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Chapter 6 Enzymes
1. An introduction to enzymes Define the terms cofactor and coenzyme. Ans: A cofactor is any chemical component required for enzyme activity; it includes both organic molecules, called coenzymes, and inorganic ions. 2. How enzymes work Draw and label a reaction coordinate diagram for an uncatalyzed reaction, S ! P, and the same reaction catalyzed by an enzyme, E. Ans: See Fig. 6-3, p. 187. 3. How enzymes work The difference in (standard) free energy content, " G', between substrate S and product P may vary considerably among different reactions. What is the significance of these differences? Ans: The difference in free energy content between substrate (or reactant) and product for each reaction reflects the relative amounts of each compound present at equilibrium. The greater the difference in free energy, the greater the difference in amounts of each compound at equilibrium. 4. How enzymes work For a reaction that can take place with or without catalysis by an enzyme, what would be the effect of the enzyme on the: (a) standard free energy change of the reaction? (b) activation energy of the reaction? (c) initial velocity of the reaction? (d) equilibrium constant of the reaction? Ans: (a) no change; (b) decrease; (c) increase; (d) no change 5. How enzymes work Sometimes the difference in (standard) free-energy content, "G', between a substrate S and a product P is very large, yet the rate of chemical conversion, S ! P, is quite slow. Why? Ans: The rate of conversion from substrate to product (or the reverse reaction, from product to substrate) does not depend on the free-energy difference between them. The rate of the reaction depends upon the activation energy of the reaction "G', which is the difference between the free-energy content of S (or P) and the reaction transition state. 6. How enzymes work Write an equilibrium expression for the reaction S ! P and briefly explain the relationship between the value of the equilibrium constant and free energy. Ans: Keq' = [P]/[S]. The value of Keq' reflects the difference between the free energy content of S and P. Free energy and equilibrium constant are related by the expression: "G' = -RT ln Keq' For each change in Keq' by one order of magnitude, "G' changes by 5.7 Kjoule/mole.

7. Enzyme kinetics as an approach to understanding mechanism What is the difference between general acid-base catalysis and specific acid-base catalysis? (Assume that the solvent is water.) Ans: Specific acid-base catalysis refers to catalysis by the constituents of water, in other words, the donation of a proton by the hydronium ion, H3O+, or the acceptance of a proton by the hydroxyl ion OH-. General acid-base catalysis refers to the donation or acceptance of a proton by weak acids and bases other than water. 8. Enzyme kinetics as an approach to understanding mechanism Michaelis-Menten kinetics is sometimes referred to as saturation kinetics. Why? Ans: According to the Michaelis-Menten model of enzyme-substrate interaction, when [S] becomes very high, an enzyme molecule's active site will become occupied with a new substrate molecule as soon as it releases a product. Therefore, at very high [S], V0 does not increase with additional substrate, and the enzyme is said to be saturated with substrate. 9. Enzyme kinetics as an approach to understanding mechanism Two different enzymes are able to catalyze the same reaction, A ! B. They both have the same Vmax, but differ their Km the substrate A. For enzyme 1, the Km is 1.0 mM; for enzyme 2, the Km is 10 mM. When enzyme 1 was incubated with 0.1 mM A, it was observed that B was produced at a rate of 0.0020 mmoles/minute. a) What is the value of the Vmax of the enzymes? b) What will be the rate of production of B when enzyme 2 is incubated with 0.1 mM A? c) What will be the rate of production of B when enzyme 1 is incubated with 1 M (in other words, 1000 mM) A? Ans: a) 0.022 mmol/min; b) 0.0022 mmol/min; c) 0.022 mmol/min 10. Enzyme kinetics as an approach to understanding mechanism An enzyme can catalyze a reaction with either of two substrates, S1 or S2. The Km for S1 was found to be 2.0 mM, and the Km, for S2 was found to be 20 mM. A student determined that the Vmax was the same for the two substrates. Unfortunately, he lost the page of his notebook and needed to know the value of Vmax. He carried out two reactions: one with 0.1 mM S1, the other with 0.1 mM S2. Unfortunately, he forgot to label which reaction tube contained which substrate. Determine the value of Vmax from the results he obtained: Tube number 1 2 Ans: Vmax = 101 11. Enzyme kinetics as an approach to understanding mechanism Write out the equation that describes the mechanism for enzyme action used as a model by Michaelis and Menten. List the important assumptions used by Michaelis and Menten to derive a rate equation for this reaction. Hint: The two equations are k1 k2 E+ ES E+P k-1 k-2 Rate of formation of product 0.5 4.8

