Chemistry of Biochemistry: Weak Acids, Buffers, and Protein Structure, Exams of Biochemistry

Download Chemistry of Biochemistry: Weak Acids, Buffers, and Protein Structure and more Exams Biochemistry in PDF only on Docsity! Page 1 CHM 222 BIOCHEMISTRY EXAM TEXT BANK QUESTIONS AND AVERIFIED ANSWERS GRADED A 2024 UPDATE 1. The dipole moment in a water molecule Which statement about hydrogen bonds is NOT true? A) Hydrogen bonds account for the anomalously high boiling point of water. B) In liquid water, the average water molecule forms hydrogen bonds with three to four other water molecules. C) Individual hydrogen bonds are much weaker than covalent bonds. D) Individual hydrogen bonds in liquid water exist for many seconds and sometimes for minutes. E) The strength of a hydrogen bond depends on the linearity of the three atoms involved in the bond. 2. A TRUE statement about hydrophobic interactions is that they: A) are the driving force in the formation of micelles of amphipathic compounds in water. B) do not contribute to the structure of water-soluble proteins. C) have bonding energies of approximately 20–40 Kjoule per mole. D) involve the ability of water to denature proteins. E) primarily involve the effect of polar solutes on the entropy of aqueous systems. 3. Hydrophobic interactions make important energetic contributions to: A) binding of a hormone to its receptor protein. B) enzyme-substrate interactions. C) membrane structure. D) three-dimensional folding of a polypeptide chain. E) All of the answers are correct. 4. Dissolved solutes alter some physical (colligative) properties of the solvent water because they change the: A) concentration of the water. B) hydrogen bonding of the water. C) ionic bonding of the water. D) pH of the water. Page 2 E) temperature of the water. 5. Osmosis is movement of a: A) charged solute molecule (ion) across a membrane. B) gas molecule across a membrane. C) nonpolar solute molecule across a membrane. D) polar solute molecule across a membrane. E) water molecule across a membrane. 6. A hydronium ion: A) has the structure H3O+. B) is a hydrated hydrogen ion. C) is a hydrated proton. D) is the usual form of one of the dissociation products of water in solution. E) All of the answers are correct. 7. The pH of a solution of 1 M HCl is: A) 0. B) 0.1. C) 1. D) 10. E) –1. 8. The pH of a solution of 0.1 M NaOH is: A) 0.1. B) 1.0. C) 12.8. D) 13. E) 14. Page 5 17. Consider an acetate buffer, initially at the same pH as its pKa (4.76). When sodium hydroxide (NaOH) is mixed with this buffer, the: A) pH remains constant. B) pH rises more than if an equal amount of NaOH is added to an acetate buffer initially at pH 6.76. C) pH rises more than if an equal amount of NaOH is added to unbuffered water at pH 4.76. D) ratio of acetic acid to sodium acetate in the buffer falls. E) sodium acetate formed precipitates because it is less soluble than acetic acid. 18. A compound is known to have a free amino group with a pKa of 8.8, and one other ionizable group with a pKa between 5 and 7. To 100 mL of a 0.2 M solution of this compound at pH 8.2 was added 40 mL of a solution of 0.2 M hydrochloric acid. The pH changed to 6.2. The pKa of the second ionizable group is: A) The pH cannot be determined from this information. B) 5.4. C) 5.6. D) 6.0. E) 6.2. 19. Three buffers are made by combining a 1 M solution of acetic acid with a 1 M solution of sodium acetate in the ratios shown below. 1 M acetic acid 1 M sodium acetate Buffer 1: 10 mL 90 mL Buffer 2: 50 mL 50 mL Buffer 3: 90 mL 10 mL Which statement is TRUE of the resulting buffers? A) pH of buffer 1 < pH of buffer 2 < pH of buffer 3 B) pH of buffer 1 = pH of buffer 2 = pH of buffer 3 C) pH of buffer 1 > pH of buffer 2 > pH of buffer 3 D) The problem cannot be solved without knowing the value of pKa. E) None of the statements is true. Page 6 20. A 1.0 M solution of a compound with 2 ionizable groups (pKa's = 6.2 and 9.5; 100 mL total) has a pH of 6.8. If a biochemist adds 60 mL of 1.0 M HCl to this solution, the solution will change to pH: A) 5.60. B) 8.90. C) 9.13. D) 9.32. E) The pH cannot be determined from this information. 21. You want to maintain pH = 7.0 for an enzyme-catalyzed reaction that will produce hydrogen ions along with the desired product. At equal concentrations, which weak acid, if any, will serve as the better buffer for the reaction: acid A, with pKa = 6.5, or acid B, with pKa = 7.5? A) acid A B) Water is as good as either of the acids available. C) acid B D) Both are equally effective. 22. In which reaction does water NOT participate as a reactant (rather than as a product)? A) conversion of an acid anhydride to two acids B) conversion of an ester to an acid and an alcohol C) conversion of ATP to ADP D) photosynthesis E) production of gaseous carbon dioxide from bicarbonate 23. Which property of water does NOT contribute to the fitness of the aqueous environment for living organisms? A) cohesion of liquid water due to hydrogen bonding B) high heat of vaporization C) high specific heat D) the density of water being greater than the density of ice E) the very low molecular weight of water Page 7 24. The ionization of water is due to the strongly electronegative element: A) hydrogen donating an electron to oxygen. B) oxygen donating an electron to hydrogen. C) hydrogen receiving an electron from oxygen. D) oxygen receiving an electron from hydrogen. E) None of the answers is correct. 25. Which attribute contributes to water's unusual properties? A) the geometry of the molecule B) the polarity of the molecule C) the ability of water molecules to hydrogen bond D) the dipole moment in a water molecule E) All of the answers are correct. 26. Which factor contributes to the bent shape of a water molecule? A) the dipole moment in a water molecule B) the unshared electron pairs on the oxygen atom C) the electronegativity difference between hydrogen and oxygen D) the unequal electron sharing between hydrogen and oxygen E) All of the answers are correct. 27. Ice is than water because . A) less dense; frozen water maintains more hydrogen bonds than liquid water B) less dense; liquid water maintains more hydrogen bonds than frozen water C) denser; frozen water maintains more hydrogen bonds than liquid water D) denser; liquid water maintains more hydrogen bonds than frozen water E) denser; frozen water cannot hydrogen bond Page 10 C) Fatty acids will form micelles to sequester hydrophobic groups from water. D) The driving force of solubilizing fatty acids is increasing entropy of the fatty acid. E) All the statements are true. 35. Which statement CORRECTLY describes the forces that drive micelle formation from amphipathic molecules, such as fatty acids, dissolved in water? A) Head groups of the molecules are sequestered in the interior of the micelle, maximizing hydrogen bonding of the hydrophobic tail with surrounding solvent molecules. B) Head groups of the molecules are exposed on the outer surface of the micelle, maximizing hydrogen bonding between hydrophobic tails. C) Head groups of the molecules are exposed on the outer surface of the micelle, minimizing the order of the surrounding solvent molecules. D) Hydrophilic tails are exposed on the outer surface of the micelle, maximizing hydrogen bonding between the tails and surrounding solvent molecules. E) Hydrophobic tails are exposed on the outer surface of the micelle, maximizing hydrogen bonding between head groups. 