Version A BIO 3513 BIOCHEMISTRY EXAM I Fall, 2010 Directions: Record your answers on a Parscore (Scantron) form X-101864

-PAR-L. Other required information on the answer sheet: 1) your name; 2) your Banner ID number; 3) Test Form = version A. Questions 1-5: Identify the following amino acids:

1. C A) threonine

2. B B) alanine

3.

D

4. E E) arginine E) valine

5. A

C) leucine D) aspartate C) threonine D) lysine

6. Which amino acid is non-polar? A) aspartate B) arginine

7. In the following peptide (adipokinetic hormone of the malaria mosquito, Anopheles gambiae), which amino acid is the amino terminus? Gln-Leu-Thr-Phe-Thr-Pro-Ala-Trp-Gly A) Leu B) Pro C) Gln D) Thr E) Gly

8. Why can't peptide bonds rotate freely? A) Chlorine atoms prevent free rotation around the bond. B) Peptide bonds have partial double bond character, due to resonance. C) Hydrogen bonding between the NH and C=O groups limits movement. D) Hydrophobic interactions between NH and C=O groups restrict C!. E) none of the above 9. An acid with a pK of 4.0 is in a solution with a pH of 7.0. What is the ratio of the deprotonated to protonated form of the acid, [A-]/[HA]? A) 1000:1 B) 10:1 C) 1:100 D) 4:7 E) none of these

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10. What is the net charge on glycine at pH 12? A) -1 B) 0 C) +1 D) +2 E) none of these 11. Collagen contains a very large amount of which amino acid? A) glycine B) valine C) alanine D) putrescine E) none of these 12. Which structure is !-helix?

A)

B) E) none of these

C)

D)

13. Which is the best method for measuring the molecular weight of a protein? A) Add 8 M urea and mercaptoethanol B) SDS polyacrylamide gel electrophoresis o C) dialysis D) heat to 75 C E) none of these 14. Which contains a "-!-" motif?

A)

B)

C)

15. Which of the following is a non-covalent interaction that stabilizes proteins in their biologically active folded state? A) peptide bonds B) hydrogen bonds C) acyl enzyme D) disulfide bonds E) none of these 2

16. The quaternary structure of ATCase is c6r6. This means that one molecule of ATCase has: A) four hydrogen bonds B) one c subunit and one r subunit C) twelve domains D) six c subunits and six r subunits E) none of these Questions 17-19 refer to the following amino acids: A) cysteine B) serine C) lysine D) isoleucine 17. Which can form an ion pair witha aspartate? C 18. Which is most likely to occur in the interior of a protein folded into its native structure? D 19. Which can form disulfide bonds? A 20. The amino acid sequences of the F helix from human myoglobin and whale myoglobin are shown below. Both proteins fold into very similar tertiary structures. Why does the substitution of K for R in human myoglobin not affect the tertiary structure? whale PIKYLEFISEAIIHVLHSRHP human PVKYLEFISEAIIQVLQSKHP A) The substitution doesn't change the structure, because both R and K are negatively charged. B) The substitution doesn't change the structure, because both R and K are positively charged. C) This sequence in human myoglobin isn't helical D) The substitution doesn't change the structure, because both R and K are nonpolar. E) none of these 21. Most unfolded proteins spontaneously refold to the biologically active state because: A) the free energy of the folded state is lower than the free energy of the unfolded state B) the pK of the folded state is lower than the pK of the unfolded state C) the free energy of the folded state is higher than the free energy of the unfolded state D) the Michaelis constant of the folded state is higher than the Vmax of the unfolded state E) none of these 22. The prosthetic group in myoglobin is: A) BPG B) acyl enzyme C) heme D) CTP E) none of these E) none of these

23. Comparing hemoglobin and myoglobin, which properties are similar? A) number of oxygen binding sites B) location of BPG binding site C. quaternary structure D) shape of oxygen binding curve E. none of these 24. When the substrate concentration is much greater than KM, the reaction velocity is close to: A) k1 B) kcat C) Vmax D) KM E) none of these. 3