Ans: The two equations are k1 k2 E+ ES E+P k-1 k-2 One assumption is that [P] = 0, so that the rate of the reaction depends exclusively on the breakdown of ES and is not influenced by the reverse reaction; that is, k-2 can be ignored and V0 = k2 [ES]. This condition is possible only if early reaction times are measured; the velocity, therefore, is an initial velocity. A second assumption is that the rate of ES formation equals the rate of ES breakdown; in other words, the reaction is at a steady state. A third assumption is [S] >> [Et], so that total [S], which equals free substrate and enzyme-bound substrate, is essentially equal to [S]. 12. Enzyme kinetics as an approach to understanding mechanism For the reaction E + S ! ES ! P, the Michaelis-Menten constant, Km, is actually a summary of three terms. What are they? How is Km determined graphically? Hint: Km = (k2 + k-1)/ k1, Ans: Km = (k2 + k-1)/ k1, where k-1 and k1 are the rate constants for the breakdown and association, respectively, of the ES complex and k2 is the rate constant for the breakdown of ES to form E + P. Km can be determined graphically on a plot of V0 vs. [S] by finding the [S] at which V0 = 1/2 Vmax. More conveniently, on a double-reciprocal plot, the x-axis intercept = 1/ Km. 13. Enzyme kinetics as an approach to understanding mechanism An enzyme catalyzes a reaction at a velocity of 20 mol/min when the concentration of substrate (S) is 0.01 M. The Km for this substrate is 1 # 10-5 M. Assuming that Michaelis-Menten kinetics are followed, what will be the reaction velocity when the concentration of S is (a) 1 # 10-5 M and (b) 1 # 10-6 M? Ans: The velocity of 20 mol/min is essentially Vmax because it is measured at [S] >> Km. (a) When [S] = 10-5 M = Km, V = 1/2 Vmax, or 10 mol/min. (b) When [S] is 10-6 M, velocity can be calculated from the Michaelis-Menten equation: V0 = Vmax [S]/( Km + [S]) = (20 mol/min)(10-6 M)/(10-5 + 10-6) = 1.8 mol/min. 14. Enzyme kinetics as an approach to understanding mechanism Give the Michaelis-Menten equation and define each term in it. Does this equation apply to all enzymes? If not, to which kind does it not apply? Ans: The Michaelis-Menten equation is: V0 = Vmax [S]/( Km + [S]), in which V0 is the initial velocity at any given concentration of S, Vmax is the velocity when all enzyme molecules are saturated with S, [S] is the concentration of S, and Km is a constant characteristic for the enzyme. This equation does not apply to enzymes that display sigmoidal V0 vs. [S] curves, but only to those giving hyperbolic kinetic plots. 15. Enzyme kinetics as an approach to understanding mechanism A biochemist obtains the following set of data for an enzyme that is known to follow Michaelis-Menten kinetics. Substrate Initial concentration velocity (M) (mol/min) 1 49

