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CH 369

Exam 1

September 24, 2014

Name: __________________________________________ eID ________________

Section I (20 points): 1 point each


1. Which of the molecules below contains a phosphodiester group?

A) (a) only
B) (b) only
C) (c) only

D) (b) and (c)


E) None of the above

2. In gel filtration the smallest proteins elute first and the largest elute last.
A) True
B) False
3. What is unique about the nature of a low-barrier H-bond as compared to a typical H-bond?
A) The H-bond forms between 2 electronegative elements.
B) Only an H nucleus is small enough to approach the lone pair electron cloud.
C) The length of the H-bond is shorter and therefore stronger.
D) A low-barrier H-bond results in less energy stabilization than in a typical H-bond.
4. 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
Scrambled version A

Page 1

5. Which of the following is NOT a common component of biomolecules?


A) Carbon
B) Hydrogen
C) Oxygen
D) Nitrogen

E) Chlorine

6. Which of the following are typical hydrogen bond interactions?


A) N!H, H!H, S!H, H!C
D) N!H, S!H, H!Si
B) N!H, O!H, S!H
E) none of the above
C) O!H, S!H, C!O
7. Since the peptide bond has partial double bond character, the atoms involved in the peptide bond are
nonpolar
A) True
B) False
8. -helix or -sheet relates to
A) primary structure
B) secondary structure

C) tertiary structure
D) quaternary structure

9. Which of the following would represent the reaction coordinate for a two-step reaction with an initial slow
step?

A) A

B) B

10. 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
D) complementary
B) stereospecificity
E) none are correct
C) denaturation
11. What is the conjugate base of the acid, HC2 O4 -?
A) H2 C2 O4

B) C2 O4 2-

C) HC2 O5 -

12. Which of the following compounds is amphipathic?


A) H2 O
D) CH3 CH2 CH2 CH2 COOH
B) CH3 CH2 CH2 CH2 CH3
E) Both A and D are correct.
C) HOOCCOOH
13. Which of the following is NOT a class of amino acid?
A) Nonpolar and neutral
D) Basic
B) Polar and neutral
E) Asymmetric
C) Acidic

Scrambled version A

Page 2

14. Which of the following amino acids is capable of participating in acid/base catalysis?
A) Thr
B) Arg
C) Met
D) Asp
E) Gln
15. Enzymes enhance the rates for slow reactions but are not needed for fast reactions.
A) True
B) False
16. In a micelle or bilayer, the surrounding water is in contact with the more _____ portion of the amphiphilic
molecule.
A) oxidized
B) reduced
C) polar
D) nonpolar
17. What are the major types of biological polymers?
A) amino acids, nucleotides, sugars
B) proteins, lipids and cholesterol
C) proteins, nucleic acids and polysaccharides

D) nucleic acids, proteins and lipids


E) none of the above

18. The heme found in myoglobin is a:


A) domain
B) prosthetic group
C) zinc finger

D) peptide
E) none of the above

19. The most recently added actin subunits in a microfilament contain bound ADP.
A) True
B) False
20. F-actin and G-actin refer to the polymeric or monomeric state of actin respectively.
A) True
B) False
Section II (62 points): 2 points each
21. In the developing fetus, fetal hemoglobin (Hb F) is synthesized beginning at the third month of gestation
and continuing until birth. After the baby is born, the concentration of Hb F declines and is replaced with
adult hemoglobin (Hb A) as synthesis of the chain declines and synthesis of the chain increases. By the
time the baby is six months old, 98% of its hemoglobin is Hb A. In the graph below, which curve
represents fetal hemoglobin?

A) A

B) B

Scrambled version A

Page 3

22. At pH ___, the pentapeptide Ala-Glu-His-Val-Cys would contain two positively charged groups and one
negatively charged group.
A) 1
B) 3
C) 5
D) 7
E) 9
23. Which of the following biomolecules always contains a building block of one of the other 4 biomolecules?
A) Amino acid
D) Lipid
B) Monosaccharide
E) none of the above
C) Nucleotide
24. What features/aspects of collagen are important in its structure
A) absence of proline
D) cross links of cysteine
B) left handed helical structure
E) none of the above
C) low glycine content
B or E accepted
25. Which of the following molecules would form a micelle?
A) NaCl
D) H3 PO4
B) CH3 COOH
E) CH3 (CH2 )1 0COO-Na+
C) CH3 CH2 CH2 CH2 CH2 CH3
26. Which of the tripeptides below has the largest number of polar R groups?
A) Tyr-Lys-Met B) Gly-Pro-Arg
C) Asp-Ser-Gln
D) Asp-His-Pro

E) Leu-Gln-Ser

27. H3 O+ is the strongest acid that can exist in a biological system.


A) True
B) False
28. A coupled reaction always involves
A) oxidation and reduction.
B) esterification.
C) reactions that produce energy and reactions that consume energy.
D) ATP as a reactant.
E) Both B and D must be true.
29. Identify the amino acid below.

