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doc RW
2011
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.
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.
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 ΔG'‡, which is the difference between the free-energy content of S (or P)
and the reaction transition state.
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:
For each change in Keq' by one order of magnitude, ΔG'° 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.
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.
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].
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.
Ans: The velocity of 20 µmol/min is essentially Vmax because it is measured at [S] >> Km. (a) When [S] =
10-5 M = Km, V = 1/2 Vmax, or 10 µmol/min. (b) When [S] is 10-6 M, velocity can be calculated from the
Michaelis-Menten equation:
V0 = Vmax [S]/( Km + [S]) = (20 µmol/min)(10-6 M)/(10-5 + 10-6) = 1.8 µmol/min.
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.
Substrate Initial
concentration velocity
(µM) (µmol/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 Vmax—the rate increases by only 1 unit when [S] increases five-fold.
(a) Km is about 8 µM, 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 µM.
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.
Substrate Initial
concentration velocity
(mM) (µmol/min)
1 167
2 250
4 334
6 376
100 498
1,000 499
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 µmol of product per minute. Because the turnover number is
5,000/min, the amount of enzyme present must be 0.1 µmol; 1 µmol of enzyme would produce 5,000 µmol
product/min.
Ans: Because the velocity measured occurs far above Km, it represents Vmax. Ten µg 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 µmol 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.
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.
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].
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.
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.
[S] 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: 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.)
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.)
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.
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.)
Ans: The strained 4-membered ring is easily opened (ΔG << 0); this energy drives the reaction that
covalently inactivates the transpeptidase.
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.
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.
Ans:
S → T → U → V → W → X → Y (most likely inhibitor)
↑ ↓
–––––––←––––––––
(most likely inhibited step)
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).
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.