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Exam CHE #2 March12th, 2010 This examination is worth 100 points. Please mark (bubble) your answer on the sheet provided. GOOD LUCK ---------------------------------------------------------------Multiple Choice: (3.5 points each) 1. What is the isoelectric point (pI) of the peptide below?
4. Which of the following molecules will have the lowest boiling point? a. the smallest ester b. the smallest ether c. the smallest alkane d. the smallest amide e. the smallest ketone 5. Which of the following statements is TRUE: a. The heme group has positively charged groups that interact with acidic amino acid side chains in Hb/Mb. b. The distal His in Hb/Mb forms a coordinate covalent bond with Fe2+ in heme. c. Mb has a polar binding pocket for O2 to allow it to bind to Fe2+ d. The heme group has negatively-charged groups that interact with basic amino acid side chains in Hb/Mb. e. Water prevents the binding of O2 to Hb/Mb because it oxidizes Fe3+ to Fe2+. 6. Which of the following statements is TRUE about 2,3-Bisphosphoglycerate (2,3-BPG)? a. 2,3-BPG has a large positive charge and binds to the OXY form of hemoglobin b. 2,3-BPG enhances the affinity of hemoglobin for O2 c. 2,3-BPG binds to the heme group of hemoglobin and O2 is released. d. 2,3-BPG binds to hemoglobin via ionic interactions between the -subunits in the DEOXY form. e. 2,3-BPG shifts the hemoglobin O2-binding curve to the left. 7. A protein denaturation curve is: a. linear b. parabolic c. hyperbolic d. sigmoidal e. logarithmic
D-A-N
a. b. c. d. e. 6.35 10.80 5.40 2.95 4.75
2. The peptide below is capped at the carboxyl terminus as a methyl ester. That is the alphacarboxyl group has been converted to a methyl ester. Calculate the net charge (consider major form) of this peptide at pH = 5.4.
H-L-T-R
a. b. c. d. e.
+1 +2 +3 -2 -3
3. Which of the following does NOT account for the stability of the triple helix of collagen? a. leucine zipper b. inter-strand H-bonding c. dispersion forces among Ala side chains d. cross-linking involving Lys side chains e. H-bonding capabilities of 4-HyP
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8. In sickle-cell anemia (with HbS), a ____ residue is mutated (changed) to a ______ residue, which adds a sticky patch to the molecule. a. D, V b. E, V c. D, L d. E, L e. E, M 9. What is the net charge of the major form of the amino acid Y at pH =10.4 (consider major form)? a. 0 b. -1 c. +1 d. -2 e. +2 10. Which of the following peptides will most likely form a stable -helix based on favorable interactions between side chains at pH = 5.7? a. H-A-Y-H-C-A-R b. W-A-V-W-A-A-W c. Q-V-M-N-K-E-S d. E-N-A-D-L-A-D e. W-A-V-L-Q-V-I 11. A new amino acid has been discovered in the basement of Blackburn Science. Tests on the side chain indicate that it can only be classified as a 4o ammonium group. What percentage of the side chains will be ionized at pH = 4.3? No, a pKa value is not necessary to answer this question. a. 75% b. 33% c. 50% d. 100% e. 0 %
12. Which of the following is NOT true about protein folding? a. The interaction of side chains enthalpically favors protein folding b. The formation of dispersion forces in the nonpolar core entropically favors protein folding c. Protein folding is a cooperative, sequential process d. Protein folding does not involve a random search of all possible conformations e. The folding of a protein into its native structure depends on the sequence of amino acids 13. At pH = 4.7, the side chain of this amino acid will tend to destabilize the helix dipole if it is near the N-terminus of the helix. a. C b. D c. H d. Q e. Y 14. Which of the following peptides can bind in the peptide-binding cleft of the HLA-A2 MHC variant (Biochemistry Chronicles movie)? a. A-I-C-S-Q-A-F-S-V b. A-W-S-C-Q-S-F-C-W c. A-G-Q-S-F-C-Q-N-T A-S-Q-F-C-S-N-A-S d. e. A-T-F-Y-A-A-Q-M-N 15. If water has to be stripped off of a substrate before it binds to an enzyme, this will: a. favor binding because energy is required to break H-bonds b. favor binding because energy is released when H-bonds are broken c. disfavor binding because energy is required to break H-bonds d. disfavor binding because energy is released when H-bonds are broken e. favor binding because there will be no consequences to stripping off the water