A) H

B) F

C) E

Scrambled version A

D) W

Page 4

E) P

30. Given the reaction below, tell whether the reactant is being oxidized or reduced.

A) Oxidized

B) Reduced

31. How many hydrogen bond acceptor GROUPS are present in the following molecule?

A) 1

B) 2

C) 3

D) 4

E) 5

32. 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
33. Under certain conditions, peptide bond formation is more thermodynamically favorable than peptide bond
hydrolysis. Would you expect chymotrypsin to catalyze peptide bond formation?
A) Yes
B) No
C) Cannot be determined
34. Which of the following amino acids is affected by oxidation/reduction?
A) M
B) S
C) C
D) L

E) D

35. Mass spectrometry is highly accurate and can therefore distinguish between the amino acid Ile and Leu.
A) True
B) False
36. The reaction catalyzed by hexokinase is given below. To which class does the enzyme belong?

A) lyase
B) ligase
C) transferase

D) oxidoreductase
E) hydrolase

37. The lysozyme molecule contains regions of helical structure. This statement refers to the _________
structure of the protein.
A) primary
B) secondary
C) tertiary
D) quaternary
Scrambled version A

Page 5

38. What is the final pH when 100 mL of 0.5 M HCl is added to 900 mL of water?
A) 1.3
D) 0.3
B) 2.3
E) none of the above
C) 13.0
39. How would chymotrypsin's catalytic triad be affected by extremely low pH values (assuming that the rest
of the protein structure remained intact)?
A) At very low pH values, His would be deprotonated and therefore able to from a hydrogen bond with
Ser.
B) At very low pH values, His would be protonated and therefore able to from a hydrogen bond with Ser.
C) At very low pH values, His would be deprotonated and therefore unable to from a hydrogen bond
with Ser.
D) At very low pH values, His would be protonated and therefore unable to from a hydrogen bond with
Ser.
40. Which of the following could form a covalent bond with acyl groups?
A) Asp and Glu
B) Lys and Arg
C) Cys and Ser
D) Tyr

Thrown out
E) C and D

41. Which of the following would NOT form a suitable buffer?


A) Acetic acid/acetate
D) Hydrochloric acid/Chloride
B) Carbonic acid/bicarbonate
E) Phosphoric acid/dihydrogen phosphate
C) Bicarbonate/carbonate
42. When pO2 =15 torr, what is the fractional saturation of myoglobin? (p5 0 = 2.8 torr)
A) 0.65
B) 0.58
C) 0.84
D) none are correct
43. The sodium acetate/acetic acid buffer is 0.1 molar in sodium acetate and 0.5 molar in acetic acid. What is
the concentration of the buffer?
A) 0.1 molar
B) 0.5 molar
C) 0.6 molar
D) 0.4 molar
E) Either A or B depending on whether acid or base is being added to the buffer.
44. A patient suffers from premature zymogen activation, so that the pancreatic enzymes are activated in the
pancreas rather than the small intestine -- causing damage to the pancreas. Which of the following would
be the most effective in preventing these effects?
A) chymotrypsin inhibitor
B) trypsin inhibitor
C) elastase inhibitor
45. In a collagen chain, the most common repeating triplet comprises all of the following accept
A) glycine
D) lysine
B) proline
E) none of the above
C) hydroxyproline

Scrambled version A

Page 6

46. The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst
because:
A) in the physiological pH range both H+ and OH are present at high concentrations.
B) in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.
C) one guanidino group is protonated, and the other is deprotonated at physiological pH.
D) the imidazole group is a strong reducing agent at physiological pH.
E) the sulfur atoms in the ring can either gain or lose a proton at physiological pH.
47. Assuming a temperature of 25o C and an entropy change of +75 J/K/ mol, the enthalpy change for a G
value of -11.0 kJ/mol is
A) + 15.2 kJ/mol
D) - 17.4 kJ/mol
B) + 22.5 kJ/mol
E) none of the above
C) + 11.3 kJ/mol
48. Ser can most likely be conservatively substituted by
A) Leu
D) Val
B) Met
E) none of the above
C) Thr
49. The height of the activation barrier determines:
A) The free energy change of the reaction.
B) The rate of the reaction.
C) The probability that the reaction will be spontaneous.
D) A and C
E) A, B and C
50. Protein structure is strongly influenced by
A) hydrophilic amino acids that want to be in the core of the protein to stabilize it.
B) the hydrophobic effect, that is the protein puts hydrophobic amino acids into the protein core to
shield them from the aqueous environment.
C) the presence of multiple loops on the protein surface that bind water and ions to make the protein
more hydrophobic.
D) all of the above
E) none of the agove
51. The power stroke in muscle contraction is associated with:
A) dissociation of ADP from the ATPase
D) the binding of ATP to ATPase
B) binding of myosin to actin
E) none of the above
C) the hydrolysis of ATP
Section III (18 points): 3 points each

Scrambled version A

Page 7

52. For the reaction in which reactant A is converted to product B, tell whether the process is favorable at (a)
4o C and (b) 37o C, given the information below.

A) Favorable at both (a) and (b)


B) Unfavorable at both (a) and (b)
C) Favorable at (a) but unfavorable at (b)

D) Unfavorable at (a) but favorable at (b)


E) No way to tell

53. Lysozyme catalyzes the hydrolysis of a polysaccharide component of bacterial cell walls. The damaged
bacteria subsequently lyse (rupture). Part of lysozyme's mechanism is shown below. The enzyme
catalyzes cleavage of a bond between two sugar residues (represented by hexagons). Catalysis involves the
side chains of Glu 35 and Asp 52. One of the residues has a pK of 4.5; the other has a pK of 5.9. Assign
the given pK values to Glu 35 and Asp 52. Would lysozyme be active at pH 8.0?

