IChO 2023 · Theory problem 7

Enzyme Kinetics

The Michaelis–Menten (MM) mechanism, introduced in 1913, describes the kinetics of enzyme catalysis. In this mechanism, enzyme \(\ce{E}\) catalyzes the conversion of substrate \(\ce{S}\) to the product \(\ce{P}\):

Figure 1

The initial rate for an enzymatic reaction following the MM mechanism is given as

\[ v_0=v_{\max}\frac{[\ce{S}]_0}{K_{\mathrm M}+[\ce{S}]_0} \tag{1} \]

when the initial concentration of \(\ce{E}\) is much lower than the initial concentration of \(\ce{S}\), \([\ce{E}]_0\ll[\ce{S}]_0\). The Michaelis constant is defined as \(K_{\mathrm M}=(k_2+k_3)/k_1\). The initial rate can also be expressed as the product of the relative flow \(j\) and \([\ce{E}]_0\):

\[ v_0=j[\ce{E}]_0 \tag{2} \]

Note: Questions 7.1 and 7.2 can have one, multiple, or no correct answer(s).

7.1 Choose the correct alternative form(s) of the initial rate (\(v_0\)) expressions (1) and (2).

\([\ce{ES}]_{\max}\) is the maximum concentration of the \(\ce{ES}\) complex.

  • (a) \(\displaystyle v_0=\frac{k_3[\ce{E}]_0[\ce{S}]_0}{K_{\mathrm M}+[\ce{S}]_0}\)
  • (b) \(\displaystyle v_0=\frac{k_3[\ce{E}]}{K_{\mathrm M}/[\ce{S}]_0+1}\)
  • (c) \(\displaystyle v_0=j[\ce{ES}]_{\max}\)
  • (d) \(\displaystyle v_0=\frac{k_3[\ce{E}]_0[\ce{ES}]_{\max}}{K_{\mathrm M}+[\ce{S}]_0}\)
  • (e) \(\displaystyle v_0=\frac{k_3[\ce{E}]_0}{K_{\mathrm M}/[\ce{S}]_0+1}\)
  • (f) \(\displaystyle v_0=\frac{j[\ce{E}]_0}{K_{\mathrm M}+[\ce{S}]_0}\)

7.2 Choose the pair(s) of axes (\(y\) vs. \(x\)) that are expected to give a linear plot.

  • (a) \(v_0\) vs. \(1/[\ce{S}]_0\)
  • (b) \(v_0\) vs. \(v_0/K_{\mathrm M}\)
  • (c) \(v_0\) vs. \(K_{\mathrm M}/v_0\)
  • (d) \(1/v_0\) vs. \(v_0/[\ce{S}]_0\)
  • (e) \(1/v_0\) vs. \(v_0/K_{\mathrm M}\)
  • (f) \([\ce{S}]_0/v_0\) vs. \([\ce{S}]_0\)

Many enzymes catalyze multi- rather than single-substrate transformations. However, if the concentration of one of the substrates is much higher than that of the other substrate or it is kept constant, the MM kinetics is also valid. Here we will look at two independent enzymatic systems that follow the MM kinetics.

Enzymatic System I

Enzyme \(\ce{E}\) converts substrates \(\ce{A}\) and \(\ce{B}\) to products \(\ce{P_A}\) and \(\ce{P_B}\). At rapid pre-equilibrium between the free enzyme and all enzyme–substrate complexes, the following equation applies:

\[ v_0= \frac{k[\ce{E}]_0[\ce{A}]_0[\ce{B}]_0} {(K+[\ce{A}]_0)(K+[\ce{B}]_0)} \tag{3} \]

where \(k\) is the rate constant of one of the reactions. The same equilibrium constant \(K\) characterizes the dissociation of either substrate from the corresponding active site of \(\ce{E}\).

7.3 Show that equation (3) takes the MM form (1) if the concentration of substrate \(\ce{B}\) is maintained at a constant value \(c_0\). Give the expression for \(v_{\max}\) in this case.

7.4 Propose a kinetic scheme for the Enzymatic System I consistent with eq. (3), showing all the intermediates and products. Indicate the reaction with a rate constant \(k\).

Enzymatic System II

Enzyme \(\ce{E}\) has five active sites, each of which is specific to one of the substrates \(\ce{S_A}\), \(\ce{S_B}\), or \(\ce{S_C}\) that are selectively transformed to products \(\ce{P_A}\), \(\ce{P_B}\), or \(\ce{P_C}\), respectively. There is at least one active site for each substrate. Each active site is independent of the others.