36. Which force plays the GREATEST role in stabilizing biological structures in membranes? A) hydrogen bonding, because it a strong non-covalent bond B) hydrophobic interactions that increase solvent entropy C) covalent interactions, because they are very stable interactions D) electrostatic interactions between oppositely charged ions E) van der Waals interactions, because of the attraction between transient dipoles 37. Which result influences the lower limit for an atom's van der Waals radius? A) The electron clouds begin to repel each other. B) The nuclei begin to repel each other. C) The transient dipole is cancelled out by the neighboring atom. D) The electron clouds begin to attract each other. E) The nuclei begin to attract each other. Page 11 38. Which list correctly shows bond/interaction strength in DECREASING order (strongest to weakest)? A) covalent bond > hydrogen bond > ionic bond > van der Waals interaction B) covalent bond > ionic bond > hydrogen bond > van der Waals interaction C) ionic bond > covalent bond > hydrogen bond > van der Waals interaction D) covalent bond > van der Waals interaction > ionic bond > hydrogen bond E) hydrogen bond > ionic bond > van der Waals interaction > covalent bond 39. When two atoms are joined together covalently, the van der Waals radius of the atoms in the covalent bond are than the radius of the atoms alone because the joined atoms are . A) shorter; pulled together by the shared electron pair B) shorter; pulled together by the attraction of the nucleus to the bonded atom C) shorter; pulled together by hydrogen bonding D) longer; repelled due to the shared electron pair E) longer; repelled due to the nuclear repulsion between bonded atoms 40. Which process would NOT disrupt the weak interactions between two biomolecules in solution? A) heating the solution B) cooling the solution C) lowering the pH of the solution D) increasing the ionic strength of the solution E) All of the answer choices would disrupt interactions between biomolecules Page 12 41. Which diagram illustrates an amphipathic molecule? 42. When water is found in a crystal structure of a biomolecule, which statement is NOT true? A) The properties of the bound water molecules are different from those of the “bulk” water of the solvent. B) The bound water molecules may provide a path for “proton hopping.” C) The bound water molecules can form an essential part of the protein's ligand binding site. D) The orientation of bound water molecules is precise. E) All of the statements are true. 43. Which of the following would have the GREATEST effect on osmotic pressure? A) M NaCl (MW = 58 g/mol) B) M CaCl2 (MW = 111 g/mol) C) M glucose (MW = 180 g/mol) D) M sucrose (MW = 342 g/mol) E) All of the answer choices would have the same effect. Page 15 B) 9.37 C) –4.63 D) 4.63 E) 13.4 52. If the Ka of an acid is 1.38 × 10–7, what is the pKa? A) 6.86 B) 7.14 C) 8.68 D) 10.7 E) 1.38 53. The conjugate base of H2PO4 –1 is: A) H3PO4. B) H2PO4 2–. C) HPO4 2–. D) HPO4 3–. E) PO4 3–. Page 16 54. According to the titration curve to the right, acid A is because the pH . A) weak; resists change when 50% titrated. B) strong; resists change when 50% titrated. C) weak; changes dramatically when 100% titrated. D) strong; changes dramatically when 100% titrated. E) It cannot be determined from the information given. 55. According to the titration curve to the right, acid A has a pKa of: A) 0.2. B) 0.5. C) 3.2. D) 3.8. E) 4.8. 56. According to the titration curve above, acid A has a buffering range of: A) 0.3 M to 0.8 M OH. Page 17 B) 0.9 to 1.0 M OH. C) pH 3.5 to pH 4.2. D) pH 2.8 to pH 3.8. E) pH 2.8 to pH 4.8. 57. Formic acid is used in the venom of some species of ants. What is the pH of a 0.2 M solution of formic acid (Ka = 1.78 × 10–4 M)? A) 8.90 B) 4.45 C) 3.75 D) 2.2 Ionization of Water, Weak Acids, and Weak Bases2 E) 1.72 58. List the acids in INCREASING order of strength (weakest to strongest): nitrous acid (Ka = 4.0 × 10–4); carbonic acid (Ka = 4.4 × 10–7); acetic acid (Ka = 1.7 × 10– 5); phosphoric acid (Ka = 7.3 × 10–3) A) acetic acid, carbonic acid, nitrous acid, phosphoric acid B) carbonic acid, acetic acid, nitrous acid, phosphoric acid C) acetic acid, nitrous acid, carbonic acid, phosphoric acid D) phosphoric acid, nitrous acid, acetic acid, carbonic acid E) carbonic acid, phosphoric acid, nitrous acid, acetic acid 59. A 0.6 M solution of a weak acid had a pH of 5.8. What is the pKa of the solution? A) 11.3 B) 10.5 C) 8.2 D) 5.7 E) 2.9 Page 20 D) vigorous exercise E) All of these treatments/actions could be used to counteract acidosis. 65. Biological buffering systems include: A) histidine. B) bicarbonate. C) phosphate. D) bicarbonate and phosphate. E) histidine, bicarbonate, and phosphate. 66. Of the seven the steps listed below, which four—in the CORRECT order—are needed to prepare 1 L of a 0.02M Tris buffer solution, pH 7.6? You have at your lab station a 0.1 M solution of Tris in its protonated form, 0.1 M solutions or HCl and NaOH, and plentiful distilled water. The Ka of Tris is 8.32 × 10–9. 1. Calculate the volume of 0.1 M Tris to use (C1V1 = C2V2). 2. Calculate the volume of 0.1 M HCl to use (C1V1 = C2V2). 3. Calculate the volume of 0.1 M NaOH to use (C1V1 = C2V2). 4. Use the Henderson-Hasselbalch equation to calculate the ratio of Tris base to protonated Tris. 5. Adjust the pH to 7.6 by adding 0.1 M NaOH. 6. Adjust the pH to 7.6 by adding 0.1 M HCl. 7. Fill to 1 L with distilled water. A) 1⟶4⟶6⟶7 B) 1⟶4⟶5⟶7 C) 1⟶2⟶4⟶7 D) 1⟶3⟶4⟶7 E) 1⟶7⟶4⟶6 Page 21 67. What is the CORRECT terminology for reactions A and B in the diagram? A) A = hydrolysis, B = condensation B) A = condensation, B = hydrolysis C) A = dehydrolysis, B = condensation D) A = phosphorylation, B = phosphatase E) A = metabolism, B = catabolism 68. Camels live in very dry habitats and do not need to consume water as frequently as animals in wetter habitats. What is a partial reason for this? A) Metabolic water is produced by oxidation of fuels such as glucose. B) Metabolic water is produced by acid/base dehydration reactions. C) Metabolic water is produced by symbiotic bacteria in the camel's gut. D) Metabolic water is produced by splitting carbon dioxide. E) None of the answers is correct. 