There are 28 questions in all. Questions 1-24 are multiple choice; 1-12 are each worth 3 points, and 13-24 are each worth 2 points. Questions 25-28 are essays and problems worth a total of 40 points.

1-2. Use these diagrams for an enzyme required for glycolysis. The left shows the reaction, and the right diagram shows a reaction intermediate in the active site.

              1. The enzyme is a/n (A) oxidoreductase; (B) hydrolase; (C) transferase;
(D) isomerase.

              2. The catalytic mechanism used by this enzyme is (A) acid-base catalysis;
(B) covalent catalysis; (C) metal ion catalysis; (D) all of the above.

              3. The Lineweaver-Burk chart on the left shows the effect of (A) adding a competitive inhibitor; (B) changing one [substrate] for an enzyme with a ping-pong mechanism; (C) changing one [substrate] for an enzyme that forms a ternary complex;
(D) adding a mixed inhibitor to an enzyme that forms a ternary complex.

4-7. The parts of the diagram labeled E represent parts of chymotrypsin, and the molecule labeled
F – – –  G represents a substrate of chymotrypsin.

              4. Changing the pH to less than 6 reduces the rate of the reaction because
(A) chymotrypsin is denatured; (B) side chain K is protonated and donates H⁺ to F–NH; (C) the concentration of the second substrate is reduced;
(D) side chain K is protonated and no longer removes H⁺ from serine.

              5. The second product of chymotrypsin includes            and is released       .
(A) F, quickly; (B) F, slowly; (C) G, quickly; (D) G, slowly.

              6. During catalysis, a covalent bond is formed between
(A) the side chains labeled I and K; (B) the side chains labeled K and L;
(C) side chain K and the substrate; (D) side chain L and the substrate.

              7. If the substrate were a serpin*, what would happen that would be different from the
F---G reaction?
(A) a covalent bond would be formed between side chain L and part of the serpin;
(B) product 1 (with a new amine terminus) would be released;
(C) the intermediate would be distorted and no second product would be released;
(D) the serpin would add water to the bond between K and L.

*The semester this was on the exam, there had been an assignment about serpins.

              8. The relationship between the rate constant for a reaction (any reaction, not just one catalyzed by an enzyme) to ΔG^† for the reaction is (A) positive; (B) inverse and exponential;
(C) determined by reactant concentration; (D) negative.

              9. The specificity constant for an enzyme with Michaelis-Menton kinetics
(A) = k_cat/K_M ; (B) allows comparison of enzyme efficiency at low [S];
(C) is limited by diffusion; (D) all of the above.

              10. The isozymes glucokinase and hexokinase have different              but the same                 .
(A) products, K_M ; (B) products, V_max; (C) V_max, product; (D) V_max, K_M .

              11. Both allosteric regulation and covalent modification (A) can be amplified;
(B) can involve either activation or inhibition; (C) are irreversible; (D) all of above.

              12. Covalent modification, unlike allosteric regulation, (A) involves R and T conformations; (B) requires two enzymes; (C) involves a competitive inhibitor;
(D) all of these are true for covalent modification only.

              13. Molecule 13 is (A) ribose with its anomeric C circled; (B) fructose with carbon 1 circled; (C) fructose with its anomeric C circled; (D) an isomer of fructose with its anomeric C circled.

              14. Molecule 14 is                                    with carbon                   circled.
(A) α-glucose, 1; (B) β-glucose, 1; (C) α-glucose, 5; (D) β-glucose, 5.

              15. Molecule 15-16 is a disaccharide consisting of a                                       residue and a                                    residue. (A) glucosamine, glucose isomer; (B) glucosamine, glucose;
(C) amine derivative of a glucose isomer, glucose; (D) glucosamine, fructose.

              16. The glycoside bond for molecule 15-16 is a/n
(A) α-(1→4); (B) β-(1→4); (C) α-(1→6); (D) β-(1→6).

              17. Disaccharide 17 (A) is a reducing sugar; (B) has an α–1→β –2-glycoside bond;
(C) consists of residues of α-glucose and an anomer of α-glucose;
(D) all of the above.

              18. Molecule 18 is a (A) purine that is adenine; (B) purine, but not adenine or guanine; (C) pyrimidine that is uracil; (D) pyrimidine, but not adenine or guanine.

              19. Molecule 19 is a/n                                   with a hydrogen acceptor                        and the atom that forms a glycoside bond                          .
(A) pyrimidine, circled, in a box; (B) pyrimidine, in a box, circled;
(C) purine, circled, in a box; (D) purine, in a box, circled.

              20. Molecule 20-22 is a/n
(A) triacylglycerol; (B) glycerophospholipid; (C) sphingolipid; (D) eicosanoid.

              21. How many carbons are in the saturated fatty acid residue in Molecule 20-22?
Write the number in the blank.

              22. The circled atom in Molecule 20-22 is part of a                      residue.
(A) fatty acid; (B) glucose; (C) sugar alcohol that is not glycerol; (D) glycerol.

              23. The unusual feature(s) of Fatty acid 23 is the (A) number of carbons;
(B) type of double bond; (C) positions of the double bonds; (D) all of the above.

              24. Molecule 24 is (A) cholesterol; (B) a steroid but not cholesterol; (C) a glycolipid; (D) a nucleolipid.

25. The two charts below are for an uninhibited enzyme E with Michaelis-Menton kinetics. The enzyme has a V_max=  600 and a K_M = 50. E catalyzes a reaction in which compound C is converted to compound H. . Write your answers below the charts.
a. Describe the interaction(s) of a mixed inhibitor X with E, C, and H.
    You may find it helpful to write a simple diagram that represents their interactions.
b. Define α or α′ for X, and write the modified Michaelis-Menton equation that shows
     the effect of X on E.
c. Add a line to each graph to show the effect of adding X. Describe X's effect for the
     Michaelis-Menton graph.

26. The diagram on the left below represents an intermediate in the reaction catalyzed by enolase. In the reversible reaction 2-phosphoglycerate ↔ phosphoenolpyruvate (PEP).
a. Either write a sentence describing the difference between substrate and product or
    draw the structures of substrate and product.
b. What co-factor(s) are required by enolase? Classify each as prosthetic or co-substrate.
c. Name the amino acid residues in the active site and explain why they are required
    for catalysis. This should include the type of mechanism enolase uses.

27. The chart on the right represents the effect of increasing [S] for an allosterically regulated enzyme in the absence of modulators. Assume that V_max= 300.
a. Which is the more appropriate term to use for this enzyme–K_M or K_0.5?
    Explain the difference between the two terms and the reason for your choice.
b. Give an approximate value for your answer to part a.
c. Add a line to the chart to represent the effect of adding an allosteric inhibitor.
     What change, if any, occurs to your answer to part b?
d. What type of inhibition (competitive, uncompetitive, or mixed) does allosteric
    inhibition resemble? Describe one similarity.

28. The protein segment below is the consensus sequence recognized and modified by protein kinase C (PKC), an enzyme involved in covalent modification. It also includes a substrate of trypsin, a serine protease with a specificity pocket for positively-charged side chains. Trypsin is involved in proteolysis.
a. Circle the side chain that is the most likely substrate for PKC and describe what
    happens to it and to the protein as a result of the reaction catalyzed by PKC.
b. Draw an arrow to a peptide bond that is a trypsin substrate and describe what
    happens to it and to the protein as a result of the reaction catalyzed by trypsin.
c. Assume that the protein containing this segment can be activated by either PKC or
    trypsin. How can the activation be reversed or ended in one case? (Your choice of
    either PKC or trypsin)

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