TEST BANK for Biochemistry 1st Edition by Roger Miesfeld & Megan McEvoy.

5. Look at the bond energies O-H, N-H, and P-H in the table below. O-H is the hardest bond to break because it has the

a. b. c. d.

greatest difference in relative affinities of the two atoms for electrons. smallest difference in relative affinities of the two atoms for electrons. smallest difference in atomic size. largest difference in atomic size.

ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Understanding 6. Given that methane (CH4) has a bond angle of and ethylene (C2H2) has a bond angle of , what is the correct bond angle for acetylene (C2H2)? a. b. c. d.

ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Applying 7. Amino acids are the building blocks for which biomolecule(s)? a. proteins b. DNA c. carbohydrates d. micelles ANS: A DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 8. The __________ differentiates amino acids from one another. a. number of silane groups b. number of phosphoryl groups c. side chains attached to the central carbon d. number of hydroxyl groups ANS: C

DIF: Medium

REF: 1.2

OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Understanding 9. A nucleotide consists of which of the following? a. nitrogenous base, four-membered sugar and phosphate groups b. phosphate base, four-membered sugar and sulfate groups c. nitrogenous base, five-membered sugar and phosphate groups d. carboxylic acid, four-membered sugar and phosphate groups ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 10. Simple sugars are made of which of the following elements? a. carbon, sulfur, and hydrogen b. carbon, oxygen, and phosphate c. carbon, oxygen, and helium d. carbon, oxygen, and hydrogen ANS: D DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 11. If energy in the form of ATP is required to make a polymeric macromolecule, which of the following will happen if there is no ATP available?

a. b. c. d.

The rate of polymer increases.

The polymer is broken down to release ATP. The polymer continues to be made at the same rate.

The enzyme degrades to release ATP.

ANS: B DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Understanding 12. Why are fewer polypeptide sequences encountered biologically than are theoretically possible? a. There is no way to make all the theoretical possibilities. b. The phosphodiester linkages don’t allow for all the possibilities.

c. Not all have useful structural and functional properties. d. Not all of the possibilities can be broken down.

ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.d. Identify the biomolecules that form polymers.

MSC: Applying

13. Humans do not have the enzyme cellulase. Is it likely that a human could survive on a plant-only diet? a. No, not enough ATP would be produced to generate energy. b. No, not enough DNA would be produced to generate energy. c. Yes, cellulase is not necessary to break down plant material. d. Yes, ATP is not necessary to maintain life.

ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Analyzing 14. Which two functional groups are involved in producing a peptide bond? a. alcohol and amino b. amino and thiol c. methyl and amino d. amino and carboxyl ANS: D DIF: Medium REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Understanding 15. Even though amylose and cellulose contain the same repeating unit of glucose, they are very different in terms of function. Why? a. A glycosidic bond cannot be cleaved. b. The orientations of the glycosidic bond are different. c. ATP cannot be generated from amylose. d. There is no structural difference between the polymers.

ANS: B DIF: Medium REF: 1.2 OBJ: 1.2.d. Identify the biomolecules that form polymers.

MSC: Applying

16. If the concentration of aspartate in the cell decreased, what would be the predicted outcome?

a. b. c. d.

increased concentration of argininosuccinate decreased concentration of citrulline decreased concentration of fumarate increased concentration of arginine

ANS: C DIF: Difficult REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Applying 17. The correct definition of a pathway intermediate is a molecule that a. is both a product and a reactant in a pathway.

b. lowers the activation energy of a reaction. c. increases the rate of a reaction. d. is only a reactant in a pathway.

ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Understanding 18. If the concentration of F is high in a cell, the pathway will MOST likely shift to produce

a. b. c. d.

more C. less C. more A. less D.

ANS: D DIF: Difficult REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Applying 19. Plasmids are small, circular DNA molecules that are used in which of the following? a. gene cloning b. production of chromatin c. cell movement d. replication of nucleus ANS: A DIF: Easy REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Remembering 20. What is the function of the chloroplast in a plant cell? a. detoxification of macromolecules b. degradation of macromolecules c. conversion of light energy to chemical energy d. conversion of glucose to ATP ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.f. Compare and contrast bacterial and eukaryotic cells.

MSC: Understanding 21. If a plasma membrane is hydrophobic, what kinds of amino acids are MOST likely to be found in the membrane? a. hydrophilic amino acids b. hydrophobic amino acids c. polar amino acids d. charged amino acids

ANS: B DIF: Medium REF: 1.2 OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Applying 22. When a ligand binds to a receptor, it causes the receptor to a. degrade. b. activate. c. deactivate. d. rapidly grow.

ANS: B DIF: Easy REF: 1.2 OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Understanding 23. How does the molecule adenosine monophosphate fit into the seven hierarchical levels that define the chemical basis of life? a. element/functional group b. biomolecule c. metabolism d. organism ANS: B DIF: Medium REF: 1.2 OBJ: 1.2.f. Compare and contrast bacterial and eukaryotic cells.

MSC: Understanding 24. The main difference between deoxyribonucleotides and ribonucleotides is that they have a different a. number of carbons in the sugar ring. b. functional group on the carbon. c. number of phosphates on the carbon. d. functional group on the carbon.

ANS: B DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Understanding

25. A hydrogen bond can best be described as a a. strong covalent interaction. b. strong ionic interaction. c. weak noncovalent interaction. d. weak covalent interaction.

ANS: C DIF: Easy REF: 1.3 OBJ: 1.3.a. Identify the three components of a nucleotide.

MSC: Remembering

26. Why can a guanine not be paired with adenine? a. Guanine is only found in RNA and adenine is found only in DNA. b. Guanine can form three hydrogen bonds and adenine can form two. c. Guanine can form only two hydrogen bonds and adenine can form three. d. Guanine can only pair with thymine.

ANS: B DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Analyzing

27. What structural feature of DNA is attributed to the fact that the two DNA strands are antiparallel? a. DNA is a left-handed helix.

b. DNA has the phosphate groups on the interior. c. DNA is a right-handed helix. d. DNA forms a pleated sheet.

ANS: C DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Applying

28. The “central dogma of molecular biology” can best be described as the transfer of information between a. nucleic acids and proteins. b. fatty acids and proteins. c. carboxylic acids and proteins. d. nucleic acids and DNA. ANS: A DIF: Easy REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Remembering

29. A segment of DNA containing 20 base pairs includes 8 adenine residues. How many uracil residues are present? a. 12 b. 8 c. 0 d. 28 ANS: C DIF: Difficult REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Analyzing

30. A genome is a set of a. proteins. b. transcripts. c. genes. d. genetic code.

ANS: C DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA. 31. Given a DNA sequence of a.

-GUAb. -AUGc. -GUAd. -GTA-

MSC: Remembering

-CAT- , what is the complementary sequence in mRNA?

ANS: A DIF: Difficult REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Applying

32. Who received the Nobel Prize in 1962 for elucidating the molecular structure of DNA? a. Albert Einstein b. Linus Pauling c. John Kendrew and Max Perutz d. Maurice Wilkins, James Watson, and Francis Crick ANS: D DIF: Easy REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Remembering

33. A single nucleotide base substitution in a wild-type DNA is an example of

a. b. c. d.

random mutation. transcription. translation. cloning.

ANS: A DIF: Easy REF: 1.4 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Remembering 34. An inherited disease comes from the mutation of DNA in a __________ cell. a. somatic b. germ-line c. adipose d. blood ANS: B DIF: Easy REF: 1.4 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Understanding 35. The RNA world model is based on the hypothesis that __________ is stable. a. RNA b. DNA c. uracil d. adenine ANS: B DIF: Medium REF: 1.2 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Understanding 36. Bioinformatics shows that 98% of human DNA is identical to that of chimpanzees. If human DNA contains 3.2 billion nucleotides, how many nucleotides are different between the two species? a. 3.1 billion b. 64 million c. 3.1 million d. 640 million ANS: B DIF: Medium REF: 1.2 OBJ: 1.4.c. Identify the relationship between protein structure and function.

MSC: Applying 37. Highly conserved gene sequences that encode proteins with the same function in different organisms are called __________ genes. a. orthologous b. conserved c. parallel d. antiparallel ANS: A DIF: Easy REF: 1.4 OBJ: 1.4.b. Differentiate between orthologous genes and paralogous genes.

MSC: Understanding 38. If a mutation was made to the gene for glucose–6–phosphate dehydrogenase that prevented it from functioning, a possible outcome would be the production of a. more NADPH. b. less NADPH.

c. more ATP. d. less ATP. ANS: B DIF: Medium REF: 1.4 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Applying 39. The appearance of new gene speciation is an example of a. gene multiplication. b. gene singulation. c. gene duplication. d. random mutation.

ANS: B DIF: Easy REF: 1.4 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Understanding 40. The amino acid sequence of a protein determines its structure. Which of the following statements is true? a. Two proteins with similar amino acid sequence should have similar structures. b. Two proteins with different amino acid sequences will have identical structures. c. Two proteins with similar amino acid sequences will always have the same function in a cell. d. It is impossible to determine how proteins will fold based on the amino acid sequence alone.

ANS: A DIF: Medium REF: 1.4 OBJ: 1.4.c. Identify the relationship between protein structure and function.

MSC: Analyzing 41. Which of the following is NOT a common functional group? a. COOH b. CH3 c. SH d. CHO ANS: D DIF: Easy REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Understanding 42. By convention, nucleic acid chains are written starting at the __________ end. a. amino b. carboxyl c. d.

ANS: D DIF: Easy REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Understanding 43. The proposal that DNA is a double helix was based on what experimental evidence? a. NMR b. IR c. HPLC d. x-ray crystallography

ANS: D DIF: Medium REF: 1.4 OBJ: 1.4.c. Identify the relationship between protein structure and function.

MSC: Understanding 44. mRNA is used for what process in the cell? a. as a template for protein synthesis b. regulation of gene expression c. regulation of RNA d. replication of DNA ANS: A DIF: Easy REF: 1.3 OBJ: 1.3.d. Define the terms transcriptome and proteome.

MSC: Understanding

45. In DNA the phosphate groups are on the outside of the helix. Why does this stabilize the structure? a. ionic interactions with the solvent b. hydrogen bonding with itself c. covalent binding to the solvent d. It does not stabilize the structure.

ANS: A DIF: Difficult REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Applying

46. What is the cause of the overall negative charge of a molecule of DNA? a. hydrogen bonding between base pairs b. the phosphate backbone c. the sugars d. the antiparallel orientation of the DNA ANS: B DIF: Difficult REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Evaluating

47. Mutations to proteins typically occur starting a. at the protein itself. b. with mRNA. c. with tRNA. d. with DNA. ANS: D DIF: Medium REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Analyzing

48. Hydrogen bonds form between hydrogen and a. oxygen. b. helium. c. carbon. d. hydrogen.

ANS: A DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Applying

49. The DNA double helix is stabilized by the interactions between nucleotides because of __________ between nucleotides. a. hydrogen bonding b. pi–pi stacking c. sigma bonds d. ionic interactions

ANS: B DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Analyzing

50. In structures of tRNA, base pairs form between a. the same strand. b. another strand of RNA. c. a strand of DNA. d. Base pairs do not form.

ANS: A DIF: Medium REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Analyzing

51. Ribose is a a. four-carbon sugar. b. five-carbon sugar. c. six-carbon sugar. d. five-carbon acid.

ANS: B DIF: Easy REF: 1.3 OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Remembering

52. The process of fermentation uses sugar to produce which molecules? a. alcohol and carbon monoxide b. alcohol and carbon dioxide c. acid and carbon monoxide d. acid and carbon dioxide ANS: B DIF: Medium REF: 1.1 OBJ: 1.1.a. List examples where biochemistry has made advancements in the lives of many humans.

MSC: Understanding 53. An example of experimental biochemistry is trying an experiment and a. quitting after it fails to prove your hypothesis. b. continuing to try with no changes to protocol. c. optimizing experimental design. d. successfully proving your hypothesis after the first attempt.

ANS: C DIF: Medium REF: 1.1 OBJ: 1.1.a. List examples where biochemistry has made advancements in the lives of many humans.

MSC: Applying 54. What side products of pyruvate are being converted into alcohol and carbon dioxide by yeast? a. CO and NADH b. CO2 and NADH c. CO2 and NAD+ d. CO and NAD+ ANS: C DIF: Difficult REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Applying 55. Pyruvate decarboxylase converts pyruvate into a. carbon dioxide and acetaldehyde.

b. carbon monoxide and acetaldehyde. c. water and glucose. d. ethanol and carbon dioxide.

ANS: A DIF: Medium REF: 1.1 OBJ: 1.1.a. List examples where biochemistry has made advancements in the lives of many humans.

MSC: Understanding 56. Which of the following is an example of a metabolic pathway? a. mitochondria b. organelles c. glycolysis d. plasma membrane ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Understanding 57. Which of the following is an example of an ecosystem? a. mammals b. plasma membrane c. insects d. forest ANS: D DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Understanding 58. A requirement for a covalent bond to form between two atoms is that a. there are unpaired electrons on each atom. b. the atoms are ions. c. both the atoms must be metals. d. one of the atoms must be a halogen.

ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.a. List the elements that are most abundant in living organisms.

MSC: Applying 59. What is the maximum number of covalent bonds a carbon atom can make? a. 2 b. 4 c. 6 d. 8 ANS: B DIF: Easy REF: 1.2 OBJ: 1.2.a. List the elements that are most abundant in living organisms.

MSC: Applying 60. The correct name for the VSEPR arrangement around a carbon in methane is a. linear. b. trigonal bipyrimidal. c. tetrahedral. d. octahedral.

ANS: C

DIF: Difficult

REF: 1.2

OBJ: 1.2.a. List the elements that are most abundant in living organisms.

MSC: Analyzing 61. Cell signaling and cell membranes are examples of functions performed by which biomolecule? a. amino acid b. nucleotide c. simple sugar d. fatty acid ANS: D DIF: Medium REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Applying 62. The figure below shows an example of which functional group?

a. b. c. d.

amino hydroxyl phosphoryl methyl

ANS: C DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Understanding 63. ATP is an abbreviation for which energy currency molecule? a. adenosine triphosphate b. adenosine thymine c. adenosine dinucleotide d. amino triphosphate ANS: A DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Understanding 64. Which of the following is the correct formula for glucose? a. C5H10O5 b. C6H12O6 c. C5H12O6 d. C6H10O6 ANS: B DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 65. What is another way to describe the amphipathic nature of a fatty acid? a. polar head and nonpolar tail

b. nonpolar head and polar tail c. polar head and double bonds in tail d. nonpolar head and double bonds in tail ANS: A DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 66. Triacylglycerols are neutral molecules made of a. three fatty acid esters covalently linked to glycine. b. three fatty acid esters covalently linked to glycerol. c. two fatty acid esters covalently linked to glycine. d. three acyls covalently linked to glycerol.

ANS: B DIF: Medium REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Remembering 67. Proteins are a polymer of __________, whereas nucleic acids are polymers of __________. a. nucleotides; fatty acid esters b. nucleotides; amino acids c. amino acids; nucleotides d. sugars; nucleotides ANS: C DIF: Medium REF: 1.2 OBJ: 1.2.d. Identify the biomolecules that form polymers.

MSC: Understanding

68. Vitamin B2 is a metabolite. Lack of vitamin B2 can lead to blurred vision and a swollen tongue.

Vitamin B2 has such a strong effect on health because metabolites a. are the catalysts that drive biochemical reactions necessary for life-sustaining processes. b. are complex chemical reactions in cells. c. process essential genetic information needed for life. d. are needed for construction of microtubules.

ANS: A DIF: Difficult REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Analyzing 69. Cyclic pathways contain several metabolites that regenerate during each turn of the cycle. Another way to describe a metabolite is that it functions as a a. reactant or product. b. catalysis. c. transition state. d. enzyme.

ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Applying 70. Enzymes and chromosome are found where in the bacterial cell? a. nucleoid b. pili c. cytoplasm d. capsule ANS: C

DIF: Easy

REF: 1.2

OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Understanding 71. What does chromatin in eukaryotic nucleus contain? a. DNA packaged with proteins. b. RNA packaged with proteins. c. ATP packaged with proteins. d. DNA packaged with ATP. ANS: A DIF: Medium REF: 1.2 OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Understanding 72. The function of chloroplasts in plant cells is to convert a. heat energy to light energy. b. heat energy to chemical energy. c. light energy to chemical energy. d. chemical energy to heat energy.

ANS: C DIF: Easy REF: 1.2 OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Applying 73. What process replicates DNA to make more DNA? a. DNA transcription b. DNA replication c. DNA translation d. RNA transcription ANS: B DIF: Easy REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Understanding

74. What process converts DNA to RNA? a. DNA transcription b. DNA replication c. DNA translation d. RNA transcription ANS: A DIF: Easy REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Understanding

75. What process describes using mRNA templates to produce proteins? a. DNA transcription b. DNA replication c. DNA translation d. mRNA translation ANS: D DIF: Easy REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Understanding

SHORT ANSWER 1. What are the three biochemical principles that together provide a framework for understanding life at the molecular level? How are they interrelated?

ANS: Hierarchical organization of biochemical processes within cells, organisms, and ecosystems underlies the chemical basis of life on Earth. DNA is the chemical basis for heredity and encodes the structural information for RNA and protein molecules, which mediate biochemical processes in cells. The function of a biomolecule is determined by its molecular structure, which is fine-tuned by evolution through random DNA mutations and natural selection. These processes cannot function without each other.

DIF: Easy REF: Introduction OBJ: 1.1.a. List examples where biochemistry has made advancements in the lives of many humans.

MSC: Understanding 2. List three examples of how biochemistry has made advancements in the lives of many humans.

ANS: A list can be found in Section 1.1 of the text. Examples include developing new pharmaceutical drugs, diagnostic tests, improved detergents, and faster ripening of fruit and vegetables.

DIF: Easy REF: 1.1 OBJ: 1.1.a. List examples where biochemistry has made advancements in the lives of many humans.

MSC: Remembering 3. Which six elements make up 97% of the weight of most organisms?

ANS: Hydrogen, oxygen, carbon, nitrogen, phosphorus, and sulfur DIF: Easy REF: 1.2 OBJ: 1.2.a. List the elements that are most abundant in living organisms.

MSC: Remembering 4. Identify the following functional groups.

ANS: Amino, hydroxyl, sulfhydryl, phosphoryl, carboxyl, methyl DIF: Easy REF: 1.2 OBJ: 1.2.b. Identify the most abundant functional groups found in biomolecules.

MSC: Understanding 5. Identify the following biomolecules.

ANS: Amino acid, nucleotide, sugar, fatty acid DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Understanding 6. What functions can polysaccharides perform?

ANS: They provide structural support to cells and energy storage.

DIF: Difficult REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Applying 7. What is an advantage of using polypeptides for storage and information transmission?

ANS: The complexity of monomeric units forms a stable arrangement that is perfect for information storage and transmission.

DIF: Difficult REF: 1.2 OBJ: 1.2.d. Identify the biomolecules that form polymers.

MSC: Evaluating

8. Explain how a linear pathway is different from a forked pathway.

ANS: In a linear pathway, a reaction generates only one product that is then used in the next reaction. In a forked pathway, two products are produced that each enter a different metabolic pathway.

DIF: Difficult REF: 1.2 OBJ: 1.2.e. Explain the role of metabolic pathways in living systems.

MSC: Analyzing 9. Compare and contrast at least three different characteristics of prokaryotic and eukaryotic cells.

ANS: Prokaryotes are often 1 in diameter, their cytoplasm contains all the enzymes and chromosomes, and they have flagella and pili. Eukaryotic cells are 10 to 100 in diameter, chromatin is contained in the nucleus, and they have a cytoskeleton.

DIF: Difficult REF: 1.2 OBJ: 1.2.f. Compare and contrast bacterial and eukaryotic cells.

MSC: Analyzing

10. Name four organelles found in a eukaryotic cell.

ANS: Many answers are correct including the following: lysosome, smooth endoplasmic reticulum, rough endoplasmic reticulum, ribosomes, peroxisome, mitochondria, nucleus, Golgi apparatus, and cytoskeleton.

DIF: Easy REF: 1.2 OBJ: 1.2.g. Name the key organelles found in a eukaryotic cell.

MSC: Remembering 11. Describe how a receptor is activated and inactivated by a ligand in the figure below.

ANS: The receptor ligand is bound to the receptor, which causes a conformation change to the active site on the protein. The ligand is then released and returns the receptor to an inactive conformation.

DIF: Difficult REF: 1.2 OBJ: 1.2.h. Explain the role of receptors in multicellular organisms.

MSC: Analyzing 12. Name the three components of a nucleotide.

ANS: Nucleotide base, five-carbon ribose, and one or more phosphate groups DIF: Easy REF: 1.3 OBJ: 1.3.a. Identify the three components of a nucleotide.

MSC: Remembering

13. Compare and contrast the bases found in DNA and RNA. ANS: DNA is composed of the deoxyribonucleotides (lacking an hydroxyl group on the position of ribose) guanine, cytosine, adenine, and thymine. RNA is composed of ribonucleotides (containing an hydroxyl group on the position of ribose) guanine, cytosine, adenine, and uracil.

DIF: Medium

REF: 1.3

OBJ: 1.3.b. Compare and contrast DNA and RNA.

MSC: Analyzing 14. Define the central dogma of molecular biology.

ANS: The central dogma of molecular biology describes how genetic information stored in DNA is used to direct the biological processes in cells.

DIF: Medium REF: 1.3 OBJ: 1.3.c. Define the central dogma of molecular biology.

MSC: Remembering

15. Compare and contrast a transcriptome and a proteome.

ANS: Although both transcriptomes and proteomes are collections of genetic material, a collection of DNA transcripts (RNA products) generated by DNA transcription is called a transcriptome, whereas a proteome is the collection of proteins produced by mRNA translation.

DIF: Difficult REF: 1.3 OBJ: 1.3.d. Define the terms transcriptome and proteome.

MSC: Analyzing

16. Differentiate between germ-line cell mutations and somatic cell mutations.

ANS: Although both are mutations in DNA, if the mutation is passed from the parent to the offspring, then the mutation is contained within the DNA of a germ-line cell. If the DNA mutation occurs during the lifetime of the organism in a somatic cell, then this disease is limited to that individual organism.

DIF: Difficult REF: 1.4 OBJ: 1.4.a. Differentiate between germ-line cell mutations and somatic cell mutations.

MSC: Analyzing 17. Differentiate between orthologous genes and paralogous genes.

ANS: Orthologous genes are highly conserved gene sequences that encode proteins with the same function in different organisms and are believed to have arisen from a common ancestral gene.

Paralogous genes are related genes within a species. Paralogous genes have orthologous genes in other species.

DIF: Difficult REF: 1.4 OBJ: 1.4.b. Differentiate between orthologous genes and paralogous genes.

MSC: Analyzing 18. Evaluate the following statement: Two amino acid sequences with high sequence conservation must have the same function in an organism.

ANS: Although two amino acid sequences with high sequence conservation may have the same structure, it does not mean that those two proteins will perform the same function in a body. As is shown in Figure 1.30, similar structures may have different function.

DIF: Difficult

REF: 1.4

OBJ: 1.4.c. Identify the relationship between protein structure and function.

MSC: Evaluating 19. For the figure below, label the and ends for each strand, the hydrogen bonds, and the pyrimidine and purine molecules, as well as the direction of polarity.

ANS:

DIF: Medium REF: 1.2 MSC: Remembering

OBJ: 1.3.b. Compare and contrast DNA and RNA.

20. Describe the difference between a deoxyribonucleotide and a ribonucleotide.

ANS: Deoxyribonucleotides are monomeric units of DNA and lack a hydroxyl group on the carbon on the position, whereas a ribonucleotide does have a hydroxyl group on the carbon on the on the position.

DIF: Medium MSC: Applying

REF: 1.2

OBJ: 1.3.b. Compare and contrast DNA and RNA.

21. Give an example of each of the following: element, biomolecule, macromolecule, metabolism, cell, organism, and ecosystem.

ANS: Any element from the periodic table is acceptable;

Biomolecules: amino acids, nucleotides, simple sugars, fatty acids; Macromolecules: DNA/RNA, proteins, carbohydrates; Metabolism: glycolysis, citrate cycle, urea cycle; Cells: cell wall, plasma membrane, organelles; Organisms: trees, mammals, fish, bird, insects; Ecosystems: rivers, islands, forest, desert.

DIF: Medium REF: 1.2 OBJ: 1.2.a. List the elements that are most abundant in living organisms.

MSC: Remembering 22. Amino acids are the building blocks of proteins. There are 20 amino acids; how do these amino acids differ from one another?

ANS: Amino acids differ from one another in the side chain attached to the central carbon.

DIF: Easy REF: 1.2 OBJ: 1.2.c. Name the four major classes of biomolecules and the primary cellular functions associated with each.

MSC: Applying 23. Describe the differences between the structures of pyrimidine and a purine.

ANS: A pyrimidine is an aromatic molecule with nitrogen at positions 1 and 3 on the ring, along with a carbonyl at position 4. Examples of pyrimidines are cytosine, thymine, and uracil. A purine is a heterocyclic aromatic molecule with nitrogen at positions 1, 3, 7, and 9. Examples of purines are guanine and adenine.

DIF: Difficult REF: 1.3 OBJ: 1.3.a. Identify the three components of a nucleotide.

MSC: Analyzing

24. What is the function of mRNA in the cell?

ANS: mRNA is used as templates for protein synthesis in a process referred to as mRNA translation.

DIF: Easy MSC: Analyzing

REF: 1.3

OBJ: 1.3.b. Compare and contrast DNA and RNA.

25. If you were a biochemist who just discovered a new protein, how would you gain insight into the function of the protein?

ANS: One way to gain insight into the function of a protein is to compare its amino acid sequence to those of other proteins to see if conserved regions appear that might suggest an important function.

This is done using the genetic code to convert the DNA sequence in the coding stand of a gene into the inferred amino acid sequence of the encoded protein.

DIF: Difficult REF: 1.4 OBJ: 1.4.c. Identify the relationship between protein structure and function.

MSC: Evaluating

Chapter 2: Physical Biochemistry: Energy Conversion, Water, and Membranes MULTIPLE CHOICE 1. Energy conversion in living systems is required for what three types of work? a. osmotic work, chemical work, mechanical work b. osmotic work, chemical work, potential work c. kinetic work, chemical work, mechanical work d. osmotic work, photosynthetic work, mechanical work ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.a. Describe how sunlight is the source of all energy on Earth.

MSC: Remembering 2. What chemical process is able to take place in the presence of solar energy? a. anaerobic respiration b. photosynthesis c. hydrogenation d. hydrolysis ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.a. Describe how sunlight is the source of all energy on Earth.

MSC: Remembering 3. Which of the following is the correct solar energy reaction that takes place on the sun?

4 a. 4 He He 4 b. He 4 He 4 c. 4 H He 4 d. H 4H ANS: C DIF: Medium REF: 2.1 OBJ: 2.1.a. Describe how sunlight is the source of all energy on Earth.

MSC: Understanding 4. What is the final molecule made from the oxidation of H2O by solar energy? a. ozone b. glucose c. fructose d. carbon dioxide ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.c. Explain the role of oxidation-reduction reactions in biological systems.

MSC: Understanding 5. The difference between an oxidation reaction and a reduction reaction is that oxidation is the __________ and reduction is the __________. a. loss of electrons; gain of electrons b. gain of electrons; loss of electrons c. loss of protons; gain of protons d. gain of protons; loss of protons ANS: A DIF: Medium REF: 2.1 OBJ: 2.1.c. Explain the role of oxidation-reduction reactions in biological systems.

MSC: Analyzing

6. Which of the following correctly describes the relationship between an ice cube melting on the table and the air surrounding it? a. The ice cube is the system and the air is the surroundings. b. The air is the system and the ice cube is the surroundings. c. The ice cube is the system and only the air is the universe. d. The air is the system and only the ice cube is the universe.

ANS: A DIF: Medium REF: 2.1 OBJ: 2.1.d. Differentiate between a system and its surroundings.

MSC: Evaluating 7. Which of the following is an example of a system? a. the universe b. the air c. a test tube with reaction components d. outer space ANS: C DIF: Easy REF: 2.1 OBJ: 2.1.d. Differentiate between a system and its surroundings.

MSC: Understanding 8. A hot pack on your arm is an example of what kind of system? a. open b. closed c. isolated d. surroundings ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.e. Differentiate among open, closed, and isolated systems.

MSC: Applying 9. Which of the following best describes an open system? a. Matter and energy are freely exchanged with the surroundings. b. Energy is exchanged with the surroundings but matter is not. c. Matter is exchanged with the surroundings but energy is not. d. Neither matter nor energy is exchanged with the surroundings.

ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.e. Differentiate among open, closed, and isolated systems.

MSC: Understanding 10. Which of the following best defines the first law of thermodynamics? a. All spontaneous processes in the universe tend toward dispersal of energy. b. Total amount of energy in the universe is a constant. c. There is no entropy at zero Kelvin. d. Entropy is a measure of disorder.

ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Understanding 11. Energy conversion in a biological system operates under constant __________ and constant __________. a. heat; pressure

b. work; heat c. pressure; volume d. volume; heat ANS: C DIF: Medium REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Applying 12. Given a biological system at 1 atm with = 16 kJ/g, what is the internal energy of the system? a. 15 kJ/g b. 16 kJ/g c. 14 kJ/g d. Not enough information is given to calculate the answer.

ANS: B DIF: Difficult REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Applying 13. The combustion of gasoline is considered exothermic because heat is a. transferred from the surroundings to the system. b. transferred from the system to the surroundings. c. transferred to the universe. d. not transferred.

ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.g. Differentiate between endothermic and exothermic reactions.

MSC: Understanding 14. Given 80 grams of water, how many calories are required to raise the temperature a. 4.184 calories b. 15.7 calories c. 80 calories d. Not enough information is given to calculate the answer.

ANS: C DIF: Medium REF: 2.1 OBJ: 2.1.g. Differentiate between endothermic and exothermic reactions.

MSC: Applying 15. The oxidation of glucose releases 15.7 kJ/g. Is this reaction spontaneous? a. Yes, because it is exothermic. b. No, because it is exothermic. c. Yes, because it is endothermic. d. The answer cannot be determined.

ANS: D DIF: Difficult REF: 2.1 OBJ: 2.1.g. Differentiate between endothermic and exothermic reactions.

MSC: Analyzing 16. In the figure below, which state of matter has the highest entropy?

?

a. b. c. d.

solid phase liquid phase gas phase all are equal entropy.

ANS: C DIF: Easy REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Remembering 17. For a reaction to be spontaneous, the change in the entropy of the universe must be a. greater than zero. b. less than zero. c. equal to zero. d. equal to 1.

ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.i. Explain the concept of entropy and its role in biological systems.

MSC: Understanding 18. The example of water freezing into ice shows a. an increase in entropy of the system. b. a decrease in entropy of the system. c. no change in the entropy of the system. d. a decrease in the entropy of the surroundings.

ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Applying 19. The change in entropy of a system is a function of a change in a. temperature and pressure. b. volume and pressure. c. enthalpy and pressure. d. enthalpy and temperature.

ANS: D DIF: Difficult REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Understanding

20. Gibbs free energy can best be defined as the a. difference between the enthalpy and entropy of a system at a given temperature. b. difference between exothermic and endothermic energy of a system at a given temperature. c. addition of enthalpy and entropy of a system at a given temperature. d. difference between pressure and volume at a given temperature.

ANS: A DIF: Difficult REF: 2.1 OBJ: 2.1.j. Define Gibbs free energy, its relation to enthalpy and entropy, and its relation to equilibrium.

MSC: Understanding 21. For a given reaction with a , the reaction is a. favorable in the reverse direction. b. favorable in the forward direction. c. unfavorable in both directions. d. favorable in both directions.

ANS: B DIF: Medium REF: 2.1 OBJ: 2.1.j. Define Gibbs free energy, its relation to enthalpy and entropy, and its relation to equilibrium.

MSC: Understanding 22. If a reaction has a and a temperatures. a. ; spontaneous b. ; spontaneous c. ; nonspontaneous d. ; nonspontaneous

, then __________ and the reaction is __________ at all

ANS: D DIF: Medium REF: 2.1 OBJ: 2.1.j. Define Gibbs free energy, its relation to enthalpy and entropy, and its relation to equilibrium.

MSC: Applying 23. If a. b. c. d.

for a reaction, then this reaction is favorable in the forward direction. is favorable in the reverse direction. is at equilibrium. cannot occur.

ANS: C DIF: Medium REF: 2.1 OBJ: 2.1.j. Define Gibbs free energy, its relation to enthalpy and entropy, and its relation to equilibrium.

MSC: Analyzing 24. If a reaction has a and in the forward direction? a. low temperatures b. high temperatures c. high pressure d. low pressure

, under which conditions would the reaction be spontaneous

ANS: A DIF: Medium REF: 2.1 OBJ: 2.1.k. Identify the impacts of enthalpy, entropy, and temperature on free energy.

MSC: Evaluating 25. The standard free energy change is defined under what set of conditions?

a. b. c. d.

1 atm, 298 K, 1 M 1 atm, 273 K, 1 M 100 kPa, 273 K, 1 M 100 kPa, 298 K, 1 M

ANS: A DIF: Difficult REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Understanding 26. If the equilibrium constant (Keq) is greater than 1, which direction will the reaction proceed? a. spontaneously to products b. spontaneously to reactants c. neither direction d. Not enough information is given to determine the direction of reaction.

ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Applying 27. If the equilibrium constant (Keq) is greater than 1, what is the value of a. b. c. d.

?

ANS: C DIF: Difficult REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Applying 28. Under what conditions could a biological reaction spontaneously proceed to reactants if the ? a. Reactant concentrations are greater than product concentrations. b. Product concentrations are greater than reactant concentrations. c. Reactant concentrations are equal to product concentrations. d. There are no conditions where this could happen.

ANS: B DIF: Difficult REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Evaluating 29. If the Gibbs free energy change value for a reaction is less than zero, this reaction is a. exergonic. b. endergonic. c. exothermic. d. endothermic.

ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.m. Differentiate between exergonic and endergonic reactions and explain how such reactions are coupled in biological systems.

MSC: Remembering 30. What chemical reaction causes ATP to be a high-energy molecule? a. cleavage of phosphoanhydride bond b. transfer of an adenylyl group to form a reactive intermediate c. hydrolysis of phosphoryl group d. oxidation of phosphoanhydride bond

ANS: B DIF: Difficult REF: 2.1 OBJ: 2.1.n. Identify the characteristics of the ATP molecule that provide such a large standard free energy change for phosphoanhydride bond cleavage.

MSC: Analyzing 31. The transfer of a phosphate from ATP to another molecule produces a(n) a. low-energy intermediate. b. highly reactive intermediate. c. neutral energy intermediate. d. It is not possible to transfer a phosphate to another molecule.

ANS: B DIF: Easy REF: 2.1 OBJ: 2.1.n. Identify the characteristics of the ATP molecule that provide such a large standard free energy change for phosphoanhydride bond cleavage.

MSC: Understanding 32. The __________ system controls the interconversion among ATP, ADP, and AMP. a. phosphorylate b. adenylate c. energy conversion d. metabolism ANS: B DIF: Easy REF: 2.1 OBJ: 2.1.o. Describe the relationship between energy charge and concentrations of ATP, ADP, and AMP. MSC: Remembering 33. Given the energy charge equation below, if a biological system has an EC = 0.8, what is true about the concentrations of ATP, ADP, and AMP in the system?

a. b. c. d.

The concentrations are all equal.

There is more ADP in the system than ATP or AMP. There is more ATP in the system than ADP or AMP. There is more AMP in the system than ATP and ADP.

ANS: C DIF: Difficult REF: 2.1 OBJ: 2.1.o. Describe the relationship between energy charge and concentrations of ATP, ADP, and AMP. MSC: Applying 34. Under steady-state conditions in a mammalian cell, the adenine nucleotide concentrations are [ATP] = 3.3 mM, [ADP] = 1.2 mM, and [AMP] = 0.2 mM. What is the energy charge of this cell? a. 0.83 b. 0.95 c. 0.72 d. 1.2 ANS: A DIF: Difficult REF: 2.1 OBJ: 2.1.o. Describe the relationship between energy charge and concentrations of ATP, ADP, and AMP. MSC: Applying 35. In a hydrogen bond between a water molecule and another water molecule, a. a hydrogen ion on the water molecule forms an ionic bond with the oxygen ion on the other water. b. the hydrogen bond typically forms between the oxygen atom of the water and the hydrogen on the other water.

c. a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other water. d. the hydrogen atom forms an ionic bond with a carbon on the other water.

ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.a. Identify hydrogen bond donors and hydrogen bond acceptors.

MSC: Applying 36. Hydrogen bonds in liquid water are formed between a. two hydrogen atoms on the same molecule. b. the oxygen of one molecule and the hydrogen of another. c. protons and hydroxides. d. two oxygen atoms on different molecules.

ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.a. Identify hydrogen bond donors and hydrogen bond acceptors.

MSC: Understanding 37. Organisms on Earth cannot easily exist at temperatures below a. hydrogen bonds cannot exist. b. water does not exist in a tetrahedron. c. ice crystals form in the organism. d. proton hopping cannot occur.

ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.b. Describe how an antifreeze protein functions.

because at that temperature

MSC: Understanding

38. Describe how an antifreeze protein functions. a. Regularly spaced tyrosine residues prevent the ice crystals from growing. b. Regularly spaced threonine resides prevent the ice crystals from growing. c. Flickering clusters of hydrogen bonds prevent the ice crystals from growing. d. The antifreeze protein prevents the water wires from forming.

ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.b. Describe how an antifreeze protein functions.

MSC: Applying

39. A hydrogen bond can form between a hydrogen atom on a(n) a. electronegative donor group and another electronegative atom. b. cationic atom and another hydrogen. c. nonpolar donor group and an electronegative atom. d. ionic atom and another anion.

ANS: A DIF: Medium REF: 2.2 OBJ: 2.2.c. Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions.

MSC: Remembering 40. The interaction between an amino group and a carboxylate group is best characterized as a. hydrogen bonds. b. ionic interactions. c. van der Waals interactions. d. a covalent bond.

ANS: B DIF: Easy REF: 2.2 OBJ: 2.2.c. Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions.

MSC: Understanding 41. The interaction between nonpolar molecules is best characterized as a. a hydrogen bond. b. ionic interactions. c. van der Waals interactions. d. a covalent bond.

ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.c. Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions.

MSC: Understanding 42. An organism in equilibrium with its environment is no longer alive because a. homeostasis is required for life. b. heterostasis is required for life. c. an organism requires only exergonic reactions to be alive. d. an organism requires only endergonic reactions to be alive.

ANS: A DIF: Easy REF: 2.1 OBJ: 2.1.f. Explain the first law of thermodynamics as it applies to biological systems.

MSC: Understanding 43. Hydrophobic interactions between nonpolar molecules result from the a. tendency to maximize water’s interaction with nonpolar molecules. b. strong attractions between nonpolar molecules. c. water becoming more ordered around the nonpolar molecule. d. water ionically bonding to the nonpolar molecule.

ANS: C DIF: Medium REF: 2.2 OBJ: 2.2.d. State the concept of the hydrophobic effect and how it impacts protein folding.

MSC: Applying 44. Limonene is a nonpolar molecule. The water molecules around it forms a. hydrogen bonds with itself and entropy decreases. b. ionic bonds with itself and the entropy decreases. c. hydrogen bonds with limonene and the entropy increases. d. covalent bonds with limonene and entropy increases.

ANS: A DIF: Difficult REF: 2.2 OBJ: 2.2.d. State the concept of the hydrophobic effect and how it impacts protein folding.

MSC: Applying 45. As a protein folds, what are the stabilizing forces that help keep the protein folded? a. hydrophilic amino acids on the interior and hydrophobic amino acids on the exterior b. increase in entropy in the surrounding water c. favorable change in free energy d. hydrophobic amino acids on the interior and hydrophilic amino acids on the exterior ANS: D DIF: Medium REF: 2.2 OBJ: 2.2.d. State the concept of the hydrophobic effect and how it impacts protein folding.

MSC: Remembering 46. Freezing point depression, boiling point elevation, and osmotic pressure are all what kind of properties?

a. b. c. d.

intrinsic properties colligative properties state functions hydrophobic effects

ANS: B DIF: Easy REF: 2.2 OBJ: 2.2.d. State the concept of the hydrophobic effect and how it impacts protein folding.

MSC: Remembering 47. The effects of solutes on the colligative properties of a solution depend only on the a. chemical properties of the solutes. b. molecular mass of the solutes. c. overall charge of the solute. d. number of solute particles.

ANS: D DIF: Easy REF: 2.2 OBJ: 2.2.e. Explain the impacts of hypotonic, isotonic, and hypertonic solutions on cells.

MSC: Remembering 48. Osmosis occurs when water diffuses through a a. semipermeable membrane from high water to low water concentration. b. nonpermeable membrane from high water to low water concentration. c. semipermeable membrane from low water to high water concentration. d. semipermeable membrane from high solute to low solute concentration.

ANS: A DIF: Easy REF: 2.2 OBJ: 2.2.e. Explain the impacts of hypotonic, isotonic, and hypertonic solutions on cells.

MSC: Remembering 49. Red blood cells are placed into a solution of unknown solute concentration. After an hour they have all burst open. The best explanation is that the solution a. had no solutes. b. had a very high concentration of solutes. c. had a very high concentration of solvent d. was at equilibrium.

ANS: A DIF: Difficult REF: 2.2 OBJ: 2.2.e. Explain the impacts of hypotonic, isotonic, and hypertonic solutions on cells.

MSC: Analyzing 50. What is the expected osmotic pressure around the cells for the plant with low turgor pressure shown below?

a. b. c. d.

hypotonic hypertonic isotonic equilibrium

ANS: B DIF: Difficult REF: 2.2 OBJ: 2.2.f. Identify the important aspects of plant, fungi, and bacterial cells that allow them to survive in a hypotonic environment.

MSC: Analyzing 51. How do plants, fungi, and bacteria avoid the damaging effects of a hypotonic environment? a. flexible cells walls b. rigid cells walls c. semipermeable cell walls d. photosynthesis ANS: B DIF: Easy REF: 2.2 OBJ: 2.2.f. Identify the important aspects of plant, fungi, and bacterial cells that allow them to survive in a hypotonic environment.

MSC: Applying 52. Which of the following is true? a. A neutral solution contains [H2O] = [H+]. b. A neutral solution does not contain any H+ or OH–. c. An acidic solution has [H+] > [OH–]. d. A basic solution does not contain H+.

ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 53. What is the concentration of OH− in a solution that contains 3.9 a. 2.6 10−11 M b. 3.9 10−4 M c. 2.7 10−2 M d. 1.0 10−14 M

10−4 M H+?

ANS: A DIF: Medium REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 54. What is the concentration of H+ in a solution of 0.05 M NaOH? a. 5 10–16 M b. 2 10–13 M c. 5 1012 M d. 140 M ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 55. Which of the following is the Kw value for pure water at a. 1 1014 b. 1 10–14 c. 7 d. 14

?

ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 56. Calculate the pH of a solution that contains 3.9 a. 4.59 b. 10.59 c. 3.41 d. 9.41

10–4M H+.

ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.h. Relate pH to the concentration of H+ or OH–.

MSC: Applying

57. Calculate the concentration of pH of a 0.023 M HCl solution. a. 12.36 b. 3.68 c. 1.64 d. 2.30 ANS: C DIF: Medium REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 58. Calculate the pH of a solution that contains 7.8 a. 1.28 b. 5.11 c. 12.72 d. 8.89

10−6 M OH−.

ANS: D DIF: Medium REF: 2.2 OBJ: 2.2.g. Calculate the concentration of H+ or OH– given the OH– or H+ concentration.

MSC: Applying 59. Which of the following acids is the strongest given their Ka values? a. HF (3.5 10–4) b. HClO2 (1.1 10–2) c. HCN (4.9 10–10) d. HNO2 (4.6 10–4) ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.i. Differentiate between weak acids and strong acids and between weak bases and strong bases. MSC: Analyzing 60. If an unknown solution has low pKa value, it can be said with certainty that it is a. a weak acid. b. a strong acid. c. pure water. d. a nonpolar solution.

ANS: B DIF: Easy REF: 2.2 OBJ: 2.2.i. Differentiate between weak acids and strong acids and between weak bases and strong bases. MSC: Applying 61. Weak acids have a high pKa because the a. HA concentration is high.

b. H+ concentration is high. c. A− concentration is high. d. HA concentration is low.

ANS: A DIF: Easy REF: 2.2 OBJ: 2.2.i. Differentiate between weak acids and strong acids and between weak bases and strong bases. MSC: Applying 62. You wish to prepare a solution with a pH of 5.44. If the pKa of the weak acid is 4.74, what ratio of weak base to weak acid should you use? a. 0.70 b. 0.20 c. 1.4 d. 5.0 ANS: D DIF: Medium REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Applying 63. Calculate the pH of a solution containing 0.105 M HA and 0.146 M A–. The Ka for the weak acid is 1.8 10–5. a. 4.88 b. 9.11 c. 4.74 d. 7.00 ANS: A DIF: Medium REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Applying 64. Given a solution with pH > pKa, what are the relative concentrations of A– and HA? a. [HA] > [A–] b. [HA] < [A–] c. [HA] = [A–] d. [HA] = [A–] = 1 ANS: B DIF: Difficult REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Analyzing 65. Which of the following are true about buffers? a. An effective buffer is made from a strong acid and strong base. b. A buffer is most resistant to changes in pH when [HA] = [A–]. c. A buffer is only resistant to changes in pH when acid is added. d. The pH range of a buffering system is 0 to 14.

ANS: B DIF: Medium REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Remembering 66. Using the figure below, which of the following best describes the titration curve?

a. b. c. d.

The equivalence point for the titration is pH = 7.

The midpoint of the titration is pH = 7.

The pKa for this weak acid is 4.76.

This is a titration of a weak base by NaOH.

ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Understanding 67. A solution of which of the following would be a good buffer system? a. HCl and NaOH b. HCl and H2O c. CH3COOH and NaCH3COO d. NaOH and KOH ANS: C DIF: Easy REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Understanding 68. A molecule with hydrophobic and hydrophilic properties is best described as a. a zwitterion. b. amphipathic. c. polar. d. nonpolar.

ANS: B DIF: Easy REF: 2.3 OBJ: 2.3.a. Identify the characteristics of a phospholipid that contribute to membrane formation.

MSC: Remembering 69. The characteristic(s) of a phospholipid is/are that they a. are overall nonpolar. b. have a polar charged head group and nonpolar hydrocarbon tails. c. have a nonpolar head group and polar hydrocarbon tails. d. are overall polar.

ANS: B DIF: Easy REF: 2.3 OBJ: 2.3.a. Identify the characteristics of a phospholipid that contribute to membrane formation.

MSC: Understanding 70. The fluidity of a membrane depends on

a. b. c. d.

the degree of saturation of the phospholipids. the number of phospholipids in the membrane. the size of the polar head group. osmotic pressure.

ANS: A DIF: Easy REF: 2.3 OBJ: 2.3.a. Identify the characteristics of a phospholipid that contribute to membrane formation.

MSC: Understanding 71. The lateral mobility of lipids with membrane depends on temperature as well as other factors.

What would be expected to happen to the lateral mobility if the temperature was decreased? a. Mobility would be unaffected. b. Mobility would increase. c. Mobility would decrease. d. The membrane would decompose.

ANS: C DIF: Medium REF: 2.3 OBJ: 2.3.c. Explain the various ways cholesterol affects membrane structure.

MSC: Applying 72. How are polar molecules like glucose transported across a membrane? a. There are holes in the membrane. b. There are proteins that allow the transportation of polar molecules across the membrane. c. Polar molecules cannot ever enter the cell. d. Polar molecules diffuse across the hydrophobic barrier.

ANS: B DIF: Easy REF: 2.3 OBJ: 2.3.c. Explain the various ways cholesterol affects membrane structure.

MSC: Applying 73. The endomembrane system encompasses which part of the cell? a. organelles b. nucleus c. cytoplasmic membrane structures d. entire cell ANS: C DIF: Easy REF: 2.3 OBJ: 2.3.d. Differentiate among the different types of membranes found in a eukaryotic cell.

MSC: Remembering 74. The endomembrane system is/are a. an intracellular network of lipid bilayers. b. energy converting organelles. c. a membrane surrounding the cell. d. nucleotide-containing membranes.

ANS: A DIF: Easy REF: 2.3 OBJ: 2.3.d. Differentiate among the different types of membranes found in a eukaryotic cell.

MSC: Remembering 75. The main function of the chloroplast is a. protein biosynthesis. b. to attach carbohydrates to lipids. c. to convert light energy into chemical energy. d. RNA synthesis.

ANS: C DIF: Easy REF: 2.3 OBJ: 2.3.d. Differentiate among the different types of membranes found in a eukaryotic cell.

MSC: Remembering SHORT ANSWER 1. Justify the following sentence: The conversion of carbon dioxide and water into glucose and oxygen is a decrease of entropy.

ANS: The balanced chemical equation of 6 CO2 (g) + 6 H2O (l) C6H12O6 (s) + 6 O2 (g) shows that 12 molecules are being converted to 7 molecules. This is an example of decreasing the disorder of the system; therefore this reaction is a decrease in entropy.

DIF: Difficult REF: 2.1 OBJ: 2.1.i. Explain the concept of entropy and its role in biological systems.

MSC: Evaluating 2. Calculate for a reaction given = 15.4 kJ/mole and spontaneous in the forward direction?

ANS: Using the equation 14.8 kJ/mole.

= 2.0 J/K at 298 K. Is this reaction

and converting the units of entropy to kJ, the final answer is

DIF: Medium REF: 2.1 OBJ: 2.1.k. Identify the impacts of enthalpy, entropy, and temperature on free energy.

MSC: Applying 3. Compare the reaction conditions for

and

.

ANS: G is the standard free energy change and measured under 1 atm and 298 K, where all reactants and products are present at 1 M. is the biochemical standard condition where the free energy change is measured under 1 atm and 298 K, where all reactants and products are present at 1 M as well as at pH 7 and the concentration of H2O is 55.5 M. DIF: Medium REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Analyzing 4. Compare the reaction conditions under which you measure Keq versus Q. ANS: Keq is the equilibrium constant, so the reaction is at equilibrium at 1 atm, 298 K, and initial concentration of 1 M of all reactants and products. Q is the mass-action ratio measured at nonequilibrium concentrations.

DIF: Medium REF: 2.1 OBJ: 2.1.l. Differentiate between standard state condition and the biochemical standard state.

MSC: Analyzing 5. Calculate the

for the net reaction given the following two reactions:

Reaction 1: Reaction 2:

. .

ANS: The net reaction is the addition of reaction 1 and 2. The net

is 5 − 12 = −7 kJ/mol.

DIF: Medium REF: 2.1 OBJ: 2.1.m. Differentiate between exergonic and endergonic reactions and explain how such reactions are coupled in biological systems.

MSC: Applying 6. Differentiate between autotrophs and heterotrophs.

ANS: Autotrophs convert solar energy to chemical energy, whereas heterotrophs cannot.

DIF: Easy REF: 2.1 OBJ: 2.1.b. Differentiate between autotrophs and heterotrophs.

MSC: Analyzing 7. How can a reaction that is endergonic occur in a biological system?

ANS: It must be paired with an exergonic reaction for a reaction in a biological system to occur.

DIF: Easy REF: 2.1 OBJ: 2.1.m. Differentiate between exergonic and endergonic reactions and explain how such reactions are coupled in biological systems.

MSC: Understanding 8. Compare a catabolic pathway versus an anabolic pathway.

ANS: Anabolic pathways synthesize biomolecules, whereas catabolic pathways extract energy from metabolic fuels. Catabolic pathways also generate ATP and reduced coenyzmes.

DIF: Medium REF: 2.1 OBJ: 2.1.o. Describe the relationship between energy charge and concentrations of ATP, ADP, and AMP. MSC: Analyzing 9. The antifreeze proteins evolved independently through convergent evolution. What does that mean?

ANS: Convergent evolution is the independent evolution of similar proteins for similar functions. For example, insect antifreeze proteins prevent the formation of ice crystals in the hemolymph by disrupting hydrogen bonding between H2O molecules. The structures of antifreeze proteins from four different organisms show that although they all contain numerous threonine residues on the protein surface, the overall structure of the proteins is quite different.

DIF: Medium REF: 2.2 OBJ: 2.2.b. Describe how an antifreeze protein functions.

MSC: Remembering

10. List the three chemical properties of ATP that account for the large standard free energy change that occurs when a phosphoanhydride bond is cleaved.

ANS: 1. Electrostatic repulsion between the charged phosphoryl groups destabilizes ATP. Repulsion is reduced on hydrolysis, and therefore the products of ATP hydrolysis are more stable than ATP itself, which favors the hydrolysis reaction.

2. The released phosphate ion has more possible resonance forms than when it is covalently attached to adenylate. Entropically, this favors the free phosphate ions compared to ATP or ADP. 3. The phosphate ion and ADP have a greater degree of solvation than ATP. This means that the phosphate ion and ADP form hydration layers and are more stable than ATP. DIF: Easy REF: 2.1 OBJ: 2.1.n. Identify the characteristics of the ATP molecule that provide such a large standard free energy change for phosphoanhydride bond cleavage.

MSC: Remembering 11. In the figure below, identify the adenine base, ribose, and phosphoanhydride bonds.

ANS:

DIF: Easy REF: 2.1 OBJ: 2.1.n. Identify the characteristics of the ATP molecule that provide such a large standard free energy change for phosphoanhydride bond cleavage.

MSC: Understanding 12. In the figure below, label which reactions are oxidations and which are reduction.

ANS:

DIF: Easy REF: 2.1 OBJ: 2.1.c. Explain the role of oxidation-reduction reactions in biological systems.

MSC: Remembering 13. Given the figure below, label the following: hydration layer, electrostatic interaction, hydrogen bond, van der Waals interaction.

ANS:

DIF: Easy REF: 2.2 OBJ: 2.2.d. State the concept of the hydrophobic effect and how it impacts protein folding.

MSC: Remembering

14. If serum pH falls blow pH 7.4, a condition called acidosis, how does the body respond?

ANS: The equilibrium of the carbonic acid–bicarbonate reaction is shifted toward H2CO3 formation to decrease H+ concentration and thereby increase the pH. This is done by lowering CO2 through hyperventilation and decreasing excretion of HCO3− by the kidneys.

DIF: Difficult REF: 2.2 OBJ: 2.2.j. Relate pH to pKa using the Henderson-Hasselbalch equation.

MSC: Analyzing 15. Compare the structure of a phospholipid bilayer and the structure of a micelle.

ANS: Phospholipid bilayers are characteristic of biological membranes and create a hydrophobic barrier between two aqueous compartments. The hydrophilic polar head groups orient toward the aqueous environment, and the hydrophobic nonpolar hydrocarbon tails form a water impermeable barrier in the interior of the membrane. Micelles are structures in which the hydrophobic tails are in the center of a globular sphere and the polar head groups are facing outward toward the water.

DIF: Easy REF: 2.3 OBJ: 2.3.a. Identify the characteristics of a phospholipid that contribute to membrane formation.

MSC: Analyzing 16. The inclusion of cholesterol in a membrane can change the behavior of the membrane. Compare how the membrane behaves at low cholesterol concentration compared with high cholesterol concentration.

ANS: When small amounts of cholesterol are added to a membrane, it prevents close packing by the phospholipids and helps the membrane increase fluidity. When large amounts are added, the cell membrane fluidity decreases due to the rigid ring structure of cholesterol.

DIF: Medium REF: 2.3 OBJ: 2.3.c. Explain the various ways cholesterol affects membrane structure.

MSC: Analyzing 17. It is known that lipid molecules in a membrane are able to move throughout the membrane.

Propose a method to determine which mode of motion is MOST likely to happen and justify your answer.

ANS: Fluorescence labeling of a phospholipid to determine that rotational movement would be the most likely to happen. This requires the least energy to perform and does not require the movement of another phospholipid.

DIF: Difficult REF: 2.3 OBJ: 2.3.c. Explain the various ways cholesterol affects membrane structure.

MSC: Evaluating 18. What are the three major types of membranes?

ANS:

Plasma membrane, endomembrane, organelle membranes DIF: Easy REF: 2.3 OBJ: 2.3.d. Differentiate among the different types of membranes found in a eukaryotic cell.

MSC: Remembering 19. Using the figure below, explain how having unsaturated fatty acid tails on phospholipids affects the fluidity of the membrane.

ANS: The kink in the tails that occurs with the inclusion of a double bond prevents the tight packing of the fatty acid tails and increases the fluidity of the membrane.

DIF: Medium REF: 2.3 OBJ: 2.3.a. Identify the characteristics of a phospholipid that contribute to membrane formation.

MSC: Understanding 20. Fill in the table below.

If the sign of H is

and if the sign of S is

Negative Positive

Positive Negative

Negative Positive

Negative Positive

ANS: If sign of H is

then the sign of G will be

Will it be spontaneous?

then the sign of G will be

Negative

and if the sign of S is Positive

Positive

Negative

Positive

Negative

Negative

Negative when temperature is low Positive when temperature is high

No at all temperatures Temperature dependent

Positive

Positive

Negative when temperature is high Positive when temperature is low

Temperature dependent

Negative

Will it be spontaneous?

Yes at all temperatures

DIF: Difficult REF: 2.1 OBJ: 2.1.k. Identify the impacts of enthalpy, entropy, and temperature on free energy.

MSC: Understanding 21. Explain why a negative

does not necessarily mean it will be a rapid reaction.

ANS: tells you whether a reaction is likely to proceed to products as written. It is not a measure of the rate at which a reaction will take place. To determine rates of reactions you need to consider the kinetics of a reaction.

DIF: Difficult REF: 2.1 OBJ: 2.1.k. Identify the impacts of enthalpy, entropy, and temperature on free energy.

MSC: Understanding 22. Water is a simple molecule that has three distinct properties. What are these properties and how are they critical for life processes?

ANS: Water is less dense as a solid than a liquid, which allows water to float. Water is a liquid over a wide range of temperatures, which allows for the existence of aquatic life and oxygen content in the atmosphere. Water is an excellent solvent that is polar and can solvate ions and polar molecules. Hydrogen bonding within water is also important as it keeps water as a solvent over a much larger temperature range then would be expected.

DIF: Difficult REF: 2.2 OBJ: 2.2.c. Differentiate among hydrogen bonds, ionic interactions, and van der Waals interactions.

MSC: Understanding 23. Explain the first and second laws of thermodynamics and how they are relevant to the field of biochemistry.

ANS: The first law of thermodynamics states that energy is neither created nor destroyed, only converted from one form to another. This is what allows energy to be taken in by plants as light and converted to chemical energy. The second law of thermodynamics states that entropy in the universe is always increasing and therefore without the input of energy to restrain entropy, the highly ordered structures of organisms would fail and the organism would die.

DIF: Difficult REF: 2.1 OBJ: 2.1.h. State the second law of thermodynamics as it applies to biological systems.

MSC: Understanding 24. Explain why adding nonpolar compounds to water is energetically unfavorable.

ANS: The addition of nonpolar compounds to water breaks the hydrogen bonds between water molecules without replacing them and leads to the formation of ordered cagelike water structures, which is energetically unfavorable.

DIF: Medium REF: 2.2 OBJ: 2.1.h. State the second law of thermodynamics as it applies to biological systems.

MSC: Understanding

25. Name and briefly describe the four types of weaker intermolecular forces found in biochemistry.

ANS: Hydrogen bonds: form between a hydrogen atom on an electronegative donor group and another electronegative atom that serves as a hydrogen-bond acceptor.

Ionic interactions: weak interactions between oppositely charged atoms or groups. van der Waals: weak interactions occurring between the dipoles of nearby electrically neutral molecule.

Hydrophobic effects: weak “interaction” is due to the tendency of hydrophobic molecules to pack close together away from water.

DIF: Easy REF: 2.2 OBJ: 2.1.h. State the second law of thermodynamics as it applies to biological systems.

MSC: Understanding

Chapter 3: Nucleic Acid Structure and Function MULTIPLE CHOICE 1. The figure below shows part of the primary structure of DNA. Identify the nucleoside.

a. b. c. d.

A B C D

ANS: C DIF: Easy REF: 3.1 OBJ: 3.1.a. Define the primary and secondary structures of DNA. MSC: Understanding 2. The figure below shows part of the primary structure of DNA. Identify the nucleotide.

a. b. c. d.

A B C D

ANS: D DIF: Easy REF: 3.1 OBJ: 3.1.a. Define the primary and secondary structures of DNA. MSC: Understanding 3. The interior stacking of the DNA bases in the double helix provides stability through a. hydrophobic and van der Waals interactions. b. hydrophilic and van der Waals interactions.

c. hydrophilic and ion–dipole interactions. d. hydrophobic and ion–dipole interactions.

ANS: A DIF: Medium REF: 3.1 OBJ: 3.1.a. Define the primary and secondary structures of DNA. MSC: Understanding 4. How many base pairs per turn does B-DNA contain? a. 10.0 b. 10.5 c. 11.0 d. 12.0 ANS: B DIF: Easy REF: 3.1 OBJ: 3.1.e. Differentiate among A-DNA, B-DNA, and Z-DNA. MSC: Remembering 5. Which form(s) of DNA exhibit(s) a right-handed helical structure? a. A-DNA b. B-DNA c. Z-DNA d. A-DNA and B-DNA ANS: D DIF: Easy REF: 3.1 OBJ: 3.1.e. Differentiate among A-DNA, B-DNA, and Z-DNA. MSC: Remembering 6. Which form(s) of DNA exhibit(s) a zigzag arrangement? a. A-DNA b. B-DNA c. Z-DNA d. A-DNA and B-DNA ANS: C DIF: Easy REF: 3.1 OBJ: 3.1.e. Differentiate among A-DNA, B-DNA, and Z-DNA. MSC: Remembering 7. Chargaff’s rule is that the amount of a. A = G and the amount of C = T. b. A = C = G = T. c. A = T and the amount of C = G. d. A = C and the amount of G = T. ANS: C DIF: Easy REF: 3.1 OBJ: 3.1.d. Restate Chargaff’s rule and explain typical base pairing in DNA structure.

MSC: Understanding 8. The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is adenine? a. 15% b. 30% c. 35% d. 70% ANS: C DIF: Difficult REF: 3.1 OBJ: 3.1.d. Restate Chargaff’s rule and explain typical base pairing in DNA structure.

MSC: Applying 9. The DNA of a bacteria was isolated and it was determined that 15% of the DNA is composed of cytosine. What percentage of the DNA is guanine? a. 15% b. 30% c. 35% d. 70% ANS: A DIF: Difficult REF: 3.1 OBJ: 3.1.d. Restate Chargaff’s rule and explain typical base pairing in DNA structure.

MSC: Applying 10. The DNA double helix is considered to be a __________ structure. a. primary b. secondary c. tertiary d. quaternary ANS: B DIF: Easy REF: 3.1 OBJ: 3.1.a. Define the primary and secondary structures of DNA. MSC: Remembering 11. DNA strands are considered to be antiparallel. This means the a. phosphodiester bonds run in the same direction. b. phosphodiester bonds run in different directions. c. base pairs form hydrogen bonds. d. phosphate backbone is on the outside of the helix.

ANS: B DIF: Easy REF: 3.1 OBJ: 3.1.b. Explain the antiparallel nature of DNA structure.

MSC: Understanding

12. When DNA is transcribed into RNA, the __________ strand has the same base sequences as the RNA transcript. a. antiparallel b. parallel c. coding d. template ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.c. Differentiate between the coding strand and the template strand.

MSC: Applying 13. When DNA is transcribed into RNA, the __________ strand has the complementary sequence to the transcribed RNA. a. antiparallel b. parallel c. coding d. template ANS: D DIF: Medium REF: 3.1 OBJ: 3.1.c. Differentiate between the coding strand and the template strand.

MSC: Applying 14. Predict the complementary strand of the following DNA sequence:

-ATCTGAATCT-

a. b. c. d.

-

-

ANS: D DIF: Medium REF: 3.1 OBJ: 3.1.b. Explain the antiparallel nature of DNA structure.

MSC: Applying

15. The basic structure of DNA is a right-handed helix formed by two __________ strands of DNA. a. antiparallel b. parallel c. coding d. template ANS: A DIF: Easy REF: 3.1 OBJ: 3.1.b. Explain the antiparallel nature of DNA structure.

MSC: Remembering

16. What is the melting temperature from the DNA absorbance shown in the figure below?

a. b. c. d.

80 C 85 C 90 C 95 C

ANS: B DIF: Medium REF: 3.1 OBJ: 3.1.f. Define the hyperchromic effect.

MSC: Applying

17. The ability to monitor the denaturation of DNA using absorbance is referred to as a. annealing. b. supercoiling. c. melting temperature. d. hyperchromic effect.

ANS: D DIF: Easy REF: 3.1 OBJ: 3.1.f. Define the hyperchromic effect.

MSC: Remembering

18. As DNA unwinds and denatures, absorbance is predicted to a. remain the same. b. decrease. c. increase. d. vary unpredictably.

ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.f. Define the hyperchromic effect.

MSC: Applying

19. The K+ ion concentration in a DNA sample is increased from 50 mM to 100 mM. The Tm will a. remain the same. b. decrease. c. increase. d. vary unpredictably.

ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Applying 20. Increasing the ion concentration increases the Tm because the ions a. bind to the phosphate groups of the DNA backbone and increase stability. b. bind to the nucleic acids and disrupt the base pairs, decreasing stability. c. increase the base length of the DNA, increasing stability. d. associate with the ribose sugars, decreasing stability.

ANS: A DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Understanding 21. DNA strands containing 20 base pairs, 40 base pairs, and 60 base pairs were denatured and the results were graphed below. Identify the curve from the 60 base pair DNA strand.

a. b. c. d.

A B C Not enough information is included to determine the curve.

ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Understanding 22. The A-T content for several DNA strands is reported below. Which strand would have the highest Tm?

a. b. c. d.

40% A-T 50% A-T 60% A-T 70% A-T

ANS: A DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Applying 23. A double helix that crosses itself in a right-handed twist is referred to as a a. positive supercoil. b. negative supercoil. c. topoisomer. d. linking number.

ANS: B DIF: Easy REF: 3.1 OBJ: 3.1.h. Differentiate between positive and negative supercoiling.

MSC: Remembering 24. A double helix that crosses itself in a left-handed twist is referred to as a a. positive supercoil. b. negative supercoil. c. topoisomer. d. linking number.

ANS: A DIF: Easy REF: 3.1 OBJ: 3.1.h. Differentiate between positive and negative supercoiling.

MSC: Remembering 25. Which of the following expresses the relationship among the linking number, twist, and writhe? a. Tw = Lk + Wr b. Lk = Tw − Wr c. Lk = Wr − Tw d. Lk = Tw + Wr ANS: D DIF: Easy REF: 3.1 OBJ: 3.1.i. Explain the relationship among linking number, twist, and writhe.

MSC: Understanding 26. Calculate the linking number for a B-DNA strand that contains 735 total base pairs. a. 50 b. 61 c. 67 d. 70 ANS: D DIF: Medium REF: 3.1 OBJ: 3.1.i. Explain the relationship among linking number, twist, and writhe.

MSC: Applying 27. The linking number of a relaxed DNA strand whose axis is not coiling is 30. Predict the twist and writhe of the DNA stand. a. Wr = 0, Tw = 30 b. Wr = 30, Tw = 0 c. Wr = 15, Tw = 15

d. Wr = 30, Tw = –30 ANS: A DIF: Medium REF: 3.1 OBJ: 3.1.i. Explain the relationship among linking number, twist, and writhe.

MSC: Applying 28. Type I topoisomerase activity results in a region of __________ DNA. a. semiconservative b. spliced c. relaxed d. unrepaired ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.j. Differentiate between type I and type II topoisomerases.

MSC: Applying 29. Predict how type I topoisomerases change the supercoil region. a. Lk = 2 b. Lk = 1 c. Lk = –1 d. Lk = –2 ANS: C DIF: Easy REF: 3.1 OBJ: 3.1.j. Differentiate between type I and type II topoisomerases.

MSC: Applying 30. Predict how type II topoisomerases change the supercoil region. a. Lk = 2 b. Lk = 1 c. Lk = –1 d. Lk = –2 ANS: D DIF: Easy REF: 3.1 OBJ: 3.1.j. Differentiate between type I and type II topoisomerases.

MSC: Applying 31. Type II topoisomerase enzymes are important in replication and transcription because they a. prevent autocleavage. b. prevent DNA cleavage. c. relieve the positive supercoiling. d. stabilize the cleaved complex.

ANS: C DIF: Medium REF: 3.1 OBJ: 3.1.j. Differentiate between type I and type II topoisomerases.

MSC: Applying 32. RNA only contains which of the following bases? a. thymine b. adenine c. uracil d. guanine ANS: C DIF: Easy REF: 3.1 OBJ: 3.1.k. List the key structural difference between DNA and RNA. MSC: Remembering

33. Several histones can bind to one DNA molecule, forming a repeating unit called a a. ribozyme. b. nucleosome. c. topoisomerase. d. nucleoside.

ANS: B DIF: Easy REF: 3.1 OBJ: 3.1.l. Identify the histone proteins and the structures they form.

MSC: Remembering 34. Which of the following binds to DNA using a specific sequence? a. histones b. Lac repressor protein c. double-stranded binding proteins d. single-stranded binding proteins ANS: B DIF: Medium REF: 3.1 OBJ: 3.1.m. Compare the general binding of histones and single-stranded binding proteins with the specific binding of the Lac repressor. MSC: Analyzing 35. What mediates the binding of histone proteins to DNA? a. ionic attractions b. London dispersion forces c. hydrophilic interactions d. hydrophobic interactions ANS: A DIF: Easy REF: 3.1 OBJ: 3.1.l. Identify the histone proteins and the structures they form.

MSC: Remembering 36. The proteins that bind to DNA in a sequence-independent manner are a. histones. b. single-stranded binding proteins. c. Lac repressor proteins. d. histones and single-stranded binding proteins.

ANS: D DIF: Medium REF: 3.1 OBJ: 3.1.m. Compare the general binding of histones and single-stranded binding proteins with the specific binding of the Lac repressor. MSC: Analyzing 37. During eukaryotic DNA condensation, nucleosomes are packed together to form a. histones. b. chromatin. c. chromosomes. d. genes.

ANS: B DIF: Easy REF: 3.2 OBJ: 3.2.a. Identify the key elements involved in DNA condensation.

MSC: Analyzing 38. The process of condensation reduced the size of DNA by a. 100-fold. b. 1,000-fold. c. 10,000-fold. d. 100,000-fold.

ANS: C DIF: Easy REF: 3.2 OBJ: 3.2.a. Identify the key elements involved in DNA condensation.

MSC: Remembering 39. Less condensed, gene-rich chromatin is referred to as a. nucleosomes. b. histones. c. heterochromatin. d. euchromatin.

ANS: D DIF: Easy REF: 3.2 OBJ: 3.2.b. Differentiate between euchromatin and heterochromatin.

MSC: Remembering 40. Chromatin that consists of more condensed regions of mostly noncoding DNA are referred to as a. nucleosomes. b. histones. c. heterochromatin. d. euchromatin.

ANS: C DIF: Easy REF: 3.2 OBJ: 3.2.b. Differentiate between euchromatin and heterochromatin.

MSC: Remembering 41. Identify the kinetochore in the following figure.

a. b. c. d.

A B C D

ANS: D DIF: Easy OBJ: 3.2.c. List the elements of a gene.

REF: 3.2 MSC: Understanding

42. __________ maintain the length of the chromosome after replication. a. Telomeres b. Centromeres c. Kinetochores d. Sister chromatids ANS: A DIF: Easy OBJ: 3.2.c. List the elements of a gene.

REF: 3.2 MSC: Understanding

43. Two identical copies of replicated DNA that remain attached until cell division are referred to as a. telomeres. b. centromeres. c. kinetochores. d. sister chromatids.

ANS: D DIF: Easy OBJ: 3.2.c. List the elements of a gene.

REF: 3.2 MSC: Remembering

44. Which protein is responsible for the proper separation of the chromosomes during cell division? a. telomeres b. centromeres c. kinetochores d. sister chromatids ANS: C DIF: Easy OBJ: 3.2.c. List the elements of a gene.

REF: 3.2 MSC: Remembering

45. Polycistronic genes that contain a coding sequence for proteins that are only involved in one biochemical process are called a. exons. b. operons. c. introns. d. promoters.

ANS: B DIF: Easy REF: 3.2 OBJ: 3.2.d. Differentiate between monocistronic and polycistronic genes.

MSC: Understanding 46. Genes found in prokaryotes that only contain a single coding sequence are referred to as a. exons. b. introns. c. polycistronic. d. monocistronic.

ANS: D DIF: Easy REF: 3.2 OBJ: 3.2.d. Differentiate between monocistronic and polycistronic genes.

MSC: Understanding 47. In a single RNA transcript, polycistronic prokaryotic genes encode __________ protein(s). a. one b. two c. three d. multiple ANS: D DIF: Medium REF: 3.2 OBJ: 3.2.d. Differentiate between monocistronic and polycistronic genes.

MSC: Applying 48. The exons of a single gene often encode for different functional domains of a protein, which can result in a. genetic recombination. b. gene regulation. c. untranslated regions.

d. termination of transcription.

ANS: A DIF: Difficult REF: 3.2 OBJ: 3.2.e. Differentiate between exons and introns.

MSC: Applying

49. In the eukaryotic cell, the NONcoding sequences on a gene are referred to as a. exons. b. operons. c. introns. d. promoter.

ANS: C DIF: Easy REF: 3.2 OBJ: 3.2.e. Differentiate between exons and introns.

MSC: Understanding

50. In the eukaryotic cell, the coding sequences on a gene are referred to as a. exons. b. operons. c. introns. d. promoter.

ANS: A DIF: Easy REF: 3.2 OBJ: 3.2.e. Differentiate between exons and introns.

MSC: Remembering

51. The mixing and matching of novel genes in eukaryotic cells occurs through a. operons. b. exon shuffling. c. promoter regions. d. untranslated regions.

ANS: B DIF: Easy REF: 3.2 OBJ: 3.2.e. Differentiate between exons and introns.

MSC: Understanding

52. A common database tool used to determine homologous genomic sequences is called a. the National Center for Biotechnology Information. b. the National Human Genome Research Institute. c. Computational Analysis. d. Basic Local Alignment Search Tool.

ANS: D DIF: Easy REF: 3.2 OBJ: 3.2.f. Explain how BLAST can be used to compare genomic sequences.

MSC: Remembering 53. Deletions or insertions into the genome cause a polymorphism called a. short tandem repeats. b. variable number tandem repeats. c. long tandem repeats. d. single nucleotide polymorphism.

ANS: A DIF: Easy REF: 3.2 OBJ: 3.2.g. Define single nucleotide polymorphisms and short tandem repeats.

MSC: Remembering 54. Individual nucleotide changes to the genome cause a polymorphism called a. short tandem repeats. b. variable number tandem repeats. c. long tandem repeats.

d. single nucleotide polymorphism.

ANS: D DIF: Easy REF: 3.2 OBJ: 3.2.g. Define single nucleotide polymorphisms and short tandem repeats.

MSC: Remembering 55. Not all single nucleotide polymorphisms cause a phenotypic change because sometimes the changes occur in the a. coding region. b. noncoding region. c. promoter sequence. d. telomeres.

ANS: B DIF: Medium REF: 3.2 OBJ: 3.2.g. Define single nucleotide polymorphisms and short tandem repeats.

MSC: Applying 56. In plasmid transformation, DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

ANS: D DIF: Medium REF: 3.3 OBJ: 3.3.a. Explain how a plasmid can transfer genetic material from one cell to another.

MSC: Understanding 57. In viral transduction, DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

ANS: A DIF: Medium REF: 3.3 OBJ: 3.3.a. Explain how a plasmid can transfer genetic material from one cell to another.

MSC: Understanding 58. In plasmid conjugation, DNA is transferred when a. bacteriophages infect bacteria. b. foreign DNA fragments are inserted into the plasmid using multiple cloning sites. c. there is a horizontal gene transfer during the bacteria mating process. d. a dead bacterium releases DNA into the environment and it is obtained by another bacterium.

ANS: C DIF: Medium REF: 3.3 OBJ: 3.3.a. Explain how a plasmid can transfer genetic material from one cell to another.

MSC: Understanding 59. Foreign DNA fragments can be inserted into plasmids using a. promoters. b. cloning vectors. c. cloning sites. d. recombinant DNA.

ANS: C DIF: Difficult REF: 3.3 OBJ: 3.3.b. List the elements of a plasmid that make it useful for producing recombinant DNA. MSC: Understanding 60. When DNA molecules from multiple sources have been connected in the laboratory, the result is referred to as a. promoters. b. cloning vectors. c. cloning sites. d. recombinant DNA. ANS: D DIF: Easy REF: 3.3 OBJ: 3.3.b. List the elements of a plasmid that make it useful for producing recombinant DNA. MSC: Remembering 61. The -galactosidase gene that is inserted into plasmid cloning vectors is used to a. cleave the DNA in a sequence-specific fashion. b. disrupt the antibiotic-resistance gene, making it nonfunctional. c. determine if the cloning has been successful. d. protect the bacteria from bacteriophage infection.

ANS: C DIF: Medium REF: 3.3 OBJ: 3.3.b. List the elements of a plasmid that make it useful for producing recombinant DNA. MSC: Applying 62. Identify the products when Smal cleaves the following DNA sequence.

a. b. c. d.

ANS: A DIF: Difficult REF: 3.3 OBJ: 3.3.c. Explain the role played by restriction enzymes in the production of recombinant DNA. MSC: Applying 63. In the production of recombinant DNA, which enzyme links matching cohesive ends using covalent interactions? a. DNA methylase b. restriction endonucleases c. reverse transcriptase

d. DNA ligase ANS: D DIF: Medium REF: 3.3 OBJ: 3.3.c. Explain the role played by restriction enzymes in the production of recombinant DNA. MSC: Understanding 64. Which enzyme is used to cleave DNA at specific sequences during the production of recombinant DNA? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase ANS: B DIF: Easy REF: 3.3 OBJ: 3.3.c. Explain the role played by restriction enzymes in the production of recombinant DNA. MSC: Understanding 65. Below are the steps involved in cloning gene sequences using mRNA. Arrange the steps in the appropriate order.

1. The double-stranded cDNA is treated with a restriction endonuclease to generate compatible ends for annealing and ligation.

2. mRNA is isolated from the cell and converted back into double-stranded sequences using reverse transcriptase to generate complementary DNA. 3. The RNA-DNA hybrid is treated with a nuclease to cleave the RNA strand, producing RNA fragments.

4. Reverse transcriptase completes the single-stranded cDNA when it reaches the end of the mRNA transcript.

5. RNA fragments serve as primers for DNA synthesis of the second strand of cDNA using DNA polymerase. a. 4, 2, 1, 5, 3 b. 2, 4, 3, 5, 1 c. 2, 3, 5, 4, 1 d. 3, 2, 5, 4, 1 ANS: B DIF: Difficult REF: 3.3 OBJ: 3.3.d. Outline the mechanism for cloning using mRNA as a starting material.

MSC: Understanding 66. The most common purpose for cloning a gene sequence using mRNA is to a. disrupt antibiotic resistance. b. determine homologous genomic sequences. c. generate a library of actively transcribed genes. d. disrupt the lacZ gene, resulting in blue-white screening.

ANS: C DIF: Medium REF: 3.3 OBJ: 3.3.d. Outline the mechanism for cloning using mRNA as a starting material.

MSC: Applying 67. When a gene sequence is cloned using mRNA, the mRNA is isolated from the cell and converted into a double-stranded sequence using which enzyme? a. DNA methylase b. restriction endonucleases c. reverse transcriptase

d. DNA ligase ANS: C DIF: Easy REF: 3.3 OBJ: 3.3.d. Outline the mechanism for cloning using mRNA as a starting material.

MSC: Understanding 68. When a gene sequence is cloned using mRNA, which enzyme is used to seal the single-strand gaps left behind in the second strand of DNA? a. DNA methylase b. restriction endonucleases c. reverse transcriptase d. DNA ligase ANS: D DIF: Easy REF: 3.3 OBJ: 3.3.d. Outline the mechanism for cloning using mRNA as a starting material.

MSC: Understanding 69. When DNA is sequenced, which analytical technique is used to separate the chain-terminated DNA fragments? a. gel electrophoresis b. blue-white screening c. antibiotic resistance d. fluorescent labeling ANS: A DIF: Easy REF: 3.3 OBJ: 3.3.e. Summarize the process used to sequence DNA.

MSC: Analyzing

70. In the second temperature phase of PCR, why does the temperature vary from 55 C to 65 C? a. different ionic strengths b. different primer concentrations c. G-C content d. different amount of hydrogen bonds ANS: C DIF: Medium REF: 3.3 OBJ: 3.3.f. List the three temperature phases of the PCR cycle and explain what occurs during each.

MSC: Analyzing 71. Identify the phase of PCR amplification where the primer is annealed.

a. b. c. d.

A B C D

ANS: B DIF: Medium REF: 3.3 OBJ: 3.3.f. List the three temperature phases of the PCR cycle and explain what occurs during each.

MSC: Understanding 72. Identify the phase of PCR amplification where DNA synthesis occurs.

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 3.3 OBJ: 3.3.f. List the three temperature phases of the PCR cycle and explain what occurs during each.

MSC: Understanding 73. Identify the phase of PCR amplification where DNA is denatured and the strands are separated.

a. b. c. d.

A B C D

ANS: A DIF: Medium REF: 3.3 OBJ: 3.3.f. List the three temperature phases of the PCR cycle and explain what occurs during each.

MSC: Understanding 74. This method of analyzing RNA transcripts relies on a predetermined collection of complementary DNA sequences. a. plasmid cloning b. viral transduction c. RNA-seq d. gene-expression microarrays ANS: D DIF: Easy REF: 3.3 OBJ: 3.3.g. Compare and contrast gene expression microarrays with RNA sequencing.

MSC: Understanding 75. Which method of analyzing RNA transcripts is considered to be an unbiased approach because it does not use a predetermined collection of complementary DNA sequence? a. plasmid cloning b. viral transduction c. RNA-seq d. gene-expression microarrays ANS: C DIF: Easy REF: 3.3 OBJ: 3.3.g. Compare and contrast gene expression microarrays with RNA sequencing.

MSC: Understanding SHORT ANSWER 1. Compare the primary and secondary structures of DNA. ANS: The primary structure of DNA refers to the sequence of deoxyribonucleotides arranged in a single chain. The secondary structure of DNA refers to when the strands of DNA bind together through hydrogen bonding of the base pairs in an antiparallel fashion. The double helix of DNA is an example of secondary structure.

DIF: Easy REF: 3.1 OBJ: 3.1.a. Define the primary and secondary structures of DNA. MSC: Analyzing 2. Compare and contrast the arrangements of A-DNA, B-DNA, and Z-DNA. ANS: All three forms have identical covalent bonds between the nucleotides. All three have antiparallel strands and exhibit Watson-Crick base pairing.

A-DNA has the widest helix (23 A in diameter) with 11 base pairs per turn, whereas the Z form is the most narrow (18 A in diameter) with 12 base pairs per turn. B-DNA is 20 A in diameter with 10.5 base pairs per turn. Both A-DNA and B-DNA have right-handed helix structures, whereas Z-DNA has a left-handed helix resulting in a zigzag structure.

DIF: Difficult REF: 3.1 OBJ: 3.1.e. Differentiate among A-DNA, B-DNA, and Z-DNA. MSC: Analyzing 3. A sequence of B-DNA contains 78,000 base pairs. Analysis shows that 42% are C-G base pairs.

Answer the following questions and show your mathematical work. a. How many pyrimidine bases are in this sequence? b. How many nucleotides are cytosines? c. How many nucleotides are thymines? d. How many hydrogen bonds does this sequence contain? e. How many turns of the double helix occur in this sequence?

ANS: a. Each base pair contains a pyrimidine and a purine, so there are 78,000 pyrimidine bases. b. C-G base pairs make up 42% of the sequence. (0.42 78,000) = 32,760 C-G base pairs.

Because there is 1 C for every base pair, there are 32,760 C. c. C-G base pairs make up 42% of the sequence, so A-T makes up 58% of the sequence.

(0.58 78,000) = 45,240 A-T base pairs. Because there is 1 T for every base pair, there are 45,240 T. d. There are 3 hydrogen bonds per C-G pair and 2 hydrogen bonds per A-T pair, so (3 bonds 32,760) + (2 bonds 45,240) = 188,760. e. 78,000/10.5 = 7428.5 DIF: Difficult REF: 3.1 OBJ: 3.1.d. Restate Chargaff’s rule and explain typical base pairing in DNA structure. | 3.1.e.

Differentiate among A-DNA, B-DNA, and Z-DNA. MSC: Applying 4. Explain the difference between the coding strand and the template strand of DNA as it relates to RNA transcription.

ANS: When DNA is transcribed into RNA, the coding strand has the same base sequence as the RNA transcript. The template strand has a complementary sequence to the transcribed RNA. DIF: Easy REF: 3.1 OBJ: 3.1.c. Differentiate between the coding strand and the template strand.

MSC: Understanding 5. DNA regions rich in A-T are more easily denatured than regions with a higher G-C content. Why is this biologically significant?

ANS: Regions rich in A-T are often the initiation sites for DNA replication or transcription. For replication or transcription to occur, the DNA strands must unwind and separate. This occurs more easily in areas rich in A-T because of the decreased base stacking interactions.

DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on

Tm. MSC: Applying 6. Why does the Tm increase as the G-C content increases?

ANS: G-C base pairs have more favorable base stacking interactions than A-T base pairs. Therefore, it takes more heat energy to disrupt the base stacking interactions of the G-C base pairs.

DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Understanding 7. How does the ionic strength of DNA affect the Tm? Explain.

ANS: Increasing the ionic strength of the solution increases the Tm. The ions bind to the phosphate groups of the DNA backbone, stabilizing the helix. Because the helix is more stable with increasing ion concentration, it takes more heat energy to denature the helix and the Tm increases.

DIF: Medium REF: 3.1 OBJ: 3.1.g. Explain the impacts of strand length, ionic strength, and A-T versus G-C content on Tm. MSC: Understanding 8. Explain the difference between a negative supercoil and a positive supercoil.

ANS: A negative supercoil is when the direction of the twist is right handed. A positive supercoil is when the direction of the supercoil is left handed.

DIF: Easy REF: 3.1 OBJ: 3.1.h. Differentiate between positive and negative supercoiling.

MSC: Understanding 9. Compare and contrast the steps used to induce a positive supercoil and a negative supercoil.

ANS: Breaking the phosphodiester bond between two adjacent bases and cleaving the DNA is the first step in generating positive or negative supercoils. If turns are removed by unwinding the cut strand before resealing, negative supercoils are formed. If turns are added before resealing the cut strand, positive supercoils are formed.

DIF: Medium REF: 3.1 OBJ: 3.1.h. Differentiate between positive and negative supercoiling.

MSC: Analyzing 10. If DNA is not cleaved, the total linking number will remain the same, even though the twist and writhe can change. Using one or two complete sentences, explain why the total linking number does not change.

ANS:

Both the twist and the writhe can change by stretching or bending. However, the linking number remains constant because of the relationship Lk = Tw + Wr. If the twist changes, the writhe will change in such a fashion that the linking number remains constant. Because these manipulations do not change the number of helical turns, the linking number remains constant.

DIF: Medium REF: 3.1 OBJ: 3.1.i. Explain the relationship among linking number, twist, and writhe.

MSC: Analyzing 11. Histones participate in the process of supercoiling DNA. Using the figure below, outline the three steps in this process labeled A, B, and C.

ANS: A, The nucleosome is assembled. A relaxed circular piece of DNA is wrapped around a histone core, which results in both negative and positive supercoiling. B, An enzyme-catalyzed double strand break removes the positive supercoil. C, The histone core is removed by protein extraction.

DIF: Medium REF: 3.1 OBJ: 3.1.l. Identify the histone proteins and the structures they form.

MSC: Analyzing 12. What are the three ways that RNA and DNA differ?

ANS: 1. RNA has a hydroxyl group on the carbon on the ribose ring, whereas DNA lacks the hydroxyl group at this position. 2. RNA contains the base uracil and DNA contains the base thymine. 3. RNA can form the catalytic molecules (ribozymes), whereas DNA does not form catalytic molecules.

DIF: Medium REF: 3.1 OBJ: 3.1.k. List the key structural difference between DNA and RNA. MSC: Analyzing 13. Why does DNA contain thymine instead of uracil?

ANS: A common reaction in cells is for cytosine to spontaneously go through a deamination reaction to form uracil. Any cytosine deamination producing uracil that is not repaired before the next round of DNA replication will change a C-G base pair to a U-A base pair, which during the next round of DNA replication will become a T-A base pair. Therefore, by having only thymine present in DNA, the presence of uracil can be more easily detected, thereby maintaining the genetic information.

DIF: Difficult REF: 3.1 OBJ: 3.1.k. List the key structural difference between DNA and RNA. MSC: Applying 14. Outline the steps involved in DNA condensation.

ANS: Double-stranded DNA wraps around histones to form nucleosome particles. These particles pack together to form chromatin fiber. Beyond these two steps, the condensation process depends on the type of DNA and the phase of the cell.

DIF: Medium REF: 3.2 OBJ: 3.2.a. Identify the key elements involved in DNA condensation.

MSC: Analyzing 15. Compare and contrast the structure of euchromatin and heterochromatin. Explain how their structure relates to biological function.

ANS: Euchromatin is less condensed and more gene rich than heterochromatin. This is because gene-rich chromatin would need to be less condensed to allow access by DNA binding proteins that regulate transcription.

DIF: Medium REF: 3.2 OBJ: 3.2.b. Differentiate between euchromatin and heterochromatin.

MSC: Analyzing 16. Compare and contrast a monocistronic gene and a polycistronic gene.

ANS: Monocistronic genes contain a promoter and a single protein-coding sequence. Polycistronic genes also contain a promoter but have multiple coding regions. Therefore, monocistronic genes only encode for one protein, whereas polycistronic genes encode for multiple proteins in a single RNA transcript.

DIF: Medium REF: 3.2 OBJ: 3.2.d. Differentiate between monocistronic and polycistronic genes.

MSC: Analyzing 17. How does the organization of prokaryotic genes differ from the organization of eukaryotic genes?

ANS: Prokaryotic genes can either be monocistronic (code for a single protein) or polycistronic (code for multiple proteins). Eukaryotic genes contain exons (coding regions) separated by introns (noncoding sequences).

DIF: Medium REF: 3.2 OBJ: 3.2.d. Differentiate between monocistronic and polycistronic genes.

MSC: Analyzing 18. What is the benefit of comparing a human disease gene to similar genes in other organisms using a bioinformatics tool such as BLAST? ANS: The comparison can lead to insight into the function of the encoded protein based on evolutionary conservation. The biochemical characterization of the protein can lead to further understanding of the biochemistry, resulting in a potential drug or treatment for the disease.

DIF: Difficult REF: 3.2 OBJ: 3.2.f. Explain how BLAST can be used to compare genomic sequences.

MSC: Analyzing 19. Many different genetic variations can be found when comparing the gene sequence of two individuals. Explain three causes of the variations.

ANS: (1) Single nucleotide polymorphisms are when nucleotides change as a result of an unrepaired error during DNA replication. A short tandem repeat can also occur where a nucleotide is deleted (2) from the sequence or inserted (3) into the sequence.

DIF: Difficult REF: 3.2 OBJ: 3.2.g. Define single nucleotide polymorphisms and short tandem repeats.

MSC: Analyzing 20. Compare the three different ways that DNA can be transferred between organisms using plasmids.

ANS: DNA can be transferred between organisms by conjugation, transformation, or transduction.

Plasmid conjugation occurs during the bacterial mating process when the donor bacterium transfers a copy of the plasmid to a recipient bacterium. Plasmid transformation occurs when a bacterium dies and the plasmid is transferred to another bacterium via a process involving the cell wall. Viral transduction occurs when a virus known as a bacteriophage infects the bacterium.

DIF: Medium REF: 3.3 OBJ: 3.3.a. Explain how a plasmid can transfer genetic material from one cell to another.

MSC: Analyzing 21. Explain why it is advantageous to use plasmids to produce recombinant DNA. ANS:

Plasmids can replicate inside a cell independent of the cell’s chromosomes, using the host cell’s replication, transcription, and translation processes to produce the proteins. Many times this is a symbiotic relationship because the genes of the plasmid produce proteins that help the organism survive. Inserting foreign DNA into a plasmid using multiple cloning sites, resulting in cloning vectors, produces recombinant DNA. The plasmids can then produce proteins that perform specific functions, like disrupting the antibiotic resistance gene of bacteria, resulting in the loss of antibiotic resistance.

DIF: Difficult REF: 3.3 OBJ: 3.3.b. List the elements of a plasmid that make it useful for producing recombinant DNA. MSC: Understanding 22. Predict the cleavage products when DNA is exposed to restriction endonucleases using the figure below.

ANS:

DIF: Difficult REF: 3.3 OBJ: 3.3.c. Explain the role played by restriction enzymes in the production of recombinant DNA. MSC: Applying 23. Explain the two methods used to determine that plasmid cloning has been successful.

ANS: Foreign DNA can be inserted to disrupt the antibiotic resistance gene of bacteria, making it nonfunctional. Antibiotic susceptibility can be used to screen to determine if DNA insertion has been successful. Plasmid cloning vectors also contain the -galactosidase gene (lacZ), which produces the -galactosidase enzyme that cleaves a substrate into a blue product. If foreign DNA has been inserted into lacZ, the enzyme function is lost and the bacteria with successful DNA insertion are white.

DIF: Difficult REF: 3.3 OBJ: 3.3.b. List the elements of a plasmid that make it useful for producing recombinant DNA. MSC: Understanding 24. Outline the steps used in the chain-termination method to determine the sequence of a region of DNA. Using the figure below, explain what occurs at steps A, B, C, D, and E.

ANS: A, Fluorescently labeled ddNTPs and unlabeled dNTPs are mixed with the DNA to be sequenced, along with DNA primer and DNA polymerase. B, Random incorporation of ddNTP in the DNA product terminates synthesis and incorporates a different fluorescent label for each ddNTP. C, The synthesis products are separated by size using gel electrophoresis.

D, Laser excitation identifies the fluorescent color associated with each DNA product. E, The DNA sequence is determined by comparing the fluorescent color with the size of the fragment.

DIF: Difficult REF: 3.3 OBJ: 3.3.e. Summarize the process used to sequence DNA.

MSC: Analyzing

25. Describe and explain what occurs at the three temperature phases in PCR. ANS: In the first temperature phase, the DNA is heated to denature and separate the strands. In the second phase, the temperature is lowered to facilitate annealing of the primer to each strand (normally in the temperature range of 55 C–65 C). The annealing temperature depends on the Tm of the primer, which is based on length and G-C content. In the third phase the temperature is raised to 72 C to allow extension of the primer and DNA synthesis.

DIF: Medium REF: 3.3 OBJ: 3.3.f. List the three temperature phases of the PCR cycle and explain what occurs during each.

MSC: Understanding

Chapter 4: Protein Structure MULTIPLE CHOICE 1. Which statement about amino acids is true? a. Most common natural amino acids in proteins are L-amino acids. b. All naturally occurring amino acids in proteins are chiral. c. Most naturally occurring amino acids in proteins are D-amino acids. d. Naturally occurring amino acids in proteins occur as a mixture of enantiomers.

ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.a. Identify the differences between D- and L-amino acids.

MSC: Analyzing 2. Of the 20 common amino acids, how many have a chiral a. 0 b. 1 c. 19 d. 20

-carbon?

ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.a. Identify the differences between D- and L-amino acids.

MSC: Analyzing 3. The chirality of naturally occurring amino acids in proteins is a. R. b. L. c. D. d. the same as glyceraldehyde.

ANS: B DIF: Easy REF: 4.1 OBJ: 4.1.a. Identify the differences between D- and L-amino acids.

MSC: Remembering 4. At what point does the isoelectric point or pI occur? a. when all of the acidic protons are neutralized with base b. at pH = 7.0 c. at the pH when all negative charges on a zwitterion counter the positive charges d. when the molecule has a single electric charge ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.b. Define the isoelectric point (pI).

MSC: Understanding

5. For the alanine titration curve shown below, which best describes point A?

a. b. c. d.

a buffer region isoelectric point second equivalence point pH = pKa

ANS: B DIF: Medium REF: 4.1 OBJ: 4.1.b. Define the isoelectric point (pI).

MSC: Understanding

6. If the titration curve shown below is for the amino acid glycine, at which point in the curve is the pI?

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 4.1 OBJ: 4.1.b. Define the isoelectric point (pI).

MSC: Evaluating

7. If the isoelectric point (pI) for an amino acid is at point A, what is the charge on the amino acid at point B?

a. b. c. d.

0 −2 +2 −1

ANS: B DIF: Difficult REF: 4.1 OBJ: 4.1.b. Define the isoelectric point (pI).

MSC: Applying

8. A polypeptide has a high pI value. Which amino acids might comprise it?

a. b. c. d.

arginine and lysine residues aspartate and glutamate residues the large nonpolar amino acids a mixture of aspartate and arginine residues

ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.c. Calculate the approximate pI of an amino acid given the pKa values for all ionizable groups.

MSC: Applying 9. Using the pKas shown, what is the isoelectric point of the amino acid tyrosine?

a. b. c. d.

<1.0 5.5 7.0 9.75

ANS: B DIF: Medium REF: 4.1 OBJ: 4.1.c. Calculate the approximate pI of an amino acid given the pKa values for all ionizable groups.

MSC: Analyzing 10. What is the pI of the dipeptide shown? (Use the pK as given.)

a. b. c. d.

0 5 9 10.5

ANS: B DIF: Difficult REF: 4.1 OBJ: 4.1.c. Calculate the approximate pI of an amino acid given the pKa values for all ionizable groups.

MSC: Analyzing 11. Which amino acid contains a hydroxyl group? a. valine b. cysteine c. threonine d. aspartate ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be

categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Remembering 12. The amino acid with the neutral side chain at neutral pH is a. asparagine. b. aspartate. c. arginine. d. glutamate.

ANS: A DIF: Medium REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Applying 13. The amino acid with the most hydrophobic side chain is a. asparagine. b. aspartate. c. valine. d. threonine.

ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Remembering 14. Which amino acid side chain from the list below is the most polar? a. Gln b. Ala c. Leu d. Phe ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Remembering 15. Which amino acid has the highest pKa? a. glutamate b. asparagine c. cysteine d. lysine ANS: D DIF: Medium REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Analyzing 16. What are the three-letter and one-letter abbreviations for the amino acid tyrosine? a. Tyo, T b. Tyr, R c. Tro, Y d. Tyr, Y ANS: D DIF: Easy REF: 4.1 OBJ: 4.1.e. State the 3-letter and 1-letter abbreviations for the 20 common amino acids.

MSC: Remembering 17. What is the peptide sequence Asp-Gln-Gly-Ser, using one-letter abbreviations for the amino acids? a. AGYS b. DNGC c. DQGS d. EGYS ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.e. State the 3-letter and 1-letter abbreviations for the 20 common amino acids.

MSC: Remembering 18. What is the approximate net charge of the molecule shown below at pH 7?

a. b. c. d.

+1 0 −1 −2

ANS: C DIF: Medium REF: 4.1 OBJ: 4.1.f. Describe the protonation states of all amino acids with ionizable groups.

MSC: Understanding 19. Consider the whole amino acid alanine at pH =7. How many atoms (including Hs) are found in the molecule? a. 15 b. 13 c. 10 d. 8 ANS: B DIF: Medium REF: 4.1 OBJ: 4.1.f. Describe the protonation states of all amino acids with ionizable groups.

MSC: Understanding 20. Which of the following are negatively charged amino acids at pH = 7? a. Glu, Asp b. Gln, Asn c. Thr, Tyr d. Cys, Asn ANS: A DIF: Medium REF: 4.1 OBJ: 4.1.f. Describe the protonation states of all amino acids with ionizable groups.

MSC: Applying 21. Which linear sequence of bonded atoms can be found in the backbone of polypeptides? a. C-N-N-C b. C-C-N-C c. N-C-C-C

d. C-O-C-N ANS: B DIF: Easy REF: 4.1 OBJ: 4.1.g. Describe the reaction that forms a peptide bond.

MSC: Remembering

22. Which represents the correct arrangement of bonding in a peptide bond? a.

b.

c.

d.

ANS: C DIF: Easy REF: 4.1 OBJ: 4.1.g. Describe the reaction that forms a peptide bond.

MSC: Remembering

23. Trace directly the covalently bonded backbone atoms from the N to C terminus of a dipeptide.

Which atoms are found in this trace? a. NCCNCC b. NCCONCCO c. NCONCO d. CNCCNC ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.g. Describe the reaction that forms a peptide bond.

MSC: Remembering

24. To what organic reaction class does peptide bond formation belong? a. condensation b. isomerization c. oxidation d. addition ANS: A DIF: Medium REF: 4.1 OBJ: 4.1.g. Describe the reaction that forms a peptide bond.

25. The peptide bond a. is most stable in the cis configuration.

MSC: Understanding

b. has a mix of single and double bond characters. c. can rotate around the carbonyl and N bond but not around the d. can function as a weak acid and weak base.

-carbon and N bond.

ANS: B DIF: Easy REF: 4.1 OBJ: 4.1.h. Identify the properties imparted by the partial double bond character of a peptide bond.

MSC: Understanding 26. The peptide bond is stronger than the ester bond. What structural feature of the peptide bond gives it additional bond strength? a. Resonance structures give the peptide bond some double bond character. b. The peptide bond is between carbon and nitrogen instead of carbon and oxygen atoms. c. The peptide bond is more polar. d. Peptide bonds can hydrogen bond.

ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.h. Identify the properties imparted by the partial double bond character of a peptide bond.

MSC: Understanding 27. The dipole moment associated with a peptide bond proceeds from which amide? a. the C to the O atom b. the C to the N atom c. the O to the H atom d. the H to the O atom ANS: D DIF: Medium REF: 4.1 OBJ: 4.1.h. Identify the properties imparted by the partial double bond character of a peptide bond.

MSC: Analyzing 28. What do Ramachandran plots show? a. Only some and angles are commonly found in proteins. b. The chiral carbon in amino acids is found largely in the S configuration. c. Peptide backbones form mostly linear chains. d. The -carbon is chiral.

