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Chap 02_9e Indicate whether the statement is true or false. 1. The amount of free energy released when bonds are broken during a reaction is higher when the molecule has more electronegative atoms. a. True b. False Indicate the answer choice that best completes the statement or answers the question. 2. The ultimate source of energy used to make ATP for all cells is: a. electricity. b. heat. c. light. d. magnetism. 3. Which of the following is true about an observed change in free energy (ΔG)? a. Free energy was created when the Big Bang occurred b. It can be calculated from the total change in energy, temperature, and change in entropy. c. If a reaction's free energy is greater than zero, it is likely to happen spontaneously. d. Free energy is comparable to unusable energy.

4. The pKa of the weak base NH3 is 9.25. When present in lysosomes, a subcellular organelle—ammonia—is almost totally protonateD) Which of the pH values listed below is most likely to be that of the lysosome lumen? a. 1 b. 5 c. 8 d. 14 5. An Archaea cell living in an abandoned mine is found to contain a very high concentration of protons. It is likely that this cell: a. has a high ph and is acidic b. has a high ph and is alkaline. c. has low ph and is acidic d. has a low pH and is alkaline. 6. What is [P]/[R] when ΔG =ΔG°´? a. –1 b. 0 c. 1 d. 2.3

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Chap 02_9e 7. Hydrolysis of ATP: a. is endothermic b. has a positive ΔG value. c. must be coupled to an energetically favorable reaction. d. none of the above 8. In the reaction NAD+ + H+ + 2e−→ NADH, NAD+ becomes: a. dehydrated b. hydrolyzed c. oxidized d. reduced 9. Which of the following is NOT one of the ways RNA differs from DNA? a. Ribonucleotides have a hydroxyl group on the 2 carbon of their sugar subunit. b. Ribonucleotides can have enzymatic activity. c. Ribonucleotides contain a phosphate group. d. Ribonucleotides can contain the base uracil. 10. A reaction with a positive ΔG value can be made energetically favorable by increasing the: a. ΔG°'. b. starting concentration of products. c. starting concentration of reactants. d. The first two answers are correct. 11. NAD+ and FAD are often referred to as: a. redox proteins. b. polymers. c. reduced dinucleotides. d. electron-carrying coenzymes. 12. Which of the following is a monosaccharide? a. fructose b. galactose c. glucose d. all of the above

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Chap 02_9e 13. When two atoms differing in electronegativity are joined in a covalent bond, then the: a. electrons are shared equally between the atoms. b. bond is nonpolar. c. resulting compound is devoid of any dipole moment. d. atom with the greater electronegativity attracts the bonded electrons more strongly. 14. Which of the following is the strongest interaction? a. hydrogen bond b. ionic bond c. phosphoanhydride bond d. van der Waals interaction 15. Which of the following is a noncovalent interaction? a. hydrophobic effect b. ionic interactions c. van der Waals interactions d. all of the above 16. Which of the following is/are a hydrophilic amino acid? a. alanine b. leucine c. tryptophan d. serine 17. Based on what you know about hydrophobic interactions, which of the following is/are composed of a bilayer? a. a cell’s membrane b. spontaneously aggregated phospholipids surrounding an aqueous interior c. lipid vesicles that have budded off the cell’s membrane d. all of the above 18. For the binding reaction A + B ➝ AB, the dissociation constant is equal to: a. [AB]/([A]+[B]) b. ([A] + [B])/[AB]. c. Keq d. The first and third answers are correct. 19. Covalent bonds between which of the following pairs of atoms are nonpolar? a. C–C b. C–H c. O–H d. A and B Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_9e 20. In a biochemical reaction in which ΔH < 0 and ΔS > 0: a. the reaction is spontaneous. b. the reaction is endothermic c. the reaction is endergonic d. ΔG is positive. 21. A 1-mL solution of 0.1 M NaOH is diluted to 1 L at 25°C. What is the pH of the resulting solution? a. 1 b. 7 c. 10 d. 13 22. What is the major structural difference between starch and cellulose? a. the types of monosaccharide subunits in the molecules b. the amount of branching that occurs in the molecule c. that humans can only ingest starch d. the type of glycosidic linkages in the molecule 23. How do phospholipids interact with water molecules? a. The polar heads interact with water; the nonpolar tails do not. b. Phospholipids don't interact with water because water is polar and lipids are nonpolar. c. The polar heads avoid water; the nonpolar tails attract water (because water is polar and opposites attract). d. Phospholipids dissolve in water. 24. A 1-mL solution of 0.05 M H2SO4 is diluted to 100 mL at 25°C. What is the pH of the resulting solution? a. 1 b. 2 c. 3 d. 4 25. Which of the following is the BEST explanation for why vegetable oil is a liquid at room temperature while animal fats are solid? a. Vegetable oil has fewer double bonds than animal fats. b. Animal fats have no amphipathic character. c. Vegetable oil has longer fatty-acid tails than do animal fats. d. Vegetable oil has more double bonds than do animal fats.