69. Carbon dioxide, produced by glucose oxidation, is not very soluble. How does the body transport this molecule through blood to be exhaled from the lungs? A) CO2 can be directly bound to hemoglobin for transport. B) CO2 can be converted to the more soluble CO for transport. C) CO2 can be converted to the more soluble HCO3 –1 for transport. D) CO2 can be bound by erythrocytes for transport. E) CO2 is only produced in the lungs. Page 22 70. Water can act as in biological reactions. A) a solvent B) a reactant C) a product D) both a solvent and reactant E) a solvent, reactant, and product 71. Which statement does NOT describe a reason that water can act as a heat buffer for cells and organisms? A) Water has a high specific heat. B) Water has an extended hydrogen-bonding network. C) Water can auto-ionize. D) A large amount of heat is required to raise the temperature of water by 1 °C. E) All of the statements describe reasons that water can act as a heat buffer. 72. The high degree of cohesion of water molecules influences which processe? A) Plants can transport dissolved nutrients from roots to leaves. B) Water can combine with carbon dioxide to form glucose. C) Loss of water causes lettuce leaves to wilt. D) Water is split by the energy of sunlight through photosynthesis. E) Water can be used as a product in respiration. 73. Which property of water has had the MOST profound consequence for aquatic organisms? A) Water has a high specific heat. B) Water has a high heat of vaporization. C) Due to hydrogen bonding, solid water is less dense than liquid water. D) Water has a high melting point. E) Nonpolar molecules are poorly soluble in water. Page 25 93. Speculate why weak forces, not strong forces, are the basis for molecular recognition among biomolecules. Page 26 Answer Key 1. D 2. A 3. E 4. A 5. E 6. E 7. A 8. D 9. D 10. E 11. D 12. D 13. B 14. E 15. D 16. E 17. D 18. C 19. C 20. A 21. A 22. E 23. E 24. D 25. E 26. B 27. A 28. C 29. C 30. D 31. B 32. B 33. A 34. D 35. C 36. B 37. A 38. B 39. A 40. B 41. D 42. E 43. B 44. E Page 27 45. A 46. C 47. D 48. A 49. B 50. B 51. D 52. A 53. C 54. A 55. D 56. E 57. D 58. B 59. A 60. B 61. C 62. A 63. D 64. B 65. E 66. B 67. A 68. A 69. C 70. E 71. C 72. A 73. C 74. 75. 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. 2 2 2 3 2 2 3 3 2 3 2 Page 30 C) Ala and Ser D) Asp and Asn E) Ser and Cys 9. Amino acids are ampholytes because they can function as either a(n): A) acid or a base. B) neutral molecule or an ion. C) polar or a nonpolar molecule. D) standard or a nonstandard monomer in proteins. E) transparent or a light-absorbing compound. 10. Titration of valine by a strong base, for example NaOH, reveals two pK's. The titration reaction occurring at pK2 (pK2 = 9.62) is: A) —COOH + OH– ⟶ —COO– + H2O. B) —COOH + —NH2 ⟶ —COO– + —NH +. C) —COO– + —NH + ⟶ —COOH + —NH . D) —NH + + OH– ⟶ —NH + H O. E) —NH2 + OH– ⟶ —NH– + H2O. 11. In a highly basic solution, pH = 13, the dominant form of glycine is: A) NH2—CH2—COOH. B) NH2—CH2—COO–. C) NH2—CH +—COO–. D) NH +—CH —COOH. E) NH +—CH —COO–. 12. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have: A) a net negative charge. B) a net positive charge. C) no charged groups. Page 31 D) no net charge. E) positive and negative charges in equal concentration. 13. At pH 7.0, converting a glutamic acid to g-carboxyglutamate, will have what effect on the overall charge of the protein containing it? A) It will become more negative B) It will become more positive. C) It will stay the same. D) There is not enough information to answer the question. E) The answer depends on the salt concentration. 14. At pH 7.0, converting a proline to hydroxyproline, will have what effect on the overall charge of the protein containing it? A) It will become more negative B) It will become more positive. C) It will stay the same. D) There is not enough information to answer the question. E) The answer depends on the salt concentration. 15. What is the approximate charge difference between glutamic acid and 𝛼-ketoglutarate at pH 9.5? A) 0 B) 1/2 C) 1 D) 11/2 E) 2 16. The formation of a peptide bond between two amino acids is an example of a(n) reaction. A) cleavage B) condensation Page 32 C) group transfer D) isomerization E) oxidation reduction 17. The peptide alanylglutamylglycylalanylleucine has: A) a disulfide bridge. B) five peptide bonds. C) four peptide bonds. D) no free carboxyl group. E) two free amino groups. 18. An octapeptide composed of four repeating glycylalanyl units has: A) one free amino group on an alanyl residue. B) one free amino group on an alanyl residue and one free carboxyl group on a glycyl residue. C) one free amino group on a glycyl residue and one free carboxyl group on an alanyl residue. D) two free amino and two free carboxyl groups. E) two free carboxyl groups, both on glycyl residues. 19. At the isoelectric pH of a tetrapeptide: A) only the amino and carboxyl termini contribute charge. B) the amino and carboxyl termini are not charged. C) the total net charge is zero. D) there are four ionic charges. E) two internal amino acids of the tetrapeptide cannot have ionizable R groups. 20. Which statement is CORRECT with respect to the amino acid composition of proteins? A) Larger proteins have a more uniform distribution of amino acids than smaller proteins. B) Proteins contain at least one each of the 20 different standard amino acids. C) Proteins with different functions usually differ significantly in their amino acid composition. Page 35 molecular weights. B) the individual bands become stained so that the isoelectric focus pattern can be visualized. C) the individual bands become visualized by interacting with protein-specific antibodies in the second gel. D) the individual bands undergo a second, more intense isoelectric focusing. E) the proteins in the bands separate more completely because the second electric current is in the opposite polarity to the first current. 29. The term specific activity differs from the term activity in that specific activity: A) is measured only under optimal conditions. B) is the activity (enzyme units) in a milligram of protein. C) is the activity (enzyme units) of a specific protein. D) refers only to a purified protein. E) refers to proteins other than enzymes. 30. Which type of structure refers to particularly stable arrangements of amino acid residues in a protein that give rise to recurring patterns? A) primary structure B) secondary structure C) tertiary structure D) quaternary structure E) None of the answers is correct. 31. Which type of structure describes the overall three-dimensional folding of a polypeptide? A) primary structure B) secondary structure C) tertiary structure D) quaternary structure E) None of the answers is correct. Page 36 32. The functional differences, as well as differences in three-dimensional structures, between two different enzymes from E. coli result directly from their different: A) affinities for ATP. B) amino acid sequences. C) roles in DNA metabolism. D) roles in the metabolism of E. coli. E) secondary structures. 