ANS: A DIF: Medium REF: 4.1 OBJ: 4.1.i. Identify phi and psi angles and explain the information in a Ramachandran plot.

MSC: Understanding 29. The and angles are the a. flatness of the peptide bond. b. torsion angles on either side of the -carbon. c. angles of each amino acid side chain. d. peptide bond plane angle.

ANS: B DIF: Easy REF: 4.1 OBJ: 4.1.i. Identify phi and psi angles and explain the information in a Ramachandran plot.

MSC: Understanding 30. The points in the Ramachandran plot are derived by

a. b. c. d.

counting the number of amino acids and placing points in allowed regions. measuring the and angles in an experimentally determined protein crystal structure. placing each amino acid in regions commonly occupied by that amino acid. experimentally measuring the optical rotation of polarized light.

ANS: B DIF: Difficult REF: 4.1 OBJ: 4.1.i. Identify phi and psi angles and explain the information in a Ramachandran plot.

MSC: Evaluating 31. How many possible unique triplet codons could there be in a genome? a. 3 b. 20 c. 36 d. 64 ANS: D DIF: Easy REF: 4.1 OBJ: 4.1.j. State the relationship between gene sequence and amino acid sequence.

MSC: Understanding 32. Use the table below to determine how many possible RNA sequences could code for the dipeptide Pro-Ala.

a. b. c. d.

1 16 8 64

ANS: B DIF: Easy REF: 4.1 OBJ: 4.1.j. State the relationship between gene sequence and amino acid sequence.

MSC: Applying 33. A __________ mutation in a gene results in the least amount of damage to the resulting protein. a. missense b. nonsense c. frameshift d. silent ANS: D DIF: Easy REF: 4.1 OBJ: 4.1.k. Define the terms reading frame, missense mutation, nonsense mutation, frameshift mutation, and silent mutation.

MSC: Evaluating 34. Using the table below, determine the kind of gene mutation illustrated.

ATG_AAT_CAC ATG_AAG_CAC

a. b. c. d.

missense mutation nonsense mutation frameshift mutation silent mutation

ANS: A DIF: Easy REF: 4.1 OBJ: 4.1.k. Define the terms reading frame, missense mutation, nonsense mutation, frameshift mutation, and silent mutation.

MSC: Analyzing 35. How many possible protein primary structures are there for a tripeptide given the 20 amino acids? a. 320 b. 400 c. 203 d. 1.27 10130 ANS: C DIF: Easy REF: 4.2 OBJ: 4.2.a. Describe protein structures at the primary, secondary, tertiary, and quaternary levels.

MSC: Understanding 36. Which interaction largely stabilizes protein secondary (2 ) structures? a. disulfide bonds b. hydrogen bonding c. hydrophobic packing d. metal ions ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.a. Describe protein structures at the primary, secondary, tertiary, and quaternary levels.

MSC: Understanding 37. All of the following are stabilizing forces in maintaining a stable protein tertiary (3 ) structure, EXCEPT a. H bonds. b. temperature. c. hydrophobic interactions. d. electrostatic attractions.

ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.a. Describe protein structures at the primary, secondary, tertiary, and quaternary levels.

MSC: Remembering 38. All of the following are types of protein secondary structure EXCEPT a. -sheets. b.

-helixes. c. -helixes. d. -turns.

ANS: C DIF: Easy REF: 4.2 OBJ: 4.2.b. Define and describe the three major types of secondary structure.

MSC: Remembering 39. Protein secondary structures such as a. ionic interactions. b. disulfide bond formation. c. van der Waals forces. d. hydrogen bond formation.

-helices and -sheets are stabilized mainly by

ANS: D DIF: Easy REF: 4.2 OBJ: 4.2.b. Define and describe the three major types of secondary structure.

MSC: Understanding 40. Which statement regarding protein secondary structures is correct? a. -strands allow -helices to interact with one another. b. Protein -helices alternate with -strands in stabilizing protein structure. c. Protein -helices are left handed, whereas -sheets are right handed in arrangement. d. Protein -helices and -strands differ in that -helices are stabilized by intrahelical hydrogen bonds, whereas -strands are stabilized by hydrogen bonds across adjacent strands.

ANS: D DIF: Medium REF: 4.2 OBJ: 4.2.b. Define and describe the three major types of secondary structure.

MSC: Understanding

41. Which of the following statements about -helices and -sheets are FALSE? a. They are both incompatible with the amino acid proline. b. They both interact with other protein elements through amino acid side chains that stick out. c. They both contain a recurring pattern of hydrogen bonds from one peptide bond to another peptide bond. d. They both give rise to similar tertiary structures.

ANS: D DIF: Medium REF: 4.2 OBJ: 4.2.b. Define and describe the three major types of secondary structure.

MSC: Analyzing 42. An -helix has the sequence: NH3+-Ser-Glu-Gly-Asp-Trp-Gln-Leu-His-Val-Phe-Ala-Lys-Val-Glu-COO-. The carbonyl oxygen (in the peptide bond) of the histidine residue is hydrogen bonded to the amide nitrogen of a. Asp. b. Lys. c. Trp. d. Ala. ANS: B DIF: Difficult REF: 4.2 OBJ: 4.2.c. Identify the characteristics of an amphipathic alpha-helix.

MSC: Evaluating 43. Which of the following statements is true about -helices? a. The center of the helix is an open channel. b. There are about seven amino acids per helical turn. c. The amide backbone dipoles line up in one direction. d. The helical backbone structure is stabilized by ionic interactions.

ANS: C DIF: Medium REF: 4.2 OBJ: 4.2.c. Identify the characteristics of an amphipathic alpha-helix.

MSC: Understanding 44. Which statement about the -helix is true? a. The hydrophobic interior of -helices is stabilized by the side chains of hydrophobic amino acids. b. The amino acid side chains point out to the sides with every third amino acid roughly lining up on one side of the helix. c.

-Helices have backbone amide groups that are hydrogen bonded to amino acid side chains. d.

-Helices have 5 amino acids per one turn of the helix.

ANS: B DIF: Medium REF: 4.2 OBJ: 4.2.c. Identify the characteristics of an amphipathic alpha-helix.

MSC: Remembering 45. What is the minimum number of amino acids needed to make one turn of an a. 3 b. 4 c. 6 d. 7 ANS: B

DIF: Medium

REF: 4.2

-helix?

OBJ: 4.2.c. Identify the characteristics of an amphipathic alpha-helix.

MSC: Understanding 46. In a standard -helix, __________ H bonds and __________ dipole moments are found per amino acid, which stabilizes the -helical structure. a. 1; 1 b. 1; 2 c. 2; 1 d. 2; 2 ANS: C DIF: Difficult REF: 4.2 OBJ: 4.2.c. Identify the characteristics of an amphipathic alpha-helix.

MSC: Evaluating 47. Which of the following statements about -sheet structures is true? a. The individual strands of all -sheet structures are connected by turns, helices, or loops. b. All amino acid side chains in antiparallel and parallel -sheet structures point to one side of the sheet. c. Parallel -sheet structures have backbone amides that directly hydrogen bond between strands, whereas antiparallel -sheets have hydrogen bonds that are offset. d. All -sheet structures form a spiraling backbone chain.

ANS: A DIF: Medium REF: 4.2 OBJ: 4.2.d. Describe beta-strand structures, beta-turns, and loops.

MSC: Understanding 48. What is a difference between parallel and antiparallel -sheet secondary structures? a. Antiparallel -sheets have a larger number of stabilizing H bonds between backbone amides than parallel -sheets. b. Parallel -sheets require a larger loop connecting together the individual peptide strands in the sheet. c. Parallel -sheets are longer than antiparallel sheets. d. Parallel -sheets have amino acid side chains alternating up and down, whereas antiparallel side chains alternate down and up.

ANS: B DIF: Difficult REF: 4.2 OBJ: 4.2.d. Describe beta-strand structures, beta-turns, and loops.

MSC: Understanding 49. How many -turns or -loops are required to construct a -sheet composed of four antiparallel strands? a. 0 b. 3 c. 4 d. 5 ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.d. Describe beta-strand structures, beta-turns, and loops.

MSC: Understanding 50. Which of the following statements about Ramachandran plots is true? a. They are good predictors of protein tertiary structure. b. They are needed to determine the secondary structure of a protein. c. They show equal distributions of and angles for -helical and -sheet containing

proteins. d. They show that -sheets and

-helices occupy different

and

angles.

ANS: D DIF: Medium REF: 4.2 OBJ: 4.2.e. Describe the common secondary structures with respect to a Ramachandran plot.

MSC: Understanding 51. Which class of protein structures does the protein shown below fit into?

a. b. c. d.

predominantly -helical predominantly -sheet intermixed -helix and -sheet domains of -helix adjacent to domains of -sheet

ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.f. Identify the four general classes of protein structure in the Protein Data Bank.

MSC: Applying 52. Which of the following statements regarding protein domains is true? a. Each protein has one unique domain. b. Multiple domains require multiple subunits and a quaternary structure. c. A domain can be composed of smaller structural units called motifs. d. A domain is a region absent of -helices and -sheets.

ANS: C DIF: Medium REF: 4.2 OBJ: 4.2.g. Differentiate between domains and motifs.

53. The common protein fold shown below is the __________ fold.

MSC: Understanding

a. Greek key b. Rossman c. FERM domain d.  barrel ANS: D DIF: Easy REF: 4.2 OBJ: 4.2.h. Differentiate among the common protein folds.

MSC: Remembering

54. The protein fold known as the Rossman fold is found in proteins that commonly bind a.

-helices. b. nucleotides. c. cytochromes. d. membranes.

ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.h. Differentiate among the common protein folds.

MSC: Remembering

55. How many different protein folds are recognized in the formal system of organization, referred to as SCOP: Structure Organization of Proteins? a. 4 b. >10 c. >100 d. >1000 ANS: D DIF: Easy REF: 4.2 OBJ: 4.2.h. Differentiate among the common protein folds.

MSC: Remembering

56. Protein tertiary structures a. require the formation of disulfide bonds in order to achieve their native state. b. are always irreversibly destroyed by the addition of denaturants, such as urea and salts, even when the denaturants are subsequently removed. c. are often disrupted by the either very low pH or very high pH values as a result of alterations in the ionization states of acidic or basic amino acids. d. are generally poorly defined and cannot be determined experimentally.

ANS: C DIF: Medium REF: 4.2 OBJ: 4.2.i. Identify the importance of cysteine in tertiary structure stabilization.

MSC: Understanding 57. Which stabilizing force in protein tertiary structures is a covalent bonding force? a. ionic bonding b. disulfide bonding c. hydrophobic interactions d. van der Waals bonding ANS: B DIF: Easy REF: 4.2 OBJ: 4.2.i. Identify the importance of cysteine in tertiary structure stabilization.

MSC: Understanding 58. The proteins collagen, silk fibroin, and hair keratin have all of the following in common, EXCEPT that they a. are fibrous proteins. b. are composed of repeating amino acid sequences. c. are composed of -helical structures. d. play important structural roles in biology.

ANS: C DIF: Easy REF: 4.2 OBJ: 4.2.j. Explain the importance of the repetitive amino acid sequence in fibrous proteins.

MSC: Understanding 59. Which one of the following statements comparing alpha keratin and silk fibroin is true? a. Both have covalently cross-linked strands. b. Both are primarily -helical in character. c. Both fibers are intracellularly located. d. Both fibers are heavily stabilized by hydrogen bonds.

ANS: D DIF: Medium REF: 4.2 OBJ: 4.2.j. Explain the importance of the repetitive amino acid sequence in fibrous proteins.

MSC: Understanding 60. What is the dominant secondary structure found in hair keratin? a.

-helices b. disulfide bonds c. -sheets d. loop structures ANS: A DIF: Easy REF: 4.2 OBJ: 4.2.j. Explain the importance of the repetitive amino acid sequence in fibrous proteins.

MSC: Remembering 61. At the interface between subunits of a protein with quaternary structure, which of the following interactions between amino acid side chains would contribute to the stability of the dimer? a. glutamate–aspartate. b. leucine–aspartate. c. glutamate–lysine. d. phenylalaninelysine.

ANS: C DIF: Medium REF: 4.2 OBJ: 4.2.k. Identify the key elements that stabilize quaternary structure in immunoglobulins.

MSC: Analyzing 62. In multi-subunit proteins, such as hemoglobin, the different subunits are usually bound to one another by all of the following EXCEPT a. hydrogen bonds. b. electrostatic interactions. c. hydrophobic interactions. d. peptide bonds.

ANS: D DIF: Easy REF: 4.2 OBJ: 4.2.k. Identify the key elements that stabilize quaternary structure in immunoglobulins.

MSC: Understanding 63. Which gives rise to a favorable enthalpic ( S) driving force for protein folding? a. The lining up of hydrogen bonds as the protein folds. b. The limiting of possible conformations as the protein folds. c. The decrease in ordered water molecules as hydrophobic amino acids pack together. d. The stabilization caused by favorable electrostatic interactions of amino acid side chains.

ANS: C DIF: Medium REF: 4.3 OBJ: 4.3.a. Summarize the three general principles of protein folding.

MSC: Understanding

64. Christian Anfinsen showed in a famous experiment that it is possible to unfold a protein and refold it to obtain a functional protein. Which two reagents were used in this experiment to unfold the protein? a. detergent and salt b. urea and -mercaptoethanol c. acid and base d. ethanol and -mercaptoethanol ANS: B DIF: Easy REF: 4.3 OBJ: 4.3.b. Outline the procedure used by Christian Anfinsen to study the folding of RNaseA. MSC: Remembering 65. In the Anfinsen experiment with the unfolding of RNaseA, what order could the chemical reagents be removed in order to achieve an inactive protein? a. Remove denaturant first and reductant second. b. Simultaneously remove denaturant and reductant. c. Remove reductant first, denaturant second, and then finally add back reductant. d. Remove reductant first and denaturant second.

ANS: D DIF: Medium REF: 4.3 OBJ: 4.3.b. Outline the procedure used by Christian Anfinsen to study the folding of RNaseA. MSC: Understanding 66. Of the three proposed models of globular protein folding, which one describes formation of an initial disordered protein interior, followed next by ordering of secondary and tertiary structures? a. mutant globule b. hydrophobic collapse model c. framework model d. nucleation model ANS: B DIF: Easy REF: 4.3 OBJ: 4.3.c. Differentiate among the three proposed models for globular protein folding.

MSC: Remembering 67. Of the three proposed models of globular protein folding, which one describes the initial formation of all secondary structures, followed by the arrangement of those secondary structures into a final tertiary structure? a. mutant globule b. hydrophobic collapse model c. framework model d. nucleation model ANS: C DIF: Easy REF: 4.3 OBJ: 4.3.c. Differentiate among the three proposed models for globular protein folding.

MSC: Remembering 68. What is the difference between clamp-type and chamber-type chaperone proteins? a. One uses ATP and the other does not. b. One folds proteins, whereas the other just protects them from unfolding. c. They are shaped differently. d. One type is found extracellularly and one intracellularly.

ANS: C DIF: Medium REF: 4.3 OBJ: 4.3.d. Differentiate between clamp-type and chamber-type chaperones.

MSC: Understanding 69. Which of the following statements about the clamp-type chaperone protein Hsp70 is correct? a. Hsp70 uses ATP binding and hydrolysis energy to assist in the folding of a protein. b. Hsp70 is a multi-subunit protein shaped like a large barrel, inside of which the folding protein is protected. c. Hsp70 is most active during cell division phases. d. Hsp70 assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds.

ANS: A DIF: Medium REF: 4.3 OBJ: 4.3.d. Differentiate between clamp-type and chamber-type chaperones.

MSC: Understanding 70. Which of the following statements about the chamber-type chaperone protein GroEL-GroES is correct? a. GroEL-GroES requires the hydrolysis of multiple ATPs to assist in the folding of a protein. b. GroEL-GroES recycles misfolded proteins by recovering individual amino acids. c. GroEL-GroES assists in protein unfolding by hydrolyzing and remaking the protein peptide bonds. d. GroEL-GroES uses GroEL as a cap, trapping an unfolded protein in the GroES chamber.

ANS: A DIF: Medium REF: 4.3 OBJ: 4.3.d. Differentiate between clamp-type and chamber-type chaperones.

MSC: Understanding 71. Cells deal with misfolded proteins by a. storing them for later energy use. b. collecting and excreting them from the cell. c. aggregating them to maintain the cell’s structural integrity. d. degrading them to individual amino acids.

ANS: D DIF: Easy REF: 4.3 OBJ: 4.3.e. Compare the major fates of misfolded proteins.

MSC: Remembering

72. It is important for cells to degrade misfolded proteins. If misfolded proteins are not degraded, the misfolded proteins may a. waste excessive ATP in attempts to refold them. b. aggregate and interfere with normal cellular function. c. eventually refold, but not until excessive and sometimes fatal levels of cellular energy are spent. d. be excreted from the cell rather than recycled for building blocks.

ANS: B DIF: Medium REF: 4.3 OBJ: 4.3.e. Compare the major fates of misfolded proteins.

MSC: Remembering

73. Cystic fibrosis results from the misfolding of proteins that never get the chance to properly insert into the membranes of lung epithelial cells and perform their function. This is generally referred to as a __________ disease. a. loss-of-function protein folding b. chaperonin-unassisted folding c. gain-of-function protein folding d. amyloid plaque–forming ANS: A

DIF: Easy

REF: 4.3

OBJ: 4.3.f. Compare loss of function with gain of function.

MSC: Remembering

74. What is believed to be the underlying cause of prion protein plaque formation? a. The PrPSc proteins are misfolded and aggregated from PrPc proteins. b. The unstructured N-terminal region of PrPc is thought to remain unfolded. c. The normal PrPc proteins are aggregated. d. The PrPSc protein adheres to and inhibits cell membranes.

ANS: A DIF: Medium REF: 4.3 OBJ: 4.3.g. Explain how PrPc is converted to PrPSc.

MSC: Understanding

75. What is a current hypothesis that explains the infectious nature of prion diseases? a. The virus responsible for prion diseases is transmissible. b. Unfavorable environmental factors negatively influence healthy cells. c. The small molecule denaturants found in infected cells are passed on to healthy cells. d. The presence of an improperly folded prion protein promotes the misfolding of normal prion proteins.

ANS: D DIF: Medium REF: 4.3 OBJ: 4.3.g. Explain how PrPc is converted to PrPSc.

MSC: Understanding

SHORT ANSWER 1. Shown is the titration curve for the amino acid aspartic acid. Draw the predominant protonation state of aspartic acid found at point A in the curve.

ANS:

DIF: Medium MSC: Applying

REF: 4.1

OBJ: 4.1.b. Define the isoelectric point (pI).

2. Calculate the pI for the following dipeptide using the pKas shown.

ANS: The pI is halfway between pKa 10.5 and 12.5; pI = 11.5.

DIF: Difficult REF: 4.1 OBJ: 4.1.c. Calculate the approximate pI of an amino acid given the pKa values for all ionizable groups.

MSC: Analyzing 3. The following amino acid is discovered in a newly isolated protein. What would it be called, and does it represent a new amino acid?

ANS: The amino acid looks like a modified serine amino acid commonly called phosphoserine. It is unlikely to be a new amino acid but is rather more likely a serine with a phosphate group added to its side chain.

DIF: Medium REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Evaluating 4. Draw the structure of the amino acid glutamate showing the predominant form found at pH 7.0 (assume NH3+ pKa 9.0; Glu pKR 4.0; COOH pKa 2.0).

ANS:

DIF: Medium REF: 4.1 OBJ: 4.1.d. Identify the structures of the 20 common amino acids and how they can be categorized into charged, hydrophilic, hydrophobic, and aromatic subfamilies.

MSC: Applying 5. The essential amino acids in adult humans are those that are required in our diet because of a lack of the biosynthetic pathway in our cells. The single-letter abbreviations for these amino acids are WVMILKFHT. Name these amino acids.

ANS: Tryptophan, valine, methionine, isoleucine, leucine, lysine, phenylalanine, histidine, and threonine DIF: Easy REF: 4.1 OBJ: 4.1.e. State the 3-letter and 1-letter abbreviations for the 20 common amino acids.

MSC: Remembering 6. Draw the structure of the amino acid cysteine showing the predominant form found at pH = 12.0 (assume NH3+ pKa 9.0; Cys pKR 8.0; COOH pKa 2.0).

ANS:

DIF: Medium REF: 4.1 OBJ: 4.1.f. Describe the protonation states of all amino acids with ionizable groups.

MSC: Applying 7. Draw the resonance structures that stabilize the peptide bonds found in proteins.

ANS:

DIF: Medium REF: 4.1 OBJ: 4.1.h. Identify the properties imparted by the partial double bond character of a peptide bond.

MSC: Understanding 8. Use the table below and write out the amino acid sequence coded by the following RNA sequence: AUG_CAC_AGG_UGA.

ANS: Met-His-Arg DIF: Easy REF: 4.1 OBJ: 4.1.j. State the relationship between gene sequence and amino acid sequence.

MSC: Applying 9. Use the table below and the following RNA sequence to determine which reading frame would give rise to the shortest peptide, or which reading frame gives rise to the first stop codon.

Frame: 1 2 3 RNA: GCG CCC CCU AAC AGG UAG CUG CGG UUC CUG

ANS: Frame 3: Beginning with reading frame 3 gives rise to the UAA stop codon after two triplet codons.

DIF: Medium REF: 4.1 OBJ: 4.1.k. Define the terms reading frame, missense mutation, nonsense mutation, frameshift mutation, and silent mutation.

MSC: Analyzing 10. List the levels of protein structure and give a brief description of each.

ANS: 1. Primary—amino acid sequence from the N to C terminus.

2. Secondary—commonly occurring folds found in proteins, such as -helix or -sheet.

3. Tertiary—the overall three-dimensional structure of the protein chain.

4. Quaternary—the arrangement of subunits in a multi-subunit protein.

DIF: Medium REF: 4.2 OBJ: 4.2.a. Describe protein structures at the primary, secondary, tertiary, and quaternary levels.

MSC: Understanding 11. Use the two-stranded antiparallel -sheet below and drawn in a -turn.

ANS:

DIF: Difficult REF: 4.2 OBJ: 4.2.d. Describe beta-strand structures, beta-turns, and loops.

MSC: Applying 12. Use the theoretical Ramachandran plot at the top to evaluate the two experimental plots on the bottom. Describe the likely secondary structures found in each experimental plot.

ANS: The middle Ramachandran plot is consistent with a protein that is largely -helical, with either some -sheet or, more likely, loops connecting the -helices. The bottom plot is consistent with a protein that is largely -sheet in structure, with some possible helical segments.

DIF: Easy REF: 4.2 OBJ: 4.2.e. Describe the common secondary structures with respect to a Ramachandran plot.

MSC: Evaluating

13. Why is the amino acid proline not commonly found in structure might proline be commonly found?

-helices or -sheets? In what secondary

ANS: Because of its cyclic nature, proline has more restricted and angles. Also, because of its lack of an NH group on its backbone amine, proline cannot hydrogen bond to stabilize the helices or sheets. Proline can often be found in turns or loops connecting helices or strands.

DIF: Medium REF: 4.2 OBJ: 4.2.e. Describe the common secondary structures with respect to a Ramachandran plot.

MSC: Evaluating 14. After analyzing all the structures of proteins found in the Protein Data Bank, scientists have found that four general classes of protein structures exist, based on their secondary structure themes.

Name the four classes of general protein structures.

ANS: Predominantly -helical, predominantly -sheet, intermixed -helix adjacent to domains of -sheet

-helix and -sheet, and domains of

DIF: Medium REF: 4.2 OBJ: 4.2.f. Identify the four general classes of protein structure in the Protein Data Bank.

MSC: Remembering 15. Identify the four images below, which represent the four classes of protein structures commonly identified across MOST structures found in the Protein Data Bank.

ANS: (a) Predominantly -helical, (b) predominantly -sheet, (c) intermixed (d) domains of -helix adjacent to domains of -sheet

-helix and -sheet, and

DIF: Medium REF: 4.2 OBJ: 4.2.f. Identify the four general classes of protein structure in the Protein Data Bank.

MSC: Understanding 16. Arrange the following in order of increasing complexity: secondary structure, tertiary structure, motif, and domain.

ANS: Secondary Structure DIF: Medium motifs.

MSC: Analyzing

Motif REF: 4.2

Domain

Tertiary Structure OBJ: 4.2.g. Differentiate between domains and

17. Draw the reaction by which a protein disulfide bond forms.

ANS:

DIF: Medium REF: 4.2 OBJ: 4.2.i. Identify the importance of cysteine in tertiary structure stabilization.

MSC: Applying 18. Collagen is an important structural protein in biological systems. It is formed by a repeating unit containing glycine, proline, and 4-hydroxyproline (4HyP). The synthesis of 4HyP from proline requires vitamin C. Draw the structure of 4HyP. ANS:

DIF: Easy REF: 4.2 OBJ: 4.2.j. Explain the importance of the repetitive amino acid sequence in fibrous proteins.

MSC: Remembering 19. In the multi-subunit protein family called immunoglobulins, the different subunits are held together by both covalent and noncovalent forces. What are the covalent forces that hold subunits together in immunoglobulins?

ANS: Cysteine disulfide bonds covalently bond together the heavy and light subunits.

DIF: Easy REF: 4.2 OBJ: 4.2.k. Identify the key elements that stabilize quaternary structure in immunoglobulins.

MSC: Remembering

20. List reagents and conditions that denature proteins.

ANS: Reagents: chaotropic agents such as urea, acids and bases, organic solvents such as ethanol, soaps or detergents, salts, reducing agents such as -mercaptoethanol.

Conditions: temperature, mechanical stress, pressure, pH. DIF: Medium REF: 4.3 OBJ: 4.3.a. Summarize the three general principles of protein folding.

MSC: Understanding 21. What specific reagents or conditions might be found on the X-axis label of the following figure?

ANS: Reagents: chaotropic agents such as urea, acids and bases (pH), organic solvents such as ethanol, soaps or detergents, salts, reducing agents such as -mercaptoethanol.

Conditions: temperature, mechanical stress, pressure, pH DIF: Medium REF: 4.3 OBJ: 4.3.a. Summarize the three general principles of protein folding.

MSC: Evaluating 22. In the famous experiment where Christian Anfinsen unfolded and refolded the protein RNaseA, in what order was the denaturant and reductant removed to give an inactive protein? Why was the protein inactive?

ANS: If the -mercaptoethanol was removed first, before the urea, the protein tended to form incorrect inter- and intramolecular disulfide bonds while in the unfolded state. The incorrect disulfide bonds stabilized largely misfolded and therefore inactive proteins.

DIF: Medium REF: 4.3 OBJ: 4.3.b. Outline the procedure used by Christian Anfinsen to study the folding of RNaseA. MSC: Understanding 23. Describe the proposed model of globular protein folding called the nucleation model.

ANS:

In the nucleation model of globular protein folding, a small localized region of the unfolded protein folds first with the correct tertiary structure. This region then serves as a center of growth around which the remaining secondary and tertiary structures fold.

DIF: Medium REF: 4.3 OBJ: 4.3.c. Differentiate among the three proposed models for globular protein folding.

MSC: Remembering 24. Describe generally how a gain-of-function protein folding disease can lead to cell death.

ANS: A gain-of-function folding disease generally results from the aggregation of misfolded proteins.

The protein aggregates interfere with normal cellular function. The misfolded proteins can result from mutations in a gene, such as in Huntington’s disease, or from the mistreatment of normal proteins, such as in Alzheimer’s disease.

DIF: Medium REF: 4.3 OBJ: 4.3.f. Compare loss of function with gain of function.

MSC: Understanding

25. Would a nonsense mutation in a gene encoding a protein be expected to result in a gain-of-function or a loss-of-function protein folding disease?

ANS: It might result in either disease or neither disease. It might be that a loss-of-function disease would be expected because the addition of a premature stop-codon would result in an incomplete and therefore nonfunctional protein. However, the incomplete protein could also aggregate and give rise to a gain-of-function folding disease. Finally, the protein may still function and fold in a relatively stable form depending on where the stop codon appeared.

DIF: Difficult REF: 4.3 OBJ: 4.3.f. Compare loss of function with gain of function.

MSC: Evaluating

Chapter 5: Methods in Protein Biochemistry MULTIPLE CHOICE 1. Why is the process of purifying proteins from cells considered challenging? a. Proteins are insoluble. b. The process is expensive and time consuming. c. There is no way to determine the structure of the protein. d. There are 10,000 to 100,000 proteins in one sample.

ANS: D DIF: Easy REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Understanding 2. Biochemical assays are important in the process of isolating proteins because they a. uniquely identify one protein. b. separate proteins based on polarity. c. isolate proteins based on size. d. determine the molecular weight of proteins.

ANS: A DIF: Difficult REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Understanding 3. Which separation technique exploits the solubility differences of proteins? a. centrifugation b. salting out c. dialysis d. ion-exchange chromatography ANS: B DIF: Easy REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Remembering 4. After using the salting out method to isolate proteins, how is ammonium sulfate removed from the solution? a. sonication b. French press c. dialysis d. centrifugation ANS: C DIF: Easy REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Remembering 5. When preparing to isolate proteins from plant cells, the first step in preparing the cell homogenate would be a. sonication. b. using a French press. c. treatment with mild detergents. d. enzymatic treatment.

ANS: D DIF: Medium REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Analyzing 6. The figure below shows how differential centrifugation can be used to isolate four subcellular fractions. Which fraction corresponds to the cytosol fraction?

a. b. c. d.

A B C D

ANS: D DIF: Easy REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Understanding 7. The figure below shows how differential centrifugation can be used to isolate four subcellular fractions. Which fraction corresponds to the mitochondrial fraction?

a. b. c. d.

A B C D

ANS: B

DIF: Easy

REF: 5.1

OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Understanding 8. The figure below shows how differential centrifugation can be used to isolate four subcellular fractions. Which fraction corresponds to the membrane fraction?

a. b. c. d.

A B C D

ANS: C DIF: Easy REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Understanding 9. After centrifugation, the purity of the protein is determined by a. absorbance measurements. b. activity units. c. total protein content. d. specific activity.

ANS: D DIF: Easy REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Remembering 10. After centrifugation, there is a 10% decrease in activity and a 75% decrease in total protein. What is purification of the target protein? a. 0.28-fold b. 1.3-fold c. 3.6-fold d. 7.5-fold ANS: C DIF: Difficult REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Applying

11. Calculate the purification of the target protein when there is a 30% decrease in activity and a 55% decrease in total protein after centrifugation. a. 0.55-fold b. 0.64-fold c. 1.6-fold d. 1.8-fold ANS: C DIF: Difficult REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Applying 12. Calculate the specific activity when 500 mg of protein has an activity of 18,000 units. a. 0.28 units/mg protein b. 36 units/mg protein c. 9000 units/mg protein d. 13,000 units/mg protein ANS: C DIF: Difficult REF: 5.1 OBJ: 5.1.b. Explain how differential centrifugation can be used to isolate different parts of the cell.

MSC: Applying 13. The figure below shows three proteins that are separated using gel filtration chromatography.

Which protein is the largest?

a. b. c. d.

squares circles triangles Not enough information is included to determine the protein.

ANS: A DIF: Medium REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Applying 14. The following peptides are separated using an anion exchange resin in ion-exchange chromatography. Which peptide is eluted first?

Peptide

Molecular Weight (g/mol)

Charge

A B

360 1080

–2 –1

C D a. b. c. d.

1800 1440

0 +1

A B C D

ANS: D DIF: Difficult REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Applying 15. Which type of chromatography separates proteins using specific binding properties? a. affinity chromatography b. gel filtration chromatography c. size exclusion chromatography d. high-performance liquid chromatography ANS: A DIF: Easy REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Remembering 16. Which of the following peptides would be eluted last when separated using gel filtration chromatography?

a. b. c. d.

Peptide

Molecular Weight (g/mol)

Charge

A B C D

360 1080 1800 1440

–2 –1 0 +1

A B C D

ANS: A DIF: Difficult REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Applying 17. Which peptide would migrate the slowest in an SDS-PAGE gel?

a. b. c. d.

A B C D

Peptide

Molecular Weight (g/mol)

A B C D

360 1080 1800 1440

ANS: C DIF: Medium REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Applying 18. Which peptide would migrate the fastest in a SDS-PAGE gel?

a. b. c. d.

Peptide

Molecular Weight (g/mol)

A B C D

360 1080 1800 1440

A B C D

ANS: A DIF: Medium REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Applying 19. Which percentage of polyacrylamide would give the best separation for small proteins? a. 5% b. 7.5% c. 10% d. 20% ANS: D DIF: Difficult REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Applying 20. Which percentage of polyacrylamide would give the best separation for large proteins? a. 5% b. 7.5% c. 10% d. 20% ANS: A DIF: Difficult REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Applying 21. The advantage of using a native PAGE gel compared with an SDS-PAGE gel is that the native PAGE gel a. separates proteins only based on molar mass. b. gives information on the charge or conformation of the protein. c. results in a better separation of small proteins. d. increases the resolution of large and small proteins.

ANS: B DIF: Medium REF: 5.1 OBJ: 5.1.e. Distinguish between native PAGE and SDS-PAGE. MSC: Analyzing 22. The advantage of using an SDS-PAGE gel compared with a native PAGE gel is that the SDS-PAGE gel

a. b. c. d.

separates proteins only based on molar mass. gives information about the charge or conformation of the protein. results in a better separation of small proteins. increases the resolution of large and small proteins.

ANS: A DIF: Easy REF: 5.1 OBJ: 5.1.e. Distinguish between native PAGE and SDS-PAGE. MSC: Analyzing 23. Two-dimensional polyacrylamide gel electrophoresis separates proteins based on a. pI and shape. b. ligand affinity and molecular weight. c. shape and ligand affinity. d. pI and molecular weight.

ANS: D DIF: Easy REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Remembering 24. In isoelectric focusing, a. negatively charged proteins migrate toward the cathode. b. negatively charged proteins migrate toward the anode. c. small proteins migrate the fastest. d. large proteins migrate the fastest.

ANS: A DIF: Easy REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Applying 25. In isoelectric focusing, a. positively charged proteins migrate toward the cathode. b. positively charged proteins migrate toward the anode. c. small proteins migrate the fastest. d. large proteins migrate the fastest.

ANS: B DIF: Easy REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Applying 26. In isoelectric focusing, a protein with a pH below the pI would a. migrate toward the anode. b. migrate toward the cathode. c. stop migrating. d. migrate, but there is no way to determine the direction.

ANS: A DIF: Difficult REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Applying 27. Which enzyme or reagent cleaves a peptide at the carboxyl side of a methionine residue? a. trypsin b. chymotrypsin c. V-8 protease d. cyanogen bromide ANS: D

DIF: Easy

REF: 5.2

OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Remembering 28. Predict the fragments of the following peptide after cleavage by trypsin.

GLMKTYPDSTA a. GLM KTYPDSTA b. GLMK TYPDSTA c. GLMKTY PDSTA d. GLMKTYPD STA ANS: B DIF: Difficult REF: 5.2 OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Applying 29. A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

Trypsin Digest

Chymotrypsin Digest

LMYK MGFCE WDER

CE LMYKW DERMGF

a. b. c. d.

ECFGMREDWKYLM LMYKWMGFCEDER LMYKWDERMGFCE CELMYKWDERMGF

ANS: C DIF: Difficult REF: 5.2 OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Applying 30. Predict the fragments of the following peptide after cleavage by the V-8 protease.

CMVAADGKLEPVS a. CMVAAD GKLEPVS b. CMVAADGKLE PVS c. CMVAADG KLEPVS d. CMVAAD GKLE PVS ANS: D DIF: Difficult REF: 5.2 OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Applying 31. Which method uses mass to charge ratios as well as a bioinformatics approach to determine the amino acid composition of a protein? a. X-ray crystallography b. nuclear magnetic resonance c. tandem mass spectrometry d. size exclusion chromatography ANS: C DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Understanding

32. In tandem mass spectrometry, the first mass spectrometer a. determines the nuclear spin of the atoms. b. determines the mass of peptide subfragments. c. uses bioinformatics to compare the masses of the peptides. d. uses electrospray ionization to select peptide fragments.

ANS: D DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Understanding 33. Which technique ionizes polypeptides by releasing them from a small metallic capillary at high voltage? a. ESI b. MALDI c. NMR d. X-ray crystallography ANS: A DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Remembering 34. Which technique ionizes polypeptides by embedding the tryptic fragments into a light-absorbing matrix and exposing it to a laser? a. ESI b. MALDI c. NMR d. X-ray crystallography ANS: B DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Remembering 35. In tandem mass spectrometry, the second mass spectrometer a. determines the nuclear spin of the atoms. b. determines the mass of peptide subfragments. c. uses bioinformatics to compare the masses of the peptides. d. uses electrospray ionization to select peptide fragments.

ANS: B DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Understanding 36. Below are the steps of solid-phase peptide synthesis: 1. The protecting groups of the amino acids are removed.

2. The peptide is released from the solid support resin.

3. An incoming amino acid is activated at the carboxyl group by DCC and added to the column.

4. Fmoc is removed by treatment with a base and the C-terminal amino acid is attached to the resin molecule.

5. The resin bound C-terminal amino acid and the incoming N-terminal amino acid are coupled.

What is the appropriate order of these steps? a. 3, 5, 4, 2, 1 b. 1, 4, 2, 5, 3 c. 4, 3, 5, 1, 2 d. 2, 4, 5, 3, 1

ANS: C DIF: Medium REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Evaluating

37. In solid-phase peptide synthesis, which reagent is used to remove the peptide from the solid resin support? a. HF b. DCC c. Fmoc d. PITC ANS: A DIF: Easy REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Remembering

38. During solid-phase peptide synthesis, 9-fluorenylmethoxycarbonyl is used a. as a blocking agent. b. as an activating agent. c. to cleave the peptide from the resin. d. to couple amino acids during the synthesis.

ANS: A DIF: Easy REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Remembering

39. The step in solid-phase peptide synthesis that occurs at number 3 is

a. b. c. d.

deblocking of the residue attached to the resin. coupling of the amino acid. cleavage from the resin. activation of the Fmoc blocked residue.

ANS: B DIF: Medium REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Understanding

40. The step in solid-phase peptide synthesis that occurs at number 2 is

a. b. c. d.

deblocking of the residue attached to the resin. coupling of the amino acid. cleavage from the resin. activation of the Fmoc blocked residue.

ANS: D DIF: Medium REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Understanding

41. During solid-phase peptide synthesis, dicyclohexylcarbodiimide is used a. as a blocking agent. b. as an activating agent. c. to cleave the peptide from the resin. d. to couple amino acids during the synthesis.

ANS: B DIF: Medium REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Remembering

42. The size of proteins studied by NMR is limited because a. a small sample size is needed. b. it is hard to determine the phases of diffracted X-rays. c. the measurements of the distances between atoms are only approximate. d. large molecules reorient slowly in solution.

ANS: D DIF: Medium REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Understanding 43. One of the most difficult steps in X-ray crystallography is a. using the correct radio frequency pulses to perturb the nuclear spin. b. determining the phases of diffracted X-rays. c. dissolving the protein in the appropriate solvent. d. obtaining a large enough sample for analysis.

ANS: B DIF: Medium REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Understanding 44. Protein NMR is more useful than X-ray crystallography for studying a. secondary structure elements. b. large proteins. c. protein unfolding. d. static protein structures.

ANS: C DIF: Medium REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Analyzing 45. The specific sites on the antigen that interacts with the antibody are called a. epitopes. b. immunoglobin light chains. c. immunoglobin heavy chains. d. variable-domain amino acid residues.

ANS: A DIF: Easy REF: 5.4 OBJ: 5.4.a. Identify the key regions of an immunoglobulin.

MSC: Remembering

46. The specific sites on the antibody that interacts with the antigen are a. epitopes. b. immunoglobin light chains. c. immunoglobin heavy chains. d. variable-domain amino acid residues.

ANS: D DIF: Easy REF: 5.4 OBJ: 5.4.a. Identify the key regions of an immunoglobulin.

47. The Fab immunoglobin fragment a. is generally found within -barrels. b. is located in polar surface groups in loop regions. c. contains the high-affinity antigen binding site.

MSC: Remembering

d. is responsible for the solubility of the antibody.

ANS: C DIF: Easy REF: 5.4 OBJ: 5.4.a. Identify the key regions of an immunoglobulin.

MSC: Remembering

48. Epitopes on protein antigens are generally located a. in the heavy chain domains. b. on polar surface groups in loop regions. c. in the light chain domains. d. in association with variable domain amino acid residues.

ANS: B DIF: Easy REF: 5.4 OBJ: 5.4.a. Identify the key regions of an immunoglobulin.

MSC: Remembering

49. Polyclonal antibodies are a. derived from B cells isolated from the spleen. b. isolated from hybridoma cells. c. a heterogeneous mixture. d. a homogenous mixture.

ANS: C DIF: Easy REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Understanding 50. Monoclonal antibodies a. recognize a single epitope. b. recognize multiple epitopes. c. are isolated from leukocytes. d. are isolated from red blood cells.

ANS: A DIF: Easy REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Understanding 51. What is the advantage of using polyclonal antibodies compared with monoclonal antibodies? a. They are less labor intensive to generate. b. They provide the ability to monitor quality continually. c. The process used to produce the antibodies provides unlimited supplies. d. They can be generated without using animals.

ANS: A DIF: Difficult REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Analyzing 52. What is the advantage of using monoclonal antibodies compared with polyclonal antibodies? a. They are less labor intensive to generate. b. They can recognize more than one epitope. c. The process used to produce the antibodies provides unlimited supplies. d. They can be generated without using animals.

ANS: C DIF: Medium REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Analyzing 53. During the production of polyclonal antibodies, how are the antigen-specific antibodies purified? a. dialysis

b. gel electrophoresis c. size exclusion chromatography d. affinity chromatography ANS: D DIF: Medium REF: 5.4 OBJ: 5.4.c. List the steps required to obtain polyclonal antibodies.

MSC: Understanding 54. The majority of serum proteins and nonspecific antibodies are removed during the generation of polyclonal antibodies by a. washing with a low pH buffer. b. gel electrophoresis. c. size exclusion chromatography. d. salting out.

ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.c. List the steps required to obtain polyclonal antibodies.

MSC: Understanding 55. Why is the supply of polyclonal antibodies limited? a. They are time consuming to produce. b. The yield is very low. c. The animals the antibodies are isolated from eventually die. d. The production is limited by the government.

ANS: C DIF: Easy REF: 5.4 OBJ: 5.4.c. List the steps required to obtain polyclonal antibodies.

MSC: Understanding 56. During the production of polyclonal antibodies, where are the antibodies isolated from? a. an immortalized tumor cell line b. liver cells c. spleen cells d. blood cells ANS: D DIF: Easy REF: 5.4 OBJ: 5.4.c. List the steps required to obtain polyclonal antibodies.

MSC: Understanding 57. Using the figure below describing monoclonal antibody generation, identify the step where the B cells are fused with the tumor cells.

a. b. c. d.

1 2 3 4

ANS: D DIF: Medium REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding 58. What cells are shown at step number 5 in the figure below?

a. b. c. d.

B cells immortalized tumor cell hybridoma cells red blood cells

ANS: C DIF: Medium REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding 59. What cells are shown at step number 2 in the figure below?

a. b. c. d.

B cells immortalized tumor cells hybridoma cells red blood cells

ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding 60. When cells isolated from the spleen are fused with long-living cells, they produce a. B cells. b. immortalized tumor cells. c. hybridoma cells. d. red blood cells.

ANS: C DIF: Medium REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding

61. Which animal is most often used to generate monoclonal antibodies? a. rabbit b. chicken c. goat d. mouse ANS: D DIF: Medium REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding 62. In monoclonal antibody generation, the cells that produce the antibody in the animal are located in __________ cells. a. heart b. liver c. spleen d. red blood ANS: C DIF: Easy REF: 5.4 OBJ: 5.4.d. List the steps required to obtain monoclonal antibodies.

MSC: Understanding 63. Most secondary antibodies used in Western blots are covalently linked to the enzyme a. luciferase. b. horseradish peroxidase. c. catalase. d. hydrolase.

ANS: B DIF: Easy REF: 5.4 OBJ: 5.4.e. Differentiate between the primary antibody and secondary antibody used in Western blotting.

MSC: Remembering 64. Which component used in a Western blot is covalently linked to an enzyme? a. SDS-PAGE gel b. primary antibody c. secondary antibody d. filter membrane ANS: C DIF: Easy REF: 5.4 OBJ: 5.4.e. Differentiate between the primary antibody and secondary antibody used in Western blotting.

MSC: Remembering 65. The part of the Western blot that contains the protein-specific recognition and facilitates the antigen-antibody interactions is the a. SDS-PAGE gel. b. primary antibody. c. tertiary antibody. d. filter membrane.

ANS: B DIF: Easy REF: 5.4 OBJ: 5.4.f. List the steps involved in Western blotting.

MSC: Understanding

66. If a protocol for a Western blot calls for the use of rabbit anti-mouse antibody, what type of antibody would this be considered? a. monoclonal primary b. polyclonal primary

c. monoclonal secondary d. polyclonal secondary ANS: D DIF: Difficult REF: 5.4 OBJ: 5.4.e. Differentiate between the primary antibody and secondary antibody used in Western blotting.

MSC: Applying 67. Below are the steps of a Western blot. What is the correct order?

1. The membrane is incubated with the secondary antibody.

2. The membrane is incubated with the primary antibody.

3. The membrane is washed with a blocking solution.

4. Proteins are transferred to a nitrocellulose membrane.

5. Protein extracts are separated by gel electrophoresis. a. 5, 4, 3, 2, 1 b. 4, 5, 2, 3, 1 c. 3, 4, 5, 1, 2 d. 2, 5, 4, 3, 1 ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.f. List the steps involved in Western blotting.

MSC: Evaluating

68. During a Western blot, the membrane is washed with a blocking solution before being treated with the primary antibody to a. retain the position of the proteins in the transfer from gel to membrane. b. facilitate antibody–antigen interactions. c. decrease nonspecific antibody binding. d. facilitate a chemical reaction that can be detected.

ANS: C DIF: Difficult REF: 5.4 OBJ: 5.4.f. List the steps involved in Western blotting.

MSC: Understanding

69. In an ELISA, the detection antibody is a __________ antibody. a. monoclonal primary b. polyclonal tertiary c. monoclonal secondary d. polyclonal secondary ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.g. Identify the key reagents required in an ELISA.

MSC: Understanding

70. In an ELISA, the capture antibody is a __________ antibody. a. monoclonal primary b. polyclonal primary c. monoclonal secondary d. polyclonal secondary ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.g. Identify the key reagents required in an ELISA.

MSC: Understanding

71. Which technique uses highly specific monoclonal antibodies in a high-throughput form to detect small amounts of antigen? a. immunofluorescence b. Western blot c. SDS-PAGE gel

d. ELISA ANS: D DIF: Medium REF: 5.4 OBJ: 5.4.g. Identify the key reagents required in an ELISA.

MSC: Understanding

72. Which technique can be combined with mass spectrometry to identify protein antigens in large cellular complexes? a. immunofluorescence b. Western blot c. immunoprecipitation d. ELISA ANS: C DIF: Medium REF: 5.4 OBJ: 5.4.h. Outline the typical procedure used to identify a protein by immunoprecipitation.

MSC: Remembering 73. Co-immunoprecipitation proteins are separated through a. affinity chromatography. b. SDS-PAGE. c. HPLC. d. size exclusion chromatography.

ANS: B DIF: Medium REF: 5.4 OBJ: 5.4.h. Outline the typical procedure used to identify a protein by immunoprecipitation.

MSC: Understanding 74. Protein-specific antibodies can be used to detect proteins within cells conserving the cell architecture using a. immunofluorescence. b. Western blot. c. immunoprecipitation. d. ELISA. ANS: A DIF: Medium REF: 5.4 OBJ: 5.4.h. Outline the typical procedure used to identify a protein by immunoprecipitation.

MSC: Understanding 75. Immunoprecipitation uses an antibody-bead combination to a. detect the antigen. b. enrich the protein solution. c. digest the proteins for use in mass spectrometry. d. separate the proteins using centrifugation.

ANS: D DIF: Difficult REF: 5.4 OBJ: 5.4.h. Outline the typical procedure used to identify a protein by immunoprecipitation.

MSC: Understanding SHORT ANSWER 1. Why is protein purification often referred to as an art and a science?

ANS:

There are between 10,000 and 100,000 different proteins in a cellular sample. To isolate just one requires that scientists rely on the differences in the chemical and physical properties of the individual proteins. Not all processes are going to work for the same protein, so a scientist must develop new protocols for each one. A scientist must rely on both the quantitative and qualitative properties of the protein to do this.

DIF: Easy REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Analyzing 2. Compare and contrast the three MOST commonly used homogenization techniques to prepare a cell extract.

ANS: All three methods are used to disrupt or remove the cell membrane to prepare the cell homogenate.

Sonication uses ultrasonic waves to disrupt the membrane through vibrational effects. Shearing uses mechanical force by pushing the cells through a small opening. Cells can also be incubated with detergents to disrupt the membrane.

DIF: Medium REF: 5.1 OBJ: 5.1.a. Identify the key steps involved in isolating proteins from whole cells.

MSC: Analyzing 3. Explain the differences among the three types of column chromatography.

ANS: Gel filtration chromatography (size exclusion chromatography) separates proteins based on their size using carbohydrate beads that retain proteins in pores. Ion-exchange chromatography contains either cation or anion resins that separate proteins based on size. Anion exchange binds to negatively charged proteins, whereas cation exchange binds to positively charged proteins.

Affinity chromatography separates proteins using specific binding properties.

DIF: Easy REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Analyzing 4. Explain how to separate the following proteins using two different types of chromatography.

Protein

Isoelectric Point (pI)

Molar Mass (kDa)

1 2 3

3.8 7.5 4.0

75 118 120

ANS: Use size exclusion chromatography to separate protein 1 from 2 and 3. Then use ion-exchange chromatography to separate 2 and 3. Because proteins 2 and 3 have such different pIs, using a buffer with a pH of 4.0 would facilitate the separation. Protein 3 would effectively have no charge, whereas protein 2 would be charged at that pH. The charge difference would result in different elution rates of the protein.

DIF: Difficult REF: 5.1 OBJ: 5.1.c. Define the different types of column chromatography.

MSC: Applying

5. What is the advantage of using sodium dodecyl sulfate (SDS) in gel electrophoresis?

ANS: Gel electrophoresis separates molecules based on size and charge. SDS is an amphipathic molecule that masks the charges on the protein. Additionally, the SDS denatures the protein, negating the effects of shape on migration. This means that an SDS-PAGE gel separates the proteins as an approximate function of molar mass.

DIF: Medium REF: 5.1 OBJ: 5.1.e. Distinguish between native PAGE and SDS-PAGE. MSC: Evaluating 6. Compare the order of migration and the separation of three proteins (25 kDa, 100 kDa, and 150 kDa) in an SDS-PAGE gel with 15% polyacrylamide gel.

ANS: The 25 kDa protein would migrate the farthest, followed by the 100 kDa and 150 kDa protein. In SDS-PAGE gels, the smallest proteins migrate faster. There would be good separation between the 25 kDa protein and the other two proteins. However, there would be more resolution between the 100 kDa and the 150 kDa proteins because of the high-percentage polyacrylamide gel.

DIF: Medium REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Analyzing 7. Contrast the way that SDS-PAGE and native PAGE gels separate proteins.

ANS: SDS-PAGE gels use several chemicals (including the SDS) that denature the protein into polypeptide chains. The addition of the SDS negates the charge and the shape of the protein, so the protein is only separated based on molar mass. In a native PAGE, the protein is not denatured and is separated based on size, molar mass, and charge.

DIF: Medium REF: 5.1 OBJ: 5.1.e. Distinguish between native PAGE and SDS-PAGE. MSC: Analyzing 8. How can the mass of an unknown protein can be determined using gel electrophoresis?

ANS: The mass of an unknown protein can be determined by comparing the migration distance in the gel to that of known proteins that serve as the molecular mass markers. The log of the masses of the known proteins can be plotted against the migration distance, forming a straight line. The molecular weight of the unknown protein can then be determined based on its migration distance in the same gel.

DIF: Medium REF: 5.1 OBJ: 5.1.d. Explain the migration process of gel electrophoresis.

MSC: Understanding 9. Explain how proteins are separated using isoelectric focusing.

ANS:

Proteins are applied to a gel strip containing a stable pH gradient. An electric field is applied and the proteins migrate toward the anode (if they are cations) or the cathode (if they are anions). Once the protein reaches its isoelectric point, where the charge is zero, it will stop migrating.

DIF: Easy REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Understanding 10. Analyze and interpret the 2-D PAGE gel shown below. What information can be determined about the proteins labeled A and B?

ANS: Protein A has a higher mass and lower pI than protein B. Protein B will have a higher pI and a lower mass.

DIF: Medium REF: 5.1 OBJ: 5.1.f. Summarize the separation methods that can be combined into 2-D PAGE. MSC: Applying 11. Why is it more advantageous to use Edman degradation instead of Sanger’s sequencing method?

ANS: Sanger’s method requires adding fresh protein after each cleavage, making the process labor intensive. The method also requires a relatively large amount of protein. The Edman degradation does not require fresh protein to be added after each step, so a much smaller amount of protein is needed.

DIF: Difficult REF: 5.2 OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Analyzing 12. A polypeptide was digested by trypsin and chymotrypsin. Use the following information to determine the polypeptide sequence.

Trypsin YMR LSSWEMYEK VEFDGSK GAWAK

Chymotrypsin MR VEF EMY DGKLSSW EKGAW

AKY ANS: VEFDGSKLSSWEMYEKGAWAKYMR DIF: Difficult REF: 5.2 OBJ: 5.2.a. Interpret the results of protease treatment followed by Edman degradation to determine the sequence of a peptide.

MSC: Applying 13. Compare and contrast electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI).

ANS: Both methods are used to ionize peptides without disintegrating them. ESI releases tryptic fragments (polypeptides) from a small metallic capillary at high voltage, causing the peptides to evaporate, forming a highly charged molecule in the gas phase. In MALDI the cleavage fragments are embedded in a light-absorbing matrix and released as a charged molecule after the flash of the laser.

DIF: Easy REF: 5.2 OBJ: 5.2.b. Identify the key steps involved in tandem mass spectrometry of tryptic digests.

MSC: Analyzing 14. How does the directionality of synthesis differ with in vivo polypeptide synthesis compared to solid-phase peptide synthesis?

ANS: In in vivo polypeptide synthesis, amino acids are added one at a time to the carboxyl terminus of the polypeptide chain. In solid-phase peptide synthesis, the amino acids are added to the amine terminus.

DIF: Easy REF: 5.2 OBJ: 5.2.c. Outline the steps of solid-phase peptide synthesis.

MSC: Analyzing

15. How does NMR spectroscopy differ from X-ray crystallography when determining the structure of a protein?

ANS: X-ray crystallography gives the atomic positions of the protein in a static crystal lattice. NMR spectroscopy uses a high-strength magnetic field to determine the relative position of specific atoms in a protein solution.

DIF: Easy REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Analyzing 16. Why is X-ray crystallography more commonly used than NMR spectroscopy when determining protein structure?

ANS: NMR is limited to proteins that are less than ~100 kDa. This occurs because large molecules reorient slowly in solution, resulting in signals that average out and are lost during the process.

Additionally, NMR requires more protein sample than X-ray crystallography.

DIF: Medium REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Analyzing 17. Describe the major difference between the types of protein samples used in X-ray crystallography and NMR spectroscopy. Then explain how this difference limits each method.

ANS: Protein samples used in NMR are in solutions, whereas the protein samples used in X-ray crystallography are in crystal form.

In X-ray crystallography, it is sometimes hard to obtain crystals of a new protein because the conditions needed to precipitate a crystal are unknown. NMR spectroscopy requires a high protein concentration, which can be hard to obtain.

DIF: Medium REF: 5.3 OBJ: 5.3.a. Compare and contrast X-ray crystallography and NMR spectroscopy as tools for determining protein structure.

MSC: Analyzing 18. Theoretically, an individual B cell could express any combination of light chain and heavy chain polypeptides to produce one of 10 antibody complexes. How does this seemingly limited production of antibodies protect us from the tens of millions of foreign antigens we encounter through our lives?

ANS: DNA recombination is the reason that we produce a multitude of unique antibodies to protect us from the tens of millions of foreign antigens. Variable domain coding sequences are joined in small DNA segments on the same chromosome. These random DNA recombination events are what generate the unique antibodies.

DIF: Difficult REF: 5.4 OBJ: 5.4.a. Identify the key regions of an immunoglobulin.

MSC: Applying

19. Explain the difference between polyclonal and monoclonal antibodies.

ANS: A polyclonal antibody is a heterogeneous mixture of immunoglobulin proteins and a monoclonal antibody is a homogenous mixture of immunoglobulin proteins. A polyclonal antibody recognizes one or more epitopes, whereas a monoclonal antibody only recognizes a single epitope.

DIF: Medium REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Analyzing 20. Describe how polyclonal antibodies are generated.

ANS: Either a rabbit, chicken, or goat is injected several times over the course of 6 to 8 weeks with an antigen. An immune response leads to the production of B-cells secreting antigen-specific antibodies. Whole blood is removed from the animal and the red blood cells are separated from the sample. The antigen-specific polyclonal antibodies are purified from the remaining animal serum using affinity chromatography.

DIF: Medium

REF: 5.4

OBJ: 5.4.c. List the steps required to obtain polyclonal antibodies.

MSC: Understanding 21. What are the advantages of using a monoclonal antibody compared with a polyclonal antibody?

ANS: Monoclonal antibodies are generated from an immortalized hybridoma cell line, resulting in an unlimited supply of antibodies. The polyclonal antibody supply is limited because the animal eventually dies. Additionally, monoclonal antibodies provide the ability to monitor quality continually using standardized diagnostic measures.

DIF: Medium REF: 5.4 OBJ: 5.4.b. Differentiate between polyclonal and monoclonal antibodies.

MSC: Analyzing 22. Explain the difference between the primary and secondary antibody using a Western blot.

ANS: The primary antibody facilitates the antigen–antibody interactions. The secondary antibody is covalently linked to an enzyme that catalyzes a chemical reaction that can be detected by a colorimetric or fluorometric assay when the substrate is added.

DIF: Easy REF: 5.4 OBJ: 5.4.e. Differentiate between the primary antibody and secondary antibody used in Western blotting.

MSC: Analyzing 23. Explain how protein samples that contain the antigenic protein are recognized using a Western blot.

ANS: The proteins are separated using gel electrophoresis and transferred to a nitrocellulose membrane.

The membrane is treated with a blocking solution to prevent nonspecific antibody binding, and then it is incubated with the primary antibody, which facilitates antigen–antibody binding. The primary antibody is removed with washing and the membrane is incubated with a secondary antibody. The secondary antibody is linked to an enzyme that causes a chemical reaction that can be detected using either colorimetric or fluorometric assays.

DIF: Medium REF: 5.4 blotting.

MSC: Understanding

OBJ: 5.4.f. List the steps involved in Western

24. Describe how an ELISA detects antigenic proteins.

ANS: ELISA uses a “sandwich” method where a primary monoclonal antibody is covalently attached to the bottom of a 96-well plate. This antibody recognizes a single epitope on the antigen. The sample is added to the well plate and incubated for several hours while the antigen–antibody binding takes place. A second primary monoclonal antibody is added to the well, recognizing a distinct epitope on the antigenic protein. A third antibody is added that recognizes the detection antibody and causes a chemical reaction that can be detected using either colorimetric or fluorometric assays.

DIF: Medium REF: 5.4 OBJ: 5.4.g. Identify the key reagents required in an ELISA.

MSC: Understanding

25. You are employed in a prominent biochemistry lab, ProteinsRUs. The company offers a $500 bonus to the person who can develop a way to perform Western blotting without having to wait to make a unique antibody for proteins under analysis. How would you propose to do this? Explain the method you would use in two to three sentences and give an example.

ANS: A faster way to perform the analysis would be to use commercially available epitope tags and gene-encoded proteins. The FLAG and myc epitopes sequences are highly antigenic, and their coding sequences can easily be added to the protein coding sequences of genes using conventional recombinant DNA techniques. This would eliminate the need to wait for antibodies to be isolated from animals.

DIF: Medium blotting.

MSC: Evaluating

REF: 5.4

OBJ: 5.4.f. List the steps involved in Western

Chapter 6: Protein Function MULTIPLE CHOICE 1. If a metabolic enzyme __________ the energy of activation of a reaction, the rate of product formation will __________. a. increases; decrease b. decreases; increase c. increases; increase d. decreases; decrease ANS: B DIF: Easy REF: 6.1 OBJ: 6.1.a. State the primary mechanism by which enzymes function as chemical catalysts.

MSC: Applying 2. Vitamin C is required for prolyl hydroxylase to function. Prolyl hydroxylase enzyme activity is necessary for the proper biosynthesis of collagen. Which of the following might result from a deficiency in vitamin C? a. higher risk of bone breakage b. a reduction in muscle contraction ability c. reduced chromosomal separation during mitosis d. brittle hair ANS: A DIF: Medium REF: 6.1 OBJ: 6.1.a. State the primary mechanism by which enzymes function as chemical catalysts.

MSC: Applying 3. Which of the following is NOT a characteristic of an enzyme active site? a. It has a three-dimensional shape. b. It plays a role in increasing the energy of activation of the reaction being catalyzed. c. It is a unique chemical environment. d. It is where the substrate of the reaction can be found.

ANS: B DIF: Medium REF: 6.1 OBJ: 6.1.a. State the primary mechanism by which enzymes function as chemical catalysts.

MSC: Remembering 4. A proposed structure of a bacterial membrane protein shows that the distance between successive amino acids in a region crossing the membrane is 3.4 Å. Recall that a typical lipid bilayer is approximately 40 Å across. Which of the following is the most likely description of the protein? a. The transmembrane region of the protein resembles the transmembrane region of the Ca2+-ATPase transporter protein. b. The primary sequence of the transmembrane region of the protein is composed of approximately nine amino acids. c. The protein contains a selectivity channel. d. The protein resembles a porin.

ANS: D DIF: Difficult REF: 6.3 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane transport.

MSC: Analyzing 5. Which of the following statements is true for hemoglobin but NOT myoglobin? a. The tertiary structure is made up of a globin fold. b. The surface of its tertiary structure contains many hydrophobic amino acids.

c. It contains a proximal histidine that coordinates the heme group. d. It contains a single carboxyl-terminal amino acid.

ANS: B DIF: Difficult REF: 6.2 OBJ: 6.2.a. Compare and contrast the structures of myoglobin and hemoglobin.

MSC: Analyzing 6. In both myoglobin and hemoglobin, O2 reversibly binds to a(n) __________ atom contained in a porphyrin ring that is tightly bound to the protein. a. calcium b. iron c. magnesium d. manganese ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.a. Compare and contrast the structures of myoglobin and hemoglobin.

MSC: Remembering 7. Which of the following is true of this compound?

a. b. c. d.

It contains a ferric ion.

It is a prosthetic group.

It is found on the surface of both hemoglobin and myoglobin.

It is coordinated to hemoglobin through interactions with a proximal cysteine.

ANS: B DIF: Medium REF: 6.2 OBJ: 6.2.a. Compare and contrast the structures of myoglobin and hemoglobin.

MSC: Understanding 8. Hemoglobin contains __________ a. 32; 4; 4 b. 32; 0; 8 c. 8; 8; 4 d. 32; 0; 4

-helices, __________ -sheets, and __________ globin folds.

ANS: D DIF: Medium REF: 6.2 OBJ: 6.2.a. Compare and contrast the structures of myoglobin and hemoglobin.

MSC: Remembering 9. A reduction in the catalytic ability of carbonic anhydrase may lead to __________ efficient oxygen delivery by hemoglobin as a result of a(n) __________ Bohr effect. a. less; increased b. more; increased

c. less; reduced d. more; reduced ANS: C DIF: Difficult REF: 6.2 OBJ: 6.2.g. List the positive and negative effectors for oxygen binding to hemoglobin.

MSC: Applying 10. An effector binds to a single subunit of a multi-subunit allosteric protein. As a result, all subunits switch to the R state. This is an example of the __________ model of allostery. a. concerted b. homotropic c. sequential d. combined ANS: A DIF: Easy REF: 6.2 OBJ: 6.2.f. Differentiate between the concerted model and the sequential model.

MSC: Understanding 11. Which of the following is a positive effector for oxygen binding to hemoglobin? a. CO2 b. O2 c. H+ d. 2,3-bisphosphoglycerate ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.g. List the positive and negative effectors for oxygen binding to hemoglobin.

MSC: Remembering 12. Below is a figure of adult hemoglobin. The arrow points to where __________ binds.

a. b. c. d.

glucose 2,3-bisphosphoglycerate O2 CO2

ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.h. Identify structural differences between adult and fetal hemoglobin that affect 2,3-BPG association. MSC: Understanding 13. Below is a fractional saturation curve for O2 binding to adult hemoglobin. Assume that curve Y represents a system at pH 7.4 and with a normal physiological level of 2,3-BPG. Curve X represents a system that

a. b. c. d.

is at pH 7.4 with a higher than normal physiological level of 2,3-BPG. has a higher pH with a normal physiological level of 2,3-BPG. has a lower pH with a normal physiological level of 2,3-BPG. is at pH 7.4 with a normal physiological level of 2,3-BPG but with an increased level of CO2.

ANS: B DIF: Difficult REF: 6.2 OBJ: 6.2.g. List the positive and negative effectors for oxygen binding to hemoglobin.

MSC: Analyzing 14. Nuclear receptors are a type of a. metabolic enzyme. b. structural protein. c. transport protein. d. cell signaling protein.

ANS: D DIF: Easy REF: 6.1 OBJ: 6.1.c. List the three major types of cell signaling proteins.

MSC: Remembering 15. The estrogen receptor is a(n) a. G protein–coupled receptor. b. receptor tyrosine kinase. c. nuclear receptor. d. intracellular signaling protein.

ANS: C DIF: Easy REF: 6.1 OBJ: 6.1.c. List the three major types of cell signaling proteins.

MSC: Remembering 16. Which of the following is NOT a transport protein? a. maltoporin b. hemoglobin c. Na+ channel d. DNA polymerase

ANS: D DIF: Easy REF: 6.1 OBJ: 6.1.b. Identify the two basic classes of membrane transport proteins.

MSC: Remembering 17. Which of the following is a genomic caretaker protein? a. topoisomerase b. insulin c. myoglobin d. tubulin ANS: A DIF: Easy REF: 6.1 OBJ: 6.1.d. Identify the two major classes of genomic caretaker proteins.

MSC: Understanding 18. Which of the following directly requires ATP to carry out its function? a. Cl− ion channel b. malate dehydrogenase c. myoglobin d. protein kinase A ANS: D DIF: Medium REF: 6.1 OBJ: 6.1.a. State the primary mechanism by which enzymes function as chemical catalysts.

MSC: Understanding 19. When oxygen binds to hemoglobin, which of the following occurs? a. The heme group becomes puckered. b. The atomic radius of the iron is decreased. c. His F7 is brought closer to the plane of the porphyrin ring. d. His E8 is brought closer to the plane of the porphyrin ring.

ANS: B DIF: Medium REF: 6.2 OBJ: 6.2.b. Analyze the structural changes that occur when oxygen binds to the heme group.

MSC: Understanding 20. Consider the following interaction between a protein and its ligand: [P] + [L]

[PL].

If [L] = 5 mM, [P] = 3 mM, and [PL] = 2 mM, what is the Ka for the interaction? a. 7.5 mM b. 15 mM c. 0.133 mM d. 0.4 mM ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.c. Differentiate between an association constant and a dissociation constant.

MSC: Applying 21. Consider the following interaction between a protein and its ligand: [P] + [L] If [L] = 5 mM, [P] = 3 mM, and [PL] = 2 mM, what is the dissociation constant? a. 7.5 mM b. 15 mM c. 0.133 mM d. 0.4 mM ANS: A

DIF: Medium

REF: 6.2

[PL].

OBJ: 6.2.c. Differentiate between an association constant and a dissociation constant.

MSC: Applying 22. The estrogen receptor is an example of a a. metabolic enzyme. b. transport protein. c. genomic caretaker protein. d. cell signaling protein.

ANS: D DIF: Easy REF: 6.1 OBJ: 6.1.c. List the three major types of cell signaling proteins.

MSC: Understanding 23. Which of the following groups are hydrogen bonded in oxyhemoglobin but not deoxyhemoglobin? a. Asp94 and Asn102 b. Asp94 and Tyr42 c. Try42 and Asp99 d. Asp99 and Asn102 ANS: A DIF: Medium REF: 6.2 OBJ: 6.2.b. Analyze the structural changes that occur when oxygen binds to the heme group.

MSC: Remembering 24. A mutation of the N-terminal valine in adult hemoglobin occurs. The amino acid is replaced with an isoleucine. Studies show that the replacement does not alter the overall structure of the protein.

Which of the following hemoglobin functions may be altered? a. affinity for 2,3-BPG b. ability to transport O2 c. ability to transport CO2 d. ability to switch from the T state to the R state ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.g. List the positive and negative effectors for oxygen binding to hemoglobin.

MSC: Analyzing 25. The fractional saturation of hemoglobin (Hb) binding to oxygen is illustrated by a. [HbO2] / ([HbO2] + [Hb]). b. ([HbO2] + [Hb]) / [HbO2]. c. [Hb] / [HbO2]. d. [HbO2] / [Hb].

ANS: A DIF: Easy REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Remembering 26. Oxygen binding is monitored for a solution of hemoglobin. During the experiment, the curve changes from sigmoidal to hyperbolic. Which of the following may be the reason for the change? a. A positive allosteric effector was added. b. A negative allosteric effector was added. c. The protein dissociated into individual subunits. d. The protein denatured.

ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Applying

27. A protein that follows the concerted model of allosteric regulation would display a binding curve that is __________. A protein that follows the sequential model of allosteric regulation would display a binding curve that is __________. a. sigmoidal; hyperbolic b. hyperbolic; sigmoidal c. sigmoidal; sigmoidal d. hyperbolic; hyperbolic ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.f. Differentiate between the concerted model and the sequential model.

MSC: Applying 28. Which of the following curves is representative of the binding of oxygen to myoglobin?

a. b. c. d.

curve A curve B curve C curve D

ANS: A DIF: Easy REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Understanding 29. Consider an allosteric protein that contains three identical subunits. Which of the following is true only if the protein follows the concerted model of allostery and NOT the sequential model of allostery? a. All three subunits exist in the R state simultaneously. b. All three subunits exist in the T state simultaneously. c. A ligand is bound to a single subunit and that subunit is in the T state. d. No ligand is bound; two subunits are in the T state and one subunit is in the L state.

ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.f. Differentiate between the concerted model and the sequential model.

MSC: Applying

30. Which of the following pairs are paralogous genes? a. chicken myoglobin; human hemoglobin subunit b. chicken hemoglobin subunit; chicken hemoglobin subunit c. human hemoglobin subunit; chicken hemoglobin subunit d. chicken hemoglobin subunit; human myoglobin ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.i. Compare the sequences of the human globins to understand the paralogous nature of their genes.

MSC: Understanding 31. The subunit of adult hemoglobin has higher sequence similarity to __________ than to __________. a. fetal subunit; myoglobin b. myoglobin; fetal subunit c. adult 1 subunit; fetal subunit d. myoglobin; adult 1 subunit ANS: A DIF: Medium REF: 6.2 OBJ: 6.2.i. Compare the sequences of the human globins to understand the paralogous nature of their genes.

MSC: Remembering 32. Look at the data in the figure below. If the sequence for the subunit was replaced with the subunit sequence from a patient with sickle cell disease, the number of

a. b. c. d.

asterisks would decrease. colons would increase. periods would decrease. asterisks would increase.

ANS: B DIF: Difficult REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Evaluating 33. Approximately how many amino acids are identical in both myoglobin and the adult hemoglobin? a. 2% b. 20% c. 38% d. 81%

-subunit of

ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.i. Compare the sequences of the human globins to understand the paralogous nature of their genes.

MSC: Remembering 34. Which of the following is NOT a symptom of anemia? a. fatigue b. shortness of breath c. cognitive decline d. excessive bleeding ANS: D DIF: Easy REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Remembering 35. Which of the following is true of sickle cell anemia? a. It is a dominant genetic disease. b. It is caused by a mutation in the -globin gene. c. It is caused by an amino acid substitution in the F helix. d. It results in a hemoglobin that contains a hydrophobic amino acid on the surface.

ANS: D DIF: Easy REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Understanding 36. Which of the following may result from a His143 a. decreased CO2 transport efficiency b. increased oxygen transport efficiency c. reduced affinity for 2,3-BPG d. sickle cell anemia

Ala143 mutation in adult hemoglobin?

ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.h. Identify structural differences between adult and fetal hemoglobin that affect 2,3-BPG association. MSC: Applying 37. Using the oxygen binding curve shown, calculate the approximate percentage of O2 that is released from hemoglobin as the pO2 changes from 13 kPa to 4 kPa.

a. b. c. d.

4% 9% 60% 91%

ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Analyzing 38. A molecule is found to be able to diffuse across a membrane. Which of the following characteristics would best describe this molecule? a. hydrophilic b. hydrophobic c. neutral d. polar ANS: B DIF: Easy REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Understanding 39. What type of transport is depicted in the figure below?

a. membrane diffusion b. passive transport of molecules down a concentration gradient

c. active transport of molecules down a concentration gradient d. active transport of molecules up a concentration gradient ANS: B DIF: Medium REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Understanding 40. The translocation rate of a solute across a membrane is measured. A plot of translocation rate versus solute concentration displays a hyperbolic curve. The translation a. could be occurring through a passive transport channel. b. could be occurring by diffusion. c. could be occurring through a passive transport carrier. d. must require an input of energy.

ANS: C DIF: Medium REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Analyzing 41. Consider a system where a passive transport channel is available for a neutral molecule X. If RTln(C2/C1) is zero, then a. no net transport will occur. b. the molecule will move from the area where the concentration is C2 to the area where the concentration is C1. c. the molecule will move from the area where the concentration is C1 to the area where the concentration is C2. d. There is no way to determine if or how transport of X will occur given the information provided.

ANS: A DIF: Difficult REF: 6.3 OBJ: 6.3.c. Evaluate the free energy of passive and active transport.

MSC: Applying 42. Passive membrane transporters CANNOT a. be small peptides. b. contain -sheets. c. contain -helices. d. contain only hydrophobic amino acids.

ANS: D DIF: Easy REF: 6.4 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane transport.

MSC: Remembering 43. Gramicidin A is involved in the __________ transport of __________ charged ions. a. active; positively b. active; negatively c. passive; positively d. passive; negatively ANS: C DIF: Easy REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Remembering 44. Which of the following accounts for some of the specificity of the K+ channel? a. The radius of solvated Na+ is smaller than the radius of solvated K+. b. The number of -strands that make up the channel.

c. The orientation of backbone carbonyl oxygen atoms in the channel. d. Alternating positive and negative amino acids in the channel pore.

ANS: C DIF: Medium REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Understanding 45. As K+ passes through the selectivity filter of the K+ channel of Streptomyces lividans it interacts with a. glycine side chains. b. amino acid carbonyl groups. c. tyrosine side chains. d. amino acid amino groups.

ANS: B DIF: Easy REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Remembering 46. In studying a transporter, it is found that no external energy input is needed to facilitate the movement of a neutral compound through the transporter. The translocation rate of the compound reaches a plateau at high levels of compound. It is a(n) a. passive transport channel. b. passive transport carrier. c. active transport channel. d. active transport carrier.

ANS: B DIF: Medium REF: 6.3 OBJ: 6.3.a. Differentiate between carriers and channels.

MSC: Applying

47. Consider the transport scenario shown. Which curve represents the overall movement of the small molecule from the extracellular environment to the cytosol?

a.

b.

c.

d.

ANS: C DIF: Difficult REF: 6.3 OBJ: 6.3.a. Differentiate between carriers and channels.

MSC: Evaluating

48. The selectivity of aquaporin for H2O relies on all EXCEPT which of the following? a. hydrogen bonding to Asn b. a 2.8 Å constriction point within the protein c. inverted -helix dipoles d. electrostatic repulsion from Asn ANS: D DIF: Medium REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Understanding 49. Which is true of the K+ channel but NOT of an aquaporin? a. Selectivity is achieved through interactions with backbone NH groups. b. It contains -helices. c. It is an active transporter. d. Selectivity is assisted through inverted -helix dipoles.

ANS: A DIF: Medium REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Analyzing 50. The E. coli maltoporin protein, but NOT the A. lividans K+ channel protein, a. is a homotetramer. b. contains mostly -helices. c. is a passive transporter.

d. uses transport dependent on interaction with amino acid side chains.

ANS: D DIF: Medium REF: 6.3 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane transport.

MSC: Analyzing 51. The transport system shown below is a(n)

a. b. c. d.

secondary active symporter. primary active transporter. secondary active antiporter.

ABC transporter.

ANS: A DIF: Easy REF: 6.3 OBJ: 6.3.f. Distinguish between primary and secondary active transporters.

MSC: Understanding 52. Which of the following is a pharmaceutical drug that targets an active transporter? a. sertraline b. malate c. gramicidin A d. 2,3-BPG ANS: A DIF: Easy REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Remembering 53. As 18 Na+ ions are exported out of the cell by the Na+-K+ ATPase membrane transport protein, __________ K+ ions are imported into the cell. a. 2 b. 12 c. 18 d. 24 ANS: B DIF: Easy REF: 6.3 OBJ: 6.3.g. Distinguish between antiporters and symporters.

MSC: Understanding

54. A cell with a membrane potential of −70 mV that contains functioning Na+-K+ ATPase membrane transport proteins will maintain an extracellular __________ concentration that is __________ than the intracellular __________ concentration. a. Na+; lower; K+ b. Na+; lower; Na+ c. K+; higher; Na+ d. K+; lower; K+

ANS: D DIF: Medium REF: 6.3 OBJ: 6.3.g. Distinguish between antiporters and symporters.

MSC: Remembering

55. The mutation that would lead to the most dramatic effect on Ca2+ transport is a mutation of a. Ser16 in phospholamban. b. Thr17 in phospholamban. c. Asp351 in SERCA. d. Ser17 in E2P. ANS: C DIF: Medium REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Applying 56. Which of the following is NOT an ABC transporter? a. cystic fibrosis transmembrane conductance regulator protein b. SERCA c. multidrug resistance protein d. maltose transporter from E. coli ANS: B DIF: Easy REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Remembering 57. Primary active ABC transporters and P-type transporters both require a. a conformational change to function. b. two ATP binding half-sites. c. solutes that move down their concentration gradients through the transporter. d. removal of inhibitory subunits to function.

ANS: A DIF: Medium REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Analyzing 58. The lactose permease from E. coli and the molybdate transporter from Archaeoglobus fulgidus both a. drive transport through the hydrolysis of ATP. b. drive transport through the use of a concentration gradient. c. undergo a conformational change that occurs on substrate binding. d. contain a selectivity filter.

ANS: C DIF: Medium REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Understanding 59. What might be the effect on the transport of lactose into the cytosol of E. coli if a drug is added that allows H+ to freely pass through the inner bacterial membrane? a. There would be no effect. b. Lactose transport would increase. c. Lactose transport would cease. d. Lactose would be transported out of the cytosol and into the periplasm.

ANS: C DIF: Medium REF: 6.3 OBJ: 6.3.f. Distinguish between primary and secondary active transporters.

MSC: Applying

60. Which of the following is NOT considered part of the thin filament? a. actin b. myosin c. troponin d. tropomyosin ANS: B DIF: Easy REF: 6.4 OBJ: 6.4.c. List the major proteins found in the sarcomere and Z disk.

MSC: Remembering 61. Titin functions to connect __________ to __________. a. myosin proteins; Z-disk proteins b. myosin proteins; thin filament proteins c. actin proteins; Z-disk proteins d. myosin proteins; tropomyosin ANS: A DIF: Easy REF: 6.4 OBJ: 6.4.c. List the major proteins found in the sarcomere and Z disk.

MSC: Understanding 62. When ATP binds to myosin, a. the troponin binding sites are exposed. b. it cannot interact with actin. c. the power stroke occurs. d. the actin nucleotide binding sites are exposed.

ANS: B DIF: Easy REF: 6.4 OBJ: 6.4.e. Restate the five steps in the actin-myosin reaction cycle.

MSC: Remembering 63. The sarcomere length of isolated heart myoblasts can be measured over time in the laboratory. The myoblasts are maintained in a buffer during the experiment. In a control experiment, Ca2+ and ATP are added to the buffer and the change in sarcomere length is analyzed. If EDTA, a chelating agent that sequesters Ca2+, was included in the buffer, the length change would be __________ compared with a control experiment without EDTA. a. smaller b. greater c. the same d. There is no way to determine the result given the information provided.

ANS: A DIF: Difficult REF: 6.4 OBJ: 6.4.d. Explain the role of Ca2+ in muscle contraction.

MSC: Applying

64. If SERCA is not functioning in a myoblast, which of the following may occur? a. Myosin will not undergo the conformational change that results in the power stroke. b. Myosin will not be able to bind to the thin filament. c. The myofibrils can shorten but not lengthen. d. The myofibrils can lengthen but not shorten.

ANS: C DIF: Medium REF: 6.4 OBJ: 6.4.d. Explain the role of Ca2+ in muscle contraction.

MSC: Applying

65. After __________ induced changes in the structure of thin filament, myosin heads containing __________ in the nucleotide binding site will bind with high affinity to actin subunits. a. ATP; ADP + Pi

b. ATP; Ca2+ c. Ca2+; ATP d. Ca2+; ADP + Pi ANS: D DIF: Easy REF: 6.4 OBJ: 6.4.e. Restate the five steps in the actin-myosin reaction cycle.

MSC: Remembering 66. Consider the following interaction between a protein and its ligand: [P] + [L] Which equation describes the dissociation constant of this interaction? a. [PL] / [P][L] b. [P][L] / [PL] c. [PL] / [P] d. [PL][P] / [L]

[PL].

ANS: B DIF: Easy REF: 6.2 OBJ: 6.2.c. Differentiate between an association constant and a dissociation constant.

MSC: Remembering 67. An oxygen binding curve of fractional saturation versus pO2 displays a sigmoidal shape. This is the oxygen binding curve for a. myoglobin. b. hemoglobin that has been dissociated into individual subunits. c. hemoglobin in the presence of 2,3-BPG. d. myoglobin in the presence of 2,3-BPG. ANS: C DIF: Medium REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Applying 68. Consider an oxygen binding curve for hemoglobin at pH 7.4. The binding curve would shift __________ if the pH is reduced to 7.2. a. to the right b. to the left c. up d. down ANS: A DIF: Medium REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Applying 69. Which of the following would shift the oxygen binding curve for hemoglobin to the left? a. a lower concentration of CO2 b. a higher pH c. a higher concentration of 2,3-BPG d. an increase in the number of hemoglobin molecules in the T state ANS: B DIF: Difficult REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Analyzing 70. Which of the following is NOT a definition of fractional saturation for a system of [P] +[L] [PL]? a. [PL] / [PL] + [P] b. [PL] + [P] / [PL]

c. [L] / [L] + Kd d. occupied binding sites / total binding sites ANS: B DIF: Medium REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Understanding 71. Which of the following statements is true of the data shown below?

a. b. c. d.

The binding of ligand to protein B follows the Bohr effect.

Both proteins display cooperative binding.

Protein A has a higher Kd for the ligand than protein B. Protein B and protein A bind to the same ligand.

ANS: D DIF: Medium REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Applying 72. Based on the data shown below, the Kd for protein A is __________ the Kd for protein B.

a. b. c. d.

equal to approximately 50% greater than six times lower than six times higher than

ANS: C DIF: Difficult REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Analyzing 73. A protein displays allosteric regulation. Which of the following is true? a. Each subunit is either in the T state or the R state, but does not switch from one state to the other.

b. Each subunit can exist in more than one conformation. c. When the protein binds to a positive allosteric effector, the subunits are more likely to be in the T state. d. A subunit must be in the R state in order to bind ligand.

ANS: B DIF: Medium REF: 6.2 OBJ: 6.2.f. Differentiate between the concerted model and the sequential model.

MSC: Understanding 74. A mutation in the subunit of hemoglobin is discovered that reduces the affinity of 2,3-BPG binding. Which of the following mutations is most likely to have this consequence? a. Val1 Ile1 b. Asp99 Glu99 c. Lys82 Asp82 d. Glu6 Val6 ANS: C DIF: Difficult REF: 6.2 OBJ: 6.2.h. Identify structural differences between adult and fetal hemoglobin that affect 2,3-BPG association. MSC: Evaluating 75. Passive transporter proteins allow molecules to move across a membrane in response to a. chemical gradients. b. ADP/ATP ratio. c. ATP/ADP ratio. d. activated signal transduction pathways.

ANS: A DIF: Easy REF: 6.1 OBJ: 6.1.b. Identify the two basic classes of membrane transport proteins.

MSC: Remembering 76. Which of the following is NOT a passive transporter protein? a. porin b. Cl− channel c. Ca2+-ATPase transporter protein d. Ca2+ channel ANS: C DIF: Easy REF: 6.1 OBJ: 6.1.b. Identify the two basic classes of membrane transport proteins.

MSC: Remembering 77. A myoblast contain(s) __________, but a myofibril does not. a. actin b. many nuclei c. myosin d. many sarcomeres ANS: B DIF: Easy REF: 6.4 OBJ: 6.4.a. Define myoblasts and myofibrils.

78. Thin filaments __________, but thick filaments do/are not. a. contain myosin b. are directly attached to the Z disk c. are part of the sarcomere d. are part of the A band ANS: B

DIF: Easy

REF: 6.4

MSC: Understanding

OBJ: 6.4.b. Distinguish between thick and thin filaments.

MSC: Remembering

SHORT ANSWER 1. Fetal and adult hemoglobin have different affinities for 2,3-BPG. Predict if O2 transport from maternal cells to fetal cells will be altered from the normal rate if the subunit of the fetal red blood cells have a Ser143 His143 mutation. Include the term T state in your answer.

ANS: When the fetal subunit contains Ser143 it has lower affinity for 2,3-BPG. 2,3-BPG binding stabilizes the T state. If Ser143 is replaced by His143 the affinity for 2,3-BPG will be the same as for adult hemoglobin, which contains His143. The affinities for both hemoglobins will be similar and O2 transport from maternal cells to fetal cells will be reduced.

DIF: Difficult REF: 6.2 OBJ: 6.2.h. Identify structural differences between adult and fetal hemoglobin that affect 2,3-BPG association. MSC: Applying 2. A newly discovered transporter protein is being investigated using an assay to determine whether transport has occurred in the cells. A nonhydrolyzable form of ATP is added to the cells, and it is found that transport is reduced. Explain these results.

ANS: The transporter protein must be involved in active transport. When ATP is added but cannot be hydrolyzed, the active transport protein is unable to function, leading to reduced transport.

DIF: Medium REF: 6.1 OBJ: 6.1.b. Identify the two basic classes of membrane transport proteins.

MSC: Applying 3. An E. coli strain is discovered that has a mutation in the gene encoding RecBCD. The mutation causes RecBCD to not function as effectively as the wild-type RecBCD. Hypothesize how the growth rate of this strain would compare with that of the wild type.

ANS: RecBCD is a genomic caretaker protein. It functions to unwind the DNA double strand to allow access for the binding of RecA, which mediates DNA repair and recombination. If RecBCD is not functioning as efficiently, then DNA repair would also be less efficient. This would likely lead to a reduction in fitness and growth rate.

DIF: Difficult REF: 6.1 OBJ: 6.1.d. Identify the two major classes of genomic caretaker proteins.

MSC: Evaluating 4. Describe the two functional units of myoglobin that are responsible for O2 binding. Include the type of chemical bond involved for each binding interaction (i.e., hydrogen bond, covalent bond, electrostatic bond, etc.).

ANS: His E7 (distal histidine) binds to O2 through a hydrogen bond. The iron (Fe) of the heme group binds to O2 by a covalent bond.

DIF: Medium

REF: 6.2

OBJ: 6.2.b. Analyze the structural changes that occur when oxygen binds to the heme group.

MSC: Applying 5. Using the following data, arrange the proteins in order from the one having the lowest affinity for the ligand to the highest.

Protein Q R S T

Kd (mM) 0.3 1.2 0.087 1.15

ANS: R, T, Q, S DIF: Medium REF: 6.2 OBJ: 6.2.c. Differentiate between an association constant and a dissociation constant.

MSC: Evaluating 6. Given the following concentrations, what is ? [Mb] = 0.07, [MbO2] = 0.69, [O2] = 3.5 kPa ANS: 0.9

DIF: Difficult REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Applying 7. A new protein has been discovered that may be allosterically regulated. The protein is purified and analyzed by SDS-PAGE followed by staining with Coomassie blue. A single band at 42 kDa is seen on the gel. Explain how these data may or may not support the belief that the protein is an allosterically regulated protein. If they do support an allosterically regulated protein, propose the most likely model of allostery followed by the protein.

ANS: These data do not support the belief that the protein is allosteric. Allosteric proteins must have quaternary structure. SDS-PAGE disrupts quaternary structure. The fact that a single band appeared on the gel does not indicate if the protein initially had quaternary structure. It may, but the subunits would be of the same molecular weight.

DIF: Difficult REF: 6.2 OBJ: 6.2.f. Differentiate between the concerted model and the sequential model.

MSC: Evaluating 8. The figure below shows the oxygen binding curves of oxygen-transport protein from four different organisms. Decide which organism is the most efficient at oxygen transport and justify your choice.

ANS: Organism D is the most efficient at oxygen transport because the difference in fractional saturation between the oxygen concentrations in the lungs versus the muscle is the greatest.

DIF: Difficult REF: 6.2 OBJ: 6.2.e. Compare and contrast oxygen binding curves for myoglobin and hemoglobin.

MSC: Evaluating 9. Look at the data in the figure below. One amino acid location is indicated by an arrow. Why is the amino acid at that location invariant among the three sequences?

ANS: This is the F8 histidine. It is responsible for coordinating the iron in the heme. It is conserved because it is required for O2 binding.

DIF: Difficult REF: 6.2 OBJ: 6.2.i. Compare the sequences of the human globins to understand the paralogous nature of their genes.

MSC: Understanding

10. What is the clinical term for reduced O2 transport efficiency from the lungs to the tissues, arising from altered hemoglobin function or reduced numbers of red blood cells per unit of blood? Provide an example of a specific type of anemia that is caused by a single point mutation.

ANS: Anemia; sickle cell anemia DIF: Easy REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Remembering 11. An increase in sickle cell disease symptoms can occur when a person with the disease is at higher altitudes. Hypothesize how allosteric regulation at high altitudes may be related to sickle cell anemia.

ANS: At high altitudes, more 2,3-bisphosphoglycerate (2,3-BPG) is made. 2,3-BPA is a negative allosteric effector of hemoglobin. It stabilizes the T state of hemoglobin. In the T state, HbS polymer formation is higher than in the R state.

DIF: Difficult REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Evaluating 12. What role do

S-Phe85 and

ANS: They interact with hemoglobin.

S

-Leu88 play in sickle cell anemia?

S-Val6 in another hemoglobin tetramer, which results in polymerization of the

DIF: Medium REF: 6.2 OBJ: 6.2.j. Identify the mutation and resulting structural change in HbS that produces sickle cell anemia.

MSC: Understanding 13. What is required for the transport of a molecule by an active transporter that is not necessary for a molecule to be transported by a passive transporter?

ANS: Energy DIF: Easy REF: 6.3 OBJ: 6.3.b. Differentiate among diffusion, passive transport, and active transport.

MSC: Understanding 14. Consider the movement of glucose into a cell by passive transport. If the extracellular concentration of glucose is 4 mM and the intracellular concentration of glucose is 2 mM, what is the free energy of transport in kJ/mol?

ANS: −1.794

DIF: Medium REF: 6.3 OBJ: 6.3.c. Evaluate the free energy of passive and active transport.

MSC: Applying 15. The E. coli maltoporin protein is a homotrimeric porin complex. A related protein is found in another bacterial species that does not form trimers but rather functions as a monomer. A comparison of the amino acid composition of a maltoporin subunit and the new porin showed similar ratios of hydrophobic/hydrophilic amino acids for the two proteins. Explain how this can be the case.

ANS: The porins are embedded in the membrane. For the trimer, the exterior of each subunit is hydrophobic in the regions interacting with the membrane as well as the regions interacting with the other subunits. For the monomer, the exterior is still hydrophobic because it needs to interact with the membrane.

DIF: Difficult REF: 6.3 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane transport.

MSC: Analyzing 16. Consider the movement of fructose into a cell by passive transport. If the extracellular concentration of fructose is 0.35 mM and the intracellular concentration of fructose is 0.42 mM, what is the free energy of transport in kJ/mol?

ANS: −0.47

DIF: Medium REF: 6.3 OBJ: 6.3.c. Evaluate the free energy of passive and active transport.

MSC: Applying 17. A passive transporter is discovered that can transport both galactose and glucose. The pore of the transporter can accommodate a single sugar at a time. If the extracellular concentrations of galactose and glucose are 0.2 and 3.6 mM, respectively, and the intracellular concentrations are 0.39 and 2.6 mM, respectively, which sugar is most likely to enter the cell through the transporter?

Provide two reasons for your answer.

ANS: Glucose is most likely to enter the cell through the transporter. First, it is at a higher overall concentration and is more likely to randomly interact with the transporter. Second, the free energy of transport for glucose is less than zero, whereas that for galactose is more than zero.

DIF: Medium

REF: 6.4

OBJ: 6.3.c. Evaluate the free energy of passive and active transport.

MSC: Analyzing 18. Explain how the five arginine residues found within the channel of Omp32 protein of the bacterium Delftia acidovorans increase the specificity of the channel.

ANS: The arginine residues are negatively charged. They line the interior of the channel and facilitate the movement of a positive molecule (malate) through the channel. They repel negatively charged molecules that attempt to enter the channel.

DIF: Medium REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Understanding 19. Using the data shown, list the porins from the most selective to the least selective.

ANS: A, D, C, B DIF: Medium REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Analyzing 20. There are two main structural differences between a typical -helix and the helix formed by gramicidin A. Describe the two structural differences and choose which structural characteristic is more important in the function of gramicidin A. Explain your choice.

ANS: A typical -helix is left handed and has a tightly packed center. The helix of gramicidin A is right handed and has a wider diameter leading to a channel within the helix. The width is more important in the function of gramicidin A because it allows for the channel through which the ions can pass.

DIF: Medium REF: 6.3 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane transport.

MSC: Analyzing 21. Predict the effect on Na+ transport through gramicidin A if the helical structure took on the conformation of a true -helix.

ANS: Na+ would no longer be transported because the helix would have a tightly packed center that would not allow the ion to enter.

DIF: Medium REF: 6.3 OBJ: 6.3.d. Distinguish between beta-barrel and alpha-helical structures used for membrane

transport.

MSC: Applying

22. Decide if the rate of malate transport by the Omp32 protein of Delftia acidovorans will be affected if the pH of the system is changed from 6.8 to 8.2. Explain your reasoning.

The pKa of amino acids with ionizable side chains are provided in the table below. Note that malic acid contains two ionizable groups with pKa of 3.40 and 5.20. Assume in this scenario that the pH change does not alter the overall conformation of the protein.

ANS: The rate will not be changed significantly because malate will remain negatively charged and the arginine groups in the porin channel will remain positively charged in this pH range.

DIF: Difficult REF: 6.3 OBJ: 6.3.e. Identify amino acid residues in transport proteins that give rise to selectivity.

MSC: Evaluating 23. You design an experiment in which you can monitor the step-by-step movement of H+ and Ca2+ through the SERCA protein, starting with the protein in the E2-ATP state and moving through the transport cycle, ultimately returning to the E2-ATP state. Your control experiment includes everything required for the system to function normally, and you easily detect four distinct conformations of the protein. You then replace the ATP in the system with ATP S, a nonhydrolyzable form of ATP, and begin the experiment again with the protein in the E2-ATP state. Predict which conformations of SERCA you will detect.

ANS: Only the E2-ATP conformation will be detected. The SERCA protein will bind the non-hydrolyzable form of ATP but cannot hydrolyze it, a requirement for the release of H+ and binding of Ca2+ in the transmembrane helices.

DIF: Difficult REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Applying 24. Phospholamban contains two phosphorylation sites, Ser16 and Thr17. Compare and contrast what directs the phosphorylation at each site and the resulting changes in activity of phospholamban.

ANS: Ser16 is phosphorylated by protein kinase A, which is activated by epinephrine. Ser17 is phosphorylated by Ca2+/calmodulin kinase II, which is activated by high levels of cytosolic Ca2+.

Both phosphorylations stop the inhibitory activity of phospholamban, leading to the activation of SERCA. DIF: Medium REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Analyzing 25. Both SERCA and the Na+-K+ ATPase contain a P domain. Explain the general function of this domain.

ANS: The P domain contains an amino acid that becomes phosphorylated. Phosphorylation leads to activation of the protein through a conformational change.

DIF: Easy REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Understanding 26. Explain how a mutation in Asp351 of SERCA might alter Ca2+ transport.

ANS: Phosphorylation of Asp351 is required for SERCA to function as a Ca2+ transporter. If Asp351 is mutated, SERCA would become inactive and Ca2+ transport would stop.

DIF: Easy REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Understanding 27. Propose how the addition of an inhibitor of the permeability glycoprotein transporter to a chemotherapy drug regimen would alter the effectiveness of the regimen.

ANS: The permeability glycoprotein transporter, also known as the multidrug resistance protein, functions to remove toxic compounds from a cell. Cancer cells can use this protein to export chemotherapy drugs. Addition of an inhibitor would result in more of the chemotherapy drugs to remain in the cancer cells, leading to a more effective regimen.

DIF: Difficult REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Evaluating 28. Complete the following bacterial ABC transporter protein process: 1. Binding of substrate carrier protein induces a conformational change to expose the substrate binding site.

2. ATP hydrolysis causes a conformational change that releases substrate.

3.

ANS: Release of ADP + Pi and binding of ATP resets the transporter.

DIF: Medium REF: 6.3 OBJ: 6.3.h. Compare and contrast P-type transporters with ABC transporters.

MSC: Applying 29. Explain why ABC transporters are channels and not carriers.

ANS: ABC transporters undergo large conformational changes, driven by the hydrolysis of ATP. DIF: Easy REF: 6.3 channels.

MSC: Understanding

OBJ: 6.3.a. Differentiate between carriers and

30. Radioactive iodine can be used in laboratory settings to label inhibitors. When working in a lab, a researcher is exposed to the radioactive iodine when some accidentally spills on her exposed wrist.

A scan with a Geiger counter the next day indicates that most of the radioactivity is located in her neck. Predict how this localization occurred and include any transporters that may be involved.

ANS: Iodine is concentrated in the thyroid, which is located in the neck. The iodine is brought in through the Na+-I− symporter. This is a secondary transporter that relies on the Na+ gradient that is established by the Na+-K+ ATPase primary active transporter.

DIF: Difficult REF: 6.3 OBJ: 6.3.f. Distinguish between primary and secondary active transporters.

MSC: Applying 31. Label the structures marked in this diagram of a sarcomere.

ANS: A is a thick filament; B is a thin filament.

DIF: Easy REF: 6.4 OBJ: 6.4.b. Distinguish between thick and thin filaments.

MSC: Remembering

32. Articulate the difference between a myoblast and a myofibril.

ANS: A myoblast is a large fused cell that contains many nuclei and shares a common plasma membrane (sarcolemma). Myofibrils are found inside myoblasts and bundles of fibers made up primarily of myosin and actin.

DIF: Easy MSC: Applying

REF: 6.4

OBJ: 6.4.a. Define myoblasts and myofibrils.

33. Construct a complete actin-myosin reaction cycle by placing the following steps in order, starting with Ca2+ binding to troponin: A. ADP release empties the nucleotide binding site in myosin.

B. Pi release induces the power stroke.

C. ATP hydrolysis induces the recovery conformation.

D. ATP binding causes myosin to dissociate from actin.

ANS: B, A, D, C DIF: Medium REF: 6.4 OBJ: 6.4.e. Restate the five steps in the actin-myosin reaction cycle.

MSC: Applying 34. Explain the relationship between P50 of oxygen binding and Kd for oxygen binding to myoglobin.

ANS: P50 is the amount of oxygen bound when half of the oxygen binding sites are saturated. It is the partial pressure of oxygen that results in a fractional saturation value of 0.5. In any ligand-binding system, the concentration of ligand required to reach a fractional saturation value of 0.5 is the Kd. In essence, the P50 is the Kd for oxygen binding to myoglobin, but because O2 is a gas the concentration is given as a partial pressure in pascals (Pa).

DIF: Difficult REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Analyzing 35. In the shift from the T to the R state in adult hemoglobin, a shift between the subunits occurs.

Explain how this shift leads to the variation of binding affinity for 2,3-BPG in the two states.

ANS: The shift from the T state to the R state makes the central cavity between the four subunits smaller.

2,3-BPG cannot bind as well to the smaller cavity, which is why there is a lower affinity for 2,3-BPG when the hemoglobin subunits are in the R state.

DIF: Medium REF: 6.2 OBJ: 6.2.h. Identify structural differences between adult and fetal hemoglobin that affect 2,3-BPG association. MSC: Understanding 36. Given the following data for myoglobin and O2 concentrations, what is  Mb] = 0.07 mM, [MbO2] = 0.69 mM, [O2] = 3.5 kPa. ANS:

0.9

DIF: Difficult REF: 6.2 OBJ: 6.2.d. Express fractional saturation of hemoglobin or myoglobin as a function of oxygen concentration.

MSC: Applying

Chapter 7: Enzyme Mechanisms MULTIPLE CHOICE 1. Binding of glucose to hexokinase causes a conformational change in the enzyme. This is an example of the __________ model of enzyme catalysis. a. substrate-induced b. lock and key c. induced-fit d. glove and hand ANS: C DIF: Easy REF: 7.1 OBJ: 7.1.a. Distinguish between the lock and key model and the induced-fit model.

MSC: Understanding 2. Which of the following is true of the induced-fit model of enzyme catalysis but NOT of the lock and key model of enzyme catalysis? a. It was proposed by Emil Fischer. b. It involves weak interactions of a substrate with an enzyme. c. It involves a conformational change of the enzyme. d. It involves noncovalent interactions of the substrate with the enzyme.

