CH 369 Exam 1

September 24, 2012

Name: ________________________________________________ eID _____________
Helpful Equations:

[ base ]
pH = pK a + log
[ acid ]

Y=

pO 2
K + pO 2

G = H T S

degrees K = 273 + C

Section I: 32 points (1 point each)

Use the following to answer questions 1-6:
Match the structure or description with the appropriate amino acid.

1.
A) Gly

B) HIs

C) Glu

D) Asn

E) Leu

A) Gly

B) His

C) Glu

D) Asn

E) Ile

F) Arg

G) Pro

H) Gln

I) Ile

J) Asn

I) Val

J) Asn

3. Amino acid with side chain that is always positively charged in biological systems
A) Gly B) His C) Glu D) Asn E) Ile F) Arg G) Pro H) Gln I) Val

J) Asn

4. Technically not hydrophobic, polar, or charged

A) Gly B) His C) Glu D) Asn E) Ile

F) Arg

G) Pro

H) Gln

I) Val

J) Asn

5. Acidic amino acid

A) Gly B) His C) Glu

2.
F) Arg

G) Pro

H) Gln

D) Asn

E) Ile

F) Arg

G) Pro

H) Gln

I) Val

J) Asn

D) Asn

E) Ile

F) Arg

G) Met

H) Gln

I) Val

J) Asn

6.
A) Gly

B) His

C) Glu

7. H3O+ is the strongest acid that can exist in a biological system.

A) True B) False

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8. Identify the AMIDO group in the following molecule.

A) (a)

B) (b)

C) (c)

9. How many hydrogen bond acceptor atoms are present in the molecule below?

A) 1

B) 2

C) 3

D) 4

E) 5

10. Of the six proteins, actin, myosin, tubulin, kinesin, keratin, and collagen, which contain nucleotide-binding sites?
A) keratin and collagen
D) actin, myosin, tubulin, and kinesin
B) myosin and kinesin
E) none of the above are correct
C) actin and tubulin
11. pleated sheets are associated with what level of protein structure?
A) Primary B) Secondary C) Tertiary D) Quaternary E) Superquaternary
12. What is the term used to define binding behavior in which the binding of one ligand alters the affinity of binding
for a second ligand?
A) cooperativity B) stereospecificity C) denaturation D) complementary E) none are correct
13. What is the predominant secondary structure in amyloid or prion fibers?
A) sheet B) helix C) random coil D) random turns E) none of the above
14. One of the principal methods that organisms use to obtain energy from chemical bonds is by
A) Substitution reactions
D) Hydration reactions
B) Dehydration reactions
E) Addition reactions
C) Oxidation/reduction reactions
15. Which of the numbered carbons in the molecule below is the alpha carbon?

A) 1

B) 2

C) 3

D) 4

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16. Proteins are effective buffers because they contain

A) a large number of amino acids
B) amino acid residues with side chains with different pKa values
C) N-terminal and C-terminal residues that can donate and accept protons
D) peptide bonds that readily hydrolyze consuming H+ and OH- ions
E) a large number of hydrogen bonds in alpha helices
17. Which of the following would be the most fully reduced molecule?
A) CH3OH B) CH3COOH C) CH3SH D) CH4 E) CH3CHO
18. The linkage in which a phosphate group is esterified to two alcohol groups is called a phosphodiester bond.
A) True B) False
19. The hydrophobic effect, resulting in the exclusion of nonpolar substances from an aqueous solution is the result of
the strong attractive force between the nonpolar molecules.
A) True B) False
20. A _________ is a compound consisting of a nitrogenous base linked to a five-carbon sugar (ribose or
deoxyribose).
A) nucleotide B) nucleoside C) purine/pyrimidine D) none of the above
21. A reaction will be spontaneous at all temperatures if what two conditions are met?
A) a decrease in enthalpy and decrease in entropy
D) an increase in enthalpy and decrease in entropy
B) a decrease in enthalpy and increase in entropy
E) none of the above
C) an increase in enthalpy and increase in entropy
22. What is true of eukaryotic cells, but NOT of prokaryotic cells?
A) Both contain a plasma membrane
B) Both have DNA
C) Both can be unicellular
D) Both have membrane-bounded cellular compartments
E) All options apply to both eukaryotes and prokaryotes
23. Non-polar molecules experience a small attractive force owing to
A) ionic interactions
D) all of the above
B) hydrogen bonding
E) none of the above
C) London dispersion forces
24. At pH 11.5, most of the amino groups found in proteins would:
A) carry a negative charge
D) bear multiple ionic charges
B) carry a positive chage
E) none of the above
C) have no charge
25. Since hydrogen bonds are stronger than London dispersion forces, the hydrogen bonds formed in a protein are
more important than the hydrophobic effect for its correct folding.
A) True B) False
26. The course of chemical reactions are determined by three factors. These are enthalpy, entropy, and
A) Heat of Reaction
D) Bond energy
B) Free energy
E) Both A and B are correct.
C) States of matter