A)
B)
C)
D)

Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be active at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be active at pH 8.0.

54. Which of the following correctly describes the sequence of events in the myosin-actin cycle?
A) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
B) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
C) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
D) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
E) myosin release from actin, myosin binds to another actin subunit, ATP binds to myosin, stretched
myosin returns to original conformation, release of Pi and ADP

Scrambled version A

Page 8

55. Hemoglobin is 50% saturated with oxygen when pO2 = 26 torr. If hemoglobin exhibited hyperbolic binding
(as myoglobin does) with 50% saturation at 26 torr, what would be the fractional saturation when (1) pO2
= 30; and (2) 100 torr? (3)In this case, what would be the effect on the oxygen saturation of Hb in the
lungs?
A) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would be less than 100% saturated with O2
B) (1) 0.79 torr; (2) 0.54 torr; (3) Hb would still be 100% saturated with O2
C) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would still be 100% saturated with O2
D) (1) 0.46 torr; (2) 0.21 torr; (3) Hb would still be 100% saturated with O2
E) (1) 0.54 torr; (2) 7.9 torr; (3) Hb would still be 100% saturated with O2
56. What amount of 0.1 M NaH2 PO4 and 0.1 M Na2 HPO4 would be required to make 0.5 L of 0.1 M, pH 7.2
phosphate buffer (pK 6.82)?
A) 418 mL 0.1 M NaH2 PO4 and 82 mL 0.1 M Na2 HPO4
B) 150 mL 0.1 M Na2 HPO4 and 350 mL 0.1 M NaH2 PO4
C) 400 mL 0.1 M NaH2 PO4 and 100 mL 0.1 M Na2 HPO4
D) 100 mL 0.1 M NaH2 PO4 and 400 mL 0.1 M Na2 HPO4
E) 353 mL 0.1 M Na2 HPO4 and 147 mL 0.1 M NaH2 PO4
57. You have a mixture of 3 proteins, listed in the table below with their relevant properties. You are
interested in isolating aspartate transaminase using ion exchange chromatography with DEAE resin. Given
the values in the table below: 1) what pH would you use in order to ensure that aspartate transaminase
protein binds to the column and that the others do not? Assume that your efforts are successful -- 2) how
will you elute aspartate transaminase from the column? Choose the correct conditions from the list below.
Protein
Aspartate transcarbamylase
Myoglobin
Aspartate transaminase

pI
9.8
7.0
5.0

A) 1) Initial pH = 10.0; 2) lower pH to 6


B) 1) Initial pH = 8; 2) raise pH to 10
C) 1) Initial pH = 4; 2) raise pH to 5 or higher

D) 1) Initial pH = 6; 2) lower pH to 5 or less


E) 1) Initial pH = 8; 2) lower pH to 7

Scrambled version A

Page 9

Answer Key - Exam1Fa14


1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.

E
B
C
B
E
B
B
B
A
A
B
D
E
D
B
C
C
B
B
A
A
B
C
E or B
E
C
A
C
A
A
B
D
A
C
B
C
B
A
D
C
D
C
C
B
Scrambled version A

Page 10

45.
46.
47.
48.
49.
50.
51.
52.
53.
54.
55.
56.
57.

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

Scrambled version A

Page 11

CH 369

Exam 1

September 24, 2014

Name: __________________________________________ eID ________________

Section I (20 points): 1 point each


1. Which of the molecules below contains a phosphodiester group?

A) (a) only
B) (b) only
C) (c) only

D) (b) and (c)


E) None of the above

2. In a micelle or bilayer, the surrounding water is in contact with the more _____ portion of the amphiphilic
molecule.
A) oxidized
B) reduced
C) polar
D) nonpolar
3. -helix or -sheet relates to
A) primary structure
B) secondary structure
4. The heme found in myoglobin is a:
A) domain
B) prosthetic group
C) zinc finger

C) tertiary structure
D) quaternary structure

D) peptide
E) none of the above

Scrambled version B

Page 1

5. Which of the following is NOT a class of amino acid?


A) Nonpolar and neutral
D) Basic
B) Polar and neutral
E) Asymmetric
C) Acidic
6. What are the major types of biological polymers?
A) amino acids, nucleotides, sugars
B) proteins, lipids and cholesterol
C) proteins, nucleic acids and polysaccharides

D) nucleic acids, proteins and lipids


E) none of the above

7. Which of the following would represent the reaction coordinate for a two-step reaction with an initial slow
step?

A) A

B) B

8. In gel filtration the smallest proteins elute first and the largest elute last.
A) True
B) False
9. Which of the following amino acids is capable of participating in acid/base catalysis?
A) Thr
B) Arg
C) Met
D) Asp
E) Gln
10. Which of the following are typical hydrogen bond interactions?
A) N!H, H!H, S!H, H!C
D) N!H, S!H, H!Si
B) N!H, O!H, S!H
E) none of the above
C) O!H, S!H, C!O
11. What is unique about the nature of a low-barrier H-bond as compared to a typical H-bond?
A) The H-bond forms between 2 electronegative elements.
B) Only an H nucleus is small enough to approach the lone pair electron cloud.
C) The length of the H-bond is shorter and therefore stronger.
D) A low-barrier H-bond results in less energy stabilization than in a typical H-bond.
12. F-actin and G-actin refer to the polymeric or monomeric state of actin respectively.
A) True
B) False
13. Which of the following is NOT a common component of biomolecules?
A) Carbon
B) Hydrogen
C) Oxygen
D) Nitrogen
14. The most recently added actin subunits in a microfilament contain bound ADP.
A) True
B) False

