Myosin is a heterohexamer. B) Myosin contains two globular heads. C) Myosin contains six different polypeptides D) Myosin aggregates to form thick filaments E) All of the answers above are true of myosin. Ans: E Level of Difficulty: Easy Section: 7.2.A Learning objective: Muscle Contraction 52. Which statement about actin is not true? A. There are two actin genes, one for F-actin and one for G-actin. B. Monomeric G-actin polymerizes to form F-actin. C. Actin filaments are polar (the ends can be distinguished). D. Actin can bind ATP. E. Actin is a common protein in nonmuscle cells. Ans: A Level of Difficulty: Moderate Section: 7.2.A Learning objective: Muscle Contraction

53. The energy needed to drive muscle contraction comes from ATP hydrolysis that is carried out by A) G-actin. B) F-actin. C) myosin heads. D) myosin tails. E) tropomyosin. Ans: C Level of Difficulty: Easy Section: 7.2.B Learning objective: Muscle Contraction 54. During muscle contraction myosin heads A) walk along thick filaments toward the M disk. B) walk along thick filaments toward the Z disk. C) walk along thin filaments toward the M disk. D) walk along the thin filaments toward the H zone. E) walk along the thin filaments toward the Z disk. Ans: E Level of Difficulty: Moderate Section: 7.2.B Learning objective: Muscle Contraction 55. Muscle contraction is triggered A) in response to an increase in the cytoplasmic Ca2+ concentration. B) in response to a decrease in the cytoplasmic Ca2+ concentration. C) in response to an increase in the cytoplasmic cAMP concentration. D) in response to a decrease in the cytoplasmic cAMP concentration. E) in response to an increase in the cytoplasmic titin concentration. Ans: A Level of Difficulty: Moderate Section: 7.2.B Learning objective: Muscle Contraction

56. Which statement about actin is correct? A) Actin is expressed only in muscle. B) Actin is expressed at low levels in most cells. C) No known function has been described for actin in nonmuscle cells. D) Nonmuscle cells only contain G actin. E) Actin is the most abundant cytoplasmic protein in many cell types. Ans: E Level of Difficulty: Moderate Section: 7.2.C Learning objective: Muscle Contraction 57. Which of the following statements about actin is not true? A) Actin is the most abundant cytoplasmic protein in many cell types. B) Actin forms microfilaments in many cell types. C) Actin plays an important role in endocytosis. D) Actin is present only as monomers in nonmuscle cells. E) Actin filaments are dynamic, they grow at one end and they lose subunits at the other end. Ans: D Level of Difficulty: Moderate Section: 7.2.C Learning objective: Muscle Contraction 58. Treadmilling refers to A) myosin heads walking along actin microfilaments. B) actin and myosin filaments sliding along each other. C) actin monomers moving through a microfilament from the + end to the – end. D) synthesis and degradation of actin monomers. E) the interactions between actin and tropomyosin. Ans: C Level of Difficulty: Moderate Section: 7.2.C Learning objective: Muscle Contraction

59. Humoral immunity refers to that part of the immune response that is mediated by A) T lymphocytes. B) antibodies. C) antigens. D) the thymus. E) the skin. Ans: B Level of Difficulty: Easy Section: 7.3.A Learning objective: Antibodies 60. Humoral immunity is mediated by soluble molecules. Which cell type produces the soluble molecules that carry out the humoral immunity? A) T cells B) B cells C) macrophages D) neutrophils E) monocytes Ans: B Level of Difficulty: Easy Section: 7.3.A Learning objective: Antibodies 61. How many different classes of antibodies are produced by the human immune system? A) 1 B) 2 C) 3 D) 4 E) 5 Ans: E Level of Difficulty: Easy Section: 7.3.A Learning objective: Antibodies

62. IgG is the most common immunoglobulin in the circulatory system and in the extravascular fluid. It is composed of two light chains and two heavy chains. What is the approximate molecular mass of an IgG molecule? A) 23 kDa B) 75 kDa C) 150 kDa D) 360 kDa E) 950 kDa Ans: C Level of Difficulty: Moderate Section: 7.3.A Learning objective: Antibodies 63. IgG is one of five classes of antibodies that can be produced by our immune system. IgGs have a molecular mass of approximately 150 kDa, what is their subunit composition? A) 2 light chains and 2 heavy chains B) 2 light chains, 2 heavy chains, and a J chain C) 4 light chains, 4 heavy chains, and a J chain D) 6 light chains, 6 heavy chains, and a J chain E) 10 light chains, 10 heavy chains , and a J chain. Ans: A Level of Difficulty: Easy Section: 7.3.A Learning objective: Antibodies 64. Which class of antibodies has been implicated in allergic reactions? A) IgA B) IgD C) IgE D) IgG E) IgM Ans: C Level of Difficulty: Moderate Section: 7.3.A Learning objective: Antibodies

65. How many antigen-binding sites are present on an IgG molecule? A) 1 B) 2 C) 3 D) 4 E) 5 Ans: B Level of Difficulty: Easy Section: 7.3.A Learning objective: Antibodies 66. How many antigen-binding sites are present on an IgM molecule? A) 2 B) 4 C) 10 D) 16 E) 25 Ans: C Level of Difficulty: Moderate Section: 7.3.A Learning objective: Antibodies 67. Fab fragments can be generated by A) reduction of IgG molecules. B) oxidation of IgG molecules. C) limited digestion of IgG molecules with papain. D) combining two light chains. E) combining two heavy chains. Ans: C Level of Difficulty: Moderate Section: 7.3.A Learning objective: Antibodies

68. Which statement about antigen-binding sites in antibodies is false? A) An antigen-binding site on an IgG is formed by the amino-terminal ~110 amino acids of a light chain and the amino terminal ~110 amino acids of a heavy chain. B) An antigen-binding site on an IgG is formed by the variable region of a light chain and the variable region of a heavy chain. C) The antigen-binding site is composed of two Ig folds. D) Antigen-binding specificity is determined by the sequences of the hypervariable sequences in both the light chain and the heavy chain. E) Antigen binding specificity is determined exclusively by the sequences in the carboxyterminal ~110 amino acids in the light chain and the heavy chain. Ans: E Level of Difficulty: Moderate Section: 7.3.B Learning objective: Antibodies 69. The Ig fold can be described as a A) globular fold composed of a helices. B) a globular fold composed of a four helix bundle. C) a globular fold composed of a b sandwich. D) a globular fold composed of b barrel. E) a coiled-coil. Ans: C Level of Difficulty: Moderate Section: 7.3.B Learning objective: Antibodies

SHORT ANSWER 70. Myoglobin is an oxygen binding protein in muscle. Describe in one sentence the overall structure of myoglobin. Ans: Myoglobin is a globular protein composed of 8 a helices that forms a hydrophobic pocket that contains the heme group. Level of Difficulty: Moderate Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 71. What is the primary physiological function of myoglobin in most mammals? Ans: The primary physiological function of myoglobin in most mammals is to increase the solubility for O2 in muscle tissue and thereby increasing the diffusion rate. Level of Difficulty: Moderate Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 72. It appears that the heme group in myoglobin binds the O2. What is the function of the polypeptide? Ans: The polypeptide performs various functions: 1. The polypeptide provides solubility for the heme group, which is very non-polar. 2. The polypeptide prevents permanent oxidation of the Fe(II). 3. The polypeptide helps coordinate the Fe(II) (His F8) 4. The polypeptide forms a H-bond with the O2 (His E7). Level of Difficulty: Difficult Section: 7.1.A Learning objective: Oxygen Binding to Myoglobin and Hemoglobin 73. Mammals and other animals have a circulatory system because diffusion is to slow to supply the tissues with oxygen in animals that are larger than 2 millimeter. Explain in one sentence why these circulatory systems contain hemoglobin or other oxygen binding proteins? Ans: Oxygen-binding proteins increase the solubility of oxygen in the fluid of the circulatory system. This is important because oxygen is not very soluble in aqueous solutions. Level of Difficulty: Difficult Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

74. The graph below shows the O2-binding curves for myoglobin (Mb) and hemoglobin (Hb). a. Label the two curves (indicate which one represents Mb and which one represents Hb).

b. Use the graph to determine the Kd of myoglobin for O2 (show your approach). c. What is the difference between myoglobin and hemoglobin that cause the O2-binding curves to so be different? d. Why is it important that hemoglobin has these particular O2-binding characteristics?

Ans: a. See graph. b. Kd equals 3-4 torr (see graph). c. Mb has one subunit, Hb has 4 subunits. The sigmoid binding curve is a consequence of positive cooperativity between the 4 O2-binding sites in Hb. The hyperbolic binding curve for myoglobin is the result of oxygen binding reaction being noncooperative. d. As a consequence of positive cooperation Hb has a high affinity for O2 when the O2 concentration is high (in the lungs) and low affinity for O2 when the O2 concentration is low (in the tissues). As a consequence Hb binds large amount of O2 in the lungs and releases large amounts of O2 in the tissues, resulting in efficient transport of O2. Level of Difficulty: Difficult Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

75. You have been studying O2 binding to a hemerythrin-like protein isolated from an exotic marine worm. Your O2-binding data are shown in the table below. a. Use the data to generate an O2-binding curve (do not forget to mark the axes). b. Use the curve to estimate the Kd for the interaction. c. Is there any evidence from your data that this hemoglobin-like protein binds O2 in a cooperative manner (briefly explain your answer)? [Ligand] in µM 21 42 79 118 257 362 535 745 900 1052

Y 0.11 0.28 0.37 0.42 0.58 0.66 0.78 0.86 0.89 0.92

October 20, 2011

Ans: a. see curve b. see curve, Kd equals 180 µM c. there is no evidence for cooperative binding of O2 to this protein, because the binding curve is hyperbolic and not sigmoid. Level of Difficulty: Difficult Section: 7.1.B Learning objective: Oxygen Binding to Myoglobin and Hemoglobin

Chapter 8: Carbohydrates Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N) O) P

eight deoxy peptidoglycan axial anomers two lactose glyceraldehyde amylopectin epimers sixteen glycogen equatorial chitin hyaluronic acid amylose

1. Glucose, with its four chiral carbon atoms, has ______ possible stereoisomers. Ans: K Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides 2. The smallest aldose is ______. Ans: H Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides 3. The monosaccharides a-D-galactose and b-D-galactose are ______. Ans: E Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

4. Bulky ring substituents preferentially occupy ______ positions in the chair conformation. Ans: M Level of Difficulty: Easy Section: 8.1.B Learning objective: Monosaccharides 5. The ______ sugars are monosaccharides in which a hydroxyl group is replaced with a hydrogen atom. Ans: B Level of Difficulty: Easy Section: 8.1.C Learning objective: Monosaccharides 6. The disaccharide commonly found in dairy products is ______. Ans: G Level of Difficulty: Easy Section: 8.2.A Learning objective: Polysaccharides 7. ______ is a homopolymer composed of b(1-4)-linked N-acetyl-D-glucosamine residues that is the principle structural component of the exoskeleton of various groups of invertebrates. Ans: N Level of Difficulty: Easy Section: 8.2.B Learning objective: Polysaccharides 8. Both a(1®4) and a(1®6) bonds can be found in the plant product______. Ans: I Level of Difficulty: Easy Section: 8.2.C Learning objective: Polysaccharides

9. An example of a homopolysaccharide in liver and muscle is ______. Ans: L Level of Difficulty: Easy Section: 8.2.C Learning objective: Polysaccharides 10. ______ is a heteropolymer composed of D-glucoronate and N-acetyl-D-glucosamine that acts as shock absorber and lubricant. Ans: O Level of Difficulty: Moderate Section: 8.2.C Learning objective: Polysaccharides 11. The main component of a bacterial cell wall is a ______. Ans: C Level of Difficulty: Easy Section: 8.3.B Learning objective: Glycoproteins

Multiple Choice 12. How many stereoisomers are possible for an aldopentose such as ribose? A) 2 B) 4 C) 8 D) 16 E) 32 Ans: C Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides 13. How many stereoisomers are possible for a ketopentose such as ribulose? A) 2 B) 4 C) 8 D) 16 E) 32 Ans: B Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This figure is used in questions 14-16

14. Which of the sugars shown in the figure above are L sugars? A) A and B B) B and C C) C and D D) A and D E) None of the above Ans: C Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides

15. Which sugar shown in the figure above is the enantiomer of sugar A? A) B B) C C) D D) B and D E) none of the above Ans: C Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides 16. Which two sugars shown in the figure above are epimers? A) A and B B) B and C C) C and D D) A and D E) None of the above Ans: A Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This figure is used in questions 17-21.

17. Which of the structures shown in the figure above is galactose? A) A B) B C) C D) D E) None of the above Ans: C Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides 18. Which structure(s) shown in the figure above represent reducing sugar(s)? A) A B) D C) C and D D) A, B, C, and D E) A, B, and C Ans: E Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides 19. Which structure shown in the figure above is a ketohexose? A) A B) B C) C D) D E) None of the above Ans: D Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

20. Which structure shown in the figure above is ribose? A) A B) B C) C D) D E) None of the above Ans: A Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides 21. The structures shown in the figure above are represented as A) Fischer projections. B) Haworth projections. C) space-filling projections. D) ball and stick models. E) None of the answers above is correct. Ans: A Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This figure is used in questions 22-25.

22. Which of the structures shown in the figure above is a glucopyranose? A) A B) B C) C D) D E) None of the above Ans: A Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides

23. Which structure shown in the figure above represents a ketose? A) A B) B C) C D) D E) None of the above Ans: E Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides 24. Which structures shown in the figure above represent possible structures of glucose? A) A B) A and B C) A and C D) A, B, and C E) None of the above Ans: B Level of Difficulty: Moderate Section: 8.1.A Learning objective: Monosaccharides 25. Which structure shown in the figure above represents deoxyribose? A) A B) B C) C D) D E) None of the above Ans: E Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

26. Alcohols react with aldehydes to form A) hemiketals. B) lactones. C) lactams. D) glycosides. E) hemiacetals. Ans: E Level of Difficulty: Easy Section: 8.1.B Learning objective: Monosaccharides 27. At equilibrium in solution, D-glucose consists of a mixture of its anomers. Which statement most accurately describes this solution? A) The solution consists of approximately equal amounts of the a- and b-anomers. B) The straight-chain form is present in high concentration. C) The a-anomer is more stable and is slightly preferred over the b-anomer. D) The b-anomer predominates over the a-anomer by a ratio of approximately 2:1. E) None of the answers above is correct. Ans: D Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This figure is used in questions 28-30.

28. The structure shown in the figure above represents a A) glucopyranose. B) ribofuranose. C) myo-inositol. D) fructofuranose. E) glucofuranose. Ans: D Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides 29. Which of the carbon atoms shown in the figure above represent the anomeric carbon? A) A B) B C) C D) D E) E Ans: E Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides 30. The configuration around which carbon atom shown in the figure above determines whether this is a D or an L sugar? A) A B) B C) C D) D E) E Ans: A Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides

31. The transformation of a monosaccharide into its ______ occurs easily and does not require the assistance of a catalyst. A) epimer B) anomer C) sugar alcohol D) diastereomer E) none of the above Ans: B Level of Difficulty: Easy Section: 8.1.B Learning objective: Monosaccharides 32. The structure below shows a Fischer projection of D-idose.

Which of the structures below represents b-D-idopyranose

Ans: E Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides

33. The structure below shows b-D-gulopyranose.

Which of the structures below represents a Fischer projection of D-gulose?

Ans: C Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides 34. Which of the following sugars is not a reducing sugar? A) glucose B) ribose C) sucrose D) starch E) galactose Ans: C Level of Difficulty: Moderate Section: 8.1.C Learning objective: Monosaccharides

35. The figure below shows structures of several types of sugars. Which one is an aldonic acid?

Ans: D Level of Difficulty: Moderate Section: 8.1.C Learning objective: Monosaccharides 36. The figure below shows structures of several types of sugars. Which one is an alditol?

Ans: B Level of Difficulty: Moderate Section: 8.1.C Learning objective: Monosaccharides

37. Uronic acids A) are aldoses where the aldehyde is oxidized to a carboxylic acid. B) are aldoses where the 1° alcohol is oxidized to a carboxylic acid. C) can be found in the pyranose or furanose forms. D) A and C are both correct. E) B and C are both correct. Ans: E Level of Difficulty: Moderate Section: 8.1.C Learning objective: Monosaccharides 38. The sialic acids A) are important constituents of glycoproteins and glycolipids. B) are N-acetyl glucosamine derivatives. C) incorporate a succinic acid derivative. D) all of the above E) none of the above Ans: A Level of Difficulty: Moderate Section: 8.1.C Learning objective: Monosaccharides 39. The bonding of alcohols to the anomeric center of a carbohydrate results in the formation of a(n) __________ bond. A) anomeric B) amide C) glycosidic D) ester E) hydrogen Ans: C Level of Difficulty: Easy Section: 8.1.C Learning objective: Monosaccharides

40. Which of the structures below represents a glucoside?

Ans: B Level of Difficulty: Easy Section: 8.1.C Learning objective: Monosaccharides 41. A saccharide that has free aldehyde group is called a(n) _____________. A) ketose B) nonreducing sugar C) reducing sugar D) aldohexose E) alditol Ans: C Level of Difficulty: Easy Section: 8.1.C Learning objective: Monosaccharides 42. D-Allose is an aldohexose. Methylation of which hydroxyl group on b-D-allopyranose prevents the molecule from mutarotating to a-D-allopyranose? A) C1 B) C2 C) C3 D) C4 E) C5 Ans: A Level of Difficulty: Easy Section: 8.1.C Learning objective: Monosaccharides

43. Which of the following is the most abundant disaccharide? A) lactose B) cellulose C) α-amylose D) maltose E) sucrose Ans: E Level of Difficulty: Easy Section: 8.2.A Learning objective: Polysaccharides 44. Which of the following is a disaccharide? A) amylose B) saccharin C) aspartame D) amylopectin E) none of the above Ans: E Level of Difficulty: Difficult Section: 8.2.A Learning objective: Polysaccharides 45. Which of these is not an artificial sweetener? A) saccharine B) aspartame C) maltose D) acesulfame E) alitame Ans: C Level of Difficulty: Moderate Section: 8.2.A Learning objective: Polysaccharides

46. Which of the following statements applies to all artificial sweeteners? A) Artificial sweeteners cannot be readily metabolized. B) Artificial sweeteners are peptides and provide important amino acids. C) Artificial sweeteners have fewer calories than sucrose. D) Artificial sweeteners are much sweeter than sucrose. E) all of the above Ans: D Level of Difficulty: Moderate Section: 8.2.A Learning objective: Polysaccharides 47. Which of the following polysaccharides cannot be digested by mammalian salivary, gastric, or pancreatic enzymes? A) cellulose B) amylopectin C) amylose D) glycogen E) starch Ans: A Level of Difficulty: Easy Section: 8.2.B Learning objective: Polysaccharides 48. Which of the following polysaccharides cannot be digested by mammalian salivary, gastric, or pancreatic enzymes? A) amylopectin B) amylose C) chitin D) glycogen E) starch Ans: C Level of Difficulty: Easy Section: 8.2.B Learning objective: Polysaccharides

49. Which of these polysaccharides is a branched polymer? A) chitin B) amylose C) cellulose D) amylopectin E) hyaluronic acid Ans: D Level of Difficulty: Moderate Section: 8.2.B Learning objective: Polysaccharides 50. Chitin differs from cellulose due to A) inversion of configuration at the anomeric carbon. B) sulfonation of the C2 OH group. C) a much greater prevalence of branching. D) replacement of the C2 OH group by an acetamido group. E) replacement of the C6 OH group by an amino group. Ans: D Level of Difficulty: Easy Section: 8.2.B Learning objective: Polysaccharides 51. Cellulose is A) a linear copolymer of glucose and galactose. B) a branched polymer of glucose. C) a linear polymer of glucose with β(1®4) linkages. D) a linear polymer of glucose with α(1®4) linkages. E) sometimes called starch. Ans: C Level of Difficulty: Easy Section: 8.2.B Learning objective: Polysaccharides

52. Which polysaccharide is found in a helically coiled conformation? A) chitin B) α-amylose C) cellulose D) lignin E) none of the above Ans: B Level of Difficulty: Moderate Section: 8.2.C Learning objective: Polysaccharides 53. Which of the following is a mixture of two types of polymers? A) cellulose B) starch C) chitin D) glycogen E) amylose Ans: B Level of Difficulty: Moderate Section: 8.2.B Learning objective: Polysaccharides 54. Starch is a mixture of A) a-amylose and amylopectin. B) glycogen and amylopectin. C) glycogen and a-amylose. D) glycogen and cellulose. E) a-amylose and maltose. Ans: A Level of Difficulty: Moderate Section: 8.2.B Learning objective: Polysaccharides

55. Which of the following is an example of a heteropolysaccharide? A) cellulose B) chitin C) starch D) glycogen E) hyaluronic acid Ans: E Level of Difficulty: Moderate Section: 8.2.D Learning objective: Polysaccharides 56. Glycoproteins A) are only found in bacteria. B) are extremely homogeneous. C) are typically less than 1% carbohydrate by weight. D) are assembled under strict genetic control. E) exhibit microheterogeneity. Ans: E Level of Difficulty: Easy Section: 8.3.A Learning objective: Glycoproteins 57. Bacterial cell walls are composed of _____. A) pectin B) chondroitin sulfate chains C) peptidoglycans D) heparin E) proteoglycans Ans: C Level of Difficulty: Easy Section: 8.3.B Learning objective: Glycoproteins

58. N-linked oligosaccharides can be covalently linked to proteins at which amino acid? A) Gly B) Ser C) Glu D) Tyr E) Asn Ans: E Level of Difficulty: Easy Section: 8.3.C Learning objective: Glycoproteins 59. Which statement about N-linked glycosylation is correct? A) N-linked oligosaccharides are attached to proteins one sugar at the time in the endoplasmic reticulum. B) N-linked sugars are attached to proteins as a 14 residue oligosaccharide during translation in the endoplasmic reticulum. C) N-linked sugars are attached to proteins as a 14 residue oligosaccharide during translation in the cytoplasm. D) N-linked sugars are attached to proteins as a 14 residue oligosaccharide after translation in the Golgi apparatus. E) N-linked oligosaccharides are attached to proteins one sugar at the time in the Golgi apparatus. Ans: B Level of Difficulty: Moderate Section: 8.3.C Learning objective: Glycoproteins 60. Which of the following sequences represents a recognition site for N-linked glycosylation where X is any amino acid except Pro? A) Gln—X—Ser B) His—X—Ser C) Arg—X—Ser D) Asn—X—Ser E) Asp—X—Ser Ans: D Level of Difficulty: Easy Section: 8.3.C Learning objective: Glycoproteins

61. O-linked oligosaccharides are commonly attached to the —OH group of _____. A) ribose B) tyrosine C) lysine D) threonine E) glycine Ans: D Level of Difficulty: Easy Section: 8.3.C Learning objective: Glycoproteins 62. Proteins that bind to specific carbohydrates are called ______. A) pectins B) oligonucleotides C) glycosaminoglycans D) lectins E) chitins Ans: D Level of Difficulty: Easy Section: 8.3.D Learning objective: Glycoproteins

SHORT ANSWER 63. We encounter a great variety of sugars in living organisms. a. Are most carbohydrates in living organisms D or L? b. Draw a Fischer projection of the smallest aldose (include all atoms). c. What is the name of this molecule? Ans: a. D

b. see drawing c. D-glyceraldehyde Level of Difficulty: Easy Section: 8.1.A Learning objective: Monosaccharides

64. We encounter a great variety of sugars in living organisms. a. Draw a Haworth projection of an aldohexose in the pyranose form (include all atoms). b. Draw the Haworth projection of the anomer of the aldose you drew in "a" above. c. Draw a circle around the carbon that determines whether this sugar is a D or an L sugar. d. How many chiral carbon atoms are present in each of the structures drawn in "a" and b" above? e. How many stereoisomers exist for these pyranoses? Ans: a. see drawing

b. see drawing c. see drawing d. 5 e. 25 = 32 Level of Difficulty: Moderate Section: 8.1.B Learning objective: Monosaccharides

65. The picture below shows a Fischer projection of D-glucose.

a. Is glucose and aldose or a ketose? b. What is the name of the molecule that is formed upon oxidation of the aldehyde to a carboxyl group? c. Draw a Fischer projection of D-galactose, which is an epimer of glucose with respect to the C4 position. d. Draw a Haworth projection of b-D-glucopyranose. e. What is the name of the linear polymer in which glucopyranose residues are linked to each other through b(1→4) glycosidic bonds. Ans: a. aldose b. D-gluconic acid c. see drawing

d. see drawing e. cellulose Level of Difficulty: Moderate Section: 8.1 and 8.2 Learning objective: Monosaccharides and Polysaccharides

66. The drawing below shows the structure of the disaccharide sucrose.

a. What are the names of the two monosaccharides that form sucrose? b. Draw squares around the carbons that determine the designation D or L for each of the monosaccharides. c. Draw circles around the anomeric carbon atoms on the drawing. d. Indicate on the drawing for each of the anomeric carbon atoms whether they are in the a or the b configuration. e. Is sucrose a reducing sugar? Explain your answer in one sentence. Ans: a. glucose (glucopyranose) and fructose (fructofuranose).

b. see drawing c. see drawing d. see drawing e. Sucrose is a nonreducing sugar because both anomeric carbons are involved in a glycosidic bond.

Chapter 9: Lipids and Biological Membranes Matching A) B) C) D) E) F) G) H) I) J) K) L) M)

amphiphiles vitamin D arachidonic acid phosphatidylethanolamine sterol gangliosides phosphatidylcholine glycerophospholipids sphingomyelins cholesterol triacylglycerols plasmalogen nonpolar

1. ______ are the lipids that are most abundant even though they are not components of membranes. Ans: K Level of Difficulty: Easy Section: 9.1.B Learning objective: Lipid Classification 2. They ______ are a class of amphipathic molecules that comprise the major lipid components of the cell membrane. Ans: H Level of Difficulty: Easy Section: 9.1.C Learning objective: Lipid Classification 3. The myelin sheath contains high levels of ______. Ans: I Level of Difficulty: Easy Section: 9.1.D Learning objective: Lipid Classification

4. A steroid-derived hormone that must be activated by hydroxylation, ______ regulates Ca2+ metabolism. Ans: B Level of Difficulty: Easy Section: 9.1.E Learning objective: Lipid Classification 5. A derivative of______ is the major lipid in lung surfactant. Ans: G Level of Difficulty: Easy Section: 9.1.F Learning objective: Lipid Classification 6. Members of the ______ family have four fused, nonplanar rings and a C3-OH group. Ans: E Level of Difficulty: Easy Section: 9.1.E Learning objective: Lipid Classification 7. A glycerophospholipid in which the C1 substituent linkage forms a vinyl ether that is more easily oxidized than its ester counterpart is called a ______. Ans: L Level of Difficulty: Easy Section: 9.1.D Learning objective: Lipid Classification 8. Glycosphingolipids with complex carbohydrate head groups that often serve as cellular receptors are ______. Ans: F Level of Difficulty: Easy Section: 9.1.D Learning objective: Lipid Classification

9. With respect to polarity, membrane lipids can be described as ______. Ans: A Level of Difficulty: Easy Section: 9.1.A Learning objective: Lipid Classification 10. Eicosanoids are 20-carbon compounds derived from ______. Ans: C Level of Difficulty: Easy Section: 9.1.F Learning objective: Lipid Classification

Multiple Choice 11. Which of the following statements are true regarding fatty acids? I. Fatty acids with fewer than 14 carbons are the most common. II. Synthesis of fatty acids occurs in 2 carbon units. III. Fatty acids with conjugated double bonds are the most common type of fatty acid. IV. In higher plants and animals, C16 and C18 species predominate. A) I, II, III, IV B) I, II, III C) I, III D) II, III, IV E) II, IV Ans: E Level of Difficulty: Moderate Section: 9.1.A Learning objective: Lipid Classification

12. Rank the melting points of the following fatty acids from highest to lowest: (1) (2) (3) (4) (5)

cis-oleic(18:1) trans-oleic (18:1) linoleic (18:2) steraic (18:0) palmitic (16:0)

A) 1 > 2 > 3 > 5 > 4 B) 4 > 5 > 2 > 1 > 3 C) 4 > 5 > 3 > 2 > 1 D) 5 > 4 > 2 > 1 > 3 E) none of the above Ans: B Level of Difficulty: Difficult Section: 9.1.A Learning objective: Lipid Classification 13. Which of the following lipid types is the least polar? A) triacylglycerols B) glycerophospholipids C) sphingolipids D) gangliosides E) glycolipids Ans: A Level of Difficulty: Easy Section: 9.1.B-D Learning objective: Lipid Classification 14. Cholesterol A) incorporation into the membrane results in increased rigidity. B) functions as a precursor to cerebrosides. C) is synthesized in two-carbon units. D) is synthesized from steroid hormones. E) all of the above Ans: A Level of Difficulty: Moderate Section: 9.1.E and F Learning objective: Lipid Classification

15. A suspension of which of the following is most likely to form a liposome? I. fatty acids II. triacylglycerols III. glycerophospholipids IV. sphingomyelins A) I, II B) II, III C) III, IV D) II, IV E) I, IV Ans: C Level of Difficulty: Moderate Section: 9.2.A Learning objective: Lipid Bilayers 16. Which of the following is true about membrane proteins embedded within the lipid bilayer? A) An increased temperature of the bilayer decreases the rate of transverse diffusion of the membrane protein. B) They undergo transverse diffusion approximately every 5 seconds at body temperature. C) They undergo transverse diffusion readily at body temperature unless their movement is restricted by other cellular components. D) As the temperature decreases, lateral diffusion of the membrane protein is restricted in bilayers with lipids which have longer chain fatty acids and fewer double bonds. E) Lateral diffusion of the membrane protein occurs independent of bilayer composition and temperature. Ans: D Level of Difficulty: Difficult Section: 9.2.B Learning objective: Lipid Bilayers

17. Which of the following statements describes integral membrane proteins? I. They protect the contents of the cell from chaotropic agents such as urea. II. They are easily dissociated from the membrane by changes in pH or high salt concentration. III. They are held tightly in place by hydrophobic effects between the membrane and hydrophobic amino acids. A) I, II, III B) I, III C) I D) II E) III Ans: E Level of Difficulty: Difficult Section: 9.3.A Learning objective: Membrane Proteins 18. Which experiment listed below did NOT verify the fluid mosaic model of membranes? A) observation of lateral movement of membrane across the cell while anchored to a microscope slide. B) monitoring the transverse diffusion of human proteins within a mouse cell membrane. C) membrane fusion between mouse and human cells. D) monitoring the lateral diffusion of fluorphores both bleached and unbleached. E) All of the above describe experiments that verified the fluid mosaic model of membranes. Ans: B Level of Difficulty: Difficult Section: 9.4.A, B Learning objective: Membrane Structure and Assembly 19. Which of the following proteins are synthesized on free ribosomes? A) mitochondrial proteins B) secretory proteins C) signal peptides D) lysosomal proteins E) transmembrane proteins Ans: A Level of Difficulty: Moderate Section: 9.4.D Learning objective: Membrane Structure and Assembly

20. The protein that forms a transmembrane pore that allows growing polypeptides to pass through the RER membrane is called the ______. A) signal recognition particle B) signal peptide C) docking protein D) translocon E) none of the above Ans: D Level of Difficulty: Easy Section: 9.4.D Learning objective: Membrane Structure and Assembly 21. Unsaturated fatty acids: A) are commonly found in plants and animals B) usually contain a double bond with cis stereochemistry C) sometimes contain multiple double bonds D) have lower melting points than the analogous saturated fatty acids E) all of the above Ans: E Level of Difficulty: Easy Section: 9.1.A Learning objective: Lipid Classification 22. Triglycerides contain more metabolic energy per unit weight than glycogen because: I. Glycogen has greater polarity than fatty acids. II. Fatty acids predominate in an anhydrous form III. Fatty acids are less oxidized than carbohydrates. IV. Triglycerides have a higher average molecular mass. A) I, II, III, IV B) I, II, III C) I, II D) II, III E) III Ans: B Level of Difficulty: Moderate Section: 9.1.B Learning objective: Lipid Classification

23. Adipocytes A) are specialized cells for the synthesis of triglycerides. B) are specialized cells for short term energy storage. C) provide compartments for efficient membrane bilayer synthesis. D) exist primarily in a thin layer surrounding major muscle groups as a rapid high energy source. E) All of the above characterize adipocytes. Ans: A Level of Difficulty: Easy Section: 9.1.B Learning objective: Lipid Classification 24. Sphingolipids I. contain a glycerol core with a phosphocholine headgroup. II. contain a modified sphingosine. III. often function as receptor components of membranes. IV. function as a precursor to sterols. A) I, II, IV B) II, IV C) I, II, III D) II, III E) II, III, IV Ans: D Level of Difficulty: Moderate Section: 9.1.D Learning objective: Lipid Classification 25. While fatty acids are most often formed by the condensation of __-carbon units, isoprenoids are assembled from __-carbon units. A) 5, 3 B) 4, 2 C) 2, 3 D) 2, 5 E) 3, 4 Ans: D Level of Difficulty: Easy

Section: 9.1.F Learning objective: Lipid Classification 26. Which of the following is comprised primarily of fatty acids and other single tailed amphiphiles? A) lipid bilayers B) two-dimensional membranes C) liposomes D) micelles E) solvent-filled vesicles Ans: D Level of Difficulty: Easy Section: 9.2.A Learning objective: Lipid Bilayers 27. Cold blooded animals modulate the fatty acid composition of their membranes as a function of temperature in order to A) adjust the membrane thickness and increase thermal insulation. B) maximize available fatty acids for metabolic use. C) ensure consistent membrane fluidity. D) compensate for decreasing cholesterol solubility. E) all of the above Ans: C Level of Difficulty: Easy Section: 9.2.B Learning objective: Lipid Bilayers 28. Which of the following amino acids from an integral membrane protein would likely contact the membrane? A) Asn B) Gln C) Glu D) Ala E) Asp Ans: D Level of Difficulty: Easy Section: 9.3.A Learning objective: Membrane Proteins

29. Transmembrane proteins I. are predominantly constructed of a single hydrophobic α-helix. II. are often constructed from bundles of hydrophobic a-helices. III. are sometimes constructed from β-barrels with hydrophobic interiors and exteriors. IV. may have transmembrane helices identified by the free energy of transfer to water. A) I, III, IV B) II, III C) II, III, IV D) I, IV E) II, IV Ans: C Level of Difficulty: Moderate Section: 9.3.A Learning objective: Membrane Proteins 30. Which of the following is (are) NOT found as covalently attached anchors in lipid-linked proteins? A) isoprenoid groups B) fatty acids C) cholesterol and other sterols D) glycosylphosphatidyl inositol groups E) All of the above are found as covalently attached anchors in lipid-linked proteins. Ans: C Level of Difficulty: Easy Section: 9.3.B Learning objective: Membrane Proteins 31. Which of the following classes of proteins associates with the membrane bilayer with the lowest energy and would therefore be most difficult to separate from the membrane? A) extrinsic proteins B) lipid-linked proteins C) transmembrane proteins D) peripheral proteins E) hydrophilic proteins Ans: C Level of Difficulty: Difficult

Section: 9.3.A Learning objective: Membrane Proteins 32. The biconcave shape of erythrocytes which maximizes rapid diffusion of oxygen is primarily maintained by A) the covalent attachment of organelles within the cell to the membrane. B) high levels of rigid cholesterol and saturated lipids that strengthen the membrane. C) a network of embedded spectrin that crosslink to other membrane proteins, D) a network of tightly-packed anion channel proteins. E) a relatively low concentration of integral membrane proteins allowing tighter packing of lipid molecules within the membrane. Ans: C Level of Difficulty: Moderate Section: 9.4.B Learning objective: Membrane Structure and Assembly 33. The _________ model describes the cell membrane as an assortment of integral proteins suspended freely in a lipid bilayer. A) FRAP B) cellular fusion C) transverse diffusion D) lateral diffusion E) fluid mosaic Ans: E Level of Difficulty: Easy Section: 9.4.A Learning objective: Membrane Structure and Assembly 34. N-terminal signal peptides function to direct proteins A) destined for secretion. B) to the endoplasmic reticulum. C) destined to be part of the lysosomes. D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section: 9.4.D Learning objective: Membrane Structure and Assembly

35. The _________, which is found embedded in the endoplasmic reticulum, is a _______ protein. A) SRP receptor…signal B) ribosome…transmembrane pore C) translocon…transmembrane pore D) translocon…peripheral E) ribosome…signal Ans: C Level of Difficulty: Moderate Section: 9.4.D Learning objective: Membrane Structure and Assembly 36. In bacteria, phospholipids are synthesized: A) on the cytoplasmic face of cell membranes B) at the rough endoplasmic reticulum C) on the extracellular face of the cell membrane D) on site at the endoplasmic reticulum. E) nonenzymatically at the site of the membrane. Ans: A Level of Difficulty: Moderate Section: 9.4.C Learning objective: Membrane Structure and Assembly 37. Which of the following segments of the integral membrane protein glycophorin most likely contains the membrane-spanning sequence? A) LSTTEVAMHTTTSSSVSKSY B) SQTNDTHKRDTYAATPRA C) VSEISVRTVYPPEEETGE D) ITLIIFGVMAGVIGTILLI E) YGIRRLIKKSPSDVKPLP Ans: D Level of Difficulty: Moderate Section: 9.3.A Learning objective: Membrane Proteins

38. Which would be most likely to be found in the membranes of mouse brain cells? A) cholesterol B) glycerolphospholipids C) GM1, GM2, or GM3 D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section: 9.1.A, B, C, D, E Learning objective: Lipid Classification 39. The signal peptide sequence I. is often used to direct proteins to the lysosome for incorporation into the lysosome. II. is usually not used for small eukaryotic proteins. III. of some transmembrane proteins is embedded into the membrane as an anchor. IV. is usually cleaved off the completed protein. A) I, IV B) I, II, IV C) II, III, IV D) I, III, IV E) I, II, III, IV Ans: D Level of Difficulty: Moderate Section: 9.4.D Learning objective: Membrane Structure and Assembly 40. Glycosphingolipids with several attached carbohydrates (including at least one sialic acid) are called: A) plasmalogens B) ceramides C) sphingiosides D) gangliosides E) cerebrosides Ans: D

Level of Difficulty: Easy Section: 9.1.C Learning objective: Lipid Classification 41. Considering the characteristics of common fatty acids found in animals described in the text, which of the structures shown below would you consider the most rare fatty acid if found in animals?

A) Structure A B) Structure B C) Structure C D) Structure D E) All structures would be equally rare. Ans: C Level of Difficulty: Moderate Section: 9.1.A Learning objective: Lipid Classification

42. Which of the structures below is an example of an w-3 polyunsaturated fatty acid?

A) Structure A B) Structure B C) Structure C D) Structure D E) None of the above Ans: B Level of Difficulty: Moderate Section: 9.1.A Learning objective: Lipid Classification

43. Which of the following statements describes one reason that plant oils are generally healthier for human consumption than animal fats? A) Plant oils usually contain more unsaturated fatty acids than animal fats. B) Plant oils usually contain more trans fatty acids than animal fats. C) Plant oils usually have a higher degree of saturation than animal fats. D) Plant oils are glycerol based rather than phospholipid based. E) Plant oils have shorter chain fatty acids than animal fats. Ans: A Level of Difficulty: Moderate Section: 9.1.A and 9.1B Learning objective: Lipid Classification 44. Lung surfactants function to decrease the likelihood of collapse of the alveoli when air is expired. Based on your knowledge of lipids and amphipathic molecules, which of the following explains the mechanism by which the dipalmitoyl phosphatidylcholine (DPPC) can accomplish this task? A) The hydrophilic head groups are bulky and expand the surface area of the alveoli. B) The inclusion of saturated fatty acids on the glycerophospholipid allows close packing of tail groups which are fully extended and prevent collapse upon expiration. C) The hydrophobic portion of the DPPC repel air, forcing the alveoli space open. D) The choline portion of the molecule is bulky, thus increasing surface area of alveoli. E) None of the above explain the mechanism. Ans: B Level of Difficulty: Difficult Section: 9.1A and C Learning objective: Lipid Classification

45. Which of the following structures correctly represents a glycerophospholipid?

A) Structure A B) Structure B C) Structure C D) Structure D E) None of the above

Ans: A Level of Difficulty: Moderate Section: 9.1C Learning objective: Lipid Classification

46. Which of the following points to the correct location of attachment for a fatty acid which

would yield a ceramide?

A) Location A B) Location B C) Location C D) Location B or C E) The correct location is not shown Ans: A Level of Difficulty: Moderate Section: 9.1D Learning objective: Lipid Classification 47. Identify the compound below:

A) a glycerolphospholipid B) sphingosine C) ceramide D) spingomylelin E) ganglioside Ans: D Level of Difficulty: Moderate Section: 9.1D Learning objective: Lipid Classification

48. Use the diagram below to answer the following question. The enzyme flipase would catalyze which of the following types of reactions?

A) Exchange of a phospholipid in position A for a cholesterol in position A. B) Exchange for a lipid in position A for a lipid in position B. C) Exchange for a phospholipid in position A with a phospholipid in position C. D) Exchange for a lipid in position B for a lipid in position D. E) Exchange for a glycerolphospholipid in position A for a spingolipid in position C. Ans: B Level of Difficulty: Moderate Section: 9.4C Learning objective: Membrane Structure and Assembly 49. Which of the following correctly ranks the steps in the secretory pathway? 1. Synthesis occurs with a leading signal peptide 2. The SRP-ribosome complex binds the SRP receptor-translocon complex 3. The signal peptide binds the SRP and GDP is replaced with GTP 4. GTP hydrolysis results in dissociation of SRP and SR 5. SRP changes in conformation arresting peptide growth 6. The nascent protein begins to fold and post-translational modification is initiated 7. Signal peptidase cleaves the protein from the signal peptide A) 1, 2, 5, 4, 6, 7, 3 B) 1, 3, 5, 2, 4, 7, 6 C) 2, 4, 1, 3, 5, 6, 7 D) 2, 4, 3, 5, 4, 6, 7 E) 1, 3, 4, 2, 5, 7, 6 Ans: B Level of Difficulty: Difficult Section: 9.4D Learning objective: Membrane Structure and Assembly

50. Which of the following correctly describes the usefulness of SNAREs? I. They are essential for proper post-translation processing. II. They are a critical element in the function of the secretory pathway. III. They are effective at overcoming electrostatic repulsion between vesicle membranes. IV. They facilitate anchoring between vesicle membranes. A) I, II, III, IV B) II, III C) III D) IV E) III, IV Ans: E Level of Difficulty: Moderate Section: 9.4F Learning objective: Membrane Structure and Assembly 51. A researcher is developing a new drug for the treatment of influenza. Based on the information presented in the text about the influenza virus, which of the following drug reactions describes the action of this new drug? A) A drug which specifically interrupts the conformational change that results from the pH change in the endosome. B) A drug which enhances the function of a normally quiescent enzyme responsible for cleavage of the carbohydrate component on glycophorin A proteins. C) A drug which readily binds the hemagglutinin tag and results in conformational change. D) All of the above are potential actions of this new drug. E) None of the above is a plausible reaction for this new drug. Ans: D Level of Difficulty: Difficult Section: 9.4F Learning objective: Membrane Structure and Assembly

52. I-cell disease results in psychomotor retardation, skeletal deformities and death. Which of the following is true regarding this disease? A) The disease results in inclusion of glycosaminoglycans and glycolipids due the absence of an essential carbohydrate marker that directs the lysosomal hydrolases to the lysosome. B) The disease results in inclusion of glycolipids due mutations in the lysosomal hydrolases that render them inactive. C) The disease results in increased expression of SNARE proteins that result in vesicle fusion and exchange of glycosaminoglycans. D) The disease results from the lack of KDEL sequences which would normally signal their return to the ER following Golgi processing. E) All of the above are true. Ans: A Level of Difficulty: Difficult Section: 9.4D Learning objective: Membrane Structure and Assembly 53. Botox is used cosmetically to reduce wrinkles for a limited time interval. The function of Botox is described by which of the following? A) Botox inhibits function of the hemagglutinin tag. B) Botox relaxes small muscles by cleaving the leader peptide prior protein folding. C) Botox functions by inhibiting function of the SNARE protein. D) Botox functions by inhibiting the lysosomal protease cathepsin D. E) None of the above describes the function of Botox. Ans: C Level of Difficulty: Moderate Section: 9.4D, E, and F Learning objective: Membrane Structure and Assembly

54. Coated vesicles are used to ensure that the enclosed protein maintains its proper orientation. Clathrin is one type of protein used to coat vesicles. Which of the following is true regarding clathrin vesicles? A) They transport proteins between successive components of the Golgi compartments. B) They transport transmembrane proteins and GPI-linked proteins from the Golgi to the plasma membrane. C) They transport proteins from the ER to the Golgi. D) They form a rigid complex capable of protecting protein structure and orientation as it is passed from hydrophobic to hydrophilic environments. E) None of the above. Ans: B Level of Difficulty: Easy Section: 9.4E Learning objective: Membrane Structure and Assembly 55. Proteins which are passed from one Golgi compartment to the next in a successive fashion do so via a mechanism called____. A) maturation B) cisternal progression C) retrograde transport D) anterograde transport E) medialgrade transport Ans: D Level of Difficulty: Easy Section: 9.4E Learning objective: Membrane Structure and Assembly 56. A researcher has designed a new drug that will block the release of certain neurotransmitters from the synaptic cleft. Which of the following reactions must be blocked by this new drug? A) The drug binds the receptors in the postsynaptic membrane and blocks neurotransmitter binding. B) The drug binds the presynaptic membrane greatly facilitating the rate of transverse diffusion, thus changing the composition of the membrane. C) The drug enhances activity of SNARE proteins, thus facilitating fusion. D) All of the above are plausible actions of this new drug. E) None of the above is a plausible action of this new drug. Ans: B Level of Difficulty: Difficult Section: 9.4F Learning objective: Membrane Structure and Assembly

57. Receptor-mediated endocytosis: A) is comparable to the activities of vesicle fusion. B) superficially resembles binding of a clathrin coated vesicle to the plasma membrane. C) superficially resembles the reverse of vesicle fusion to the plasma membrane. D) mimics the function of the Golgi apparatus. E) functions much like the SNARE mediated fusion process. Ans: C Level of Difficulty: Easy Section: 9.4E and F Learning objective: Membrane Structure and Assembly 58. Which of the following processes presented in this chapter is (are) readily reversible with the help of enzymes known as thioesterases? A) myristoylation B) glycosylphosphotidylinositalation C) palmitoylation D) all of the above E) none of the above Ans: C Level of Difficulty: Moderate Section: 9.3B Learning objective: Membrane Proteins 59. Which of the following lipids would NOT likely be found in a lipid raft? I. glycosphingolipids II. glycerophospholipids III. cholesterol IV. palmitoleic acid A) I, IV B) I, II, IV C) II, IV D) III, IV E) IV Ans: C Level of Difficulty: Easy Section: 9.1A, D, E, 9.4C Learning objective: Lipid Classification and Membrane Structure and Assembly

60. Lipid bilayers with high concentrations of gangliosides are rare. Which of the following explanations is correct? A) The hydrophobic tails on gangliosides form a conical shape rather than a cylindrical shape making close packing difficult. B) Gangliosides contain large headgroups making close packing difficult. C) Gangliosides contain trans fatty acids resulting in a bent hydrophobic tail making close packing difficult. D) All of the above are correct. E) None of the above is correct. Ans: B Level of Difficulty: Moderate Section: 9.1D Learning objective: Lipid Classification

Chapter 10: Membrane Transport Matching A) Porins B) gap junctions C) symport D) active E) ion channel F) secondary active G) channel-forming H) carrier ionophores I) passive-mediated J) uniport K) simple diffusion L) anti-ion transport

1. ______ are transporters that bind the substance to be transported on one side of the membrane then diffuse through the membrane and release the substance on the other side. Ans: H Level of Difficulty: Easy Section: 10.2.A Learning objective: Passive-Mediated Transport 2. An example of nonmediated transport is ______. Ans: K Level of Difficulty: Easy Section: 10.1 Learning objective: Thermodynamics of Transport 3. The GLUT1 transporter functions via _____ transport. Ans: I Level of Difficulty: Easy Section: 10.2.E Learning objective: Passive-Mediated Transport