ANS: C DIF: Easy REF: 7.1 OBJ: 7.1.a. Distinguish between the lock and key model and the induced-fit model.

MSC: Understanding 3. Enzymes usually bind substrates with __________ affinity and __________ specificity. a. high; high. b. high; low c. low; low d. low; high ANS: A DIF: Easy REF: 7.1 OBJ: 7.1.b. List three critical aspects of enzyme structure and function.

MSC: Remembering 4. Enzyme active sites a. are nonspecific. b. are a pocket or cleft. c. always exclude water. d. can only bind a single substrate at a time.

ANS: B DIF: Medium REF: 7.1 OBJ: 7.1.b. List three critical aspects of enzyme structure and function.

MSC: Understanding 5. What is the rate enhancement as a result of the presence of an enzyme if the uncatalyzed rate of the reaction is 1.2 102 mmol/sec and the catalyzed rate is 2.4 104 mmol/sec? a. 0.005 b. 200 c. 2.88 106 d. 2 ANS: B

DIF: Medium

REF: 7.1

OBJ: 7.1.c. Restate Henry Eyring’s transition state theory.

MSC: Applying

6. The transition state of a reaction is a. higher in free energy than the product. b. lower in free energy than the ground state of the substrate. c. easily isolated. d. equal to the G‡ of the uncatalyzed reaction minus the G‡ of the catalyzed reaction.

ANS: A DIF: Medium REF: 7.1 OBJ: 7.1.c. Restate Henry Eyring’s transition state theory.

MSC: Understanding

7. Consider the reaction coordinate diagram shown below. X is __________; Y is __________.

a. transition state; activation energy b. G‡ of catalyzed reaction; transition state c. activation energy of catalyzed reaction; transition state d. G‡ of uncatalyzed reaction; transition state ANS: D DIF: Medium REF: 7.1 OBJ: 7.1.d. Illustrate the energetic advantage of a catalyst with a reaction coordinate diagram.

MSC: Understanding 8. Which of the following is a holoenzyme? a. pyruvate kinase with a bound K+ b. alcohol dehydrogenase c. nitrite reductase d. hexokinase ANS: A DIF: Medium REF: 7.1 OBJ: 7.1.e. Differentiate between an apoenzyme and a holoenzyme.

MSC: Applying 9. Nitrite reductase contains two histidine amino acids that coordinate a Cu2+ ion. When the ion is present in the enzyme, the ion is a __________ and the enzyme is a __________. a. cofactor; apoenzyme b. cofactor; holoenzyme c. coenzyme; apoenzyme d. coenzyme; holoenzyme

ANS: B DIF: Medium REF: 7.1 OBJ: 7.1.e. Differentiate between an apoenzyme and a holoenzyme.

MSC: Understanding 10. Which of the following is a prosthetic group? a. Mg2+ b. NADH c. Zn2+ d. heme ANS: D DIF: Easy REF: 7.1 OBJ: 7.1.f. Define cofactors, coenzymes, and prosthetic groups.

MSC: Remembering 11. The dihydrolipoyl transacetylase enzyme contains a lipoyl group. The lipoyl group is a(n) a. ion. b. apoenzyme. c. prosthetic group. d. holo group.

ANS: C DIF: Easy REF: 7.1 OBJ: 7.1.f. Define cofactors, coenzymes, and prosthetic groups.

MSC: Remembering 12. Which of the following is true of a coenzyme but NOT true of a prosthetic group? a. It contains an organic component. b. It is loosely associated with the enzyme. c. It is necessary for enzyme function. d. It is present in a holoenzyme but not an apoenzyme.

ANS: B DIF: Medium REF: 7.1 OBJ: 7.1.f. Define cofactors, coenzymes, and prosthetic groups.

MSC: Analyzing 13. Hexokinase catalyzes the phosphorylation of glucose to glucose 6-phosphate. Hexokinase belongs to which enzyme class? a. transferase b. ligase c. oxidoreductase d. hydrolase ANS: A DIF: Easy REF: 7.1 OBJ: 7.1.g. List the six enzyme classes and describe the type of reaction each catalyzes.

MSC: Remembering 14. Which answer correctly pairs the enzyme class with the type of reaction catalyzed? a. lyase; formation of two products by hydrolyzing a substrate b. transferase; transfer of H or O atoms c. isomerase; intramolecular rearrangements d. oxidoreductase; transfer of groups within molecules ANS: C DIF: Medium REF: 7.1 OBJ: 7.1.g. List the six enzyme classes and describe the type of reaction each catalyzes.

MSC: Analyzing

15. An enzyme that requires the coenzyme nicotinamide adenine dinucleotide belongs to which enzyme class? a. transferases b. isomerases c. ligases d. oxidoreductases ANS: D DIF: Difficult REF: 7.1 OBJ: 7.1.g. List the six enzyme classes and describe the type of reaction each catalyzes.

MSC: Understanding 16. An enzyme can increase the rate of a reaction inside a cell by __________ the energy of the __________. a. lowering; transition state b. increasing; product c. lowering; substrate d. increasing; transition state ANS: A DIF: Easy REF: 7.2 OBJ: 7.2.a. List three major ways that enzymes increase the rate of a reaction.

MSC: Remembering 17. A reaction coordinate diagram comparing an uncatalyzed reaction with an enzyme-catalyzed reaction can directly illustrate that the enzyme __________, but will not directly illustrate that the enzyme __________. a. orients the substrates appropriately for the reaction to occur; provides an alternative path for product formation b. provides an alternative path for product formation; stabilizes the transition state c. stabilizes the transition state; orients the substrates appropriately for the reaction to occur d. stabilizes the transition state; provides an alternative path for product formation ANS: C DIF: Difficult REF: 7.2 OBJ: 7.2.a. List three major ways that enzymes increase the rate of a reaction.

MSC: Analyzing 18. Which of the following is a way that an enzyme can increase the rate of a reaction inside a cell? a. increasing the temperature of the cell b. increasing the pressure inside the cell c. increasing the substrate concentration inside the cell d. orienting substrates appropriately for the reaction to occur ANS: D DIF: Easy REF: 7.2 OBJ: 7.2.a. List three major ways that enzymes increase the rate of a reaction.

MSC: Remembering 19. Below is a ribbon diagram of an enzyme. Four regions of the enzyme are indicated. Which is most likely the active site?

a. b. c. d.

A B C D

ANS: A DIF: Medium REF: 7.2 OBJ: 7.2.b. State the ways that an enzyme active site creates a microenvironment.

MSC: Analyzing 20. A mutation of Lys229 in aldolase leads to a loss of enzyme activity. This is most likely because the a. active site can no longer exclude water. b. active site can no longer include water. c. enzyme can no longer hold the intermediate in the correct orientation for catalysis. d. product will remain bound to the enzyme active site.

ANS: C DIF: Difficult REF: 7.2 OBJ: 7.2.b. State the ways that an enzyme active site creates a microenvironment.

MSC: Analyzing 21. Refer to the reaction coordinate diagram below. At what point is there a maximum number of interactions between the enzyme and the compound that it is binding?

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 7.2 OBJ: 7.2.c. Illustrate the stabilization of a transition state with a reaction coordinate diagram.

MSC: Analyzing 22. Refer to the reaction coordinate diagram below. The change in the activation energy of the reaction because of the presence of an enzyme is illustrated by the energy of __________ minus the energy of __________.

a. b. c. d.

B; A B; C B; D C; D

ANS: B DIF: Medium REF: 7.2 OBJ: 7.2.c. Illustrate the stabilization of a transition state with a reaction coordinate diagram.

MSC: Applying 23. Enzymes from four different species catalyze the same reaction. Based on the reaction coordinate diagrams below, which species contains an enzyme that experiences more bonding interactions with the transition state of the reaction?

a. b. c. d.

species A species B species C species D

ANS: A DIF: Difficult REF: 7.2 OBJ: 7.2.c. Illustrate the stabilization of a transition state with a reaction coordinate diagram.

MSC: Analyzing 24. The conversion of L-proline to D-proline is shown below. Which of the following characteristics would most likely be found in a transition state analog that inhibits an enzyme that catalyzes the reaction?

a. b. c. d.

planar positively charged at the -carbon tetrahedral geometry at the -carbon double bonds within the ring

ANS: A DIF: Medium REF: 7.2 OBJ: 7.2.d. Differentiate between the transition state and a transition state analog.

MSC: Applying 25. Many medicinal drugs are transition state analogs. They are good drugs because they can interact with the target enzyme active site and are a. higher in energy than the transition state. b. identical in structure to the transition state. c. stable.

d. polar.

ANS: C DIF: Medium REF: 7.2 OBJ: 7.2.d. Differentiate between the transition state and a transition state analog.

MSC: Applying 26. Reaction coordinate diagrams clearly show that the energy of an enzyme bound to a transition state is higher than the energies of the E + S, E + P, and ES that occur along the same reaction coordinate. The energy of an enzyme bound to a transition state analog would lie __________ in the diagram. a. above the E + S but below the transition state b. below the E + S c. above the transition state d. above E + S but below ES ANS: B DIF: Medium REF: 7.2 OBJ: 7.2.d. Differentiate between the transition state and a transition state analog.

MSC: Analyzing 27. All of the following are common catalytic reaction mechanisms in enzyme active sites EXCEPT __________ catalysis. a. acid–base b. covalent c. metal ion d. van der Waals ANS: D DIF: Easy REF: 7.2 OBJ: 7.2.e. List the three most common reaction mechanisms in enzyme active sites.

MSC: Remembering 28. If an enzyme carries out acid–base catalysis, which of the following amino acids could act as general acid? a. phenylalanine b. glycine c. histidine d. alanine ANS: C DIF: Medium REF: 7.2 OBJ: 7.2.e. List the three most common reaction mechanisms in enzyme active sites.

MSC: Applying 29. When a nucleophile present in the enzyme attacks an electrophilic substrate to form an enzyme-substrate intermediate, this is an example of __________ catalysis. a. covalent b. acid–base c. metal ion d. hydrophobic ANS: A DIF: Easy REF: 7.2 OBJ: 7.2.e. List the three most common reaction mechanisms in enzyme active sites.

MSC: Remembering 30. The three general categories of enzyme-mediated reactions, which are determined on the basis of the work they accomplish, include all EXCEPT a. coenzyme-dependent redox reactions.

b. reversible covalent modification. c. hydrophobic collapse reactions. d. metabolite transformation reactions.

ANS: C DIF: Easy REF: 7.2 OBJ: 7.2.f. State the three general categories of enzyme-mediated reactions (which are determined on the basis of the work they accomplish).

MSC: Remembering 31. The regulation of a biomolecule through the addition or removal of a molecular tag involves __________ reactions. a. coenzyme-dependent redox b. reversible covalent modification c. metabolite transformation d. isomerization ANS: B DIF: Easy REF: 7.2 OBJ: 7.2.f. State the three general categories of enzyme-mediated reactions (which are determined on the basis of the work they accomplish).

MSC: Understanding 32. Which pair correctly matches the coenzymes most often used to mediate the described redox reactions? a. NAD+/NADH; redox at C–O bonds b. NADP+/NADPH; redox at C–C bonds c. FAD/FADH2; redox at C–O bonds d. FMN/FMNH2; redox at C–O bonds ANS: A DIF: Medium REF: 7.2 OBJ: 7.2.f. State the three general categories of enzyme-mediated reactions (which are determined on the basis of the work they accomplish).

MSC: Applying 33. In a reversible covalent modification reaction involving the phosphorylation of a target protein, which of the following amino acids is LEAST likely to be modified with a phosphate group? a. Ser b. Phe c. Tyr d. Thr ANS: B DIF: Medium REF: 7.2 OBJ: 7.2.f. State the three general categories of enzyme-mediated reactions (which are determined on the basis of the work they accomplish).

MSC: Applying 34. Which type of reaction does not change the molecular formula of the product compared with that of the substrate? a. condensation b. reduction c. hydrolysis d. isomerization ANS: D DIF: Easy REF: 7.2 OBJ: 7.2.g. Define the three types of reactions that are the most commonly observed in metabolic pathways.

MSC: Remembering

35. The conversion of 2-phosphoglycerate to phosphoenolpyruvate is an example of which type of reaction? a. hydrolysis b. dehydration c. isomerization d. condensation ANS: B DIF: Medium REF: 7.2 OBJ: 7.2.g. Define the three types of reactions that are the most commonly observed in metabolic pathways.

MSC: Applying 36. The catalytic triad of chymotrypsin is composed of His57, Ser195, and a. Gly193. b. Glu103. c. Asp120. d. Asp102.

ANS: D DIF: Medium REF: 7.3 OBJ: 7.3.a. List the amino acids that compose the catalytic triad of chymotrypsin.

MSC: Remembering 37. The side chains of the amino acids that make up the catalytic triad of chymotrypsin contain all EXCEPT a. a hydroxyl group. b. a carboxylic acid. c. an aromatic group. d. an imidazole.

ANS: C DIF: Difficult REF: 7.3 OBJ: 7.3.a. List the amino acids that compose the catalytic triad of chymotrypsin.

MSC: Analyzing 38. Which amino acid acts as a general acid and a general base in the mechanism of chymotrypsin? a. Ser195 b. His57 c. Gly193 d. Asp102 ANS: B DIF: Medium REF: 7.3 OBJ: 7.3.a. List the amino acids that compose the catalytic triad of chymotrypsin.

MSC: Understanding 39. Which of the following is true of the tetrahedral intermediate in the chymotrypsin mechanism? a. It is lower in free energy than the substrate. b. It is partially positively charged. c. All bonds are the same length. d. It contains an oxyanion.

ANS: D DIF: Medium REF: 7.3 OBJ: 7.3.b. Illustrate the structure of the tetrahedral intermediate in the chymotrypsin mechanism.

MSC: Analyzing 40. Both the substrate and the tetrahedral intermediate, when associated with chymotrypsin,

a. b. c. d.

contain an oxyanion. interact with the oxyanion hole. undergo a nucleophilic attack. hydrogen bond to Asp102.

ANS: C DIF: Difficult REF: 7.3 OBJ: 7.3.b. Illustrate the structure of the tetrahedral intermediate in the chymotrypsin mechanism.

MSC: Analyzing 41. The substrate binding pocket of __________ contains a(n) __________, which facilitates substrate specificity. a. trypsin; Ser b. chymotrypsin; Asp c. trypsin; Asp d. elastase; Gly ANS: C DIF: Medium REF: 7.3 OBJ: 7.3.c. Compare and contrast the binding pockets of chymotrypsin, trypsin, and elastase.

MSC: Understanding 42. A mutation results in the change of Ser to Asp in the substrate binding pocket of chymotrypsin.

Most likely, the mutant enzyme will a. no longer catalyze the hydrolysis of a peptide bond because Asp cannot facilitate the nucleophilic attack. b. no longer catalyze the hydrolysis of a peptide bond because Asp is unable to be deprotonated by His57. c. preferentially hydrolyze substrates containing phenylalanine. d. preferentially hydrolyze substrates containing lysine.

ANS: C DIF: Difficult REF: 7.3 OBJ: 7.3.c. Compare and contrast the binding pockets of chymotrypsin, trypsin, and elastase.

MSC: Analyzing 43. The substrate binding pocket of __________ is best at accommodating substrates with small side chains. a. elastase b. chymotrypsin c. enolase d. trypsin ANS: A DIF: Easy REF: 7.3 OBJ: 7.3.c. Compare and contrast the binding pockets of chymotrypsin, trypsin, and elastase.

MSC: Understanding 44. Which of the following functions as a general base in the mechanism of enolase? a. Lys345 b. His57 c. Mg2+ d. Glu211 ANS: A DIF: Easy REF: 7.3 OBJ: 7.3.d. Identify the roles of Lys345, Glu211, and the Mg2+ ions in the enolase mechanism.

MSC: Understanding

45. Which of the following is NOT a function of the Mg2+ ions in the mechanism of enolase? a. orientation of substrate in the active site b. stabilizing the intermediate c. making the proton at the C-2 position more acidic d. electrophilic attack on the scissile bond ANS: D DIF: Medium REF: 7.3 OBJ: 7.3.d. Identify the roles of Lys345, Glu211, and the Mg2+ ions in the enolase mechanism.

MSC: Applying 46. The role of Glu211 in the mechanism of enolase is to a. facilitate the orientation of the phosphate group of the substrate. b. act as a general base on the substrate. c. act as a general acid on the intermediate. d. make the proton at the C-2 position more acidic.

ANS: C DIF: Medium REF: 7.3 OBJ: 7.3.d. Identify the roles of Lys345, Glu211, and the Mg2+ ions in the enolase mechanism.

MSC: Understanding 47. The glutamate side chain in the active site of HMG-CoA reductase acts as a general base only after a. the mevalonate binds to the active site. b. the hydride from the second NADPH attacks the carbonyl center of the aldehyde. c. a conformational change triggers the exchange of NADP+ for NADPH. d. CoA is reduced to CoA-SH. ANS: C DIF: Difficult REF: 7.3 OBJ: 7.3.e. State the four steps in the HMG-CoA reductase mechanism.

MSC: Evaluating 48. The hemithioacetal intermediate formed during the action of HMG-CoA reductase is stabilized by a. Lys267. b. Asp283. c. His381. d. Glu83.

ANS: A DIF: Medium REF: 7.3 OBJ: 7.3.e. State the four steps in the HMG-CoA reductase mechanism.

MSC: Understanding 49. The mechanism of HMG-CoA reductase involves a. two NADPH. b. one NADPH. c. two NADH. d. one NADH. ANS: A DIF: Easy REF: 7.3 OBJ: 7.3.e. State the four steps in the HMG-CoA reductase mechanism.

MSC: Remembering 50. Place the following HMG-CoA reductase steps in the correct order: A. Reduction of aldehyde B. Breakdown of hemithioacetal C. Reduction of thioester D. Cofactor exchange

a. b. c. d.

A, D, C, B C, D, B, A A, B, D, C C, B, D, A

ANS: B DIF: Difficult REF: 7.3 OBJ: 7.3.e. State the four steps in the HMG-CoA reductase mechanism.

MSC: Analyzing 51. For a reaction of S a. k. b. k. c. 1 / v. d. [S] / v.

P, the rate constant of the reaction is equal to

ANS: A DIF: Easy REF: 7.4 OBJ: 7.4.a. Define the velocity of a reaction in terms of the rate constant.

MSC: Remembering 52. For a reaction of Q + R P, the rate constant a. is equal to [Q][R] / [P]. b. has units of s−1. c. is a second-order rate constant. d. is equal to [P] / [Q][R].

ANS: C DIF: Medium REF: 7.4 OBJ: 7.4.a. Define the velocity of a reaction in terms of the rate constant.

MSC: Understanding 53. If the rate constant for a reaction is determined to be equal to v / [Q][R], the reaction is the conversion of a. Q to R. b. R to Q. c. R plus Q to a product. d. It is impossible to determine the reaction given the information provided.

ANS: C DIF: Medium REF: 7.4 OBJ: 7.4.a. Define the velocity of a reaction in terms of the rate constant.

MSC: Applying 54. On a plot of [product] versus time for an enzyme-catalyzed reaction, the v0 is equal to the a. slope of the line / [S]. b. [P] at the lowest time point. c. slope of the line. d. y-intercept.

ANS: C DIF: Medium REF: 7.4 OBJ: 7.4.b. Differentiate between initial velocity and maximum velocity.

MSC: Applying 55. The initial velocity of an enzyme-catalyzed reaction is followed at various substrate concentrations. At very high substrate concentrations it is observed that the initial velocity no longer increases as more substrate is added. The velocity under these conditions is known as a. the ultimate velocity. b. the maximum velocity.

c. v[S]. d. optimal velocity.

ANS: B DIF: Easy REF: 7.4 OBJ: 7.4.b. Differentiate between initial velocity and maximum velocity.

MSC: Remembering 56. In the steady-state condition assumed in Michaelis–Menten kinetics, __________ is relatively constant. a. [ES] b. [S] c. v0 d. [ES] / [S] ANS: A DIF: Easy REF: 7.4 OBJ: 7.4.c. State the three assumptions made when using Michaelis–Menten kinetics.

MSC: Understanding 57. Which of the following is an assumption made when using Michaelis–Menten kinetics? a. The conversion of E + P ES does not occur. b. k1 > k2 c. v0 = vmax at low [S] d. The conversion of EP E + P is rapid.

ANS: D DIF: Easy REF: 7.4 OBJ: 7.4.c. State the three assumptions made when using Michaelis–Menten kinetics.

MSC: Understanding 58. In the figure below, KM is indicated at

a. b. c. d.

A. B. C. D.

ANS: D DIF: Medium REF: 7.4 OBJ: 7.4.d. Define the Michaelis constant.

59. KM is equal to

MSC: Remembering

a. k1 / (k−1 + k2). b. (k−1 + k2) / k1. c. 1/2 vmax. d. vmax[S] / v0.

ANS: B DIF: Medium REF: 7.4 OBJ: 7.4.d. Define the Michaelis constant.

MSC: Remembering

60. The y-axis of a Lineweaver–Burk plot is a. v0. b. 1 / vo. c. Km / vmax. d. 1 / [S].

ANS: B DIF: Easy REF: 7.4 OBJ: 7.4.e. Compare and contrast a Michaelis–Menten plot with a Lineweaver–Burk plot.

MSC: Remembering 61. A plot of 1 / v0 versus 1/[S] is called a __________ plot. Data in this plot have a slope equal to __________. a. Lineweaver–Burk; Km/vmax b. Lineweaver–Burk; −1/Km c. Michaelis–Menten; Km/vmax d. Michaelis–Menten; vmax ANS: A DIF: Medium REF: 7.4 OBJ: 7.4.e. Compare and contrast a Michaelis–Menten plot with a Lineweaver–Burk plot.

MSC: Understanding 62. Below is a Lineweaver–Burk plot in which the axis labels have been removed. Interpret the plot to determine the vmax.

a. b. c. d.

0.2 5 3 0.33

ANS: B DIF: Difficult REF: 7.4 OBJ: 7.4.e. Compare and contrast a Michaelis–Menten plot with a Lineweaver–Burk plot.

MSC: Applying

63. The specificity constant is equal to a. [Et][S] / v0. b. Km / v0. c. kcat / Km. d. kcat / [Et].

ANS: C DIF: Medium REF: 7.4 OBJ: 7.4.f. Calculate the specificity constant for an enzyme given kcat and Km. MSC: Remembering 64. An experiment is performed in which the kinetics of an enzyme-catalyzed reaction at different pHs is monitored. It is found that the Km does not change but that the kcat increases as the pH goes above 7. Which of the following is true? a. A chemical group within the enzyme that has a pKa of around 7 is likely involved in the catalytic mechanism. b. A chemical group with a pKa of around 7 must be deprotonated in order for substrate to bind. c. A chemical group with a pKa of around 7 must be positively charged in order for the substrate to bind. d. Protons are acting as positive heterotropic allosteric effectors of this enzyme.

ANS: A DIF: Difficult REF: 7.4 OBJ: 7.4.g. Explain why pH and temperature affect enzyme velocity.

MSC: Analyzing 65. Which of the following is NOT a primary mechanism that affects catalytic efficiency? a. binding of regulatory molecules b. covalent modification c. proteolytic processing d. cofactor degradation ANS: D DIF: Easy REF: 7.5 OBJ: 7.5.a. List the three primary mechanisms that affect catalytic efficiency.

MSC: Understanding 66. A kinase adds a phosphate group to a target enzyme, altering the catalytic efficiency of the enzyme. This is an example of a. covalent modification. b. proteolytic processing. c. binding of regulatory molecules. d. feedback inhibition.

ANS: A DIF: Easy REF: 7.5 OBJ: 7.5.a. List the three primary mechanisms that affect catalytic efficiency.

MSC: Understanding 67. Acetylcholinesterase is an important enzyme in the nervous system. Acetylcholinesterase activity is blocked by the nerve agent sarin gas, which forms a covalent bond with a Ser in the active site of the enzyme. Sarin gas is a(n) a. allosteric effector. b. competitive inhibitor. c. reversible inhibitor. d. irreversible inhibitor.

ANS: D DIF: Easy REF: 7.5 OBJ: 7.5.b. Distinguish between reversible and irreversible inhibition in terms of the types of interactions observed between inhibitor and enzyme.

MSC: Applying 68. Which type of interaction is more likely to be found between an enzyme and an irreversible inhibitor? a. covalent bond b. hydrogen bond c. ionic interaction d. van der Waals interaction ANS: A DIF: Easy REF: 7.5 OBJ: 7.5.b. Distinguish between reversible and irreversible inhibition in terms of the types of interactions observed between inhibitor and enzyme.

MSC: Remembering 69. Which of the following pairs correctly matches the type of interaction observed between an inhibitor and an enzyme with the type of inhibition? a. ionic; irreversible b. covalent; irreversible c. hydrogen bonding; reversible d. hydrophobic; irreversible ANS: C DIF: Easy REF: 7.5 OBJ: 7.5.b. Distinguish between reversible and irreversible inhibition in terms of the types of interactions observed between inhibitor and enzyme.

MSC: Remembering 70. A mixture of enzyme and inhibitor is run through a size-exclusion chromatography column. The activity of the enzyme is assessed before and after the chromatography. The enzyme has more activity after the chromatography step. Which of the following is true? a. The enzyme was not eluted fully from the column. b. The enzyme was denatured during chromatography. c. The inhibitor is a reversible inhibitor. d. The inhibitor is an irreversible inhibitor.

ANS: C DIF: Medium REF: 7.5 OBJ: 7.5.b. Distinguish between reversible and irreversible inhibition in terms of the types of interactions observed between inhibitor and enzyme.

MSC: Applying 71. An inhibitor that binds only to the ES complex and not free enzyme is known as a(n) __________ inhibitor. a. irreversible b. competitive c. uncompetitive d. mixed ANS: C DIF: Easy REF: 7.5 OBJ: 7.5.c. Differentiate between the three classes of reversible inhibitors.

MSC: Remembering 72. In the formation of an ESI complex, __________ inhibition can result. a. mixed b. competitive c. covalent d. anticompetitive

ANS: A DIF: Easy REF: 7.5 OBJ: 7.5.c. Differentiate between the three classes of reversible inhibitors.

MSC: Understanding 73. The Lineweaver–Burk plot shows data obtained for an enzyme in the absence and presence of a reversible inhibitor. Which type of inhibitor was used in the experiment?

a. b. c. d.

competitive uncompetitive mixed noncompetitive

ANS: D DIF: Medium REF: 7.5 OBJ: 7.5.d. Illustrate the difference between the kinetics of the reversible inhibitors with Lineweaver–Burk plots.

MSC: Applying 74. The Lineweaver–Burk plot shows data obtained for an enzyme in the absence and presence of a noncompetitive inhibitor. If the [I] is increased significantly in the experiment, the Vmaxapp would __________ and the Kmapp would __________.

a. b. c. d.

decrease; decrease stay the same; decrease decrease; stay the same stay the same; stay the same

ANS: C DIF: Medium REF: 7.5 OBJ: 7.5.d. Illustrate the difference between the kinetics of the reversible inhibitors with Lineweaver–Burk plots.

MSC: Applying 75. A Lineweaver–Burk plot displays parallel lines for an enzyme in the absence and presence of increasing amounts of an inhibitor. The inhibitor in this experiment a. binds both the free enzyme and the ES complex. b. is competitive. c. alters the Km but not the vmax. d. is uncompetitive.

ANS: D DIF: Medium REF: 7.5 OBJ: 7.5.d. Illustrate the difference between the kinetics of the reversible inhibitors with Lineweaver–Burk plots.

MSC: Applying 76. Which answer correctly classifies the compound with its relationship to aspartate transcarbamoylase? a. ATP; allosteric inhibitor b. ATP; allosteric activator c. CTP; allosteric activator d. CTP; substrate ANS: B DIF: Easy REF: 7.5 OBJ: 7.5.e. Identify the roles of ATP and CTP in the regulation of aspartate transcarbamoylase.

MSC: Understanding 77. Which of the following statements are true? a. ATCase is regulated by feedback inhibition. b. CTP is an allosteric activator of ATCase. c. ATP is an allosteric inhibitor of ATCase. d. GTP is an allosteric inhibitor of ATCase.

ANS: A DIF: Easy REF: 7.5 OBJ: 7.5.e. Identify the roles of ATP and CTP in the regulation of aspartate transcarbamoylase.

MSC: Understanding 78. When compared with the T state of aspartate transcarbamoylase, the R state a. has dissociated into two C3R3 complexes. b. has greater separation of the catalytic subunits. c. is bound to CTP. d. has substrate bound in the ATP binding site.

ANS: B DIF: Easy REF: 7.5 OBJ: 7.5.f. Distinguish between the T and R states of aspartate transcarbamoylase.

MSC: Understanding 79. A plot of vo versus [S] for aspartyl transcarbamoylase displays three sigmoidal lines. If the line in the middle represents the enzyme activity in the absence of any allosteric effectors, then the line to the __________ represents the enzyme in the __________ when bound to __________. a. right; R state; CTP b. right; T state; CTP c. left; R state; GTP d. left; T state; GTP ANS: B

DIF: Medium

REF: 7.5

OBJ: 7.5.f. Distinguish between the T and R states of aspartate transcarbamoylase.

MSC: Understanding 80. An enzyme undergoes a mutation that causes it to lose the ability to be regulated via phosphorylation. Which of the following mutations may lead to this loss of regulation? Assume that the overall structure is not altered by the mutation. a. Ser Thr b. Thr Ser c. Tyr Phe d. Ser Tyr ANS: C DIF: Medium REF: 7.5 OBJ: 7.5.g. List the three amino acid residues targeted by kinase enzymes.

MSC: Applying 81. Phosphorylation of __________ in glycogen phosphorylase shifts the enzyme to the __________. a. Tyr397; T state b. Tyr397; R state c. Ser14; T state d. Ser14; R state ANS: D DIF: Easy REF: 7.5 OBJ: 7.5.h. Relate the phosphorylation state of glycogen phosphorylase with its activity.

MSC: Remembering 82. When __________ is increased, __________ is activated, which acts on glycogen phosphorylase, leading to a decrease in the activity of the enzyme. a. glucagon; phosphorylase kinase b. epinephrine; phosphorylase kinase c. insulin; protein phosphatase 1 d. glucagon; protein phosphatase 1 ANS: C DIF: Easy REF: 7.5 OBJ: 7.5.h. Relate the phosphorylation state of glycogen phosphorylase with its activity.

MSC: Understanding 83. What is the appropriate order of the following steps?

A. Glutamine binding to uridylyltransferase B. Adenylation of glutamine synthetase C. Deuridylation of glutamine synthetase adenylyltransferase a. C, B, A b. A, C, B c. A, B, C d. C, A, B ANS: B DIF: Medium REF: 7.5 OBJ: 7.5.i. Explain the roles of adenylation and uridylation in the control of glutamine synthetase.

MSC: Applying 84. Glutamine synthetase is in the R state when Tyr397 is a. deadenylated. b. uridylated. c. phosphorylated. d. dephosphorylated.

ANS: A DIF: Easy REF: 7.5 OBJ: 7.5.i. Explain the roles of adenylation and uridylation in the control of glutamine synthetase.

MSC: Remembering 85. Procathepsin B is a lysosomal protease that is first translated as a proenzyme. On autocleavage it is fully activated. Procathepsin B is a. a zymogen. b. in the T state after autocleavage. c. an allosteric enzyme. d. inactive at low pH. ANS: A DIF: Easy OBJ: 7.5.j. Define the term zymogen.

REF: 7.5 MSC: Understanding

SHORT ANSWER 1. An enzyme is crystallized in preparation for X-ray crystallography. The crystal is then soaked in a solution of substrate and the crystal shatters. Propose a reason for this result.

ANS: The enzyme follows the induced-fit model of enzyme catalysis. Adding the substrate caused the enzyme to change conformation, which caused the crystal to shatter.

DIF: Difficult REF: 7.1 OBJ: 7.1.a. Distinguish between the lock and key model and the induced-fit model.

MSC: Evaluating 2. Explain the two ways that catalytic efficiency of enzymes can be controlled within a cell.

ANS: Catalytic efficiency can be controlled by the binding of regulatory molecules or by covalent modification.

DIF: Medium REF: 7.1 OBJ: 7.1.b. List three critical aspects of enzyme structure and function.

MSC: Understanding 3. What is Henry Eyring’s transition state theory?

ANS: Henry Eyring’s transition state theory states that the conversion of substrate to product involves a high-energy transition state in which a molecule can either become a product or remain a substrate.

DIF: Medium REF: 7.1 OBJ: 7.1.c. Restate Henry Eyring’s transition state theory.

MSC: Remembering

4. Consider the reaction coordinate diagram shown below for the conversion of substrate (S) to product (P) via two different reaction pathways that involve different transition states (‡ and ‡*). Assume that one pathway involves a catalyst and one does not. Decide which pathway involves the catalyst and explain your logic.

ANS: The pathway containing the ‡* transition state involves the catalyst. The role of a catalyst is to lower the G‡ by providing more favorable reaction conditions. The ‡* transition state has a lower G, resulting in a lower G‡.

DIF: Medium REF: 7.1 OBJ: 7.1.d. Illustrate the energetic advantage of a catalyst with a reaction coordinate diagram.

MSC: Evaluating 5. Consider the reaction coordinate diagram shown below for the conversion of substrate (S) to product (P). Assume that a hypothetical enzyme is added that destabilizes the substrate (S) so that it has the free energy of S*, but otherwise the reaction is the same (in other words, it still goes through the transition state indicated in the diagram). Justify why the hypothetical enzyme is a catalyst.

ANS: The role of a catalyst is to lower the activation energy ( G‡) of a reaction. The activation energy in the presence of the hypothetical protein is lowered; therefore the hypothetical protein is a catalyst.

DIF: Difficult REF: 7.1 OBJ: 7.1.d. Illustrate the energetic advantage of a catalyst with a reaction coordinate diagram.

MSC: Evaluating 6. A patient presents with symptoms associated with the disease beriberi. An analysis of pyruvate dehydrogenase complex activity shows significantly reduced levels from normal. Predict how a deficiency in a coenzyme may be the culprit. Specify the coenzyme involved.

ANS:

Beriberi disease is caused by reduced pyruvate dehydrogenase complex activity. Pyruvate dehydrogenase complex activity can be reduced if the cofactor thiamine pyrophosphate is lacking, leading to an apoenzyme.

DIF: Medium REF: 7.1 OBJ: 7.1.e. Differentiate between an apoenzyme and a holoenzyme.

MSC: Applying 7. Propose an experiment to determine the presence of a predicted hydrophobic channel in a newly discovered enzyme. At your disposal you have the purified enzyme, the ability to analyze the enzyme by X-ray crystallography, a spectrophotometer, the enzyme substrate, and polyethylene glycol. Be sure to explain how the results will determine if the protein contains a hydrophobic channel.

ANS: To determine the presence of a predicted hydrophobic channel, determine the structure of the enzyme in the presence of polyethylene glycol using X-ray crystallography. If a channel is there, the hydrophobic polyethylene glycol should bind into the channel.

DIF: Difficult REF: 7.2 OBJ: 7.2.b. State the ways that an enzyme active site creates a microenvironment.

MSC: Evaluating 8. Justify how an enzyme that catalyzes a hydrolysis reaction does not contradict the concept that enzyme active sites are microenvironments that exclude excess water.

ANS: An enzyme that catalyzes a hydrolysis reaction uses water as a substrate within the microenvironment of the active site. Excess water that is not specifically acting as a substrate in the reaction mechanism is still excluded.

DIF: Difficult REF: 7.2 OBJ: 7.2.g. Define the three types of reactions that are the most commonly observed in metabolic pathways.

MSC: Evaluating 9. Complete the following statement: The NH groups of Ser195 and Gly193 in chymotrypsin are able to stabilize the intermediate of the reaction by ANS: forming hydrogen bonds with the oxyanion.

DIF: Medium REF: 7.3 OBJ: 7.3.b. Illustrate the structure of the tetrahedral intermediate in the chymotrypsin mechanism.

MSC: Applying 10. Using words, define initial velocity (v0) for an enzyme-catalyzed reaction.

ANS: Initial velocity (v0) for an enzyme-catalyzed reaction is the reaction rate at the beginning of the reaction before the substrate concentration has changed significantly.

DIF: Medium REF: 7.4 OBJ: 7.4.b. Differentiate between initial velocity and maximum velocity.

MSC: Understanding 11. Connect the use of v0 to the ability to treat k−2 as negligible in Michaelis–Menten kinetics.

ANS: By considering the reaction at an early time, when the velocity is the initial velocity (v0), no appreciable product has been generated. Therefore the back reaction, where ES forms from EP with a rate constant k−2, is negligible.

DIF: Medium REF: 7.4 OBJ: 7.4.c. State the three assumptions made when using Michaelis–Menten kinetics.

MSC: Analyzing 12. Given the following parameters, calculate Km. v0 vmax [S] [P]

22.5 mM/s 45 mM/s 50 mM 125 mM

ANS: 50 mM DIF: Difficult MSC: Applying

REF: 7.4

OBJ: 7.4.d. Define the Michaelis constant.

13. Given the following data for lactate dehydrogenase, calculate the specificity constant.

Km ( M) Vmax ( M/min) kcat (min−1)

14.7 24.5 6270

103

ANS: The specificity constant is kcat/Km. 0.426 min-1/ M. DIF: Difficult REF: 7.4 OBJ: 7.4.f. Calculate the specificity constant for an enzyme given kcat and Km. MSC: Applying 14. Given the following kinetic data for the action of hexokinase for two different substrates (glucose and fructose), determine which is the preferred substrate of the enzyme and explain your answer.

Substrate Glucose Fructose

Km ( M) 180 200

kcat (s−1) 250 200

ANS: Glucose is the preferred substrate for hexokinase because the specificity constant (kcat/Km) is 1.38 M−1s−1 for glucose and is 1 M−1s−1 for fructose. A larger specificity constant indicates stronger substrate preference.

DIF: Difficult

REF: 7.4

OBJ: 7.4.f. Calculate the specificity constant for an enzyme given kcat and Km. MSC: Analyzing 15. The activity of an enzyme is monitored as a function of temperature. At low temperature very little activity is seen; the activity peaks as the temperature increases and then dramatically decreases to zero as higher temperatures are attained. Explain why the activity drops off completely at higher temperatures.

ANS: The higher temperature destabilizes the protein structure to the point where the enzyme is no longer folded properly. The enzyme cannot act as a catalyst when unfolded.

DIF: Medium REF: 7.4 OBJ: 7.4.g. Explain why pH and temperature affect enzyme velocity.

MSC: Applying 16. Hexokinase catalyzes the first step of glycolysis, which occurs in the cell cytoplasm. The protocol for an in vitro enzyme activity assay of hexokinase suggests that the assay is carried out at a pH of 7.4. Predict what may occur if the assay is carried out at a pH of 8.8 instead. Explain your reasoning.

ANS: The enzyme activity would be lower at the higher pH. The cytoplasm has a near neutral pH and hexokinase likely has optimal activity at that pH. DIF: Difficult REF: 7.4 OBJ: 7.4.g. Explain why pH and temperature affect enzyme velocity.

MSC: Applying 17. In vivo arginine decarboxylase activity is monitored over several days in the absence and presence of protease inhibitors. The activity is greatly reduced when protease inhibitors are present.

Arginine decarboxylase is not a protease. Interpret these findings.

ANS: Arginine decarboxylase activity is regulated by proteolytic processing. When the proteases responsible for activating arginine decarboxylase are inhibited, the activity of arginine decarboxylase is reduced.

DIF: Difficult REF: 7.5 OBJ: 7.5.a. List the three primary mechanisms that affect catalytic efficiency.

MSC: Applying 18. A plot of v0 versus substrate concentration for aspartate transcarbamoylase displays a sigmoidal curve. Explain how the plot would change in the presence of CTP. ANS: CTP is an allosteric inhibitor of aspartate transcarbamoylase. Its presence would shift the curve to the right.

DIF: Easy REF: 7.5 OBJ: 7.5.e. Identify the roles of ATP and CTP in the regulation of aspartate transcarbamoylase.

MSC: Understanding

19. Describe two conformational changes that occur when aspartate transcarbamoylase shifts from the R state to the T state.

ANS: The catalytic subunits are brought closer together. The catalytic subunits rotate.

DIF: Medium REF: 7.5 OBJ: 7.5.f. Distinguish between the T and R states of aspartate transcarbamoylase.

MSC: Understanding 20. What three amino acids are targeted for phosphorylation by kinases?

ANS: Serine, threonine, tyrosine DIF: Easy REF: 7.5 OBJ: 7.5.g. List the three amino acid residues targeted by kinase enzymes.

MSC: Remembering 21. Define the term zymogen.

ANS: Zymogen is the inactive precursor of an enzyme, or proenzyme, that must be cleaved by a protease to generate the active enzyme.

DIF: Easy REF: 7.5 MSC: Remembering

OBJ: 7.5.j. Define the term zymogen.

Chapter 8: Cell Signaling Systems MULTIPLE CHOICE 1. A ligand binds to a transmembrane protein. This causes a conformational change in the protein that is detected by an intracellular protein. The intracellular protein is an enzyme that adds phosphate groups to target proteins. The phosphorylated proteins cause a physiological change within the cell. This is an example of a. a metabolic pathway. b. homeostasis. c. a signal transduction pathway. d. an allosteric inhibition pathway.

ANS: C DIF: Easy REF: 8.1 OBJ: 8.1.a. Define cell signaling pathway.

MSC: Understanding

2. Which of the following does NOT participate in a signal transduction pathway? a. second messenger b. first messenger c. receptor protein d. lipid transporter ANS: D DIF: Easy REF: 8.1 OBJ: 8.1.a. Define cell signaling pathway.

MSC: Remembering

3. Construct a functional signal transduction pathway by placing the following actors in the correct order: A. upstream signaling protein B. second messenger C. receptor protein D. first messenger E. target proteins F. downstream signaling protein a. D, E, C, A, B, F b. C, D, A, B, F, E c. D, C, A, B, F, E d. D, C, B, A, F, E ANS: C DIF: Medium REF: 8.1 OBJ: 8.1.a. Define cell signaling pathway.

MSC: Applying

4. First messengers, but NOT second messengers a. bind to a protein. b. act as a transcription factor. c. are located extracellularly. d. are an allosteric effector.

ANS: C DIF: Easy REF: 8.1 OBJ: 8.1.b. Distinguish between first messengers and second messengers.

MSC: Understanding 5. Which of the following is an example of a first or second messenger? a. peptide hormone b. G protein–coupled receptor

c. protein kinase d. cyclic nucleotide phosphodiesterase ANS: A DIF: Easy REF: 8.1 OBJ: 8.1.b. Distinguish between first messengers and second messengers.

MSC: Remembering 6. Which of the following list includes ONLY first messengers? a. cortisol, insulin, prostaglandins b. nitric oxide, estradiol, heme c. insulin, glucagon, glucose d. Ca2+, testosterone, protein kinase A ANS: A DIF: Medium REF: 8.1 OBJ: 8.1.b. Distinguish between first messengers and second messengers.

MSC: Understanding 7. Estradiol is secreted by the ovaries, travels through the bloodstream, and interacts with estrogen receptors on breast epithelial cells. In this scenario estradiol is acting through which type of mechanism? a. synacrine b. paracrine c. endocrine d. autocrine ANS: C DIF: Medium REF: 8.1 OBJ: 8.1.c. Differentiate among endocrine, paracrine, and autocrine hormones.

MSC: Analyzing 8. A Western blot analysis of the expression of estrogen receptors in ovarian tissues at different times of the estrous cycle showed approximately four times greater protein levels at day 2 compared with day 10 of the cycle. Which of the following may be true given these data? a. Estrogen is acting as an endocrine signal in the ovaries. b. Estrogen is acting as an autocrine signal in the ovaries. c. Ovaries only secrete estrogen early in the estrous cycle. d. Ovarian tissue is responsive to estrogen only early in the estrous cycle.

ANS: B DIF: Difficult REF: 8.1 OBJ: 8.1.c. Differentiate among endocrine, paracrine, and autocrine hormones.

MSC: Evaluating 9. Acetylcholine is a neurotransmitter that stimulates muscle contraction. Acetylcholine is acting as a(n) a. endocrine signal. b. paracrine signal. c. autocrine signal. d. second messenger.

ANS: B DIF: Easy REF: 8.1 OBJ: 8.1.c. Differentiate among endocrine, paracrine, and autocrine hormones.

MSC: Understanding 10. Cyclic GMP is the __________ during vasodilation. a. first messenger b. second messenger

c. paracrine signal d. activator of nitric oxide synthetase ANS: B DIF: Easy REF: 8.1 OBJ: 8.1.d. Differentiate between endocrine, paracrine, and autocrine hormones.

MSC: Remembering 11. Muscle relaxation in response to nitric oxide would be reduced if a(n) __________ was present. a. stimulator of cGMP phosphodiesterase b. inhibitor of protein kinase A c. inhibitor of acetylcholine esterase d. stimulator of guanylate cyclase ANS: A DIF: Medium REF: 8.1 OBJ: 8.1.d. Differentiate between endocrine, paracrine, and autocrine hormones.

MSC: Analyzing 12. The levels of the second messenger involved in vasodilation are increased by __________ and decreased by __________. a. cGMP cyclase; guanylate phosphodiesterase b. guanylate phosphodiesterase; cGMP cyclase c. guanylate cyclase; cGMP phosphodiesterase d. cGMP phosphodiesterase; guanylate cyclase ANS: C DIF: Medium REF: 8.1 OBJ: 8.1.d. Differentiate between endocrine, paracrine, and autocrine hormones.

MSC: Applying 13. Which class of proteins interacts with a heterotrimeric intracellular protein? a. receptor tyrosine kinases b. TNF receptor family c. G protein–coupled receptors d. nuclear transmembrane proteins ANS: C DIF: Easy REF: 8.1 OBJ: 8.1.e. Compare G protein–coupled receptors, receptor tyrosine kinases, and ligand-gated ion channels.

MSC: Remembering 14. Ligand binding causes which of the following to form trimers? a. tumor necrosis factor receptors b. receptor tyrosine kinases c. G protein–coupled receptors d. nicotinic acetylcholine receptors ANS: A DIF: Easy REF: 8.1 OBJ: 8.1.e. Compare G protein–coupled receptors, receptor tyrosine kinases, and ligand-gated ion channels.

MSC: Remembering 15. What characteristic is true for both RTKs and GPCRs? a. The receptor binds to intracellular proteins only when activated. b. When activated, the receptor has enzymatic activity. c. The receptor transmits ions. d. The receptor undergoes a conformational change on activation.

ANS: D DIF: Medium REF: 8.1 OBJ: 8.1.e. Compare G protein–coupled receptors, receptor tyrosine kinases, and ligand-gated

ion channels.

MSC: Applying

16. Which of the following is a GTPase? a. b. c. d.

ANS: C DIF: Medium REF: 8.2 OBJ: 8.2.a. List the name and function of each component of the heterotrimeric G protein.

MSC: Remembering 17. The subunit of trimeric G proteins can function to a. regulate ion channels. b. activate adenylate cyclase. c. inhibit phospholipase A. d. inhibit phosphodiesterase.

ANS: B DIF: Medium REF: 8.2 OBJ: 8.2.a. List the name and function of each component of the heterotrimeric G protein.

MSC: Remembering 18. Levels of diacylglycerol increase in a cell on binding of a ligand to a taste receptor. Which trimeric G protein subunit is most likely to be bound to GTP? a. b. c. d.

ANS: A DIF: Medium REF: 8.2 OBJ: 8.2.a. List the name and function of each component of the heterotrimeric G protein.

MSC: Applying 19. Which of the following is activated or increased in a liver cell on exposure to either glucagon or epinephrine? a. GTP b. phospholipase C c. cAMP d. DAG ANS: C DIF: Medium REF: 8.2 OBJ: 8.2.b. Distinguish between the shared pathways and parallel pathways of glucagon and epinephrine activity.

MSC: Understanding 20. An estrogen-dependent breast cancer cell line is grown in a medium that contains estrogen. Cell proliferation is monitored over time. In a separate experiment, the cell line is grown in a medium that lacks estrogen but includes bisphenol A, a compound found in polycarbonate plastics. When monitored, cell proliferation is higher than in the presence of estrogen. A possible explanation of these results is that bisphenol A a. inhibits the binding of estrogen to the estrogen receptor. b. is an agonist of the estrogen receptor. c. inhibits adenylate cyclase. d. is toxic to the cell line.

ANS: B DIF: Difficult REF: 8.2 OBJ: 8.2.c. Differentiate between receptor agonists and receptor antagonists.

MSC: Applying 21. Which of the following compounds is a pharmaceutical adrenergic receptor agonist? a. dopamine b. metoprolol c. norepinephrine d. clonidine ANS: D DIF: Medium REF: 8.2 OBJ: 8.2.c. Differentiate between receptor agonists and receptor antagonists.

MSC: Analyzing 22. When bound to GTP, obtains a conformation that promotes interaction with a. adenylate cyclase. b. PKA. c. the G protein–coupled receptor. d. phospholipase C. ANS: A DIF: Easy REF: 8.2 OBJ: 8.2.c. Differentiate between receptor agonists and receptor antagonists.

MSC: Understanding 23. When the regulatory subunit of PKA is bound to cAMP, a. it dissociates into monomers. b. the pseudosubstrate is phosphorylated. c. it cannot bind to catalytic subunit of PKA. d. it is part of a tetramer.

ANS: C DIF: Medium REF: 8.2 OBJ: 8.2.e. Identify the key steps in protein kinase A activation.

MSC: Applying 24. When PKA is inactive, which of the following is true? a. The pseudosubstrate of the PKA regulatory subunits is bound in the active site of the catalytic subunits. b. The regulatory subunits are bound by cAMP. c. The regulatory subunits are bound by GTP. d. ATP is unable to bind the catalytic subunits.

ANS: A DIF: Medium REF: 8.2 OBJ: 8.2.e. Identify the key steps in protein kinase A activation.

MSC: Understanding 25. Liver cells were monitored for changes in metabolic enzymatic activity after exposure to glucagon.

The enzymes that showed changes in activity were then analyzed to assess if they had been covalently modified. Which of the following results were likely observed? a. Enzymes that showed lower activity were not phosphorylated. b. Enzymes that showed higher activity were methylated. c. Enzymes that showed altered activity (higher or lower) were phosphorylated. d. Enzymes that showed altered activity (higher or lower) were methylated.

ANS: C DIF: Medium REF: 8.2 OBJ: 8.2.f. List the metabolic responses in the liver after glucagon binding to beta2-adrenergic

receptors.

MSC: Applying

26. If protein kinase A is activated in a liver cell in response to glucagon binding to the 2-adrenergic receptor, which of the following will result? a. Glycogen synthesis will be turned on. b. Glycogen degradation will be turned on. c. Glucose synthesis will be turned off. d. GLUT1 expression will be upregulated.

ANS: B DIF: Medium REF: 8.2 OBJ: 8.2.f. List the metabolic responses in the liver after glucagon binding to beta2-adrenergic receptors.

MSC: Applying 27. Which of the following prevents GPCR from reassociating with the

complex?

a. -arrestin b. GTPase activating protein c. cAMP phosphodiesterase d. RGS ANS: A DIF: Medium REF: 8.2 OBJ: 8.2.g. Define the terms guanine nucleotide exchange factor, GTPase activating protein, G protein receptor kinase, beta-adrenergic receptor kinase, and beta-arrestin.

MSC: Understanding 28. The __________ is a specific type of __________. a. GRK; ARK b. -adrenergic receptor kinase; -arrestin c. regulator of G protein signaling; GTPase activating protein d. GTPase activating protein; guanine nucleotide exchange factor ANS: C DIF: Medium REF: 8.2 OBJ: 8.2.g. Define the terms guanine nucleotide exchange factor, GTPase activating protein, G protein receptor kinase, beta-adrenergic receptor kinase, and beta-arrestin.

MSC: Understanding 29. Which scenario would allow -arrestin to bind to the GPCR? a. ARK is internalized into the endosome. b. The receptor is phosphorylated. c. is bound to GDP. d. The regulatory subunit of -arrestin is removed.

ANS: B DIF: Medium REF: 8.2 OBJ: 8.2.h. Restate the role of beta-adrenergic receptor kinase and beta-arrestin in terminating the signal of G protein–coupled receptors. MSC: Applying 30. Below is the molecular structure of a single bovine -arrestin subunit. Two locations are indicated.

What is most likely to interact with the protein at these locations?

a. ARK b. GTP-bound c. dephosphorylated GPCR d. phosphorylated GPCR ANS: D DIF: Difficult REF: 8.2 OBJ: 8.2.h. Restate the role of beta-adrenergic receptor kinase and beta-arrestin in terminating the signal of G protein–coupled receptors. MSC: Applying 31. Below is a schematic representation of a dimerized receptor tyrosine kinase. Where is the kinase function located?

a. b. c. d.

A B C D

ANS: D DIF: Medium REF: 8.3 OBJ: 8.3.a. List the steps that follow binding of epidermal growth factor to its receptor.

MSC: Remembering 32. Place the following steps in proper order: A. phosphorylation of RTK cytoplasmic tails B. activation of downstream signaling pathways C. ligand binding, receptor dimerization, and kinase activation D. protein binding to RTK phosphotyrosines and phosphorylation of target proteins a. C, D, A, B b. C, B, A, D

c. C, A, D, B d. B, C, A, D ANS: C DIF: Medium REF: 8.3 OBJ: 8.3.a. List the steps that follow binding of epidermal growth factor to its receptor.

MSC: Analyzing 33. If there were a technique that allowed one to isolate EGFR1 and EGFR2 at discrete steps along their activation pathway, which of the following would be isolated? a. A dimer in which EGFR2 contains phosphotyrosines but EGFR1 does not. b. A dimer in which EGFR1 contains phosphotyrosines but EGFR2 does not. c. A monomer of EGFR1 that contains phosphotyrosines. d. A monomer of EGFR2 that contains phosphotyrosines.

ANS: A DIF: Difficult REF: 8.3 OBJ: 8.3.a. List the steps that follow binding of epidermal growth factor to its receptor.

MSC: Evaluating 34. Which of the following proteins contains an SH3 domain? a. growth factor receptor-bound 2 (GRB2) b. phosphoinositide-3 kinase (PI-3K) c. SOS protein d. RasGAP ANS: A DIF: Medium REF: 8.3 OBJ: 8.3.b. Differentiate between SH2 and SH3 domains.

MSC: Remembering

35. Below is shown a short sequence of a protein. Which of the following domains would most likely bind this sequence?

a. b. c. d.

SH2 SH3 SH2a SHP

ANS: B DIF: Difficult REF: 8.3 OBJ: 8.3.b. Differentiate between SH2 and SH3 domains.

MSC: Applying

36. If GRB2 were truncated so that the N-terminal domain was missing, the truncated protein would be unable to bind the a. phosphorylated Tyr of the SOS protein. b. phosphorylated Tyr of the RTK substrate. c. proline-rich sequence of the SOS protein.

d. protein-rich sequence of the RTK substrate.

ANS: C DIF: Difficult REF: 8.3 OBJ: 8.3.b. Differentiate between SH2 and SH3 domains.

MSC: Analyzing

37. Which of the following is true of a recessive oncogene mutation but NOT a dominant oncogene mutation? a. It results in a disease phenotype any time the mutation is present in a cell. b. It results in a disease phenotype only when both copies of the mutated oncogene are present in the same cell. c. It is a gain-of-function mutation. d. It is a mutation in a tumor suppressor gene.

ANS: B DIF: Medium REF: 8.3 OBJ: 8.3.c. Define the terms oncogene, dominant mutation, recessive mutation, and tumor suppressor.

MSC: Understanding 38. A mutation causes a cell to divide uncontrollably. Analysis of the cell shows that both copies of the gene must have the mutation. From this information, it can be determined that the mutation is a. dominant. b. recessive. c. in a gene coding a kinase. d. in a tumor suppressor gene.

ANS: B DIF: Easy REF: 8.3 OBJ: 8.3.c. Define the terms oncogene, dominant mutation, recessive mutation, and tumor suppressor.

MSC: Applying 39. The insulin receptor is a type of a. G protein–linked receptor. b. receptor tyrosine kinase. c. oncogene. d. MEK. ANS: B DIF: Easy REF: 8.3 OBJ: 8.3.d. Explain the concept of autophosphorylation as it applies to the insulin receptor.

MSC: Remembering 40. On binding of an insulin molecule to the insulin receptor, a conformational change occurs that a. increases the affinity of a second insulin binding site. b. causes the dimerization of the receptor. c. brings the L1 region of the subunit closer to the membrane. d. stimulates tyrosine autophosphorylation in the subunits.

ANS: D DIF: Medium REF: 8.3 OBJ: 8.3.e. List the steps that follow binding of insulin to its receptor.

MSC: Understanding 41. On binding of an insulin molecule to the insulin receptor, which region of the receptor becomes phosphorylated?

a. b. c. d.

CR TM TK L1

ANS: C DIF: Easy REF: 8.3 OBJ: 8.3.e. List the steps that follow binding of insulin to its receptor.

MSC: Remembering 42. Construct a functional pathway out of the following steps.

A: Phosphorylation of subunits of the insulin receptor occurs.

B: Insulin binds to subunits of the insulin receptor.

C: PI-3K is activated.

D: IRS is phosphorylated. a. C, A, B, D b. B, D, A, C c. B, A, C, D d. B, A, D, C ANS: D DIF: Easy REF: 8.3 OBJ: 8.3.e. List the steps that follow binding of insulin to its receptor.

MSC: Applying 43. On insulin binding to the insulin receptor, MAP kinase signaling proteins are activated. Which of the following proteins are part of this signaling pathway? a. Shc b. IRS c. PI-3K d. GLUT-1 ANS: A DIF: Easy REF: 8.3 OBJ: 8.3.e. List the steps that follow binding of insulin to its receptor.

MSC: Remembering

44. Which of the following occurs after activation of the PI-3K signaling pathway? a. Glycogen synthesis rates decrease. b. GRB2 is activated. c. GLUT-1 levels decrease. d. Glucose uptake increases.

ANS: D DIF: Easy REF: 8.3 OBJ: 8.3.f. Name the two primary metabolic results of activation of the PI-3K signaling pathway.

MSC: Remembering 45. A new protein is discovered that contains a pleckstrin homology domain. Which of the following is likely to bind to the protein? a. PIP3 b. PI-3K c. phosphorylated tyrosines d. Ca2+ ANS: A DIF: Easy REF: 8.3 OBJ: 8.3.e. List the steps that follow binding of insulin to its receptor.

MSC: Understanding 46. Caspases contain a. phosphorylated tyrosines when activated. b. death domains. c. an active site cysteine residue. d. SODD. ANS: C DIF: Easy REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Remembering

47. A caspase is a a. protease. b. kinase. c. phosphatase. d. transmembrane receptor.

ANS: A DIF: Easy REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Remembering

48. Caspase 3 is responsible for a. activating caspase 8. b. phosphorylating Fas. c. degrading key regulatory molecules. d. dephosphorylating FasL. ANS: C DIF: Medium REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Understanding

49. Predict which bond of a target protein would be cleaved by caspase 3 executioner enzyme.

a. b. c. d.

1 2 3 4

ANS: D DIF: Difficult REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Applying

50. If a mutation occurred in SODD that prohibited its interaction with the DD of TNF receptor, the TNF receptor would a. no longer form a trimer. b. no longer be able to release TNF- . c. bind TRADD, even in the absence of TNF- . d. bind NFB, even in the absence of TNF- .

ANS: C DIF: Difficult REF: 8.4 OBJ: 8.4.b. Differentiate between silence of death domain and TNF receptor–associated death domain proteins.

MSC: Applying 51. Both the silence of death domain and TNF receptor–associated death domain proteins a. inhibit downstream signaling. b. activate downstream signaling. c. are phosphorylated when TNF- is bound to its receptor. d. bind TNF receptor death domains.

ANS: D DIF: Medium REF: 8.4 OBJ: 8.4.b. Differentiate between silence of death domain and TNF receptor–associated death domain proteins.

MSC: Applying 52. Which protein is part of the TNF receptor–activated programmed cell death signaling pathway? a. FADD b. TRAF2 c. NFB-inducing kinase d. IKK ANS: A DIF: Medium REF: 8.4 OBJ: 8.4.c. Identify the key elements of the TNF-alpha mediated apoptotic pathway.

MSC: Remembering 53. Place the following steps of the apoptotic pathway in their proper order.

A. CASP3 cleavage of cellular proteins B. Cleavage of procaspase 8 C. Cleavage of procaspase 3 D. Assembly of DD and DED protein complexes a. D, C, B, A b. B C, A, D

c. D, B, C, A d. D, C, A, B ANS: C DIF: Medium REF: 8.4 OBJ: 8.4.c. Identify the key elements of the TNF-alpha mediated apoptotic pathway.

MSC: Applying 54. Below shows the cell survival pathway promoted by TNF- . A complex is indicated with a question mark. What is this complex?

a. b. c. d.

inactive NFB active NFB active CASP3 NIK

ANS: B DIF: Difficult REF: 8.4 OBJ: 8.4.d. Identify the key elements of the TNF-alpha mediated cell survival pathway.

MSC: Applying 55. Which of the following acts as a transcription factor in the cell survival pathway activated by TNF- ? a. p50:p65 complex b. NIK:RIP complex c. IB d. IKK

ANS: A DIF: Easy REF: 8.4 OBJ: 8.4.d. Identify the key elements of the TNF-alpha mediated cell survival pathway.

MSC: Remembering 56. Phosphorylation of which of the following is necessary for the increased expression of antiapoptotic genes? a. RIP b. TNF receptor c. FADD d. IKK ANS: D DIF: Easy REF: 8.4 OBJ: 8.4.d. Identify the key elements of the TNF-alpha mediated cell survival pathway.

MSC: Understanding 57. Which of the following is true of active NFB? a. It is a dimer. b. It is phosphorylated. c. It is in a complex with a DD. d. It has been proteolytically activated.

ANS: A DIF: Medium REF: 8.4 OBJ: 8.4.d. Identify the key elements of the TNF-alpha mediated cell survival pathway.

MSC: Understanding 58. Consider a mutant cell that does not form DISC on TNF signaling. Which of the following would occur in this mutant cell if exposed to TNF- ? a. Caspase 3 would be activated. b. TNF- would bind to the TNF receptor. c. Caspase 8 would be activated. d. The cell would undergo apoptosis.

ANS: B DIF: Difficult REF: 8.4 OBJ: 8.4.e. Compare the activation of procaspase 3 with the activation of other zymogens such as chymotrypsinogen. MSC: Applying 59. Which of the following is true of procaspase 8? a. It is proteolytically active. b. It can cleave caspase 3. c. It can be activated by proteolysis. d. It is a kinase.

ANS: C DIF: Medium REF: 8.4 OBJ: 8.4.e. Compare the activation of procaspase 3 with the activation of other zymogens such as chymotrypsinogen. MSC: Understanding 60. Consider a mutation in procaspase 3 that changes Asp28 to an amino acid that is no longer a substrate for autocleavage. This mutant would a. no longer be cleaved by caspase 8. b. no longer obtain a quaternary structure. c. be partially activated. d. be fully activated.

ANS: C DIF: Difficult REF: 8.4 OBJ: 8.4.e. Compare the activation of procaspase 3 with the activation of other zymogens such as

chymotrypsinogen.

MSC: Applying

61. Cell-specific responses to signaling molecules are possible because a. nuclear receptor expression is cell specific. b. target palindromic DNA sequences are ubiquitous. c. signaling molecules are hydrophobic and can pass through the plasma membrane. d. only some cells express gated channels for the signaling molecules.

ANS: A DIF: Easy REF: 8.5 OBJ: 8.5.a. List the parameters that govern the cell-specific physiologic responses controlled by nuclear receptors.

MSC: Understanding 62. Cultures of two different cell types are exposed to the same signaling ligand. Analysis of gene expression shows that only one of the cell types responded to the ligand. Which of the following may account for this difference? a. The ligand was only bioavailable to one of the cell types. b. Only one of the cell types contained accessible target gene DNA sequences. c. Only one cell type contained DNA. d. The ligand could only pass through the membrane of one of the cell types.

ANS: B DIF: Medium REF: 8.5 OBJ: 8.5.a. List the parameters that govern the cell-specific physiologic responses controlled by nuclear receptors.

MSC: Analyzing 63. Which of the following DNA sequences is MOST likely to be bound by a steroid receptor? a. AGGAGAACATCATGTTCT b. AGGAGATAGGAGAACT c. TTTGATCCAGTTTCCAGT d. CCCAAGTTCCCAAG ANS: A DIF: Difficult REF: 8.5 OBJ: 8.5.b. Differentiate between steroid receptors and metabolite receptors.

MSC: Applying 64. Which of the following is a metabolite receptor? a. aldosterone receptor b. glucocorticoid receptor c. progesterone receptor d. thyroid hormone receptor ANS: D DIF: Medium REF: 8.5 OBJ: 8.5.b. Differentiate between steroid receptors and metabolite receptors.

MSC: Remembering 65. The ligands for metabolite receptors are often derived from dietary nutrients, including all EXCEPT which of the following? a. essential amino acids b. vitamins c. unsaturated fatty acids d. saturated fatty acids ANS: D DIF: Medium REF: 8.5 OBJ: 8.5.b. Differentiate between steroid receptors and metabolite receptors.

MSC: Remembering

66. This Zn2+-containing homodimer is part of

a. b. c. d.

the glucocorticoid receptor.

PPAR -RXR .

TRADD. the retinoic acid receptor.

ANS: A DIF: Difficult REF: 8.5 OBJ: 8.5.c. Distinguish DNA binding of the glucocorticoid receptor from DNA binding by PPARgamma-RXRalpha.

MSC: Understanding 67. The PPAR -RXR heterodimer interacts with DNA via a. the LXXLL sequences. b. leucine zipper motifs. c. zinc finger motifs. d. basic leucine zipper motifs.

ANS: C DIF: Easy REF: 8.5 OBJ: 8.5.c. Distinguish DNA binding of the glucocorticoid receptor from DNA binding by PPARgamma-RXRalpha.

MSC: Understanding 68. Removal of which metal ion would likely alter the structure of the GR DNA-binding domain and preclude it from binding to DNA? a. Zn2+ b. Mg2+ c. Ca2+ d. Fe2+ ANS: A DIF: Easy REF: 8.5 OBJ: 8.5.c. Distinguish DNA binding of the glucocorticoid receptor from DNA binding by PPARgamma-RXRalpha.

MSC: Applying 69. Below is shown the structure of a homodimer of the GR DNA-binding domain. Four areas are highlighted. Which is most likely to interact with DNA?

a. b. c. d.

A B C D

ANS: D DIF: Difficult REF: 8.5 OBJ: 8.5.c. Distinguish DNA binding of the glucocorticoid receptor from DNA binding by PPARgamma-RXRalpha.

MSC: Understanding 70. A class of proteins that assist other proteins to fold are known as __________ proteins. a. folding assist b. proteasome c. chaperonin d. overseer ANS: C DIF: Easy REF: 8.5 OBJ: 8.5.d. Define the terms chaperonin protein and glucocorticoid response elements.

MSC: Remembering 71. Hsp90 is a type of a. chaperonin. b. kinase. c. response element. d. heat sensing protease.

ANS: A DIF: Easy REF: 8.5 OBJ: 8.5.d. Define the terms chaperonin protein and glucocorticoid response elements.

MSC: Remembering 72. A response element is a. any protein whose expression is changed in response to a signal. b. a sequence of regulatory DNA. c. a domain of the glucocorticoid receptor that binds DNA. d. a sequence of DNA coding for a steroid or metabolite receptor.

ANS: B DIF: Easy REF: 8.5 OBJ: 8.5.d. Define the terms chaperonin protein and glucocorticoid response elements.

MSC: Understanding 73. Which of the following is NOT an expected effect of the binding of the glucocorticoid response element by GR? a. upregulation of annexin I

b. inhibition of the inflammatory response c. upregulation of cyclooxygenase-2 d. decreased interaction of p65 and p50 of NFB ANS: C DIF: Medium REF: 8.5 OBJ: 8.5.d. Define the terms chaperonin protein and glucocorticoid response elements.

MSC: Understanding 74. The __________ domain functions as a protein–protein interaction module and is located in the cytoplasmic tail of TNF receptors. a. death b. SH2 c. SH3 d. RIP ANS: A DIF: Easy REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Remembering

75. The result of TRADD proteins binding to TNF receptors is that a. TRADD is phosphorylated. b. an activated adaptor complex is formed. c. downstream signaling proteins are inactivated. d. TNF is degraded.

ANS: B DIF: Easy REF: 8.3 OBJ: 8.4.b. Differentiate between silence of death domain and TNF receptor–associated death domain proteins.

MSC: Remembering SHORT ANSWER 1. Explain how the conformational organization of a nuclear receptor homodimer allows it to recognize inverted repeat sequences of DNA. ANS: The homodimer is organized head to head, which allows it to recognize inverted repeat sequences of DNA. DIF: Medium REF: 8.5 OBJ: 8.5.b. Differentiate between steroid receptors and metabolite receptors.

MSC: Understanding 2. Nuclear receptors are ligand-activated transcription factors that control a wide range of physiologic responses. The responses are governed by cell-specific expression of nuclear receptors and coregulatory proteins and accessibility of target gene DNA sequences. What else governs the responses?

ANS: Ligand bioavailability DIF: Easy REF: 8.5 OBJ: 8.5.a. List the parameters that govern the cell-specific physiologic responses controlled by nuclear receptors.

MSC: Understanding 3. What is the TNF receptor–TRADD-FADD–procaspase 8 adaptor complex also known as?

ANS: The death-inducing signaling complex (DISC) DIF: Medium REF: 8.4 OBJ: 8.4.c. Identify the key elements of the TNF-alpha mediated apoptotic pathway.

MSC: Remembering 4. Differentiate between the caspase in the apoptotic pathway that is activated by autocleavage and the caspase that is activated by another enzyme. Clearly name each caspase.

ANS: Caspase 8 is activated by autocleavage. Caspase 3 is activated by caspase 8.

DIF: Medium REF: 8.4 OBJ: 8.4.c. Identify the key elements of the TNF-alpha mediated apoptotic pathway.

MSC: Analyzing 5. Activation of caspases ultimately leads to the programmed death of the cell. What is this process known as? Explain why this may be a beneficial outcome to the organism.

ANS: Apoptosis. Apoptosis is advantageous to the organism as a whole because it prevents a damaged or inappropriate cell from surviving.

DIF: Easy REF: 8.4 OBJ: 8.4.a. Define apoptosis, death domain, and caspase.

MSC: Remembering

6. An inhibitor of PTEN is accidentally ingested by an infant. The infant displays symptoms of hypoglycemia. How would inhibiting PTEN lead to this outcome?

ANS: PTEN removes the phosphate from PIP3 to regenerate PIP2, thereby shutting off the PI-3K signaling pathway. If this inhibition is blocked, cells will continue to increase glucose uptake even when insulin is not present and glucose levels are low, leading to hypoglycemia.

DIF: Difficult REF: 8.3 OBJ: 8.3.f. Name the two primary metabolic results of activation of the PI-3K signaling pathway.

MSC: Applying 7. Predict how the flux of glucose through glucose transporters will change when PI-3K is activated.

ANS: The flux of glucose through glucose transporters increases when PI-3K is activated.

DIF: Easy REF: 8.3 OBJ: 8.3.f. Name the two primary metabolic results of activation of the PI-3K signaling pathway.

MSC: Applying 8. The PI-3K signaling pathway is activated by the binding of __________ to its receptor. This leads to an increase in glucose uptake and in __________ synthesis.

ANS: Insulin; glycogen

DIF: Easy REF: 8.3 OBJ: 8.3.f. Name the two primary metabolic results of activation of the PI-3K signaling pathway.

MSC: Remembering 9. On binding of insulin to the insulin receptor, the receptor becomes phosphorylated. What is the name of the protein that carried out this phosphorylation?

ANS: The insulin receptor DIF: Medium REF: 8.3 OBJ: 8.3.d. Explain the concept of autophosphorylation as it applies to the insulin receptor.

MSC: Understanding 10. A culture of insulin-responsive cells are analyzed after stimulation with insulin. The insulin receptors are then isolated (assume that during the isolation protocol the insulin is removed from the receptor). Half of the sample is analyzed by SDS-PAGE followed by Coomassie blue staining.

The other half of the sample is analyzed via SDS-PAGE followed by a Western blot. The primary antibody used in the blot recognizes phosphorylated tyrosine residues. Predict how many bands will be seen on the SDS-PAGE compared with the Western blot and explain your answer.

ANS: There will be two bands on the SDS-PAGE, corresponding to the and subunits of the insulin receptor. There will be one band on the Western blot, corresponding to the subunit which contains the phosphorylated tyrosine residues.

DIF: Difficult REF: 8.3 OBJ: 8.3.d. Explain the concept of autophosphorylation as it applies to the insulin receptor.

MSC: Evaluating 11. Oncogenic Ras protein chronically stimulates the MAP kinase pathway. Why is Ras not inactivated in this situation?

ANS: Because Ras can no longer hydrolyze GTP DIF: Easy REF: 8.3 OBJ: 8.3.c. Define the terms oncogene, dominant mutation, recessive mutation, and tumor suppressor.

MSC: Understanding 12. Explain why the retinoblastoma gene is considered a tumor suppressor.

ANS: The retinoblastoma gene is considered a tumor suppressor because under normal conditions it functions to inhibit uncontrolled cell proliferation.

DIF: Easy REF: 8.3 OBJ: 8.3.c. Define the terms oncogene, dominant mutation, recessive mutation, and tumor suppressor.

MSC: Understanding 13. GRB2 contains both SH2 and SH3 domains. Contrast the role of each domain in the function of GRB2.

ANS: The SH2 domain of GRB2 identifies phosphorylated tyrosines on target proteins, whereas the SH3 domain recognizes proline-rich domains on target proteins.

DIF: Medium REF: 8.3 OBJ: 8.3.b. Differentiate between SH2 and SH3 domains.

MSC: Analyzing

14. Illustrate how a conformational change is critical in the two-step model of EGF function.

ANS: After dimerization of the receptor, the EGFR1 cytoplasmic kinase domain is activated, which phosphorylates the cytoplasmic tail of EGFR2. This induces a conformation change that activates the kinase domain of EGFR2 and phosphorylation of EGFR1.

DIF: Medium REF: 8.3 OBJ: 8.3.a. List the steps that follow binding of epidermal growth factor to its receptor.

MSC: Applying 15. Construct the order of signaling termination through the -adrenergic receptor that includes the following steps: A. Internalization of the receptor into endosomes B. Dissociation of heterotrimeric G protein complex from the receptor C. Phosphorylation of the receptor D. Recruitment of ARK to the receptor E. -arrestin association with GPCR ANS: B, D, C, E, A DIF: Medium REF: 8.2 OBJ: 8.2.h. Restate the role of beta-adrenergic receptor kinase and beta-arrestin in terminating the signal of G protein–coupled receptors. MSC: Analyzing 16. What is a protein that promotes GDP-GTP exchange in G proteins known as?

ANS: Guanine nucleotide exchange factor DIF: Easy REF: 8.2 OBJ: 8.2.g. Define the terms guanine nucleotide exchange factor, GTPase activating protein, G protein receptor kinase, beta-adrenergic receptor kinase, and beta-arrestin.

MSC: Understanding 17. Endosomal fractions can be isolated from cells using differential centrifugation. Using this technique, would you expect to find more or fewer -adrenergic receptors in the purified endosomes in a wild-type liver cell that had been stimulated with glucagon OR in a mutant liver cells that lacks -adrenergic receptor kinase that had been stimulated with glucagon? In explaining your answer describe the role of -adrenergic receptor kinase.

ANS: Fewer -adrenergic receptors would be found in the mutant cells because -adrenergic receptor kinase phosphorylates the receptor, marking it for recycling through the endosomal pathway.

DIF: Difficult REF: 8.2 OBJ: 8.2.g. Define the terms guanine nucleotide exchange factor, GTPase activating protein, G protein receptor kinase, beta-adrenergic receptor kinase, and beta-arrestin.

MSC: Analyzing 18. Glycogen synthesis was monitored in a liver cell in the presence of glucagon binding to the 2-adrenergic receptor and after its removal. How would the activity of enzymes involved in glycogen synthesis and glycogen degradation be altered if the experiment were carried out after the cells were treated with caffeine, an inhibitor of cAMP phosphodiesterase? Explain your reasoning.

ANS: If cAMP phosphodiesterase is inhibited, the level of cAMP in the cell will remain high even when glucagon is removed. Therefore protein kinase A (PKA) would remain activated. This would lead to the phosphorylation of enzymes involved in glycogen synthesis, leading to their inhibition. So the rates of glycogen synthesis would be low even when glucagon was removed.

DIF: Difficult REF: 8.2 OBJ: 8.2.f. List the metabolic responses in the liver after glucagon binding to beta2-adrenergic receptors.

MSC: Evaluating 19. Glycogen metabolism is regulated when glucagon binds to 2-adrenergic receptors on liver cells.

Describe the type of covalent modification that leads to this regulation and distinguish how the modification effects the rate of glycogen synthesis and glycogen degradation.

ANS: Phosphorylation activates enzymes involved in glycogen degradation and inactivates enzymes involved in glycogen synthesis.

DIF: Difficult REF: 8.2 OBJ: 8.2.f. List the metabolic responses in the liver after glucagon binding to beta2-adrenergic receptors.

MSC: Analyzing 20. Compare and contrast the pseudosubstrate found in the regulatory subunit of protein kinase A with a substrate of protein kinase A. ANS: Substrates of protein kinase A contain a Ser, which can be phosphorylated. The pseudosubstrate contains an Ala instead of Ser. Although both can bind the active site of the PKA catalytic subunit, the pseudosubstrate cannot be phosphorylated.

DIF: Medium REF: 8.2 OBJ: 8.2.e. Identify the key steps in protein kinase A activation.

MSC: Analyzing 21. Protein kinase A is immunoprecipitated from two different liver samples. The immunoprecipitate is then analyzed with SDS-PAGE. The first sample shows a single band on the gel, whereas the second displays two bands. Propose an explanation for why the results are different.

ANS:

Protein kinase A can be bound by regulatory subunits. In the sample with the single band, protein kinase A alone was precipitated. However, in the sample displaying two bands, the antibody precipitated protein kinase A that was bound to the regulatory subunits. During the SDS-PAGE, the subunits dissociated, resulting in two bands.

DIF: Difficult REF: 8.2 OBJ: 8.2.e. Identify the key steps in protein kinase A activation.

MSC: Evaluating 22. Contrast the structures and nucleotide binding properties of cyclase versus protein.

when interacting with adenylate

ANS: When interacting with adenylate cyclase, the switch II helix of is positioned to promote the interaction and is bound to GTP. Alternatively, when interacting with protein, the switch II helix of

is positioned to promote that interaction and

is bound to GDP.

DIF: Difficult REF: 8.2 OBJ: 8.2.d. Explain the differences between the GDP-bound and GTP-bound states of the G-alpha subunit.

MSC: Analyzing 23. Below is a figure of

protein bound to

protein. What is the name of the portion indicated

by the arrow, and which protein is it a part of?

ANS: It is the switch II helix and it is part of the

protein.

DIF: Medium REF: 8.2 OBJ: 8.2.d. Explain the differences between the GDP-bound and GTP-bound states of the G-alpha subunit.

MSC: Understanding

24. Some breast cancers express estrogen receptors and are estrogen dependent. Tamoxifen is a chemotherapy agent used in the treatment of estrogen-responsive breast cancers. What is tamoxifen in relation to the estrogen receptor and why does it have this effect?

ANS: Tamoxifen is an antagonist of the estrogen receptor in these cancers because it blocks the binding of estrogen to the estrogen receptors.

DIF: Medium REF: 8.2 OBJ: 8.2.c. Differentiate between receptor agonists and receptor antagonists.

MSC: Applying 25. Outline the steps that occur in the shared pathway of glucagon and epinephrine signaling in a liver cell. Include the specific receptors, G protein subunits, upstream signaling protein, and second messengers.

ANS: Glucagon binds specifically to glucagon receptors and activates signaling, which stimulates adenylate cyclase activity to produce the second messenger cAMP. Epinephrine binds the 2 receptor, which also activates signaling, which stimulates adenylate cyclase activity to produce the second messenger cAMP. DIF: Difficult REF: 8.2 OBJ: 8.2.b. Distinguish between the shared pathways and parallel pathways of glucagon and epinephrine activity.

MSC: Analyzing 26. A liver cell is exposed to glucagon and epinephrine and glucose export is monitored. On addition of an adenylate cyclase inhibitor, the level of glucose export is reduced but not eliminated. Propose a reason for this partial reduction.

ANS: Epinephrine can bind to two different receptors on the cell to stimulate two parallel signal transduction pathways. Only one of the pathways involves adenylate cyclase. When it is inhibited, the other pathway still functions to stimulate glucose export.

DIF: Difficult REF: 8.2 OBJ: 8.2.b. Distinguish between the shared pathways and parallel pathways of glucagon and epinephrine activity.

MSC: Evaluating 27. Define the main characteristics of a signal transduction pathway and give a specific example of such a pathway.

ANS: A signal transduction pathway is a linked set of biochemical reactions that are initiated by ligand-induced activation of a receptor protein and terminated by a measurable cellular response.

Examples include tumor necrosis factor pathway and epidermal growth factor receptor pathway.

DIF: Easy REF: 8.1 MSC: Remembering

OBJ: 8.1.a. Define cell signaling pathway.

Chapter 9: Glycolysis: A Paradigm of Metabolic Regulation MULTIPLE CHOICE 1. Metabolism is best defined as a collection of a. biochemical reactions that convert chemical energy into work. b. biochemical reactions that convert mechanical energy into work. c. enzymes that convert glucose into carbon dioxide. d. enzymes that convert amino acids into proteins.

ANS: A DIF: Easy REF: 9.1 OBJ: 9.1.a. List the major metabolic pathways in animals.

MSC: Remembering

2. Catabolic pathways are always paired with anabolic pathways. Why? a. Catabolic pathways build up new molecules and anabolic break down molecules. b. Catabolic pathways break down molecules and anabolic build up new molecules. c. Both require ATP to operate. d. Both require redox reactions to operate.

ANS: A DIF: Medium REF: 9.1 OBJ: 9.1.c. Distinguish between catabolic pathways and anabolic pathways.

MSC: Analyzing 3. What may be the root cause of the slowing of the flux of metabolites through the glycolysis and gluconeogenesis pathways in your body? a. elevated levels of amino acids in the body b. elevated levels of glycogen in the body c. lowered levels of protein synthesis d. lowered levels of enzyme activity ANS: D DIF: Medium REF: 9.1 OBJ: 9.1.d. Explain how flux through a pathway changes in response to substrate concentration and enzyme activity. MSC: Evaluating 4. Flux is defined as the rate at which __________ is/are interconverted. a. enzymes b. metabolites c. sugars d. energy ANS: B DIF: Easy flux.

MSC: Remembering

REF: 9.1

OBJ: 9.1.e. Define metabolic

5. In the reaction A B, if at equilibrium [B] >> [A], what can be said about the directionality of the reaction? a. strongly favored in the forward direction b. strongly favored in the reverse direction c. strongly favored in both directions d. Not enough information is given.

ANS: A DIF: Medium REF: 9.1 OBJ: 9.1.d. Explain how flux through a pathway changes in response to substrate concentration and enzyme activity. MSC: Applying

6. For the following reaction A→ B, if at equilibrium directionality of the reaction? a. strongly favored in the forward direction b. strongly favored in the reverse direction c. strongly favored in both directions d. Not enough information is given.

> 0, what can be said about the

ANS: B DIF: Medium REF: 9.1 OBJ: 9.1.d. Explain how flux through a pathway changes in response to substrate concentration and enzyme activity. MSC: Applying 7. How can an unfavorable reaction ( > 0) still occur in a metabolic pathway? a. Link it to another unfavorable reaction. b. Link it to a favorable reaction. c. They cannot be used in metabolic pathway reactions. d. Increase the temperature of the reaction.

ANS: B DIF: Easy REF: 9.1 OBJ: 9.1.g. Explain how reaction coupling allows an unfavorable (Delta)G value to be part of a metabolic pathway. MSC: Understanding 8. Which of the following metabolic pathways is only found in plants? a. glycolysis b. citrate cycle c. photosynthesis d. urea cycle ANS: C DIF: Easy REF: 9.1 OBJ: 9.1.b. List the major metabolic pathways in plants.

MSC: Remembering

9. Which of the following pathways are found in both plants and animals? a. photosynthesis and carbon fixation b. urea cycle c. nitrogen fixation d. citrate cycle ANS: D DIF: Easy REF: 9.1 OBJ: 9.1.b. List the major metabolic pathways in plants.

10. Calculate the net

a. b. c. d.

MSC: Remembering

for the following series of reactions:

14 kJ/mol –6 kJ/mol 6 kJ/mol 0 kJ/mol

ANS: B DIF: Easy REF: 9.1 OBJ: 9.1.g. Explain how reaction coupling allows an unfavorable (Delta)G value to be part of a metabolic pathway. MSC: Applying

11. Is the net reaction favorable for the following series of coupled reactions?

a. b. c. d.

Yes, No, Yes, No,

<0 <0 >0 >0

ANS: A DIF: Medium REF: 9.1 OBJ: 9.1.g. Explain how reaction coupling allows an unfavorable (Delta)G value to be part of a metabolic pathway. MSC: Applying 12. Review the figure below. Shared intermediates are used so effectively in coupled reactions because they

a. b. c. d.

allow products to diffuse through membrane to increase concentration gradient. increase the value of . decrease the value of Q. limit product diffusion and allow intermediates to channel from one enzyme to the next.

ANS: D DIF: Medium REF: 9.1 OBJ: 9.1.g. Explain how reaction coupling allows an unfavorable (Delta)G value to be part of a metabolic pathway. MSC: Understanding 13. Which of the following is an energy conversion pathway? a. urea cycle b. citrate cycle c. nitrogen fixation and assimilation d. fatty acid degradation and synthesis ANS: B DIF: Easy REF: 9.1 OBJ: 9.1.f. Distinguish between energy conversion pathways and metabolite synthesis and degradation pathways.

MSC: Understanding 14. What is the main difference between energy conversion pathways and metabolite synthesis pathways? a. Energy conversion pathways produce ATP. b. Energy conversion pathways deplete ATP. c. Metabolite synthesis pathway uses ATP to break down metabolites.

d. Metabolite synthesis pathway uses ATP to break down pyruvate.

ANS: A DIF: Easy REF: 9.1 OBJ: 9.1.f. Distinguish between energy conversion pathways and metabolite synthesis and degradation pathways.

MSC: Understanding 15. A shared intermediate can be defined as a molecule that is a. a reactant in a pathway. b. the final product of a pathway. c. the final product of a pathway and the reactant of the next pathway. d. favorable to produce.

ANS: C DIF: Easy OBJ: 9.1.h. Define shared intermediate.

REF: 9.1 MSC: Remembering

16. In the following series of reactions, what is the shared intermediate?

a. b. c. d.

glucose-6-P fructose-6-P ATP fructose-1,6-P

ANS: B DIF: Medium OBJ: 9.1.h. Define shared intermediate.

REF: 9.1 MSC: Applying

17. Which of the following is the correct formula for glucose? a. C12H22O11 b. C6H12O6 c. C6H6O6 d. C14N2H18O5 ANS: B DIF: Easy REF: 9.2 OBJ: 9.2.a. Distinguish between glucose and fructose.

MSC: Remembering

18. Compare the structure of an aldose to a ketose. a. Ketose has a carbon backbone with an aldehyde group at the end of the molecule, whereas aldose has a ketone group at the end of the molecule. b. Ketose has a carbon backbone with a ketone group at the end of the molecule, whereas aldose has an aldehyde group at the end of the molecule. c. Both have a carbon backbone where ketose has a ketone group at the end of the molecule, and aldose also has an aldehyde group at the end of the molecule. d. Both have a carbon backbone where ketose has a ketone group on the second carbon in the molecule, and aldose also has an aldehyde group at the end of the molecule.

ANS: D DIF: Medium OBJ: 9.2.c. Define aldose and ketose.

REF: 9.2 MSC: Analyzing

19. A chiral center is an atom with a. two different functional groups and a strong dipole.

b. four different functional groups and which lacks a plane of symmetry. c. all the same functional groups and a plane of symmetry. d. the ability to hydrogen bond.

ANS: B center.

MSC: Applying

DIF: Easy

REF: 9.2

OBJ: 9.2.d. Define chiral

20. Glucose and fructose are both C6H12O6. What is the structural difference between them? a. Glucose is a five-membered ring and fructose is a six-membered ring. b. Fructose is a five-membered ring and glucose is a six-membered ring. c. Glucose is a linear molecule and fructose is a ring. d. Glucose is found in the boat conformation and fructose is a chair conformation.

ANS: B DIF: Easy REF: 9.2 OBJ: 9.2.a. Distinguish between glucose and fructose.

MSC: Applying

21. Explain the difference between a Fisher projection and a Haworth projection. a. Fischer projections illustrate the cyclic form, whereas Haworth projections represent the linear form. b. The Haworth projection illustrates the six-membered rings, whereas the Fischer projection represents the five-membered rings. c. Haworth projections illustrate the cyclic form, whereas Fischer projections represent the linear form. d. Fischer projections show the boat conformation, whereas Haworth projections show the chair conformation.

ANS: C DIF: Medium REF: 9.2 OBJ: 9.2.b. Explain the difference between a Haworth projection and a Fisher projection.

MSC: Applying 22. Define aldose. a. Only aldose molecules have CH2OH. b. Aldose molecules have ketone functional groups. c. Aldose molecules have aldehyde functional groups. d. Aldose molecules are all five-membered rings.

ANS: C DIF: Easy OBJ: 9.2.c. Define aldose and ketose.

REF: 9.2 MSC: Remembering

23. Define ketose. a. Only ketose molecules have CH2OH. b. Ketose molecules have ketone functional groups. c. Ketose molecules have aldehyde functional groups. d. Ketose molecules are all five-membered rings.

ANS: B DIF: Easy OBJ: 9.2.c. Define aldose and ketose.

REF: 9.2 MSC: Remembering

24. Distinguish between D and L isomers. a. D is right handed and L is left handed. b. D is left handed and L is right handed. c. D and L only differ in the position of one chiral center. d. D is the boat conformation and L is the chair conformation.

ANS: A

DIF: Easy

REF: 9.2

OBJ: 9.2.e. Distinguish between D and L isomers. MSC:

Understanding

25. What is the relationship between the molecules in the figure below?

a. b. c. d.

They are isomers.

They are anomers.

They are epimers.

They are identical.

ANS: C DIF: Medium REF: 9.2 OBJ: 9.2.f. Differentiate among epimers, anomers, and isomers.

MSC: Applying 26. Anomers differ from each other by changes at the __________ carbon. a. chiral b. C-2 c. C-3 d. C-1 ANS: D DIF: Medium REF: 9.2 OBJ: 9.2.f. Differentiate among epimers, anomers, and isomers.

MSC: Understanding 27. Which of following is an anomeric pair? a. D-glucose and D-fructose b. D-glucose and L-fructose c. D-glucose and L-glucose d. -D-glucose and b--glucose ANS: D DIF: Medium REF: 9.2 OBJ: 9.2.f. Differentiate among epimers, anomers, and isomers.

MSC: Understanding 28. During the cyclization of D-glucose, where is a new chiral center formed? a. C-1 b. C-3 c. C-4 d. C-5 ANS: A DIF: Easy REF: 9.2 OBJ: 9.2.g. Demonstrate the cyclization of linear glucose to cyclic glucopyranose.

MSC: Understanding

29. The test using copper to determine blood glucose levels is called a __________ test. a. glycolysis b. phosphorylation c. Benedict’s d. McKee’s ANS: C DIF: Easy REF: 9.2 OBJ: 9.2.h. Explain the significance of Benedict’s test.

MSC: Remembering

30. A carbohydrate that reacts with oxidizing agents such as Cu+2 is called a(n) __________ sugar. a. oxidizing b. reducing c. rentose d. aldose ANS: B DIF: Medium REF: 9.2 OBJ: 9.2.i. Differentiate between a reducing and a nonreducing sugar.

MSC: Remembering 31. Sucrose is a nonreducing sugar. Why? a. Sucrose does not contain an aldehyde functional group. b. Sucrose does not react with heat. c. Sucrose is a pyranose that cannot be reacted with copper. d. Sucrose is a disaccharide that cannot be converted to an open chain.

ANS: D DIF: Medium REF: 9.2 OBJ: 9.2.i. Differentiate between a reducing and a nonreducing sugar.

MSC: Understanding 32. Name the following disaccharide using descriptive nomenclature.

a. b. c. d.

Glc( 1 2)Fru Glc( 1 2)Glc Gal( 1 4)Glc Glc( 1 4)Glc

ANS: C DIF: Difficult REF: 9.2 OBJ: 9.2.k Demonstrate the difference between an alpha-1,4 linkage and a beta-1,4 linkage.

MSC: Remembering 33. In the following figure, what is the linkage between the two monosaccharide units and is this a reducing sugar?

a. b. c. d.

1 1 1 1

2, nonreducing 1, nonreducing 2, reducing 2, reducing

ANS: A DIF: Medium REF: 9.2 OBJ: 9.2.k Demonstrate the difference between an alpha-1,4 linkage and a beta-1,4 linkage.

MSC: Understanding 34. The glycolytic pathway is responsible for passing molecules to which other pathways? a. citrate cycle and nitrogen fixation b. photosynthesis and oxidative phosphorylation c. citrate cycle and oxidative phosphorylation d. urea cycle and fatty acid synthesis ANS: C DIF: Easy REF: 9.3 OBJ: 9.3.a. Describe the glycolytic pathway.

MSC: Understanding

35. Which of the following is NOT a reason why glycolysis is considered one of the core metabolic pathways in nature? a. Glycolytic enzymes are hugely conserved among all living organisms. b. It is a primary pathway for ATP generation under anaerobic conditions. c. Metabolites of glycolysis are precursors for a large number of interdependent pathways. d. It is a primary pathway for nitrogen generation.

ANS: D DIF: Easy REF: 9.3 OBJ: 9.3.b. List the three primary reasons why glycolysis is considered one of the core metabolic pathways in nature. MSC: Understanding 36. Which of the following is the correct net reaction for glycolysis? a. glucose + 2 ATP 2 lactate + 2 ADP + 2 Pi b. glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate + 2 ATP + 2 NADH + 4 H+ c. glucose + 2 ADP + 2 Pi 2 CH3CH2OH + 2 CO2 + 2 ATP d. glucose + 2 ADP + 2 Pi + 2 NAD+ 2 pyruvate + 2 ATP + 2 NADH + 2 H+ + 2H2O ANS: D DIF: Easy REF: 9.3 OBJ: 9.3.d. Identify the overall net reaction of glycolysis.

MSC: Understanding

37. What does glycolysis accomplish for the cell? a. It generates ADP for the cell to be used in other cycles. b. It generates ATP and pyruvate for the cell to be used in other cycles. c. It generates glucose to be used for storage. d. It generates CO2 that is exhaled.

ANS: B DIF: Medium REF: 9.3 OBJ: 9.3.d. Identify the overall net reaction of glycolysis.

MSC: Applying

38. In which of the following metabolic conversions is ATP “consumed” during glycolysis? a. 1,3-Bisphosphoglycerate 3-phosphoglycerate b. glucose glucose-6-phosphate c. 2-Phosphoglycerate 3-phosphoglycerate d. glucose-6-phosphate fructose-6-phosphate ANS: B DIF: Medium REF: 9.3 OBJ: 9.3.e. Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.

MSC: Remembering 39. Which of the following best defines substrate-level phosphorylation? a. direct transfer of a Pi to an ADP b. direct transfer of a Pi to an ATP c. indirect transfer of a Pi to an ATP d. indirect transfer of a Pi to glucose ANS: A DIF: Medium REF: 9.3 OBJ: 9.3.f. Define substrate-level phosphorylation.

MSC: Remembering

40. Which of the following compounds contains a “high-energy” bond and is used to produce ATP by substrate-level phosphorylation in glycolysis? a. glucose b. fructose-1,6-BP c. 3-phosphoglycerate d. 1,3-bisphosphoglycerate ANS: D DIF: Medium REF: 9.3 OBJ: 9.3.f. Define substrate-level phosphorylation.

MSC: Applying

41. The first reaction in glycolysis that produces a high-energy compound is catalyzed by a. aldolase. b. triose phosphate isomerase. c. enolase. d. phosphofructokinase-1.

ANS: D DIF: Easy REF: 9.3 OBJ: 9.3.h. Explain how phosphofructokinase-1 couples ATP hydrolysis with a phosphoryl transfer reaction.

MSC: Remembering 42. Fructose-1,6-bisphosphate is cleaved by aldolase. What is required for the reaction to proceed? a. production of endergonic intermediate b. substrate phosphorylation c. cleaving of high-energy phosphate bond d. formation of Schiff base intermediate ANS: D DIF: Medium REF: 9.3 OBJ: 9.3.i. Identify how fructose-1,6-biphosphatase is cleaved by aldolase.

MSC: Understanding 43. Which coenzyme is required to convert glyceraldehyde-3-P into 1,3-bisphosphosphoglycerate? a. FAD+ b. NAD+ c. ATP d. Pi

ANS: B DIF: Easy REF: 9.3 OBJ: 9.3.j. Explain how glyceraldehyde-3-P is converted into 1,3-bisphosphoglycerate by glyceraldehyde-3-P dehydrogenase.

MSC: Understanding 44. How does phosphoglycerate kinase make glycolysis energy neutral at this step? a. It uses ATP to produce 3-phosphoglycerate. b. It produces 2 ATP along with 3-phosphoglycerate. c. It results in a reaction at equilibrium. d. It results in a reaction is endergonic.

ANS: B DIF: Medium REF: 9.3 OBJ: 9.3.k. Describe how phosphoglycerate kinase replaces 2 ATP previously invested in glycolysis.

MSC: Applying 45. What advantage is there to phosphoglycerate kinase having an open and closed configuration? a. It allows water to be trapped in the active site along with the substrate. b. It forces covalent binding of the substrate to the enzyme active site. c. The induced-fit mechanism maximizes accessibility of active site without sacrificing hydrophobic environment. d. Changing of the configuration of the enzyme makes the reaction exergonic.

ANS: C DIF: Medium REF: 9.3 OBJ: 9.3.k. Describe how phosphoglycerate kinase replaces 2 ATP previously invested in glycolysis.

MSC: Applying 46. Predict how oxygen saturation would be affected if an individual has defective hexokinase enzymes. a. 2,3-BPG levels are elevated and oxygen binding decreases. b. 2,3-BPG levels are reduced and oxygen binding increases. c. 2,3-BPG levels are elevated and oxygen binding increases. d. 2,3-BPG levels are reduced and oxygen binding decreases.

ANS: B DIF: Difficult REF: 9.3 OBJ: 9.3.l. Explain why individuals with defects in glycolytic enzymes have altered oxygen-transport capabilities.

MSC: Applying 47. The enzyme phosphoglycerate mutase operates at reversibility of that reaction a. is spontaneous. b. occurs rapidly. c. occurs at equilibrium. d. is nonspontaneous.

? 0 kJ/mol. That indicates that the

ANS: C DIF: Easy REF: 9.3 OBJ: 9.3.m. Demonstrate how phosphoglycerate mutase is a reversible reaction.

MSC: Applying 48. Using the table below, explain why glycolysis is an overall favorable reaction pathway.

a. b. c. d.

Overall the pathway is Overall the pathway is Overall the pathway is Overall the pathway is

> 0. = 0. < 0. < 1.

ANS: B DIF: Easy REF: 9.3 OBJ: 9.3.n. Demonstrate using Gibbs free energy that glycolysis is an overall favorable reaction pathway.

MSC: Applying 49. To produce 4 ATP requires 122 kJ/mol. Which reactions in the glycolytic pathway produce enough energy to be able to overcome this deficit? a. hexokinase, phosphofructokinase-1, and pyruvate kinase b. hexokinase, phosphofructokinase-1, and pyruvate kinase c. phosphofructokinase-1, aldolase, and pyruvate kinase d. hexokinase, enolase, and pyruvate kinase ANS: B DIF: Easy REF: 9.3 OBJ: 9.3.n. Demonstrate using Gibbs free energy that glycolysis is an overall favorable reaction pathway.

MSC: Applying 50. 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. 1,3-Bisphosphoglycerate + ADP 3-Phosphoglycerate + ATP c. 2-phosphoglyerate phosphoenolpyruvate d. fructose-6-phosphate fructose-1,6-bisphosphate ANS: D DIF: Medium REF: 9.3 OBJ: 9.3.g. List the three irreversible enzymatic reactions in glycolysis.

MSC: Applying 51. In glycolysis, fructose 1,6-bisphosphate is converted to two products with a standard free-energy change ( ) of 23.8 kJ/mol. Under what conditions (encountered in erythrocytes) will the free-energy change ( ) be negative, enabling the reaction to proceed to products? a. The free-energy change will be negative if the concentrations of the two products are high relative to that of fructose 1,6-bisphosphate.

b. The reaction will not go to the right spontaneously under any conditions because the is positive. c. Under standard conditions, enough energy is released to drive the reaction to the right. d. The free-energy change will be negative when there is a high concentration of fructose 1,6-bisphosphate relative to the concentration of products.

ANS: D DIF: Difficult REF: 9.3 OBJ: 9.3.n. Demonstrate using Gibbs free energy that glycolysis is an overall favorable reaction pathway.

MSC: Analyzing 52. Where in the body is glucokinase found? a. small intestine b. liver c. heart d. thyroid ANS: B DIF: Easy REF: 9.4 OBJ: 9.4.a. Explain the role of glucokinase in regulation of the glycolytic pathway.

MSC: Remembering 53. Hexokinase has a Km of 0.1 mM for glucose, whereas glucokinase has a Km of 10 mM for glucose. What does that mean for their relative affinities for glucose? a. Glucokinase has a higher affinity. b. Hexokinase has a higher affinity. c. Km does not measure affinity. d. They are different enzymes and affinity cannot be compared between enzymes.

ANS: B DIF: Easy REF: 9.4 OBJ: 9.4.a. Explain the role of glucokinase in regulation of the glycolytic pathway.

