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Name: __________________________ Date: _____________

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.

2. Consider the following metabolic reaction:


2-Phosphoglycerate  3-Phosphoglycerate G°' = -4.40 kJ/mol
What can be said about this reaction when the concentration of 2-phosphoglycerate is 0.490 mM
and the concentration of 3-phosphoglycerate is 2.90 mM at 25°C?
A) This reaction is endergonic under these conditions.
B) This reaction is exergonic under these conditions.
C) This reaction is at equilibrium under these conditions.
D) This reaction is not favorable under standard conditions.
E) 40 kJ of work can be done by this reaction under these conditions.

3. In most organisms, replication proceeds in a ______ manner from the ______.


A) unidirectional, chromosome ends
B) bidirectional, replication origin
C) bidirectional, theta site
D) bidirectional, lagging strand
E) none of the above

4. Which of the following best describes the structure of RNA-DNA hybrids?


A) They are most similar to A-DNA
B) They are most similar to B-DNA
C) They are most similar to Z-DNA.
D) Their structure is intermediate to those of A-DNA and B-DNA.

Use the following to answer questions 5-8:

Consider the structure of the coenzyme NADP


O
B
NH 2
O

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

5. Which arrow points at a phosphate ester bond?


A) A
B) B
C) C
D) D
E) E

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6. Which arrow points at an amide bond?
A) A
B) B
C) C
D) D
E) E

7. Which arrow points at a glycosidic bond?


A) A
B) B
C) C
D) D
E) E

8. Which arrow points at an anhydride bond?


A) A
B) B
C) C
D) D
E) E

Use the following to answer question 9:

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

10. In redox half-reactions, a more positive standard reduction potential means


A) the oxidized form has a higher affinity for electrons
B) the oxidized form has a lower affinity for electrons
C) the primary ionic form has a higher positive charge
D) the reduced form is more reactive
E) none of the above

11. Which of the following is not true about enzymes?


A) Enzymes catalyze reactions in the forward direction only.
B) Enzymes are often very specific for their substrates.
C) Enzyme activities can often be regulated.
D) Enzymes typically act under milder conditions of temperature and pH than chemical
catalysts.
E) Enzymes typically catalyze reactions at much higher rates than chemical catalysts.

12. Alterations in genetic information are caused by:


A) point mutations
B) faulty recombination
C) transposition of genes
D) A and B
E) A, B and C

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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

19. In a hydrogen bond between a water molecule and another biomolecule:


A) a hydrogen ion on the water molecule forms an ionic bond with a hydride ion on the other
molecule.
B) the partial charge on a hydrogen of the water interacts with the partial charge on a hydrogen
of the other molecule.
C) the hydrogen bond will typically form between a hydrogen atom and either a nitrogen,
sulfur, or oxygen atom.
D) a hydrogen on the water molecule forms a covalent bond to a hydrogen atom on the other
molecule.
E) the hydrogen atom is located between an oxygen atom of the water and a carbon atom of the
other molecule.

20. In eukaryotes, glycolysis typically occurs in the


A) mitochondrion
B) cytosol
C) lysosome
D) nucleus
E) golgi apparatus

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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.

24. Proteins that bind specific carbohydrates are called ______.


A) pectins
B) oligonucleotides
C) glycosaminoglycans
D) lectins
E) chitins

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

26. Unsaturated fatty acids:


A) are commonly found in plants and animals
B) usually contain a double bond with cis stereochemistry
C) sometimes contain multiple double bonds
D) have lower melting points than the analogous saturated fatty acids
E) all of the above

27. Enzyme activity in cells is controlled by processes including:


A) temporary covalent modifications.
B) modulation of expression levels.
C) feedback inhibition.
D) binding to allosteric effectors.
E) all of the above.

28. Which statement below does not describe fibrous proteins?


A) Domains are compact and globular.
B) These proteins are usually dominated by a single type of secondary structure.
C) These proteins usually perform a protective, connective, or supportive role in the organism.
D) Domains are usually stiff and elongated.
E) The proteins are usually water soluble.