Scrambled version B

Page 2

E) Chlorine

15. What is the conjugate base of the acid, HC2 O4 -?


A) H2 C2 O4

B) C2 O4 2-

C) HC2 O5 -

16. Since the peptide bond has partial double bond character, the atoms involved in the peptide bond are
nonpolar
A) True
B) False
17. 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
18. 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
D) complementary
B) stereospecificity
E) none are correct
C) denaturation
19. Enzymes enhance the rates for slow reactions but are not needed for fast reactions.
A) True
B) False
20. Which of the following compounds is amphipathic?
A) H2 O
D) CH3 CH2 CH2 CH2 COOH
B) CH3 CH2 CH2 CH2 CH3
E) Both A and D are correct.
C) HOOCCOOH
Section II (62 points): 2 points each
21. H3 O+ is the strongest acid that can exist in a biological system.
A) True
B) False
22. What features/aspects of collagen are important in its structure
A) absence of proline
D) cross links of cysteine
B) left handed helical structure
E) none of the above
C) low glycine content
B or E accepted
23. Identify the amino acid below.

A) H

B) F

C) E

Scrambled version B

D) W

Page 3

E) P

24. 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
25. Mass spectrometry is highly accurate and can therefore distinguish between the amino acid Ile and Leu.
A) True
B) False
26. What is the final pH when 100 mL of 0.5 M HCl is added to 900 mL of water?
A) 1.3
D) 0.3
B) 2.3
E) none of the above
C) 13.0
27. Which of the following amino acids is affected by oxidation/reduction?
A) M
B) S
C) C
D) L

E) D

28. Which of the tripeptides below has the largest number of polar R groups?
A) Tyr-Lys-Met B) Gly-Pro-Arg
C) Asp-Ser-Gln
D) Asp-His-Pro

E) Leu-Gln-Ser

29. Which of the following would NOT form a suitable buffer?


A) Acetic acid/acetate
D) Hydrochloric acid/Chloride
B) Carbonic acid/bicarbonate
E) Phosphoric acid/dihydrogen phosphate
C) Bicarbonate/carbonate
30. When pO2 =15 torr, what is the fractional saturation of myoglobin? (p5 0 = 2.8 torr)
A) 0.65
B) 0.58
C) 0.84
D) none are correct
31. How would chymotrypsin's catalytic triad be affected by extremely low pH values (assuming that the rest
of the protein structure remained intact)?
A) At very low pH values, His would be deprotonated and therefore able to from a hydrogen bond with
Ser.
B) At very low pH values, His would be protonated and therefore able to from a hydrogen bond with Ser.
C) At very low pH values, His would be deprotonated and therefore unable to from a hydrogen bond
with Ser.
D) At very low pH values, His would be protonated and therefore unable to from a hydrogen bond with
Ser.
32. The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst
because:
A) in the physiological pH range both H+ and OH are present at high concentrations.
B) in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.
C) one guanidino group is protonated, and the other is deprotonated at physiological pH.
D) the imidazole group is a strong reducing agent at physiological pH.
E) the sulfur atoms in the ring can either gain or lose a proton at physiological pH.
Scrambled version B

Page 4

33. Ser can most likely be conservatively substituted by


A) Leu
D) Val
B) Met
E) none of the above
C) Thr
34. Under certain conditions, peptide bond formation is more thermodynamically favorable than peptide bond
hydrolysis. Would you expect chymotrypsin to catalyze peptide bond formation?
A) Yes
B) No
C) Cannot be determined
35. Which of the following molecules would form a micelle?
A) NaCl
D) H3 PO4
B) CH3 COOH
E) CH3 (CH2 )1 0COO-Na+
C) CH3 CH2 CH2 CH2 CH2 CH3
36. The sodium acetate/acetic acid buffer is 0.1 molar in sodium acetate and 0.5 molar in acetic acid. What is
the concentration of the buffer?
A) 0.1 molar
B) 0.5 molar
C) 0.6 molar
D) 0.4 molar
E) Either A or B depending on whether acid or base is being added to the buffer.
37. Which of the following biomolecules always contains a building block of one of the other 4 biomolecules?
A) Amino acid
D) Lipid
B) Monosaccharide
E) none of the above
C) Nucleotide
38. Given the reaction below, tell whether the reactant is being oxidized or reduced.

A) Oxidized

B) Reduced

39. A coupled reaction always involves


A) oxidation and reduction.
B) esterification.
C) reactions that produce energy and reactions that consume energy.
D) ATP as a reactant.
E) Both B and D must be true.

Scrambled version B

Page 5

40. Protein structure is strongly influenced by


A) hydrophilic amino acids that want to be in the core of the protein to stabilize it.
B) the hydrophobic effect, that is the protein puts hydrophobic amino acids into the protein core to
shield them from the aqueous environment.
C) the presence of multiple loops on the protein surface that bind water and ions to make the protein
more hydrophobic.
D) all of the above
E) none of the agove
41. How many hydrogen bond acceptor GROUPS are present in the following molecule?

