BMB 514 -- Exam I -- September 15, 2003
Tear off and keep this for your record of your answers.
ANSWER GRID
Version of the Exam: 1A
1. 6. 11. 16. 21. 26.
2. 7. 12. 17. 22. 27.
3. 8. 13. 18. 23. 28.
4. 9. 14. 19. 24. 29.
5. 10. 15. 20. 25. 30.



BMB 514 -- Exam I -- September 15, 2003 Name ___________________________
BEFORE you begin the exam, please complete the following information on your response sheet:
(a) your name and signature (b) your student number (PID)
(c) your college -- in the area under SECTION: mark 001 for CHM student
mark 002 for COM student
(d) your version of the exam is 1A - mark this in the area under FORM
  • There are 30 questions on this exam. For each question, mark the letter corresponding to what you consider is the BEST answer on the response sheet provided.
  • When you leave the exam room, please turn in your RESPONSE SHEET and your EXAM to the proctors standing by the doors INSIDE the auditorium. Once you exit the auditorium, please DO NOT return until we have reopened the doors (~8:45 a.m.).
  • There will be answer keys to this exam outside A-133 Life Sciences after the exam is completed. You may wish to copy your responses from the response sheet onto the answer grid on the first page of this exam so that you can check your results. You can tear off the first page and take it with you.
  • You have 60 minutes to complete this exam. We will close the exam promptly at 8:30 .a.m. Once we withdraw the boxes for the response sheets from the doors, no additional response sheets will be accepted.
  • Do well and good luck.
Abbreviations for Amino Acids

Ionizable Group		 pKa
Amino Acid 3-Letter
Abbreviation		 Amino Acid 3-Letter
Abbreviation
Alanine
Arginine
Asparagine
Aspartic Acid
Cysteine
Glutamine
Glutamic Acid
Glycine
Histidine
Isoleucine		 Ala
Arg
Asn
Asp
Cys
Gln
Glu
Gly
His
Ile		 Leucine
Lysine
Methionine
Phenylalanine
Proline
Serine
Threonine
Tryptophan
Tyrosine
Valine		 Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val		 a-COOH of any aa
b-COOH of Asp
g-COOH of Glu
imidazole of His
SH of Cys
a-NH2 of any aa
phenolic OH of Tyr
e-NH2 of Lys
guanidino of Arg		 2
4
4
6
8
9
10
10
12
For Questions 1-3, select the amino acid from the list below (A - E) that represents the most appropriate match with the description in each question.
A. Arginine
B. Glutamic acid
C. Histidine
D. Serine
E. Phenylalanine

1. Is nearly always found buried in the interior of a globular protein.

2. Contains a hydroxyl group in its side chain.

3. Can serve as a buffer at pH 6.8.

4. The major interaction in which the side chain of threonine could participate is:

A. acid-base dissociation
B. disulfide bonding
C. hydrogen bonding
D. hydrophobic interaction
E. amide bond formation
5. Which of the following statements about protein structure is correct?
A. The information required for the correct folding of a protein is contained in the specific sequence of amino acids along the polypeptide chain.
B. The formation of a disulfide bond in a protein requires that the two participating cysteine residues be adjacent to each other in the primary sequence of the protein.
C. The stability of quarternary structure in proteins is mainly due to covalent bonds between the subunits.
D. The denaturation of proteins always leads to irreversible loss of secondary and tertiary structure.
E. Proteins consisting of one polypeptide can have quarternary structure.
6. b-pleated sheets:
A. are composed of adjacent polypeptides that must be of the opposite polarity.
B. are a form of tertiary structure.
C. are favored by amino acid sequences that contain the repeating motif, Gly-X-Y.
D. are stabilized by hydrogen bonding between carbonyl and amide groups of the main chain.
E. are stabilized by hydrogen bonding between the R-groups of the amino acid residues.
7. Select the non-protein component that forms part of an active enzyme.
A. Apoenzyme
B. Coenzyme
C. Holoenzyme
D. Isoenzyme
E. Allosteric enzyme
8. Although the free sulfhydryl group (-SH) of Cys residues exhibits the property of a weak acid, it loses the ionizable proton upon oxidation into a disulfide bond. Given this information, what will be the net charge of the following polypeptide at pH 6?

A. -2
B. -1
C. 0
D. +1
E. +2
9. Conversion of Fe+2 to Fe+3 in hemoglobin would:
A. convert hemoglobin to myoglobin
B. dissociate the tetramer to dimers
C. denature the globin polypeptide irreversibly
D. increase the capacity of hemoglobin to bind O2
E. prevent the binding of O2 to the heme prosthetic group
10. Which of the following statements concerning the binding of oxygen by hemoglobin is correct?