MSC: Understanding 54. If blood glucose levels are elevated, what does glucokinase do in response? a. inhibits glycolysis b. stimulates the production of more hexokinase c. stimulates the release of insulin d. inhibits production of 2,3-BPG ANS: C DIF: Medium REF: 9.4 OBJ: 9.4.a. Explain the role of glucokinase in regulation of the glycolytic pathway.

MSC: Understanding 55. If you are unable to digest milk products, what is the metabolic root of that issue? a. maltase b. lactase c. sucrose d. glucose oxidase ANS: B DIF: Easy REF: 9.4 OBJ: 9.4.g. Describe metabolic roots of lactose intolerance.

MSC: Understanding

56. In the presence of lactase, lactose is cleaved into the monosaccharides glucose and a. glucose. b. fructose. c. galactose. d. maltose.

ANS: C DIF: Easy REF: 9.4 OBJ: 9.4.g. Describe metabolic roots of lactose intolerance.

MSC: Understanding

57. The rate limiting step can be defined as a level of enzyme activity that can be regulated to be __________ even when substrate levels are __________. a. high; high b. low; high c. high; low d. low; low ANS: B DIF: Easy OBJ: 9.4.c. Define rate limiting step.

REF: 9.4 MSC: Remembering

58. What effect do elevated levels of ATP have on glycolysis? a. decrease the affinity of PFK-1 for fructose-6-P and slow rate of the pathway b. increase the affinity of PFK-1 for fructose-6-P and increase the rate of the pathway c. increase the concentration of PFK-1 in the R-state d. increase the concentration of glucose entering glycolysis ANS: A DIF: Medium REF: 9.4 OBJ: 9.4.b. Explain how the conversion of phosphofructokinase-1 between the T and R state is allosterically controlled by ATP, ADP, and AMP. MSC: Understanding 59. In the presence of high concentrations of ADP and F6P, how does the equilibrium shift between the T state and R state of PFK-1? High concentrations of ADP and F6P a. shift equilibrium to the R state. b. shift equilibrium to the T state. c. do not bind to PFK. d. cancel each other out and have no effect.

ANS: A DIF: Medium REF: 9.4 OBJ: 9.4.b. Explain how the conversion of phosphofructokinase-1 between the T and R state is allosterically controlled by ATP, ADP, and AMP. MSC: Applying 60. If a person has a deficiency in fructose-1-P, what effects does that have on the body? a. Fructose-6-P concentrations increase. b. Fructose-6-P is depleted. c. ATP concentrations increase. d. Glucose-6-P concentrations increase.

ANS: A DIF: Difficult REF: 9.4 OBJ: 9.4.b. Explain how the conversion of phosphofructokinase-1 between the T and R state is allosterically controlled by ATP, ADP, and AMP. MSC: Applying 61. List three ways in which flux is controlled through glycolysis. a. regulation of aldolase, PFK-1, and supply and demand of intermediates b. regulation of glucokinase, fructokinase, and number of intermediates c. regulation of glucokinase, PFK-1, and concentration of glucose d. regulation of glucokinase, PFK-1, and supply and demand of intermediates ANS: D DIF: Difficult REF: 9.4 OBJ: 9.4.d. List three ways in which substrate availability and enzyme activity levels control flux through the glycolytic pathway.

MSC: Applying 62. Galactosemia is deficiency in which enzyme?

a. b. c. d.

galactokinase galactose-1-P uridyltransferase UDP-galactose 4-epimerase phosphoglucomutase

ANS: B DIF: Difficult REF: 9.4 OBJ: 9.4.i. Describe the effect of defective galactose-1-P uridylyltransferase.

MSC: Understanding 63. An infant who obtains nourishment from milk and who has galactosemia is unable to convert a. galactose-1-P to glucose-6-P. b. glucose-6-P to galactose-1-P. c. galactose-1-P to glucose-1-P. d. glucose-1-P to galactose-1-P. ANS: C DIF: Difficult REF: 9.4 OBJ: 9.4.i. Describe the effect of defective galactose-1-P uridylyltransferase.

MSC: Applying 64. Glucokinase is a molecular sensor for which molecule? a. glucose b. lactose c. galactose d. maltose ANS: A DIF: Easy REF: 9.4 OBJ: 9.4.e. Explain why glucokinase is a molecular sensor.

MSC: Remembering

65. Which enzyme is the main regulator of glycolysis? a. hexokinase b. PFK-1 c. pyruvate kinase d. aldolase ANS: B DIF: Easy REF: 9.4 OBJ: 9.4.f. List the allosteric activators and inhibitors of phosphofructokinase-1.

MSC: Understanding 66. What is the potential metabolic fate of pyruvate under aerobic conditions? a. produce lactate b. produce ethanol c. produce carbon dioxide and water d. produce glucose ANS: C DIF: Easy REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Understanding

67. What is the potential metabolic fate of pyruvate during strenuous exercise? a. produce lactate b. produce ethanol c. produce carbon dioxide and water d. produce glucose ANS: A DIF: Medium REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Understanding

68. The NADH that is produced by glycolysis under anaerobic conditions is regenerated to NAD+ by the conversion of a. acetaldehyde ethanol. b. lactate pyruvate. c. phosphoenolpyruvate pyruvate. d. pyruvate lactate.

ANS: D DIF: Medium REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Applying

69. What would the effect be of a lack of lactate dehydrogenase? a. buildup of glucose b. buildup of CO2 c. deficiency of ATP d. deficiency of pyruvate ANS: C DIF: Medium REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Understanding

70. What is the fate of pyruvate in the presence of yeast, Saccharomyces cerevisiae? a. converts to CO2 and ethanol b. converts to H2O and CO2 c. converts to lactate and ethanol d. converts to lactate and glucose ANS: A DIF: Medium REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Applying

71. Which of these cofactors participates directly in MOST of the redox reactions in the fermentation of glucose to lactate? a. ADP b. ATP c. NAD+/NADH d. FAD/FADH2 ANS: C DIF: Medium REF: 9.5 OBJ: 9.5.a. List the potential metabolic fates of pyruvate.

MSC: Remembering

72. When a mixture of glucose 6-phosphate and fructose 6-phosphate is incubated with the enzyme phosphohexose isomerase, the final mixture contains twice as much glucose 6-phosphate as fructose 6-phosphate. Which one of the following statements is MOST correct, when applied to the reaction below (R = 8.315 J/mol·K and T = 298 K)?

Glucose 6-phosphate  fructose 6-phosphate a. is +1.7 kJ/mol. b. is –1.7 kJ/mol. c. is zero. d. It is not possible to calculate ANS: A DIF: Difficult REF: 9.3 OBJ: 9.3.n. Demonstrate using Gibbs free energy that glycolysis is an overall favorable reaction pathway.

MSC: Applying 73. Fructose 1,6-bisphosphate is converted to two products with a standard free energy of 23.8 kJ/mol.

Under what condition(s) will this reaction become spontaneous?

a. spontaneous under any conditions b. spontaneous under all conditions c. when there is a high concentration of products relative to the concentration of fructose 1,6-bisphosphate d. when there is a low concentration of products relative to the concentration of fructose 1,6-bisphosphate ANS: D DIF: Medium REF: 9.3 OBJ: 9.3.n. Demonstrate using Gibbs free energy that glycolysis is an overall favorable reaction pathway.

MSC: Applying 74. During glycolysis, the steps between glucose and formation of glyceraldehyde-3-phosphate a. consume 2 ATP and 2 NADH. b. consume 2 ATP. c. produce 2 ADP and 2 NADH. d. produce 2 ATP and 2 NADH. ANS: B DIF: Easy REF: 9.3 OBJ: 9.3.e. Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.

MSC: Applying 75. Which reaction in glycolysis is a redox reaction? a. glyceraldehyde-3-P 1,3-bisphosphoglycerate b. glucose glucose-6-P c. 2-phosphoglycerate phosphoenolpyruvate d. fructose-6-P fructose-1,6-BP ANS: A DIF: Easy REF: 9.3 OBJ: 9.3.a. Describe the glycolytic pathway.

MSC: Understanding

SHORT ANSWER 1. Using glucose metabolism, justify the following statement: Metabolic pathways are highly interdependent and are exquisitely controlled by enzyme activity levels and substrate bioavailability.

ANS: Using the example from the textbook: Before your first meal, blood glucose levels begin to decline, which triggers glucagon release from the pancreas. Glucagon signaling in liver cells activates both glycogen degradation and gluconeogenesis and at the same time inhibits the catabolism of glucose by the glycolytic pathway. This activity causes a release of glucose from the liver into the bloodstream, where it acts as an energy source. After eating a meal, your insulin levels increase as a result of elevated blood glucose. Insulin signaling in the liver leads to stimulation of glucose uptake and glycogen synthesis as well as an increase in glucose catabolism by the glycolytic pathway. These pathways are always active—the only change being the flux through the pathways depending on glucose concentrations.

DIF: Difficult REF: 9.1 OBJ: 9.1.c. Distinguish between catabolic pathways and anabolic pathways.

MSC: Evaluating 2. List the major metabolic pathways in animals and classify each as either an energy conversion pathway or a synthesis/degradation pathway

ANS: Pentose phosphate pathway, gluconeogenesis, urea cycle, fatty acid degradation, and synthesis are all metabolite synthesis and degradation pathways. Glycolysis, citrate cycle, and oxidative phosphorylation are all energy conversion pathways.

DIF: Easy REF: 9.1 OBJ: 9.1.a. List the major metabolic pathways in animals.

MSC: Remembering

3. List the major metabolic pathways in plants and classify each as either an energy conversion pathway or a synthesis/degradation pathway.

ANS: Pentose phosphate pathway, gluconeogenesis, fatty acid degradation, and synthesis are all metabolite synthesis and degradation pathways. Glycolysis, citrate cycle, oxidative phosphorylation, and photosynthesis and carbon fixation are all energy conversion pathways.

DIF: Easy REF: 9.1 plants.

MSC: Remembering

OBJ: 9.1.b. List the major metabolic pathways in

4. Illustrate both the Fisher and Haworth projections for glucose and fructose ANS:

DIF: Medium REF: 9.2 OBJ: 9.2.b. Explain the difference between a Haworth projection and a Fisher projection.

MSC: Applying 5. Given figures A and B below, label the chiral center on each and state if the molecule is a D or L enantiomer.

ANS: Molecule A is the D enantiomer and molecule B is the L enantiomer.

DIF: Medium REF: 9.2 MSC: Understanding

OBJ: 9.2.d. Define chiral center.

6. Differentiate among epimers, anomers, and isomers.

ANS: Epimers are two monosaccharides of same molecular formula that differ in the position of hydroxyl group around only one carbon atom. Anomers differ from each other at the anomeric carbon. Isomers have same formula but a different arrangement of atoms in the molecule.

DIF: Medium REF: 9.2 OBJ: 9.2.f. Differentiate among epimers, anomers, and isomers.

MSC: Analyzing 7. Demonstrate the cyclization of linear glucose to cyclic glucopyranose.

ANS:

DIF: Difficult REF: 9.2 OBJ: 9.2.g. Demonstrate the cyclization of linear glucose to cyclic glucopyranose.

MSC: Analyzing

8. Benedict’s test is a redox reaction between glucose and copper. Draw the reaction between glucose and copper.

ANS: See Figure 9.13a. The glucose is oxidized to a carboxylic acid and copper is reduced from Cu+2 to Cu+.

DIF: Medium test.

MSC: Applying

REF: 9.2

OBJ: 9.2.h. Explain the significance of Benedict’s

9. Explain why disaccharides are more common in nature than monosaccharides.

ANS: Disaccharides are sugars formed by a condensation reaction between two monosaccharides. They are the degradation product of oligosaccharides, with 3 notable disaccharides being lactose, sucrose, and maltose.

DIF: Medium REF: 9.2 OBJ: 9.2.j. List the three common disaccharides in nature.

MSC: Understanding

10. List three common disaccharides in nature and draw the structures of each.

ANS: Lactose, sucrose, trehalose, and maltose.

DIF: Easy REF: 9.2 OBJ: 9.2.j. List the three common disaccharides in nature.

MSC: Remembering

11. Describe how the glycolytic pathway provides aerobic energy to the citrate cycle and oxidative phosphorylation.

ANS: The glycolytic pathway generates ATP and pyruvate, which are required for the other pathways.

DIF: Medium MSC: Applying

REF: 9.3

OBJ: 9.3.a. Describe the glycolytic pathway.

12. In your own words explain why glycolysis is considered one of the core metabolic pathways in nature.

ANS: Glycolysis, or the glycolytic pathway, is considered one of the three core metabolic pathways in nature for three primary reasons: 1. Glycolytic enzymes are hugely conserved among all living organisms. 2. Glycolysis is the primary pathway for ATP generation under anaerobic conditions and in cells lacking mitochondria. 3. Metabolites of glycolysis are precursors for a large number of interdependent pathways.

DIF: Medium REF: 9.3 OBJ: 9.3.b. List the three primary reasons why glycolysis is considered one of the core metabolic pathways in nature. MSC: Understanding 13. List the 10 enzymes required for glycolysis.

ANS: Hexokinase, phosphoglucoisomerase, phosphofructokinase-1, aldolase, triose phosphate isomerase, glyceraldehyde-3-phosphate dehydrogenase, phosphoglycerate kinase, phosphoglycerate mutase, enolase, and pyruvate kinase.

DIF: Medium REF: 9.3 MSC: Remembering

OBJ: 9.3.c. List the 10 enzymes of glycolysis.

14. Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.

ANS: In glycolysis the first five reactions require an investment of 2 ATP to produce high-energy compounds that are then used in stage 2 to generate 4 ATP with substrate-level phosphorylation.

DIF: Medium

REF: 9.3

OBJ: 9.3.e. Distinguish between the energy investment of stage 1 and stage 2 of glycolysis.

MSC: Understanding 15. Three reactions in glycolysis operate far from equilibrium and are potential sites for major flux control. List the three enzymes and explain why each enzyme is or is not the major control site of glycolysis.

ANS: Hexokinase, phosphofructokinase-1, and pyruvate kinase are irreversible and hence potential sites for control flux. These enzymes catalyze highly favorable reactions ( <<0) and are regulated to control flux through the pathway. Hexokinase catalyzes the first reaction of the pathway and is not required if the glycogen is the source of the glucose 6-phosphate. Pyruvate kinase is the final reaction of the cycle and is not a good candidate for regulating the entire pathway.

Phosphofrucokinase-1 catalyzes the third reaction of the pathway, produces a highly exergonic reaction, and is heavily regulated by other substrates.

DIF: Difficult REF: 9.3 OBJ: 9.3.g. List the three irreversible enzymatic reactions in glycolysis.

MSC: Analyzing 16. Draw the five steps required by aldolase to convert fructose 1,6-bisphosate into glyceraldehyde-3-phosphate and dihydroxyacetone phosphate.

ANS: See Figure 9.28 below.

DIF: Difficult REF: 9.3 OBJ: 9.3.i. Identify how fructose-1,6-biphosphatase is cleaved by aldolase.

MSC: Evaluating 17. Illustrate how glyceraldehyde-3-P is converted into 1,3-bisphosphoglycerate by glyceraldehyde-3-P dehydrogenase using the appropriate mechanisms.

ANS: See Figure 9.31 below.

DIF: Difficult REF: 9.3 OBJ: 9.3.j. Explain how glyceraldehyde-3-P is converted into 1,3-bisphosphoglycerate by glyceraldehyde-3-P dehydrogenase.

MSC: Applying 18. Why do individuals with defects in glycolytic enzymes have altered oxygen transport capabilities?

ANS: It is due to increased or decreased levels of 2,3-BPG. If glycolytic enzymes corresponding to reactions upstream of 1,3-bisphosphoglycerate formation are defective, then 2,3-BPG levels are reduced. This shifts the oxygen saturation curve to the left (see Figure 6.17). In contrast, individuals with defects downstream of 1,3-bisphosphoglycerate contain higher levels of 2,3-BPG, which results in decreased oxygen binding capability.

DIF: Difficult REF: 9.3 OBJ: 9.3.l. Explain why individuals with defects in glycolytic enzymes have altered oxygen-transport capabilities.

MSC: Evaluating 19. Draw the mechanism for bisphosphoglycerate mutase and explain how this reaction has an effect on oxygen transport.

ANS:

As shown in Figure 9.34, bisphosphoglycerate mutase converts 1,3-bisphosphoglycerate into 2,3-bisphosphoglycerate. 2,3-Bisphosphoglycerate is an allosteric regulator of hemoglobin. The result is a metabolic link between glycolytic flux and oxygen transport. This link explains why individuals with defects in glycolytic enzymes have altered oxygen-transport capabilities. If glycolytic enzymes corresponding to reactions upstream of 1,3-BPG formation are defective, then 2,3-BPG levels are reduced. The shifts the oxygen saturation curve to the left (see Figure 6.17). In contrast, individuals with defects in glycolytic enzymes downstream of 1,3-BPG contain higher levels of 2,3-BPG, which results in decreased oxygen binding capability.

DIF: Difficult REF: 9.3 OBJ: 9.3.l. Explain why individuals with defects in glycolytic enzymes have altered oxygen-transport capabilities.

MSC: Evaluating 20. Using the figure below, discuss how ATP, ADP, AMP, and fructose-2,6-BP are an allosteric regulator of phosphofructokinase-1.

ANS: The activity of PFK-1 is inhibited by high ATP concentrations where PFK-1 activity is maximally induced in the presence of fructose-2,6-BP. Elevated ADP and/or AMP levels also cause an increase in PFK-1 activity to favor fructose-6-P binding.

DIF: Medium REF: 9.4 OBJ: 9.4.f. List the allosteric activators and inhibitors of phosphofructokinase-1.

MSC: Analyzing 21. Describe how molecules such as maltose can enter glycolysis.

ANS: Maltose is cleaved by maltase to form two molecules of glucose. Glucose can then enter glycolysis. See Figure 9.48 for the entire pathway.

DIF: Difficult REF: 9.4 OBJ: 9.4.a. Explain the role of glucokinase in regulation of the glycolytic pathway.

MSC: Analyzing 22. NAD+ is required for the oxidative step of glycolysis. Briefly discuss how NAD+ is regenerated from NADH under aerobic and anaerobic conditions.

ANS:

Under aerobic conditions, electrons pass from the reduced coenzyme (NADH) through a series of electron carriers to oxygen, the final oxidizing agent. This regenerates the oxidized coenzyme (NAD+). Under anaerobic conditions, the electrons of NADH are transferred to pyruvate to form lactate, the end-product of glycolysis under anaerobic conditions.

DIF: Difficult REF: 9.5 OBJ: 9.5.c. Explain why there is a metabolic requirement for NAD+ in glycolysis.

MSC: Analyzing 23. Explain why people who have the genetic disease lactate dehydrogenase deficiency cannot maintain intense exercise.

ANS: These people cannot maintain sustained periods of intense exercise because of an inability to use glycolysis to produce ATP needed for muscle concentration under anaerobic conditions. If the lactate dehydrogenase reaction is not fully functional, NADH oxidation to regenerate NAD+ does not occur at a rate high enough to sustain glycolysis. This causes the muscle cells to run out of ATP quickly, leading to fatigue and even muscle damage.

DIF: Difficult REF: 9.5 OBJ: 9.5.c. Explain why there is a metabolic requirement for NAD+ in glycolysis.

MSC: Analyzing 24. Explain why in the production of beer, the yeast are first grown under aerobic conditions and then shifted to anaerobic conditions.

ANS: The oxygen is needed for the production of unsaturated fatty acids to produce strong cell membranes. If the membranes contain sufficient levels of sterols, the cells are much stronger, more cells will thrive to finish the fermentation, and the yeast may complete the fermentation significantly faster. If they do not have sufficient levels of sterols, the yeast cells may be killed off by the alcohol that they are producing.

DIF: Difficult REF: 9.5 OBJ: 9.5.c. Explain why there is a metabolic requirement for NAD+ in glycolysis.

MSC: Analyzing 25. Describe galactose metabolism. If a person has galactosemia, what does that indicate about his or her galactose metabolic pathway?

ANS: First galactose is phosphorylated by galactokinase to form galactose-1-P. Second, the enzyme galactose-1-P uridylytransferase converts galactose-1-P and UDP-glucose into glucose-1-P and USP-galactose. Third, the glucose-1-P product of the previous reaction is converted by phosphoglucomutase into glucose-6-P, which can enter the glycolytic pathway. Fourth, the UDP-galactose that was produced in the second reaction is converted back to UDP-glucose by the enzyme UDP-galactose 4-epimerase. The UDP-glucose that is produced from this reaction can now be used by galactose-1-P uridylyltransferase in another reaction.

DIF: Difficult REF: 9.5 OBJ: 9.5.c. Explain why there is a metabolic requirement for NAD+ in glycolysis.

MSC: Analyzing

Chapter 10: The Citrate Cycle MULTIPLE CHOICE 1. Which molecules function as electron acceptors in the citrate cycle? a. NAD+, FAD b. NADH, FADH2 c. GDP, ADP d. GTP, ATP ANS: A DIF: Easy REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Remembering 2. In two turns of the citrate cycle, how many electrons are transferred from the citrate cycle intermediates to NAD+ and FAD? a. 4 b. 8 c. 12 d. 16 ANS: D DIF: Easy REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Applying 3. The primary function of NAD+ in the citrate cycle is that it a. functions as an electron donor. b. is oxidized to produce GTP. c. acts as an electron acceptor. d. phosphorylates ADP. ANS: C DIF: Easy REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Remembering 4. Regeneration of NAD+ and FAD inside the mitochondrial matrix is required because a. anabolic reactions generally require them. b. they produce GDP through the citrate cycle. c. they transport pyruvate through the matrix. d. they maintain flux through the citrate cycle.

ANS: D DIF: Medium REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Analyzing 5. Where do citrate cycle reactions in eukaryotic cells take place? a. cytosol b. mitochondrial matrix c. endoplasmic reticulum d. nucleus ANS: B DIF: Easy REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Remembering

6. The primary function of the citrate cycle is to oxidize a. glucose. b. pyruvate. c. acetyl-CoA. d. citrate.

ANS: C DIF: Easy REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Remembering

7. How many ATP are produced from two turns of the citrate cycle? a. 9 b. 10 c. 18 d. 20 ANS: D DIF: Medium REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Applying

8. Which of the following is a reactant in the net reaction of the citrate cycle? a. CO2 b. H2O c. GTP d. CoA ANS: B DIF: Easy REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Remembering

9. Which of the following is a product of the net reaction of the citrate cycle? a. FAD b. H2O c. H+ d. NAD+ ANS: C DIF: Easy REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Remembering

10. Which molecule in the net reaction of the citrate cycle contributes to the inhibition of pyruvate dehydrogenase? a. FAD b. H2O c. H+ d. NADH ANS: D DIF: Medium REF: 10.1 OBJ: 10.1.b. State the net reaction of the citrate cycle.

MSC: Applying

11. Which enzyme regulates the flux of acetyl-CoA through the citrate cycle? a. pyruvate dehydrogenase b. citrate synthase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: A DIF: Easy REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Remembering

12. Which enzyme in the citrate cycle is activated by CoA? a. pyruvate dehydrogenase b. citrate synthase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: A DIF: Easy REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Applying 13. Which enzyme of the citrate cycle catalyzes the oxidative decarboxylation reaction that produces CO2, NADH, and succinyl-CoA? a. pyruvate dehydrogenase b. citrate synthase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: D DIF: Easy REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Remembering 14. The poison compound 1080 converts fluoroacetate to fluorocitrate. Which enzyme in the citrate cycle is inhibited by this poison? a. aconitase b. citrate synthase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: A DIF: Difficult REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Applying 15. Which enzyme in the citrate cycle produces NADH? a. aconitase b. citrate synthase c. isocitrate dehydrogenase d. fumarase ANS: C DIF: Easy REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Remembering 16. Which enzyme requires CoASH to produce acetyl-CoA? a. pyruvate dehydrogenase b. citrate synthase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: A DIF: Easy REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Remembering 17. Calculate the below.

of a coupled redox reaction with O2 and ferredoxin (Fe2+) using the table

a. b. c. d.

−1.25 −0.39 0.39 1.25

ANS: D DIF: Difficult REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Applying 18. Identify the strongest oxidant in the table below.

a. b. c. d.

O2 oxaloacetate pyruvate ferredoxin

ANS: A DIF: Easy REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Understanding 19. Identify the strongest reductant in the table below.

a. b. c. d.

O2 oxaloacetate pyruvate ferredoxin

ANS: D DIF: Easy REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Understanding 20. Calculate the the table below.

of a redox reaction of pyruvate and hydrogen under standard conditions using

a. b. c. d.

18.33 kJ/mol 36.66 kJ/mol 54.99 kJ/mol 73.32 kJ/mol

ANS: B DIF: Medium REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Applying 21. In linked metabolic pathways, the oxidants in subsequent reactions must a. result in negative values at each reaction step. b. result in positive values at each reaction step. c. have progressively lower standard reduction potentials. d. have progressively higher standard reduction potentials.

ANS: D DIF: Medium REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Understanding 22. Coenzyme A is derived from which of the following vitamins? a. thiamine b. pantothenic acid c. riboflavin d. niacin ANS: B DIF: Easy REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Remembering 23. Which vitamin is the precursor to the coenzyme that functions as a reductant in the pyruvate dehydrogenase complex in the final step of the reaction? a. thiamine

b. pantothenic acid c. riboflavin d. niacin ANS: C DIF: Medium REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Remembering 24. Pantothenic acid is essential for life because it is the vitamin precursor to the molecule that a. provides a reactive disulfide that can participate in redox reactions within the enzyme active site of pyruvate dehydrogenase. b. can accept one or two electrons in redox reactions in the cell. c. is involved in at least 200 redox reactions in the cell. d. is a cofactor in the biosynthetic pathways that produce fatty acids, acetylcholine, heme, and cholesterol.

ANS: D DIF: Medium REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Analyzing 25. Thiamine pyrophosphate functions as a coenzyme in which reactions in the citrate cycle? a. pyruvate dehydrogenase and succinate dehydrogenase b. pyruvate dehydrogenase and -ketoglutarate dehydrogenase c. malate dehydrogenase and succinate dehydrogenase d. malate dehydrogenase and -ketoglutarate dehydrogenase ANS: B DIF: Difficult REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Remembering 26. The disease beriberi is a result of which vitamin deficiency? a. thiamine b. pantothenic acid c. riboflavin d. niacin ANS: A DIF: Easy REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Remembering 27. Identify the coenzyme that provides a reactive disulfide that participates in the redox reaction in the active site of pyruvate dehydrogenase. a. NAD+ b. coenzyme A c. lipoamide d. thiamine pyrophosphate ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Understanding 28. Classify the reaction that occurs at step 5 in the reaction schematic of the pyruvate dehydrogenase reaction below.

a. b. c. d.

isomerization addition oxidation reduction decarboxylation

ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Analyzing 29. Classify the reaction that occurs at step 1 in the reaction schematic of the pyruvate dehydrogenase reaction below.

a. b. c. d.

isomerization addition oxidation reduction decarboxylation

ANS: D DIF: Easy REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Analyzing 30. Classify the reaction that occurs at step 4 in the reaction schematic of the pyruvate dehydrogenase reaction below.

a. b. c. d.

isomerization addition oxidation reduction decarboxylation

ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Analyzing 31. Identify the E1 subunit in the reaction schematic of the pyruvate dehydrogenase reaction below.

a. b. c. d.

pyruvate dehydrogenase dihydrolipoyl dehydrogenase dihydrolipopyl acetyltransferase flavin adenine dinucleotide

ANS: A DIF: Easy REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Understanding 32. Identify the E2 subunit in the reaction schematic of the pyruvate dehydrogenase reaction below.

a. b. c. d.

pyruvate dehydrogenase dihydrolipoyl dehydrogenase dihydrolipopyl acetyltransferase flavin adenine dinucleotide

ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Understanding 33. What is the purpose of the first 3 steps in the pyruvate dehydrogenase reaction? a. regenerate the oxidized form of lipoamide b. form NADH c. transfer electrons d. form acetyl-CoA ANS: D DIF: Medium REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Applying 34. Which coenzyme in the citrate cycle is affected by arsenic? a. coenzyme A b. thiamine pyrophosphate c. dihydrolipopyl acetyltransferase d. flavin adenine dinucleotide ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Remembering 35. Which of the following is the cause of the irreversible blockage of the catalytic activity of lipoamide-containing enzymes? a. cheilosis b. pellagra c. beriberi d. arsenic poisoning ANS: D DIF: Easy REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Understanding 36. A patient seeks medical attention for ulcerous skin lesions. The patient is diagnosed with a. arsenic exposure. b. a deficiency in vitamin B3. c. beriberi. d. cheilosis.

ANS: A DIF: Medium REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Applying 37. Which two enzymes in the citrate cycle are affected by arsenic poisoning? a. pyruvate dehydrogenase and succinate dehydrogenase b. pyruvate dehydrogenase and -ketoglutarate dehydrogenase c. malate dehydrogenase and succinate dehydrogenase d. malate dehydrogenase and -ketoglutarate dehydrogenase

ANS: B DIF: Medium REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Remembering 38. Arsenite affects the lipoamide coenzymes of the pyruvate dehydrogenase reaction by a. acting as a competitive inhibitor. b. covalently modifying the coenzyme. c. being a noncompetitive inhibitor. d. modifying the coenzyme through electrostatic interactions.

ANS: B DIF: Medium REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Understanding 39. If acetyl-CoA is not metabolized by the citrate cycle, the molecule in the cell a. undergoes fatty acid metabolism. b. is transported across the cell membrane. c. is used to synthesize amino acids. d. is used during glycolysis.

ANS: A DIF: Easy REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Analyzing 40. How would an increase in Ca2+ be expected to affect the pyruvate dehydrogenase reaction? a. The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity. b. The last step of the pyruvate dehydrogenase reaction is blocked, resulting in a decrease in activity. c. The E1 subunit is phosphorylated by pyruvate dehydrogenase kinase, and the catalytic activity of pyruvate dehydrogenase decreases. d. The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.

ANS: D DIF: Medium REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Applying 41. How is the pyruvate dehydrogenase reaction regulated? a. pH and enzyme conformation b. pH and the protonation state of the active site c. allosteric control and covalent modification d. product inhibition ANS: C DIF: Easy REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Understanding 42. How would a high NADH to NAD+ ratio be expected to affect the pyruvate dehydrogenase reaction? a. The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an increase in pyruvate dehydrogenase activity. b. The last step of the pyruvate dehydrogenase reaction is blocked, resulting in a decrease in activity. c. The E1 subunit is phosphorylated by pyruvate dehydrogenase kinase, and the catalytic

activity of pyruvate dehydrogenase decreases. d. The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.

ANS: B DIF: Medium REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Applying 43. How would an increased level of acetyl-CoA be expected to affect the pyruvate dehydrogenase reaction? a. The pyruvate dehydrogenase kinase enzyme activity would increase, resulting in an inhibition of pyruvate dehydrogenase activity. b. The last step of the pyruvate dehydrogenase reaction would be blocked, resulting in a decrease in activity. c. The E1 subunit would be phosphorylated by pyruvate dehydrogenase kinase, and the catalytic activity of pyruvate dehydrogenase would decrease. d. The pyruvate dehydrogenase phosphatase-1 enzyme would increase, resulting in pyruvate dehydrogenase activation at an accelerated rate.

ANS: A DIF: Medium REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Applying 44. The reaction catalyzed by __________is the most endergonic reaction in the citrate cycle. a. fumarase b. succinate dehydrogenase c. malate dehydrogenase d. aconitase ANS: C DIF: Easy REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Remembering 45. The reaction catalyzed by __________ is the most exergonic reaction in the citrate cycle. a. citrate synthase b. fumarase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: D DIF: Easy REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Remembering 46. Why is the of the condensation of oxaloacetate and acetyl-CoA highly favorable? a. The addition of inorganic phosphate provides energy, resulting in the highly favorable nature of this reaction. b. Allosteric regulations of the reaction cause a release of energy, making the reaction thermodynamically favorable. c. The iron-sulfur cluster in the enzyme reduces the activation energy of the reaction, resulting in the favorable . d. The hydrolysis of the thioester bond in citryl-CoA results in the highly exergonic reaction.

ANS: D DIF: Medium REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Understanding

47. The reaction catalyzed by __________ is likely to be reversible under cellular conditions according to the . a. malate dehydrogenase b. citrate synthase c. succinate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: C DIF: Medium REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Applying 48. According to the , which of the following exergonic reactions is most likely irreversible under normal cellular conditions and is considered to be the rate-limiting step of the citrate cycle? a. citrate synthase b. fumarase c. isocitrate dehydrogenase d.

-ketoglutarate dehydrogenase ANS: C DIF: Easy REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Remembering 49. Which reactions in the citrate cycle produce CO2?

a. b. c. d.

1 and 2 2 and 3 3 and 4 4 and 5

ANS: C DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 50. Which reactions in the citrate cycle produce NADH?

a. b. c. d.

1, 2, and 4 3, 4, and 8 3, 6, and 7 5, 6, and 8

ANS: B DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 51. Which reaction in the citrate cycle produces GTP?

a. b. c. d.

3 4 5 6

ANS: C DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 52. Which reaction in the citrate cycle produces FADH2?

a. b. c. d.

3 4 5 6

ANS: D DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 53. Which reaction in the citrate cycle produces NADH?

a. b. c. d.

4 5 6 7

ANS: D DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 54. Which reaction in the citrate cycle produces CO2?

a. 1 b. 2 c. 3

d. 5 ANS: C DIF: Medium REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 55. A high concentration of which molecule would inhibit citrate synthase in the citrate cycle? a. AMP b. ADP c. NAD+ d. ATP ANS: D DIF: Easy REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Understanding 56. What enzyme in the citrate cycle is activated by high concentrations of AMP? a. isocitrate dehydrogenase b.

-ketoglutarate dehydrogenase c. citrate synthase d. succinyl-CoA synthetase ANS: B DIF: Easy REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Understanding 57. An in vitro study shows that isocitrate dehydrogenase is activated in the citrate cycle. What is a possible explanation for the activation? a. high levels of ATP b. low levels of ATP c. high levels of NADH d. low levels of AMP ANS: B DIF: Medium REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Applying 58. An in vitro study shows that -ketoglutarate dehydrogenase is inhibited in the citrate cycle. What is a possible explanation for this inhibition? a. high levels of ATP b. low levels of Ca2+ c. low levels of NADH d. high levels of ADP ANS: A DIF: Medium REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Applying 59. High levels of ATP would result in the inhibition of which enzyme in the citrate cycle? a. succinate dehydrogenase b. isocitrate dehydrogenase c. malate dehydrogenase d. fumarase ANS: B DIF: Easy REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high

concentrations of AMP, ADP, or ATP.

MSC: Applying

60. In the citrate cycle, a high concentration of NADH would result in a. activation of citrate synthase. b. inhibition of -ketoglutarate dehydrogenase. c. inhibition of fumarase. d. activation of -ketoglutarate dehydrogenase.

ANS: B DIF: Medium REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Applying 61. An in vitro study shows that citrate synthase is inhibited in the citrate cycle. What is a possible explanation for this inhibition? a. high levels of ADP b. low levels of succinyl-CoA c. high levels of NADH d. high levels of AMP ANS: C DIF: Easy REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Applying 62. A high NADH to NAD+ ratio would inhibit which enzyme in the citrate cycle? a. succinate dehydrogenase b. succinyl-CoA synthetase c. aconitase d. isocitrate dehydrogenase ANS: D DIF: Easy REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Applying 63. The regulatory mechanism in the citrate cycle involving the NADH to NAD+ ratio is considered to be an example of regulation by a. pH and protonation state. b. product inhibition. c. covalent modification. d. pH and enzyme conformation.

ANS: B DIF: Medium REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Applying 64. A low NADH to NAD+ ratio would activate which enzyme in the citrate cycle? a. succinyl-CoA synthetase b. fumarase c. citrate synthase d. succinate dehydrogenase ANS: C DIF: Medium REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Applying 65. The citrate cycle is considered to be a(n) __________ pathway.

a. b. c. d.

anabolic catabolic anaplerotic amphibolic

ANS: D DIF: Easy REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Remembering

66. Which anaplerotic reaction balances the input of oxaloacetate with acetyl-CoA in the citrate cycle by converting pyruvate into oxaloacetate? a. pyruvate carboxylase b. malate dehydrogenase c. malic enzyme d. pyruvate kinase ANS: A DIF: Easy REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Understanding

67. The anaplerotic reaction catalyzed by pyruvate carboxylase requires which coenzyme? a. niacin b. biotin c. riboflavin d. thiamine ANS: B DIF: Easy REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Remembering

68. When the citrate cycle is inhibited, which two metabolites are exported to the cytosol for fatty acid and cholesterol synthesis? a. malate and succinyl-CoA b. succinyl-CoA and -ketoglutarate c.

-ketoglutarate and citrate d. citrate and malate ANS: D DIF: Easy REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Understanding

69. Which citrate cycle intermediate is siphoned off the citrate cycle during starvation? a. succinyl-CoA b. malate c.

-ketoglutarate d. fumarate ANS: B DIF: Difficult REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Applying

70. Which anaplerotic reactions do plants, yeast, and bacteria use to generate oxaloacetate? a. pyruvate carboxylase b. malic enzyme c. phosphoenolpyruvate carboxylase d. malate dehydrogenase ANS: C DIF: Medium REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Remembering

71. Which citrate cycle metabolite is used as a precursor for heme biosynthesis?

a. succinyl Co-A b. oxaloacetate c.

-ketoglutarate d. malate ANS: A DIF: Easy REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Understanding 72. What is the fate of oxaloacetate when it is not used in the citrate cycle? a. cholesterol synthesis b. heme synthesis c. amino acid synthesis d. gluconeogenesis ANS: C DIF: Medium REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Applying 73. Predict the fate of -ketoglutarate when it is not used in the citrate cycle. a. cholesterol synthesis b. heme synthesis c. gluconeogenesis d. amino acid synthesis ANS: D DIF: Easy REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Applying 74. Which citrate cycle intermediate is also used in gluconeogenesis? a. oxaloacetate b.

-ketoglutarate c. fumarate d. succinate ANS: A DIF: Medium REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Analyzing 75. Predict the fate of succinyl-CoA in the cell when it is not in the citrate cycle. a. cholesterol synthesis b. heme synthesis c. gluconeogenesis d. amino acid synthesis ANS: B DIF: Easy REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Applying SHORT ANSWER 1. Describe the fate of NADH and FADH2 produced in the citrate cycle.

ANS:

NADH and FADH2 enter the electron transport system, where they are oxidized to NAD+ and FAD. They produce ATP by the process of oxidative phosphorylation.

DIF: Medium REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Understanding 2. Compare and contrast the functions of NAD+ and FAD in the citrate cycle.

ANS: Both NAD+ and FAD act as coenzymes. They accept electrons from the citrate cycle intermediates and are oxidized in the electron transport chain. The citrate cycle requires three NAD+ molecules, which accept a total of six electrons. In contrast, the cycle only requires one FAD molecule, which accepts two electrons.

DIF: Medium REF: 10.1 OBJ: 10.1.a. Describe the role of NAD+ and FAD in the citrate cycle.

MSC: Analyzing 3. Use the overall net reaction of the citrate cycle to explain why excess NADH inhibits the pyruvate dehydrogenase reaction.

ANS: NADH is a product in the balanced citrate cycle reaction. The pyruvate dehydrogenase reaction produces acetyl-CoA, which is a reactant in the balanced citrate cycle. When the cell has excess NADH, there is no reason to produce more. The pyruvate dehydrogenase reaction is inhibited so that the reactant acetyl-CO is diverted to fatty acid synthesis and more NADH is not produced.

DIF: Difficult cycle.

MSC: Applying

REF: 10.1

OBJ: 10.1.b. State the net reaction of the citrate

4. What two features of the citrate cycle make it unique compared with linear metabolic pathways?

ANS: Oxaloacetate is both the substrate for the first reaction and the last reaction, unlike linear metabolic pathways. Because of this, if just one citrate cycle intermediate is added to the cells, the concentrations of all the intermediates increase. Additionally, the enzymes pyruvate dehydrogenase and pyruvate carboxylase control the flow of acetyl-CoA and oxaloacetate into the citrate cycle.

DIF: Difficult REF: 10.1 OBJ: 10.1.c. List the functions of the key enzymes of the citrate cycle.

MSC: Analyzing 5. Use the figure below to answer the following questions.

A. The electrochemical cell shown here is measuring the reduction potential of Fe2+/Fe3+ using a reference hydrogen half reaction. Write each half reaction on the figure and show the flow of electrons.

B. Do these oxidants have a higher or lower affinity for electrons compared with H+? Explain how you know this using information from the experiment.

ANS: A. The reference hydrogen half reaction should be written on the left side of the cell with the electrons flowing from the left to the right. The iron half reaction should be on the right side of the cell.

B. These oxidants have a higher affinity for electrons than H+ because the standard reduction potential is greater than 0 (0.77 V).

DIF: Medium REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Applying 6. Using the table below, calculate and determine if the conversion from malate to oxaloacetate is favorable under standard biochemical conditions.

Malate + NAD+ → Oxaloacetate + H+ + NADH

ANS: Calculate the for the coupled redox reaction. = –0.17 – (–0.32) = +0.15 Then, use this value to determine Gibbs free energy. = –nF = –(2)(96.48 kJ/V mol)(+0.15 V) = –28.94 kJ/mol This calculation shows that the conversion from malate to oxaloacetate is favorable because is less than 0 under standard biochemical conditions.

DIF: Difficult REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Applying 7. Explain what redox reaction values mean regarding spontaneity. How does the spontaneity affect the arrangement of multiple redox reactions in a linked metabolic pathway?

ANS: Redox reactions with positive values proceed spontaneously, whereas redox reactions with negative values do not proceed spontaneously. In linked metabolic pathways, the oxidants in subsequent reactions must have progressively more positive standard reduction potentials than in the previous reactions.

DIF: Medium REF: 10.1 OBJ: 10.1.d. Explain how change in free energy can be found from differences in reduction potential.

MSC: Understanding | Applying

8. Corn-rich diets in Europe in the 1700s resulted in the disease pellagra. Though Mexico also had a corn-rich diet at the time, this disease was rare there. Propose a reason for this observation.

ANS: Pellagra is the result of a niacin deficiency. Niacin is the precursor to NAD+ and NADP+, which are needed for approximately 200 redox reactions in the cell, as well as the citrate cycle. Niacin is present in corn but is bound to a protein that greatly reduces the ability of the vitamin to be absorbed by the small intestine. Unlike in Europe, in Mexico the corn was soaked in a lime solution (calcium oxide), which released niacin from the protein when the corn was heated.

Therefore, niacin deficiency was rare in Mexico.

DIF: Difficult REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Evaluating 9. Coenzyme A does not readily cross the cell membrane. However, coenzyme A functions as an acyl carrier in the citrate cycle in the mitochondrial matrix. Explain how coenzyme A crosses the cell membrane to participate in the citrate cycle.

ANS: Coenzyme A is degraded in the gut to pantothenic acid. Pantothenic acid is absorbed and transported through the circulatory system to various tissues, where it is transported across the cell membrane. Once inside the cell it is converted back to coenzyme A by several phosphorylation reactions and reactions that require ASTP, cysteine, and cytidine triphosphate.

DIF: Medium REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Understanding 10. Explain why riboflavin is critical to the citrate cycle.

ANS: Riboflavin is the precursor to flavin adenine dinucleotide (FAD). FAD is a coenzyme in the pyruvate dehydrogenase complex, functioning as a reductant. It is also covalently bound to the enzyme succinate dehydrogenase and participates in the conversion of succinate to fumarate.

DIF: Medium REF: 10.2 OBJ: 10.2.a. Explain the importance of the vitamins niacin, riboflavin, pantothenic acid, and thiamine to the citrate cycle.

MSC: Understanding 11. Outline the five reaction steps of the conversion from pyruvate to acetyl-CoA. ANS: Step 1: Pyruvate dehydrogenase catalyzes a decarboxylation reaction once it binds pyruvate, releasing carbon dioxide. This forms hydroxyethyl-TPP. Step 2: Hydroxyethyl-TPP reacts with the disulfide group of the lipoamide moiety on dihydrolipoyl acetyltransferase, generating acetyl-dihydrolipoamide.

Step 3: Dihydrolipoyl transacetylase catalyzes the transfer of an acetyl group to CoA to yield acetyl-CoA. Step 4: Dihydrolipoyl dehydrogenase oxidizes lipoic acid to the disulfide form.

Step 5: An electron transfer from dihydrolipoyl dehydrogenase-FADH2 regenerates NADH. DIF: Difficult REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA.

MSC: Analyzing 12. Compare the two roles of lipoic acid in the pyruvate dehydrogenase reaction.

ANS: Lipoic acid provides a reactive disulfide that participates in redox reactions at the enzyme active site. Lipoic acid forms the lipoamide that participates in the transfer of the acetyl group.

DIF: Difficult REF: 10.2 OBJ: 10.2.b. Classify the organic reaction that converts pyruvate into acetyl-CoA. MSC: Analyzing 13. Explain how arsenic affects the pyruvate dehydrogenase reaction.

ANS: Arsenite covalently modifies lipoamide coenzymes in the pyruvate dehydrogenase complex. For example, the arsenite binds with the sulfide groups of dihydrolipoyl acetyl transferase. This results in the oxidized form of the lipoamide that cannot be regenerated.

DIF: Medium REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Understanding 14. You have a patient who has been traveling through India and Bangladesh who is presenting with ulcerous skin lesions. What could cause this issue and what is your recommendation?

ANS: The symptom plus the travel locales are indicative of arsenic poisoning. The patient should have his or her water tested for arsenic and avoid drinking from the water supply because it could be contaminated. Arsenic is also present in some paints, so the patient should avoid paints as well.

DIF: Difficult REF: 10.2 OBJ: 10.2.c. Summarize the effect of arsenic on pyruvate dehydrogenase.

MSC: Applying 15. You exercise vigorously for 30 minutes. Which chemical compounds would you expect to be elevated that would affect the regulation of pyruvate dehydrogenase? State the substances and explain how they would affect the regulation.

ANS: Muscle contraction results in an increase in calcium ions as well as an increased demand for ATP. The NADH to NAD+ ratio is also low when cells are active metabolically. These chemicals shift the metabolic flux toward catabolic pathways, so they would activate pyruvate dehydrogenase to produce acetyl-CoA, which would produce ATP through the citrate cycle. These molecules function as signals to turn on the oxidative enzymes to produce energy.

DIF: Difficult REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Applying 16. Compare the two ways the pyruvate dehydrogenase reaction is controlled by the cell.

ANS:

Pyruvate dehydrogenase is regulated by allotter control and covalent modification. The allosteric control includes NADH to NAD+ ratio and CoA to acetyl-CoA ratio. When NADH to NAD+ ratio is high, NADH competes with NAD+ for binding with dihydrolipoyl dehydrogenase, preventing the reoxidation of NADH in the last step of the reaction. When acetyl-CoA levels are high, acetyl CoA competes with CoA for binding to dihydrolipoyl acetyltransferase, blocking pyruvate decarboxylation. Covalent modification includes the phosphorylation of the pyruvate dehydrogenase enzyme catalyzed by pyruvate dehydrogenase kinase. This covalent modification deactivates the pyruvate dehydrogenase enzyme.

DIF: Difficult REF: 10.2 OBJ: 10.2.d. Hypothesize why the activity of pyruvate dehydrogenase is so tightly controlled by the cell.

MSC: Analyzing 17. The of the conversion from malate to oxaloacetate in the last reaction of the citrate cycle is very large, indicating this reaction is not thermodynamically favorable. Propose an explanation for how this reaction can proceed in the forward direction despite the very positive value.

ANS: The oxaloacetate concentrations are kept very low in the cell by the conversion to citrate in the first reaction, which is strongly exergonic. This allows the reaction to proceed in the forward direction even though it is endergonic.

DIF: Medium REF: 10.3 OBJ: 10.3.a. Classify the eight reactions of the citrate cycle as either exergonic or endergonic.

MSC: Evaluating 18. Briefly describe the eight reactions from the citrate cycle, including the identity of the organic reactions and the energetic products.

ANS: In the first reaction, oxaloacetate undergoes a condensation reaction with acetyl-CoA to form citrate. Citrate then undergoes an isomerization reaction to form isocitrate, which undergoes an oxidative decarboxylation reaction to form -ketoglutarate. -Ketoglutarate undergoes another decarboxylation reaction to form succinyl-CoA. During each of these decarboxylation reactions, CO2 is released and an NADH molecule is produced. The thiol bond from succinyl-CoA is cleaved, producing GTP via a substrate level phosphorylation. Succinate undergoes to redox reaction, producing fumarate and an FADH2 molecule. Fumarate undergoes a hydration reaction to form malate, and malate undergoes a redox reaction to form oxaloacetate and the final NADH molecule.

DIF: Difficult REF: 10.3 OBJ: 10.3.b. Identify the steps of the citrate cycle in which NADH, FADH2, CO2, and GTP are produced.

MSC: Understanding 19. ATP regulates the citrate cycle but is not found as a direct product of any of the reactions. Explain how ATP regulates the cycle and identify the enzymes that ATP regulates.

ANS: ATP is an example of feedback inhibition. Low levels of ATP in the cell signal that the cell needs more energy, and the citrate cycle is activated. Conversely, high levels of ATP in the cell signal that no more is needed, and the citrate cycle is inhibited. The three enzymes in the citrate cycle that ATP regulates are citrate synthase, isocitrate dehydrogenase, and -ketoglutarate dehydrogenase.

DIF: Medium REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Understanding 20. Hypothesize how high concentrations of the following would either inhibit or activate the specific enzymes of the citrate cycle and the citrate cycle as a whole.

A. AMP B. ATP C. ADP ANS: A. High levels of AMP would activate -ketoglutarate dehydrogenase, resulting in the activation of the citrate cycle.

B. High levels of ATP inhibit the citrate cycle by inhibiting citrate synthase, isocitrate dehydrogenase, and -ketoglutarate dehydrogenase, resulting in the inhibition of the citrate cycle.

C. High levels of ADP would activate isocitrate dehydrogenase and citrate synthase, resulting in the activation of the citrate cycle.

DIF: Medium REF: 10.4 OBJ: 10.4.a. Hypothesize whether the citrate cycle would be activated or inhibited by high concentrations of AMP, ADP, or ATP. MSC: Evaluating 21. Explain the effect a high concentration of NADH has on the citrate cycle.

ANS: High NADH implies that the cell does not need energy, resulting in the inhibition of the citrate cycle. Specifically, high NADH concentrations inhibit the citrate cycle by inhibiting citrate synthase, isocitrate dehydrogenase, and -ketoglutarate dehydrogenase.

DIF: Easy REF: 10.4 OBJ: 10.4.b. Describe the effect of high concentrations of NADH on the citrate cycle.

MSC: Understanding 22. Predict what happens to citrate in a cell when ATP and NADH concentrations are high.

ANS: The citrate cycle is inhibited under these conditions, so citrate is exported from the mitochondria to the cytosol. In the cytosol, citrate is cleaved by citrate lyase, releasing acetyl-CoA and oxaloacetate.

DIF: Medium REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Applying

23. Predict the fate of acetyl-CoA and oxaloacetate when the citrate cycle is inhibited.

ANS: Acetyl Co-A is used in the cytosol for cholesterol and fatty acid biosynthesis. Oxaloacetate can either be converted to malate in the cytosol by malate dehydrogenase or it can be converted to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase for gluconeogenesis. Oxaloacetate also functions as a precursor to the amino acids aspartate and glutamate.

DIF: Medium REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA in the cell.

MSC: Applying

24. Compare and contrast the anaplerotic nature of the pyruvate carboxylase reaction and the phosphoenolpyruvate carboxylase reaction.

ANS: Both reactions help replenish oxaloacetate in the citrate cycle. The pyruvate carboxylase reaction replenishes oxaloacetate from pyruvate. Phosphoenolpyruvate carboxylase replenishes the citrate cycle intermediate from the reactants phosphoenolpyruvate and bicarbonate.

DIF: Difficult REF: 10.5 OBJ: 10.5.a. List the anaplerotic reactions of the citrate cycle.

MSC: Analyzing

25. In the following figure, identify and explain the specific pathways (A–F) that are shared with the citrate cycle intermediates.

ANS: A. Succinyl-CoA and glycine synthesize -aminolevulinic acid via -aminolevulinic acid synthase, which is an essential component for heme biosynthesis.

B. -Ketoglutarate undergoes a transamination reaction to form the carbon backbone of the amino acids aspartate and glutamate.

C. Oxaloacetate undergoes a transamination reaction to form the carbon backbone of the amino acids aspartate and glutamate.

D. Oxaloacetate is a substrate for phosphoenolpyruvate carboxykinase, generating phosphoenolpyruvate for glucose synthesis.

E. Acetyl Co-A is used in fatty acid biosynthesis.* F. Acetyl Co-A is used in cholesterol biosynthesis.* *Note: E and F can be interchangeable.

DIF: Difficult REF: 10.5 OBJ: 10.5.b. Describe the potential fates of oxaloacetate, alpha-ketoglutarate, and succinyl-CoA

in the cell.

MSC: Understanding

Chapter 11: Oxidative Phosphorylation MULTIPLE CHOICE 1. The major purpose of the electron transport system is to a. reduce oxygen to water. b. reoxidize NADH and use that energy to pump protons across a membrane. c. produce ATP. d. produce NADH for cellular respiration.

ANS: B DIF: Medium REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Understanding 2. Approximately how many more ATPs are made from one glucose molecule under aerobic conditions with oxidative phosphorylation than under anaerobic conditions? a. 0 b. 2 c. 30 d. 104 ANS: C DIF: Medium REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Analyzing 3. The ultimate electron acceptor of the mitochondrial electron transport system is a. O2. b. NADH. c. H2O. d. cytochrome c.

ANS: A DIF: Easy REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Understanding 4. What are the principle physiological electron donors for the mitochondrial electron transport pathway? a. FADH2 and NADH b. FADH2, NADH, and NADPH c. NADH only d. UQH2, NADH, and FADH2 ANS: A DIF: Easy REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Remembering 5. Which process or pathway describes the coupling of the oxidation reaction of NADH with the formation of ATP? a. electron transport system b. chemiosmotic theory c. proton motive force d. oxidative phosphorylation ANS: D

DIF: Medium

REF: 11.1

OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Remembering 6. Which of the following statements about the chemiosmotic theory is true? a. It requires an enclosed mitochondrial membrane. b. The membrane ATPase (or ATP synthase) has no significant role in the theory. c. Energy is coupled through a transmembrane electron gradient. d. It explains how ATP energy is used to create a pH gradient.

ANS: A DIF: Medium REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Analyzing 7. Protons are pumped by mitochondria during active electron transport a. into the thylakoid lumen. b. outside the outer mitochondrial membrane. c. into the mitochondrial matrix. d. outside the inner mitochondrial membrane.

ANS: D DIF: Easy REF: 11.1 OBJ: 11.1.b. Compare the direction of proton flow in the mitochondrion to that in the chloroplast.

MSC: Understanding 8. In the mitochondrial electron transport system, the electron from NADH moves from __________ the mitochondria through the protein complexes to __________ the mitochondria. a. outside; outside b. outside; inside c. inside; inside d. inside; outside ANS: C DIF: Medium REF: 11.1 OBJ: 11.1.b. Compare the direction of proton flow in the mitochondrion to that in the chloroplast.

MSC: Remembering 9. Which statement comparing chloroplasts and mitochondria is true? a. Chloroplasts and mitochondria each contain two membranes. b. Chloroplasts and mitochondria use electrons from NADH to create a proton gradient. c. Chloroplasts pump protons outside the organelle, while mitochondria pump protons inside the inner part of the organelle. d. Chloroplasts and mitochondria use energy from a proton gradient to make ATP. ANS: D DIF: Medium REF: 11.1 OBJ: 11.1.b. Compare the direction of proton flow in the mitochondrion to that in the chloroplast.

MSC: Analyzing 10. Mitochondria a. selectively transport molecules from the cytoplasm to the intermembrane space. b. maintain a pH gradient across the inner mitochondrial membrane. c. are found one per cell. d. have a matrix that is continuous with the cytoplasm.

ANS: B DIF: Medium REF: 11.1 OBJ: 11.1.c. Describe the structure of the mitochondrion.

11. Mitochondria

MSC: Understanding

a. have a porous inner membrane and nonporous outer membrane. b. have a higher pH inside the matrix than outside during active electron transport. c. have an outer membrane that is composed of lipids and protein electron transport complexes. d. generate ATP for the cell under anaerobic and aerobic conditions.

ANS: B DIF: Medium REF: 11.1 OBJ: 11.1.c. Describe the structure of the mitochondrion.

MSC: Understanding

12. Studies of the inner mitochondrial membrane reveal its composition to be approximately 20% lipid bilayer and 80% protein. What is true of these proteins? a. Abundant collagen proteins form connective tissues to strengthen the membrane against the pH gradient. b. High levels of proteins are required to metabolize glucose in the glycolysis pathway for rapid energy production. c. The proteins form highly folded cristae structures. d. The proteins are largely electron transport complexes and ATP synthase enzymes.

ANS: D DIF: Medium REF: 11.1 OBJ: 11.1.c. Describe the structure of the mitochondrion.

MSC: Understanding

13. As electrons from NADH pass through the electron transport system, a. the oxidized form of ADP is reduced to ATP. b. the reduction potential of the mitochondria becomes more thermodynamically favorable. c. the resulting electron gradient is used to make ATP. d. protons are pumped across the mitochondrial membrane to create a pH gradient.

ANS: D DIF: Medium REF: 11.1 OBJ: 11.1.d. Describe the role of the electron transport system.

MSC: Understanding 14. What is the fate of NADH after it donates its electrons to the electron transport system? a. NAD+ is excreted from the cell and sent to the liver for final degradation. b. NADH is used for cellular biosynthesis. c. NAD+ is re-reduced by the TCA cycle or glycolysis and returns to electron transport system, where the process is repeated. d. NAD+ is fed into the TCA cycle for oxidation of CO2.

ANS: C DIF: Difficult REF: 11.1 OBJ: 11.1.d. Describe the role of the electron transport system.

MSC: Evaluating 15. The energy released during mitochondrial electron transport processes is used to a. make ATP. b. pump protons across the membrane. c. heat the mitochondria. d. synthesize carbohydrates.

ANS: B DIF: Medium REF: 11.1 OBJ: 11.1.d. Describe the role of the electron transport system.

MSC: Analyzing 16. What would happen to the ETC and oxidative phosphorylation pathway in the presence of excess NADH if the mitochondrial matrix were not closed, but opened up to the cytoplasm? a. The ETC complexes would function as normal, but no ATP would be made.

b. The ETC and synthesis of ATP would continue as normal. c. The ETC complexes would transfer electrons from NADH to O2, but no protons would be pumped. d. The NADH would react directly with O2, generating excess heat.

ANS: A DIF: Difficult REF: 11.1 OBJ: 11.1.d. Describe the role of the electron transport system.

MSC: Applying 17. The TCA cycle is dependent on O2 to a. enable the regeneration of the NAD+ by the electron transport system. b. oxidize the sugar carbons to CO2. c. support cellular combustion reactions. d. serve as a substrate for the oxidoreductase enzymes.

ANS: A DIF: Difficult REF: 11.1 OBJ: 11.1.d. Describe the role of the electron transport system.

MSC: Applying 18. Use the table below to answer the question.

Standard Reduction Potentials ( NAD+ + H+ + 2 e− FAD + 2 H+ + 2 e− O2 + 4 H+ + 4 e−

NADH FADH2 2 H2O

) for Half Reactions −0.32 V −0.22 V +0.82 V

In the direction indicated, which of the following reactions are thermodynamically favored?

I. NAD+ + H2O O2 + NADH II. FADH2 + H2O O2 + FAD III. NADH + O2 H2O + NAD+ a. I and II b. I and III c. I, II, and III d. III only ANS: D DIF: Easy REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Evaluating 19. Which reaction does the concept of oxidative phosphorylation refer to? a. O2 + ADP + Pi 2 H2O + ATP b. NADH + H+ + 1/2 O2 NAD+ + H2O c. ADP + Pi ATP d. NADH + 1/2 O2 + H+ + ADP + Pi NAD+ + ATP + H2O ANS: D DIF: Difficult REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Understanding 20. A decrease in __________ would be LEAST likely to affect the processes of the electron transport system. a. oxygen concentrations in the cell b. the TCA cycle activity c. cellular CO2 concentrations

d. the concentration of cellular NADH ANS: C DIF: Difficult REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Analyzing 21. Which of the following is NOT a part of oxidative phosphorylation? a. NADH is oxidized to NAD+. b. O2 is reduced to H2O. c. Electrons from O2 are transferred to ATP. d. The pumping of protons is coupled with the formation of ATP. ANS: C DIF: Medium REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Analyzing 22. The first enzyme in the electron transport system is referred to as complex I, otherwise known as a. ATP synthase. b. NADH-ubiquinone oxidoreductase. c. succinate dehydrogenase. d. cytochrome c oxidase.

ANS: B DIF: Medium REF: 11.1 OBJ: 11.1.f. Name the major enzymes of the electron transport system.

MSC: Understanding 23. The last enzyme in the electron transport system, where O2 is reduced to water, is called a. NADH-ubiquinone oxidoreductase. b. ATP synthase. c. ubiquinone cytochrome c oxidoreductase. d. cytochrome c oxidase.

ANS: D DIF: Medium REF: 11.1 OBJ: 11.1.f. Name the major enzymes of the electron transport system.

MSC: Remembering 24. Which of the following is an electron carrier in the mitochondrial electron transport system? a. proton b. water c. quinone d. ATP ANS: C DIF: Easy REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Understanding 25. The electron transport complexes found in the electron transport system a. contain multiple electron transfer cofactors that facilitate electron transfer through the complexes. b. are bound to the outer mitochondrial membrane. c. pump protons from outside the mitochondria to the mitochondrial matrix on electron transfer. d. absorb light energy that results in electron transfer.

ANS: A DIF: Easy REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Analyzing 26. Identify the correct order of electron transfers in the electron transport chain starting from FADH2. a. complex I complex II complex III complex IV b. complex II complex III cytochrome c complex IV c. complex II coenzyme Q complex IV ATP synthase d. complex I coenzyme Q complex III complex IV ANS: B DIF: Easy REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Understanding 27. Which is the only electron carrier in the electron transport system that is not embedded in a membrane? a. ATP b. cytochrome c c. coenzyme Q d. complex I ANS: B DIF: Easy REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Understanding 28. Which statement is true of the mitochondrial electron transport system? a. All the electron carriers are located in enzyme complexes. b. All the electrons in the chain end up on O2 to produce water. c. The pH drops in the mitochondria as electrons pass through the system. d. Protons are pumped from the inner membrane space to the mitochondrial matrix during the electron transfer.

ANS: B DIF: Medium REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Analyzing 29. For one electron entering the electron transport chain at complex I, how many times is it handed off between redox active cofactors on its way through the enzyme complexes to end up on O2? a. ~2000 b. ~200 c. ~20 d. ~2 ANS: C DIF: Difficult REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Evaluating 30. Which one of the following is involved in the flow of electrons from NADH through the electron transport system to molecular oxygen (O2)? a. ATP synthase b. complex II c. complex III d. ATP ANS: C DIF: Easy REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Remembering

31. Which is NOT involved in the transfer of reducing equivalents from succinate to molecular oxygen (O2)? a. cytochrome c b. coenzyme Q c. complex I d. complex II ANS: C DIF: Easy REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Remembering 32. What is the reaction catalyzed by complex III in the electron transport system? a. UQH2 + O2 UQ + H2O b. UQH2 + complex IV+ UQ + complex IV c. FADH2 + UQ FAD + UQH2 d. UQH2 + cytochrome c+ UQ + cytochrome c ANS: D DIF: Medium REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Remembering 33. A characteristic of complex III is that it a. transports electrons from cytochrome c to complex IV. b. is reduced by FADH2. c. uses the Q cycle mechanism to oxidize ubiquinone. d. participates in electron transfer when the donor is NADH but not when the donor is succinate (or FADH2).

ANS: C DIF: Medium REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Understanding 34. The electron transport chain component that transfers electrons directly to oxygen is a. complex I. b. cytochrome c. c. complex IV. d. NADH. ANS: C DIF: Easy REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Understanding 35. Complex IV in the mitochondrial electron transport chain belongs to which enzyme class? a. lyase b. hydrolase c. transferase d. oxidoreductase ANS: D DIF: Difficult REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Applying 36. What is the location of the electron transport system protein called cytochrome c? a. cytoplasm

b. mitochondrial matrix c. inner mitochondrial membrane d. intermembrane space ANS: D DIF: Easy REF: 11.2 OBJ: 11.2.c. Hypothesize why cytochrome c is highly conserved in nature.

MSC: Remembering 37. What active site cofactor is found in the electron transport system protein called cytochrome c? a. heme b. FeS cluster c. Flavin d. quinone ANS: A DIF: Easy REF: 11.2 OBJ: 11.2.c. Hypothesize why cytochrome c is highly conserved in nature.

MSC: Remembering 38. The structure of the electron transport system protein called cytochrome c is highly conserved in nature because the a. enzyme has the rare ability to bind O2 and reduce it. b. protein active site contains a cofactor unique to the electron transport system. c. protein is located inside the mitochondria of eukaryotic cells. d. protein plays an important role in the electron transport system and in other critical cellular pathways such as apoptosis.

ANS: D DIF: Difficult REF: 11.2 OBJ: 11.2.c. Hypothesize why cytochrome c is highly conserved in nature.

MSC: Evaluating 39. What enzyme uses the proton motive force for its driving force? a. complex IV b. ATP synthase c. complex III d. complex I ANS: B DIF: Easy REF: 11.2 OBJ: 11.2.d. Explain the role of the proton motive force.

MSC: Remembering

40. What best describes the driving force for ATP synthesis in the mitochondria? a. Electron transport from electron transport system complexes. b. The higher pH inside the mitochondria that results from electron transfer. c. The large drops in G resulting from electron transfer in the ETC. d. The substrate level phosphorylations of the TCA cycle and glycolysis.

ANS: B DIF: Medium REF: 11.2 OBJ: 11.2.d. Explain the role of the proton motive force.

MSC: Evaluating

41. Protons in the mitochondria are a. the driving force for the electron transfers in the electron transport system. b. pumped by mitochondrial electron transport system enzymes. c. pumped inside the mitochondria using ATP energy. d. the cause of a lower pH inside the mitochondria than outside the mitochondria.

ANS: B

DIF: Medium

REF: 11.2

OBJ: 11.2.d. Explain the role of the proton motive force.

MSC: Analyzing

42. ATP synthase is located in or on the a. cytoplasm. b. intermembrane space of the mitochondria. c. inner mitochondrial membrane. d. outer mitochondrial membrane.

ANS: C DIF: Easy REF: 11.3 OBJ: 11.3.a. Describe the organization and structure of ATP synthase.

MSC: Remembering 43. The catalytic headpiece of the ATP synthase enzyme is primarily composed of which subunits? a. a hexameric 3 3 ring b. a circle of 10 c subunits c. the F0 subunit d. , , and subunits ANS: A DIF: Medium REF: 11.3 OBJ: 11.3.a. Describe the organization and structure of ATP synthase.

MSC: Remembering 44. The ATP synthase enzyme contains a central stalk embedded in the mitochondrial membrane.

What part of this stalk rotates? a. the 3 3 ring b. the F1 subunit c. the d, h, and OSCP subunits d. the ring of c subunits ANS: D DIF: Medium REF: 11.3 OBJ: 11.3.a. Describe the organization and structure of ATP synthase.

MSC: Remembering 45. ATP synthesis occurs a. on the outer mitochondrial membrane. b. at the ATP synthase complex after ADP and Pi are transported into the mitochondria. c. as a result of the leakage of H+ back out of the mitochondria. d. from the electron transfer reactions through complex IV. ANS: B DIF: Medium REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Evaluating 46. What is the driving force for ATP synthesis by the ATP synthase enzyme? a. The electron transfers through the protein complexes. b. ADP + Pi ATP c. The oxidation of NADH to NAD+. d. The pH gradient across the inner mitochondrial membrane.

ANS: D DIF: Medium REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Understanding 47. An ATP synthase enzyme with more than 10 c subunits in the F0 stalk would a. require more protons to complete one 360 rotation.

b. result in more ATP synthesis per 360 turn. c. require fewer protons to rotate 360 . d. result in less ATP synthesis per 360 turn.

ANS: A DIF: Difficult REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Applying 48. What would happen to a mutated ATP synthase enzyme where the proton binding aspartate residue on the c subunits was mutated to an alanine? a. The enzyme would make ATP as normal in the presence of a proton gradient. b. The enzyme would not make ATP in the presence of a proton gradient. c. The enzyme would make ATP without the need for a proton gradient. d. The rotor would rotate in response to a proton gradient, but no ATP would be made.

ANS: B DIF: Difficult REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Evaluating 49. In yeast, it is estimated that approximately __________ H+ are required by ATP synthase per ATP synthesized. a. 1 b. 3 c. 9 d. 10 ANS: B DIF: Easy REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Remembering 50. Which part of the native ATP synthase enzyme is stationary and does NOT rotate during ATP synthesis? a. the rotor b. the circle of c subunits c. the central subunit connecting the rotor to the catalytic headpiece d. the catalytic headpiece ANS: D DIF: Difficult REF: 11.3 OBJ: 11.3.c. State the three basic principles of the binding change mechanism.

MSC: Analyzing 51. The resting state of the three subunits in the ATP synthase enzyme is best described as a. one O, one L, and one T conformation. b. all in O conformations. c. all in L conformations. d. one L and two O conformations.

ANS: A DIF: Medium REF: 11.3 OBJ: 11.3.c. State the three basic principles of the binding change mechanism.

MSC: Applying 52. The __________ causes the catalytic headpiece of ATP synthase to change conformation. a. rotation of the circle of the 3 3 subunits b. movement of the circle of ~10 c subunits c. interaction with the rotating central subunit

d. binding of ADP and Pi ANS: C DIF: Medium REF: 11.3 OBJ: 11.3.c. State the three basic principles of the binding change mechanism.

MSC: Understanding 53. What type of transport is illustrated by the mitochondrial ATP/ADP translocase? a. symporter b. antiporter c. facilitated diffusion d. primary active transporter ANS: B DIF: Medium REF: 11.4 OBJ: 11.4.a. Describe how ADP, ATP, and Pi are moved across the inner mitochondrial membrane.

MSC: Applying 54. During transfer of ATP, ADP, and Pi, some of the proton gradient is lost in the a. movement of ATP into the mitochondria by the ATP/ADP translocase. b. movement of ATP out of the mitochondria. c. transport of ADP into the mitochondria by the ADP translocase. d. transport of Pi into the mitochondria by the phosphate translocase.

ANS: D DIF: Medium REF: 11.4 OBJ: 11.4.a. Describe how ADP, ATP, and Pi are moved across the inner mitochondrial membrane.

MSC: Remembering 55. Which one of the following correctly designates the number of ATPs generated by the reducing molecules shown below? a. NADH from the TCA cycle—1.5 ATP b. NADH from the cytosol (glycerol phosphate shuttle)—2.25 ATP c. NADH from the cytosol (malate-aspartate shuttle)—1.5 ATP d. FADH2 from the TCA cycle—1.5 ATP ANS: D DIF: Medium REF: 11.4 OBJ: 11.4.b. Distinguish between mechanisms of electron transfer from NADH into the mitochondrial matrix in liver versus muscle cells.

MSC: Remembering 56. Which one of the following statements about the glycerol phosphate shuttle is true? a. It involves the transfer of electrons from cytoplasmic NADH to dihydroxyacetone phosphate (DHAP) to yield glycerol phosphate. b. It is more efficient than the malate aspartate shuttle. c. NADH produced in the cytoplasm by glycolysis ultimately leads to NADH in mitochondria. d. Glycerol phosphate diffuses into the mitochondria.

ANS: A DIF: Difficult REF: 11.4 OBJ: 11.4.b. Distinguish between mechanisms of electron transfer from NADH into the mitochondrial matrix in liver versus muscle cells.

MSC: Understanding 57. Which mechanism is the most efficient at moving NADH equivalents from the cytoplasm into the mitochondria? a. citrate shuttle b. malate-aspartate shuttle

c. glyoxylate shunt d. glycerol phosphate shuttle ANS: B DIF: Easy REF: 11.4 OBJ: 11.4.b. Distinguish between mechanisms of electron transfer from NADH into the mitochondrial matrix in liver versus muscle cells.

MSC: Remembering 58. How many ATPs are obtained from one acetyl-CoA run once through the TCA cycle, assuming that all resulting NADH and FADH2 is used by the electron transport chain and oxidative phosphorylation to make ATP? a. 6.5 b. 9 c. 10 d. 11 ANS: C DIF: Difficult REF: 11.4 OBJ: 11.4.c. State net yield of ATP per glucose in liver and muscle cells.

MSC: Applying 59. How many ATPs are produced from the complete metabolism of one glucose molecule, assuming that all resulting NADH and FADH2 is used by the electron transport chain and oxidative phosphorylation to make ATP? a. 4 b. 16 c. 32 d. 102 ANS: C DIF: Easy REF: 11.4 OBJ: 11.4.c. State net yield of ATP per glucose in liver and muscle cells.

MSC: Remembering 60. Electrons from a succinate molecule can enter into the ETC and result in enough pumped protons to make how many ATPs? a. 2.0 b. 1.5 c. 1.0 d. 2.5 ANS: B DIF: Difficult REF: 11.4 OBJ: 11.4.c. State net yield of ATP per glucose in liver and muscle cells.

MSC: Applying 61. If the mitochondrial ATP synthase were inhibited, but the electron transport chain was allowed to run continuously, the pH of the cytoplasm would a. decrease. b. increase. c. remain unchanged. d. increase immediately and then decrease.

ANS: A DIF: Medium REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Applying

62. Inhibitors of the electron transport system, such as cyanide (CN−) and carbon monoxide (CO), inhibit complex IV by binding to the heme iron cofactor. What is the resulting effect on oxidative phosphorylation? a. Electrons pass through the electron transport system, but no protons are pumped. b. Protons are pumped, but no electron transport occurs. c. The electron transport system occurs normally, but no ATP is synthesized. d. Electron transport is disabled, and no protons are pumped.

ANS: D DIF: Difficult REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Understanding 63. The drug oligomycin inhibits ATP synthase by preventing protons from flowing through the enzyme. Oligomycin must bind to the __________ of ATP synthase. a. catalytic headpiece b. F1 subunit c. ATP binding site d. F0 subunit of ANS: D DIF: Medium REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Applying 64. The main activator molecule of the ATP synthesis and the electron transport system is a. ATP. b. H+. c. ADP. d. NAD+.

ANS: C DIF: Medium REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Understanding 65. What is the effect of oligomycin, an ATP synthase inhibitor, on the mitochondrial oxidative phosphorylation pathway? a. The mitochondria cannot reduce NADH or make ATP. b. No proton gradient is formed, and no ATP is synthesized. c. Protons leak back into the cytoplasm. d. The proton gradient is formed, but no ATP synthesis can occur.

ANS: D DIF: Medium REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Applying 66. What would happen if mitochondria were treated with a proton gradient uncoupler, such as 2,4-dinitrophenol? a. Electron transfer would stop. b. Complex I would become reduced, and complexes III and IV would become oxidized. c. Protons would be pumped by the mitochondrial electron transport chain, although no ATP would be synthesized. d. Reducing equivalents, in the form of NADH, would no longer be consumed.

ANS: C DIF: Difficult REF: 11.5 OBJ: 11.5.b. Classify the role of 2,4-dinitrophenol as it relates to the electron transport system.

MSC: Applying

67. What happens to patients given the proton gradient uncoupler 2,4-dinitrophenol? a. They undergo rapid decrease in body temperature as a result of lack of mitochondrial electron transport. b. They experience lower cellular pH as a result of rapid proton gradient dissipation. c. Their mitochondrial membranes fail as a result of rapid proton gradient release. d. Their body temperatures rise as a result of heat release from gradient uncoupling.

ANS: A DIF: Medium REF: 11.5 OBJ: 11.5.b. Classify the role of 2,4-dinitrophenol as it relates to the electron transport system.

MSC: Applying 68. What is the cellular location of eukaryotic thermogenin (or uncoupling protein)? a. mitochondrial inner membrane b. mitochondrial matrix c. cytoplasm d. both cytoplasm and mitochondrial matrix ANS: A DIF: Easy REF: 11.5 OBJ: 11.5.c. Explain why some uncouplers (such as thermogenin) are adaptive to survival in certain animals.

MSC: Understanding 69. Which animal would have the lowest levels of brown adipose tissue? a. newborn human b. hibernating squirrel c. migrating duck d. polar bear ANS: C DIF: Medium REF: 11.5 OBJ: 11.5.c. Explain why some uncouplers (such as thermogenin) are adaptive to survival in certain animals.

MSC: Evaluating 70. Thermogenin (or uncoupling protein) is not toxic like 2,4-dinitrophenol because the protein a. is typically expressed in adipose tissues where ample fat calories are found. b. is less efficient at proton dissipation. c. cannot leave the mitochondria. d. is naturally occurring and not synthetic.

ANS: A DIF: Difficult REF: 11.5 OBJ: 11.5.c. Explain why some uncouplers (such as thermogenin) are adaptive to survival in certain animals.

MSC: Evaluating 71. Brown adipose tissue is brown in color because of a. increased levels of thermogenin, or uncoupling protein. b. increased muscle fiber content. c. increased numbers of mitochondria. d. decreased levels of lipid.

ANS: C DIF: Medium REF: 11.5 OBJ: 11.5.d. Describe brown adipose tissue and explain its role in certain species.

MSC: Evaluating 72. What is the primary fuel metabolized by the mitochondria in brown adipose tissue of hibernating animals? a. glucose

b. NADH c. lipid d. ATP ANS: C DIF: Easy REF: 11.5 OBJ: 11.5.d. Describe brown adipose tissue and explain its role in certain species.

MSC: Understanding 73. The role of brown adipose tissue is to a. efficiently generate ATP from fat tissue. b. metabolize excess fat calories. c. store excess calories as fat. d. generate heat for the organism.

ANS: D DIF: Easy REF: 11.5 OBJ: 11.5.d. Describe brown adipose tissue and explain its role in certain species.

MSC: Understanding 74. Which tissue types are affected the most by inherited mitochondrial disorders? a. those tissues with the highest levels of mitochondria and high levels of activity b. heart tissue c. liver tissue d. those tissues with the lowest levels of mitochondria ANS: A DIF: Medium REF: 11.5 OBJ: 11.5.e. Identify the reason why mitochondrial disorders are passed through the maternal line only.

MSC: Analyzing 75. How are many mitochondrial diseases passed on from parents to offspring? a. through the mother only b. through the father only c. through an equal distribution from both parents d. by random mutations in the mitochondrial genome ANS: A DIF: Easy REF: 11.5 OBJ: 11.5.e. Identify the reason why mitochondrial disorders are passed through the maternal line only.

MSC: Remembering SHORT ANSWER 1. Give the chemical reaction between the mitochondrial electron transport system’s original electron donor and final electron acceptor.

ANS: NADH + H+ + 1/2 O2

H2O + NAD+

DIF: Easy REF: 11.1 OBJ: 11.1.a. Summarize the purpose of the electron transport system.

MSC: Understanding 2. Submitochondrial particles are inside-out pieces of the inner mitochondrial membrane formed through the sonication of mitochondria. Draw a diagram of these inside-out particles clearly showing (A) where electron transport from NADH occurs, (B) the direction of proton pumping, (C) the location of ATP synthesis, and (D) where O2 reacts.

ANS:

DIF: Difficult REF: 11.1 OBJ: 11.1.b. Compare the direction of proton flow in the mitochondrion to that in the chloroplast.

MSC: Applying 3. On the left hand side of the figure, label the regions above and below the lipid membrane assuming the process occurs in mitochondria. On the right hand side, label the regions assuming the process occurs in chloroplasts.

ANS:

DIF: Easy REF: 11.1 OBJ: 11.1.b. Compare the direction of proton flow in the mitochondrion to that in the chloroplast.

MSC: Analyzing 4. Use the following picture of a mitochondrion and label the (A) matrix, (B) crista, (c) inner membrane space, (D) cytoplasm, (E) inner membrane, (F) outer membrane, (G) location of the ATP synthesis, (H) location of elevated pH, and (I) the location of the electron transport system complexes.

ANS:

In addition, (D) the cytoplasm is outside the outer membrane; (H) the location of elevated pH is in the inner membrane space; and (I) the location of the electron transport system is on the inner membrane.

DIF: Easy REF: 11.1 OBJ: 11.1.c. Describe the structure of the mitochondrion.

MSC: Remembering

5. Use the table below to (A) write out the balanced reaction between NADH and O2 that drives the electron transport system and (B) compute the standard reduction potential.

Standard Reduction Potentials ( NAD+ + H+ + 2 e− FAD + 2 H+ + 2 e− O2 + 4 H+ + 4 e− ANS: 2NADH + O2 + 2H+

) for Half Reactions −0.32 V −0.22 V −0.82 V

NADH FADH2 2 H2O

2H2O + 2NAD+

= +1.14 V

DIF: Medium REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Evaluating

6. The free energy released from the electron transport system reaction NADH + 1/2 O2 + H+ H2O + + NAD is ’= −220 kJ/mol. How many moles of ATP could theoretically be made assuming 100% efficiency in energy coupling through the chemiosmotic theory, and that ADP+Pi ATP ’= 30.5 kJ/mol?

ANS: 220 kJ/mol / 30.5 kJ/mol = 7.2 moles of ATP, or 7 moles of ATP DIF: Easy REF: 11.1 OBJ: 11.1.e. State the overall reaction of the electron transport system.

MSC: Applying 7. List the common enzyme names of the major enzyme complexes in the oxidative phosphorylation pathway, which are required to couple NADH oxidation with ATP synthesis.

ANS: Complex I (NADH–ubiquinone oxidoreductase) Complex III (ubiquinone cytochrome c oxidoreductase) Complex IV (cytochrome c oxidase) ATP synthase DIF: Medium REF: 11.1 OBJ: 11.1.f. Name the major enzymes of the electron transport system.

MSC: Remembering 8. List the major enzymes and enzyme complexes in the oxidative phosphorylation pathway, which are required to couple FADH2 oxidation with ATP synthesis.

ANS: Complex II (succinate dehydrogenase) Complex III (ubiquinone cytochrome c oxidoreductase) Complex IV (cytochrome c oxidase) ATP synthase DIF: Medium REF: 11.1 OBJ: 11.1.f. Name the major enzymes of the electron transport system.

MSC: Remembering 9. List the order of enzymes, enzyme complexes, and membrane soluble electron carriers that an electron is passed through on its way from NADH to O2 in the electron transport system.

ANS: NADH

complex I

ubiquinone

complex III

cytochrome c

complex IV

DIF: Easy REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Remembering 10. Use the structure of the oxidized coenzyme Q (ubiquinone) shown below and draw the two-electron reduced form.

O2

ANS:

DIF: Difficult REF: 11.2 OBJ: 11.2.a. List the major components of the electron transport system.

MSC: Applying 11. Label the figure with the following items: a. complex I b. O2 c. NADH d. complex IV e. ubiquinone f. cytochrome c g. complex III h. H+ pumping direction

ANS:

DIF: Difficult REF: 11.2 OBJ: 11.2.b. Describe the roles of complexes I, III, and IV of the electron transport system.

MSC: Applying 12. Draw a diagram of the mitochondrion and indicate which side of the organelle has a net positive charge and which side has a net negative charge as a result of proton pumping.

ANS:

Outside the inner membrane is positive.

Inside the inner membrane is negative.

DIF: Easy force.

MSC: Applying 13. Label the locations of enzyme.

REF: 11.2

OBJ: 11.2.d. Explain the role of the proton motive

, , , and c, and the F0 and F1 subunits on the following ATP synthase

ANS: Note that the

and

labels are interchangeable in the labeled figure below.

DIF: Medium REF: 11.3 OBJ: 11.3.a. Describe the organization and structure of ATP synthase.

MSC: Remembering 14. On the figure below label the clearly identify the positions of the three functional units of ATP synthase: the rotor, the catalytic headpiece, and the stator.

ANS:

DIF: Medium REF: 11.3 OBJ: 11.3.a. Describe the organization and structure of ATP synthase.

MSC: Understanding 15. Describe the process by which proton flow through the c subunits forces the rotation of the ATP synthase spindle in the mitochondrial membrane. Please include the roles of aspartic acid residues and the half-channels in your description.

ANS: Protons from the high concentration side of the mitochondrial membrane pass through a half-channel in the a subunit of the F0 component of ATP synthase. The protons protonate and neutralize an aspartic acid residue on one of the c subunits in about the 10 c subunit spindle. The neutralized Asp residue is free to rotate into the hydrophobic membrane exposed circumference of the spindle. This rotation exposes the adjacent c subunit to a second half-channel, which is exposed to the low concentration side of the mitochondrial membrane. The proton leaves the Asp residue, leaving it charged. This charged c subunit then rotates to the first half-channel, where the protonation/rotation/deprotonation processes repeat. See Figure 11.32, the two-channel model.

DIF: Difficult REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Understanding 16. Explain how ATP synthase can be used as primary active transporter of H+ and pump protons.

ANS: ATP synthase can be run in the reverse direction, by using ATP hydrolysis to drive conformational changes in the 3 3 subunits, which interact with the rotor spindle subunit and turn the c subunits in the opposite direction.

DIF: Medium REF: 11.3 OBJ: 11.3.b. Explain the mechanism whereby proton flow through ATP synthase results in ATP synthesis.

MSC: Applying 17. List the conformation types and the changes to the substrates in a single synthase catalytic head piece during one 360o rotation of the rotor.

subunit on the ATP

ANS: A subunit begins in the O or open form, where ADP and Pi can enter its active site. A 120 rotation of the central subunit causes an O form conformational change to the L, or loose form.

This locks the ADP and Pi in the active site. A second 120 rotation of the central subunit changes the L conformation into the T or tight conformation, which forces ATP formation. A third 120 rotation converts the T conformation into the O conformation, where ATP is released and another ADP and Pi are free to bind for the process to repeat.

DIF: Difficult REF: 11.3 OBJ: 11.3.c. State the three basic principles of the binding change mechanism.

MSC: Understanding 18. Which directions across the mitochondria must H+, ATP, ADP, and Pi travel during active mitochondrial ATP synthesis?

ANS: H+ travels back into the mitochondria; ATP travels out to the cytoplasm; ADP and Pi travel into the mitochondria.

DIF: Easy REF: 11.4 OBJ: 11.4.a. Describe how ADP, ATP, and Pi are moved across the inner mitochondrial membrane.

MSC: Understanding 19. Add to the malate-aspartate shuttle scheme below the missing reactant and products a, b, c, and d.

ANS:

DIF: Medium REF: 11.4 OBJ: 11.4.b. Distinguish between mechanisms of electron transfer from NADH into the mitochondrial matrix in liver versus muscle cells.

MSC: Applying 20. For the metabolism of one glucose to two pyruvate molecules, set up a table showing the differences in the number of ATP obtained in the muscle and the liver assuming that the NADH and FADH2 is used by the electron transport chain and oxidative phosphorylation to make ATP.

Molecules

Liver

Muscle

______ ATP

______ ATP

Liver −1 ATP −1 ATP 2 NADH (= 5 ATP with malate-aspartate shuttle)

Muscle −1 ATP −1 ATP 2 NADH (= 3 ATP with glycerol phosphate shuttle)

2 ATP 2 ATP 7 ATP

2 ATP 2 ATP 5 ATP

TOTAL ANS: Molecules Hexokinase PFK1 Glyceraldehyde-3-P dehydrogenase Phosphoglycerate kinase Pyruvate kinase TOTAL

There would be two more ATP in the liver than in the muscle cells as a result of the prevalence of the different NADH shuttle systems.

DIF: Difficult REF: 11.4 OBJ: 11.4.c. State net yield of ATP per glucose in liver and muscle cells.

MSC: Applying 21. For each molecule below, list the number of ATP obtained assuming that the electron transport chain and oxidative phosphorylation are active.

NADH (from the TCA cycle) FADH2 (from the TCA cycle) NADH (from the cytoplasm, malate aspartate shuttle) NAD+ (from the mitochondria) ANS: NADH (from the TCA cycle) FADH2 (from the TCA cycle) NADH (from the cytoplasm, malate aspartate shuttle) NAD+ (from the mitochondria)

2.5 2.5 2.5 0

DIF: Medium REF: 11.4 OBJ: 11.4.c. State net yield of ATP per glucose in liver and muscle cells.

MSC: Remembering 22. Why are 2,4-dintrophenol and thermogenin referred to as uncouplers?

ANS:

They uncouple the electron transport system’s proton gradient from the synthesis of ATP and thus uncouple the oxidation from the phosphorylation in oxidative phosphorylation.

DIF: Easy REF: 11.5 OBJ: 11.5.a. List the major activators and inhibitors of the electron transport system and ATP synthesis.

MSC: Applying 23. The structure of 2,4-dinitrophenol is shown below. Explain how it functions to uncouple a proton gradient across the mitochondrial membrane.

ANS:

2,4-dinitrophenol is nonpolar enough that it readily crosses the inner mitochondria membrane. It releases a proton to the low [H+] concentration side of the membrane (inside the inner membrane) and then crosses the membrane to pick up a proton on the high [H+] concentration side (outside the inner membrane). This process is repeated and results in a rapid loss of the proton gradient.

DIF: Medium REF: 11.5 OBJ: 11.5.b. Classify the role of 2,4-dinitrophenol as it relates to the electron transport system.

MSC: Applying 24. Explain the origin of the brown color of brown adipose tissue.

ANS: Brown adipose tissue is brown because of the large numbers of mitochondria and the iron proteins found in their electron transport systems.

DIF: Easy REF: 11.5 OBJ: 11.5.d. Describe brown adipose tissue and explain its role in certain species.

MSC: Understanding 25. Explain why many mitochondrial diseases are inherited from the mother only.

ANS: Many of the proteins in the mitochondrial oxidative phosphorylation pathway are coded for by mitochondrial DNA. Because mitochondria and mitochondrial DNA only come from the mother’s egg cell, any mutations in the mitochondrial DNA would be inherited from the mother.

DIF: Easy REF: 11.5 OBJ: 11.5.e. Identify the reason why mitochondrial disorders are passed through the maternal line only.

MSC: Understanding

Chapter 12: Photosynthesis MULTIPLE CHOICE 1. The term greenhouse effect refers to the idea that a. the global production of plant matter is increasing. b. the capacity of the earth’s plant matter to store CO2 is increasing. c. the temperature of the earth is increasing because of heat trapped by gases such as CO2. d. tropical rainforests are gradually being eliminated.

ANS: C DIF: Medium REF: 12.1 OBJ: 12.1.a. Hypothesize how the loss of forests could exacerbate the greenhouse effect.

MSC: Understanding 2. The Biosphere 2 project, in Tucson, Arizona, was an experiment involving a large sealed terrarium with humans and photosynthetic plants living in balance. Why did the project have to be interrupted after only a few months? a. Levels of CO2 rose to dangerous levels. b. The humans ran out of food. c. The plants stopped producing oxygen. d. The rate of photosynthesis was too high.

ANS: A DIF: Easy REF: 12.1 OBJ: 12.1.a. Hypothesize how the loss of forests could exacerbate the greenhouse effect.

MSC: Remembering 3. The __________ is driven directly by photons from the sun in photosynthesis light reactions. a. pumping of protons b. synthesis of ATP c. transfer of electrons d. synthesis of glucose ANS: C DIF: Medium REF: 12.1 OBJ: 12.1.b. List the five steps used by photosynthetic organisms to convert solar energy into chemical energy.

MSC: Understanding 4. In the five steps used by photosynthetic organisms to convert solar energy into chemical energy, which molecules store the solar energy before sugar synthesis? a. chlorophylls b. NADH and FADH2 c. H2O and O2 d. ATP and NADPH ANS: D DIF: Medium REF: 12.1 OBJ: 12.1.b. List the five steps used by photosynthetic organisms to convert solar energy into chemical energy.

MSC: Understanding 5. All of the following are true of both chloroplasts and mitochondria EXCEPT that they a. have one highly folded membrane. b. produce ATP inside the organelle. c. produce NADPH inside the organelle. d. are present in photosynthetic plant cells.

ANS: C

DIF: Medium

REF: 12.1

OBJ: 12.1.c. Name the key structures found within the chloroplast.

MSC: Analyzing 6. The chloroplast contains a highly folded membrane called the a. thylakoid. b. lumen. c. inner membrane. d. matrix.

ANS: A DIF: Easy REF: 12.1 OBJ: 12.1.c. Name the key structures found within the chloroplast.

MSC: Remembering 7. What is the overall reaction for the Calvin cycle, or dark reactions? a. 2 H2O + 2 NADP+ + 3 ADP + 3 Pi O2 + 2 NADPH + 3 ATP b. 3 CO2 + 6 NADPH + 9 ATP + 6 H2O Glyceraldehyde-3-phosphate + 6 NADP+ + 9 ADP + 9 Pi c. 6 CO2 + 6 NADPH + 12 ATP Glucose + NADP+ + ADP + Pi d. Glucose 9 ATP + 12 NADPH + 6 CO2 + 6 H2O ANS: B DIF: Medium REF: 12.1 OBJ: 12.1.d. State the overall net reactions for photosynthetic electron transport and for the Calvin cycle.

MSC: Analyzing 8. What is the overall balanced reaction for the light reactions of photosynthesis? a. O2 + 2 NADPH + 3 ATP 2 H2O + 2 NADP+ + 3 ADP + 3 Pi b. 3 CO2 + 6 NADPH + 9 ATP + 6 H2O Glyceraldehyde-3-phosphate + 6 NADP+ + 9 ADP + 9 Pi c. O2 + 8 photons + NADP+ + 3 ATP 2 H2O + NADP+ + 3 ADP + 3 Pi d. 2 H2O + 8 photons + 2 NADP+ + 3 ADP + 3 Pi O2 + 2 NADPH + 3 ATP ANS: D DIF: Medium REF: 12.1 OBJ: 12.1.d. State the overall net reactions for photosynthetic electron transport and for the Calvin cycle.

MSC: Analyzing 9. The O2 generated from photosynthesis is derived from a. CO2 reduction to glyceraldehyde-3-phosphate. b. CO2 reduction to glycerate-3-phosphate. c. water molecules that directly reduce PSI*. d. water molecules that directly reduce PSII*.

ANS: D DIF: Medium REF: 12.1 OBJ: 12.1.d. State the overall net reactions for photosynthetic electron transport and for the Calvin cycle.

MSC: Analyzing 10. Which enzyme in the photosynthesis light reactions does NOT transfer electrons? a. ATP synthase b. photosystem II c. photosystem I d. cytochrome b6f ANS: A DIF: Easy REF: 12.1 OBJ: 12.1.d. State the overall net reactions for photosynthetic electron transport and for the Calvin cycle.

MSC: Understanding

11. Chlorophyll absorbs a. heat energy and reaches an excited state. b. photon energy and becomes excited or oxidized. c. an electron during photon excitation. d. all wavelengths of light.

ANS: B DIF: Difficult REF: 12.2 OBJ: 12.2.a. List the three possible outcomes from excitation of an electron in a chlorophyll molecule.

MSC: Analyzing 12. On excitation by a photon, a fate of the excited chlorophyll molecule is to a. transfer an electron to an acceptor molecule. b. transfer an electron to ATP. c. relax and release a proton to a neighboring chlorophyll. d. relax and accept an electron from a nearby donor.

ANS: A DIF: Difficult REF: 12.2 OBJ: 12.2.a. List the three possible outcomes from excitation of an electron in a chlorophyll molecule.

MSC: Evaluating 13. For photosynthesis, sunlight energy drives electron transfer. Where are the electrons ejected from when light is absorbed? a. photons released by chlorophyll b. NADPH c. light-harvesting pigments in PSI and PSII d. oxygen ANS: C DIF: Medium REF: 12.2 OBJ: 12.2.a. List the three possible outcomes from excitation of an electron in a chlorophyll molecule.

MSC: Understanding 14. Heme and chlorophyll have similar overall structures. What is common between the two molecules? a. color b. hydrophobic tail c. polycyclic planar structure d. metal ion found at their center ANS: C DIF: Medium REF: 12.2 OBJ: 12.2.b. Compare the structures of chlorophyll and heme.

MSC: Analyzing

15. Chlorophyll absorbs light energy efficiently because of the a. metal ion in the center of the molecule. b. ring structure. c. planar structure. d. alternating double and single bonds.

ANS: D DIF: Difficult REF: 12.2 OBJ: 12.2.b. Compare the structures of chlorophyll and heme.

MSC: Understanding

16. Which of the following is a photosynthetic light harvesting pigment? a. FeS cluster b. NADPH c. plastoquinone d. -carotene

ANS: D DIF: Medium REF: 12.2 OBJ: 12.2.c. Name the key pigments associated with the photosynthetic reaction center.

MSC: Remembering 17. Which is the orange pigment commonly found in plant’s light harvesting complexes? a. chlorophyll b. phycocyanobilin c. porphyrin d. -carotene ANS: D DIF: Easy REF: 12.2 OBJ: 12.2.c. Name the key pigments associated with the photosynthetic reaction center.

MSC: Remembering 18. Approximately how many light-harvesting chromophores are found per photosystem enzyme, such as in PSI or PSII? a. 2 b. about a dozen c. about 100 to 200 d. about 1000 to 2000 ANS: C DIF: Easy REF: 12.2 OBJ: 12.2.c. Name the key pigments associated with the photosynthetic reaction center.

MSC: Remembering 19. The following picture is an example of what phenomenon?

a. b. c. d.

resonance energy transfer electron transfer photoexcitation fluorescence

ANS: A DIF: Medium REF: 12.2 OBJ: 12.2.d. Define resonance energy transfer as it applies to the photosystems.

MSC: Analyzing 20. Resonance energy transfer from one chlorophyll in the photosystems results in a. a reduced neighboring pheophytin molecule. b. a neighboring chlorophyll in an excited state. c. heat release. d. the release of a photon.

ANS: B DIF: Medium REF: 12.2 OBJ: 12.2.d. Define resonance energy transfer as it applies to the photosystems.

MSC: Understanding

21. Which of the following is an electron transfer molecule in photosynthesis light reactions? a. plastoquinone b. photon c. paraquat d. ATP ANS: A DIF: Easy REF: 12.2 OBJ: 12.2.e. List the components of the Z scheme of plant photosynthesis.

MSC: Remembering 22. The photosynthetic Z scheme describes the a. synthesis of glucose from CO2. b. movement of electrons driven by the absorption of light energy. c. production of O2. d. reduction of NADPH. ANS: B DIF: Medium REF: 12.2 OBJ: 12.2.e. List the components of the Z scheme of plant photosynthesis.

MSC: Understanding 23. Where do electrons from photosystem II (PSII) come from to re-reduce the oxidized P680+ state? a. O2 b. NADPH c. plastocyanin d. H2O ANS: D DIF: Medium REF: 12.2 OBJ: 12.2.f. Restate the mechanism used by the O2-evolving complex to connect a four-electron reduction with a single-electron oxidation.

MSC: Understanding 24. What group in photosystem II (PSII) directly reacts with H2O during its light-driven oxidation? a. oxygen evolving center b. P680 c. tyrosine d. pheophytin ANS: A DIF: Medium REF: 12.2 OBJ: 12.2.f. Restate the mechanism used by the O2-evolving complex to connect a four-electron reduction with a single-electron oxidation.

MSC: Analyzing 25. To form one O2, __________ electrons must leave two water molecules, and to form one NADPH, __________ electrons must be delivered to one NADP+. a. 2; 2 b. 2; 4 c. 4; 2 d. 4; 4 ANS: C DIF: Difficult REF: 12.2 OBJ: 12.2.f. Restate the mechanism used by the O2-evolving complex to connect a four-electron reduction with a single-electron oxidation.

MSC: Analyzing 26. Which enzyme in the photosynthetic Z scheme catalyzes the PQ cycle, which is analogous to Complex III and the Q cycle in the mitochondrial electron transport chain? a. photosystem II

b. plastocyanin c. cytochrome b6f d. photosystem I ANS: C DIF: Medium REF: 12.2 OBJ: 12.2.g. Compare and contrast the PQ cycle with the Q cycle of mitochondrial electron transport.

MSC: Remembering 27. Which is NOT a correct analogy between the photosynthetic PQ cycle and the mitochondrial electron transport chain Q cycle? a. Plastocyanin is analogous to cytochrome c. b. Plastoquinone is analogous to coenzyme Q. c. Cytochrome b6f is analogous to Complex III. d. Photosystem I is analogous to Complex I. ANS: D DIF: Difficult REF: 12.2 OBJ: 12.2.g. Compare and contrast the PQ cycle with the Q cycle of mitochondrial electron transport.

MSC: Applying 28. Which electron carrier molecule in the photosynthetic electron transport chain is largely hydrophobic and found floating in the thylakoid membrane? a. heme b. chlorophyll c. pheophytin d. plastoquinone ANS: D DIF: Easy REF: 12.2 OBJ: 12.2.g. Compare and contrast the PQ cycle with the Q cycle of mitochondrial electron transport.

MSC: Analyzing 29. During photophosphorylation, the protons are pumped into the __________, and the ATP is made in the __________. a. thylakoid lumen; cytoplasm b. thylakoid lumen; stroma c. stroma; thylakoid lumen d. cytoplasm; stroma ANS: B DIF: Medium REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Understanding 30. Which complex in the photosynthetic electron transport chain pumps protons as electrons pass through it? a. plastocyanin b. cytochrome b6f c. photosystem I d. photosystem II ANS: B DIF: Easy REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Understanding 31. In addition to the pumping of protons with the photosynthetic electron transport, what else contributes to establishing a proton gradient? a. the loss of electrons from NADPH

b. the reduction of P680+ c. the movement of plastocyanin d. the formation of O2 from two H2O ANS: D DIF: Difficult REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Evaluating 32. Electrons from plastocyanin are passed on to a. P700+. b. P680+. c. cytochrome b6f. d. O2.

ANS: A DIF: Medium REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Understanding 33. The herbicide paraquat operates by stealing electrons from photosystem I (PSI). Which of the following is true of chloroplasts treated with paraquat? a. NADPH levels drop. b. Photosystem II is not re-reduced. c. Plastocyanin has nowhere to donate electrons. d. No protons are pumped across the chloroplast membranes.