4. ______ are bacterial proteins forming a b barrel structure with a central aqueous channel. Ans: A Level of Difficulty: Easy Section: 10.2.B Learning objective: Passive-Mediated Transport 5. Connexin proteins make up the structure of ______. Ans: B Level of Difficulty: Easy Section: 10.2.E Learning objective: Passive-Mediated Transport 6. A transporter that moves two substances simultaneously in the same direction is an example of a(n) __________. Ans: C Level of Difficulty: Easy Section: 10.2.E Learning objective: Passive-Mediated Transport 7. KcsA is an example of a ______ ionophore. Ans: G Level of Difficulty: Easy Section: 10.2.C Learning objective: Passive-Mediated Transport 8. The Ca2+–ATPase requires ATP directly and is therefore an example of ______ transport. Ans: D Level of Difficulty: Easy Section: 10.3.B Learning objective: Active Transport

9. The Na+–glucose transport system requires generation of a gradient by another transporter and is therefore an example of ______ transport. Ans: F Level of Difficulty: Easy Section: 10.3.D Learning objective: Active Transport 10. KcsA is an example of a(n) _________. Ans: E Level of Difficulty: Easy Section: 10.2.C Learning objective: Passive-Mediated Transport

Multiple Choice 11. Which of the following compounds would cross a biological membrane most readily by nonmediated diffusion? A) water B) acetone C) hexane D) acetic acid E) methanol Ans: C Level of Difficulty: Easy Section: 10.1 Learning objective: Thermodynamics of Transport 12. Which of the following is an example of nonmediated transport? A) simple diffusion B) facilitated diffusion C) passive transport D) active transport E) all of the above Ans: A Level of Difficulty: Easy Section: 10.1 Learning objective: Thermodynamics of Transport

13. Which statement does not describe the transport of ions by valinomycin? A) Mutations in the peptide sequence may alter ability to transport through the membrane. B) Transport may be active or passive. C) The active site binds K+ with greater affinity than Na+ D) Transport results in equilibration of a concentration gradient across membranes. E) All of the above do describe transport by valinomycin. Ans: B Level of Difficulty: Moderate Section: 10.2.A Learning objective: Passive-Mediated Transport 14. Which of the following statements is true regarding ion channels? A) Protein structure studies indicate a flexible pore size capable of transporting ions of varying size. B) Ions require waters of hydration for sufficient passage through the entire channel. C) Ion channels maintain sodium and potassium ion concentrations that are greater in the extracellular fluid than in the cytosol. D) Channel rigidity minimizes energy states for appropriately sized ions. E) None of the above is true regarding ion channels. Ans: D Level of Difficulty: Difficult Section: 10.2.C Learning objective: Passive-Mediated Transport 15. Which of the following channels open in response to an extracellular stimulus such as a neurotransmitter? A) mechanoselective channels B) ligand-gated channels C) signal-gated channels D) voltage-gated channels E) All of these are sensitive to an extracellular stimulus.. Ans: B Level of Difficulty: Easy Section: 10.2.C Learning objective: Passive-Mediated Transport

16. D-Glucose and D-mannitol are similarly soluble, but D-glucose is transported through the erythrocyte membrane four times as rapidly as D-mannitol. What is the most likely explanation? A) D-glucose undergoes simple diffusion more rapidly than mannitol because glucose is less polar. B) D-glucose and D-mannitol enter the erythrocyte via an ion-gated channel. C) D-glucose and D-mannitol are transported via a system that distinguishes the two sugars. D) D-glucose flux through the membrane is linear whereas D-mannitol flux is described by a hyperbolic curve. E) None of the above provides the explanation. Ans: C Level of Difficulty: Easy Section: Box 10.2 and 10.2E Learning objective: Passive-Mediated Transport 17. D-glucose is added to cells and the rate of glucose transport is plotted against D-glucose concentration. In the presence of the D-galactose derivative 6-O-benzyl-D-galactose, the curve is shifted to the right, indicating that D-glucose and the D-galactose derivative both compete for a place in the binding site. Which of the following is true? A) The D-galactose derivative occupies some of the available binding sites. B) Given the same concentration of glucose available, the number of binding sites with Dglucose present would decrease. C) Given the same concentration of glucose, the rate of D-glucose flux would remain the same with the D-galactose derivative added. D) Presumably a higher concentration of D-glucose would be required in order to maintain the same rate of D-glucose flux as before the D-galactose derivative was added. E) All of the above are true. Ans: E Level of Difficulty: Difficult Section: Box 10.2 and 10.2 E Learning objective: Passive-Mediated Transport

18. Which of the following is not an example of a passive-mediated transporter? A) aquaporins B) the Kv ion channel C) GLUT1 D) lactose permease E) none of the above Ans: D Level of Difficulty: Easy Section: 10.2 Learning objective: Passive-Mediated Transport 19. Which of the following is (are) characteristic of the (Na+–K+)–ATPase? I. It binds Na+ and K+ simultaneously prior to binding ATP II. It is covalently modified by phosphorylation at an Asp residue when Na+ is present. III. Transport of Na+ and K+ occur in a 1:1 ratio, thus maintaining a balanced gradient until opening of the gated portion of the channel. IV It is essential for excitation of nerve cells. A) I, II, IV B) II, III, IV C) II, IV D) II, III E) II Ans: C Level of Difficulty: Difficult Section: 10.3.D Learning objective: Active Transport

20. Which of the transporters listed below differs from the others? A) (Na+–K+)–ATPase B) Na+–glucose transporter C) lactose permease D) KcsA E) Ca2+–ATPase Ans: D Level of Difficulty: Easy Section: 10.3 Learning objective: Active Transport 21. When the cardiac glycoside, digitoxin, is used for heart failure, the effects include: I. inhibition of phosphate hydrolysis from E2 of the (Na+–K+)–ATPase pump II. activation of the (Na+–K+)–ATPase pump III. increase in intracellular Na+ concentration IV. increase in Ca2+ concentration in the sarcoplasmic reticulum A) I, II, III, IV B) I, III, IV C) II, III, IV D) II, III E) I, III Ans: B Level of Difficulty: Difficult Section: 10.3.A Learning objective: Active Transport

22. Which features allow the KcsA channel to selectively transport K+? I. The entrance of the channel contains hydrophobic residues which forces the removal of waters of hydration. II. It is attracted to the entrance of the channel via electrostatic interactions. III. The “selectivity filter” involves a narrowing of the channel, allowing only dehydrated K+ access. IV. As K+ is transported through the channel it interacts with −C=O groups from the protein. A) I, II, III, IV B) II, III, IV C) II, III D) III, IV E) I, III Ans: B Level of Difficulty: Difficult Section: 10.2.C Learning objective: Passive-Mediated Transport 23. Gated ion channels I. exist because active transporters cannot maintain the gradient at a rate equal to nongated ion flow. II. remain open unless acted on by an external stimulus. III. remain open to all ions that are smaller than the pore diameter. IV. can transport varying ions. A) I, II B) I, III C) II, III D) II, IV E) I Ans: E Level of Difficulty: Difficult Section: 10.2.C Learning objective: Passive-Mediated Transport

24. Which does not occur when neurons are stimulated? A) Local depolarization results from the opening of Na+ ion channels allowing Na+ to exit the cell. B) Neighboring Na+ ion channels open in response to the change in membrane potential, resulting in a wave of depolarization. C) Depolarization stimulates the opening of ion-gated K+ channels, resulting in repolarization . D) Recovery involves the movement of Na+ out of the cell and K+ into the cell, resulting in the membrane regaining its resting potential. E) All of the above do occur when neuron are stimulated. Ans: A Level of Difficulty: Moderate Section: 10.2.C Learning objective: Passive-Mediated Transport 25. Vanilomycin A) is a cyclic polypeptide that functions as a K+ carrier. B) is a transmembrane polypeptide that transports K+. C) is a cyclic polypeptide that functions as a Na+ carrier. D) is a transmembrane polypeptide that transports Na+. E) is a b-barrel pore transporter that transfers K+. Ans: A Level of Difficulty: Easy Section: 10.2.C Learning objective: Passive-Mediated Transport 26. ClC Cl– channels I. assist in transport by forming a strong electrical dipole with the N-terminal end positively charged. II. effectively funnel ions into the pore via electrostatic interactions with basic amino acids. III. have a selectivity filter constructed from the N-terminal ends of α-helices, whose dipoles attract Cl– ions. IV. rely on the side chain hydroxyl groups from Ser and Tyr. A) I, II, II, IV B) I, II, IV C) II, II, IV D) III, IV E) I, IV

Ans: A Level of Difficulty: Difficult Section: 10.2.C Learning objective: Passive-Mediated Transport 27. Which statement about aquaporins is false? A) They transport water and hydronium ions efficiently. B) They exclusively transport water molecules at a high rate. C) They use hydrogen bonding to side chain NH2 groups of two Asn residues to exclude proton transport within the pore. D) They have a narrow constriction approximately equal to the van der Waals diameter of a water molecule. E) They use Arg and His side chains to remove associated water molecules from the ‘transported’ H2O. Ans: A Level of Difficulty: Moderate Section: 10.2.D Learning objective: Passive-Mediated Transport 28. Which of the following correctly rank the steps in erythrocyte glucose transport by GLUT1? I. Glucose binding results in a conformational change, opening the binding site on the opposite side of the membrane II. Glucose binds to the transporter on one side of the membrane III. The transporter reverts to initial conformation IV. The glucose disassociates A) II, I, III, IV B) II, I, IV, III C) IV, III, II, I D) I, II, IV, III E) IV, II, III, I Ans: B Level of Difficulty: Moderate Section: 10.2.E Learning objective: Passive-Mediated Transport

29. Which of the following is true about the (Na+–K+)–ATPase transporter? A) Three potassium ions bind to the cytostolic face of the transporter in the E1 state. B) GTP binds to it and is hydrolyzed to form GDP and a high energy phosphorylated glutamyl residue. C) Formation of the high-energy phosphorylated glutamyl residue triggers a conformational shift from the E1 form to the E2 form. D) Phosphate hydrolysis of the E2 state releases potassium ions to the cytosol and results in rearrangement to the E1 state. E) All of the above correctly describe this transporter. Ans: D Level of Difficulty: Difficult Section: 10.3.A Learning objective: Active Transport 30. Ouabain inhibits the (Na+–K+)–ATPase pump, resulting in A) K+ ions moving into the cell along a concentration gradient B) K+ ions bringing water molecules into the cell in order to maintain an osmotic balance C) extra K+ ions and water in cells causing them to swell and lyse D) an increase in the strength of heart muscle contractions when small amounts of Ouabain are used E) all of the above Ans: D Level of Difficulty: Easy Section: 10.3.A Learning objective: Active Transport 31. Lactose permease uses a ___________ gradient generated ______ to cotransport lactose across the cell membrane. A) potassium; via the Na+/K+ pump B) potassium; via oxidative metabolism C) proton; via the Na+/K+ pump D) proton; via oxidative metabolism E) chloride; within the intestinal lumen Ans: D Level of Difficulty: Moderate Section: 10.3.D Learning objective: Active Transport

32. The Kv channel is transiently closed by ___________. A) a spherical globular segment on the N-terminus B) a C-terminal segment activated by proteolysis C) proteoglycan residues D) an ion larger than the selectivity filter blocking entry E) tightly-bound Ca2+ Ans: A Level of Difficulty: Moderate Section: 10.2.C Learning objective: Passive-Mediated Transport 33. A graph of the rate of glucose transport via the GLUT1 transporter vs. glucose concentration would have a ________ shape indicating that higher glucose concentrations increase the rate of transport until all the sites are saturated. A) hyperbolic B) sigmoidal C) bell D) linear E) exponential Ans: A Level of Difficulty: Easy Section: 10.2.E Learning objective: Passive-Mediated Transport 34. In the intestinal epithelium, glucose enters the cell in symport with ______, which is subsequently ejected by ________. A) K+; the Na+/K+ pump B) H+; oxidative metabolism C) Na+; the Na+/K+ pump D) Na+; the GLUT1 transporter E) Cl–; MDR transporter Ans: C Level of Difficulty: Moderate Section: 10.3.D Learning objective: Active Transport

35. The concentration of cytosolic Ca2+ is _________ the extracellular concentration of Ca2+. A) dependent upon B) equal to C) 4 orders of magnitude greater than D) 2 order of magnitude greater than E) much less than Ans: E Level of Difficulty: Easy Section: 10.3.B Learning objective: Active Transport 36. Drug resistance is frequently traced to I. the MDR transporter. II. overexpression of P-glycoprotein. III. increased number of specific ABC transporters. IV. the evolution of selectivity filters. A) I, II, III B) II, III C) I, III D) III, IV E) II, IV Ans: A Level of Difficulty: Moderate Section: 10.3.C Learning objective: Active Transport 37. A pore that simultaneously transports two different molecules in different directions is called A) a symport. B) a uniport . C) a gap junction. D) an equilibrium channel. E) an antiport. Ans: E Level of Difficulty: Easy Section: 10.2.E Learning objective: Passive-Mediated Transport

38. Gap junctions A) connect the cytoplasm to the extracellular solution thus allowing transfer of small molecules out of the cell into the extracellular solution. B) are essential communication channels between the cell and the extracellular solution. C) allow exchange of small molecules between cells within an organ. D) allow intercellular exchange of macromolecules. E) All of the above. Ans: C Level of Difficulty: Difficult Section: 10.2.E and Box 10-1 Learning objective: Passive-Mediated Transport 39. The rapid transport of K+ ions by the KcsA ion channel moves up to ____ ions per ______. A) 106; minute B) 101; second C) 1023; minute D) 108; second E) 108; hour Ans: D Level of Difficulty: Easy Section: 10.2.C Learning objective: Passive-Mediated Transport 40. In the body hydrogen ions produced from the reaction of carbonic anhydrase are transported into the lumen of the stomach via an ATP utilizing proton pump. The removal of hydrogen ions drives formation of bicarbonate ions and a concentration gradient is formed. Bicarbonate is transported out at the same time that chloride ions are transferred in. Based on this information, which of the following is FALSE? A) The pump driving the driving the hydrogen ions into the lumen must undergo a conformational change. B) The pump driving bicarbonate out and chloride in must be an antiport system. C) The pump driving bicarbonate out and chloride in must require ATP directly. D) The bicarbonate-chloride pump requires ATP indirectly. E) The bicarbonate-chloride pump must require activity of the proton pump. Ans: C Level of Difficulty: Difficult Section: 10.3.C Learning objective: Active Transport

41. Based on the diagram below, which of the following statements is TRUE?

A) F requires ATP directly B) B is an example of symport C) B is gradient driven D) B requires ATP directly E) None of the above are true Ans: E Level of Difficulty: Difficult Section: 10.3.C Learning objective: Active Transport 42. Based on the figure below, this system represents _______.

A) primary active transport B) passive transport C) nonmediated transport D) secondary active transport E) A and D Ans: A Level of Difficulty: Moderate Section: 10.3.C Learning objective: Active Transport

43. Which of the following methods will allow you to determine if a substance used mediated transport? A) Measure the rate of transport to determine if it is high or low relative to other transport systems. B) Evaluate the flux at several different concentrations of the substance and look for hyperbolic dependence. C) Monitor transport rates at a variety of concentrations and confirm a linear dependence. D) Compare rate of transport in an in vitro system to those in vivo. E) None of the above. Ans: B Level of Difficulty: Moderate Section: Box 10-2 Learning objective: Active Transport 44. The greater the magnitude of the concentration gradient: A) the more rapid the rate of diffusion. B) the more likely mediated transport is required. C) the easier it is to reverse the flux. D) the higher number of ATPs required to diffuse. E) All of the above are true. Ans: A Level of Difficulty: Moderate Section: 10.1 Learning objective: Thermodynamics of Transport 45. The E. coli maltoporin utilizes what has been termed the greasy slide. Which of the following statements best describe the function of the greasy slide? A) There is a pathway of phospholipids that line the inside of the channel and facilitate transport. B) A series of aromatic side chains arrange in a helical pattern matching the relative curvature of the protein backbone, thus provided little restriction to transport. C) Hydroxyl groups on glucose hydrogen bond with polar and charged side chains lining the channel, thus resulting in a series of interactions mimicking a screw-like pathway. D) Constriction in the channel removes waters of hydration, thus making the substrate more hydrophobic and "greasy." E) Amino acids side chains lining the channel are small and non-bulky, making steric constriction essentially non-existent.

Ans: C Level of Difficulty: Moderate Section: 10.2B Learning objective: Passive-Mediated Transport 46. Of the transport proteins discussed in the chapter, in general, which of the following do they have in common? A) utilize conformational changes to control flux B) require hydrophobic amino acid side chains to line the pores C) utilize stereospecifcity to selectively transport D) transport ionized substances E) move in the direction of the gradient Ans: A Level of Difficulty: Moderate Section: 10.2E Learning objective: Passive-Mediated Transport 47. A patient has low levels of potassium. Which of the following could be affected? I. levels of calcium available for cardiac muscle II. amount of glucose transported through the intestinal lumen III. amount of lactose metabolized IV. chloride ion transport may slow A) I, IV B) II, IV C) II, III D) II, IV E) I, II, IV Ans: E Level of Difficulty: Difficult Section: 10.3.A, B, C, D Learning objective: Active Transport 48. What type of gradient is required for efficient lactose transport in E. coli? A) sodium B) potassium C) proton D) magnesium E) calcium

Ans: C Level of Difficulty: Easy Section: 10.3.D Learning objective: Active Transport 49. Which of the following correctly describes the reason for the specificity of valinomycin? A) The K+ ion is the only ion small enough to fit through the ion channel. B) The K+ radius is the ideal size for a large binding affinity because it minimizes steric strain and potential for degrees of rotation. C) It selectively binds to the entrance of the transporter which is lined with negatively charged amino acids. D) All of the above describe the specificity. E) None of the above describe the specificity. Ans: B Level of Difficulty: Difficult Section: 10.2.A Learning objective: Passive-Mediated Transport 50. Which of the following is evidence for aquaporins? A) Kidney cells are otherwise incapable of maintaining a gradient. B) Kidney cell transport of water molecules can be inhibited by mercuric ions. C) Water, a polar substance, cannot cross the hydrophobic membrane without mediation. D) Rapid rates of water transport require mediation. E) Studies measuring flux of water molecules in the kidney yielded only linear plots of flux vs. [H2O] despite the large excess in water. Ans: B Level of Difficulty: Moderate Section: 10.2.C Learning objective: Passive-Mediated Transport

Chapter 11: Enzyme Catalysis Matching A) B) C) D) E) F) G) H) I) J) K) L) M) N)

high deprotonated protonated catalytic mechanism covalent rate-determining step leaving group formation of ES amino acid low coenzymes concerted acid-base orientation oxidation

1. For efficient nucleophilic catalysis, a group such as the sulfhydryl on a cysteine residue must be able to form a good ______, in addition to being a good nucleophile. Ans: G Level of Difficulty: Easy Section: 11.3.B Learning objective: Catalytic Mechanisms 2. If an enzyme-catalyzed reaction has a low rate at low pH and high rate at higher pH, this implies that a group on either the enzyme or the substrate must be ______ for an efficient reaction. Ans: B Level of Difficulty: Easy Section: 11.3.A Learning objective: Catalytic Mechanisms

3. On a transition state diagram for a multistep reaction, the step with the greatest DG is the ______. Ans: F Level of Difficulty: Easy Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate 4. On a transition state diagram for a one-step very spontaneous reaction a large peak (high D G‡)would imply a ______ rate for the reaction. Ans: J Level of Difficulty: Easy Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate 5. Metal ion cofactors can coordinate to the substrate or stabilize electrostatic effects by enabling proper ______in the active site. Ans: M Level of Difficulty: Easy Section: 11.3.C Learning objective: Catalytic Mechanisms 6. Large rate enhancement in enzyme catalysis may occur when binding the substrate via _________ attachment. Ans: E Level of Difficulty: Easy Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate 7. Metal ion cofactors offer various ______ states that allow enzymes to accomplished oxidation reduction reactions. Ans: N Level of Difficulty: Easy Section: 11.3.C Learning objective: Catalytic Mechanisms

8. Since proteins are limited in their abilities to catalyze oxidation-reduction reactions, enzymes often employ ______ to assist with catalysis. Ans: K Level of Difficulty: Easy Section: 11.1.C Learning objective: General Properties of Enzymes 9. Some serine proteases are believed to have developed by convergent evolution, because the ______ sequences of some serine proteases show no resemblance to those of others. Ans: I Level of Difficulty: Easy Section: 11.5.B Learning objective: Serine Proteases 10. Clustering several amino acid residues with appropriate pK values at an active site can promote a(n) _________ catalytic mechanism. Ans: L Level of Difficulty: Easy Section: 11.3.A Learning objective: Catalytic Mechanisms

Multiple Choice 11. An uncatalyzed reaction has a rate of 4.2 × 10–7 sec–1. When an enzyme is added the rate is 3.2 × 104 sec–1. Calculate the rate enhancement caused by the enzyme. A) 3.2 × 104 B) 7.4 × 10–3 C) 1.3 × 10–2 D) 7.6 × 1010 E) The data are not appropriate for the calculation requested. Ans: D Level of Difficulty: Moderate Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate

12. Which of these amino acid groups would not make a good nucleophilic catalyst? A) amino B) sulfhydryl C) imidazole D) methyl E) hydroxyl Ans: D Level of Difficulty: Easy Section: 11.3.B Learning objective: Catalytic Mechanisms 13. The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst because I. the imidazole group has a pKa in the physiological pH range. II. in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated. III. one guanidino group is protonated, and the other is deprotonated at physiological pH. IV. the imidazole group is a strong reducing agent at physiological pH. A) I, II B) I C) II, IV D) II, III E) IV Ans: A Level of Difficulty: Moderate Section: 11.3.A Learning objective: Catalytic Mechanisms 14. A new serine protease was discovered that preferentially cleaves a peptide bond adjoining a negatively charged side chain. Which of the following is true? A) The specificity pocket would mimic that of chymotrypsin. B) The specificity pocket would mimic that of trypsin. C) The specificity pocket is likely lined with amino acids such as Arg and Lys. D) It likely reacts much slower than chymotrypsin. E) It likely reaction much faster than chymotrypsin. Ans: C Level of Difficulty: Moderate Section: 11.5.C Learning objective: Serine Proteases

15. If you add enzyme to a solution containing only the product(s) of a reaction, would you expect any substrate to form? A) It depends on the time interval and temperature of reaction. B) It depends on the concentration of products added. C) It depends on the energy difference between E + P and the transition state. D) All of the above may determine if product forms. E) None of the above determines if product forms. Ans: C Level of Difficulty: Difficult Section: 11.3.E Learning objective: Catalytic Mechanisms 16. Which one of the following is correct? I. All enzymes are highly specific for the reactions they catalyze. II. Prosthetic groups are loosely associated with the polypeptide chain of an enzyme. III. If an enzyme-catalyzed reaction requires a group with a low pK to be deprotonated and a group with a higher pK to be protonated, the pH vs. rate curve will have a peak in the middle of the two pK values. IV. When comparing types of catalysis, the proximity effect provides the largest rate enhancement. A) I, II, III, IV B) I, III C) I D) III E) IV Ans: D Level of Difficulty: Difficult Section: 11.3 Learning objective: Catalytic Mechanisms

17. Which of the following amino acid residues would not provide a side chain for acid-base catalysis at physiological pH? (Assume pK values of each amino acid are equal to the pK value for the free amino acid in solution.) I. leucine II. lysine III. aspartic acid IV. histidine A) I, II, III B) I, II C) I D) II E) I, III Ans: A Level of Difficulty: Difficult Section: 11.3.A Learning objective: Catalytic Mechanisms 18. Which of the following amino acid residues would provide a side chain capable of increasing the hydrophobicity of a binding site? A) histidine B) lysine C) isoleucine D) arginine E) serine Ans: C Level of Difficulty: Moderate Section: 11.3 Learning objective: Catalytic Mechanisms

19. Which of the following is TRUE about enzymes? I. Enzymes typically catalyze reactions at much higher rates than chemical catalyst. II. Enzymes are often very specific for their substrates. III. Enzyme activities can often be regulated. IV. Enzymes typically act under milder conditions of temperature and pH than chemical catalysts. A) I, II, III B) I, II, III, IV C) II, II D) III, IV E) II, III, IV Ans: B Level of Difficulty: Moderate Section: 11.3.E Learning objective: Catalytic Mechanisms 20. In affinity labeling, a technique used to study enzyme mechanisms, A) A compound designed to bind at the active site reacts with and therefore permits the identification of a nearby group. B) A fluorescent group is attached to the substrate to identify the position of the active site. C) Highly purified enzyme is obtained by affinity chromatography for mechanistic studies. D) A radioactive isotope is incorporated into the substrate to identify the position of the active site. E) Genetic modification of amino acid residues is used to alter the binding affinity of the active site. Ans: A Level of Difficulty: Moderate Section: 11.5.A Learning objective: Serine Proteases

21. Which of the following is TRUE regarding cofactors? A) Coenzymes are often separate from the enzyme and do not need recharged. B) Metal ions must be covalently attached to function as a cofactor. C) Cofactor is a broad term used for all enzyme "helpers". D) Prosthetic groups can dissociate readily and be regenerated for use in another enzyme. E) An apoenzyme implies that a cofactor is present.

Ans: C Level of Difficulty: Easy Section: 11.1.C Learning objective: General Properties of Enzymes 22. A peptide with the sequence "Glu-Ser-Val-Asp-Lys" will likely be cut next to "Val" rapidly by _______ and very slowly by ____. I. chymotrypsin II. trypsin III. trypsinogen IV. elastase A) I,IV B) I, II C) II, III D) IV, II E) IV, I Ans: E Level of Difficulty: Easy Section: 11.5.B Learning objective: Serine Proteases 23. Alcohol dehydrogenase catalyzes the conversion of methanol to _________ and is, therefore, classified as a(an)________. A) acetic acid; transferase B) formaldehyde; oxidoreductase C) acetic acid; oxidoreductase D) ethanol; lyase E) formaldehyde; transferase Ans: B Level of Difficulty: Easy Section: 11.1.A Learning objective: General Properties of Enzymes 24. Carbohydrate metabolic enzymes bind D-glucose specifically. D-glucose has an estimated caloric value of 1 kcal per 4 grams of carbohydrate. Based on the methods used to convert the energy of D-glucose into a useable form, what would you estimate the caloric value of L-glucose to be using the same method?

A) 1 kcal per 4 grams B) 1 kcal per 2 grams C) 1 kcal per 8 grams D) 0 kcal per 4 grams E) 2 kcal per 8 grams Ans: D Level of Difficulty: Difficult Section: 11.1.B Learning objective: General Properties of Enzymes 25. Glu 35 of lysozyme is found in a nonpolar environment. Which of the following is true? A) Its pK is lower than the usual value in this environment. B) Its pK is higher than the usual value in this environment. C) Its pK would not change in this environment. D) Its pK would depend on the sample buffer. E) None of the above is correct. Ans: B Level of Difficulty: Easy Section: 11.4B Learning objective: Activation Energy and the Reaction Coordinate 26. ______ metals are the most common metallic enzyme cofactors. A) Actinide B) Alkali C) Heavy D) Rare earth E) Transition Ans: E Level of Difficulty: Easy Section: 11.3.C Learning objective: Catalytic Mechanisms

27. Curved arrows are conventionally used to illustrate the movement of A) electron pairs. B) single electrons. C) protons. D) anions. E) All of the above use this convention. Ans: A Level of Difficulty: Easy Section: 11.3 Learning objective: Catalytic Mechanisms 28. Proton transfer from an acid, lowering the free energy of a reaction’s transition state, is characteristic of A) electrostatic catalysis. B) nucleophilic catalysis. C) general base catalysis. D) general acid catalysis. E) concerted acid-base catalysis. Ans: D Level of Difficulty: Easy Section: 11.3.A Learning objective: Catalytic Mechanisms 29. Simultaneous stimulation of a reaction by general acid and general base catalysis is defined as A) covalent catalysis. B) electrostatic catalysis. C) proximity catalysis. D) concerted acid-base catalysis. E) transition state catalysis. Ans: D Level of Difficulty: Easy Section: 11.3.A Learning objective: Catalytic Mechanisms

30. A pH versus rate curve with an inflection point at pH~4 suggests the involvement of a(n) ________ in the catalytic step. A) proton abstraction that requires a metal ion in close proximity B) proton transfer with a pK close to 4 C) proton donation that is mediated by a coenzyme D) free proton surrounded by a hydrophobic environment E) redox cofactor Ans: B Level of Difficulty: Moderate Section: 11.3.A Learning objective: Catalytic Mechanisms 31. The catalytic mechanism of bovine pancreatic RNase A relies upon acid-base catalysis involving the amino acid __________. A) imidazole B) lysine C) histidine D) aspartic acid E) glutamic acid Ans: C Level of Difficulty: Easy Section: 11.3.A Learning objective: Catalytic Mechanisms 32. Consider the Schiff base formation reaction discussed in the catalytic mechanisms section of the chapter. What would probably happen if the carboxylate group was stabilized by a nearby positive charge? A) The Schiff base would donate a lone pair of electrons to the substrate. B) The Schiff base would form prior to decarboxylation. C) The reaction would proceed with nucleophilic attack on the enzyme by the electrophilic substrate. D) All of the above would be possible given the discussed mechanism with a stabilized carboxyl group. E) None of the above is plausible considering the discussed mechanism with a stabilized carboxylate group. Ans: E Level of Difficulty: Difficult Section: 11.3.B Learning objective: Catalytic Mechanisms

33. During the course of a catalytic reaction the following occurs: 1) Substrate is covalently bound and oriented with proximity to the active site residues. 2) Negative charge builds up on the substrate and is stabilized. 3) Oxidation of the enzyme followed by reduction to complete the catalytic cycle. What type of chemical species can facilitate these reactions? A) nucleophilic amino acids B) electrophilic groups C) prosthetic phosphate groups D) transition metal anions E) transition metal cations Ans: E Level of Difficulty: Moderate Section: 11.3.C Learning objective: Catalytic Mechanisms 34. Which of the following processes would yield and increase in rate? A) the proximity of the reacting groups B) the rotational motions of the substrates and catalytic groups C) the orientations of the substrates and catalytic groups D) all of the above E) none of the above Ans: D Level of Difficulty: Easy Section: 11.3.D Learning objective: Catalytic Mechanisms 35. Enzymes that bind reaction transition states with greater affinity than substrates or products A) have a lower free energy ES complex than E + S. B) increase reaction rates by decreasing the concentration of the transition state . C) progress slowly due to the stability of the transition state complex. D) compensate for small differences in the energy of the free substrate and free product. E) All of the above are correct. Ans: A Level of Difficulty: Difficult Section: 11.3.E Learning objective: Catalytic Mechanisms

36. Lysozyme requires _____ for effective catalysis. I. an Asp in a nonpolar environment II. a negatively charged Asp III. a Glu that functions as an acid catalyst IV. a Glu that is deprotonated A) I, II, III, IV B) I, III C) II, III D) II, IV E) I, IV Ans: C Level of Difficulty: Moderate Section: 11.4 Learning objective: Lysozyme 37. Zymogens are not enzymatically active because A) the active site amino acids have been mutated. B) they have not yet bound the proper cofactor. C) their environment has the wrong pH. D) they are not yet shaped such that essential proximity and orientation catalysis can occur. E) None of the above is correct. Ans: D Level of Difficulty: Moderate Section: 11.5.D Learning objective: Serine Proteases 38. Serine proteases use _________ to catalyze the cleavage of a peptide bond. I. covalent catalysis II. proximity and orientation effects III. general base catalysis IV. electrostatic catalysis A) I, II B) II C) III D) I, II, III E) I, II, III, IV

Ans: E Level of Difficulty: Easy Section: 11.5.C Learning objective: Serine Proteases 39. Which of the following would result in the greatest decrease in function of the catalytic triad found in serine proteases? A) Mutation to Ser, Cys, Asp B) Mutation to Ser, His, Asp C) Mutation to Cys, His, Asp D) Mutation to Ser, His, Glu E) Mutation to Cys, His, Glu Ans: C Level of Difficulty: Difficult Section: 11.5.B Learning objective: Serine Proteases 40. In the lysozome reaction the D ring in NAM is in the ________ conformation providing a contribution of catalytic energy via the ____ distortion. A) half-chair; electrostatic B) chair; strain C) boat; strain D) boat; electrostatic E) half-chair; strain Ans: E Level of Difficulty: Easy Section: 11.4.B Learning objective: Lysozyme

41. Enzyme X catalyzes the addition of a hydroxyl group to substrate Y. In the process a metal cofactor is reduced and then reoxidized. What class of enzyme is X? A) oxidoreductase B) ligase C) hydrolase D) isomerase E) lyase Ans: A Level of Difficulty: Easy Section: 11.1.A and B Learning objective: General Properties of Enzymes 42. The transition state of an enzyme and substrate reaction A) must always bind the enzyme active site with lower energy than the products. B) is stabilized by enhancing the reverse reaction of E + S→ES. C) is composed of true covalent bonds which decrease its energy. D) is stabilized due to the specificity of the active site for the substrate. E) is stabilized by decreasing the effective concentration. Ans: D Level of Difficulty: Moderate Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate 43. Proximity effects A) result from active site specificity. B) result from substrate channeling. C) result in increased effective concentration of substrate. D) lower the energy of activation. E) All of the above of the above are correct. Ans: D Level of Difficulty: Difficult Section: 11.3.D Learning objective: Catalytic Mechanisms

44. In the serine protease trypsin, the specificity for one substrate over another describes what type of catalysis? A) proximity B) acid-base C) covalent D) strain E) none of the above Ans: A Level of Difficulty: Moderate Section: 11.5.A, B, C Learning objective: Serine Proteases 45. Which type of catalysis may be carried out using redistribution of electron density to facilitate the transfer of a proton? I. proximity II. acid-base III. covalent IV. strain A) I B) II C) III D) II, III E) II, IV Ans: D Level of Difficulty: Difficult Section: 11.3.B Learning objective: Catalytic Mechanisms 46. In trypsin the specificity for one substrate over another comes from A) the negatively charged pocket. B) the positively charge pocket. C) the hydrophobic pocket. D) the amino acid serine. E) the amino acid histidine. Ans: A Level of Difficulty: Easy Section: 11.5.A, B, C

47. Which of the following is TRUE regarding transition state? A) The free energy between the transition state and the reactants must be negative. B) The transition state can be stabilized by covalent catalysis. C) The transition state represents the ES complex. D) Transition state analogs bind the substrate not the enzyme E) All of the above are true. Ans: B Level of Difficulty: Moderate Section: 11.2 Learning objective: Activation Energy and the Reaction Coordinate 48. Research scientists are trying to clone a gene. In order to accomplish this task they join two pieces of DNA. Which class of the enzymes below might accomplish this task? A) oxidoreductase B) ligase C) hydrolase D) isomerase E) lyase Ans: B Level of Difficulty: Moderate Section: 11.1.A Learning objective: General Properties of Enzymes

49. The enzyme pictured below is shown in two configurations, A (open) and B (closed). Upon binding substrate in the active site, the enzyme converts the structure shown in B. Which of the following is true based on the given information?

A) The enzyme requires a high concentration of substrate to function B) This example exemplifies the “lock-and-key” model. C) This enzyme must require ATP. D) This example exemplifies the of “induced fit” model. E) None of these are true. Ans: D Level of Difficulty: Moderate Section: 11.1.B Learning objective: General Properties of Enzymes 50. Why can histidine NOT act as a base in the lysosome (an organelle where the pH is close to 4.5)? A) Histidine has a positive charge at pH 4.5. B) Histidine has a side chain pK close to 6. C) Histidine would be protonated at pH 4.5. D) All of the above are correct. E) None of the above is correct. Ans: D Level of Difficulty: Moderate Section: 11.3.A Learning objective: Catalytic Mechanisms

51. A recent discovery has suggested that a gene mutation results in several amino acid substitutions within an active site. The following substitutions have been identified and are each expected to form the active site: Normal protein amino acids Valine Leucine Valine Serine Histidine Aspartate

Substitutions Lysine Arginine Arginine Deleted and replaced with a coenzyme capable of covalent binding Histidine (note no mutation) Glutamate

It was also noticed that a coenzyme molecule containing a hydroxyl (—OH) group binds to the mutated protein in approximately the same location as the original serine but does not alter the structure of the protein in anyway. Based on your knowledge of amino acids, enzymes, and catalysis, which of the following is a REASONABLE conclusion? A) The mutant protein cleaves on the carboxy side of phenylalanine. B) The mutant protein cleaves peptide bonds on the carboxy side of glutamate or aspartate. C) The mutant protein cleaves peptide bonds on the carboxy side of lysine or arginine. D) The mutant protein functions identical to chymotrypsin. E) The mutant protein has no function. Ans: B Level of Difficulty: Difficult Section: 11.5.A, B, C Learning objective: Serine Proteases

52. The following diagram shows a portion of a reaction sequence of an enzyme. What type(s) of catalysis is (are) occurring in this first step?

A) proximity catalysis B) acid-base catalysis C) covalent catalysis D) All of the above are occurring. E) None of the above is occurring. Ans: B Level of Difficulty: Moderate Section: 11.5.A, B, C Learning objective: Serine Proteases 53. Acid-base catalysis may be accomplished by: A) active site specificity B) charge delocalization C) buffer effects D) induced strain E) conformational change Ans: B Level of Difficulty: Difficult Section: 11.3.A Learning objective: Catalytic Mechanisms

Chapter 12: Enzyme Kinetics, Inhibition and Control

Matching A) isozymes B) [A] C) the rate constant D) Ping Pong E) bimolecular F) ES complex G) random ordered H) competitive inhibition I) unimolecular J) [A]2 K) competitive inhibition L) phosphorylation M) small KS N) large KS O) uncompetitive inhibition P) [B] 1. The E+Sà E+P reaction is ______. Ans: E Level of Difficulty: Easy Section: 12.1.A Learning objective: Reaction Kinetics 2. Assume a first order reaction, the rate of the reaction 2A®B is dependent on ______. Ans: B Level of Difficulty: Easy Section: 12.1.A Learning objective: Reaction Kinetics 3. If AàB is a zero-order reaction, the rate is dependent on ______. Ans: C Level of Difficulty: Easy Section: 12.1.B Learning objective: Reaction Kinetics

4. A two-substrate enzymatic reaction in which one product is produced before the second substrate binds to the enzyme has a ______ mechanism. Ans: D Level of Difficulty: Easy Section: 12.1.D Learning objective: Reaction Kinetics 5. The type of enzyme inhibition in which Vmax is unaffected is ______. Ans: K Level of Difficulty: Moderate Section: 12.2.A Learning objective: Enzyme Inhibition 6. In uncompetitive inhibition, the inhibitor binds only to the ______. Ans: F Level of Difficulty: Moderate Section: 12.2.B Learning objective: Enzyme Inhibition 7. A common type of covalent modification of regulatory enzymes involves ______ of serine residues. Ans: L Level of Difficulty: Moderate Section: 12.3.B Learning objective: Control of Enzyme Activity 8. A lead compound for a new drug should bind to its target protein with a very ______. Ans: M Level of Difficulty: Moderate Section: 12.4.A Learning objective: Drug Design

9. Different enzymes that catalyze the same reaction, although may be found in different tissues, are known as ______. Ans: A Level of Difficulty: Easy Section: 12.3.B Learning objective: Control of Enzyme Activity 10. In ______, the inhibitor binds to a site involved in both substrate binding and catalysis. Ans: H Level of Difficulty: Easy Section: 12.2.C Learning objective: Enzyme Inhibition

Multiple Choice 11. A lead compound would be most promising if it had: A) KI = 4.7 × 105 M. B) KI = 1.5 × 108 M. C) KI = 1.5 × 10-8 M. D) KI = 4.7 × 10-5 M. E) KM = 4.7 × 105 M. Ans: C Level of Difficulty: Moderate Section: 12.4.A Learning objective: Drug Design 12. What is the velocity of a first-order reaction at 37oC when the reactant concentration is 6 × 10-2 M and the rate constant is 8 × 103 sec-1? A) 1.33 × 105 M-1•sec-1 B) 1.33 × 105 M•sec C) 7.5 × 10-2 M•sec D) 4.8 × 102 M•sec-1 E) Not enough data are given to make this calculation Ans: D Level of Difficulty: Moderate Section: 12.1.A Learning objective: Reaction Kinetics

13. Reaction that is first order with respect to A and B A) is dependent on the concentration of A and B. B) is dependent on the concentration of A. C) has smaller rate constants than first-order reactions regardless of reactant concentration. D) is independent of reactant concentration. E) is always faster than first-order reactions due to loss of concentration dependence. Ans: A Level of Difficulty: Moderate Section: 12.1.A Learning objective: Reaction Kinetics 14. For a reaction A + B ® C, if the concentration of B is much larger than A so that [B] remains constant during the reaction while [A] is varied, the kinetics will be A) sigmoidal. B) pseudo-first-order. C) unimolecular. D) zero-order. E) hyperbolic. Ans: B Level of Difficulty: Easy Section: 12.1.A Learning objective: Reaction Kinetics 15. KM is A) a measure of the catalytic efficiency of the enzyme. B) equal to half of Vmax C) the rate constant for the reaction ES ® E + P. D) the [S] that half-saturates the enzyme. E) a ratio of substrate concentration relative to catalytic power. Ans: D Level of Difficulty: Moderate Section: 12.1.B Learning objective: Reaction Kinetics

16. In order for an enzymatic reaction obeying the Michaelis-Menten equation to reach 3/4 of its maximum velocity, A) [S] would need to be equal to KM B) [S] would need to be ½ KM C) [S] would need to be 3KM D) [S] would need to be ¾ KM E) not enough information is given to make this calculation Ans: C Level of Difficulty: Moderate Section: 12.1.C Learning objective: Reaction Kinetics 17. The KM can be considered to be the same as the dissociation constant KS for E + S binding if A) the concentration of [ES] is unchanged. B) ES ® E + P is fast compared to ES ® E + S. C) k1 >> k2 D) k2 << k-1. E) this statement cannot be completed because KM can never approximate KS. Ans: D Level of Difficulty: Difficult Section: 12.1.C Learning objective: Reaction Kinetics 18. Find kcat for a reaction in which Vmax is 4 × 10-4 mol•min-1 and the reaction mixture contains one microgram of enzyme (the molecular weight of the enzyme is 200,000 D). A) 2 × 10-11 min-1 B) 8 × 107 min-1 C) 8 × 109 min-1 D) 2 × 10-14 min-1 E) 4 × 108 min-1 Ans: B Level of Difficulty: Difficult Section: 12.1.C Learning objective: Reaction Kinetics

19. An enzyme is near maximum efficiency when A) its turnover number is near Vmax. B) kcat/KM is near 108 M-1s-1. C) k1 << k-1. D) kcat/KM is equal to kcat. E) KM is large when k2 exceeds k1. Ans: B Level of Difficulty: Easy Section: 12.1.C Learning objective: Reaction Kinetics 20. Find the initial velocity for an enzymatic reaction when Vmax = 6.5 × 10–5 mol•sec–1, [S] = 3.0 × 10–3 M, KM = 4.5 × 10–3 M and the enzyme concentration at time zero is 1.5 × 10-2 µM. A) 3.9 × 10–5 mol•sec–1 B) 2.6 × 10–5 mol•sec–1 C) 1.4 × 10–2 mol•sec–1 D) 8.7 × 10–3 mol•sec–1 E) Not enough information is given to make this calculation. Ans: B Level of Difficulty: Moderate Section: 12.1.C Learning objective: Reaction Kinetics 21. When [S] = KM, n0 = (_____)× (Vmax). A) [S] B) 0.75 C) 0.5 D) KM E) kcat Ans: C Level of Difficulty: Moderate Section: 12.1.A Learning objective: Reaction Kinetics

22. [S] = KM for a simple enzymatic reaction. When [S] is doubled the initial velocity is A) 2 Vmax B) equal to Vmax C) (1/3) Vmax D) 0.5 Vmax E) 2 KM/[S] Ans: C Level of Difficulty: Moderate Section: 12.1.C Learning objective: Reaction Kinetics 23. Irreversible enzyme inhibitors A) inactivate the enzyme B) inhibit competitively C) maximize product by minimizing ESàE+S D) behave allosterically E) function via Ping Pong mechanism Ans: A Level of Difficulty: Easy Section: 12.2.C Learning objective: Enzyme Inhibition 24. A Lineweaver-Burk plot is also referred to as I. a sigmoidal plot. II. a linear plot. III. a Michaelis–Menten plot. IV. a double reciprocal plot. A) II B) II, III C) IV D) II, IV E) III, IV Ans: D Level of Difficulty: Moderate Section: 12.1.C Learning objective: Reaction Kinetics

25. Parallel lines on a Lineweaver-Burk plot indicate I. an increase in KM. II. decrease in KM. III. decrease in Vmax. IV. uncompetitive inhibition. A) I, IV B) II, III, IV C) I or II, III D) I or III, II E) I, III, IV Ans: C Level of Difficulty: Difficult Section: 12.2.B Learning objective: Enzyme Inhibition 26. Fourth-order reactions. A) have three or more sequential rate determining steps. B) require a ‘Ping Pong’ mechanism. C) are best analyzed using Lineweaver-Burk plots. D) exist only when enzymatically catalyzed. E) none of the above. Ans: E Level of Difficulty: Moderate Section: 12.1.A Learning objective: Reaction Kinetics

27. Pseudo-first-order reaction kinetics would be observed for the reaction A + B g C A) if [A] or [B] > [C]. B) if [C]>[A] and [C]>[B]. C) if [A] or [B] = 0. D) if [C] = 0. E) none of the above Ans: E Level of Difficulty: Easy Section: 12.1.A Learning objective: Reaction Kinetics The following questions (29 and 30) refer to the overall transformation shown in the following reaction:

28. Which of the following is (are) true? A) The [ES] will remain constant if k2>k1 and k−1< k2. B) The reaction is zero order with respect to [S] if [S]>>[E] C) It describes a double displacement reaction D) All of the above are true. E) None of the above is true. Ans: B Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics 29. For the reaction, the steady state assumption A) implies that k1=k−1 B) implies that k−1 and k2 are such that the [ES] = k1[ES] C) [P]>>[E] D) [S] = [P] E) ES breakdown occurs at the same rate as ES formation Ans: E Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics

30. The Michaelis constant KM is defined as I. (k–1 + k2)/k1 II. ½ Vmax III. [S] = [ES] IV. [ES]/2 A) I B) I, II C) II D) I, IV E) II, IV Ans: A Level of Difficulty: Easy Section: 12.1.B Learning objective: Reaction Kinetics 31. The catalytic efficiency of an enzyme can never exceed A) k2. B) k1. C) k–1. D) k–1 + k2. E) (k–1 + k2)/k1. Ans: B Level of Difficulty: Easy Section: 12.1.B Learning objective: Reaction Kinetics The following questions (33 and 34) refer to the diagram (with boxes where it has been left incomplete):

32. This diagram refers to a (an) A) Ping Pong reaction. B) ordered bisubstrate reaction. C) random bisubstrate reaction. D) double order ping pong reaction E) X, Y, and Z must be provided in order to answer correctly Ans: C Level of Difficulty: Easy Section: 12.1.D Learning objective: Reaction Kinetics 33. Which of the following is correct in regards to the diagram above? A) X=A, Y=B, Z=P B) X=B, Y=A, Z=Q C) X=E, Y=A, Z=E D) X=E, Y=B, Z=Q E) X=E, Y=B, Z=P Ans: B Level of Difficulty: Moderate Section: 12.1.D Learning objective: Reaction Kinetics 34. A compound that distorts the active site, rendering the enzyme catalytically inactive is called A) a uncompetitive inhibitor B) an allosteric effector C) an inactivator D) a competitive inhibitor E) none of the above Ans: D Level of Difficulty: Easy Section: 12.2.B Learning objective: Enzyme Inhibition

35. Compounds that function as “mixed inhibitors” I. interfere with substrate binding to the enzyme. II. bind to the enzyme reversibly. III. can bind to the enzyme/substrate complex. A) I B) II C) III D) II, III E) I, II, III Ans: E Level of Difficulty: Easy Section: 12.2.C Learning objective: Enzyme Inhibition 36. Enzyme activity in cells is controlled by which of the following? I. covalent modifications II. modulation of expression levels III. feedback inhibition IV. allosteric effectors A) I B) II C) III D) III, IV E) I, II, III, IV Ans: E Level of Difficulty: Easy Section: 12.3 Learning objective: Control of Enzyme Activity

37. Allosteric activators A) bind via covalent attachment. B) stabilize conformations with higher Ks. C) stabilize conformations with higher substrate affinity. D) all of the above E) none of the above. Ans: C Level of Difficulty: Easy Section: 12.3.A Learning objective: Control of Enzyme Activity 38. Protein kinases are involved in A) the digestion of drugs to potentially toxic byproducts. B) the degradation of enzymes to the component amino acids. C) the phosphorylation of a wide variety of proteins. D) the metabolism of drugs to water soluble, excretable compounds. E) all of the above Ans: C Level of Difficulty: Easy Section: 12.3.B Learning objective: Control of Enzyme Activity 39. ________ clinical trials are focused on evaluating the efficacy of new drug candidates, and usually use _____ test. A) Phase 1; single blind B) Phase 1; double blind C) Phase 2; single blind D) Phase 2; double blind E) Phase 3; double blind Ans: C Level of Difficulty: Easy Section: 12.4.C Learning objective: Drug Design

40. Determine the KM and Vmax from the following graph. (Note: On the x-axis the minor tick mark spacing is 0.005; on the y-axis the minor tick mark spacing is 0.002) 0.05

0.04

1/v

0.03

0.02

0.01

-0.05

-0.025

0.025

0.05

-0.01

0.075

0.1

0.125

0.15

0.175

0.2

0.225

1/[S]

A) KM = [0.006]; Vmax = 0.0075/s B) KM = [0.196]; Vmax = 0.0075/s C) KM = [165]; Vmax = 33/s D) KM = [33]; Vmax = 167/s E) KM = [270]; Vmax x = 68/s Ans: D Level of Difficulty: Moderate Section: 12.1.C Learning objective: Reaction Kinetics

41. I propose to design a new drug which will act as an inhibitor for an enzyme. If I have used all current information about the mechanism of this enzyme to design this inhibitor and I carefully engineer it with similar chemical properties of the transition state, what type of inhibitor am I attempting to engineer and how will I know if I have succeeded? A) A competitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in Vmax. B) A competitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in KM. C) A uncompetitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in KM. D) A uncompetitive inhibitor, collect kinetic data both in the presence and absence of inhibitor and watch for a change in Vmax. E) None of the above.