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Chap 02_9e 26. Which of the following is a negatively charged amino acid? a. alanine b. aspartate c. glutamine d. histidine 27. Photosynthesis by plants and certain microbes traps the energy in light and uses it to: a. Reduce glucose into carbon dioxide. b. synthesize ATP from ADP and inorganic phosphate. c. generate ATP from the oxidation of reduced inorganic compounds. d. none of the above 28. A nucleotide can vary in _____. a. the base b. the sugar c. the phosphate group d. the sugar and the base 29. Which of the following is the weakest interaction? a. hydrogen bond b. ionic bond c. phosphoanhydride bond d. van der Waals interaction 30. Adenosine is a: a. component of RN b. nucleoside. c. pyrimidine. d. a and b 31. If the equilibrium constant for the reaction A→B is 0.5 and the initial concentration of A is 25 mM and of B is 12.5 mM, then the reaction: a. will proceed in the direction it is written, producing a net increase in the concentration of B. b. will produce energy, which can be used to drive ATP synthesis. c. will proceed in the reverse direction, producing a net increase in the concentration of A. d. is at equilibrium.

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Chap 02_9e 32. Cysteine often plays an important role in stabilizing protein structure. Explain how this works.

33. You discover that you suffer from a deficiency in the amino acid tryptophan. At the pharmacy, you find both ᴅ tryptophan and L-tryptophan supplements. Which do you purchase? Why?

34. The enzyme alcohol dehydrogenase is capable of catalyzing the oxidation of a number of different substances, including ethanol, ethylene glycol, and methanol, to an aldehyde. The metabolic products of both ethylene glycol and methanol are highly toxic to humans. A standard medical treatment for prevention of ethylene glycol or methanol poisoning is the administration of a dose of ethanol. Why is this treatment effective?

35. Triacylglycerol and cholesterol esters are nonpolar; in contrast, phospholipids are amphipathic molecules. Biomembranes are based on phospholipids rather than on triacylglycerols. Why?

36. The interactions between two proteins such as an antibody and an antigen or a hormone and its receptor are quite strong despite the fact that these interactions consist of relatively weak noncovalent bonds. How can this be?

37. How do cells maintain a relatively constant pH despite the fact that many metabolic processes produce acids?

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Chap 02_9e 38. What produces the dipole of a water molecule?

39. A solution of 8 M urea is sometimes used in the isolation of protein molecules. When the solution is prepared by dissolving urea in water at room temperature, it becomes cold. How should the ΔG for this process change if you tried to dissolve urea in the cold room, rather than at room temperature?

40. What is the effect of an enzyme on the end equilibrium concentration of reactants and products?

41. Under what conditions is the ΔG for a reaction different from the ΔG°´?

42. Phosphoglucomutase converts glucose 1-phosphate, the product of the reaction catalyzed by glycogen phosphorylase, into glucose 6-phosphate. The Keq for this reaction is 19 under standard conditions. What is the Δ °´ for the reaction?

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Chap 02_9e Answer Key 1. False 2. c 3. b 4. b 5. c 6. b 7. d 8. d 9. c 10. c 11. d 12. d 13. d 14. c 15. d 16. d 17. d 18. b 19. d 20. a 21. c 22. d 23. a 24. c 25. a 26. b Copyright Macmillan Learning. Powered by Cognero.