33. One method used to prevent disulfide bond interference with protein sequencing procedures is: A) cleaving proteins with proteases that specifically recognize disulfide bonds. B) protecting the disulfide bridge against spontaneous reduction to cysteinyl sulfhydryl groups. C) reducing disulfide bridges and preventing their re-formation by further modifying the —SH groups. D) removing cystines from protein sequences by proteolytic cleavage. E) sequencing proteins that do not contain cysteinyl residues. 34. A nonapeptide was determined to have the following amino acid composition: (Lys)2, (Gly) 2, (Phe) 2, His, Leu, Met. The native peptide was incubated with 1-fluoro-2,4- dinitrobenzene (FDNB) and then hydrolyzed; 2,4-dinitrophenylhistidine was identified by HPLC. When the native peptide was exposed to cyanogen bromide (CNBr), an octapeptide and free glycine were recovered. Incubation of the native peptide with trypsin gave a pentapeptide, a tripeptide, and free Lys. 2,4-Dinitrophenyl-histidine was recovered from the pentapeptide, and 2,4-dinitrophenylphenylalanine was recovered from the tripeptide. Digestion with the enzyme pepsin produced a dipeptide, a tripeptide, and a tetrapeptide. The tetrapeptide was composed of (Lys) 2, Phe, and Gly. The native sequence was determined to be: A) Gly–Phe–Lys–Lys–Gly–Leu–Met–Phe–His. B) His–Leu–Gly–Lys–Lys–Phe–Phe–Gly–Met. C) His–Leu–Phe–Gly–Lys–Lys–Phe–Met–Gly. D) His–Phe–Leu–Gly–Lys–Lys–Phe–Met–Gly. E) Met–Leu–Phe–Lys–Phe–Gly–Gly–Lys–His. Page 37 35. Even when a gene is available and its sequence of nucleotides is known, chemical studies of the protein are still required to determine: A) molecular weight of the protein. B) the amino-terminal amino acid. C) the location of disulfide bonds. D) the number of amino acids in the protein. E) whether the protein has the amino acid methionine in its sequence. 36. The term “proteome” has been used to describe: A) regions (domains) within proteins. B) regularities in protein structures. C) the complement of proteins expressed by an organism's genome. D) the structure of a protein-synthesizing ribosome. E) the tertiary structure of a protein. 37. A major advance in the application of mass spectrometry to macromolecules came with the development of techniques to overcome which problem? A) Macromolecules were insoluble in the solvents used in mass spectrometry. B) Mass spectrometric analyses of macromolecules were too complex to interpret. C) Mass spectrometric analysis involved molecules in the gas phase. D) Most macromolecules could not be purified to the degree required for mass spectrometric analysis. E) The specialized instruments required were prohibitively expensive. 38. Identify the pair of peptides below that CANNOT be distinguished by tandem mass spectrometry. A) VTSPLYANEGK and VTCPLYANEGK B) VTSPLYANEGK and VTSPLYADEGK C) VTSPLYANEGK and VTSPIYANEGK D) VTSPLYANEGK and VSTPLYANEGK E) All of the answer choices are correct. Page 40 E) Only some amino acids are negatively charged. 46. The MOST useful way to classify amino acids is by: A) molecular weight. B) pKa. C) polarity. D) propensity in proteins. E) alphabetical order. 47. The protein bovine serum albumin (BSA), has a MW of about 66,400. Using the Lambert-Beer Law, calculate the concentration of a sample of BSA with an absorbance at 280 nm of 1.3, assuming the molar extinction coefficient at 280 nm is 43,824 M– 1cm– 1. A) 0.51 mg/mL B) 0.86 mg/mL C) 1.97 mg/mL D) 2.56 mg/mL E) 3.78 mg/mL 48. The pKa of lysine's carboxyl group, amino group, and side chain are 2.2, 9.0, and 10.5, respectively. If lysine is in a pH 13 solution, what is the net charge on each lysine molecule? A) –2 B) –1 C) 0 D) +1 E) +2 49. Amino acids without ionizable R-groups can act as a zwitterion in a(n) solution. A) nonpolar B) boiling C) acidic Page 41 D) basic E) neutral 50. According to the diagram, which pH range offers the GREATEST buffering power for this amino acid? A) 0.5–1.5 B) 0–1 C) 1–2 D) 2–3 E) 1–3 Page 42 51. According to the diagram, which estimate is BEST of this amino acid's isoelectric point? A) 0.5 B) 1 C) 1.5 D) 6 E) 11 Page 45 54. According to the diagram, at pH 1, what is the average net charge on this amino acid? A) + 1 B) + 0.5 C) 0 D) –0.5 E) –1 Page 46 55. According to the diagram, at pH 2, what is the average net charge on this amino acid? A) +1 B) + 0.5 C) 0 D) –0.5 E) –1 Page 47 56. According to the diagram, does this amino acid have a titratable R-group? A) yes, as evidenced by the steep center of the curve B) yes, as evidenced by the two relatively flat parts of the curve C) no, as evidenced by only two relatively flat parts of the curve D) no, as evidenced by the steepness of the center of the curve E) It cannot be determined from this graph. 57. When the ribosome forms a peptide bond, which two atoms form a covalent bond? A) the 𝛼 carbon and the amino nitrogen B) the amino nitrogen and carboxylic acid carbon C) the 𝛼 carbon and the carboxylic acid carbon D) the amino nitrogen and the 𝗉 carbon E) It depends on the amino acids being joined. Page 50 64. According to the table, ion-exchange chromatography would be the LEAST effective method to separate which protein mixture? Protein MW pI A 12,500 3.2 B 13,200 5.7 C 13,500 10.5 D 25,200 6.3 E 36,900 5.8 F 78,400 6.1 A) proteins A, B, and C B) proteins A, C, and E C) proteins B, E, and F D) proteins B, C, and E E) All of the answers are correct. 65. According to the table, size-exclusion (gel-filtration) chromatography could NOT be used to separate which protein mixture? Protein MW pI A 12,500 3.2 B 13,200 5.7 C 13,500 10.5 D 25,200 6.3 E 36,900 5.8 F 78,400 6.1 A) proteins A, D, and F B) proteins C, E, and F C) proteins B, E, and F D) proteins A, B, and C E) All of the answers are correct. 66. A protein with a high percentage of lysine and arginine residues would be BEST purified and concentrated with which type of column? A) cation exchange B) anion exchange C) size-exclusion chromatography Page 51 D) affinity chromatography E) reverse-phase chromatography 67. A protein with a high percentage of aspartate and glutamate residues would be BEST purified and concentrated with which type of column? A) cation exchange B) anion exchange C) size-exclusion chromatography D) affinity chromatography E) reverse-phase chromatography 68. If protein A has a pI of 3.1, protein B has a pI of 6.8, and protein C has a pI of 8.9, which protein would elute FIRST from a cation exchange column at pH 7? A) protein A B) protein B C) protein C D) All three proteins would elute at the same time from the column. E) Not enough information about the proteins is given in the problem. Page 52 69. The gel below illustrates the purification of the RecA protein from E. coli. This gel was loaded from the top. Which statement BEST describes how proteins “run” in an SDS gel? A) The proteins are separated primarily by molecular weight—the largest MW proteins are on the bottom, and the smallest are on the top. B) The proteins are separated primarily by molecular weight—the smallest MW proteins are on the bottom, and the largest are on the top. C) The proteins are separated primarily by charge—the protein with the smallest pI is on the top, and the protein with the largest pI is on the bottom. D) The proteins are separated primarily by charge—the protein with the largest pI is on the top, and the protein with the smallest pI is on the bottom. E) The proteins are separated primarily by their propensity to precipitate—as electrophoresis progresses, the heat generated by the current denatures proteins faster or slower. The slowest to denature is on the bottom, and the fastest to denature is on the top. Page 55 77. Only one of the common amino acids has no free 𝛼-amino group. Name this amino acid. 78. Briefly describe the five major groupings of amino acids. 