Ans: A Level of Difficulty: Difficult Section: 12.2.A Learning objective: Enzyme Inhibition 42. An extremely efficient enzyme called “efficase” catalyzes the conversion of “A” to “B.” A researcher decides to mutate the enzyme in order to try to improve its performance. Following active site mutations, a significant reduction in the value of KM and Vmax was observed. Which of the following may have occurred? A) The affinity of the enzyme for the substrate was increased to a point which did not favor propagation (continuation) of the reaction. B) The decrease in Vmax was not related to the decrease in KM. C) If the reaction was first-order, the change in KM cannot have affected Vmax. D) The stability of E+S (E+A as written above) was increased, thereby increasing the KM. E) The reverse reaction (breakdown of EA to E+A) was favored, slowing the Vmax. Ans: E Level of Difficulty: Very Difficult Section: 12.1.B Learning objective: Reaction Kinetics 43. Enzyme E is responsible for conversion of substrate X to product U. As a result of this conversion electrons are transported to a coenzyme (FAD) within Enzyme E. In order for the reaction to be completed, a second substrate NAD+ must also bind Enzyme E and collect stored electrons (which converts it to product, NADH). The graph below shows the data while varying X, with fixed concentrations of NAD+. What type of multi-substrate mechanism does enzyme E utilize?

Substrates: Products:

X ¯ U

NAD+ ¯ NADH

A) sequential – Ordered B) sequential – Random C) simultaneous addition D) Ping Pong E) Sequential but the data cannot differentiate between ordered and random.

Ans: B Level of Difficulty: Very Difficult Section: 12.2.B Learning objective: Reaction Kinetics 44. The following data were collected under conditions indicated in the graph below during the time period of 0-5 seconds. Upon plotting the Lineweaver-Burk plot, the information given in the table below was determined. Based on this available information which of the following is FALSE? x-intercept y-intercept slope

- 0.002 (Units on the x-axis are 1/M) 0.005 (Units on the y-axis are 1/s) 2.50

A) The Vmax equals 200 M/s B) The Ks equals 500 M C) The kapp equals 200 per second D) The data was collected prior to reaching steady state. E) The kcat cannot be determined for this information. Ans: A Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics

45. In the plot below, can the KM be determined? If so, what is its value?

A) Yes, it is 30 mM. B) Yes, it is 30 mM/sec. C) Yes, it is 60 mM/sec D) Yes, it is 60 mM E) No this data does not follow Michaelis-Menten kinetics Ans: A Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics

46. Following several experiments, the data presented on the graph below was obtained. What can you determine from this graph?

A) This data may have been collected both in the absence (solid line) and presence (dashed line) of a competitive inhibitor. B) This data may have been collected both in the absence (solid line) and presence (dashed line) of a mixed (noncompetitive) inhibitor. C) This data may have been collected both in the absence (solid line) and presence (dashed line) of mechanism based inhibitor. D) This data may have been collected both in the absence (solid line) and presence (dashed line) of an inhibitor which binds the active site. E) More than one of the above are correct. Ans: B Level of Difficulty: Difficult Section: 12.2.A, B, C Learning objective: Enzyme Inhibition 47. KM A) is the concentration of substrate where the enzyme achieves ½ Vmax. B) is equal to Ks. C) measures the stability of the product D) is high if the enzyme has high affinity for the substrate. E) All of the above are correct. Ans: A Level of Difficulty: Easy Section: 12.1.B Learning objective: Reaction Kinetics

48. At substrate concentrations much lower than the enzyme concentration, A) the rate of reaction is expected to be inversely proportional to substrate concentration. B) the rate of reaction is expected to be directly proportional to substrate concentration. C) first order enzyme kinetics are not observed. D) the KM is lower. E) the rate of reaction is independent of substrate concentration. Ans: B Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics 49. The breakdown of dopamine is catalyzed by the enzyme monoamine oxidase (MAO). What is the final concentration of product if the starting dopamine concentration is 0.050 M and the reaction runs for 5 seconds. (Assume the rate constant for the reaction is 0.249 s−1.) A) 0.050 M B) 0.014 M C) 0.018 M D) 1.2 M E) 0.025 M Ans: B Level of Difficulty: Moderate Section: 12.1.A Learning objective: Reaction Kinetics

50. A lab recently developed a new drug which is hypothesized to inhibit the enzyme cyclooxygenase-2 (COX-2) and reduce inflammation. In their first test they monitored the reaction of substrate as it is converted to product in the presence of the new drug (data shown below). If the hypothesis is correct the observed initial rate will be at least 2 times slower than the normal reaction without the drug. If the normal initial rate is 30 mM/s, does the data below indicate that the team has designed a successful inhibitor?

Substrate concentration (mM)

90 80 70 60 50 40 30 20 10 0 0

Time (seconds)

A) Yes. B) No. C) This cannot be determined with the information given. D) The data is dependent on the maximal velocity. E) The answer is dependent on the substrate concentration. Ans: A Level of Difficulty: Difficult Section: 12.1.A Learning objective: Reaction Kinetics

51. From the graph below plotting data that was collected under steady state conditions, velocity on the y-axis in units of μM/s and substrate concentration of the x-axis in units of μM, what is the Vmax?

A) 0.24 μM/s B) 18 μM C) 0.2 μM D) 0.24 μM E) 0.12 μM/s Ans: A Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics 52. From the graph below plotting data that was collected under steady state conditions, velocity on the y-axis in units of μM/s and substrate concentration of the x-axis in units of μM, what is the KM?

A) 0.24 μM/s B) 18 μM C) 0.2 μM D) 0.24 μM E) 0.12 μM/s

Ans: B Level of Difficulty: Difficult Section: 12.1.B Learning objective: Reaction Kinetics 53. Based on the figures below, which of the following expressions would be correct?

A) Vmax = 1/B B) C = 1/ Vmax C) D= Vmax D) D = 1/ Vmax E) A = 1/ Vmax Ans: D Level of Difficulty: Moderate Section: 12.1.B Learning objective: Reaction Kinetics 54. Based on the figure in the question above (question 54), which of the following expressions would correctly define KM? A) A= KM B) KM = A/2 C) B = KM D) C = - KM E) D= 1/ KM Ans: C Level of Difficulty: Moderate Section: 12.1.B Learning objective: Reaction Kinetics

55. A new drug has been discovered which inhibits the reaction catalyzed by enzyme A. Based on the information shown below, what is this drug?

A) competitive inhibitor B) uncompetitive inhibitor C) mixed inhibitor D) allosteric activator E) More information is required to answer the question. Ans: A Level of Difficulty: Moderate Section: 12.2.A Learning objective: Enzyme Inhibition

Chapter 13: Biochemical Signaling Matching A) B) C) D) E) F) G) H) I) J) K) L) M)

receptors phosphoinositide rhodopsin calmodulin insulin hypothalamus cortisol adrenal cortex cyclic AMP RasGAP islets of Langerhans adenylate cyclase (AC) receptor tyrosine kinase (RTK)

1. Proteins that bind molecules and elicit a cellular response are called _____. Ans: A Section: Intro Level of Difficulty: Easy Learning Objective: Biochemical Signaling 2. A molecule that often functions as a second messenger is ______. Ans: I Section: 13.3 Level of Difficulty: Easy Learning Objective: Heterotrimeric G Proteins 3. The gland that is predominately responsible for producing the hormone that is released in response to consumption of a meal particularly high in carbohydrates. Ans: K Section: 13.1.A Level of Difficulty: Moderate Learning Objective: Hormones

4. Isoproterenol functions as an agonist for receptors that bind hormones synthesized in the ___. 175

Ans: H Section: 13.1.B Level of Difficulty: Moderate Learning Objective: Hormones 5. A release of _____ would result in the stimulation of the liver to synthesize glycogen. Ans: E Section: 13.1.A Level of Difficulty: Easy Learning Objective: Hormones 6. The first G protein-coupled receptor (GPCR) to be structurally analyzed at the atomic level was _____. Ans: C Section: 13.3.A Level of Difficulty: easy Learning Objective: Heterotrimeric G Proteins 7. The ____ signaling pathway undergoes autophosphorylation resulting in kinase activation. Ans: M Section: 13.2.A Level of Difficulty: Easy Learning Objective: Receptor Tyrosine Kinase 8. The ____ signaling pathway relies on GTP dependent hydrolysis for subsequent synthesis of cAMP. Ans: L Section: 13.3.C Level of Difficulty: Easy Learning Objective: Heterotrimeric G Proteins

9. Cytosolic calcium ion levels are altered by the _____ signaling pathway. Ans: B Section: 13.4.A Level of Difficulty: Easy 176

Learning Objective: The Phosphoinositide Pathway 10. The hormone _____ is responsible for a variety of actions including the ability to cope with stress. Ans: G Section: 13.1.C Level of Difficulty: Easy Learning Objective: Hormones

Multiple Choice 11. Insulin binds to a receptor that I. is coupled to a G protein. II. possesses tyrosine kinase activity. III. possesses serine/threonine phosphatase activity. IV. interact with proteins homologous to Src A) I, II, III B) II only C) I, III D) II, IV E) I, IV Ans: D Section: 13.2.B Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 12. Which of the following proteins is a phosphatase activated by Ca2+ essential for T cell proliferation? A) calcineurin B) calmodulin (CaM) C) rhodopsin D) RasGAP E) MAPK Ans: A Section: 13.2.D Level of Difficulty: Easy Learning Objective: Receptor Tyrosine Kinases 13. The ability of receptors to adapt to long-term stimulation by responding to changes in stimulation levels rather than absolute values of stimulation is called A) dual-specificity. B) intrasteric sensitivity. 177

C) autoinhibition. D) desensitization. E) switch regional detection. Ans: D Section: 13.3.A Level of Difficulty: Easy Learning Objective: Heterotrimeric G Proteins 14. Cancer causing viruses often contain: I. oncogenes. II. genes encoding variant proteins. III. genes encoding cell proliferation inhibitors. IV. genes capable of inducing malignant transformation. A) I only B) III only C) IV only D) I, II, IV E) I, II, III, IV Ans: D Section: 13.2.B and Box 13-3 Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 15. The interaction (cross-talk) of various signaling pathways A) allows for dual-specificity within different cell types. B) is necessary for effective signal transduction. C) occurs during autoinhibition of a pathway. D) accounts for the ability of a signaling pathway to undergo desensitization. E) can be minimized by scaffold proteins. Ans: E Section: 13.2.B Level of Difficulty: Easy Learning Objective: Receptor Tyrosine Kinases

16. Phospholipase C cleaves PIP2, resulting in an increased cytosolic concentration of I. IP3 (inositolpolyphosphate-3) II. protein kinase C III. cAMP 178

IV. Ca2+ A) I only B) II only C) I, III D) I, IV E) IV only Ans: D Section: 13.4.A Level of Difficulty: Difficult Learning Objective: The Phosphoinositide Pathway 17. The b cells of the islets of Langerhans secrete ______ in response to ______ glucose levels in the muscle and/or adipose tissue. A) insulin; low B) insulin; elevated C) glucagon; low D) glucagon; elevated E) somatostatin; elevated Ans: B Section: 13.1.A Level of Difficulty: Moderate Learning Objective: Hormones 18. The a cells of the islets of Langerhans secrete _____ in response to ____ glucose levels in the liver. A) insulin; low B) insulin; elevated C) glucagon; low D) glucagon; elevated E) somatostatin; elevated Ans: C Section: 13.1.A Level of Difficulty: Moderate Learning Objective: Hormones

19. Heterotrimeric G proteins I. consist of three subunits, Ga, Gb, and Gg. II. function as an autoinhibtory segment. III. can function as a mediator to adenylate cyclase activity. IV. are anchored to the cytoplasmic side of the membrane. 179

A) I, II, IV B) I, III, IV C) I, IV D) I, III E) I only Ans: B Section: 13.3.A Level of Difficulty: Difficult Objective: Heterotrimeric G Proteins 20. The insulin signaling pathway includes which of the following steps? A) ligand-induced dimerization of the receptor and phosphorylation of IRS-1 and/or IRS-2 proteins B) autophosphorylation and phosphorylation of IRS-1 and/or IRS-2 proteins C) IRS-1–induced dimerization of the receptor, autophosphorylation, and phosphorylation of SH2 domains D) autophosphorylation and dephosphorylation of IRS-1 and/or SH2 domains E) none of the above Ans: B Section: 13.2.B Level of Difficulty: Difficult Learning Objective: Receptor Tyrosine Kinases

21. Which of the following is (are) an advantage(s) of protein phosphorylation in regards to biochemical signaling? I. Phosphorylation is rapid and specific. II. Phosphorylation is enzymatically reversible. III. Phosphorylation can be amplified by cascade systems. IV. Phosphorylation results in covalent modification of enzymes. 180

A) I, II, III, IV B) II, III, IV C) II, III D) I, II E) III only Answer: A Section: 13.2 Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 22. Which of the following is (are) the result of insulin binding to its receptor? I. MAPK activation, which regulates gene expression via Fos, Jun and Myc. II. PI3K activation leading to an increase in glucose transport. III. High affinity binding of SH2 domains to phosphorylated tyrosines. IV. Autophosphorylation resulting in activation of tyrosine kinase. A) II, III, IV B) I, II, III, IV C) II, III D) I, II E) III only Ans: B Section: 13.2.B and 13.4.D Level of Difficulty: Difficult Learning Objective: Receptor Tyrosine Kinases and Epilog

23. Ras is an example of I. a protein anchoted by prenylation. II. a heterotrimeric G protein. III. a kinase activated protein. IV. a GTP dependent protein. 181

A) I, II, III, IV B) I, III, IV C) I, III D) II, III, IV D) IV only Ans: B Section: 13.2.B Level of Difficulty: Difficult Learning Objective: Receptor Tyrosine Kinases 24. Somatostatin I. inhibits the release of insulin. II. inhibits the release of glucagon. III. stimulates the release of insulin. IV. stimulates the release of glucagon. A) I only B) II only C) I and II D) III and IV E) IV only Ans: C Section: 13.1.A Level of Difficulty: Moderate Learning Objective: Hormones

25. Catecholamines mediate their effects through I. α-adrenoreceptors. II. β-adrenoreceptors. III. receptor tyrosine kinases. IV. monomeric G protein receptors . A) I only B) II only 182

C) I and II D) III and IV E) IV only Ans: C Section: 13.1.B Level of Difficulty: Moderate Learning Objective: Hormones 26. Which of the following hormones functions by binding to receptors that function directly as transcription factors? A) steroids B) insulin C) epinephrine D) glucagon E) somatostatin Ans: A Section: 13.1.C Level of Difficulty: Easy Learning Objective: Hormones 27. Which of the following are produced in the adrenal cortex? I. Glucorticoids II. mineralcorticoides III. androgens IV. estrogens A) I only B) I, II C) II only D) II, IV E) I, II, III, IV Ans: E Section: 13.1.C Level of Difficulty: Moderate Learning Objective: Hormones 28. Which of the following proteins has a structural motif called an "EF hand"? A) insulin B) calmodulin (CaM) C) receptor tyrosine kinases (RTK) D) cAMP-dependent protein kinase E) scaffold proteins Ans: B 183

Section: 13.4.B Level of Difficulty: Easy Learning Objective: The Phosphoinositide Pathway

29. Which of the following is (are) associated with cAMP binding to cAMP-dependent protein kinase A? I. cAMP binds to the regulatory subunits. II. Tetrameric regulatory subunits and catalytic subunits dissociate. III. Catalytic subunits phosphorylate multiple targets with specific serine and threonine residues. IV. cAMP is membrane bound via phosphoinositol attachment. A) I, II, III, IV B) I, II, III C) I, II D) II, III, IV E) III, IV Ans: B Section: 13.3.C Level of Difficulty: Difficult Learning Objective: Heterotrimeric G Proteins 30. Which of the following statements concerning the action of G proteins on adenylate cyclase is true? I. G proteins always serve to activate adenylate cyclase. II. G proteins always serve to inhibit adenylate cyclase. III. Some G proteins activate adenylate cyclase, while others inhibit it. IV. G proteins do not act on adenylate cyclase at all. A) I only B) II, III C) I, III D) II only E) III only Ans: E Section: 13.3.C Level of Difficulty: Moderate Learning Objective: Heterotrimeric G Proteins 31. Which of the following increases the affinity of SH2 binding to phosphor-tyrosine? A) The absence of a Ser or Thr residue in the binding region. 184

B) The presence of an Arg residue deep in the binding pocket. C) The presence of an Arg residue near the binding pocket entrance. D) The absence of a Ser residue deep in the binding pocket. E) None of the above. Ans: B Section: 13.2.B Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 32. Recently a researcher has discovered several unidentified proteins (UPS-1 through UPS-3) that are up regulated (produced in higher levels) by the cell in response to the inclusion of high levels of an artificial sweetener called "sugarish". The research ran a PAGE gel of the protein samples after the cells were treated with different concentrations of "sugarish" (0-5 nm). One sample was also treated with the detergent SDS. The results are shown below. Which of the following are possible conclusions given these results and the knowledge you have gained from this chapter?

I. UPS-1 functions as a dimer. II. UPS-1 interacts with UPS-2. III. UPS-1 interacts with UPS-3. IV. UPS-2 interacts with UPS-3. A) I, II, III, IV B) II, III, IV C) I, II D) I, III E) II, III Ans: A Section: 13.2.B Level of Difficulty: Very Difficult Learning Objective: Receptor Tyrosine Kinases and Epilog 185

33. Considering the same unidentified proteins discussed in the question 32 above (UPS-1 through UPS-3) what can you conclude from the following observations and the knowledge you gained in this chapter? OBSERVATIONS: 1) UPS-1 is capable of autophosphorylation. 2) UPS-2 becomes phosphorylated only when UPS-1 is phosphorylated. 3) UPS-2, when phosphorylated interacts with UPS-3 and activates the Ras protein. 4) Recombinant UPS-2 protein that has a mutation resulting in the replacement of tyrosine for serine in the binding region loses all function. 5) The proteins Jun and Fos are expressed at high levels in the presence of UPS-1,2,3. A) The UPS signaling system functions as a heterotrimeric G protein signaling cascade. B) Sugarish appears to solicit a similar insulin response to that expected from glucose. C) Sugarish must be sensitive to the phosphoinositide pathway. D) Calmodulin (CaM) would likely alter the activity of the UPS proteins. E) None of the above are possible conclusions. Ans: B Section: 13.2.B and Epilog Level of Difficulty: Very Difficult Learning Objective: Receptor Tyrosine Kinases

34. Based on the following figure, which of the following are possible?

186

I. "A" could be adenylate cyclase. II. "B" is a receptor protein. III. "C" could be an inactive Ras protein. IV. "D" could be an SH2 domain. A) I, II, III, IV B) I, II, III C) II, III, IV D) I only E) III only Ans: E Section: 13.2.B Level of Difficulty: Difficult Learning Objective: Receptor Tyrosine Kinases

35. The virulent form of bubonic plague carries a protein called YopH. Which of the following is true? A) YopH functions as a MAPK specific inhibitor. B) YopH functions as a Ras inhibitor. C) YopH functions as a receptor tyrosine kinase. D) YopH functions as a protein tyrosine phosphatase. E) YopH functions as β propeller. Ans: D Section: 13.2.D Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 187

36. Which of the following functions as a regulatory protein by dephosphorylating activated enzymes? A) receptor tyrosine kinase B) phosphoprotein phosphatase C) heterotrimeric G protein phosphorylase D) guanine nucleotide exchange factor E) Sos protein Ans: B Section: 13.2.D Level of Difficulty: Easy Learning Objective: Receptor Tyrosine Kinases 37. Which of the following generalizations explains how anabolic steroids can affect muscle growth? A) Anabolic steroids increase the level of testosterone, a hormone predominately found in males. B) Anabolic steroids easily pass through the membrane and bind steroid receptors which migrate to the nucleus and function as a transcription factor. C) Anabolic steroids are water soluble and can transport to the muscle tissue readily. D) Anabolic steroids alter the phosphoinositide pathway, thereby increasing levels of calcium in the cytosol and subsequently increase the strength of muscle contraction. E) None of the above is correct. Ans: B Section: 13.1.C Level of Difficulty: Moderate Learning Objective: Hormones

38. Which of the following sets of terms has a member that does not belong? A) rhodopsin – heterotrimeric G protein – desensitization B) autoinhibitor segment – receptor tyrosine kinase – SH2 188

C) propranolol – β-adrenoreceptor – antagonist D) transcortin – aldosterone – adrenal cortex E) adenylate cyclase – cholera toxin – heterotrimeric G protein Ans: B Section: 13.1, 13.2, 13.3 Level of Difficulty: Very Difficult Learning Objective: Hormones, Receptor Tyrosine Kinase, Heterotrimeric G Proteins 39. The activity of protein kinase A is affected by which of the following? I. caffeine II. levels of cAMP III. phosphodiesterases IV. cholera toxin A) I only B) II only C) I, IV D) I, II, III E) I, II, III, IV Ans: E Section: 13.3 Level of Difficulty: Moderate Learning Objective: Heterotrimeric G Proteins 40. Which of the following are activated either directly or indirectly by a heterotrimeric G protein subunit? I. phospholipase C II. Herceptin ® III. calmodulin (CaM) sensitive kinase IV. MAPK A) I, II, III, IV B) I, II C) I, III D) II, III, IV E) I, II, IV Ans: C Section: 13.3 and 13.4 Level of Difficulty: Difficult Learning Objective: Heterotrimeric G Proteins and The Phosphoinositide pathway

189

41. Oncogenes I. function as cell cycle inhibitors. II. encode a protein which block cell cycle inhibition. III. are expressed by cells that have higher levels of human growth hormone. IV. can function as transcription factors. A) I, III, IV B) II, III C) III, IV D) II, IV E) II Ans: D Section: 13.2.B and Box 13-3 Level of Difficulty: Moderate Learning Objective: Receptor Tyrosine Kinases 42. Scaffold proteins limit A) oncogene transfer. B) MAPK activity. C) cross-talk. D) cell differentiation. E) signal amplification. Ans: C Section: 13.2.B Level of Difficulty: Easy Learning Objective: Receptor Protein Kinases

43. Autoinhibition in the SH2 and SH3 domains A) occurs when a SH2 phospho-Tyr forms a salt bridge with an Arg on SH3. B) occurs when a SH2 phospho-Tyr binds a Pro segment on the SH3 domain, therefore blocking the active site and burying the required Tyr. C) occurs when a salt bride forms between the active site phosphor-Tyr on SH3 and the Glu on the activation loop. D) occurs when the salt bridge between Glu and Arg is broken. E) None of the above is correct. 190

Ans: B Section: 13.2.C Level of Difficulty: Moderate Learning Objective: Receptor Protein Kinases 44. Which of the following best describe the mechanism of calmodulin (CaM) mediated activation? A) Ca2+ binding to calmodulin (CaM) results in conformational change that exposes a hydrophobic patch capable of binding to calcium sensitive protein kinase B) a conformational change induced by the binding of Ca2+ results in the release of the phosphate group in calmodulin (CaM) C) calmodulin (CaM) sensitive protein kinase dimerizes forming a joint active site capable of tightly binding Ca2+ D) phosphorylation of a tyrosine on calmodulin induced a conformational change that results in release of Ca2+ from the cytosol. E) none of the above. Ans: A Section: 13.4.B Level of Difficulty: Moderate Learning Objective: The Phosphoinositide Pathway

45. Which of the following describes the similarity between the following words? DAG, cAMP, IP3 A) All of them induce conformational changes in PKA. B) All of them activate adenylate cyclase. C) All of them require phosphorylation in order to function. D) All of them function as second messengers. E) All them result from the activity of phosphoprotein lipase. Ans: D Section: 13.3C, 13.4.A and C Level of Difficulty: Easy Learning Objective: Heterotrimeric G Proteins, The Phosphoinositide Pathway 46. Sildenafil (Viagra®) A) inhibits activity of a phosphoprotein phosphatase. B) increases the relative concentration of cGMP. C) increases the relative concentration of nitric oxide in the blood. D) A, B, and C E) A and B 191

Ans: B Section: 13.3.D Level of Difficulty: Moderate Learning Objective: Heterotrimeric G Proteins 47. Which of the following correctly states an essential step in the function of heterotrimeric G protein function? A) A cascade of events must occur that ultimately activate protein kinase C. B) Binding of a hormone to a receptor must signal the exchange of GDP for GTP. C) Binding of GTP to the receptor protein must induce a change in conformation of the receptor. D) Binding of cAMP to the α subunit of the G protein must initiate translocation of the subunit. E) All of the above are correct. Answer: B Section: 13.3 Level of Difficulty: Moderate Learning Objective: Heterotrimeric G Proteins 48. Which of the following activities would lead to a decrease in the level of IP3 in the cytosol? A) increased activity of inositol polyphosphate 5-phosphatase B) increased activity of phospholipase C C) increased activation of protein kinase C D) increased Ca2+ concentration E) all of the above Ans: A Section: 13.4.A Level of Difficulty: Moderate Learning Objective: The Phosphoinositide Pathway 49. Anthrax toxin functions by altering levels of cAMP. The toxin also contains an edema factor, which requires the activity of calmodulin (CaM) for proper function. Based on this information, which of the following can you conclude? A) The toxin alters cAMP dependent cell signaling. B) Calcium levels affect the function of the edema factor. C) Unlike other toxins, the anthrax toxin does not function by altering biochemical signaling. D) A and B E) A and C Ans: D Section:13.3.C, 13.4.B Level of Difficulty: Difficult Learning Objective: Heterotrimeric G Proteins and The Phosphoinositide Pathway 192

50. Which of the following is always true of hormones? A) Hormones always bind membrane bound receptors. B) Hormones elicit specific cellular responses. C) Hormones are secreted from a gland via a robust network of ducts. D) The release of hormones is influenced by adrenal receptors. E) All of the above are true. Ans: B Section: 13.1 Level of Difficulty: Easy Learning Objective: Hormones

193

Chapter 14: Introduction to Metabolism Matching A) B) C) D) E) F) G) H) I) J) K) L) M)

anabolic adenylate kinase e°' catabolic phosphorylase kinase obligate aerobes acyl phosphate proteomics reduction pyrophosphatase autotrophs oxidation DG°’

1. Prokaryotes that are able to synthesize all of their cellular components from simple molecules such as CO2, H2O, NH3, and H2S are called ______. Ans: K Level of Difficulty: Easy Section: 14.1.A Learning objective: Overview of Metabolism 2. Organisms that require oxygen for nutrient breakdown are called ______. Ans: F Level of Difficulty: Easy Section: 14.1.A Learning objective: Overview of Metabolism 3. Biomolecules are synthesized from simpler components in ______ pathways. Ans: A Level of Difficulty: Easy Section: 14.1 Learning objective: Overview of Metabolism

4. 1,3-Bisphosphoglycerate is an example of a(n) ______. Ans: G Level of Difficulty: Easy Section: 14.2.C Learning objective: High-Energy Compounds 5. The enzyme ______ catalyzes the reaction, PPi ® 2 Pi. Ans: J Level of Difficulty: Easy Section: 14.2.B Learning objective: High-Energy Compounds 6. The enzyme ______ catalyzes the transfer of a phosphoryl group from ATP to AMP. Ans: B Level of Difficulty: Easy Section: 14.2.C Learning objective: High-Energy Compounds 7. A metabolic reaction resulting in the formation of FADH2 is an example of a(n) ___ reaction. Ans: I Level of Difficulty: Easy Section: 14.3.B Learning objective: Oxidation-Reduction Reactions 8. The reaction NADH ® NAD+ is an example of _____. Ans: E Level of Difficulty: Easy Section: 14.3.A Learning objective: Oxidation-Reduction Reactions

9. The standard reduction potential under biochemical standard state conditions is symbolized as ______. Ans: C Level of Difficulty: Easy Section: 14.2.B Learning objective: Oxidation-Reduction Reactions 10. The study of the complete set of proteins synthesized in the cell in response to changing conditions is called ______. Ans: H Level of Difficulty: Easy Section: 14.4.C Learning objective: Experimental Approaches to the Study of Metabolism

Multiple Choice 11. Organisms that can grow in either the presence or absence of oxygen are classified as A) obligate aerobes B) facultative anaerobes C) autotrophs D) heterotrophs E) obligate anaerobes Ans: B Level of Difficulty: Easy Section: 14.1.A Learning objective: Overview of Metabolism

12. Which of the choices correctly ranks the following compounds from lowest level of oxidation to highest level of oxidation? 1 2 3 CH3CHO CH2=CH2 CH3CO2H A) 1< 2< 3 B) 2< 1< 3 C) 1< 3< 2 D) 3< 2< 1 E) 2< 3< 1 Ans: B Level of Difficulty: Moderate Section: 14.1.B, Box 14-1 Learning objective: Overview of Metabolism, Box 14-1 13. Consider the following metabolic reaction: Succinyl-CoA + Acetoacetate ® Acetoacetyl-CoA + Succinate What is the Keq for this reaction at 25°C? A) 1.66 B) 0.602 C) 1.00 D) 4.22 x 102 E) 3.21 Ans: A Level of Difficulty: Moderate Section: 14.2 Learning objective: High-Energy Compounds

DG°' = –1.25 kJ/mol

14. Consider the following metabolic reaction: Succinyl-CoA + Acetoacetate ® Acetoacetyl-CoA + Succinate

DG°' = –1.25 kJ/mol

The DG°' for the hydrolysis of Succinyl-CoA is –33.9 kJ/mol. What is the DG°' for the hydrolysis of Acetoacetyl-CoA: Acetoacetyl-CoA ® Acetoacetate + CoA A) –35.2 kJ/mol B) –32.7 kJ/mol C) +32.7 kJ/mol D) +35.2 kJ/mol E) none of the above Ans: B Level of Difficulty: Difficult Section: 14.2.B Learning objective: High-Energy Compounds 15. Consider the following metabolic reaction: Succinyl-CoA + Acetoacetate ® Acetoacetyl-CoA + Succinate

DG°' = –1.25 kJ/mol

This reaction is A) favorable under standard conditions. B) not favorable under standard conditions. C) nonspontaneous as written regardless of reactant concentrations D) spontaneous as written only when [succinate] and [acetoacetyl-CoA] are high. E) favorability of this reaction as written depends on temperature and reactant concentrations Ans: A Level of Difficulty: Moderate Section: 14.2.B Learning objective: High-Energy Compounds

16. The Keq is 0.503 at 25°C for the following reaction. What is the DG°' for this reaction? D-Glucose-6-phosphate ® D-Fructose-6-phosphate

DG°'= ?

A) –2.87 × 103 J/mol B) +1.70 kJ/mol C) +143 J/mol D) The DG°' cannot be determined with the given information. E) The DG°' can be determined with the given information but the correct answer is not shown. Ans: B Level of Difficulty: Moderate Section: 14.2.B Learning objective: High-Energy Compounds 17. Consider the following metabolic reaction: 2-Phosphoglycerate ® 3-Phosphoglycerate

DG°' = −4.40 kJ/mol

What can be said about this reaction when the concentration of 2-phosphoglycerate is 0.490 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 25°C? I. This reaction is endergonic under these conditions. II. This reaction is exergonic under these conditions. III. This reaction is at equilibrium under these conditions. IV. This reaction is not favorable under standard conditions. A) I, IV B) II only C) III only D) IV only E) None of the above Ans: C Level of Difficulty: Difficult Section: 14.2.B Learning objective: High-Energy Compounds

18. Consider the following metabolic reaction: 3-Phosphoglycerate ® 2-Phosphoglycerate

DG°' = +4.40 kJ/mol

What is the DG for this reaction when the concentration of 2-phosphoglycerate is 0.290 mM and the concentration of 3-phosphoglycerate is 2.90 mM at 37°C? A) +10.3 kJ/mol B) –1.53 kJ/mol C) –1.30 kJ/mol D) –5.93 kJ/mol E) –4.40 kJ/mol Ans: B Level of Difficulty: Difficult Section: 14.2.B Learning objective: High-Energy Compounds 19. Which of the numbered arrows in the figure points toward a high-energy phosphoanhydride bond?

A) 1 B) 2 C) 3 D) 4 E) 5 Ans: E Level of Difficulty: Easy Section: 14.2.A Learning objective: High-Energy Compounds

20. Given that the standard reduction potential of oxaloacetate is –0.166 V and the standard

reduction potential of NAD+ is –0.315 V. What is the De°' for the oxidation of malate by NAD+: Malate + NAD+ ® Oxaloacetate + NADH + H+ A) –4.81 V B) + 4.81 V C) –0.149 V D) +0.149 V E) +0.052 V Ans: C Level of Difficulty: Moderate Section: 14.3.B Learning objective: Oxidation-Reduction Reactions 21. The conversion of triacylglycerides into fatty acids for the purpose of energy generation is an example of which of the following? A) heterotropism B) anaerobism C) catabolism D) anabolism E) glycolysis Ans: C Level of Difficulty: Easy Section: 14.1.A Learning objective: Overview of Metabolism 22. ATP contains ________ bonds. A) one phosphoanhydride and two phosphoester B) two phosphoester and one glycosidic C) three phosphoanhydride D) one amide and three phosphoanhydride E) one phosphoester and two phosphoanhydride Ans: E Level of Difficulty: Moderate Section: 14.2.A Learning objective: High-Energy Compounds

23. The vitamin ______ is one of the components of coenzyme A, which is involved in _____. A) pantothenic acid; carboxylation B) pantothenic acid; acyl transfer C) cobalamin; acyl transfer D) riboflavin; carboxylation E) niacin; electron transfer Ans: B Level of Difficulty: Moderate Section: 14.1.B Learning objective: Overview of Metabolism 24. The ______ is equal to the rate of synthesis minus the rate of breakdown of the metabolic intermediates. A) metabolic rate B) Keq C) rate determining step D) flux E) none of the above Ans: D Level of Difficulty: Easy Section: 14.1.E Learning objective: Overview of Metabolism 25. Cells control or regulate the flux through metabolic pathways by means of I. allosteric control of enzymes. II. covalent modification of enzymes. III. genetic control of the concentrations of enzymes. IV. genetic expression of allosteric effectors. A) I, II, III, IV B) II, III C) I, II, IV D) I, II, III E) I, IV Ans: D Level of Difficulty: Easy Section: 14.1.E Learning objective: Overview of Metabolism

26. Which of the following are factors that contribute to the large negative standard free energy change for the reaction shown below? ATP ® ADP + Pi A) the increase in resonance stabilization in the reactants compare to the products B) the precipitation of the insoluble Pi C) the addition of a water molecule to the hydrophilic ATP molecule D) the decrease in negative charge repulsion in the products compared to reactants E) all of the above Ans: D Level of Difficulty: Difficult Section: 14.2.A Learning objective: High-Energy Compounds 27. Which of the following is (are) true regarding vitamins? I. They are essential organic molecules an organism is unable to synthesize. II. Some water soluble vitamins mediate electron-transfer reactions. III. In humans, the water soluble vitamins converted into organic coenzymes. IV. In humans, the fat soluble vitamins mediate group transfer reactions. A) I, II, III, IV B) I, II, III C) II, III, IV D) I only E) II, IV Ans: B Level of Difficulty: Moderate Section: 14.1.B Learning objective: Overview of Metabolism 28. While ____ is always involved in reactions that require the transfer of 2 electrons, ____ can participate in reactions that transfer either 1 or 2 electrons. A) O2; NAD+ B) NAD+; FAD C) NAD+; O2 D) flavin; niacin E) FAD; NAD+ Ans: B

Level of Difficulty: Easy Section: 14.3.A Learning objective: Oxidation-Reduction Reactions 29. The term "Nutrition" involves which of the following components? I. food intake II. metabolic utilization of food III. the intake requirement of oxygen IV. the control of metabolic flux A) I only B) II only C) I, II D) I, II, III D) I, II, III, IV Ans: C Level of Difficulty: Moderate Section: 14.1.A Learning Objective: Overview of Metabolism 30. Obligate aerobes A) perish under conditions with O2. B) use oxidizing agents such as sulfate or nitrate as a primary food source. C) resemble the earliest life forms. D) all of the above E) none of the above Ans: E Level of Difficulty: Easy Section: 14.1.A Learning objective: Overview of Metabolism

31. In the catabolic pathway major nutrients are _________ broken down resulting in the synthesis of __________ . A) exergonically; ADP B) endergonically; ADP C) exergonically; ATP D) endergonically; NADP+ E) endergonically; ATP

Ans: C Level of Difficulty: Easy Section: 14.1.C Learning objective: Overview of Metabolism 32. In eukaryotes, glycolysis typically occurs in the A) mitochondrion. B) cytosol. C) lysosome. D) rough endoplasmic reticulum. E) smooth endoplasmic reticulum. Ans: B Level of Difficulty: Easy Section: 14.1.C Learning objective: Overview of Metabolism 33. Which compound is in the highest oxidation state? A) carbon monoxide B) carbon dioxide C) ethanol D) A, B, and C are equal E) A and B are equal Ans: B Level of Difficulty: Moderate Section: 14.1.C Learning objective: Overview of Metabolism 34. Acyl phosphates such as 1,3-bisphosphoglycerate have a ______ phosphoryl group transfer potential compared to ATP, which can be recognized by the _______ DG°' values for hydrolysis. A) greater; more positive B) greater; more negative C) lower; more positive D) lower; more negative E) none of the above Ans: B Level of Difficulty: Easy Section: 14.2.C Learning objective: High-Energy Compounds

35. Consider the following metabolic reaction important in muscle and nerve cells: ATP + creatine D phosphocreatine + ADP

DG°' = +12.6 kJ/mol

Under intracellular conditions, the DG for the reaction, which is catalyzed by the enzyme creatine kinase, is ~0 kJ/mol. From this information we can conclude that A) creatine kinase catalysis would not be necessary under intracellular conditions. B) ATP has a greater phosphoryl group transfer potential compared to phosphocreatine. C) at equilibrium, most intracellular creatine is phosphorylated. D) the reaction operates close to equilibrium in cells. E) None of the above is a correct conclusion. Ans: D Level of Difficulty: Moderate Section: 14.2.C Learning objective: High-Energy Compounds 36. The terminal electron acceptor in an aerobic organisms is A) CO2. B) NAD+. C) FAD. D) O2. E) H2O. Ans: D Level of Difficulty: Easy Section: 14.3.A Learning objective: Oxidation-Reduction Reactions 37. In redox half-reactions, a more positive standard reduction potential means I. the oxidized form has a higher affinity for electrons. II. the oxidized form has a lower affinity for electrons. III. the reduced form has a higher affinity for electrons. IV. the greater the tendency for the oxidized form to accept electrons. A) I only B) II only C) II, III D) I, IV E) II, IV

Ans: D Level of Difficulty: Moderate Section: 14.3.C Learning objective: Oxidation-Reduction Reactions 38. ______ is the most reliable systems biology approach to assess gene expression. A) genomics B) transcriptomics C) proteomics D) metabolmics E) none of the above Ans: C Level of Difficulty: Easy Section: 14.4.C Learning objective: Experimental Approaches to the Study of Metabolism 39. Acetyl-CoA contains a ____ bond which often provides the energy required for substratelevel phosphorylation. A) phosphoester B) phosphoanhydride C) phosphothioester D) ester E) thioester Ans: E Level of Difficulty: Easy Section: 14.2.D Learning objective: High-Energy Compounds 40. The enzyme inorganic pyrophosphatase catalyzes the hydrolysis of bonds in ___. A) ATP B) ADP C) AMP D) PPi E) phosphate Ans: D Level of Difficulty: Easy Section: 14.2.B Learning objective: High-Energy Compounds

41. Which of the following increase the phosphate transfer potential of compound? I. electrostatic repulsion between charged groups on the reactant II. resonance stabilization of the hydrolysis products III. greater energy of solvation of the hydrolysis products IV. the presence of a enol group in the reactants A) I, II B) I, IV C) I, II, IV D) II, IV E) I, II, III, IV Ans: E Level of Difficulty: Moderate Section: 14.2.A Learning objective: High Energy Compounds 42. I have discovered a new metabolic enzyme which utilizes NAD+ as a coenzyme. Which of the following could be true based on this information? A) It is involved in a catabolic pathway. B) It is involved in an anabolic pathway. C) It performs acyl group transfer. D) It catalyzes a hydrolytic cleavage. E) It catalyzes the reduction of the enzyme's substrate. Ans: A Level of Difficulty: Moderate Section: Intro, 14.1 Learning objective: Overview of Metabolism

43. What are the correct coenzyme forms that correspond to X and Y in the following reaction as catalyzed by lactate dehydrogenase? Pyruvate + X → Lactate + Y A) X = NADH B) X = NADPH C) X = NAD+ D) X = FAD E) X = NADH

Y = NAD+ Y = NADP+ Y = NADH Y = FADH2 Y = NADP+

Ans: A Level of Difficulty: Moderate Section: 14.1.C Learning objective: Overview of Metabolism 44. Negative feedback inhibition is one type of _______ metabolic control. A) allosteric B) hormonal C) covalent modification D) genetic E) signal transduction Ans: A Level of Difficulty: Easy Section: 14.1.E Learning objective: Overview of Metabolism 45. If Z = ATP formed via substrate level phosphorylation in the diagram below, which of the following compounds (represented by an uppercase letter) contains a high-energy bond?

A) Compound A B) Compound B C) Compound C D) All have equally high energy. E) All have equally low energy. Ans: B Level of Difficulty: Difficult Section: 14.2.C Learning objective: High Energy Compounds

46. If the diagram below represents a catabolic pathway, and enzyme 1 requires NAD+, what type of reaction does enzyme 1 catalyze?

A) reduction B) oxidation C) isomerization D) any of the aboveE) none of the above Ans: B Level of Difficulty: Moderate Section: 14.1.C Learning objective: Overview of Metabolism 47. NADH is a derivative of A) niacin. B) riboflavin. C) lipoic acid. D) thiamine. E) vitamin A. Ans: A Level of Difficulty: Easy Section: 14.1.B Learning objective: Overview of Metabolism

48. Use the table below to rank the redox centers in order of increasing ability to produce a favorable electron flow. Redox Center

e°'

- 0.002

- 0.198

- 0.225

- 0.053

+ 0.002

A) D, Q, F, C, Z B) Q, F, C, D, Z C) Z, Q, F, C, D D) Z, F, C, D, Q E) Z, Q, C, Q, D Ans: B Level of Difficulty: Moderate Section: 14.3.C Learning objective: Oxidation-Reduction Reactions 49. A researcher is interested in determining if a long term change in the carbohydrate content of an individual's diet alters the levels of expression of carbohydrate metabolizing enzymes. Which of the following would address this question? A) proteomics B) DNA microarrays C) genomics D) lipidomics E) none of the above Ans: B Level of Difficulty: Easy Section: 14.4.C Learning objective: Experimental Approaches to the Study of Metabolism

50. Compound "K" is the ultimate product of a linear metabolic pathway consisting of ten enzymatically catalyzed reactions as shown below. 1

A® B ® C ® D ® E ® F ® G ® H ® I ® J® K Complete the following description. If "K" inhibits activity of enzyme "5", then enzyme "5" is under ___ control. If enzyme "3" becomes activated in response to activity of protein kinase A only when compound "A" is present, then enzyme "3" is under ___ control. If enzyme "2" is only expressed in the presence of high concentrations of "A," then enzyme "2" is under ___ control. If all of these are true, high concentrations of "__" will decrease the flux through the pathway. A) covalent modification; allosteric; genetic; A B) allosteric; covalent modification; genetic; K C) genetic; allosteric; genetic; K D) allosteric; genetic; genetic; K E) allosteric; genetic; genetic; A Ans: B Level of Difficulty: Difficult Section: 14.1.E Learning objective: Overview of Metabolism

51. Identify the structure pictured below.

A) NAD+ B) NADH C) FAD D) FADH2 E) Coenzyme A (CoA)

Ans: A Level of Difficulty: Moderate Section: 14.3.A Learning objective: Oxidation-Reduction Reactions 52. What type of metabolic control is described in the figure below?

A) feed forward activation B) product Inhibition C) feedback Inhibition D) hormonal control E) signal transduction control

Ans: C Level of Difficulty: Moderate Section: 14.2.E Learning objective: Overview of Metabolism

Chapter 15: Glucose Catabolism Matching Choose the correct answer from the list. Not all the answers will be used. A) fructose-1,6-bisphosphatase B) pentose phosphate C) pyruvate decarboxylase D) hypoglycemia E) phosphofructokinase F) NADP+ G) thiamine pyrophosphate H) ATP I) galactosemia J) NAD+ K) fluoride ion L) pyruvate M) glucogenic N) FAD 1. The enzyme ______ , which catalyzes the formation of acetyaldehyde and CO2 from pyruvate, is not present in animals. Ans: C Section: 15.3.B Level of Difficulty: Moderate Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 2. Vitamin B1 is a component of the coenzyme ______ essential for development of an electron sink necessary for decarboxylation of pyruvate. Ans: G Section: 15.3.B Level of Difficulty: Moderate Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 3. Glycolysis forms ____ under either aerobic or anaerobic conditions. Ans: H Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis 4. The products of glycolysis include: ATP, NADH, and ______. 112

Ans: L Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis 5. The coenzyme ______ is the oxidizing agent in both aerobic and anaerobic glycolysis. Ans: J Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis 6. ______ is an inhibitor of enolase which was useful in elucidating the glycolytic pathway. Ans: K Section: 15.2.I Level of Difficulty: Moderate Learning Objective: The Reactions of Glycolysis 7. A genetic deficiency of a single transferase enzyme required for sugar group exchange causes the medical condition known as _____ which results in failure to thrive, mental retardation, and potential liver damage. Ans: I Section: 15.5.B Level of Difficulty: Moderate Learning Objective: Metabolism of Hexoses Other than Glucose 8. The enzyme _____ is the major control point for glycolysis in muscle. Ans: E Section: 15.2.C, 15.4.A Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis, Regulation of Glycolysis 9. NADPH used in lipid biosynthesis is produced by the ______ pathway. Ans: B Section: 15.6 Level of Difficulty: Easy Learning Objective: The Pentose Phosphate Pathway

113

10. The enzyme _____ participates in a regulatory substrate cycle along with phosphofructokinase. Ans: A Section: 15.4.B Level of Difficulty: Moderate Learning Objective: Regulation of Glycolysis

Multiple Choice 11. Glucose is converted to ______ in skeletal muscle under anaerobic conditions. A) lactate B) acetyaldehyde C) fructose D) glycogen E) acetyl-CoA Ans: A Section: 15.3.A Level of Difficulty: Easy Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 12. Aerobic glycolysis produces a net yield of ______ ATP. A) 1 B) 2 C) 3 D) 4 E) more than 4 Ans: B Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis

13. Which of the following enzymes catalyzes the transfer of a phosphoryl group from ATP to glucose?

114

A) hexokinase B) phosphoglucose isomerase C) glucose-6-phosphatase D) phosphoglucose mutase E) A transfer such as this does not occur in glycolysis. Ans: A Section: 15.2.A Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis 14. The enzymes that catalyze glycolysis are located in the A) endoplasmic reticulum. B) mitochondrial matrix. C) cytosol. D) inner mitochondrial membrane. E) outer mitochondrial membrane. Ans: C Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis 15. The enzyme _____forms a Schiff base upon formation of the enzyme-substrate complex allowing aspartate mediated cleavage of the substrate. A) hexokinase B) phosphoglucose isomerase C) glucose-6-phosphatase D) phosphoglucose mutase E) aldolase Ans: E Section: 15.2.D Level of Difficulty: Moderate Learning Objective: The Reactions of Glycolysis

115

16. Phosphofructokinase is allosterically _____ by high concentrations of _____. I. activated; ATP II. inhibited; ATP III. inhibited; fructose-2,6-bisphosphate IV. activated; fructose -2,6-bisphosphate A) I, III B) II, III C) II, IV D) I, IV E) none of the above Ans: D Section: 15.4.A Level of Difficulty: Moderate Learning Objective: Regulation of Glycolysis 17. In alcoholic fermentation, acetaldehyde is produced by A) the decarboxylation of pyruvate. B) the carboxylation of pyruvate. C) the decarboxylation of lactate. D) the carboxylation of lactate. E) none of the above Ans: A Section: 15.3.B Level of Difficulty: Easy Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate

18. The metabolism of mannose requires _____ to produce ____ for entry into the glycolytic pathway. A) hexokinase; glucose-6-phosphate B) hexokinase; fructose-6-phosphate C) phosphomannose isomerase; glucose-6-phosphate D) phosphomannose isomerase; fructose-6-phosphate E) phosphofructokinase; bisphosphoglycerate Ans: D Section: 15.5.C Level of Difficulty: Difficult 116

Learning Objective: Metabolism of Hexoses Other than Glucose 19. Glycolytic synthesis of ATP occurs via A) oxidation. B) reduction. C) substrate-level phosphorylation. D) oxidative phosphorylation. E) photophosphorylation. Ans: C Section: 15.2.G Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis 20. Experimental evidence indicates that glyceraldehyde-3-phosphate dehydrogenase contains a critical ______ residue in its active site, as shown by its inactivation by iodoacetamide. A) alanine B) aspartate C) cysteine D) methionine E) lysine Ans: C Section: 15.2.F Level of Difficulty: Difficult Learning Objective: The Reactions of Glycolysis 21. Which is the net equation for aerobic glycolysis? A) B) C) D) E)

Glucose + 2 ATP ® 2 lactate + 2 ADP + 2 Pi Glucose + 2 ADP + 2 Pi + 2 NAD+ ® 2 pyruvate + 2 ATP + 2 NADH + + 2 H2O 4 H+ Glucose + 2 ADP + 2 Pi ® 2 lactate + 4 ATP + 4 H+ Glucose + 2 ATP + 2 NAD+® 2 pyruvate + 4 ATP + 4 NADH + 4 H+ Glucose + 2 ADP + 2 Pi + 2 NAD+® 2 lactate + 4 ATP + 2 NADH + 4 H+

Ans: B Section: 15.1 Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis 22. In which of the following metabolic conversions is ATP required during glycolysis? I. fructose-6-phosphate ® fructose-1,6-bisphosphate 117

II. glucose ® glucose-6-phosphate III. fructose-1,6-bisphosphate ® dihydroxyacetone phosphate + glyceraldehyde-3-phosphate IV. glucose-6-phosphate ® fructose-6-phosphate A) I only B) II only C) I, II D) I, III E) I, IV Ans: C Section: 15.1, 15.2.A Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 23. Consider the following portion of the glycolytic sequence catalyzed by the enzymes above the arrows. Which products(s) will produce ATP? O C

HC OH CH2OPO3-2

II.