ANS: A DIF: Difficult REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Evaluating 34. Per O2 molecule generated in photosynthesis light reactions, approximately how many protons are moved across the thylakoid membrane? a. 3 b. 4 c. 8 d. 12 ANS: D DIF: Medium REF: 12.3 OBJ: 12.3.a. State the number of protons translocated into the lumen and the number of ATP produced for each O2 produced by the O2-evolving complex.

MSC: Remembering 35. Approximately how many ATP are synthesized per O2 molecule generated in photosynthesis light reactions? a. 3 b. 4 c. 8 d. 12 ANS: A DIF: Medium REF: 12.3 OBJ: 12.3.a. State the number of protons translocated into the lumen and the number of ATP produced for each O2 produced by the O2-evolving complex.

MSC: Remembering 36. The primary difference between ATP synthesis during the photosynthetic light reactions and ATP synthesis in the mitochondrial electron transport chain is the a. cellular location of the proton motive force. b. enzyme catalyzing the ATP synthesis.

c. number of ATP produced per 360 rotation of the F1 subunit of ATP synthase. d. number of NADPH required to produce ATP. ANS: A DIF: Difficult REF: 12.3 OBJ: 12.3.a. State the number of protons translocated into the lumen and the number of ATP produced for each O2 produced by the O2-evolving complex.

MSC: Evaluating 37. The energy derived from photosynthesis and used to make ATP is manifested in what form? a. an acidic stroma b. an electron gradient in the thylakoid membrane c. an acidic thylakoid lumen d. an acidic cytoplasm ANS: C DIF: Easy REF: 12.3 OBJ: 12.3.a. State the number of protons translocated into the lumen and the number of ATP produced for each O2 produced by the O2-evolving complex.

MSC: Understanding 38. Under what conditions does cyclic photophosphorylation take place? a. in an acidic stroma b. with high levels of NADPH c. with high levels of ATP d. with an inactivated photosystem I ANS: B DIF: Medium REF: 12.3 OBJ: 12.3.b. Explain the importance of cyclic photophosphorylation.

MSC: Understanding 39. Which protein or enzyme is NOT involved in the cyclic photophosphorylation pathway? a. ferredoxin b. photosystem II c. cytochrome b6f d. plastocyanin ANS: B DIF: Easy REF: 12.3 OBJ: 12.3.b. Explain the importance of cyclic photophosphorylation.

MSC: Applying 40. In the chloroplasts, photosystem I (PSI) and photosystem II (PSII) are known to localize in different regions. PSI generally localizes in the __________, whereas PSII localizes in the __________. a. thylakoid lumen; thylakoid grana b. thylakoid lamellae; thylakoid grana c. stroma; thylakoid lumen d. thylakoid grana; thylakoid lamellae ANS: B DIF: Medium REF: 12.3 OBJ: 12.3.c. State three reasons why the localization of PSI and PSII to different regions of the thylakoid membrane makes sense.

MSC: Understanding 41. What is a reason for keeping photosystem I (PSI) and photosystem II (PSII) separate in the chloroplasts? a. They are involved in different pathways and not involved with each other. b. They would quench each other by energy transfer. c. They have different sunlight exposure requirements. d. They have different ATP consumption requirements.

ANS: B DIF: Difficult REF: 12.3 OBJ: 12.3.c. State three reasons why the localization of PSI and PSII to different regions of the thylakoid membrane makes sense.

MSC: Analyzing 42. Regulation of photosystem II (PSII) enzyme activity is accomplished by phosphorylation. Higher levels of __________ stimulates the phosphorylation and tuning down of PSII activity. a. oxidized NADP+ b. reduced plastoquinone (PQH2) c. reduced NADPH d. ATP ANS: B DIF: Difficult REF: 12.3 OBJ: 12.3.c. State three reasons why the localization of PSI and PSII to different regions of the thylakoid membrane makes sense.

MSC: Analyzing 43. In what location of the cell does the Calvin cycle occur? a. chloroplast grana b. thylakoid lumen c. chloroplast stroma d. cytoplasm ANS: C DIF: Easy REF: 12.4 OBJ: 12.4.a. List the products of the light reactions that are required for the Calvin cycle.

MSC: Understanding 44. The Calvin cycle requires which species from the light reactions? a. ATP and NADPH b. reducing electrons c. CO2 and ATP d. NADH and FADH2 ANS: A DIF: Easy REF: 12.4 OBJ: 12.4.a. List the products of the light reactions that are required for the Calvin cycle.

MSC: Remembering 45. Why are Calvin cycle reactions also referred to as the dark reactions? a. They occur primarily at night. b. They absorb, and do not reflect, the sunlight energy. c. They do not absorb sunlight energy. d. They do not require sunlight energy.

ANS: C DIF: Difficult REF: 12.4 OBJ: 12.4.a. List the products of the light reactions that are required for the Calvin cycle.

MSC: Evaluating 46. The three stages of the Calvin cycle are a. (1) fix CO2, (2) make a C3 sugar, and (3) make glucose. b. (1) fix CO2, (2) use NADPH and ATP, and (3) regenerate the starting C5 molecule. c. (1) use ATP, NADPH, and CO2, (2) make a C3 molecule, and (3) regenerate the starting C3 molecule. d. (1) use a C5 sugar, (2) reduce CO2 with NADPH, and (3) use ATP to regenerate the starting C5 molecule.

ANS: B DIF: Difficult REF: 12.4 OBJ: 12.4.b. Define the three stages of the Calvin cycle.

MSC: Analyzing

47. The first stage of the three-stage Calvin cycle a. generates CO2. b. uses ATP and NADPH from the light reactions. c. occurs in the plant cell cytoplasm. d. is catalyzed by the enzyme rubisco.

ANS: D DIF: Easy REF: 12.4 OBJ: 12.4.b. Define the three stages of the Calvin cycle.

MSC: Analyzing

48. Which is a characteristic of the second stage of the three-stage Calvin cycle? a. It uses ATP and NADPH. b. It is similar to a series of reactions in pentose phosphate pathway. c. It is catalyzed by an enzyme called rubisco. d. It begins and ends with a C5 sugar.

ANS: A DIF: Medium REF: 12.4 OBJ: 12.4.b. Define the three stages of the Calvin cycle.

MSC: Understanding

49. The third stage of the three-stage Calvin cycle a. uses ATP and NADPH from the light reactions. b. generates a glucose molecule for the plant. c. is similar to the reactions found in the glycolysis pathway. d. regenerates a C5 sugar for the Calvin cycle to continue.

ANS: D DIF: Medium REF: 12.4 OBJ: 12.4.b. Define the three stages of the Calvin cycle.

MSC: Understanding

50. Overall, the net balanced reaction of the Calvin cycle converts 3 CO2 into one a. ribulose-5-phosphate. b. glyceraldehyde-3-phosphate. c. acetyl-CoA. d. glucose.

ANS: B DIF: Easy REF: 12.4 OBJ: 12.4.c. State the net Calvin cycle reaction that produces one molecule of glyceraldehyde-3-phosphate.

MSC: Understanding 51. The formation of one net glyceraldehyde-3-phosphate during the net Calvin cycle reactions requires __________ NADPH and __________ ATP. a. 3; 3 b. 3; 6 c. 6; 6 d. 6; 9 ANS: D DIF: Difficult REF: 12.4 OBJ: 12.4.c. State the net Calvin cycle reaction that produces one molecule of glyceraldehyde-3-phosphate.

MSC: Remembering 52. What is the name of the enzyme that catalyzes the reaction shown below?

a. b. c. d.

ribulose bisphosphate carboxylase acetyl-CoA carboxylase glyceraldehyde-3-phosphate dehydrogenase pyruvate carboxylase

ANS: A DIF: Medium REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Evaluating 53. Ribulose bisphosphate carboxylase (rubisco) a. is the most abundant enzyme in the biosphere, comprising as much as 50% of plant cell protein. b. catalyzes the reaction of C5 molecule and CO2 with a C6 sugar product. c. is located in the thylakoid lumen. d. requires NADPH and ATP to fix CO2.

ANS: A DIF: Medium REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Evaluating 54. The five-step mechanism of ribulose bisphosphate carboxylase (rubisco) a. is an overall thermodynamically unstable reaction. b. involves C1, C3, C4, C5, and C6 molecules in the enzyme mechanism intermediates. c. adds a CO2 molecule to a C5 ribulose sugar, yielding an unstable C6 molecule that cleaves into two C3 molecules. d. involves the incorporation of 3 CO2 molecules to yield one 3-phosphoglycerate molecule.

ANS: C DIF: Difficult REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Evaluating 55. Which of the following is NOT required to activate rubisco? a. carbamate formation of the active site lysine b. activation by CO2 c. binding of the biotin cofactor d. binding of Mg2+ ANS: C DIF: Medium REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Analyzing 56. The final product that is formed by the enzyme rubisco is a. 3-phosphoglycerate. b. ATP. c. ribulose-1,5-bisphosphate. d. glyceraldehyde-3-phosphate.

ANS: A DIF: Easy REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Understanding 57. The reactions in stage 2 of the Calvin cycle are the same as those of the gluconeogenesis/glycolysis pathway in the a. cellular location of the pathways. b. use of NADPH as reductant. c. C3 sugars in the pathways. d. enzyme locations.

ANS: C DIF: Medium REF: 12.4 OBJ: 12.4.e. Compare and contrast stage 2 of the Calvin cycle with the reactions of glycolysis.

MSC: Analyzing 58. Which of the following is true of stage 2 of the Calvin cycle? a. Stage 2 involves the net incorporation of CO2 into the six-carbon glucose molecule. b. Almost all of the NADPH and ATP from the light reactions are used in stage 2. c. Stage 2 reactions are localized on the thylakoid membrane of the chloroplasts. d. C3, C4, C5, and C6 sugars are all involved in stage 2 reactions.

ANS: B DIF: Difficult REF: 12.4 OBJ: 12.4.e. Compare and contrast stage 2 of the Calvin cycle with the reactions of glycolysis.

MSC: Evaluating 59. When transketolase acts on fructose-6-phosphate and glyceraldehyde-3-phosphate, the products are a. 3-phosphoglycerate and two molecules of glyceraldehyde-3-phosphate. b. dihydroxyacetone phosphate and glucose-6-phosphate. c. xylulose-5-phosphate and erythrose-4-phosphate. d. xylulose-5-phosphate and ribose-5-phosphate.

ANS: C DIF: Difficult REF: 12.4 OBJ: 12.4.f. Name the key enzymes of the carbon shuffle reactions.

MSC: Applying 60. Which of the following groups of molecules are found in the shuffling reactions of stage 3 of photosynthesis? a. C1, C2, C3, C4, C5, C6, and C7 sugars b. NADPH and ATP c. erythrose-4-phosphate, glyceraldehyde-3-phosphate, and xylulose-5-phosphate d. 3-phosphoglycerate, 1,3-bisphosphoglycerate, and glyceraldehyde-3-phosphate ANS: C DIF: Medium REF: 12.4 OBJ: 12.4.f. Name the key enzymes of the carbon shuffle reactions.

MSC: Understanding 61. Transketolase requires the coenzyme a. cobalamin (vitamin B12). b. pyridoxal phosphate. c. tetrahydrofolic acid. d. thiamine pyrophosphate.

ANS: D DIF: Medium REF: 12.4 OBJ: 12.4.f. Name the key enzymes of the carbon shuffle reactions.

MSC: Remembering

62. Which is a way that light controls the Calvin cycle activity? a. Calvin cycle enzymes are inhibited by the lower H+, which is pumped out of the stroma by light reactions. b. Reduced ferredoxin from the light reactions keeps thioredoxin reduced, which keeps Calvin cycle enzymes in an active form. c. High levels of ATP and NADPH from the light reactions inhibit the Calvin cycle enzymes. d. Calvin cycle or dark reaction enzyme activators are present at higher levels in the dark.

ANS: B DIF: Difficult REF: 12.4 OBJ: 12.4.g. State the three mechanisms used to control Calvin cycle activity by light.

MSC: Evaluating 63. Which species from the light reactions keeps thioredoxin reduced so that it can activate enzymes in the Calvin cycle? a. ferredoxin b. plastoquinone c. P700 d. NADPH ANS: A DIF: Medium REF: 12.4 OBJ: 12.4.g. State the three mechanisms used to control Calvin cycle activity by light.

MSC: Remembering 64. What is the process depicted below, where plants react with O2?

a. b. c. d.

photorespiration photosynthesis photogeneration photoglycolate pathway

ANS: A DIF: Easy REF: 12.4 OBJ: 12.4.h. Explain why limiting exposure of rubisco to oxygen is important for plants.

MSC: Analyzing 65. Under what condition(s) do the wasteful side reaction of O2 with rubisco become significant? a. higher levels of CO2 than O2 b. at night c. increased temperature and intense light d. increased rubisco concentrations ANS: C DIF: Medium REF: 12.4 OBJ: 12.4.h. Explain why limiting exposure of rubisco to oxygen is important for plants.

MSC: Understanding 66. In C3 plants CO2 is first incorporated into __________, whereas in C4 and CAM plants the CO2 is first incorporated into __________. a. 3-phosphoglycerate; oxaloacetate b. dihydroxyacetone phosphate; malate c. 3-phosphoglycerate; malate d. glyceraldehyde-3- phosphate; erythrose-4-phosphate ANS: A DIF: Easy REF: 12.4 OBJ: 12.4.i. Differentiate among C3, C4, and CAM plants.

MSC: Understanding

67. C4 plants are thought to be more efficient than C3 plants because they a. make larger sugar molecules from CO2. b. can concentrate the CO2 in chloroplasts and therefore minimize side reactions with O2. c. can produce sugar molecules at night in addition to during the day. d. can live in dry climates.

ANS: B DIF: Medium REF: 12.4 OBJ: 12.4.i. Differentiate among C3, C4, and CAM plants.

MSC: Evaluating

68. Which cell type in C4 plants is isolated from O2 exposure as they perform Calvin cycle reactions? a. Hatch-Slack cells b. bundle sheath cells c. guard cells d. mesophyll cells ANS: B DIF: Easy REF: 12.4 OBJ: 12.4.j. Outline the reactions that take place in the mesophyll cell and the bundle sheath cell of C4 plants.

MSC: Remembering 69. Which statement regarding CAM plants is true? a. They use one cell type to absorb and store CO2 before utilizing it in the Calvin cycle in another cell type. b. They are more efficient than C4 plants. c. They absorb CO2 at night and release it to the Calvin cycle during the day. d. They store CO2 in 3-phosphoglycerate before releasing it to the Calvin cycle.

ANS: C DIF: Medium REF: 12.4 OBJ: 12.4.k. Distinguish the reactions that occur during the day from those that occur at night in CAM plants.

MSC: Analyzing

70. What is the name of the plant leaf openings that open during the night and close during the day in CAM plants? a. mesophyll cells b. stomata c. guard cells d. malate pore proteins ANS: B DIF: Easy REF: 12.4 OBJ: 12.4.k. Distinguish the reactions that occur during the day from those that occur at night in CAM plants.

MSC: Understanding 71. What is the cellular location of the plant glyoxylate cycle? a. chloroplast stroma b. cytoplasm c. mitochondria d. glyoxysome ANS: D DIF: Easy REF: 12.5 OBJ: 12.5.a. Identify the organelles required by the glyoxylate cycle.

MSC: Remembering 72. Which of the following is true of the glyoxylate cycle? a. It allows plants to produce glucose from fats and two-carbon molecules like acetate. b. It occurs in plant cells as an alternative to photosynthesis. c. It bypasses all regulated steps of the TCA cycle. d. It results in a net production of ATP and NADH without proceeding through the TCA cycle.

ANS: A DIF: Medium REF: 12.5 OBJ: 12.5.a. Identify the organelles required by the glyoxylate cycle.

MSC: Analyzing 73. The glyoxylate cycle reaction shown below is catalyzed by which enzyme class?

a. b. c. d.

lyase hydrolase transferase oxidoreductase

ANS: A DIF: Easy REF: 12.5 OBJ: 12.5.b. Name the two enzymes that are unique to the glyoxylate cycle.

MSC: Understanding 74. The glyoxylate cycle enzymes a. are active at night when sugar reserves are high and lipid synthesis is activated. b. bypass the decarboxylation steps of the TCA cycle, resulting in the net synthesis of a sugar molecule from acetyl-CoA. c. replace the mitochondrial TCA cycle enzymes. d. require ATP and NADPH from the light reactions.

ANS: B DIF: Difficult REF: 12.5 OBJ: 12.5.b. Name the two enzymes that are unique to the glyoxylate cycle.

MSC: Analyzing 75. Unlike plant cells, animal cells lack the glyoxylate enzymes a. isocitrate lyase and malate synthase. b. rubisco and transaldolase. c. acetyl-CoA carboxylase and citrate synthase. d. isocitrate dehydrogenase and -ketoglutarate dehydrogenase.

ANS: A DIF: Easy REF: 12.5 OBJ: 12.5.b. Name the two enzymes that are unique to the glyoxylate cycle.

MSC: Remembering SHORT ANSWER 1. Hypothesize how the combustion of large quantities of fossil fuels could affect the cycle shown below. Then explain how this could be further complicated by the global loss of vegetation, such as by the cutting of rain forests.

ANS: The formation of CO2 from burning fossil fuels, in addition to the natural production of CO2 as depicted in the figure, could outpace the fixation of CO2 by natural photosynthetic processes, resulting in increased levels of atmospheric CO2. This could be further exacerbated by depleting the plants which carry out photosynthesis.

DIF: Medium REF: 12.1 OBJ: 12.1.a. Hypothesize how the loss of forests could exacerbate the greenhouse effect.

MSC: Applying 2. List the five steps of photosynthesis, whereby solar energy is converted into chemical energy.

ANS: (1) Photons oxidize chlorophyll, which is reduced by stealing electrons from H2O to give O2. (2) The electron transfers driven by the photons result in proton pumping and a proton gradient. (3) The electrons lost from chlorophyll make reduced NADPH. (4) The proton gradient is used to make ATP by ATP synthase. (5) The ATP and NADPH are used to drive carbon fixation reactions, making sugars from CO2.

DIF: Difficult REF: 12.1 OBJ: 12.1.b. List the five steps used by photosynthetic organisms to convert solar energy into chemical energy.

MSC: Applying 3. Label the parts of the chloroplast on the figure below.

ANS:

DIF: Medium REF: 12.1 OBJ: 12.1.c. Name the key structures found within the chloroplast.

MSC: Remembering 4. List the three possible fates of an electron in an excited state chlorophyll molecule.

ANS: See Figure 12.9 below. (1) Electron transfer to a neighboring electron acceptor. (2) Relaxation of the electron back to its ground state with loss of heat or photon energy. (3) Relaxation of the electron back to its ground state with resonance energy transfer to a nearby energy acceptor.

DIF: Easy REF: 12.2 OBJ: 12.2.a. List the three possible outcomes from excitation of an electron in a chlorophyll molecule.

MSC: Applying 5. Heme and chlorophyll have the same porphyrin cofactor, yet they have largely different roles.

Compare their color and the metal ions employed by each.

ANS: Chlorophyll = green, Mg2+; heme = red/brown, Fe2+/3+ DIF: Easy REF: 12.2 OBJ: 12.2.b. Compare the structures of chlorophyll and heme.

MSC: Analyzing

6. Describe the arrangement of light-harvesting complexes relative to the reaction center in a plant’s photosystem enzymes.

ANS: The reaction center is centrally located and it is surrounded by light-harvesting complexes (LHCs).

The LHCs are thought to absorb photons and transfer that energy through resonance energy transfer to the reaction center, which is composed of a pair of chlorophyll molecules that ultimately eject an electron.

DIF: Medium REF: 12.2 OBJ: 12.2.c. Name the key pigments associated with the photosynthetic reaction center.

MSC: Applying 7. Draw the reaction that corresponds to the energy transfer between an excited chlorophyll molecule and its neighbor.

ANS: Chl1* + Chl2

Chl1 + Chl2* (* denotes excited state)

DIF: Medium REF: 12.2 OBJ: 12.2.d. Define resonance energy transfer as it applies to the photosystems.

MSC: Applying

8. List the four proteins/enzymes and the one molecule involved in the electron transfers in the photosynthetic Z scheme, and show their positions in the “Z” shape.

ANS: (1) Photosystem 1 (PSI), (2) photosystem II (PSII), (3) cytochrome b6f, (4) plastocyanin and plastoquinone. The top line of the Z scheme’s “Z” shape is PSII, while the bottom line is PSI. The diagonal of the “Z” is represented by electron transfers through plastoquinone, cytochrome b6f, and plastocyanin.

DIF: Medium REF: 12.2 OBJ: 12.2.e. List the components of the Z scheme of plant photosynthesis.

MSC: Applying 9. Trace the path of each electron through the photosynthetic pathway, starting from H2O and proceeding to the cytochrome b6f complex.

ANS: See Figure 12.20 below. H2O photosystem II (oxygen evolving center [OEC, Mn4Ca cluster] TyrZ+ → P680+ pheophytin+ PQA PQB} cytochrome b6f

DIF: Difficult REF: 12.2 OBJ: 12.2.f. Restate the mechanism used by the O2-evolving complex to connect a four-electron reduction with a single-electron oxidation.

MSC: Applying 10. Which two proteins do electrons move between in the PQ cycle?

ANS: The PQ cycle moves electrons from PQB of photosystem II to the copper protein plastocyanin.

DIF: Medium REF: 12.2 OBJ: 12.2.g. Compare and contrast the PQ cycle with the Q cycle of mitochondrial electron transport.

MSC: Remembering 11. Draw a picture of the chloroplast and show the location of and direction in which protons are pumped during photosynthetic light reactions.

ANS: See Figure 12.7 below. Protons are pumped into the thylakoid lumen by the cytochrome b6f complex.

DIF: Medium REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Applying 12. Trace the electron from plastocyanin to NADPH in the photosynthetic electron transport system.

ANS: See Figure 12.30 below. plastocyanin phylloquinone Fx FA FB}

photosystem II {P700+ Chl ChlAo ferredoxin ferredoxin-NADP+ reductase

DIF: Difficult REF: 12.2 OBJ: 12.2.h. Identify where protons are translocated across the thylakoid membrane.

MSC: Applying

NADPH

13. Draw the path of electrons in the cyclic photophosphorylation pathway showing the main enzymes and electron carriers involved and demonstrating its cyclic nature.

ANS: See Figure 12.38 below. photosystem I plastocyanin photosystem I

ferredoxin

plastoquinone

cytochrome b6f

DIF: Difficult REF: 12.3 OBJ: 12.3.b. Explain the importance of cyclic photophosphorylation.

MSC: Applying 14. Briefly describe the three stages of the Calvin cycle.

ANS: (1) The enzyme rubisco catalyzes the fixation of CO2, by incorporating it onto a C5 molecule to give two C3 molecules. (2) The two C3 molecules (glycerate-3-phosphate) are converted into two other C3 molecules (glyceraldehyde-3-phosphate) utilizing ATP and NADPH from the light reactions. (3) The C3 molecules are rearranged through transferase reactions to regenerate the starting C5 molecule.

DIF: Medium cycle.

MSC: Applying

REF: 12.4

OBJ: 12.4.b. Define the three stages of the Calvin

15. Write out the overall net Calvin cycle reaction assuming three CO2 molecules are the starting reactant.

ANS: 3 CO2 + 6 NADPH + 9 ATP + 6 H2O

glyceraldehyde-3-phosphate + 6 NADP+ + 9 ADP+ + 9 Pi

DIF: Difficult REF: 12.4 OBJ: 12.4.c. State the net Calvin cycle reaction that produces one molecule of glyceraldehyde-3-phosphate.

MSC: Understanding 16. In the figure below, identify A and B in the active site of rubisco.

ANS: A is the active site Mg2+ ion. B is the active site lysine carbamate group. Both are required for activity.

DIF: Medium REF: 12.4 OBJ: 12.4.d. List the five steps in the reaction catalyzed by rubisco.

MSC: Analyzing 17. Fill in the missing cofactors in the reactions below which correspond to stage 2 of the Calvin cycle reactions.

ANS:

DIF: Easy REF: 12.4 OBJ: 12.4.e. Compare and contrast stage 2 of the Calvin cycle with the reactions of glycolysis.

MSC: Understanding 18. Name the two key enzymes involved in swapping carbons between sugars in the carbon shuffling reactions of stage 3 of the Calvin cycle, and describe the differences in their reactions.

ANS:

Transaldolase and transketolase. Transaldolase combines a C3 ketose sugar with an aldose, making a new ketose product. Transketolase requires two reactants, a ketose and an aldolase, and it transfers a C2 group making a new ketose and leaving a new aldose as products. It uses thiamine pyrophosphate as a cofactor.

DIF: Medium REF: 12.4 OBJ: 12.4.f. Name the key enzymes of the carbon shuffle reactions.

MSC: Analyzing 19. Use the figure below to show how light exposure results in an activated rubisco enzyme.

ANS:

As sunlight activates the light reactions to pump protons into the thylakoid lumen, the pH rises in the stroma and Mg2+ ions are displaced from the lumen into the stroma. Both Mg2+ and the higher pH in the stroma activate rubisco.

DIF: Difficult REF: 12.4 OBJ: 12.4.g. State the three mechanisms used to control Calvin cycle activity by light.

MSC: Applying 20. Explain why the rubisco enzyme’s unproductive side reaction with O2, called photorespiration, is a concern even when the O2 affinity for rubisco is 30 times less than that of CO2.

ANS: The concentration of O2 in the air is much higher than that of CO2 (500 times higher).

DIF: Easy REF: 12.4 OBJ: 12.4.h. Explain why limiting exposure of rubisco to oxygen is important for plants.

MSC: Understanding 21. What is the main difference between C4 and CAM plants?

ANS: CAM plants open up their stomata at night and absorb CO2 by storing it in malate until light activates the Calvin cycle. The C4 plants absorb CO2 during the day with active Calvin cycle reactions. However, the cells where CO2 is absorbed (mesophyll cells) are separate from those cells performing the carbon fixation with rubisco (bundle sheath cells).

DIF: Difficult REF: 12.4 OBJ: 12.4.i. Differentiate among C3, C4, and CAM plants.

MSC: Applying

22. Identify the cell types of cells A and B below, and then identify the plant type in which the cell arrangements are found.

ANS: A is a mesophyll cell. B is a bundle sheath cell. They are found in C4 plants.

DIF: Easy REF: 12.4 OBJ: 12.4.j. Outline the reactions that take place in the mesophyll cell and the bundle sheath cell of C4 plants.

MSC: Understanding 23. Explain how the bundle sheath and mesophyll cells in C4 plants cooperate to accomplish the delivery of CO2 to the Calvin cycle.

ANS: In the surface mesophyll cells, CO2 is absorbed and reacts with phosphoenolpyruvate to give oxaloacetate before it is converted into malate and transported to the bundle sheath cells. In the bundle sheath cells malate is decarboxylated to release CO2 and pyruvate. The released CO2 is used by rubisco to make glycerate-3-phosphate and support the Calvin cycle. The pyruvate molecule is transported back to the mesophyll cells, where it is converted to phosphoenolpyruvate to react with another CO2.

DIF: Difficult REF: 12.4 OBJ: 12.4.j. Outline the reactions that take place in the mesophyll cell and the bundle sheath cell

of C4 plants.

MSC: Applying

24. Explain how CAM plants cooperate to accomplish the delivery of CO2 to the Calvin cycle.

ANS: CO2 is absorbed at night, when it is cool. CO2 reacts with phosphoenolpyruvate to give oxaloacetate before it is converted into malate. The malate is stored until daylight conditions, where malate is decarboxylated in the chloroplasts to release CO2 and pyruvate. The released CO2 is used by rubisco to make glycerate-3-phosphate and support the Calvin cycle. The pyruvate molecule is converted into starch, where it is stored until night and converted back into phosphoenolpyruvate to react with another CO2.

DIF: Difficult REF: 12.4 OBJ: 12.4.k. Distinguish the reactions that occur during the day from those that occur at night in CAM plants.

MSC: Applying 25. At what stage of plant growth is the glyoxylate cycle most common, and why?

ANS: The glyoxylate cycle is most common in seedling growth as the fats stored in seeds are converted into carbohydrate molecules for energy production.

DIF: Easy REF: 12.5 OBJ: 12.5.a. Identify the organelles required by the glyoxylate cycle.

MSC: Applying

Chapter 13: Carbohydrate Structure and Function MULTIPLE CHOICE 1. Which glycan is a major component of plant cell walls? a. cellulose b. chitin c. starch d. glycogen ANS: A DIF: Easy REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Remembering 2. Which simple sugar major group ranges in size from 3 to 20 branched and unbranched sugar residues? a. monosaccharides b. disaccharides c. oligosaccharides d. polysaccharides ANS: C DIF: Easy REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Remembering 3. Which of the following is classified as a monosaccharide? a. sucrose b. glucose c. lactose d. maltose ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Remembering 4. Which disaccharide can be found in fermented beverages such as beer? a. sucrose b. glucose c. lactose d. maltose ANS: D DIF: Medium REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Applying 5. Which glucose homopolymer would be used if a person had to sprint quickly? a. sucrose b. galactose c. starch d. glycogen ANS: D DIF: Medium REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Applying

6. Which glucose homopolymer is generated during daylight hours in plants? a. sucrose b. galactose c. starch d. glycogen ANS: C DIF: Easy REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Applying 7. One of the functions of simple sugars includes a. enzymatically removing glycans through hydrolysis reactions. b. functioning as a structural component in invertebrate exoskeletons. c. acting as metabolic intermediates in energy conversion pathways. d. enzymatically linking glycans to proteins and lipids.

ANS: C DIF: Easy REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Understanding 8. One of the functions of polysaccharides includes a. enzymatically removing glycans through hydrolysis reactions. b. functioning as a structural component in invertebrate exoskeletons. c. acting as metabolic intermediates in energy conversion pathways. d. enzymatically linking glycans to proteins and lipids.

ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Understanding 9. Glycoconjugates are linked to proteins or lipids via a. London forces. b. ionic bonds. c. covalent bonds. d. hydrogen bonds.

ANS: C DIF: Easy REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Remembering 10. The following figure shows the cellular processes that synthesize, secrete, and recognize glycoconjugates in eukaryotic cells. Identify the cellular structure where glycosyltransferase enzymes function.

a. b. c. d.

1 2 3 4

ANS: B DIF: Difficult REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Understanding 11. The following figure shows the cellular processes that synthesize, secrete, and recognize glycoconjugates in eukaryotic cells. Identify where lectins are located on the figure.

a. b. c. d.

1 2 5 6

ANS: D DIF: Difficult REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Understanding 12. The following figure shows the cellular processes that synthesize, secrete, and recognize glycoconjugates in eukaryotic cells. Identify the cell surface glycoconjugates.

a. b. c. d.

1 2 5 6

ANS: C DIF: Difficult REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Understanding 13. Which of the following oligosaccharides are found in high abundance in some types of vegetables and have been known to cause intestinal distress? a. lacto-N-tetraose b. verbascose c. amylose d. amylopectin ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Remembering 14. Raffinose-series oligosaccharides are hard for humans to digest because a. humans do not have the enzyme necessary to hydrolyze the glycosidic bonds. b. they bind to bifidobacteria in the gut. c. they function as soluble decoys that inhibit pathogenic bacteria from invading the epithelial cells. d. humans have a large number of competing glycan binding sites.

ANS: A DIF: Easy REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Understanding 15. Eating large amounts of vegetables can cause flatulence because of the presence of a. glucose. b. lactose. c. starch. d. raffinose.

ANS: D

DIF: Medium

REF: 13.1

OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Remembering 16. The structure of raffinose, stachyose, and verbascose differ in the number of __________ units attached to a __________. a. galactose; lactose b. glucose; sucrose c. galactose; sucrose d. glucose; lactose ANS: C DIF: Medium REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Understanding 17. The product Beano contains __________, which helps humans digest raffinose-series oligosaccharides. a.

-galactosidase b. -galactosidase c. lactase d. amylase ANS: A DIF: Medium REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Applying 18. The growth rate of nonruminating animals often decreases when they eat feed containing __________ because of the inability to digest it. a. glucose b. lactose c. starch d. raffinose ANS: D DIF: Medium REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Remembering 19. The image below shows a(n) __________ glycosidic bond.

a. b. c. d.

-1,4-1,4-1,6-1,6-

ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

20. The image below shows a(n) __________ glycosidic bond.

MSC: Understanding

a. b. c. d.

-1,4-1,4-1,6-1,6-

ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Understanding

21. What type of bond is responsible for the rigid nature of the polysaccharide fibril structure? a. London forces b. ionic bonds c. covalent bonds d. hydrogen bonds ANS: D DIF: Medium REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Remembering

22. What would the predicted enzymatic product be when cellulose is exposed to cellulase? a. pectin b. hemicellulose c. cellotetraose d. glucose ANS: C DIF: Medium REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Applying

23. How are glycosaminoglycans attached to proteins? a. London forces b. ionic bonds c. covalent bonds d. hydrogen bonds ANS: C DIF: Medium REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Understanding

24. The glycosaminoglycan __________ sulfate is responsible for providing structural support in the cornea of the eye. a. chondroitin b. keratan c. heparan d. chitin

ANS: B DIF: Difficult REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

25. Which glycan contains both a. amylopectin b. amylose c. chitin d. cellulose

-1,4 glycosidic bonds and

MSC: Remembering

-1,6 glycosidic bonds?

ANS: A DIF: Easy REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Understanding 26. Compared with glycogen, amylopectin contains __________ glycosidic bonds. a. more -1,6 b. fewer -1,6 c. only -1,4 d. only -1,6 ANS: B DIF: Difficult REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Analyzing 27. Approximately how many glucose molecules would be present in an amylose polymer with 15 turns of the helix? a. 60 b. 75 c. 90 d. 105 ANS: C DIF: Difficult REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Applying 28. Compared with amylopectin, amylose has __________ glycosidic bonds. a. more -1,6 b. fewer -1,6 c. only -1,4 d. only -1,6 ANS: C DIF: Difficult REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Analyzing 29. Amylose can form stable left-handed helical structures because of a. London forces. b. ionic bonds. c. covalent bonds. d. hydrogen bonds.

ANS: D DIF: Medium REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Remembering 30. Which glycan contains a covalently linked dimeric protein that functions as a protein anchor?

a. b. c. d.

amylose glycogen amylopectin cellulose

ANS: B DIF: Easy REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Understanding 31. The glycan group on glycoproteins and glycolipids on the red blood cells all contain the glycan subgroup(s) a. O. b. Gal. c. GalNAc. d. Gal and GalNAc. ANS: A DIF: Easy REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Understanding 32. A person who only expresses the GTA enzyme and not the GTB enzyme will have which blood type? a. O b. A c. B d. AB ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying 33. A person who only expresses the GTB enzyme and not the GTA enzyme will have which blood type? a. O b. A c. B d. AB ANS: C DIF: Medium REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying 34. If one homozygous parent expresses the GTA glycosyltransferase and the other homozygous parent expresses the GTP glycosyltransferase, what is the probability of a child with a blood type of O? a. 0% b. 25% c. 75% d. 100% ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying

35. Two homozygous parents express the GTA glycosyltransferase. What is the probability of a child with an A blood type? a. 0% b. 25% c. 75% d. 100% ANS: C DIF: Medium REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying 36. What is the blood type of a person who fails to express either the GTA or GTB glycosyltransferases? a. O b. A c. B d. AB ANS: A DIF: Easy REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying 37. What type of antigen(s) is/are expressed on the red blood cell of a personal with type A blood? a. antigen A b. antigen B c. both antigen A and antigen B d. neither antigen A or antigen B ANS: A DIF: Easy REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Understanding 38. What type of antibody or antibodies is/are found in the plasma of a person with type O blood? a. anti-A b. anti-B c. neither anti-A or anti-B d. both anti-A and anti-B ANS: D DIF: Easy REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Understanding 39. Because of antibody recognition, which of the following blood types can donate to a person with type O blood? a. A b. B c. AB d. O ANS: D DIF: Easy REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Applying 40. What type of antibody or antibodies is/are found in the plasma of a person with type AB blood? a. anti-A

b. anti-B c. neither anti-A or anti-B d. both anti-A and anti-B ANS: C DIF: Easy REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Remembering 41. What type of antibody or antibodies is/are found in the plasma of a person with type A blood? a. anti-A b. anti-B c. neither anti-A or anti-B d. both anti-A and anti-B ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Remembering 42. What type of antibody or antibodies is/are found in the plasma of a person with type B blood? a. anti-A b. anti-B c. neither anti-A or anti-B d. both anti-A and anti-B ANS: A DIF: Medium REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Remembering 43. Compared with Gram-negative bacteria, Gram-positive bacteria have a a. thicker peptidoglycan layer. b. thinner peptidoglycan layer. c. thinner outer membrane. d. thicker outer membrane.

ANS: A DIF: Difficult REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Analyzing 44. Gram-positive bacteria have a peptidoglycan layer that consists of __________, which provides structural support and influences the uptake of charged biomolecules. a. starch b. lipopolysaccharides c. lipoteichoic acid d. hyaluronic acid ANS: C DIF: Easy REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Remembering 45. The outer membrane of Gram-negative bacteria contains glycolipids called a. cellulose. b. lipopolysaccharides. c. lipoteichoic acid. d. hyaluronic acid.

ANS: B

DIF: Easy

REF: 13.2

OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Remembering 46. Crystal violet stains Gram-positive bacteria because Gram-positive bacteria have a(n) a. outer membrane layer that collapses, trapping the crystal violet molecules. b. thinner peptidoglycan layer that allows the crystal violet molecules to pass through the pores. c. thinner peptidoglycan layer that collapses, trapping the crystal violet molecules. d. thicker peptidoglycan layer that collapses, trapping the crystal violet molecules.

ANS: D DIF: Medium REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Analyzing 47. Gram-negative bacteria resist staining with crystal violet because Gram-negative bacteria have a(n) a. outer membrane layer that collapses, releasing the crystal violet molecules. b. thinner peptidoglycan layer that does not retain the crystal violet molecules. c. thinner peptidoglycan layer that collapses, releasing the crystal violet molecules. d. thicker peptidoglycan layer that collapses, releasing the crystal violet molecules.

ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Analyzing 48. Gram-negative bacteria contain which potent inflammatory agent in animals? a. cellulose b. lipopolysaccharide c. lipoteichoic acid d. hyaluronic acid ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Understanding 49. Which enzyme does penicillin target in bacteria? a. -lactamase b. peptidase c. transpeptidase d.

-galactosidase ANS: C DIF: Easy REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

50. Which functional group on penicillin forms a complex with transpeptidase of the bacterial wall? a. sulfide b. amine c. hydroxyl d. carbonyl ANS: D DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

51. Which enzyme is produced by penicillin-resistant bacteria? a. -lactamase b. peptidase

MSC: Understanding

c. transpeptidase d.

-galactosidase ANS: A DIF: Easy REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

52. Which amino acid does penicillin form a complex with on transpeptidase? a. aspartic acid b. lysine c. alanine d. serine ANS: D DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

53. How is penicillin inactivated by penicillin-resistant bacteria? a. Transpeptidase binds to methicillin. b. The carbonyl carbon of the -lactam ring binds to transpeptidase. c. The -lactam ring in penicillin is hydrolyzed. d. The serine in transpeptidase binds to penicillin.

ANS: C DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

54. Penicillin kills bacteria by inhibiting the biosynthesis of the cell wall. How does penicillin cause the inhibition? a. The transpeptidase of the bacteria binds to methicillin. b. The carbonyl carbon of the -lactam ring of penicillin binds to transpeptidase. c. The -lactam ring in penicillin is hydrolyzed. d. The glycine in transpeptidase binds to penicillin.

ANS: B DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

55. What type of inhibitor is penicillin classified as? a. reversible b. competitive c. suicide d. uncompetitive ANS: C DIF: Medium REF: 13.2 OBJ: 13.2.e. Distinguish between penicillin and synthetic compounds such as methicillin.

MSC: Remembering 56. What is an advantage of using methicillin compared with penicillin? a. Penicillin is susceptible to inactivation by mutant transpeptidase enzymes. b. Methicillin is resistant to -lactamase activity. c. Penicillin does not bind transpeptidase as well as methicillin. d. Methicillin does not bind transpeptidase.

ANS: B DIF: Easy REF: 13.2 OBJ: 13.2.e. Distinguish between penicillin and synthetic compounds such as methicillin.

MSC: Analyzing 57. Both methicillin and penicillin are inactive when exposed to

a. transpeptidase. b. transpeptidase and -lactamase. c. -lactamase. d. variant transpeptidase.

ANS: D DIF: Medium REF: 13.2 OBJ: 13.2.e. Distinguish between penicillin and synthetic compounds such as methicillin.

MSC: Analyzing 58. What method is used to release the N-linked glycan groups from the membrane-associated glycoconjugates shown in 1 in the figure below?

a. b. c. d.

enzymatic cleavage using PNGaseF chemical cleavage using a -elimination reaction chemical cleavage using a Schiff base intermediate enzymatic cleavage using -galactosidase

ANS: A DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 59. What method is used to release the O-linked glycan groups from the membrane-associated glycoconjugates shown in 2 in the figure below?

a. enzymatic cleavage using PNGaseF b. chemical cleavage using a -elimination reaction c. chemical cleavage using a Schiff base intermediate

d. enzymatic cleavage using -galactosidase ANS: B DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 60. What is the first step when analyzing glycan groups on a glycoprotein? a. The glycan groups must undergo liquid chromatography to separate the different components of the mixture. b. Mass spectrometry should be used to identify the glycans based on their mass to charge ratio. c. The glycan groups must be separated from the protein moiety using a cleavage reaction. d. The glycan groups must undergo column chromatography to separate the glycan groups from the lipid moiety.

ANS: C DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 61. Why are glycans more difficult to structurally analyze compared with proteins or nucleic acids? a. Proteins are smaller than most glycans. b. Nucleic acids are polar, whereas most glycans are nonpolar. c. Sugar synthesis is a template-directed process. d. Glycans have sugar isomers with identical masses.

ANS: D DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 62. One common way to characterize glycans is to a. digest the glycan into fragments using trypsin and chymotrypsin. b. use affinity chromatography to recognize the different sugars. c. incubate fluorescently labeled glycoproteins with lectin. d. use ELISA to determine the structure.

ANS: C DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 63. A a. b. c. d.

-elimination reaction is used in glycan characterization to label the antibody arrays. fluorescently label glycoproteins. cleave the O-linked glycans. cleave the N-linked glycans.

ANS: C DIF: Easy REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Understanding 64. Which fluorescent dye is used to label glycans before HPLC? a. 2-aminobenzamide b. sodium hydroxide and sodium borohydride c. sodium cyanoborohydride d. PNGaseF ANS: A

DIF: Easy

REF: 13.3

OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Remembering 65. Which technique provides information about the arrangement of sugars in a glycan fraction? a. glycan arrays b. MALDI-TOF c. mass spectrometry d. high-performance liquid chromatography ANS: D DIF: Easy REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Understanding 66. Which technique can identify N-linked glycans in a mixed sample? a. lectin arrays b. glycan arrays c. mass spectrometry d. high-performance liquid chromatography ANS: C DIF: Easy REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Understanding 67. The glycan fragment shown on the right has been cleaved by glycosylase enzymes, and HPLC analysis has produced the peaks 1 to 6.

Which of the following fragments corresponds to peak 5?

a. b.

c.

d.

ANS: A DIF: Medium REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Applying 68. The glycan fragment shown below on the right has been cleaved by glycosylase enzymes and HPLC analysis has produced the peaks 1 to 6. Which of the following fragments corresponds to peak 1?

a.

b.

c.

d.

ANS: D DIF: Medium REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Applying 69. The glycan fragment shown below on the right has been cleaved by glycosylase enzymes, and HPLC analysis has produced the peaks 1 to 6. Which of the following fragments corresponds to peak 6?

a.

b.

c.

d.

ANS: D DIF: Medium REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Applying 70. Glycan arrays can be coupled with __________ to qualitatively compare fractionated cell extracts from different sources. a. MALDI-TOF b. HPLC c. size exclusion chromatography d. mass spectrometry ANS: B DIF: Difficult REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Understanding 71. To detect lectins on the surface of pathogenic and nonpathogenic bacteria, __________ would be used. a. HPLC b. MALDI-TOF c. a glycan array d. column chromatography ANS: C DIF: Difficult REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Applying 72. In a lectin array, how are lectin proteins attached to the solid support? a. van der Waals interactions b. hydrogen bonding c. covalent bonding d. ionic interactions ANS: C DIF: Easy REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Remembering 73. Arrays made with chemically synthesized glycans are used to investigate glycan-binding properties a. of different arrangements of sugar groups using HPLC. b. by comparing the mass-to-charge ratio of the fragments with known glycan groups. c. of different types of pathogenic bacteria using HPLC. d. by comparing the affinity of lectins with structurally related glycan groups.

ANS: D DIF: Easy REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Understanding 74. The figure below is a fluorescence readout from a lectin array. What can be deduced from A?

a. b. c. d.

There is no interaction between the glycan and the lectin in the well.

There is a glycan–lectin interaction in the well.

There is an interaction, but there is no way to determine the species that are interacting.

Glycan cleavage from the glycoconjugate has been achieved.

ANS: A DIF: Medium REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Applying 75. The figure below is a fluorescence readout from a lectin array. What can be deduced from B?

a. b. c. d.

There is no interaction between the glycan and the lectin in the well.

There is a glycan–lectin interaction in the well.

There is an interaction, but there is no way to determine the species that are interacting.

Glycan cleavage from the glycoconjugate has been achieved.

ANS: B DIF: Medium REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Applying

SHORT ANSWER 1. Give an example of a mono-, di-, and polysaccharide and explain the biological importance of each.

ANS: Answers will vary depending on the examples the students choose. An example of a representative answer would be as follows: Monosaccharide: Glucose is a common monosaccharide that is also known as grape sugar or blood sugar. Glucose is the monomer unit that makes up many polysaccharides including starch and glycogen.

Disaccharide: Lactose is a disaccharide that is found in milk and milk products. It is also the common disaccharide in human milk oligosaccharides.

Polysaccharide: Cellulose is one of the most abundant polysaccharides in the biosphere. It is a major component of plant cell walls.

DIF: Easy REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Remembering | Understanding 2. Explain the connection the disaccharide lactose has to lacto-N-tetraose and lacto-N-fucopentaose I that is found in human breast milk.

ANS: Lactose is a disaccharide that is found in milk and milk products. It is also the common disaccharide in human milk oligosaccharides. Both lacto-N-tetraose and lacto-N-fucopentaose I are modifications of lactose.

DIF: Medium REF: 13.1 OBJ: 13.1.a. Name examples of biologically important mono-, di-, and polysaccharides.

MSC: Analyzing 3. Approximately 11 different monosaccharides are used as building blocks of glycan groups in glycoconjugates. However, a predictive sugar code has been difficult to identify. Propose three reasons for this difficulty.

ANS: Unlike other biological molecules (DNA, proteins), carbohydrate addition to proteins and lipids is not a template-directed process, making it difficult to predict the structure. Molecules of the same protein can contain similar but not identical glycan structures because of the cellular environment, which can be difficult to predict. Additionally, limitations in glycan analytical methods and instrument sensitivity make it very difficult to decipher the glycan structures.

DIF: Difficult REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Evaluating 4. Explain the difference between simple sugars, polysaccharides, and glycoconjugates.

ANS:

Simple sugars are the building blocks of polysaccharides and glycoconjugates. They also can function as metabolic intermediates in energy conversion pathways. Polysaccharides are polymers of monosaccharides that function in a variety of ways including acting as a structural component of invertebrate exoskeletons (chitin) and forming plant walls (cellulose). Glycoconjugates are proteins or lipids that are covalently linked to glycans. They participate in cellular communication.

DIF: Easy REF: 13.1 OBJ: 13.1.b. Differentiate among simple sugars, polysaccharides, and glycoconjugates.

MSC: Analyzing 5. Explain how sucrose is related to raffinose, stachyose, and verbascose.

ANS: The raffinose-series oligosaccharides (raffinose, stachyose, and verbascose) are related because they are modifications of the same disaccharide. The disaccharide that relates them is sucrose.

DIF: Difficult REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Analyzing 6. Why do humans experience intestinal distress when eating some vegetables?

ANS: The human gut does not contain the enzyme necessary to hydrolyze the -1,6 glycosidic bond of the raffinose-series oligosaccharides. The undigested carbohydrates end up in the lower intestine, where bacteria that do contain -1,6 galactosidase ferment the compounds, resulting in the production of gas.

DIF: Medium REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Applying 7. The growth rate of pigs and chickens is often decreased when they eat raffinose-series oligosaccharides that are present in soybean-based feeds. Propose a method where pigs and chickens can still eat the soybean-based feeds but also grow at the same rate.

ANS: The food could be pretreated with an enzyme that degrades the raffinose-series oligosaccharides in the feed. Aspergillis niger secretes -galactosidase that could be used for this purpose.

DIF: Difficult REF: 13.1 OBJ: 13.1.c. Explain why humans and other nonruminating animals cannot digest raffinose-series oligosaccharides.

MSC: Applying 8. Why can cows digest grass but humans cannot?

ANS: Cows (and other ruminating herbivores) contain microorganisms that secrete the enzyme cellulase, which can break the -1,4 glycosidic bonds in cellulose. The ability of the cows to regurgitate their food maximizes the mechanical and enzymatic breakdown of the grass.

DIF: Difficult REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Applying

9. Compare and contrast the structure of chitin and cellulose.

ANS: Both contain -1,4 glycosidic bonds. Chitin consists of repeating GlcNAc hexosamine units, whereas cellulose contains repeating units of the glucose disaccharide cellobiose.

DIF: Medium REF: 13.1 OBJ: 13.1.d. Describe the structures of cellulose and chitin.

MSC: Analyzing

10. Compare and contrast the structure of glycogen, amylose, and amylopectin.

ANS: All the glycans contain exclusively glucose units and exhibit -1,4 glycosidic bonds, but amylopectin and glycogen also have -1,6 glycosidic bonds. This results in a linear structure for amylose and a branched structure for amylopectin and glycogen. Glycogen is more highly branched and contains more glucose units than amylopectin. Furthermore, glycogen has a covalently linked dimeric protein called glycogenin that functions as an anchor.

DIF: Medium REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Analyzing 11. What are the biological implication of the increased branching in glycogen compared with amylopectin and amylose?

ANS: The increased branching in glycogen results in more glucose units with nonreducing ends. This means that glycogen can be used as a fast energy source if the body requires it.

DIF: Difficult REF: 13.1 OBJ: 13.1.e. State the similarities and differences among amylose, amylopectin, and glycogen.

MSC: Applying 12. Compare the glycosyltransferase enzyme expression that results in the ABO blood groups.

ANS: Human ABO blood types are determined by the expression of one, both, or neither glycosyltransferase enzymes -1,3-N-acetylgalactosaminyltransferase (GTA) and -1,3-N-galactosylaminyltransferase (GTB). If neither is expressed, the blood type is O. If GTA is expressed, the GalNAc sugar residue is attached and the blood type is A. If GTB is expressed, the Gal sugar residue is attached and the blood type is B. If both GTA and GTB are expressed, both GalNAc and Gal sugar residues are expressed, resulting in the AB blood type.

DIF: Difficult REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Analyzing 13. A father’s blood type is B and a mother’s blood type is O. Is it possible for their baby to be born with type A blood? If so, how?

ANS:

This is not possible. Blood type inheritance is a codominant genetic trait, meaning individuals inherit one copy of each of the GTA or GTB enzymes from each parent. A mother with a blood type of O and a father with a blood type of B cannot produce a baby with a blood type of A. DIF: Difficult REF: 13.2 OBJ: 13.2.a. Explain the relationship of glycosyltransferases to biochemical properties of human blood groups.

MSC: Applying 14. Type O blood is sometime referred to as a universal donor. Explain what this means.

ANS: Type O individuals can donate packed red blood cells to blood types A, B, AG, and O. They do not express A or B glycoconjugate antigens, which means there is no immunological response.

DIF: Medium REF: 13.2 OBJ: 13.2.b. List the expected blood group–related antibodies found in each of the four human blood types.

MSC: Applying 15. Differentiate Gram-positive bacteria and Gram-negative bacteria.

ANS: Gram-positive bacteria have a thicker peptidoglycan cell wall compared with Gram-negative bacteria. Furthermore, Gram-positive bacteria lack an outer membrane, whereas Gram-negative bacteria have an outer membrane. The thick peptidoglycan layer of Gram-positive bacteria will trap crystal violet dye, whereas Gram-negative will not.

DIF: Medium REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Analyzing 16. Outline the methods used to stain both Enterococcus faecalis and Escherichia coli.

ANS: Enterococcus faecalis is a Gram-positive bacteria. A crystal violet stain and an iodine mordent would be applied to the cells and then washed with ethanol, resulting in a purple stain. Escherichia coli is a Gram-negative bacteria. The process for staining is similar to the Gram-positive bacteria, except a red safranin counterstain is applied, turning the cells red.

DIF: Difficult REF: 13.2 OBJ: 13.2.c. Differentiate between Gram-positive and Gram-negative bacteria with regard to biochemistry and properties.

MSC: Analyzing 17. Explain how penicillin functions.

ANS: Penicillin blocks bacterial cell wall biosynthesis by inhibiting the enzyme transpeptidase.

Penicillin specifically forms a suicide inhibitor complex between the serine residue in transpeptidase and the carbonyl carbon in the -lactam ring of the penicillin molecule. This inhibits the cell wall biosynthesis, resulting in bacterial death.

DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

18. Why are some bacteria resistant to penicillin?

ANS: Some bacteria produce an enzyme called -lactamase. This hydrolyzes the -lactam ring of penicillin, making the antibiotic inactive. Because -lactamase is a secreted enzyme, it basically functions as a protective shield for the bacteria.

DIF: Medium REF: 13.2 OBJ: 13.2.d. Describe the mechanism of action of penicillin.

MSC: Understanding

19. How do the antibacterial properties of penicillin compare with methicillin?

ANS: Penicillin forms a suicide inhibitor complex between the serine residue in transpeptidase and the carbonyl carbon in the -lactam ring of the penicillin molecule. This inhibits the cell wall biosynthesis, resulting in bacterial death. Similarly, methicillin also inactivates the transpeptidase enzyme, resulting in bacteria death. Methicillin is not affected by -lactamase, which can render penicillin ineffective.

DIF: Medium REF: 13.2 OBJ: 13.2.e. Distinguish between penicillin and synthetic compounds such as methicillin.

MSC: Analyzing 20. Compare the mechanisms of resistance that bacteria have developed with penicillin and methicillin.

ANS: Penicillin-resistant bacteria express the enzyme -lactamase, which inactivates the penicillin by hydrolyzing the -lactam ring. In contrast, methicillin-resistant bacteria express variant transpeptidases that do not react with methicillin, resulting in active transpeptidase.

DIF: Medium REF: 13.2 OBJ: 13.2.e. Distinguish between penicillin and synthetic compounds such as methicillin.

MSC: Analyzing 21. What challenges are encountered during the structural characterization of glycans on glycoconjugates? Compare the two approaches used to overcome the characterization challenges presented by glycans.

ANS: Glycans have multiple bonding arrangements because they can have as many as 11 different sugars. There are sugar stereoisomers that can be present in the glycan conjugates that have the same mass, making mass spectrometry techniques challenging. Additionally, glycan structures can be different in small ways between identical classes of glycoconjugates.

Liquid chromatography can be used to sequence glycans using specific elution profiles generated by specific glycosidase enzymes. Liquid chromatography gives information about the arrangement of sugars in the glycan fraction produced from the enzyme cleavage. Mass spectrometry is used to identify the glycan fragment based on the mass-to-charge ratio.

DIF: Difficult REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Analyzing

22. Compare the methods used to cleave the O-linked and N-linked glycans from glycoproteins.

ANS: N-linked glycans are enzymatically cleaved using the peptide N-glycosidase F (PNGaseF).

O-linked glycans are chemically cleaved using a -elimination reaction with the reagents sodium hydroxide and sodium borohydride.

DIF: Medium REF: 13.3 OBJ: 13.3.a. Explain how techniques for structural characterization overcome challenges associated with glycan structures.

MSC: Analyzing 23. Compare the information about glycan structure that is determined from liquid chromatography with the information obtained from mass spectrometry.

ANS: High-performance liquid chromatography provides information about the arrangement of sugars in the glycan fraction. Mass spectrometry identifies common glycans in a mixed glycan sample using their mass-to-charge ratios.

DIF: Medium REF: 13.3 OBJ: 13.3.b. Differentiate between information about glycan structure provided by liquid chromatography and information provided by mass spectrometry.

MSC: Analyzing 24. Compare the two basic types of arrays developed for glycobiology research.

ANS: The first type is a protein array that can detect labeled glycoproteins in experimental samples.

Lectin proteins or antibodies are covalently attached to the array for the detection of glycoproteins.

The second array contains glycan groups that are covalently bound to glycoproteins for the detection of labeled lectin proteins or antibodies.

DIF: Medium REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Analyzing 25. Explain the information that glycan arrays provide about the cell.

ANS: Glycan arrays analyze the complete set of cellular glycan groups (glycome) under a variety of conditions. Additionally, glycan arrays can detect lectins on the surface of pathogenic and nonpathogenic bacteria.

DIF: Medium REF: 13.3 OBJ: 13.3.c. Describe what type of information about a cell might be obtained through a glycan array. MSC: Understanding

Chapter 14: Carbohydrate Metabolism MULTIPLE CHOICE 1. The pentose phosphate pathway occurs in the a. cytoplasm. b. nucleus. c. Golgi apparatus. d. mitochondria.

ANS: A DIF: Easy REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Remembering 2. The main function of the pentose phosphate pathway is to provide a. the cell with backup capability when glycolysis is inhibited. b. energy and reducing power. c. a mechanism for the utilization of the carbon skeletons of excess amino acids. d. a source of ribose and NADPH. ANS: D DIF: Easy REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Understanding 3. The pentose phosphate pathway a. resembles the TCA cycle in that it couples the loss of CO2 with the formation of NADH. b. allows 5C sugars to converge with or diverge from the glycolysis pathway. c. contains 2C, 3C, 4C, 5C, 6C, and 7C sugar molecules. d. enables the production of ATP from glucose.

ANS: B DIF: Medium REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Analyzing 4. The pentose phosphate pathway a. can be used to make seduheptulose-7-phosphate for use in RNA and DNA synthesis. b. is linked at its start and at its end to the glycolysis pathway. c. converges glycolysis intermediates with TCA cycle intermediates. d. occurs in the mitochondrial matrix of cells.

ANS: B DIF: Difficult REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Analyzing 5. Which of the following is NOT a role played by the pentose phosphate pathway? a. converting pyruvate into TCA cycle intermediates b. making NADPH for other metabolic pathways c. converting 6C glucose into 5C ribose d. converting DNA backbone sugars into glycolysis intermediates ANS: A DIF: Difficult REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Analyzing

6. The products of the oxidative portion of the pentose phosphate pathway are carbon dioxide and a. 2 NADH + 1 hexose phosphate. b. 2 NADP+ + 1 pentose phosphate. c. 2 NADPH + 1 hexose phosphate. d. 2 NADPH + 1 pentose phosphate.

ANS: D DIF: Easy REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Understanding 7. Which is the substrate or product of the reactions that comprise the oxidative branch of the pentose phosphate pathway? a. sedoheptulose-7-phosphate b. glyceraldehyde-3-phosphate c. ribulose-5-phosphate d. ribose-5-phosphate ANS: C DIF: Difficult REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Remembering 8. Which enzyme class catalyzes the following pentose phosphate pathway reaction?

a. b. c. d.

lyase transferase oxidoreductase isomerase

ANS: B DIF: Medium REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Applying 9. Which of the following molecules is found in the nonoxidative phase of the pentose phosphate pathway? a. ATP b. NADPH c. fructose-6-phosphate d. CO2 ANS: C DIF: Difficult REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Evaluating

10. What enzyme class in the nonoxidative phase of the pentose phosphate pathway allows for the reaction of ribose-5-phosphate and xylulose-5-phosphate to produce glyceraldehyde-3-phosphate and seduheptulose-7-phosphate? a. isomerase b. hydrolase c. transferase d. oxidoreductase ANS: C DIF: Medium REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Applying 11. Which of the following molecules is found in the nonoxidative phase of the pentose phosphate pathway? a. glucose-6-phosphate b. sedoheptulose-7-phosphate c. phosphoenolpyruvate d. CO2 ANS: B DIF: Medium REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Understanding 12. Which enzyme class catalyzes the following pentose phosphate pathway reaction (note that there may be some missing reactants and products)?

a. b. c. d.

lyase isomerase transferase oxidoreductase

ANS: D DIF: Medium REF: 14.1 OBJ: 14.1.c. Name the pentose phosphate pathway enzymes that produce NADPH. MSC: Applying 13. Starting from the oxidative phase of the pentose phosphate pathway, how many ATP and high-energy reduced molecules, respectively, are made in going from one glucose molecule to glyceraldehyde-3-phosphate and fructose-6-phosphate? a. 0; 0 b. 0; 2 c. 2; 0 d. 2; 2 ANS: B DIF: Easy REF: 14.1 OBJ: 14.1.c. Name the pentose phosphate pathway enzymes that produce NADPH. MSC: Understanding

14. Which enzyme in the pentose phosphate pathway catalyzes the following reaction?

a. b. c. d.

glucose-6-phosphate dehydrogenase transaldolase 6-phosphogluconate dehydrogenase ribulose-5-phosphate epimerase

ANS: C DIF: Medium REF: 14.1 OBJ: 14.1.c. Name the pentose phosphate pathway enzymes that produce NADPH. MSC: Remembering 15. Which enzyme in the pentose phosphate pathway is regulated to control flux through the pathway? a. glucose-6-phosphate dehydrogenase b. transaldolase c. 6-phosphogluconate dehydrogenase d. ribulose-5-phosphate epimerase ANS: A DIF: Easy REF: 14.1 OBJ: 14.1.d. Identify the control mechanisms for the pentose phosphate pathway.

MSC: Understanding 16. What molecule activates the pentose phosphate pathway? a. NADP+ b. ribulose-5-phosphate c. ADP d. NADH ANS: A DIF: Medium REF: 14.1 OBJ: 14.1.d. Identify the control mechanisms for the pentose phosphate pathway.

MSC: Analyzing 17. If the ratio of NADP+ to NADPH were high, the a. net production of ATP would occur. b. pentose phosphate pathway oxidative phase would be activated. c. cellular levels of nucleotides would have to increase from an activated pentose phosphate pathway. d. pentose phosphate pathway would be inhibited.

ANS: B DIF: Difficult REF: 14.1 OBJ: 14.1.d. Identify the control mechanisms for the pentose phosphate pathway.

MSC: Evaluating 18. Which enzyme uses cellular NADPH to regenerate reduced glutathione? a. glucose-6-phosphate dehydrogenase

b. glutathione peroxidase c. glutathione reductase d. hemoglobin ANS: C DIF: Medium REF: 14.1 OBJ: 14.1.e. Define the roles of glutathione, glutathione peroxidase, and glutathione reductase.

MSC: Remembering 19. How would individuals with decreased levels of the pentose phosphate enzyme glucose-6-phosphate dehydrogenase respond to oxidative stress? a. Higher than normal levels of NADPH would accumulate. b. They would not have the ability to regenerate reduced glutathione as rapidly. c. They would rapidly neutralize cellular levels of H2O2 and other reactive oxygen species. d. They would compensate with higher than normal levels of pentose phosphate pathway activity.

ANS: B DIF: Difficult REF: 14.1 OBJ: 14.1.e. Define the roles of glutathione, glutathione peroxidase, and glutathione reductase.

MSC: Applying 20. Which of the following metabolites is NOT a gluconeogenesis substrate in humans? a. pyruvate b. lactate c. oxaloacetate d. acetate ANS: D DIF: Easy REF: 14.2 OBJ: 14.2.a. List the three major sources of carbon for gluconeogenesis in animals.

MSC: Understanding 21. Which of the following metabolites has carbon atoms that can end up in glucose via the gluconeogenesis pathway in humans? a. CO2 b. glycerol c. ATP d. NADH ANS: B DIF: Easy REF: 14.2 OBJ: 14.2.a. List the three major sources of carbon for gluconeogenesis in animals.

MSC: Understanding 22. Two moles of pyruvate molecules running through the gluconeogenesis pathway to give 1 mole of glucose requires the hydrolysis of __________ moles of ATP equivalents. a. 0 b. 2 c. 4 d. 6 ANS: D DIF: Medium REF: 14.2 OBJ: 14.2.b. State the overall reaction for gluconeogenesis starting with pyruvate.

MSC: Remembering 23. How many moles of NADH are required in gluconeogenesis to convert 2 moles of pyruvate molecules into 1 mole of glucose? a. 0

b. 1 c. 2 d. 4 ANS: C DIF: Medium REF: 14.2 OBJ: 14.2.b. State the overall reaction for gluconeogenesis starting with pyruvate.

MSC: Remembering 24. Which pathway is opposite to gluconeogenesis? a. TCA cycle b. glycogen synthesis pathway c. pentose phosphate pathway d. glycolysis pathway ANS: D DIF: Easy REF: 14.2 OBJ: 14.2.b. State the overall reaction for gluconeogenesis starting with pyruvate.

MSC: Understanding 25. The gluconeogenesis pathway a. converts NADH into NAD+ so that glycolysis can continue. b. provides energy for the cell. c. increases the ratio of ATP to ADP in the cell. d. converts two 3C sugars into a 6C sugar.

ANS: D DIF: Easy REF: 14.2 OBJ: 14.2.b. State the overall reaction for gluconeogenesis starting with pyruvate.

MSC: Applying 26. In the reaction catalyzed by pyruvate carboxylase (the first reaction in gluconeogenesis), CO2 is a. lost from oxaloacetate. b. activated by ATP energy. c. activated by the cofactor NADH. d. added to the phosphoenolpyruvate product.

ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Analyzing 27. The conversion of pyruvate to phosphoenolpyruvate (PEP) in gluconeogenesis a. requires the net input of two equivalents of NADH. b. occurs in two steps and is catalyzed by the enzymes pyruvate carboxylase and phosphoenolpyruvate carboxykinase. c. is a thermodynamically spontaneous reaction that gives rise to a stable product. d. requires lactate as a precursor.

ANS: B DIF: Difficult REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Analyzing 28. The gluconeogenesis reaction shown below is missing some reactants and products. What class of enzyme catalyzes this reaction?

a. b. c. d.

lyase hydrolase transferase oxidoreductase

ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Applying 29. The first two reactions of gluconeogenesis are required to reverse reaction 10 (or the last reaction) of glycolysis. How many ATP equivalents are used by these first two reactions of gluconeogenesis? a. 1 b. 2 c. 3 d. 4 ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Remembering 30. What molecules are missing from boxes in the gluconeogenesis reaction shown below?

a. b. c. d.

Ser-Pi; Ser-Pi H2O; Pi ADP; ATP ATP; ADP

ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Understanding 31. In the gluconeogenesis pathway, the enzyme glucose-6-phosphatase reverses which step in glycolysis? a. the formation of glucose b. the reaction catalyzed by pyruvate dehydrogenase c. the reaction catalyzed by hexokinase d. the formation of fructose-1,6-bisphosphate ANS: C DIF: Difficult REF: 14.2 OBJ: 14.2.d. Name the three enzymes of glycolysis that are bypassed in gluconeogenesis.

MSC: Applying 32. How many of the 10 glycolysis reactions use the same enzyme in the gluconeogenesis pathway? a. 10

b. 7 c. 5 d. 3 ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.d. Name the three enzymes of glycolysis that are bypassed in gluconeogenesis.

MSC: Analyzing 33. Which enzyme in the glycolysis pathway catalyzes a reaction that requires two enzymes to reverse in the gluconeogenesis pathway? a. pyruvate kinase b. phosphofructokinase I c. pyruvate dehydrogenase d. glycogen phosphorylase ANS: A DIF: Medium REF: 14.2 OBJ: 14.2.d. Name the three enzymes of glycolysis that are bypassed in gluconeogenesis.

MSC: Remembering 34. Cytoplasmic levels of NADH must be maintained in order for gluconeogenesis to occur. What generates NADH for this pathway? a. the glycolysis pathway b. the TCA cycle c. the mitochondrial electron transport chain d. the movement of NADH equivalents from inside the mitochondria via malate transport ANS: D DIF: Medium REF: 14.2 OBJ: 14.2.e. Summarize the movement of oxaloacetate from the mitochondrial matrix to the cytosol.

MSC: Understanding 35. Which correctly describes the role of the transport system shown below?

a. It provides an alternate fate for pyruvate degradation. b. It provides a source of NADH for gluconeogenesis via malate transport. c. It converts NADH equivalents into reduced forms of carbon.

d. It allows for pyruvate transport into and out of the mitochondria.

ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.e. Summarize the movement of oxaloacetate from the mitochondrial matrix to the cytosol.

MSC: Analyzing 36. Of the four molecules listed below, three of them reciprocally regulate phosphofructokinase 1 (PFK1) and fructose-1,6-bisphosphatase. Which molecule does NOT fit? a. pyruvate b. fructose-2,6-bisphosphate c. citrate d. AMP ANS: A DIF: Easy REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Understanding 37. Gluconeogenesis is favored when citrate levels are __________, when AMP levels are __________, and when ATP levels are __________. a. low; low; high b. high; low; high c. low; high; low d. high; high; low ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Evaluating 38. Gluconeogenesis would most likely be allosterically activated simultaneously along with which other metabolic process? a. glycolysis b. pentose phosphate pathway c. glycogen synthesis d. TCA cycle ANS: C DIF: Easy REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Applying 39. The regulated reactions of gluconeogenesis have/are a. large positive G values. b. those that are counter to regulated reactions in glycolysis. c. reversible reactions. d. activated by molecules indicating a low energy charge in the cell.

ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Understanding 40. The hormone insulin activates phosphofructokinase 2 (2PFK2). This leads to a(n) __________ in concentration of fructose 2,6 bisphosphate, which favors the __________ pathway. a. increase; glycolysis b. increase; gluconeogenesis c. decrease; glycolysis

d. decrease; gluconeogenesis ANS: A DIF: Difficult REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Evaluating 41. Which hormone slows down glycolysis while stimulating gluconeogenesis through the phosphorylation of phosphofructokinase 2 (PFK2) and fructose-2,6-bisphosphatase? a. insulin b. protein kinase c. ATP d. glucagon ANS: D DIF: Medium REF: 14.2 OBJ: 14.2.f. Recall the reciprocal regulation of PFK-1 and fructose-1,6-bisphosphatase.

MSC: Analyzing 42. Which pair of opposite enzymes in the glycolysis and gluconeogenesis pathway are not allosterically regulated but rather regulated by compartmentalization? a. pyruvate kinase/PEP carboxykinase b. phosphofructokinase 1/fructose-1,6-bisphosphatase c. phosphofructokinase 2/fructose-2,6-bisphosphatase d. hexokinase/glucose-6-phosphatase ANS: D DIF: Easy REF: 14.2 OBJ: 14.2.g. State the strategy used to prevent hexokinase activity when gluconeogenesis is active.

MSC: Remembering 43. What controls the activity of the opposing enzymes hexokinase and glucose-6-phosphatase from the glycolysis and gluconeogenesis pathways? a. levels of ATP b. cellular compartmentalization and separation of the two enzymes c. fructose-2,6-bisphosphate concentration d. phosphorylation of the enzymes ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.g. State the strategy used to prevent hexokinase activity when gluconeogenesis is active.

MSC: Remembering 44. Which molecule allosterically activates pyruvate carboxylase? a. AMP b. NAD+ c. epinephrine d. acetyl-CoA ANS: D DIF: Easy REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Evaluating 45. Which of the following molecules would inhibit the regulated steps in gluconeogenesis? a. ATP b. ADP c. pyruvate

d. NADH ANS: B DIF: Easy REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Understanding 46. The enzymes that catalyze the regulated steps in glycolysis are a. phosphofructokinase, pyruvate dehydrogenase, and lactate dehydrogenase. b. hexokinase, phosphofructokinase, and pyruvate dehydrogenase. c. aldolase, phosphofructokinase, and pyruvate kinase. d. hexokinase, phosphofructokinase, and pyruvate kinase.

ANS: D DIF: Medium REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Remembering 47. Which of the following molecules might inhibit the regulated enzymes in glycolysis? a. NAD+ b. ATP c. AMP d. fructose-2,6-bisphosphate ANS: B DIF: Easy REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Analyzing 48. Which of the following molecules would activate phosphofructokinase 1 (PFK1)? a. NADH b. AMP c. ATP d. pyruvate ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Applying 49. Which of the following molecules would inhibit the last reaction of glycolysis? a. ATP b. glucose c. AMP d. NAD+ ANS: A DIF: Easy REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Analyzing 50. The Cori cycle a. transports pyruvate from working muscles to the liver, where it is converted back to glucose. b. is important in organisms respiring aerobically. c. involves the conversion of muscle pyruvate to alanine followed by transport to the liver. d. relies on functioning lactate dehydrogenase in both muscle and liver tissues.

ANS: D DIF: Medium REF: 14.2 OBJ: 14.2.i. Explain the Cori cycle as a link between muscle and liver.

MSC: Analyzing

51. What triggers the Cori cycle? a. a buildup of cellular NAD+ b. oxygen-limited working muscle cells c. low levels of glucose in the muscle cells d. elevated glucagon levels ANS: B DIF: Medium REF: 14.2 OBJ: 14.2.i. Explain the Cori cycle as a link between muscle and liver.

MSC: Evaluating 52. The Cori cycle a. requires both glycolysis and gluconeogenesis pathways. b. removes lactic acid from liver cells and delivers it to muscle cells. c. involves the regeneration of NADH equivalents for the working muscles. d. converts glucose into lactic acid.

ANS: A DIF: Difficult REF: 14.2 OBJ: 14.2.i. Explain the Cori cycle as a link between muscle and liver.

MSC: Evaluating 53. The branching enzyme of glycogen synthesis is involved in a. making the (1,6) branch points. b. making (1,4) linkages at the branch points. c. breaking the (1,6) branches and smoothing out the glycogen chain. d. transferring 3 glucose units from a branch point to the end of a growing glycogen chain.

ANS: A DIF: Easy REF: 14.3 OBJ: 14.3.a. List the names and functions for the enzymes of glycogen metabolism.

MSC: Applying 54. Which one of the following is involved in the breakdown of glycogen? a. inorganic phosphate b. ATP c. branching enzyme d. hexokinase ANS: A DIF: Easy REF: 14.3 OBJ: 14.3.a. List the names and functions for the enzymes of glycogen metabolism.

MSC: Remembering 55. The glycogen phosphorylase enzyme a. makes (1,4) links at the nonreducing end of glycogen. b. uses Pi (phosphate) as a nucleophile in the cleavage of glucose units off of the glycogen chain. c. cleaves the (1,6) linkages of glucose units in the glycogen polymer. d. releases free glucose units as its immediate product.

ANS: B DIF: Medium REF: 14.3 OBJ: 14.3.a. List the names and functions for the enzymes of glycogen metabolism.

MSC: Understanding 56. How many high-energy NTP molecules are hydrolyzed for each glucose monomer added to a growing glycogen polymer? a. 0

b. 1 c. 2 d. 3 ANS: C DIF: Medium REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Understanding 57. In the elongation of glycogen, activated glucose units are attached to which hydroxyl of the terminal residue of the growing glycogen chain? a. C-1 b. C-3 c. C-4 d. C-6 ANS: C DIF: Medium REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Applying 58. In the glycogenesis pathway, what is the leaving group in the last step where glucose is added to the growing glycogen chain? a. UDP-glucose b. pi c. glucose-1-phosphate d. UDP ANS: D DIF: Medium REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Remembering 59. In the glycogenesis pathway, which enzyme catalyzes the formation of a. debranching enzyme b. glycogen synthase c. glycogen phosphorylase d. branching enzyme

(1,6) linkages?

ANS: D DIF: Easy REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Understanding 60. In the breakdown of glycogen by glycogen phosphorylase, the immediate predominant product is a. glucose. b. glucose-1-phosphate. c. UDP-glucose. d. glucose-6-phosphate.

ANS: B DIF: Easy REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Remembering 61. The branching enzyme a. couples the formation of glycogen with UDP loss from UDP-glucose. b. makes (1,4) linkages with the transfer of seven glucose units. c. breaks (1,6) branch points and remakes (1,4) linkages.

d. catalyzes the cleavage of

(1,4) links and the formation of

(1,6) links.

ANS: D DIF: Medium REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Analyzing 62. In the glycogenesis pathway, the role of the glucose-6-phosphate isomerization reaction is to a. create a more stable intermediate for the subsequent reaction. b. decrease the concentration of glucose-6-phosphate, thereby driving the pathway forward. c. ensure that the charged molecule stays in the cell. d. prepare the anomeric carbon for nucleophilic attack.

ANS: D DIF: Difficult REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Applying 63. In the breakdown of glycogen, the debranching enzyme catalyzes the formation of a. glucose-1-phosphate. b. glucose. c.

(1,6) branched glycogen. d. glucose-6-phosphate.

ANS: B DIF: Medium REF: 14.3 OBJ: 14.3.c. Classify the reactions catalyzed by the debranching enzyme.

MSC: Evaluating 64. Which enzyme catalyzes the following reaction?

a. b. c. d.

debranching enzyme glycogen phosphorylase branching enzyme glycogen synthase

ANS: A DIF: Difficult REF: 14.3 OBJ: 14.3.c. Classify the reactions catalyzed by the debranching enzyme.

MSC: Understanding 65. The debranching enzyme does NOT catalyze the a. formation of (1,6) linkages. b. cleavage of (1,6) linkages. c. formation of (1,4) linkages. d. cleavage of (1,4) linkages.

ANS: A DIF: Medium REF: 14.3 OBJ: 14.3.c. Classify the reactions catalyzed by the debranching enzyme.

MSC: Understanding 66. Which statement of the debranching enzyme is true? a. It catalyzes the addition of free glucose to a nonreducing end of glycogen. b. Its product is glucose-1-phosphate. c. It evenly distributes branch points across the glycogen polymer. d. It is one enzyme with three unique catalytic activities.

ANS: D DIF: Medium REF: 14.3 OBJ: 14.3.c. Classify the reactions catalyzed by the debranching enzyme.

MSC: Understanding 67. The role of glycogenin is to a. catalyze the formation of UDP-glucose. b. act as a hormone to regulate glucose levels. c. serve as the origin of the glycogen polymer. d. enable glycogen to fold properly.

ANS: C DIF: Medium glycogenin.

MSC: Understanding

REF: 14.3

OBJ: 14.3.d. Define

REF: 14.3

OBJ: 14.3.d. Define

68. What class of biomolecule is glycogenin? a. hormone b. carbohydrate c. enzyme d. lipid ANS: C DIF: Easy glycogenin.

MSC: Understanding

69. The activation of glycogen phosphorylase will lead to a(n) __________ in blood glucose concentrations and is stimulated by the hormone __________. a. decrease; insulin b. decrease; glucagon c. increase; insulin d. increase; glucagon ANS: D DIF: Easy REF: 14.3 OBJ: 14.3.e. Summarize the activity of glycogen phosphorylase and glycogen synthase in the presence of glucagon, epinephrine, or insulin.

MSC: Applying 70. The hormone insulin stimulates __________ and inhibits __________, leading to a(n) __________ in the glucose levels. a. glycogen synthase; glycogen phosphorylase; decrease b. glycogen phosphorylase; glycogen synthase; decrease c. glycogen synthase; glycogen phosphorylase; increase d. glycogen phosphorylase; glycogen synthase; increase ANS: A DIF: Medium REF: 14.3 OBJ: 14.3.e. Summarize the activity of glycogen phosphorylase and glycogen synthase in the presence of glucagon, epinephrine, or insulin.

MSC: Applying

71. What is the name of the enzyme that removes phosphate groups from the regulated glycogen metabolism enzymes to reverse their activity? a. phosphorylase kinase b. protein phosphatase 1 c. insulin d. protein kinase A ANS: B DIF: Medium REF: 14.3 OBJ: 14.3.e. Summarize the activity of glycogen phosphorylase and glycogen synthase in the presence of glucagon, epinephrine, or insulin.

MSC: Remembering 72. Because muscles lack receptors for glucagon, what hormone activates muscle glycogen phosphorylase? a. insulin b. adrenaline c. glycogenin d. UDP-glucose ANS: B DIF: Easy REF: 14.3 OBJ: 14.3.f. Differentiate between glycogen metabolism in the liver and glycogen metabolism in the muscle.

MSC: Understanding 73. Why is it important that muscle cells are unresponsive to glucagon? a. Muscle cells store glycogen for its own energy needs and not the needs of other tissues. b. The muscles do not store glycogen. c. The muscles release glucose to other tissues in need. d. Muscle cells respond to insulin instead.

ANS: A DIF: Difficult REF: 14.3 OBJ: 14.3.f. Differentiate between glycogen metabolism in the liver and glycogen metabolism in the muscle.

MSC: Applying 74. McArdle disease is due to a deficiency in muscle glycogen phosphorylase activity. The result of this deficiency is an inability to a. form (1,4) linkages in glycogen. b. form glucose-1-phosphate during the breakdown of glycogen. c. store glycogen. d. cleave (1,6) linkages.

ANS: B DIF: Medium REF: 14.3 OBJ: 14.3.g. List the most commonly occurring glycogen storage diseases and the cause of each.

MSC: Applying 75. A patient is found to have a mutated enzyme that results in fewer branch points in glycogen.

Which one of the following would best characterize the way in which the patient’s glycogen is altered relative to normal glycogen? a. an increase in the proportion of (1,6) linkages relative to (1,4) linkages b. a change in the stereochemical configuration at the reducing end c. some (1,4) linkages in place of (1,4) linkages d. a decreased ratio of nonreducing to reducing ends ANS: D DIF: Difficult REF: 14.3 OBJ: 14.3.g. List the most commonly occurring glycogen storage diseases and the cause of each.

MSC: Applying

SHORT ANSWER 1. List the three metabolic molecules that regulate the activity of the pentose phosphate pathway.

ANS: (1) Levels of NADPH regulate flux through the oxidative phase of the pathway. (2) Levels of nucleotides regulate the production of 5C ribose from the pathway. (3) The levels of ATP regulate the amount of glucose directed through the pentose phosphate pathway versus the glycolysis pathway.

DIF: Medium REF: 14.1 OBJ: 14.1.a. List the three metabolic states of the cell that regulate flux through the pentose phosphate pathway. MSC: Applying 2. What is the overall net reaction of the pentose phosphate pathway, where glucose-6-phosphate is entirely converted to CO2? Please include any cofactors produced for the cell.

ANS: glucose-6-phosphate + 12 NADP+ + 6 H2O

6 CO2 + 12 NADPH + 12 H+

DIF: Medium REF: 14.1 OBJ: 14.1.b. State the net reactions for the oxidative phase and the nonoxidative phase of the pentose phosphate pathway.

MSC: Applying 3. What class of enzymes in the oxidative phase of the pentose phosphate pathway is responsible for the production of NADPH? ANS: Dehydrogenases, or oxidoreductases DIF: Easy REF: 14.1 OBJ: 14.1.c. Name the pentose phosphate pathway enzymes that produce NADPH. MSC: Understanding 4. What would happen to cellular glucose-6-phosphate if the pentose phosphate pathway is inhibited?

ANS: The glucose-6-phosphate could be catabolized by the glycolysis pathway. Alternatively, the glucose-6-phosphate could be polymerized as glycogen.

DIF: Difficult REF: 14.1 OBJ: 14.1.d. Identify the control mechanisms for the pentose phosphate pathway.

MSC: Applying 5. What is the cellular role of glutathione in red blood cells?

ANS: Glutathione acts as an antioxidant to prevent cysteine oxidation in hemoglobin and to neutralize the harmful oxidizing effects of reactive oxygen species, which might come from hemoglobin if reduced forms of oxygen escape.

DIF: Medium

REF: 14.1

OBJ: 14.1.e. Define the roles of glutathione, glutathione peroxidase, and glutathione reductase.

MSC: Understanding 6. Fill in the names of the enzymes involved in the important cellular glutathione detoxification system shown below.

ANS:

DIF: Medium REF: 14.1 OBJ: 14.1.e. Define the roles of glutathione, glutathione peroxidase, and glutathione reductase.

MSC: Analyzing 7. What are the three main sources of carbon in animals making glucose with the gluconeogenesis pathway?

ANS: (1) Glycerol from fats, (2) lactate from the Cori cycle, and (3) the breakdown of amino acids that give pyruvate DIF: Difficult REF: 14.2 OBJ: 14.2.a. List the three major sources of carbon for gluconeogenesis in animals.

MSC: Applying 8. Give the overall balanced reaction for the gluconeogenesis pathway, beginning from pyruvate.

Please include any energy currency molecules required by the pathway.

ANS: 2 pyruvate + 2NADH + 4ATP + 2 GTP + 6 H2O 2 GDP + 9 Pi

glucose + 2 NAD+ + 2H+ + 4 ADP +

DIF: Difficult REF: 14.2 OBJ: 14.2.b. State the overall reaction for gluconeogenesis starting with pyruvate.

MSC: Remembering 9. Name the enzymes of the gluconeogenesis pathway that are required to form the unstable phosphoenolpyruvate molecule from pyruvate starting material.

ANS: Pyruvate carboxylase and phosphoenolpyruvate carboxykinase DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Remembering 10. Name the four enzymes of the gluconeogenesis pathway that are NOT found in the glycolysis pathway.

ANS: Pyruvate carboxylase, phosphoenolpyruvate carboxykinase, fructose-1,6-bisphosphatase, glucose-6-phosphatase DIF: Medium REF: 14.2 OBJ: 14.2.c. Name the four enzymes required for gluconeogenesis that are not used in glycolysis.

MSC: Remembering 11. List the three enzymes in glycolysis that are bypassed in gluconeogenesis and match them with the enzymes in gluconeogenesis that replace them.

ANS: (1) Hexokinase is replaced by glucose-1-phosphatase. (2) Phosphofructokinase I is replaced by fructose-1,6-bisphosphatase. (3) Pyruvate kinase is replaced by two enzymes, pyruvate carboxylase and phosphoenolpyruvate carboxykinase.

DIF: Difficult REF: 14.2 OBJ: 14.2.d. Name the three enzymes of glycolysis that are bypassed in gluconeogenesis.

MSC: Applying 12. During vigorous exercise the lactate produced in the muscle travels to the liver for recycling.

Explain why starting with lactate is beneficial for the liver gluconeogenesis pathway.

ANS: Lactate in the liver (1) can be converted into pyruvate and is thus a carbon source for gluconeogenesis; and (2) the conversion of lactate to pyruvate, catalyzed by lactate dehydrogenase, creates an NADH that can be used in gluconeogenesis.

DIF: Difficult REF: 14.2 OBJ: 14.2.e. Summarize the movement of oxaloacetate from the mitochondrial matrix to the cytosol.

MSC: Applying 13. The opposing glycolysis and gluconeogenesis enzymes hexokinase and glucose-6-phosphatase are located with which cellular locations, respectively?

ANS: Hexokinase is found in the cytoplasm, whereas glucose-6-phosphatase is found in the lumen of the endoplasmic reticulum.

DIF: Medium REF: 14.2 OBJ: 14.2.g. State the strategy used to prevent hexokinase activity when gluconeogenesis is active.

MSC: Remembering 14. Name the enzymes in the glycolysis or gluconeogenesis pathway that could be inhibited by ATP. ANS: In glycolysis, enzymes that are inhibited by ATP include fructose-1,6-bisphosphatase and pyruvate kinase.

DIF: Medium REF: 14.2 OBJ: 14.2.h. Identify the activators and inhibitors of glycolysis and gluconeogenesis.

MSC: Understanding 15. Explain how the Cori cycle leads to the regeneration of NAD+ for muscles with an active glycolysis pathway.

ANS: After glycolysis and the formation of pyruvate, the NADH made in glycolysis is converted back to NAD+ by lactate dehydrogenase as it forms lactate from the pyruvate. The lactate then leaves the muscle cells and travels to the liver, where it is converted back to pyruvate and then glucose, before returning to the muscle tissue.

DIF: Medium REF: 14.2 OBJ: 14.2.i. Explain the Cori cycle as a link between muscle and liver.

MSC: Applying 16. Draw a diagram indicating the organs, metabolic pathways, and key molecules involved in the circular Cori cycle.

ANS:

DIF: Difficult REF: 14.2 OBJ: 14.2.i. Explain the Cori cycle as a link between muscle and liver.

MSC: Applying 17. Name the enzymes that catalyze the two opposing glycogen polymerization and depolymerization reactions found in glycogen synthesis and glycogen breakdown.

ANS: Glycogen synthase catalyzes glycogen synthesis, while glycogen phosphorylase catalyzes the breakdown of glycogen.

DIF: Easy REF: 14.3 OBJ: 14.3.a. List the names and functions for the enzymes of glycogen metabolism.

MSC: Remembering 18. Draw a glucose molecule and indicate which atom is linked to glycogen during the glycogen synthesis process.

ANS: The C1 of the incoming glucose unit is linked to the growing glycogen chain.

DIF: Medium REF: 14.3 OBJ: 14.3.b. State the net reactions for glycogen synthesis and degradation.

MSC: Applying 19. Name each of the distinct catalytic activities of the debranching enzyme.

ANS: The debranching enzyme approaches a branch with four glucose units from an (1,6) branch point. First the enzyme removes three glucose residues by hydrolyzing the (1,4) linkage. The enzyme then moves those three residues to the end of another branch and forms an (1,4) linkage.

Finally the enzyme hydrolyzes away the fourth glucose residue by hydrolyzing the (1,6) branch point.

DIF: Medium REF: 14.3 OBJ: 14.3.c. Classify the reactions catalyzed by the debranching enzyme.

MSC: Remembering 20. Draw the structure of the short glycogen disaccharide linked to glycogenin through its tyrosine amino acid.

ANS:

DIF: Difficult MSC: Applying

REF: 14.3

OBJ: 14.3.d. Define glycogenin.

21. State whether enzymes are phosphorylated or dephosphorylated in the glycogen metabolism pathways on the binding of adrenaline to liver or muscle cell receptors and state how this affects their activity.

ANS: Adrenaline leads to the phosphorylation of glycogen synthase and its inactivity while leading to phosphorylation of glycogen phosphorylase and its activation.

DIF: Medium REF: 14.3 OBJ: 14.3.e. Summarize the activity of glycogen phosphorylase and glycogen synthase in the presence of glucagon, epinephrine, or insulin.

MSC: Applying 22. State how glucagon functions to increase blood glucose levels.

ANS: It activates a phosphorylation cascade that phosphorylates and stimulates glycogen phosphorylase and inhibits glycogen synthase. This process occurs mainly in liver tissues, which have glucagon receptors. The liver tissues release the glucose to the blood.

DIF: Easy

REF: 14.3

OBJ: 14.3.e. Summarize the activity of glycogen phosphorylase and glycogen synthase in the presence of glucagon, epinephrine, or insulin.

MSC: Applying 23. State the role of the liver and the role of the muscles and explain their need for different glycogen metabolism regulation.

ANS: The liver stores glycogen to meet the needs of the body through maintaining blood glucose levels.

It therefore responds to insulin and glucagon, as well as adrenaline. The muscles must provide physical work for the body and thus respond to adrenaline. They also respond to insulin as a means of storing glucose; however, they do not respond to glucagon or release glucose when blood levels are low. The muscle glycogen metabolism enzymes are also sensitive to allosteric control through cellular levels of ATP and AMP. DIF: Difficult REF: 14.3 OBJ: 14.3.f. Differentiate between glycogen metabolism in the liver and glycogen metabolism in the muscle.

MSC: Understanding 24. von Gierke disease is a common glycogen storage disease caused by a deficiency in glucose-6-phosphatase. Explain how a deficiency in this gluconeogenesis enzyme leads to glycogen storage issues.

ANS: A deficiency in glucose-6-phosphatase gives rise to an elevated glucose-6-phosphate level, which activates glycogen synthase and is incorporated into glycogen. Individuals with this disease have large amounts of glycogen in cells.

DIF: Medium REF: 14.3 OBJ: 14.3.g. List the most commonly occurring glycogen storage diseases and the cause of each.

MSC: Applying 25. Cori disease arises from a deficient debranching enzyme. Describe the consequences for glycogen metabolism.

ANS: Individuals with Cori disease have glycogen molecules with shorter outer branches that cannot be fully degraded.

DIF: Medium REF: 14.3 OBJ: 14.3.g. List the most commonly occurring glycogen storage diseases and the cause of each.

MSC: Applying

Chapter 15: Lipid Structure and Function MULTIPLE CHOICE 1. Classify the following fatty acid.

a. b. c. d.

saturated unsaturated monounsaturated polyunsaturated

ANS: A DIF: Easy REF: 15.1 OBJ: 15.1.a. Differentiate among saturated, monounsaturated, and polyunsaturated fatty acids.

MSC: Analyzing 2. Identify the polyunsaturated fatty acid. a.

b.

c.

d.

ANS: C DIF: Easy REF: 15.1 OBJ: 15.1.a. Differentiate among saturated, monounsaturated, and polyunsaturated fatty acids.

MSC: Understanding 3. A fatty acid that has more than one double bond is referred to as a. monosaturated. b. monounsaturated. c. polysaturated. d. polyunsaturated.

ANS: D DIF: Easy REF: 15.1 OBJ: 15.1.a. Differentiate among saturated, monounsaturated, and polyunsaturated fatty acids.

MSC: Remembering 4. Predict the structure of a fatty acid that is cis 16:1 ( 9).

a.

b.

c.

d.

ANS: C DIF: Medium REF: 15.1 OBJ: 15.1.b. Convert the common nomenclature for fatty acids into a drawing of the structure.

MSC: Applying 5. Predict the structure of a fatty acid that is trans 16:1 ( 9). a.

b.

c.

d.

ANS: A DIF: Medium REF: 15.1 OBJ: 15.1.b. Convert the common nomenclature for fatty acids into a drawing of the structure.

MSC: Applying 6. Predict the structure of a fatty acid that is trans 18:2 ( 9,11).

a.

b.

c.

d.

ANS: B DIF: Medium REF: 15.1 OBJ: 15.1.b. Convert the common nomenclature for fatty acids into a drawing of the structure.

MSC: Applying 7. Using common nomenclature, name the following fatty acid.

a. b. c. d.

trans 16:2 ( 11,13) cis 16:2 ( 11,13) trans 16:2 ( 3,5) cis 16:2 ( 3,5)

ANS: D DIF: Medium REF: 15.1 OBJ: 15.1.c. Use the structure of the fatty acid to derive the common nomenclature for fatty acids.

MSC: Applying 8. Using common nomenclature, name the following fatty acid.

a. b. c. d.

trans 18:1 ( 10) cis 18:1 ( 10) trans 18:1 ( 8) cis 18:1 ( 8)

ANS: A DIF: Medium REF: 15.1 OBJ: 15.1.c. Use the structure of the fatty acid to derive the common nomenclature for fatty acids.

MSC: Applying 9. Using common nomenclature, name the following fatty acid.

a. b. c. d.

trans 14:1 ( 7) cis 14:1 ( 7) trans 14:7 ( 1) cis 14:7 ( 1)

ANS: B DIF: Medium REF: 15.1 OBJ: 15.1.c. Use the structure of the fatty acid to derive the common nomenclature for fatty acids.

MSC: Applying 10. Predict the fatty acid with the highest melting point. a.

b.

c.

d.

ANS: D DIF: Easy REF: 15.1 OBJ: 15.1.d. Predict the melting point of a fatty acid based on chain length and degree of saturation.

MSC: Applying 11. Predict the fatty acid with the lowest melting point. a. trans 14:1 ( 7) b. cis 14:2 ( 7,9) c. trans 14:2 ( 7,9) d. cis 14:3 ( 7,9,11) ANS: D DIF: Easy REF: 15.1 OBJ: 15.1.d. Predict the melting point of a fatty acid based on chain length and degree of saturation.

MSC: Applying 12. Predict the fatty acid with the highest melting point.

a. b. c. d.

trans 14:1 ( 7) cis 14:2 ( 7,9) trans 14:2 ( 7,9) cis 14:3 ( 7,9,11)

ANS: A DIF: Easy REF: 15.1 OBJ: 15.1.d. Predict the melting point of a fatty acid based on chain length and degree of saturation.

MSC: Applying 13. One disadvantage of using partial hydrogenation in the food industry is that a. the shelf life of the oils is not as long. b. trans fats are formed during the process. c. the oils tend to become rancid and have foul odors. d. the oils cost more than animal fats.

ANS: B DIF: Easy REF: 15.1 OBJ: 15.1.e. Distinguish between hydrogenation and partial hydrogenation.

MSC: Analyzing 14. One advantage of using hydrogenation in the food industry is a. decreased processing time. b. reduction in heart disease. c. increased shelf life. d. decreased melting point.

ANS: C DIF: Easy REF: 15.1 OBJ: 15.1.e. Distinguish between hydrogenation and partial hydrogenation.

MSC: Analyzing 15. Partial hydrogenation can result in the formation of a.

-3 fatty acids. b. -6 fatty acids. c. cis double bonds. d. trans double bonds.

ANS: D DIF: Easy REF: 15.1 OBJ: 15.1.e. Distinguish between hydrogenation and partial hydrogenation.

MSC: Remembering 16. Identify the a.

-3 fatty acid.

b.

c.

d.

ANS: D DIF: Medium REF: 15.1 OBJ: 15.1.f. Differentiate between omega-3 and omega-6 fatty acids.

MSC: Understanding 17. Identify the a.

b.

-6 fatty acid.

c.

d.

ANS: C DIF: Medium REF: 15.1 OBJ: 15.1.f. Differentiate between omega-3 and omega-6 fatty acids.

MSC: Understanding 18. Predict the essential -6 fatty acid. a. trans 18:2 ( 9,12) b. cis 18:2 ( 9,12) c. trans 18:2 ( 6,9) d. cis 18:2 ( 6,9) ANS: B DIF: Difficult REF: 15.1 OBJ: 15.1.f. Differentiate between omega-3 and omega-6 fatty acids.

MSC: Applying 19. Identify the wax. a.

b.

c.

d.

ANS: C DIF: Easy MSC: Understanding

REF: 15.1

OBJ: 15.1.g. Define wax.

20. Compared with a fatty acid, a wax a. contains a glycerol backbone. b. has long hydrocarbon chains with a carboxylate group. c. has long hydrocarbon chains connected with an ester linkage. d. contains a polar phosphate group.

ANS: C MSC: Analyzing

DIF: Medium

REF: 15.1

OBJ: 15.1.g. Define wax.

21. A wax is defined as a. long chain fatty alcohols esterified to hydrocarbon chains. b. three fatty acids linked to a glycerol backbone. c. a long hydrocarbon chain with a carboxylate group at the end. d. two fatty acids and a phosphate group linked to a glycerol backbone.

ANS: A DIF: Medium MSC: Remembering

REF: 15.1

OBJ: 15.1.g. Define wax.

22. During the process of saponification, fatty acid molecules are released from triacylglycerols by treatment(s) with a strong a. base. b. acid. c. base and heat. d. acid and heat.

ANS: C DIF: Easy REF: 15.1 OBJ: 15.1.h. Name two aspects of everyday life that have benefited from our knowledge of triacylglycerol chemistry.

MSC: Remembering 23. Soap traps dirt particles in a. triacylglycerols. b. micelles. c. steroids. d. glycerophospholipids.

ANS: B DIF: Easy REF: 15.1 OBJ: 15.1.h. Name two aspects of everyday life that have benefited from our knowledge of triacylglycerol chemistry.

MSC: Remembering 24. Spices such as eugenol are added to oils to enhance the flavor because of a. hydrogen bonds. b. dipole–dipole interactions. c. hydrophilic interactions. d. hydrophobic interactions.

ANS: D DIF: Easy REF: 15.1 OBJ: 15.1.h. Name two aspects of everyday life that have benefited from our knowledge of triacylglycerol chemistry.

MSC: Remembering 25. Free fatty acids released from adipose tissue are transported throughout the body by a carrier protein called a. adipocyte.

b. albumin. c. lipase. d. colipase.

ANS: B DIF: Easy REF: 15.2 OBJ: 15.2.a. Compare the movement of triacylglycerols through the circulatory system with the movement of fatty acids.

MSC: Remembering 26. The water-soluble enzyme in the small intestine that hydrolyzes the acyl ester bonds in triacylglycerols is a. adipocyte. b. albumin. c. lipase. d. colipase.

ANS: C DIF: Easy REF: 15.2 OBJ: 15.2.a. Compare the movement of triacylglycerols through the circulatory system with the movement of fatty acids.

MSC: Remembering 27. Triacylglycerols are transported though the blood as a. glycerophospholipids. b. sphingolipids. c. cerebrosides. d. very low density lipoprotein particles.

ANS: D DIF: Easy REF: 15.2 OBJ: 15.2.a. Compare the movement of triacylglycerols through the circulatory system with the movement of fatty acids.

MSC: Remembering 28. Which particles transport triacylglycerols to adipose tissue for storage? a. apolipoproteins b. adipocytes c. chylomicrons d. perilipin ANS: C DIF: Easy REF: 15.2 OBJ: 15.2.b. State the role of chylomicrons.

MSC: Understanding

29. Chylomicrons are produced in a. liver cells. b. intestinal epithelial cells. c. stomach cells. d. adipocytes.

ANS: B DIF: Easy REF: 15.2 OBJ: 15.2.b. State the role of chylomicrons.

MSC: Remembering

30. Chylomicrons contain a monolayer on the outside of the particle consisting of a. cerebrosides and phospholipids. b. cerebrosides and sphingolipids. c. phospholipids and cholesterol. d. cholesterol and sphingolipids.

ANS: C DIF: Medium REF: 15.2 OBJ: 15.2.b. State the role of chylomicrons.

MSC: Remembering

31. VLDLs are produced in a. liver cells. b. intestinal epithelial cells. c. stomach cells. d. adipocytes.

ANS: A DIF: Easy REF: 15.2 OBJ: 15.2.c. Summarize the events in the liver that lead to VLDL formation.

