Spring 2012 BIBC 102 midterm Hampton et al. Metabolic Biochemistry Midterm Tuesday May 8, 2012; 3:30-5:50

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1 Metabolic Biochemistry Midterm Tuesday May 8, 2012; 3:30-5:50 Good afternoon and goooood evening. This midterm has two purposes. One is to solidify your knowledge of the frequently-used ideas and information that form the basis of metabolism. The second is to discern how much you know. As you know, we try to serve these two purposes with the minimum of anxiety by making the midterm option, and scoring it so that it can only help you. Specifically, if averaging in the midterm helps you at the end of the quarter, we will use it in the scoring. If it hurts you out it goes! This way, it is more about what you end up learning rather than exactly when you learn it. My advice (which I never followed as a student): read the whole question before you start your answer. And please, feel free to ask questions. That is why we are circulating around like coelecanths who must move to get that lactate out of our bloodstreams. Please believe me when I say we are not about tricking you or trying to be crafty and fooly. This is a very straightforward exam, and what we ask for is what we want. Period. Enjoy, to the extent that this is possible in a midterm Also, this is the shortest test I have ever written. Here's the thing: if you write a long test, people complain it is too long, despite being given more chances to show what they know. If you write a short test, people complain it is too short, and so doesn't give them enough chances to show what they know, even though they have more time to work on the fewer pages. What-uver! Summation Page 2 (out of 15) Page 3 (out of 14) Page 4 (out of 15) Page 5 (out of 27) Page 6 (out of 19) Page 7 (out of 10) Total (out of 100)

2 Spring 2012 BIBC 102 midterm Hampton et al. ID # (7 pts) The parts of proteins a) Here are three amino acids. Under each write that amino acids one letter code H C W b) Which of these functions in the chymostrypsin catalytic triad?. You can use the full name if you want: Histidine (His) c) What does that amino acid do in the catalytic triad? (one sentence) Histidine accepts and donates protons during the reaction that cleaves the peptide bond I mentioned that using license plates is one of the best ways to learn the amino acid one letter code. d) For the plate at the right, write the four amino acids that are spelled out. You can use three letter abbreviations, like Pro for proline: MetAlaLysGlu; Methionine-Alanine-Lysine-Glutamate 2 (3 pts) How fast and how far a) Draw a reaction coordinate graph showing the relationship of ΔG and ΔG for a reaction with a negative free energy change, ΔG using S and P as we do in class. ΔG' b) For another reaction, the ΔG o for the S to P reaction is S positive. At equilibrium, what can you say about the concentrations of S and P? (one sentence) P At equilibrium, the concentration of S will be greater than P if the ΔG'o for the reaction is positive. 3 (4pts) Reductio ad absurdum- To the right is a biochemical reaction. We will talk about this reaction later, but here we'll just discuss the chemistry. a) For the reaction as drawn what is getting reduced and what is getting oxidized? (one sentence) The left metabolite (A) is getting reduced, and the NADH is getting oxidized b) This reaction is spontaneous. Is the value of the E'o, positive or negative, and is the ΔG'o positive or negative? For a spontaneous reaction, the ΔG'o is negative; and the E'o is positive 4 (1pt) Backwards and forwards- Suppose and enzyme accelerates the rate of a forward reaction by a factor of 105. What is the effect of the enzyme on the reverse reaction (one sentence)? The acceleration of the reverse rate will be identical, an increase of 105 2

3 5) (3 pts) Who're these jerks, Lineweaver and Burke? Rate data for enzyme A and enzyme B are both plotted on a Lineweaver Burke plot. Both data sets form lines, with identical X intercepts, but A has a larger value for the Y (vertical axis) intercept than B. a) Which (A, B, neither) has a higher Km? Neither (same) b) Which (A, B, neither) has a higher Vmax B (smaller 1/V max ) c) Which (A, B, both, neither) show Michaelis- Menton behavior? both (lines) 6 (11pts) Enzyme rules and regulations- The picture shows a generic linear metabolic pathway, in which A goes to F by 5 enzyme steps. Ecd is the enzyme that catalyses the C to D reaction a) Suppose in cellular conditions the conversion of A to F, catalyzed by five enzymes (one for each arrow) is spontaneous, that is, it has a negative ΔG value. Would the reaction be spontaneous in the absence of the enzymes? Yes or no, and why (one sentence) Yes, the five reaction pathway would still have the same free energy change; this is unaffected by enzymes (or any catalyst for that matter) b) Would the A to F reaction proceed as fast without the enzymes? Yes or no, and why (one sentence) The reaction would proceed much (probably MUCH MUCH) more slowly without the enzymes. The enzyme, Ecd, undergoes allosteric regulation. Specifically, metabolites A and E are each allosteric regulators of Ecd. c) How should A regulate enzyme Ecd in order to ensure that not too much C accumulates (one sentence) If A was an allosteric activator of Ecd, then when A is high, the increased production of C by the upstream enzymes will be compensated by faster removal. d) How should metabolite E regulate the enzyme Ecd in order to ensure that not too much F gets made? (one sentence) If E was an allosteric inhibitor of Ecd, the increased production of F would be slowed when E gets high, thus limiting further F production e) Draw a rate graph (using the axes) for an allosteric enzyme with and without an added allosteric inhibitor. Label the axes, and indicate which curve is which. f) Name one allosteric enzyme we have discussed in class. Any one. Don't care which: Phosphofructokinase (PFK-1), citrate synthase, PDH complex, isocitrate dehyrogenase, αketoglutarate dehydrogenase, etc. V o no inh [S] plus inh

