page1 (of9) Name_____Presto Metabolino______________ BIBC102 Midterm 1 Sp 2009 Stu. ID#__________________________________ 1) (2 pts) Define catabolism and anabolism. One sentence each should be fine. Catabolism- group of metabolic pathways that break down molecules to gain energy and precursors for biosynthesis Anabolism-group of metabolic pathways that build macromolecules such as RNA, DNA, lipids, proteins and various cell and organ structures 2) (3 pts) Two peptides are listed below using the one letter code for each amino acid. a) RKDE b) LYWF i) Which peptide is more hydrophobic __b__: L, Y, W and F are all have hydrophobic R groups ii) Which peptide has more charged groups __ a __ R, K positive R groups; D, E neg. R groups iii) Write each peptide, using the usual first three letter for each amino acid. Example: APL would be AlaProLeu a) ArgLysAspGlu b) LeuTyrTrpPhe 3) (3 pts) Entropy reduction, acid-base catalysis, metal ion catalysis, and covalent intermediate formation are four ways that enzymes catalyze reactions. a) Which is one the chymotrypsin mechanism does NOT use: Metal Ion Catalysis (no metal ions in mechanism b) Which most directly involves the catalytic triad serine: Cov. intermediate formation (attached to Ser OH group) c) Which most directly involves the catalytic triad histidine: acid-base catalysis (His R group accepts and donates H+ during reaction cycle) 4) (2 pts) a) For a given reaction converting S to P. Draw a sketch of the energy diagram to depict the ΔG and the ΔG‡ 5) (2 pts) For a simple, Michaelis-Menton type enzyme, write the term for fraction f of maximum rate as a function of substrate concentration. Hint: the term only goes between 0 and 1 f = S/(S+Km) S P ΔG‡ ΔGpage2 (of9) Name_____Presto Metabolino______________ BIBC102 Midterm 1 Sp 2009 Stu. ID#__________________________________ 6) (2 pts) As you know, kcat,= Vmax/ ET What property of an enzyme does kcat describe, in English? kcat describes the number of reactions catalyzed per second per enzyme molecule at maximum velocity 7) (3 pts) You have a beaker with S and P in equilibrium. You add an enzyme E that increases the S to P rate by 107. Describe what happens to the P to S rate, and the ratio [P]/[S]. One sentence: The P to S rate will increase by 107 (just like the S to P rate) and the ratio will stay the same 8) (4 pts) The following branched pathway has a reaction catalyzed by Rase, that "decides" how much S becomes P1 or P2. a) Describe a plausible scheme in which P1 and P2 are allosteric regulators of Rase that would tend to keep the production of each product in balance. (One sentence) : Let P1 be an allosteric inhibitor of Rase, and P2 be an allosteric activator of Rase, that way, high P1 will promote the synthesis of P2, and high P2 will promote the synthesis of P1. b) Draw a graph showing the Rase reaction rate as a function of S with no added regulator, added P1 or added P2, according to your scheme. No regulator is in BLACK, plus P1 is in RED, and plus P2 is in GREEN 9) (4 pts) The picture below is the "business end" of the NAD cofactor. a) Is this the oxidized form or the reduced form? _oxidized from_ b) Draw the other form next to the one depicted. Anything like this is fine; key points: no charge, no aromatic, two Hs c) Name one enzyme that uses this cofactor in its catalytic cycle: ox red none + P1 + P2page3 (of9) Name_____Presto Metabolino______________ BIBC102 Midterm 1 Sp 2009 Stu. ID#__________________________________ Lactate dehydrogenase, isocitrate dehydrogenase, PDH, aKGDH, 10) (1 pt) An enzyme allows ATP to drive a chemical reaction. The reaction without ATP has a ΔG'o of 10 kjoule/mole, and the ATP ΔG'o is -36 kjoule/mole. What is the ΔG'o of the enyzmatically catalyzed reaction? ______10 + (-36) = -26 kjoule/mole____ 11 (4 pts) The following skeletal picture of glucose has the carbons each labeled with a number. a) Which carbon(s) is oxidized by NAD+ in glycolysis ? ___3, 4___ b) Which carbons receive phosphate from ATP in glycolysis? ____1, 6________ c) Which pairs of carbons end up being indistinguishable as glycolysis proceeds? a) 1 and 5; b) 3 and 4; c) 1 and 6; B and C; d) none Write all the correct options (a-d) below: Correct letters: b (3 and 4), c (1 and 6) 12) (2 pts) Draw the structure of glyceraldehyde 3 phosphate. any number of variations accepted… 13) (2 pts) The product of the glyceraldehyde 3 phosphate dehydrogenase enzyme is 1,3 bisphosphoglycerate. Where do each of these phosphates come from during glycolysis? The 1-P is on the carboxyl (One sentence) The 1 phosphate comes from free phosphate ion that enters the G3PDH reaction, and the 3 P comes from ATP added during the preparatory phase. 14) (3 pts) In class we discussed the two hexokinase isozymes: hexokinse and liver-specific glucokinase. a) Sketch an enzyme rate curve as a function of glucose concentration for each isozyme, to the right. No need for concentrations. b) Why are the liver-specific isozyme's kinetic properties useful? One sentence The liver-specific glucokinase has a saturation curve that allows it to act over the broad range of glucose concentrations encountered by the liver without saturationpage4 (of9) Name_____Presto Metabolino______________ BIBC102 Midterm 1 Sp 2009 Stu. ID#__________________________________ 15) (5 pts) Word problem!! You have developed a drug, Tristatin, that is a potent inhibitor of the triose phosphate isomerase (TPI). You add Tristatin to cells in culture, using enough to completely inhibit TPI. Let's think about the effect of this drug. a) Write the reaction catalyzed by TPI. Use the provided structure to complete the reaction. If you need cofactors or other stuff, add them. Write the names of reactants and products. TPI converts DHAP into G3P, allowing use of all six glucose carbons in later glycolysis steps TPI DHAP G3P We will now explore the effects of complete inhibition of TPI by Tristatin on glycolysis. b) How many ATP will be produced per glucose molecule in drubg treated cells? ____2 total____ c) How many ATP will be consumed per glucose molecule in drug treated cells?____2 total_____ d) How many NADH will be produced per glucose molecule in treated cells? ____1 total_____ e) Which
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