79. A B C D E Tyr-Lys-Met Gly-Pro-Arg Asp-Trp-Tyr Asp-His-Glu Leu-Val-Phe Which one of the above tripeptides: (a) is most negatively charged at pH 7? (b) will yield DNP-tyrosine when reacted with l-fluoro-2,4-dinitrobenzene and hydrolyzed in acid? (c) contains the largest number of nonpolar R groups? (d) contains sulfur? (e) will have the greatest light absorbance at 280 nm? 80. The “signature sequence” shown below represents a portion of a protein from four different organisms. a. At which position(s) are amino acid residues invariant? b. At which position(s) are amino acids limited to positively charged residues? c. At which position(s) are amino acids limited to negatively charged residues? d. At which position(s) are amino acids limited to nonpolar residues? 81. Describe the structures of the amino acids phenylalanine and aspartate in the ionization state you would expect at pH 7.0. Why is aspartate very soluble in water, whereas phenylalanine is much less soluble? 82. Name two uncommon amino acids that occur in proteins. By what route do they get into proteins? 83. Why do amino acids, when dissolved in water, become zwitterions? 3 Page 56 84. As more OH– equivalents (base) are added to an amino acid solution, what titration reaction will occur around pH = 9.5? 85. In the amino acid glycine, what effect does the positively charged —NH + group have on the pKa of an amino acid's —COOH group? 86. How does the shape of a titration curve confirm the fact that the pH region of greatest buffering power for an amino acid solution is around its pK's? 87. What is the pI, and how is it determined for amino acids that have nonionizable R groups? 88. The amino acid histidine has a side chain for which the pKa is 6.0. Calculate what fraction of the histidine side chains will carry a positive charge at pH 5.4. Be sure to show your work. 89. The amino acid histidine has three ionizable groups, with pKa values of 1.8, 6.0, and 9.2. (a) Which pKa corresponds to the histidine side chain? (b) In a solution at pH 5.4, what percentage of the histidine side chains will carry a positive charge? 90. What is the uniquely important acid-base characteristic of the histidine R group? 91. How can a polypeptide have only one free amino group and one free carboxyl group? 92. Hydrolysis of peptide bonds is an exergonic reaction. Why, then, are peptide bonds quite stable? 93. What is the structure components of Gly–Ala–Glu in the ionic form that predominates at pH 7. 94. If the average molecular weight of the 20 standard amino acids is 138, why do biochemists divide a protein's molecular weight by 110 to estimate its number of amino acid residues? Page 57 95. Lys residues make up 10.5% of the weight of ribonuclease. The ribonuclease molecule contains 10 Lys residues. Calculate the molecular weight of ribonuclease. 96. Why do smaller molecules elute after large molecules when a mixture of proteins is passed through a size-exclusion (gel filtration) column? 97. For each of these methods of separating proteins, describe the principle of the method, and tell what property of proteins allows their separation by this technique. (a) ion-exchange chromatography (b) size-exclusion (gel filtration) chromatography (c) affinity chromatography 98. A biochemist is attempting to separate a DNA-binding protein (protein X) from other proteins in a solution. Only three other proteins (A, B, and C) are present. The proteins have the following properties: pI protein X 7.8 22,000 yes What type of protein separation techniques might she use to separate: (a) protein X from protein A? (b) protein X from protein B? (c) protein X from protein C? 99. What factors would make it difficult to interpret the results of a gel electrophoresis of proteins in the absence of sodium dodecyl sulfate (SDS)? 100. How can isoelectric focusing be used in conjunction with SDS gel electrophoresis? 101. You are given a solution containing an enzyme that converts B into A. Describe what you would do to determine the specific activity of this enzyme solution. 102. As a protein is purified, both the amount of total protein and the activity of the purified protein decrease. Why, then, does the specific activity of the purified protein increase? (isoelectric point) Size Mr Bind to DNA? protein A 7.4 82,000 yes protein B 3.8 21,500 yes protein C 7.9 23,000 no Page 60 Answer Key 1. C 2. B 3. C 4. A 5. C 6. A 7. A 8. E 9. A 10. D 11. C 12. B 13. A 14. C 15. B 16. B 17. C 18. C 19. C 20. C 21. B 22. C 23. A 24. E 25. B 26. E 27. B 28. A 29. B 30. B 31. D 32. B 33. C 34. C 35. C 36. C 37. C 38. C 39. A 40. C 41. B 42. D 43. C 44. E Page 61 45. A 46. C 47. C 48. B 49. E 50. E 51. D 52. B 53. C 54. A 55. B 56. C 57. B 58. A 59. A 60. D 61. E 62. B 63. A 64. C 65. D 66. A 67. B 68. A 69. B 70. B 71. E 72. C 73. D 74. D 75. C 76. 77. 78. 79. 80. 81. 82. 83. 84. 85. 86. 87. 88. 89. 90. Page 62 91. 92. 93. 94. 95. 96. 97. 98. 99. 100. 101. 102. 103. 104. 105. 106. 107. 108. 109. 110. 111. 112. 113. Name: Date: 1. Which interactions are NOT considered to be “weak” in proteins? A) hydrogen bonds B) hydrophobic interactions C) ionic bonds D) peptide bonds E) van der Waals forces 2. The MOST important contribution to the stability of a protein's conformation appears to be the: A) entropy increase from the decrease in ordered water molecules forming a solvent shell around it. B) maximum entropy increase from ionic interactions between the ionized amino acids in a protein. C) sum of free energies of formation of many weak interactions among the hundreds of amino acids in a protein. Page 65 10. Roughly how many amino acids are there in one turn of an 𝛼 helix? A) 1 B) 2.8 C) 3.6 D) 4.2 E) 10 11. In the 𝛼 helix, the hydrogen bonds: A) are roughly parallel to the axis of the helix. B) are roughly perpendicular to the axis of the helix. C) occur mainly between electronegative atoms of the R groups. D) occur only between some of the amino acids of the helix. E) occur only near the amino and carboxyl termini of the helix. 