Figure 2

For \(\ce{E}\), it is known that:

  1. The affinity for \(\ce{S_C}\) is higher than for \(\ce{S_B}\).

  2. The plot of \(v_{0i}\) vs. \(v_{0i}/[\ce{S_i}]_0\), known as Eadie–Hofstee plot, for \(\ce{S_A}\), \(\ce{S_B}\), \(\ce{S_C}\), with rate given per active site (\(v_{0i}\)), is shown below, but the scale and the legend are omitted.

Figure 3
  1. When \(\ce{E}\) is saturated with \(\ce{S_A}\), \(\ce{S_B}\), \(\ce{S_C}\), the catalytic turnover number (TON) for \(\ce{S_C}\) per site is \(10200\ \mathrm{min^{-1}}\), and 2023 product \(\ce{P_A}\), \(\ce{P_B}\), \(\ce{P_C}\) molecules in total are synthesized per second. At the same time, no more than \(5.94\times10^6\) molecules of \(\ce{P_A}\) and \(\ce{P_B}\) are detected to form per hour.

  2. At equimolar concentrations of \(\ce{S_A}\), \(\ce{S_B}\), \(\ce{S_C}\), which are at least 1000-times lower than corresponding \(K_{\mathrm M,i}\) values, the \(\ce{P_A}\), \(\ce{P_B}\), \(\ce{P_C}\) concentrations become proportional to the catalytic efficiency \((\varepsilon_i=k_{i3}/K_{\mathrm M,i})\), and their ratio is \(3:2:5\), respectively.

  3. Two \(\ce{ES_i}\) complexes have equal rate constants for dissociation to \(\ce{E}\) and \(\ce{S_i}\). The activation barrier for the reaction of \(\ce{ES_C}\) into the initial compounds is \(1266\ \mathrm{J\,mol^{-1}}\) higher than for the reaction into the final products. Assume that the pre-exponential factors are equal for both reactions and \(T=25\,^\circ\mathrm C\).

  4. For \(\ce{E + S_i}\) reaction: \(k_{\mathrm{c1}}=1.57\times10^7\ \mathrm{M^{-1}\,s^{-1}}\) and \(k_{\mathrm{a1}}=k_{\mathrm{b1}}\).

7.5 Fill in the table below and provide your calculations. Hints:

  • Use information from points 1 and 2 to find the relation (\(<\), \(>\), \(=\)) between constants \(K_{\mathrm M,A}\), \(K_{\mathrm M,B}\) and \(K_{\mathrm M,C}\).
  • Information from points 3 and 5 allows you to complete the first column (number of active sites for each substrate) and the last row (all the constants for substrate \(\ce{S_C}\)) of the table. Check that the sum of active sites is equal to 5.
# of active sites \(k_1\) \(k_2\) \(k_3\) \(K_{\mathrm M}\)
\(\ce{S_A}\)
\(\ce{S_B}\)
\(\ce{S_C}\) \(1.57\times10^7\ \mathrm{M^{-1}\,s^{-1}}\)

Official English text of the problem.

Answers

  • 7.1: (a), (c), (e).
  • 7.2: (b), (f).
  • 7.3: \(\displaystyle v_{\max}=\frac{k[\ce{E}]_0c_0}{K+c_0}\), with \(K_{\mathrm M,A}=K\).
  • 7.4: Rapid binding equilibria \(\ce{E + A <=> EA}\), \(\ce{E + B <=> EB}\), \(\ce{EA + B <=> EAB}\), and \(\ce{EB + A <=> EAB}\), each with dissociation constant \(K\), followed by \(\ce{EAB ->[k] E + P_A + P_B}\).
  • 7.5: \(K_{\mathrm M,A}=K_{\mathrm M,B}>K_{\mathrm M,C}\). The upper, middle, and shallow lines represent \(\ce{S_A}\), \(\ce{S_B}\), and \(\ce{S_C}\), respectively. The completed table is:
Substrate # of active sites \(k_1\;(\mathrm{M^{-1}\,s^{-1}})\) \(k_2\;(\mathrm{s^{-1}})\) \(k_3\;(\mathrm{s^{-1}})\) \(K_{\mathrm M}\;(\mathrm M)\)
\(\ce{S_A}\) 1 \(1.96\times10^7\) \(1.02\times10^2\) \(9.08\times10^2\) \(5.14\times10^{-5}\)
\(\ce{S_B}\) 1 \(1.96\times10^7\) \(4.05\times10^2\) \(6.05\times10^2\) \(5.14\times10^{-5}\)
\(\ce{S_C}\) 3 \(1.57\times10^7\) \(1.02\times10^2\) \(1.70\times10^2\) \(1.73\times10^{-5}\)