MSC: Remembering 32. The biosynthesis of triacylglycerols in animals uses which citrate cycle intermediate in the liver? a. malate b. acetyl-CoA c. isocitrate d. succinate ANS: B DIF: Medium REF: 15.2 OBJ: 15.2.c. Summarize the events in the liver that lead to VLDL formation.

MSC: Analyzing 33. In addition to triacylglycerols, which other lipid synthesized in the liver is transported by VLDLs? a. sphingophospholipid b. cerebroside c. ganglioside d. cholesterol ANS: D DIF: Medium REF: 15.2 OBJ: 15.2.c. Summarize the events in the liver that lead to VLDL formation.

MSC: Analyzing 34. Identify the lipase whose activity is regulated by protein G58. a. colipase b. monoacylglycerol lipase c. hormone-sensitive lipase d. adipose triglyceride lipase ANS: D DIF: Medium REF: 15.2 OBJ: 15.2.d. List the three major lipases found in human adipocytes.

MSC: Understanding 35. The lipase-mediated release of fatty acids can always be expected to occur when a person is a. reading a book. b. watching TV. c. running from a bear. d. eating.

ANS: C DIF: Medium REF: 15.2 OBJ: 15.2.d. List the three major lipases found in human adipocytes.

MSC: Applying 36. The lipase-mediated release of fatty acids can always be expected to occur when a person is a. hungry. b. walking. c. studying. d. watching TV.

ANS: A DIF: Medium REF: 15.2 OBJ: 15.2.d. List the three major lipases found in human adipocytes.

MSC: Applying 37. Arrange the following steps of glucagon signaling in the correct order.

1. A hydrolysis reaction cleaves a fatty acid from the stored triacylglycerols to generate diacylglycerol and a fatty acid.

2. The regulatory protein G58 binds to adipose triglyceride lipase.

3. Perilipin is phosphorylated on the surface of lipid droplets.

4. Albumin transports the free fatty acid.

5. A GDP–GTP exchange stimulates cyclic AMP production by the enzyme adenylate cyclase. a. 2, 5, 3, 4, 1 b. 5, 2, 4, 3, 1 c. 5, 3, 2, 1, 4 d. 2, 3, 5, 1, 4 ANS: C DIF: Difficult REF: 15.2 OBJ: 15.2.e. State the steps required for glucagon to cause release of fatty acids from adipocytes.

MSC: Analyzing 38. Which step in glucagon signaling occurs in the Gs protein?

1. A hydrolysis reaction cleaves a fatty acid from the stored triacylglycerols to generate diacylglycerol and a fatty acid.

2. The regulatory protein G58 binds to adipose triglyceride lipase.

3. Perilipin is phosphorylated on the surface of lipid droplets.

4. Albumin transports the free fatty acid.

5. A GDP–GTP exchange stimulates cyclic AMP production by the enzyme adenylate cyclase. a. 1 b. 2 c. 3 d. 5 ANS: D DIF: Medium REF: 15.2 OBJ: 15.2.e. State the steps required for glucagon to cause release of fatty acids from adipocytes.

MSC: Understanding 39. Which is the step in glucagon signaling where adipose triglyceride lipase mediates a reaction?

1. A hydrolysis reaction cleaves a fatty acid from the stored triacylglycerols to generate diacylglycerol and a fatty acid.

2. Perilipin is phosphorylated on the surface of lipid droplets.

3. Albumin transports the free fatty acid.

4. A GDP–GTP exchange stimulates cyclic AMP production by the enzyme adenylate cyclase. a. 1 b. 2 c. 3 d. 4 ANS: A DIF: Medium REF: 15.2 OBJ: 15.2.e. State the steps required for glucagon to cause release of fatty acids from adipocytes.

MSC: Understanding 40. In comparison with glycerophospholipids, the structure of cerebrosides contains a a. fatty acid. b. sphingosine. c. choline.

d. steroid ring.

ANS: B DIF: Medium REF: 15.3 OBJ: 15.3.a. List the major types of lipids found in a typical plasma membrane.

MSC: Analyzing 41. In comparison with gangliosides, the structure of phosphatidylcholine contains a a. fatty acid. b. sugar moiety. c. glycerol moiety. d. steroid ring.

ANS: C DIF: Medium REF: 15.3 OBJ: 15.3.a. List the major types of lipids found in a typical plasma membrane.

MSC: Analyzing 42. In comparison with glycerophospholipids and sphingolipids, cholesterol contains a a. fatty acid. b. phosphate group. c. glycerol moiety. d. steroid ring.

ANS: D DIF: Easy REF: 15.3 OBJ: 15.3.a. List the major types of lipids found in a typical plasma membrane.

MSC: Analyzing 43. The outer layer of the plasma membrane of human erythrocytes contains mostly __________ lipids. a. phosphatidylinositol b. phosphatidylserine c. phosphatidylcholine d. phosphatidylethanolamine ANS: C DIF: Medium REF: 15.3 OBJ: 15.3.b. Differentiate between the lipids found in the outer monolayer of a plasma membrane and those found in the inner monolayer.

MSC: Understanding 44. The inner layer of the plasma membrane of human erythrocytes contains mostly __________ lipids. a. phosphatidylserine b. ganglioside c. phosphatidylcholine d. sphingomyelin ANS: A DIF: Medium REF: 15.3 OBJ: 15.3.b. Differentiate between the lipids found in the outer monolayer of a plasma membrane and those found in the inner monolayer.

MSC: Understanding 45. The total content of __________ is approximately the same in both the inner and outer layer of the plasma membrane of human erythrocytes. a. phosphatidylinositol b. sphingomyelin c. phosphatidylcholine d. cholesterol ANS: D

DIF: Medium

REF: 15.3

OBJ: 15.3.b. Differentiate between the lipids found in the outer monolayer of a plasma membrane and those found in the inner monolayer.

MSC: Understanding 46. Lipid rafts are thought to be discrete membrane regions that contain high concentrations of a. phosphatidylinositol. b. gangliosides. c. phosphatidylcholine. d. cholesterol.

ANS: D DIF: Easy REF: 15.3 OBJ: 15.3.c. Define the fluid mosaic model and lipid rafts.

MSC: Understanding

47. Compared with other areas of the membrane, lipid rafts contain more a. sphingolipids. b. phosphatidylcholine. c. phosphatidylinositol. d. gangliosides.

ANS: A DIF: Medium REF: 15.3 OBJ: 15.3.c. Define the fluid mosaic model and lipid rafts.

MSC: Analyzing

48. One of the functions of the lipid rafts is to a. act as a storage mechanism for fatty acids. b. control fluidity of the membrane. c. coordinate cell signaling. d. maintain sodium levels in the cell.

ANS: C DIF: Medium REF: 15.3 OBJ: 15.3.c. Define the fluid mosaic model and lipid rafts.

MSC: Understanding

49. Snake venom often secretes phospholipase A2 enzymes, which cleave a. glycerophospholipids. b. ceramides. c. sphingosines. d. gangliosides.

ANS: A DIF: Easy REF: 15.3 OBJ: 15.3.d. Distinguish between glycerophospholipids and sphingolipids.

MSC: Remembering 50. Which type of fatty acid plays important roles in cell recognition such as in ABO blood groups? a. sphingomyelins b. gangliosides c. cerebrosides d. glycerophospholipids ANS: B DIF: Easy REF: 15.3 OBJ: 15.3.d. Distinguish between glycerophospholipids and sphingolipids.

MSC: Understanding 51. The addition of phosphocholine to ceramides generates a. glycerophospholipids. b. gangliosides. c. cerebrosides. d. sphingomyelin.

ANS: D DIF: Easy REF: 15.3 OBJ: 15.3.d. Distinguish between glycerophospholipids and sphingolipids.

MSC: Understanding 52. Which membrane lipids are derivatives of long chain amino alcohols synthesized from palmitate and serine? a. phosphatidylinositol b. phosphatidylcholine c. sphingosines d. phosphatidylethanolamine ANS: C DIF: Easy REF: 15.3 OBJ: 15.3.e. List the four alcohols used to produce the most abundant glycerophospholipids in eukaryotic membranes.

MSC: Understanding 53. Which of the following amino alcohols act as the functional group attached to a phosphate in a glycerophospholipid? a. lysine b. serine c. glycine d. alanine ANS: B DIF: Easy REF: 15.3 OBJ: 15.3.e. List the four alcohols used to produce the most abundant glycerophospholipids in eukaryotic membranes.

MSC: Understanding 54. Which of the following amino alcohols act as the functional group attached to a phosphate in a glycerophospholipid? a. methanolamine b. ethanolamine c. propanolamine d. butanolamine ANS: B DIF: Easy REF: 15.3 OBJ: 15.3.e. List the four alcohols used to produce the most abundant glycerophospholipids in eukaryotic membranes.

MSC: Understanding 55. Tay-Sachs disease, Fabry disease, and Niemann-Pick disease are all symptomatic because of a. defects in sphingolipid metabolism. b. improper glycan storage. c. cleavage of glycerophospholipids. d. reduced cholesterol synthesis.

ANS: A DIF: Medium REF: 15.3 OBJ: 15.3.f. Identify the missing enzymes that give rise to Tay-Sachs disease, Fabry disease, and Niemann-Pick disease.

MSC: Analyzing 56. Which missing enzyme results in Tay-Sachs disease? a. phospholipase A2 b. sphingomyelinase c.

-galactosidase A d. hexosaminidase A ANS: D DIF: Medium REF: 15.3 OBJ: 15.3.f. Identify the missing enzymes that give rise to Tay-Sachs disease, Fabry disease, and

Niemann-Pick disease.

MSC: Understanding

57. Which missing enzyme results in Fabry disease? a. phospholipase A2 b. sphingomyelinase c.

-galactosidase A d. hexosaminidase A ANS: C DIF: Medium REF: 15.3 OBJ: 15.3.f. Identify the missing enzymes that give rise to Tay-Sachs disease, Fabry disease, and Niemann-Pick disease.

MSC: Understanding 58. Which missing enzyme results in Niemann-Pick disease? a. phospholipase A2 b. sphingomyelinase c.

-galactosidase A d. hexosaminidase A ANS: B DIF: Medium REF: 15.3 OBJ: 15.3.f. Identify the missing enzymes that give rise to Tay-Sachs disease, Fabry disease, and Niemann-Pick disease.

MSC: Understanding 59. Which of the following membranes would have the greatest fluidity based on the following percentage of cholesterol in the membrane? a. 10% b. 25% c. 30% d. 40% ANS: A DIF: Medium REF: 15.3 OBJ: 15.3.g. Explain how cholesterol affects membrane fluidity.

MSC: Applying 60. Which of the following membranes would have the least amount of fluidity based on the following percentage of cholesterol in the membrane? a. 10% b. 25% c. 30% d. 40% ANS: D DIF: Medium REF: 15.3 OBJ: 15.3.g. Explain how cholesterol affects membrane fluidity.

MSC: Applying 61. Which of the following molecules aid in the absorption of dietary lipids? a. prostaglandin b. cortisol c. glycocholate d. aldosterone ANS: C DIF: Easy REF: 15.4 OBJ: 15.4.a. List the major lipids that are involved in cell signaling.

MSC: Understanding 62. Cortisol is a glucocorticoid that regulates

a. b. c. d.

blood pressure. ion transport in the kidneys. testosterone. liver metabolism.

ANS: D DIF: Medium REF: 15.4 OBJ: 15.4.a. List the major lipids that are involved in cell signaling.

MSC: Understanding 63. A patient is having problems regulating blood pressure and has poor kidney function. Which steroid could be responsible for this? a. progesterone b. cortisol c. aldosterone d. estradiol ANS: C DIF: Medium REF: 15.4 OBJ: 15.4.a. List the major lipids that are involved in cell signaling.

MSC: Applying 64. Mineralocorticoids and glucocorticoids are synthesized in the a. kidneys. b. adrenal glands. c. liver. d. corpus luteum.

ANS: B DIF: Easy REF: 15.4 OBJ: 15.4.b. List the major sites within the human body where steroid hormones are synthesized.

MSC: Remembering 65. Which steroid hormone is synthesized in the ovaries? a. cortisol b. progesterone c. testosterone d. estradiol ANS: D DIF: Easy REF: 15.4 OBJ: 15.4.b. List the major sites within the human body where steroid hormones are synthesized.

MSC: Remembering 66. Which steroid hormone is synthesized in the corpus luteum? a. cortisol b. progesterone c. testosterone d. estradiol ANS: B DIF: Easy REF: 15.4 OBJ: 15.4.b. List the major sites within the human body where steroid hormones are synthesized.

MSC: Remembering 67. 7-Dehydrocholesterol is converted to cholecalciferol (Vitamin D3) by a. P450C1 hydroxylase. b. P450C12 hydroxylase. c. P450C25 hydroxylase. d. ultraviolet light.

ANS: D DIF: Medium REF: 15.4 OBJ: 15.4.c. Summarize the route that converts 7-dehydrocholesterol into 1,25-hydroxyvitamin D3.

MSC: Understanding 68. Vitamin D3 is converted to 25-hydroxyvitamin D3 in the __________ cells. a. skin b. kidney c. muscle d. liver ANS: D DIF: Easy REF: 15.4 OBJ: 15.4.c. Summarize the route that converts 7-dehydrocholesterol into 1,25-hydroxyvitamin D3.

MSC: Understanding 69. 25-Hydroxyvitamin D3 is converted to 1,25-hydroxyvitamin D3 by a. P450C1 hydroxylase. b. P450C12 hydroxylase. c. P450C25 hydroxylase. d. ultraviolet light.

ANS: A DIF: Medium REF: 15.4 OBJ: 15.4.c. Summarize the route that converts 7-dehydrocholesterol into 1,25-hydroxyvitamin D3.

MSC: Understanding 70. Which eicosanoid modulates the secretion of proteoglycans that protects the stomach lining from the effects of low pH? a. prostaglandin b. prostacyclin c. thromboxane d. leukotriene ANS: A DIF: Easy REF: 15.4 OBJ: 15.4.e. Differentiate among prostacyclins, prostaglandins, thromboxanes, and leukotrienes.

MSC: Understanding 71. Which eicosanoid controls platelet formation? a. prostaglandin b. prostacyclin c. thromboxane d. leukotriene ANS: B DIF: Easy REF: 15.4 OBJ: 15.4.e. Differentiate among prostacyclins, prostaglandins, thromboxanes, and leukotrienes.

MSC: Understanding 72. Which eicosanoid regulates blood vessel constriction? a. prostaglandin b. prostacyclin c. thromboxane d. leukotriene ANS: C

DIF: Easy

REF: 15.4

OBJ: 15.4.e. Differentiate among prostacyclins, prostaglandins, thromboxanes, and leukotrienes.

MSC: Understanding 73. Which eicosanoid acts as an inflammatory mediator that also regulates smooth muscle contraction? a. prostaglandin b. prostacyclin c. thromboxane d. leukotriene ANS: D DIF: Easy REF: 15.4 OBJ: 15.4.e. Differentiate among prostacyclins, prostaglandins, thromboxanes, and leukotrienes.

MSC: Understanding 74. Compared with the COX-2 enzyme, COX-1 has a. a larger active site. b. a smaller active site. c. a more elongated three-dimensional structure. d. more -barrels.

ANS: B DIF: Difficult REF: 15.4 OBJ: 15.4.d. Distinguish between COX-1 and COX-2.

MSC: Analyzing

75. Inhibition of the COX-1 enzyme results in a. reduced pain and fever. b. reduced mucin secretion. c. increased risk of heart disease. d. increased platelet aggregation.

ANS: B DIF: Easy REF: 15.4 OBJ: 15.4.d. Distinguish between COX-1 and COX-2.

MSC: Understanding

SHORT ANSWER 1. Compare and contrast saturated, monounsaturated, and polyunsaturated fatty acids.

ANS: Saturated, monounsaturated, and polyunsaturated fatty acids contain a carboxylic acid head group and a hydrocarbon chain. The hydrocarbon chain of saturated fatty acids only contains single bonds. Monounsaturated fatty acids contain one double bond in their hydrocarbon side chain, whereas polyunsaturated fatty acids contain more than one double bond in the hydrocarbon side chain.

DIF: Easy REF: 15.1 OBJ: 15.1.a. Differentiate among saturated, monounsaturated, and polyunsaturated fatty acids.

MSC: Analyzing 2. Predict the following fatty acid structures. a. cis 18:2 ( 9,12) b. trans 18:1 ( 9) c. trans 20:2 ( 11,13) ANS:

a.

b.

c.

DIF: Difficult REF: 15.1 OBJ: 15.1.b. Convert the common nomenclature for fatty acids into a drawing of the structure.

MSC: Applying 3. Using common nomenclature, name the following fatty acid structures.

a.

b.

c.

ANS: a. cis 14:1 ( 9) b. cis 16:2 ( 6,9) c. trans 18:3 ( 7,9,11) DIF: Medium REF: 15.1 OBJ: 15.1.c. Use the structure of the fatty acid to derive the common nomenclature for fatty acids.

MSC: Applying

4. Why do long chain, saturated fatty acids have a higher melting point than unsaturated fatty acids?

ANS: Long chain, saturated fatty acids do not contain double bonds, whereas unsaturated fatty acids contain double bonds with the cis confirmation. The cis double bonds introduce a bend in the chain, resulting in less contact between molecules. Because saturated fatty acid molecules have more contact, they have more London forces, which results in a higher melting point.

DIF: Medium REF: 15.1 OBJ: 15.1.d. Predict the melting point of a fatty acid based on chain length and degree of saturation.

MSC: Understanding 5. What is partial hydrogenation? Outline the pros and cons of using partial hydrogenation in the food industry.

ANS: Hydrogenation is a commercial process where carbon double bonds are reduced to single bonds, raising the melting point. Partial hydrogenation is used to convert plant oils into margarine by only hydrogenating a percentage of the double bonds, resulting in the formation of trans double bonds in many remaining double bonds. The pros of this process are that plant oils are cheaper than animal fats and have a longer shelf life. The con of this process is that consumption of trans fats has been correlated to an increase cardiovascular disease.

DIF: Medium REF: 15.1 OBJ: 15.1.e. Distinguish between hydrogenation and partial hydrogenation.

MSC: Understanding | Analyzing 6. Propose a reason that a diet rich in -3 fatty acids would result in a decrease in cardiovascular disease.

ANS: This may be due to the binding of -3 fatty acid derivatives to peroxisome proliferator–activated receptors. These peroxisome proliferator–activated receptors regulate the expression of lipid-metabolizing enzymes in response to ligand binding. While the mechanism is not completely understood, the regulation of the lipid metabolizing enzymes is believed to decrease cardiovascular disease.

DIF: Difficult REF: 15.1 OBJ: 15.1.f. Differentiate between omega-3 and omega-6 fatty acids.

MSC: Evaluating 7. Compare and contrast the structure of a wax to that of a fatty acid.

ANS: Fatty acids contain a carboxylic acid head group and a hydrocarbon chain and can contain all single carbon bonds or carbon double bonds. Similarly, waxes can contain either single carbon bonds or carbon double bonds. In contrast to fatty acids, waxes consist of two long hydrocarbon chains linked with an ester bond.

DIF: Medium MSC: Analyzing

REF: 15.1

OBJ: 15.1.g. Define wax.

8. Describe the two ways triacylglycerols have been used to improve daily life.

ANS: Triacylglycerols improve daily life through cooking. Many spices are hydrophobic, so they are more soluble in fats and oils. Triacylglycerols also improve life through the process of making soap for cleaning. Fat is used in saponification to make soap.

DIF: Easy REF: 15.1 OBJ: 15.1.h. Name two aspects of everyday life that have benefited from our knowledge of triacylglycerol chemistry.

MSC: Analyzing 9. Outline the six steps required for the absorption and transport of dietary triacylglycerols.

ANS: (1) Triacylglycerols are emulsified by bile acids. (2) Triacylglycerols are hydrolyzed by intestinal lipases, generating free fatty acids that pass through the intestinal epithelial cell. (3) Triacylglycerols are resynthesized inside the intestinal epithelial cells. (4) Triacylglycerols are packaged into large lipoproteins called chylomicrons. (5) Chylomicrons are exported to the lymphatic system. (6) Chylomicrons enter the circulatory system through the left subclavian vein.

DIF: Difficult REF: 15.2 OBJ: 15.2.a. Compare the movement of triacylglycerols through the circulatory system with the movement of fatty acids.

MSC: Analyzing 10. Compare and contrast chylomicrons and VLDLs. ANS: Both function as transporters of triacylglycerols through the blood. Chylomicrons are large lipoprotein molecules that are produced in intestinal epithelial cells. VLDLs are low-density lipoproteins that are synthesized and exported by liver cells.

DIF: Difficult MSC: Analyzing

REF: 15.2

OBJ: 15.2.b. State the role of chylomicrons.

11. A television commercial states that high triacylglycerols in the bloodstream could be a result of diet. Two ways to transport triacylglycerols through the bloodstream are chylomicrons and VLDLs. Explain the statement from the commercial in terms of these two transportation systems.

ANS: Chylomicrons function to transport dietary triacylglycerols from intestinal epithelial cells; therefore, they are related to the diet claim from the commercial. VLDLs transport triacylglycerols that have been synthesized in the liver from the degradation of carbohydrates and proteins, which are also a component of diet.

DIF: Difficult REF: 15.2 OBJ: 15.2.c. Summarize the events in the liver that lead to VLDL formation.

MSC: Applying 12. List the three major lipases in human adipocytes and explain the regulatory mechanism for one of the lipases.

ANS: Adipose triglyceride lipase, hormone-sensitive lipase, and monoacylglycerol lipase are the three major lipases in human adipocytes. The regulatory protein G58 controls the lipase activity of adipose triglyceride lipase in response to epinephrine and glucagon signaling.

DIF: Medium REF: 15.2 OBJ: 15.2.d. List the three major lipases found in human adipocytes.

MSC: Understanding 13. Free fatty acids inside cells can act as a detergent and dissolve membranes. How is this prevented inside the cells?

ANS: The released fatty acids are contained within a fatty acid binding protein in the cytosol. The human adipocyte fatty acid binding protein 4 has a flexible loop with a Phe residue that acts as a lid. It opens and closes, providing access to the interior hydrophobic binding pocket.

DIF: Difficult REF: 15.2 OBJ: 15.2.e. State the steps required for glucagon to cause release of fatty acids from adipocytes.

MSC: Applying 14. List and describe the major types of lipids found in a typical plasma membrane.

ANS: The three major types are glycerophospholipids, sphingolipids, and cholesterol.

Glycerophospholipids contain two fatty acids and a phosphate group attached to a glycerol.

Sphingolipids contain sphingosines. Cholesterol contains a rigid, four-ring steroid center.

DIF: Easy REF: 15.3 OBJ: 15.3.a. List the major types of lipids found in a typical plasma membrane.

MSC: Understanding 15. The inner monolayer and outer monolayer of a plasma membrane have different lipid compositions. Describe the composition and explain the role of the uneven distribution of membrane lipids.

ANS: The outer monolayer contains phosphatidylcholine, sphingomyelin, and ganglioside sphingolipids.

The inner monolayer contains phosphatidylethanolamine, phosphatidylserine, and phosphatidylinositol. The uneven distribution of the membrane lipids determines the varying physical properties of the membrane such as fluidity, charge, and thickness, as well as mediators of signaling pathways.

DIF: Medium REF: 15.3 OBJ: 15.3.b. Differentiate between the lipids found in the outer monolayer of a plasma membrane and those found in the inner monolayer.

MSC: Analyzing | Understanding 16. Define lipid rafts and explain their function.

ANS: Lipid rafts are assemblies of lipids and proteins in the fluid mosaic model. They coordinate cell signaling processes, membrane trafficking, and neurotransmission.

DIF: Easy REF: 15.3 OBJ: 15.3.c. Define the fluid mosaic model and lipid rafts.

17. Compare glycerophospholipids with sphingolipids.

MSC: Understanding

ANS: Both glycerophospholipids and sphingolipids contain at least one fatty acid. Glycerophospholipids have two fatty acids bound to a glycerol backbone with a phosphate polar head group. The structure of sphingolipids varies compared with glycerophospholipids because some, such as cerebrosides and gangliosides, contain a glycan group, whereas sphingomyelin contains a phosphate head group with choline. All sphingolipids are derived from sphingosine.

DIF: Medium REF: 15.3 OBJ: 15.3.d. Distinguish between glycerophospholipids and sphingolipids.

MSC: Analyzing 18. List the four most abundant glycerophospholipids in eukaryotic membranes and compare and contrast their structure.

ANS: The four most abundant glycerophospholipids are phosphatidylserine, phosphatidylethanolamine, phosphatidylcholine, and phosphatidylinositol. The structure of the phospholipids is similar in that they contain a glycerol backbone, two fatty acid tails, and a phosphate head group. The structure of these phospholipids differs based on their alcohol precursors, which are attached to the phosphate polar head group: serine, ethanolamine, choline, and inositol.

DIF: Difficult REF: 15.3 OBJ: 15.3.e. List the four alcohols used to produce the most abundant glycerophospholipids in eukaryotic membranes.

MSC: Analyzing 19. Explain how snake venom can lead to tissue damage and eventual death without treatment.

ANS: Snake venom often contains secreted phospholipase A2 enzymes that cleave the glycerophospholipids. This results in free fatty acids that break down membranes from the detergent effect, resulting in tissue damage. If untreated, this can lead to massive internal bleeding.

DIF: Difficult REF: 15.3 OBJ: 15.3.d. Distinguish between glycerophospholipids and sphingolipids.

MSC: Applying 20. Compare and contrast the enzyme deficiencies that result in Tay-Sachs disease, Fabry disease, and Niemann-Pick disease.

ANS: All of these diseases are the result of defects in the enzymes that are responsible for sphingolipid degradations that result in the buildup of metabolic precursors. Hexosaminidase A is defective in patients with Tay-Sachs disease, resulting in a buildup of GM2 ganglioside in the spleen and brain.

Fabry disease results from defects in the enzyme -galactosidase A, and Niemann-Pick disease is due to defects in sphingomyelinase.

DIF: Difficult REF: 15.3 OBJ: 15.3.f. Identify the missing enzymes that give rise to Tay-Sachs disease, Fabry disease, and Niemann-Pick disease.

MSC: Analyzing 21. How do cholesterol concentrations affect membrane fluidity?

ANS:

High concentrations of cholesterol prevent the lateral movement of phospholipids, decreasing the membrane fluidity in that region. Low concentrations of cholesterol allow the lateral movement of phospholipids, increasing the membrane fluidity in that region.

DIF: Medium REF: 15.3 OBJ: 15.3.g. Explain how cholesterol affects membrane fluidity.

MSC: Understanding 22. Compare and contrast the site of synthesis and the physiological function of the following steroids: cortisol, aldosterone, and testosterone.

ANS: All three are synthesized in the adrenal cortex, with testosterone also synthesized in the testes.

Testosterone is important in the development of male reproductive organs. Aldosterone regulates ion transport in the kidney as well as blood pressure. Cortisol regulates liver metabolism as well as cell functions in the immune system and the brain (adaption to stress).

DIF: Difficult REF: 15.4 OBJ: 15.4.b. List the major sites within the human body where steroid hormones are synthesized.

MSC: Analyzing 23. Compare the lipid signaling molecules derived from cholesterol to those derived from the acid arachidonate.

-6 fatty

ANS: Cholesterol is the precursor to the steroid hormones such as mineralocorticoids, glucocorticoids, progesterones, androgens, estrogens, and vitamin D. These molecules are important for the development of reproductive organs, ion transport in the kidneys, and blood pressure regulation, among many other functions. The cell signaling molecules that are derived from -6 fatty acid arachidonate include prostaglandins, prostacyclins, thromboxanes, and leukotrienes. These are all immunoregulatory molecules.

DIF: Difficult REF: 15.4 OBJ: 15.4.a. List the major lipids that are involved in cell signaling.

MSC: Analyzing 24. Summarize the conversion of 7-hydroxycholestrol into 1,25-hydroxyvitamin D. ANS: Skin cells absorb energy from ultraviolet light, converting 7-hydroxycholestrol to vitamin D3.

Vitamin D3 is transported to the liver, where it is converted to 25-hydroxyvitamin D3 by P450C25 hydroxylase. Then, in the kidney, 25-hydroxyvitamin D3 is converted to 1,25-hydroxyvitamin D3

by P450C1 hydroxylase.

DIF: Difficult REF: 15.4 OBJ: 15.4.c. Summarize the route that converts 7-dehydrocholesterol into 1,25-hydroxyvitamin D3.

MSC: Evaluating 25. Compare the results when anti-inflammatory drugs inhibit COX-1 and COX-2 enzymes.

ANS:

COX-1 produces prostaglandins that stimulate mucin secretion and protect the lining of the stomach. When inhibited, bleeding ulcers can occur. COX-2 produces prostaglandins that cause swelling, pain, and fever. Anti-inflammatory drugs reduce these symptoms.

DIF: Easy COX-2.

MSC: Analyzing

REF: 15.4

OBJ: 15.4.d. Distinguish between COX-1 and

Chapter 16: Lipid Metabolism MULTIPLE CHOICE 1. How many passes through the fatty acid oxidation pathway are required to degrade palmitic acid? a. 1 b. 7 c. 8 d. 16 ANS: B DIF: Easy REF: 16.1 OBJ: 16.1.a. State the net reaction for fatty acid degradation of palmitate.

MSC: Applying 2. What is the cellular location of the fatty acid oxidation pathway? a. cytoplasm b. peroxisome c. mitochondrial matrix d. smooth endoplasmic reticulum ANS: C DIF: Easy REF: 16.1 OBJ: 16.1.a. State the net reaction for fatty acid degradation of palmitate.

MSC: Understanding 3. What precursors are required for the breakdown of palmitate? a. 14 ATP and 14 NADH b. ATP and CoA c. acetyl-CoA d. NADH and FADH2 ANS: B DIF: Easy REF: 16.1 OBJ: 16.1.a. State the net reaction for fatty acid degradation of palmitate.

MSC: Analyzing 4. What is the key enzyme involved in priming fatty acids for degradation? a. acetyl-CoA carboxylase b. fatty acyl-CoA synthetase c. carnitine acyltransferase I d. fatty acyl hydrolase ANS: B DIF: Easy REF: 16.1 OBJ: 16.1.b. List the key enzymes of fatty acid metabolism.

MSC: Understanding

5. Which enzyme is responsible for assembly of palmitate from activated acetyl-CoA fragments? a. acyl-CoA dehydrogenase b. acetyl-CoA carboxylase c. fatty acyl-CoA synthetase d. fatty acid synthase ANS: D DIF: Easy REF: 16.1 OBJ: 16.1.b. List the key enzymes of fatty acid metabolism.

MSC: Understanding

6. Which enzyme catalyzes the modification of a fatty acid, so that it can be transported into the mitochondria for oxidation?

a. b. c. d.

acyl-CoA dehydrogenase acetyl-CoA carboxylase fatty acyl-CoA synthetase carnitine acyltransferase I

ANS: D DIF: Easy REF: 16.1 OBJ: 16.1.b. List the key enzymes of fatty acid metabolism.

MSC: Understanding

7. In order for a fatty acyl-CoA to be moved into the mitochondria for -oxidation, it must be a. transported by the carnitine–acylcarnitine translocase. b. activated by ATP. c. reduced by NADH and FADH2. d. hydrolyzed into acetyl-coA fragments.

ANS: A DIF: Medium REF: 16.1 OBJ: 16.1.c. Summarize the events that move a fatty acid from the cytosol to the mitochondrial matrix before oxidation.

MSC: Evaluating 8. Which molecule is used to transport fatty-acyl groups into the mitochondria? a. CoA-SH b. ATP c. biotin d. carnitine ANS: D DIF: Easy REF: 16.1 OBJ: 16.1.c. Summarize the events that move a fatty acid from the cytosol to the mitochondrial matrix before oxidation.

MSC: Remembering 9. Carnitine is a. used for transporting fatty acids into the cell. b. attached to the growing fatty acid chain in fatty acid synthesis. c. attached to fatty acid groups that are moved into the mitochondria for degradation. d. attached to acetyl groups to activate them for addition to the growing fatty acid chain in fatty acid synthesis.

ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.c. Summarize the events that move a fatty acid from the cytosol to the mitochondrial matrix before oxidation.

MSC: Understanding 10. How many high-energy FADH2 and NADH molecules, respectively, are made from each pass through the -oxidation pathway? a. 1 FADH2; 2 NADH b. 1 FADH2; 0 NADH c. 0 FADH2; 2 NADH d. 1 FADH2; 1 NADH ANS: D DIF: Easy REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Remembering 11. Which of the following is NOT an intermediate in the -oxidation of a fatty acid? a.

b.

c.

d.

ANS: B DIF: Medium REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Analyzing 12. What enzyme class catalyzes the following reaction?

a. b. c. d.

ligase hydratase transferase oxidoreductase

ANS: B DIF: Medium REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Analyzing 13. What enzyme class catalyzes the following reaction? (Note that there may be some missing reactants and products.)

a. b. c. d.

lyase hydrolase transferase dehydrogenase

ANS: D DIF: Medium REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Analyzing 14. Which cofactor is utilized in the following fatty acid oxidation reaction?

a. b. c. d.

ATP NAD+ FAD NADP+

ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Remembering 15. Why is the fatty acid oxidation pathway also referred to as the -oxidation pathway? a. The carbon adjacent to the fatty acyl-CoA reacts with oxygen. b. The pathway utilizes NAD+ and FAD as cofactors. c. A carbon atom that is two carbons away from the carboxylic acid end of the fatty acid chain is oxidized. d. The resulting products are referred to as -bodies.

ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Understanding 16. How many total NADH + FADH2s are made in the -oxidation pathway from the breakdown of the following fatty acid to all acetyl-CoAs?

a. b. c. d.

6 8 4 2

ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.e. Calculate the ATP yield from the complete oxidation of palmitate.

MSC: Applying 17. The complete -oxidation of 1 mole of palmitic acid (16:0) yields __________ moles of ATP after TCA cycle and oxidative phosphorylation processes. a. 8 b. 32 c. 106 d. 156 ANS: C DIF: Easy REF: 16.1 OBJ: 16.1.e. Calculate the ATP yield from the complete oxidation of palmitate.

MSC: Remembering 18. Why is less ATP obtained from the average carbon in a sugar molecule than from a carbon in a fat molecule? a. The sugar carbons require more water weight during cellular storage. b. The carbons in fatty acids are a more reduced form of carbon than those in sugars. c. The sugar carbons yield more NADH than ATP. d. The sugar carbons are derived from CO2.

ANS: B DIF: Difficult REF: 16.1 OBJ: 16.1.e. Calculate the ATP yield from the complete oxidation of palmitate.

MSC: Evaluating 19. About __________ more ATPs can be obtained from one 16:0 fatty acid than from one glucose molecule. a. 32 b. 106 c. 2 d. 75 ANS: D DIF: Difficult REF: 16.1 OBJ: 16.1.e. Calculate the ATP yield from the complete oxidation of palmitate.

MSC: Applying 20. How many ATPs are obtained from the complete -oxidation of one mole of stearoyl-CoA (18Cs) compared with three molecules of glucose (3 6C = 18Cs)? a. 106 versus 32 b. 100 versus 100 c. 36 versus 90 d. 120 versus 90 ANS: D DIF: Medium REF: 16.1 OBJ: 16.1.f. Compare the products of beta-oxidation from stearoyl-CoA with the beta-oxidation products of oleoyl-CoA. MSC: Applying 21. How many more passes through -oxidation does the saturated fat stearic acid (18:0) require, compared with the monounsaturated fat oleic acid (18:1)? a. 0 b. 1 c. 2 d. 17 ANS: A DIF: Easy REF: 16.1 OBJ: 16.1.f. Compare the products of beta-oxidation from stearoyl-CoA with the beta-oxidation products of oleoyl-CoA. MSC: Understanding 22. What is the primary difference in the oxidation of stearic acid (18:0) and oleic acid (18:1)? a. Stearic acid requires one more pass through the fatty acid oxidation pathway. b. Oleic acid will yield one less FADH2 product molecule. c. Oleic acid cannot be fully metabolized. d. Stearic acid yields less ATP. ANS: B DIF: Difficult REF: 16.1 OBJ: 16.1.f. Compare the products of beta-oxidation from stearoyl-CoA with the beta-oxidation products of oleoyl-CoA. MSC: Analyzing 23. How many more enzymes does the oxidation of oleoyl-CoA (18:1) require than the oxidation of stearoyl-CoA (18:0)? a. 0 b. 1 c. 2 d. 3 ANS: B

DIF: Medium

REF: 16.1

OBJ: 16.1.f. Compare the products of beta-oxidation from stearoyl-CoA with the beta-oxidation products of oleoyl-CoA. MSC: Understanding 24. The -oxidation of mono- and polyunsaturated fatty acids a. requires an extra cycle through the pathway. b. involves the reduction of the double bonds and then the continuation of -oxidation. c. yields succinyl-CoA. d. involves isomerization and in some cases reduction of the double bonds before the continuation of -oxidation.

ANS: D DIF: Medium REF: 16.1 OBJ: 16.1.g. Explain the difference between oxidation of a monounsaturated fatty acid and a polyunsaturated fatty acid.

MSC: Evaluating 25. How do we deal with the double bonds during the degradation of unsaturated fatty acids? a. Convert the three-carbon propionyl-CoA to succinyl-CoA and feed it into the TCA cycle. b. Converge them with the TCA cycle to produce acetyl-CoAs. c. Isomerize the position of the double bonds to converge them with the -oxidation pathway. d. Reduce them to single bonds and feed the saturated fatty acid into the -oxidation pathway.

ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.g. Explain the difference between oxidation of a monounsaturated fatty acid and a polyunsaturated fatty acid.

MSC: Evaluating 26. The following fatty acid __________ be metabolized by __________.

a. will; being run through the -oxidation pathway until the double bond is isomerized for the pathway to continue b. will not; not being recognized by -oxidation pathway enzymes c. will not; entering the pathway as normal but eventually inhibiting the enzymes d. will; being run through the -oxidation pathway as normal ANS: A DIF: Medium REF: 16.1 OBJ: 16.1.g. Explain the difference between oxidation of a monounsaturated fatty acid and a polyunsaturated fatty acid.

MSC: Evaluating 27. How many more enzymes does the oxidation of a polyunsaturated fat such as linoleoyl-CoA (18:2) require than the oxidation of stearoyl-CoA (18:0)? a. 0 b. 1 c. 2 d. 3 ANS: C DIF: Medium REF: 16.1 OBJ: 16.1.g. Explain the difference between oxidation of a monounsaturated fatty acid and a polyunsaturated fatty acid.

MSC: Understanding

28. What extra enzyme types are often required in the degradation of polyunsaturated fats by the -oxidation pathway? a. reductase and isomerase b. hydrolase and isomerase c. oxidoreductase and reductase d. synthase and isomerase ANS: A DIF: Medium REF: 16.1 OBJ: 16.1.g. Explain the difference between oxidation of a monounsaturated fatty acid and a polyunsaturated fatty acid.

MSC: Understanding 29. What molecule is the odd chain fatty acid product propionyl-CoA converted into? a. butyryl-CoA b. succinyl-CoA c. citrate d. palmitate ANS: B DIF: Medium REF: 16.1 OBJ: 16.1.h. Summarize the reactions that occur in the last round of beta-oxidation of a fatty acid with an odd number of carbons.

MSC: Remembering 30. Which is found in the ketone body pathway? a. succinyl-CoA. b. propionyl-CoA. c. dihydroxyacetone phosphate. d. hydroxybutyrate.

ANS: D DIF: Medium REF: 16.1 OBJ: 16.1.i. Hypothesize about the conditions that would stimulate ketogenesis.

MSC: Understanding 31. Which of the following are ketone bodies? a. acetyl-CoA, hydroxymethylglutaryl-CoA b. -ketoacyl-ACP, hydroxymethylglutaryl-CoA c. methylmalonyl-CoA, acetyl-CoA d. hydroxybutyrate, acetoacetate ANS: D DIF: Easy REF: 16.1 OBJ: 16.1.i. Hypothesize about the conditions that would stimulate ketogenesis.

MSC: Remembering 32. Ketone bodies are a. transported to the liver for degradation. b. an alternate storage form of glucose. c. used as a fuel source by muscle cells as well as brain cells. d. polymerized to form fatty acids.

ANS: C DIF: Easy REF: 16.1 OBJ: 16.1.i. Hypothesize about the conditions that would stimulate ketogenesis.

MSC: Understanding 33. How many acetyl-CoAs per ketone body are delivered to cells in need of energy? a. 1 b. 2 c. 3

d. 4 ANS: B DIF: Medium REF: 16.1 OBJ: 16.1.i. Hypothesize about the conditions that would stimulate ketogenesis.

MSC: Applying 34. Both the synthesis and -oxidation of saturated fatty acids a. require FAD. b. require NADPH. c. occur in the cytosol. d. involve acetyl-CoA. ANS: D DIF: Easy REF: 16.2 OBJ: 16.2.a. Compare and contrast fatty acid synthesis with fatty acid degradation.

MSC: Analyzing 35. A difference between FA synthesis and -oxidation is that FA synthesis __________, whereas -oxidation __________. a. reactions use ATP; reactions directly yield ATP b. occurs in the mitochondria; takes place in the cytoplasm c. uses NADH; uses NADPH d. uses acyl-ACP; uses acyl-CoA ANS: D DIF: Medium REF: 16.2 OBJ: 16.2.a. Compare and contrast fatty acid synthesis with fatty acid degradation.

MSC: Analyzing 36. The same four reactions that are central to the -oxidation pathway are also present in the fatty acid synthesis pathway, except they are reversed. What is a key difference between the four reactions in these two pathways? a. One set of reactions synthesizes an ATP, whereas the other set uses an ATP. b. One set occurs in the muscle, whereas the second pathway occurs in the liver. c. One pathway adds three carbon atoms at a time, whereas the other removes two carbons. d. Four enzymes are used in one, whereas one enzyme is used in the other.

ANS: D DIF: Medium REF: 16.2 OBJ: 16.2.a. Compare and contrast fatty acid synthesis with fatty acid degradation.

MSC: Analyzing 37. Which of the following do -oxidation and fatty acid synthesis have in common? a. the presence of an oxidized fatty acyl -carbon with a hydroxyl or carbonyl group as a pathway intermediate b. their cellular location c. their use of NADH d. the number of enzymes involved in the pathways ANS: A DIF: Difficult REF: 16.2 OBJ: 16.2.a. Compare and contrast fatty acid synthesis with fatty acid degradation.

MSC: Analyzing 38. What enzyme catalyzes the following reaction in the first step of fatty acid synthesis?

a. b. c. d.

fatty acyl-CoA synthetase acetyl-CoA carboxylase fatty acid synthase fatty acyl-CoA dehydrogenase

ANS: B DIF: Medium REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Evaluating 39. The synthesis of fatty acids requires which cofactor? a. FADH2 b. NADH c. thiamine pyrophosphate (TPP) d. NADPH ANS: D DIF: Easy REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Understanding 40. What cofactor, common to carboxylase enzymes, is used by acetyl-CoA carboxylase? a. NADPH b. FAD c. biotin d. pyridoxal phosphate ANS: C DIF: Easy REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Remembering 41. What enzyme catalyzes the following fatty acid synthesis reaction?

a. b. c. d.

fatty acid synthase fatty acyl-CoA synthetase fatty acyl-CoA dehydrogenase acetyl-CoA carboxylase

ANS: A DIF: Easy REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Understanding 42. The synthesis of palmitic acid a. occurs in mitochondria. b. involves the acyl carrier protein (ACP). c. uses FAD and NADP+. d. requires ATP. ANS: D DIF: Easy REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Analyzing

43. Which is true of the acyl carrier protein (ACP)? a. It transports the fatty acid chain during oxidation and synthesis. b. It directs the growing fatty acid chain from one enzyme active site to another in the fatty acid synthesis pathway. c. It requires ATP for proper function. d. It catalyzes the delivery of fatty acyl chains from the mitochondria to the cytosol.

ANS: B DIF: Medium REF: 16.2 OBJ: 16.2.c. Distinguish between the roles of the acyl carrier protein and the KS domain.

MSC: Understanding 44. What are the different roles played the acyl carrier protein (ACP) and the ketoacyl synthase (KS) domain during fatty acid synthesis? a. The ACP carries the growing fatty acid chain more than the KS domain. b. The KS domain holds the growing fatty acid chain, whereas the ACP delivers two carbon fragments. c. The KS domain associates with the fatty acid synthase enzyme, whereas the ACP does not. d. The ACP delivers two carbon fragments one at a time, whereas the KS domain passes them on to the fatty acid.

ANS: A DIF: Difficult REF: 16.2 OBJ: 16.2.c. Distinguish between the roles of the acyl carrier protein and the KS domain.

MSC: Evaluating 45. Which enzyme activates acetyl-CoA so that it can be added to the growing fatty acid chain during the synthesis of palmitate? a. acetyl-CoA carboxylase b. fatty acyl-CoA synthase c. acyl-CoA dehydrogenase d. fatty acid synthase ANS: A DIF: Easy REF: 16.2 OBJ: 16.2.d. State the net reaction for the synthesis of palmitate.

MSC: Understanding 46. The introduction of 14CO2 into a cell actively synthesizing fatty acids results in 14C labeled a. malonyl-CoA. b. acetyl-CoA. c. acyl-CoA. d. palmitate.

ANS: A DIF: Easy REF: 16.2 OBJ: 16.2.d. State the net reaction for the synthesis of palmitate.

MSC: Understanding 47. For every two carbons that are added to a growing fatty acid chain in the fatty acid synthesis pathway, __________ ATPs and __________ NADPHs are required. a. 0; 1 b. 1; 2 c. 2; 1 d. 0; 2 ANS: B DIF: Easy REF: 16.2 OBJ: 16.2.d. State the net reaction for the synthesis of palmitate.

MSC: Applying 48. How are double bonds added to fatty acid chains in humans? a. The smooth endoplasmic reticulum is involved in elongating and unsaturating fatty acids. b. FAD is used as an oxidant to create the double bonds in the smooth endoplasmic reticulum. c. Unsaturated fatty acids are not made by humans and are therefore essential fats. d. Fatty acid desaturase enzymes use O2 and NADH to add double bonds to fatty acids.

ANS: D DIF: Medium REF: 16.2 OBJ: 16.2.e. Summarize the events that convert palmitate into oleoyl-CoA. MSC: Understanding 49. Which fatty acid can be synthesized from scratch in humans by desaturase enzymes? a. 20:4, 5,8,11,14 b. 18:2, 9,13 c. 20:2, 6,9 d. 16:2, 9,11 ANS: C DIF: Difficult REF: 16.2 OBJ: 16.2.e. Summarize the events that convert palmitate into oleoyl-CoA. MSC: Applying 50. What class of enzyme is the human desaturase enzyme? a. isomerase b. oxidoreductase c. ATPase d. transferase ANS: B DIF: Easy REF: 16.2 OBJ: 16.2.e. Summarize the events that convert palmitate into oleoyl-CoA. MSC: Understanding 51. In triacylglycerol synthesis, from where is the glycerol backbone derived? a. fatty acyl-CoA b. pyruvate c. dihydroxyacetone phosphate d. acetyl-CoA ANS: C DIF: Easy REF: 16.2 OBJ: 16.2.f. Outline the steps for triacylglycerol production from dihydroxyacetone phosphate.

MSC: Understanding 52. The synthesis of both triacylglycerols and membrane phospholipids occurs from which immediate precursor? a. phosphatidic acid b. glycerol c. phosphatidylserine d. diacylglycerol ANS: A DIF: Easy REF: 16.2 OBJ: 16.2.f. Outline the steps for triacylglycerol production from dihydroxyacetone phosphate.

MSC: Understanding 53. Membrane phospholipids are synthesized in which cellular location?

a. b. c. d.

cytoplasm mitochondrial intermembrane space mitochondrial matrix smooth endoplasmic reticulum

ANS: D DIF: Easy REF: 16.2 OBJ: 16.2.g. Explain how phosphatidylethanolamine is produced from phosphatidic acid.

MSC: Remembering 54. Which group is responsible for activating phosphatidic acid for the synthesis of phospholipids? a. CoA b. ATP c. CO2 d. CTP ANS: D DIF: Medium REF: 16.2 OBJ: 16.2.g. Explain how phosphatidylethanolamine is produced from phosphatidic acid.

MSC: Remembering 55. Which correctly describes the synthesis of phosphatidylethanolamine? a. Activated ethanolamine is added to a phosphatidic acid precursor. b. Phosphatidylserine is decarboxylated. c. Diacylglycerol is activated by CTP. d. Triacylglycerol is phosphorylated with ATP. ANS: B DIF: Difficult REF: 16.2 OBJ: 16.2.g. Explain how phosphatidylethanolamine is produced from phosphatidic acid.

MSC: Remembering 56. The NADPH required by the fatty acid synthesis pathway comes from the a. pentose phosphate pathway and the shuttle of citrate from the mitochondria. b. mitochondria. c. breakdown of glucose. d. TCA cycle and the shuttle of citrate from the mitochondria.

ANS: A DIF: Difficult REF: 16.2 OBJ: 16.2.h. Summarize the movement of acetyl-CoA from the matrix to the cytosol.

MSC: Applying 57. The acetyl-CoA for fatty acid synthesis comes from the a. breakdown of fats. b. TCA cycle. c. mitochondria via the citrate shuttle. d. breakdown of cytoplasmic pyruvate.

ANS: C DIF: Easy REF: 16.2 OBJ: 16.2.h. Summarize the movement of acetyl-CoA from the matrix to the cytosol.

MSC: Understanding 58. The rate-limiting reaction is catalyzed by __________ in the synthesis of saturated fatty acids in the __________. a. fatty acid synthase; cytosol b. fatty acid synthase; mitochondrion c. acetyl-CoA carboxylase; cytosol d. citrate synthase; mitochondrion

ANS: C DIF: Medium REF: 16.2 OBJ: 16.2.i. Define the role of AMP-activated protein kinase in the control of fatty acid synthesis.

MSC: Evaluating 59. The regulation of Acetyl-CoA carboxylase is a. activated by glucagon. b. activated by acyl-CoA binding. c. stimulated by citrate. d. inactivated by insulin.

ANS: C DIF: Difficult REF: 16.2 OBJ: 16.2.i. Define the role of AMP-activated protein kinase in the control of fatty acid synthesis.

MSC: Understanding 60. Which of the following stimulate fatty acid synthesis when their concentrations are high? a. citrate and insulin b. glucagon and citrate c. insulin and acyl-CoA d. citrate, insulin, and palmitoyl-CoA ANS: A DIF: Medium REF: 16.2 OBJ: 16.2.j. List the regulatory mechanisms that prevent futile cycling in the lipid metabolism pathways.

MSC: Evaluating 61. Which of the following causes inhibition of fatty acid synthesis? a. increased insulin b. increased AMP-activated protein kinase (AMPK) c. decreased cytoplasmic acyl-CoA d. increased cytoplasmic acetyl-CoA ANS: B DIF: Difficult REF: 16.2 OBJ: 16.2.j. List the regulatory mechanisms that prevent futile cycling in the lipid metabolism pathways.

MSC: Evaluating 62. The smallest precursor molecule cholesterol is derived from a. squalene. b. isoprene. c. arachidonic acid. d. acetyl-CoA. ANS: D DIF: Easy REF: 16.3 OBJ: 16.3.a. List the four stages of cholesterol synthesis.

MSC: Understanding

63. The final formation of cholesterol from squalene involves a. condensation with HMG-CoA and mevalonate. b. more than 19 reactions including cyclization and oxidation. c. oxidation and the addition of acyl-CoA. d. dimerization and oxidation of squalene.

ANS: B DIF: Medium REF: 16.3 OBJ: 16.3.a. List the four stages of cholesterol synthesis.

MSC: Understanding

64. Which enzyme catalyzes the rate-limiting step of cholesterol synthesis?

a. b. c. d.

cholesterol synthase HMG-CoA reductase thiolase HMG-CoA synthase

ANS: B DIF: Medium REF: 16.3 OBJ: 16.3.b. Identify the rate-limiting step of cholesterol synthesis.

MSC: Remembering 65. All of the following are metabolic fates of cholesterol EXCEPT a. the majority of cholesterol is catabolized to bile salts. b. cholesterol may be present in membranes. c. cholesterol is a precursor for nucleotides. d. steroids are derived from cholesterol.

ANS: C DIF: Easy REF: 16.3 OBJ: 16.3.c. Summarize the major metabolic fates of cholesterol.

MSC: Understanding 66. During the conversion of VLDL to IDL, the a. IDL becomes increasingly enriched in cholesterol. b. core of IDL becomes increasingly enriched in TAGs. c. LDL intermediate is formed. d. IDL becomes depleted in protein.

ANS: A DIF: Easy REF: 16.3 OBJ: 16.3.d. List the five major classes of lipoproteins and their roles in lipid transport.

MSC: Evaluating 67. Which one of the following lipoproteins functions to transport cholesterol from the peripheral tissues to the liver? a. VLDL b. LDL c. HDL d. chylomicron ANS: C DIF: Easy REF: 16.3 OBJ: 16.3.d. List the five major classes of lipoproteins and their roles in lipid transport.

MSC: Understanding 68. What enzyme is activated by HDL to release cholesterol from the cell membranes of peripheral tissues? a. phosphatidylcholine esterase b. HDL apolipase c. cholesterol esterase d. lecithin-cholesterol acyltransferase ANS: D DIF: Easy REF: 16.3 OBJ: 16.3.e. Explain how HDL particles transport cholesterol to the liver.

MSC: Remembering 69. The uptake of LDLs by cells is triggered by the a. absorption of the LDL triacylglycerol and phospholipid core. b. hydrolysis of LDL phospholipids by phospholipase enzymes. c. binding of the apoB-100 lipoprotein on LDL to the LDL receptor.

d. formation of cholesterol plaques.

ANS: C DIF: Medium REF: 16.3 OBJ: 16.3.f. Summarize the endocytosis of LDL particles by cells.

MSC: Analyzing 70. By what process are LDL particles removed selectively from the blood serum? a. through targeted digestion by serum lipases b. by receptor-mediated endocytosis c. They are replenished with triacylglycerols and never removed. d. They form atherosclerotic plaques.

ANS: B DIF: Medium REF: 16.3 OBJ: 16.3.f. Summarize the endocytosis of LDL particles by cells.

MSC: Understanding 71. Which lipid is thought to give rise to the plaques that can clog arteries? a. HDL b. LDL c. VLDL d. chylomicrons ANS: B DIF: Easy REF: 16.3 OBJ: 16.3.g. Explain the connection between elevated levels of LDL and atherosclerosis.

MSC: Understanding 72. LDLs are referred to as “bad cholesterol” because a. they are the blood serum particle with the highest concentration of cholesterol. b. they contain cholesterol that is not as easily degraded. c. their cholesterol has no specific cellular purpose other than to form plaques. d. LDL levels surge after meals high in fat.

ANS: A DIF: Medium REF: 16.3 OBJ: 16.3.g. Explain the connection between elevated levels of LDL and atherosclerosis.

MSC: Evaluating 73. Cholesterol biosynthesis and cholesterol uptake is stimulated by a. the binding of SREs to cholesterol uptake genes. b. the binding of SREBPs to SREs and activating the transcription of cholesterol synthesizing genes. c. increased levels of cholesterol binding to the SREBPs. d. the uptake of LDLs through the LDL receptor.

ANS: B DIF: Medium REF: 16.3 OBJ: 16.3.h. Define sterol regulatory element binding proteins and sterol regulatory elements.

MSC: Understanding 74. The sterol regulatory element (SRE) is a(n) __________ and the sterol regulatory element binding protein (SREBP) is a(n) __________. a. allosteric activator; enzyme b. transport activator; transport protein c. receptor; hormone d. DNA promoter; transcription activator ANS: D DIF: Medium REF: 16.3 OBJ: 16.3.h. Define sterol regulatory element binding proteins and sterol regulatory elements.

MSC: Understanding 75. All of the following genes are activated by the interaction of the SREBP with the SRE, EXCEPT for a. HMG-CoA reductase. b. LDL receptor. c. HMG-CoA synthase. d. cholesterol esterase.

ANS: D DIF: Medium REF: 16.3 OBJ: 16.3.h. Define sterol regulatory element binding proteins and sterol regulatory elements.

MSC: Applying SHORT ANSWER 1. Draw the overall balanced reaction for the breakdown of palmitic acid (16:0) to give all acetyl-CoA products. Please include all cofactors involved in the process.

ANS: palmitate + 7 NAD+ + 7 FAD + 8 CoA + 7 H2O + ATP → 8 acetyl-CoA + 7 NADH + 7H+ + 7 FADH2 + AMP + 2 Pi DIF: Difficult REF: 16.1 OBJ: 16.1.a. State the net reaction for fatty acid degradation of palmitate.

MSC: Remembering 2. Diagram the process by which the palmitoyl-CoA molecule moves from the cytosol into the mitochondria for degradation.

ANS:

DIF: Difficult REF: 16.1 OBJ: 16.1.c. Summarize the events that move a fatty acid from the cytosol to the mitochondrial matrix before oxidation.

MSC: Applying

3. As in glycolysis and the degradation of glucose, the degradation of fatty acids also requires an initial investment of ATP energy. State the reaction or reactions where ATP energy is needed before fatty acids can be oxidized.

ANS: The enzyme fatty acyl-CoA synthetase uses an ATP molecule, which gets hydrolyzed to AMP and 2 Pi, to couple the fatty acid with a CoA cofactor.

DIF: Difficult REF: 16.1 OBJ: 16.1.c. Summarize the events that move a fatty acid from the cytosol to the mitochondrial matrix before oxidation.

MSC: Applying 4. Starting from the 6C fatty acyl-CoA molecule shown below, draw the reactants and products, including all cofactors used for one round of the -oxidation pathway and list the enzyme types involved in each step.

ANS:

DIF: Difficult REF: 16.1 OBJ: 16.1.d. Classify the four reactions involved in the beta-oxidation pathway.

MSC: Applying 5. Start with the following molecule. (A) Write the balanced equation for the products formed from its complete oxidation in the -oxidation pathway and (B) show how many ATPs would be obtained from the complete metabolism of those products.

ANS:

DIF: Difficult REF: 16.1 OBJ: 16.1.e. Calculate the ATP yield from the complete oxidation of palmitate.

MSC: Applying 6. Draw and name the two products obtained from the last round of -oxidation of an odd-chain fatty acid.

ANS: Acetyl-CoA and propionyl-CoA

DIF: Easy REF: 16.1 OBJ: 16.1.h. Summarize the reactions that occur in the last round of beta-oxidation of a fatty acid with an odd number of carbons.

MSC: Understanding 7. What is the name of the enzyme that adds another carbon atom to propionyl-CoA in the degradation of odd-chain fatty acids?

ANS: Propionyl-CoA carboxylase DIF: Medium REF: 16.1 OBJ: 16.1.h. Summarize the reactions that occur in the last round of beta-oxidation of a fatty acid with an odd number of carbons.

MSC: Remembering 8. Describe the metabolic conditions under which ketone bodies are produced.

ANS: When carbohydrate levels run low, typically under starving conditions, there are depleted levels of oxaloacetate, which is needed in the mitochondrial TCA cycle. The metabolism of fats in the liver mitochondria performing -oxidation leads to elevated levels of acetyl-CoA (which cannot be metabolized in the TCA cycle because of the depletion of oxaloacetate). The acetyl-CoA is thus converted into ketone bodies.

DIF: Difficult REF: 16.1 OBJ: 16.1.i. Hypothesize about the conditions that would stimulate ketogenesis.

MSC: Applying 9. Draw the structure of malonyl-CoA, the activated form of acetyl-CoA for fatty acid synthesis.

ANS:

DIF: Medium REF: 16.2 OBJ: 16.2.b. Classify the four reactions involved in the fatty acid synthesis cycle.

MSC: Applying 10. Identify the name of the group shown below that is common to CoA and the acyl carrier protein.

ANS: Phosphopantetheine, or vitamin B5 DIF: Medium REF: 16.2 OBJ: 16.2.c. Distinguish between the roles of the acyl carrier protein and the KS domain.

MSC: Remembering 11. Draw the overall balanced reaction for the synthesis of palmitic acid (16:0) from acetyl-CoA precursors. Please include all the high-energy cofactors required for the process.

ANS: 8 acetyl-CoA + 7 ATP + 14 NADPH + 14H+ 14 NADP+ + 6 H2O

palmitate + 8 CoA + 7 ADP + 7 Pi +

DIF: Difficult REF: 16.2 OBJ: 16.2.d. State the net reaction for the synthesis of palmitate.

MSC: Remembering 12. In the fatty acid synthesis pathway, how many ATPs and NADPHs are needed to add two carbons to the growing fatty acid chain starting with an acetyl-CoA? ANS: One ATP to activate the acetyl-CoA to malonyl-CoA and two NADPH to reduce the -carbon.

DIF: Difficult REF: 16.2 OBJ: 16.2.d. State the net reaction for the synthesis of palmitate.

MSC: Applying 13. Explain how humans can create oleoyl-CoA (18:1

9

) from stearoyl-CoA (18:0).

ANS: By using a fatty acid desaturase

DIF: Medium REF: 16.2 OBJ: 16.2.e. Summarize the events that convert palmitate into oleoyl-CoA. MSC: Remembering 14. Name the steps involved in converting glycerol into triacylglycerol.

ANS: (1) Glycerol is first phosphorylated to make glycerol-3-phosphate. (2) Glycerol-3-phosphate has the first acyl group added to yield lysophosphatidic acid. (3) A second acyl group is added to yield phosphatidic acid. (4) Finally, the third acyl group is added to give the final triacylglycerol. All added acyl groups begin as CoA derivatives.

DIF: Difficult REF: 16.2 OBJ: 16.2.f. Outline the steps for triacylglycerol production from dihydroxyacetone phosphate.

MSC: Applying 15. Fill in the missing names or structures in the following triacylglycerol synthesis scheme.

ANS:

DIF: Difficult REF: 16.2 OBJ: 16.2.f. Outline the steps for triacylglycerol production from dihydroxyacetone phosphate.

MSC: Evaluating 16. Name the enzyme in the following reaction:

ANS: Phosphatidylserine decarboxylase DIF: Medium REF: 16.2 OBJ: 16.2.g. Explain how phosphatidylethanolamine is produced from phosphatidic acid.

MSC: Applying 17. Describe the roles of the citrate shuttle with regards to the fat synthesis pathway.

ANS: The citrate shuttle moves acetyl-CoA from the mitochondria into the cytosol by first combining it with oxaloacetate to form citrate. (1) Once citrate enters the cytoplasm it is cleaved to give back oxaloacetate and release acetyl-CoA for fat synthesis. (2) Oxaloacetate then reenters the mitochondria as either malate or pyruvate after enzymatic conversion. If converted to pyruvate, NADPH is produced as a by-product that is also used in the fat synthesis pathway.

DIF: Medium REF: 16.2 OBJ: 16.2.h. Summarize the movement of acetyl-CoA from the matrix to the cytosol.

MSC: Applying 18. Describe the role that AMP-activated protein kinase (AMPK) plays in the regulation of fatty acid synthesis.

ANS:

AMPK is activated by phosphorylation as a result of AMP binding. The active AMPK goes on to phosphorylate acetyl-CoA carboxylase and inhibit it by forming the monomeric form of this key enzyme that controls the committed step in fatty acid synthesis.

DIF: Difficult REF: 16.2 OBJ: 16.2.i. Define the role of AMP-activated protein kinase in the control of fatty acid synthesis.

MSC: Applying 19. List the four key steps in the synthesis of cholesterol.

ANS: (1) Three acetyl-coA molecules are combined into HMG-CoA and then mevalonate. (2) CO2 is lost from mevalonate to give the isoprenoid, isopentenyl diphosphate. (3) Six molecules of isopentenyl diphosphate are combined to form squalene. (4) Through many cyclization reactions, squalene is converted into cholesterol.

DIF: Medium synthesis.

MSC: Applying

REF: 16.3

OBJ: 16.3.a. List the four stages of cholesterol

20. The rate-limiting step of cholesterol synthesis involves controlling the fate of HMG-CoA. What other pathways is HMG-CoA involved in?

ANS: HMG-CoA could be converted into ketone bodies or into mevalonate for cholesterol synthesis.

DIF: Difficult REF: 16.3 OBJ: 16.3.b. Identify the rate-limiting step of cholesterol synthesis.

MSC: Applying 21. List the primary three physiological roles played by cholesterol or cholesterol derivatives.

ANS: Cholesterol is converted to bile acids for emulsifying fats in the small intestine. Cholesterol is added to membranes to change their fluidity. Cholesterol is a precursor for steroid hormones, such as the sex hormones or cortisone.

DIF: Medium REF: 16.3 OBJ: 16.3.c. Summarize the major metabolic fates of cholesterol.

MSC: Remembering 22. List the five classes of lipoproteins and briefly state the body origin of each.

ANS: (1) Chylomicrons, which originate from the intestines after a fatty meal. (2) HDL, which originates from peripheral tissues with fats and cholesterol for degradation by the liver. (3) VLDL, which originates from the liver with fats and cholesterol for storage. (4) IDL, which originates from VLDLs. (5) LDL, which originates from IDLs. DIF: Difficult REF: 16.3 OBJ: 16.3.d. List the five major classes of lipoproteins and their roles in lipid transport.

MSC: Applying

23. Identify the molecular components of the following lipoprotein.

ANS: (A) Cholesterol, (B) triacylglycerol, (C) cholesterol ester, (D) phospholipid, and (E) apolipoproteins DIF: Medium REF: 16.3 OBJ: 16.3.d. List the five major classes of lipoproteins and their roles in lipid transport.

MSC: Applying 24. List in order the three most abundant molecule types found in an HDL. ANS: HDLs are composed of proteins as the most abundant component, followed by cholesterol, and then triacylglycerols.

DIF: Medium REF: 16.3 OBJ: 16.3.e. Explain how HDL particles transport cholesterol to the liver.

MSC: Evaluating 25. What are the known components of atherosclerotic plaques?

ANS: Cholesterol, various lipids, and macrophage cells called foam cells DIF: Medium REF: 16.3 OBJ: 16.3.g. Explain the connection between elevated levels of LDL and atherosclerosis.

MSC: Remembering

Chapter 17: Amino Acid Metabolism MULTIPLE CHOICE 1. The 10 amino acids that animals need to take in through their diet are called the __________ amino acids. a. common b. essential c. optional d. degradation ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Remembering 2. Nitrogen in biological compounds ultimately comes from what source? a. ammonia b. nitrate c. nitrogen gas d. bacteria ANS: C DIF: Easy REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Remembering 3. The process of nitrogen fixation reduces N2 to a. NAD+. b. nitrate. c. ammonia. d. nitrite.

ANS: B DIF: Easy REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Remembering 4. Which of the following is the correct net reaction of nitrogen fixation in bacteria? a. N2 + 8H+ + 8e + 16 ATP + 16 H2O 2NH3 + H2 + 16 ADP + 16 Pi b. N2 + 8H+ + 8e + 16 ADP + 16 H2O 2NH3 + H2 + 16 ATP + 16 Pi c. 2N2 + 8H+ + 8e + 16 ATP + 16 H2O NH3 + 4H2 + 16 ADP + 16 Pi d. 2NH3 + H2 + 16 ADP + 16 Pi N2 + 8H+ + 8e + 16 ATP + 16 H2O ANS: A DIF: Medium REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Understanding 5. What is the net reaction of nitrogen assimilation in plants? a. Glutamate + ADP + Pi + NADP+ -Ketoglutarate + NH4+ + ATP + NADPH + H+ b.

-Ketoglutarate + NH4+ + ATP + NADPH + H+ Glutamate + ADP + Pi + NADP+ c.

-Ketoglutarate + NH4+ + ADP + NADPH + H+ Glutamate + ATP + Pi + NADP+ + + d.

-Ketoglutarate + NH4+ + ATP + NADP + H Glutamate + ADP + Pi + NADPH ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.b. State the net reaction of nitrogen assimilation in plants.

MSC: Understanding 6. What are the four key enzymes in nitrogen fixation and assimilation in plants and bacteria? a. nitrogenase synthetase, glutamine complex, glutamate synthase, glutamate dehydrogenase b. nitrogenase complex, glutamine synthetase, glutamate synthase, glutamate dehydrogenase c. glutamine synthetase, glutamate synthase, glutamate dehydrogenase, glutamate oxidase d. nitrogenase complex, glutamine synthetase, glycine synthase, glutamine dehydrogenase ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Remembering 7. How does biological fixation convert nitrogen to ammonia? a. by reducing nitrogen b. by combining nitrogen with carbon c. through the ATP-dependent process catalyzed by nitrogenase complex d. through the NADH-dependent process catalyzed by glutamate dehydrogenase ANS: C DIF: Medium REF: 17.1 OBJ: 17.1.c. List the three processes used to overcome the high energy barrier required to break the N2 triple bond. MSC: Understanding 8. How does atmospheric fixation occur given the high energy barrier to convert nitrogen to nitrogen oxides? a. through the oceans that break the triple bond of nitrogen and allow for the combination with water b. through clouds that allow for nitrogen to combine with oxygen c. in the soil by bacteria that reduce nitrogen to ammonia d. through lightning that breaks the triple bond of nitrogen and allows for the combination with oxygen ANS: D DIF: Medium REF: 17.1 OBJ: 17.1.c. List the three processes used to overcome the high energy barrier required to break the N2 triple bond. MSC: Understanding 9. The Haber process is 98% efficient. How does it achieve that level of efficiency? a. low temperatures and atmospheric pressure b. low pressures and recycling unreacted nitrogen c. high pressures and recycling nitrogen d. high pressures and high concentrations of nitrogen ANS: C DIF: Difficult REF: 17.1 OBJ: 17.1.c. List the three processes used to overcome the high energy barrier required to break the N2 triple bond. MSC: Understanding 10. Using nitrogenase to reduce N2 should require 2 ATP to be invested, but it actually takes 16 ATP. Why? a. It is harder to break the nitrogen triple bond than expected and requires more energy input. b. Extra energy is required to produce H2. c. To regenerate the MoFe protein requires the input of ATP. d. To keep the nitrogenase complex associated requires an input of 4 ATP. ANS: B DIF: Difficult REF: 17.1 OBJ: 17.1.d. State the six steps of the nitrogenase reaction.

MSC: Applying

11. Because nitrogenase is inhibited by oxygen, under what conditions can the enzyme operate to reduce N2? a. aerobic conditions b. anaerobic conditions c. high pressure d. high temperature ANS: B DIF: Easy REF: 17.1 OBJ: 17.1.d. State the six steps of the nitrogenase reaction.

MSC: Applying

12. To increase the efficiency of the nitrogenase reaction, some plants have symbionts. The plant increases the efficiency of the reaction by providing __________, whereas bacteria provide(s) __________. a. fumerate and malate; additional NH3 b. fumerate and malate; ATP c. ATP; amino acids d. NADH; ATP ANS: A DIF: Difficult REF: 17.1 OBJ: 17.1.d. State the six steps of the nitrogenase reaction.

MSC: Understanding

13. Bacteria in the genus Nitrosomonas are able to oxidize ammonia to what final product? a. NO2 b. NO3 c. NO4 d. NO2 ANS: D DIF: Easy REF: 17.1 OBJ: 17.1.e. Distinguish between Nitrosomonas and Nitrobacter in terms of the product of nitrification.

MSC: Remembering 14. Nitrite is oxidized by Nitrobacter bacteria to a. NO2. b. NO2 . c. NO . d. NO3 .

ANS: D DIF: Easy REF: 17.1 OBJ: 17.1.e. Distinguish between Nitrosomonas and Nitrobacter in terms of the product of nitrification.

MSC: Remembering 15. Agricultural fertilizers provide the ground with nitrate and nitrite, but only ammonia can be assimilated by plants. What process converts nitrate and nitrite to ammonia? a. nitrification b. ammonia assimilation c. nitrogen fixation d. nitrogen assimilation ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.e. Distinguish between Nitrosomonas and Nitrobacter in terms of the product of nitrification.

MSC: Remembering 16. Both Nitrosomonas and Nitrobacter have a key role in nitrification. Nitrosomonas produces __________, whereas Nitrobacter produces __________.

a. b. c. d.

ammonia; nitrite nitrite; nitrate nitrate; nitrite nitrite; ammonia

ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.e. Distinguish between Nitrosomonas and Nitrobacter in terms of the product of nitrification.

MSC: Analyzing 17. In the nitrogen cycle, one main method for ammonia entering is a. decomposition of organic material by invertebrates. b. from the atmosphere. c. through denitrification. d. by leghemoglobin.

ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.f. Recall the key elements of the nitrogen cycle.

MSC: Understanding

18. The nitrogen balance in the biosphere incorporates which of the following processes? a. nitrogen fixation, nitrogen assimilation, and nitrate reduction b. nitrogen oxidation and nitrogen reduction c. nitrogen fixation, nitrification, and nitrate reduction d. nitrogen oxidation and nitrate assimilation ANS: C DIF: Easy REF: 17.1 OBJ: 17.1.f. Recall the key elements of the nitrogen cycle.

MSC: Understanding

19. If plants and bacteria were unable to produce glutamate from ammonia, a possible outcome would be that plants would a. be able to produce more nucleotides. b. no longer be able to produce other amino acids. c. not be able to complete glycolysis. d. be able to produce more ATP. ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Applying 20. Which three enzymes mediate ammonia assimilation? a. glutamine synthase, glutamate synthetase, glutamate hydrogenase b. glutamine synthetase, glutamate synthase, glutamate dehydrogenase c. glutamine oxidase, glutamate reductase, glutamate dehydrogenase d. glutamine dehydrogenase, glutamate synthase, glutamate oxidase ANS: B DIF: Easy REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Remembering 21. Glutamine synthetase uses ammonia to covert glutamate into a. glutamine. b. nitrate. c.

-ketoglutarate. d. histidine.

ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Understanding 22. In the absence of ATP for glutamine synthetase to use, what would happen to the concentration of glutamine in the cell? a. increase b. decrease c. no change d. Not enough information is given.

ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Applying 23. Which of the following is the correct net reaction for the combined reaction of glutamine synthetase and glutamate synthase? a.

-ketoglutarate + NH4+ + ATP + NADH + H+ NAD+ + ADP + Pi + glutamate b. NAD+ + ADP + Pi + glutamate -ketoglutarate + NH4+ + ATP + NADH + H+ c.

-ketoglutarate + NH4+ + ATP + NADH + H+ NAD+ + ADP + Pi + glutamine + + d. glutamate + NH4+ + ATP + NADH + H NAD + ADP + Pi + -ketoglutarate ANS: A DIF: Medium REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Understanding 24. Given that glutamate dehydrogenase has a Km of 1 mM and dehydrogenase only operates best when a. there is a high concentration of nitrogen available. b. there is a low concentration of nitrogen available. c. operates regardless of nitrogen concentration. d. Not enough information is given.

G of +30 kJ/mol, glutamate

ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Applying 25. Adenylylation of Try397 regulates glutamine synthetase by a. lowering activation energy. b. inhibiting activity. c. increasing activation energy. d. increasing rate of reaction.

ANS: B DIF: Medium REF: 17.1 OBJ: 17.1.h. Recall the allosteric regulators of glutamine synthetase.

MSC: Applying 26. Aminotransferase reactions operate at G 0. What occurs when there is high substrate availability? a. Mostly reactants are made. b. Mostly products are made. c. Equal amount of products and reactants are made. d. This reaction is thermodynamically unfavorable.

ANS: B DIF: Easy REF: 17.1 OBJ: 17.1.i. Predict the products of an aminotransferase reaction.

MSC: Applying

27. What would the products be for the reaction below?

a.

-keto acid and glutamate b. oxaloacetate and glutamate c. pyruvate and glutamate d. histidine and glutamate ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.i. Predict the products of an aminotransferase reaction.

MSC: Applying 28. How can the body easily adjust the relative levels of some amino acids using aminotransferases? a. Add ATP to the cell to produce more amino acids. b. Use common intermediates to interconvert between amino acids. c. Phosphorylate the amino acids to prevent them from being used. d. Remove NADH from the cell to produce more amino acids.

ANS: B DIF: Difficult REF: 17.1 OBJ: 17.1.i. Predict the products of an aminotransferase reaction.

MSC: Analyzing 29. Aminotransferase reaction is an example of what kind of kinetics? a. ternary b. ping-pong c. cooperative d. reversible ANS: B DIF: Easy REF: 17.1 OBJ: 17.1.j. Identify the different forms of pyridoxal phosphate observed during an aminotransferase reaction. MSC: Remembering 30. In the overall reaction of aminotransferase, how many amino acids are produced? a. 1 b. 2 c. 3 d. 0 ANS: A DIF: Easy REF: 17.1 OBJ: 17.1.j. Identify the different forms of pyridoxal phosphate observed during an aminotransferase reaction. MSC: Understanding 31. How many different forms of pyridoxal phosphate are observed in the aminotransferase reaction? a. 7 b. 6 c. 5 d. 4

ANS: D DIF: Easy REF: 17.1 OBJ: 17.1.j. Identify the different forms of pyridoxal phosphate observed during an aminotransferase reaction. MSC: Understanding 32. Nitrogen balance is best described as when the daily intake of __________ equals the amount of __________ lost by excretion. a. ammonia; nitrogen b. nitrogen; nitrogen c. glucose; glucose d. nitrogen; ammonia ANS: B DIF: Easy OBJ: 17.2.a. Define nitrogen balance.

REF: 17.2 MSC: Remembering

33. A negative nitrogen balance in a person would be an indicator of a. accumulation of nitrogen in the body. b. a diet heavy in protein. c. starvation. d. overall good health.

ANS: C DIF: Easy OBJ: 17.2.a. Define nitrogen balance.

REF: 17.2 MSC: Applying

34. After food enters the stomach, gastrin triggers the release of __________ and secretion of __________. a. gastric juices; pepsinogen b. gastric juices; chyme c. chime; enteropeptidase d. secreton; enteropeptidase ANS: B DIF: Medium REF: 17.2 OBJ: 17.2.b. Distinguish between hormones released from the stomach and those released from the duodenum.

MSC: Remembering 35. Compare the function of pepsin with that of secretin. a. Pepsin cleaves trypsin, whereas secretin activates proteolytic zymogens. b. Pepsin activates trypsinogen, whereas secretin neutralizes pH back to 7. c. Pepsin denatures proteins, whereas secretin cleaves polypeptide bonds. d. Pepsin cleaves polypeptide bonds, whereas secretin neutralizes pH back to 7.

ANS: D DIF: Medium REF: 17.2 OBJ: 17.2.b. Distinguish between hormones released from the stomach and those released from the duodenum.

MSC: Analyzing 36. In the duodenum, enteropeptidase a. cleaves trypsinogen to form trypsin. b. cleaves chymotrypsinogen to form chymotrypsin. c. generates peptides and amino acids. d. neutralizes the pH of the duodenum to a pH of 7.

ANS: A DIF: Easy REF: 17.2 OBJ: 17.2.b. Distinguish between hormones released from the stomach and those released from the duodenum.

MSC: Applying

37. It is important that proteolytic enzymes in the lysosome are optimized to work at low pH because low pH a. enhances protein denaturing. b. deactivates cysteine proteases. c. makes it easier for ATP to be converted to ADP + Pi. d. enhances the degradation of ubiquitinated proteins.

ANS: A DIF: Difficult REF: 17.2 OBJ: 17.2.c. State the two pathways for degradation of cellular proteins in eukaryotes.

MSC: Analyzing 38. Eukaryotic proteasome selectively degrade which type of proteins? a. all proteins; they are not selective b. ubiquitinated proteins c. phosphorylated proteins d. ATP-dependent proteins ANS: B DIF: Easy REF: 17.2 OBJ: 17.2.c. State the two pathways for degradation of cellular proteins in eukaryotes.

MSC: Remembering 39. What specific characteristic must a target protein have to be recognized by an ubiquitinating protein? a. phosphorylated residue b. N terminus c. C terminus d.

-helix ANS: A DIF: Easy REF: 17.2 OBJ: 17.2.c. State the two pathways for degradation of cellular proteins in eukaryotes.

MSC: Understanding 40. The two mechanisms to regulate protein ubiquitination are biochemical changes to a. target proteins and E1 ligases. b. E1 and E2 ligases. c. target proteins and E3 ligases. d. the E2-ubiquitin-E3 complex.

ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.c. State the two pathways for degradation of cellular proteins in eukaryotes.

MSC: Remembering 41. Cells cannot store amino acids that accumulate as a result of protein degradation. The carbon skeletons that remain a. enter the urea cycle. b. are used to produce new amino acids. c. enter the citrate cycle. d. are used to produce DNA and RNA. ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.e. Summarize the possible fates of the carbon atoms from amino acid catabolism.

MSC: Remembering 42. In the production of urea, the carbon atom comes from a. water.

b. carbamoyl phosphate. c. aspartate. d. the citrate cycle.

ANS: D DIF: Easy REF: 17.2 OBJ: 17.2.e. Summarize the possible fates of the carbon atoms from amino acid catabolism.

MSC: Applying 43. What nitrogen source is used to produce carbamoyl phosphate? a. alanine b. urea c. ammonia d. glutamine ANS: A DIF: Easy REF: 17.2 OBJ: 17.2.f. Recall the routes by which the nitrogen from amino acids is converted into carbamoyl phosphate or aspartate.

MSC: Understanding 44. When amino acids from dietary proteins enter a cell, how are they able to enter the urea cycle? a. through conversion to glutamine b. through conversion to aspartate c. by degrading down to ammonia d. by getting phosphorylated ANS: B DIF: Easy REF: 17.2 OBJ: 17.2.f. Recall the routes by which the nitrogen from amino acids is converted into carbamoyl phosphate or aspartate.

MSC: Applying 45. The urea cycle’s function is to __________ the body of an organism. a. remove excess sugar from b. remove excess water-soluble vitamins from c. remove excess nitrogen from d. add additional nitrogen to ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Applying 46. Which of the following is the net reaction of the urea cycle? a. Urea + Fumerate + 2 ADP + 2Pi + AMP + PPi NH+ + HCO3- + aspartate + 3ATP b. NH+ + HCO3 + aspartate + 3ATP urea + fumerate + 2 ADP + 2Pi + AMP + PPi c. NH+ + HCO3 + fumerate + 3ATP urea + aspartate + 2 ADP + 2Pi + AMP + PPi d. NH+ + HCO3 + aspartate + 2 ADP + 2Pi + AMP + PPi urea + fumerate + 3ATP ANS: B DIF: Medium REF: 17.2 OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Understanding 47. Which of the following is the key regulated enzyme in urea synthesis? a. carbamoyl phosphate synthetase I b. glutamate dehydrogenase c. arginase d. argininosuccinase ANS: A

DIF: Easy

REF: 17.2

OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Understanding 48. What is a possible outcome to the urea cycle if the cell is unable to produce enough aspartate? a. Flux would be accelerated through the cycle. b. There would be a buildup of citrulline. c. There would be a buildup of urea. d. The cycle would maintain equilibrium.

ANS: B DIF: Easy REF: 17.2 OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Applying 49. Which intermediate is shared by the urea cycle and the citric acid cycle? a. citrulline b. argininosuccinate c. aspartate d. malate ANS: B DIF: Easy REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Understanding 50. Which intermediates of the Krebs bicycle would be found in the cytosol? a. fumerate and argininosuccinate b. citrulline and malate c. arginine and oxaloacetate d. urea and ammonia ANS: A DIF: Easy REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Understanding 51. The recycling of fumerate helps offset the energy cost of the urea cycle because fumerate helps generate a. arginine to produce 2 ATP. b. citrulline to produce NADPH, which can generate 3 ATP. c. oxaloacetate to produce NADH, which can generate 2.5 ATP. d. urea, which will make more ATP. ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Applying 52. If there was a loss of efficiency in the urea cycle, there would be a buildup of a. fumarate. b. urea. c. glutamine. d. glucose.

ANS: C DIF: Easy REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Applying

53. A no-protein diet with high doses of L-arginine helps patients with argininosuccinase deficiency because it __________ the concentration of __________. a. increases; fumerate that is metabolized by the citric acid cycle to lower ammonia levels b. increases; ammonia in the diet to keep them regulated c. increases; ornithine that is needed to maintain flux through the urea cycle d. decreases; citrulline to prevent ammonia toxicity ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Analyzing 54. Alanine, cysteine, glycine, and serine are all considered __________ amino acids. a. glucogenic b. ketogenic c. nonessential d. urea ANS: A DIF: Easy REF: 17.2 OBJ: 17.2.i. Classify amino acids as exclusively glucogenic, exclusively ketogenic, or both glucogenic and ketogenic.

MSC: Understanding 55. Glucogenic amino acids give rise to which molecule? a. pyruvate b. urea c. ketone bodies d. glucose ANS: A DIF: Medium REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Understanding 56. Group 2 pathways can be correctly described as pathways that a. degrade glucogenic amino acids to generate -ketoglutarate. b. convert phenylalanine to tyrosine. c. degrade alanine. d. convert fumerate to oxaloacetate.

ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.j. Differentiate among group 1, group 2, and group 3 amino acid degradation pathways.

MSC: Understanding 57. Using the figure below, determine which of the following is NOT a final product from group 1 amino acid degradation.

a. b. c. d.

glycine pyruvate acetoacetyl-CoA acetyl-CoA

ANS: A DIF: Medium REF: 17.2 OBJ: 17.2.j. Differentiate among group 1, group 2, and group 3 amino acid degradation pathways.

MSC: Understanding 58. If no NAD+ was available, the group 2 amino acid degradation pathway would experience a

a. b. c. d.

buildup of urea. buildup of glutamate. depletion of proline. depletion of histidine.

ANS: B DIF: Medium REF: 17.2 OBJ: 17.2.j. Differentiate among group 1, group 2, and group 3 amino acid degradation pathways.

MSC: Applying 59. Alkaptonuria is a disease coming from a deficiency in which pathway? a. group 1 b. group 2 c. group 3 d. urea ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.k. Explain the genetic diseases alkaptonuria and phenylketonuria.

MSC: Applying 60. A person who has alkaptonuria is easily diagnosed from his or her black urine. What causes the black color? a. oxidation of phenylalanine b. oxidation of homogentisate c. reduction of acetoacetyl-CoA d. dehydration ANS: B DIF: Medium REF: 17.2 OBJ: 17.2.k. Explain the genetic diseases alkaptonuria and phenylketonuria.

MSC: Understanding

61. A person who has phenylketonuria will have a buildup of which molecule in the cell? a. tyrosine b. phenylalanine c. pyruvate d. alanine ANS: B DIF: Difficult REF: 17.2 OBJ: 17.2.k. Explain the genetic diseases alkaptonuria and phenylketonuria.

MSC: Applying 62. A person who has phenylketonuria must avoid which food additive? a. protein b. methanol c. aspartame d. phenylalanine ANS: C DIF: Medium REF: 17.2 OBJ: 17.2.k. Explain the genetic diseases alkaptonuria and phenylketonuria.

MSC: Remembering 63. Aspartate is a(n) __________ amino acid, so if a person had a diet that contained no aspartate, __________. a. essential; death would occur b. nonessential; aspartate could be synthesized from other intermediates c. essential; aspartate could be synthesized from other intermediates d. nonessential; death would occur ANS: B DIF: Medium REF: 17.3 OBJ: 17.3.b. Classify the 20 amino acids as essential or nonessential for humans.

MSC: Applying 64. Arginine, leucine, and lysine are all essential amino acids. This means that they are a. only available from a person’s diet. b. produced from other intermediates. c. not needed for a body to function. d. the main intermediates to the urea cycle.

ANS: A DIF: Medium REF: 17.3 OBJ: 17.3.b. Classify the 20 amino acids as essential or nonessential for humans.

MSC: Applying 65. A possible outcome if E. coli was depleted in NADPH would be a. buildup of lysine. b. depletion of asparagine. c. buildup of aspartate. d. depletion of methionine.

ANS: D DIF: Difficult REF: 17.3 OBJ: 17.3.c. Summarize the synthesis of amino acids from oxaloacetate and pyruvate in E. coli.

MSC: Applying 66. The shikimate pathway can be defined as the pathway that involves the a. condensation of phosphoenolpyruvate and erythrose-4-phosphate. b. synthesis of essential amino acids from pyruvate.

c. synthesis of essential amino acids from oxaloacetate. d. condensation of oxaloacetate and shikimate.

ANS: A DIF: Medium OBJ: 17.3.d. Define shikimate pathway.

REF: 17.3 MSC: Remembering

67. What is the mechanism by which Roundup works? a. Glyphosate is a competitive inhibitor to plant EPSP synthase. b. Urea is a competitive inhibitor to plant chorismate synthase. c. Glyphosate is an activator to plant EPSP synthase. d. Anthranilate is an activator to chorismate synthase.

ANS: A DIF: Medium REF: 17.3 OBJ: 17.3.e. Explain the mechanism by which glyphosate inhibits the production of the aromatic amino acids in plants.

MSC: Understanding 68. What amino acid serves as the precursor to heme? a. histidine b. asparagine c. glycine d. glutamine ANS: C DIF: Easy REF: 17.4 OBJ: 17.4.a. List the starting reactants for the heme biosynthetic pathway.

MSC: Understanding 69. Diseases affecting heme biosynthesis as a result of deficiencies in the heme biosynthetic pathway are called a. porphyrias. b. albinism. c. shikimate. d. alkaptonuria.

ANS: A DIF: Easy REF: 17.4 OBJ: 17.4.b. Compare and contrast the known porphyrias.

MSC: Remembering

70. Jaundice is indicative of what process working inefficiently? a. heme synthesis b. bilirubin removal from blood c. urea synthesis d. amino acid degradation ANS: B DIF: Easy REF: 17.4 OBJ: 17.4.c. Identify the key enzymes, intermediates, and products of heme catabolism.

MSC: Understanding 71. Which metabolic process is the cause of albinism? a. inefficient production of dopamine b. the enzyme tyrosinase working inefficiently c. overproduction of NADPH d. low levels of ATP available in the cell ANS: B DIF: Difficult MSC: Understanding

REF: 17.4

72. A person unable to produce new melanocytes is likely to have

OBJ: 17.4.e. Define albinism.

a. b. c. d.

black hair. red hair. gray hair. hair loss.

ANS: C DIF: Easy REF: 17.4 OBJ: 17.4.d. Summarize the synthesis of the catecholamines.

MSC: Applying

73. Which of the following is the reaction for nitric oxide synthase? a. citrulline + NO + 1.5 NADP+ L-arginine + 1.5 NADPH + H+ + 2O2 b. L-arginine + 1.5 NADPH + H+ + 2O2 citrulline + NO + 1.5 NADP+ c. L-arginine + 1.5 NADPH + H+ + 2O2 dopamine + NO + 1.5 NADP+ d. L-arginine + 1.5 NADP+ + H+ + 2O2 citrulline + NO + 1.5 NADPH ANS: D DIF: Difficult REF: 17.4 OBJ: 17.4.f. State the reaction for nitric oxide synthase.

MSC: Understanding

74. What molecule signals the endothelial cell to produce NO? a. dopamine b. phosphate c. acetylcholine d. citrulline ANS: C DIF: Medium REF: 17.4 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Remembering 75. Why do angina patients carry nitroglycerine with them? a. as a rapid source of NO for blood vessel dilation b. as a source of ammonia for muscle relaxation c. to inhibit acetylcholine release from neurons d. to inhibit cGMP phosphodiesterase ANS: A DIF: Easy REF: 17.4 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Applying SHORT ANSWER 1. What purpose does nitrogen fixation and assimilation serve in the biosphere?

ANS: Nitrogen fixation takes place in bacteria and is the primary process by which atmospheric nitrogen gas is converted to ammonium and nitrogen oxides in the biosphere. Nitrogen assimilation is the process by which plants and bacteria incorporate nitrogen into organic compounds.

DIF: Medium REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Applying 2. What is the difference between nitrogen fixation and nitrogen assimilation?

ANS:

Nitrogen fixation is carried out by bacteria in both soil and aquatic environments. Leguminous plants incorporate nitrogen from bacterially synthesized amino acids into their own amino acids.

Nonleguminous plants incorporate ammonia produced by nitrogen fixing soil bacteria directly into amino acids by nitrogen assimilation.

DIF: Medium REF: 17.1 OBJ: 17.1.a. State the net reaction of nitrogen fixation in bacteria.

MSC: Understanding 3. What are the six steps of the nitrogenase reaction?

ANS: (1) Exchange of 2 ADP for 2 ATP with reduction of 4 Fe-4S redox center; (2) reduced Fe protein forms a complex with the oxidized MoFe protein; (3) ATP is hydrolyzed and electron is transferred from the 4 Fe-4 S cluster to the P cluster in the MoFe protein; (4) ADP-bound Fe protein dissociates from the FeMo cofactor, which releases an electron to reduce N2; (5) a second electron transfer to N2 the N2H2 is generated; (6) oxidized MoFe protein is recycled to obtain another electron transfer to the MoFe cofactor to complete the reduction of N2.

DIF: Difficult REF: 17.1 OBJ: 17.1.d. State the six steps of the nitrogenase reaction.

MSC: Remembering

4. Using the figure below, illustrate the two final products and identify the amino group on glutamine that gets transferred.

ANS:

DIF: Medium REF: 17.1 OBJ: 17.1.g. Name the three enzymes that mediate ammonia assimilation.

MSC: Applying 5. What are the allosteric regulators of glutamine synthetase?

ANS: Glucosamine-6-phosphate, carbamoyl phosphate, AMP cytidine triphosphate, histidine, tryptophan, alanine, glycine, and serine

DIF: Easy REF: 17.1 OBJ: 17.1.h. Recall the allosteric regulators of glutamine synthetase.

MSC: Remembering 6. For the figure below, summarize the interdependent regulation of glutamine synthetase and glutamine synthetase adenylyltransferase.

ANS: Covalent modification of glutamine synthetase by adenylylation at Tyr397 inhibits enzyme activity. Both adenylylation and deadenylylation of glutamine synthetase are mediated by the enzyme glutamine synthetase adenylyltransferase. In turn, the enzyme activity is controlled by uridylylation of Try51 in the PII regulatory subunit by uridylyltransferase.

DIF: Difficult REF: 17.1 OBJ: 17.1.h. Recall the allosteric regulators of glutamine synthetase.

MSC: Evaluating 7. Distinguish between the first and second stages of the aminotransferase reaction.

ANS: In the first stage of the reaction the -amino group of the amino acid substrate is transferred to the enzyme-bound PLP group to form pyridoxamine phosphate and an -keto acid. In the second stage this nitrogen is transferred to an incoming -keto acid to form the amino acid product.

DIF: Difficult REF: 17.1 OBJ: 17.1.j. Identify the different forms of pyridoxal phosphate observed during an aminotransferase reaction. MSC: Analyzing 8. Differentiate between proteins being degraded by an ATP-dependent process compared with the ATP-independent process.

ANS: An ATP-independent process degrades the proteins inside lysosomes. An ATP-dependent process degrades proteins containing a polymer of ubiquitin protein and occurs in the proteasome.

DIF: Difficult

REF: 17.2

OBJ: 17.2.c. State the two pathways for degradation of cellular proteins in eukaryotes.

MSC: Analyzing 9. Outline the process of protein degradation by the ubiquitin proteasome pathway.

ANS: The ubiquitin proteasome pathway takes target proteins and covalently binds ubiquitin subunits to lysine residues. Binding of the polyubiquitinated target protein to the 19S proteasomal complex initiates protein unfolding and hydrolysis of the ubiquitin subunits. The unfolded protein is then degraded into oligopeptides.

DIF: Easy REF: 17.2 OBJ: 17.2.d. Outline the process of protein degradation by the ubiquitin proteasome.

MSC: Analyzing 10. During vigorous anaerobic exercise, glycogen degradation leads to the buildup of pyruvate. How does the alanine-glucose cycle prevent a toxic buildup?

ANS: The alanine-glucose cycle removes excess nitrogen from muscle cells, using alanine as the carrier.

The alanine aminotransferase reaction in liver cells removes the nitrogen from alanine to generate pyruvate and glutamate. The pyruvate is then used to produce glucose via gluconeogenesis, and the glucose is exported back to muscle cells, where it can be used as a source of energy for muscle contraction or converted to glycogen DIF: Difficult REF: 17.2 OBJ: 17.2.f. Recall the routes by which the nitrogen from amino acids is converted into carbamoyl phosphate or aspartate.

MSC: Evaluating 11. How is carbamoyl phosphate synthetase I allosterically regulated in the urea cycle?

ANS: This key reaction in urea synthesis is allosterically regulated by N-acetylglutamate, a metabolite that signals high levels of glutamate in the cell. The enzyme N-acetylglutamate synthase catalyzes the formation of N-acetylglutamate from glutamate and acetyl-CoA and is activated by arginine, a urea cycle intermediate. The net result is that glutamate and arginine stimulate flux through the urea cycle by increasing the rate of carbamoyl phosphate synthesis.

DIF: Difficult REF: 17.2 OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Analyzing 12. Why does carbamoyl phosphate synthetase I require two equivalents of ATP? ANS: The reaction mechanism for carbamoyl phosphate synthetase has three steps. In the first step bicarbonate is phosphorylated by ATP to form carboxyphosphate, which is then attacked by ammonia in the second step to release the phosphate and generate carbamate. In the final step, a second ATP molecule is used to phosphorylate carbamate to form the produce of the reaction, carbamoyl phosphate.

DIF: Medium REF: 17.2 OBJ: 17.2.g. State the net reaction and key enzymes of the urea cycle.

MSC: Applying

13. How can individuals with urea cycle deficiencies be treated with sodium phenylbutyrate?

ANS: One way to remove excess nitrogen in individuals with urea cycle deficiencies is to treat them with phenylbutyrate. Phenylbutyrate is metabolized to the compound phenylacetylglutamine by the enzyme glutamine N-acetyltransferase and is excreted in the urine. This results in increased synthesis of glutamine from glutamate and ammonia by the glutamate synthase reaction, thereby lowering ammonia levels in the blood.

DIF: Medium REF: 17.2 OBJ: 17.2.h. Explain the Krebs bicycle that connects the citrate cycle and the urea cycle.

MSC: Evaluating 14. Classify the 20 amino acids as glucogenic, ketogenic, or both.

ANS:

DIF: Easy REF: 17.2 OBJ: 17.2.i. Classify amino acids as exclusively glucogenic, exclusively ketogenic, or both glucogenic and ketogenic.

MSC: Remembering 15. The carbon skeletons of all 20 amino acids side chains are derived from just seven metabolic intermediates and their associated pathways. What are those intermediates and pathways?

ANS: Three glycolytic pathway intermediates: 3-phosphoglycerate, phosphoenolpyruvate, pyruvate. Two pentose phosphate pathway intermediates: ribose-5-phosphate and erythose-4-phosphate. Two citrate cycle intermediate: -ketoglutarate and oxaloacetate.

DIF: Medium

REF: 17.3

OBJ: 17.3.a. Name the seven metabolic intermediates and their associated pathways that provide the carbon skeletons for all 20 amino acids. MSC: Applying 16. How is the synthetic pathway for nonessential amino acids different than for essential amino acids?

ANS: The nonessential amino acids have carbon skeletons that are similar to those of common metabolic precursors and require only one or a few reaction steps to synthesize. Essential amino acids have complex structures that require many reaction steps to synthesize, which is why humans must gain them from outside sources.

DIF: Easy REF: 17.3 OBJ: 17.3.b. Classify the 20 amino acids as essential or nonessential for humans.

MSC: Understanding 17. Using the figure below, summarize the synthesis of amino acids from oxaloacetate and pyruvate in E. coli.

ANS: Nine amino acids are synthesized from oxaloacetate and pyruvate. The oxaloacetate and pyruvate pathways are linked by -ketobutyrate, which is shared product in the two pathways. Essential amino acids in humans are shown in bold in Figure 17.49 in the text.

DIF: Difficult REF: 17.3 OBJ: 17.3.c. Summarize the synthesis of amino acids from oxaloacetate and pyruvate in E. coli.

MSC: Analyzing 18. How are Roundup Ready soybeans resistant to the herbicide?

ANS: Glyphosate-resistant crops were developed so that farmers could spray their crops with glyphosate throughout the growing season to kill weeds that compete with crop plants for nutrients and water.

By reducing weed growth through aerial spraying of glyphosate, it is possible to achieve significantly higher crop yield with improved quality of the crops.

DIF: Medium REF: 17.3 MSC: Understanding

OBJ: 17.3.d. Define shikimate pathway.

19. Compare and contrast the known porphyrias.

ANS: See Figure 17.55 in the text. Some of the porphyrias are caused by defects in liver enzymes, whereas others are caused by enzyme defects in erythrocyte precursor cells.

DIF: Medium REF: 17.3 OBJ: 17.4.b. Compare and contrast the known porphyrias.

MSC: Analyzing

20. Summarize the synthesis of the catecholamines.

ANS: Tyrosine is the metabolons precursor to the catecholamines dopamine, norepinephrine, and epinephrine. Tetrahydrobiopterin is a redox factor that oxidizes tyrosine to L-dopa. L-Dopa is then decarboxylated to produce dopamine, which can be converted to norepinephrine and epinephrine.

DIF: Medium REF: 17.3 OBJ: 17.4.d. Summarize the synthesis of the catecholamines.

MSC: Evaluating

21. Summarize the mechanism for control of endothelial nitric oxide.

ANS: Calcium-calmodulin binds to the endothelial nitric oxide synthase enzyme in response to receptor-mediated signaling through G protein–coupled receptors. See Figure 17.64 in the text.

DIF: Medium REF: 17.3 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Evaluating 22. What are the key enzymes, intermediates, and products of heme catalysis?

ANS:

As shown in Figure 17.54 in the text, -aminolevulinate synthase catalyzes a reaction combining glycine and succinyl-CoA to produce -aminolevulinate. This is then exported to the cytosol, where it condenses with another molecule of -aminolevulinate to generate porphobilinogen. In the subsequent reactions, four molecules of porphobilinogen are dominated and combined to synthesize the heme precursor uroporphyrinogen III. In the next two reactions, six CO2 are removed from uroporphyrinogen III to form protoporphyrinogen to protoporphyrin, and the enzymes ferrochelatase incorporates Fe+2 into the heme ring.

DIF: Medium REF: 17.4 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Remembering 23. Explain the mechanism by which glyphosate inhibits the production of aromatic amino acids in plants.

ANS: Glyphosate is a competitive inhibitor of the enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSP), which is required to convert shikimate-3-phosphate to 5-enolpyruvylshikimate-3-phosphate in one of the final three steps leading to chorismate. When a plant is sprayed with glyphosate, EPSP synthase activity is inhibited, leading to insufficient levels of chorismate. The plants are then unable to synthesize tryptophan, tyrosine, and phenylalanine and die.

