Version B BIO 3513 BIOCHEMISTRY EXAM I Fall, 2011 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 B. Questions 1-5: Identify the following amino acids:

1.

2.

A C)

3. B tryptophan

4.

E E) arginine

5. C

A) proline

B) methionine

D) threonine

6. Of the amino acids shown in questions 1-5, which would most likely be located on the surface of a protein folded into its functional tertiary structure? A) both 3 and 5 B) both 2 and 4 C) both 1 and 4 D) 5 E) none of these 7. Why does myoglobin lack quaternary structure? A) It has only one polypeptide chain that doesn't associate with other chains B) It remains unfolded until oxygen binds C) It isn't allosteric D) Heme-containing proteins don't have quaternary structure E) none of these 8. Which amino acid is required for the chains of the collagen triple helix to associate? A) alanine B) leucine C) peptone D) glycine E) none of these 9. Which of the following noncovalent interactions is caused by unfavorable interactions with water molecules rather than an attractive force? A) ion pair B) hydrophobic effect C) hydrogen bond D) van der Waals interaction E) none of these 10. Why is the peptide bond shorter and stronger than a single bond? A) hydrogen bonds B) cis-trans isomerization C) resonance stabilization D) ion pairs E) none of these 11. Treating ribonuclease with urea and mercaptoethanol causes: A) unfolding and loss of activity B) refolding and gain of activity C) unfolding and activation D) refolding and inactivation E) none of these

12. In the proteins shown below, which one contains both -helix and -sheet secondary structure?

D) A) B) C) E) none of these

13. A secondary structure motif is: A) the transition state of an enzyme B) a combination of secondary structures that is repeated in many proteins C) a compact globular region of a protein connected by a flexible segment D) a newly synthesized protein E) none of these 14. A domain is: A) the active site of an enzyme B) a combination of secondary structures that is repeated in many proteins C) a compact globular region of a protein connected by a flexible segment D) an unfolded protein E) none of these 15. Which amino acid can react in pairs to form covalent crosslinks between one protein chain and another: A) valine B) leucine C) glycine D) cysteine E) none of these 16. Researchers took cells expressing two proteins, X and O, and found a way to make the cells express them joined together as XO in a single polypeptide chain. The figure to the right shows the results of SDS-polyacrylamide gel electrophoresis of extracted proteins from cells containing X, O, and XO. The positions to which the three proteins migrated are indicated by triangles. The + and - signs indicate the electrophoresis electrodes. Which triangle marks the position of XO? A 17. The quaternary structure of hemoglobin is: A) one and one subunit B) two and two subunits C) three and three subunits D) four and four subunits E) none of these

Questions 18 and 19 refer to the diagram to the right. The dashed line indicates an enzymecatalyzed reaction and the solid line is the same reaction without the enzyme. 18. Which letter marks the transition state of the uncatalyzed reaction? A 19. Which letter marks the free energy of activation of the catalyzed reaction? C 20. Which of the following is not a property of an enzyme active site? A) a three-dimensional cleft or crevice B) contains amino acids from many different parts of the sequence C) has a complementary shape to the substrate D) is formed only from the protein backbone and never from amino acid side chains E) none of these 21. Identify the oxygen binding site in myoglobin: A) histidine B) valine C) heme iron atom D) ATP E) none of these 22. 2,3-Bisphosphoglycerate is a heterotropic allosteric inhibitor because: A) it stabilizes the T state B) it stabilizes the R state C) it is a competitive inhibitor D) it generates more oxygen to bind to hemoglobin E) none of these 23. An increase in H+ concentration increases oxygen delivery to the tissues by hemoglobin because: A) O2 is more soluble at low pH B) H+ stabilizes the R state, which has low O2 affinity C) H+ stabilizes the T state, which has low O2 affinity D) O2 is less soluble at low pH E) none of these 24. Hemoglobin S contains a mutation of glutamate to valine at position 6 on the chains . This causes sickle cell disease by: A) forming a hydrophobic site that becomes exposed in deoxyhemoglobin B) forming an ion pairing site that becomes exposed in deoxyhemoglobin C) forming a hydrophobic site that becomes exposed in oxyhemoglobin D) forming an ion pairing site that becomes exposed in oxyhemoglobin E) none of these 25. When an enzyme inhibitor binds to part of the active site that overlaps with the substrate binding site, it is known as: A) uncompetitive B) noncompetitive C) competitive D) pseudocompetitive E) none of these

26. Which curve in the figure below best represents oxygen binding to myoglobin? A) I B) II C) III D) both I and II E) none of these