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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

29. The monosaccharides -D-galactose and -D-galactose are ______.

30. Glucose, with its four chiral carbons, has ______ possible stereoisomers.

31. The disaccharide commonly found in dairy products is ______.

32. The smallest aldose is ______.

33. Bulky ring substituents preferentially occupy ______ positions in the chair conformation.

34. Both (14) and (16) bonds can be found in the plant product ______.

35. The vitamin ______ is one of the components of Coenzyme A.


A) biotin
B) pantothenic acid
C) cobalamin
D) riboflavin
E) niacin

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

37. The isoelectronic point of an amino acid is the point where:


A) The pK of the carboxylic acid is the same as the amino group
B) Sodium ions are attracted to the amino groups
C) the solubility of the amino acid is maximized
D) the amino acid racemizes
E) the amino acid carries no net electrical charge

38. The least abundant amino acid in proteins is:


A) V
B) W
C) G
D) F
E) A

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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

40. Recombinant DNA technology can be used for


A) constructing mutant proteins
B) the industrial production of useful proteins
C) producing transgenic organisms
D) correcting genetic defects
E) all of the above

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

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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.

48. Which of the following is an example of a heteropolysaccharide?


A) cellulose
B) chitin
C) starch
D) glycogen
E) glycosaminoglycan

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.

52. The Edman degradation is used to:


A) Determine a protein's N-terminal amino acid
B) Remove DNA from a protein sample
C) Separate subunits of a multi-subunit protein
D) Remove protein from a DNA sample
E) Determine a protein's C-terminal amino acid

53. Myoglobin's secondary structure is primarily composed of ______________.


A) parallel -sheets
B) antiparallel -sheets
C) -helices
D) -bends
E) –helices

54. Which of the statements about viruses is not true:


A) Viruses are much simpler than cells
B) Viruses are the simplest living organisms
C) Viruses lack the necessary metabolic apparatus to reproduce
D) Viruses are dependent on host cells
E) all the statements are true

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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

56. Which of the following statements about keratin is false?


A) Its primary structure consists of a 7-residue repeat, with nonpolar residues predominating at
the first and fourth residues.
B) The classification of keratin as “hard” or “soft” is determined by the proportion of proline
residues.
C) It consists of coiled-coil structures, which form dimers and then associate to form
protofilaments.
D) The coiled-coil structures account for the springiness of hair and wool fibers.
E) Individual chains are cross-linked by disulfide bonds.

57. A gene knockout is:


A) a gene that has been inactivated or removed from an organism.
B) a dominant gene that knocks-out expression of other genes.
C) a gene inserted in place of another gene.
D) a particularly attractive gene.
E) none of the above

58. Which of the following statements is/are true?


A) amino acids can be derived from purines and pyrimidines
B) purines and pyrimidines can be derived from amino acids
C) no protein contains every standard amino acid
D) A and C
E) B and C

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

60. Hydrophobic interactions between nonpolar molecules or groups:


A) result from the tendency to maximize water's contact with nonpolar molecules.
B) are the result of strong attractions between nonpolar regions.
C) are the result of strong repulsion between water and nonpolar regions.
D) depend on strong permanent dipoles in the nonpolar molecules.
E) require the presence of surrounding water molecules.

61. In B-form DNA


A) the bases are all in the syn conformation and the sugars all have a 3' endo pucker.
B) the bases are all in the syn conformation and the sugars all have a 2' endo pucker.
C) the bases are all in the anti conformation and the sugars all have a 3' endo pucker.
D) the bases are all in the anti conformation and the sugars all have a 2' endo pucker.
E) have fairly even mixes of syn vs. anti, and of 2' vs. 3' endo pucker.

62. Free radicals are likely to cause


A) pyrimidine dimers.
B) point mutations.
C) insertions.
D) deletions.
E) base excision.

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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.

64. Which of the following statements does not apply to collagen?


A) It contains hydroxylated amino acids.
B) The polypeptide forms a left-handed helix.
C) Hydrogen bonds between the -OH groups of Hyp residues stabilize the helix.
D) There is an absolute requirement for glycine every third position.
E) The triple helical structure twists in the right-handed direction.

65. SDS-PAGE separates proteins primarily due to differences in:


A) isoelectronic points
B) size
C) polarity
D) solubility
E) sequence

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)

68. ______________ is an emerging technique for protein sequencing.