A) 1

B) 2

C) 3

D) 4

E) 5

42. The reaction catalyzed by hexokinase is given below. To which class does the enzyme belong?

A) lyase
B) ligase
C) transferase

D) oxidoreductase
E) hydrolase

43. The power stroke in muscle contraction is associated with:


A) dissociation of ADP from the ATPase
D) the binding of ATP to ATPase
B) binding of myosin to actin
E) none of the above
C) the hydrolysis of ATP
44. In a collagen chain, the most common repeating triplet comprises all of the following accept
A) glycine
D) lysine
B) proline
E) none of the above
C) hydroxyproline

Scrambled version B

Page 6

45. In the developing fetus, fetal hemoglobin (Hb F) is synthesized beginning at the third month of gestation
and continuing until birth. After the baby is born, the concentration of Hb F declines and is replaced with
adult hemoglobin (Hb A) as synthesis of the chain declines and synthesis of the chain increases. By the
time the baby is six months old, 98% of its hemoglobin is Hb A. In the graph below, which curve
represents fetal hemoglobin?

A) A

B) B

46. The height of the activation barrier determines:


A) The free energy change of the reaction.
B) The rate of the reaction.
C) The probability that the reaction will be spontaneous.
D) A and C
E) A, B and C
47. At pH ___, the pentapeptide Ala-Glu-His-Val-Cys would contain two positively charged groups and one
negatively charged group.
A) 1
B) 3
C) 5
D) 7
E) 9
48. The lysozyme molecule contains regions of helical structure. This statement refers to the _________
structure of the protein.
A) primary
B) secondary
C) tertiary
D) quaternary
49. Assuming a temperature of 25o C and an entropy change of +75 J/K/ mol, the enthalpy change for a G
value of -11.0 kJ/mol is
A) + 15.2 kJ/mol
D) - 17.4 kJ/mol
B) + 22.5 kJ/mol
E) none of the above
C) + 11.3 kJ/mol
50. A patient suffers from premature zymogen activation, so that the pancreatic enzymes are activated in the
pancreas rather than the small intestine -- causing damage to the pancreas. Which of the following would
be the most effective in preventing these effects?
A) chymotrypsin inhibitor
B) trypsin inhibitor
C) elastase inhibitor
Thrown out
51. Which of the following could form a covalent bond with acyl groups?
A) Asp and Glu
B) Lys and Arg
C) Cys and Ser
D) Tyr
E) C and D

Scrambled version B

Page 7

Section III (18 points): 3 points each


52. Which of the following correctly describes the sequence of events in the myosin-actin cycle?
A) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
B) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
C) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
D) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
E) myosin release from actin, myosin binds to another actin subunit, ATP binds to myosin, stretched
myosin returns to original conformation, release of Pi and ADP
53. Lysozyme catalyzes the hydrolysis of a polysaccharide component of bacterial cell walls. The damaged
bacteria subsequently lyse (rupture). Part of lysozyme's mechanism is shown below. The enzyme
catalyzes cleavage of a bond between two sugar residues (represented by hexagons). Catalysis involves the
side chains of Glu 35 and Asp 52. One of the residues has a pK of 4.5; the other has a pK of 5.9. Assign
the given pK values to Glu 35 and Asp 52. Would lysozyme be active at pH 8.0?

A)
B)
C)
D)

Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be active at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be active at pH 8.0.

54. For the reaction in which reactant A is converted to product B, tell whether the process is favorable at (a)
4o C and (b) 37o C, given the information below.

A) Favorable at both (a) and (b)


B) Unfavorable at both (a) and (b)
C) Favorable at (a) but unfavorable at (b)

D) Unfavorable at (a) but favorable at (b)


E) No way to tell

Scrambled version B

Page 8

55. You have a mixture of 3 proteins, listed in the table below with their relevant properties. You are
interested in isolating aspartate transaminase using ion exchange chromatography with DEAE resin. Given
the values in the table below: 1) what pH would you use in order to ensure that aspartate transaminase
protein binds to the column and that the others do not? Assume that your efforts are successful -- 2) how
will you elute aspartate transaminase from the column? Choose the correct conditions from the list below.
Protein
Aspartate transcarbamylase
Myoglobin
Aspartate transaminase

pI
9.8
7.0
5.0

A) 1) Initial pH = 10.0; 2) lower pH to 6


B) 1) Initial pH = 8; 2) raise pH to 10
C) 1) Initial pH = 4; 2) raise pH to 5 or higher

D) 1) Initial pH = 6; 2) lower pH to 5 or less


E) 1) Initial pH = 8; 2) lower pH to 7

56. What amount of 0.1 M NaH2 PO4 and 0.1 M Na2 HPO4 would be required to make 0.5 L of 0.1 M, pH 7.2
phosphate buffer (pK 6.82)?
A) 418 mL 0.1 M NaH2 PO4 and 82 mL 0.1 M Na2 HPO4
B) 150 mL 0.1 M Na2 HPO4 and 350 mL 0.1 M NaH2 PO4
C) 400 mL 0.1 M NaH2 PO4 and 100 mL 0.1 M Na2 HPO4
D) 100 mL 0.1 M NaH2 PO4 and 400 mL 0.1 M Na2 HPO4
E) 353 mL 0.1 M Na2 HPO4 and 147 mL 0.1 M NaH2 PO4
57. Hemoglobin is 50% saturated with oxygen when pO2 = 26 torr. If hemoglobin exhibited hyperbolic binding
(as myoglobin does) with 50% saturation at 26 torr, what would be the fractional saturation when (1) pO2
= 30; and (2) 100 torr? (3)In this case, what would be the effect on the oxygen saturation of Hb in the
lungs?
A) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would be less than 100% saturated with O2
B) (1) 0.79 torr; (2) 0.54 torr; (3) Hb would still be 100% saturated with O2
C) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would still be 100% saturated with O2
D) (1) 0.46 torr; (2) 0.21 torr; (3) Hb would still be 100% saturated with O2
E) (1) 0.54 torr; (2) 7.9 torr; (3) Hb would still be 100% saturated with O2