12. In an 𝛼 helix, the R groups on the amino acid residues: A) alternate between the outside and the inside of the helix. B) are found on the outside of the helix spiral. C) cause only right-handed helices to form. D) generate the hydrogen bonds that form the helix. E) stack within the interior of the helix. 13. Thr and/or Leu residues tend to disrupt an 𝛼 helix when they occur next to each other in a protein because: A) an amino acids like Thr is highly hydrophobic. B) covalent interactions may occur between the Thr side chains. C) electrostatic repulsion occurs between the Thr side chains. D) steric hindrance occurs between the bulky Thr side chains. E) the R group of Thr can form a hydrogen bond. Page 66 14. A D-amino acid would interrupt an 𝛼 helix made of L-amino acids. Another naturally occurring hindrance to the formation of an 𝛼 helix is the presence of: A) a negatively charged Arg residue. B) a nonpolar residue near the carboxyl terminus. C) a positively charged Lys residue. D) a Pro residue. E) two Ala residues side by side. 15. An 𝛼 helix would be destabilized most by: A) an electric dipole spanning several peptide bonds throughout the 𝛼 helix. B) interactions between neighboring Asp and Arg residues. C) interactions between two adjacent hydrophobic Val residues. D) the presence of an Arg residue near the carboxyl terminus of the 𝛼 helix. E) the presence of two Lys residues near the amino terminus of the 𝛼 helix. 16. The major reason that antiparallel 𝗉-stranded protein structures are more stable than parallel 𝗉-stranded structures is that the latter: A) are in a slightly less extended configuration than antiparallel strands. B) do not have as many disulfide crosslinks between adjacent strands. C) do not stack in sheets as well as antiparallel strands. D) have fewer lateral hydrogen bonds than antiparallel strands. E) have weaker hydrogen bonds laterally between adjacent strands. 17. Amino acid residues commonly found in the middle of 𝗉 turn are: A) Ala and Gly. B) hydrophobic. C) Pro and Gly. D) those with ionized R-groups. E) two Cys. Page 67 18. A sequence of amino acids in a certain protein is found to be -Ser-Gly-Pro-Gly-. The sequence is most probably part of a(n): A) antiparallel 𝗉 sheet. B) parallel 𝗉 sheet. C) 𝛼 helix. D) 𝛼 sheet. E) 𝗉 turn. 19. The three-dimensional conformation of a protein may be strongly influenced by amino acid residues that are very far apart in sequence. This relationship is in contrast to secondary structure, where the amino acid residues are: A) always side by side. B) generally near each other in sequence. C) invariably restricted to about 7 of the 20 standard amino acids. D) often on different polypeptide strands. E) usually near the polypeptide chain's amino terminus or carboxyl terminus. 20. The 𝛼-keratin chains indicated by the diagram below have undergone one chemical step. To alter the shape of the 𝛼-keratin chains—as in hair waving—what subsequent steps are required? A) chemical oxidation and then shape remodeling B) chemical reduction and then chemical oxidation C) chemical reduction and then shape remodeling D) shape remodeling and then chemical oxidation Page 70 29. Proteostasis is the cellular process by which: A) proteins are synthesized. B) proteins are folded. C) proteins are modified. D) proteins are degraded. E) protein levels are maintained. 30. An average protein will NOT be denatured by: A) a detergent such as sodium dodecyl sulfate. B) heating to 90°C. C) iodoacetic acid. D) pH 10. E) urea. 31. Which factor is LEAST likely to result in protein denaturation? A) altering net charge by changing pH B) changing the salt concentration C) disruption of weak interactions by boiling D) exposure to detergents E) mixing with organic solvents such as acetone 32. Experiments on denaturation and renaturation after the reduction and reoxidation of the —S—S— bonds in the enzyme ribonuclease (RNase) have shown that: A) folding of denatured RNase into the native, active conformation, requires the input of energy in the form of heat. B) native ribonuclease does not have a unique secondary and tertiary structure. C) the completely unfolded enzyme, with all —S—S— bonds broken, is still enzymatically active. D) the enzyme, dissolved in water, is thermodynamically stable relative to the mixture of amino acids whose residues are contained in RNase. E) the primary sequence of RNase is sufficient to determine its specific secondary and tertiary structure. Page 71 33. Which statement concerning the process of spontaneous folding of proteins is FALSE? A) It may be an essentially random process. B) It may be defective in some human diseases. C) It may involve a gradually decreasing range of conformational species. D) It may involve initial formation of a highly compact state. E) It may involve initial formation of local secondary structure. 34. Protein S will fold into its native conformation only when protein Q is also present in the solution. However, protein Q can fold into its native conformation without protein S. Protein Q, therefore, may function as a for protein S. A) proteasome B) molecular chaperone C) protein precursor D) structural motif E) supersecondary structural unit 35. Which factor is NOT known to be involved in the process of assisted folding of proteins? A) chaperonins B) disulfide interchange C) heat shock proteins D) peptide bond condensation E) peptide bond isomerization 36. Proteins in their functional, folded conformation are called proteins. A) native B) unique C) intrinsic D) inherent E) natural Page 72 37. Disulfide bonds are more likely to be formed of the cell, due to the environment there. A) inside; oxidizing B) inside; reducing C) outside; oxidizing D) outside; reducing E) inside; hydrophobic 38. Which group of amino acids would be MOST likely to be found in the core of protein that is folded into a three-dimensional structure and soluble in water? A) N, Y, and K B) I, M, and V C) V, T, and R D) M, S, and Y E) F, Y, and W 39. A salt bridge would be MOST likely to be found: A) in the interior of a protein of a bacterium that lives in humans. B) on the exterior of a protein of a bacterium that lives in humans. C) in the interior of a protein of a thermophilic archaeal organism. D) on the exterior of a protein of a thermophilic archaeal organism. E) A salt bridge would be equally likely to be found in any of these cases. 