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27. The DNA "backbone" is composed of

A) An amide bond between deoxyribose and a nitrogenous base
B) A glycosidic bond between deoxyribose and a nitrogenous base
C) A phosphodiester bond between the 3'- and 5'-hydroxyl groups of adjacent deoxyribose residues
D) A phosphodiester bond between the 2'- and 5'-hydroxyl groups of adjacent deoxyribose residues
E) None of the above are correct.
28. Members of the lipid category include:
A) cholesterol B) palmitate C) glucose

D) A and B

E) A, B and C

29. The synthesis of glucose-6-phosphate in the cell is carried out by the following reaction: glucose + ATP <-->
glucose-6-phosphate + ADP. If the G of the hydrolysis of ATP is -30.5 kJ/mol and the G of the
phosphorylation of glucose is 13.8 kJ/mol, what is the G of the overall reaction?
A) +44.3 B) -44.3 C) +16.7 D) -16.7 E) none of the above
30. What is the pH of a 2 x 10-10 M solution of HCl?
A) 9.7 B) 10 C) 7.0 D) 4.3 E) none of the above
31. Which of the following would NOT form a suitable buffer?
A) Acetic acid/acetate
D)
B) Carbonic acid/bicarbonate
E)
C) Bicarbonate/carbonate

Hydrochloric acid/Chloride
Phosphoric acid/dihydrogen phosphate

32. Which makes the greatest contribution to the over all stability of DNA
A) hydrogen bonds B) ionic bonds C) base stacking D) A and B

E) none of the above

Section II: 50 points (2 points each)

33. You wish to prepare 0.5 L of 0.2 M phosphate buffer at pH 7.7. Which is the relevant equation and pKa?
A) H3PO4 <---> H2PO4-1+ H+, pKa 2.2
C) H2PO4-1 <---> HPO4-2 + H+, pKa 6.8
B) HPO4-2 <---> PO4-3 + H+, pKa 12.4
D) none of the above
34. Which of the following amino acids would be the best for buffering near neutral pH?
A) Glutamic acid B) Histidine C) Tyrosine D) Lysine E) Arginine
35. What is the net charge on the following molecule at pH 9.5? Table of pK values on exam cover.
Ala-Cys-Lys-Arg-Glu-Gln-Gly-Val-Tyr-Pro
A) -2 B) -1 C) 0 D) +1 E) +2
36. Calculate the pH of 500 mL of water to which 15 mL of 1.0 M KOH has been added.
A) 1.54 B) 12.5 C) 15.5 D) -1.54 E) 5.5
37. You have a short piece of synthetic RNA that you want to use as a probe to identify a gene in a sample of DNA.
The RNA probe has a tendency to hybridize with sequences that are only weakly complementary. Should you
increase or decrease the temperature to improve your chances of tagging the correct sequence?
A) Increase B) Decrease
38. Place the following steps of the myosin-actin reaction cycle in the correct order (assume one cycle has just
finished):
1. Myosin binds to actin
2. Hydrolysis of ATP, myosin lever rotates, increases affinity of myosin for actin
3. Pi and ADP release, lever returns to original position, thin filament moves relative to thick filament
4. ATP binds to myosin head, releases actin
A) 2, 4, 1, 3 B) 2, 4, 3, 1 C) 4, 2, 1, 3 D) 3, 2, 4, 1 E) 1, 2, 3, 4 F) none of the above
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39. Which of the following ranks the amino acids correctly from most to least soluble?
A) Phe > Ile > Trp > Ser > His > Asp
D) Asp > His > Ser > Trp > Ile > Phe
B) His > Asp > Ser > Ile > Trp > Phe
E) His > Asp > Ser > Ile > Phe > Trp
C) Asp > His > Ser > Ile > Trp > Phe
40. Which of the following would make the best buffer solution when combined together?
A) 6M NaC2H3O2 , H2O, 1M HC2H3O2
D) H2O, 1M HC2H3O2, 1M NaC2H3O2
B) H2O, 1M HC2H3O2
E) H2O, 1M HC2H3O2, 1M NaOH
C) H2O, 1M NaOH, 1M H2SO4
41. A rapidly growing microtubule will contain more
A) ATP at the (+) end.
B) ATP at the (-) end.
C) ADP at the (+) end.
D) ADP at the (-) end.

E)
F)
G)
H)

GTP at the (+) end.