2 96 8 349 50 621 100 676 1,000 698 5,000 699 (a) Vmax for the enzyme is __________. Explain in one sentence how you determined Vmax. (b) Km for the enzyme is _________. Explain in one sentence how you determined Km. Ans: (a) Vmax is about 700. In a plot of V vs. [S], the asymptote is Vmax. Simple inspection of the data shows the approach to Vmaxthe rate increases by only 1 unit when [S] increases five-fold. (a) Km is about 8 M, the [S] at which the velocity is half-maximal. Because Vmax is about 700, 1/2 Vmax is about 350. The [S] at that rate is about 8 M. 16. Enzyme kinetics as an approach to understanding mechanism Why is the Lineweaver-Burk (double reciprocal) plot (see Box 6-1, p. 197) more useful than the standard V vs. [S] plot in determining kinetic constants for an enzyme? (Your answer should probably show typical plots.) Ans: The plot of V vs. [S] is hyperbolic; maximum velocity is never achieved experimentally, because it is impossible to do experiments at infinitely high [S]. The Lineweaver-Burk transformation of the Michaelis-Menten equation produces a linear plot that can be extrapolated to infinite [S] (where 1/[S] becomes zero), allowing a determination of Vmax. 17. Enzyme kinetics as an approach to understanding mechanism An enzyme catalyzes the reaction A ! B. The initial rate of the reaction was measured as a function of the concentration of A. The following data were obtained: [A], micromolar 0.05 0.1 0.5 1 5 10 50 100 500 1,000 5,000 10,000 20,000 V0, nmoles/min 0.08 0.16 0.79 1.6 7.3 13 40 53 73 76 79 80 80

a) What is the Km of the enzyme for the substrate A? b) What is the value of V0 when [A] = 43? The above data was plotted as 1/ V0 vs. 1/[A], and a straight line was obtained. c) What is the value of the y-intercept of the line? d) What is the value of the x-intercept of the line?

Ans: a) 50 micromolar; b) 37 nmoles/min; c) 0.0125 (nmole/min)-1; d) $0.02 micromolar-1 18. Enzyme kinetics as an approach to understanding mechanism The turnover number for an enzyme is known to be 5,000 min-1. From the following set of data, calculate the Km and the total amount of enzyme present in these experiments. Substrate concentration (mM) 1 2 4 6 100 1,000 Initial velocity (mol/min) 167 250 334 376 498 499

(a) Km = __________. (b) Total enzyme = __________ mol. Ans: Km = about 2 mM (the concentration of S needed to achieve one-half of Vmax, which is about 500). The total enzyme present is producing about 500 mol of product per minute. Because the turnover number is 5,000/min, the amount of enzyme present must be 0.1 mol; 1 mol of enzyme would produce 5,000 mol product/min. 19. Enzyme kinetics as an approach to understanding mechanism When 10 g of an enzyme of Mr 50,000 is added to a solution containing its substrate at a concentration one hundred times the Km, it catalyzes the conversion of 75 mol of substrate into product in 3 min. What is the enzyme's turnover number? Ans: Because the velocity measured occurs far above Km, it represents Vmax. Ten g of the enzyme represents 10 # 10-6 g/(5 # 104 g/mol), or 2 # 10-10 mol of enzyme. In 3 minutes, this amount of enzyme produced 75 mol of product, equivalent to 25 # 10-6 mol of product per minute. The turnover number is therefore: (25 # 10-6 mol/min)/(2 # 10-10 mol) = 12.5 # 104 min-1. 20. Enzyme kinetics as an approach to understanding mechanism Fifteen (15) g of an enzyme of Mr 30,000 working at Vmax catalyzes the conversion of 60 mol of substrate into product in 3 min. What is the enzyme's turnover number? Ans: The amount of enzyme present is 15 # 10-6 g, which is (15 # 10-6 g)/(3 # 104 g/mol) = 5 # 10-10 mol of enzyme. The rate of product formation is 60 # 10-6 mol/3 min, or 20 # 10-6 mol of product per minute. The turnover number is therefore (20 # 10-6 mol/min)/(5 # 10-10 mol of enzyme), or 4 # 10-4 min-1. 21. Enzyme kinetics as an approach to understanding mechanism How does the total enzyme concentration affect turnover number and Vmax? Ans: The turnover number, kcat, is the number of substrate molecules converted to product in a given time by a single enzyme molecule, so turnover number is not affected by the total enzyme concentration, [Et]. For any given reaction, however, Vmax can change because Vmax is the product of turnover number # the total enzyme concentration, or Vmax = kcat [Et]. 22. Enzyme kinetics as an approach to understanding mechanism Enzymes with a kcat / Km ratio of about 108 M-1s-1 are considered to show optimal catalytic efficiency.