DIF: Difficult REF: 17.3 OBJ: 17.3.e. Explain the mechanism by which glyphosate inhibits the production of the aromatic amino acids in plants.

MSC: Understanding 24. How does Viagra interact with the mechanism of endothelial nitric oxide synthase?

ANS: As illustrated in Figure 17.64 in the text, sildenafil (Viagra) maintains the vasodilated state in erectile tissue by inhibiting the activity of cGMP phosphodiesterase, which has the net result of increasing intracellular cGMP levels by delaying its degradation.

DIF: Difficult REF: 17.4 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Understanding 25. Summarize the role of the glycine in the biosynthesis of heme, tyrosine for epinephrine and pheomelanins, and arginine for nitric oxide.

ANS: Glycine is required for heme biosynthesis in the first reaction of the pathway, which is catalyzed by the enzyme -aminolevulinate synthase. Glycine provides all four nitrogen atoms to the heme ring. Tyrosine is the amino acid precursor in the synthesis of epinephrine and in the synthesis of pheomelanin. Cysteine is also required for pheomelanin synthesis. Arginine is the amino acid substrate for nitric oxide production by the enzyme nitric oxide synthase.

DIF: Difficult REF: 17.4 OBJ: 17.4.g. Summarize the mechanism for control of endothelial nitric oxide synthase.

MSC: Evaluating

Chapter 18: Nucleotide Metabolism MULTIPLE CHOICE 1. Which of the following is NOT a general role of nucleotides in cells? a. energy conversion reactions b. signal transduction pathways c. genetic information storage d. proteolysis ANS: D DIF: Easy REF: 18.1 OBJ: 18.1.a. List the major roles of nucleotides.

MSC: Remembering

2. Which of the following is a coenzyme that is derived from ATP? a. coenzyme Q b. FAD c. heme d. Fe4-S4 cluster ANS: B DIF: Easy REF: 18.1 OBJ: 18.1.a. List the major roles of nucleotides.

MSC: Understanding

3. The molecule below is a precursor to the formation of which of the following second messengers?

a. b. c. d.

ADP cAMP NAD+ PKA

ANS: B DIF: Medium REF: 18.1 OBJ: 18.1.a. List the major roles of nucleotides.

MSC: Understanding

4. Which of the following is synthesized by a complex that requires an electrochemical gradient to function? a. ATP b. cAMP c. GTP d. ribose ANS: A DIF: Easy REF: 18.1 OBJ: 18.1.a. List the major roles of nucleotides.

MSC: Understanding

5. Which of the following is a benefit of nucleotide salvage pathways compared with de novo synthesis?

a. b. c. d.

increased variety of nucleotides produced increased half-life of mRNA reduced energy expenditure decreased regulation of nucleotide homeostasis

ANS: C DIF: Easy REF: 18.1 OBJ: 18.1.b. Define nucleotide salvage pathways.

MSC: Understanding

6. The conversion of ribose-1-phosphate to ATP via the salvage pathway would require the activity of several enzymes. Choose the answer that lists them in the order that they would act in this pathway. a. PRPP synthetase; phosphopentomutase; kinase; kinase; phosphoriboxyl transferase b. PRPP synthetase; phosphoriboxyl transferase; phosphopentomutase; kinase; kinase c. phosphopentomutase; PRPP synthetase; phosphoriboxyl transferase; kinase; kinase d. phosphopentomutase; phosphoriboxyl transferase; kinase; PRPP synthetase; kinase ANS: C DIF: Difficult REF: 18.1 OBJ: 18.1.b. Define nucleotide salvage pathways.

MSC: Analyzing

7. To synthesize nucleotide monophosphates from oligonucleotides in a test tube, which enzyme must be included in the reaction mixture? a. phosphodiesterases b. nucleotidases c. kinases d. phosphopentomutase ANS: A DIF: Medium REF: 18.1 OBJ: 18.1.b. Define nucleotide salvage pathways.

MSC: Applying

8. In purines, __________ nitrogen atoms and __________ carbon atoms originate from glycine. a. 0; 2 b. 1; 1 c. 2; 1 d. 1; 2 ANS: D DIF: Medium REF: 18.2 OBJ: 18.2.a. Identify the origin of nitrogen and carbon atoms in the purine ring system.

MSC: Remembering 9. The nitrogen atoms of a purine originate from all of the following amino acids EXCEPT a. glycine. b. aspartate. c. cysteine. d. glutamine.

ANS: C DIF: Medium REF: 18.2 OBJ: 18.2.a. Identify the origin of nitrogen and carbon atoms in the purine ring system.

MSC: Understanding 10. The carbon atoms of a purine originate from glycine and a. N10-formyl-THF. b. aspartate. c. glycinamide. d. glutamate.

ANS: A

DIF: Easy

REF: 18.2

OBJ: 18.2.a. Identify the origin of nitrogen and carbon atoms in the purine ring system.

MSC: Remembering 11. Which nitrogen originates from aspartate?

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 18.2 OBJ: 18.2.a. Identify the origin of nitrogen and carbon atoms in the purine ring system.

MSC: Remembering 12. If HCO3 that is radioactively labeled with 13C is available, which carbon atom in the molecule below would ultimately be expected to be radioactive?

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 18.2 OBJ: 18.2.a. Identify the origin of nitrogen and carbon atoms in the purine ring system.

MSC: Applying 13. Purine biosynthesis takes place in two stages. The first stage begins with ribose-5-phosphate and ends with a. 5-phosphoriboxylamine. b. 5-aminoimidazole ribonucleotide. c. inosine- -monophosphate. d. 5-aminoimidazole-4-carboxamide ribonucleotide.

ANS: B DIF: Easy REF: 18.2 OBJ: 18.2.b. Summarize the two stages of IMP biosynthesis.

MSC: Understanding

14. A product of the first stage of purine biosynthesis is __________, whereas __________ is a by-product of the second stage. a. fumarate; glycine b. glutamine; glutamate c. fumarate; glutamate d. glutamate; fumarate ANS: D DIF: Difficult REF: 18.2 OBJ: 18.2.b. Summarize the two stages of IMP biosynthesis.

MSC: Remembering

15. The transformation of ribose-5-phosphate to AIR in the first stage of purine biosynthesis in E. coli consumes the equivalent of 5 ATP. The second stage consumes a. an additional 5 ATP. b. more than 5 ATP. c. less than 5 ATP and generates 1 ATP. d. less than 5 ATP. ANS: D DIF: Medium REF: 18.2 OBJ: 18.2.b. Summarize the two stages of IMP biosynthesis.

MSC: Understanding

16. In analyzing the intermediates formed during the conversion of IMP to GMP and AMP, which molecule would one expect to find in the conversion to GMP but NOT in the conversion to AMP? a. xanthosine- -monophosphate b. adenylosuccinate c. 5-phosphoriboxylamine d. 5-aminoimidazole ribonucleotide ANS: A DIF: Difficult REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

17. A mutation in the gene encoding which of the following enzymes would affect the synthesis of both AMP and GMP? a. adenylosuccinate synthetase b. PRPP synthetase c. IMP dehydrogenase d. GMP synthase ANS: B DIF: Medium REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

18. Analysis of AMP and GMP synthesized in E. coli grown in medium containing 15N-labeled aspartate would show that a. AMP contained twice as much 15N than GMP. b. GMP contained twice as much 15N than AMP. c. AMP contained three times as much 15N than GMP. d. they contain the same levels of 15N. ANS: A DIF: Difficult REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Analyzing

19. A person wishes to determine the role of PRPP synthetase in a newly discovered organism. He or she decides that a good way to do this would be to see what happens when PRPP synthetase is inhibited. Which of the following could be added to a cell from this organism to inhibit PRPP synthetase? a. GDP b. AMP c. ATP d. GTP ANS: A DIF: Medium REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

20. Analysis of enzyme activities in a cell in the absence and presence of AMP and GMP is completed.

Which enzyme would show lower activity when AMP is added but not when GMP is added? a. glutamine-PRPP aminotransferase b. adenylosuccinate synthase c. IMP dehydrogenase d. PRPP synthetase ANS: B DIF: Difficult REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

21. Place the steps converting GMP to uric acid in the correct order.

A. Conversion to guanine B. Conversion to guanosine C. Conversion to xanthine D. Conversion to uric acid a. A; C; B; D b. A; B; C; D c. B; C; A; D d. B; A; C; D ANS: D DIF: Difficult REF: 18.2 OBJ: 18.2.e. Outline the biosynthesis of uric acid.

MSC: Analyzing

22. Which of the following is an intermediate in the conversion of AMP to uric acid but NOT an intermediate in the conversion of GMP to uric acid?

a. b. c. d.

A B C D

ANS: B DIF: Difficult REF: 18.2 OBJ: 18.2.e. Outline the biosynthesis of uric acid.

MSC: Understanding

23. A person is carrying out in vitro synthesis of uric acid from GMP. He or she wants to include all substrates and enzymes necessary. All EXCEPT __________ should be included in the reaction mixture.

a. b. c. d.

adenosine deaminase purine nucleoside phosphorylase guanine deaminase xanthine oxidase

ANS: A DIF: Easy REF: 18.2 OBJ: 18.2.e. Outline the biosynthesis of uric acid.

MSC: Applying

24. If GMP radiolabeled at the nitrogen atom indicated by the * were metabolized to uric acid, which of the following molecules along the pathway would also be radioactive?

a. b. c. d.

uric acid guanine NH4+ xanthine

ANS: C DIF: Difficult REF: 18.2 OBJ: 18.2.e. Outline the biosynthesis of uric acid.

MSC: Analyzing

25. Uric acid is processed to allantoic acid, which is then secreted. In which of the following organisms does this occur? a. insects b. bony fish c. marine invertebrates d. amphibians ANS: B DIF: Easy REF: 18.2 OBJ: 18.2.f. Identify the fates of uric acid in various organisms.

MSC: Remembering 26. Which of the following organisms would generate this compound?

a. b. c. d.

nonprimate mammals birds cartilaginous fish primates

ANS: C DIF: Medium REF: 18.2 OBJ: 18.2.f. Identify the fates of uric acid in various organisms.

MSC: Understanding 27. Marine invertebrates express enzymes that allow for the conversion of uric acid to NH4+. What is the correct order of the action of enzymes in this pathway?

1. Urate oxidase 2. Allantoicase 3. Urease 4. Allantoinase a. 2; 3; 4; 1 b. 1; 2; 4; 3 c. 3; 4; 2; 1 d. 1; 4; 2; 3 ANS: D DIF: Difficult REF: 18.2 OBJ: 18.2.f. Identify the fates of uric acid in various organisms.

MSC: Analyzing 28. Nonprimate mammals convert uric acid to allantoin. This reaction, catalyzed by urate oxidase, also generates which of the following products? a. H2O b. H2O2 c. O2 d. NH4+ ANS: B DIF: Difficult REF: 18.2 OBJ: 18.2.f. Identify the fates of uric acid in various organisms.

MSC: Remembering 29. Samples from a bird, reptile, amphibian, and primate were analyzed by Western blotting for the expression of allantoinase, the enzyme that converts allantoin to allantoic acid. Unfortunately the researcher forgot the order that the samples were loaded into the gel. Luckily, only a single sample indicated allantoinase. Which sample contained allantoinase? a. bird b. reptile c. amphibian d. primate ANS: C DIF: Medium REF: 18.2 OBJ: 18.2.f. Identify the fates of uric acid in various organisms.

MSC: Applying 30. An enzyme panel analysis of a patient reveals a lack of __________, which is an indication of Lesch-Nyhan syndrome. a. PRPP synthetase b. adenosine deaminase c. HGPRT d. xanthine oxidase ANS: C DIF: Easy REF: 18.2 OBJ: 18.2.g. Name the deficient enzymes in Lesch-Nyhan syndrome and severe combined immunodeficiency. MSC: Applying 31. The conversion of hypoxanthine to IMP is catalyzed by __________, which is deficient in __________. a. HGPRT; Lesch-Nyhan syndrome

b. adenosine deaminase; ADA-SCID c. xanthine oxidase; Lesch-Nyhan syndrome d. purine nucleoside phosphorylase; ADA-SCID ANS: A DIF: Easy REF: 18.2 OBJ: 18.2.g. Name the deficient enzymes in Lesch-Nyhan syndrome and severe combined immunodeficiency. MSC: Remembering 32. The possibility of ADA-SCID is indicated by __________ than normal activity of __________. a. lower; ribonucleotide reductase b. higher; adenosine deaminase c. lower; HGPRT d. higher; xanthine oxidase ANS: A DIF: Difficult REF: 18.2 OBJ: 18.2.g. Name the deficient enzymes in Lesch-Nyhan syndrome and severe combined immunodeficiency. MSC: Analyzing 33. The conversion of adenosine to inosine is catalyzed by __________, which is deficient in __________. a. HGPRT; Lesch-Nyhan syndrome b. adenosine deaminase; ADA-SCID c. xanthine oxidase; Lesch-Nyhan syndrome d. purine nucleoside phosphorylase; ADA-SCID ANS: B DIF: Easy REF: 18.2 OBJ: 18.2.g. Name the deficient enzymes in Lesch-Nyhan syndrome and severe combined immunodeficiency. MSC: Remembering 34. Aspartate contains four carbons. If all are radioactively labeled, how many carbons of UMP will be radioactively labeled? a. 0 b. 2 c. 3 d. 4 ANS: C DIF: Difficult REF: 18.2 OBJ: 18.3.a. Identify the origin of nitrogen and carbon atoms in the pyrimidine ring system.

MSC: Applying 35. A nitrogen of a pyrimidine ring arises from which amino acid? a. aspartate b. asparagine c. glycine d. alanine ANS: A DIF: Easy REF: 18.3 OBJ: 18.3.a. Identify the origin of nitrogen and carbon atoms in the pyrimidine ring system.

MSC: Remembering 36. Which of the following is the precursor of the indicated carbon atom in a pyrimidine ring?

a. b. c. d.

aspartate glycine carbamoyl phosphate orotate

ANS: C DIF: Medium REF: 18.3 OBJ: 18.3.a. Identify the origin of nitrogen and carbon atoms in the pyrimidine ring system.

MSC: Understanding 37. How many of the nitrogens in orotidine- -monophosphate arise from glutamine? a. 0 b. 1 c. 2 d. 3 ANS: B DIF: Easy REF: 18.3 OBJ: 18.3.a. Identify the origin of nitrogen and carbon atoms in the pyrimidine ring system.

MSC: Understanding 38. During the biosynthesis of UMP from carbamoyl phosphate and aspartate, dihydroorotate is converted to which of the following compounds? a. carbamoyl aspartate b. orotate c. orotidine- -monophosphate d. quinone ANS: B DIF: Medium REF: 18.3 OBJ: 18.3.b. Summarize the six reactions of UMP biosynthesis.

MSC: Remembering 39. If a mutation of the decarboxylase enzyme that functions in the biosynthetic pathway of UMP caused the pathway to halt at that step, which of the following would no longer occur? a. reduction of a quinone b. production of orotidine- -monophosphate c. generation of CO2 d. generation of glutamate ANS: C DIF: Medium REF: 18.3 OBJ: 18.3.b. Summarize the six reactions of UMP biosynthesis.

MSC: Applying 40. What enzymatic activity is NOT required during the biosynthesis of UMP from carbamoyl phosphate and aspartate? a. dehydrogenase b. decarboxylase c. phosphoribosyl transferase d. synthetase

ANS: D DIF: Medium REF: 18.3 OBJ: 18.3.b. Summarize the six reactions of UMP biosynthesis.

MSC: Understanding 41. How many ATP are converted to ADP during the biosynthesis of CTP from UMP? a. 0 b. 1 c. 2 d. 3 ANS: D DIF: Easy REF: 18.3 OBJ: 18.3.c. Outline the conversion of UMP to CTP. 42.

MSC: Remembering

15

N-labeled aspartate is provided to bacteria during the biosynthesis of pyrimidine trinucleotides.

The radiolabeled nitrogen would ultimately be found in a. neither UTP or CTP. b. both UTP and CTP. c. UTP but not CTP. d. CTP but not UTP. ANS: B DIF: Difficult REF: 18.3 OBJ: 18.3.c. Outline the conversion of UMP to CTP.

MSC: Applying

43. A mutation in __________ may alter the rate at which UT is converted to CTP. a. CTP synthetase b. UTP dehydrogenase c. CTP transferase d. UTP decarboxylase ANS: A DIF: Easy REF: 18.3 OBJ: 18.3.c. Outline the conversion of UMP to CTP.

MSC: Applying

44. How many PRPP are required to synthesize two UMP and two CTP from carbamoyl aspartate? a. 0 b. 2 c. 4 d. 8 ANS: C DIF: Medium REF: 18.3 OBJ: 18.3.c. Outline the conversion of UMP to CTP.

MSC: Understanding

45. CTP synthetase is inhibited by __________ and activated by __________. a. CTP; GTP b. CTP; UMP c. ATP; GTP d. GTP; UMP ANS: A DIF: Medium REF: 18.3 OBJ: 18.3.d. State the major regulatory sites in pyrimidine biosynthesis.

MSC: Remembering 46. The biosynthesis of CTP is allosterically regulated at many steps. Which of the following is a major point of regulation? a. dihydroorotate dehydrogenase b. UMP kinase

c. nucleoside diphosphate kinase d. UMP synthase ANS: D DIF: Medium REF: 18.3 OBJ: 18.3.d. State the major regulatory sites in pyrimidine biosynthesis.

MSC: Understanding 47. Consider a cell that is provided aspartate in which all carbons are radioactively labeled.

Compounds in the cell are analyzed after the biosynthesis and subsequent breakdown of pyrimidines. Which of the following compounds would display no radioactivity signal during the analysis? a. -alanine b. glutamine c. -aminoisobutyrate d. dihydrouracil ANS: B DIF: Difficult REF: 18.3 OBJ: 18.3.e. Summarize the degradation of pyrimidines.

MSC: Applying

48. Complete the following pathway of the degradation of UMP. UMP Uridine __________ Dihydrouracil -alanine a. uracil; N-carbamoyl– -aminoisobutyrate b. N-carbamoyl–uracil; -alanine CoA c. uracil; N-carbamoyl– -alanine d. orotate; uracil

__________

ANS: C DIF: Medium REF: 18.3 OBJ: 18.3.e. Summarize the degradation of pyrimidines.

49.

NH4+ + HCO3- +

MSC: Applying

-aminoisobutyrate is a breakdown product of a. dATP. b. dUMP. c. dCMP. d. dTMP. ANS: D DIF: Easy REF: 18.3 OBJ: 18.3.e. Summarize the degradation of pyrimidines.

MSC: Remembering

50. Consider the breakdown of the four compounds below. Which would be expected to generate -alanine? a. dATP b. dGMP c. dCMP d. dTMP ANS: C DIF: Easy REF: 18.3 OBJ: 18.3.e. Summarize the degradation of pyrimidines.

MSC: Applying

51. What is the name of the compound below, which is an intermediate in the breakdown of some pyrimidines?

a. N-carbamoyl– -alanine b. N-carbamoyl– -aminoisobutyrate c. dihydrothymine d. -aminoisobutyrate ANS: B DIF: Medium REF: 18.3 OBJ: 18.3.e. Summarize the degradation of pyrimidines.

MSC: Understanding

52. The chemotherapy agent 5-fluorouracil is usually degraded by which of the following enzymes, which requires administration of higher doses? a. -ureidopropionase b. thymidine phosphorylase c. dihydropyrimidine dehydrogenase d. dihydropyrimidinase ANS: C DIF: Easy REF: 18.3 OBJ: 18.3.f. Explain how a deficiency of dihydropyrimidine dehydrogenase causes problems for cancer patients who use 5-fluorouracil.

MSC: Understanding 53. Dihydropyrimidine dehydrogenase deficiencies can lead to an intolerance of high doses of 5-fluorouracil because 5-fluorouracil __________ dihydropyrimidine dehydrogenase. a. is usually metabolized by b. inhibits c. allosterically activates d. denatures ANS: A DIF: Easy REF: 18.3 OBJ: 18.3.f. Explain how a deficiency of dihydropyrimidine dehydrogenase causes problems for cancer patients who use 5-fluorouracil.

MSC: Understanding 54. Which answer INCORRECTLY pairs a substrate and subsequent product of dihydropyrimidine dehydrogenase? a. thymine; dihydrothymine b. uracil; dihydrouracil c. adenine; dihydroadenine d. 5-fluorouracil; fluorodihydrouracil ANS: C DIF: Medium REF: 18.3 OBJ: 18.3.f. Explain how a deficiency of dihydropyrimidine dehydrogenase causes problems for cancer patients who use 5-fluorouracil.

MSC: Understanding 55. An oncologist has a patient with dihydropyrimidine dehydrogenase deficiency. Which of the following is a chemotherapy agent that the doctor should be cautious about using with this patient because of serious side effects? a. primaquine b. -alanine c. 5-dihydrothymine

d. 5-fluorouracil ANS: D DIF: Easy REF: 18.3 OBJ: 18.3.f. Explain how a deficiency of dihydropyrimidine dehydrogenase causes problems for cancer patients who use 5-fluorouracil.

MSC: Applying 56. Dihydropyrimidine dehydrogenase deficiencies exist in approximately __________ of humans and can result in complications when 5-fluorouracil is administered as a __________ therapy. a. 15%; cancer b. 5%; cancer c. 15%; autoimmunity d. 5%; autoimmunity ANS: B DIF: Easy REF: 18.3 OBJ: 18.3.f. Explain how a deficiency of dihydropyrimidine dehydrogenase causes problems for cancer patients who use 5-fluorouracil.

MSC: Remembering 57. To determine the role of glutaredoxin in the generation of deoxyribonucleotides by ribonucleotide reductase, which organisms would be the best to study? a. bony fish b. bacteria c. humans d. amphibians ANS: B DIF: Easy REF: 18.4 OBJ: 18.4.a. Differentiate deoxynucleoside diphosphate production in bacteria and most animals.

MSC: Applying 58. To purify glutathione reductase to carry out a kinetics analysis, which organism would be the best source of the enzyme? a. cod fish b. chimpanzee c. E. coli d. turtle ANS: C DIF: Easy REF: 18.4 OBJ: 18.4.a. Differentiate deoxynucleoside diphosphate production in bacteria and most animals.

MSC: Applying 59. Order the following steps involving the regeneration of ribonucleotide reductase that occurs in most animals so that it may carry out the formation of deoxyribonucleotides. (Note that not all steps are shown.)

1. Reduction of thioredoxin 2. Reduction of ribonucleotide reductase 3. Oxidation of thioredoxin reductase 4. Reduction of thioredoxin reductase a. 3; 4; 1; 2 b. 2; 1; 3; 4 c. 4; 1; 2; 3 d. 4; 3; 1; 2 ANS: D DIF: Difficult REF: 18.4 OBJ: 18.4.a. Differentiate deoxynucleoside diphosphate production in bacteria and most animals.

MSC: Analyzing

60. The biosynthesis of deoxynucleosides is important, yet different organisms require different sets of enzymes to carry it out. If 100 different species were analyzed, which enzyme is most likely to be found in all of them? a. ribonucleotide reductase b. thioredoxin c. glutaredoxin d. glutathione reductase ANS: A DIF: Easy REF: 18.4 OBJ: 18.4.a. Differentiate deoxynucleoside diphosphate production in bacteria and most animals.

MSC: Applying 61. Tyr122 is important in the mechanism of the E. coli ribonucleotide reductase. The function of this amino acid in the mechanism is to a. carry out a nucleophilic attack on the substrate. b. coordinate water in the active site. c. generate the Cys439 radical species. d. hydrogen-bond to the phosphates of the substrate.

ANS: C DIF: Medium REF: 18.4 OBJ: 18.4.b. Restate the importance of Tyr122 and the multiple cysteine residues in the E. coli ribonucleotide reductase mechanism.

MSC: Understanding 62. Identify the carbon atom that is attacked by Cys439 in the first step of the E. coli ribonucleotide reductase mechanism.

a. b. c. d.

A B C D

ANS: C DIF: Medium REF: 18.4 OBJ: 18.4.b. Restate the importance of Tyr122 and the multiple cysteine residues in the E. coli ribonucleotide reductase mechanism.

MSC: Remembering 63. The importance of stable free radicals in the mechanism of E. coli ribonucleotide reductase was identified in the early 1970s. The existence of stable radicals in a protein had not been previously observed. Which of the following amino acids can exist as a stable radical in ribonucleotide reductase? a. Cys b. His c. Ser d. Glu ANS: A

DIF: Easy

REF: 18.4

OBJ: 18.4.b. Restate the importance of Tyr122 and the multiple cysteine residues in the E. coli ribonucleotide reductase mechanism.

MSC: Remembering 64. Several cysteines play important roles in the mechanism of E. coli ribonucleotide reductase. Which is NOT a role carried out by cysteine in this enzyme? a. donation of a hydrogen atom to the substrate b. removal of a hydrogen atom from the substrate c. donation of a proton to ultimately form water d. reduction of thioredoxin ANS: D DIF: Difficult REF: 18.4 OBJ: 18.4.b. Restate the importance of Tyr122 and the multiple cysteine residues in the E. coli ribonucleotide reductase mechanism.

MSC: Understanding 65. In severe combined immunodeficiency disease (SCID), ribonucleotide reductase activity is __________ because of an overabundance of __________. a. activated; dATP b. activated; cAMP c. inhibited; dATP d. inhibited; cAMP ANS: C DIF: Easy REF: 18.4 OBJ: 18.4.c. Explain the regulation of ribonucleotide reductase.

MSC: Remembering 66. Contrast the binding of nucleotides to the activity site and specificity site on the R1 subunit of E. coli ribonucleotide reductase by choosing the nucleotide that can bind to the specificity site but NOT the activity site. a. ATP b. dTTP c. dATP d. dCDP ANS: B DIF: Medium REF: 18.4 OBJ: 18.4.c. Explain the regulation of ribonucleotide reductase.

MSC: Analyzing 67. If an alteration occurred in the activity site of the R1 subunit of E. coli ribonucleotide reductase that allowed dATP to bind but precluded ATP binding to the site, a possible result would be that ribonucleotide reductase a. would remain active under all conditions. b. would be decreased when dATP bound both the activity and specificity sites. c. activity would be increased when ATP bound the specificity site. d. activity would be decreased when dCDP bound the catalytic site.

ANS: B DIF: Medium REF: 18.4 OBJ: 18.4.c. Explain the regulation of ribonucleotide reductase.

MSC: Applying 68. To study the allosteric regulation of E. coli ribonucleotide reductase in a cell-free in vitro system, which of the following would be a good choice to add to the system? a. glucose b. ATP c. Ca2+ d. IP3

ANS: B DIF: Easy REF: 18.4 OBJ: 18.4.c. Explain the regulation of ribonucleotide reductase.

MSC: Applying 69. Place the following steps in their proper order starting with dUMP and N5,N10-methylenetetrahydrofolate as substrates.

1. Formation of tetrahydrofolate 2. Formation of N5,N10-methylenetetrahydrofolate 3. Formation of 7,8-dihydrofolate a. 2; 1; 3 b. 1; 3; 2 c. 1; 2; 3 d. 3; 1; 2 ANS: D DIF: Medium REF: 18.4 OBJ: 18.4.d. List the steps in the conversion of dUMP to dTMP. MSC: Analyzing 70. When analyzing the production of dTMP by thymidylate synthase in a cell-free system, which of the following compounds would be found as an additional product of this enzyme? a. 7,8-dihydrofolate b. NADP+ c. N5,N10-methylenetetrahydrofolate d. glycine ANS: A DIF: Easy REF: 18.4 OBJ: 18.4.d. List the steps in the conversion of dUMP to dTMP. MSC: Applying 71. Which enzyme activity would be directly inhibited by the addition of methotrexate? a. thymidine kinase b. thymidylate synthase c. dihydrofolate reductase d. serine hydroxymethyltransferase ANS: C DIF: Easy REF: 18.4 OBJ: 18.4.e. Name the enzymes of thymidylate synthesis that are inhibited by 5-fluorodeoxyuridine, methotrexate, and aminopterin.

MSC: Understanding 72. Which enzyme activity would be directly reduced if fluorodeoxyuridine- -monophosphate is present? a. thymidine kinase b. thymidylate synthase c. dihydrofolate reductase d. serine hydroxymethyltransferase ANS: B DIF: Easy REF: 18.4 OBJ: 18.4.e. Name the enzymes of thymidylate synthesis that are inhibited by 5-fluorodeoxyuridine, methotrexate, and aminopterin.

MSC: Understanding 73. A compound is added to a cell and dihydrofolate reductase activity is reduced. If this compound is __________, it can be predicted that a similar result would be seen if __________ were added instead. a. methotrexate; aminopterin

b. methotrexate; raltitrexed c. aminopterin; raltitrexed d. aminopterin; fluorodeoxyuridine- -monophosphate ANS: A DIF: Medium REF: 18.4 OBJ: 18.4.e. Name the enzymes of thymidylate synthesis that are inhibited by 5-fluorodeoxyuridine, methotrexate, and aminopterin.

MSC: Applying 74. Reduction in dTMP biosynthesis is NOT dependent upon __________. a. methotrexate b. aminopterin c. raltitrexed d. dihydrofolate ANS: D DIF: Easy REF: 18.4 OBJ: 18.4.e. Name the enzymes of thymidylate synthesis that are inhibited by 5-fluorodeoxyuridine, methotrexate, and aminopterin.

MSC: Understanding SHORT ANSWER 1. Describe how the levels of cAMP would change in a liver cell before and after exposure to glucagon. Compare these with the levels expected if the cell were previously exposed to an inhibitor of adenylate cyclase.

ANS: After exposure to glucagon, the levels of cAMP would increase. An inhibitor of adenylate cyclase would prohibit the synthesis of cAMP even in the presence of glucagon.

DIF: Difficult MSC: Analyzing

REF: 18.1

OBJ: 18.1.a. List the major roles of nucleotides.

2. Contrast the role of kinases and nucleotidases in the nucleotide salvage pathway.

ANS: Kinases add phosphates to nucleotide monophosphates and diphosphates to generate nucleotide triphosphates. Alternatively, nucleotidases remove the phosphoryl group from the nucleotide.

DIF: Difficult MSC: Applying

REF: 18.1

OBJ: 18.1.b. Define nucleotide salvage pathways.

3. Explain how a general inhibitor of endonucleases would alter the homeostasis of mRNA and affect the nucleotide salvage pathway.

ANS: Endonucleases break down mRNA. If inhibited, mRNA would be altered because mRNA would remain longer than normal. The nucleotide salvage pathway would be halted because mRNA is the primary source for oligonucleotides entering the pathway.

DIF: Difficult MSC: Applying

REF: 18.1

OBJ: 18.1.b. Define nucleotide salvage pathways.

4. The enzymes required to convert PRPP to IMP in animal cells form a large protein complex called a(n) __________. Describe the experimental evidence proving the existence of this complex.

ANS: Purinosome; Evidence for the existence of purinosomes came from tissue culture experiments using human cancer cells grown in purine-depleted media. By expressing in these cells, fluorescent recombinant proteins fused to the coding sequences of purine biosynthetic enzymes. Therefore, it was possible to visualize the location of these purine biosynthetic enzymes in live cells.

DIF: Medium REF: 18.2 OBJ: 18.2.b. Summarize the two stages of IMP biosynthesis.

MSC: Understanding

5. An E. coli strain that is unable to synthesize purines because of a mutation in the gene encoding the AIR synthetase is transfected with the human gene coding for hTrifGART. Would this strain would be able to undergo mitosis in purine-depleted media? Explain your answer.

ANS: Mitosis will require the production of new purine bases. The hTrifGART is a trifunctional enzyme that can carry out the reaction catalyzed by AIR synthase. Thus the strain should be able to undergo mitosis in purine-depleted media.

DIF: Difficult REF: 18.2 OBJ: 18.2.b. Summarize the two stages of IMP biosynthesis.

MSC: Evaluating

6. Contrast the energy required to drive the synthesis of AMP from IMP with that required to drive the synthesis of GMP from IMP. ANS: The synthesis of ATP requires energy from GTP, whereas the synthesis of GTP requires energy from ATP. DIF: Easy REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Understanding

7. Relate the broad substrate specificity of nucleoside diphosphate kinase to its role in the consumption and synthesis of nucleoside triphosphates.

ANS: Nucleoside diphosphate kinase is able to use all nucleoside triphosphates as donors of phosphate groups to generate all nucleoside triphosphates.

DIF: Medium REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

8. Explain how the feedback inhibition of IMP dehydrogenase by GMP can increase the flux of the ATP synthesis pathway.

ANS: IMP is a common precursor for both GMP and ATP. Inhibition of IMP dehydrogenase by GMP decreases the flux of that pathway, while allowing for more IMP to be utilized in the ATP synthesis pathway.

DIF: Difficult REF: 18.2 OBJ: 18.2.c. Compare the biosynthesis of AMP and GMP.

MSC: Applying

9. Glutamine-PRPP amidotransferase is a tetrameric enzyme that displays sigmoidal kinetics when no inhibitors are present. In the presence of either GTP or ATP the kinetics curve is sigmoidal. Why does this difference in kinetics occur?

ANS: Both GTP and ATP are allosteric inhibitors.

DIF: Difficult REF: 18.2 OBJ: 18.2.d. Explain the major regulatory sites in purine biosynthesis.

MSC: Analyzing 10. Describe how feedback inhibition by GDP may affect the flux of the ATP synthesis pathway.

ANS: GDP inhibits glutamine-PRPP amidotransferase, which is an upstream enzyme in the ATP synthesis pathway. Its inhibition would reduce the flux of the ATP synthesis pathway.

DIF: Medium REF: 18.2 OBJ: 18.2.d. Explain the major regulatory sites in purine biosynthesis.

MSC: Applying 11. Propose a pathway by which AMP could be converted to hypoxanthine in a cell if there is a mutation that inactivated the enzyme AMP deaminase.

ANS: AMP could be converted to adenosine by -nucleotidase and then converted to inosine by adenosine deaminase. Inosine could be converted to hypoxanthine by purine nucleoside phosphorylase.

DIF: Difficult MSC: Applying

REF: 18.2

OBJ: 18.2.e. Outline the biosynthesis of uric acid.

12. Mutations in HGPRT cause Lesch-Nyhan syndrome. Mutations can lead to two different outcomes, both of which result in a reduction of guanine salvaging in cells. Contrast the two classes of mutations in HGPRT that can lead to the same result.

ANS: Some mutations decrease enzyme activity, whereas others destabilize the protein structure.

DIF: Medium REF: 18.2 OBJ: 18.2.g. Name the deficient enzymes in Lesch-Nyhan syndrome and severe combined immunodeficiency. MSC: Analyzing 13. Two biosynthesis steps are necessary to incorporate the carbon from HCO3 into carbamoyl aspartate. Describe the intermediate compound generated during this conversion.

ANS: Carbamoyl phosphate, which is formed from HCO3- and glutamine, is generated through the activity of carbamoyl phosphate synthetase II. DIF: Medium REF: 18.3 OBJ: 18.3.a. Identify the origin of nitrogen and carbon atoms in the pyrimidine ring system.

MSC: Understanding

14. The oxidation of dihydroorotate to orotate, which occurs during the biosynthesis of UMP, uses what molecule as an electron acceptor?

ANS: Quinone DIF: Medium REF: 18.3 OBJ: 18.3.b. Summarize the six reactions of UMP biosynthesis.

MSC: Understanding 15. A part of the pathway of UMP biosynthesis is shown below. What intermediate is missing? What is the enzyme that generates this compound in the pathway? What is the enzyme that uses this compound as a substrate in the pathway?

Carbamoyl phosphate + Aspartate

Carbamoyl aspartate

__________

Orotate

ANS: Dihydroorotate is missing. Dihydroorotase generates this compound and dihydroorotate dehydrogenase uses this compound as a substrate.

DIF: Medium REF: 18.3 OBJ: 18.3.b. Summarize the six reactions of UMP biosynthesis.

MSC: Understanding 16. Contrast the source of the nitrogen required for the conversion of UTP to CTP in humans and bacteria.

ANS: Humans use glutamine, whereas bacteria use ammonia (NH4+).

DIF: Medium MSC: Analyzing

REF: 18.3

OBJ: 18.3.c. Outline the conversion of UMP to CTP.

17. Identify the error in the diagram of the regulation of flux through the pyrimidine biosynthetic pathway shown below.

ANS: UMP does not activate UMP synthase.

DIF: Difficult

REF: 18.3

OBJ: 18.3.d. State the major regulatory sites in pyrimidine biosynthesis.

MSC: Evaluating 18. How would the flux of the pyrimidine biosynthetic pathway in E. coli cells be affected if the enzyme level of PRPP synthetase is upregulated? Explain your reasoning.

ANS: An upregulation of PRPP synthetase would increase the levels of PRPP. PRPP is an allosteric activator of CAD. Therefore flux through the pathway would increase.

DIF: Difficult REF: 18.3 OBJ: 18.3.d. State the major regulatory sites in pyrimidine biosynthesis.

MSC: Evaluating 19. Compare the regulatory effects of ATP and CTP on ATCase in E. coli.

ANS: ATP activates ATCase, whereas CTP inhibits ATCase.

DIF: Medium REF: 18.3 OBJ: 18.3.d. State the major regulatory sites in pyrimidine biosynthesis.

MSC: Understanding 20. Distinguish between the enzyme requirements for the regeneration of NADP+ needed during dNDP formation in humans and bacteria.

ANS: Humans use thioredoxin and thioredoxin reductase. Bacteria use glutaredoxin and glutathione reductase.

DIF: Medium REF: 18.4 OBJ: 18.4.a. Differentiate deoxynucleoside diphosphate production in bacteria and most animals.

MSC: Analyzing 21. What would be the effect on the enzyme activity of a mutant ribonucleotide reductases in which the metal-coordinated Tyr is missing? Explain your reasoning in the context of the role of the Tyr in the mechanism of the enzyme.

ANS: The enzyme would not be active because the Tyr radical is important in abstracting a hydrogen atom from Cys439, leading to the formation of a radical in the active site.

DIF: Medium REF: 18.4 OBJ: 18.4.b. Restate the importance of Tyr122 and the multiple cysteine residues in the E. coli ribonucleotide reductase mechanism.

MSC: Analyzing 22. The activity site of ribonucleotide reductase can bind two different molecules, whereas the specificity site can bind several. Construct a situation where the activity of the enzyme is inhibited by choosing the identity of the molecules bound to each site.

ANS: The enzyme would be inhibited if dATP is bound to the activity site and ATP, dATP, dGTP, or dTTP were bound to the specificity site.

DIF: Difficult REF: 18.4 OBJ: 18.4.c. Explain the regulation of ribonucleotide reductase.

MSC: Applying 23. What is the name of the enzyme that catalyzes the methylation of dUMP to generate dTMP? Describe the mechanism of the enzyme and include the coenzyme requirement.

ANS: Thymidylate synthase. This enzyme reaction converts dUMP (deoxyuridylate) to dTMP (deoxythymidylate, or simply thymidylate; see Table 3.1) through a mechanism involving a C1 transfer from the coenzyme N 5, N 10-methylenetetrahydrofolate.

DIF: Easy REF: 18.4 OBJ: 18.4.d. List the steps in the conversion of dUMP to dTMP. MSC: Remembering 24. What is the name of the compound below, which is part of the pathway that regenerates N5,N10-methylenetetrahydrofolate?

ANS: Tetrahydrofolate DIF: Medium REF: 18.4 OBJ: 18.4.d. List the steps in the conversion of dUMP to dTMP. MSC: Remembering 25. An in vitro experiment with all precursors available for the conversion of dUMP to dTMP would also need to include thymidylate synthase and two additional enzymes necessary for the regeneration of N5,N10-methylenetetrahydrofolate. What are the two enzymes?

ANS: Serine hydroxymethyltransferase and dihydrofolate reductase DIF: Medium REF: 18.4 OBJ: 18.4.d. List the steps in the conversion of dUMP to dTMP.

MSC: Applying 26. What would be the effect on thymidylate synthase activity if raltitrexed is present?

ANS: Thymidylate synthase activity would be reduced.

DIF: Easy REF: 18.4 OBJ: 18.4.e. Name the enzymes of thymidylate synthesis that are inhibited by 5-fluorodeoxyuridine, methotrexate, and aminopterin.

MSC: Understanding

Chapter 19: Metabolic Integration MULTIPLE CHOICE 1. Which of the following is unlikely to affect metabolic homeostasis? a. physical activity b. tissue dysfunction c. psychological stress d. telomere duplication ANS: D DIF: Easy REF: 19.1 OBJ: 19.1.a. Define the terms energy balance and metabolic homeostasis.

MSC: Remembering 2. Metabolic homeostasis relies on maintaining a. maximum ATP synthase activity. b. optimal metabolite concentrations. c. maximum flux through the citric acid cycle. d. minimal inhibition of gluconeogenesis.

ANS: B DIF: Easy REF: 19.1 OBJ: 19.1.a. Define the terms energy balance and metabolic homeostasis.

MSC: Understanding 3. Which organ is responsible for regulating physiological levels of glucose? a. liver b. muscle c. adipose tissue d. brain ANS: A DIF: Easy REF: 19.1 OBJ: 19.1.b. Summarize the major metabolic roles of the liver, muscle, adipose tissue, brain, and kidney.

MSC: Remembering 4. Skeletal muscle can use all of the following as metabolic fuel EXCEPT a. glucose. b. free fatty acids. c. chylomicrons. d. ketone bodies.

ANS: C DIF: Easy REF: 19.1 OBJ: 19.1.b. Summarize the major metabolic roles of the liver, muscle, adipose tissue, brain, and kidney.

MSC: Remembering 5. Which of the following is secreted by visceral fat? a. glucagon b. adipokines c. somatostatin d. phosphocreatine ANS: B DIF: Medium REF: 19.1 OBJ: 19.1.b. Summarize the major metabolic roles of the liver, muscle, adipose tissue, brain, and kidney.

MSC: Remembering

6. A comparison of kidney and liver would show that both a. accept blood through the portal vein. b. express glucokinase. c. express phosphoenolpyruvate carboxykinase. d. express adipokines.

ANS: C DIF: Difficult REF: 19.1 OBJ: 19.1.b. Summarize the major metabolic roles of the liver, muscle, adipose tissue, brain, and kidney.

MSC: Analyzing 7. The blood-brain barrier results from __________, which allow glucose and __________ to enter the brain. a. astrocytes; ketone bodies b. astrocytes; triacylglycerols c. hepatocytes; ketone bodies d. hepatocytes; triacylglycerols ANS: A DIF: Medium REF: 19.1 OBJ: 19.1.b. Summarize the major metabolic roles of the liver, muscle, adipose tissue, brain, and kidney.

MSC: Remembering 8. Predict the metabolic outcome of a partial inhibition of lipoprotein lipase. a. Neurons in the brain would no longer use free fatty acids as a fuel source. b. Rates of glycogen breakdown in heart muscle would increase. c. Levels of ketone bodies in the blood would decrease. d. Liver lactate dehydrogenase activity levels would decrease.

ANS: C DIF: Difficult REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Evaluating 9. Which tissue participates in the Cori cycle in order to maintain metabolic homeostasis? a. skeletal muscle b. adipose tissue c. kidney d. brain ANS: A DIF: Medium REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Understanding 10. Which tissue participates in the triacylglycerol cycle in order to maintain metabolic homeostasis? a. skeletal muscle b. liver c. kidney d. brain ANS: B DIF: Medium REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Understanding 11. The synthesis of dihydroxyacetone phosphate from amino acid backbones and lactate is carried out by the __________ pathway. a. triacylglycerol b. lactate

c. triphosphate d. glyceroneogenesis ANS: D DIF: Easy REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Remembering 12. The pancreatic cell type that is responsible for the production of somatostatin is the __________ cells. a. acinar b. c. d.

ANS: D DIF: Easy REF: 19.1 OBJ: 19.1.d. State the role of the pancreas in controlling metabolic homeostasis.

MSC: Remembering 13. Which of the following activates triacylglycerol hydrolysis and fatty acid export in adipose tissue? a. insulin b. glucagon c. somatostatin d. LpL ANS: B DIF: Medium REF: 19.1 OBJ: 19.1.d. State the role of the pancreas in controlling metabolic homeostasis.

MSC: Understanding 14. Glucagon-like peptide-1 (GLP-1) is a hormone peptide secreted by intestinal L cells. It is secreted in response to the nutrient detection in the small intestine. The resulting physiological response is the lowering of blood glucose levels. Which of the following is a potential mechanism for how GLP-1 causes this physiological response? a. stimulation of glucagon release b. stimulation of insulin release by pancreatic cells c. increase in the apoptosis rate of pancreatic cells d. downregulation of GLUT4 ANS: B DIF: Difficult REF: 19.1 OBJ: 19.1.e. Compare the effects of insulin and glucagon on metabolic pathways in the liver, skeletal muscle, adipose tissue, and brain. MSC: Applying 15. Glucagon stimulates glucose export by increasing metabolic flux through gluconeogenesis in the a. liver. b. skeletal muscle. c. adipose. d. brain.

ANS: A DIF: Easy REF: 19.1 OBJ: 19.1.e. Compare the effects of insulin and glucagon on metabolic pathways in the liver, skeletal muscle, adipose tissue, and brain. MSC: Understanding 16. What is the expected outcome in a liver cell after exposure to insulin? a. activation of fructose-1,6-bisphosphatase b. allosteric inhibition of protein phosphatase 1 c. phosphorylation of phosphofructokinase-2/fructose-2,5-bisphosphatase

d. increased cytoplasmic concentration of fructose-2,6-bisphosphate ANS: D DIF: Difficult REF: 19.1 OBJ: 19.1.e. Compare the effects of insulin and glucagon on metabolic pathways in the liver, skeletal muscle, adipose tissue, and brain. MSC: Applying 17. The expected outcome in adipose tissue after exposure to glucagon would be an increased a. glucose uptake through GLUT4. b. glycerol synthesis. c. fatty acid uptake from lipoprotein particles. d. triacylglycerol hydrolysis.

ANS: D DIF: Medium REF: 19.1 OBJ: 19.1.e. Compare the effects of insulin and glucagon on metabolic pathways in the liver, skeletal muscle, adipose tissue, and brain. MSC: Applying 18. Which of the following would show increased activity levels in a liver cell after exposure to insulin? a. phosphorylase kinase b. phosphofructokinase-1 c. glycogen phosphorylase d. fructose-1,6-bisphosphatase ANS: B DIF: Medium REF: 19.1 OBJ: 19.1.e. Compare the effects of insulin and glucagon on metabolic pathways in the liver, skeletal muscle, adipose tissue, and brain. MSC: Understanding 19. Analysis of various cell types after exposure to insulin would show an increase in triacylglycerol synthesis in which of the following? a. brain b. skeletal muscle c. liver d. pancreas ANS: C DIF: Easy REF: 19.1 OBJ: 19.1.f. Contrast the effect of insulin on liver and muscle cells.

MSC: Applying 20. On exposure to insulin, the liver responds by upregulating __________, which in turn causes the upregulation of __________. a. protein phosphatase 2A; acetyl-CoA carboxylase b. protein phosphatase 2A; glycogen synthase c. protein phosphatase 1; phosphorylase kinase d. protein phosphatase 1; glycogen phosphorylase ANS: A DIF: Medium REF: 19.1 OBJ: 19.1.f. Contrast the effect of insulin on liver and muscle cells.

MSC: Applying 21. Analysis of enzyme activity in both liver and muscle cells on insulin exposure would show an increase in the activity of which of the following? a. glucokinase b. protein phosphatase 2A c. glycogen phosphorylase d. pyruvate dehydrogenase complex

ANS: D DIF: Medium REF: 19.1 OBJ: 19.1.f. Contrast the effect of insulin on liver and muscle cells.

MSC: Applying 22. Analysis of enzyme activity in both liver and muscle cells on insulin exposure would show a decrease in the activity of a. glycogen phosphorylase. b. fructose-1,6-bisphosphatase. c. pyruvate dehydrogenase complex. d. phosphofructokinase-1.

ANS: A DIF: Medium REF: 19.1 OBJ: 19.1.f. Contrast the effect of insulin on liver and muscle cells.

MSC: Applying 23. Which of the following is NOT one of the three peroxisome proliferator–activated receptor nuclear receptor proteins that function in metabolic homeostasis? a. PPAR b. PPAR c. PPAR d. PPAR ANS: B DIF: Medium REF: 19.1 OBJ: 19.1.g. Explain the role of peroxisome proliferator–activated receptors in control of metabolic homeostasis.

MSC: Remembering 24. PPARs have a variety of functions in lipid metabolism that include all EXCEPT a. regulation of lipid transport. b. mobilization of fatty acid oxidation. c. mobilization of lipid synthesis. d. decreasing insulin sensitivity.

ANS: D DIF: Easy REF: 19.1 OBJ: 19.1.g. Explain the role of peroxisome proliferator–activated receptors in control of metabolic homeostasis.

MSC: Understanding 25. Enzyme activities after PPAR signaling were monitored in both liver and skeletal muscle. When compared with activities before PPAR signaling, which of the following would have been found to increase in liver but NOT in skeletal muscle? a. acyl CoA dehydrogenase b. enoyl-CoA hydratase c. transketolase d. acetyl-CoA acetyltransferase ANS: C DIF: Difficult REF: 19.1 OBJ: 19.1.g. Explain the role of peroxisome proliferator–activated receptors in control of metabolic homeostasis.

MSC: Analyzing 26. The graph below shows the relative changes in concentration of glucose, fatty acids, and ketone bodies during 40 days of starvation. Choose the answer that correctly labels the data on the graph.

a. b. c. d.

X = fatty acids; Y = glucose; Z = ketone bodies X = glucose; Y = fatty acids; Z = ketone bodies X = ketone bodies; Y = glucose; Z = fatty acids X = ketone bodies; Y = fatty acids; Z = glucose

ANS: C DIF: Difficult REF: 19.1 OBJ: 19.1.h. Summarize the changes in metabolic flux that occur during starvation.

MSC: Analyzing 27. Which of the following changes in metabolic flux would be expected to occur during long periods without food? a. decreased release of fatty acids from adipose tissue b. decreased gluconeogenesis in liver and kidney cells c. decreased ketogenesis in liver cells d. protein degradation in skeletal muscle ANS: D DIF: Easy REF: 19.1 OBJ: 19.1.h. Summarize the changes in metabolic flux that occur during starvation.

MSC: Understanding 28. During periods of starvation, gluconeogenesis increases in the liver. Which of the following is a major substrate for glucose biosynthesis under these conditions? a. glutamate b. alanine c. urea d. fatty acids ANS: B DIF: Easy REF: 19.1 OBJ: 19.1.h. Summarize the changes in metabolic flux that occur during starvation.

MSC: Remembering 29. A lack of energy balance may lead to a. type 1 diabetes. b. a BMI value of less than 30, indicating obesity. c. type 2 diabetes. d. increased skeletal muscle breakdown.

ANS: C

DIF: Easy

REF: 19.2

OBJ: 19.2.a. Define the terms energy balance and set point.

MSC: Understanding

30. The average amount of adipose tissue the body maintains at physiological homeostasis is known as the a. energy balance. b. adipose energy balance. c. BMI. d. set point.

ANS: D DIF: Easy REF: 19.2 OBJ: 19.2.a. Define the terms energy balance and set point.

MSC: Remembering

31. The set point can be increased as a result of a. a sedentary lifestyle. b. starvation. c. negative energy imbalance. d. weight loss.

ANS: A DIF: Easy REF: 19.2 OBJ: 19.2.a. Define the terms energy balance and set point.

MSC: Understanding

32. Human gene variants favoring individuals with a capacity to store extra fat during times of feast are known as a. Neel variants. b. thrifty genes. c. leptos genes. d. Pima variants.

ANS: B DIF: Easy REF: 19.2 OBJ: 19.2.b. Explain the thrifty gene hypothesis.

MSC: Remembering

33. Thrifty genes are __________ during times of starvation and __________ when physical activity is low. a. beneficial; beneficial b. beneficial; detrimental c. detrimental; detrimental d. detrimental; beneficial ANS: B DIF: Easy REF: 19.2 OBJ: 19.2.b. Explain the thrifty gene hypothesis.

MSC: Understanding

34. Leptin is a a. mutated form of insulin. b. hormone receptor expressed in adipocytes. c. adipocyte peptide hormone. d. recessive gene that causes obesity.

ANS: C DIF: Easy REF: 19.2 OBJ: 19.2.c. Summarize the effects of leptin.

MSC: Remembering

35. Neuronal samples from wild-type mice were monitored in the absence and presence of leptin via Western blotting. The data are shown below. Choose the answer that correctly identifies the NPY/AGRP neuronal samples obtained in the absence and then the presence of leptin.

a. b. c. d.

B; C D; B A; C C; A

ANS: C DIF: Difficult REF: 19.2 OBJ: 19.2.c. Summarize the effects of leptin.

MSC: Evaluating

36. The net effect of leptin signaling in humans includes a. decreased appetite. b. decreased basal metabolic rates. c. increased set point. d. decreased thrifty gene expression.

ANS: A DIF: Medium REF: 19.2 OBJ: 19.2.c. Summarize the effects of leptin.

MSC: Understanding

37. What might occur if a mutation in the leptin receptor causes it to be always activated, even in the absence of leptin? a. JAK2 will be activated. b.

-MSH secretion will be low. c. NPY secretion will be high. d. AGRP secretion will be high.

ANS: A DIF: Medium REF: 19.2 OBJ: 19.2.c. Summarize the effects of leptin.

MSC: Applying

38. DB mice display the __________ phenotype and express __________ leptin levels when compared with OB mice. a. same; higher b. same; lower c. different; higher d. different; lower ANS: A DIF: Medium REF: 19.2 OBJ: 19.2.c. Summarize the effects of leptin.

MSC: Understanding

39. Which of the following neurons is a second-order neuron and therefore does NOT respond directly to leptin? a. POMC

b. orexigenic c. NPY d. AGRP ANS: B DIF: Easy REF: 19.2 OBJ: 19.2.d. Distinguish between anorexigenic and orexigenic neurons.

MSC: Understanding 40. When basal metabolic rates are decreased and appetite is increased, which type of neurons are likely activated? a. anorexigenic b. orexigenic c. POMC d. ghrelin ANS: B DIF: Medium REF: 19.2 OBJ: 19.2.d. Distinguish between anorexigenic and orexigenic neurons.

MSC: Understanding 41. Modify the schematic below by properly labeling the four neurons (W, X, Y, and Z).

a. b. c. d.

W = orexigenic; X = anorexigenic; Y = POMC; Z = NPY/AGRP W = anorexigenic; X = orexigenic; Y = NPY/AGRP; Z = POMC W = anorexigenic; X = orexigenic; Y = POMC; Z = NPY/AGRP W = anorexigenic; X = orexigenic; Y = NPY/AGRP; Z = POMC

ANS: C DIF: Difficult REF: 19.2 OBJ: 19.2.d. Distinguish between anorexigenic and orexigenic neurons.

MSC: Applying 42. Anorexigenic neurons express the __________ receptor. a. MC4 b. Y1/Y5 c. Y2 d. NPY ANS: A DIF: Difficult REF: 19.2 OBJ: 19.2.d. Distinguish between anorexigenic and orexigenic neurons.

MSC: Remembering 43. A patient has been diagnosed with metabolic syndrome. To establish the diagnosis, the doctor likely performed several tests. A test that the doctor was UNLIKELY to perform would be a. an assessment of abdominal obesity. b. fasting followed by glucose tolerance test to establish insulin sensitivity. c. monitoring of blood pressure. d. a blood test for lipid levels.

ANS: B DIF: Medium REF: 19.2 OBJ: 19.2.e. List the five symptoms of metabolic syndrome.

MSC: Applying

44. Analysis of a patient with metabolic syndrome would indicate low a. HDL levels. b. LDL levels. c. blood pressure. d. visceral fat.

ANS: A DIF: Easy REF: 19.2 OBJ: 19.2.e. List the five symptoms of metabolic syndrome.

MSC: Applying

45. Whipple surgery, sometimes carried out on patients battling pancreatic cancer, is one of the most demanding surgeries to perform. It involves removing parts of the pancreas and rerouting aspects of the digestive track. Which of the following side effects may result from Whipple surgery? a. type 1 diabetes b. type 2 diabetes c. leptin insensitivity d.

-MSH overproduction ANS: B DIF: Medium REF: 19.2 OBJ: 19.2.f. Differentiate between type 1 and type 2 diabetes.

MSC: Analyzing

46. Compared with a normal patient, a person with type 1 diabetes would display __________ during a glucose tolerance test. a. lower starting blood glucose level b. more rapid rise in blood glucose levels after drinking the glucose solution c. more rapid recovery to normal blood glucose levels after drinking the glucose solution d. reduction in blood glucose levels after drinking the glucose solution ANS: A DIF: Medium REF: 19.2 OBJ: 19.2.f. Differentiate between type 1 and type 2 diabetes.

MSC: Analyzing

47. After a meal is consumed by an individual with chronically elevated levels of free fatty acids, __________ is expected to occur. a. increased glucose uptake b. increased activation of protein kinase C c. increased glycogen synthesis d. activation of the phosphoinoside-3 kinase pathway ANS: B DIF: Medium REF: 19.2 OBJ: 19.2.g. Evaluate the proposed mechanism for the inhibition of insulin signaling by free fatty acids. MSC: Applying 48. Which protein will be phosphorylated in a muscle cell in an obese individual with elevated serum levels of free fatty acids?

a. b. c. d.

protein kinase C insulin receptor IRS1 GLUT1

ANS: C DIF: Medium REF: 19.2 OBJ: 19.2.g. Evaluate the proposed mechanism for the inhibition of insulin signaling by free fatty acids. MSC: Applying 49. Muscle cells from normal and obese type 2 diabetic patients were analyzed for plasma membrane lipid content. Which of the following would likely be elevated in the diabetic patient? a. IR b. IRS1 c. IP3 d. DAG ANS: D DIF: Medium REF: 19.2 OBJ: 19.2.g. Evaluate the proposed mechanism for the inhibition of insulin signaling by free fatty acids. MSC: Applying 50. Activation of __________ in __________ leads to downregulation of adiponectin. a. IKK; adipocytes b. p38 MAP kinase; adipocytes c. p38 MAP kinase; liver cells d. JNK; adipocytes ANS: A DIF: Medium REF: 19.2 OBJ: 19.2.h. Summarize the effects of elevated TNF-alpha on insulin signaling.

MSC: Understanding 51. Which of the following would be expected to be degraded by the proteasome in a cell that has been exposed to TNF- ? a. IRS1 b. phosphorylated IRS1 c. phosphorylated I B d. NF B ANS: C DIF: Medium REF: 19.2 OBJ: 19.2.h. Summarize the effects of elevated TNF-alpha on insulin signaling.

MSC: Understanding 52. TNF- causes the __________ of insulin signaling in __________. a. inhibition; muscle cells b. activation; liver cells c. activation; adipocytes d. activation; kidney cells ANS: A DIF: Easy REF: 19.2 OBJ: 19.2.h. Summarize the effects of elevated TNF-alpha on insulin signaling.

MSC: Understanding 53. What might be the outcome of a mutation that causes the adiponectin receptor to be constitutively activated? a. very low levels of GLUT4 in muscle cell membranes b. high levels of acetyl-CoA carboxylase activity

c. insulin resistance d. highly activated AMPK ANS: C DIF: Medium REF: 19.2 OBJ: 19.2.i. State the role of adiponectin in insulin sensitivity.

MSC: Applying

54. Adiponectin is a. a lipid hexamer. b. a multimeric protein. c. produced by the pancreas. d. produced at high levels in obese people.

ANS: B DIF: Easy REF: 19.2 OBJ: 19.2.i. State the role of adiponectin in insulin sensitivity.

MSC: Remembering

55. Serum levels of high-molecular-weight adiponectin are __________ in obese individuals, in part because of __________ suppression of adiponectin expression. a. decreased; TNAb. decreased; insulin c. increased; TNAd. increased; insulin ANS: A DIF: Easy REF: 19.2 OBJ: 19.2.i. State the role of adiponectin in insulin sensitivity.

MSC: Remembering

56. Metformin is a(n) a.

-glucosidase inhibitor. b. sulfonylurea inhibitor of pancreatic ATP-dependent K+ channels. c. AMPK stimulator. d. PPAR agonist.

ANS: C DIF: Easy REF: 19.2 OBJ: 19.2.j. Identify the mechanisms by which metformin and thiazolidinediones function as treatments for type 2 diabetes.

MSC: Remembering 57. Monitoring fatty acid metabolism in a patient before and after administration of metformin would show a decrease of fatty acid synthesis in __________ and an increase in fatty acid oxidation in __________. a. liver; heart b. liver; adipose tissue c. adipose tissue; liver d. skeletal muscle; heart ANS: A DIF: Easy REF: 19.2 OBJ: 19.2.j. Identify the mechanisms by which metformin and thiazolidinediones function as treatments for type 2 diabetes.

MSC: Applying 58. Thiazolidinedione activates PPAR in adipose tissue. This results in the upregulation of a. TNF- . b. plasminogen activator inhibitor 1. c. interleukin-6. d. phosphoenolpyruvate carboxykinase.

ANS: D DIF: Medium REF: 19.2 OBJ: 19.2.j. Identify the mechanisms by which metformin and thiazolidinediones function as treatments for type 2 diabetes.

MSC: Understanding

59. Which of the following drugs stimulate adrenergic receptor signaling? a. ephedrine b. lorcaserin c. orlistat d. thiazolidinedione ANS: A DIF: Easy REF: 19.3 OBJ: 19.3.a. Compare the mechanisms of action for ephedrine, lorcaserin, and orlistat.

MSC: Remembering 60. Orlistat and olestra can both lead to undigested lipids in the colon, yet they do so by contrasting mechanisms. Orlistat __________, whereas olestra __________. a. inhibits pancreatic lipase; activates PPAR b. inhibits pancreatic lipase; is a fat substitute that is not a substrate for pancreatic lipase c. is a fat substitute that is not a substrate for pancreatic lipase; inhibits pancreatic lipase d. activates PPAR ; inhibits pancreatic lipase ANS: B DIF: Medium REF: 19.3 OBJ: 19.3.a. Compare the mechanisms of action for ephedrine, lorcaserin, and orlistat.

MSC: Applying 61. Which of the following functions by specifically targeting neuronal control of food consumption? a. ephedrine b. olestra c. lorcaserin d. orlistat ANS: C DIF: Easy REF: 19.3 OBJ: 19.3.a. Compare the mechanisms of action for ephedrine, lorcaserin, and orlistat.

MSC: Understanding 62. Most fad diets do not work because a. they cost too much. b. 40% of people do not “stick to it.” c. they increase caloric intake. d. they slow metabolism because of a lack of micronutrient consumption.

ANS: B DIF: Easy REF: 19.3 OBJ: 19.3.b. Hypothesize as to why most fad diets do not work.

MSC: Understanding 63. Fad diets may lead to biochemical outcomes that are unfavorable. Which diet may lead to ketoacidosis? a. Atkins diet b. Ornish diet c. Weight Watchers d. olestra-rich diet ANS: A DIF: Difficult REF: 19.3 OBJ: 19.3.b. Hypothesize as to why most fad diets do not work.

MSC: Analyzing 64. The numerical value of a food that indicates how quickly glucose is released into the blood is called the

a. b. c. d.

calorie.

GRP (glucose-release point). set point. glycemic index.

ANS: D DIF: Easy OBJ: 19.3.c. Define glycemic index.

REF: 19.3 MSC: Remembering

65. Which list correctly places the foods in order of lowest to highest glycemic index? a. corn chips < soda < cherries b. peanuts < donut < skim milk c. broccoli < soda < corn chips d. donut < broccoli < pretzel ANS: C DIF: Difficult OBJ: 19.3.c. Define glycemic index.

REF: 19.3 MSC: Applying

66. What are the concentrations of glucose that would be expected of a healthy individual after an 8-hour fast and after consuming a large soft pretzel? a. 80 mg/dL; 130 mg/dL b. 130 mg/dL; 180 mg/dL c. 75 mg/dL; 100 mg/dL d. 125 mg/dL; 75 mg/dL ANS: A DIF: Medium OBJ: 19.3.c. Define glycemic index.

REF: 19.3 MSC: Applying

67. A steep drop in blood glucose concentration occurs after consumption of high glycemic index foods because of a(n)

a. b. c. d.

insulin spike. glucagon spike. insulin drop. catecholamine spike.

ANS: A DIF: Medium OBJ: 19.3.c. Define glycemic index.

REF: 19.3 MSC: Applying

68. What is the fuel source for ATP production that is used in a 200-meter sprint?

a. b. c. d.

muscle phosphocreatine liver glycogen muscle glycogen adipose tissue fatty acids

ANS: A DIF: Easy REF: 19.3 OBJ: 19.3.d. Distinguish the energy source for muscle in a 10-km run versus a 200-meter sprint.

MSC: Understanding 69. What fuel source will last the longest before being depleted during intense exercise? a. liver glycogen b. muscle phosphocreatine c. muscle ATP d. adipose tissue fatty acids ANS: D DIF: Easy REF: 19.3 OBJ: 19.3.d. Distinguish the energy source for muscle in a 10-km run versus a 200-meter sprint.

MSC: Understanding 70. During intense exercise, muscle ATP stores will be depleted in about a. 3 minutes. b. 5 minutes. c. 30 seconds. d. 3 seconds.

ANS: D DIF: Easy REF: 19.3 OBJ: 19.3.d. Distinguish the energy source for muscle in a 10-km run versus a 200-meter sprint.

MSC: Understanding 71. When AMPK is bound by AMP and is phosphorylated at Thr172, __________ activity will __________. a. glycogen synthase; increase b. phosphofructokinase-2; decrease c. acetyl-CoA carboxylase; increase d. hormone-sensitive lipase; decrease ANS: C DIF: Medium REF: 19.3 OBJ: 19.3.e. List the enzymes and pathways activated by AMPK. MSC: Applying 72. Analysis of phosphorylated proteins in a cell with a fully active AMPK would reveal that __________ is phosphorylated. a. cytochrome oxidase b. cytochrome c c. phosphofructokinase-2 d. PPAR ANS: C DIF: Medium REF: 19.3 OBJ: 19.3.e. List the enzymes and pathways activated by AMPK. MSC: Applying 73. Fully active AMPK results in an increase in all pathways listed EXCEPT a. glycolytic flux. b. fatty acid oxidation. c. oxidative phosphorylation.

d. fatty acid synthesis.

ANS: D DIF: Easy REF: 19.3 OBJ: 19.3.e. List the enzymes and pathways activated by AMPK. MSC: Understanding 74. AMPK can be activated by a. high-fat diet. b. exercise. c. fasting. d. PPAR .

ANS: B DIF: Easy REF: 19.3 OBJ: 19.3.e. List the enzymes and pathways activated by AMPK. MSC: Understanding 75. Reduced levels of __________ molecular-weight serum adiponectin in obese individuals results in __________ activation of AMPK signaling in muscle cells. a. low; decreased b. low; increased c. high; decreased d. high; increased ANS: B DIF: Easy REF: 19.3 OBJ: 19.3.e. List the enzymes and pathways activated by AMPK. MSC: Understanding SHORT ANSWER 1. What is the process of maintaining optimal metabolic concentrations and managing chemical energy reserves in tissues? Describe the three primary factors that influence this process.

ANS: Metabolic homeostasis. Metabolic homeostasis is influenced by genetic inheritance, nutrition, and exercise.

DIF: Easy REF: 19.1 OBJ: 19.1.a. Define the terms energy balance and metabolic homeostasis.

MSC: Understanding 2. What are the two aspects of energy within an organism that must be considered to determine the energy balance?

ANS: Energy input and energy expenditure DIF: Medium REF: 19.1 OBJ: 19.1.a. Define the terms energy balance and metabolic homeostasis.

MSC: Understanding 3. The exchange of fatty acids and triacylglycerols between the liver and adipose tissue is an ongoing process that helps maintain metabolic homeostasis. What is the name of this process?

ANS:

Triacylglycerol cycle DIF: Medium REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Remembering 4. Distinguish between the main energy sources of brain versus cardiac muscle.

ANS: The brain requires glucose, whereas cardiac muscle requires fatty acids and ketone bodies.

DIF: Medium REF: 19.1 OBJ: 19.1.c. List the principles of metabolic flux required to maintain metabolic homeostasis.

MSC: Analyzing 5. How can hormone(s) cause the upregulation of the glucose transporter type 4 protein in liver and adipose cells?

ANS: Pancreatic beta ( ) cells secrete insulin, which causes the upregulation of the glucose transporter type 4 protein in liver and adipose cells. Insulin stimulates the translocation of the transporter to the plasma membrane.

DIF: Difficult REF: 19.1 OBJ: 19.1.d. State the role of the pancreas in controlling metabolic homeostasis.

MSC: Applying 6. Membrane fractions of skeletal muscle and adipose tissue were purified. Before purification the samples were exposed to insulin or glucagon. The samples were then analyzed via Western blotting using antibodies against GLUT4 and GLUT2. A loading control was included in the analysis. The results are shown below. Assume that sample A is skeletal muscle. Which sample corresponds to skeletal muscle that has been exposed to insulin? Explain your choice.

ANS: Samples C or D could be skeletal muscle that has been exposed to insulin because insulin increases the translocation of GLUT4 to the plasma membrane in skeletal muscle.

DIF: Difficult

REF: 19.1

OBJ: 19.1.d. State the role of the pancreas in controlling metabolic homeostasis.

MSC: Applying 7. Whipple surgery, sometimes carried out on patients battling pancreatic cancer, is one of the most demanding surgeries to perform. It involves removing parts of the pancreas and rerouting aspects of the digestive track. A complication of the surgery can be the development of diabetes. Why could this complication develop? Include the types of cells and hormones that are involved.

ANS: If too many beta ( ) cells are removed during the surgery, patients may not be able to produce enough insulin. The low insulin levels may lead to diabetes.

DIF: Difficult REF: 19.1 OBJ: 19.1.d. State the role of the pancreas in controlling metabolic homeostasis.

MSC: Applying 8. Liver and skeletal muscle both respond to insulin by exhibiting an increased metabolic flux through glycolytic and glycogen synthesis pathways. Yet the tissues also exhibit different responses in how glucose is transported into the cells on insulin stimulation. What are these differences?

ANS: Skeletal muscle, but not liver, increases the level of GLUT4 protein on the cell surface.

DIF: Medium REF: 19.1 OBJ: 19.1.f. Contrast the effect of insulin on liver and muscle cells.

MSC: Applying 9. What is the physiological importance of PPAR

signaling in liver cells after overnight fasting?

ANS: PPAR signaling after overnight fasting stimulates the liver to increase rates of fatty acid oxidation, resulting in elevated production and export of ketone bodies and glucose to the peripheral tissues.

DIF: Medium REF: 19.1 OBJ: 19.1.g. Explain the role of peroxisome proliferator–activated receptors in control of metabolic homeostasis.

MSC: Evaluating 10. Are thiazolidinediones agonists or antagonists of PPAR ?

ANS: Agonists DIF: Easy REF: 19.1 OBJ: 19.1.g. Explain the role of peroxisome proliferator–activated receptors in control of metabolic homeostasis.

MSC: Remembering 11. Humans have evolved to utilize ketone bodies as a partial replacement for glucose during times of starvation before moving toward muscle protein as an energy source. Why is this beneficial?

ANS:

Preserving muscle protein increases chances that the body will be strong enough to obtain food and thereby prevent death.

DIF: Medium REF: 19.1 OBJ: 19.1.h. Summarize the changes in metabolic flux that occur during starvation.

MSC: Applying 12. During starvation, acetyl-CoA generated by fatty acid oxidation is used to generate ketone bodies.

Relate how rates of fatty acid oxidation and flux through the citric acid cycle can lead to increased ketogenesis in this situation.

ANS: The acetyl-CoA generated by fatty acid oxidation cannot be metabolized by the citrate cycle because of oxaloacetate being shunted toward gluconeogenesis. Under these conditions acetyl-CoA is used to generate ketone bodies.

DIF: Difficult REF: 19.1 OBJ: 19.1.h. Summarize the changes in metabolic flux that occur during starvation.

MSC: Applying 13. When calories consumed/day is equal to the calories expended/day, a person is considered to have a(n) __________. Describe the role of leptin in this process.

ANS: Energy balance. Leptin synthesis in visceral adipose tissue is proportional to the amount of stored fat. Leptin functions as a metabolic regulator that activates neuronal signaling pathways in the brain that decrease appetite and increase energy expenditure. Therefore, when the amount of stored fat in adipose tissue suddenly increases, leptin signaling inhibits further fat storage to maintain energy balance. Similarly, if fat storage suddenly decreases, leptin levels decrease, and fat storage increases because it is not subject to leptin suppression.

DIF: Medium REF: 19.2 OBJ: 19.2.a. Define the terms energy balance and set point.

MSC: Understanding

14. Propose an experimental design using identical twins that would support the thrifty gene hypothesis.

ANS: Follow identical twins who have lived in different environments or who have different lifestyles.

DIF: Difficult MSC: Applying

REF: 19.2

OBJ: 19.2.b. Explain the thrifty gene hypothesis.

15. Proposed by James Neel, the __________ explains the high rates of obesity in developed countries. Describe how fat storage is involved in this proposal.

ANS: Thrifty gene hypothesis. The thrifty gene hypothesis states that humans contain metabolic gene variants that provide protection against famine by maximizing fat storage during times of feast.

These same gene variants contribute to the epidemic of obesity.

DIF: Medium REF: 19.2 MSC: Understanding

OBJ: 19.2.b. Explain the thrifty gene hypothesis.

16. This is a Western blot of wild-type neurons after exposure to leptin. Choose the sample (A, B, C, or D) that represents the expected data for POMC neurons and explain the reason for your choice.

ANS: Sample B represents the data from POMC neurons. On leptin signaling in POMC neurons, STAT3 is phosphorylated. NPY gene expression is not altered in these neurons.

DIF: Difficult MSC: Evaluating

REF: 19.2

OBJ: 19.2.c. Summarize the effects of leptin.

17. A patient presents with insulin resistance, hypertension, and hyperlipidemia. What condition would you diagnose this patient as having?

ANS: Metabolic syndrome DIF: Medium REF: 19.2 OBJ: 19.2.e. List the five symptoms of metabolic syndrome.

MSC: Applying

18. A physician believes her patient has metabolic syndrome. In her examining room, she checks the patient’s visceral fat levels and blood pressure. She then writes out a prescription for the patient to obtain bloodwork. The bloodwork includes a glucose tolerance test. What additional bloodwork should the physician order for the patient?

ANS: Analysis of LDL and HDL levels, otherwise known as a lipid profile DIF: Difficult REF: 19.2 OBJ: 19.2.e. List the five symptoms of metabolic syndrome.

MSC: Applying

19. If the bottom curve in this experiment represents the results from a normal human, the top curve represent the results from a human with what disease?

ANS: Type 2 diabetes DIF: Medium REF: 19.2 OBJ: 19.2.f. Differentiate between type 1 and type 2 diabetes.

MSC: Analyzing

20. Insulin-resistant diabetes, once called adult-onset diabetes, is now known as __________. Describe the main characteristics of this type of diabetes and contrast them to the main characteristics of childhood-onset diabetes.

ANS: Type 2 diabetes; Insulin-resistant type 2 diabetes is characterized at initial diagnosis by high levels of circulating insulin and desensitization of insulin receptor signaling in muscle, liver, and adipose tissue. In contrast, type 1 diabetes is due to insufficient insulin production by the pancreatic  cells and is treatable with insulin injections.

DIF: Medium REF: 19.2 OBJ: 19.2.f. Differentiate between type 1 and type 2 diabetes.

MSC: Understanding

21. Design a blood test that could distinguish between those with type 1 diabetes and type 2 diabetes.

ANS: Administer insulin and monitor blood glucose levels over time. A type 1 diabetic will show a response to the insulin, whereas a type 2 diabetic will not.

DIF: Medium REF: 19.2 OBJ: 19.2.f. Differentiate between type 1 and type 2 diabetes.

MSC: Analyzing

22. Differentiate the roles of the two different phosphorylation sites of insulin receptor substrate 1 (IRS1). Include the specific amino acids that are phosphorylated as well as the signaling pathway involved in your answer.

ANS: Phosphorylation of tyrosine (Tyr) results in activation of the phosphoinositide-3 kinase signaling pathway. Phosphorylation of serine (Ser) inhibits phosphorylation of the tyrosine (Tyr). This results in inhibition of the phosphoinositide-3 kinase signaling pathway.

DIF: Difficult REF: 19.2 OBJ: 19.2.g. Evaluate the proposed mechanism for the inhibition of insulin signaling by free fatty

acids. MSC:

Analyzing

23. Compare the phosphorylation state of IRS1 in a normal muscle cell on TNFof a muscle cell exposed to insulin.

exposure with that

ANS: On TNF- exposure IRS1 would be phosphorylated on a serine, whereas insulin exposure results in a phosphorylated tyrosine on IRS1.

DIF: Medium REF: 19.2 OBJ: 19.2.h. Summarize the effects of elevated TNF-alpha on insulin signaling.

MSC: Analyzing 24. Compare the activation levels of AMPK signaling in a normal-weight versus an obese person in response to adiponectin exposure.

ANS: A normal-weight person would have high levels of AMPK signaling, whereas an obese person would have minimally activated AMPK signaling levels.

DIF: Medium REF: 19.2 OBJ: 19.2.i. State the role of adiponectin in insulin sensitivity.

MSC: Analyzing

25. Samples of adipose tissue from a patient were analyzed by Western blot. Samples were obtained before and after treatment with a drug aimed to treat type 2 diabetes. Given the data shown, determine which sample (A or B) was obtained after drug administration. Discuss your reasoning and include the name of the drug that was used in the study.

ANS: Sample B was obtained after administration of thiazolidinedione. Thiazolidinedione is known to upregulate the expression of lipoprotein lipase in adipose tissue.

DIF: Difficult REF: 19.2 OBJ: 19.2.j. Identify the mechanisms by which metformin and thiazolidinediones function as treatments for type 2 diabetes.

MSC: Analyzing 26. Both metformin and thiazolidinedione ultimately activate AMPK signaling. Yet the two drugs achieve this outcome by different means. Contrast the ways that these drugs activate AMPK signaling.

ANS: Metformin is a guanidine analog that elevates AMP levels, which activates AMPK signaling.

Thiazolidinedione activated PPAR -regulated gene expression, which increases adiponectin levels.

Adiponectin then acts through its receptor to activate AMPK signaling.

DIF: Difficult REF: 19.2 OBJ: 19.2.j. Identify the mechanisms by which metformin and thiazolidinediones function as treatments for type 2 diabetes.

MSC: Analyzing

Chapter 20: DNA Replication, Repair, and Recombination MULTIPLE CHOICE 1. The best definition for DNA replication is when a cell copies its __________ genome and is __________ cell division. a. entire; a required element of b. partial; a required element of c. entire; not required for d. partial; not required for ANS: A DIF: Easy REF: 20.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Remembering 2. Semiconservative, as it relates to DNA replication, can be defined as when the original duplex DNA template a. remains intact to make a new DNA duplex. b. is broken into fragments. c. is separated into single strands before replications. d. can only be replicated once.

ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 3.

15

N is heavier than 14N because it has more a. protons. b. electrons. c. neutrons. d. nitrogens.

ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Understanding

4. If 15N DNA replicated using conservative replication in 14N media, the outcome would be that new DNA has a. a single intermediate density. b. a lower density. c. only the higher density. d. one high density and one low density strand.

ANS: D DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Applying 5. What is the name for the relationship between the original DNA and replicate DNA? a. father and son b. parent and children c. parent and daughter

d. mother and daughter ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 6. A replication fork is necessary because it allows a. for DNA replication to start on a single strand. b. for DNA replication to start on the double strand. c. DNA to break into half to start replication. d. DNA to unwind completely to start replication.

ANS: A DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Applying 7. Bidirectional replication is defined as replication a. with one replication fork. b. with two replication forks. c. that unwinds the DNA completely to replicate. d. that replicates the DNA in a given direction.

ANS: B DIF: Medium REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 8. All DNA is synthesized in which direction? a. b. c. d.

ANS: A DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 9. How can DNA strands be synthesized using bidirectional replication? a. They are not synthesized simultaneously. b. One strand is synthesized , whereas the other is . c. They are synthesized through Okazaki fragments. d. They are synthesized using RNA polymerases.

ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Applying 10. The role of Mg2+ in DNA replication is to __________ the incoming deoxynucleotide. a. stabilize the positive charges on b. act as a nucleophile to attack the -phosphoryl group in c. stabilize the negative charges on

d. protonate ANS: C DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Applying 11. The -hydroxyl group used to initiate DNA synthesis comes from a. a RNA primer. b. the magnesium ion. c. uracils, always. d. amino acids, always.

ANS: A DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Analyzing 12. Which enzyme synthesizes the RNA primer for DNA replication? a. DNA polymerase b. DNA primase c. DNA polymerization d. DNA Pol III ANS: B DIF: Easy REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Understanding 13. DNA polymerase does not make mismatched base pairs because a. there are no hydrogen bonds that line up between the mismatches. b. the active site does not fit mismatches well. c. the mismatched pairs make covalent bonds instead of hydrogen bonds. d. the DNA primer does not allow for mismatched pairs.

ANS: B DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Understanding 14. What is a major function of prokaryotic DNA polymerase I besides replication? a. very slow polymerization rate (1–2 nucleotides) to prevent mistakes b. DNA translation c. unlimited processivity d. checking for exonuclease activity ANS: D DIF: Difficult REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Applying 15. Which are the major prokaryotic DNA polymerases? a. Pol I, Pol III, and Pol  b. Pol I, Pol II, and Pol III c. Pol I, Pol II, and Pol  d. Pol I, Pol III, and Pol  ANS: B DIF: Difficult REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Remembering

16. Which prokaryotic polymerase is mainly responsible for DNA proofreading? a. Pol I b. Pol II c. Pol III d. Pol ANS: A DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Remembering 17. Which of the following functions does a reverse transcriptase perform? a. proofreading b. exonuclease activity c. convert RNA to DNA d. convert DNA to RNA ANS: C DIF: Medium REF: 20.1 OBJ: 20.1.c. Describe the function of reverse transcriptase.

MSC: Understanding

18. HIVRT is closely related to which DNA polymerase? a. Pol I b. Pol II c. Pol III d. Pol IV ANS: A DIF: Medium REF: 20.1 OBJ: 20.1.c. Describe the function of reverse transcriptase.

MSC: Remembering

19. The complete complex that contains the enzymes and proteins required to replicate DNA is called the a. primase. b. polymerase. c. replisome. d. DNA gyrase.

ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Remembering 20. What is the correct order of the following steps to synthesize new DNA? 1. Addition of an RNA primer 2. Extension of the RNA primer 3. Conversion of double-stranded DNA to single-stranded DNA 4. Synthesize new DNA a. 1; 2; 3; 4 b. 2; 3; 4; 1 c. 3; 1; 2; 4 d. 4; 1; 3; 2 ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Analyzing 21. Why do helicase and gyrase need to work together?

a. b. c. d.

Gyrase adds the RNA primer and helicase removes it.

Helicase unwinds DNA and gyrase relieves the torsional strain.

Helicase synthesizes DNA and gyrase prevents helicase from dissociating.

Gyrase synthesizes RNA primers and helicase.

ANS: B DIF: Easy REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Understanding 22. The main function of the primosome is to a. synthesize primers for leading strand synthesis. b. synthesize primers for lagging strand synthesis. c. bind to single-stranded DNA to prevent reannealing. d. synthesize new DNA on leading and lagging strand.

ANS: B DIF: Medium REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Remembering 23. The function of the -clamp is to a. keep the torsional strain reduced. b. add the RNA primer. c. keep the Pol III complex associated with the DNA. d. separate the DNA into a single strand.

ANS: C DIF: Easy REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Remembering 24. What is the specific site on the E. coli genome where DNA replication can initiate? a. oriC b. DnaA c. primase d. SeqA ANS: A DIF: Easy REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding 25. The two key elements of the oriC include a. three 13-bp repeats and four 9-bp repeats with enriched G-C base pairs. b. three 13-bp repeats and four 9-bp repeats with enriched A-T pairs. c. 20 subunits of A-T pairs. d. the RNA primer.

ANS: B DIF: Difficult REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Remembering 26. What would happen first if a cell was no longer able to produce DnaA? a. DnaC would not be able to bind to DnaB. b. DnaB would not bind to primase. c. The genome would not be unwound. d. Pol III would not be able to bind to the DNA. ANS: B

DIF: Easy

REF: 20.1

OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Applying 27. The function of Dam methylase in DNA synthesis is to methylate the a. new DNA strand. b. old DNA strand. c. RNA primer. d. primase.

ANS: A DIF: Easy REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Applying 28. Tus-Ter terminates DNA synthesis by a. breaking the single-strand DNA and preventing further synthesis. b. forcing the primase to dissociate. c. blocking the opening of helicase. d. methylating the DNA strand.

ANS: C DIF: Medium REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding 29. Eukaryotic genomes overcome the slow synthesis rate by a. eliminating the need for unwinding the DNA. b. providing more replication origins. c. using multiple primases. d. only replicating part of the DNA in one cycle.

ANS: B DIF: Easy REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Applying 30. The role of CDK in DNA synthesis is to a. remove the histones. b. block further production of pre-RCs while converting pre-RC to RPC. c. block further production of methylated DNA. d. terminate synthesis.

ANS: B DIF: Easy REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding 31. What would a possible outcome be if no primer could be added at the end of a linear chromosome during replication? a. DNA synthesis would restart on the same strand. b. DNA synthesis would be enhanced. c. The chromosome would be shortened every subsequent replication. d. The chromosome would be elongated every subsequent replication.

ANS: C DIF: Difficult REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Applying 32. What is the function of telomerase in termination of DNA synthesis?

a. b. c. d.

remove the telomeres reverse transcription of the telomeres bind to single-strand DNA to prevent refolding shorten the DNA strand after each replication

ANS: B DIF: Difficult REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding 33. What would a possible outcome be if all eukaryotic cells had telomerase activity? a. Cells would die sooner. b. Cells would have increased synthesis. c. The rate of synthesis would increase. d. Cells would live indefinitely.

ANS: D DIF: Medium REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Analyzing 34. Which of the following would cause a genetic mutation? a. DNA makes too many copies in the cell. b. DNA synthesis does not occur. c. DNA damage is not corrected. d. Death of a cell occurs.

ANS: C DIF: Easy REF: 20.2 OBJ: 20.2.a. Describe the relationship between DNA damage and cancer.

MSC: Understanding 35. The most common DNA mutation is the substitution of one base for another. What is the likely outcome from that mutation? a. increased DNA replication b. an alteration of the protein’s coding sequence c. prevention of further synthesis d. cell death ANS: B DIF: Easy REF: 20.2 OBJ: 20.2.a. Describe the relationship between DNA damage and cancer.

MSC: Analyzing 36. Most cancers are caused by which kind of DNA mutation? a. base substitution b. abasic site c. somatic d. nucleotide deletions ANS: C DIF: Easy REF: 20.2 OBJ: 20.2.a. Describe the relationship between DNA damage and cancer.

MSC: Applying 37. When do somatic mutations occur? a. G1 phase b. S phase c. G2 phase d. after zygote formation

ANS: D DIF: Easy REF: 20.2 OBJ: 20.2.a. Describe the relationship between DNA damage and cancer.

MSC: Understanding 38. Which of the following is the most common type of DNA damage? a. deamination of cytosine b. deamination of uracil c. methylation of adenine d. methylation of tyrosine ANS: A DIF: Easy REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Understanding

39. When a cytosine is deaminated to form uracil and removed by glycosylase enzymes, a __________ site is generated. a. nonbasic b. abasic c. dibasic d. deaminated ANS: B DIF: Easy REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Applying

40. Cytosine can be deaminated because it has a free __________ that can be removed. a. keto group b. amine c. amide group d. ester group ANS: B DIF: Easy REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Analyzing

41. Spending time in the sun is a possible cause of DNA damage because UV radiation a. causes an abasic site to form. b. produces photoproducts. c. causes protein misfolding. d. produces methylated thymidine.

ANS: B DIF: Medium REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Applying

42. What is a possible outcome when UV light reacts with riboflavin or tryptophan? a. methylated riboflavin b. reactive oxygen species c. spontaneous deglycosylation d. production of an abasic site ANS: B DIF: Easy REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Applying

43. The DNA alkylation of guanine is possible because the __________ of guanine is __________ and reacts rapidly with __________ alkylating agents. a. N-7; nucleophilic; electrophilic b. N-5; nucleophilic; electrophilic c. N-7; electrophilic; nucleophilic

d. N-5; electrophilic; nucleophilic ANS: A DIF: Difficult REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Applying

44. If a cell has many ROS species, what is the most likely reaction with DNA? a. Nothing, because ROS do not react with DNA. b. G-C to T-A replacement c. O-alkylation of thymine d. single point excision ANS: B DIF: Difficult REF: 20.2 OBJ: 20.2.b. List the major causes of damage to DNA.

MSC: Applying

45. What is the mechanism by which replication errors are fixed in E. coli? a. degrading of the entire DNA strand to start over b. base excision c. mismatch repair d. abasic repair ANS: B DIF: Easy REF: 20.2 OBJ: 20.2.d. Distinguish between base excision repair and nucleotide excision repair.

MSC: Understanding 46. What is the function of the MutS-MutL-MutH protein complex? a. base excision b. mismatch repair c. DNA adenylation d. DNA methylation ANS: B DIF: Difficult REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Understanding 47. Base excision repair removes which kind of bases? a. mismatched b. methylated c. those damaged by ROS d. uracil ANS: C DIF: Medium REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Understanding 48. If a strand of DNA has a large lesion that distorts the helical nature of the DNA, what would be the mechanism of repair? a. mismatch repair b. abasic repair c. base excision d. nucleotide excision ANS: D DIF: Difficult REF: 20.2 OBJ: 20.2.d. Distinguish between base excision repair and nucleotide excision repair.

MSC: Applying 49. What is NOT a likely repair system used if a strand of DNA has a pyrimidine dimer?

a. b. c. d.

mismatch repair direct repair pathway base excision nucleotide excision

ANS: A DIF: Medium REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Applying 50. What are the mechanisms for excision nucleotide repairs in eukaryotes? a. global genomic and mismatch b. global genomic and base excision c. transcription-coupled and partial genomic d. transcription-coupled and global genomic ANS: D DIF: Medium REF: 20.2 OBJ: 20.2.d. Distinguish between base excision repair and nucleotide excision repair.

MSC: Applying 51. Which of the following is a specialized direct DNA repair process? a. DNA photolyase system b. nucleotide excision repair c. base excision repair d. DNA mismatch repair ANS: A DIF: Medium REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Understanding 52. Which of the following best describes base excision? a. removal and replacement of individual bases that have been damaged by various chemical reactions b. repair of large lesions that distort DNA c. removal of individual bases that have been phosphorylated d. repair of small lesions that distort DNA ANS: A DIF: Medium REF: 20.2 OBJ: 20.2.d. Distinguish between base excision repair and nucleotide excision repair.

MSC: Applying 53. DNA photolyase specifically seeks out what kind of DNA damage? a. base mismatch b. abasic sites c. pyrimidine dimers d. phosphorylated base ANS: C DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Applying 54. Methenyltetrahydrofolate (MTHF) absorbs light to form *MTHF. What does the star on MTHF signify? a. radical b. excited c. cation

d. anion ANS: B DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 55. MGMT is called the suicide enzyme because its active site permanently becomes a. phosphorylated. b. methylated. c. protonated. d. ionized.

ANS: B DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 56. What DNA damage can the MGMT enzyme repair? a. phosphorylated adenine b. methylated guanine c. pyrimidine dimers d. mismatched bases ANS: B DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 57. What role does PARP1 have in repairing a single-strand DNA break? a. recognizes the break b. removes the methyl group from guanine c. replaces the mismatched pair d. absorbs light to become excited ANS: A DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 58. Homologous recombination repairs what kind of DNA damage? a. single-strand break b. double-strand break c. mismatched pairs d. pyrimidine dimers ANS: B DIF: Difficult REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 59. Homologous recombination can only be used in late S phase or G2 phase because it a. requires the presence of an intact sister chromatid as a template. b. does not require the presence of a homologous template. c. requires the cell to be in cell division. d. requires the cell to be in the resting phase.

ANS: A DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing

60. What role do BRCA1 and BRCA2 play in DNA repair? a. find the double-strand break b. assist with strand invasion c. repair pyrimidine dimers d. synthesize new DNA bases ANS: B DIF: Difficult REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 61. Mutation of the BRCA protein can lead to a. breast cancer. b. lymphoma. c. arthritis. d. bone tumors.

ANS: A DIF: Easy REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 62. Individuals with mutations of BRCA have increased incidence of cancer because of their a. increased ability to form pyrimidine dimers. b. decreased ability to repair single-strand DNA breaks. c. decreased ability to repair double-strand DNA breaks. d. increased ability to form methylated guanine.

ANS: C DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 63. If one parent has Lynch syndrome but the other does not, what is the likelihood that the child will also have Lynch syndrome? a. 10% b. 25% c. 50% d. 100% ANS: C DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Analyzing 64. Lynch syndrome is a genetic deficiency in __________ repairs. a. DNA excision b. single-strand c. double-strand d. mismatch ANS: D DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 65. In what stage of the cell cycle does homologous recombination largely occur? a. G1 b. S c. G2

d. meiosis ANS: D DIF: Easy REF: 20.3 OBJ: 20.3.a. Explain the role of meiosis in contributing to genetic diversity.

MSC: Remembering 66. DNA crossover is important during meiosis because it allows a. the organization of genes on the chromosome to change. b. DNA repair to occur. c. exchange of genetic information. d. base excision to occur.

ANS: C DIF: Medium REF: 20.3 OBJ: 20.3.a. Explain the role of meiosis in contributing to genetic diversity.

MSC: Analyzing 67. A Holliday junction can best be defined as a region of a. quadruplex DNA. b. duplex DNA. c. DNA damage. d. DNA pyrimidine duplexes.

ANS: A DIF: Medium REF: 20.3 OBJ: 20.3.a. Explain the role of meiosis in contributing to genetic diversity.

MSC: Remembering 68. Lysogeny by bacteriophages causes what result to the host DNA? a. integration of virus DNA into host DNA b. production of new bacteriophage particles c. cell death d. formation of Holliday junctions ANS: A DIF: Easy REF: 20.3 OBJ: 20.3.c. Compare bacteriophage lytic and lysogenic cycles.

MSC: Understanding 69. If a bacteriophage activates the lytic cycle, what is the result to the host DNA? a. integration of virus DNA into host DNA b. production of new bacteriophage particles c. cell death d. formation of Holliday junctions ANS: B DIF: Easy REF: 20.3 OBJ: 20.3.c. Compare bacteriophage lytic and lysogenic cycles.

MSC: Analyzing 70. An HIV infection begins with what first step? a. fusion of the cell membrane and viral envelope b. release of viral DNA and synthesis of cDNA c. protein synthesis and processing d. budding of infectious virus ANS: A DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Understanding

71. An advantage of viral DNA using LTR to produce a four-nucleotide overhang on the 3 end is to a. start replication. b. help with alignment of the viral DNA to the host DNA. c. start a base mismatch repair sequence. d. help with cell meiosis.

ANS: B DIF: Medium REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Applying 72. The definition of a transposon is a segment of a. DNA that can move from one region to another. b. RNA that can move from one region to another. c. DNA that is easily transcribed. d. DNA that is in need of repair.

ANS: A DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Remembering 73. The definition of a retrotransposon is a segment of a. DNA that goes through an RNA intermediate to be moved. b. RNA that goes through a DNA intermediate to be moved. c. DNA that needs to be excised. d. DNA that is folded incorrectly.

ANS: A DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Remembering 74. The importance of V(D)J recombination is that it gives rise to new a. viruses being formed. b. DNA combinations. c. antibodies. d. RNA combinations.

ANS: C DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Applying 75. AZT is such a good HIV drug because it a. prevents new DNA from being replicated. b. prevents HIV from binding to the cell. c. allows DNA to repair itself after viral DNA is added. d. allows DNA to be replicated at a slower rate.

ANS: A DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Applying SHORT ANSWER 1. Describe the Meselson-Stahl experiment and how it provided biochemical evidence that DNA replication is semiconservative.

ANS: Escherichia coli grown in 15N-containing medium contain heavy DNA. When allowed to divide in 14 N-containing medium, a hybrid DNA is produced that contains one strand of heavy DNA and one strand of light DNA. A second round of division produces one hybrid DNA molecule and one light DNA molecule. This result could only occur through semiconservative replication.

DIF: Difficult REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 2. Using the figure below, identify conservative replication, dispersive replication, and semiconservative replication.

ANS: In this image conservative replication is on the left, dispersive replication is in the middle, and semiconservative replication is on the right.

DIF: Easy REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Remembering 3. Describe the experiment that demonstrated that complete unwinding of the chromosome does not occur.

ANS: John Cairnes grew E. coli in the presence of 3H-thymidine. This method then allowed him to visualize individual molecules of replicating DNA by the use of autoradiography. Even individual molecules in the midst of replication could be seen. The experiment showed that both single-stranded and double-stranded regions are found within DNA molecules. He was able to demonstrate that DNA replicates through the use of a replication fork.

DIF: Difficult REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Applying

4. Describe how Okazaki fragments allow for simultaneous synthesis of double-stranded DNA. ANS: For double-stranded DNA to be continuously synthesized, one strand is synthesized continuously and the other is synthesized in fragments known as Okazaki fragments. The continuously synthesized strand is called the leading strand, whereas the strand containing the Okazaki fragments is called the lagging strand and is synthesized discontinuously. DNA synthesis is only possible in the to direction. Therefore, as the replication fork unwinds it can only expose a small amount of template DNA on the lagging strand in the to direction.

DIF: Medium REF: 20.1 OBJ: 20.1.a. Define the terms semiconservative and bidirectional in regard to genome duplication.

MSC: Applying 5. Describe the differences among Pol I, Pol II, and Pol III in prokaryotic organisms.

ANS: Pol III is the main polymerizing enzyme that can perform exonuclease for proofreading.

Pol I is involved in proofreading of newly synthesized DNA, DNA repair, and removal of RNA primers. Pol I has both and exonuclease activity. Pol II has the main function of DNA repair.

DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Applying 6. Describe the differences between Pol

, Pol , and Pol

in eukaryotic organisms.

ANS: Pol  has an extremely high processivity but slow reaction rate and contains exonuclease activity. Pol is responsible for leading strand synthesis and is also capable of proofreading. Pol is most often associated with lagging strand synthesis.

DIF: Medium REF: 20.1 OBJ: 20.1.b. Categorize the major eukaryotic and prokaryotic DNA polymerases by name and function.

MSC: Applying 7. How does reverse transcriptase convert RNA to DNA? ANS: Reverse transcriptase first uses the single-stranded RNA as a template to produce a DNA-RNA hybrid. This is then converted into double-stranded DNA using the reverse transcriptase again. As with DNA polymerases a free -hydroxyl group is required for the polymerase reaction to take place. This hydroxyl group is provided by the end of the transfer RNA. DIF: Medium REF: 20.1 OBJ: 20.1.c. Describe the function of reverse transcriptase.

8. Explain the trombone model of DNA synthesis.

ANS:

MSC: Understanding

The trombone model of DNA synthesis at the fork proposes that the Pol III core on the lagging strand template alternates between bound and unbound forms. The Pol III core on the lagging strand template synthesizes an Okazaki fragment from the 3 end of one RNA primer until it reaches the 5 end of the RNA primer farther down the lagging strand template. This primer extension and DNA synthesis on the lagging strand template resemble the slide arm of a trombone as the loop is extended. Once the Pol III core releases the lagging strand template DNA strand, the DNA loop shrinks in size much like the retraction of the trombone arm. Reassociation of the Pol III core with the lagging strand template at the site of the next RNA primer starts the process over again with synthesis of the next Okazaki fragment.

DIF: Difficult REF: 20.1 OBJ: 20.1.d. Identify the major prokaryotic and eukaryotic replication fork proteins.

MSC: Understanding 9. How is Dam methylase able to be a control mechanism for DNA replication initiation?

ANS: Methylation by Dam methylase is used to distinguish the original strand in newly synthesized DNA from the new strand. At oriC the hemimethylated state lasts substantially longer, generally about a third of the cell cycle. This is an important control mechanism in replication initiation at oriC because it apparently prevents a second round of initiation from occurring before the first round has been completed.

DIF: Difficult REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding 10. Using the figure below, explain the replication and termination of DNA synthesis in E. coli.

ANS: DNA synthesis proceeds bidirectionally until the DNA replication forks reach each other halfway around the genome at the termination region. Resolution of the two opposing replication forks produces two daughter DNA molecules, each containing one old strand of DNA and one nascent DNA strand.

DIF: Medium REF: 20.1 OBJ: 20.1.e. Compare initiation and termination of replication in prokaryotes and eukaryotes.

MSC: Understanding

11. Describe the Ames test.

ANS: The test determines whether or not a substance is mutagenic to a particular strain of bacteria, Salmonella typhimurium, which lacks the ability to produce histidine because of mutations in the genes for histidine synthesis. The bacteria are first exposed to the agent being tested. If the bacteria are able to grow in a medium that is not supplemented with the amino acid histidine, this indicates a back mutation has occurred as a result of exposure to the agent that allowed the histidine synthesis genes to regain their function.

DIF: Medium REF: 20.2 OBJ: 20.2.a. Describe the relationship between DNA damage and cancer.

MSC: Understanding 12. Compare the two different outcomes of cytosine deamination as replication proceeds.

ANS:

As shown in Figure 20.34, there are two different outcomes of cytosine deamination depending on whether replication occurs before or after repair. If replication occurs with the uracil in place, one of the daughter strands will incorporate an adenine base as a complement to the uracil, which will result in conversion of a C-G base pair to T-A. If replication takes place with an abasic site present, a cytosine is often inserted opposite the abasic site. This results in a C-G to G-C mutation.