GTP at the (-) end.
GDP at the (+) end.
GDP at the (-) end.

42. The Bohr effect on hemoglobin is:

A) the increase in oxygen affinity in the presence of excess heme
B) the decrease in oxygen affinity in the presence of dissolved CO2
C) the decrease in oxygen affinity in the presence of 2,3-bisphophoglycerate
D) the increase in oxygen affinity in the presence of carbon monoxide
E) none of the above
43. 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) It is defined as that oxygen partial pressure at which half of the oxygen binding sites are occupied.
C) It is a measure of the affinity of myoglobin for oxygen.
D) If Y > K, then myoglobin is less than 50% saturated with oxygen.
E) It is the value of pO2 at which Y = 0.5.
44. You add 2.0 mL of 1 M HCl to 1 L of 0.1 M Hepes buffer, pH 8.0 (pKa 7.6). Which is the correct statement?
A) The amount of conjugate base increases by 0.002 mole and the acid decreases by 0.002 mole
B) The amount of acid increases by 0.002 mole and the conjugate base decreases by 0.002 mole
C) The amount of acid and conjugate base both increase by 0.002 mole
D) The amount of acid and conjugate base both decrease by 0.002 mole
E) none of the above
45. Which of the following deoxyoligonucleotides will hybridize with a DNA
containing the sequence (5') AGACTGGTC (3')?
A) (5')TCTGACCAG (3')
D) (5')GACCAGTCT(3')
B) (5')GAGTCAACT(3')
E) (5')TCTGGATCT(3')
C) (5')CTCATTGAG(3')
F) none of the above
46. A triple helix is the right-handed helical structure formed by three left-handed helical polypeptide chains in
____________.
A) myosin B) collagen C) kinesin D) keratin E) none of the above
47. Which of the following biomolecules always contains a building block of one of the other 4 biomolecules?
A) Amino acid B) Monosaccharide C) Nucleotide D) Lipid E) none of the above

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48. What factor(s) limit(s) the conformation of the protein backbone?

A) double-bond character of the C-N bond
D) A and B
B) steric strain limitations
E) A, B, and C
C) hydrogenbonding interactions
49. Which of the following molecules would form a micelle?
A) NaCl B) CH3COOH C) CH3CH2CH2CH2CH2CH3

D) H3PO4

E) CH3(CH2)10COO-Na+

50. Based on the following Tm values, what can be said about the these two strands of DNA? Tm values (C): Strand
A = 80 Strand B = 100
A) Strand A has a higher percentage of adenine bases.
B) Strand B has a higher percentage cytosine bases.
C) Strand B has stronger stacking interactions (van der Waals).
D) All of the above
51. A polypeptide has a high pI value. Which of the following amino acids are likely to be present?
A) Glycine B) Serine C) Valine D) Aspartic acid E) Arginine
52. Of the following amino acids, which one is NOT hydrophobic.
A) Lys B) Leu C) Met D) Val E) Ala
53. Which of the tripeptides below has the largest number of polar R groups?
A) Tyr-Lys-Met B) Gly-Pro-Arg C) Asp-Trp-Phe D) Asp-His-Glu

E) Leu-Gln-Ser

54. Which of the following is NOT true about peptide bonds?

A) They can be broken by proteases.
B) Water is released when they are formed.
C) They can be broken by a reducing reagent such as 2-mercaptoethanol.
D) They have partial double bond character.
E) They are found along the "backbone" of a protein.
55. You are performing site-directed mutagenesis to test predictions about which residues are essential for a protein's
function. Which of each pair of amino acid substitutions listed below would you expect to disrupt protein function
the most?
A) Val replaced by Ala
D) Lys replaced by Arg
B) Pro replaced by His
E) none of the above
C) Gln replaced by Asn
56. When pO2=15 torr, what's the myoglobin's fractional saturation? (K = 2.8 torr)
A) 0.65 B) 0.58 C) 0.84 D) none are correct
57. Which of the four primary alcohols in the table below would be the best solvent for ammonium ions?

A) 1-butanol

B) 1-propanol

C) ethanol

D) methanol

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Section III: 18 points (3 points each)

58. Biochemists sometimes link a recombinant (cloned) protein to a small fluorescent protein known as GFP. The
fluorophore of GFP is a derivative of three consecutive amino acids that undergo cyclization of the polypeptide
chain and an oxidation. Using the structure below, identify: 1) the three amino acid residues and 2) the bond that
results from oxidation.

