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1. Enzymes that hydrolyze the internal peptide bonds (not the peptide bonds of the terminal amino
acids) of a protein are:
A) oxidoreductases.
B) lyases.
C) endopeptidases.
D) nucleases.
E) exopeptidases.
O P O N
A H
O
H
O
H H
OH OH NH2
O P O
N
C
N
O
N N
H
O
H
D
H H
OH O
E
O P O
Page 1
6. Which arrow points at an amide bond?
A) A
B) B
C) C
D) D
E) E
Choose the correct answer from the list. Not all the answers will be used.
A) positively cooperative
B) cyanosis
C) His E7
D) decrease
E) R
F) hydrogen bonds
G) increase
H) symmetry
I) His F8
J) ion pairs
K) T
L) hemolytic anemia
9. Mutations that favor the oxidation of the heme iron to the +3 oxidation state can cause ______.
A) B
Page 2
13. Cyanide (CN-) inhibits electron transport at
A) Complex I
B) Complex II
C) Complex III
D) Complex IV
E) Coenzyme Q
14. A first step in purifying a protein that was initially associated with fatty substances would be:
A) Coomassie Brilliant Blue dye staining.
B) analytical ultracentrifugation.
C) ELISA.
D) Western blotting.
E) hydrophobic chromatography.
15. Triglycerides contain more metabolic energy per unit weight than glycogen because:
A) the carbohydrate glycerol is readily metabolized
B) anhydrous glycogen cannot be cleaved by glycogen phosphorylase
C) fatty acids are less oxidized than carbohydrates
D) triglycerides have a higher average molecular mass
E) none of the above
16. Which of the following amino acids has a charged polar side chain at pH 7?
A) Leu
B) Ala
C) Met
D) Trp
E) Glu
17. Natural polypeptides most commonly contain linear polypeptides between 100 and 1000
residues in length. Polypeptides outside this range may be disfavored because:
A) larger polypeptides would likely be insoluble.
B) smaller polypeptides do not form stable folded structures
C) small polypeptides typically assemble into prion-like aggregates.
D) A & B
E) A & C
18. [S] = KM for a simple enzymatic reaction. When [S] is doubled, the rate becomes _____ Vmax.
A) 2
B) 1
C) 0.67
D) 0.5
E) 0.1
Page 3
21. Conformation(s) that has (have) both a favorable hydrogen bonding pattern and and values
that fall within the allowed Ramachandran conformational regions is (are)
A) helix
B) collagen helix
C) sheet
D) All of the above
E) None of the above
22. At equilibrium in solution, D-glucose consists of a mixture of its anomers. Which statement most
accurately describes the solution?
A) The solution consists of approximately equal amounts of the - and -anomers.
B) The straight-chain form is present in high concentration.
C) The -anomer is more stable and is slightly preferred over the -anomer.
D) The -anomer predominates over the -anomer by a ratio of approximately 2:1.
E) None of the above.
23. KM is:
A) a measure of the catalytic efficiency of the enzyme.
B) the rate at which the enzyme dissociates from the substrate.
C) the rate constant for the reaction ES E + P.
D) the [S] that half-saturates the enzyme.
E) the rate at which the enzyme binds the substrate.
25. Which of the following is the best explanation for the hydrophobic effect?
A) It is caused by an affinity of hydrophobic groups for each other
B) It is caused by the affinity of water for hydrophobic groups
C) It is an entropic effect, caused by the desire of water molecules to increase their entropy by
forming highly ordered structures (called clathrates) around the hydrophobic groups
D) It is an entropic effect, caused by the desire of water molecules to increase their entropy by
excluding hydrophobic groups, which they must otherwise surround with highly ordered
structures (called clathrates)
E) It is an entropic effect caused by the desire of hydrophobic groups to increase their entropy
by associating with other hydrophobic groups
Page 4
Use the following to answer questions 29-34:
Choose the correct answer from the list. Not all the answers will be used.
A) eight
B) deoxy
C) peptidoglycan
D) axial
E) anomers
F) two
G) lactose
H) glyceraldehyde
I) amylopectin
J) epimers
K) sixteen
L) glycogen
M) equatorial
30. Glucose, with its four chiral carbons, has ______ possible stereoisomers.
33. Bulky ring substituents preferentially occupy ______ positions in the chair conformation.
34. Both (14) and (16) bonds can be found in the plant product ______.
36. Which of the following amino acid residues would not provide a side chain for acid-base
catalysis?