A. The Bohr effect results in a lower affinity for oxygen at higher pH values.
B. Carbon dioxide increases the oxygen affinity of hemoglobin by binding to the terminal amino groups of the polypeptide chains.
C. The oxygen affinity of hemoglobin increases as the percent saturation increases.
D. The hemoglobin tetramer binds four molecules of 2,3-diphosphoglycerate (DPG).
E. Oxyhemoglobin and deoxyhemoglobin have the same affinity for protons (H+).

11. Hemoglobin resembles myoglobin in that they both:
A. bind one O2 per heme group.
B. are tetrameric proteins.
C. exhibit sigmoidal O2-saturation curves.
D. bind 2,3-diphosphoglycerate (DPG).
E. store oxygen in the muscle
12. A decrease in P50 of hemoglobin for oxygen can be brought about in vivo by:
A. acidemia
B. alkalemia
C. increased 2,3-diphosphoglycerate (DPG) in red blood cells.
D. All of the above.
E. None of the above.
13. The isohydric transport of CO2:
A. causes a drastic fluctuation of pH in the plasma.
B. has nothing to do with the buffering capacity of hemoglobin.
C. does not involve the formation of carbaminohemoglobin.
D. is dependent on the higher affinity of HbF for O2.
E. is augmented by the ability of the red blood cell to exchange HCO3- for Cl-
14. During a short-distance race (e.g., 100-meter dash), the runner's muscles produce a large amount of lactic acid from anaerobic metabolism. This would decrease the pH of blood and may cause cramps. A common practice of competitive short-distance runners is to breathe rapidly and deeply for about half a minute just before the race. The purpose of this hyperventilation is to achieve:
A. Metabolic acidosis.
B. Metabolic alkalosis.
C. Respiratory acidosis.
D. Respiratory alkalosis.
E. Acid-base normalcy.
15. A sample of urine from a patient with ketosis contains 28 mmoles of total acetoacetic acid-acetoacetate (i.e., HA + A- = 28 mmoles). The pKa for acetoacetic acid is 4.5; the pH of the urine is also 4.5. Assuming that Na+ ions are excreted as a counter-ion with equivalent amounts of the conjugate base (acetoacetate), what is the amount of Na+ excreted?
A. 7 mmoles
B. 14 mmoles
C. 28 mmoles
D. 35 mmoles
E. 42 mmoles
16. A 3-year old child was brought to the hospital with a cough, respiratory distress, and cyanosis. Physical examination suggested a lower respiratory tract infection. Other laboratory data available:
 
Patient
Normal
pO2 (mmHg)
29
80-100
PCO2
75
35-45
pH
7.1
7.35-7.45


[Other useful values:        (a) pKa of carbonic acid, 6.1;
                                         (b) solubility coefficient for CO2 at 37 oC, 0.03 mM/mmHg]
What is the plasma bicarbonate concentration?
A. 8.7 mM
B. 22.5 mM
C. 24 mM
D. 29 mM
E. 40 Mm
17. Isozymes:
A. are enzymes of similar structures catalyzing different reactions.
B. are enzymes with the same optimum pH.
C. may have different Km values while catalyzing the same reaction.
D. always have the same Vmax but different Km values.
E. are enzymes inhibited by the same inhibitors.
18. The rate of a reaction, catalyzed by a Michaelis-Menten enzyme, was measured using several substrate concentrations that were much lower than Km. The dependence of reaction rate on substrate concentration can best be described as:
A. proportional to the substrate concentration.
B. equal to Vmax.
C. equal to Km.
D. independent of enzyme concentration.
E. dependent on the overall free energy change of the reaction.

19. A competitive inhibitor of a Michaelis-Menten enzyme:
 
Km
Vmax
A.
B.
C.
D.
E.
increase
decrease
no change
no change
decrease

no change
no change
increase
decrease
decrease

A. increase no change
B. decrease no change
C. no change increase
D. no change decrease
E. decrease decrease
20. A negative allosteric effector of a regulated enzyme:
A. binds to the substrate binding site
B. increases the affinity of the enzyme for the substrate
C. prevents subunit-subunit interaction of oligomeric proteins
D. shifts the v versus [S] curve to the right
E. increases the Vmax of the reaction.

21. A patient comes to you complaining of fatigue and the blood profile suggests that the patient may have anemia. Using your considerable biochemistry skills, you pinpoint the problem to a mutation in the patient's gene encoding methionine synthase, which catalyzes the following reaction:

The patient's enzyme has a Km value for homocysteine of 10-3M, about 10,000-fold higher than normal. You dream of replacing the patient's defective methionine synthase with the "best" enzyme possible from the following list. Comparing equimolar amounts of enzyme and using 1mM homocysteine and 1mM N5-methyl THF, which of the following enzymes would you choose?