Fumarase, which catalyzes the reversible-dehydration reaction fumarate + H2O malate has a ratio of turnover number to the Michaelis-Menten constant (kcat / Km) of 1.6 # 108 for the substrate fumarate and 3.6 # 107 for the substrate malate. Because the turnover number for both substrates is nearly identical, what factors might be involved that explain the different ratio for the two substrates? Ans: If the turnover number is nearly identical for both substrates, then the Km for malate must be much larger than for fumarate. Similar turnover numbers suggest no significant differences in rate of conversion of substrate to product, but the different Km values could possibly be explained by a stronger binding affinity of the enzyme for fumarate than for malate or some other aspect of the reaction mechanism that affects Km. 23. Enzyme kinetics as an approach to understanding mechanism Methanol (wood alcohol) is highly toxic because it is converted to formaldehyde in a reaction catalyzed by the enzyme alcohol dehydrogenase: NAD+ + methanol ! NADH + H+ + formaldehyde Part of the medical treatment for methanol poisoning is to administer ethanol (ethyl alcohol) in amounts large enough to cause intoxication under normal circumstances. Explain this in terms of what you know about examples of enzymatic reactions. Ans: Ethanol is a structural analog of methanol, and competes with methanol for the binding site of alcohol dehydrogenase, slowing the conversion of methanol to formaldehyde, and allowing its clearance by the kidneys. The effect of ethanol is that of a competitive inhibitor. 24. Enzyme kinetics as an approach to understanding mechanism You measure the initial rate of an enzyme reaction as a function of substrate concentration in the presence and absence of an inhibitor. The following data are obtained: V0 $Inhibitor +Inhibitor 0.0001 33 17 0.0002 50 29 0.0005 71 50 0.001 83 67 0.002 91 80 0.005 96 91 0.01 98 95 0.02 99 98 0.05 100 99 0.1 100 100 0.2 100 100 a) What is the Vmax in the absence of inhibitor? b) What is the Km in the absence of inhibitor? c) When [S] = 0.0004, what will V0 be in the absence of inhibitor? d) When [S] =0.0004, what will V0 be in the presence of inhibitor? e) What kind of inhibitor is it likely to be? Ans: a) 100; b) 0.0002; c) 66.7; d) 40; e) competitive 25. Enzyme kinetics as an approach to understanding mechanism An enzyme follows Michaelis-Menten kinetics. Indicate (with an "x") which of the kinetic parameters at the [S]

left would be altered by the following factors. Give only one answer for each.