A) leucine
B) serine
C) lysine
D) aspartic acid
E) histidine
Page 5
39. Non-covalent forces that stabilize protein structure include all of the following except
__________.
A) the hydrophobic effect
B) salt bridges
C) metal-ion coordination
D) hydrogen bonding
E) disulfide bridges
41. RNA occurs primarily as single strands, often giving rise to _______ structures.
A) diploid
B) stem-loop
C) parallel
D) tautomeric
E) haploid
42. Given that the standard reduction potential of oxaloacetate is –0.166 V and the standard
reduction potential of NAD+ is –0.315 V. What is the °' for the oxidation of malate by
NAD+: Malate + NAD+ Oxaloacetate + NADH + H+
A) –4.81 V
B) + 4.81 V
C) –0.149 V
D) +0.149 V
E) +0.0523 V
43. How many NADH are produced when one acetyl group is oxidized in the citric acid cycle?
A) 1
B) 2
C) 3
D) 4
E) more than 4
44. In the absence of ascorbic acid, prolyl oxidase is unable to oxidize proline residues in collagen to
hydroxyproline, resulting in:
A) sickle-cell anemia
B) prion diseases
C) amyloid formation
D) the disease scurvy
E) brittle hair and nails
45. A protein that has had few changes in its amino acid sequence over evolutionary history is
labeled:
A) a fibrinopeptide.
B) evolutionarily conservative.
C) random.
D) a product of pseudogenes.
E) phylogenetic.
46. At pH 1, lysine (pKs are -carboxylate 2.16, -amino 9.06, -amino 10.54) would be charged as
follows:
A) 0 -carboxylate, -1 -amino, -1 -amino, -2 net charge
B) -1 -carboxylate, +1 -amino, +1 -amino, +1 net charge
C) +1 -carboxylate, +2 -amino, +2 -amino, +5 net charge
D) 0 -carboxylate, +1 -amino, +1 -amino, +2 net charge
E) +2 -carboxylate, +1 -amino, +1 -amino, +4 net charge
Page 6
47. An enzyme-linked immunosorbent assay requires:
A) a radioactive substrate.
B) a coupled enzymatic reaction.
C) aromatic amino acids.
D) an antibody that binds the protein of interest.
E) a catalytic antibody.
49. A technique that can be used to separate proteins based primarily their surface non-polar residues
is called:
A) Ion-exchange chromatography
B) Gel filtration chromatography
C) Afffinity chromatography
D) Gel electrophoresis
E) Hydrophobic interaction chromatography
50. Polynucleotides are cleaved at recognition sites within the strands by:
A) bacteriophages
B) DNA ligase
C) type III restriction endonucleases
D) reverse transcriptase
E) type II restriction endonucleases
51. Which one of these characteristics is not true for the helix?
A) There are 3.6 amino acids per turn.
B) There is a requirement for glycine every third amino acid residue.
C) A hydrogen bond forms between the carbonyl oxygen of the nth amino acid residue and the
-NH group of the (n + 4)th amino acid residue.
D) Proline is typically not found in the helix.
E) It is right-handed.
Page 7
55. 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) Fructose-1,6-bisphosphate dihydroxyacetone phosphate +
glyceraldehyde-3-phosphate
E) Glucose-6-phosphate fructose-6-phosphate
59. Gel electrophoresis generally separates nucleic acids on the basis of:
A) shape
B) sequence
C) size
D) charge-density
E) none of the above
Page 8
63. The disulfide bond between two cysteine molecules:
A) is a peptide bond.
B) is an ionic bond that is stable at physiological pH.
C) is a covalent bond formed by oxidation.
D) is a hydrogen bond between the two sulfhydryl groups.
E) is a weak ion-induced dipole attraction.
66. In situ hybridization often uses radioactively labeled probes. When probing for a gene
containing the sequence 'AGCTAACGGG' (standard notation), the probe should have a sequence
containing
A) just 'TT'; in order to recognize all related genes
B) 'TGCCC', in order to bind selectively to the 3' end of the gene of interest
C) 'CCCGTTAGCT', in order to very selectively bind the target in an antiparallel fashion
D) a gene conferring antibiotic resistance
E) DNA ligase
67. In replicating circular DNA, the “bubble” or “eye” shapes that are observed, are called ______
structures.