Solution

7.1

For the MM mechanism, enzyme conservation gives

\[ [\ce{E}]_0=[\ce{E}]+[\ce{ES}]. \]

At substrate saturation, essentially all enzyme is present as the complex, so

\[ [\ce{ES}]_{\max}=[\ce{E}]_0, \qquad v_{\max}=k_3[\ce{E}]_0. \]

Substitution into equation (1) gives

\[ v_0= \frac{k_3[\ce{E}]_0[\ce{S}]_0}{K_{\mathrm M}+[\ce{S}]_0} = \frac{k_3[\ce{E}]_0}{K_{\mathrm M}/[\ce{S}]_0+1}. \]

Thus (a) and (e) are correct. Also, equation (2) becomes

\[ v_0=j[\ce{E}]_0=j[\ce{ES}]_{\max}, \]

so (c) is correct.

In (b), \([\ce{E}]\) is the free-enzyme concentration, which generally differs from the total concentration \([\ce{E}]_0\). In (d), replacing the numerator’s substrate concentration with \([\ce{ES}]_{\max}\) does not preserve the MM expression. In (f), the additional concentration denominator is incorrect; it also gives units of \(\mathrm{s^{-1}}\), whereas \(v_0\) has units of concentration per time.

Therefore,

\[ \boxed{\text{7.1: (a), (c), (e).}} \]

7.2

Write \(s=[\ce{S}]_0\), \(V=v_{\max}\), and \(K=K_{\mathrm M}\), with \(V\) and \(K\) constant:

\[ v_0=\frac{Vs}{K+s}. \]

Each proposed choice gives the following relation between its stated \(y\) and \(x\):

Option Relation Linear?
(a) \(\displaystyle y=\frac{V}{1+Kx}\) No
(b) \(y=Kx\) Yes
(c) \(\displaystyle y=\frac{K}{x}\) No
(d) \(\displaystyle y=\frac{1}{V-Kx}\) No
(e) \(\displaystyle y=\frac{1}{Kx}\) No
(f) \(\displaystyle y=\frac{K}{V}+\frac{x}{V}\) Yes

For (b), the linearity follows directly from \(x=v_0/K_{\mathrm M}\): the line passes through the origin with slope \(K_{\mathrm M}\).

For (f), rearranging the MM equation gives the Hanes–Woolf form:

\[ \frac{[\ce{S}]_0}{v_0} = \frac{K_{\mathrm M}}{v_{\max}} +\frac{[\ce{S}]_0}{v_{\max}}. \]

Its slope is \(1/v_{\max}\), and its vertical intercept is \(K_{\mathrm M}/v_{\max}\).

Therefore,

\[ \boxed{\text{7.2: (b), (f).}} \]

7.3

Set \([\ce{B}]_0=c_0\) in equation (3):

\[ v_0= \frac{k[\ce{E}]_0[\ce{A}]_0c_0} {(K+[\ce{A}]_0)(K+c_0)}. \]

Collecting the factors independent of \([\ce{A}]_0\),

\[ v_0= \underbrace{\frac{k[\ce{E}]_0c_0}{K+c_0}}_{v_{\max}} \frac{[\ce{A}]_0}{K+[\ce{A}]_0}. \]

This is the MM form, with

\[ \boxed{ v_{\max}=\frac{k[\ce{E}]_0c_0}{K+c_0}, \qquad K_{\mathrm M,A}=K. } \]

7.4

A suitable scheme allows the two substrates to bind independently in either order. The singly bound complexes are \(\ce{EA}\) and \(\ce{EB}\); both routes lead to the doubly bound complex \(\ce{EAB}\):

\[ \begin{aligned} &\ce{E + A <=> EA},\\ &\ce{E + B <=> EB},\\ &\ce{EA + B <=> EAB},\\ &\ce{EB + A <=> EAB}. \end{aligned} \]

Each binding equilibrium has dissociation constant \(K\). Only the doubly bound complex undergoes the product-forming step:

\[ \boxed{\ce{EAB ->[k] E + P_A + P_B}.} \]

The overall substrate conversion is

\[ \ce{A + B -> P_A + P_B}. \]

Thus, a drawing would show a binding square with \(\ce{E}\), \(\ce{EA}\), \(\ce{EB}\), and \(\ce{EAB}\) at its corners, and an irreversible arrow labelled \(k\) from \(\ce{EAB}\) to \(\ce{E + P_A + P_B}\).