Scrambled version B

Page 9

Answer Key - Exam1Fa14


1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.

E
C
B
B
E
C
A
B
D
B
C
A
E
B
B
B
B
A
B
D
A
E or B
A
D
B
A
C
C
D
C
D
B
C
A
E
C
C
A
C
B
B
C
A
D
Scrambled version B

Page 10

45.
46.
47.
48.
49.
50.
51.
52.
53.
54.
55.
56.
57.

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

Scrambled version B

Page 11

CH 369

Exam 1

September 24, 2014

Name: __________________________________________ eID ________________

Section I (20 points): 1 point each


1. Which of the molecules below contains a phosphodiester group?

A) (a) only
B) (b) only
C) (c) only

D) (b) and (c)


E) None of the above

2. 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
D) complementary
B) stereospecificity
E) none are correct
C) denaturation
3. The most recently added actin subunits in a microfilament contain bound ADP.
A) True
B) False
4. -helix or -sheet relates to
A) primary structure
B) secondary structure

C) tertiary structure
D) quaternary structure
Scrambled version C

Page 1

5. In gel filtration the smallest proteins elute first and the largest elute last.
A) True
B) False
6. Which of the following would represent the reaction coordinate for a two-step reaction with an initial slow
step?

A) A

B) B

7. Which of the following compounds is amphipathic?


A) H2 O
D) CH3 CH2 CH2 CH2 COOH
B) CH3 CH2 CH2 CH2 CH3
E) Both A and D are correct.
C) HOOCCOOH
8. In a micelle or bilayer, the surrounding water is in contact with the more _____ portion of the amphiphilic
molecule.
A) oxidized
B) reduced
C) polar
D) nonpolar
9. Since the peptide bond has partial double bond character, the atoms involved in the peptide bond are
nonpolar
A) True
B) False
10. Which of the following amino acids is capable of participating in acid/base catalysis?
A) Thr
B) Arg
C) Met
D) Asp
E) Gln
11. 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
12. The heme found in myoglobin is a:
A) domain
B) prosthetic group
C) zinc finger

D) peptide
E) none of the above

13. Which of the following are typical hydrogen bond interactions?


A) N!H, H!H, S!H, H!C
D) N!H, S!H, H!Si
B) N!H, O!H, S!H
E) none of the above
C) O!H, S!H, C!O

Scrambled version C

Page 2

14. Which of the following is NOT a class of amino acid?


A) Nonpolar and neutral
D) Basic
B) Polar and neutral
E) Asymmetric
C) Acidic
15. Enzymes enhance the rates for slow reactions but are not needed for fast reactions.
A) True
B) False
16. What is the conjugate base of the acid, HC2 O4 -?
A) H2 C2 O4

B) C2 O4 2-

17. What are the major types of biological polymers?


A) amino acids, nucleotides, sugars
B) proteins, lipids and cholesterol
C) proteins, nucleic acids and polysaccharides

C) HC2 O5 -

D) nucleic acids, proteins and lipids


E) none of the above

18. Which of the following is NOT a common component of biomolecules?


A) Carbon
B) Hydrogen
C) Oxygen
D) Nitrogen

E) Chlorine

19. What is unique about the nature of a low-barrier H-bond as compared to a typical H-bond?
A) The H-bond forms between 2 electronegative elements.
B) Only an H nucleus is small enough to approach the lone pair electron cloud.
C) The length of the H-bond is shorter and therefore stronger.
D) A low-barrier H-bond results in less energy stabilization than in a typical H-bond.
20. F-actin and G-actin refer to the polymeric or monomeric state of actin respectively.
A) True
B) False
Section II (62 points): 2 points each
21. How many hydrogen bond acceptor GROUPS are present in the following molecule?

A) 1

B) 2

C) 3

D) 4

E) 5

22. At pH ___, the pentapeptide Ala-Glu-His-Val-Cys would contain two positively charged groups and one
negatively charged group.
A) 1
B) 3
C) 5
D) 7
E) 9

Scrambled version C

Page 3

23. The imidazole side chain of histidine can function as either a general acid catalyst or a general base catalyst
because:
A) in the physiological pH range both H+ and OH are present at high concentrations.
B) in the physiological pH range, the nitrogen in the ring can be easily protonated/deprotonated.
C) one guanidino group is protonated, and the other is deprotonated at physiological pH.
D) the imidazole group is a strong reducing agent at physiological pH.
E) the sulfur atoms in the ring can either gain or lose a proton at physiological pH.
24. In the developing fetus, fetal hemoglobin (Hb F) is synthesized beginning at the third month of gestation
and continuing until birth. After the baby is born, the concentration of Hb F declines and is replaced with
adult hemoglobin (Hb A) as synthesis of the chain declines and synthesis of the chain increases. By the
time the baby is six months old, 98% of its hemoglobin is Hb A. In the graph below, which curve
represents fetal hemoglobin?