III.

CO2C OPO3 CH2

A) I, IV B) II, IV C) II only D) III, IV E) IV only Ans: B Section: 15.2.F Level of Difficulty: Difficult Learning Objective: The Reactions of Glycolysis

118

-2

IV.

24. The reaction below is catalyzed by yeast alcohol dehydrogenase. Which of the following corresponds to X and Y in this reaction? O

CH3CH + X

A) X = NADH+ B) X = NAD+ C) X = NADH + H+ D) X = NAD + H+ E) X = NADPH + H+

CH3CH2 + Y

Y = NAD + H+ Y = NADH + H+ Y = NAD+ Y = NADH+ Y = NADP+

Ans: C Section: 15.3.B Level of Difficulty: Moderate Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 25. During glycolysis, the steps between glucose and formation of the triose phosphates collectively A) consume two ATP and two NADH molecules. B) consume two ATP molecules. C) produce two ADP and two NADH molecules. D) produce two ATP and two NAD+ molecules. E) consume two NAD+ molecules. Ans: B Section: 15.1, 15.2.A – 15.2.E Level of Difficulty: Easy Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 26. In skeletal muscle cells, oxidation of NADH generated from anaerobic glycolysis occurs during which of the following reactions? A) acetaldehyde ® ethanol B) lactate ® pyruvate C) phosphoenolpyruvate ® pyruvate D) pyruvate ® lactate E) glyceraldehyde-3-phosphate ® 1,3-bisphosphoglycerate Ans: D Section: 15.3.A Level of Difficulty: Easy Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate

119

27. Which of the following metabolic conversions is considered to be the major control point of glycolysis? A) fructose-1,6-bisphosphate ® dihydroxyacetone phosphate + glyceraldehyde-3-phosphate B) glucose ® glucose-6-phosphate C) 2-phosphoglyerate ® phosphoenolpyruvate D) fructose-6-phosphate ® fructose-1,6-bisphosphate E) phosphoenolpyruvate ® pyruvate Ans: D Section: 15.2.C, 15.4.A Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis, Regulation of Glycolysis 28. Individuals with galactosemia A) cannot catabolize galactose via glycolysis. B) lack the enzyme hexokinase which is required for phosphorylation of galactose. C) lack the enzyme galactokinase which is required for interconversion between glucose-1phosphate and galactose-1-phosphate. D) cannot synthesize galactose from glucose. E) lack adequate uridine diphosphosphate. Ans: A Section: 15.5.B Level of Difficulty: Difficult Learning Objective: Metabolism of Hexoses Other than Glucose

120

29. Which of the following compounds contains a “high-energy” bond and is used to produce ATP by substrate-level phosphorylation in glycolysis? O

C OH A)

CH2OPO 3-2 O C O

C OPO 3-2 B)

CH2OPO 3-2

CO2-2

C OPO3 C)

CH2 O

CH3CCO2O

CH3C OPO 3-2

Ans: C Section: 15.2.J Level of Difficulty: Difficult Learning Objective: The Reactions of Glycolysis

30. Which enzyme has an intermediate of the form presented below? OH H3C

TPP

A) phosphofructokinase B) aldolase C) pyruvate decarboxylase D) glyceraldehyde-3-phosphate dehydrogenase E) triose phosphate isomerase Ans: C Section: 15.3.B 121

Level of Difficulty: Moderate Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 31. If glucose labeled at the C-1 position with 14C passes through glycolysis, on which carbon of pyruvate will the radiolabel be found? A) 1 B) 2 C) 3 D) It will be released in CO2 rather than present in pyruvate. E) Not enough information is given to predict. Ans: C Section: 15.2 Level of Difficulty: Difficult Learning Objective: The Reactions of Glycolysis 32. Which of the following best explains why an enzyme hasn't evolved to catalyze the following reaction as the first step of glycolysis? glucose + Pi —> glucose-6-phosphate I. The use of ATP is required for this step to serve as a regulatory control point. II. The use of ATP is important because it helps keep its concentration low. Otherwise the high [ATP] would slow glycolysis too much through feedback inhibition. III. The large positive DG˚' of this reaction would need to be overcome by an exceedingly high [Pi]. IV. Inorganic phosphate cannot be specifically placed on the carbon in the 6th position. A) I, III B) I, II C) II, IV D) I only E) III only Ans: C Section: 15.2.A Level of Difficulty: Very Difficult Learning Objective: The Reactions of Glycolysis

33. Which glycolytic enzyme catalyzes a reaction with an enediolate intermediate?

122

A) phosphoglucomutase B) triose phosphate isomerase C) phosphofructokinase D) aldolase E) none of the above Ans: B Section: 15.2.B Level of Difficulty: Moderate Learning Objective: The Reactions of Glycolysis 34. Which of the following is true regarding glycolysis? I. There is a net oxidation of substrate carbon atoms. II. There is no net release of free energy. III. Pyruvate is generated only during aerobic glycolysis. IV. There is 2 ATP formed for every 2 glucose molecules. . A) I only B) I, IV C) I, III, IV D) IV only E) II, IV Ans: A Section: 15.1, 15.2.F Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 35. The reaction catalyzed by the enzyme aldolase has a DG˚' ≈ +23 kJ/mol. In muscle cells, the reaction proceeds in this same, forward direction. How can this occur? A) This DG˚' means it is thermodynamically favored. B) The enzyme changes the ∆G of the reaction in cells to something favorable. C) The concentration of reactant(s) must be significantly greater than product(s) in cells. D) The concentration of product(s) must be significantly greater than reactant(s) in cells. E) none of the above Ans: C Section: 15.2.D Level of Difficulty: Difficult Learning Objective: The Reactions of Glycolysis

36. Conversion of galactose to glucose 123

I. requires an epimerase. II. requires uridine diphosphate. III. requires a transferase IV. requires an isomerase. A) I, II, III, IV B) I, II, III C) II, III, IV D) II, III E) I, III Ans: B Section: 15.5.B Level of Difficulty: Difficult Learning Objective: Metabolism of Hexoses Other than Glucose 37. Methanol is highly toxic, not because of its own activity, but because it is converted metabolically into formaldehyde, which is the actual poison. What enzyme catalyzes this conversion? A) methanol caboxylase B) methanol transferase C) alcohol transmutase D) alcohol carboxylase E) alcohol dehydrogenase Ans: E Section: 15.3.B Level of Difficulty: Difficult Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 38. Which of the following reactions does not occur in mammals? A) pyruvate + NADH → lactate + NAD+ B) ribulose-5-phosphoate → ribose-5-phosphate C) mannose + ATP → mannose-6-phosphate + ADP + Pi D) 6-phophogluconate + NADP+ → ribulose-5-phosphate + NADPH + CO2 E) pyruvate + NADH + H+ → CO2 + ethanol + NAD+ Ans: E Section: 15.3.B Level of Difficulty: Moderate Learning Objective: Fermentation: The Anaerobic Fate of Pyruvate 39. Which enzyme is involved in substrate level phosphorylation in glycolysis? 124

A) Hexokinase B) Pyruvate kinase C) Glyceraldehyde-3phosphate dehydrogenase D) Aldolase E) None of the above. Ans: B Section: 15.2.J Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis 40. Which of the following best describes the entry of mannose into glycolysis? A) hydrolyzed into two glucose units, they enter normally B) phosphorylated at C-1; UMP moiety transferred from UDP-glucose; epimerized at C-2; released from UMP moiety on next transfer as G1P C) phosphorylated at C-1; UMP moiety transferred from UDP-glucose; epimerized at C-4; released from UMP moiety on next transfer as G1P D) phosphorylated at C-6; epimerized at C-2 to produce G6P E) phosphorylated at C-6; isomerized to produce F6P Ans: E Section: 15.5.C Level of Difficulty: Moderate Learning Objective: Metabolism of Hexoses Other than Glucose 41. Which of the following is correct regarding the hexose monophosphate shunt? I. NADH is generated by the oxidation of glucose-6-phosphate. II. Glyceraldehyde-3-phosphate is generated in the reaction. III. The pathway requires a transaldolase. IV. The pathway generates 3 ATP per 1 glucose-6-phosphate. A) I, II, III B) I, II, III, IV C) II, III, IV D) II, III E) III, IV Ans: D Section: 15.6 Level of Difficulty: Moderate Learning Objective: The Pentose Phosphate Pathway 42. Select the enzyme from the list which would catalyze the reaction shown below. 125

A) hexokinase (HK) B) pyruvate kinease (PK) C) enolase D) phosphoglucomutase (PGM) E) G3P dehydrogenase (G3PDH) Ans: A Section: 15.2.A Level of Difficulty: Easy Learning Objective: The Reactions of Glycolysis 43. Of the reaction types listed below, which type of reaction is NOT used in glycolysis? A) oxidation B) phosphorylation C) dehydration D) isomerization E) All are used in glycolysis. Ans: E Section: 15.1 Level of Difficulty: Easy Learning Objective: Overview of Glycolysis 44. During reactions utilizing the enzymes shown below, in which case(s) is ATP produced? I. phosphofructokinase (PFK) II. phosphoglycerate kinase (PGK) III. pyruvate kinase (PK) A) I B) II C) III D) I, II E) II, III Ans: E Section: 15.1, 15.2.G, 15.2.J Level of Difficulty: Easy Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 126

45. Which of the following best describes the control exhibited by phosphofructokinase (PFK)? A) It is allosterically inhibited by ATP and citrate. B) It is allosterically activated by F2,6P. C) It is allosterically activated by ATP and citrate. D) Both A and B are correct. E) Both B and C are correct. Ans: D Section: 15.4.A Level of Difficulty: Moderate Learning Objective: Regulation of Glycolysis 46. ATP A) inhibits activity of phosphofructokinase (PFK) allosterically. B) activates activity of phosphofructokinase (PFK) allosterically. C) inhibits activity of phosphofructokinase (PFK) hormonally. D) activates activity of phosphofructokinase (PFK) hormonally. E) does not alter phosphofructokinase (PFK) activity. Ans: A Section: 15.4.A Level of Difficulty: Moderate Learning Objective: Regulation of Glycolysis Use the following reactions to answer questions 47-49: I. 1,3-Bisphosphoglycerate (BPG) ® 3-phosphoglycerate(3PG) II. Glucose ® glucose-6-phosphate (G6P) III. 2-Phosphoglycerate (2PG) ® 3-phosphoglycerate (3PG) IV. Glycerol-3-phosphate (GAP) ® 1,3-Bisphosphoglycerate (BPG) V. Glucose-6-phosphate (G6P) ® fructose-6-phosphate (F6P)

47. In which reaction above is ATP required? A) I, II B) II only C) III only D) IV, V E) None of the reactions I-V requires ATP. Ans: B 127

Section: 15.1, 15.2.A Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 48. Which reaction above is an oxidation reaction? A) I, III B) II, III C) III only D) IV only E) None of the reactions I-V is oxidation reactions. Ans: D Section: 15.1, 15.2.F Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 49. In which reaction above is at least 1 NADH formed? A) II only B) III only C) IV only D) IV, V E) None of the reaction I-V form NADH. Ans: C Section: 15.1, 15.2.F Level of Difficulty: Moderate Learning Objective: Overview of Glycolysis, The Reactions of Glycolysis 50. The utilization of fructose in glycolysis in the liver A) requires UDP-glucose. B) requires one extra ATP. C) uses GTP rather than ATP. D) bypasses phosphofructokinase (PFK) regulation. E) enters glycolysis as fructose bisphosphate (FBP). Ans: D Section: 15.5.A Level of Difficulty: Moderate Learning Objective: Metabolism of Hexoses Other than Glucose

128

Chapter 16: Glycogen Metabolism and Gluconeogenesis Matching Choose the correct answer from the list. Not all the answers will be used. A) B) C) D) E) F) G) H) I) J) K) L)

phosphorylase a gluconeogenesis glucagon glucose-6-phosphatase cAMP biotin insulin glycogenolysis liver glucose-1-phosphate dolichol muscle

1. The breakdown of glycogen is referred to as ______. Ans: H Section: 16.1 Level of Difficulty: Easy Learning Objective: Glycogen Breakdown 2. Glucose can be synthesized from noncarbohydrate precursors by______. Ans: B Section: Intro Level of Difficulty: Easy Learning Objective: Gluconeogenesis 3. Carboxylation of pyruvate in humans requires ______ as an essential dietary nutrient. Ans: F Section: 16.4.A Level of Difficulty: Easy Learning Objective: Gluconeogenesis 4. ______ activates glycogen breakdown. Ans: E Section: 16.3.B Level of Difficulty: Easy Learning Objective: Control of Glycogen Metabolism 5. An enzyme present in the endoplasmic reticulum of liver cells is ______. Ans: D Section: 16.1.C 122

Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown 6. ______ cells lack receptors for the hormone glucagon. Ans: L Section: 16.3.C Level of Difficulty: Easy Learning Objective: Control of Glycogen Metabolism 7. Low blood glucose (< 5mM) levels result in the release of ______. Ans: C Section: 16.3.C Level of Difficulty: Easy Learning Objective: Control of Glycogen Metabolism 8. The first step in the breakdown of glycogen is catalyzed by ______. Ans: A Section: 16.1.A Level of Difficulty: Easy Learning Objective: Glycogen Breakdown 9. Both glycogen synthesis and glycogen breakdown share the metabolite ______. Ans: J Section: 16.2.A Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown & Synthesis 10. The membrane-bound polyisoprenol involved in the synthesis of N-linked glycoproteins is called ______. Ans: K Section: 16.5 Level of Difficulty: Easy Learning Objective: Other Carbohydrate Biosynthetic Pathways

Multiple Choice 11. Which of the following enzymes catalyzes the conversion of glucose-1-phosphate to glucose6-phosphate? A) B) C) D) E)

glucose-1-isomerase glucokinase glucose-1-phosphatase phosphoglucomutase glycogen phosphorylase

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Ans: D Section: 16.1C Level of Difficulty: Easy Learning Objective: Glycogen Breakdown

12. Individuals with McArdle's disease lack the ____ in the ____, A) B) C) D) E)

debranching enzyme; liver phosphoglucomutase; liver glycogen phosphorylase; muscle phosphoglucomutase; muscle glycogen phosphorylase; liver

Ans: C Section: 16.1.C, Box 16-2 Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown, Box 16-2 13. In glycogen synthesis, the intermediate between glucose-1-phosphate and glycogen is A) B) C) D) E)

UDP–glucose . UDP-glycogen. glucose-1,6-bisphosphate. glucose-6-phosphate. glucose.

Ans: A Section: 16.2.A Level of Difficulty: Easy Learning Objective: Glycogen Synthesis 14. Which of the following aides in formation of a primer for glycogen synthesis ? A) B) C) D) E)

glycogen synthase UDP-glucose pyrophosphatate glycogenin UDP–glycogen amylo-(1,4®1,6)-transglycosylase

Ans: C Section: 16.2.B Level of Difficulty: Moderate Learning Objective: Glycogen Synthesis

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15. Which of the following enzymes directly converts phosphorylase b into the more active form, phosphorylase a? A) B) C) D) E)

cAMP-dependent protein kinase phosphorylase kinase protein kinase A adenylate cyclase phosphoprotein phosphatase-1

Ans: B Section: 16.1.A, 16.3.B Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown, Control of Glycogen Metabolism 16. The biotin prosthetic group of pyruvate carboxylase is covalently attached to a ______ residue of the enzyme? A) B) C) D) E)

valine serine lysine arginine the biotin is attached non-covalently

Ans: C Section: 16.4.A Level of Difficulty: Easy Learning Objective: Gluconeogenesis 17. Which of the following serves as the free energy source for the metabolic conversion of oxaloacetate to phosphoenolpyruvate, which is catalyzed by PEP carboxykinase? A) B) C) D) E)

hydrolysis of PPi hydrolysis of ATP hydrolysis of GTP hydrolysis of an internal phosphoanhydride bond hydrolysis of a thioester intermediate

Ans: C Section: 16.4.A Level of Difficulty: Easy Learning Objective: Gluconeogenesis 18. What is the net energetic cost of converting two pyruvate to one glucose by gluconeogenesis in ATP equivalents? A) B) C) D) E)

2 3 4 6 8 125

Ans: D Section: 16.4.B Level of Difficulty: Moderate Learning Objective: Gluconeogenesis 19. Muscle cells are not able to supply glucose for other tissues because A) B) C) D) E)

they lack the GLUT2 transporter. they lack pyruvate carboxylase. they lack glucose-6-phosphatase. they lack the malate-aspartate shuttle. they lack glycogen phosphorylase.

Ans: C Section: 16.1.C Level of Difficulty: Difficult Learning Objective: Glycogen Breakdown

20. Which of the following statements about glycogen is true? I. Glycogen is a polymer of glucose in a(1®6) linkages with a(1®4) linked branches every 8–14 residues. II. UDP–glucose is produced from glycogen by the action of the enzyme phosphorylase. III. In glycogen breakdown, glucose residues are sequentially removed from the nonreducing ends. IV. The breakdown of glycogen in skeletal muscle ultimately supplies glucose-6phosphate, which can enter glycolysis to generate ATP. A) I, II, III, IV B) I, II C) II, III, IV D) III, IV E) III only Ans: D Section: 16.1 Level of Difficulty: Difficult Learning Objective: Glycogen Breakdown 21. Which of the following metabolic conversions does not occur in gluconeogenesis? A) B) C) D) E)

oxaloacetate ® phosphoenolpyruvate fructose-1,6-bisphosphate ® fructose-6-phosphate GTP ® CO2 + GDP NADH + H+ ® NAD+ 1,3-bisphosphoglycerate ® 3-phosphoglycerate 126

Ans: E Section: 16.4 Level of Difficulty: Moderate Learning Objective: Gluconeogenesis 22. Which of the following is correct concerning the metabolic reaction shown below? Pyruvate + CO2 + ATP

® oxaloacetate + ADP + Pi

I. This metabolic reaction is catalyzed by pyruvate carboxykinase. II. The enzyme that catalyzes this reaction is activated by high concentrations of acetyl-CoA . III. The enzyme that catalyzes this reaction is covalently bonded to the coenzyme pyridoxal-5ꞌ-phosphate. IV. The enzyme that catalyzes this reaction is located in the endoplasmic reticulum of the cell . A) I, II B) I only C) II only D) II, III E) II, III, IV Ans: C Section: 16.4.A Level of Difficulty: Difficult Learning Objective: Gluconeogenesis 23. What molecules correspond to correspond to X and Y in the following gluconeogenic reaction? Fructose-1,6-bisphosphotase + X ® Fructose-6-phosphate + Y A) B) C) D) E)

X = NADH + H+ X = ATP X = NAD+ X = GTP X = H2 O

Y = NAD+ Y = ADP + Pi Y = NADH + H+ Y = GTP + Pi Y = Pi

Ans: E Section: 16.4.B Level of Difficulty: Moderate Learning Objective: Gluconeogenesis

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24. Which of the following metabolic conversions involved in glucose synthesis requires the direct expenditure of ATP? I. 3-Phosphoglycerate ® 1,3-bisphosphoglycerate II. Glyceraldehyde-3-phosphate + dihydroxyacetone phosphate ® fructose1,6-bisphosphate III. Fructose-1,6-bisphosphate ® fructose-6-phosphate IV. 1,3-Bisphosphoglycerate ® glyceraldehyde-3-phosphate A) I only B) II, III C) III only D) II, IV E) I, IV Ans: A Section: 16.4.B Level of Difficulty: Moderate Learning Objective: Gluconeogenesis 25. Which statement is TRUE concerning the metabolic reaction shown below? HOCH2

-2

O3POCH2

OPO3-2

A) B) C) D) E)

The enzyme that catalyzes this reaction is called a mutase. The enzyme that catalyzes this reaction is called a kinase. This reaction requires the free energy of ATP hydrolysis. This reaction requires multiple steps catalyzed by a phosphorylase and a mutase. The oxidation level of glucose-1-phosphate is higher than that of glucose-6phosphate.

Ans: A Section: 16.1.C Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown

128

26. The diagram represents a “substrate cycle” in glucose metabolism. Which of the following statements about the cycle is true?

A) B) C) D) E)

Reactions I & II are catalyzed by the same enzyme and help establish equilibrium between the two metabolites. Reaction II produces ATP by substrate-level phosphorylation. Reaction II is catalyzed by an allosteric enzyme that is inhibited by fructose-26-bisphosphate. Reaction I is involved in the biosynthesis of glucose. Reaction II occurs under low-energy conditions when the cell needs ATP.

Ans: C Section: 16.4.C Level of Difficulty: Difficult Learning Objective: Gluconeogenesis 27. Increased levels of epinephrine in the blood will I. II. III. IV.

activate adenylate cyclase in liver and muscle cells. stimulate glycogen synthesis. inhibit glycolysis in the muscle cell. stimulate gluconeogenesis in the muscle cell.

A) I only B) I, II C) I, II, III D) II only E) I, II, III, IV Ans: A Section: 16.3.C Level of Difficulty: Difficult Learning Objective: Control of Glycogen Metabolism

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28. Avidin, a protein intact in raw egg whites, prevents the absorption of biotin in the intestine resulting in biotin deficiency. Which of the following is affected in individuals who consume large amounts of raw egg? A) B) C) D) E)

Oxaloacetate ® phosphoenolpyruvate 1,3-Bisphosphoglycerate ® glyceraldehyde-3-phosphate Fructose-1,6-bisphosphate ® fructose-6-phosphate Pyruvate ® oxaloacetate Phosphoenolpyruvate ® 2-phosphoglycerate

Ans: D Section: 16.4.A Level of Difficulty: Difficult Learning Objective: Gluconeogenesis

29. Which enzyme has an intermediate of the form presented below? CH 2OPO 32O

H H OH

H OPO 32-

OH H

A) B) C) D) E)

phosphofructokinase glycogen phosphorylase phosphohexose isomerase phosphoglucomutase none of the above

Ans: D Section: 16.1.C Level of Difficulty: Difficult Learning Objective: Glycogen Breakdown

30. Which statement is true regarding the activation of pyruvate carboxylase by acetyl-CoA? A) B) C) D) E)

Feedback activation enhances flux through glycolysis. Feedforward activation enhances the entry of pyruvate through the TCA cycle as Acetyl-CoA. Ensures that gluconeogenesis occurs rather than pyruvate conversion to acetyl-CoA. Ensures that ATP is not wasted in the production of oxaloacetate. Feedback inhibition ensures that excess glucose-6-phosphate is not produced. 130

Ans: C Section: 16.1.C Level of Difficulty: Difficult Learning Objective: Gluconeogenesis 31. What is the net ATP yield for a muscle cell that stores one dietary glucose molecule as glycogen and then releases it and sends it through glycolysis? A) B) C) D) E)

0 1 2 3 4

Ans: C Section: 16.1 Level of Difficulty: Difficult Learning Objective: Glycogen Breakdown 32. Which of the following best describes the function of the glycogen debranching enzyme in glycogenolysis? A) B) C) D) E)

It cleaves a(1®6) branch points releasing glucose-6-phosphate. It cleaves a(1®6) branch points releasing glucose-1-phosphate. It cleaves a(1®6) branch points releasing glucose. It transfers an a(1®4) linked trisaccharide unit to the nonreducing end of an alternate branch, then cleaves the a(1®6) branch point releasing glucose-1phosphate. It transfers an a(1®4) linked trisaccharide to the nonreducing end of an alternate branch, then cleaves the a(1®6) branch point releasing glucose.

Ans: E Section: 16.1.B Level of Difficulty: Easy Learning Objective: Glycogen Breakdown

131

33. If cAMP levels are high I. Glycogenolysis will occur in muscle cells but not liver cells. II. Glucose released from muscle glycogen will enter glycolysis. III. Glucose released from liver glycogen will exit liver cells via the GLUT4 transporter. IV. Glucose will enter liver cells resulting in glycogen synthesis. A) I, II, IV B) I, II C) II, III, IV D) II only E) III only Answer: D Section: 16.3.C Level of Difficulty: Very Difficult Learning Objective: Control of Glycogen Breakdown

34. Which of the following best explains the energetically favorable formation of UDP–glucose in the liver and muscle? A) B) C) D) E)

DG°¢ for the reaction glucose-1-phosphate + UTP ® UDP–glucose + PPi is very negative. DG°¢ for the reaction glucose-1-phosphate + UTP ® UDP–glucose + PPi is very positive. DG°¢ for the reaction PPi ® 2Pi is very negative. DG°¢ for the reaction PPi ® 2Pi is very positive. DG°¢ for the overall reaction is very positive.

Ans: C Section: 16.2.A Level of Difficulty: Moderate Learning Objective: Glycogen Synthesis

35. Hexokinase does not catalyze the final step in gluconeogenesis as written below because glucose-6-phosphate + ADP ® glucose + ATP A) B) C) D) E)

the phosphate bond in glucose-6-phosphate does not have a high enough free energy to form ATP. ATP inhibits hexokinase and blocks the reaction from occurring as written. hexokinase is only reversible when high levels of ATP are present. hexokinase does not bind glucose-6-phosphate. none of the above 132

Ans: A Section: 16.4.B Level of Difficulty: Difficult Learning Objective: Gluconeogenesis 36. Which of the following best describes the role of fructose-2,6-bisphosphate (FBP) in liver cells? A) B) C) D) E)

It is an intermediate in glycolysis. It is an intermediate in gluconeogenesis. It is an intermediate in both glycolysis and gluconeogenesis. FBP is a potent allosteric activator of phosphofructokinase and an inhibitor of fructose bisphosphatase. FBP is a potent allosteric activator of fructose bisphosphatase and an inhibitor of phosphofructokinase.

Ans: D Section: 16.4.C Level of Difficulty: Moderate Learning Objective: Gluconeogenesis

37. Which of the following is true regarding the reaction shown below? pyruvate + HCO3− + ATP ® oxaloacetate + ADP + Pi I. II. III. IV.

It requires the direct transport of oxaloacetate across the membrane. It utilizes the malate-aspartate shuttle in some species. It is essential for gluconeogenesis. Its reactants require the function of enzymes which are only found in the cytosol.

A) I only B) II, III C) II, III, IV D) III only E) II, IV Ans: B Section: 16.4.B Level of Difficulty: Difficult Learning Objective: Gluconeogenesis

133

38. The synthesis of N-linked oligosaccharides occur in the _____ while O-linked oligosaccharides are synthesized in the ______. A) B) C) D) E)

Golgi apparatus; endoplasmic reticulum cytosol; Golgi apparatus mitochondrial matrix; endoplasmic reticulum endoplasmic reticulum; Golgi apparatus Golgi apparatus; mitochondrial matrix

Ans: D Section: 16.5 Level of Difficulty: Easy Learning Objective: Other Carbohydrate Biosynthetic Pathways

39. Levels of glucose-6-phosphate (G6P) are affected by which of the following? I. glycogen breakdown II. activity of the pentose phosphate pathway III. galactose preparation for entry into glycolysis A) I, II B) I, II, III C) III D) II, E) I, III Ans: B Section: 15.5, 15.6, 16.1 Level of Difficulty: Difficult Learning Objective: Chapter 15 sections, Glygocen Breakdown 40. The breakdown of glycogen produces G1P. Which of the following is FALSE regarding G1P? A) It is involved in the utilization of fructose by glycolysis in the liver. B) It is involved in the utilization of fructose by glycolysis in the muscle. C) It is involved in utilization of galactose by glycolysis. D) It is converted to G6P by phosphoglucoisomerase (PGI). E) It is produced as an intermediate in the central glycolytic sequence. Ans: D Section: 15.1, 15.5, 16.1C, 16.2 Level of Difficulty: Difficult Learning Objective: Chapter 15 sections, Glycogen Breakdown, Glycogen Synthesis

134

41. The glycogen debranching enzyme is required for A) the transfer of 3-glucose units from one branch to another. B) the transfer of phosphate from one position to another. C) cleaving a(1à6) sugar linkages D) A and C E) A, B and C Ans: D Section: 16.1.B Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown 42. Which of the following describes a sequence which will ultimately activate glycogen breakdown in a muscle? A) epinephrine binds β receptors. àcAMP à PKA àphosphorylase kinase àglycogen phosphorylase B) epinephrine bind α receptors à Ca2+ increase à phosphorylase kinase à glycogen phosphorylase C) glucagon à glucagon receptors à cAMP à PKA à phosphorylase kinase à glycogen phosphorylase D) PP1 binding to unphosphorylated Gm à dephosphorylates glycogen phosphorylase and phosphorylase kinase E) All of these will activate glycogen breakdown in a muscle. Ans: A Section: 16.3.C Level of Difficulty: Difficult Learning Objective: Control of Glycogen Metabolism

43. Phosphoprotein phosphatase -1 (PP1) A) catalyzes the phosphorylation of phosphorylase kinase. B) increases glycogen breakdown when active. C) catalyzes the dephosphorylation of phosphorylase kinase. D) catalyzes the dephosphorylation of glycogen phosphorylase. E) Both C and Dare correct. Ans: E Section: 16.3.B Level of Difficulty: Moderate Learning Objective: Control of Glycogen Metabolism

135

44. Which of the following will NOT activate glycogen phosphorylase in the liver? A) epinephrine B) glucagon C) eating a high carbohydrate meal D) cAMP E) All of the above will activate glycogen phosphorylase. Ans: C Section: 16.3.C Level of Difficulty: Difficult Learning Objective: Control of Glycogen Metabolism

45. Patient “G” has a glycogen storage disease which results in decreased muscle glycogen levels. Muscle biopsies indicate poor glycogen structure in the muscle. Which of the following enzymes might be related to the cause? A) muscle debranching enzyme B) muscle glycogen phosphorylase C) liver debranching enzyme D) muscle glycogen synthase E) liver glycogen synthase Ans: D Section: 16.1 Level of Difficulty: Difficult Learning Objective: Glycogen Synthesis 46. Which of the following overall sequences is correct with regard to gluconeogenesis? A) Oxaloacetate à PEP à G6P à Glucose B) Pyruvate à FBP à PEP à Glucose C) Lactate à PEP à Pyruvate à G6P D) Oxaloacetate à F6P à FBP à Glucose E) F6P à FBP à Glucose à G6P Ans: A Section: 16.4 Level of Difficulty: Moderate Learning Objective: Gluconeogenesis

136

47. Which enzyme below is NOT required for the synthesis of branched glycogen? A) glycogen phosphorylase B) glycogen synthase C) branching enzyme D) phosphoglucomutase E) All are required for synthesis of glycogen. Ans: A Section: 16.1 Level of Difficulty: Easy Learning Objective: Glycogen Synthesis 48. A deficiency in muscle glycogen phosphorylase would result in A) normal muscle glycogen structure. B) abnormal muscle glycogen structure. C) elevated muscle glycogen levels D) A and C E) B and C Ans: D Section: 16.2.A, B, C Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown 49. The Cori cycle is effective because A) it allows the use of the lactate generated during anaerobic glycolysis to produce pyruvate. B) it uses less ATP than gluconeogenesis. C) it uses the compound DHAP and G3P generated during glycolysis to transport reducing equivalents. D) A and B E) A and C Ans: A Section: Box 16-1, 16.1 Level of Difficulty: Moderate Learning Objective: Glycogen Breakdown, Box 16-1

137

50. A deficiency in the enzyme PEPCK (PEP carboxykinase) would A) block function of the malate/aspartate shuttle. B) block transfer of reducing equivalents across the membrane in the heart and liver. C) inhibit formation of ATP via oxidative phosphorylation. D) inhibit formation of NADH. E) decrease flux through gluconeogenesis. Ans: E Section: 16.4 Level of Difficulty: Difficult Learning Objective: Gluconeogenesis

138

Chapter 17: Citric Acid Cycle Matching Choose the correct answer from the list. Not all the answers will be used. A) oxaloacetate B) malate synthase C) malate D) malonate E) Krebs F) aconitase G) succinyl-CoA synthetase H) a-ketoglutarate I) carbon dioxide J) malate dehydrogenase K) isocitrate L) succinate dehydrogenase

1. The citric acid cycle is also called the ______ cycle. Ans: E Level of Difficulty: Easy Section: 17.1 Learning Objective: Overview of the Citric Acid Cycle 2. ______ is the first compound that is oxidized in the citric acid cycle. Ans: K Section: 17.3.C Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle 3. ______ catalyzes a substrate-level phosphorylation reaction within the citric acid cycle. Ans: G Section: 17.3.E Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle 4. ______ is used in the first reaction of the citric acid cycle and regenerated upon completion of one turn of the citric acid cycle. Ans: A Section: 17.1 Level of Difficulty: Easy Learning Objective: Overview of the Citric Acid Cycle 5. A membrane-bound enzyme of the citric acid cycle that catalyzes an oxidation reaction is ______. Ans: L Section: 17.3.F

132

Level of Difficulty: Easy Learning Objective: Enzymes of the Citric Acid Cycle 6. The name of a citric acid cycle intermediate that is derived from the Latin word for "apple" is ______. Ans: C Section: 17.1 Level of Difficulty: Easy Learning Objective: Overview of the Citric Acid Cycle 7. The enzyme ______ is unique because it contains an iron-sulfur cluster but does not participate in a redox reaction. Ans: F Section: 17.3.B Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle 8. The compound ______ is a structural analog and competitive inhibitor of the enzyme succinate dehydrogenase. Ans: D Section: 17.3.F Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle 9. The enzyme ______ is part of the glyoxylate cycle that occurs in plants, bacteria, and fungi. Ans: B Section: 17.5.C Level of Difficulty: Moderate Learning Objective: Reactions Related to the Citric Acid Cycle 10. _____ and pyruvate can be combined in an ATP dependent reaction that regenerates one of the key intermediates in the citric acid cycle. Ans: I Section: 17.5.B Level of Difficulty: Moderate Learning Objective: Reactions Related to the Citric Acid Cycle

Multiple Choice 11. Which of the following coenzymes is required by E1 of the pyruvate dehydrogenase complex for catalytic activity? A) B) C) D)

thiamine pyrophosphate lipoamide coenzyme A NAD+ 133

FAD

Answer: A Section: 17.2.B Level of Difficulty: Easy Learning Objective: Synthesis of Acetyl-Coenzyme A 12. E2 of the pyruvate dehydrogenase complex contains a lipoyl group that is covalently attached via an amide linkage to a ______ residue on the enzyme? A) tyrosine B) serine C) lysine D) arginine E) cysteine Answer: C Section: 17.2.B Level of Difficulty: Easy Learning Objective: Synthesis of Acetyl-Coenzyme A 13. Which of the following is an intermediate between citrate and isocitrate in the citric acid cycle? A) B) C) D) E)

succinyl-CoA citryl-CoA oxalosuccinate succinyl-phosphate cis-aconitate

Answer: E Section: 17.3.B Level of Difficulty: Easy Learning Objective: Enzymes of the Citric Acid Cycle

14. Condensation of ____ with oxaloacetate yield citrate. A) B) C) D) E)

acetyl-CoA α-ketoglutarate isocitrate citrophosphate oxalosuccinate

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Answer: A Section: 17.3.A Level of Difficulty: Easy Learning Objective: Enzymes of the Citric Acid Cycle 15. During the oxidation of isocitrate, _____ is decarboxylated to form a-ketoglutarate. A) B) C) D) E)

hydroxyethyl-TPP carboxybiotin oxalosuccinate succinyl-phosphate none of the above

Answer: C Section: 17.3.C Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle 16. The reaction catalyzed by _____ requires an enzyme bound flavin coenzyme. A) B) C) D) E)

isocitrate dehydrogenase a-ketoglutarate dehydrogenase succinyl-CoA synthetase succinate dehydrogenase malate dehydrogenase

Answer: D Section: 17.3.F Level of Difficulty: Easy Learning Objective: Enzymes of the Citric Acid Cycle 17. In eukaryotes, the citric acid cycle occurs in the _____ and therefore requires that reactants of the citric acid cycle be transported from the _____. A) B) C) D) E)

cytosol; mitochondrial matrix mitochondrial matrix; cytosol endoplasmic reticulum; mitochondrial matrix inner mitochondrial membrane; mitochondrial matrix outer mitochondrial membrane; cytosol

Answer: B Section: 17.1 Level of Difficulty: Moderate Learning Objective: Overview of the Citric Acid Cycle 18. How many NADH are produced when one acetyl group is oxidized in the citric acid cycle? A) B) C)

1 2 3 135

D) 4 E) more than 4 Answer: C Section: 17.1 Level of Difficulty: Easy Learning Objective: Overview of the Citric Acid Cycle 19. Which of the following utilizes intermediates of the citric acid cycle?

A) B) C) D) E)

I. gluconeogenesis II. amino acid biosynthesis III. fatty acid oxidation IV. glycolysis I only II only I, II, III I, II I, IV

Answer: D Section: 17.5 Level of Difficulty: Moderate Learning Objective: Reactions Related to the Citric Acid Cycle 20. The reaction catalyzed by pyruvate carboxylase is an example of a(n) ______ reaction because it replenishes the citric acid cycle intermediates that have been siphoned off for use in other reactions. A) amphibolic B) amphipathic C) anaplerotic D) cataplerotic E) none of the above Answer: C Section: 17.5.B Level of Difficulty: Easy Learning Objective: Reactions Related to the Citric Acid Cycle

21. Which of the following is oxidized by a multienzyme complex that requires five different coenzymes? O

O2C

CH2 C

CO2-

136

CH2 CH CO2-

O2C O

CH3 C

SCoA

C) D)

A and B

A, B, and C

Answer: C Section: 17.2.A Level of Difficulty: Moderate Learning Objective: Synthesis of Acetyl-Coenzyme A 22. The isomerization of citrate to isocitrate A) B) C) D)

is the reaction of the citric acid cycle that occurs spontaneously without enzymatic catalysis. protects cells from the toxic effects of arsenite ion. converts a tertiary alcohol, which cannot easily be oxidized, to a secondary alcohol that can be oxidized. is one major regulatory step for the citric acid cycle because it functions as a rate limiting step. A and B

E) Answer: C Section: 17.3.B Level of Difficulty: Difficult Learning Objective: Enzymes of the Citric Acid Cycle

23. Which of the following is(are) TRUE concerning the metabolic reaction shown below? Pyruvate + NAD+ + CoA-SH ® Acetyl-CoA + NADH + H+ + CO2 I. The enzyme that catalyzes this reaction contains a pyridoxal phosphate prosthetic group. II. This reaction is an oxidative decarboxylation.

137

III. The enzyme that catalyzes this metabolic conversion is activated by high concentrations of ATP. I, II, III II, III II only III only I, II

A) B) C) D) E) Answer: C Section: 17.2.B Level of Difficulty: Difficult Learning Objective: Synthesis of Acetyl-Coenzyme A

24. Which of the following causes pyruvate dehydrogenase kinase to catalyze the phosphorylation and inactivation of E1 in the pyruvate dehydrogenase complex? A) B) C) D) E)

elevated concentrations of NADH and ATP elevated concentrations of NAD+ and ADP insulin elevated concentrations of acetyl-CoA C and D

Answer: A Section: 17.4.A Level of Difficulty: Difficult Learning Objective: Regulation of the Citric Acid Cycle

25. If acetyl-CoA labeled with 14C, as shown in the figure to the right, were used as the substrate for the citric acid cycle, which of the following intermediates would be produced during the first round of the cycle? OH H O2*C

C C

CH2 CO2

H CO2

138

O CoAS

C *CH3

OH H O2C

C C *CH2 CO2 H CO2

OH H O2C

C C

CH2 *CO2

H CO2

OH H O2C *C C CH2 CO2 H CO2

OH H O2C C *C CH2 CO2 H CO2

Answer: B Section: 17.1 Level of Difficulty: Difficult Learning Objective: Overview of the Citric Acid Cycle

26. Which of the following uses inherent length and flexibility to facilitate transfer of an acetyl group? A) B) C) D) E)

FAD NAD+ lipoamide thiamine pyrophosphate coenzyme A

Answer: C Section: 17.2.B Level of Difficulty: Moderate Learning Objective: Synthesis of Acetyl-Coenzyme A 27. Which of the following structures represents a molecule that is added to succinate to form CoA and malate? O

O2C

CO2

CH3 C O

139

O2CCH2 C

CO2

O O D)

C C O O

H C

CO2

Answer: E Section: 17.5.C Level of Difficulty: Difficult Learning Objective: Reactions Related to the Citric Acid Cycle 28. Which of the following best describes the importance of the citric acid cycle as a central pathway of metabolism? A) B) C) D)

It allows recovery of energy from carbohydrates only. It allows recovery of energy from fatty acids only. It allows recovery of energy from amino acids only. It allows recovery of energy from several metabolic fuels that are broken down to acetyl-CoA. A and B

E) Answer: D Section: 17.1 Level of Difficulty: Easy Learning Objective: Overview of the Citric Acid Cycle

29. Which of the following coenzymes is required by the pyruvate dehydrogenase complex for reoxidation of E3? A) B) C) D) E)

thiamine pyrophosphate pyridoxal phosphate coenzyme A FAD NAD+

Answer: E Section: 17.2.B 140

Level of Difficulty: Difficult Learning Objective: Synthesis of Acetyl-Coenzyme A 30. Which of the following enzymes catalyzes a reaction with the pictured compound as an COOintermediate? A) B) C) D) E)

a-ketoglutarate dehydrogenase succinyl-CoA synthetase succinate dehydrogenase fumarase malate dehydrogenase

Answer: B Section: 17.3.E Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle

CH2 CH2 C 2-O P 3

31. Which of the following can be said about the isocitrate product of aconitase? A) B) C) D) E)

The product always has the R configuration. The product always has the S configuration. The product is not chiral. The product can exist in either the R or S configuration in eukaryotes. If the product is in the R configuration it has by passed the cis-aconitate intermediate.

Answer: A Section: 17.3.B Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle

32. Which of the following enzymes of the citric acid cycle is inhibited by ATP? A) B) C) D) E)

citrate synthase isocitrate dehydrogenase a-ketoglutarate dehydrogenase succinyl-CoA synthetase A and B

Answer: B Section: 17.4.B 141

Level of Difficulty: Moderate Learning Objective: Regulation of the Citric Acid Cycle 33. Which of the following organisms does not utilize the glyxolate cycle? A) B) C) D) E)

trees bacteria fungi mammals All of the above utilize the glyxolate cycle when necessary.

Answer: D Section: 17.5.C Level of Difficulty: Easy Learning Objective: Reactions Related to the Citric Acid Cycle OH

34. The figure at right represents an intermediate in the reaction catalyzed by which of the following enzymes? A) B) C) D) E)

enolase aldolase pyruvate decarboxylase glyceraldehyde-3-phosphate dehydrogenase lactate dehydrogenase

H3C

TPP

Answer: C Section: 17.2.B Level of Difficulty: Moderate Learning Objective: Synthesis of Acetyl-Coenzyme A

35. Which of the following amino acid residues facilitates the transfer of a phosphate group in the reaction producing succinate and GTP? A) B) C) D) E)

aspartate glutamate histidine lysine serine

Answer: C Section: 17.3.E 142

Level of Difficulty: Difficult Learning Objective: Enzymes of the Citric Acid Cycle 36. Which of the following citric acid cycle intermediates can be converted to aspartate via transamination? A) B) C) D) E)

citrate a-ketoglutarate succinate fumarate oxaloacetate

Answer: E Section: 17.5.A Level of Difficulty: Moderate Learning Objective: Reactions Related to the Citric Acid Cycle 37. Considering the reactions within the citric acid cycle, which of the following molecules will be produced from the intermediate pictured on the right? A) B) C) D) E)

citrate isocitriate succinate succinyl-CoA α-ketoglutarate

O-

CH 2 C

COO -

Answer: B Section: 17.3.B Level of Difficulty: Moderate Learning Objective: Enzymes of the Citric Acid Cycle

38. Consider the following reaction which has a ∆G˚' ≈ +30 kJ/mol. malate + NAD+ → oxaloacetate + NADH + H+ In muscle cells, the reaction proceeds as written. Which of the following explains how the reaction occurs as written despite the positive value for DG°'? A) It is thermodynamically favored under standard conditions. B) In the cell, it is kinetically favored, even though it’s thermodynamically unfavorable.

143

C) D) E)

The concentration of malate must be higher than oxaloacetate for this reaction to occur in the cell. [H+] must be higher in muscle than under standard conditions, thus altering ∆G˚ to ∆G˚'. None of the above

Answer: C Section: 17.5 Level of Difficulty: Difficult Learning Objective: Reactions Related to the Citric Acid Cycle 39. Germinating plant seeds can convert acetyl-CoA (obtained from fatty acids stored as oils) into carbohydrates, whereas animals are incapable of converting fatty acids into glucose. This difference is due to the fact that: A) B) C) D)

animals have glycogen and don’t need to make glucose from fatty acids. plants use the glyoxylate cycle to convert two acetyl CoA to oxaloacetate, a precursor for gluconeogenesis. plant seeds use photosynthesis to make sugar. animals use the citric acid cycle selectively for energy production, whereas plants primarily use glycolysis. B and D

E) Answer: B Section: 17.5.C Level of Difficulty: Moderate Learning Objective: Reactions Related to the Citric Acid Cycle

40. How many electrons are transferred from one acetyl group during the citric acid cycle? A) 2 B) 4 C) 6 D) 8 E) 10 Answer: D Section: 17.4 Level of Difficulty: Easy Learning Objective: Regulation of the Citric Acid Cycle 41. An individual with a shortage of B vitamins (which include thiamine and riboflavin) may feel fatigued as a result of decreased pyruvate dehydrogenase activity. Which of the following would be TRUE regarding this shortage? A) B)

The amount of acetyl CoA produced from carbohydrate metabolism that enters the citric acid cycle would be decreased. A decrease in the amount of NADH would likely decrease activity of citrate synthase.