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Chap 02_9e 27. b 28. d 29. d 30. d 31. d 32. Two adjacent sulfhydryl (SH) groups can oxidize to form a covalent disulfide (S–S) bond. Disulfide bonds can stabilize the structure of folded peptides or sometimes link two separate peptide chains together. 33. You should choose L-tryptophan. All amino acids can exist as one of two stereoisomers (ᴅ or L) because of asymmetry around the α carbon. Proteins consist of the L form of amino acids, and as these stereoisomers possess distinct biological properties and are not readily interconverted, you should choose the form that is normally utilized by cells. 34. The ethanol-like ethylene glycol and methanol are capable of binding to the enzyme, alcohol dehydrogenase, and competing with its other substrates. A sufficient dosage of ethanol can out-compete the other substrates, and hence the ethylene glycol and methanol are not metabolized to toxic products. Gradually the ethylene glycol or methanol will be excreted from the body. 35. Biomembranes are based on phospholipids rather than on triacylglycerols because phospholipids as amphipathic molecules can form planar lipid bilayers, whereas the nonamphipathic nonpolar triacylglycerols cannot. Their amphipathic property, the presence of a polar and nonpolar domain at opposite ends of the same molecule, allows phospholipids to form hydrophilic associations with water at the same time as forming hydrophobic associations with each other through their hydrophobic tails. Triacylglycerols are strictly hydrophobic in nature and hence in an aqueous environment tend to associate with one another to form lipid droplets. This minimizes the contact of triacylglycerol with water. Recall the old adage: oil and water do not mix. 36. Two proteins can bind tightly because of molecular complementarity, in which multiple noncovalent bonds participate. Although each individual bond is weak, the cumulative effect of many noncovalent bonds is a relatively strong and highly specific interaction. 37. All cells contain buffers such as phosphate ions that can absorb or release protons or hydroxyl ions to stabilize pH changes near neutral pH. 38. The dipole of a water molecule is caused by the difference in electronegativity between O and H. The oxygen atom has a greater electronegativity than the hydrogen atom. As a result, oxygen attracts the electrons in the O–H bond more strongly, and the oxygen side of the bond has a slight net negative charge. This results in a dipole moment. 39. Urea will be less soluble at cold temperatures than at room temperature because the decrease in temperature will decrease the term TΔS, increasing the value of ΔG, because ΔG = ΔH − TΔS. The values of ΔH and ΔS are relatively independent of temperature. 40. An enzyme has no effect on the end equilibrium concentration of reactants and products.

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Chap 02_9e 41. ΔG°´ is the Gibbs free energy of a reaction under standard conditions: pH 7.0, 1 M initial concentration of all reactants and products except protons and water, 1 atm pressure, 298°K (25°C). Variation of any of these parameters from standard conditions, depending on the reaction, can produce a different ΔG value. 42. −1.741 kcal/mol, ΔG°´ = −2.3RT log Keq, ΔG°´ = −2.3 (1.987) (298) log Keq

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Chap 03_9e Indicate the answer choice that best completes the statement or answers the question. 1. Which of the following is NOT part of a zinc-finger motif? a. zinc ion b. proline residue c. cysteine residue d. histidine residue

2. Starting with 1 mCi (milliCurie) of a phosphorus-32-labeled compound, how long would it take until only 0.125 mCi remains? a. 14.3 days b. 28.6 days c. 42.9 days d. 57.2 days 3. The conversion of inactive chymotrypsinogen to active chymotrypsin is an example of: a. proteolytic activation. b. positive cooperativity. c. allostery. d. ligand-induced activation. 4. Proteomics allows researchers to: a. examine where a protein is located within the cytosol of a cell. b. compare thousands of samples from different people in the same experiment. c. examine which proteins differ in abundance between a normal sample and a disease sample. d. use antibodies to label specific proteins on an SDS-PAGE gel. 5. The correct order for molecular chaperone–mediated protein folding is: I – exchange of ATP for ADP on chaperone II – chaperone undergoes conformational change, which affects protein folding III – chaperone binds to exposed hydrophobic residues on unfolded protein IV – folded protein is released a. I, II, III, IV b. III, II, I, IV c. III, I, II, IV d. II, III, I, IV 6. You disrupt all hydrogen bonds in a protein. What level of structure will be preserved? a. secondary structure b. primary structure c. tertiary structure d. quaternary structure Copyright Macmillan Learning. Powered by Cognero.

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Chap 03_9e 7. Changes in the conformational shape of an enzyme that diminish the size of its ligand-binding pocket are likely to affect an enzyme’s: a. specificity. b. affinity. c. epitope. d. specificity and affinity. 8. Which of the following methods can separate proteins based on their mass? a. centrifugation b. ion exchange chromatography c. SDS polyacrylamide gel electrophoresis d. centrifugation and SDS polyacrylamide gel electrophoresis 9. Kinases, which are responsible for the activation or inactivation of a number of proteins, add phosphate groups onto: a. tryptophan residues. b. serine residues. c. cysteine residues. d. tryptophan and cysteine residues. 10. Which of the following plays a role in the degradation of proteins? a. RNAi b. ubiquitin c. proteasome d. b and c 11. All the following statements about molecular chaperones are true EXCEPT: a. they play a role in the proper folding of proteins. b. they are located in every cellular compartment. c. they are found only in mammals. d. they bind a wide range of proteins. 12. Which of the following does NOT impose limits on protein folding? a. ability of side chains to form hydrogen and ionic bonds b. backbone sequence of the polypeptide c. rotations of the planes around the peptide bonds d. size of side chains