A) (theta)
B) (phi)
C) (rho)
D) (sigma)
E) (delta)
70. Secondary structural elements are often observed in groupings commonly called ________.
A) motifs
B) domains
C) clusters
D) lobes
E) rolls
Page 9
71. Which of the following is at a higher level of oxidation than CH3CHO?
A) CH3CH2OH
B) CH3CH3
C) CH2=CH2
D) CH3CO2H
E) none of the above
74. How many electrons can be carried by the prosthetic group in cytochrome?
A) 1
B) 2
C) 3
D) 1 or 2
E) none of the above
75. The process by which ATP is formed from ADP in glycolysis is referred to as
A) oxidation
B) reduction
C) substrate-level phosphorylation
D) oxidative phosphorylation
E) photophosphorylation
76. At pH 7, arginine (pKs are -carboxylate 1.82, -amino 8.99, guanidino 12.48) would be
charged as follows:
A) 0 -carboxylate, 0 -amino, +1 guanidino, +1 net charge
B) +1 -carboxylate, 0 -amino, -1 guanidino, 0 net charge
C) +1 -carboxylate, -1 -amino, -1 guanidino, -1 net charge
D) -1 -carboxylate, +1 -amino, +1 guanidino, +1 net charge
E) -1 -carboxylate, 0 -amino, +1 guanidino, 0 net charge
Page 10
Use the following to answer question 79:
The following question(s) refer to the diagram (with boxes where it has been left incomplete):
81. The quantitation of proteins due to their absorbance at ~280nm (UV region) is made possible by
the large extinction coefficients of the ________ amino acids.
A) anionic
B) dansylated
C) cleaved
D) polar
E) aromatic
82. Myoglobin and a single chain of hemoglobin have similar ______ structures.
A) primary
B) secondary
C) tertiary
D) quaternary
E) none of the above
83. Consider the following reaction which has a G' +30 kJ/mol.
malate + NAD+ —> oxaloacetate + NADH + H+
In muscle cells, the reaction proceeds as written, i.e., from left to right. How can this occur?
A) It is thermodynamically favored under standard conditions.
B) In the cell, it is kinetically favored, even though it's thermodynamically unfavored.
C) The concentration of malate must be higher than oxaloacetate for this reaction to occur in
the cell.
D) [H+] must be higher in muscle than under standard conditions, thus altering G to G'.
E) The enzyme can only catalyze the reaction in that direction.
85. What group is attached to the ring in thymine and is not found on uracil?
A) ribose
B) CH3
C) NH3
D) OCH3
E) none of the above
Page 11
86. DNA polymerase from Thermus aquaticus is used in PCR because:
A) it is a soluble protein
B) the genes from Thermus aquaticus are readily distinguished from 'normal' organisms
C) the enzyme is readily deactivated by heat, effectively halting the reaction
D) it is stable to PCR reaction conditions
E) it is not infectious
91. Which of the following coenzymes is NOT used by the pyruvate dehydrogenase complex?
A) thiamine pyrophosphate
B) pyridoxal phosphate
C) coenenzyme A
D) FAD
E) NAD+
93. For -sheets, the terms 'parallel' and 'anti-paralllel' refer to ___________.
A) the 'direction' of the associated peptide strands
B) the orientation of the amide crosslinks
C) the quaternary structure of the protein
D) the orientation of the hydrogen bonding
E) the topology of the reverse turns
Page 12
95. Pol I synthesizes new DNA with very high fidelity, due to its
A) processivity.
B) proofreading capabilities.
C) helicase functionality.
D) ligase functionality.
E) semiconservative nature.
96. ATP contains one ________ bond and two ______ bonds.
A) phosphoanhydride; phosphoester
B) phosphoester; glycosidic
C) glycosidic; amide
D) amide; phosphoanhydride
E) phosphoester; phosphoanhydride
Page 13
Answer Key
1. C
2. C
3. B
4. D
5. E
6. B
7. D
8. A
9. (No Answer Provided)
10. A
11. A
12. E
13. D
14. E
15. C
16. E
17. B
18. C
19. C
20. B
21. D
22. D
23. D
24. D
25. D
26. E
27. E
28. A
29. E
30. K
31. G
32. H
33. M
34. I
35. B
36. A
37. E
38. B
39. E
40. E
41. B
42. C
43. C
44. D
45. B
46. D
47. D
48. E
49. E
50. E
51. B
52. A
53. C
54. B
55. B
56. B
57. A
58. B
59. C
60. E
61. D
62. B
63. C
Page 14
64. C
65. B
66. C
67. A
68. B
69. C
70. A
71. D
72. E
73. D
74. A
75. C
76. D
77. A
78. E
79. D
80. E
81. E
82. C
83. C
84. B
85. B
86. D
87. B
88. A
89. A
90. D
91. B
92. B
93. A
94. A
95. B
96. E
97. B
98. B
99. A
100. B
101. A
Page 15