144

Flux through the citric acid cycle would cease until adequate pyruvate is available. none of the above all of the above

D) E) Answer: A Section: 17.4 Level of Difficulty: Difficult Learning Objective: Regulation of the Citric Acid Cycle

42. Which of the following would decrease activity of the citric acid cycle overall? I. high concentration of NADH II. high concentration of Ca2+ III. high concentration of ATP IV. high concentration of citrate A) B) C) D) E)

I only I, II, III, IV I, III I, III, IV I, IV

Answer: D Section: 17.4 Level of Difficulty: Difficult Learning Objective: Regulation of the Citric Acid Cycle 43. Which of the following steps of the citric acid cycle conserves the energy of a high energy thioester bond? A) the reaction catalyzed by succinate dehydrogenase. B) the reaction that produces oxalacetate. C) the condensation reaction that produces citrate. D) the reaction catalyzed by α-ketoglutarate dehydrogenase. E) the conversion of citrate to isocitrate. Answer: D Section: 17.3.E Level of Difficulty: Moderate Learning Objective: Enzymes of the citric acid cycle

44. Which of the following enzymatic reactions is favorable both under physiological conditions and under standard conditions? A) B) C)

The reaction catalyzed by isocitrate dehydrogenase. The reaction catalyzed by malate dehydrogenase. The reaction catalyzed by succinate dehydrogenase. 145

D) all of the above E) none of the above Answer: A Section: 17.4 Level of Difficulty: Moderate Learning Objective: Regulation of the citric acid cycle 45. One turn of the citric acid cycle generates A) 2 FADH2, 3 ATP, 1 NADH B) 1 NAD+, 2FADH2, 1 ATP C) 1 GTP, 3 NADH, 1 FADH2 D) 1 FAD, 2 ATP, 3 NADH E) 1 FADH2, 1GTP, 2 NADH Answer: C Section: 17.1 Level of Difficulty: Moderate Learning Objective: Overview of the citric acid cycle

46. Which reaction below produces GTP in the citric acid cycle? A) isocitrate à a-ketoglutarate B) a-ketoglutarate à succinyl CoA C) succinyl CoA à succinate D) fumarate à malate E) malate à oxaloacetate Answer: C Section: 17.1 Level of Difficulty: Moderate Learning Objective: Overview of the citric acid cycle

47. Which of the following statements correctly and most accurately describes the function of FAD in the pyruvate dehydrogenase enzyme complex?

146

A) B) C) D) E)

NADH passes electrons to FAD to form FADH2. Lipoamide passes electrons through FADH2, which almost instantly passes them to NAD thus forming NADH. FADH2 donates electrons to lipoamide thus regenerating FAD. Lipoamide oxidizes NADH to NAD by passing electrons to FAD. NAD accepts electrons directly from lipoamide, which has gained them via oxidation of FADH2.

Answer: B Section: 17.2.B Level of Difficulty: Difficult Learning Objective: Synthesis of Acetyl-Coenzyme A 48. Which of the following is TRUE regarding the discovery of the citric acid cycle? I. One of the first discoveries was the involvement of coenzyme A in the production of GTP. II. Krebs had knowledge of the sequence of reactions before he was able to demonstrate the link of the cycle to glucose metabolism. III. The citric acid cycle was the first cyclic pathway discovered. IV. Krebs demonstrated the involvement of the citric acid cycle in oxidation of amino acid and fatty acids. A) B) C) D) E)

I, II, III, IV I, II, III II, III III, IV II, IV

Answer: B Section: 17.1, Box 17-1 Level of Difficulty: Moderate Learning Objective: Overview of the citric acid cycle, Box 17-1

147

49. Which of the following represents a point of regulation for the citric acid cycle? I. pyruvate dehydrogenase complex II. aconitase III. isocitrate dehydrogenase IV. fumarase A) I, II, III, IV B) I, II, IV C) II, III D) I, III E) I, IV Answer: D Section: 17.4 Level of Difficulty: Moderate Learning Objective: Regulation of the citric acid cycle 50. Bioinformatics has identified some enzymes used in the citric acid cycle in primitive bacteria. Once such a cycle utilized many of the citric acid cycle intermediates but occurred in the reverse direction. Researchers suspect which of the following based on this information? A) B) C) D) E)

Researchers suspect that the "original" citric acid cycle was used by all species. Researchers suspect that portions of the reverse cycle may have been responsible for fixing CO2 Researchers suspect that early methods for converting pyruvate to acetyl CoA did not exist. Researchers suspect that the current "clockwise" version of the citric acid cycle could be used to help humans feed off CO2. Researchers suspect that primitive prokaryotic use of the citric acid enzymes were focused on the production of CO2 rather than the use of CO2.

Answer: B Section: Box 17-3 Level of Difficulty: Difficult Learning Objective: Box 17-3

148

Chapter 18: Electron Transport and Oxidative Phosphorylation Matching Choose the correct answer from the list. Not all the answers will be used. A) shuttle B) matrix C) respiration D) copper E) heme F) tunnel G) plasma membrane H) coenzyme Q I) cytosol J) antioxidant K) wire L) proton pump 1. The inner mitochondrial membrane divides the mitochondrion into the inner membrane space and the ______. Ans: B Section: 18.1.A Level of Difficulty: Easy Learning Objective: The Mitochondrion 2. Complexes I and II each transfer electrons to ______. Ans: H Section: 18.2.B Level of Difficulty: Easy Learning Objective: Electron Transport 3. Electrons from cytosolic NADH are transferred to the matrix via electron ______ systems. Ans: A Section: 18.1.B Level of Difficulty: Easy Learning Objective: The Mitochondrion 4. Protons moving through a transmembranc channel by "jumping" through an arrangement of hydrogen-bonded groups are described as moving through a proton ______. Ans: K Section: 18.2.C Level of Difficulty: Moderate Learning Objective: Electron Transport 5. Bacteriorhodopsin is an example of a light-driven ______ . Ans: L Section: 18.2.C Level of Difficulty: Easy Learning Objective: Electron Transport 143

6. The cytochromes within complex III all contain _____ groups. Ans: E Section: 18.2.B Level of Difficulty: Moderate Learning Objective: Electron Transport 7. Cytochrome c oxidase contains four redox centers: two heme groups and two redox centers containing_______. Ans: D Section: 18.2.B Level of Difficulty: Easy Learning Objective: Electron Transport 8. Bacteria carry out electron transport in the _____. Ans: G Section: 18.3.A Level of Difficulty: Easy Learning Objective: Oxidative Phosphorylation 9. The stoichiometric relationship of ATP synthesis to ______ is referred to as the P/O ratio. Ans: C Section: 18.3.C Level of Difficulty: Easy Learning Objective: Oxidative Phosphorylation 10. Molecules that prevent oxidative damage by the superoxide radical possess ______ properties. Ans: J Section: 18.4.B Level of Difficulty: Easy Learning Objective: Control of Oxidative Metabolism

Multiple Choice 11. A typical eukaryotic cell contains up to ____ mitochondria each bound by a smooth outer membrane. A) 2 B) 20 C) 2000 D) 20,000 E) 200,000 Answer: C Section: 18.1.A Level of Difficulty: Easy Learning Objective: The Mitochondrion 144

12. Approximately how many ATP molecules are synthesized from the oxidation of 1 NADH? A) 1 B) 1.5 C) 2 D) 2.5 E) 3 Answer: D Section: 18.2.A Level of Difficulty: Easy Learning Objective: Electron Transport 13. According to the proposed reaction sequence presented in the chapter, cytochrome c oxidase obtains a fourth electron from a ____ residue adjacent to the heme a3-ligated O2, thus forming a transient radical. A) serine B) threonine C) tyrosine D) phenylalanine E) tryptophan Answer: C Section: 18.2.F Level of Difficulty: Moderate Learning Objective: Electron Transport 14. One method used by newborn mammals to generate heat is referred to as nonshivering thermogenesis. This method utilizes a protein channel called ________ which is present in high levels inside the mitochondria of _____tissue. A) thermogenin; muscle B) UCP-1; muscle C) thermogenin; brown adipose D) UCP-1; white adipose E) UCP-2; brown adipose Answer: C Section: 18.3.D, Box 18-4 Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation, Box 18-4 15. Based on the estimation presented in the chapter, how many ATP per glucose are synthesized by the aerobic metabolism in eukaryotes? A) 2 B) 4 C) 32 D) 38 E) 60 Answer: C Section: 18.3.C 145

Level of Difficulty: Easy Learning Objective: Oxidative Phosphorylation 16. Some degenerative diseases, such as Parkinson’s disease, are associated with ______ damage to ______. A) oxidative; mitochondria B) thermogenic; mitochondria C) free radical; nuclei D) oxidative; nuclei E) thermogenic; nuclei Answer: A Section: 18.4.B Level of Difficulty: Easy Learning Objective: Control of Oxidative Metabolism 17. The electrons formed from the aerobic oxidation of glucose are I. ultimately transferred to O2 after several other transfer reactions. II. transferred to the coenzymes NAD+ and FAD. III. directly transferred to O2 during the citric acid cycle. IV. transferred to succinate and arachidonic acid. A) I only B) II only C) I, II D) II, III, IV E) I, II, III Answer: C Section: 18.1 Level of Difficulty: Moderate Learning Objective: The Mitochondrion 18. Which of the following statements about the mitochondrial inner membrane is TRUE? I. The inner membrane is permeable to CO2, H2O, and small ions. II. The inner membrane contains several transport proteins and membrane bound enzymes. III. In general, a higher inner membrane surface area correlates to a higher rate of respiration. IV. The number of cristae reflects the respiratory activity of the cell. A) I, II, III, IV B) I, II, III C) II only D) II, III, IV E) III, IV Answer: D Section: 18.1.A, B Level of Difficulty: Moderate Learning Objective: The Mitochondrion 146

19. Which of the following is TRUE regarding the complexes within the electron transport system? I. Complex II contributes twice as many protons to the gradient than Complex I II. Inhibition of Complex II would decrease the total number of electrons moving through the electron transport chain. III. Inhibition of Complex II would not alter the amount of free energy generated from electrons originating from NADH. IV. Complex I can accept electrons with higher potential than Complex II is able to accept. A) I, II, III, IV B) I, II, III C) II only D) II, III E) III, IV Answer: D Section: 18.2.A-D Level of Difficulty: Moderate Learning Objective: Electron Transport 20. Which of the following correctly ranks redox centers found in Complex I from lower to higher potential? A correct answer will contain redox centers which are found in only Complex I and will also rank those redox centers in order of lower to higher reduction potential. A) FMN, Heme b560, [2Fe-2S], CoQ B) ubiquinone, [4Fe-4S], [2Fe-2S], FMN C) FMN, [2Fe-2S], [4Fe-4S] D) Heme b560, [2Fe-2S], [4Fe-4S], FAD E) FAD, [2Fe-2S], [4Fe-4S], Heme b560 Answer: C Section: 18.2.B, 18.2.C Level of Difficulty: Moderate Learning Objective: Electron Transport

21. Based on the information in the chapter, which of the following is TRUE regarding Complex III? I. A large portion of Complex III dissociates from the membrane bound portion of the complex. II. Complex III contains three identical cytochrome redox centers. III. The Q cycle allows stepwise reoxidation of the two electrons from CoQH2. IV. A change in conformation of iron sulfur protein (ISP) ensures that the Reiske center is reduced preferentially by CoQ.-. A) I only B) I, II C) III only 147

D) E)

III, IV I, III, IV

Answer: C Section: 18.2.E Level of Difficulty: Difficult Learning Objective: Electron Transport 22. Which of the prosthetic groups listed can accept or donate either one or two electrons due to the stability of the semiquinone state? A) cytochrome c B) NADH C) CoQ D) [2Fe-2S] E) Rieske center Answer: C Section: 18.2.E Level of Difficulty: Moderate Learning Objective: Electron Transport 23. Which of the following statements is(are) TRUE about oxidative phosphorylation? I. Electron transport provides energy to pump protons into the intermembrane space. II. An electrochemical gradient is formed across the inner mitochondrial membrane. III. Potassium and sodium ions form an ionic gradient across the inner mitochondrial membrane. IV. Complexes I, II, III, IV actively transport protons into the intermembrane space during electron transport. A) I, II, III, IV B) I, II, IV C) II, III, IV D) I, IV E) II, IV Answer: B Section: 18.2.A-F; 18.3A Level of Difficulty: Moderate Learning Objective: Electron Transport; Oxidative Phosphorylation

24. Which of the following are TRUE statements regarding the structure of ATP synthase? A) It has a membrane-embedded component called F0 and a component found in the matrix referred to as F1. B) The g subunit acts as the proton "wire" allowing equilibration of the ion gradient. C) Research indicates that the F1 portion of the protein rotates in a circular counterclockwise direction. D) A and B 148

E) A, B, and C Answer: A Section: 18.3.B Level of Difficulty: Difficult Learning Objective: Oxidative Phosphorylation 25. The rate of oxidative phosphorylation I. is regulated by the availability of ADP and Pi. II. is reduced when the ratio of [NADH]/[NAD+] is high. III. increases with a higher concentration of reduced cytochrome c IV. is regulated by activity of the ADP-ATP translocator. A) I, II, IV B) I, III, IV C) II, III D) I, III, IV E) II, IV Answer: D Section: 18.4.A Level of Difficulty: Moderate Learning Objective: Control of Oxidative Metabolism 26. What is the net result of the successive reactions catalyzed by superoxide dismutase and catalase? A) conversion of the free radical O2×to H2O2, which is converted to water and O2 B) conversion of the free radical O2× to H2O2, which is converted to water and GSSG and water C) conversion of the free radical O2× to peroxide, which is converted to CO2 and water D) conversion of the free radical O2× to carbon dioxide and water E) none of the above Answer: A Section: 18.4.B Level of Difficulty: Difficult Learning Objective: Control of Oxidative Metabolism

27. Phosphate (Pi) is transported into the mitochondria from the cytosol by a phosphate carrier which is driven by the A) hydrolysis of ATP. B) simultaneous transport of H+ into the mitochondrion. C) simultaneous transport of ADP into the mitochondrion. D) simultaneous transport of H+ out of the mitochondrion. E) simultaneous transport of ATP out of the mitochondrion. Answer: B Section: 18.1.B 149

Level of Difficulty: Difficult Learning Objective: The Mitochondrion 28. Consider the following half-reactions:

eo¢ = –0.315 V eo¢ = 0.815 V

NAD+ + H+ + 2 e– « NADH 1/2 O2 + 2 H+ + 2 e– « H2O

What is the eo¢ for the following redox equation? O2 + 2 NADH + 2 H+ ® 2 H2O + 2 NAD+ A) –1.130 V B) –0.500 V C) +0.500 V D) +1.130 V E) none of the above Answer: D Section: 18.2.A Level of Difficulty: Difficult Learning Objective: Electron Transport 29. Cyanide (CN–) I. inhibition can be restored by addition of succinate. II. inhibition can be restored by addition of cytochrome c. III.inhibits electron transport which stops consumption of oxygen. IV. blocks transfer of electrons from CoQ to Complex III. A) I, III, IV B) I, III C) II, III, IV D) I only E) III only Answer: E Section: 18.2.B Level of Difficulty: Difficult Learning Objective: Electron Transport

30. Rotenone and amytal I. inhibition can be restored by addition of succinate II. inhibition can be restored by addition of cytochrome c. III. blocks consumption of oxygen. IV. blocks transfer of electrons from CoQ to Complex III. A) I, II, III, IV B) I, II, III C) II, III, IV D) III only E) IV only 150

Answer: B Section: 18.2.B Level of Difficulty: Difficult Learning Objective: Electron Transport 31. Antimycin A I. inhibition can be restored by addition of succinate. II. inhibition can be restored by addition of cytochrome c. III. blocks consumption of oxygen. IV. blocks transfer of electrons from CoQ to Complex III. A) I, II, III, IV B) I, II, III C) II, III, IV D) II, III E) III only Answer: C Section: 18.2.B Level of Difficulty: Difficult Learning Objective: Electron Transport 32. In the electron transport chain, FMN can adopt ____ oxidation state(s) and is capable of accepting or donating ____ electron(s). A) 2; 2 B) 2; 1 or 2 C) 3; 2 D) 3; 1 or 2 E) 3; 1 Answer: D Section: 18.2.C Level of Difficulty: Moderate Learning Objective: Electron Transport

33. Which of the following is TRUE regarding heme proteins? I. Heme groups are capable of transferring electrons across large distances provided that some molecular network exists as a "path." II. Heme groups are often buried in protein structure because the protein protects the heme and prevents it from indiscriminately transferring electrons. III. The rate of electron transfer from a reduced heme is physiologically significant. IV. Heme groups are often differentiated by their absorption spectrum. A) I, III B) I, III, IV. C) I, II D) II, IV E) I, II, III, IV Answer: E 151

Section: 18.2.E, Box 18-1 Level of Difficulty: Moderate Learning Objective: Electron Transport, Box 18-1 34. Which of the following best describes the function of cytochrome c oxidase? A) Cytochrome c oxidase oxidizes four consecutive cytochrome c molecules, via one-electron transfers, while simultaneously reducing one O2 to two H2O. B) Cytochrome c oxidase oxidizes two consecutive cytochrome c molecules, via two-electron transfers, while simultaneously reducing one O2 to two H2O. C) Cytochrome c oxidase oxidizes four consecutive cytochrome c molecules, via one-electron transfers, while simultaneously reducing two O2 to two H2O. D) Cytochrome c oxidase oxidizes two consecutive cytochrome c molecules, via two- electron transfers, while simultaneously reducing two O2 to two H2O. Answer: A Section: 18.2.F Level of Difficulty: Moderate Learning Objective: Electron Transport 35. Cyclonite is a poison that blocks electron transfer between cytochromes bL and bH. When this poison is added to a suspension of isolated mitochondria, and when spectroscopic analysis is performed, A) the coenzyme Q pool will be found in the reduced state, and cytochrome c will be found in the oxidized state. B) the coenzyme Q pool will be found in the oxidized state, and cytochrome c will be found in the reduced state. C) the coenzyme Q pool will be found in both oxidized & reduced states, and cytochrome c will be found in only one state. D) the coenzyme Q pool will be found in only one state, and cytochrome c will be found in both oxidized & reduced states. E) both the coenzyme Q pool and cytochrome c will be found in both oxidized & reduced states. Answer: A Section: 18.2.E Level of Difficulty: Difficult Learning Objective: Electron Transport

36. Which statement(s) concerning the mitochondrial F0F1 ATP synthase is FALSE? I. The F1 subunit includes rotating sets of ab dimers. II. The F0 subunit includes a ring of between 9 and 12 proton-carrying polypeptides. III. The F1 subunit undergoes a series of conformational changes throughout the course of reaction. A) I, II, III B) II, III 152

C) D) E)

I only III only None of the options (I – III) is false. Options I-IV are all true.

Answer: C Section: 18.3.B Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation 37. A poison that prevents the transfer of electrons from the last [Fe-S] cluster of Complex I to coenzyme Q is added to a suspension of actively respiring mitochondria. Which of the following will be observed? A) ATP production would be impaired due to the uncoupling of oxidative phosphorylation from electron transport. B) ATP production would be reduced due to inhibition of the CoQ subunit of ATP synthase. C) ATP production would be reduced due to a decrease in the number of protons pumped out of the mitochondrial matrix. D) ATP production would be halted completely due to the block in electron transport through the electron transport chain. E) ATP production would be maintained at the normal rate due to functional overlap between Complex I and Complex II. Answer: C Section: 18.2, 18.3 Level of Difficulty: Difficult Learning Objective: Electron Transport, Oxidative Phosphorylation 38. The effects of a poison on actively respiring mitochondria are being studied to determine its mode of action. When the poison is added, every component of the electron transport chain is found to be in its reduced form based on spectroscopic analysis, and ATP production ceases entirely. It is reasoned that the poison is either blocking the final transfer of electrons to oxygen or is blocking the ATP synthase. Which of the following experiments will help unravel this dilemma? A) Add a second blocking agent to interfere with either Complex I or Complex II along with the poison. B) Add an artificial electron donor along with the poison. C) Add an uncoupling agent along with the poison. D) Any of the above would allow differentiation between these two possibilities. E) None of the above will help distinguish between these two possibilities. Answer: C Section: 18.2, 18.3 Level of Difficulty: Difficult Learning Objective: Electron Transport, Oxidative Phosphorylation

39. Which statement concerning Complex II of the electron transport chain is FALSE? 153

I. This complex oxidizes FADH2 and reduces coenzyme Q. II. This complex includes the covalently bound enzyme succinate dehydrogenase. III. This complex pumps protons from the matrix to the intermembrane space. IV. This complex also oxidizes succinate to fumarate in the citric acid cycle. A) I, II B) II only C) II, III D) III only E) IV only Answer: D Section: 18.2.D Level of Difficulty: Moderate Learning Objective: Electron Transport 40. In theory how many protons could be pumped under standard state conditions by Complex III per mol of CoQ oxidized, considering the following information? (NOTE: mt = mitochondria) coenzyme Q + 2H+ + 2 e- → coenzyme QH2

eo¢ ' ≈ 0.040 V eo¢ ≈ 0.270 V

cytochrome c (Fe3+) + e- → cytochrome c (Fe2+) H+ (outside mt) → H+ (inside mt) DG ≈ -20kJ/mol Faraday constant (F) ≈ 100 kJ/Vmol ∆Gº' = -nF∆E0' A) four or less protons B) greater than four protons but less than or equal to six protons C) greater than six protons but less than or equal to eight protons D) greater than 8 protons E) Cannot be determined from the information provided. Answer: B Section: 18.2.A Level of Difficulty: Difficult Learning Objective: Electron Transport 41. ATP forms (is produced) I. upon transition from the loose to the tight form of the α and β subunit complex of ATP synthase. II. as a result of the flux of electrons through the channel formed by Fo III. as a result of the positive ions pumped into the matrix of the mitochondrion. A) B) C) D) E) Answer: D

I, II, III II, III I, III I only II only

154

Section: 18.3.A, B Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation 42. The structure of ATP synthase changes in conformation as a result of A) the rotation of the α and β subunits. B) the rotation of the β subunit. C) the rotation of ATP. D) the rotation of the g subunit. E) all of the above. Answer: D Section: 18.3.B Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation 43. In the electron transport chain, electrons are passed from redox center to redox center ____. A) spontaneously due to the redox potential gradient. B) in an ATP dependent fashion. C) as a result of the addition of free energy. D) as a result of the proton gradient. E) with the assistance of a carrier protein. Answer: A Section: 18.2.B Level of Difficulty: Moderate Learning Objective: Electron Transport 44. Electrons from FADH2 are delivered to ____ and electrons from NADH are delivered to ____ of the electron transport chain. A) Complex I; Complex II B) Complex I; Complex III C) Complex II; Complex III D) Complex II; Complex I E) Complex I; Complex IV Answer: D Section: 18.2.C, D Level of Difficulty: Easy Learning Objective: Electron Transport 45. All of the following inhibit electron transport EXCEPT A) oxaloacetate B) rotenone C) anitimycin A D) cyanide E) All of the above inhibit electron transport, 155

Answer: A Section: 18.2.B Level of Difficulty: Easy Learning Objective: Electron Transport 46. Which conformation of the active sites in ATP synthase allows binding of substrates? A) L state B) O state C) T state D) C state E) A and B Answer: A Section: 18.3.B Level of Difficulty: Easy Learning Objective: Oxidative Phosphorylation 47. ___ the gradient with the synthesis of ATP via oxidative phosphorylation. I. The Fo portion of ATP synthase II. Thermogenin uncouples III. 2,4-dinitrophenol (DNP) dissipates IV. An ionophore capable of transporting potassium ions across the membrane A) I, II, III, IV B) II, III, IV C) II, III D) II only E) I, IV Answer: C Section: 18.3.B, D Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation 48. Use the table below to rank the redox centers in order to produce a favorable electron flow.

A) B) C) D)

Redox Center

eo¢

D F Q C Z

- 0.002 - 0.198 - 0.225 - 0.053 + 0.002

D, Q, F, C, Z Q, F, C, D, Z Z, Q, F, C, D Z, F, C, D, Q 156

E) Z, Q, C, Q, D Answer: B Section: 18.2.B Level of Difficulty: Moderate Learning Objective: Electron Transport 49. In a newly discovered electron transport complex a researcher has identified the redox center Fe-S, cytochrome c, and coenzyme Q. The researcher also knows that this complex ultimately passes its electrons to oxygen. What is most likely the redox center which completes this task? A) Fe-S B) 2Fe-2S C) coenzyme Q D) cytochrome c E) None of the above Answer: D Section: 18.2.B Level of Difficulty: Difficult Learning Objective: Electron Transport 50. An animal with the UCP-1 protein would I. generate excess heat. II. have lower energy levels. III. generate ATP efficiently via oxidative phosphorylation. A) I B) I, II C) I, II, III D) I, III E) II, III Answer: B Section: 18.3.D, Box 18-4 Level of Difficulty: Moderate Learning Objective: Oxidative Phosphorylation, Box 18-4

157

Chapter 19: Photosynthesis Matching Choose the correct answer from the list below. Not all the answers will be used. A) photosynthetic reaction center B) tyrosyl radical C) thylakoid D) H2O E) CF1CF0 F) Z-scheme G) NADPH H) plastoquinone I) H+ J) RuBP carboxylase K) CO2 L) 2 OH– M) O2 1. The light reactions of photosynthesis occur in the _____ membrane of the chloroplast. Ans: C Section: 19.1.A Level of Difficulty: Easy Learning Objective: Chloroplasts 2. Light-harvesting antennas gather photons and pass the energy to the ______ . Ans: A Section: 19.1.B Level of Difficulty: Easy Learning Objective: Chloroplasts 3. The electron pathway from water to NADP+, referred to as the ____, allows two loci for photochemical events. Ans: F Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 4. ______ carries electrons between PSII and PSI. Ans: H Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 5. PSII oxidizes ____. Ans: D 151

Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 6. The electrons abstracted by the oxygen evolving center (OEC) are relayed to a ______. Ans: B Section: 19.2 Level of Difficulty: easy Learning Objective: The Light Reactions 7. Electron transport through the cytochrome b6f complex generates a _____ gradient. Ans: I Section: 19.2 Level of Difficulty: easy Learning Objective: The Light Reactions 8. The chloroplast ATP synthase is also called ______. Ans: E Section: 19.2.D Level of Difficulty: easy Learning Objective: The Light Reactions 9. In the Calvin cycle, ______ is “fixed” to generate carbohydrate molecules. Ans: K Section: 19.3.A Level of Difficulty: easy Learning Objective: The Dark Reactions 10. The most abundant biological catalyst is ______. Ans: J Section: 19.3.A Level of Difficulty: easy Learning Objective: The Dark Reactions

Multiple Choice 11. Which of the following is the site of ATP synthesis in chloroplasts? A) B)

smooth outer membrane inner membrane space 152

C) stroma D) thylakoid membrane E) thylakoid compartment Answer: D Section: 19.2.D Level of Difficulty: Easy Learning Objective: Chloroplasts 12. An assembly of antenna pigments, or light harvesting complex, A) B) C) D)

are often cytosolic proteins containing multiple chlorophylls. are nearly identical in structure from species to species. are likely optimized to allow efficient transfer of energy throughout pigments. contain an alternating structure of lipid molecules and chlorophylls allowing maximal incorporation in the membrane. none of the above

E) Answer: C Section: 19.1.B Level of Difficulty: Moderate Learning Objective: Chloroplasts

13. Electron transfer in PbRC is approximately ____ efficient. A) B) C) D) E)

25%. 50%. 75%. 96%. 100%.

Answer: E Section: 19.2.B Level of Difficulty: Easy Learning Objective: The Light Reactions 14. Light dependent ATP synthesis is called A) B) C) D) E)

photophosphorylation. substrate-level phosphorylation. oxidative phosphorylation. pyrophosphorylation. none of the above

Answer: A Section: 19.2.D Level of Difficulty: Easy Learning Objective: The Light Reactions 15. The photosynthetic electron transport system includes the transmembrane complexes PSI, PSII and A) B)

PSIII. cytochrome a3. 153

C) D) E)

cytochrome b6f. cytochrome c. proton translocating ATP synthase

Answer: C Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 16. Which of the following is TRUE regarding the oxygen evolving complex (OEC)? I. All states have high reduction potentials that exceed that of water. II. The OEC is made up of magnesium atoms that bridge oxygen atoms together. III. Current evidence indicates that the OEC cycles between five states in which the metal atoms exist in a variety of combinations of oxidation states. IV. During the course of reaction, protons and electrons are abstracted from one water molecule yielding one O2. A) I, II, III, IV B) I, III C) I, II D) III only E) III, IV Answer: B Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions 17. In the dark reactions of photosynthesis, glyceraldehyde-3-phosphate is converted to dihydroxyacetone phosphate by___. A) B) C) D) E)

phosphoglucoisomerase triose phosphate isomerase glyceraldehyde-3-phosphate dehydrogenase phosphotriose epimerase phosphoglycerate kinase

Answer: B Section: 19.3.A Level of Difficulty: Easy Learning Objective: The Dark Reactions 18. Synthesis of sucrose requires which of the following? I. glyceraldehyde-3-phosphate and/or dihydroxyacetone phosphate II. sucrose phosphate kinase III. sucrose phosphate phosphatase IV. UTP A) I, II, III, IV B) I, II, IV C) I, III, IV D) II, III 154

E) II, III, IV Answer: C Section: 19.3.B Level of Difficulty: Moderate Learning Objective: The Dark Reactions 19.

Which statement about carotenoids is FALSE? A) B) C) D) E)

b-Carotene is an example of a common accessory pigment.. Carotenoids are often used ensure complete coverage of the spectrum. Carotenoids are contained in the prosthetic ring structure of chlorophylls. b-Carotene aides in light absorption for photosynthesis.. All of the above statements are true.

Answer: C Section: 19.1.B Level of Difficulty: Moderate Learning Objective: Chloroplasts 20.

The groups that initially absorb light in the Rps. viridis photosynthetic reaction center are observed to be arranged with ______, and are called the ______. A) B) C) D) E)

twofold symmetry, special pair anti-parallel symmetry, RHC trifold symmetry, tri-harvest center shared menaquinone prosthetic groups, shared pair none of the above

Answer: A Section: 19.2.B Level of Difficulty: Moderate Learning Objective: The Light Reactions 21.

In plants and cyanobacteria, PSII ______, and PSI ______. A) B) C) D) E)

oxidizes H2O, reduces NAD+ oxidizes H2O, reduces NADP+ oxidizes O2, reduces FAD oxidizes H2O, reduces FAD none of the above are true

Answer: B Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 22.

The oxygen evolving center I. is a part of PSI known as the water splitting enzyme. II. breaks two H2O molecules into four protons, four electrons and O2. III. requires four light-dependent reactions to generate O2. 155

IV. frees an electron from oxygen for replacement of the photooxidized electron in P680. A) I, II, III, IV B) I, II C) II, III, IV D) II, III E) I, IV Answer: D Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions 23.

Which of the following are possible functions for the activated electrons from PSI? I. reduction of NAD+ II. reduction of NADP+ III. formation of ATP IV. formation of a proton gradient V. formation of an ionic gradient A) B) C) D) E)

I, II I, III II, III II, IV I, V

Answer: D Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions

24.

The major sugar transported to nonphotosynthesizing cells is A) B) C) D) E)

sucrose. fructose. UDP-glucose. fructose-6-phosphate. glyceraldehyde-3-phosphate.

Answer: A Section: 19.3.B Level of Difficulty: Easy Learning Objective: The Dark Reactions 25.

Which of the following is(are) FALSE about photorespiration? A) B)

RuBP carboxylase oxygenates ribulose bisphosphate to form 2phosphoglycolate and 3-phosphoglycerate. The reaction provides an additional mechanism to generate ATP and NADPH. 156

C) D) E)

The C4 cycle minimizes the need for photorespiration. CO2 and O2 compete for binding the RuBP carboxylase active site. Photorespiration is thought to function as a protective mechanism to allow dissipation of unused energy.

Answer: B Section: 19.3.D Level of Difficulty: Moderate Learning Objective: The Dark Reactions 26. Which of the following would decrease the activity of RuBP carboxylase? I. a change in the pH of the stroma from 6.7 to 7.9 II. an increase in the concentration of Mn2+ in the stroma III. an uncoupling protein embedded in the thylakoid membrane IV. presence of the transition state analog CA1P A) I, II, III, IV B) I, III, IV C) II, III, IV D) III, IV E) I, III Answer: D Section: 19.3.C Level of Difficulty: Difficult Learning Objective: The Dark Reactions

27.

Which of the following statements about photosynthetic pigments is FALSE? A) B) C) D) E)

Carotenoid pigments absorb light in the 400-500 nm range Chlorophylls a and b absorb both long and short wavelength light Phycoerythrin absorbs blue and green light. Phycocyanin absorbs yellow light around the 600 nm range Bacteriochlorophyll a overlaps the absorption wavelengths of chlorophylls a and b

Answer: E Section: 19.1.B Level of Difficulty: Moderate Learning Objective: Chloroplasts 28. Which of the following statements about the OEC is FALSE? I. It is located at the lumenal surface of the D1 subunit II. It has a low reduction potential in all states III. It contains Mn4CaO4 or Mn4CaO5 IV. Part of the cluster is liganded to the amino acids Asp and Glu A) II, III B) II only C) III only D) II, IV 157

E) II, III Answer: B Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions 29. Which mechanism is the method by which antenna complex chlorophylls funneled energy toward the reaction centers? A) B) C) D) E)

fluorescence internal conversion resonance energy transfer (exciton transfer) electron transfer none of the above

Answer: C Section: 19.2.A Level of Difficulty: Easy Learning Objective: The Light Reactions 30. Which of the following statements concerning Z-scheme photosynthesis is TRUE? A) B) C) D) E)

Water is reduced by a Mn-containing cluster. Electrons are carried by lipid-soluble plastoquinones, which participate in a Q cycle. Ferredoxin oxidizes NADPH. Transfer occurs stepwise from PSI to PSII with increasing potential. A proton gradient is not generated to drive ATP synthesis.

Answer: B Section: 19.2.C Level of Difficulty: moderate Learning Objective: The Light Reactions 31. Which of the following statements concerning crassulacean acid metabolism (CAM) is TRUE? A) B) C) D)

It allows desert plants to collect CO2 at night for use during the day in the Calvin cycle. Desert plants utilize CAM to transport CO2 to bundle sheath cells where the Calvin cycle takes place. It permanently fixes CO2 in place of RuBisCo, avoiding the oxygenase reaction. CAM facilitates transport of photorespiration products back to the Calvin cycle. All of the above are true.

E) Answer: A Section: 19.3.D Level of Difficulty: Difficult Learning Objective: The Dark Reactions

158

32. A houseplant has been mutated so that its chlorophyll is more efficient at fluorescence than normal. What will be the likely result? A) B) C) D) E)

Both forms of the light reactions will improve and the plant will better tolerate low light conditions. Z-scheme photosynthesis will be favored over cyclic photophosphorylation, making additional illumination at long wavelengths necessary. Cyclic photophosphorylation will be favored over Z-scheme, making additional illumination at short wavelengths necessary. Both forms of the light reaction will be impaired and the plant will be less tolerant to low light conditions. none of the above

Answer: D Section: 19.2.A Level of Difficulty: Difficult Learning Objective: The Light Reactions

33. A houseplant is treated with a compound that inactivates plastocyanin. Which of following might allow the plant to survive? A) B) C) D) E)

supplement with light with a wavelength of 680 nm or less supplement with light with a wavelength greater than 680 nm addition of an uncoupling agent thus allowing ATP synthesis to resume addition of an oxidant capable of oxidizing NADPH, thus decreasing photorespiration. none of the above

Answer: E Section: 19.2.D Level of Difficulty: Difficult Learning Objective: The Light Reactions 34. It is believed that the ratio of cyclic photophosphorylation to Z-scheme photosynthesis changes in response to metabolic demands. How would this ratio in chloroplasts performing the following reaction compare to that in chloroplasts performing only the Calvin cycle? Calvin cycle + reduction of nitrite (NO2-) to NH3 A) B) C)

The ratio of cyclic photophosphotylation to Z-scheme is increased in chloroplasts performing the above reaction compared to those performing only the Calvin cycle The ratio of cyclic photophosphotylation to Z-scheme is decreased in chloroplasts performing the above reaction compared to those performing only the Calvin cycle The ratio of cyclic photophosphotylation to Z-scheme is depends primarily on the level of light available and would therefore not be altered by the above reaction 159

D) E)

The ratio of cyclic photophosphotylation to Z-scheme is depends primarily on the availability of plastocyanin and would therefore not be altered by the above reaction none of the above

Answer: B Section: 19.2.D Level of Difficulty: Difficult Learning Objective: The Light Reactions 35. The major difference between pheophytins and chlorophylls is A) B) C) D) E)

pheophytins contain iron in their centers while chlorophylls contain magnesium. chlorophylls contain iron in their centers while pheophytins contain magnesium. heophytins contain no metal ion in their centers. pheophytins are linear, rather than cyclic tetrapyrroles. none of the above

Answer: C Section: 19.2.C Level of Difficulty: Easy Learning Objective: The Light Reactions 36. Which of the following statements concerning cyclic photophosphorylation is FALSE? A) B) C) D) E)

Only PSI is used. Plastocyanin is oxidized by the photosystem. NADPH donates electrons to the plastoquinone pool. Ferredoxin accepts electrons from the photosystem and reduces the cytochrome bf complex. This system is used to pump protons and form an electrochemical gradient to drive the formation of ATP.

Answer: C Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions 37. Binding of oxygen to RuBisCo A) B) C) D) E)

destroys enzymatic function because oxygen is a suicide inhibitor of the enzyme. targets the enzyme for proteolytic degradation. decreases the enzyme's Km for oxygen since binding is cooperative. activates the enzyme for carbon fixing reactions. costs the cell ATP since energy is required to replace intermediates necessary for carbon fixation.

Answer: E Section: 19.3.D 160

Level of Difficulty: Easy Learning Objective: The Dark Reactions 38. Which of the following correctly identifies the products and amounts produced from noncyclic electron transport? A) B) C) D) E)

4 ATP per O2 plus 2 NADPH per 4 electrons liberated from 2 H2O 5 ATP per O2 plus 1 NADPH per 4 electrons liberated from 2 H2O 2.5 ATP per O2 plus 2 NADPH per 2 electrons liberated from 2 H2O 9 ATP per O2 plus 2 NADPH per 4 electrons liberated from 2 H2O 5 ATP equivalents

Answer: E Section: 19.2.D Level of Difficulty: Moderate Learning Objective: The Light Reactions 39. Based on comparison of oxidative phosphorylation to photophosphoylation, which of the following is TRUE? A) B) C) D) E)

Photophosphoylation cannot be uncoupled by an ionophore like can be done with oxidative phosphorylation. The formation of a proton gradient is required for adequate function of both photoand oxidative phosphorylation. Although sequence similarities exist between the ATP synthases from each process, little structural similarity is observed. Photophosphorylation is not dependent on spontaneous electron flow whereas oxidative phosphorylation requires that electron flow be spontaneous. None of the above is true.

Answer: B Section: 19.2.D Level of Difficulty: Moderate Learning Objective: The Light Reactions 40. A radioactive labeled carbon entering the Calvin cycle as 14CO2 A) B) C) D) E)

would be removed from the cycle as various carbohydrate side products in the first round of the cycle. could be identified only in the triose intermediates within the cycle. would only be observed in intermediates following three rounds of the cycle. could be observed in any of the intermediates within the cycle during the first or subsequent rounds of the cycle. would be rapidly removed by transketolase catalyzed reactions.

Answer: D Section: 19.3.A Level of Difficulty: Moderate Learning Objective: The Dark Reactions 161

41. Synthesis of starch requires I. ATP II. glucose-1-phosphate III. ADP-glucose phosphatase IV. ADP-glucose A) I, II, III B) II, III, IV C) I, III, IV D) I, II, IV E) II, III Answer: D Section: 19.3.B Level of Difficulty: Easy Learning Objective: The Dark Reactions 42. Which of the following correctly represents the Q cycle? (Note: Portions are omitted for simplicity) A)

162

Answer: B Section: 19.2.C Level of Difficulty: Moderate Learning Objective: The Light Reactions 43. In photorespiration, reduction of hydroxypyruvate to glycerate requires ____ and occurs in the ____. A) NADPH; mitochondrion B) NADH; peroxisome C) NADPH; chloroplast D) NADH; chloroplast E) none of the above Answer: B Section: 19.3.D Level of Difficulty: Easy Learning Objective: The Dark Reactions 44. Which of the following is TRUE regarding the difference between chlorophyll structures and heme? A) B) C) D)

Chlorophyll structures contain copper rather than iron. Chlorophyll structures typically have five rings while heme typically has four. Chlorophyll often has fewer R groups attached to the ring system that heme. Chlorophyll metal atoms coordinate to the nitrogen atoms from the ring where as heme iron atoms coordinate to carbon atoms. all of the above

E) Answer: B Section: 19.1.B Level of Difficulty: Easy Learning Objective: Chloroplasts

163

45. The protein which passes electrons to NADP+ thus forming the NADPH generated from noncyclic electron transport is A) ferridoxin-NADP+ reductase. B) ferridoxin NADPH dehydrogenase. C) ferridoxin FAD dehydrogenase. D) FAD reductase. E) FAD dehydrogenase. Answer: A Section: 19.2C Level of Difficulty: Easy Learning Objective: The Light Reactions 46. Electrons from FB in PSI that follow the cyclic pathways are returned from ____ via ____ to the plastoquinone pool. A) plastocyanin; plastoquinone B) PSI; cytochrome b6 C) PSI; plastoquinone D) plastocyanin; cytochrome b6 E) cytochrome b6; plastoquinone Answer: B Section: 19.2C Level of Difficulty: Moderate Learning Objective: The Light Reactions 47. Electrons abstracted from water by ___ are relayed to ___ via formation of a ____. A) OEC; P680+; plastoquinone B) PSII; cytochrome b6; plastoquinone C) OEC; P680+; tyrosyl radical D) OEC; cytochrome b6; tyrosyl radical E) OEC; P960+; tyrosyl radical Answer: C Section: 19.2C Level of Difficulty: Easy Learning Objective: The Light Reactions 48. Light activation of P680 results in which of the following? I. electron transfer as follows: QA à QB àChlα àPheoα II. electron transfer from PSI directly back to the Pheoα-QA complex III. reduction of S4 of the OEC to S1 of the OEC IV. reduction of cytochrome b6f A) I, III, IV B) I, II C) II, III D) I only E) IV only 164

Answer: E Section: 19.2C Level of Difficulty: Moderate Learning Objective: The Light Reactions 49. The redox centers PSII, PbRC, PbRC from Rps. viridis, and cytochrome b6f A) B)

have identical prosthetic groups that differ only in sequence of arrangement and spatial orientation. have some degree of symmetry either based on their prosthetic groups or based on tertiary protein structure. all become reduced due to activity of the OEC. all of the above none of the above

C) D) E) Answer: B Section: 19.2.B-C Level of Difficulty: Moderate Learning Objective: The Light Reactions

50. Which of the following is a product of the Calvin cycle? I. ATP II. Glyceraldehyde-3-phosphate III. NADPH IV. CO2 A) I only B) I, III C) II only D) II, IV E) I, III, IV Answer: C Section: 19.3.A Level of Difficulty: Easy Learning Objective: The Dark Reactions

165

Chapter 20: Lipid Metabolism Matching Choose the correct answer from the list. Not all the answers will be used. A) HDL B) propionyl-CoA C) LDL D) Dihydroxyacetone phosphate E) malonyl-CoA F) ACP G) chylomicrons H) phosphopantetheine I) flavin J) albumin K) ketone bodies L) cholesterol 1. Lipoproteins formed in the intestinal mucosal cells are called ________. Ans: G Section: 20.1.B Level of Difficulty: Easy Learning Objective: Lipid Digestion, Absorption, and Transport 2. Cholesterol and other lipids are transported from tissues to the liver by ________. Ans: A Section: 20.1.B Level of Difficulty: Easy Learning Objective: Lipid Digestion, Absorption, and Transport 3. The glycerol backbone of triacylglycerols is catabolized to ________ . Ans: D Section: 20.1.B Level of Difficulty: Easy Learning Objective: Lipid Digestion, Absorption, and Transport 4. Free fatty acids bind to ________ for circulation in the bloodstream. Ans: J Section: 20.2 Level of Difficulty: Easy Learning Objective: Fatty Acid Oxidation 5. Cells take up ____ by receptor mediated endocytosis. Ans: C Section: 20.1.B Level of Difficulty: Easy Learning Objective: Fatty Acid Oxidation 159

6. The b oxidation of odd-numbered fatty acids results in ________ as a final product. Ans: B Section: 20.2.E Level of Difficulty: Easy Learning Objective: Fatty Acid Oxidation 7. The molecules acetoacetate, acetone, and D-b-hydroxybutyrate are metabolic fuels termed ________. Ans: K Section: 20.3 Level of Difficulty: Easy Learning Objective: Ketone Bodies 8. Acyl carrier protein (ACP) contains a ________ prosthetic group. Ans: H Section: 20.4.C Level of Difficulty: Easy Learning Objective: Fatty Acid Biosynthesis 9. Fatty acid synthesis requires both acetyl-CoA and ________ as initiator molecules. Ans: E Section: 20.4.B Level of Difficulty: Easy Learning Objective: Fatty Acid Biosynthesis 10. ________ is formed from ordered sequence of condensation of isoprene units. Ans: L Section: 20.7.A Level of Difficulty: Easy Learning Objective: Cholesterol Metabolism

Multiple Choice 11. Digestion of triacylglycerols is aided by the cholesterol derivatives synthesized by the liver known as A) B) C) D) E)

bile acids. lipoproteins. lanosterols. chylomicrons. colipases.

Answer: A 160

Section: 20.1.A Level of Difficulty: Moderate Learning Objective: Lipid Digestion, Absorption, and Transport 12. Which of the following would result in a net increase in uptake of LDL by the liver? A) increased availability of LDL receptors B) high levels of cholesterol synthesis C) increased availability of clathrin triskelions D) all of the above E) none of the above Answer: B Section: 20.1.B Level of Difficulty: Difficult Learning Objective: Lipid Digestion, Absorption, and Transport 13. Which of the following is required for entry of fatty acids into the oxidation pathway? I. priming via the enzyme acyl CoA synthetase II. conservation of free energy from ATP hydrolysis by use of a thioester linkage III. transport to the cytosol for oxidation via a carnitine carrier protein IV. hydrolysis of carnitine palmitoyl transfer protein A) I, II B) I, II, III C) I, II, III, IV D) III, IV E) I, III Answer: A Section: 20.2.A Level of Difficulty: Difficult Learning Objective: Fatty Acid Oxidation

14. Which of the following vitamins is part of the prosthetic group 5¢-deoxyadenosylcobalamin? A) B) C) D) E)

B1 B2 B6 B12 none of the above

Answer: D Section: 20.2.E Level of Difficulty: Easy 161

Learning Objective: Fatty Acid Oxidation 15. ______, a condition in which acetoacetate production exceeds it metabolism and results in a sweet breath odor due to nonenyzmatic ___ of acetoacetate to _____. A) B) C) D) E)

ketosis; decarboxylation; hydroxylbutryate ketosis; carboxylation; hydroxylbutryate ketosis; carboxylation; acetone glyceroneogenesis; decarboxylation; hydroxylbutryate glyceroneogenesis; decarboxylation; acetone

Answer: C Section: 20.3 Level of Difficulty: Moderate Learning Objective: Ketone Bodies 16. Triacylglycerols are synthesized by ____ during times of starvation via a process known as ____. A) B) C) D) E)

Dihydroxyacetone phosphate; ketosis Dihydroxyacetone phosphate; glyceroneogenesis acetyl CoA; ketosis acetyl CoA; glyceroneogenesis ketone bodies; ketosis

Answer: B Section: 20.4.E Level of Difficulty: Moderate Learning Objective: Fatty Acid Biosynthesis 17. Two phosphatidylglycerol molecules condense to form the molecule ______, and glycerol is eliminated as the side product. A) B) C) D) E)

phosphatidic acid cardiolipin plasmalogen sphingomyelin squalene

Answer: B Section: 20.6.B Level of Difficulty: Easy Learning Objective: Synthesis of Other Lipids 18. The activity of lipases is controlled in part by a process known as ____ which functions effectively due to the ____ where lipases are active. A) B) C) D) E)

interfacial activation; lipid-water interface lipase activation; lipid-water interface lipase activation; bile salt-water interface micelle activation; water-salt interface none of the above

Answer: A 162

Section: 20.1.A Level of Difficulty: Moderate Learning Objective: Lipid Digestion, Absorption, and Transport 19. Which of the following accurately ranks lipoproteins from highest to lowest density? A) chylomicrons > HDL > LDL > IDL > VLDL B) HDL > IDL > LDL > VLDL > chylomicrons C) HDL > LDL > IDL > VLDL > chylomicrons D) chylomicrons > VLDL > IDL > LDL > HDL E) VLDL > IDL > LDL > HDL > chylomicrons Answer: C Section: 20.1.B Level of Difficulty: Moderate Learning Objective: Lipid Digestion, Absorption, and Transport 20. Which of the following statements about apolipoproteins (with the possible exception of apoB-100) is TRUE? I. The apolipoproteins are water-soluble and loosely associate with the lipoproteins. II. The apolipoproteins contain helices with hydrophobic and hydrophilic groups on opposite sides of the helical cylinder. III. The apolipoproteins are synthesized in the intestinal tissues. IV. The apolipoproteins appear to float on the surface of phospholipids. A) I only B) I and II C) III, IV D) I, II, III E) I, II, IV Answer: E Section: 20.1.B Level of Difficulty: Moderate Learning Objective: Lipid Digestion, Absorption, and Transport

21. Knoop’s experiments with fatty acids A) B) C) D) E)

involved the novel use of chemical labels to elucidate metabolic mechanisms. demonstrated that fatty acids are broken down by two carbons at a time by oxidation at the ω carbon. demonstrated a distinct difference in the mechanism of odd chain versus. even chain fatty acid oxidation. A and B A, B, and C 163

Answer: A Section: 20.2 Level of Difficulty: Difficult Learning Objective: Fatty Acid Oxidation 22. Which of the following statements about peroxisomes is FALSE? A) B) C) D) E)

b oxidation in peroxisomes can shorten very long fatty acids. Mammalian peroxisomes can synthesize some lipids, including bile salts. In plants, peroxisomes and glyoxysomes serve as the site of b oxidation. Long chain fatty acids are transported into the peroxisome via a carnitine carrier protein where they are activated for oxidation. b oxidation in peroxisomes varies slightly from the mitochondrial process.

