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exam 1a 2009 - no answers

exam 1a 2009 - no answers - Biochemistry 460 Exam#1A NAME...

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Unformatted text preview: Biochemistry 460, Exam #1A February 13, 2009 NAME WRITE YOUR NAME LEGIBLY ON EVERY PAGE NAME (print, no nicknames): CHECK TO BE SURE YOU HAVE 7 PAGES INCLUDING COVER PAGE. I swear/affirm that I have neither given nor received any assistance with this exam. Signature: Date: BIOCHEMISTRY 460 EXAM 1A February 13, 2009 Please put your name on every page. Page 1 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME A NON-PROGRAMMABLE CALCULATOR MAY BE USED ON THIS EXAM. No programmable calculators are permitted, and no sharing of calculators. We have a couple of spare calculators to lend in an emergency. SHOW YOUR WORK FOR ALL CALCULATIONS, AND BE SURE TO STATE UNITS OF ANY NUMERICAL ANSWERS. If the reasoning, calculations, or answer are shown anywhere other than in the space provided, make a note in the space provided and put answer on BACK OF SAME PAGE so the grader for that page will have it. USEFUL CONSTANTS: R (gas constant) = 8.315 Jmol1Kelvin1 = 8.315 x 103 kJmol1Kelvin1 If temperature = 25 C, absolute temperature T = 298 K (Assume this temperature unless problem states otherwise.) Use these "generic" pKa values only when no precise pKa for a specific group is given. Ionizable group in peptides and proteins a-carboxyl side chain carboxyl Imidazole a-amino Thiol aromatic hydroxyl e-amino Guanidino Approximate ("generic") pKa in peptides & proteins (from Berg, Tymoczko & Stryer, Biochemistry, 5th ed., 2001) 3.1 4.1 6.0 8.0 8.3 10.9 10.8 12.5 p. 3 (20 points) p. 4 (26 points) p. 5 (17 points) p. 6 (22 points) p. 7 (15 points) EXAM TOTAL: (100 points) Page 2 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME 1- A tetrapeptide structure is shown below: A. (4 pts) Circle a group of 6 atoms in the tetrapeptide that are coplanar (all in the same plane),excluding atoms in cyclic structures. There is more than one correct answer, but circle only 6 atoms total; if you circle more than 6 atoms, the grader will assume you mean the first 6 atoms you circle starting from the left. B. (4 pts) The structure is drawn in a certain state of ionization. Under which of the following pH conditions would this peptide exist predominantly in the state of ionization shown above? a) pH 10 C. b) pH 7.5 c) pH 5 d) pH 1 (4 pts) Which residue (A, B, C or D) has an R group that can be involved in TWO (2) hydrogen bonds in the form shown above? D. (4 pts) Which residue (A, B, C or D) has the most hydrophobic R group? E. (4 pts) Draw one clear ARROW ( - ) to any ONE of the peptide bonds in this structure. Draw only one arrow. If you draw more than one, the grader will assume you mean the arrow closest to left end. Page 3 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME 2- The structure of the enzyme citrate synthase, a homodimer, is shown below. A. (3 pts) What is the principal type of secondary structure seen in the structure above? B. (3 pts) What type of axis of rotational symmetry is apparent in this structure? C. (6 pts) Name 3 of the 4 types of noncovalent interactions that might be expected to stabilize the tertiary and quaternary structures of a protein such as this one. (Disulfide bonds are covalent bonds, so don't give that as an answer.) D. (4 pts) What principles would dictate the folding of this globular protein in aqueous solution? 3. In a muscle cell, when the ATP required to provide the energy for muscle contraction is depleted, another "energy storage" compound, creatine phosphate, can provide the energy to produce ATP from ADP in the following reaction: ADP + creatine phosphate ATP + creatine A. (5 pts) Write the expression defining the equilibrium constant for this reaction in terms of the concentrations of the reactants and products at equilibrium. What would be the UNITS of Keq for this reaction? B. (5 pts) The standard free energy change (G') for this reaction is 12.6 kJ/mol. Calculate Keq for the reaction. Show your work and state units of answer. Page 4 