Ans: (a) Km; (b) both; (c) both; (d) neither 26. Examples of enzymatic reactions The enzymatic activity of lysozyme is optimal at pH 5.2 and decreases above and below this pH value. Lysozyme contains two amino acid residues in the active site essential for catalysis: Glu35 and Asp52. The pK values for the carboxyl side chains of these two residues are 5.9 and 4.5, respectively. What is the ionization state of each residue at the pH optimum of lysozyme? How can the ionization states of these two amino acid residues explain the pH-activity profile of lysozyme? Ans: For the enzyme to be active, it is likely that Asp52 is unprotonated and Glu35 is protonated. When the pH is below 4.5, Asp52 becomes protonated, and when it is above 5.9, Glu35 is deprotonated, either of which decreases the activity of the enzyme. (See Fig. 6-20, p. 207.) 27. Examples of enzymatic reactions Why does pH affect the activity of an enzyme? Ans: The state of ionization of several amino acid side chains is affected by pH, and the activity of many enzymes requires that certain of the amino acid residue side chains be in a specific ionization state. (See Fig. 6-20, p. 207.) 28. Examples of enzymatic reactions Chymotrypsin belongs to a group of proteolytic enzymes called the serine proteases, many of which have an Asp, His, and Ser residue that is crucial to the catalytic mechanism. The serine hydroxyl functions as a nucleophile. What do the other two amino acids do to support this nucleophilic reaction? Ans: In chymotrypsin, histidine functions as a general base, accepting a proton from the serine hydroxyl, thereby increasing serine's reactivity as a nucleophile. The negatively charged Asp stabilizes the positive charge that develops on the His. 29. Examples of enzymatic reactions For serine to work effectively as a nucleophile in covalent catalysis in chymotrypsin, a nearby amino acid, histidine, must serve as general base catalyst. Briefly describe, in words, how these two amino acids work together. Ans: The serine is a polar hydroxyl, with the oxygen functioning as an electronegative nucleophile. A nearby histidine residue, with pKa % 6.0, however, functions as a base to abstract the proton from the serine hydroxyl group. The result is to substantially increase the electronegativity of the serine oxygen, making it a much stronger nucleophile. This, in turn, lowers the activation energy of the covalent catalysis between serine and the carbonyl carbon of the substrate peptide bond. (See Fig. 6-21, pp. 208-209.) 30. Examples of enzymatic reactions Penicillin and related antibiotics contain a 4-membered &-lactam ring. Explain why this feature is important

to the mechanism of action of these drugs. Ans: The strained 4-membered ring is easily opened ("G << 0); this energy drives the reaction that covalently inactivates the transpeptidase. 31. Regulatory enzymes On the enzyme hexokinase, ATP reacts with glucose to produce glucose 6-phosphate and ADP five orders of magnitude faster than ATP reacts with H2O to form phosphate and ADP. The intrinsic chemical reactivity of the OH group in water is about the same as that of the glucose molecule, and water can certainly fit into the active site. Explain this rate differential in two sentences or less. Ans: The binding of glucose to hexokinase induces a conformation change that brings the amino acid residues that facilitate the phosphoryl transfer into position in the active site. Binding of water alone does not induce this conformational change. 32. Examples of enzymatic reactions Why is a transition-state analog not necessarily the same as a competitive inhibitor? Ans: The structure of a competitive inhibitor may be similar to the structure of the free substrate. Similar structure will mean that the competitive inhibitor can associate with the enzyme at the active site, effectively blocking the normal substrate from binding. A transition-state analog, however, is similar in structure to the transition-state of the reaction catalyzed by the enzyme. Often a transition-state analog will bind tightly to an enzyme, and is not easily competed away by substrate. 33. Regulatory enzymes The scheme S ! T ! U ! V ! W ! X ! Y represents a hypothetical pathway for the metabolic synthesis of compound Y. The pathway is regulated by feedback inhibition. Indicate where the inhibition is most likely to occur and what the likely inhibitor is: Ans: S ! T ! U ! V ! W ! X ! Y (most likely inhibitor) ' ( ) (most likely inhibited step) 34. Regulatory enzymes Explain how a biochemist might discover that a certain enzyme is allosterically regulated. Ans: The enzyme would show kinetics that do not fit the Michaelis-Menten equation; the plot of V vs. [S] would be sigmoidal, not hyperbolic. The enzyme kinetics would be affected by molecules other than the substrate(s). 35. Regulatory enzymes What is a zymogen (proenzyme)? Explain briefly with an example. Ans: A zymogen is an inactive form of an enzyme that is activated by one or more proteolytic cleavages in its sequence. Chymotrypsinogen, trypsinogen, and proelastase are all zymogens, becoming chymotrypsin, trypsin, and elastase, respectively, after proper cleavage.