Answer: D Section: 20.2.F Level of Difficulty: Difficult Learning Objective: Fatty Acid Oxidation 23. An important structural lipid found in nerve cell membranes, ______, is a type of ______. A) B) C) D) E)

sphingomyelin, phospholipid phosphatidylcholine, phospholipid palmitate, glycerophospholipid glucagon, hormone none of the above

Answer: A Section: 20.6.B Level of Difficulty: Moderate Learning Objective: Synthesis of Other Lipids 24. Pain and inflammation are triggered by ___ which are synthesized by an enzyme inhibited by ____. A) B) C) D) E)

cardiolipins; aspirin prostaglandins; aspirin analgesics; statins prostaglandins; COX-1 cyclooxygen; NSAIDS

Answer: B Section: 20.6.C Level of Difficulty: Moderate Learning Objective: Synthesis of Other Lipids 25. Cholesterol is a precursor to I. prostaglandins II. vitamin K 164

III. steroid hormones such as androgens IV. bile acids A) I, III, IV B) I, II, III, IV C) III only D) IV only E) III, IV Answer: E Section: 20.7 Level of Difficulty: Easy Learning Objective: Cholesterol Metabolism 26. Which of the following best describes arachidonic acid? A) B) C) D) E)

a 20-carbon isoprene-based intermediate of cholesterol synthesis a 20-carbon fatty acid essential for cholesterol synthesis a 20-carbon isoprene-based compound used for synthesis of prostaglandins a 20-carbon fatty acid used for synthesis of prostaglandins a 2-carbon compound that functions in conjunction with a fatty acid carrier protein for transport of primed fatty acids

Answer: D Section: 20.6.C Level of Difficulty: Easy Learning Objective: Synthesis of Other Lipids 27. Which of the following compounds are required to make sphingosine? I. palmitoyl-CoA II. serine III. acetyl-CoA IV. isoprene V. arachidonic acid A) I, II B) I, III C) II, IV D) IV, V E) II, V Answer: A Section: 20.6.B Level of Difficulty: Moderate Learning Objective: Synthesis of Other Lipids

28. In which location listed below does the following reaction take place? A) B)

HMG-CoA → acetoacetate + Acetyl-CoA cytosol of cardiomyocytes mitochondria of cardiomyocytes 165

C) D) E)

cytosol of liver cells mitochondria of liver cells all of the above

Answer: D Section: 20.3 Level of Difficulty: Moderate Learning Objective: Ketone Bodies 29. In which cellular compartment does the following reaction take place? HMG-CoA + 2 NADPH → mevalonate + 2 NADP+ + Acetyl-CoA A) cytosol of liver cells B) mitochondria of liver cells C) cells in the intestinal lumen D) lysosomal fluid E) all of the above Answer: A Section: 20.7.A Level of Difficulty: Moderate Learning Objective: Cholesterol Metabolism 30. Which enzyme catalyses the key regulatory step of cholesterol synthesis? A) B) C) D) E)

b-ketothiolase HMG-CoA synthase HMG-CoA reductase mevalonate-5-phosphotransferase phenyltransferase

Answer: C Section: 20.7.A Level of Difficulty: Easy Learning Objective: Cholesterol Metabolism 31. Sphinganine is an intermediate in the synthesis of which of the following? I. ceramides II. spingomyelins III. cerebrosides IV. prostaglandins A) I only B) I, II C) I, II, III D) II, III E) I, II, IV Answer: C Section: 20.6.B Level of Difficulty: Difficult 166

Learning Objective: Synthesis of Other Lipids 32. Which of the following is TRUE regarding the enzyme acetyl-CoA carboxylase? I. It catalyzes the first committed step in fatty acid oxidation. II. It requires S-adenosylmethionine. III. It produces malonyl CoA IV. It uses acetyl CoA A) I, II, III, IV B) I only C) I, III, IV D) III, IV E) III only Answer: D Section: 20.4.B Level of Difficulty: Difficult Learning Objective: Fatty Acid Biosynthesis 33. What is the net production of ATP from complete catabolism of the following fatty acid to CO2 and H2O? A) B) C) D) E)

< 50 51 – 90 91 - 120 121 - 150 151 +

C OH

Answer: B Section: 20.4.B Level of Difficulty: Moderate Learning Objective: Fatty Acid Biosynthesis 34. Which of the following could be produced by the reaction of two or more of phosphatidic acids with two or more glycerol-3-phosphates? I. phosphatidylglycerol II. cardiolipin III. phosphatidylinositol IV. gangliosides A) I, II, III, IV B) II, III C) I, III D) I, II E) III only

Answer: D Section: 20.6.A Level of Difficulty: Difficult 167

Learning Objective: Synthesis of Other Lipids 35. The mechanism of the condensing enzyme (KS) of fatty acid synthase is best described as A) B) C) D) E)

base catalysis using a glu residue in the active site acid catalysis using a glu residue in the active site base catalysis using a cys residue in the active site acid catalysis using a cys residue in the active site covalent catalysis using a cys residue in the active site

Answer: E Section: 20.4.C Level of Difficulty: Difficult Learning Objective: Fatty Acid Biosynthesis 36. Which statement concerning fatty acid synthesis is TRUE? I. The process occurs in the cytosol. II. In eukaryotes, the process occurs on a single large protein. III. The growing acyl chain is carried on an acyl carrier protein instead of coenzyme A. IV. The process requires two NADPH per acetyl group (2 carbons) added. A) I, II B) II, III C) I, II, III, IV D) III, IV E) I, III, IV Answer: C Section: 20.4.C Level of Difficulty: Moderate Learning Objective: Fatty Acid Biosynthesis 37. Which of the following diets would most likely promote the formation of ketone bodies? A) B) C) D) E)

high simple carbohydrates, low fat high complex carbohydrates, high fructose high fat, high protein, low carbohydrate low fat, high protein, high complex carbohydrates high fructose; high whole grain carbohydrates

Answer: C Section: 20.3 Level of Difficulty: Difficult Learning Objective: Ketone Bodies

38. Which statement concerning phospholipid synthesis is true? 168

A) B) C) D) E)

Addition of polar “head groups” to diacylglycerol usually involves CDP derivatives. Addition of polar “head groups” to diacylglycerol usually involves UDP adducts. Addition of fatty acyl “tails” to glycerol usually involves CDP adducts. Addition of fatty acyl “tails” to glycerol usually involves UDP adducts. None of the above is true.

Answer: A Section: 20.6.A Level of Difficulty: moderate Learning Objective: Synthesis of Other Lipids 39. An enzyme that is inhibited by the statin group of drugs (e.g. Lipitor®) is A) B) C) D) E)

phospholipase a2. hormone sensitive lipase. HMG CoA reductase. desaturase. glycerol kinase.

Answer: C Section: 20.7 Level of Difficulty: Easy Learning Objective: Cholesterol Metabolism 40. Which of the following is the source of the two carbon fragments in fatty acids biosynthesis? A) B) C) D) E)

acetyl CoA malonyl CoA palmitic acid propionyl CoA ceramides

Answer: B Section: 20.4.C Level of Difficulty: Easy Learning Objective: Fatty Acid Biosynthesis 41. Which of the following is the starting metabolite in ketone body biosynthesis? A) B) C) D) E)

acetyl CoA malonyl CoA propionlyl CoA acetyl CoA and propionyl CoA acetyl CoA and malonyl CoA

Answer: A Section: 20.3 Level of Difficulty: Learning Objective: Ketone Bodies

169

42. Which of the following is FALSE regarding HMG-CoA reductase? A) B) C) D) E)

HMG-CoA reductase is highly regulated. The active site is tightly bound by statins. HMG-CoA reductase levels are increased as a result of high cholesterol concentrations in the ER HMG-CoA reductase levels are decreased as a result of high cholesterol concentrations in the ER. HMG-CoA reductase is levels are decreased by the same factor that down regulated production of the LDL receptors

Answer: C Section: 20.7.A.B Level of Difficulty: Moderate Learning Objective: Cholesterol Metabolism 43. Considering the figure below, what compound would be formed by action of acyl-CoA dehydrogenase?

Answer: A Section: 20.2.C Level of Difficulty: Moderate Learning Objective: Fatty Acid Oxidation 170

44. Which of the following drugs acts by acetylating a serine residue preventing adequate enzyme activity? A) B) C) D) E)

ibuprofen acetaminophen Vioxx® aspirin Celebrex®

Answer: D Section: 20.6.C Level of Difficulty: Easy Learning Objective: Synthesis of Other Lipids 45. PGH2 is synthesized from ______ and triggers pain and ________. A) B) C) D) E)

cardiolipins; foam cell development steroids; fever salicylic acid; foam cell development NSAIDS; COX-1 arachidonate; inflammation

Answer: E Section: 20.6.C Level of Difficulty: Easy Learning Objective: Synthesis of Other Lipids 46. Which of the following enzymes is NOT involved in the tricarboxylate transport system? A) B) C) D) E)

citrate synthase ATP citrate lyase malate dehydrogenase malic enzyme All are involved in the transport of acetyl-CoA into the cytosol

Answer: E Section: 20.4.A Level of Difficulty: Easy Learning Objective: Fatty Acid Biosynthesis 47. Which of the following components would be condensed to form acetoacetate? A) B) C) D) E)

acetyl CoA and acetyl-CoA HMG-CoA and acyl-CoA acetone and betahydroxybutyrate malonyl-CoA and acyl-CoA DHAP and glycerol-3-phosphate 171

Answer: A Section: 20.3 Level of Difficulty: Easy Learning Objective: Ketone Bodies 48. Which of the following is the correct sequence of events in cholesterol synthesis? (Note: not all events in the sequence are included) A) B) C) D) E)

HMG-CoA > isopentyl pyrophosphate > farnesyl pyrophosphate > geranyl pyrophosphate isopentyl pyrophosphate > squalene > oxidosqualene > geranyl pyrophosphate dimethylallyl pyrophosphate > geranyl pyrophosphate > farnesyl pyrophosphate > squalene HMG –CoA > phosphomevalonate > squalene > farnesyl pyrophosphate mevalonate > dimethylallyl pyrophosphate > farnesyl pyrophosphate > gernayl pyrophosphate

Answer: C Section: 20.7 Level of Difficulty: Difficult Learning Objective: Cholesterol Metabolism 49. Which of the following compounds is produced by the multistep cyclization of squalene? A) B) C) D) E)

lanosterol geranyl pyrophosphate fanesyl pyrophosphate isoprene isopentyl pyrophosphate

Answer: A Section: 20.7 Level of Difficulty: Easy Learning Objective: Cholesterol Metabolism 50. Which of the following is NOT an example of a problem sometimes associated with unsaturated fatty acid breakdown? A) B) C) D) E)

β, g double bond α, β double bond unanticipated isomerization inhibition of hydratase by a double bond All of the above are problems.

Answer: B Section: 20.2.D Level of Difficulty: Moderate Learning Objective: Fatty Acid Oxidation

172

51. LDL taken up by the liver is A) B) C) D) E)

broken down into fatty acids and amino acids. taken up by the ER and used to control synthesis of HMG CoA reductase and LDL receptor synthesis. converted into clathrin and recycled. irreversibly bound to LDL receptors. excreted in a clathrin coated vesicle.

Answer: B Section: 20.2.B Level of Difficulty: Moderate Learning Objective: Lipid Digestion, Absorption, and Transport

173

Chapter 21: Amino Acid Metabolism Matching Choose the correct answer from the list. Not all the answers will be used. A) ribosomes B) jaundice C) channeling D) 26S proteasome E) glutamine synthetase F) alanine G) glutamate H) vitamin B6 I) anammox J) glutamine transferase K) THF L) autotroph M) vitamin D N) lysosomes O) diazotrophs 1. _____ are involved in the nonselective degradation of proteins in well nourished cells. Answer: N Section: 21.1.A Level of Difficulty: Easy Learning Objective: Protein Degradation 2. ATP-dependent degradation of ubiquitinated proteins is mediated by ______. Answer: D Section: 21.1.C Level of Difficulty: Easy Learning Objective: Protein Degradation 3. Aminotransferases utilize a coenzyme synthesized from ______. Answer: H Section: 21.2.A Level of Difficulty: Easy Learning Objective: Amino Acid Deamination 4. A phenomenon in which intermediates are directly transferred from one active site to another is ______. Answer: C Section: 21.3.A Level of Difficulty: Easy Learning Objective: The Urea Cycle 5. The amino acid ______ has been thought to act as a transfer system for NH3, safely allowing the toxic molecule to be transported from the liver to the kidneys. Answer: G 167

Section: 21.2.B Level of Difficulty: Moderate Learning Objective: Amino Acid Deamination 6. The cofactor ______ is used to transfer C1 units such as methyl, formyl, and methenyl groups. Answer: K Section: 21.4.D Level of Difficulty: Easy Learning Objective: Breakdown of Amino Acids 7. The enzyme ______ is critical to regulating nitrogen metabolism. Answer: E Section: 21.5.A Level of Difficulty: Easy Learning Objective: Amino Acid Biosynthesis 8. Infants who cannot properly degrade bilirubin develop ______. Answer: B Section: 21.6.A Level of Difficulty: Easy Learning Objective: Other Products of Amino Acid Metabolism 9. Organisms known as _____ can fix nitrogen into metabolically useful molecules. Answer: O Section: 21.7 Level of Difficulty: Easy Learning Objective: Nitrogen Fixation

Multiple Choice 10. Which of the following describes the steps required prior to ATP-dependent degradation of proteins? I. Ubiquitin is transferred to cysteine on a ubiquitin-conjugating enzyme. II. The protein is linked to at least four tandemly linked ubiquitin units. III. Activated ubiquitin is transferred to a lysine of the previously bound protein. IV. Ubiquitin is attached via a thioester to a unbiquitin-activiating enzyme. A) I, II, III, IV B) IV, I, III, II C) II, I, III, IV D) IV, II, I, III 168

E) IV, II, III, I Answer: B Section: 21.1.B Level of Difficulty: Difficult Learning Objective: Protein Degradation 11. The majority of amino acids are deaminated by a ______ reaction. A) A) B) C) D)

transaminmation reduction condensation transacetylation oxidation

Answer: A Section: 21.2 Level of Difficulty: Easy Learning Objective: Amino Acid Deamination 12. The aminotransferase reaction, in which an enzyme-PLP Schiff base forms, I. is ATP dependent. II. results in formation of a hydroxylaldehyde. III. results in formation of an a-ketoacid. IV. requires an active site lysine. A) I, III, IV B) I, IV C) II, III D) I, II, III E) II, III, IV Answer: A Section: 21.2.A Level of Difficulty: Difficult Learning Objective: Amino Acid Deamination 13. Which of the following reaction sequences could result in glucose synthesis? A) B) C) D) E)

fumarate à arginine à urea fumarate à malate à oxaloacetate citrulline à urea à aspartate urea à arginine à ornithine none of the above

Answer: B Section: 21.3.A Level of Difficulty: Moderate Learning Objective: The Urea Cycle 14. Ketogenic amino acids can be converted to I. glucose 169

II. fatty acids III. ketone bodies IV. pyruvate A) I, III B) II, IV C) I, II D) I,II, III E) I, IV Answer: B Section: 21.4 Level of Difficulty: Easy Learning Objective: Breakdown of Amino Acids 15. The amino acids Ala, Cys, Gly, Ser, and Thr are all degraded to the metabolic intermediate ___ and are considered ____. A) B) C) D) E)

acetyl-CoA; glucogenic acetyl-CoA; ketogenic pyruvate; glucogenic pyruvate; ketogenic acetoacetate; ketogenic

Answer: C Section: 21.4.A Level of Difficulty: Moderate Learning Objective: Breakdown of Amino Acids 16. Which of the following glycolytic intermediates is the common precursor to serine, cysteine, and glycine? A) B) C) D) E)

fructose-6-phosphate glyceraldehyde-3-phosphate dihydroxyacetone phosphate 3-phosphoglycerate pyruvate

Answer: D Section: 21.5.A Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis 17. The neurotransmitters, dopamine, epinephrine, and norepinephrine are synthesized from the amino acid A) B) C) D) E)

tryptophan tyrosine glutamate aspartate lysine

Answer: B Section: 21.6.B 170

Level of Difficulty: easy Learning Objective: Other Products of Amino Acid Metabolism 18. Nitrogenase I. can be found in most bacteria and a few invertebrate animals. II. contains unique redox centers that contain both Fe and Mo. III. changes in conformation as a result of ATP hydrolysis. IV. carries out a reaction that reduces nitrogen to NO. A) I, II, III, IV B) II, III, IV C) II, III D) III, IV E) IV only Answer: C Section: 21.7 Level of Difficulty: Moderate Learning Objective: Nitrogen Fixation 19. The total cost of nitrogen reduction is ____ and ___ transferred electrons. A) B) C) D) E)

8 ATP; 4 12 ATP; 8 12 ATP; 6 16 ATP; 8 16 ATP; 6

Answer: D Section: 21.7.A Level of Difficulty: Moderate Learning Objective: Nitrogen Fixation 20. The lifetime of a protein in cells actively involved in metabolism A) is longer in eukaryotes than in prokaryotes. B) ranges from months to years. C) is independent of the function and activity of the protein. D) can change in response to changes in metabolic hormone levels. E) none of the above Answer: D Section: 21.1.A Level of Difficulty: Moderate Learning Objective: Protein Degradation 21. What are KFERQ proteins? I. Proteins that contain the KFERQ pentapeptide sequence (or a similar sequence) . II. Proteins that are selectively degraded in tissues that atrophy after a prolonged fast (starvation). III. A special set of enzymes that are activated in response to starvation. 171

A) I, II B) I, II, III C) II, III D) I, III E) I only Answer: A Section: 21.1.A Level of Difficulty: Moderate Learning Objective: Protein Degradation 22. Proteins targeted for destruction via the ubiquitin pathway include I. proteins with a destabilizing N-end rule component. II. proteins with a PEST sequence. III. proteins that contain the RING finger E3 component named E3a. IV. protein with polyubiquitin proteins. A) I only B) II only C) I, II, III D) I, II, IV E) II, IV Answer: D Section: 21.1.B Level of Difficulty: Moderate Learning Objective: Protein Degradation 23. The presence of SGOT and SGPT in the serum indicate potential A) B) C) D) E)

starvation and brain tissue damage. inflammation. heart attack or liver damage. lung or breast cancer. none of the above

Answer: C Section: 21.2.A Level of Difficulty: Easy Learning Objective: Amino Acid Deamination 24. Oxidative deamination of glutamate I. generates NAD(P)H and a-ketoglutarate. II. is inhibited by glutamate. III. is activated by GTP. IV. eliminates the keto group from a-ketoacids. A) I only B) I, II C) I, III D) II, IV E) III, IV 172

Answer: A Section: 21.2.B Level of Difficulty: Difficult Learning Objective: Amino Acid Deamination 25. Which of the following statements about maple syrup urine disease is FALSE? I. It is caused by a genetic deficiency in the enzyme BCKDH. II. The disease is fatal unless promptly treated. III. There is a buildup of the branched-chain a-keto acids. IV. Patients with the disease excrete urine that smells like maple syrup. A) I only B) II only C) I, III D) III, IV E) All of the statements are true. Answer: E Section: 21.4.D Level of Difficulty: Moderate Learning Objective: Breakdown of Amino Acids 26. Which of the following statements about phenylalanine is(are) TRUE? A) B) C) D) E)

The enzymatic degradation of phenylalanine requires the biopterin cofactor. Individuals with defects in phenylalanine catabolism require tyrosine in their diet. An inability to hydroxylate phenylalanine results in increased blood levels of phenylalanine, causing mental retardation. A and C A, B, and C

Answer: D Section: 21.4.G Level of Difficulty: Moderate Learning Objective: Breakdown of Amino Acids 27. Which of the following statements about tryptophan synthase is FALSE? A) B) C) D) E)

Indole can pass between active sites via a channel in the enzyme. Tryptophan synthase catalyzes two distinct reaction steps to form tryptophan. The enzyme is a tetramer of four identical subunits. The enzyme has two states, an "open" and "closed", to ensure that bound indole is not lost to solvent. The indole group is produced following release of glyceraldehyde-3phosphate from the indole-glycerol-3-phosphate.

Answer: C Section: 21.5.B Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis 173

28. Heme biosynthesis A)

requires that synthesis of the protoporphryin ring occur in the mitochondria due to difficulties in transporting large molecule. is inhibited in lead poisoning. can be completed using enzymes from the cytosol. A and B A, B, and C

B) C) D) E) Answer: B Section: 21.6.A Level of Difficulty: Moderate Learning Objective: Other Products of Amino Acid Metabolism

29. _____ catalyzes the synthesis of ____, a molecule that signals vasodilation, from the precursor _____ A) B) C) D) E)

NOS; nitric oxide (NO); arginine Nitrous oxidase; nitrous oxide; arginine Arginate; nitric oxide (NO); citrulline Citrulline dehydrogenase; nitrous oxide; citrulline none of the above

Answer: A Section: 21.6.C Level of Difficulty: Moderate Learning Objective: Other Products of Amino Acid Metabolism 30. Which of the following is(are) advantages to the constant degradation and reformation of proteins? A) B) C) D) E)

Nutrients can be stored as proteins, which can be used during periods of metabolic need. Damaged proteins are eliminated so they do not accumulate. Metabolism can be efficiently regulated by the synthesis and degradation of enzymes. All of the above are advantages. None of the above is an advantage.

Answer: D Section: 21.1 Level of Difficulty: Moderate Learning Objective: Protein Degradation 31. The activity of bacterial glutamine synthetase is I. inhibited allosterically by tryptophan. II. inhibited allosterically by glucosamine-6-phosphate. III. activated by nine allosteric feedback inhibitors. IV. altered by covalent modification. A) I, III B) III, IV C) I, II 174

D) E)

I, IV I, II, III, IV

Answer: E Section: 21.5.A Level of Difficulty: Difficult Learning Objective: Amino Acid Biosynthesis 32. Which enzyme catalyses a reaction via an enzyme-bound adenylated intermediate? A) B) C) D) E)

glutamine synthetase argininosuccinate synthetase carbamoyl phosphate synthetase I Ac-CoA decarboxylase arginase

Answer: B Section: 21.3.A Level of Difficulty: Difficult Learning Objective: The Urea Cycle 33. In which cellular location listed below does the following reaction take place? arginine → urea + ornithine A) B) C) D) E)

cytosol mitochondrial matrix lysosome A or B none of the above

Answer: A Section: 21.3.A Level of Difficulty: Moderate Learning Objective: The Urea Cycle 34. In which cellular location listed below does the following reaction take place? A) B) C) D) E)

ornithine + carbamoyl-phosphate → citrulline cytosol mitochondrial matrix lysosome A or B none of the above

Answer: B Section: 21.3.A Level of Difficulty: Moderate Learning Objective: The Urea Cycle 35. What species are combined to produce carbamoyl phosphate? A) B)

NH3 , PO43−, HCO3− NH4+, PO43−, Ac-CoA, releasing CoA-SH 175

C) D) E)

glycine & inorganic phosphate, releasing CO2 acetate & NH4+, releasing CO2 alanine & inorganic phosphate, releasing acetate

Answer: A Section: 21.3.A Level of Difficulty: Moderate Learning Objective: The Urea Cycle 36. A number of compounds, including neurotransmitters, are synthesized from amino acids via decarboxylations. The enzymes catalyzing these steps usually use _______ as a cofactor. A) B) C) D) E)

pyridoxal-5ꞌ-phosphate thiamine pyrophosphate biotin cobalt containing compounds [vitamin B12] tetrahydrofolate

Answer: A Section: 21.6.B Level of Difficulty: Moderate Learning Objective: Other Products of Amino Acid Metabolism 37. Which of the following is TRUE regarding catabolism of leucine? A) B) C) D) E)

The pathway begins with aspartate. The pathway requires a-ketoglutarate. The pathway requires TPP. The pathway generates HMG-CoA. none of the above

Answer: B Section: 21.4.E Level of Difficulty: Moderate Learning Objective: Breakdown of Amino Acids 38. The metabolite chorismate A) B) C) D) E)

allosterically enhances production of aromatic amino acids. is an important intermediate in the production of Trp, Tyr, and Phe. is a derivative of glucose. A and B B and C

Answer: E Section: 21.5.B Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis 39. The pictured compound, glutamate-5-semialdehyde, is an intermediate in the biosynthesis of which of the following amino acids? A)

O +H3N

C CH

histidine

CH2 H 2C

176

C O

O-

B) C) D) E)

arginine methionine threonine More than one of the above is made from this intermediate.

Answer: B Section: 21.5.A Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis 40. Which of the following amino acids is NOT synthesized from aspartate? A) B) C) D) E)

threonine methionine lysine cysteine All of the above are synthesized from aspartic acid.

Answer: D Section: 21.5 Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis 41. Which of the following is TRUE about glutamine? I. It is formed from a-ketoglutarate. II. It donates an amino group to aspartate to form asparagine. III. It is directly required for ornithine synthesis. IV. It is a precursor to homoserine. A) I, II B) I, II, III C) II, III, IV D) II, IV E) I, III Answer: A Section: 21.5.A Level of Difficulty: Difficult Learning Objective: Amino Acid Biosynthesis 42. Individuals with an alanine to valine mutation in N5, N10 – methylenetetrahydrofolate reductase (MTHFR) I. typically have higher levels of homocysteine. II. have increased risk for cardiovascular disease. III. typically have increased incidence of oxidative damage to the walls of blood vessels. IV. are at increased risk, if female, of giving birth to a child with a neural tube defect. A) I, II B) II, III C) I only D) IV only E) I, II, III, IV 177

Answer: E Section: 21.4.D Level of Difficulty: Moderate Learning Objective: Breakdown of Amino Acids 43. Which of the following control the urea cycle? I. substrate concentration of the cycle enzymes II. allosteric activation of carbamoyl phosphate synthetase I III. concentration of glutamate IV. availability of glucose A) I, III B) II, III C) II, IV D) I, II, III E) I, IV Ans: D Section: 21.3.B Level of Difficulty: Moderate Learning Objective: Urea Cycle 44. Enzyme A is involved in the metabolism of metabolite C to metabolite D. Enzyme A is part of a linear pathway involving ten enzymes ultimately converting B àF. High levels of F directly alter the activity of enzyme A and result in control over the overall pathway. Enzyme A A) B) C) D) E)

likely has high rates of degradation and synthesis. is likely a nonessential enzyme. likely has low rates of degradation and synthesis. is likely involved in a nonessential pathway. none of the above

Ans: A Section: 21.1 Level of Difficulty: Difficult Learning Objective: Protein Degradation 45. Which of the following is required for synthesis of tryptophan? A) B) C) D) E)

serine phosphoenolpyruvate erythrose-4-phosphate all of the above none of the above

Ans: D Section: 21.5.B Level of Difficulty: Moderate Learning Objective: Amino Acid Biosynthesis

178

46. A mutation in GDH of patients with HI/HA (hypoglycemia/hyperammonemia) results in a decrease in allosteric control of GDH via GTP. Which of the following will be observed in the patients? A) B) C) D) E)

an increase in ammonia an increase in glutamate an increase in NADH A and B A and C

Ans: E Section: 21.2 Level of Difficulty: Difficult Learning Objective: Amino Acid Deamination 47. Which of the following require a cyclic carbohydrate precursor for synthesis? I. histidine II. alanine III. arginine IV. tyrosine A) I, II B) II only C) I, III D) I , IV E) II, IV Ans: D Section: 21.5.A.B Level of Difficulty: Difficult Learning Objective: Amino Acid Biosynthesis 48. Which of the following are essential amino acids for adult humans? A) B) C) D) E)

Arg, His, Gly, Try Met, Lys, His, Val His, Leu, Tyr, Ala Met, Gly, Thr, Ser Ala, Arg, Cys, Ser

Ans: B Section: 21.5.A Level of Difficulty: Easy Learning Objective: Amino Acid Biosynthesis 49. The synthesis of which of the following uses an aminotransferase in the first step of the synthesis? A) B) C) D)

glutamine proline serine valine 179

E) all of the above Ans: A Section: 21.5.A and B Level of Difficulty: Moderate Learning Objective: Amino acid Biosynthesis 50. Which of the following amino acid breakdown reactions would be catalyzed by an aminotransferase? A) B) C) D) E)

Threonine à Acetyl CoA Alanine à Pyruvate Asparagine à Aspartate Homocysteine à Methionone HMG-CoA à Acetoacetate

Ans: B Section: 21.4.A-E Level of Difficulty: Moderate Learning Objective: Amino Acid Breakdown

180

Chapter 22: Mammalian Fuel Metabolism: Integration and Regulation Matching Choose the correct answer from the list. Not all the answers will be used. A) a-adrenergic receptor B) b-adrenergic receptor C) Cori cycle D) urea cycle E) leptin F) phosphatase G) liver H) hormones I) acetyl CoA J) ketone bodies K) urea L) kidney M) brain N) pancreas 1. The activity of the _____ enzyme glucokinase increases with high blood glucose. Ans: G Section: 22.1.D Level of Difficulty: Easy Learning Objective: Organ Specialization 2. ______ and other waste products from the blood are excreted by the kidney. Ans: K Section: 22.1.E Level of Difficulty: Easy Learning Objective: Organ Specialization 3. The ____ provides a pathway for the metabolic use of lactate for production of glucose. Ans: C Section: 22.1.F Level of Difficulty: Easy Learning Objective: Organ Specialization

4. The endocrine glands secrete ______ which result in numerous cellular responses. Ans: H Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism 175

5. Epinephrine binding to the ______ causes an increase in intracellular [Ca2+]. Ans: A Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism 6. Following prolonged starvation, ______ are used as fuel by the brain. Ans: J Section: 22.4.A Level of Difficulty: Easy Learning Objective: Disturbances in Fuel Metabolism 7. ______ is the degradation product of glucose, fatty acids, and ketogenic amino acids. Ans: I Section: 22.1 Level of Difficulty: Easy Learning Objective: Organ Specialization 8. During starvation the _____ generate as much as 50% of the body's glucose supply. Ans: L Section: 22.1.E Level of Difficulty: Easy Learning Objective: Organ Specialization 9. The ______ stores very little glycogen and therefore requires a steady supply of glucose from the blood. Ans: M Section: 22.1.A Level of Difficulty: Easy Learning Objective: Organ Specialization 10. Mice lacking the protein ______ are genetically obese. Ans: E Section: 22.3.C Level of Difficulty: Easy Learning Objective: Metabolic Homeostasis

Multiple Choice 11. Glucose is the preferred fuel of muscles because A) B)

it can be metabolized under anaerobic conditions. it can be generated from ketone bodies even during starvation. 176

C) D) E)

the heart muscle uses glucose exclusively as a fuel. it is the most efficient energy storage available. all of the above

Ans: A Section: 22.1.B Level of Difficulty: Moderate Learning Objective: Organ Specialization 12. The glucose transporter in muscle cells is A) B) C) D) E)

insulin. glucagon. GLUT2. GLUT4. none of the above

Ans: D Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism 13. Which of the following reactions is catalyzed by adenylate cyclase? A) B) C) D) E)

ATP ® cAMP + PPi cAMP ® AMP ATP ® cATP ADP ® cAMP + Pi AMP ® cAMP

Ans: A Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism

14. Phospholipase C cleaves PIP2, generating A) B) C) D) E)

IP3 and DAG (inositol-1,4,5-trisphosphate and 1,2-diacylglycerol). cAMP and PPi. cAMP and DAG (1,2-diacylglycerol). IP3 and PPi. IP3 and Pi.

Ans: A Section: 22.2 Level of Difficulty: Moderate 177

Learning Objective: Hormonal Control of Fuel Metabolism 15. A balanced meal containing fatty acids, carbohydrates, and protein is digested. Which of the following is TRUE? I. Carbohydrates are absorbed by the stomach and delivered to the liver. II. Fatty acids are absorbed by the intestinal mucosa and circulated through the lymph. III. Proteins are digested into monomer amino acids and absorbed by the intestinal mucosa after which the majority is delivered to the liver. A) I, II, III B) I, II C) II, III D) I, III E) III only Ans: C Section: 22.4.A Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism 16. Animals lack the ability to produce glucose from ______. A) B) C) D) E)

other sugars fatty acids pyruvate amino acids starches

Ans: B Section: 22.4.A Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism

17. The common products of fuel metabolism in mammals are A) B) C) D) E)

oxaloacetate and acetyl- CoA. pyruvate and acetyl-CoA. ATP and acetyl-CoA. pyruvate and glucose. none of the above

Ans: B Section: 22.1 Level of Difficulty: Easy 178

Learning Objective: Organ Specialization 18. Which of the following mechanisms for ATP regeneration are listed in order utilized? A) B) C) D) E)

glycolysis, phosphocreatine, oxidative phosphorylation phosphocreatine, glycolysis, oxidative phosphorylation phosphocreatine, oxidative phosphorylation, glycolysis, phosphocreatine, oxidative phosphorylation, glycolysis, gluconeogenesis none of the above

Ans: B Section: 22.1.B Level of Difficulty: Moderate Learning Objective: Organ Specialization 19. Glucokinase is regulated by _______ and _____. A) B) C) D) E)

glucokinase regulatory protein, fructose-6-phosphate fructose-6-phosphate, glucose glucose-6-phosphate; glucose ATP; glucose-6-phosphate all of the above

Ans: A Section: 22.1.D Level of Difficulty: Easy Learning Objective: Organ Specialization 20. The metabolic fate(s) of glucose-6-phosphate include I. glycogen and glucose. II. ribose-5-phosphate III. acetyl-CoA. IV. DNA and RNA. A) I B) I, II C) I, III D) III, IV E) I, II, III, IV Ans: E Section: 22.1.D Level of Difficulty: Difficult Learning Objective: Organ Specialization 21. Which of the following statements concerning the response of hepatocytes to insulin is FALSE? A) B) C) D)

Phosphorylase kinase is inactivated, decreasing glycogenolysis. Glycogen synthase is activated. Transcription of glucokinase increases. Glucose uptake is increased in the liver. 179

E) The liver stores glucose as glycogen or triacylglycerols. Ans: D Section: 22.2 Level of Difficulty: Difficult Learning Objective: Hormonal Control of Fuel Metabolism 22. Which of the following is TRUE regarding pancreatic b cells? A) B) C) D) E)

Insulin is secreted by the b cells in response to the increase in b cell glucose receptor binding. Glucagon is secreted by the b cells in response to the increase in b cell glucose receptor binding. Insulin is secreted by the b cells in response to high glucose levels. Insulin is secreted by the b cells in response to low glucose levels. Glucagon is secreted by the b cells in response to high glucose levels.

Ans: C Section: 22.1 Level of Difficulty: Moderate Learning Objective: Hormonal Control of Fuel Metabolism 23. Which of the following are effects of insulin secretion? I. Muscle and adipose tissue are stimulated to take up glucose. II. Glycogen synthesis increases in the liver. III. Gluconeogenesis is inhibited in the liver and kidney. IV. Lipolysis increases in the adipose tissue. A) I, II B) I C) I, II, III D) I, III E) II, IV Ans: C Section: 22.2 Level of Difficulty: Difficult Learning Objective: Hormonal Control of Fuel Metabolism

24. Which of the following proteins stimulates the appetite? A) B) C) D) E)

leptin ghrelin adiponectin insulin PYY3-36 180

Ans: B Section: 22.3.B Level of Difficulty: Easy Learning Objective: Metabolic Homeostasis 25. Which of the following is FALSE relating to leptin? A) B) C) D) E)

Obese mice lacking leptin tend to overeat. Leptin seems to function by different mechanisms in mice and humans. Obesity in humans leads to a decrease in leptin production. Obesity leads to leptin resistance. none of the above

Ans: C Section: 22.3.B Level of Difficulty: Moderate Learning Objective: Metabolic Homeostasis 26. Which of the following statements is TRUE regarding the blood glucose level of non-insulin dependent diabetics tend to compare to that of normal individuals? A) B) C) D)

Blood glucose levels of diabetics tend to be very stable, but at a higher level. Blood glucose levels of diabetics tend to be variable and higher. Blood glucose levels decrease more rapidly following a meal, often dropping lower than is tolerable. Blood glucose levels average the same level in diabetics, but reach higher peaks for short periods. none of the above

E) Ans: B Section: 22.4.B Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism 27. Insulin-dependent (type 1) diabetes A) B) C) D) E)

is associated with a deficiency of pancreatic β-cells. is associated with a deficiency of insulin receptors. is associated with a deficiency of signal transduction can be treated with injections of leptin. can be treated with injections of ghrelin.

Ans: A Section: 22.4.C Level of Difficulty: Easy Learning Objective: Disturbances in Fuel Metabolism 28. Aerobic activity in response to stress results in which of the following? I. Glycolysis occurs in the muscle. II. Glycolysis occurs in the liver. III. Glycogenolysis occurs in the muscle. 181

IV. Glycogenolysis occurs in the liver. A) I, III, IV B) I, II, IV C) II, IV D) II, IV E) III, IV Ans: A Section: 22.2 Level of Difficulty: Moderate Learning Objective: Hormonal Control of Fuel Metabolism 29. The interorgan pathway that allows transport of nitrogen from muscle to the liver utilizes ____ as an amino group acceptor in the transamination reaction generating _____. A) B) C) D) E)

acetyl-CoA; alanine acetyl-CoA; glutamine pyruvate; glutamine pyruvate; glutamate pyruvate; alanine

Ans: E Section: 22.1.F Level of Difficulty: Moderate Learning Objective: Organ Specialization 30. Which of the following best describes the function of AMP-dependent protein kinase (AMPK)? A) B) C) D) E)

It activates ATP-generating metabolic pathways and inhibits biosynthetic pathways. It activates biosynthetic pathways and inhibits ATP-generating metabolic pathways. It activates both ATP-generating and biosynthetic pathways. It inhibits both ATP-generating and biosynthetic pathways. None of the above is correct.

Ans: A Section: 22.3.A Level of Difficulty: Easy Learning Objective: Metabolic Homeostasis

31. At low glucose concentrations (≤5mM), the majority of glucose produced by liver cells is due to the action of A) B)

glucokinase. hexokinase. 182

C) D) E)

glucose-6-phosphatase. AMP-dependent protein kinase (AMPK). AMP-responsive tyrosine kinase.

Ans: C Section: 22.1.D Level of Difficulty: Easy Learning Objective: Organ Specialization 32. In an average individual the liver glycogen is depleted during starvation in approximately A) B) C) D) E)

45-60 minutes. 4-6 hours. 18-24 hours. 55-60 hours. 5-7 days.

Ans: D Section: 22.4.A Level of Difficulty: Easy Learning Objective: Disturbances in Fuel Metabolism 33. Excess glucosylation of lens proteins in diabetics leads to A) B) C) D) E)

cataracts. retinal degeneration. glaucoma. ketosis. fatty liver disease.

Ans: A Section: 22.4.B Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism 34. Based on the information given in the chapter complete the following statement about the graph shown below: The curve labeled ___ corresponds to activity of glucokinase under conditions with no inhibition. The binding of ____ to the regulating protein would result in kinetic behavior represented by curve ____.

183

A) B) C) D) E)

B; F6P; A A; glucose; B B; F6P; C C; F6P; B B; glucose; C

Ans: C Section: 22.1.D Level of Difficulty: Difficult Learning Objective: Organ Specialization 35. The majority of glucose in the brain A) B) C) D) E)

is used to store adequate glycogen for extended periods of starvation. is used to produce ATP for membrane Na+-K+ ATPase required for nerve impulse transmission. is synthesized from fatty acids due to the need for high ATP levels. is synthesized in the adipose tissue and transported to the brain. is synthesized from ketone bodies under conditions of prolonged fasting.

Ans: B Section: 22.1.A Level of Difficulty: Moderate Learning Objective: Organ Specialization 36. Synthesis of triacylglycerols is dependent on A) B) C) D) E)

the availability of glycerol-3-phosphate. the uptake of glucose from the bloodstream. the enzyme responsible for reduction of dihydroxyacetone phosphate. the circulation of lipoprotein. all of the above

Ans: E Section: 22.1.C Level of Difficulty: Moderate Learning Objective: Organ Specialization 37. Adipose tissue 184

A) B) C) D) E)

secretes hormones that regulate metabolism. synthesizes both glucose and triacylglycerols. contains enough stored energy to survive about one month. A and B A and C

Ans: A Section: 22.1.C Level of Difficulty: Easy Learning Objective: Organ Specialization 38. Which of the following can generate glucose? I. kidney II. liver III. adipose tissue IV. muscle A) I, II, III, IV B) I, II, IV C) I, II D) II, IV E) II only Ans: C Section: 22.1.A Level of Difficulty: Moderate Learning Objective: Organ Specialization 39. Which of the following occurs during starvation? I. The kidney generates approximately half the glucose required for the body. II. The brain utilizes ketone bodies as a fuel source. III. The adipose tissue releases fatty acids. IV. Gluconeogenesis occurs in the liver. A) I, II, III, IV B) I, II, III C) I, II D) II, III E) II, III, IV Ans: B Section: 22.1.A-E Level of Difficulty: Difficult Learning Objective: Organ Specialization 40. Which of the following metabolizes ketone bodies? I. brain II. liver III. muscle IV. adipose tissue A) I, II, III, IV 185

B) C) D) E)

I, II, III I, III II only III only

Ans: C Section: 22.1.B-E Level of Difficulty: Moderate Learning Objective: Organ Specialization 41. Metabolism in the muscle is controlled hormonally by A) B) C) D) E)

glucagon insulin epinephrine B and C A, B, C

Ans: E Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism 42. Which of the following is part of the regulation of metabolism? A) B) C) D) E)

receptor tyrosine kinase adenylate cyclase phosphoinositide pathway all of the above none of the above

Ans: D Section: 22.2 Level of Difficulty: Easy Learning Objective: Hormonal Control of Fuel Metabolism 43. The muscle and liver A) B) C) D) E)

both increase glucose uptake in response to insulin. both increase glycogenolysis in response to glucagon. both increase glycogenolysis in response to insulin. both decrease gluconeogenesis in response to insulin. none of the above

Ans: E Section: 22.2 Level of Difficulty: Moderate Learning Objective: Hormonal Control of Fuel Metabolism

44. Glucose uptake A)

in the liver is mediated by GLUT4. 186

B) C) D) E)

in the muscle is increased in response to insulin due to increased expression of GLUT4. in the brain is adjusted relative to the concentration of glucose. A and B A, B, C

Ans: B Section: 22.2 Level of Difficulty: Moderate Learning Objective: Hormonal Control of Fuel Metabolism 45. Activation of AMPK activity is A) B) C) D) E)

accomplished by AMP induced conformational changes facilitating phosphorylation. accomplished by ATP induced conformational change facilitating phosphorylation. inhibited by high levels of AMP due to conformational changes burying the phosphorylation site. increased by high levels of ATP due to conformational changes burying the phosphorylation site. none of the above

Ans: A Section: 22.3.A Level of Difficulty: Moderate Learning Objective: Metabolic Homeostasis 46. Evidence suggests that the lifespan of a rodent may be extended A) B) C) D) E)

30% by a 60% reduction in calorie intake. 50% by a 30-40% reduction in calorie intake. 40% by a 50% reduction in calorie intake. 50% by reducing caloric intake by half. 50% by minimizing carbohydrate rich calorie sources.

Ans: B Section: 22.4.A Level of Difficulty: Easy Learning Objective: Disturbances in Fuel Metabolism 47. Type 2 diabetes I. can develop due to a mutation in the insulin receptor II. can develop in individuals with insulin resistance. III. results in hypersensitivity to insulin release. IV. are treated with drugs that decrease AMPK activity. A) I, II, IV B) I, II C) II, IV D) III, IV 187

E) I, IV Ans: B Section: 22.4.B Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism 48. During prolonged starvation the majority of the stored caloric energy comes from fat stores. Which of the following provides the second largest caloric energy total? A) B) C) D) E)

muscle glycogen liver glycogen blood glucose muscle protein All are approximately equal.

Ans: D Section: 22.4.A Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism 49. Which of the following are characteristics of metabolic syndrome? I. insulin resistance II. inflammation III. increased risk for type 1 diabetes. IV. hypersensitivity to insulin A) I, II B) I, II, III C) I, II, III, IV D) I, III E) I only Ans: A Section: 22.4.C Level of Difficulty: Easy Learning Objective: Disturbances in Fuel Metabolism 50. Metformin and thiazolidinediones (TZDs) are used to treat ____ and produce a(an) ______ in AMPK activity. A) B) C) D) E)

type 2 diabetes; decrease type 2 diabetes; increase type 1 diabetes; decrease type 1 diabetes; increase both type 1 and type 2 diabetes; decrease

Ans: B Section: 22.4.B Level of Difficulty: Moderate Learning Objective: Disturbances in Fuel Metabolism

188

Chapter 23: Nucleotide Metabolism Matching Choose the correct answer from the list. Not all the answers will be used. A) fumarate B) NADPH C) salvage D) uric acid E) oxidation F) XMP G) iron H) allopurinol I) IMP J) oxidation K) therapeutic L) suicide M) molybdenum N) FADH O) Malonyl-CoA P) reduction Q) antifolate 1. The precursor to AMP and GMP is ______. Ans: I Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 2. In purine synthesis the byproduct released when aspartate functions as an amino group donor is ________. Ans: A Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 3. During the turnover of nucleic acids some purines can be reincorporated into nucleotides via _____ pathways. Ans: C Section: 23.1.D Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 4. Deoxyribonucleotides are synthesized by ______ of the corresponding ribonucleotide’s 2¢ carbon. Ans: P Section: 23.3.A 183

Level of Difficulty: Easy Learning Objective: Formation of Deoxyribonucleotides 5. Class I ribonucleotide reductases (RNR) contain a(n) ______ prosthetic group. Ans: G Section: 23.3.A Level of Difficulty: Easy Learning Objective: Formation of Deoxyribonucleotides 6. The electrons used to convert an NDP to a dNDP ultimately come from ______. Ans: B Section: 23.3.A Level of Difficulty: Easy Learning Objective: Formation of Deoxyribonucleotides 7. Mechanism-based inhibitors are also called _____ substrates. Ans: L Section: 23.3.B Level of Difficulty: Easy Learning Objective: Formation of Deoxyribonucleotides 8. ______ compounds are effective anticancer agents. Ans: Q Section: 23.3.B Level of Difficulty: Easy Learning Objective: Formation of Deoxyribonucleotides 9. Purines are degraded to ______. Ans: D Section: 23.4.A Level of Difficulty: Easy Learning Objective: Nucleotide Degradation 10. Gout is treated using the compound ______. Ans: H Section: 23.4.B Level of Difficulty: Easy Learning Objective: Nucleotide Degradation

Multiple Choice 11. John Buchanan began the elucidation of the synthesis of purine nucleotides by studying _______ excreted by pigeons fed isotopically labeled compounds. A) B) C) D)

xanthine hypoxanthine uric acid b-alanine 184

b-aminoisobutyrate

Ans: C Section: 23.1 Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 12. Hydroxylation of IMP to form GMP occurs in conjunction with the ________ of _______. A) B) C) D) E)

oxidation; NADH reduction; NAD+ oxidation; NADPH reduction; NADP+ none of the above

Ans: B Section: 23.1.B Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides 13. The symptoms of Lesch–Nyhan syndrome are caused by a deficiency of which of the following enzymes? A) B) C) D) E)

adenine phosphoribosyltransferase HGPRT (hypoxanthine–guanine phosphoribosyltransferase) adenosine deaminase dihydrofolate reductase xanthine oxidase

Ans: B Section: 23.1.D Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides

14. The first step in pyrimidine biosynthesis is the formation of A) B) C) D) E)

carbamoyl phosphate. carbamoyl aspartate. β-aminoisobutyrate. dihydroorotate. none of the above

Ans: A Section: 23.2.A Level of Difficulty: Easy 185

Learning Objective: Synthesis of Pyrimidine Ribonucleotides 15. Which of the following correctly describes the formation of CTP? A) B) C) D) E)

UTP + Glutamine + ATP + H2O ® Glutamate + ADP + Pi + CTP UMP + ATP + H2O + Glutamine ® CMP + Glutamate + ADP + Pi TTP + N5,N10-Methylenetetrahydrofolate ® CTP + Dihydrofolate UMP + Glutamine ® Glutamate + CTP CMP + Glutamine + ATP ® CTP + Glutamate + ADP + Pi

Ans: A Section: 23.2.B Level of Difficulty: Easy Learning Objective: Synthesis of Pyrimidine Ribonucleotides 16. The synthesis of the dNTPs required for DNA production must be controlled by ________ in order to ensure minimal ________ activity from excess of one dNTP over the other dNTPs. A) B) C) D) E)

feedback inhibition; mutagenic feed forward activation; synthesis substrate availability; mutagenesis secondary messenger systems; synthesis feed forward; mutagenic

Ans: A Section: 23.3.A Level of Difficulty: Moderate Learning Objective: Formation of Deoxyribonucleotides

17. Which of the choices correctly represents the synthesis of dTTP as represented by the following reactions? I. dUMP + N5,N10-methylenetetrahydrofolate ® dTMP + dihydrofolate II. dTMP + ATP ® dTTP + Pi III. dUTP + H2O ® dUMP + PPi IV. dUTP + N5,N10-methylenetetrahydrofolate ® dTTP + dihydrofolate A)

I ® II ® IV 186

B) C) D) E)

IV only III ® IV ® I ® II III ® I ® II III ® I

Ans: D Section: 23.3.A,B Level of Difficulty: Difficult Learning Objective: Formation of Deoxyribonucleotides

18. The conversion of dUMP to dTMP by thymidylate synthase requires which of the following cofactors? I.

thioredoxin

II.