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME 3. A. (3 pts) The enzyme creatine kinase catalyzes the reaction: ADP + creatine phosphate ATP + creatine The enzyme: a) b) c) d) e) shifts the equilibrium to the right shifts the equilibrium to the left increases the forward rate constant only increases the reverse rate constant only does not change the equilibrium, but increase the rates of both the forward and back reactions. B. (2 pts) Choose best description of an enzyme: a) It allows a chemical reaction to proceed extremely fast b) It increases the rate at which a chemical reaction approaches equilibrium relative to its uncatalyzed rate c) It makes a reaction thermodynamically favorable C. (6 pts) Which of the following would be brought about any enzyme catalyzing the simple reaction below? (Please choose ALL correct answers) where K'eq=[P]/[S] (a) (b) (c) (d) (e) (f) (g) (h) Decreased equilibrium constant K'eq Increased rate constant, kF, of the forward reaction Increased equilibrium constant K'eq Increased free activation energy G Decreased free activation energy G More negative free standard free energy Go' Increased rate constant, kR, of the reverse reaction Decreased rate constant, kR, of the reverse reaction D. (6pts) Name 3 characteristics (chemical, physical, spatial) of an enzyme's active site. Page 5 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME 4) A. (3 pts) Where does 2-3BPG interact with hemoglobin, and what types bonds or interactions mediate this interaction? B. The plot below shows the relationship of fractional saturation to oxygen concentration (expressed as pO2, in torr) in normal adult human hemoglobin. a- (2 pts) The binding curve is sigmoidal. What does it indicate? b- (2 pts) Label on the graph Kd (or P50) for normal Hb c- (3 pts) The affinity for a mutant of hemoglobin is Kd = 10 torr. Draw a curve for this mutant, indicating its Kd on the graph. How does the affinity of the mutant change (i.e. increase or decrease) compared to normal Hb? Explain why. C. (4 points) A team of biochemists use genetic engineering to modify the interface region between Hb subunits. The resulting Hb variants exist in solution as dimers. Are these variants likely to bond oxygen more weakly or more tightly as compared to wild type Hb? Explain your answer. 5) True/False (8 points total, 2 pts each) T / F G'folding for lysozyme is -62 kJ/mol. It indicates that lysozyme would be in its folded state. T / F Anfinsen's experiments concluded that the primary structure is not sufficient to specify the tertiary structure. T / F Homologs that perform identical or similar functions in different organisms are called paralogs. T / F 35% sequence identity between two proteins suggests that they are homologous. Page 6 of 7 Total _________ Biochemistry 460, Exam #1A February 13, 2009 NAME 6) Protein -antitrypsin Histone H1d HIV-1 Protease Insulin Src kinase Transferrin Molecular Weight (kD) 45.0 21.2 13.3 5.8 60.0 90.0 pI 5.4 10.9 8.66 5.6 4.8 7.95 Biological Function Inhibits a the protease trypsin Binds DNA in eukaryotic cells Cleaves polypeptides at specific sites Hormone involved in blood sugar regulation Protein kinase involved in cell signaling Transports iron in the bloodstream A. (5 points) Which protein above is most likely to be rich in amino acids arginine and lysine? What would its charge be at physiological pH (~7.4)? How does the amino acid composition (and hence the pI) of this protein relate to its biological function? Explain your logic for full credit. B. (5 points) Imagine you analyze the set of proteins above using SDS-PAGE. Draw and label the resulting stained gel (right). Be sure to label the direction of electrophoresis (i.e. positive and negative) C. (5 points) Explain in biochemical terms why green fluorescent protein is a useful tag for visualizing proteins in cells while the use of the enzyme firefly luciferase, which catalyzes a reaction that emits light, is limited. (In other words, what are the properties of green fluorescent protein that led to its widespread use in biology?) Page 7 of 7 Total _________ ...
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