A) A

B) B

25. What is the final pH when 100 mL of 0.5 M HCl is added to 900 mL of water?
A) 1.3
D) 0.3
B) 2.3
E) none of the above
C) 13.0
26. How would chymotrypsin's catalytic triad be affected by extremely low pH values (assuming that the rest
of the protein structure remained intact)?
A) At very low pH values, His would be deprotonated and therefore able to from a hydrogen bond with
Ser.
B) At very low pH values, His would be protonated and therefore able to from a hydrogen bond with Ser.
C) At very low pH values, His would be deprotonated and therefore unable to from a hydrogen bond
with Ser.
D) At very low pH values, His would be protonated and therefore unable to from a hydrogen bond with
Ser.
27. Given the reaction below, tell whether the reactant is being oxidized or reduced.

A) Oxidized

B) Reduced
Scrambled version C

Page 4

28. Under certain conditions, peptide bond formation is more thermodynamically favorable than peptide bond
hydrolysis. Would you expect chymotrypsin to catalyze peptide bond formation?
A) Yes
B) No
C) Cannot be determined
29. Assuming a temperature of 25o C and an entropy change of +75 J/K/ mol, the enthalpy change for a G
value of -11.0 kJ/mol is
A) + 15.2 kJ/mol
D) - 17.4 kJ/mol
B) + 22.5 kJ/mol
E) none of the above
C) + 11.3 kJ/mol
30. In a collagen chain, the most common repeating triplet comprises all of the following accept
A) glycine
D) lysine
B) proline
E) none of the above
C) hydroxyproline
31. The sodium acetate/acetic acid buffer is 0.1 molar in sodium acetate and 0.5 molar in acetic acid. What is
the concentration of the buffer?
A) 0.1 molar
B) 0.5 molar
C) 0.6 molar
D) 0.4 molar
E) Either A or B depending on whether acid or base is being added to the buffer.
32. Which of the following would NOT form a suitable buffer?
A) Acetic acid/acetate
D) Hydrochloric acid/Chloride
B) Carbonic acid/bicarbonate
E) Phosphoric acid/dihydrogen phosphate
C) Bicarbonate/carbonate
33. H3 O+ is the strongest acid that can exist in a biological system.
A) True
B) False
34. The lysozyme molecule contains regions of helical structure. This statement refers to the _________
structure of the protein.
A) primary
B) secondary
C) tertiary
D) quaternary
35. Mass spectrometry is highly accurate and can therefore distinguish between the amino acid Ile and Leu.
A) True
B) False
36. Ser can most likely be conservatively substituted by
A) Leu
D) Val
B) Met
E) none of the above
C) Thr

Scrambled version C

Page 5

37. Which of the following molecules would form a micelle?


A) NaCl
D) H3 PO4
B) CH3 COOH
E) CH3 (CH2 )1 0COO-Na+
C) CH3 CH2 CH2 CH2 CH2 CH3
38. Identify the amino acid below.

A) H

B) F

C) E

D) W

E) P

39. The power stroke in muscle contraction is associated with:


A) dissociation of ADP from the ATPase
D) the binding of ATP to ATPase
B) binding of myosin to actin
E) none of the above
C) the hydrolysis of ATP
40. Protein structure is strongly influenced by
A) hydrophilic amino acids that want to be in the core of the protein to stabilize it.
B) the hydrophobic effect, that is the protein puts hydrophobic amino acids into the protein core to
shield them from the aqueous environment.
C) the presence of multiple loops on the protein surface that bind water and ions to make the protein
more hydrophobic.
D) all of the above
E) none of the agove
41. The height of the activation barrier determines:
A) The free energy change of the reaction.
B) The rate of the reaction.
C) The probability that the reaction will be spontaneous.
D) A and C
E) A, B and C
42. Which of the following amino acids is affected by oxidation/reduction?
A) M
B) S
C) C
D) L
43. What features/aspects of collagen are important in its structure
A) absence of proline
D) cross links of cysteine
B) left handed helical structure
E) none of the above
C) low glycine content
B or E accepted

Scrambled version C

Page 6

E) D

44. A coupled reaction always involves


A) oxidation and reduction.
B) esterification.
C) reactions that produce energy and reactions that consume energy.
D) ATP as a reactant.
E) Both B and D must be true.
45. When pO2 =15 torr, what is the fractional saturation of myoglobin? (p5 0 = 2.8 torr)
A) 0.65
B) 0.58
C) 0.84
D) none are correct
46. A patient suffers from premature zymogen activation, so that the pancreatic enzymes are activated in the
pancreas rather than the small intestine -- causing damage to the pancreas. Which of the following would
be the most effective in preventing these effects?
A) chymotrypsin inhibitor
B) trypsin inhibitor
C) elastase inhibitor
47. Which of the tripeptides below has the largest number of polar R groups?
A) Tyr-Lys-Met B) Gly-Pro-Arg
C) Asp-Ser-Gln
D) Asp-His-Pro

E) Leu-Gln-Ser

48. Which of the following could form a covalent bond with acyl groups? Thrown out
A) Asp and Glu
B) Lys and Arg
C) Cys and Ser
D) Tyr
E) C and D
49. 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
50. Which of the following biomolecules always contains a building block of one of the other 4 biomolecules?
A) Amino acid
D) Lipid
B) Monosaccharide
E) none of the above
C) Nucleotide
51. The reaction catalyzed by hexokinase is given below. To which class does the enzyme belong?