N5,N10-methylenetetrahydrofolate

III.

S-adenosylmethionine A) B) C) D) E)

I and II I only II only II and III I and III

Ans: C Section: 23.3.B Level of Difficulty: Moderate Learning Objective: Formation of Deoxyribonucleotides 19. Myoadenylate deaminase deficiency is most evident in ______ tissue. A) B) C) D) E)

liver connective neural muscle brain

Ans: D Section: 23.4.A Level of Difficulty: Easy Learning Objective: Nucleotide Degradation 20. Which of the following organisms excrete uric acid? I. primates II. marine invertebrates III. insects IV. mammals other than primates A) I, IV B) I, III C) IV only 187

D) E)

I only II, III

Ans: B Section: 23.4.B Level of Difficulty: Easy Learning Objective: Nucleotide Degradation 21. Which of the following is not required for purine biosynthesis? I. aspartate II. glycine III. glutamine IV. formyl addition to tetrahydrofolate A) I only B) II, IV C) II, III D) IV only E) All of the above are required. Ans: E Section: 23.1.A Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides 22. Atoms from which of the following amino acids are utilized in pyrimidine biosynthesis? I. II. III. IV.

glutamine glycine asparagine aspartate A) I, II B) I. III C) I, IV D) II, III E) II, IV

Ans: C Section: 23.2.A Level of Difficulty: Easy Learning Objective: Synthesis of Pyrimidine Ribonucleotides

23. The proposed mechanism of the Class I RNR involves A) B) C) D) E)

electron transfer directly from substrate to tyrosine 122. electron transfer from substrate to various cysteine residues. an exposed tyrosine which accepts an electron from the ribosyl radical. electron donation to external reducing agents. none of the above

Ans: B Section: 23.3.A 188

Level of Difficulty: Difficult Learning Objective: Formation of Deoxyribonucleotides 24. The thymidylate synthase reaction is unique because A) B) C) D) E)

THF is regenerated by the same enzyme. THF is regenerated via a two-step reaction. THF is oxidized to DHF; no other reaction alters the THF oxidation state. None of the above is correct. All of the above are correct.

Ans: C Section: 23.3.B Level of Difficulty: Difficult Learning Objective: Formation of Deoxyribonucleotides 25. Which of the following statements about nucleotide synthesis is (are) true? I. II. III.

Most dietary nucleotides are salvaged and used in DNA synthesis. Most nucleotides in cells are from de novo pathways. Most nucleotides in cells are salvaged and used in RNA synthesis. A) I, II B) I only C) II only D) II, IV E) III only

Ans: C Section: 23.4 Level of Difficulty: Moderate Learning Objective: Nucleotide Degradation 26. Which of the following sequences for uric acid catabolism is correct for marine invertebrates? A) B) C) D) E)

uric acid ®allantoin®allantoic acid®urea®NH4+ uric acid ® allantoic acid®urea®NH4+ uric acid ®allantoin® urea®NH4+ uric acid ®allantoin®allantoic acid®urea none of the above

Ans: A Section: 23.4.B Level of Difficulty: Easy Learning Objective: Nucleotide Degradation 27. The disease gout is characterized by high levels of ____, which forms crystal deposits in joints and is treated by inhibition of _______. A) B) C) D)

uric acid; urate oxidase uric acid; xanthine oxidase urea; urate oxidase xanthine; xanthine oxidase 189

E) none of the above Ans: B Section: 23.4.B Level of Difficulty: Moderate Learning Objective: Nucleotide Degradation 28. The end products of pyrimidine catabolism are A) B) C) D) E)

uric acid and glyoxylic acid. uric acid and allantoin. b-alanineand b-aminoisobutyrate. b-alanine and a-ketoglutarate. none of the above

Ans: C Section: 23.4.A Level of Difficulty: Moderate Learning Objective: Nucleotide Degradation 29. The symptoms of severe combined immunodeficiency syndrome (SCID) are caused by a deficiency of which of the following enzymes? A) B) C) D) E)

adenine phosphoribosyltransferase HGPRT (hypoxanthine–guanine phosphoribosyltransferase) adenosine deaminase dihydrofolate reductase xanthine oxidase

Ans: C Section: 23.4.A Level of Difficulty: Easy Learning Objective: Nucleotide Degradation

30. The synthesis of 5-phosphoribosylamine from PRPP is I. inhibited allosterically by ATP and GTP. II. activated by PRPP via feed forward activation. III. controlled by cAMP dependent phosphorylation. A) I, II, III, B) I, II 190

C) D) E)

II, III II only III only

Ans: B Section: 23.1.C Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides 31. Addition of pyrophosphate to which of the following occurs during the first step of purine biosynthesis? A) B) C) D) E)

5-phosphoribosyl phosphate ribulose-5-phosphate ribose-5-phosphate ribose phosphribosylamine

Ans: C Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 32. Which of the following pathways produces the sugar moiety used for nucleotide synthesis? A) B) C) D) E)

glycolysis Calvin cycle pentose phosphate glycogen metabolism none of the above

Ans: C Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 33. The amino group added to the C6 position of IMP to form AMP is derived from A) B) C) D) E)

aspartate. asparagine. glutamine. a-ketoglutarate. arginine.

Ans: A Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 34. The amino group added to the C2 position on IMP to form GMP is derived from A) B)

aspartate aspargine 191

C) D) E)

glutamine a-ketoglutarate arginine

Ans: C Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 35. Orotate is synthesized from A) B) C) D) E)

glycine and carbamoyl phosphate. arginine and carbamoyl phosphate. aspartate and carbamoyl phosphate. aspartate and glutamine. asparagine and glutamine.

Ans: C Section: 23.2.A Level of Difficulty: Moderate Learning Objective: Synthesis of Pyrimidine Ribonucleotides 36. Which best describes the synthesis of purine nucleotides? A) B) C) D) E)

The basic ring structure, orotate, is synthesized and then linked to PRPP. This is then modified to produce either GMP or AMP. The basic ring structure, inosine, is synthesized and then linked to PRPP. This is then modified to produce either GMP or AMP. The basic ring structure, orotate, is synthesized stepwise on PRPP. This is then modified to produce either GMP or AMP. The basic ring structure, inosine, is synthesized stepwise on PRPP. This is then modified to produce either GMP or AMP. The basic ring structure, orotate, is synthesized and then linked to PRPP. This is then modified to produce either UMP or CMP.

Ans: D Section: 23.1.A, 23.1.B Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides

37. Individuals that do not consume adequate folic acid have serious problems with the A) B) C) D)

synthesis of dATP. synthesis of dCTP. synthesis of dGTP. synthesis of dTTP. 192

E) all of the above Ans: B Section: 23.1.A, 23.3.B Level of Difficulty: Difficult Learning Objective: Synthesis of Purine Ribonucleotides, Formation of Deoxyribonucleotides 38. What category of reaction converts orotate monophosphate (OMP) into uracil monophosphate (UMP)? A) B) C) D) E)

a transamination a methylation a decarboxylation a carboxylation none of the above

Ans: C Section: 23.2.B Level of Difficulty: Moderate Learning Objective: Synthesis of Pyrimidine Ribonucleotides 39. Which of the following statements is TRUE? A) B) C) D) E)

PRPP is an effective feedback inhibitor of nucleotide synthesis. GTP serves as the energy input for AMP synthesis from IMP. Oxidation of ribosyl moieties to produce deoxynucleotides occurs at the diphosphate level. Thymidylate synthase methylates dUTP to produce dTTP. All of the above are true.

Ans: B Section: 23.1.B Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides 40. Which of the following reactions is NOT catalyzed by nucleoside diphosphate kinase? A) B) C) D) E)

GDP + ATP ® GTP + ADP UDP + ATP ® UTP + ADP CDP + ATP ® CTP + ADP dGDP + ATP ® dGTP + ADP It catalyzes all the above.

Ans: C Section: 23.1.B, 23.3.A Level of Difficulty: Difficult Learning Objective: Synthesis of Purine Ribonucleotides, Formation of Deoxyribonucleotides 41. Which of the following is correct regarding pyrimidine synthesis? 193

!"#$%!(')

A) carbamoyl phosphate + PRPP !⎯⎯⎯⎯⎯⎯# aspartate + Pi + dihydroorotate !"#$%!(')

B) carbamoyl phosphate + aspartate + quinone !⎯⎯⎯⎯⎯⎯# quinone

Orotate + Pi +

H2O + reduced

!"#$%!(')

C) dihydroorotate + quinone !⎯⎯⎯⎯⎯⎯# orotate + reduced quinine D) A and C E) None of the above Ans: B Section: 23.2.A Level of Difficulty: Difficult Learning Objective: Synthesis of Pyrimidine Ribonucleotides 42. In animals, elevated levels of PRPP will A) B) C) D) E)

activate pyrimidine biosynthesis. activate purine biosynthesis. activate both pyrimidine and purine biosynthesis. inhibit pyrimidine biosynthesis; activate purine biosynthesis. inhibit purine biosynthesis; activate pyrimidine biosynthesis.

Ans: C Section: 23.1.C; 23.2.C Level of Difficulty: Moderate Learning Objective: Synthesis of Purine Ribonucleotides and Synthesis of Pyrimidine Ribonecleotides

Using the diagram above, answer questions 43 - 45. C may be used to represent either or both of the atoms labeled C. 43. Glycine contributes to the ring at position _____. A) B) C) D) E)

A B C D E 194

Ans: E Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 44. Formate contributes to the ring at position _____. A) B) C) D) E)

A B D B, D F

Ans: B Section: 23.1.A Level of Difficulty: Easy Learning Objective: Synthesis of Purine Ribonucleotides 45. Rank the additions to the rings in order of formation. A) B) C) D) E)

C, B, A, F, D, E C, E, D, C, F, A, B A, C ,D ,E ,F ,B D, F, A, C, B, E C, F, A, C, B ,E ,D

Ans: B Section: 23.1.A Level of Difficulty: Difficult Learning Objective: Synthesis of Purine Ribonucleotides 46. A final common product from both purine degradation and pyrimidine degradation is A) B) C) D) E)

uric acid. aspartate. ribose-1-phosphate. ribose-5-phosphate. malonyl-CoA.

Ans: B Section: 23.4.A and C Level of Difficulty: Moderate Learning Objective: Nucleotide Degradation 47. The last step in purine degradation I. generates hydrogen peroxide as a byproduct. II. utilizes molecular oxygen. III. is inhibited by methotrexate. IV. requires NAD+. A) I, II, III, IV B) I, II, IV 195

C) D) E)

II, IV I, II, IV I, II

Ans: E Section: 23.4.A Level of Difficulty: Difficult Learning Objective: Nucleotide Degradation 48. Recombinant forms of the enzyme urate oxidase are available for therapeutic purposes. Based on the information in this chapter, in which of the following conditions might this therapy be useful? A) B) C) D) E)

myoadenylate deaminase deficiency severe combined immunodeficiency disease gout toxoplasmosis folate deficiency

Ans: C Section: 23.4.B Level of Difficulty: Difficult Learning Objective: Nucleotide Degradation 49. The anticancer drug methotrexate inhibits nucleotide synthesis. Which of the following explains why it also inhibits the synthesis of histidine and methionine? A) B) C) D) E)

The synthetic pathways for these amino acids require tetrahydrofolate for group transfer reactions. These amino acids are derivatives of the nucleotides UTP and GTP. Without the synthesis of nucleotides, there is not sufficient energy for the synthesis of the amino acids. <ethotrexate inhibits also inhibits the precursors for these amino acids. all of the above

Ans: A Section: 23.3.B Level of Difficulty: Difficult Learning Objective: Formation of Deoxyribonucleotides 50. Acyclovir is a derivative of which of the following? A) B) C) D) E)

a pyrimidine a purine malonic semialdehyde dihydrofolate thioredoxin

Ans: B Section: 23.4.B Level of Difficulty: Easy Learning Objective: Nucleotide Degradation 196

Chapter 24: Nucleic Acid Structure Matching Choose the correct answer from the list. Not all the answers will be used. A) type I B) ribocatalyzers C) C2¢-endo D) repressors E) ethidium F) type II G) C3¢-endo H) hybridized I) interchanged J) supercoiled K) cooperative L) non-cooperative M) underwound N) ribozymes O) deuterium P) zinc finger Q) leucine zipper 1. The 2-deoxyribose groups assume the ____ conformation in B-DNA. Ans: C Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 2. Naturally occurring circular DNA is typically _______. Ans: M Section: 24.1.C Level of Difficulty: Easy Learning Objective: The DNA Helix 3. Single-strand breaks in DNA are transiently created by ______ topoisomerases. Ans: A Section: 24.1.D Level of Difficulty: Easy Learning Objective: The DNA Helix 4. _________ topoisomerases that make double-strand breaks in DNA in a controlled fashion. Ans: F Section: 24.1.D Level of Difficulty: Easy 191

Learning Objective: The DNA Helix 5. The denaturation of DNA is a ______ cooperative process. Ans: K Section: 24.2.A Level of Difficulty: Easy Learning Objective: Forces Stabilizing Nucleic Acid Structures 6. Complementary DNA and RNA strands can be ______. Ans: H Section: 24.2.C Level of Difficulty: Easy Learning Objective: Forces Stabilizing Nucleic Acid Structures 7. RNA catalysts are called ______. Ans: N Section: 24.2.C Level of Difficulty: Easy Learning Objective: Forces Stabilizing Nucleic Acid Structures 8. ________, an ion that intercalates into double-stranded DNA, is often used for staining gels. Ans: E Section: 24.3.B Level of Difficulty: Easy Learning Objective: Fractionation of Nucleic Acids 9. In prokaryotes, many of the _____ that bind to DNA contain a HTH motif. Ans: D Section: 24.4.B Level of Difficulty: Moderate Learning Objective: DNA-Protein Interactions

10. Heptad repeats are found in the ______ region of DNA binding proteins. Ans: Q Section: 24.4.C Level of Difficulty: Easy Learning Objective: DNA-Protein Interactions 192

Multiple Choice 11. Which of the following scientists is now accredited with generating the X-ray diffraction photograph that played a pivotal role in the discovery of the structure of B-DNA? A) B) C) D) E)

James Watson Francis Crick Maurice Wilkins Rosalind Franklin all of the above

Ans: D Section: 24.1.A Level of Difficulty: Easy Learning Objective: The DNA Helix 12. The chromosomes of some viruses and bacteria are ______ and often ______. A) B) C) D) E)

linear; single stranded linear; supercoiled circular; single stranded circular; supercoiled none of the above

Ans: D Section: 24.1.C Level of Difficulty: Moderate Learning Objective: The DNA Helix 13. Which of the following would NOT result in the relaxation of supercoiled DNA? A) B) C) D) E)

heating the DNA to induce denaturation nicking one strand treatment with pancreatic DNaseI treatment with type II topoisomerase treatment with type I topoisomerase

Ans: A Section: 24.1.C Level of Difficulty: Moderate Learning Objective: The DNA Helix 14. Which of the following prokaryotic enzymes can introduce negative supercoils? A) B) C) D) E)

topoismerase IA topoismerase III DNA gyrase all of the above none of the above

Ans: C Section: 24.1.D 193

Level of Difficulty: Easy Learning Objective: The DNA Helix 15. Heat-denatured DNA exhibits ______ UV absorbance, which is called the ______. A) B) C) D) E)

increased; hyperchromic effect decreased; hyperchromic effect increased; hypochromic effect decreased; hypochromic effect identical; renaturation effect

Ans: A Section: 24.2.A Level of Difficulty: Moderate Learning Objective: Forces Stabilizing Nucleic Acid Structures 16. tRNA molecules are I. extensively base-paired. II. stabilized by hydrogen bonds. III. stabilized by stacking interactions. IV. stabilized by covalent cross links. A) I, II B) II, III C) I, II, III D) I, III E) I, II, IV Ans: C Section: 24.2.C Level of Difficulty: Moderate Learning Objective: Forces Stabilizing Nucleic Acid Structures

17. Which of the following materials would be useful for a researcher seeking to purify chromosomal DNA of lysed E. coli cells from cellular proteins and RNA? A) B) C) D) E)

ethidium bromide hydroxyapatite acridine orange proflavin DNA gyrase

Ans: B Section: 24.3.A Level of Difficulty: Easy 194

Learning Objective: Fractionation of Nucleic Acids 18. The sequence-specific binding of BamHI to DNA depends primarily on A) B) C) D) E)

hydrogen bonding and allows binding to less specific sequences as well. hydrogen bonding and precludes binding to any other sequence. stacking interactions and could be mimicked using an intercalation molecule. hydrogen bonding and could be mimicked using an intercalation molecule. none of the above

Ans: B Section: 24.4.A Level of Difficulty: Difficult Learning Objective: DNA-Protein Interactions 19. Histone H1 binds to ____ which allows attachment to _____. A) B) C) D) E)

the nucleosome core particle; nucleases linker DNA; the next nucleosome the nucleosome core particle; the next nucleosome linker DNA; nucleases none of the above

Ans: B Section: 24.5.B Level of Difficulty: Moderate Learning Objective: Eukaryotic Chromosome Structure 20. What evidence suggests that a biological function exists for Z-DNA? A) B) C) D) E)

Z-DNA is unique because it is made up of alternating pyrimidine and purine residues in the anti and syn conformation. The left-handed nature of Z-DNA allows phosphate separation which is stabilizing.. X-ray structure of the protein Za binding Z-DNA has been identified. A and B A, B, and C

Ans: C Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 21. Which of the following statements about the structure and conformation of DNA is FALSE? A) B) C) D) E)

DNA binding proteins distort DNA structure Changes in ionic strength can alter DNA structure Specific sequences can cause deviations in conformation. Changes in DNA conformation result from energy minimizations and do not relate to in vivo conditions. All of the above are true. 195

Ans: D Section: 24.1.B Level of Difficulty: Difficult Learning Objective: The DNA Helix 22. Which of the following topoisomerases require(s) ATP hydrolysis for energy? I. type IA II. type IB III. type II A) I only B) II only C) III only D) I, II E) I, II, III Ans: C Section: 24.1.D Level of Difficulty: Easy Learning Objective: The DNA Helix 23. An effective antibiotic is ___, which inhibits ______. A) B) C) D) E)

ciprofloxacin, DNA gyrase doxorubicin, Type IA topoisomerase novobiocin, ATPase camptothecin, Type II topoisomerase none of the above

Ans: A Section: 24.1.D Level of Difficulty: Easy Learning Objective: The DNA Helix

24. The DNA helix is stabilized by I. hydrogen bonds between phosphate groups. II. stacking interactions. III. an entropically favored interaction between hydrophobic groups. IV. favorable electrostatic interactions. A) I, II, III, IV B) I, II, IV C) II, IV D) III, IV E) II, III 196

Ans: C Section: 24.2.B Level of Difficulty: Difficult Learning Objective: Forces Stabilizing Nucleic Acid Structures 25. Indirect readout refers to I. a protein’s ability to form hydrogen bonds through a network of water molecules. II. the 5¢ to 3¢ sequence on the opposite strand of a DNA helix. III. a protein’s ability to recognize a specific DNA sequence by its backbone conformation and flexibility. IV. the protein's ability to make hydrogen bonds with nonesterified phosphate oxygens A) B) C) D) E)

I, III, IV II, IV III, IV I, III I, IV

Ans: C Section: 24.4.B Level of Difficulty: Moderate Learning Objective: DNA-Protein Interactions 26. Which of the following statements about zinc fingers is FALSE? A) B) C) D) E)

Zinc fingers contain Cys and His residues. Zinc is tetrahedrally coordinated as part of a small compact protein domain. More than one finger can be found in a protein; as many as 60 have been observed. Zinc fingers are the predominant DNA-binding motif of restriction enzymes. A zinc finger recognizes specific sequences of DNA via its N-terminal helices.

Ans: D Section: 24.4.A, 24.4.C Level of Difficulty: Difficult Learning Objective: DNA-Protein Interactions

27. The sugar pucker is___ in the ___form. A) B) C) D) E)

C2'-endo; A-DNA C3'-endo; B-DNA C2'-endo for pyrimidines and C3'-endo for purines: Z-DNA C2'-endo for purines and C3'-endo for pyrimidines: B-DNA C2'-endo for purines and C3'-endo for pyrimidines: A-DNA

Ans: C Section: 24.1.A Level of Difficulty: Moderate 197

Learning Objective: The DNA Helix 28. During which of the following processes are RNA−DNA hybrids observed? A) B) C) D) E)

transcription, both eukaryotic and prokaryotic translation, both eukaryotic and prokaryotic replication, both eukaryotic and prokaryotic transcription, prokaryotic only replication, prokaryotic only

Ans: A Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 29. Which of the following best describes the structure of RNA-DNA hybrids? I. They are most similar to A-DNA. II. They are most similar to B-DNA. III. They are most similar to Z-DNA. IV. They are most similar to RNA. A) I only B) II only C) I, II D) III only E) IV only Ans: D Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix

30. Southern blots identify _____, Northern blots identify ____, and Western blots identify ______. A) B) C) D) E)

DNA, proteins, RNA DNA, RNA, proteins RNA, proteins, DNA RNA, DNA, proteins proteins, DNA, RNA

Ans: B Section: 24.3.B Level of Difficulty: Moderate 198

Learning Objective: Fractionation of Nucleic Acids 31. Western blots, or ____, identify ______ using ______. A) B) C) D) E)

Northern blots; RNA; antibodies immunoblots; proteins; antibodies Southern blots; proteins; radioactivity immunoblots; DNA; antibodies Northern blots; DNA; antibodies

Ans: B Section: 24.3.B Level of Difficulty: Moderate Learning Objective: Fractionation of Nucleic Acids 32. Two circular DNAs are isolated, both with 1000 bp, are electrophoresed side-by-side:

A) B) C) D) E)

#1: twist (T) = +100, writhing number (W) = −5 #2: twist (T) = +1000, writhing number (W) = +5 DNA #1 should migrate further. DNA #2 should migrate further. They should migrate the same distance. More information is required to determine. This cannot be determined regardless of additional information.

Ans: C Section: 24.1.C, 24.3.B Level of Difficulty: Difficult Learning Objective: The DNA Helix, Fractionation of Nucleic Acids

33. Which the following sequences of DNA is most likely to form Z-DNA in vitro? A) B) C) D)

5'-ATATATATATATATATATAT-3' 3'-TATATATATATATATATATA-5' 5'-AAAAAAAAAAAAAAAAAAAA-3' 3'-TTTTTTTTTTTTTTTTTTTT-5' 5'-GCGCGCGCGCGCCGCGCGCG-3' 3'-CGCGCGCGCGCGCGCGCGCG-5' 5'-GGGGGGGGGGGGGGGGGGGG-3' 3'-CCCCCCCCCCCCCCCCCCCC-5' 199

5'-GATCGATCGATCGATCGATC-3' 3'-CTAGCTAGCTAGCTAGCTAG-5'

Ans: C Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix

34. Which atoms, or groups attached to them, face into the major groove of B- DNA? H O

N 8

deoxyribose

7 6

1 N 3

N N

N 3

deoxyribose

A) B) C) D) E)

purine 1 & 2; pyrimidine 2 & 3 purine 2 & 3; pyrimidine 2 purine 8 & 9; pyrimidine 1 & 6 purine 6 & 7; pyrimidine 4 & 5 purine 6 & 7; pyrimidine 2

Ans: D Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix

35. Which atoms, or groups attached to them, face into the minor groove of B-DNA?

200

H O

N 8

deoxyribose

7 6

1 N 3

N 3

N N

deoxyribose

A) B) C) D) E)

purine 1 & 2; pyrimidine 2 & 3 purine 2 & 3; pyrimidine 2 purine 8 & 9; pyrimidine 1 & 6 purine 6 & 7; pyrimidine 4 & 5 purine 6 & 7; pyrimidine 2

Ans: B Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 36. A circular 25000 base pair DNA molecule with no supercoils will have _____ helical twists if it is B-DNA. A) B) C) D) E)

about 2.5 about 25 about 250 about 2500 about 25000.

Ans: D Section: 24.1.A Level of Difficulty: Easy Learning Objective: The DNA Helix 37. If a circular DNA containing no supercoils is incubated with ethidium bromide A) B) C) D) E)

the number of twists will increase, positive supercoils will develop, and the linking number will remain the same. the number of twists will decrease, positive supercoils will develop, and the linking number will remain the same. the number of twists will increase, negative supercoils will develop, and the linking number will remain the same. the number of twists will decrease, negative supercoils will develop, and the linking number will remain the same. the linking number will be altered, and both the writhing number and twist will adjust accordingly.

Ans: B Section: 24.1.A, 24.3.B Level of Difficulty: Difficult Learning Objective: The DNA Helix, Fractionation of Nucleic Acids 201

38. In A-DNA A) B) C) D) E)

the glycosidic bond is in the syn conformation with a C3'-endo sugar pucker. the glycosidic bond is in the syn conformation with a C2'-endo sugar pucker. the glycosidic bond is in the anti conformation with a C3'-endo sugar pucker. the glycosidic bond is in the anti conformation with a C2'-endo sugar pucker. the glycosidic bond conformation and sugar pucker is dependent on the base.

Ans: C Section: 24.1.A Level of Difficulty: Easy Learning Objective: The DNA Helix 39. Which of the following can be determined from a Northern blot? A) B) C) D) E)

the size of a gene transcript the abundance of a gene transcript the tissue specificity of gene transcript the stage-specificity of a gene transcript all of the above

Ans: E Section: 24.3.B Level of Difficulty: Moderate Learning Objective: Fractionation of Nucleic Acids 40. Which of the following best describes the structure of a nucleosome? A) B) C) D) E)

approximately 150 bp of DNA wrapped around a set of two H2A/H2B and two H3/H4 dimers with H1 on the outside approximately 15 bp of DNA wrapped around an octamer of H1 with H2A,B, H3 and H4 on the outside approximately 150 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside approximately 1500 bp of DNA wrapped around a tetramer of either H2A/H2B or H3/H4 with H1 on the outside approximately 200 bp of DNA wrapped around a tetramer of H2A,H2B,H3, and H4 with H1 on the outside

Ans: A Section: 24.4.B Level of Difficulty: Moderate Learning Objective: Eukaryotic Chromosome Structure 41. Hammerhead ribozyme A) B) C) D)

contains a catalytic core with a Fe2+ at its center. utilizes hydrogen bonding to position itself favorably for nucleophilic attack. enhances the rate of cleavage of itself by a factor of five. A and C 202

B and C

Ans: B Section: 24.2.C Level of Difficulty: Difficult Learning Objective: Forces Stabilizing Nucleic Acid Structures 42. Which of the following is used to allow effective gel electrophoresis of DNAs > 100,000 base pairs? A) B) C) D) E)

hydroxyapatite treatment prior to gel loading Northern blots pulsed-field gel electrophoresis Southern Blot Western Blot

Ans: C Section: 24.3.B Level of Difficulty: Easy Learning Objective: Fractionation of Nucleic Acids 43. Based on the information in this chapter, which of the following sequences would likely bind a repressor if double stranded? A) B) C) D) E)

5' TGAGCA3' 5' TGATCA3' 5' TACGTCA3' All of the above would bind the repressor with equal efficiency None of the above would bind would the repressor.

Ans: B Section: 24.4B Level of Difficulty: Difficult Learning Objective: DNA-Protein Interactions 44. Which of the following is FALSE regarding DNA binding to proteins? A) B) C) D) E)

Most eukaryotic transcription factors contain a conserved DNA-binding basic region. The basic regions typically bind in the major groove of its target DNA. Eukaryotic transcription factors either contain an HTH motif or resemble the met repressor. all of the above none of the above

Ans: C Section: 24.4.C Level of Difficulty: Easy Learning Objective: DNA-Protein Interactions 45. Nucleosomes 203

I. reduce the contour length of DNA 7-fold. II. are bound together by linker histones. III. come together to form a zigzag double helix. IV. contain a histone octamer. A) I, II, III, IV B) II, III C) III, IV D) I, IV E) II, IV Ans: A Section: 24.4.A, B, C Level of Difficulty: Moderate Learning Objective: Eukaryotic Chromosome Structure 46. Which of the following is NOT a requirement of genetic material? A) B) C) D)

The lifetime of the material must be such that it can undergo repeated decoding. The material must be accessible for replication, transcription, and translation. The material must be capable of duplication. The material must perform a read only function to minimize damaging changes in structure. none of the above

E) Ans: D Section: 24.1 Introduction Level of Difficulty: Difficult Learning Objective: The DNA Helix 47. In B-DNA A) B) C) D) E)

the width of the base pair varies depending on the bases involved. the base planes are rotated approximately 90° from the axis of the helix. the sugar pucker must be variable depending on the base attached. the helix twist is approximately 10° per base pair. all of the above

Ans: B Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 48. Which of the following is FALSE about RNA? A) B) C) D) E)

It may be double stranded in viral genomes. It may form double stranded stems by binding its complementary bases within the same strand. It always forms a single strand that resembles the structure of B-DNA. It is only synthesized as a single strand. It may be involved in the control of gene expression. 204

Ans: C Section: 24.1.A Level of Difficulty: Moderate Learning Objective: The DNA Helix 49. Which of the following is TRUE regarding the rotation of the bonds in DNA? A) B) C) D) E)

The vertex angles of the ribose rind are 108°. The ribose ring always puckers at C3'. Noncovalent interactions between the ribose ring and the phosphate group constrain rotation. A and B B and C

Ans: C Section: 24.1.B Level of Difficulty: Difficult Learning Objective: The DNA Helix 50. E. coli topoisomerase III I. contains a hole capable of holding duplex DNA that is lined with negatively charged residues. II. binds the sugar-phosphate backbone such that base recognition is possible. III. functions by nucleophilic attack on the binding phosphate group. A) I, II B) II, III C) I, III D) I only E) II only Ans: B Section: 24.1.D Level of Difficulty: Difficult Learning Objective: The DNA Helix

205

Chapter 25: DNA Replication, Repair and Recombination Matching Choose the correct answer from the list. Not all the answers will be used. A) SSB B) Tus C) primosome D) ARS E) ATS F) primer G) transposons H) nick translation I) photolyase J) processive K) G-loops L) G-quartets M) accurate N) lagging strand synthesis O) MCM P) abortive 1. Enzymes that undergo many rounds of polymerization catalysis before dissociating from the substrate are described as highly ______. Ans: J Section: 25.2.A Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 2. The RNA segment to which DNA residues are added during replication is the ______. Ans: F Section: 25.1 Level of Difficulty: Easy Learning Objective: Overview of DNA Replication 3. The process whereby nucleotides are removed from the 5¢ end of one DNA segment while nucleotides are added to the 3¢ end of the immediately preceding DNA segment is called ______. Ans: H Section: 25.2.A Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 4. DNA separated at the replication fork is stabilized by ______ . 199

Ans: A Section: 25.2.B Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 5. E. coli primer synthesis is catalyzed by a ______. Ans: C Section: 25.2.B Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 6. Termination of replication fork movement in E. coli involves the binding of the ______ protein at a Ter site. Ans: B Section: 25.2.D Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 7. In yeast, DNA replication begins at sequences known as ______. Ans: D Section: 25.3.B Level of Difficulty: Moderate Learning Objective: Eukaryotic DNA Replication 8. G-rich polynucleotides can form _______ Ans: L Section: 25.3.C Level of Difficulty: Easy Learning Objective: Eukaryotic DNA Replication 9. Direct reversal of pyrimidine dimers in prokaryotic cells is catalyzed by a DNA _____. Ans: I Section: 25.5.A Level of Difficulty: Easy Learning Objective: DNA Repair

10. Genes can be moved by _______. Ans: G Section: 25.6 Level of Difficulty: Easy 200

Learning Objective: Recombination

Multiple Choice 11. Replication of circular DNA occurs at the “bubbles” or “eyes”, also called ______ . A) q structures B) f bubbles C) q bubbles D) s structures E) s bubbles Ans: A Section: 25.1 Level of Difficulty: Easy Learning Objective: Overview of DNA Replication 12. Pol I synthesizes new DNA with very high fidelity, due to its A) high processivity. B) 3¢ ® 5¢ exonuclease activity. C) helicase association with the primase. D) 5¢ ® 3¢ exonuclease activity. E) all of the above. Ans: B Section: 25.2.A Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 13. Pol I is proteolytically cleaved to yield the ____, which lacks 5¢®3¢ exonuclease activity. A) Klenow fragment B) Klentaq1 polymerase C) Okazaki fragment D) ligase E) primase Ans: A Section: 25.2.A Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication

14. Which of the following would result in single stranded DNA? A) B) C) D) E) Ans: C

Klenow fragment Klentaq I DnaB DnaG pol III 201

Section: 25.2 Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 15. E. coli leading and lagging strand synthesis takes place at the A) the Klenow fragment binding site. B) Pol III & Tus interface. C) multiprotein replisome. D) origin recognition complex. E) telomere. Ans: C Section: 25.2 Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication 16. Capping is important because A) it likely protects the telomere ends from becoming shortened. B) it likely prevents DNA repair mechanisms from initiating at the telomeres. C) it likely results in increased processivity on the eukaryotic chromosome. D) all of the above E) none of the above Ans: B Section: 25.3.C Level of Difficulty: Difficult Learning Objective: Eukaryotic DNA Replication 17. Free radical damage to DNA often results in I. pyrimidine dimers II. point mutations III. insertions IV. base excision I only. II only. I, II. II, III. I, IV.

A) B) C) D) E) Ans: C Section: 25.4.A Level of Difficulty: Moderate Learning Objective: DNA Damage 18. The presence of proflavin is likely to induce A) B) C)

pyrimidine dimers. point mutations. deletions. 202

D) transversions. E) Any of the above may occur. Ans: C Section: 25.4.A Level of Difficulty: Difficult Learning Objective: DNA Damage 19. Positive correlations between mutagenesis and carcinogenesis A) are increased with teleomere capping. B) are reverted via nick translation. C) are examined using the Ames test. D) increase with photoreactivation. E) None of the above is correct . Ans: C Section: 25.4.B Level of Difficulty: Easy Learning Objective: DNA Damage 20. When a section of DNA is damaged and polymerization cannot proceed, _____ repair can reconstitute the damaged replication fork. A) mismatch B) nucleotide excision C) recombination D) photoreactivation E) base excision Ans: C Section: 25.6.E Level of Difficulty: Moderate Learning Objective: DNA Repair 21. In most organisms, replication proceeds in a ______ manner from the ______. A) discontinuous; leading strand B) unidirectional; chromosome ends C) bidirectional; replication origin D) bidirectional; chromosome ends E) discontinuous; chromosome ends Ans: C Section: 25.1 Level of Difficulty: Easy Learning Objective: Overview of DNA Replication 22. Lagging stands are polymerized in the ______ direction, and the DNA fragments are about ______ nucleotides (nt) long in eukaryotic cells. A) B)

5¢ to 3¢, 100–200 5¢ to 3¢, 1000–2000 203

C) 3¢ to 5¢, 100–400 D) 3¢ to 5¢, 1000–50000 E) none of the above Ans: A Section: 25.1 Level of Difficulty: Moderate Learning Objective: Overview of DNA Replication 23. Which of the following statements about Pol I is FALSE? A) B) C) D) E)

Experiments demonstrate that Pol I exhibits exonuclease activity. Pol I is not the primary replicase in E. coli. Mutation analysis demonstrates that Pol I functions in DNA repair. Mutation analysis demonstrates the Pol I activity is not essential for cell viability. Experiments have successfully utilized Pol I to radioactively label DNA in lab experiments.

Ans: D Section: 25.2.A Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 24. Which of the following statement(s) about DNA polymerase III (Pol III) is (are) TRUE? I. DNA polymerase III has greater accuracy than RNA polymerase. II. Pol III is the primary replicase of E. coli. III. Pol III does not contain 5¢ to 3¢ exonuclease activity. I, II. II, III. III only. I only. I, II, III.

A) B) C) D) E) Ans: E Section: 25.2.A Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication

25. DNA ligase can be activated by which of the following? I. The coupled hydrolysis of NAD+ to (NMN+) + AMP. II. The coupled hydrolysis of ATP to AMP + PPi. III. The coupled hydrolysis of GTP to GMP + PPi. I only II only III only I, II I, III

A) B) C) D) E) Ans: D Section: 25.2.C Level of Difficulty: Moderate

204

Learning Objective: Prokaryotic DNA Replication 26. Which of the following statements about the fidelity of replication is FALSE? A) B)

Cells maintaining an equal concentration of each dNTP helps maintain fidelity. DNA polymerase catalyzes synthesis in a two-stage reaction, ensuring the proper base is added. Cells viability is removed when DNA point mutations are incorporated. Pol I and Pol III are both involved in increasing fidelity. Specific repair systems repair and maintain DNA.

C) D) E) Ans: C Section: 25.2.A, 25.4.A Level of Difficulty: Difficult Learning Objective: Prokaryotic DNA Replication, DNA Damage

27. Synthesis of telomeres requires the enzyme ______, which is a type of ______. A) telomerase, helicase B) telomerase, ribonucleoprotein C) ribonuclease, riboprotein D) ribotelase, ligase E) none of the above Ans: B Section: 25.3.C Level of Difficulty: Moderate Learning Objective: Eukaryotic DNA Replication 28. Which of the following statements about DNA methylation is TRUE? I. Methylation plays a role in genomic imprinting. II. Methylation can influence gene regulation. III. Methylation plays a role in restriction modification systems. IV. Methylation occurs in prokaryotic cells, but not eukaryotic cells. I, II, III, IV I, II, III II, III II, III, IV II only

A) B) C) D) E) Ans: B Section: 25.4.A Level of Difficulty: Learning Objective: DNA Damage

29. Defects in the proteins ______, which associate with RAD-51, are correlated with several types of cancer. A) B) C)

BRCA1 and BRCA2 RecU and RecB Pol a and Pol b 205

D) DSB and NHEJ E) RecA and RecUGA Ans: A Section: 25.6.B Level of Difficulty: Difficult Learning Objective: Recombination 30. Which of the following are TRUE about transposons? I. They are normal components of plasmids. II. They often carry genes for antibiotic resistance. III. They insert at a target sequence that is a repetitive unit of about 200 bp. A) I, II, III B) I, II C) II, III D) II only E) III only Ans: B Section: 25.6.C Level of Difficulty: Difficult Learning Objective: Recombination 31. The experiments of Reiji Okazaki allowed determination that DNA synthesis occurs in I. a continuous fashion. II. different ways on the lagging strand than the leading strand. III. resulted in new synthesized DNA fragments containing the radioactive isotope. I, II, III II, III I, II I, III II only

A) B) C) D) E) Ans: B Section: 25.1 Level of Difficulty: Moderate Learning Objective: Overview of DNA Replication

32. A prokaryotic replisome typically contains two molecules of DNA pol III, but only one molecule of DNA pol I. Why? A) B) C) D)

The DNA pol I works on the leading strand, while DNA pol IIIs work on the Okazaki fragments. since there are several of those, it takes more proteins to keep up. DNA pol I has a built-in proofreading exonuclease; DNA pol III does not. The second DNA pol III is needed to follow the first to accomplish the necessary proofreading. The DNA pol IIIs work at one replication fork, while the DNA pol I works at the other. This way they don't meet exactly at the other side of the chromosome. The DNA pol IIIs do most of the work. DNA pol I only has to work on the telomers. 206

DNA pol I replaces the RNA primers with DNA, which really only needs to be done repetitively on one strand, while both strands are worked on by the DNA pol IIIs.

Ans: E Section: 25.2.C Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 33. Which of the following statements about telomerase is FALSE? I. Telomerase is an RNA polymerase. II. Telomerase has a 5'—>3' polymerase activity. III. Telomerase uses RNA as a template. IV. The product of the telomerase-catalyzed reaction is rich in G and T. I only II only II, III I, III II, IV

A) B) C) D) E) Ans: A Section: 25.3.C Level of Difficulty: Moderate Learning Objective: Eukaryotic DNA Replication

Use the following information to answer the next 3 questions (Questions 34 0 36): Suppose that an error in replication occurred at position 324 in the E. coli sequence below, and that a GATC motif used to regulate replication and restriction is located about 300 bp away. Note that the A on the bottom (shown by the underlining) strand is methylated. 5' 3'

10 ... 310 320 330 GGACGGATCC ...TAAGCTGGTGGTGGTGGGCGCCGGCGGTGT CCTGCCTAGG ...ATTCGACCACCACCACCCGCGGCAGCCACA

34. What kind of mutation has occurred? A) B) C) D) E)

transition transversion insertion deletion none of the above

Ans: B Section: 25.4.A Level of Difficulty: Moderate Learning Objective: DNA Damage

207

35. What enzymes would be used to repair this error? A) methyl-directed mismatch repair enzymes B) nucleotide excision repair enzymes C) methyl-directed double strand break repair enzymes D) UvrABC plus UvrD E) None of the above systems can repair this error Ans: A Section: 25.5.D Level of Difficulty: Difficult Learning Objective: DNA Repair 36. E. coli DNA repair enzymes act on the sequence. Which of the following will result? A) The underlined A will be changed to a C. B) The underlined G will be changed to a T. C) The underlined A will be methylated. D) The underlined G will be methylated. E) More than one of the above is correct Ans: B Section: 25.5.D Level of Difficulty: Moderate Learning Objective: DNA Repair 37. Which of the following activities does E. coli DNA polymerase III contain? I. 5'→3' polymerase II. 5'→3' exonuclease III. 3'→5' exonuclease I only I, II II only I, III I, II, III

A) B) C) D) E) Ans: D Section: 25.1.A Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 38. Which of the following enzymes catalyze the creation of AP sites for base excision repair? A) exonuclease B) endonuclease C) ligase D) glycosylase E) methylase Ans: D Section: 25.5.B Level of Difficulty: Easy Learning Objective: DNA Repair 208

39. Suppose Meselson & Stahl had observed the following data in their famous experiment involving a switch from medium containing 15N to 14N. What would they have concluded about the nature of DNA replication?

A) They still would have concluded that DNA replication is semiconservative. B) They would have concluded that DNA replication is conservative. C) They would have concluded that DNA replication is dispersive/random. D) None of the above is correct. E) Cannot be determined with the information given. Ans: C Section: 25.1 Level of Difficulty: Difficult Learning Objective: Overview of DNA Replication 40. Deamination of cytosine leads to the formation of A) thymine. B) 5-methylcytosine. C) uracil. D) 5-bromouracil. E) 5-methyluracil. Ans: C Section: 25.3.B Level of Difficulty: Easy Learning Objective: Eukaryotic DNA Replication

209

41. The DNA sequence shown below is copied by the Klenow fragment. Which of the following would most likely result? 5' TGCGTGCACTCGA 3' A) identical B) 5' TGCGT 3' C) 5' TGCAGTGACGCT 3' D) cannot predict E) none of the above Ans: C Section: 25.2.A Level of Difficulty: Difficult Learning Objective: Prokaryotic DNA Replication 42. Which of the following would result in increased processivity in E.coli? A) b (sliding) clamp B) primosome C) helicase D) Dna B E) Dna G Ans: A Section: 25.2.C Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 43. In molecular biology labs researchers often use E.coli strains that are RecA minus (recA−) when transforming a cloned gene into a plasmid which explains why

A) B) C) D) E)

I. a Rec A-strain would have fewer replication errors. II. a Rec A-strain would have less opportunity forming DNA mutations. III. a Rec A-strain would increase error repair. I only. II only. III only. I, II II, III

Ans: B Section: 25.5.E Level of Difficulty: Difficult Learning Objective: DNA Repair

210

44. Which of the following can be extended by DNA polymerase? A) a single strand of DNA ending in a nucleotide with a free 3' OH B) a RNA single strand with a ribonucleotide with a free 3' OH C) a single strand DNA end in a deoxyribonucleotide with free 5' P D) a RNA single strand E) all of the above Ans: A Section: 25.1 Level of Difficulty: Moderate Learning Objective: Overview of DNA Replication 45. Which of the following describes the Holliday junction? A) point where DNA base excision repair initiates B) crossover point involving 4-stranded DNA structure in homologous recombination C) insertion point of a gene flanked in transposons D) point where MutS binds to initiate SOS response E) none of the above Ans: B Section: 25.6 Level of Difficulty: Easy Learning Objective: Recombination 46. Bacteria have obtained the b-lactamase gene which encodes a protein that renders all blactem antibodies such as ampicillin and penicillin inactive. Which of the following would result in an increased number of bacteria with this ability? I. a transposon with the b-lactamase gene II. a recombination event within the original strain that results in a point mutation inactivating b-lactamase III. an insertion in the original strain rendering transposase inactive IV. a deletion in the insertion sequence of the transposon A) I, II, III, IV B) I only C) II only D) II, III E) III, IV Ans: B Section: 25.6.C Level of Difficulty: Difficult Learning Objective: Recombination

211

47. A new DNA polymerase exhibits: (1) high processivity, (2) low fidelity, and (3) ability to replace RNA with DNA. Which of the following is probably TRUE? A) B) C) D) E)

It has 3’ exonuclease activity. It has 5’exonuclease activity. It has RNA primase activity. It is not associated with a clamp. both A and B

Ans: B Section: 25.1.A Level of Difficulty: Difficult Learning Objective: Prokaryotic DNA Replication 48. Considering the following eukaryotic DNA polymerases, which of the following has the highest fidelity? A) DNA pol a B) DNA pol b C) DNA pol d D) All have high fidelity E) All have low fidelity Ans: C Section: 25.3A Level of Difficulty: Moderate Learning Objective: Eukaryotic DNA Replication 49. Use the following diagram to complete the sentences below

“ ______ is the enzyme which catalyzes phosphodiester bond formation on both strands. Processivity of DNA pol is increased when associated with ____. DNA untwisting is accomplished by ______.” A, C, B A, B, C B, C, A A, D, B A, E, B

A) B) C) D) E) Ans: D Section: 25.2.A, B, C Level of Difficulty: Moderate Learning Objective: Prokaryotic DNA Replication 50. Which of the following describes the usefulness of primase? 212

A) It removes RNA bases and replaces them with DNA bases. B) It seals nicks. C) It adds an RNA starter sequence which can be elongated. D) It is only required on the leading strand. E) It unwinds the DNA. Ans: C Section: 25.2.B Level of Difficulty: Easy Learning Objective: Prokaryotic DNA Replication

213

Chapter 26: Transcription and RNA Processing Matching Choose the correct answer from the list. Not all the answers will be used. A) Rho (r) B) introns C) sigma (s) D) sense E) operons F) structural G) Pribnow H) promoters I) antisense J) exons K) nucleolus L) TATA M) sense N) AAAA (poly A) O) Ribosome 1. Eukaryotic RNA molecules are altered by removal of intervening sequences called ______. Ans: B Section: 26.3.A Level of Difficulty: Easy Learning Objective: Posttranscriptional Processing 2. An AT-rich region found in eukaryotic promoters is called the ______ box. Ans: L Section: 26.2.B Level of Difficulty: Easy Learning Objective: Transcription in Eukaryotes 3. The DNA strand that serves as a template during transcription is known as the ______ or noncoding strand. Ans: I Section: 26.1.B Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription

4. Prokaryotic contain nucleotide sequences know as _____ which contain related genes with related functions. Ans: E 207

Section: 26.1.B Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription 5. Protein-coding genes are also known as ______ genes. Ans: F Section: 26.1.B Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription 6. Eukaryotic rRNA genes are transcribed and processed in the ______. Ans: K Section: 26.3.B Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 7. Termination of bacterial transcription requires the ______ factor. Ans: A Section: 26.1.D Level of Difficulty: Moderate Learning Objective: Prokaryotic RNA Transcription 8. The expressed sequences of eukaryotic pre-mRNAs are known as ______. Ans: J Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 9. In eukaryotes, RNA polymerase does not include a removable ______ factor. Ans: C Section: 26.2.A, 26.2.C Level of Difficulty: Moderate Learning Objective: Transcription in Eukaryotes

10. CpG islands function analogously to prokaryotic ______. Ans: H Section: 26.2.B Level of Difficulty: Moderate Learning Objective: Transcription in Eukaryotes 208

Multiple Choice 11. In prokaryotes, the _____ factor recognizes base sequences in the _____ which facilitates RNA polymerase binding and initiates RNA synthesis. A) B) C) D) E)

s; promoter regulatory; enhancer s; enhancer regulatory; promoter omega; promoter

Ans: A Section: 26.1.B Level of Difficulty: Moderate Learning Objective: Prokaryotic RNA Transcription 12. The term rRNA refers to ______ RNA. A) B) C) D)

ribosomal retroviral recombinant rho factor

Ans: A Section: 26.1 Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription 13. Transcriptional activators that can have variable positions and orientations are called A) B) C) D) E)

core promoter elements. upstream promoter elements. CpG islands. enhancers. Inr elements.