40. Which residues are MOST likely to be enriched in an intrinsically disordered protein that is soluble in water? A) Y, K, W B) E, C, F C) V, I, L D) R, K, A E) H, F, W Page 75 46. The secondary structure is formed more readily than other types of secondary structures, most likely due to . A) 𝗉 turn; hydrogen bonds with solvent molecules B) 𝗉 sheet; R-group contacts C) 𝗉 sheet; internal hydrogen bonds D) 𝛼 helix; R-group contacts E) 𝛼 helix; internal hydrogen helical bonds 47. The secondary structure shown below is an example of a(n): A) parallel 𝗉 sheet. B) antiparallel 𝗉 sheet. C) right-handed 𝛼 helix. D) left-handed 𝛼 helix. E) 𝗉 turn. 48. Which peptide could form an amphipathic 𝛼 helix? A) Nterm-RIFHKVAE-Cterm B) Nterm-RIHFKMEA-Cterm C) Nterm-RHKEMVAI-Cterm D) Nterm-ALIWSQDK-Cterm E) None of the answers is correct. Page 76 49. The secondary structure shown below is an example of a(n): A) parallel 𝗉 sheet. B) antiparallel 𝗉 sheet. C) right-handed 𝛼 helix. D) left-handed 𝛼 helix. E) 𝗉 turn. 50. Proline residues are infrequently found in due to their . A) 𝛼 helices; decreased ability to serve as hydrogen-bond donors B) 𝛼 helices; large positive charge that disrupts the repeating structure C) 𝗉 sheets; decreased ability to serve as hydrogen-bond donors D) 𝗉 sheets; large positive charge that disrupts the repeating structure E) 𝗉 turns; decreased flexibility as an amino acid 51. Which method would be BEST to use to monitor protein secondary structure during the titration of a denaturing agent? A) x-ray crystallography B) electron microscopy C) circular dichroism D) mass spectrometry E) liquid chromatography Page 77 52. Long-range interactions between residues on a single polypeptide chain could BEST be classified as structure. A) primary B) secondary C) tertiary D) quaternary E) globular 53. Interactions between residues on separate polypeptide chains could be best classified as structure. A) primary B) secondary C) tertiary D) quaternary E) global 54. A protein will often have properties that allow it to be both strong and flexible. A) macromolecular B) fibrous C) globular D) helical E) membrane 55. The dimensions of an 𝛼 helix from a fibrous protein such as keratin differ slightly from an 𝛼 helix from a globular protein. What is the reason for this difference in helical dimensions? A) An 𝛼 helix from a fibrous protein is left-handed, not right-handed. B) An 𝛼 helix from a fibrous protein contains mainly hydrophobic residues, elongating the helix. C) An 𝛼 helix from a fibrous protein contains mainly polar residues, elongating the helix. D) An 𝛼 helix from a fibrous protein forms a coiled-coil, distorting the helix. E) An 𝛼 helix from a fibrous protein contains mainly Gly residues for more efficient packing. Page 80 63. What is the CORRECT way to classify the protein below according to its secondary- structure elements? A) all 𝗉 B) 𝛼 + 𝗉 C) 𝛼/𝗉 D) 𝗉/𝛼/𝗉 E) 𝛼/𝗉/𝛼 64. Intrinsically disordered proteins may: A) wrap around their targets. B) have multiple interaction partners. C) function as molecular “scavengers.” D) lack a hydrophobic core. E) All of the answers are correct. 65. If a protein is not folded correctly or becomes partially unfolded, what could NOT be a consequence? A) The protein may form an inactive aggregate that leads to disease. B) The protein may be remodeled by a chaperone. C) The protein may be degraded by the proteasome. D) The protein may be refolded. E) All of these consequences are possible. Page 81 66. Which disease is NOT one characterized by or associated with an unfolded protein aggregate? A) Alzheimer disease B) diabetes C) Parkinson disease D) scurvy E) All of these diseases are linked to unfolded protein aggregates. 67. The image below plots the denaturation of ribonuclease A as a function of guanidine hydrochloride (GdnHCl) concentration, monitored by circular dichroism. The shape of the curve in the figure supports which statement? A) The addition of GdnHCl has little effect on protein secondary structure. B) Increasing temperature causes the protein to become unfolded. C) Unfolding of this protein is a cooperative process. D) Ribonuclease A is a heat-stable protein. E) The peptide bonds of the protein are broken around 3.4 M GdnHCl. Page 82 68. Which image below shows that there are folding intermediates with substantial stability along nearly every folding pathway? A) I B) II C) III D) IV E) None of the answers is correct. 69. Which of the images below depict a protein-folding pathway with no stable folding intermediates? A) I B) III C) IV D) I and III E) II and IV Page 85 88. Explain what is meant by motifs in protein structure. 89. In a 𝗉𝛼𝗉 loop, and describe what is found in the interior of the loop. 90. Describe the quaternary structure of hemoglobin. 91. What is the rationale for many large proteins containing multiple copies of a polypeptide subunit? 92. Explain (succinctly) the theoretical and/or experimental arguments in support of this statement: “The primary sequence of a protein determines its three-dimensional shape and thus its function.” 93. Each of the following reagents or conditions will denature a protein. For each, describe in one or two sentences what the reagent/condition does to destroy native protein structure. (a) urea (b) high temperature (c) detergent (d) low pH 94. How can changes in pH alter the conformation of a protein? 95. Once a protein has been denatured, how can it be renatured? If renaturation does not occur, what might be the explanation? 96. What are two mechanisms by which “chaperone” proteins assist in the correct folding of polypeptides? 97. What important concepts regarding protein thermal denaturation can be inferred from the egg white of a boiled egg? Page 86 98. Identify and quantify the secondary structures present in this protein: 99. Two proteins, X and Y, have similar tertiary structures. The quaternary structures of the proteins are indicated by the diagram below. What differences can be expected in the surfaces of the polypeptides X and Y? 100. In a classic experiment by Christian Anfinsen in the 1950s, it was shown that ribonuclease A could be denatured and then refolded into a catalytically active protein. What control experiment demonstrated that ribonuclease A did not need a chaperone to become properly folded? 101. Briefly describe the process by which a protein aggregate is degraded by autophagy. Page 87 Answer Key 1. D 2. A 3. D 4. C 5. E 6. B 7. A 8. D 9. A 10. C 11. A 12. B 13. D 14. D 15. E 16. E 17. C 18. E 19. B 20. D 21. A 22. D 23. A 24. E 25. D 26. C 27. B 28. D 29. E 30. C 31. B 32. E 33. A 34. B 35. D 36. A 37. C 38. B 39. C 40. D 41. C 42. A 43. C 44. C Page 90 E) segment of mRNA synthesized by RNA polymerase. 4. Which statement about enzymes that interact with DNA is TRUE? A) E. coli DNA polymerase I is unusual in that it possesses only a 5' ⟶ 3' exonucleolytic activity. B) Endonucleases degrade circular but not linear DNA molecules. C) Exonucleases degrade DNA at a free end. D) Many DNA polymerases have a proofreading 5' ⟶ 3' exonuclease. E) Primases synthesize a short stretch of DNA to prime further synthesis. 5. E. coli DNA polymerase III: A) can initiate replication without a primer. B) is efficient at nick translation. C) is the principal DNA polymerase in chromosomal DNA replication. D) represents over 90% of the DNA polymerase activity in E. coli cells. E) requires a free 5'-hydroxyl group as a primer. 