WRITE YOUR NAME AND I.D. NUMBER LEGIBLY ON EVERY PAGE – PAGES WILL BE SEPARATED FOR GRADING! CHECK TO BE SURE YOU HAVE 7 PAGES, NAME (print): INCLUDING COVER PAGE. 5-digit course ID # I swear/affirm that I have neither given nor received any assistance with this exam. Signature: Date: BIOCHEMISTRY 460 SECOND HOUR EXAMINATION FORM A (yellow) June 19, 2006 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 J•mol–1•Kelvin–1 = 8.315 x 10–3 kJ•mol–1•Kelvin–1 If temperature = 25 °C, absolute temperature T = 298 K (Assume this temperature unless problem states otherwise.) F (Faraday constant) = 96.5 kJ/(V•mol) Potentially useful equations: Michaelis-Menten Equation: Vo= Vmax[S][S] + Km Free energy of transport: ! "Gt= RT lnC2C1+ zF"V where F is the Faraday constant (96.5 kJ/V•mol), z is the charge on the solute, and ΔV is the membrane potential (charge gradient across the membrane) Use these “generic” pKa values only when no precise pKa for a specific group is given. Ionizable group in peptides and proteins Approximate ("generic") pKa in peptides & proteins (from Berg, Tymoczko & Stryer, Biochemistry, 5th ed., 2001) α-carboxyl 3.1 side chain carboxyl 4.1 imidazole 6.0 α-amino 8.0 thiol 8.3 aromatic hydroxyl 10.9 ε-amino 10.8 guanidino 12.5Biochemistry 460, Exam #2 Form A NAME June 19, 2006 5-digit course ID# page 2 1. (4 pts) Suppose that a homodimeric enzyme with a phosphoserine residue is less active than the enzyme with the free Ser-OH. Briefly state how the cell would remove the phosphate group if it needed to activate the enzyme. Be as specific as you can about the mechanism the cell would use, with type of reaction (e.g., group transfer reaction, redox reaction, condensation reaction, etc.), and what type of enzyme (as specific a category as possible, e.g. serine protease). 2. (9 pts) A. (3 pts) The fatty acid that is the precursor for all of the eicosanoids (a class of lipids that includes prostaglandins, involved in inflammatory response) is ___________________ acid. B. (3 pts) The source of that eicosanoid precursor fatty acid is the 2nd position of membrane glycerophospholipids. What specific enzyme is responsible for removal of the fatty acid from the phospholipid? Phospholipase_ _____. C. (3 pts) Nonsteroidal antiinflammatory drugs such as aspirin, ibuprofen (Advil), Celebrex, etc. inhibit 1) the phospholipase that cleaves the precursor fatty acid from membrane phospholipids. 2) the first enzyme in the biosynthetic pathway of prostaglandins, cyclooxygenase (prostaglandin H2 synthase). 3) the action of prostaglandins on their cellular targets. 4) None of the above. 3. (4 pts) A mutation in the regulatory (R) subunit of protein kinase A (PKA) that prevented the R subunits from binding cyclic AMP (cAMP) would cause A. PKA to be inactive even in the presence of cAMP. B. PKA to be inactive even in the absence of cAMP. C. PKA to be active even in the presence of cAMP. D. PKA to be active even in the absence of of cAMP. 4. (4 pts) The figure below shows an abbreviated version of the biosynthetic pathway for purine nucleotides, AMP and GMP. The enzyme catalyzing each step is designated by a number (E1, etc.) A. Which enzyme would be regulated by [GMP] to specifically control the amount of GMP produced? ______ Briefly explain your choice for the regulated step (no credit without correct explanation.) B. What would you expect to be the effect on the enzyme’s activity of increasing the GMP concentration? /21 p. 2 (21 points) p. 3 (17 points) p. 4 (17 points) p. 5 (18 points) p. 6 (12 points) p. 7 (15 points) TOTAL: (100 points)Biochemistry 460, Exam #2 Form A NAME June 19, 2006 5-digit course ID# page 3 5. (4 pts) Suppose you have a membrane preparation whose glycerophospholipids have nothing but fatty acyl chains with 18 C atoms and 1 double bond at the C1 and C2 positions of the glycerol. If you wanted to decrease the transition temperature (lower the "melting point") of the membrane preparation, you would substitute fatty acid chains of: (Circle one choice in A, and one choice in B.) A. 1) shorter chainlength 2) longer chainlength 3) Chainlength doesn't affect transition temp. B. 1) fewer double bonds 2) more double bonds 3) Double bonds don't affect transition temp. 6. (4 pts) Suppose a given cell type is transporting a solute S into the cell from the outside by facilitated diffusion. Hint: draw a diagram if that helps you think about this. On the axes below, sketch a plot that shows the effect of solute concentration outside the cell [S1] on the rate of transport of S into the cell by facilitated diffusion. 7. (9 pts) Suppose that the cytosolic (intracellular) concentration of Ca2+ is 10–7 M and the extracellular concentration of Ca2+ is 1.5 x 10–3 M. The membrane potential (ΔV) is – 0.06 V, inside of cell negative relative to outside. As one mechanism for maintaining the low cytosolic Ca2+ concentration, the cell transports Ca2+ ions out of the cell with a Ca2+-ATPase located in the plasma membrane. A. (3 pts) Judging by the name of the enzyme and the nature of the process, which term describes the transport process catalyzed by the plasma membrane Ca2+-ATPase? 1) secondary active transport 2) primary active transport 3) facilitated diffusion B. (6 pts) Consider the free energy change for transporting Ca2+ ions across the plasma membrane out of the cell at 298 K. You do NOT have to do a calculation, but the Faraday constant and gas constant are on cover of exam if needed. NOTE: the charge on a Ca2+ ion is +2; it's a divalent cation. You may find it useful to sketch a diagram of the transport process involved here. The equation (cover sheet) for the free energy change for transport of a
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