DIF: Medium DNA. MSC: Evaluating

REF: 20.2

OBJ: 20.2.b. List the major causes of damage to

13. Contrast missense mutations, nonsense mutations, and silent mutations.

ANS: It takes three nucleotide bases in DNA to specify an amino acid codon in RNA. A DNA mutation in one of the three nucleotide bases in a codon might not result in a change of the amino acid sequence, which is called a silent mutation. Alternatively a single nucleotide change could result in incorporation of a chemically similar or dissimilar amino acid; such mutations are called missense mutations. If the mutation results in the substitution of the original amino acid with one that is chemically similar, then it is called a conservative missense mutation, whereas if the substituted amino acid is chemically dissimilar, then it is called a nonconservative missense mutation. A nonsense mutation is one in which the nucleotide change converts an amino acid codon into a stop codon that terminated the protein synthesis process before the true end of the protein is reached.

DIF: Difficult DNA. MSC: Evaluating

REF: 20.2

OBJ: 20.2.b. List the major causes of damage to

14. Explain the mechanism of base excision repair.

ANS:

Base excision repair is mediated by short-patch and long-patch mechanism. Short-patch base excision repair removes only one nucleotide, whereas long-patch base excision repair removes up to 10 nucleotides. Using Figure 20.39 in the text as an example, after formation of an abasic site, the AP1 endonuclease cleaves the phosphodiester backbone to generate an abasic deoxyribose phosphate (dRP), which is either removed by the enzyme lyase or displaced by Pol I as a result of DNA synthesis.

DIF: Medium REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Understanding 15. Explain the mechanism of nucleotide excision repair.

ANS: Nucleotide excision repair is initiated by recognition of the lesion by UvrAB complex. Nicks in the DNA are created by UvrB and UvrC. UvrD removes the polynucleotide containing the lesion, followed by gap repair using Pol I and ligase.

DIF: Medium REF: 20.2 OBJ: 20.2.c. Explain the importance of the DNA mismatch repair system.

MSC: Understanding 16. Distinguish between base excision and nucleotide excision repair.

ANS: Base excision repair is responsible for removal and replacement of individual bases that have been damaged by various chemical reactions. Nucleotide excision repair is used for large lesions that distort the helical nature of DNA. DIF: Medium REF: 20.2 OBJ: 20.2.d. Distinguish between base excision repair and nucleotide excision repair.

MSC: Analyzing 17. Describe the mechanism for repair of DNA damage by photolyase.

ANS: As shown in Figure 20.41 in the text, DNA is repaired in a six-step mechanism. (1) Light is absorbed by the folate coenzymes (MTHF). (2) Energy is transferred from MTHF* to FADH- to generate the excited state *FADH-. (3) Electron transfer occurs from *FADH- to the cyclobutane dimer substrate. (4) Radical reaction breaks the first bond. (5) Radical reaction breaks the second bond. (6) An electron is transferred to FADH, and the adjacent pyrimidines are restored to their normal structure.

DIF: Difficult REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 18. Explain the suicide mechanism for MGMT. ANS: As shown in Figure 20.42 in the text, the MGMT enzyme uses a suicide mechanism to remove the CH3 group from O6-methylguanine. An active site cysteine residue displaces the methyl group to produce a homocysteine residue. This modification inactivates the protein, which is then degraded to metabolize the homocysteine.

DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Understanding 19. How is an individual with Lynch syndrome at higher risk for cancer?

ANS: Lynch syndrome is caused by autosomal dominant mutations in the gene encoding the human mismatch repair enzymes hMLH1 and hMSH2. Mutations in just one copy of either of these DNA repair enzyme genes lead to HNPCC at a relatively early age, which is in large part the result of the critical role in maintaining genome integrity.

DIF: Medium REF: 20.2 OBJ: 20.2.e. Describe the repair pathways for double-strand DNA breaks.

MSC: Evaluating 20. How do Holliday junctions work in DNA recombination?

ANS: Double-strand DNA breaks are first made as shown in Figure 20.48. After the break a 3 single-stranded DNA overhang can cross over to bind homologous sequences in another DNA molecule. Ligation of the ends forms a region where multiple DNA strands come together, called a Holliday junction. Holliday junctions can be moved along the now-joined chromosomes by helicase activity.

DIF: Easy REF: 20.3 OBJ: 20.3.b. State the significance of a Holliday junction in recombination.

MSC: Understanding 21. Use the following figure to distinguish between the two possible outcomes from Holliday junctions.

ANS: A resolvase can bind at either sites 1 or 2. If binding occurs such that cuts are made at sites 1 followed by ligation, then the products show no crossover. If binding occurs such that cuts are made at sites 2 followed by ligation, crossover occurs.

DIF: Easy REF: 20.3 OBJ: 20.3.b. State the significance of a Holliday junction in recombination.

MSC: Analyzing 22. Compare bacteriophage lytic and lysogenic cycles.

ANS: After bacteriophage infections, the viral DNA can enter a lytic cycle or undergo lysogeny. A lytic cycle causes production of large amounts of the virus, followed by cell lysis. Lysogeny causes the phage DNA to be replicated with each bacterial replication.

DIF: Easy REF: 20.3 OBJ: 20.3.c. Compare bacteriophage lytic and lysogenic cycles.

MSC: Analyzing 23. Describe the HIV infection cycle.

ANS: The HIV infection (as shown in Figure 20.54 in the text) requires conversion of the viral genome to cDNA that is then integrated into the host cell genome by a recombination event. After binding of the virus to the CD4 receptor and membrane fusion, the RNA genome is inserted into the host cell. Reverse transcriptase uses the single-stranded RNA to produce a cDNA-RNA hybrid. The RNase activity of reverse transcriptase degrades the RNA, then forms duplex DNA by polymerization of the complementary strand.

DIF: Medium REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Understanding 24. Describe the mechanism of retroviral DNA integration into a eukaryotic genome.

ANS: HIV integration into the host cell genome is initiated by integrase binding both ends of the viral DNA and removing several nucleotides to crease a 5 overhang. The host DNA is captured and cleaved to produce complementary ends. Integrase facilitates strand transfer to join the ends of viral and host DNA, followed by gap repair to complete the integration process as illustrated in Figure 20.55.

DIF: Difficult REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Understanding 25. What is the difference between a transposon move and a retrotransposon move?

ANS: Transposons move by a cut-and-paste mechanism mediated by transposase enzymes and inverted repeat sequences. Retrotransposons move through a RNA intermediate, which is transcribed into cDNA by the enzyme reverse transcriptase. Insertion requires an integrase enzyme and LTR sequences.

DIF: Easy REF: 20.3 OBJ: 20.3.d. Describe the mechanism of retroviral DNA integration into a eukaryotic host cell genome.

MSC: Analyzing

Chapter 21: RNA Synthesis, Processing, and Gene Silencing MULTIPLE CHOICE 1. The RNA type directly involved in protein synthesis is a. small nuclear RNA. b. short interfering RNA. c. ribosomal RNA. d. long nc RNA. ANS: C DIF: Easy REF: 21.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Analyzing 2. Which class of RNA molecules is unique to eukaryotic organisms? a. transfer RNA b. ribosomal RNA c. small nuclear RNA d. messenger RNA ANS: C DIF: Easy REF: 21.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Applying 3. Which class of RNA molecule is typically the shortest in length? a. transfer RNA b. messenger RNA c. small nuclear RNA d. micro RNA ANS: D DIF: Medium REF: 21.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Remembering 4. Which of the following is a coding RNA molecule? a. short interfering RNA. b. TERC RNA. c. small nucleolar RNA. d. messenger RNA. ANS: D DIF: Easy REF: 21.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Remembering 5. RNA is typically more susceptible to backbone hydrolysis than DNA because of the a. presence of simpler nucleotides. b. presence of a OH group. c. presence of a OH group. d. lack of thymine nucleotides.

ANS: B DIF: Medium REF: 21.1 OBJ: 21.1.b. Name the three ways in which RNA is a highly dynamic biomolecule.

MSC: Evaluating

6. RNA is a highly dynamic biomolecule in that it a. can fold and hydrogen bond with itself, DNA, proteins, or small molecules to adopt largely modified tertiary structures. b. is less capable of forming stable H-bonds than DNA. c. is often shorter than DNA. d. is largely composed of a phosphate backbone.

ANS: A DIF: Medium REF: 21.1 OBJ: 21.1.b. Name the three ways in which RNA is a highly dynamic biomolecule.

MSC: Analyzing 7. How are RNA structures different from protein structures? a. RNA is single stranded, whereas proteins are not. b. RNA can H-bond with itself, whereas proteins cannot. c. RNA mutations can lead to nonfunctioning proteins, whereas protein mutations do not. d. RNA adopts less defined tertiary structures than proteins.

ANS: D DIF: Difficult REF: 21.1 OBJ: 21.1.b. Name the three ways in which RNA is a highly dynamic biomolecule.

MSC: Evaluating 8. RNA is a dynamic biomolecule because it can a. be a component in protein synthesis, regulate protein synthesis, and be synthesized and function in cell nucleus. b. catalyze its own synthesis. c. contain a ribose sugar backbone. d. be stable to hydrolysis.

ANS: A DIF: Medium REF: 21.1 OBJ: 21.1.b. Name the three ways in which RNA is a highly dynamic biomolecule.

MSC: Analyzing 9. Of the following protein synthesizing RNA molecules, which codes for a protein? a. tRNA b. siRNA c. mRNA d. rRNA ANS: C DIF: Easy REF: 21.1 OBJ: 21.1.c. Define the protein-synthesizing RNA molecules.

MSC: Remembering

10. Which protein-synthesizing RNA molecule carries an amino acid to the ribosome active site? a. rRNA b. tRNA c. mRNA d. siRNA ANS: A DIF: Easy REF: 21.1 OBJ: 21.1.c. Define the protein-synthesizing RNA molecules.

11. Which RNA molecule does NOT bind to the ribosome? a. tRNA b. rRNA c. mRNA d. snRNA

MSC: Remembering

ANS: D DIF: Medium REF: 21.1 OBJ: 21.1.c. Define the protein-synthesizing RNA molecules.

MSC: Analyzing

12. Which of the following RNA molecules has the LEAST number of different sequences in a given organism? a. tRNA b. rRNA c. mRNA d. snRNA ANS: B DIF: Difficult REF: 21.1 OBJ: 21.1.c. Define the protein-synthesizing RNA molecules.

MSC: Evaluating

13. Prokaryotic mRNA is commonly processed through a. splicing by RNaseP enzymes. b. immediate translation during transcription. c. addition of 7-methylguanylate cap. d. removal of exons.

ANS: B DIF: Difficult REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Analyzing 14. Which is often removed from eukaryotic mRNA before translation? a. poly(A) tails b. exons c. polycistrons d. introns ANS: D DIF: Medium REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Remembering 15. The most significant influence on why mRNA is processed differently in prokaryotes than eukaryotes is the fact that a. eukaryotes separate transcription and translation with a nucleus. b. prokaryotes are often polycistronic. c. eukaryotes are multicellular organisms. d. prokaryotes do not add a poly(A) tail.

ANS: A DIF: Difficult REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Evaluating 16. A 7-methylguanylate cap and poly(A) tail is added to mRNA to a. differentiate the mRNA from the tRNA. b. facilitate binding and translation by the ribosome. c. increase mRNA splicing efficiency. d. signify the start and end of the gene sequence.

ANS: B DIF: Medium REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Understanding 17. Which enzyme is important in the processing of tRNA and mRNA from prokaryotes?

a. b. c. d.

RNaseP snRNA reverse transcriptase ribozyme

ANS: A DIF: Easy REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Remembering 18. Long noncoding RNA (lncRNA) is generated from a. the tips of chromosomes. b. the transcription of genomic DNA. c. the splicing of used mRNA. d. an infection of viral RNA. ANS: B DIF: Easy REF: 21.1 OBJ: 21.1.e. List four mechanisms by which lncRNA could regulate cellular processes.

MSC: Understanding 19. It has been estimated that as much as __________ % of the human genome is transcribed into noncoding RNA, whereas __________ % of the E. coli genome is noncoding RNA. a. 10; 90 b. 90; 10 c. 50; 10 d. 25; 2 ANS: C DIF: Medium REF: 21.1 OBJ: 21.1.e. List four mechanisms by which lncRNA could regulate cellular processes.

MSC: Understanding 20. A knockout mutation in the X-inactive specific transcript (XIST) lncRNA of mice would result in a. one inactivated X chromosome in female mice. b. the inhibited transcription and translation of X-linked proteins. c. two inactive X chromosomes in female mice. d. two active X chromosomes in female mice.

ANS: D DIF: Difficult REF: 21.1 OBJ: 21.1.e. List four mechanisms by which lncRNA could regulate cellular processes.

MSC: Evaluating 21. Long noncoding RNAs (lncRNAs) are found on a. exons of protein-coding genes. b. introns of protein-coding genes. c. non-functional rRNA. d. protein-coding mRNA. ANS: B DIF: Easy REF: 21.1 OBJ: 21.1.e. List four mechanisms by which lncRNA could regulate cellular processes.

MSC: Understanding 22. Which is true of RNA polymerases in both prokaryotic and eukaryotic organisms? a. They are composed of an analogous core. b. There is a single enzyme type per organism. c. They make copies of RNA from either DNA or RNA templates. d. They have the same number of cofactors in prokaryotes and eukaryotes.

ANS: A DIF: Easy REF: 21.2 OBJ: 21.2.a. Define the sigma factor and promoter region.

MSC: Analyzing

23. Eukaryotic RNA polymerase a. is a ribozyme. b. contains as many as five protein subunits in the final functional enzyme. c. synthesizes all RNA types. d. has a common core structure resembling that of prokaryotic RNA polymerase.

ANS: D DIF: Medium REF: 21.2 OBJ: 21.2.a. Define the sigma factor and promoter region.

MSC: Analyzing

24. What are factors in RNA synthesis? a. DNA promoter regions b. RNA polymerases c. transcription factors d. receptor proteins ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.a. Define the sigma factor and promoter region.

MSC: Remembering

25. What do factors bind to in RNA synthesis? a. DNA promoters and RNA polymerase b. RNA promoters and DNA c. DNA and RNA d. transcription factors ANS: A DIF: Medium REF: 21.2 OBJ: 21.2.a. Define the sigma factor and promoter region.

MSC: Applying

26. The function of DNase I is that it a. cuts DNA whenever DNA binding proteins are present. b. cuts double-stranded DNA by cutting phosphodiester bonds. c. cuts DNA binding proteins. d. makes an RNA copy of DNA. ANS: B DIF: Easy REF: 21.2 OBJ: 21.2.b. Explain the process of DNase I footprinting.

MSC: Understanding

27. The information gained from the DNA footprinting technique is the a. DNA sequence. b. promotor region of a gene. c. location of a gene in DNA. d. location of a DNA binding protein on DNA. ANS: D DIF: Medium REF: 21.2 OBJ: 21.2.b. Explain the process of DNase I footprinting.

MSC: Applying

28. Which biochemical lab technique is used in the DNA footprinting technique? a. gel electrophoresis b. polymerase chain reaction c. plasmid ligation d. cloning ANS: A

DIF: Medium

REF: 21.2

OBJ: 21.2.b. Explain the process of DNase I footprinting.

MSC: Applying

29. Using the DNA footprinting technique, which of the following were/was identified as binding site(s) for factors? a. -35 box b. -5 and -35 box c. -10 and -35 box d. -10 box ANS: C DIF: Easy REF: 21.2 OBJ: 21.2.b. Explain the process of DNase I footprinting.

MSC: Remembering

30. The DNA sequence of prokaryotic gene promotors were found to be a. largely conserved. b. distinct for each gene. c. capable of binding different promoters. d. strong binders of DNA polymerase.

ANS: A DIF: Medium REF: 21.2 OBJ: 21.2.c. Distinguish between a strong promoter and a weak promoter.

MSC: Analyzing 31. Strong prokaryotic promoters a. bind tightly to the transcription factors. b. have factors that are larger, more stable proteins. c. generally result in a higher rate of transcription. d. are less common in prokaryotes.

ANS: C DIF: Difficult REF: 21.2 OBJ: 21.2.c. Distinguish between a strong promoter and a weak promoter.

MSC: Evaluating 32. Weak prokaryotic promoters a. can bind to different transcription factors. b. have a DNA sequence that is significantly different from that of other common promotors. c. can be easily bound to factors. d. give weak DNA footprinting signals.

ANS: B DIF: Difficult REF: 21.2 OBJ: 21.2.c. Distinguish between a strong promoter and a weak promoter.

MSC: Evaluating 33. What prokaryotic promoter would most likely control a housekeeping gene? a. weak promoter b. -10 and -35 box c. TATA box d. strong promoter ANS: D DIF: Medium REF: 21.2 OBJ: 21.2.c. Distinguish between a strong promoter and a weak promoter.

MSC: Applying 34. Eukaryotic promoters, but NOT prokaryotic promoters, a. are located before the transcription start site. b. bind transcription factors.

c. are located after the transcription start site. d. assist in activating transcription.

ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.d. Compare and contrast eukaryotic and prokaryotic promoters.

MSC: Analyzing 35. Approximately how many different types of RNA promotors are needed in eukaryotic systems? a. 1 b. 2 c. 3 d. 4 ANS: C DIF: Easy REF: 21.2 OBJ: 21.2.d. Compare and contrast eukaryotic and prokaryotic promoters.

MSC: Understanding 36. Eukaryotic transcription promoters a. require multiple DNA binding regions. b. are largely conserved across the genome. c. can stimulate DNA polymerases by direct binding. d. control translational as well as transcriptional events.

ANS: A DIF: Difficult REF: 21.2 OBJ: 21.2.d. Compare and contrast eukaryotic and prokaryotic promoters.

MSC: Evaluating 37. Eukaryotic transcription promoters a. are typically found after the transcription start site. b. have a single sequence and bind one RNA polymerase type. c. may bind to both transcription factors and RNA polymerases. d. are all controlled by a ubiquitous factor.

ANS: C DIF: Difficult REF: 21.2 OBJ: 21.2.d. Compare and contrast eukaryotic and prokaryotic promoters.

MSC: Evaluating 38. The __________ strand of DNA is transcribed into mRNA. a. leading b. coding c. lagging d. template ANS: D DIF: Medium REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Remembering 39. Which is NOT required in the prokaryotic transcription initiation complex? a. a primer b. RNA polymerase c. initiation factor d. a ribonucleotide triphosphate (NTP) ANS: A DIF: Easy REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Understanding

40. In which direction is mRNA synthesized by RNA polymerase? a. in the to direction b. with to phosphodiester linkages c. in the to direction d. It depends on whether the sense or antisense strand is transcribed.

ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Evaluating 41. In E. coli, __________ RNA-DNA base pairs are maintained and about __________ base pairs of single-stranded DNA are maintained in the transcription bubble. a. 20; 80 b. 8; 17 c. 17; 20 d. 200; 1000 ANS: B DIF: Medium REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Remembering 42. At what point during transcription does the a. in the initiation phase b. in the termination phase c. before the elongation phase d. during the elongation phase

factor dissociate from the RNA polymerase?

ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Remembering 43. Prokaryotic transcription could terminate by a. association of a factor with the DNA. b. RNA with GC stem loop structures. c. a G-rich region on the DNA. d. RNA polymerase without the elongation factor.

ANS: B DIF: Medium REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Evaluating 44. The initiation of transcription in eukaryotes a. occurs in the same manner as prokaryotic transcription. b. requires the complete unfolding of the gene into single-stranded DNA. c. requires many more transcription factors than prokaryotic transcription. d. uses RNA polymerase as well as helicase and primase.

ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Analyzing 45. The initiation, elongation, and termination of eukaryotic transcription is controlled by the a. extent of phosphorylation and dephosphorylation of the RNA polymerase. b. presence of initiation, elongation, and termination factors binding to RNA polymerase.

c. unwinding the double-stranded DNA. d. length of the RNA transcript.

ANS: A DIF: Medium REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Analyzing 46. The C-terminal domain (CTD) of the eukaryotic RNA polymerase II is involved in the transcriptional process of a. addition of a poly(A) tail. b. removal of exons. c. directing RNA to the cytoplasm. d. product phosphorylation.

ANS: A DIF: Medium REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Analyzing 47. A difference between transcription in prokaryotes and eukaryotes is the a. lack of need for a primer. b. presence of a transcription bubble. c. addition of a poly(A) tail. d. direction of transcription on the DNA template.

ANS: C DIF: Medium REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Evaluating 48. Eukaryotic RNA polymerase II facilitates the a. removal of exons. b. addition of 7-methylguanylate cap. c. addition of a poly(A) tail. d. translation of the RNA transcript.

ANS: B DIF: Easy REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Understanding 49. Most post-transcriptional RNA processing reactions are catalyzed by a. DNAzymes. b. ribozymes. c. ligases. d. transferases.

ANS: B DIF: Easy REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Remembering 50. Trans activity refers to the __________ for a ribozyme. a. cleavage of another identical RNA molecule b. intermolecular cleavage of substrate c. intramolecular cleavage d. conserved activity of all enzymes ANS: B DIF: Medium REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Understanding 51. The following is referred to as the __________ ribozyme.

a. b. c. d.

stem-loop hairpin hammerhead cloverleaf

ANS: C DIF: Easy REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Remembering 52. Cis-acting enzymes are a. self-operating enzymes. b. enzymes that operate on a target molecule. c. intermolecular-operating enzymes. d. enzymes that operate on other enzymes.

ANS: A DIF: Medium REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Understanding 53. Which is true of ribozymes? a. They have conserved primary sequences. b. They are not true catalysts. c. They are transcription factors. d. They have conserved secondary and tertiary structures.

ANS: D DIF: Medium REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Evaluating 54. What is a difference between group I and group II introns? a. intron cleaving versus exon ligating abilities

b. cis versus trans cleaving capabilities c. linear versus lariat intron products d. nucleophilic versus electrophilic hydroxyl attacks ANS: C DIF: Medium REF: 21.3 OBJ: 21.3.b. Differentiate between group I and group II introns.

MSC: Analyzing 55. What do group I introns require that group II introns do not? a. ATP hydrolysis b. metal ion cofactors c. guanosine cofactor binding d. external RNA substrate ANS: C DIF: Easy REF: 21.3 OBJ: 21.3.b. Differentiate between group I and group II introns.

MSC: Remembering 56. Group I and group II introns are similar in their a. requirement for metal ion cofactors. b. requirement for exogenous nucleoside binding. c. DNA composition. d. intron lariat structure.

ANS: A DIF: Difficult REF: 21.3 OBJ: 21.3.b. Differentiate between group I and group II introns.

MSC: Evaluating 57. The group I and group II introns catalyze which class of reaction? a. transferase b. cleavage c. hydrolysis d. transesterification ANS: D DIF: Medium REF: 21.3 OBJ: 21.3.b. Differentiate between group I and group II introns.

MSC: Applying 58. The spliceosome a. is a cis-acting ribozyme. b. resembles group II introns in its mechanism and product. c. performs the same function in prokaryotes and eukaryotes. d. is a protein enzyme.

ANS: B DIF: Medium REF: 21.3 OBJ: 21.3.c. Describe the mechanism of spliceosome-mediated trans splicing.

MSC: Understanding 59. What best describes the composition of the spliceosome? a. small nuclear ribonucleoprotein b. RNA only c. protein d. mRNA ANS: A DIF: Medium REF: 21.3 OBJ: 21.3.c. Describe the mechanism of spliceosome-mediated trans splicing.

MSC: Evaluating 60. Identify the location of action of the spliceosome. a. nuclear pore b. nucleus c. rough endoplasmic reticulum d. cytoplasm ANS: B DIF: Easy REF: 21.3 OBJ: 21.3.c. Describe the mechanism of spliceosome-mediated trans splicing.

MSC: Applying 61. The roles of U1, U2, U4, U5, and U6 in the spliceosome complex are to a. bind mRNA and facilitate the splicing reaction. b. bind the small nuclear RNA. c. carry the products from the nucleus to the cytoplasm. d. bind proteins and hold the complex together.

ANS: A DIF: Medium REF: 21.3 OBJ: 21.3.c. Describe the mechanism of spliceosome-mediated trans splicing.

MSC: Remembering 62. A common RNA base modification is a. methylation. b. amination. c. carboxylation. d. hydroxylation.

ANS: A DIF: Easy REF: 21.3 OBJ: 21.3.d. Distinguish a modified base in RNA from an unmodified base.

MSC: Remembering 63. More than 100 different RNA base modifications have been identified, and most of those are found in a. mRNA. b. rRNA. c. snRNA. d. tRNA. ANS: D DIF: Easy REF: 21.3 OBJ: 21.3.d. Distinguish a modified base in RNA from an unmodified base.

MSC: Understanding 64. Which is central to the addition of the 7-methylguanosine cap to mRNA? a. RNA polymerase 1 b. guanine-N7 methyltransferase c. GMP d. snoRNA ANS: B DIF: Difficult REF: 21.3 OBJ: 21.3.e. Summarize the events that convert a precursor mRNA into a mature mRNA. MSC: Applying 65. Which enzyme is responsible for adding the poly(A) tail to mRNA? a. cleavage stimulatory factor (CStF)

b. poly(A) polymerase c. cleavage and polyadenylation specificity factor (CPSF) d. poly(A) binding protein ANS: B DIF: Medium REF: 21.3 OBJ: 21.3.e. Summarize the events that convert a precursor mRNA into a mature mRNA. MSC: Understanding 66. Which is the correct order of mRNA degradation? a. (1) poly(A) tail removal; (2) 7-methylguanosine cap removal; (3) RNA hydrolysis b. (1) 7-methylguanosine cap removal; (2) RNA hydrolysis; (3) poly(A) tail removal c. (1) 7-methylguanosine cap removal; (2) poly(A) tail removal; (3) RNA hydrolysis d. (1) RNA hydrolysis; (2) Poly(A) tail removal; (3) 7-methylguanosine cap removal ANS: A DIF: Medium REF: 21.3 OBJ: 21.3.f. Identify the events that lead to mRNA decay.

MSC: Understanding

67. Which enzyme degrades the poly(A) tail in the degradation of mRNA? a. poly(A) binding protein b. exosome c. CCR4 d. DCP1 and DCP2 ANS: C DIF: Easy REF: 21.3 OBJ: 21.3.f. Identify the events that lead to mRNA decay.

MSC: Evaluating

68. Different mRNAs can be obtained from the same gene by a. terminating transcription at different stop codons. b. splicing the mRNA with different exons. c. adding the 7-methylguanosine cap at different sites. d. alternate folding of mRNA. ANS: B DIF: Easy REF: 21.3 OBJ: 21.3.g. List the three mechanisms that generate two or more distinct mRNA products from the same gene.

MSC: Analyzing 69. Many noncoding RNAs are involved in gene silencing. Gene silencing refers to a. the splicing of mRNA into alternative transcripts. b. defense mechanisms against RNA viruses. c. mechanisms inhibiting gene expression. d. the modification of genes through RNA-mediated mutation.

ANS: C DIF: Medium REF: 21.4 OBJ: 21.4.a. Define gene silencing, RNA interference, antisense RNA, and sense RNA. MSC: Analyzing 70. Which type of RNA facilitates RNA interference by resulting in degraded mRNA? a. snoRNA b. siRNA c. miRNA d. rRNA ANS: B DIF: Easy REF: 21.4 OBJ: 21.4.a. Define gene silencing, RNA interference, antisense RNA, and sense RNA. MSC: Remembering

71. Antisense RNA binds to __________ and sense RNA binds to __________. a. template DNA; coding DNA b. tRNA; mRNA c. coding DNA; template DNA d. mRNA; coding DNA ANS: A DIF: Difficult REF: 21.4 OBJ: 21.4.a. Define gene silencing, RNA interference, antisense RNA, and sense RNA. MSC: Applying 72. The enzyme responsible for making siRNA is a. RISC. b. snoRNA. c. exosome. d. dicer.

ANS: D DIF: Easy REF: 21.4 OBJ: 21.4.b. Explain how the RNAi pathway degrades mRNA. MSC: Remembering 73. miRNA is a. involved in stimulating gene expression. b. derived from degraded mRNA. c. expressed in the nucleus and is involved in regulating gene expression. d. derived from degraded virus RNA strands.

ANS: C DIF: Medium REF: 21.4 OBJ: 21.4.c. Compare and contrast the miRNA pathways with the RNAi pathway.

MSC: Evaluating 74. Which RNA molecule is expressed in the genome to regulate gene expression? a. RNAi b. snoRNA c. miRNA d. siRNA ANS: C DIF: Easy REF: 21.4 OBJ: 21.4.c. Compare and contrast the miRNA pathways with the RNAi pathway.

MSC: Remembering 75. What is the biggest difference between miRNA and siRNA? a. One is derived from the nucleus and one is derived from double-stranded RNA. b. One regulates gene expression, whereas the other regulates protein synthesis. c. One binds to mRNA and suppresses its translation and one binds to mRNA and signals degradation. d. One binds to the DNA gene and inhibits transcription and one binds to the mRNA and signals degradation.

ANS: A DIF: Medium REF: 21.4 OBJ: 21.4.c. Compare and contrast the miRNA pathways with the RNAi pathway.

MSC: Analyzing SHORT ANSWER 1. List the classes and types of noncoding RNAs that are found typically in eukaryotic organisms.

ANS: Short noncoding RNAs include (1) micro RNA, (2) short interfering RNA, and (3) PIWI-interacting RNA. Small noncoding RNAs include (1) small nuclear RNA and (2) small nucleolar RNA. Long noncoding RNAs include (1) RNaseP RNA, (2) TERC RNA, and (3) long noncoding RNA. DIF: Difficult REF: 21.1 OBJ: 21.1.a. List the major types of RNA in eukaryotic and prokaryotic cells.

MSC: Remembering 2. Using the picture below, describe the three ways that RNA is a highly dynamic biomolecule.

ANS:

(1) Part a illustrates that RNA is synthesized and degraded in the nucleus where it mainly functions. (2) Part b illustrates that RNA can bind small molecules (or large ones such as RNA, DNA, or proteins) and change from one defined tertiary structure into another. (3) Part c illustrates the ready interaction of RNA with RNA or DNA through base pairing.

DIF: Medium REF: 21.1 OBJ: 21.1.b. Name the three ways in which RNA is a highly dynamic biomolecule.

MSC: Applying 3. Name the RNA molecules involved in protein expression and synthesis that are found in both prokaryotic and eukaryotic organisms, and name the RNA molecules involved in protein expression and synthesis only in eukaryotic organisms.

ANS: (1) rRNA, (2) tRNA, and (3) mRNA are found in both organisms. While eukaryotes employ additional microRNA (miRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA), and long noncoding RNA (lncRNA) are involved in gene regulation and have RNA processing roles.

DIF: Difficult REF: 21.1 OBJ: 21.1.c. Define the protein-synthesizing RNA molecules.

MSC: Analyzing

4. List the three main ways that eukaryotic mRNA molecules are processed before translation, which prokaryotic organisms to do not require.

ANS: (1) The addition of a 7-methylguanylate cap, (2) the addition of a poly(A) tail, and (3) the removal of introns and splicing of exons DIF: Medium REF: 21.1 OBJ: 21.1.d. Differentiate between prokaryotic and eukaryotic mRNA. MSC: Remembering 5. List the four ways that long noncoding RNAs are thought to function.

ANS: lncRNAs may (1) base pair to mRNA and regulate translation or processing, (2) base pair to single-stranded DNA and regulate transcription, (3) form functional protein-RNA complexes involved in catalyzing reactions or activating genes, and (4) be involved in sensing small molecules and function in sensing pathways.

DIF: Difficult REF: 21.1 OBJ: 21.1.e. List four mechanisms by which lncRNA could regulate cellular processes.

MSC: Applying 6. Describe the difference between

factors for housekeeping genes and those for other genes.

ANS: Housekeeping genes are those that are steadily expressed in a cell and therefore the factors needed to initiate their transcription are always present. On the other hand, genes that are needed only at certain times or in response to certain conditions would require factors to be present only in those instances.

DIF: Difficult

REF: 21.2

OBJ: 21.2.a. Define the sigma factor and promoter region.

MSC: Applying

7. Draw a picture of the gel electrophoresis results after DNA footprinting experiments on the following DNA strand.

ANS:

DIF: Difficult REF: 21.2 OBJ: 21.2.b. Explain the process of DNase I footprinting.

MSC: Applying

8. Would a weak or a strong promotor be more active in a prokaryotic cell? Explain your answer.

ANS: It may depend on the organism and on the metabolic state or cellular environment. In general, the strong promotor would be one with higher levels of transcription and would therefore be more active.

DIF: Medium REF: 21.2 OBJ: 21.2.c. Distinguish between a strong promoter and a weak promoter.

MSC: Analyzing 9. The picture below shows the TATA binding protein. What is its role?

ANS: The TATA binding protein is a eukaryotic transcription factor that binds to RNA polymerase II to initiate transcription.

DIF: Medium REF: 21.2 OBJ: 21.2.d. Compare and contrast eukaryotic and prokaryotic promoters.

MSC: Understanding 10. Draw a double-stranded piece of DNA, label the transcribed and in which direction.

and

ends, and show which strand is

ANS:

DIF: Difficult REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Applying 11. Describe two ways that termination can occur in the transcription of prokaryotic genes.

ANS:

(1) The protein Rho binds to a C-rich region on the growing RNA transcript and destabilizes the RNA/DNA base pairs, causing transcription to stop and the polymerase complex to dissociate. (2) A GC-rich region on the RNA transcript forms stem-loop structures that hang up the polymerase, followed by a U-rich region that forms weaker RNA-DNA base pairs, which leads to polymerase complex dissociation.

DIF: Difficult REF: 21.2 OBJ: 21.2.e. Summarize the events of and proteins required for initiation, elongation, and termination in prokaryotic RNA synthesis.

MSC: Applying 12. Describe the composition and processing of the C-terminal domain (CTD) of eukaryotic RNA polymerase II, as well as its role in transcription.

ANS: The CTD is a repeating peptide sequence rich with serine, tyrosine, and threonine amino acids, which are subjected to various levels of phosphorylation. The levels of phosphorylation can influence the rate of transcription, as well as the CTD’s interaction with RNA transcript modifying enzymes and other transcription cofactors.

DIF: Difficult REF: 21.2 OBJ: 21.2.f. Identify the key differences between eukaryotic and prokaryotic transcription.

MSC: Applying 13. Name the types of catalysis in ribozymes illustrated in the two figures below.

ANS: Acid-base catalysis is on the left, and metal ion catalysis is on the right.

DIF: Medium REF: 21.3 OBJ: 21.3.a. Distinguish between cis and trans activities of a ribozyme.

MSC: Applying 14. List two differences and two similarities between group I and group II introns.

ANS: Differences: (1) Group I requires a guanosine cofactor; group II does not. (2) Group I gives a linear intron product, whereas the group II intron product is a lariat structure. Similarities: (1) They are self-splicing. (2) They excise introns. (3) They are ribozymes. (4) They have similar tertiary structures. (5) They require metal ion cofactors.

DIF: Medium REF: 21.3 OBJ: 21.3.b. Differentiate between group I and group II introns.

MSC: Applying

15. What reaction is catalyzed by the spliceosome?

ANS: The removal of introns and splicing together of exons in eukaryotic mRNA. DIF: Easy REF: 21.3 OBJ: 21.3.c. Describe the mechanism of spliceosome-mediated trans splicing.

MSC: Applying 16. Why must tRNA contain base modifications?

ANS: tRNAs have very similar secondary and tertiary structures and this therefore necessitates that bases be modified as the main way for aminoacyl tRNA synthetases to recognize them.

DIF: Medium REF: 21.3 OBJ: 21.3.d. Distinguish a modified base in RNA from an unmodified base.

MSC: Applying 17. What RNA types are required for eukaryotic rRNA and mRNA processing? Where does this processing occur?

ANS: Small nucleolar RNA (snoRNA) is involved in rRNA processing in the nucleus, while small nuclear RNA (snRNA) is involved in mRNA processing in the nucleus.

DIF: Medium REF: 21.3 OBJ: 21.3.d. Distinguish a modified base in RNA from an unmodified base.

MSC: Applying 18. Describe the timing and location of removal of introns and splicing of exons in mRNA. ANS: After the addition of the 7-methylguanosine cap and before the end of transcription, the first introns are removed. Removal of introns and exon splicing continues and complete splicing occurs after transcription ends.

DIF: Difficult REF: 21.3 OBJ: 21.3.e. Summarize the events that convert a precursor mRNA into a mature mRNA. MSC: Applying 19. Describe what is depicted in the figure below and explain the role of Ras-related nuclear protein (Ran).

ANS: The different classes of RNAs are transported in distinctly controlled ways. They all pass through nuclear pore complexes on their way from the nucleus to the cytoplasm; however, distinct ribonucleoprotein complexes are assembled to mediate their transport. Ran plays the role of assisting their transport through the nuclear pore complex.

DIF: Medium REF: 21.3 OBJ: 21.3.e. Summarize the events that convert a precursor mRNA into a mature mRNA. MSC: Understanding 20. When does rRNA, tRNA, and mRNA degradation typically occur?

ANS: rRNA and tRNA degradation typically occurs when they are damaged. mRNA degradation can occur after damage or as a strategy to control protein levels in the cell.

DIF: Medium REF: 21.3 OBJ: 21.3.f. Identify the events that lead to mRNA decay.

MSC: Understanding

21. List the three general ways that a single gene can give rise to multiple different mRNA transcripts.

ANS: (1) Using alternate promoter sites; (2) adding the poly(A) tail at alternate locations; and (3) performing alternate splicing of exons and removal of introns DIF: Medium REF: 21.3 OBJ: 21.3.g. List the three mechanisms that generate two or more distinct mRNA products from the same gene.

MSC: Applying 22. List the three different ways that mRNA splicing can give rise to different mRNA transcripts.

ANS: (1) Exons can be skipped or spliced over. (2) Some introns can be retained in the mRNA. (3) A given intron can use alternate donor splice sites or acceptor sites during the splicing.

DIF: Difficult REF: 21.3 OBJ: 21.3.g. List the three mechanisms that generate two or more distinct mRNA products from the same gene.

MSC: Applying 23. Define RNA interference (RNAi) and name the RNA class responsible for RNAi. ANS: RNA interference refers to the suppression of protein expression with the use of small interfering RNAs (siRNA) that bind to and result in the degradation of mRNA. DIF: Medium REF: 21.4 OBJ: 21.4.a. Define gene silencing, RNA interference, antisense RNA, and sense RNA. MSC: Understanding 24. In the following RNAi scheme, label the mRNA, siRNA, RISC, dicer, and double-stranded RNA.

ANS:

DIF: Medium REF: 21.4 OBJ: 21.4.b. Explain how the RNAi pathway degrades mRNA. MSC: Analyzing 25. Explain why RNAi requires some double-stranded RNA to initiate the process.

ANS: The enzyme called dicer will cut any double-stranded RNA and generate the siRNA that is required for binding to mRNA and initiating the mRNA hydrolysis by the RNA-induced silencing complexes (RISC).

DIF: Difficult REF: 21.4 OBJ: 21.4.b. Explain how the RNAi pathway degrades mRNA. MSC: Applying

Chapter 22: Protein Synthesis, Posttranslational Modification, and Transport MULTIPLE CHOICE 1. Which molecule contains both an amino acid acceptor stem and an anticodon? a. tRNA b. mRNA c. rRNA d. RNAi ANS: A DIF: Easy REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Understanding

2. The adaptor molecule in translation is a. aminoacyl-tRNA synthetase. b. mRNA. c. rRNA. d. tRNA. ANS: D DIF: Easy REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Understanding

3. tRNA must be __________ before binding to the ribosome to allow for translation to occur. a. charged with a codon b. charged with an anticodon c. charged with an amino acid d. bound by ATP ANS: C DIF: Medium REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

4. The tRNA sequence a. AGG. b. GGA. c. UCC. d. CCU.

anticodon loop that recognizes the

ANS: A DIF: Medium REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Understanding codon UCC could have the

MSC: Applying

5. The anticodon of tRNA is made up of __________ bases. a. 2 b. 3 c. 4 d. 5 ANS: B DIF: Easy REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Remembering

6. Consider an in vitro experiment in which all components needed for protein synthesis are present.

If tRNAs charged with radioactively labeled amino acids are added, over time the radioactivity would be located in which of the following components? a. mRNA

b. aminoacyl tRNA synthetase c. nascent protein d. codons ANS: C DIF: Medium REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Applying

7. Which of the following mRNA codons would NOT be recognized by a tRNA that is charged with an amino acid? a. CAA b. GUU c. CUC d. UAA ANS: D DIF: Difficult REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Applying

8. Where would an amino acid be attached to the tRNA below?

a. b. c. d.

A B C D

ANS: A DIF: Easy REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Remembering

9. Which of the following is considered the adaptor molecule in protein synthesis? a. mRNA b. DNA c. tRNA d. rRNA ANS: C DIF: Easy REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Remembering

10. What region of the amino acid below would become covalently attached to a tRNA?

a. b. c. d.

A B C D

ANS: D DIF: Medium REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Applying

11. An analysis of noncanonical base pairings between the -position of the tRNA anticodon and the -position of the mRNA codon would show the pairing a. I-G. b. G-A. c. I-U. d. I-I. ANS: C DIF: Medium REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Analyzing 12. Which base location in the figure below is LEAST discriminating in the bases that it can pair with as described by the wobble hypothesis?

a. b. c. d.

A B C D

ANS: D DIF: Medium REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Understanding 13. In yeast, the number of tRNA genes is __________ the number of __________. a. equivalent to; amino acids b. less than; amino acids c. equivalent to; mRNAs d. greater than; codons ANS: B DIF: Easy REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Understanding 14. Noncanonical base pairings are observed between the third position of the codons and the first position of the anticodons. This concept is known as the a. nonsense rule. b. noncanonical hypothesis. c. wobble hypothesis. d. 3:1 hypothesis.

ANS: C DIF: Easy REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Remembering 15. Noncanonical base pairings of A and I would contain __________ hydrogen bonds. The base pairing of C and I would contain __________ hydrogen bonds. a. 1; 3 b. 1; 2 c. 2; 2 d. 2; 1 ANS: C DIF: Easy REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Understanding 16. Inosine is formed through a a. deamination of adenosine. b. deamination of cytosine. c. demethylation of thymine. d. deamination of guanosine.

ANS: A DIF: Difficult REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Understanding 17. How many potential codons does the following mRNA sequence contain?

CUCUCUCUCUCUC a. 0 b. 1 c. 2 d. 3 ANS: C DIF: Medium REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Applying 18. If the following mRNA was added to a cell-free translation system, how many unique protein sequences would be generated?

ACCACCACCACCACCACCACCACCACCACCACCACCACCACC a. 14 b. 7 c. 2 d. 3 ANS: D DIF: Medium REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Applying 19. The wobble hypothesis was first proposed by a. Leder. b. Nirenberg. c. Holley. d. Crick.

ANS: D DIF: Easy REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Remembering 20. Which component of the Nirenberg-Leder experiment, that assigned triplet codons to specific amino acids, was radioactively labeled? a. ribosome b. aminoacyl-tRNA c. tRNA d. mRNA ANS: B DIF: Medium REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Understanding 21. In an iteration of the Nirenberg-Leder experiment to assign triplet codons to specific amino acids, radioactively labeled aminoacyl-tRNA with the anticodon of CUG was used. The radioactivity was retained on the filter at the end of the experiment. Which mRNA was used in this iteration of the experiment? a. CAG b. GAC c. CTG d. GTC ANS: B DIF: Medium REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Applying 22. Which of the following catalyzes the formation of a bond between an amino acid and a tRNA? a. aminoacyl-tRNA synthetase b. aminoacyl-tRNA hydrolase c. tRNA linking enzyme d. ribosome ANS: A

DIF: Easy

REF: 22.2

OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Understanding 23. A full catalytic cycle of an aminoacyl-tRNA synthetase generates __________ as a product. a. ATP b. ADP c. H2O d. AMP ANS: D DIF: Difficult REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Understanding 24. All aminoacyl-tRNA synthetases are a. monomeric. b. tetrameric. c. able to bind ATP. d. able to bind ADP. ANS: C DIF: Medium REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Understanding 25. Different tRNAs for the same amino acid that bind alternate codons are known as __________ tRNAs. a. cognate b. isoacceptor c. variable d. class I and class II ANS: B DIF: Easy REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Remembering 26. Aminoacyl-tRNA synthetases carry out editing a. before activation of amino acid with ATP. b. at a site that is distinct from the active site. c. at the same time that the amino acid is transferred to the d. by binding to an editing subunit.

group.

ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Understanding 27. Both prokaryotes and eukaryotes recognize __________ as a start codon. a. AUG b. UAC c. GUA d. CAU ANS: A DIF: Easy REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Remembering

28. The prokaryotic ribosome contains __________ subunits. The eukaryotic ribosome contains __________ subunits. a. 30S and 70S; 40S and 60S b. 40S and 60S; 30S and 80S c. 30S and 50S; 40S and 60S d. 30S and 60S; 40S and 50S ANS: C DIF: Easy REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Remembering 29. What is the identity of the protein labeled with the question mark in the eukaryotic preinitiation complex shown below?

a. b. c. d.

PABP eIF5B eIF4E eIF2

ANS: A DIF: Difficult REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Remembering 30. Eukaryotes are directed to begin scanning the mRNA for the start codon based on binding of the a. Shine-Dalgarno sequence. b. poly(A) tail and cap. c. Met-tRNAifMet. d. 16S rRNA. ANS: B DIF: Easy REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Remembering 31. A common feature of translation in both eukaryotes and prokaryotes is a. hydrolysis of ATP to facilitate translocation of the ribosome. b. hydrolysis of GTP to promote binding of the AA-tRNAAA. c. a P site that can contain uncharged tRNA. d. an E site that can contain a tRNA covalently bound to a nascent polypeptide.

ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Understanding 32. Where might the molecule shown below be located in both the prokaryotic and eukaryotic ribosome?

a. b. c. d.

A site E site 40S complex 70S complex

ANS: A DIF: Easy REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Understanding 33. tRNA interacts with ribosomes at one of three sites: the E site, the P site, and the __________ site. a. T b. M c. SD d. A ANS: D DIF: Easy REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Remembering 34. The Shine-Dalgarno sequence of mRNA base pairs with the __________ rRNA within the prokaryote __________ ribosomal subunit. a. 23S; 30S b. 16S; 50S c. 16S; 30S d. 5S; 50S ANS: C

DIF: Easy

REF: 22.2

OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Remembering 35. tRNAs interact with the ribosome only after a. they bind the free mRNA. b. the small and large subunits have come together. c. the first peptide bond in the nascent chain is formed. d. the AUG start codon is positioned in the E site.

ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Understanding 36. Below are examples of sequences from seven different E. coli genes. The underlined sequences are known as __________ sequences and the bolded AUG sequences are known as the __________ codon.

a. b. c. d.

Shine-Dalgarno; start Shine-Dalgarno; S initiation factor; start initiation factor; S

ANS: A DIF: Easy REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Remembering 37. What characteristics of eukaryotic mRNA are recognized through specific interactions during the formation of the translation initiation complex? a. cap b. Shine-Dalgarno sequence c. poly(A) tail d. GTP-binding site ANS: C DIF: Easy REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Remembering 38. The eukaryotic 48S preinitiation complex is purified and the components are identified. Which of the following would be found in this complex? a. 60S ribosomal subunit b. Met-rRNAMet c. EF-Tu d. eIF4 ANS: D

DIF: Difficult

REF: 22.2

OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Remembering 39. Prokaryotic mRNA will directly interact with __________ during translation. a. release factors b. 23S rRNA c. Kozak sequence d. GTP ANS: A DIF: Medium REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Understanding 40. Ribosomal rRNA interacts with all EXCEPT __________ during the process of translation. a. mRNA b. tRNA c. ribosomal proteins d. PABP ANS: D DIF: Medium REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Understanding 41. Release factor hydrolyzes GTP during the __________ step of translation. a. initiation b. elongation c. translocation d. termination ANS: D DIF: Easy REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Remembering 42. Secondary downstream of the cap structure in the mRNA is unwound during the __________ step of translation. a. initiation b. elongation c. translocation d. termination ANS: A DIF: Easy REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Remembering 43. A nucleophilic amino group of the amino acid bound to the terminus of A-site tRNA attacks the electrophilic carbonyl carbon in the ester bond between the terminus of P-site tRNA and its bound amino acid during the __________ step of translation. a. initiation b. elongation c. translocation d. termination ANS: B DIF: Easy REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying

44. In the image below, which group will be attacked by the nucleophilic amino group of the next amino acid brought into the ribosome?

a. b. c. d.

A B C D

ANS: D DIF: Difficult REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying 45. After the initiation complex is complete, what occurs next in the process of translation? a. peptide bond formation b. EF-G•GTP binding c. EF-Tu•GTP AA–tRNAAA binding d. RF2 binding ANS: C DIF: Medium REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying 46. Place the following steps in the elongation phase of translation in their proper order.

A. Peptide bond formation occurs.

B. GTP is hydrolyzed, and the ribosome moves one codon in the direction.

C. GTP is hydrolyzed, and EF-Tu•GDP is released.

D. tRNA is released from the E site. a. A; C; B; D b. A; B; C; D c. B; D; C; A d. C; A; B; D ANS: D DIF: Medium REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying 47. Place the following steps in the initiation phase in a prokaryote in their proper order.

A. mRNA binds to the complex.

B. GTP is hydrolyzed.

C. IF1, IF2, and IF3 bind the 30S subunit. a. C; B; A b. C; A; B c. A; B; C d. B; C; A ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying 48. How many GTP are hydrolyzed during a single round of translation elongation in a eukaryote? a. 0 b. 1 c. 2 d. 6 ANS: C DIF: Easy REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Remembering 49. Which of the following is NOT a component that is released from the ribosome on translation termination? a. RF2 b. nascent polypeptide c. tRNA d. Met-tRNAfMet ANS: D DIF: Easy REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Understanding 50. Which antibiotic functions by inhibiting cell wall synthesis? a. penicillin b. linezolid c. tetracycline d. rifampin ANS: A DIF: Easy REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Remembering

51. Which antibiotic functions by inhibiting DNA gyrase? a. vancomycin b. coumermycin c. aminoglycosides d. clindamycin ANS: B DIF: Easy REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Remembering 52. The antibiotics streptomycin, tetracycline, and chloramphenicol all interfere with a. cell membrane formation. b. protein synthesis. c. nucleic acid synthesis. d. cell wall formation.

ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Applying 53. Which antibiotic would be a good choice to use as a research tool if investigating the role of DNA gyrase in a cell? a. coumermycin b. penicillin c. tetracycline d. bacitracin ANS: A DIF: Medium REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Applying 54. An experiment with bacteria that has been exposed to an antibiotic reveals that the translocation step has been inhibited. Which antibiotic was likely used? a. chloramphenicol b. erythromycin c. tetracycline d. streptomycin ANS: B DIF: Medium REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Applying 55. If a protein is covalently modified by ubiquitin, it will be a. degraded. b. secreted. c. targeted to the nucleus. d. anchored to the plasma membrane.

ANS: A DIF: Easy REF: 22.3 OBJ: 22.3.a. Identify the significance of the most common posttranslational modifications of proteins.

MSC: Understanding 56. Gene expression can be controlled by the modification of histones by all of the following EXCEPT a. phosphorylation. b. methylation.

c. acetylation. d. glycosylation.

ANS: D DIF: Difficult REF: 22.3 OBJ: 22.3.a. Identify the significance of the most common posttranslational modifications of proteins.

MSC: Understanding 57. A newly discovered protein is found to be modified by a lipid. Where is this protein most likely located? a. nucleus b. proteasome c. cell membrane d. extracellular matrix ANS: C DIF: Medium REF: 22.3 OBJ: 22.3.a. Identify the significance of the most common posttranslational modifications of proteins.

MSC: Applying 58. Enzyme-mediated protein modification in eukaryotic cells is a means of regulating the activity of the protein. Which of the following is UNLIKELY to result from such a modification? a. phosphorylation b. methylation c. glycosylation d. hydration ANS: D DIF: Easy REF: 22.3 OBJ: 22.3.a. Identify the significance of the most common posttranslational modifications of proteins.

MSC: Understanding 59. All glycoproteins have __________ covalently added posttranslationally. a. carbohydrates b. phosphates c. methyl groups d. acetyl groups ANS: A DIF: Easy REF: 22.3 OBJ: 22.3.a. Identify the significance of the most common posttranslational modifications of proteins.

MSC: Understanding 60. In the ER, prenylation can occur. Prenylation is the attachment of an isoprenoid group to a __________ residue via a(n) __________. a. lysine; amide b. cysteine; thioester c. threonine; ester d. serine; ester ANS: B DIF: Easy REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Understanding 61. Which sequence is MOST likely to be prenylated in the ER? (The … represents additional amino acids N-terminal to those shown.) a. …Cys-Leu-Leu-Phe-Ala-Lys b. …Leu-Phe-Leu-Cys-Ile-Phe c. …Phe-Ile-Leu-Ser-Ile-Leu

d. …Cys-Leu-Cys-Leu-Lys-Phe ANS: B DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Applying 62. Which sequence is MOST likely to be modified with the fatty acid myristoylate in the ER? (The … represents additional amino acids N-terminal to those shown.) a. Cys-Leu-Ala-Ile-Ser-Phe… b. Leu-Gly-Phe-Ala-Ser-Phe… c. Gly-Leu-Phe-Ala-Ile-Ser… d. Phe-Leu-Cys-Gly-Leu-Ile… ANS: C DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Applying 63. Choose the sequence that is MOST likely to be modified with the fatty acid palmitoylate in the ER. (The … represents additional amino acids N-terminal or C-terminal to those shown.) a. …Phe-Leu-Cys-Gly-Leu-Ile… b. …Gly-Leu-Phe-Ala-Ile-Ser… c. …Tyr-Leu-Ala-Ile-Ser-Phe… d. …Ala-Thr-Leu-Phe-Ser-Gly… ANS: A DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Applying 64. A protein is targeted to the plasma membrane. Its final functional location is as a subunit of a transmembrane protein that interacts with the central subdomain of the membrane. Analysis of this protein would most likely show modification with a a. myristoylate. b. palmitoylate. c. isoprenoid. d. phosphate.

ANS: B DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Applying 65. Which sequence is MOST likely to contain an O-linked oligosaccharide in the ER? (The … represents additional amino acids N-terminal or C-terminal to those shown.) a. …Phe-Leu-Cys-Gly-Leu-Ile… b. …Gly-Leu-Phe-Ala-Ile-Gly… c. …Tyr-Leu-Ala-Ile-Gly-Phe… d. …Ala-Thr-Leu-Phe-Ser-Gly… ANS: D DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Applying 66. An experimental prep is able to separate the following membrane fractions: nuclear membrane, Golgi apparatus membrane, transport vesicle membrane, and mitochondrial membrane. The membrane fractions can then be analyzed via Western blotting for the presence of specific proteins. Which fraction would indicate the presence of t-SNAREs?

a. b. c. d.

nuclear membrane Golgi apparatus membrane transport vesicle membrane mitochondrial membrane

ANS: B DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Analyzing 67. Which of the following sequences is most likely a nuclear localization signal? a. Lys-Lys-Arg-Gly-Arg b. Glu-Asp-Asp-Gly-Glu c. Ile-Leu-Phe-Leu-Gly d. Lys-Asp-Arg-Glu-Glu ANS: A DIF: Easy REF: 22.3 OBJ: 22.3.c. Explain how Ran regulates the transport of proteins in and out of the nucleus.

MSC: Understanding 68. At any time during nuclear import and export, Ran can be found associated with all EXCEPT a. GTP. b. exportin. c. GMP. d. importin.

ANS: B DIF: Easy REF: 22.3 OBJ: 22.3.c. Explain how Ran regulates the transport of proteins in and out of the nucleus.

MSC: Understanding 69. An inhibitor of __________ would specifically prohibit the release of Ran from importin. a. GTP-GDP exchange in Ran b. exportin c. the signal peptide peptidase d. GAP ANS: D DIF: Medium REF: 22.3 OBJ: 22.3.c. Explain how Ran regulates the transport of proteins in and out of the nucleus.

MSC: Applying 70. During the import of one protein from the cytosol to the nucleus via Ran-dependent nuclear import, __________ high-energy phosphate molecule(s) are hydrolyzed. a. 2 ATP b. 1 GTP c. 1 GTP and 1 ATP d. 2 GTP ANS: B DIF: Easy REF: 22.3 OBJ: 22.3.c. Explain how Ran regulates the transport of proteins in and out of the nucleus.

MSC: Understanding 71. Place the following steps in proper order for the translation of a membrane-bound protein.

A. GTP binds to SRP. B. Protein synthesis occurs on free ribosome.

C. Protein synthesis halts.

D. SRP binds to the signal peptide sequence.

a. b. c. d.

A; B; C; D B; D; C; A D; C; B; A A; B; D; C

ANS: A DIF: Medium REF: 22.3 OBJ: 22.3.d. Express how the ER signal peptide causes ribosomes to bind to the translocator.

MSC: Understanding 72. What step in the process of translation of a nascent protein into the lumen of the ER requires an input of energy provided by the hydrolysis of GTP? a. binding of SRP to the signal peptide sequence b. release of SRP from the ribosome c. transfer of the signal peptide sequence into the translocon d. binding of SRP to the SRP receptor ANS: C DIF: Medium REF: 22.3 OBJ: 22.3.d. Express how the ER signal peptide causes ribosomes to bind to the translocator.

MSC: Understanding 73. Which protein would initially have been translated on free ribosomes? a. lysosomal-associated membrane protein 1 (LAMP-1) b. insulin receptor subunit c. collagen d. histone subunit H2A ANS: D DIF: Medium REF: 22.3 OBJ: 22.3.d. Express how the ER signal peptide causes ribosomes to bind to the translocator.

MSC: Analyzing 74. A __________ is NOT a characteristic of the ER signal peptide sequence. a. N-terminal segment containing negatively charged amino acids b. segment containing hydrophobic amino acids c. C-terminal segment containing hydrophobic amino acids d. protease cleavage site ANS: A DIF: Easy REF: 22.3 OBJ: 22.3.d. Express how the ER signal peptide causes ribosomes to bind to the translocator.

MSC: Remembering SHORT ANSWER 1. Aminoacyl-tRNA synthetase contains two binding sites. Describe the consequence of a mutation that changed the specificity of the amino acid binding site of an aminoacyl-tRNA synthetase from Glu to Asp. ANS: Proteins would be synthesized that might contain an Asp where a Glu was coded for in the mRNA. DIF: Medium REF: 22.1 OBJ: 22.1.a. Describe the role of tRNA in protein synthesis.

MSC: Analyzing

2. Why does the genetic code require triplet codons to code for the 20 different amino acids? Why would duplet codons be inadequate to perform the job?

ANS: There are four bases; if duplet codons were used, then only 4 4 = 16 codons would be available.

Given the 20 different amino acids, 16 codons is not enough to cover all the amino acids. Triplet codons lead to 64 different codon possibilities, more than enough to cover the 20 amino acids.

DIF: Difficult REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Analyzing 3. Explain what is meant by the statement, “The genetic code is universal.”

ANS: A universal genetic code implies that mRNA from any species could be translated by the protein components of any other species.

DIF: Medium REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Understanding 4. Although the genetic code is considered universal, this may not be fully true when comparing the human nuclear code with the human mitochondrial code. Describe how and provide a specific example.

ANS: In humans, the preferred codon usage varies for nuclear versus mitochondrial DNA. For example, in mitochondria both AUG and AUA code for methionine, whereas in nuclei only AUG codes for methionine and AUA codes for isoleucine.

DIF: Difficult REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Analyzing 5. The rate of translation of an identical mRNA sequence is measured in cells from two different species—E. coli and human. It is found that the rate is slower in E. coli cells. What is a possible reason for this finding?

ANS: Codons are not used at the same frequency in different organisms. This could lead to a slower translation rate.

DIF: Medium REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Analyzing 6. How does the wobble hypothesis allow for fewer than 63 tRNAs to effectively recognize 63 codons?

ANS: The wobble hypothesis states that base pairing rules may be relaxed at the third position of the codon. This allows a single tRNA to recognize more than one codon.

DIF: Medium REF: 22.1 OBJ: 22.1.b. Explain the cause and adaptive advantage of redundancy in the genetic code.

MSC: Applying 7. How was the selectivity of the nitrocellulose filter essential in the Nirenberg-Leder experiment, which was able to assign triplet codons to specific amino acids?

ANS: The nitrocellulose filter would allow aminoacylated tRNAs to pass but not proteins, such as the ribosome. If aminoacylated tRNAs bind to the codon in complex with the ribosome, the complex would not pass through the membrane.

DIF: Difficult REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Applying 8. Nirenberg and Matthaei determined the genetic code experimentally by using a cell-free translation system. Two components, however, were restricted in their system. One was the use of a single type of mRNA. What was the other component that was restricted? How did this restriction allow them to determine the genetic code?

ANS: The other component that was restricted was the free amino acids available. Only a single type of amino acid was added for each test condition. If the mRNA coded for this amino acid, then protein would be generated. If the mRNA did not code for this amino acid, no protein would be generated.

DIF: Difficult REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Analyzing 9. In the experiment illustrated below, based off the original by Nirenberg and Matthaei, in which tube would the resulting protein be found? Explain your answer.

ANS: The Pro tube would contain poly-Pro. This is because the codon for proline is CCC.

DIF: Medium REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Applying 10. Nirenberg and Leder completed the experiment illustrated below. If the tRNA used had an anticodon that recognizes UAA and the mRNA added contained repeats of UAA, what would be the expected result? Would the membrane contain any radioactivity, and if so, which amino acid would be retained on the membrane?

ANS: The membrane would not contain radioactivity. UAA is a stop codon and no radioactive amino acid would be attached.

DIF: Difficult REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Evaluating 11. Radioactively labeled aminoacyl-tRNAs were used in the Nirenberg-Leder experiment to assign triplet codons to specific amino acids. Why was this important in the experimental design?

ANS: If the radiolabeled aminoacyl-tRNA was able to interact with the mRNA within the ribosome, the complex would be retained on the filter. The radioactivity allowed the scientists to determine the location of the aminoacyl-tRNA and thus determine if it had bound to the ribosome or not.

DIF: Difficult REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Evaluating 12. Radioactively labeled aminoacyl-tRNAs were used in the Nirenberg-Leder experiment to assign triplet codons to specific amino acids. If the aminoacyl-tRNA contains an anticodon of AGG and the mRNA included contains a codon of UCA, where will the radioactivity be located at the end of the experiment? Explain your reasoning.

ANS:

The codon and anticodon will not interact. Therefore the aminoacyl-tRNA will not interact with the ribosome and will flow through the filter.

DIF: Difficult REF: 22.1 OBJ: 22.1.c. Analyze classic experiments that revealed the nature of the genetic code.

MSC: Analyzing 13. Describe the steps of the mechanism of aminoacyl-tRNA synthetase. Clarify the role of ATP in the process.

ANS: Stage 1: E + ATP + AA E(AA–AMP) + PPi. Stage 2: E(AA–AMP) + tRNA AA–tRNA + E + AMP. In stage 1 of the aminoacyl-tRNA synthetase reaction, free energy from ATP is used to form an aminoacyl-adenylate. This reaction activates the amino acid by preserving the free energy of the phosphodiester bond in the aminoacyl-AMP intermediate (Figure 22.12). The amino acid is then transferred to the acceptor stem of tRNA in stage 2, driven by the cleavage of aminoacyl-AMP. DIF: Medium REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Applying 14. The of the two combined catalytic steps of tRNA synthetase is near equilibrium. How does this reaction occur in an essentially irreversible fashion in a cell?

ANS: PPi is released after the first step. Its subsequent hydrolysis to 2Pi makes the process irreversible.

DIF: Medium REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Understanding 15. Differentiate between the mechanisms of type I and type II aminoacyl-tRNA synthetases.

ANS: Class I enzymes initially link the aminoacyl group to their cognate tRNA on the -hydroxyl group of the terminal adenosine in the acceptor stem before moving the group by a transesterification reaction to the -hydroxyl group of the ribose. Class II enzymes directly charge the -hydroxyl of the adenosine.

DIF: Difficult REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Analyzing 16. Differentiate between type I and type II aminoacyl-tRNA synthetases in how they interact with the tRNA and acceptor stem.

ANS: Class I aminoacyl-tRNA synthetases bind the D-loop side of the tRNA and interact with the acceptor stem in the minor groove, whereas class II enzymes recognize the opposite side of the tRNA and bind the acceptor stem in the major groove.

DIF: Difficult

REF: 22.2

OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Analyzing 17. Contrast the discrimination at the active site and at the editing site of aminoacyl-tRNA synthetases, so that combined they ensure that tRNAs are charged with the correct amino acid.

ANS: Structurally dissimilar amino acids are rejected at the active site, whereas incorrectly charged aminoacyl tRNAs are hydrolyzed at the editing site.

DIF: Medium REF: 22.2 OBJ: 22.2.a. Describe the role and structure of tRNA synthetases.

MSC: Analyzing 18. Contrast both the structure and function of a prokaryotic initiator tRNA with a prokaryotic Met-tRNAMet. ANS: The initiator tRNA is modified by the addition of an N-formyl group. The initiator tRNA is able to bind to an otherwise empty ribosome and match with the AUG codon. Met-tRNAMet is only able to bind after protein synthesis has been initiated.

DIF: Medium REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Analyzing 19. Does the figure below represent a prokaryotic or eukaryotic translation system? Describe the clues used to form a decision.

ANS: This is a prokaryotic translation system. The mRNA contains a Shine-Dalgarno sequence, which is unique to prokaryotes. The ribosome is made up of a 30S subunit and contains 16S rRNA, also unique to prokaryotes.

DIF: Medium REF: 22.2 OBJ: 22.2.b. Identify similarities and differences in translation between prokaryotes and eukaryotes.

MSC: Analyzing

20. Below are seven examples of sequences found in E. coli. Differentiate between the underlined and bolded sequences. Explain where each would ultimately be located in the 70S initiation complex and what types of interactions are required to achieve these locations.

ANS: The underlined regions are the Shine-Dalgarno sequences and the bolded are the start codons. In the 70S initiation complex the Shine-Dalgarno sequences will pair with the 16s rRNA of the small subunit. This will orient the start codon within the 30S initiation complex so that when the 50S subunit engages the AUG will be aligned with the P site.

DIF: Difficult REF: 22.2 OBJ: 22.2.c. Explain how ribosomes interact with mRNA and tRNA during translation.

MSC: Analyzing 21. Draw out the peptidyl transferase reaction that is catalyzed by the ribozyme activity of the 23S rRNA in the large ribosomal subunit.

ANS:

DIF: Difficult REF: 22.2 OBJ: 22.2.d. Describe the three steps in the mechanism of protein synthesis.

MSC: Applying 22. Identify the antibiotic shown below and illustrate how it functions to inhibit bacterial cell growth.

ANS: This is streptomycin. It alters the structure of the 30S subunit, causing errors in translation.

DIF: Difficult REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Applying 23. Compare the chemical structures of puromycin with an aminoacylated tRNA. How do their similarities allow puromycin to function as an antibiotic?

ANS: Both an aminoacylated tRNA and puromycin contain a peptide bond. The structural similarities allow both to bind to the A site of the ribosome. Puromycin functions as a peptidyl acceptor to terminate translation.

DIF: Difficult REF: 22.2 OBJ: 22.2.e. Differentiate mechanisms of blocking protein synthesis by antibiotics.

MSC: Analyzing 24. Differentiate among the trafficking of vesicles coated with COPI, COPII, or clathrin.

ANS: Transport from the Golgi apparatus to the endoplasmic reticulum and within the Golgi apparatus is mediated by cytoplasmic coat I (COPI)–coated vesicles, whereas transport from the ER to the Golgi is mediated by cytoplasmic coat II (COPII)–coated vesicles. Transport from the trans-Golgi network or from the plasma membrane occurs in clathrin-coated vesicles.

DIF: Medium REF: 22.3 OBJ: 22.3.b. Explain how proteins are modified and packaged as they move through the endoplasmic reticulum and Golgi apparatus. MSC: Analyzing 25. Relate the importance of the binding of Ran to importin to its role in nuclear import.

ANS: Ran binds importin once importin has carried its cargo protein into the nucleus. This binding allows importin to release its cargo protein.

DIF: Medium REF: 22.3 OBJ: 22.3.c. Explain how Ran regulates the transport of proteins in and out of the nucleus.

MSC: Applying 26. Describe the function of the SRP receptor.

ANS: The SRP receptor is responsible for binding the SRP-ribosome complex. This brings the SRP-ribosome in close contact with the translocon protein to allow the peptide sequence to be inserted.

DIF: Easy REF: 22.3 OBJ: 22.3.d. Express how the ER signal peptide causes ribosomes to bind to the translocator.

MSC: Understanding

Chapter 23: Gene Regulation MULTIPLE CHOICE 1. The control point for most gene regulation occurs at the initiation of a. transcription. b. RNA processing. c. protein synthesis. d. protein modifications.

ANS: A DIF: Medium REF: 23.1 OBJ: 23.1.a. Define trans-acting factors and cis-acting sites.

MSC: Understanding

2. The phrase trans-acting factors is short for __________ factor protein. a. translation b. transcription c. transunion d. transform ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.a. Define trans-acting factors and cis-acting sites.

MSC: Understanding

3. Which of the following best describes how trans- and cis-acting factors operate? a. Cis-acting factors can bind to specific DNA sequences whereas trans-acting sites are DNA sequences. b. Trans-acting factors can bind to specific DNA sequences whereas cis-acting sites are DNA sequences. c. Trans- and cis-acting factors can both bind to specific DNA sequences. d. Trans- and cis-acting factors can both only bind to DNA elements to which they are physically linked.

ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.a. Define trans-acting factors and cis-acting sites.

MSC: Analyzing

4. One of the most common binding interactions between proteins and DNA are __________ bonds. a. ionic b. covalent c. hydrogen d. polar ANS: C DIF: Medium REF: 23.1 OBJ: 23.1.b. Name four amino acids that commonly make specific contacts with nucleotide bases.

MSC: Understanding 5.

-Helices are usually found in DNA binding proteins because they a. are the only secondary feature found in proteins. b. are the only stable secondary feature in proteins. c. have the appropriate diameter to fit into the major groove of DNA. d. have the appropriate diameter to fit into the minor groove of DNA. ANS: C DIF: Easy REF: 23.1 OBJ: 23.1.b. Name four amino acids that commonly make specific contacts with nucleotide bases.

MSC: Understanding 6. A helix-turn-helix motif can best be described as a(n) __________ followed by a(n) __________. a.

-helix; -helix b.

-helix; -helix c. -helix; -helix d. -helix; -helix ANS: B DIF: Easy REF: 23.1 OBJ: 23.1.c. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

MSC: Remembering 7. In a leucine zipper, the leucine resides are found every seventh amino residue. This forces the supersecondary structure to be a(n) a.

-helix. b. -sheet. c. coiled-coil. d. hairpin turn.

ANS: C DIF: Easy REF: 23.1 OBJ: 23.1.c. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

MSC: Understanding 8. A protein that has a weak affinity for a DNA site and is at ___________ concentrations of protein will bind to DNA __________. a. low; strongly b. high; strongly c. low; indiscriminately d. high; indiscriminately ANS: B DIF: Difficult REF: 23.1 OBJ: 23.1.c. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

MSC: Applying 9. In cooperative DNA binding, the binding of a. both proteins must occur at the same time. b. one protein molecule is more favored when another one is bound to a nearby site on the DNA. c. one protein molecule is less favored when another one is bound to a nearby site on the DNA. d. one protein molecule is only possible if two other molecules are bound to a nearby site on the DNA. ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.d. Identify the role of cooperativity in gene regulation.

MSC: Applying 10. Which of the following is NOT a common mechanism for modifying transcription factor activity? a. allosteric activation b. covalent modification c. ionic modification d. positive modulation ANS: C DIF: Easy REF: 23.1 OBJ: 23.1.e. Define the different mechanisms of positive and negative gene regulation by ligand

binding.

MSC: Remembering

11. The best description of how allosteric regulation works is that a ligand __________ the transcriptional regulatory protein, which __________ the protein’s affinity for DNA. a. covalently modifies; increases b. covalently modifies; decreases c. binds to; causes conformational changes that affect d. binds to; causes conformational changes that can only decrease ANS: C DIF: Medium REF: 23.1 OBJ: 23.1.e. Define the different mechanisms of positive and negative gene regulation by ligand binding.

MSC: Understanding 12. What kind of control mechanism is ligand-induced binding of an activator protein? a. positive b. negative c. neutral d. covalent ANS: A DIF: Difficult REF: 23.1 OBJ: 23.1.e. Define the different mechanisms of positive and negative gene regulation by ligand binding.

MSC: Understanding 13. In negative autoregulation, a. proteins activate their own expression. b. proteins repress their own expression. c. a regulatory protein controls DNA expression. d. a regulatory protein turns off DNA expression.

ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.f. Compare negative and positive autoregulation.

MSC: Understanding

14. The figure below shows __________ autoregulation and will __________.

a. b. c. d.

positive; reach a steady state positive; be zero in the absence of an activator negative; reach a steady state negative; be zero in the absence of an activator

ANS: C DIF: Medium REF: 23.1 OBJ: 23.1.f. Compare negative and positive autoregulation.

MSC: Understanding

15. Which of the following best describes when a pattern of gene expression is altered without change in the DNA sequence? a. epigenetic states b. negative autoregulation c. positive autoregulation d. meiosis ANS: A DIF: Easy REF: 23.1 OBJ: 23.1.f. Compare negative and positive autoregulation.

MSC: Remembering

16. When IPTG is added to a cell, what is the predicted outcome? a. Protein synthesis stops. b. Protein overproduction occurs. c. The DNA sequence coding for a given protein is altered. d. An epigenetic state occurs.

ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Applying 17. IPTG causes the lac promoter to a. bind irreversibly to the DNA. b. dissociate from the DNA. c. perform ligand-regulated repression. d. perform ligand-activated deregulation.

ANS: B DIF: Difficult REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Applying 18. What by-product can be measured for in a cell if lacZ is being used as a reporter gene? a. luciferase b. chloramphenicol acetyltransferase c. -galactosidase d. GFP ANS: C DIF: Medium REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Applying 19. When running an assay for luciferase, what reporter gene has been inserted into the plasmid? a. lacZ b. luc c. cat d. gfp ANS: B DIF: Medium REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Applying 20. A reporter gene can be defined as a gene that a. has a product that is easy to detect. b. prevents protein synthesis. c. overproduces proteins.

d. causes an epigenetic sate.

ANS: A DIF: Medium REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Understanding 21. Operons can be defined as units of DNA containing _________ gene(s) under control of __________ promotor(s). a. one; one b. multiple; one c. multiple; multiple d. one; multiple ANS: B DIF: Medium REF: 23.2 OBJ: 23.2.a. Name the key elements of the lac operon.

MSC: Remembering

22. The function of the lac operon is to provide a. the enzymes needed to utilize the disaccharide lactose. b. the enzymes needed to produce lactose. c. lactose. d. glucose and galactose to make lactose.

ANS: A DIF: Medium REF: 23.2 OBJ: 23.2.a. Name the key elements of the lac operon.

MSC: Understanding

23. When there is no lactose in a cell, production of lac operon a. increases. b. decreases. c. turns off completely. d. production of lac operon does not depend on lactose concentration.

ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.a. Name the key elements of the lac operon.

MSC: Understanding

24. An unusual structural feature of the lac repressor is that it is a a. homodimer. b. homotetramer. c. heterodimer. d. heterotetramer.

ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.b. State the roles of the lac repressor and CRP in regulation of the lac operon.

MSC: Understanding 25. A result of the DNA bend induced by the lac repressor binding is that the __________ groove of the DNA is widened to allow binding of the lac repressor __________. a. minor; -helix b. major; -helix c. minor; -helix d. major; -helix ANS: B DIF: Difficult REF: 23.2 OBJ: 23.2.b. State the roles of the lac repressor and CRP in regulation of the lac operon.

MSC: Understanding 26. Allolactose acts as a(n)

a. b. c. d.

repressor by causing the lac repressor to bind. inducer by binding to the lac repressor and causing it to dissociate. repressor by increasing the binding affinity of the lac repressor. inducer by binding to CRP.

ANS: B DIF: Medium REF: 23.2 OBJ: 23.2.b. State the roles of the lac repressor and CRP in regulation of the lac operon.

MSC: Understanding 27. The function of CRP in lac operon expression is to __________ the promoter by causing RNA polymerase to __________. a. stimulate; dissociate b. stimulate; bind tighter c. inhibit; dissociate d. inhibit; bind tighter ANS: B DIF: Medium REF: 23.2 OBJ: 23.2.b. State the roles of the lac repressor and CRP in regulation of the lac operon.

MSC: Understanding 28. What will happen to the lac operon when there are elevated levels of glucose in a cell? a. CRP binds strongly. b. Transcription occurs at a very high rate of expression. c. Transcription occurs at a very low rate of expression. d. The lac repressor is bound.

ANS: C DIF: Medium REF: 23.2 OBJ: 23.2.b. State the roles of the lac repressor and CRP in regulation of the lac operon.

MSC: Understanding 29. A regulon can best be described as units of DNA containing __________ gene(s) under control of __________ promotor(s). a. one; one b. multiple; one c. multiple; multiple d. one; multiple ANS: C DIF: Medium REF: 23.2 OBJ: 23.2.d. Differentiate between an operon and a regulon.

MSC: Remembering

30. What is the function of the SOS regulatory system in the cell? a. DNA repair b. DNA translation c. lactose degradation d. glucose inhibition ANS: A DIF: Easy REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Understanding 31. When DNA is damaged, what protein is activated? a. LexA repressor b. RecA c. SOS operon d. lac operon

ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Understanding 32. The function of RecA* is to a. inhibit expression of its own gene. b. repress SOS genes. c. stimulate LexA autocleavage. d. allow LexA to accumulate.

ANS: C DIF: Easy REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Understanding 33. When LexA is autocleaved by RecA*, the SOS genes a. are repressed. b. are activated. c. are unaffected. d. produce operons.

ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Applying 34. Once RecA is no longer activated, what happens to the SOS regulon? a. LexA builds up and represses the SOS regulon. b. LexA autocleaves and SOS regulon is activated. c. LexA binds to the RecA. d. LexA binds to the SOS regulon.

ANS: A DIF: Easy REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Applying 35. When bacteriophage a. lysis b. lysogeny c. lyophilize d. lysine

integrates into the E. coli genome, what is that lifestyle called?

ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.f. Differentiate between the lytic and lysogenic stages of bacteriophage lambda in terms of what genes are active.

MSC: Remembering 36. When bacteriophage generates progeny viruses that kill the bacterial host E. coli genome, what is that lifestyle called? a. lytic b. lysogeny c. lyophilize d. lysine ANS: A DIF: Easy REF: 23.2 OBJ: 23.2.f. Differentiate between the lytic and lysogenic stages of bacteriophage lambda in terms of what genes are active.

MSC: Remembering

37. High concentration of CI protein in the cell __________ expression of the __________. a. prevents; lytic promoter b. allows; lytic promoter c. prevents; trp operon d. allows; attenuator sequence ANS: A DIF: Easy REF: 23.2 OBJ: 23.2.g. Define the roles of the promoters, CI binding sites, and the Cro binding site.

MSC: Applying 38. The role of the CI protein in the lysogenic pathway is that the a. lysogenic pathway is favored when CI binds. b. lytic pathway is favored when CI binds. c. CI protein activates the PR promoter. d. CI protein inhibits the PRM promoter.

ANS: A DIF: Easy REF: 23.2 OBJ: 23.2.g. Define the roles of the promoters, CI binding sites, and the Cro binding site.

MSC: Applying 39. When Cro is bound to OR3, the a. lysogenic pathway is favored. b. lytic pathway is favored. c. Cro protein inhibits the PR promoter. d. CI protein activates the PRM promoter.

ANS: B DIF: Medium REF: 23.2 OBJ: 23.2.g. Define the roles of the promoters, CI binding sites, and the Cro binding site.

MSC: Applying 40. If PRM is autoactivated and PR is inhibited, then __________ is/are bound. a. CI b. Cro c. both CI and Cro d. neither CI and Cro ANS: A DIF: Medium REF: 23.2 OBJ: 23.2.g. Define the roles of the promoters, CI binding sites, and the Cro binding site.

MSC: Applying 41. When the Trp repressor is bound to the trp operon, it results in the __________ by RNA polymerase. a. inhibition of transcriptional initiation b. disruption of transcriptional elongation c. initiation d. enhancement of transcriptional elongation ANS: A DIF: Medium REF: 23.2 OBJ: 23.2.h. Name the two mechanisms used for control of the trp operon.

MSC: Applying 42. When trp operon is attenuated, what does that mean for the trp operon? a. inhibition of transcriptional initiation by RNA polymerase b. disruption of transcriptional elongation by RNA polymerase c. initiation by RNA polymerase

d. enhancement of transcriptional elongation by RNA polymerase ANS: B DIF: Medium REF: 23.2 OBJ: 23.2.h. Name the two mechanisms used for control of the trp operon.

MSC: Applying 43. When there is a large presence of tryptophan, what effect that does that have on the Trp repressor? a. Trp repressor is bound. b. Trp repressor is not bound. c. There is initiation of RNA polymerase. d. Transcriptional elongation by RNA polymerase is enhanced.

ANS: A DIF: Medium REF: 23.2 OBJ: 23.2.h. Name the two mechanisms used for control of the trp operon.

MSC: Applying 44. The correct mRNA secondary structure of transcriptional termination is __________ stem-loop structure. a. 2-3 b. 3-4 c. 1-3 d. 2-4 ANS: B DIF: Easy REF: 23.2 OBJ: 23.2.i. Explain how mRNA secondary structure plays a role in control of the trp operon.

MSC: Understanding 45. Transcriptional elongation is favored by the trp operon when tryptophan levels are a. high. b. low. c. constant. d. The trp operon is not affected by tryptophan levels.

ANS: B DIF: Difficult REF: 23.2 OBJ: 23.2.i. Explain how mRNA secondary structure plays a role in control of the trp operon.

MSC: Applying 46. Together, the eight histone molecules are called the histone a. octane. b. octamer. c. dimer. d. tetramer.

ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.a. Define the structure of a nucleosome.

MSC: Remembering

47. By wrapping DNA around the histone octamer, how much smaller can DNA be? a. tenfold b. eightfold c. sevenfold d. twofold ANS: C DIF: Easy REF: 23.3 OBJ: 23.3.a. Define the structure of a nucleosome.

MSC: Remembering

48. A nucleosome can best be described as a protein core containing __________ molecules each of __________ histones and a segment of DNA. a. four; four b. two; four c. two; two d. four; two ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.a. Define the structure of a nucleosome.

MSC: Remembering

49. The portion of the histone that can be acetylated is the a. head. b. body. c. tail. d. arm.

ANS: C DIF: Easy REF: 23.3 OBJ: 23.3.b. State the three broad classes of nucleosome modifications.

MSC: Remembering 50. What is a result of histone acetylation? a. repression of transcription b. increased transcriptional activity c. no effect d. remodeling of histone ANS: B DIF: Difficult REF: 23.3 OBJ: 23.3.b. State the three broad classes of nucleosome modifications.

MSC: Applying 51. Which amino acid residues on histones are acetylated? a. histidine b. lysine c. arginine d. serine ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.b. State the three broad classes of nucleosome modifications.

MSC: Understanding 52. Histone acetylation leads to transcriptional activation by a. increasing the interaction between the histone tail and DNA. b. decreasing the interaction between the histone tail and DNA. c. strengthening the interactions between nucleosomes. d. removing binding sites for additional transcriptional factors.

ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.c. Identify three biochemical consequences of histone acetylation.

MSC: Analyzing 53. When histones are acetylated, the nucleosome–histone interaction a. is weakened. b. is strengthened. c. dissociates the nucleosome from the histone. d. covalently binds the nucleosome to the histone.

ANS: A DIF: Medium REF: 23.3 OBJ: 23.3.c. Identify three biochemical consequences of histone acetylation.

MSC: Applying 54. When the lysine side chain in a histone is acetylated, the amino group is now a. positively charged. b. neutral. c. negatively charged. d. removed.

ANS: B DIF: Difficult REF: 23.3 OBJ: 23.3.c. Identify three biochemical consequences of histone acetylation.

MSC: Understanding 55. What function do HAT and HDAC perform in the chromatin-modifying process? a. Both HAT and HDAC activate the gene. b. Both HAT and HDAC repress the gene. c. HAT represses the gene and HDAC activates the gene. d. HAT activates the gene and HDAC represses the gene.

ANS: D DIF: Difficult REF: 23.3 OBJ: 23.3.c. Identify three biochemical consequences of histone acetylation.

MSC: Analyzing 56. Bromodomain-containing complexes bind to __________ lysines in histones. a. methylated b. acetylated c. brominated d. chlorinated ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.d. Differentiate between bromodomains and chromodomains.

MSC: Understanding 57. Lysine methylation has what effect on the histone? a. leaves a positive charge on the amino acid b. leaves a neutral charge on the amino acid c. binds more strongly to the histone d. removes chromatin docking sites ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.e. Compare and contrast acetylation and methylation of histones.

MSC: Applying 58. The Swi-Snf complex affects chromatin by a. creating extra nucleosomes near the promoter. b. being a promoter. c. creating a nucleosome-free region near the promoter. d. transcribing the chromatin.

ANS: C DIF: Difficult REF: 23.3 OBJ: 23.3.f. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

MSC: Applying

59. Why are long tracts of A residues not found in regions of stable nucleosome positioning? a. They are too flexible. b. They are too stiff. c. DNA cannot have long tracts of A residues. d. DNA cannot have A residues.

ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.f. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

MSC: Analyzing 60. The pioneer factor can be defined as the a. last transcription factor protein complex to bind. b. first transcription factor protein complex to bind. c. last cis-acting site in a chain. d. first cis-acting site in a chain.

ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.f. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

MSC: Understanding 61. A function of transcriptional activator proteins is to a. recruit gene promotors. b. initiate RNA synthesis. c. recruit chromatin modifiers. d. initiate DNA synthesis.

ANS: C DIF: Easy REF: 23.3 OBJ: 23.3.g. State the two primary functions of transcriptional activator proteins.

MSC: Analyzing 62. What are the two key protein complexes recruited to the preinitiation complex by activator proteins? a. mediator complex and DNA polymerase b. mediator complex and TFIID c. TFIID and RNA polymerase d. TFIID and DNA polymerase ANS: B DIF: Difficult REF: 23.3 OBJ: 23.3.g. State the two primary functions of transcriptional activator proteins.

MSC: Understanding 63. The function of an insulator sequence in DNA is to a. amplify the action of enhancers. b. counteract the action of enhancers. c. inhibit promoters. d. activate RNA synthesis.

ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.g. State the two primary functions of transcriptional activator proteins.

MSC: Applying 64. In yeast, the sugar galactose is converted to what molecule to enter glycolysis? a. glucose

b. fructose c. glucose-6-phosphate d. fructose-6-phosphate ANS: C DIF: Easy REF: 23.3 OBJ: 23.3.h. Understand how galactose regulates its own metabolism in yeast.

MSC: Understanding 65. The proteins encoded by GAL1, GAL2, GAL7, and GAL10 are all needed for converting __________ to glucose-6-phosphate. a. glucose b. fructose c. galactose d. galactose ANS: D DIF: Medium REF: 23.3 OBJ: 23.3.h. Understand how galactose regulates its own metabolism in yeast.

MSC: Understanding 66. Predict the state of yeast when GAL 80 is bound to GAL 4 activation domain. a. high glucose concentration b. low glucose concentration c. high galactose concentration d. low galactose concentration ANS: D DIF: Difficult REF: 23.3 OBJ: 23.3.h. Understand how galactose regulates its own metabolism in yeast.

MSC: Applying 67. The eve stripe 2 enhancer can be defined as multiple __________ sites for at least four __________. a. trans-binding; transcription factor proteins b. cis-binding; transcription factor proteins c. cis-binding; insulator genes d. cis-binding; gene promoters ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.i. Describe the role of the eve stripe 2 enhancer and its associated transcription factors.

MSC: Understanding 68. Bicoid, Hunchback, Giant, and Kruppel are all transcription factor proteins involved in __________ pattern. a. even-skipped expression b. odd-skipped expression c. even-skipped transcription d. odd-skipped transcription ANS: A DIF: Medium REF: 23.3 OBJ: 23.3.i. Describe the role of the eve stripe 2 enhancer and its associated transcription factors.

MSC: Understanding 69. Introducing Oct4, Sox2, c-Myc, or Klf4 into a differentiated cell causes a. cell death. b. a pluripotent state. c. no change.

d. cell meiosis.

ANS: B DIF: Medium REF: 23.3 OBJ: 23.3.j. Define the pluripotent state. MSC: Analyzing 70. Pluripotent state can be defined as a __________ cell. a. differentiated b. predifferentiated c. G1 state of the d. S state of the ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.j. Define the pluripotent state. MSC: Remembering 71. What are the two main types of stem cells? a. somatic and embryonic b. somatic and epithelial c. stromal and somatic d. stromal and embryonic ANS: A DIF: Easy REF: 23.3 OBJ: 23.3.j. Define the pluripotent state. MSC: Remembering 72. iPS cells can be defined as __________ cells. a. differentiated b. dedifferentiated c. embryonic stem d. somatic stem ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.j. Define the pluripotent state. MSC: Understanding 73. Stem cells can undergo two different pathways: cell __________ and cell __________. a. proliferation; dedifferentiation b. proliferation; differentiation c. differentiation; dedifferentiation d. differentiation; integration ANS: B DIF: Easy REF: 23.3 OBJ: 23.3.j. Define the pluripotent state. MSC: Remembering 74. Producing an iPS cell is remarkable because the pathway a. for conversion is general, not specific. b. is a highly irreversible reaction. c. for conversion is very specific and limited. d. produces a very unstable cell.

ANS: A DIF: Difficult REF: 23.3 OBJ: 23.3.k. Explain how pluripotency can be induced.

75. What are two medical applications that iPS could be used for? a. type 1 diabetes and Parkinson’s b. type 2 diabetes and Parkinson’s c. Alzheimer’s and Parkinson’s d. Alzheimer’s and type 2 diabetes

MSC: Applying

ANS: A DIF: Medium REF: 23.3 OBJ: 23.3.k. Explain how pluripotency can be induced.

MSC: Understanding

SHORT ANSWER 1. Why are Arg, Lys, Gln, and Asn commonly found to make specific contact with nucleotide bases?

ANS: These amino acids are able to form hydrogen bonds with the nucleotides. They are able to function as either a hydrogen bond donor or acceptor.

DIF: Medium REF: 23.1 OBJ: 23.1.b. Name four amino acids that commonly make specific contacts with nucleotide bases.

MSC: Understanding 2. Draw the four combinations of nucleotides and label the major groove in each as either an H-bond donor, an H-bond acceptor, or hydrophobic.

ANS: As shown in Figure 23.4, the A-T base pair in the major groove is acceptor–donor–acceptor– , whereas T-A is –acceptor–donor–acceptor. The G-C base pair is acceptor–acceptor–donor, but C-G is donor–acceptor–acceptor.

DIF: Medium REF: 23.1 OBJ: 23.1.b. Name four amino acids that commonly make specific contacts with nucleotide bases.

MSC: Applying

3. How does entropy drive protein-DNA complex formations?

ANS: Entropy is often increased by the release of bound water molecules and cations when a protein-DNA complex is formed. This increase in entropy makes the interaction thermodynamically favorable.

DIF: Difficult REF: 23.1 OBJ: 23.1.c. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

MSC: Applying 4. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

ANS: Helix-turn-helix is approximately 20 amino acids long and consists of two -helices connected by a short turn. Zinc-finger motif is approximately 30 amino acids long and coordinates on a zinc atom with two cysteine and two histidine residues. The leucine zipper leucine amino acids are found approximately every seven amino acids, which allows interactions between similarly spaced leucines on the other protein subunit, creating a coiled-coiled structure. Helix-loop-helix proteins are characterized by a loop region between the DNA binding on -helix and the dimerization -helix.

DIF: Difficult REF: 23.1 OBJ: 23.1.c. Differentiate among the helix-turn-helix, zinc-finger DNA-binding, leucine zipper, and helix-loop-helix motifs.

MSC: Applying 5. Using the figure below, explain how cooperativity works.

ANS: Weak interactions between the three components will allow the components to interact. When the third component binds to a binary complex, the same interactions form, but only small amounts of entropy are lost when the three protein complexes form, so it is strongly favored.

DIF: Medium REF: 23.1 OBJ: 23.1.d. Identify the role of cooperativity in gene regulation.

MSC: Applying 6. Define the different mechanism of positive and negative gene regulation by ligand binding.

ANS: As shown in Figure 23.10 a and d, negative control turns off expression of a gene by either ligand-induced binding of a repressor protein or ligand-induced dissociation of activator binding.

Positive control occurs either through ligand-induced binding of an activator protein or ligand-induced dissociation of repressor binding to DNA.

DIF: Medium REF: 23.1 OBJ: 23.1.e. Define the different mechanisms of positive and negative gene regulation by ligand binding.

MSC: Understanding 7. Compare negative and positive autoregulation.

ANS: In negative autoregulation a protein represses its own expression, giving rise to negative feedback, which acts to modulate fluctuations in the level of the regulator. When repressor protein levels are high at the onset, negative autoregulation does not occur until repressor protein levels are high enough to affect transcription rates. In positive autoregulation, a protein activates its own expression. This confers positive feedback and is often used in regulatory circuits to drive regulatory decisions or switches toward a particular regulatory state.

DIF: Medium REF: 23.1 OBJ: 23.1.f. Compare negative and positive autoregulation.

MSC: Analyzing

8. How can the lac promoter and IPTG be used to produce large amounts of a specific protein?

ANS: As shown in Figure 23.16, the lac promoter can be used to regulate the expression of a target gene using IPTG, an inhibitor of the lac repressor. Regulation of transcription by the lac promoter uses IPTG to inhibit lac repressor binding to the lac operator, which allows for overproduction of proteins.

DIF: Medium REF: 23.1 OBJ: 23.1.g. Explain how the lac promoter and IPTG can be used to produce large amounts of a specific protein.

MSC: Understanding 9. Name the key elements of the lac operon.

ANS: The regulatory region and the structural genes are the key elements of the lac operon. The regulatory region contains cis-acting sites that control lac operon expression and regulation. The structural genes (lacZ, lacY, and lacA) are needed to break down lactose into glucose and galactose.

DIF: Medium operon.

REF: 23.2

OBJ: 23.2.a. Name the key elements of the lac

MSC: Understanding 10. Compare and contrast the structures of the lac repressor protein and CRP. ANS: The lac repressor is a homotetramer, whereas the CRP protein is a dimer.

DIF: Easy REF: 23.2 OBJ: 23.2.c. Compare and contrast the structures of the lac repressor protein and CRP. MSC: Analyzing 11. State the four distinct transcription states in the SOS regulon.

ANS: (1) When the system is in the OFF state, the LexA protein acts to repress several dozen SOS genes in the SOS regulon. LexA also inhibits expression of its own gene and expression of the RecA gene. (2) DNA damage leads to activation of the RecA protein (RecA*). (3) RecA* stimulates LexA autocleavage, which reduces the amount of LexA repressor in the cell, thereby increasing the expression of the SOS regulon genes. (4) When DNA is repaired and replication can resume, RecA is no longer active. This enables LexA to accumulate, allowing a return to the OFF state.

DIF: Medium REF: 23.2 OBJ: 23.2.e. State the four distinct transcription states in the SOS regulon.

MSC: Remembering 12. Differentiate between the lytic and lysogenic stages of bacteriophage  in terms of what genes are active.

ANS: Using Figure 23.31 for reference, it can be seen that transcriptional regulation is the molecular basis of control for the bacteriophage  lysogenic and lytic pathways. The lysogenic state is favored when CI binds tightly and cooperatively to sites OR1 and OR2, which activates its own expression from PRM and represses PR. Cro binds tightly to OR3, repressing PRM without affecting its own expression from PR. This regulatory state is stable because Cro continues to be made and CI is repressed.

DIF: Difficult REF: 23.2 OBJ: 23.2.f. Differentiate between the lytic and lysogenic stages of bacteriophage lambda in terms of what genes are active.

MSC: Analyzing 13. Compare the two mechanisms used for control of the trp operon.

ANS: The first mechanism is by the action of the Trp repressor that inhibits transcriptional initiation by RNA polymerase, whereas the second mechanism involves disruption of transcriptional elongation

by RNA polymerase through a mechanism called attenuation.

DIF: Medium REF: 23.2 OBJ: 23.2.h. Name the two mechanisms used for control of the trp operon.

MSC: Analyzing 14. Describe the three broad classes of nucleosome modifications.

ANS: (1) Histones in nucleosomes undergo a wide variety of posttranslational modifications on their amino acid side chains; (2) the positions of nucleosome relative to the DNA sequence can be changed; some nucleosomes contain histone variants, (3) in which a particular histone is replaced by a closely related protein.

DIF: Medium REF: 23.3 OBJ: 23.3.b. State the three broad classes of nucleosome modifications.

MSC: Understanding 15. Describe the three biochemical consequences of histone acetylation.

ANS: First, it weakens the interaction between the histone tail and the DNA by removing an electrostatic interaction and therefore destabilizing the nucleosome. Second, acetylation weakens interactions between nucleosomes, thereby disassembling the higher-order chromatin structures. Third, histone acetylation provides binding sites for additional transcription factors.

DIF: Medium REF: 23.3 OBJ: 23.3.c. Identify three biochemical consequences of histone acetylation.

MSC: Understanding 16. Differentiate between where bromodomains and chromodomains bind.

ANS: Bromodomain-containing complexes bind to acetylated lysines in histones.

Chromodomain-containing complexes bind to methylated lysines in histones.

DIF: Easy REF: 23.3 OBJ: 23.3.d. Differentiate between bromodomains and chromodomains.

MSC: Analyzing 17. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

ANS: As shown in Figure 23.47 from the text, pioneer factors are the first transcription factors to bind a promoter or enhancer region, leading to changes that allow other factors to bind. Several mechanisms can enable their binding. The nucleosomes might be positioned so that the binding site is free. The DNA near the end of the portion wrapped around the core can dissociate briefly, exposing that site. Some pioneer transcription factors can bind to DNA that is wrapped in a nucleosome and initiate chromatin remodeling to expose the cis-acting site.

DIF: Medium REF: 23.3 OBJ: 23.3.f. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

MSC: Remembering 18. Explain how transcription of the yeast PHO5 gene is regulated.

ANS: Transcription of the yeast PHO5 gene is regulated by PHO4-mediated removal of nucleosomes near the PHO5 promoter. Under conditions of low phosphate levels, PHO4 is dephosphorylated and translocated to the nucleus, where it binds to a regulatory element called UASp1. This leads to repositioning of the neighboring nucleosome, exposing a second PHO4 protein. Eventually, a total of four nucleosomes are removed from a region of the PHO5 promoter, thereby establishing a nucleosome-free region to facilitate the binding of additional transcription factors.

DIF: Medium REF: 23.3 OBJ: 23.3.f. List the chain of events that occurs after a pioneer factor binds to a cis-acting sequence.

MSC: Analyzing 19. Describe the two primary functions of transcriptional activator proteins.

ANS: (1) Recruit chromatin modifiers to DNA regions near genes and (2) recruit components of the general transcriptional machinery to gene promoter sequences DIF: Medium REF: 23.3 OBJ: 23.3.g. State the two primary functions of transcriptional activator proteins.

MSC: Understanding 20. Describe the transcriptional regulation of the GAL1 and GAL10 genes in yeast.

ANS: The GAL4 protein binds to the UASG. In the absence of galactose, the GAL80 regulatory protein binds to the GL4 protein activation domain and inhibits the recruitment of transcription factors to GL1 and GAL10 gene promoters. On addition of galactose, GAL3 binds galactose, which induces a protein conformation change in GAL3 that promotes its binding to GAL80. Once this happens, GAL80 protein is no longer able to bind and inhibit GAL4.

DIF: Difficult REF: 23.3 OBJ: 23.3.h. Understand how galactose regulates its own metabolism in yeast.

MSC: Understanding

21. How can pluripotency be induced?

ANS: Reprogramming of differentiated cells to iPS cells is done by introduction of the four transcription factors (Oct4, Sox2, Klf4, c-Myc). A human tissue sample is grown in culture and then viruses carrying the transcription factor genes are introduced into the cells. After continued growth for several weeks, a few cells become iPS cells. These iPS cells are then expanded in culture and further characterized.

DIF: Medium REF: 23.3 induced.

MSC: Understanding

OBJ: 23.3.k. Explain how pluripotency can be

22. What are the two main approaches being considered for treatment using iPS cell technology?

ANS: The first approach is to reintroduce cells into the patient that might correct the patient’s disease.

Two disease states are being considered: type 1 diabetes and Parkinson’s. The second approach is to use the iPS cells to help identify disease mechanism and to screen for drugs that correct disease phenotype.

DIF: Medium induced.

MSC: Evaluating

REF: 23.3

OBJ: 23.3.k. Explain how pluripotency can be

23. How is transcription factor recruitment used in eukaryotic gene regulatory circuits?

ANS: Recruitment refers to the property of trans-acting factors, bound to cis-acting sites near the genes to be regulated, to interact with other proteins or protein complexes and bring them to the vicinity of the gene to be regulated. Three different classes of proteins or complexes are recruited. The first is proteins that act to modify the side chains of histones in nucleosomes. The second is chromatin remodeling machines, which move nucleosomes around. The third is components of the general transcription machinery, such as the mediator complex and TFIID, which are brought to the vicinity of the gene so that a preinitiation complex can assemble at the transcription start site.

DIF: Difficult REF: 23.3 OBJ: 23.3.b. State the three broad classes of nucleosome modifications.

MSC: Evaluating 24. Explain the expression of the Drosophila even-skipped gene.

ANS: Expression of the Drosophila even-skipped gene occurs in a series of seven stripes along the axis of the embryo, where each stripe has a separate set of regulatory controls. The eve stripe 2 enhancer region contains cis-acting sites for four different transcription factors that function together to restrict expression of the even structural gene to a small number of cells.

DIF: Difficult REF: 23.3 OBJ: 23.3.i. Describe the role of the eve stripe 2 enhancer and its associated transcription factors.

MSC: Understanding 25. What are the four transcription factors involved in the eve stripe 2 enhancer region?

ANS: Bicoid, Hunchback, Giant, and Kruppel DIF: Easy REF: 23.3 OBJ: 23.3.i. Describe the role of the eve stripe 2 enhancer and its associated transcription factors.

MSC: Understanding