CH 369 Exam 1

Name: __________________________ eID _____________ Grade_______________

September 15, 2011

I. (10 points total, 1 point each) True/False

1. The first step in the folding of disordered polypeptide chains into stable proteins is the formation of primary structural
elements.
A) True B) False
2. Ice is H-bonded to a similar extent as liquid water.
A) True B) False
3. The bundles of myosin tails that assemble to bind actin in a muscle cell are called thin filaments.
A) True B) False
4. A spontaneous process has a G<0.
A) True B) False
5. If gas molecules in an enclosed space are allowed to enter a second chamber, the resulting redistribution of gas molecules
represents an increase in entropy.
A) True B) False
6. The formation of a dipeptide from two amino acids requires oxidation of the -carbon.
A) True B) False
7. Weak acids are only partially ionized in aqueous solution..
A) True B) False
8. The terms "protein" and "polypeptide" are interchangeable.
A) True B) False
9. By convention, the sequence of nucleotide residues in a nucleic acid molecule is written lef t to right starting with the 5'
end.
A) True B) False
10. The pH at the midpoint of an acid/base titration is equal to the pK of the corresponding base.
A) True B) False
II. (4 points total, 0.5 points each) Match the structure of the amino acid with its correct name.

11.
A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

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12.

13.
A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

A) Leu

B) Ala

C) Ile

D) His

E) Gln

F) Arg

G) Thr

H) Trp

I) Asn

J) Glu

14.

15.

16.

17.

18.

III. (33 points total, 1.5 points each) Multiple choice

19. Choose the correct answer from the list. Not all the answers will be used.
Edman's reagent can be used to identify the ______ of a protein.
A) electrophoresis
G) three-dimensional shape
B) positive charge
H) enzyme-linked immunosorbent assay
C) cation exchange
I) negative charge
D) foaming
J) N-terminal amino acid
E) high level expression
K) chromophore
F) hydrophobic
20. The movement of kinesin along the protofilament:
A) can be described as by a hand-over over-hand model
B) requires the coordinated action of both heads
C) requires the hydrolysis of ATP

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D) all of the above

E) none of the above

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21. While the binding of O2 to myoglobin as a function of pO2 is described by a simple __________ curve, thebinding to
hemoglobin is described by a more complex ______ curve.
A) sigmoidal; hyperbolic
D) sigmoidal; bell-shaped
B) hyperbolic; sigmoidal
E) hyperbolic; concave
C) exponential; hyperbolic
22. Molecular chaperones assist proteins in the formation of ________.
A) aggregates B) 3 structure C) amide bonds D) 1 structure

E) none of the above

23. The biological classification system categorizes organisms into the domains:
A) bacteria, eukarya, and vertebrate.
D) eukarya and bacteria.
B) archaea and eukarya.
E) none of the above
C) bacteria, eukarya, and archaea.
24. Amino acid side-chain residues have:
A) a positive charge in every situation
B) pKs that assure the solubility of every protein
C) different pKs in peptides as compared to the free amino acids
D) constant pKs no matter what aqueous environment they are found in
E) polar functional groups
25. Choose the correct answer from the list. Not all the answers will be used.
The most abundant chemical element in the human body is
A) nitrogen.
F) H TS.
B) q/T.
G) polymers.
C) H.
H) equilibrium.
D) thermophiles.
I) halobacteria.
E) carbon.
J) entropy.
26. Which of the following is not true of eukaryotes:
A) They contain organelles like mitochondria, chloroplasts, ribosomes, and a nucleus
B) They are usually 10 to 100 microns in diameter
C) They can be both uni or multicellular
D) They are also called archaea
E) All of the above are true of eukaryotes
27. Choose the correct answer from the list. Not all the answers will be used.
Octane molecules dispersed in water tend to aggregate because that allows water molecules to be more
A) hydrogen bond(s).
F) rotational.
B) tetrahedral structure arrangement.
G) dissolved but only partially ionized.
C) higher electronegativity.
H) disordered.
D) base versus acid.
I) insoluble.
E) acid versus base.
28. Hydrogen bonds within liquid water:
A) are attractions between the protons of the oxygen nuclei.
B) are dipole-dipole attractions.
C) are ion-induced dipole attractions.
D) are attractions between two hydrogen atoms.
E) are attractions between the H+ and OH ions of the liquid.
29. In a large part, Francis and Crick's proposal of a double-helical structure for DNA was based on evidence from:
A) NMR (nuclear magnetic resonance) spectroscopy
D) x-ray crystallography
B) IR (infrared) spectroscopy
E) electron microscopy
C) atomic force microscopy
30. Polynucleotides are cleaved at recognition sites within the strands by:
A) restriction endonucleases B) bacteriophages C) DNA ligase D) reverse transcriptase

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31. Choose the correct answer from the list. Not all the answers will be used.
The 104.5 bond angle in the water molecule is the result of the ______ of electron orbitals around oxygen.
A) hydrogen bond(s)
F) negative entropy
B) positive entropy
G) rotation
C) insoluble
H) disordered
D) higher electronegativity
I) tetrahedral structure arrangement
E) dissolved but only partially ionized
32. For -sheets, the terms 'parallel' and 'anti-paralllel' refer to ___________.
A) the topology of the reverse turns
D) the orientation of the hydrogen bonding
B) the orientation of the amide crosslinks
E) the 'direction' of the associated peptide strands
C) the quaternary structure of the protein
33. 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.
34. The stability of the DNA helix is mainly due to
A) hydrogen bonding between phosphate groups.
B) stacking and hydrophobic interactions.
C) attractive ionic interactions.