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16. This type of enzyme catalyzes the addition of groups to double bonds or the formation of double bonds via the removal of groups a. Ligase b. Dehydrogenase c. Isomerase d. Lyase e. Kinase 17. Consider a Lineweaver-Burk plot that has two lines. Line #1 is a control (no inhibitor) and Line #2 was generated in the presence of a competitive inhibitor. Line #1 has an x-intercept value of -6.8 mM-1 and Line #2 has an xintercept value of -2.7 mM-1. The value of for Line #2 is equal to: a. 7.2 b. 3.8 c. 9.5 d. 4.1 e. 2.5 18. Which of the following statements about chaperones is NOT true: a. The chaperone GroEL, discussed in class, has a large cavity that is initially lined with nonpolar amino acids to lure unfolded proteins into the cavity b. The chaperone GroEL, discussed in class, has a large cavity that is initially lined with polar amino acids to lure unfolded proteins into the cavity c. They prevent proteins from folding prematurely as they emerge from the ribosome d. They aid in the self-assembly (folding) of proteins e. They prevent unfolded proteins from aggregating
19. The Hb O2-binding curve is __________ and shifts to the _______ as the [H+] is increased. a. sigmoidal, right b. hyperbolic, left c. sigmoidal, left d. hyperbolic, right e. hypermoidal, right 20. Which of the following is a valid unit for Vmax? a. sec-1 b. mmoles/L c. moles/sec d. mM e. mM/mL 21. The N of H1N1 stands for: a. Neokinase b. Neuraminidase c. Neutral d. Neodynium e. Naturase 22. Which of the following is FALSE about Tamiflu? a. It is a pro-drug and must undergo ester hydrolysis to be effective b. It blocks the active site of Hemagglutinin c. It binds to its target via an induced-fit process d. It resembles the transition state of the reaction it was designed to block e. Mutations have reduced the effectiveness against some H1N1 strains 23. A -Turn has: a. many bulky amino acid side chains b. (n, n+4) backbone H-bonding c. (n, n+3) backbone H-bonding d. (n, n+4) side chain H-bonding e. (n, n+3) side chain H-bonding
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24. Which of the following statements is NOT true about enzymatic catalysis? a. Enzymes that form a ternary complex can bind the two substrates in a random or ordered fashion. b. Enzymes decrease the effective concentration of substrates c. Enzymes can use amino acid side chains that act as acids or bases in the active site to help catalyze reactions. d. Enzymes do not alter the Grxn of a reaction e. Enzymes are more complementary to transition states of reactions. 25. Consider the antiparallel -strand below, with four important side chains identified by numbers. Below are various combinations of side chains that can be present in the -strand. Which combination will result in the MOST STABLE strand at pH = 7?
a. b. c. d. e.
1 = W, 2 = A, 3 = A, 4 = A 1 = R, 2 = H, 3 = D, 4 = K 1 = D, 2 = E, 3 = C, 4 = L 1 = C, 2 = A, 3 = C, 4 = K 1 = D, 2 = K, 3 = C, 4 = C
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26. Consider the peptide below. Studies have shown that the peptide below will NOT form a stable -helix in water UNLESS sodium ions are also present in the solution. EXPLAIN (7 points)
E-A-A-E-A-A-E
27. Sketch a plot of v (rate) versus [S] for an enzyme-catalyzed reaction following the MichaelisMenten model. Identify Vmax and Km on the plot. (6 points)
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