A) NMR spectroscopy
B) Mass spectrometry
C) Gel electrophoresis
D) Phylogenetic analysis
E) Limited proteolysis

69. Zwitterions are:


A) amino acids
B) ionic molecules that are racemic
C) molecules that bear both negatively and positively charged groups
D) side chain carboxylate anions
E) delocalized ions

70. Secondary structural elements are often observed in groupings commonly called ________.
A) motifs
B) domains
C) clusters
D) lobes
E) rolls

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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

72. Cloning DNA is often necessary in order to sequence it because:


A) Plasmid DNA is a serious biohazard
B) uridine must be replaced by thymidine
C) the resulting antiparallel complementary strand can be readily sequenced
D) it is necessary to produce large amounts of RNA for sequencing to be accurate
E) the small amounts of DNA available from most organisms can not be easily sequenced

73. Chargaff's rules for DNA state that:


A) G+C = 39-46% in mammals
B) A=U and G=C
C) the minor groove is shallower than the major groove
D) A=T and G=C
E) the sense strand is a right-handed helix

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

77. Genomic DNA is ______, producing _________.


A) transcribed; mRNA
B) translated; tRNA
C) transcribed; protein
D) translated; protein
E) translated; rRNA

78. A Lineweaver-Burk plot is also called:


A) a sigmoidal plot
B) a linear plot
C) a double–displacement plot
D) a Michaelis–Menten plot
E) a double reciprocal plot

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Use the following to answer question 79:

The following question(s) refer to the diagram (with boxes where it has been left incomplete):

79. Which reactant/product should be in the box labeled with a Z?


A) A
B) B
C) P
D) Q
E) E

80. Which of these characteristics does not describe the  sheet?


A) Side chains are located both above and below the sheet.
B)  sheets usually exhibit right-handed twists.
C) There are two forms, parallel and antiparallel.
D) The sheets contain as few as two and as many as 22 polypeptide chains.
E) Parallel  sheets containing fewer than five chains are the most common.

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.

84. Western blots identify ______ using ______.


A) RNA, antibodies
B) proteins, antibodies
C) enzymes, substrates
D) RNA, ELISA
E) none of the above

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

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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

87. Transfer RNA molecules are involved in:


A) transcription
B) translation
C) duplication
D) gene shuffling
E) recombination

88. In alcoholic fermentation, acetaldehyde is produced by


A) the decarboxylation of pyruvate
B) the carboxylation of pyruvate
C) the decarboxylation of lactate
D) the carboxylation of lactate
E) None of the above

89. Nucleotides contain phosphate groups bonded to the:


A) C3 or C5 atoms
B) C3 or C3 atoms
C) C5 or N9 atoms
D) C3 or N9 atoms
E) none of the above

90. When [S] = KM, ν0 = _______Vmax.


A) 2
B) 1
C) 0.67
D) 0.5
E) 0.1

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+

92. What is abortive initiation of transcription by RNA polymerase?


A) initiation at non-promoter sites prior to dissociation of the polymerase.
B) synthesis of short transcripts about 10 nucleotides long prior to commitment to elongation.
C) pausing by the polymerase during elongation.
D) failure to undergo the closed to open transition in the pre-initiation complex.
E) None of the above

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

94. Cholesterol is commonly found in which of the following organisms?


A) mammals
B) plants
C) yeast and fungi
D) bacteria
E) all of the above

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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

97. The formation of a dipeptide from two amino acids requires:


A) side-chain complementarity
B) loss of water
C) oxidation of the -carbon
D) reduction of the -carbon
E) base catalysis

98. The electrons formed from the oxidation of glucose are


A) directly transferred to O2 during the citric acid cycle.
B) transferred to the coenzymes NAD+ and FAD.
C) transferred to succinate and arachidonic acid.
D) A and B
E) none of the above

99. The strongest non-covalent interactions are:


A) ionic interactions
B) hydrogen bonds
C) dipole-dipole interaction
D) London dispersion forces
E) van der Waal forces

100. Halophiles and thermophiles are


A) early versions of eukaryotic cells.
B) highly evolved for their specific environments
C) relatively inefficient and unevolved organisms
D) more complex than eukaryotes
E) extremely slow growing

101. ___________ is an example of a very slowly evolving protein.


A) Histone H4
B) Hemoglobin
C) Cytochrome c
D) Fibrinopeptides
E) none of the above

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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

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