To verify the rate law, let \(a=[\ce{A}]_0\) and \(b=[\ce{B}]_0\). Rapid pre-equilibrium gives

\[ [\ce{EA}]=\frac{[\ce{E}]a}{K}, \qquad [\ce{EB}]=\frac{[\ce{E}]b}{K}, \qquad [\ce{EAB}]=\frac{[\ce{E}]ab}{K^2}. \]

The enzyme balance is therefore

\[ \begin{aligned} [\ce{E}]_0 &=[\ce{E}]+[\ce{EA}]+[\ce{EB}]+[\ce{EAB}]\\ &=[\ce{E}] \left(1+\frac{a}{K}\right) \left(1+\frac{b}{K}\right). \end{aligned} \]

Consequently,

\[ [\ce{EAB}] = \frac{[\ce{E}]_0ab}{(K+a)(K+b)}, \]

and the reaction rate is

\[ v_0=k[\ce{EAB}] = \frac{k[\ce{E}]_0[\ce{A}]_0[\ce{B}]_0} {(K+[\ce{A}]_0)(K+[\ce{B}]_0)}, \]

as required. Each of the two products forms at this rate.

7.5

Let \(n_A,n_B,n_C\) be the numbers of sites specific to the three substrates. They are positive integers satisfying

\[ n_A+n_B+n_C=5. \]

First, rearrange the MM equation into the Eadie–Hofstee form:

\[ v_{0i} = v_{\max,i} - K_{\mathrm M,i}\frac{v_{0i}}{[\ce{S_i}]_0}. \]

The slope is \(-K_{\mathrm M,i}\), and the vertical intercept is the maximum rate per site, proportional to \(k_{i3}\).

The graph contains two parallel, steeper lines and one shallower line. Using the stated affinity comparison, \(K_{\mathrm M,C}<K_{\mathrm M,B}\). Therefore, the shallow line must correspond to \(\ce{S_C}\), and the two parallel lines correspond to \(\ce{S_A}\) and \(\ce{S_B}\):

\[ \boxed{K_{\mathrm M,A}=K_{\mathrm M,B}>K_{\mathrm M,C}.} \]

The turnover constant for a C site is

\[ k_{\mathrm{c3}} = 10200\ \mathrm{min^{-1}} \left(\frac{1\ \mathrm{min}}{60\ \mathrm s}\right) = 170\ \mathrm{s^{-1}}. \]

The maximum allowed combined A-and-B production rate is

\[ \frac{5.94\times10^6}{3600} = 1650\ \text{molecules per second}. \]

Thus, C sites must produce at least

\[ 2023-1650=373\ \text{molecules per second}. \]

For one enzyme molecule,

\[ 170n_C\ge373, \qquad n_C\ge2.194. \]

Since \(n_C\) is an integer, \(n_C\ge3\). At least one site is required for each of A and B, so \(n_C\le3\). Hence

\[ \boxed{n_A=1,\qquad n_B=1,\qquad n_C=3.} \]

The site count is indeed \(1+1+3=5\).

Next, the two reactions of the C complex are

\[ \ce{ES_C ->[k_{c2}] E + S_C}, \qquad \ce{ES_C ->[k_{c3}] E + P_C}. \]

Their equal Arrhenius pre-exponential factors give

\[ \frac{k_{\mathrm{c2}}}{k_{\mathrm{c3}}} = \exp\left[ -\frac{E_{\mathrm a,c2}-E_{\mathrm a,c3}}{RT} \right]. \]

Using \(T=298.15\ \mathrm K\) and \(R=8.314\ \mathrm{J\,mol^{-1}\,K^{-1}}\),

\[ \frac{k_{\mathrm{c2}}}{k_{\mathrm{c3}}} = \exp\left[ -\frac{1266}{8.314(298.15)} \right] \approx0.6001. \]

Therefore,

\[ \boxed{k_{\mathrm{c2}}\approx102.0\ \mathrm{s^{-1}}.} \]

It follows that

\[ K_{\mathrm M,C} = \frac{k_{\mathrm{c2}}+k_{\mathrm{c3}}}{k_{\mathrm{c1}}} = \frac{102.0+170}{1.57\times10^7} \approx1.7326\times10^{-5}\ \mathrm M, \]

so

\[ \boxed{K_{\mathrm M,C}=1.73\times10^{-5}\ \mathrm M.} \]

To use the low-concentration product ratio, the number of sites must be included. At a common substrate concentration \(s\ll K_{\mathrm M,i}\),

\[ v_i = n_i[\ce{E}]_0 \frac{k_{i3}s}{K_{\mathrm M,i}+s} \approx n_i[\ce{E}]_0\frac{k_{i3}}{K_{\mathrm M,i}}s = n_i[\ce{E}]_0\varepsilon_i s. \]