A) lyase
B) ligase
C) transferase

D) oxidoreductase
E) hydrolase

Section III (18 points): 3 points each

Scrambled version C

Page 7

52. Lysozyme catalyzes the hydrolysis of a polysaccharide component of bacterial cell walls. The damaged
bacteria subsequently lyse (rupture). Part of lysozyme's mechanism is shown below. The enzyme
catalyzes cleavage of a bond between two sugar residues (represented by hexagons). Catalysis involves the
side chains of Glu 35 and Asp 52. One of the residues has a pK of 4.5; the other has a pK of 5.9. Assign
the given pK values to Glu 35 and Asp 52. Would lysozyme be active at pH 8.0?

A)
B)
C)
D)

Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 4.5; Asp 52 has a pK of 5.9; Lysozyme would be active at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be inactive at pH 8.0.
Glu 35 has a pK of 5.9; Asp 52 has a pK of 4.5; Lysozyme would be active at pH 8.0.

53. For the reaction in which reactant A is converted to product B, tell whether the process is favorable at (a)
4o C and (b) 37o C, given the information below.

A) Favorable at both (a) and (b)


B) Unfavorable at both (a) and (b)
C) Favorable at (a) but unfavorable at (b)

D) Unfavorable at (a) but favorable at (b)


E) No way to tell

54. What amount of 0.1 M NaH2 PO4 and 0.1 M Na2 HPO4 would be required to make 0.5 L of 0.1 M, pH 7.2
phosphate buffer (pK 6.82)?
A) 418 mL 0.1 M NaH2 PO4 and 82 mL 0.1 M Na2 HPO4
B) 150 mL 0.1 M Na2 HPO4 and 350 mL 0.1 M NaH2 PO4
C) 400 mL 0.1 M NaH2 PO4 and 100 mL 0.1 M Na2 HPO4
D) 100 mL 0.1 M NaH2 PO4 and 400 mL 0.1 M Na2 HPO4
E) 353 mL 0.1 M Na2 HPO4 and 147 mL 0.1 M NaH2 PO4

Scrambled version C

Page 8

55. Which of the following correctly describes the sequence of events in the myosin-actin cycle?
A) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
B) myosin release from actin, ATP binds to myosin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
C) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, release of Pi
and ADP, stretched myosin returns to original conformation
D) ATP binds to myosin, myosin release from actin, myosin binds to another actin subunit, stretched
myosin returns to original conformation, release of Pi and ADP
E) myosin release from actin, myosin binds to another actin subunit, ATP binds to myosin, stretched
myosin returns to original conformation, release of Pi and ADP
56. Hemoglobin is 50% saturated with oxygen when pO2 = 26 torr. If hemoglobin exhibited hyperbolic binding
(as myoglobin does) with 50% saturation at 26 torr, what would be the fractional saturation when (1) pO2
= 30; and (2) 100 torr? (3)In this case, what would be the effect on the oxygen saturation of Hb in the
lungs?
A) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would be less than 100% saturated with O2
B) (1) 0.79 torr; (2) 0.54 torr; (3) Hb would still be 100% saturated with O2
C) (1) 0.54 torr; (2) 0.79 torr; (3) Hb would still be 100% saturated with O2
D) (1) 0.46 torr; (2) 0.21 torr; (3) Hb would still be 100% saturated with O2
E) (1) 0.54 torr; (2) 7.9 torr; (3) Hb would still be 100% saturated with O2
57. You have a mixture of 3 proteins, listed in the table below with their relevant properties. You are
interested in isolating aspartate transaminase using ion exchange chromatography with DEAE resin. Given
the values in the table below: 1) what pH would you use in order to ensure that aspartate transaminase
protein binds to the column and that the others do not? Assume that your efforts are successful -- 2) how
will you elute aspartate transaminase from the column? Choose the correct conditions from the list below.
Protein
Aspartate transcarbamylase
Myoglobin
Aspartate transaminase

pI
9.8
7.0
5.0

A) 1) Initial pH = 10.0; 2) lower pH to 6


B) 1) Initial pH = 8; 2) raise pH to 10
C) 1) Initial pH = 4; 2) raise pH to 5 or higher

D) 1) Initial pH = 6; 2) lower pH to 5 or less


E) 1) Initial pH = 8; 2) lower pH to 7

Scrambled version C

Page 9

Answer Key - Exam1Fa14


1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
13.
14.
15.
16.
17.
18.
19.
20.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
31.
32.
33.
34.
35.
36.
37.
38.
39.
40.
41.
42.
43.
44.

E
A
B
B
B
A
D
C
B
D
B
B
B
E
B
B
C
E
C
A
B
B
B
A
A
D
A
A
C
D
C
D
A
B
B
C
E
A
A
B
B
C
E or B
C
Scrambled version C

Page 10

45.
46.
47.
48.
49.
50.
51.
52.
53.
54.
55.
56.
57.

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

Scrambled version C

Page 11

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