4 8 (13 pts) Coat Hanger!! You knew this was coming! Usually when you encounter glycolysis in your real lives, the molecules or the pathway are mentioned, and you need to put that in context. So this question is geared to that idea. You will notice a "parts list" in the box where the standard abbreviation for each metabolite for the glycolytic pathway is indicated. a) Put the molecules in order, using the spaces provided. Each number represents an enzyme. For example, number 11 is lactate dehydrogenase. There, don't say I never did you any favors. Answer the following questions. Some might need more than one number b) Which enzyme(s) use ATP as a substrate in the reaction direction as written? number(s): 1, 3 b) Which enzyme(s) converts a three carbon ketone to a three carbon aldehyde? number(s): 5 d) Which enzyme(s) reaction produces ATP as a product in the direction written? number(s): 7, 10 e) Which reaction is needed to restore NAD+ for continued glycolysis number 11 Glu-6P Fru-6P Fru-1,6bP G3P DHAP 1,3bPG 3PG 2PG PEP The molecule below is called 6- phosphogluconate f ) (2 pts f-g) What is the name of the pathway in which this is made: Pentose phosphate pathway (oxidative phase) Pyr Lac g) Complete the pathway reaction that includes this molecule as a substrate, including the new structures. You do not have to know the enzymes name, but you do need to know that the reaction includes NADP as a substrate (oops ) + NADP+

5 Spring 2012 BIBC 102 midterm Hampton et al. ID # (8pts) P to the D to the H.The pyruvate dehydrogenase (PDH) complex is a key part of energy metabolism. Here are a few questions about this remarkable nanomachine: a) Draw the structure of pyruvate in the box. Indicate with a bracket the two carbons that end up in a product of the PDH b) Name the product of PDH reaction that contains these two pyruvate carbons? AcCoA, or CH3-CO-SCoA, or acetyl-coa b) Where in the mitochondrion does PDH function?: Mitochondrial matrix c) What common carrier molecule is a substrate of PDH CoASH, coenzyme A, CoA The picture shows one of the cofactors of the PDH. d) What is the three letter abbreviation of this cofactor? ans: TPP (thiamine pyrophosphate) e) What is its molecular function in the PDH (one sentence) It allows creation of a carbanion that attacks carbonyls in enzyme reactions f) The PDH is regulated by many inputs. When AMP is abundant, what happens to PDH activity, and why does this make sense (one sentence) AMP indicates a lack of ATP, and this is an allosteric activator of PDH, thus enhancing production of Krebs cycle "fuel" when more energy is needed 10 (19 pts) It's complex. This cartoon depicts the electron transport chain. Use the numbers best associated with the statement, or answer T/F for questions referring to the numbers, as needed. a) NAD+ 2 b) ADP 13 c) Q/QH2 7 d) succinate _5 e) NADH oxidoreductase _3 f) Complex III 8 j) succinate dehydrogenase 4 m) fumarate 6 n) ATP synthase 12 T or F: o) F 4 in the picture is a glycolytic enzyme p) T 15 is a proton that just crossed a membrane q) F The lipid bilayer depicted is the mitochondrial outer membrane r) T The complexes labeled "3" and "4" have a common substrate s) T One of the substrates of "10" is a product of "8" 5 g) oxidized cyt c 9 h) O2 11 i) ATP 14 k) cytochrome c oxidase 10 l) complex II 4

6 11 (16 pts) Krebs be turnin', acetate burnin'! a) Where in the cell does the Krebs cycle occur? ans: Mitochondrial matrix b) Suppose 10,000 turns of the Krebs cycle occur in a cell. How many acetyl groups are consumed by this occurrence ans: 10,000 c) How many CO2 molecules are produced from those acetyl groups? ans: 20,000 d) Suppose 10,000 turns of the glyoxalate cycle occur in a cell. How many acetyl groups are consumed by this occurrence ans: 20,000 e) How many CO2 molecules are produced from those acetyl groups? ans: 0, none The molecule on the right is a key metabolite of the Krebs cycle. f) How many carbons are there in this molecule 6 g) What is the name of this molecule? ans: citrate, citric acid h) Notice two - CH2- CO2- groups can be found on this metabolite. In the enzymatic formation of this molecule, one of these groups comes from acetyl- CoA. What Krebs cycle molecule does the other one come from? Give the full name: oxaloacetate The next molecule on the right is also from the Krebs cycle. i) How many carbons are there in this molecule 6 j) What is the name of this molecule? ans: isocitrate k) Notice there is a - CH2- CO2- group on this molecule. Has this group been through the Krebs cycle before or not? Yes or no, and why (one sentence) No, the acetyl group that is not hydroxylated in isocitrate is ALWAYS the one that just came from AcCoA and so has not been through the cycle yet 12 (3 pts) Here are 4 dicarboxylic acid names. Next to each write the carbon number Glutaric 5 Oxalic 2 Succinic 4 Malonic 3 Draw the structure of glutarate (glutaric acid): C-CH 2 -CH 2 -CH 2 -CO 2 -

7 13 (10 pts) Rogue s Gallery! For each structure, write it s name and the pathway where it arises in the spaced provided. glyceraldehyde-3- phosphate glycolysis fructose 1,6 bisphosphate glycolysis α-ketoglutarate Krebs fumarate Krebs phosphoenolpyruvate glycolysis