The specified \(s/K_{\mathrm M,i}\le10^{-3}\) justifies this approximation. Consequently,

\[ n_A\varepsilon_A:n_B\varepsilon_B:n_C\varepsilon_C = 3:2:5. \]

With the site counts already found,

\[ \varepsilon_A:\varepsilon_B:3\varepsilon_C = 3:2:5, \]

or equivalently,

\[ \boxed{\varepsilon_A:\varepsilon_B:\varepsilon_C=9:6:5.} \]

Because \(K_{\mathrm M,A}=K_{\mathrm M,B}\),

\[ \frac{k_{\mathrm{a3}}}{k_{\mathrm{b3}}} = \frac{\varepsilon_A}{\varepsilon_B} = \frac32. \]

At saturation, the total production rate gives

\[ k_{\mathrm{a3}}+k_{\mathrm{b3}}+3k_{\mathrm{c3}}=2023\ \mathrm{s^{-1}}, \]

hence

\[ k_{\mathrm{a3}}+k_{\mathrm{b3}} = 2023-3(170) = 1513\ \mathrm{s^{-1}}. \]

Combining the sum and ratio,

\[ \boxed{ k_{\mathrm{a3}}=\frac35(1513)=907.8\ \mathrm{s^{-1}}, } \]

\[ \boxed{ k_{\mathrm{b3}}=\frac25(1513)=605.2\ \mathrm{s^{-1}}. } \]

Thus the higher of the two parallel lines is A, and the lower is B.

The ratio \(\varepsilon_A/\varepsilon_C=9/5\) now determines the common A-and-B Michaelis constant:

\[ \frac{k_{\mathrm{a3}}/K_{\mathrm M,A}} {k_{\mathrm{c3}}/K_{\mathrm M,C}} = \frac95, \]

so

\[ \begin{aligned} K_{\mathrm M,A} &=\frac{5k_{\mathrm{a3}}}{9k_{\mathrm{c3}}}K_{\mathrm M,C}\\ &=\frac{5(907.8)}{9(170)} \left(1.7326\times10^{-5}\right)\ \mathrm M\\ &\approx5.1399\times10^{-5}\ \mathrm M. \end{aligned} \]

Therefore,

\[ \boxed{ K_{\mathrm M,A}=K_{\mathrm M,B}=5.14\times10^{-5}\ \mathrm M. } \]

Finally, \(k_{\mathrm{a1}}=k_{\mathrm{b1}}\) and \(K_{\mathrm M,A}=K_{\mathrm M,B}\) imply

\[ k_{\mathrm{a2}}+k_{\mathrm{a3}} = k_{\mathrm{b2}}+k_{\mathrm{b3}}. \]

Thus,

\[ k_{\mathrm{b2}}-k_{\mathrm{a2}} = k_{\mathrm{a3}}-k_{\mathrm{b3}} = 302.6\ \mathrm{s^{-1}}. \]

The A and B dissociation rate constants cannot be the equal pair. If instead \(k_{\mathrm{b2}}=k_{\mathrm{c2}}\approx102.0\ \mathrm{s^{-1}}\), then

\[ k_{\mathrm{a2}}\approx102.0-302.6=-200.6\ \mathrm{s^{-1}}, \]

which is impossible. The equal pair must therefore be A and C:

\[ \boxed{k_{\mathrm{a2}}=k_{\mathrm{c2}}\approx102.0\ \mathrm{s^{-1}},} \]

\[ \boxed{ k_{\mathrm{b2}}\approx102.0+302.6 =404.6\ \mathrm{s^{-1}}. } \]

The common association rate constant is

\[ \begin{aligned} k_{\mathrm{a1}}=k_{\mathrm{b1}} &=\frac{k_{\mathrm{a2}}+k_{\mathrm{a3}}}{K_{\mathrm M,A}}\\ &\approx \frac{102.0+907.8}{5.1399\times10^{-5}}\\ &=1.9646\times10^7\ \mathrm{M^{-1}\,s^{-1}}. \end{aligned} \]

To three significant figures,

\[ \boxed{ k_{\mathrm{a1}}=k_{\mathrm{b1}} =1.96\times10^7\ \mathrm{M^{-1}\,s^{-1}}. } \]

The unrounded values satisfy the two saturation constraints:

\[ 907.8+605.2+3(170)=2023\ \text{products per second}, \]

\[ (907.8+605.2)(3600) = 5.4468\times10^6 < 5.94\times10^6 \quad\text{A-and-B products per hour}. \]

They also give the required low-concentration total-product ratio:

\[ n_A\varepsilon_A:n_B\varepsilon_B:n_C\varepsilon_C = 9:6:15 = 3:2:5. \]

The solution was checked against the official solution.