Chemistry 6720, quiz 4 handout

Here are the quiz 4 questions you will answer online using the quiz tool in canvas instructure. Some of the questions deal with citric acid cycle enzymes that use mechanistic strategies covered in the lectures. Since we did not cover all of those specific enzymes in lecture, be sure to review the citric acid cycle ahead of taking the quiz online so you can answer the appropriate questions regarding mechanistic strategies/themes for the enzymes. In doing so, practice drawing mechanisms for each enzyme of the citric acid cycle. You will probably need to look up the mechanisms for isocitrate dehydrogenase, aconitase, succinate dehydrogenase, and succinyl-CoA synthetase in a general biochemistry text. I will not be asking specific details of the mechanisms for those 4 enzymes, but you will still need to be generally familiar with how they operate to answer a few of the questions below. You do not need to know the chemistry of FAD reduction for the quiz. Be sure to note the quiz deadline in canvas to be sure you get your answers submitted by the deadline.

1. Shown at the right is a Fischer projection for D-glucose. Use the strategy described in the lecture to assign the configurations (R or S) of the chiral centers at C2, C3, C4, and C5.

2. Using the structures shown to the right, assign the methyl groups of isopropanol, and the hydrogens at C2 and C3 of succinate, as either ProR or ProS. Use the strategy covered in lecture to guide you in making the assignments.

3. Which faces of acetaldehyde, acetyl chloride, glycinate, pyruvate, and methylethylketone are shown here?

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Chemistry 6720, quiz 4 handout

4. Match the following classes of enzymes with the product that will be formed from substrate oxidation by the enzyme. a. primary alcohol dehydrogenase = b. aldehyde dehydrogenase = c. (primary) amine dehydrogenase = d. secondary alcohol dehydrogenase =

5. What is the primary purpose of the catalytic Zn2+ ion in the liver alcohol dehydrogenase mechanism?

6. Which of the following show INCORRECT electron pushing for alcohol dehydrogenase reaction(s)? Check all the options that are INCORRECT. Correct and incorrect electron pushing diagrams will appear in the online quiz.

7. Order the following steps properly, from first to last, for the reaction catalyzed by GAPDH (steps will be provided in the online quiz; review the mechanism ahead of time to prepare).

8. Which of the following dehydrogenases catalyze the dehydrogenation of an alcohol functional group? Select all the correct answers (choices provided on online quiz).

9. Which of the following dehydrogenases catalyze reactions involving oxidative decarboxylation? a. lactate dehydrogenase b. pyruvate dehydrogenase c. malate dehydrogenase d. isocitrate dehydrogenase e. alpha-ketoglutarate dehydrogenase f. succinate dehydrogenase

10. Match the following enzymes with the unique chemistry used for the transformations. a. type I aldolase = b. Type II aldolase = c. Claisen condensation = d. carboxylation with bicarbonate as the substrate

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Chemistry 6720, quiz 4 handout

11. Classify the following reactions based on the type of enzyme. a. ATP + glucose → glucose-6-phosphate + ADP = b. glucose-6-phosphate → fructose-6-phosphate = c. glucose-6-phosphate → glucose-1-phosphate = d. Glyceraldehyde-3-phosphate → dihydroxyacetone phosphate = e. Glyceraldehyde-3-phosphate → 1,3-diphosphoglycerate = f. 2-phosphoglycerate → phosphoenolpyruvate =

12. The following diagrams depicts the initial step for which types of reaction?

13. Which glycolytic enzymes will form a cis-enediolate during catalysis?

14. Match the indicated enzymes associated with an appropriate answer that relates to the mechanism of the transformation. Note that alcohol dehydrogenase is involved only in anaerobic glycolysis in microorganisms that produce ethanol as the fermentation product. a. alcohol dehydrogenase = b. glyceraldehyde-3-phosphate dehydrogenase = c. triose phophate isomerase = d. type I aldolase = e. phosphoglycerate kinase =

15. Which glycolytic enzymes will form a covalent adduct with the substrate or an intermediate formed during the reaction? 16. During the reaction catalyzed by aldolase, in the direction relevant to the reaction that occurs in glycolysis, what will occur in the next step for each of the intermediates shown below? Intermediate structures will be shown on the online quiz.

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Chemistry 6720, quiz 4 handout

17. Correctly order the following sequence of events in the reaction catalyzed by triosephosphate isomerase in the direction shown below. Note some of the steps may occur in a concerted fashion, yet these steps can still be placed in the sequence based on which electron pushing step occurs first. Sequence will be shown on the online quiz.

18. Molecules of dihydroxyacetone phosphate (DHAP) were labelled with T in the positions shown below to give the molecules (shown as Fischer projections) labelled (1) and (2). Either (1) or (2) was then mixed with triose phosphate isomerase and allowed to react until equilibrium was reached. At that point, the glyceraldehy-3-phosphate (G3P) product was isolated and the amount of T present determined by liquid scintillation counting. For the reaction with (1), no T was found to be present in G3P. For the reaction with (2), one mol of T was present for each mol G3P formed. What does this tell you about the stereochemistry associated with the mechanism of the reaction?

T H HO C T HO 1C H 1 C O 2C O 2 2- CH O PO 2- 3 CH2O PO3 3 2 3

(1) (2) 19. Match the following citric acid cycle enzymes with the type of reaction they catalyze. Enzymes: Aconitase, alpha-ketoglutarate dehydrogenase, citrate synthase, fumarase, isocitrate dehydrogenase, malate dehydrogenase, succinate dehydrogenase, succinyl-CoA synthetase Reaction types: Isomerization, oxidative decarboxylation requiring TPP, claisen condensation, substrate hydration, oxidative decarboxylation not requiring TPP, alcohol dehydrogenation, dehydrogenation of a C-C bond, substrate level phosphorylation

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Chemistry 6720, quiz 4 handout

20. Match the following citric acid cycle enzymes with the unique chemistry involved in the enzymatic transformation. Enzymes can be used more than once, but there is only one correct match for each feature. Note: some of these were not covered in lecture, so you might have to do some research to answer them. Enzymes: Fumarase, aconitase, succinyl-CoA synthetase, isocitrate dehydrogenase, alpha- ketoglutarate dehydrogenase, citrate synthase Features: net substrate hydration, prochiral arm discrimination for hydroxyl group movement, substrate level phosphorylation, dehydration and rehydration, phosphorolysis = succinyl-CoA synthetase, oxidative decarboxylation not using TPP, oxidative decarboxylation using TPP, isomerization, carbon-carbon bond formation =

21. Match the following roles to the correct cofactors in the reaction catalyzed by pyruvate dehydrogenase. a. Accepts the acetyl group from reduced lipoamide b. Oxidizes FADH2 c. Initial electron acceptor in oxidation of pyruvate d. Attacks and attaches to the central carbon in pyruvate e. Oxidizes the reduced form of lipoic acid

22. During the reaction catalyzed by pyruvate dehydrogenase, what will occur in the next step for the intermediates shown below? Intermediate structures will be provided on the online quiz.

23. According to the figure provided in my lecture notes, what are the cofactor roles of biotin in biotin-dependent carboxylases?

24. and 25. The transformations of the following substrates in the citric acid cycle will be initiated how?

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