6. The proofreading function of DNA polymerase does NOT involve: A) a 3' ⟶ 5' exonuclease. B) base pairing. C) detection of mismatched base pairs. D) phosphodiester bond hydrolysis. E) reversal of the polymerization reaction. 7. The 5' ⟶ 3' exonuclease activity of E. coli DNA polymerase I is involved in: A) formation of a nick at the DNA replication origin. B) formation of Okazaki fragments. C) proofreading of the replication process. D) removal of RNA primers by nick translation. E) sealing of nicks by ligase action. Page 91 8. Prokaryotic DNA polymerase III: A) contains a 5' ⟶ 3' proofreading activity to improve the fidelity of replication. B) does not require a primer molecule to initiate replication. C) has a 𝗉 subunit that acts as a circular clamp to improve the processivity of DNA synthesis. D) synthesizes DNA in the 3' ⟶ 5' direction. E) synthesizes only the leading strand; DNA polymerase I synthesizes the lagging strand. 9. Which compound is NOT required for initiation of DNA replication in E. coli? A) DnaB (helicase) B) DnaG (primase) C) Dam methylase D) DNA ligase E) DnaA (a AAA+ ATPase) 10. At replication forks in E. coli: A) DNA helicases make endonucleolytic cuts in DNA. B) DNA primers are degraded by exonucleases. C) DNA topoisomerases make endonucleolytic cuts in DNA. D) RNA primers are removed by primase. E) RNA primers are synthesized by primase. 11. Which factor is NOT required for elongation during DNA replication in E. coli? A) DnaB (helicase) B) DnaG (primase) C) DnaC D) a 𝗉-sliding clamp E) a clamp loader Page 92 12. In contrast to bacteria, eukaryotic chromosomes need multiple DNA replication origins because: A) eukaryotic chromosomes cannot usually replicate bidirectionally. B) eukaryotic genomes are not usually circular, like the bacterial chromosome is. C) the processivity of the eukaryotic DNA polymerase is much less than the bacterial enzyme. D) their replication rate is much slower, and it would take too long with only a single origin per chromosome. E) they have a variety of DNA polymerases for different purposes, and need a corresponding variety of replication origins. 13. The function of the eukaryotic DNA replication factor PCNA (proliferating cell nuclear antigen) is similar to that of the 𝗉 subunit of bacterial DNA polymerase III in that it: A) facilitates replication of telomeres. B) forms a circular sliding clamp to increase the processivity of replication. C) has a 3ʹ ⟶ 5ʹ proofreading activity. D) increases the speed but not the processivity of the replication complex. E) participates in DNA repair. 14. The Ames test is used to: A) detect bacterial viruses. B) determine the rate of DNA replication. C) examine the potency of antibiotics. D) measure the mutagenic effects of various chemical compounds. E) quantify the damaging effects of UV light on DNA molecules. 15. In a mammalian cell, DNA repair systems: A) are extraordinarily efficient energetically. B) are generally absent, except in egg and sperm cells. C) can repair deletions, but not mismatches. D) can repair most types of lesions except those caused by UV light. E) normally repair more than 99% of the DNA lesions that occur. Page 95 accuracy. C) replication proceeds much faster than normal, resulting in many more mistakes. D) the DNA polymerases involved cannot facilitate base-pairing as well as DNA polymerase III. E) the DNA polymerases involved lack exonuclease proofreading activities. 25. In homologous recombination in E. coli, the protein that moves along a double-stranded DNA, unwinding the strands ahead of it and degrading them, is: A) chi. B) DNA ligase. C) RecA protein. D) RecBCD enzyme. E) RuvC protein (resolvase). 26. In homologous recombination in E. coli, the protein that assembles into long, helical filaments that coat a region of DNA is: A) DNA methylase. B) DNA polymerase. C) histone. D) RecA protein. E) RecBCD enzyme. 27. In homologous genetic recombination, RecA protein is involved in: A) formation of Holliday intermediates and branch migration. B) introduction of negative supercoils into the recombination products. C) nicking the two duplex DNA molecules to initiate the reaction. D) pairing a DNA strand from one duplex DNA molecule with sequences in another duplex, regardless of complementarity. E) resolution of the Holliday intermediate. 28. Which statement is FALSE? A) In vitro, the strand-exchange reaction can include formation of a Holliday intermediate. Page 96 B) In vitro, the strand-exchange reaction is accompanied by ATP hydrolysis. C) In vitro, the strand-exchange reaction may involve transient formation of a three- or four-stranded DNA complex. D) In vitro, the strand-exchange reaction needs RecA protein. E) In vitro, the strand-exchange reaction requires DNA polymerase. 29. Which feature is NOT applicable to homologous recombination during meiosis? A) a double strand break B) cleavage of two crossover events C) alignment of homologous chromosomes D) formation of a single Holliday intermediate E) exposed 3ʹ ends invade the intact duplex DNA of the homolog 30. Which statement does NOT describe a feature of site-specific recombination? A) A specific recombinase enzyme is required. B) The energy of the phosphodiester bond is preserved in covalent enzyme- DNA linkage. C) Recombination sites have non-palindromic sequences. D) Formation of Holliday intermediates is required. E) Insertions or deletions can result from site-specific recombination. 31. Which statement is FALSE about transposition of DNA? A) The diversity of immunoglobins is in part due to DNA recombination by transposition. B) Transposition occurs in both prokaryotes and eukaryotes. C) Enzymes are not required for transposition. D) The first step of transposition can be single- or double-stranded DNA cleavage. E) Transposition can lead to simple movement of a DNA region or duplication of that region in a new location. 32. Which phrase describes a role for E. coli DNA Pol III? A) lagging strand synthesis only B) base excision repair only Page 97 C) mismatch repair only D) both lagging strand synthesis and mismatch repair E) All of these are roles for DNA Pol III. 33. Which statement is FALSE regarding DnaA? A) DnaA is a sequence that is part of oriC in E. coli. B) DnaA is an important component in DNA replication initiation. C) DnaA affects the writhe in oriC in E. coli. D) All of the statements are false. E) None of the statements is false. 34. How many rounds of replication would result in a 1:1 distribution of hybrid to new DNA helices in the Meselson and Stahl experiment? A) one B) two C) three D) four E) five 35. If DNA replication was conservative, what would be observed after two rounds of the Meselson and Stahl experiment? A) 1:1 high-density to low-density bands. B) 1:1 high-density to hybrid-density bands. C) 1:2 high-density to low-density bands. D) 1:2 high-density to hybrid-density bands. E) 1:4 high-density to low-density bands. 36. DnaA binds to what sites in the E. coli origin? A) R sites only B) I sites only C) DUE sites only