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Chap 03_9e 13. A misfolded protein targeted to the proteasome will undergo: a. unfolding using energy released by ATPases. b. entry into the proteasome through the narrow channel in the beta channel. c. death by a thousand cuts in the alpha subunit rings. d. complete cleavage into its amino acid monomers. 14. Which of the following is defined as the tertiary structure of a protein? a. the primary amino acid sequence b. structural domains such as a DNA-binding domain c. folded structures such as an α helix d. structural features such as a turn 15. Which of the following is true about protein folding? a. Amino acids cluster in the primary sequence so that all the hydrophobic amino acids are near each other to facilitate folding into the hydrophobic core of the tertiary structure. b. All known proteins have well-ordered conformations. c. Amino acids with hydrophobic, nonpolar side chains stabilize the tertiary structure through hydrogen bonding with water molecules surrounding the proteins. d. Elements from the secondary structure are maintained in the tertiary structure. 16. For an enzyme-catalyzed reaction, doubling the concentration of enzyme will: a. double the Vmax. b. halve the Vmax. c. double the Km. d. halve the Km. 17. Mass spectrometry techniques are used in proteomics for all of the following purposes EXCEPT: a. identification of thousands of proteins’ amino acid sequences within a single cell. b. characterization of proteolytically digested pieces of proteins from the sample. c. identification of all the protein complexes present in certain yeast species. d. identification of proteins within each organelle in liver tissue. 18. Two proteins that have a similar function: a. will share similar amino acid sequences if they are homologs. b. must have similar amino acid sequences. c. will have identical primary structures. d. belong in families together.

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Chap 03_9e 19. Hsp90 family members are present in all organisms except: a. archaea b. bacteria c. fungi. d. plants. 20. Eggs are protein-rich foods. An uncooked egg can catalyze a reaction via an enzyme that breaks down bacterial cell walls. After cooking, this activity is almost abolished This is likely because: a. the enzyme became denatured b. bacteria can grow on cooked eggs. c. the cell membranes were liquefied d. cooking sped up chemical reactions. 21. A chunk of tissue is treated so that each cell’s membrane is broken open to release the contents inside, and then subjected to differential centrifugation. Which of the following is true at the end of the centrifugation? a. Depending on the speed of the centrifugation, the proteasome is more likely to be in the supernatant than a chaperone. b. Proteins of similar density will be found in the same fraction (either pellet or supernatant). c. The pellet contains the least dense material. d. The pellet will contain a purified protein for further analysis. 22. GTPases serve in many signal transduction pathways and the presence of GTP or GDP dictates whether the pathway is on or off, respectively. Which of the following statements is true regarding guanine nucleotide exchange factors (GEF) and their role in these signaling pathways? a. They hydrolyze GTP into GDP and Pi. b. They decrease the GTPase activity of the G-protein. c. They catalyze the dissociation of GDP on the G-protein to therefore promote the replacement of GTP. d. none of the above 23. The Km for an enzyme-catalyzed reaction: a. determines the shape of the kinetics curve. b. determines the Vmax for the reaction. c. is a measure of the affinity of the substrate for the enzyme. d. is a measure of the rate of the reaction. 24. All the following statements about enzymes are true except: a. they function in an aqueous environment. b. they lower the activation energy of a reaction. c. they increase the rate of a reaction. d. a single enzyme typically reacts with many different substrates.

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Chap 03_9e 37. Which of the following is true about enzymes? a. The catalytic site is responsible for substrate specificity. b. Reactions catalyzed by enzymes give the products more free energy than reactions that occur spontaneously. c. The rate of an enzymatic reaction is always proportional to the concentration of the substrate . d. Enzymes increase reaction rates by lowering the activation energy needed to reach the transition state. 38. Western blotting is a method for detecting: a. DNA b. RNA c. protein. d. carbohydrate. 39. Modification of proteins by ubiquitin and ubiquitin-like E3 ligases can stimulate all of the following EXCEPT: a. recognition of intracellular viruses. b. regulation of the cell cycle. c. mRNA stability. d. nuclear import. 40. What is Western blotting? How can this technique be used to detect proteins?

41. Describe the general mechanism by which a multisubunit protein can be activated by binding an allosteric effector molecule.

42. How can gel filtration chromatography separate proteins based on their mass?

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Chap 03_9e 43. Many proteins contain one or more motifs built from particular combinations of secondary structure. Describe the three common structural motifs discussed in this chapter.

44. Describe the types of bonds/interactions that hold together or stabilize the primary, secondary, tertiary, and quaternary structures of proteins.

45. What is positive cooperativity?

46. What is the basis for separation of proteins by two-dimensional gel electrophoresis? Why is this better for resolving a mixture of proteins?

47. Describe the mechanism by which the bacterial chaperonin GroEL promotes protein folding.

48. What types of bonds are apt to be more common in the nonaqueous, interior environment of a protein than in the aqueous, surface environment of a protein?

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