27. A hemoglobin molecule has one O2 bound. The affinity for a second O2 is: A) the same as the first B) lower than the first C) higher than the first D) the same as myoglobin E) none of these OMIT 28. Comparing hemoglobin at an oxygen pressure of 100 torr with hemoglobin at an oxygen pressure of 20 torr: A) at 100 torr hemoglobin is mostly in the T state B) at 20 torr hemoglobin is entirely in the R state C) at 20 torr some hemoglobin molecules are in the R state and some in the T state D) at 100 torr hemoglobin dissociates into separate and subunits E) none of these 29. The velocity of an enzyme reaction can be measured as: A) the rate of disappearance of product B) the rate of appearance of substrate C) the rate of disappearance of enzyme D) the rate of appearance of product E) none of these 30. An example of general acid-base catalysis is: A) the reaction of penicillin with transpeptidase B) the role of active site histidine in cleavage of peptide bonds by chymotrypsin C) the mechanism of competitive inhibition D) the role of water in cleavage of peptide bonds by chymotrypsin E) none of these 31. At certain steps in the catalytic mechanism of chymotrypsin, the enzyme: A) generates a reactive carbanion to attack the peptide carbonyl carbon B) donates a proton to the peptide carbonyl oxygen C) removes a proton from the peptide amide nitrogen D) stabilizes tetrahedral oxyanion intermediates by hydrogen bonding E) none of these

32. Allosteric enzymes show non-Michaelis-Menten kinetics because: A) substrate molecules bind to and stabilize the more active R state B) substrate molecules bind to and stabilize the less active T state C) the enzyme-substrate complex dissociates D) the transition state is modified E) none of these 33. An enzyme has KM = 30 M and Vmax = 1000 M/sec. What is the velocity when the substrate concentration is 30 M? A) 1000 M/sec B) 500 M/sec C) 30 M/sec D) 30000 M2/sec E) none of these 34. For the enzyme in question 33, what is the turnover number when the total enzyme concentration is 1 M? A) 1000 sec-1 B) 10-3 sec-1 C) 33.3 sec-1 D) 500 sec-1 E) none of these 35. For the reactions in the table to the right, which one does not go spontaneously from left to right? B

36. The standard free energy change for the reaction shown below is Go = 4.6 kJ/mol. What is the free energy change, G, for this reaction when the concentrations of 3phosphoglycerate and 2-phosphoglycerate are equal? (hint: ln(1)=0). 3-phosphoglycerate 2-phosphoglycerate A) 0 kJ/mol B) 1 kJ/mol C) -4.6 kJ/mol D) 4.6 kJ/mol E) none of these 37. In a series of linked metabolic reactions, feedback inhibition and feedback activation often occur by: A) changing the pH-activity profile of the enzyme B) heterotropic allosteric activation or inhibition C) unfolding the enzyme D) changing the prosthetic group of the enzyme E) none of these

Questions 38-40 refer to the following statements: A) the substrate concentration at Vmax/2 B) the velocity at substrate concentrations much larger than KM C) the number of substrate molecules that the enzyme can convert to product per unit time when the active sites are fully saturated D) the rate constant when nearly all the active sites are empty E) none of these 38. What is kcat? C 39. What is KM? A 40. What is Vmax? B 41. If an enzyme inhibitor cannot be reversed by increasing the substrate concentration, which type of inhibition is it? A) uncompetitive B) capitalistic C) competitive D) anticompetitive E) none of these 42. In catalytic mechanisms involving covalent intermediates part of the substrate transiently forms a covalent bond with: A) the enzyme B) water C) a substrate molecule D) a product molecule E) none of these 43. Penicillin inhibits transpeptidase by: A) competitive inhibition B) noncompetitive inhibition C) covalent modification D) lowering the activation free energy E) none of these 44. An acid has its pKa equal to 3.6. The acid (AH) and its salt (A ) are mixed together to use as a buffer. If the buffer is prepared with the concentration of the acid equal to the concentration of the salt, what is the pH? A) 1 B) 10 C) -log(3.6) D) 3.6 E) none of these 45. The amino acid sequences below correspond to one chain of a two-chain protein isolated from the pancreas of humans and elephants. Explain why the sequences are, or are not, likely to fold into similar tertiary structures. human GIVEQCCTSICSLYQLENYCN elephant GIVEQCCTSVCSLYQLENYCN A) They will fold into similar tertiary structures because the amino acid sequences are nearly identical, and the only differences are amino acids of similar polarity (I and V). B) They will not fold into similar tertiary structures because the amino acid sequences are not identical. C) They will fold into similar tertiary structures because they have the same N- and Cterminal amino acids. D) They will not fold into similar tertiary structures because the differences (I and V) are due to a mutation. E) None of these