D) A and B
E) B and C

35. Kw, the ionization constant of water, is _____ at _____.

A) 1014; 0C B) 1014; 25C C) 1014; 25C D) 10-7; 25C

E) 107; 25K

36. Choose the correct answer from the list. Not all the answers will be used.
Cytosine, uracil, and thymine are structural derivatives of
A) exons.
F) phosphodiester.
B) introns.
G) chain-terminator.
C) purine.
H) diploid.
D) cloning.
I) transformed.
E) pyrimidine.
J) ampicillin.
37. Consider the structure of the coenzyme NADP
amide (amido group)

diphosphoric acid
ester

imine

bond

amine

Which arrow points at a phosphate ester bond?

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

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38. Choose the correct answer from the list. Not all the answers will be used.
The term used to indicate the degree of randomness within a system is
A) H.
F) flux.
B) G.
G) phylogenetic.
C) q/T.
H) carbon.
D) H TS.
I) polymers.
E) entropy.
J) equilibrium.
39. Choose the correct answer from the list. Not all the answers will be used.
______ is found in bone, teeth, cartilage, and tendons.
A) Peptide group
F) Molecular chaperone
B) Regular secondary structure
G) Collagen
C) Forbidden conformation
H) Tertiary structure
D) Alpha
I) Keratin
E) Ribonuclease A
J) Hydropathy value
40. Choose the correct answer from the list. Not all the answers will be used.
Gibbs free energy is defined as G =
A) equilibrium.
F) G.
B) carbon.
G) flux.
C) H TS.
H) q/T.
D) entropy.
I) polymers.
E) H.
J) nitrogen.
IV. (38 points total, 2 points each) Multiple choice
41. Which one of the three structures below would not exist at any pH (pKs are -carboxylate 2.0, -amino 10.2, sulfhydryl
8.0)?

A)

B)

C)

42. Which one of the three structures below would predominate at pH 7.0 (pKs are -carboxylate 2.0, -amino 10.2,
sulfhydryl 8.0)?

A)

B)

C)

Pk (8) > pH (7) =? protonated

43. Which one of the three structures below would exist at pH 10 (pKs are -carboxylate 2.0, -amino 10.2, sulfhydryl 8.0)?

A)

B)

C)

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44. In the graph below, which curve represents fetal hemoglobin?

A)

B)

45. Which of the following amino acids has a charged polar side chain at pH 7?
A) Trp B) Ala C) Glu D) Leu E) Met
46. Lysine can form a salt bridge by associating with a nearby _____ residue.
A) Glu B) Gly C) Ser D) Gln E) Pro
negative

polar

polar

polar

lysine= positive

hydrophobic

47. Which one of the two forms of the amino acid illustrated below would predominate at pH 3.9 (pKs are -carboxylate 2.1,
-amino 9.8, side carboxy 3.9)?
pH = pK = [A-] = [HA]

A)

B)

C) Neither predominates

48. Non-covalent forces that stabilize protein structure include all of the following except __________.
A) disulfide bridges
D) metal-ion coordination
B) salt bridges
E) hydrogen bonding
C) the hydrophobic effect
49. 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.
50. Would Glu 35 of lysozyme, which is found in a non-polar environment, be expected to be more or less acidic than an
external, well hydrated Glu residue?
A) more acidic
D) it would depend on the sample buffer
B) less acidic
E) none of the above
C) the pK would not change Glu is negative charge
51. DNA polymerase from Thermus aquaticus is used in PCR because:
A) it is not infectious
B) it is a soluble protein
C) the genes from Thermus aquaticus are readily distinguished from 'normal' organisms
D) the enzyme is readily deactivated by heat, effectively halting the reaction
E) it is stable to PCR reaction conditions

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52. In order to perform PCR, the following reagents must be included:

A) DNA fragment, primers flanking the region of interest, dNTPs, DNA Polymerase
B) DNA fragment, primers flanking the region of interest, dNTPs, ddNTPS, DNA Polymerase
C) DNA fragment, one primer, dNTPs, DNA Polymerase, DNA ligase
D) DNA fragment, primers flanking the region of interest, dNTPs, DNA Ligase
E) none of the above
53. At pH 7, arginine (pKs are -carboxylate 1.82, -amino 8.99, guanidino 12.48) would be charged as follows:
A) +1 -carboxylate, 0 -amino, -1 guanidino, 0 net charge
B) +1 -carboxylate, -1 -amino, -1 guanidino, -1 net charge
C) -1 -carboxylate, +1 -amino, +1 guanidino, +1 net charge
D) -1 -carboxylate, 0 -amino, +1 guanidino, 0 net charge
E) 0 -carboxylate, 0 -amino, +1 guanidino, +1 net charge
54. Which of the following statements about water is incorrect?
A) Water is an excellent solvent for polar molecules.
B) Pure water has a concentration of approximately 55.5 M.
C) Non-polar molecules do not dissolve in water, but form a separate phase.
H is positive
D) Cations are solvated by shells of water molecules oriented with their hydrogen atoms pointed toward the ions.
charge => repel
E) Amphiphilic detergents often form micelles with the polar groups on the outside exposed to the water (solvent) and
the non-polar groups sequestered in the interior.
55. Choose the correct answer from the list. Not all the answers will be used.
A solution of buffer at a pH of 8.5 with a pK of = 7.5 would have more capacity to buffer the addition of
A) H2PO4.
F) insoluble.
B) hydrogen bond(s).
G) H3PO4.
C) HPO4 2.
H) rotational.
D) acid versus base.
I) base versus acid.
E) disordered.
56. 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

57. Phosphate, with a pK2 of = 6.82, will be mostly in the HPO42 form at pH 7.2. At pH 5.82 it is mostly in the ______ form.
A) H3PO4 B) rotational C) H2PO4 D) insoluble E) HPO4 2
pK 6.82 > pH 5.82 => protonate

58. What is the ratio of citric acid (pK1 = 3.09) to monosodium citrate in a 1.0 M citric acid solution with a pH = 2.09?
A) 10:11 B) 1:11 C) 10:1 D) 1:1 E) 1:10
59. DNA sequencing using the Sanger method requires:
A) template, primer, DNA polymerase, mRNA, dNTPs, ddNTP
B) template, primer, DNA polymerase, dNTPs, ddNTP
C) template, primer, DNA polymerase, rRNA, dNTPs, ddNTP
D) template, primer, DNA polymerase, mRNA, dNTPs
E) none of the above
V. (15 points total, 3 points each) Multiple choice [Note: these problems may require extra time, do not attempt until the rest of the
exam is complete.]
60. Which of the following statements does not apply to the K value in the equation for the oxygen binding curve of
myoglobin?
A) It is numerically equal to p50.
B) If Y > K, then myoglobin is less than 50% saturated with oxygen.
C) It is defined as that oxygen partial pressure at which half of the oxygen binding sites are occupied.
D) It is the value of pO2 at which Y = 0.5.
E) It is a measure of the affinity of myoglobin for oxygen.

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61. What is the volume (in mL) of 17.4 M glacial acetic acid (pK 4.76) that would have to be added to 500 mL of a solution of
0.20 M sodium acetate in order to achieve a pH of 5.0?
A) 3.3 mL B) 1.74 mL C) 33 mL D) 17.4 mL
62. If an enzyme-catalyzed reaction has a low rate at low pH and high rate at higher pH, this implies that a group on either the
enzyme or the substrate must be ______ for an efficient reaction.
A) motion
H) leaving group
B) orient
I) oxidoreductase
C) rate-determining
J) coenzymes
D) short peptides
K) deprotonated
E) concerted acid-base
L) protonated
F) amino acid
M) least resistance
G) high
N) low

63. One liter of a 0.10 M Tris buffer (pK 8.30) is prepared and adjusted to a pH of 8.2. What are the concentrations of
conjugate acid and weak base at this pH?
A) [HA] = 79 mM; [A-] = 21 mM
D) [HA] = 28 mM; [A-] = 72 mM
B) [HA] = 56 mM; [A ] = 44 mM
E) [HA] = 44 mM; [A-] =56 mM
C) [HA] = 21 mM; [A ] = 79 mM

64. What is the ratio of conjugate base to weak acid if 1.5 mL of 3.0 M HCl is added to 1.0 L of the buffer prepared in
question 63? What is the new pH?
A) ratio = 1.53; pH = 8.50 B) ratio = 0.94; pH = 8.27 C) ratio = 0.65; pH = 8.12 D) ratio = 1.06; pH = 8.33

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Answer Key
1.
2.
3.
4.
5.
6.
7.
8.
9.
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25.
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27.
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31.
32.
33.
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35.
36.
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38.
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44.
45.
46.
47.
48.
49.
50.
51.
52.
53.
54.
55.
56.
57.
58.
59.

B
A
B
A
A
B
A
B
A
B
J
H
G
F
D
C
B
I
J
D
B
B
C
C
E
D
H
B
D
A
I
E
C
B
C
E
E
E
G
C
B
A
C
A
C
A
C
A
C
B
E
A
C
D
D
A
C
C
B
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60.
61.
62.
63.
64.

B
A
K
B
C

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