A)
B)
C)

Met-Tyr-Ala; c
Ser-Tyr-Gly; a
Ser-Phe-Gly; c

D)
E)
F)

Ser-Tyr-Gly; b
Ser-Phe-Gly; a
Met-Tyr-Ala; b

59. You have a mixture of 3 proteins, listed in the table below with their relevant properties. You are interested in
isolating ferrocytochrome using ion exchange chromatography with carboxymethylcellulose (CM) resin. Given
the values in the table below: 1) what pH would you use in order to ensure that ferrocytochrome protein binds to
the column and that the others do not? Assume that your efforts are successful -- 2) how will you elute the
ferrocytochrome from the column? Choose the correct conditions from the list below.
Protein
pI
alcohol dehydrogenase
6.8
ferrocytochrome
10.0
hexokinase
4.9
A) 1) Initial pH = 10.0; 2) lower pH below 10
B) 1) Initial pH = 8.0; 2) raise pH to 10
C) 1) Initial pH = 11; 2) lower pH to below 10

D)
E)

1) Initial pH = 4; 2) raise pH to 10
1) Initial pH = 6; 2) raise pH to 10

Use the following to answer questions 60-61:

While most human beings are able to hold their breath for only a minute or two, other species are able to stay
under water for much longer periods of time. For example deep sea-diving mammals, such as whales and seals,
are able to stay under water for long periods of time because their muscles contain many-fold higher
concentrations of myoglobin than humans. Crocodiles are also able to stay submerged for periods of time
exceeding one hour, which allows the crocodile to kill small animals by drowning them. However, the crocodile
does not have large amounts of myoglobin in its muscle, as the deep sea-diving mammals. In 1995, Nagai and
colleagues suggested that bicarbonate (HCO3-) binds to hemoglobin to promote the dissociation of oxygen.
60. The researchers decided to modify human hemoglobin to be more like crocodile hemoglobin. They identified 3
amino acid residues that most likely contacted the bicarbonate directly and these were located at the alpha/beta
dimer interface. These amino acid differences are most likely to affect:
A) The transition from oxy to deoxy state when bicarbonate binds
B) Prevent allosteric communication between the subunits
C) The formation of alpha helices around the heme group
D) The overall 3D structure of the Hb such that bicarbonate binding favors the oxy state
E) none of the above
F) all of the above
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61. Consider the hypothesis that bicarbonate serves as an allosteric modulator of oxygen binding in crocodiles. What
would be the source of bicarbonate in crocodile tissues while submerged in water?
A) CO2 is produced by metabolic processes and forms carbonic acid.
B) Carbonic acid rapidly dissociates to form protons and bicarbonate in the presence of carbonic anhydrase.
C) CO2 comes the atmosphere and is held in the crocodile lungs.
D) A and B
E) B and C
F) all of the above
62. What amount of 0.1 M NaH2PO4 and 0.1 M Na2HPO4 would be required to make 0.5 L of 0.1 M, pH 7.2
phosphate buffer (pKa 6.8)
A) 418 mL 0.1 M NaH2PO4 and 82 mL 0.1 M Na2HPO4
B) 334 mL 0.1 M NaH2PO4 and 166 mL 0.1 M Na2HPO4
C) 143 mL 0.1 M Na2HPO4 and 357 mL 0.1 M NaH2PO4
D) 400 mL 0.1 M NaH2PO4 and 100 mL 0.1 M Na2HPO4
E) 100 mL 0.1 M NaH2PO4 and 400 mL 0.1 M Na2HPO4
F) 357 mL 0.1 M Na2HPO4 and 143 mL 0.1 M NaH2PO4
63. The oxygen-binding curves for normal hemaglobin (Hb A) and a mutant hemoglobin (Hb Great Lakes) are shown
in the figure below. Which of the two hemoglobins: 1) has a higher affinity for oxygen when pO2 = 20 torr; and
2) is most efficient at delivering oxygen from arterial blood (pO2 = 75 torr) to active muscle (pO2 = 20 torr)?

A)
B)
C)
D)

1) Hb A; 2) Hb A
1) Hb A; 2) Hb Great Lakes
1) Hb Great Lakes; 2) Hb A
1) Hb Great Lakes; 2) Hb Great Lakes

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E)
F)
G)
H)

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1) same affinity; 2) Hb A
1) same affinity; 2) Hb Great Lakes
1) Hb Great Lakes; 2) same efficiency
1) Hb A; 2) same efficiency

Answer Key
1.
2.
3.
4.
5.
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52.
53.

E
D
F
A
C
G
A
C
B
D
B
A
A
C
B
B
D
A
B
B
B
D
C
C
B
B
C
D
D
C
D
C
C
B
B
B
A
C
D
D
E
B
D
B
D
B
C
E
E
D
E
A
D
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54.
55.
56.
57.
58.
59.
60.
61.
62.
63.

C
B
C
D
B
B
A
D
F
C

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