25. The energy difference between the substrate and the transition state is: A) the pK of the reaction. B) the energy difference between the substrate and the product. C) the free energy of activation. D) the maximum velocity. E) none of the above. 26. The value of KM is equal to the: A) product concentration at initial reaction conditions. B) substrate concentration when the reaction rate is half its maximal value. C) enzyme concentration. D) activation energy. E) none of these. 27. In which type of inhibition does the inhibitor bind to the enzyme-substrate complex? A) competitive B) uncompetitive C) introverted D) diffident E) none of the above 28. A typical enzyme active site is: A) distributed over the entire surface of the enzyme. B) a small cleft or crevice in the surface of the enzyme. C) not involved with interacting the substrate. D) a mirror image of the inactive site, which is on the opposite side of the enzyme. E) none of these 29. What does Vmax indicate? A) the amount of product per unit time converted into enzyme when half the active sites have substrate bound B) the substrate concentration when the reaction rate is half its maximal value C) the amount of product per unit time produced by an enzyme with all active sites have substrate bound D) the concentration of enzyme without inhibitor E) none of the above 30. In the oxygen binding curves below, curve I is hemoglobin in red blood cells. Which statement is correct? A) Curve III is curve I after an increase in the BPG concentration B) Curve II is curve I after a decrease in the BPG concentration C) Curve II shows non-cooperative binding of oxygen D) Curve III shows oxygen binding to myoglobin E) none of these

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31. An enzyme has a maximum velocity of 10-6 M/sec at a total enzyme concentration of 10-8 M. What is the turnover number for this enzyme? A) 10-14 B) 1000 C) 100 D) 0.01 E) none of these 32. A competitive inhibitor: A) increases the rate of catalysis B) diminishes the rate of catalysis by unfolding enzyme molecules C) can be overcome by increasing the amount of substrate D) binds to the enzyme-substrate complex E) none of these 33. Which amino acids in chymotrypsin are found in the active site and participate in the catalytic mechanism? A) Ser, His, Asp B) His, Phe C) Asp, Leu D) Ala, His, Met E) none of these 34. Which of the following is a mechanism by which enzymes increase reaction rates? A) causing the temperature of the substrate to increase B) covalent intermediate C) using nuclear fusion energy D) general chaos catalysis E) none of these 35. Which of the following contributes to the catalytic mechanism of chymotrypsin? A) A zinc ion polarizes a water molecule B) Conversion of active site Ser into a powerful nucleophile C) A magnesium ion polarizes a water molecule and positions it to attack the substrate D) The enzyme undergoes a conformational change from the R state to the T state E) none of these 36. What is the function of the oxyanion hole of chymotrypsin? A) Converts the active site Ser into a powerful nucleophile B) Converts the active site Val into a strong acid C) Stabilizes the tetrahedral intermediate D) Converts the active site Arg into a strong ion pair E) none of these 37. How can a series of reactions be regulated to maintain a specific concentration of final product without building up high concentrations of intermediates? A) competitive inhibition B) feedback inhibition C) prior restraint D) acylation E) none of these 38. When a molecule of O2 binds to a heme in deoxyhemoglobin: A) it has a lower affinity than O2 binding to hemoglobin with 2 oxy hemes B) it forms ion pairs C) it oxidizes the iron D) it has a higher affinity than O2 binding to oxyhemoglobin E) none of these 5

39. Many allosteric enzymes have two types of subunits, termed: A) merotropic and regulatory B) catalytic and isotropic C) catalytic and regulatory D) catatonic and regulonic E) none of these 40. The catalytic rate of an allosteric enzyme in the T form is _________ than the catalytic rate in the R form. A) lower B) equal C) higher D) no E) none of these 41. The effects of substrate binding to one subunit of an allosteric enzyme on substrate binding to another subunit are referred to as _______ effects. A) heterotropic B) homotropic C) isobaric D) xenophobic E) none of these 42. When an enzyme catalyzes a reaction involving more than one substrate, a common reaction type is known as: A) double-cross B) secretive C) double-dealing D) sequential E) none of these 43. Penicillin inhibits bacterial cell wall synthesis by: A) competitive inhibition of oxygen binding to myoglobin B) uncompetitive inhibition of BPG binding to hemoglobin C) feedback inhibition of ATP binding to ATCase D) covalent modification of active site serine in glycopeptide transpeptidase E) none of these 44. On the graph below, curve B represents the rate vs. substrate graph for ATCase in the absence of regulatory molecules. Which curve best represents the kinetics in the presence of the allosteric regulator ATP?

D) none of these

45. How is specificity determined by chymotrypsin? A) hydrogen bonding of the peptide bond to the active site Arg B) binding of a large, non-polar substrate side chain into a deep pocket on the enzyme C) acylation of a His residue D) conformational change upon binding of inhibitor E) none of these

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