Enzyme
Km (homocysteine)
Km (N5-methyl THF)
Vmax (mole/min)
A.
B.
C.
D.
E.
10-6M
10-6
10-5
10-7
10-7
10-6M
10-6
10-7
10-6
10-7
104
105
104
104
105

22. The rates of an enzyme-catalyzed reaction are shown in the graphs below for several concentrations of substrate. The solid line depicts the data collected from the reaction carried out in the absence of any inhibitor. The dotted line depicts the corresponding data in the presence of an inhibitor. From the data presented, which of the following is true?

Vmax (no inhibitor) Vmax (+inhibitor  Km (no inhibitor) Km' (+ inhibitor)
A
 0.2 (mmole)-1(sec) 0.2 (mmole)-1(sec) -1.4 (mM)-1 -0.8 (mM)-1
B
 5 (mmole) (sec)-1 5 (mmole) (sec)-1 0.71 mM 1.25 mM
C
 5 (mmole) (sec)-1 5 (mmole) (sec)-1 1.25 mM 0.71 mM
D
 5(mmole) (sec)-1 0.2(mmole) (sec)-1 1.25 mM 0.71 mM
E
 0.71 mM 1.25 mM 5 (mmole)(sec)-1 5 (mmole)(sec)-1
23. ATP and the coenzyme derivatives of niacin and pantothenate play central roles in metabolism. What two chemical structures are shared in these three critical molecules?
A. Ribose and adenine
B. glucose and thiol group
C. phosphoanhydride bonds and glucose
D. Ribose and activated thiol group
E. Adenine and phosphoanhydride bond

24. Which of the following correctly pairs the COENZYME DERIVATIVE with what it carries?
A. Thiamine Pyrophosphate, Nitrogen
B. Riboflavin, Hydrogen
C. Coenzyme A, Hydrogen
D. Tetrahydrofolate, carbon
E. Cobamide coenzymes, Nitrogen
25. What is the name of the following coenzyme derivative and identify its active site using the correct Roman numeral?
A. Flavin mononucleotide, V
B. Flavin adenine dinucleotide, II
C. Nicotinamide adenine dinucleotide, III
D. Coenzyme A, I
E. Nicotinamide adenine dinucleotide, IV
26. Which of the following is NOT true about the following 2 sugar structures:
A. They are isomers
B. They are D-sugars
C. They are C-3 epimers
D. When in ring form can combine to make lactose
E. They are reducing sugars
27. Which of the following best describes the following structure:
A. It is a furanose.
B. It is the main building block of amylopectin.
C. It is a building block of cartilage.
D. It is b-D-glucosamine.
E. It combines with fructose to make maltose.
28. Aldolase catalyzes the breakdown of fructose 1,6-bisphosphate (F1,6P) to dihydroxyacetone phosphate (DHAP) and glyceraldehyde 3-phosphate (GA3P). Given that the DGo'= +2.5 kcal/mol and RTln = 1.43Log10 calculate the free energy change (G') for this reaction given the intracellular concentrations of F1,6P = 10 M, DHAP = 0.1 M and GA3P is 1 M.
A. +5.36 kcal/mol
B. -0.36 kcal/mol
C. +1.07 kcal/mol
D. +3.93 kcal/mol
E. -1.79 kcal/mol
29. If the above equation is allowed to go to equilibrium, which of the following best describes its equilibrium constant?
A. Keq = 0
B. Keq = -0.86
C. Keq < 1
D. Keq > 10
E. There is not enough information to calculate Keq
30. Maintenance of the intracellular concentrations of ATP is a metabolic priority. Which of the following best describes ATP?
A. Since ATP is a B vitamin its inclusion in our diet is essential.
B. Structurally it is composed of glucose, adenine and phosphates.
C. The complete hydrolysis of ATP to Adenosine + 3Pi would yield 7.3 kcal of energy.
D. The kinetics of ATP hydrolysis are slow owing to ATP stability.
E. The energy released in the conversion of ATP to ADP + Pi is higher than any other chemical reaction within the cell.
BMB 514
Exam I
September 15, 2003
ANSWER KEY
Version of the Exam: 1A

1. E 6. D 11. A 16. B 21. E 26. C
2. D 7. B 12. B 17. C 22. B 27. C
3. C 8. B 13. E 18. A 23. A 28. B
4. C 9. E 14. D 19. A 24. D 29. C
5. A 10. C 15. B 20. D 25. A 30. D