Ans: D Section: 25.2.B Level of Difficulty: Moderate Learning Objective: Transcription in Eukaryotes

14. Most ______ have well defined 3¢ ends terminating in poly(A) tails of ~ 250 nt. A) B) C) D) E)

prokaryotic mRNAs eukaryotic mRNAs prokaryotic rRNAs eukaryotic rRNAs all of the above 209

Ans: B Section: 25.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 15. The fact that some eukaryotic rRNAs are self-splicing indicates that A) B) C) D) E)

RNA structures are highly variable. RNAs can contain modified bases. eukaryotes have multiple RNA polymerases. RNA can act as an enzyme or catalyst. None of the above is correct.

Ans: E Section: 25.3.B Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 16. The precursors of most eukaryotic rRNAs are synthesized by I. RNA polymerase I. II. RNA polymerase II. III. RNA polymerase III. A) I or III B) I or II C) I only D) II only E) III only Ans: C Section: 25.2.A Level of Difficulty: Easy Learning Objective: Transcription in Eukaryotes 17. The precursors of eukaryotic mRNAs are synthesized by ______. I. RNA polymerase I. II. RNA polymerase II. III. RNA polymerase III. A) I or III B) I or II C) I only D) II only E) III only Ans: D Section: 25.2.A Level of Difficulty: Easy Learning Objective: Transcription in Eukaryotes 18. The precursors of 5S rRNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs are synthesized by ______. 210

I. RNA polymerase I. II. RNA polymerase II. III. RNA polymerase III. A) I or III B) I or II C) I only D) II only E) III only Ans: E Section: 26.2 Level of Difficulty: Easy Learning Objective: Transcription in Eukaryotes 19. Imagine that a new drug is proposed which is hypothesized to selectively bind the transcription factor TBP. Which of the following would be affected? I. RNA polymerase I II. RNA polymerase II III. RNA polymerase III IV. E. coli RNA polymerase A) I, II, III, IV B) I, II, III C) I only D) II only E) IV only Ans: B Section: 26.2.C Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes

20. All cellular RNAs are transcribed from A) B) C) D) E)

DNA templates. RNA templates. either DNA or RNA templates, but not both in the same organism. a combination of DNA and RNA templates. none of the above

Ans: A Section: 26.1 Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription 21. Which of the following statements best describes the role of s factors in bacterial gene expression? A) B) C)

s factors determine which RNA polymerase is used during transcription. s factors mediate the excision of intronic sequences. s factors can be used to express certain genes necessary based on cell type. 211

D) E)

s factors bind to the TATA box and initiate transcription. none of the above

Ans: C Section: 26.1.A Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription 22. In eukaryotes all three RNA polymerases recognize A) B) C) D) E)

the promoter sequence bound by s factor. a single promoter sequence named TF II D. class I promoters. promoters with TATA boxes. none of the above.

Ans: E Section: 26.2.B Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes 23. How does the preinitiation complex begin to form at a TATA box–containing promoter? A) B) C) D) E)

RNAP binds to the sigma factor. RNAP binds to the initiator (Inr) element. TATA-binding protein binds to the TATA box. RNAP binds to the Rho factor. none of the above.

Ans: C Section: 26.2.C Level of Difficulty: Moderate Learning Objective: Transcription in Eukaryotes 24. In eukaryotes, mRNAs are synthesized in the cell ______, whereas most translation occurs in the ______. A) B) C) D) E)

nucleus, nucleosome. nucleus, cytosol. cytosol, nucleosome. cytosol, nucleus. nucleosome, cytosol.

Ans: B Section: 26.3.A Level of Difficulty: Easy Learning Objective: Posttranscriptional Processing 25. Which of the following types of RNA undergo posttranscriptional modifications? A) B) C)

mRNA rRNA tRNA 212

D) E)

all of the above none of the above

Ans: D Section: 26.3 Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 26. Why is TBP referred to as a universal transcription factor?

A) B) C) D) E)

I. TBP is present in both prokaryotic and eukaryotic organisms. II. TBP catalyzes the initiation of all RNA polymersase in both prokaryotes and eukaryotes. III. TBP is required for initiation by RNAP I, RNAP II, and RNAP III. I, II, III I, II I, III II, III III only

Ans: C Section: 26.2.C Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes 27. Which of the following is required for correct translation in eukaryote initiation? A) B) C) D) E)

poly(A) tail. 5' cap consisting of 7-methylguanosine. intron excision. alternative splicing. exon skipping.

Ans: B Section: 26.3.A Level of Difficulty: Easy Learning Objective: Posttranscriptional Processing 28. Which of the following are components of the spliceosome? I. primary transcript RNA. II. snRNPs. III. primary transcript RNA binding proteins. A) I, II B) I, III C) II, III D) I, II, III E) III only Ans: E Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 213

29. The processing of pre-rRNAs includes ______. I. nucleolytic cleavage. II. snoRNA-assisted methylation. III. snRNP-assisted methylation. A) I, II B) I, III C) II, III D) I, II, III E) III only Ans: A Section: 26.3.B Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 30. Which of the following is correct regarding splicing? A) B) C) D) E)

CPSFs are products of RNA sequences designed to recognize the 3'OH at the splice site. PABIII recognizes the A rich sequences at the 5' end of the splice site. Lariats are the sequence recognized by the cleavage site. smURFs are used to recognize the poly A tail and initiate slicing snRNPs are the protein product of U rich RNAs that partially complement the 5' splice junction.

Ans: E Section: 26.3.A Level of Difficulty: Difficult Learning Objective: Posttranscriptional Processing 31. Splicing I. occurs in the cytosol. II. results from 2' -OH on the exon attack on the 5' splice site. III. is completed when the 3' -OH on the newly cut exon attacks the 5'-terminal phosphate on the next exon. A) I, II B) I, III C) I only D) II only E) III only Ans: E Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 32. What is abortive initiation of transcription by RNA polymerase? A)

initiation at nonpromoter sites prior to dissociation of the polymerase. 214

B) C) D) E)

synthesis of short transcripts about 10 nucleotides long prior to commitment to elongation. pausing by the polymerase during elongation. failure to undergo the closed to open transition in the pre-initiation complex. none of the above

Ans: B Section: 26.1.C Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription 33. The Pribnow box is a _____ sequence that is _____ and is located at approximately ____ position of the promoter. A) B) C) D) E)

conserved; AT rich; -10 dispersive; AT rich; -10 conserved; GC rich; -35 dispersive; GC rich; -35 conserved; variable in sequence; 0

Ans: A Section: 26.1.B Level of Difficulty: Moderate Learning Objective: Prokaryotic RNA Transcription 34. E. coli RNA polymerase contains multiple subunits, which of the following combinations would result in promoter recognition but no RNA synthesis? A) B) C) D) E)

s and β a and b s, β, β' a, β, β' ω, β, a

Ans: A Section: 26.1.A Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription

35. Which of the following types of splicing RNAs uses a free nucleotide to perform a nucleophilic attack? I. group I introns II. group II introns III. self splicing introns A) I, II, III B) I, II C) I, III D) II, III E) none of the above Ans: C 215

Section: 26.3.C Level of Difficulty: Difficult Learning Objective: Posttranscriptional Processing 36. The phosphorylation of the CTD of RNA polymerase II is important for which phase of transcription? A) B) C) D) E)

initial binding of the promoter conversion from the pre-initiation (closed) complex to the initiation (open) complex progression from initiation to elongation termination of transcription none of the above

Ans: C Section: 26.2.A Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes 37. Which of the following describes the cap nucleotide linkage on a eukaryotic mRNA? I. 5'→5' linkage II. 5'→3' linkage III. 3'→5' linkage IV. 3'→3' linkage A) I or II B) I or III C) I only D) II only E) II or IV Ans: C Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 38. Which of the following best describes the cap nucleotide on a eukaryotic mRNA? A) B) C) D) E)

A C m7G T U

Ans: C Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing

216

39. In which of the following types of eukaryotics RNAs are introns completely removed most of the time, although exceptions can occur? I. mRNA II. rRNA III. tRNA A) I, II B) I, III C) II, III D) I, II, III E) none of the above Ans: A Section: 26.3.A, 26.3.C Level of Difficulty: Easy Learning Objective: Posttranscriptional Processing 40. Which of the following best describes the function of poly(A) tails for eukaryotic mRNAs? A) B) C) D) E)

They are required for accurate translation. They have a protective role against degradation. They signal transcription termination. They function as splice sites. No role has been observed for these features.

Ans: B Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 41. Which of the following would result in the tightest binding association between E. coli RNA polymerase and DNA? A) B) C) D) E)

core enzyme binding single stranded DNA at the promoter region open complex bound to the Pribnow box core enzyme binding duplex DNA following promoter recognition haloenzyme binding duplex DNA at the promoter site haloenzyme binding duplex DNA following promoter recognition

Ans: C Section: 26.1.B Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription 42. Which of the following if TRUE regarding prokaryotic DNA polymerase?

A) B) C)

I. Abortive initiation is common. II. RNA polymerase processivity increases with the β clamp. III. The error rate is 1 in 106. IV. Initiation of transcription begins at the −10 position. I, II, III I only III only 217

D) E)

III, IV II, III, IV

Ans: B Section: 26.1.B, C Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription 43. Which of the following DNA sequences would most likely result in transcription termination? A) B)

5' GCGCCTAGGCGCATTTTT 3' 3' CGCGGATCCGCGTAAAAA 5 ' 5' GCGCCCGCTTTTTT 3' 3' CGCGGGCCAAAAAA 5'

5' GCGCCCGCAAAAAA 3' 3' CGCGGGCCTTTTTT 5'

5' GCGCCTAGGCGCAAAAAAA 3' 3' CGCGGATCCGCGTTTTTTT 5'

none of the above

Ans: A Section: 26.1.D Level of Difficulty: Difficult Learning Objective: Prokaryotic RNA Transcription 44. Which is TRUE regarding structure and function of RNAPII?

A) B) C) D) E)

I. Distortion of the DNA by ~90° isolates the template base such that it can be properly paired. II. The "clamp" moves over the DNA increasing processivity. III. RNAPII accomplishes proofreading by forcing mispaired nucleotides against the "wall" causing distortion such that mispairs can be cleaved by the "rudder." I, II, III I, II II, III II only III only

Ans: B Section: 26.2.A Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes 45. In eukaryotes, which of the following would decrease the rate of transcription? 218

A) B) C) D) E)

mutation in the nucleotide sequences at −10 and −35 mutation in the nucleotide sequences at −10 and +5 mutation in the nucleotide sequences at −70 and −90 mutation at the s binding site all of the above

Ans: C Section: 26.2.B Level of Difficulty: Difficult Learning Objective: Transcription in Eukaryotes 46. Which of the following eukaryotic proteins are encoded by genes which have no known introns? A) B) C) D) E)

interferons tropomyosin SXL protein all of the above none of the above

Ans: A Section: 26.3.A Level of Difficulty: Moderate Learning Objective: Posttranscriptional Processing 47. What function is accomplished by snoRNAs? A) B) C) D) E)

spicing site recognition capping of the mRNA methylation of tRNAs methylation of rRNA splicosome catalytic site recognition

Ans: D Section: 26.3.B Level of Difficulty: Easy Learning Objective: Posttranscriptional Processing 48. Which of the following increases the stability of the elongation complex during transcription in E. coli? A) B) C) D) E)

formation of the open complex dissociation of the s subunit mutations in the promoter region production of abortive transcripts All of the above increase the stability.

Ans: B Section: 26.1.C Level of Difficulty: Moderate Learning Objective: Prokaryotic RNA Transcription 219

49. Which of the following is FALSE regarding prokaryotic transcription termination? A) B) C) D) E)

It can occur in a factor dependent fashion. It can occur in a factor independent fashion. It may involve the Rho protein. all of the above none of the above

Ans: E Section: 26.1.D Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription 50. The function of the TATA box is A) B) C) D) E)

to recognize the s subunit and correctly line up the RNA polymerase. to terminate active RNA transcription. to form a hairpin for RNA transcription termination. to provide a binding location for the Rho protein. to stimulate formation of the transcription bubble.

Ans: A Section: 26.2.B Level of Difficulty: Easy Learning Objective: Prokaryotic RNA Transcription

220

Chapter 27: Protein Synthesis Matching Choose the correct answer from the list. Not all the answers will be used. A) AUG B) sense C) release factors D) noninitiator E) hairpin F) preproteins G) genetic code H) penicillin I) proproteins J) proofreading K) UUA L) synonyms M) nucleotide cypher N) streptomycin O) nonsense P) revising Q) cloverleaf 1. Codons that specify the same amino acid are called ______. Ans: L Section: 27.1.C Level of Difficulty: Easy Learning Objective: The Genetic Code 2. The fidelity of amino acid attachment to a tRNA is enhanced by the ______ ability of the corresponding aaRS. Ans: J Section: 27.2.B Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 3. A mutation that converts an aminoacyl-coding codon to a Stop codon is known as a ______ mutation. Ans: O Section: 27.4.C Level of Difficulty: Moderate Learning Objective: Translation 4. Some proteins are synthesized as inactive precursors called ______. Ans: I 214

Section: 27.5.B Level of Difficulty: Easy Learning Objective: Posttranslational Processing 5. The ______ is composed of three-nucleotide codons that do not overlap and are read sequentially by the protein-synthesizing machinery. Ans: G Section: 27.1.A Level of Difficulty: Easy Learning Objective: The Genetic Code 6. Translation termination requires ______ that recognize Stop codons. Ans: C Section: 27.4.C Level of Difficulty: Easy Learning Objective: Translation 7. Almost all known tRNAs can be arranged in the so-called ______ secondary structure. Ans: Q Section: 27.2.A Level of Difficulty: Easy Learning Objective: Transfer RNA and Its Aminoacylation 8. EF-Tu binds all ______ aminoacyl tRNAs but that of tRNAsec. Ans: D Section: 27.4.B Level of Difficulty: Moderate Learning Objective: Translation 9. At low concentrations the antibiotic ______ causes misreading of the mRNA. Ans: N Section: 27.4.B Level of Difficulty: Moderate Learning Objective: Translation 10. The start codon is usually ______. Ans: A Section: 27.4.A Level of Difficulty: Easy Learning Objective: Translation

215

Multiple Choice 11. Insertions or deletions of one or two nucleotides can cause A) B) C) D) E)

frameshift mutations. degenerate mutations. synonymous mutations. wobble codons. transpeptidation.

Ans: A Section: 27.1.A Level of Difficulty: Easy Learning Objective: The Genetic Code 12. The correct amino acid is covalently attached to a tRNA by the corresponding ______ which is specific for each ______. A) B) C) D) E)

aminoacyl-tRNA synthetase (aaRS); amino acid aminoacyl-tRNA synthetase (aaRS); species elongation factor; amino acid elongation factor; species none of the above

Ans: A Section: 27.2.B Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 13. In E. coli, base-pairing between an mRNA’s ______ and the 3¢ end of the 16S rRNA permits the ribosome to select the proper initiation codon, thus minimizing ______. A) B) C) D) E)

start codon; abortive initiation Shine–Dalgarno sequence; abortive initiation start codon; frameshift mutations Shine–Dalgarno sequence; frameshift mutations none of the above

Ans: D Section: 27.4.A Level of Difficulty: Difficult Learning Objective: Translation 14. In E. coli, which of the following factors function to ensure the proper binding of tRNAfMet during mRNA binding and ribosomal subunit assembly?

A) B)

I. IF-1 II. IF-2 III. IF-3 IV. EF-Ts I only I, II 216

C) D) E)

I, III II, IV I, II, III

Ans: C Section: 27.4.A Level of Difficulty: Easy Learning Objective: Translation 15. Which of the following is a ribonucleoprotein required for the delivery of membrane and secretory proteins to the endoplasmic reticulum? A) B) C) D) E)

protein-conducting channel (PCC) small ubiquitin-related modifier (SUMO) trigger factor calnexin signal recognition particles (SRP)

Ans: E Section: 27.5 Level of Difficulty: Moderate Learning Objective: Posttranslational Processing 16. Codons that do not specify amino acids but signal the ribosome to terminate polypeptide chain elongation are termed A) B) C) D) E)

frameshifts. anticodon. Stop codons. suppressors. terminators.

Ans: C Section: 27.1.A Level of Difficulty: Easy Learning Objective: The Genetic Code 17. The thermodynamic requirement for proofreading is met by A) B) C) D) E)

aminoacyl-tRNA binding to the ribosomal A site. hydrolysis of GTP by EF-Tu transpeptidation mediated by IF-2. transpeptidation mediated by RF-3 none of the above.

Ans: B Section: 27.4.B Level of Difficulty: Easy Learning Objective: Translation 18. The structural similarities of EF-G and the EF-Tu·tRNA complex indicate A)

EF-G may be used as a substitute for EF-Tu. 217

B) C) D) E)

EF-G may play a role in displacing the tRNA growing peptide. EF-G may mediate a change in conformation that facilitates EF-Tu binding. EF-G may be involved in facilitating binding of initiation factors. EF-G and EF-Tu are both required for proper initiation.

Ans: B Section: 27.4.B Level of Difficulty: difficult Learning Objective: Translation 19. Inhibitors of translation may be effective as A) B) C) D) E)

antibiotics. anticancer agents. research on translation. all of the above none of the above

Ans: D Section: 27.4.B Level of Difficulty: Easy Learning Objective: Translation 20. Proteins are properly folded with the assistance of A) B) C) D) E)

protein-conducting channels (PCCs). small ubiquitin-related modifiers (SUMOs). trigger factors. chaperones. signal recognition particles (SRPs).

Ans: D Section: 27.5.A Level of Difficulty: Moderate Learning Objective: Posttranslational Processing 21. The triplet code allows many amino acids to be specified by more than one codon. Such a code is said to be A) B) C) D) E)

replicative. synonymous. duplicative. universal. degenerate.

Ans: E Section: 27.1 Level of Difficulty: Easy Learning Objective: The Genetic Code 22. Based on the structure shown below, which of the following correctly represents the sequence that would be present at the "XYZ" position? 218

A) B) C) D) E)

UGG TGG ACC Cannot be determined from the given data. None of the above is the correct sequence.

Ans: C Section: 27.1.B Level of Difficulty: Difficult Learning Objective: The Genetic Code 23. Which of the following is NOT a feature of tRNA structure? A) B) C) D) E)

acceptor or amino acid stem D arm anticodon loop 3¢ terminal phosphate arm variable arm

Ans: D Section: 27.2.A Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 24. Class I and Class II aminoacyl–tRNA synthetases differ in their

A) B) C) D) E)

I. structural motifs. II. anticodon recognition. III. site of aminoacylation. IV. amino acid specificity. I only II, III II, IV II only I, II, III, IV

Ans: E Section: 27.2.B Level of Difficulty: Difficult Learning Objective: Transfer RNA and Its Aminoacylation 25. The site on the ribosome complex which binds the new incoming amino acid- tRNA is called the A)

P site. 219

B) A site. C) E site. D) 50 S site. E) 30 S site. Ans: B Section: 27.3.A Level of Difficulty: Moderate Learning Objective: Ribosomes 26. Polypeptide synthesis A) B) C) D) E)

proceeds from the C-terminus to the N-terminus. proceeds from the N-terminus to the C-terminus. proceeds in both directions simultaneously. proceeds in either direction once initiated. proceeds randomly.

Ans: B Section: 27.4 Level of Difficulty: Easy Learning Objective: Translation 27. Which of the following is NOT associated with eukaryotic translation initiation? A) B) C) D) E)

Shine–Dalgarno sequence a formylated Met−tRNAfmet base pairing between the mRNA and 16S rRNA initiation factors IF-1, IF-2, and IF-3 all of the above

Ans: E Section: 27.4.A Level of Difficulty: Easy Learning Objective: Translation 28. The steps required for peptide elongation at the ribosome are, respectively, A) B) C) D) E)

initiation, elongation and termination. decoding, transpeptidation, and translocation. initiation, elongation, and release. aa-tRNA binding, GTP-peptidation, and translocation. none of the above

Ans: B Section: 27.4.B Level of Difficulty: Moderate Learning Objective: Translation

29. Posttranslational modifications to proteins include all of the following, except A)

glycosylation. 220

B) C) D) E)

phosphorylation. amino acid derivatization. peptide joining. proteolysis.

Ans: D Section: 27.5.B Level of Difficulty: Moderate Learning Objective: Posttranslational Processing 30. The signal recognition particle (SRP) is a _____, and its function is to ______. A) B) C) D) E)

DNA:protein complex, transport proteins into the eukaryotic nucleus multisubunit protein, modify proteins ribosome complex, catalyze posttranslational modification ribonucleoprotein, bind the N-terminal end of growing polypeptides for membrane translocation none of the above

Ans: D Section: 27.5.B Level of Difficulty: Moderate Learning Objective: Posttranslational Processing 31. Which of the following correctly describes the sequence of events in formation of the ribosome assembly and associated RNAs and proteins? A) B) C) D)

small ribosome subunit associates with large subunit; mRNA associates next; IF with bound NTP brings in first f-Met-tRNA; IF then hydrolyses bound NTP. IF with bound NTP binds f-Met-tRNA; small ribosome subunit associates next; mRNA associates next; then large subunit; IF then hydrolyses bound NTP. small subunit associates with mRNA; IF w/ bound NTP brings in first f-MettRNA; IF then hydrolyses bound NTP; large subunit associates large subunit associates with mRNA; IF w/ bound NTP brings in first f-MettRNA; small subunit associates; IF then hydrolyses bound NTP. none of the above

E) Ans: C Section: 27.4.A Level of Difficulty: Difficult Learning Objective: Translation

32. Which of the following is TRUE regarding the Shine-Dalgarno sequence? A) B) C) D) E)

It functions as a promoter sequence which recognizes and bonds the sigma factor. It is part of the operator sequence used to control translation. It is a nucleotide sequence involved in initiation of translation. It is a nucleotide sequence involved in termination of translation. none of the above 221

Ans: C Section: 27.4.A Level of Difficulty: Moderate Learning Objective: Translation 33. What happens when a stop codon is reached by a ribosome? A) B) C)

D) E)

A termination tRNAter binds to the codon and is used to release the growing peptide from the P site tRNA. The ribosome then is likely to dissociate. A termination tRNAter binds to the codon and the growing peptide is transferred to it. When the peptidyl-tRNAter reaches the P site, the ribosome is signaled to release the protein. The ribosome then is likely to dissociate. A termination tRNAter binds to the codon and the growing peptide is transferred to it. When the peptidyl-tRNAter reaches the P site, the ribosome dissociates. A separate peptidyl transferase then releases the protein from tRNAter. A release factor binds to the codon and is used to release the growing peptide from the P site tRNA. A release factor binds to the codon and the ribosome dissociates. A separate peptidyl transferase then releases the protein from the last tRNA to which was attached.

Ans: D Section: 27.4.C Level of Difficulty: Difficult Learning Objective: Translation 34. Which of following best describes the process for attachment of amino acid to the appropriate tRNAs? (Note: AA = amino acid, Pi = phosphate, PPi = pyrophosphate) A) B) C) D) E)

AA + ATP → AA-P + ADP then AA-P + tRNA → AA-tRNA + Pi AA + ATP → AA-AMP + PPi thenAA-AMP + tRNA → AA-tRNA + AMP tRNA + ATP → tRNA-P + ADP then tRNA-P + AA → AA-tRNA + Pi tRNA + ATP → tRNA-AMP + PPi then tRNA-AMP + AA → AA-tRNA + AMP AA + GTP → AA-GMP + PPi then AA-GMP + tRNA → AA-tRNA + GMP

Ans: B Section: 27.2.B Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 35. Which linkage best describes the covalent bond between an amino acid (AA) and its cognate tRNA? A) B) C) D) E)

amino group of AA linked to 5' –OH of tRNA amino group of AA linked to 5' phosphate of tRNA carboxyl group of AA linked to 3' –OH of tRNA carboxyl group of AA linked to 3' phosphate of tRNA none of the above

Ans: C 222

Section: 27.2.B Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 36. Which of the following best describes the method used for error minimization or proofreading to ensure the correct charging of the tRNAs? A) B) C) D) E)

The enzymes catalyzing the addition always proofread after the first step. The enzymes catalyzing the addition always proofread after the second step. Some of the enzymes catalyzing the addition proofread after the first step, some after the second. Ribosomes themselves proofread the linkage when the AA-tRNA reaches the A site. No proofreading of this process occurs.

Ans: C Section: 27.2.B Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation 37. During translation, the reaction catalyzed by peptidyl transferase is coupled to which of the following? A) B) C) D) E)

ATP → ADP + Pi ATP → AMP + PPi GTP → GDP + Pi GTP → GMP + PPi Release of the tRNA in the P site

Ans: E Section: 27.4.B Level of Difficulty: Moderate Learning Objective: Translation 38. During translation, translocation of the ribosome is driven by which of the following? A) B) C) D) E)

ATP → ADP + Pi ATP → AMP + PPi GTP → GDP + Pi GTP → GMP + PPi Release of the tRNA in the P site

Ans: C Section: 27.4.B Level of Difficulty: Moderate Learning Objective: Translation 39. Which of following describes proofreading for the addition of amino acids (AAs) to the growing peptide? A)

An RNA component of the ribosome ensures that the correct AA is associated with the A site before addition occurs. 223

B) C) D) E)

An RNA component of the ribosome ensures that the correct AA has been added, but before the peptidyl-tRNA is shifted to the P site. The EF-Tu • GTP complex ensures that the correct AA is associated with the A site before addition occurs. EF-G ensures that the correct AA has been added, but before the peptidyltRNA is shifted to the P -site. No proofreading of this process occurs.

Ans: C Section: 27.4.B Level of Difficulty: Difficult Learning Objective: Translation 40. Which of the following best describes the preparation of fMet-tRNAfmet for translation in prokaryotes? A) B) C) D)

Met is first formylated, then added to a tRNA specific for the start codon that differs from that designed to carry Met. Met is first added to a tRNA specific for the start codon that differs from that designed to carry Met, then is formylated. Met is first formylated, then added to a "regular" tRNA; the fact that it has the formyl group allows use in the initiation codon. Met is first added to a "regular" tRNA, then is formylated; the fact that it has the formyl group allows use in the initiation codon. f-Met isn't used in prokaryotes, only in eukaryotes.

E) Ans: B Section: 27.4.A Level of Difficulty: Difficult Learning Objective: Translation

41. Approximately 1.6% of patients with cystic fibrosis have an amino acid mutation from Glu to Asp at position 551. The normal sequence is: GCAUGGAC….UGUGAGGGU… Which of the following sequences would constitute this amino acid mutation? A) GCAUGGAC…..UGUGAUGGU… B) GCAUGGAC…..UGUGAAGGU… C) GCAUGGAC…..UGUGGGGGU… D) GCAUGGAC…..UGUGUGGGU… E) GCAUGGAC…..UGUUAAGGU… Ans: Section: 27.1.C Level of Difficulty: Difficult Learning Objective: The Genetic Code 42. The Shine-Dalgarno sequence is A) B) C) D)

used to align ribosome subunits and initiation translation. functions as a stop codon. is used to align RNA polymerase. is used during transcription termination. 224

E) all of the above Ans: A Section: 27.4.A Level of Difficulty: Easy Learning Objective: Translation 43. Which of the following is a function of the ribosome? I. bind mRNA and allow codon recognition II. mediate the binding of proteins necessary for initiation, elongation, and termination III. catalyze synthesis of peptide bonds IV. translocates such that multiple codons can be read I only I, II I, IV II only I, II, III, IV

A) B) C) D) E) Ans: E Section: 27.3 Level of Difficulty: Moderate Learning Objective: Ribosomes

44. The sequence steps involved in elongation of the newly synthesized protein are ordered as follows: (Note: AA=amino acid) A) AA-tRNA binding, peptide bond formation, translocation, tRNA release. B) translocation, AA-tRNA binding, tRNA release, peptide bond formation. C) tRNA release, AA-tRNA binding, translocation, peptide bond formation. D) translocation, peptide bond formation, AA-tRNA binding, tRNA release. E) peptide bond formation, tRNA release, AA-tRNA binding, translocation. Ans: A Section: 27.4.B, C Level of Difficulty: Moderate Learning Objective: Translation 45. A mutation in the DNA sequence prior to (on the 5ꞌside of) the ATG start site will result in which of the following? I. decreased binding efficiency of the TATA binding protein II. decreased promoter efficiency III. frameshift mutation A) I B) II C) III D) I, II E) I, II, III Ans: C Section: 27.1.A 225

Level of Difficulty: Moderate Learning Objective: The Genetic Code 46. Which of the following best describes the wobble hypothesis? I. The degree of variance in base pairing is greater at the 5' end of the anticodon, thus accounting for more than one codon. II. The degree of variance in base pairing is greater at the 3' end of the anticodon, thus accounting for more than one codon III. Non-Watson-Crick base pairing is sometimes allowed in the last position of the anticodon-codon pairing. I only II only I and III II and III III only

A) B) C) D) E) Ans: C Section: 27.2.C Level of Difficulty: Moderate Learning Objective: Transfer RNA and Its Aminoacylation

47. Structural studies of the bacterial ribosome indicate which of the following important points regarding function? A) B) C)

The domains of the 30S subunit appear flexible during protein synthesis. The large subunit of the ribosome appears to undergo domain motion during protein synthesis. The small and large subunits of the ribosome appear static throughout protein synthesis. all of the above none of the above

D) E) Ans: A Section: 27.3.A Level of Difficulty: Moderate Learning Objective: Ribosomes

48. A silent mutation occurs when a nucleotide mutation results in the identical amino acid in place upon completion of translation. If the original sequence is as follows, which example below represents a silent mutation? GUACAAGCAUGAAGUUUGGUAAGCG GUGCAAGCAUGAAGUUUGGUAAGCG GUACAAGCAUGAAAUUUGGUAAGCG GUACAAGCAUGAAGUUGGGUAAGCG GUACAGGCAUGAAGUUUGGUAAGCG GUACAAGCAUGAAGUUUGGUAACCG

A) B) C) D) E) Ans: B Section: 27.1.C; 27.4.A Level of Difficulty: Difficult

226

Learning Objective: The Genetic Code and Translation 49. Considering elongation of peptides via ribosome-mediated peptide synthesis, how many ATP equivalents are required for addition of on amino acid to the growing peptide chain and translocation such that the assembly is prepared for the subsequent addition of another amino acid? A) 0 B) 1 C) 2 D) 3 E) 4 Ans: C Section: 27.4.B Level of Difficulty: Difficult Learning Objective: Translation 50. Which of the following is(are) used to assist in protein folding? I. calnexin II. calreticulin III. DnaK IV. GroEL A) I, II B) III, IV C) II, IV D) I, III E) I, II, III, IV Ans: E Section: 27.5.A and C Level of Difficulty: Easy Learning Objective: Posttranslational Processing

227

Chapter 28: Regulation of Gene Expression Matching Choose the correct answer from the list. Not all the answers will be used. A) globin B) M phase C) G0 phase D) necrosis E) euchromatin F) S phase G) riboswitch H) histone I) insulators J) heterochromatin K) Mediator L) 1,6-allolactose M) apoptosis N) orphan O) galactose 1. Genes without a known function are called ______ genes. Ans: N Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization 2. To induce expression of the lac operon, _______ can be added to the cell medium. Ans: L Section: 28.2.A Level of Difficulty: Easy Learning Objective: Regulation of Prokaryotic Gene Expression 3. In bacteria, riboflavin can inhibit its own synthesis by binding to an mRNA element termed a ______. Ans: G Section: 28.2.D Level of Difficulty: Moderate Learning Objective: Regulation of Prokaryotic Gene Expression 4. The ______ proteins can undergo posttranslational modification by acetylation, phosphorylation, methylation, and ubiquitination. Ans: H Section: 28.3.A Level of Difficulty: Easy 221

Learning Objective: Regulation of Eukaryotic Gene Expression 5. Transcriptionally active DNA in eukaryotes is called ______. Ans: E Section: 28.3.A Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 6. RNAP II holoenzyme contains RNAP II and the protein complex called ______. Ans: K Section: 28.3.B Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 7. Enhancer activity can be blocked by the presence of sequences called _____. Ans: I Section: 28.3.B Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 8. Mitosis and cell division take place during ______ of the cell cycle. Ans: B Section: 28.4.A Level of Difficulty: Easy Learning Objective: The Cell Cycle, Cancer, and Apoptosis 9. DNA is synthesized during ______ of the cell cycle. Ans: F Section: 28.4.A Level of Difficulty: Easy Learning Objective: The Cell Cycle, Cancer, and Apoptosis 10. Cell death caused by trauma is called ______. Ans: D Section: 28.4.C Level of Difficulty: Easy Learning Objective: The Cell Cycle, Cancer, and Apoptosis

Multiple Choice 11. An organism’s metabolic complexity and morphology are not always consistent with the amount of its genetic material. This inconsistency is called A) B)

genomic degeneracy. the C-value paradox. 222

C) D) E)

nucleotide polymorphism. chromatin reorganization. Prader-Willi syndrome.

Ans: B Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization 12. In humans, approximately ______ of the genome encodes proteins. A) B) C) D) E)

0.4% 1.4% 14% 24% 44%

Ans: B Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization 13. A database of _____ is being compiled to examine possible genetic links to the susceptibility to disease or infection.. A) B) C) D) E)

CpG islands ORFs SNPs LINEs SINEs

Ans: C Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization 14. In eukaryotic cells, methylated bases are present in palindromic ______, which are often found in upstream promoter regions. A) B) C) D) E)

CpG islands ORFs SNPs LINEs SINEs

Ans: A Section: 28.1.A, 28.3.A Level of Difficulty: Easy Learning Objective: Genome Organization, Regulation of Eukaryotic Gene Expression 15. Which of the following relates to the observation that males and females make approximately equal amounts of X-chromosome gene products? 223

A) B) C) D) E)

the phenomenon is known as dosage compensation inactivation of one of the X-chromosomes unequal distribution of X-chromosome genes. A and B B and C

Ans: D Section: 28.3.A Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 16. The apparent correlation between histone modification and control over gene expression is termed A) B) C) D) E)

architectural model. polymorphism. chromatin remodeling. the histone code. acetylation.

Ans: D Section: 28.3.A Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 17. Gene regulation by the JAK-STAT pathway relays signals initiated by A) B) C) D) E)

phosphorylated cytokines binding to hormone response elements. steroids binding to steroid receptors inducing phosphorylation of tyrosine. methylation of the SH2 domain. bromodomain recruitment of coactivators. ligand binding induced dimerization of cytokine receptor.

Ans: E Section: 28.3.B Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 18. RNA interference is a mechanism of posttranscriptional RNA-dependent A) B) C) D) E)

chromatin-remodeling. gene silencing. histone methylation. coactivation. apoptosis.

Ans: B Section: 28.3.C Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 19. "Programmed" cell death is called 224

A) B) C) D) E)

imprinting. silencing. necrosis. coactivation. apoptosis.

Ans: E Section: 28.4.C Level of Difficulty: Easy Learning Objective: The Cell Cycle, Cancer, and Apoptosis 20. Which of the following statements about repetitive DNA sequences is FALSE? A) B) C) D) E)

Both centromeres and telomeres contain repetitive DNA sequences. Short tandem repeats, such as (CA)n, may be due to replication slippage. Large sections of repetitive sequences are observed in prokaryotic and eukaryotic cells. Familial relationships can be determined by analysis of repetitive DNA. Repetitive sequences are found in some protein-coding genes.

Ans: C Section: 28.1.C Level of Difficulty: Moderate Learning Objective: Genome Organization 21. Which of the following events are necessary for efficient expression of the lac operon? I. The lac repressor must bind inducer and dissociate from the operator site. II. CAP must bind cAMP. III. CAP and the repressor must simultaneously bind to RNAP. A) I, II, III B) I, II C) I, III D) II, III E) I only Ans: B Section: 28.2.A and B Level of Difficulty: Difficult Learning Objective: Regulation of Prokaryotic Gene Expression 22. How does the transcriptional machinery gain access to the nucleosome-sequestered DNA? I. Methylation of DNA prevents histone binding. II. Chromatin-remodeling complexes allow sections of DNA to be transiently exposed to transcription factors. III. The transcription proteins have higher affinity for DNA and push the histones away from binding sites. A) I, II, III B) I, II C) II, III 225

D) E)

I, III II only

Ans: A Section: 28.3.A Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 23. HMG proteins are I. a set of small conserved proteins containing about 50% charged amino acids. II. regulation elements Moderated by the trp attenuation leader sequence. III. able to alter DNA conformation by causing it to bend, unwind, and form loops. IV. architectural proteins that regulate gene expression. A) I, II B) I, III C) II, IV D) I, III, IV E) I, II, III Ans: D Section: 28.3.A Level of Difficulty: Difficult Learning Objective: Regulation of Eukaryotic Gene Expression

24. Activators and repressors bind to target DNA sites called A) B) C) D) E)

enhancers and silencers, respectively. CpG islands. epigenic centers. all of the above none of the above

Ans: A Section: 28.3.B Level of Difficulty: Easy Learning Objective: Regulation of Eukaryotic Gene Expression 25. Upstream transcription factors typically contain the following domain(s) I. a DNA binding domain. II. an activation domain, which often is rich in negative charges. III. an ATP binding domain, which is used to promote conformational change in the DNA. A) I, II B) I, II, III C) I, II D) II, III E) none of the above Ans: A 226

Section: 28.3.B Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 26. Hormone response elements I. are DNA segments that contain repeated sequences separated by several bases. II. bind members of the nuclear receptor superfamily of proteins. III. are highly conserved sequences found in prokaryotic and eukaryotic cells. A) I, II, III B) I, II C) II, III D) I, III E) II only Ans: B Section: 28.3.B Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 27. Eukaryotic posttranscriptional control of gene expression does NOT include A) B) C) D) E)

differential degradation of mRNA. attenuation. interference by RNA sequences. phosphorylation of eIF2. decapping of the mRNA 5¢ end.

Ans: B Section: 28.3.C Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 28. How many nucleotide pairs does a bacterial genome typically contain? A) B) C) D) E)

103 – 104 105 – 106 106 – 107 108 – 109 none of the above

Ans: C Section: 28.1.A Level of Difficulty: Moderate Learning Objective: Genome Organization 29. How many nucleotide pairs does a mammalian genome typically contain? A) B) C) D)

105 – 106 106 – 107 108 – 109 109 – 1010 227

E) none of the above Ans: D Section: 28.1.A Level of Difficulty: Moderate Learning Objective: Genome Organization 30. Human cancers are often caused by a mutation in ___, which generally functions to restrain uncontrolled cell proliferation. A) B) C) D) E)

the cyclin gene the p53 gene a high mobility group (HMG) gene an activator region a silencer region

Ans: B Section: 28.4.B Level of Difficulty: Moderate Learning Objective: The Cell Cycle, Cancer, and Apoptosis 31. The p53 protein functions as a ___ arresting the cell cycle in the ___ phase. A) B) C) D) E)

cyclin; G2 tumor suppressor; G2 cyclin; Go tumor suppressor; Go tumor suppressor; S

Ans: B Section: 28.4.B Level of Difficulty: Moderate Learning Objective: The Cell Cycle, Cancer, and Apoptosis 32. Which of the following is correct regarding the function of the lac repressor protein? A) B) C) D)

In the presence of allolactose, the protein binds the operator inhibiting transcription. In the absence of allolactose, the protein binds the operator inhibiting transcription. In the presence of allolactose, the protein binds the operator enhancing transcription. In the absence of allolactose, the protein binds the operator enhancing transcription. None of the above.

E) Ans: B Section: 28.2.A Level of Difficulty: Moderate Learning Objective: Regulation of Prokaryotic Gene Expression

33. Which stage of transcription does the lac repressor affect in order to accomplish its function? 228

A) B) C) D) E)

initial binding of RNAP to the promoter DNA initiation of transcription after RNAP has bound the promoter preventing abortive initiation transcription termination none of the above

Ans: B Section: 28.2.A Level of Difficulty: Moderate Learning Objective: Regulation of Prokaryotic Gene Expression 34. Which of the following correctly describes the function of the repressor protein controlling expression of the trp operon? A) B) C) D) E)

In the presence of tryptophan, the trp repressor tryptophan complex binds the operator inhibiting transcription. In the absence of tryptophan, the trp repressor tryptophan complex binds the operator inhibiting transcription. In the presence of tryptophan, the trp repressor tryptophan complex binds the operator enhancing transcription. In the absence of tryptophan, the trp repressor tryptophan complex binds the operator enhancing transcription. None of the above.

Ans: A Section: 28.2.C Level of Difficulty: Moderate Learning Objective: Regulation of Prokaryotic Gene Expression 35. Euchromatin is A) B) C) D) E)

DNA that is tightly condensed and transcriptionally active. DNA that is tightly condensed and transcriptionally inactive. DNA that is not condensed and transcriptionally active. DNA that is not condensed and transcriptionally inactive. DNA that is not condensed, but may or may not be transcriptionally active.

Ans: C Section: 28.3.A Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 36. Heterochromatin is A) B) C) D) E)

Ans: B Section: 28.3.A 229

Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 37. A mutant strain of E. coli lacks a binding site for CAP at the promoter for the lac operon. How does expression of the operon compare to wild type? (The bold face row indicates units of activity observed in wild type.) no glucose present

Wild type à A) B) C) D) E)

−IPTG

+ IPTG

100

glucose present −IPTG + IPTG 1 5

5 5 1 1 100

100 100 5 5 100

1 5 5 1 100

5 100 100 50 100

Ans: D Section: 28.2.B Level of Difficulty: Difficult Learning Objective: Regulation of Prokaryotic Gene Expression 38. What type of mutation causes conditions such as Huntington’s disease and Fragile X syndrome? A) B) C) D) E)

an excess of trinucleotide repeats in a protein-coding gene a mutation in the p53 tumor suppressor a mutation in a cyclin-dependent protein kinase a mutation in the retinoblastoma gene a mutation in caspase-activated DNase

Ans: A Section: 28.1.C Level of Difficulty: Easy Learning Objective: Genome Organization 39. How do steroid hormones influence gene expression? A) B) C) D) E)

They bind cell surface receptors which influence the concentration of second messengers. They migrate between the cytosol and nucleus binding the hormone response elements to affect transcription. They bind to histones, influencing their ability to form nucleosomes. They bind to histones, influencing their ability to be methylated. None of the above.

Ans: B Section: 28.3.B Level of Difficulty: Moderate 230

Learning Objective: Regulation of Eukaryotic Gene Expression 40. Which of the following best describes caspases? A) B) C) D) E)

They are cysteine proteases that participate in apoptosis. They are cyclin-dependent protein kinases that regulate the cell cycle. They are tumor suppressor DNA-binding proteins. They are a class of high mobility group (HMG) proteins. They are DNA repair enzymes involved in splicing immunoglobulin genes.

Ans: A Section: 28.4.C Level of Difficulty: Moderate Learning Objective: The Cell Cycle, Cancer, and Apoptosis 41. Which of the following are requirements for genetic information? I. Information must be tapped in an orderly fashion. II. Information must be available to direct responses in changes to internal or external conditions. III. Information must be removable following development. A) I, II, III B) I, II C) II, III D) I, III E) I only Ans: B Section: 28.Introduction Level of Difficulty: Moderate Learning Objective: Genome Organization 42. Of the human genome approximately 80% ___. A) is made up of exonic DNA. B) may be transcribed. C) is made up of protein encoding genes. D) A and C E) A and B Ans: B Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization

43. On average a single nucleotide polymorphism occurs ____ in humans. A)

every 2050 base pairs 231

B) C) D) E)

every 250 base pairs every 1250 base pairs every 2 replications every 2 million base pairs

Ans: C Section: 28.1.A Level of Difficulty: Easy Learning Objective: Genome Organization 44. Which of the following genes rarely occur in multiple copies? I. histone proteins II. protein-coding genes III. gene clusters A) I, II, III B) I, II C) I, III D) II only E) III only Ans: D Section: 28.1.B Level of Difficulty: Easy Learning Objective: Genome Organization 45. Considering the E. coli trp operon, which of the following is TRUE? I. The formation of the 2-3 hairpin is highly favored over the 1-2 hairpin when trp is low. II. When the concentration of Trp-tRNATrp is low, the ribosome halts on tandem Trp codon of segment 1. III. Formation of the 2-3 hairpin facilitates transcription and translation of the trp operon. IV. The attenuator system has no effect when Trp levels are high. A) I, II, III, IV B) I, II, III C) II, III D) II, III, IV E) II, IV Ans: C Section: 28.2.C Level of Difficulty: Difficult Learning Objective: Regulation of Prokaryotic Gene Expression

46. In prokaryotes, which of the following are effective at controlling gene expression relative to the concentration of a metabolite or catabolite? I. CAP or CRP 232

II. long terminal repeats (LTRs) III. riboswitches IV. SWI/SNF A) I, II, III, IV B) I, II, III C) I, III D) II, IV E) III, IV Ans: C Section: 28.2.B, C Level of Difficulty: Moderate Learning Objective: Regulation of Prokaryotic Gene Expression 47. Which of the following is TRUE regarding eukaryotic mRNAs? I. They uniformly stable. II. The poly (A) tail appears to partially Moderate the rate of degradation. III. The 5' cap appears to partially Moderate the rate of degradation. IV. They have decay times ranging from 10-30 minutes. A) I, II B) II, III C) II, IV D) III, IV E) II only Ans: B Section: 28.3.C Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 48. Which of the following would likely result in the formation of RNAi? A) B) C) D) E)

injection of antisense RNA from a human into human cells injection of sense RNA into C. elegans injection of antisense RNA from yeast into a human all of the above none of the above

Ans: E Section: 28.3.C Level of Difficulty: Difficult Learning Objective: Regulation of Eukaryotic Gene Expression

49. The process of somatic recombination I. results in antibody diversity. II. involves selection of individual members of clustered gene sequences. III. involves selection and recombination of specific exons on the k and/or l chain. 233

A) B) C) D) E)

I, II, III I, III I, III II, III none of the above

Ans: A Section: 28.3.D Level of Difficulty: Moderate Learning Objective: Regulation of Eukaryotic Gene Expression 50. Progression through the cell cycle I. is regulated by cyclins. II. is controlled by Cdks. III. is altered by CKIs. A) I only B) II only C) III only D) II , III E) I, II, III Ans: E Section: 28.4.A Level of Difficulty: Easy Learning Objective: The Cell Cycle, Cancer, and Apoptosis

234