IChO 2024 · Theory problem 3

Tyrosinase

The enzyme tyrosine 3-monooxygenase has an important biological role because it catalyzes the initial and rate-limiting step in the biosynthesis of the neurotransmitter dopamine. In this first step, L-DOPA is produced from the amino acid L-tyrosine (Tyr) in the presence of dissolved oxygen, tetrahydrofolic acid and ferrous ions. In a subsequent step, another enzyme transforms L-DOPA into dopamine.

Figure 1

The activity of the tyrosine 3-monooxygenase enzyme is described well by the simplest model of enzyme action, the Michaelis-Menten equation. This gives the rate of the formation (\(r\)) of L-DOPA as a function of the enzyme (E) and substrate Tyr (S) concentrations as follows:

\[ r=\frac{k[E][S]}{K_{\mathrm M}+[S]} \]

The following values of enzymatic turnover frequency (\(k=250\ \mathrm{min^{-1}}\)) and Michaelis constant (\(K_{\mathrm M}=0.49\ \mathrm{mmol\,dm^{-3}}\)) can be used in this task when needed.

Catechol (1,2-dihydroxybenzene) inactivates the enzyme tyrosine 3-monooxygenase irreversibly by turning it into an inactive form. When a carefully purified sample of catechol is mixed with the enzyme with the exclusion of dissolved oxygen, no change is seen at all. So the reaction of catechol with dissolved oxygen, which produces o-quinone, must be important.

Figure 2

This process can be studied in the absence of the enzyme. A test experiment in a reactor not in contact with ambient air at \(37\,^\circ\mathrm C\) and at pH 7.5 gave the following kinetic data:

time (min) catechol concentration (\(\mathrm{mmol\,dm^{-3}}\)) oxygen concentration (\(\mathrm{mmol\,dm^{-3}}\)) o-quinone concentration (\(\mu\mathrm{mol\,dm^{-3}}\))
0 2.00 0.200 0
20.0 1.97 0.170 30
40.0 1.94 0.140 60
60.0 1.91 0.111 89
80.0 1.88 0.083 117
100.0 1.85 0.054 146

3.1 — 5.0 pt

Identify the only by-product (which is not one of the molecules shown in the table above) and write the balanced equation of the process with molecular formulas based on the kinetic data.

3.2 — 2.0 pt

Calculate the initial rate (\(r_0\)) of o-quinone formation in this experiment with an appropriate unit.

The rate law of the process was determined by varying the initial concentrations of the reactants. Changing the oxygen concentration did not influence the initial rate of the process. Using different catechol concentrations gave the following initial rates for o-quinone formation:

catechol concentration (\(\mathrm{mmol\,dm^{-3}}\)) initial rate of o-quinone formation (\(\mu\mathrm{mol\,dm^{-3}\,min^{-1}}\))
1.0 0.75
4.0 3.0
6.0 4.5
8.0 6.0
10.0 7.5

3.3 — 5.0 pt

Determine the rate law of the reaction between catechol and oxygen producing o-quinone. Calculate the rate constant of this process (\(k_{\mathrm{catechol}}\)) with an appropriate unit.

In separate experiments, it was confirmed that neither o-quinone, nor the by-product inactivates the enzyme alone, nor even in combination.

An experiment in which the enzyme is reacted with catechol in the presence of dissolved oxygen did show inactivation, though.

The experiment was done in an open vessel so that any oxygen consumed in the process could be continuously replenished from air. The initial concentration of the enzyme was \(4.2\ \mathrm{nmol\,dm^{-3}}\), the initial concentration of catechol was \(2.00\ \mathrm{mmol\,dm^{-3}}\) at \(37\,^\circ\mathrm C\) and at pH 7.5.

Samples were taken regularly from the enzyme-catechol reaction mixture, and the activity of the enzyme was assayed by adding L-tyrosine, tetrahydrofolic acid and ferrous ions. During the enzyme activity measurements, the concentration of added L-tyrosine was \(10.0\ \mathrm{mmol\,dm^{-3}}\) and the concentration of L-DOPA in each assay sample was measured after 2.0 minutes. The following results were obtained:

Figure 3
inactivation reaction time \(t\) (min) L-DOPA concentration after 2.0 minutes from the start of the assay \([\mathrm{DOPA}]\) (\(\mu\mathrm{mol\,dm^{-3}}\))
0 2.0
20.0 1.9
40.0 1.7
60.0 1.3
70.0 1.00
80.0 0.72
90.0 0.38

3.4 — 4.0 pt

Derive a formula that allows you to calculate the actual concentration of active enzyme (\([E]\)) from the data of these experiments in terms of \(k\) (\(=250\ \mathrm{min^{-1}}\)), \(K_{\mathrm M}\) (\(=0.49\ \mathrm{mmol\,dm^{-3}}\)), and/or reagent concentrations.

The change in the active enzyme concentration as a function of time is well described by a parabola (\([E]=[E]_0-k_{\mathrm{obs}}t^2\)), where \(k_{\mathrm{obs}}\) is an observed rate constant (i.e. one that can be written later as a combination of elementary rate constants and initial concentrations), and \([E]_0\) is the initial concentration of the enzyme.

3.5 — 3.0 pt

Give the value of \(k_{\mathrm{obs}}\) with an appropriate unit.

3.6 — 3.0 pt

Determine the first half-life of the enzyme inactivation reaction. Derive a formula that gives the first half-life as a function of the initial enzyme concentration and of \(k_{\mathrm{obs}}\).

The first half-lives for enzyme inactivation were determined using other initial catechol concentrations. The dependences of active enzyme concentrations on time were very well described by parabolas in these cases as well.

catechol concentration (\(\mathrm{mmol\,dm^{-3}}\)) first half-life (min)
1.0 140
4.0 35
6.0 23
8.0 17.5
10.0 14

3.7 — 6.0 pt

Derive a rate equation of the enzyme inactivation process consistent with all the experimental observations.

3.8 — 3.0 pt

What are the reactants of the rate determining step for the enzyme inactivation process? Select the ONLY correct option on the answer sheet.

A) \(\ce{\text{catechol} + O2 ->} \ldots\)
B) \(\ce{\text{catechol} + \text{o-quinone} ->} \ldots\)
C) \(\ce{\text{o-quinone} + O2 ->} \ldots\)
D) \(\ce{\text{enzyme} + 2 \text{catechol} ->} \ldots\)
E) \(\ce{\text{enzyme} + O2 ->} \ldots\)
F) \(\ce{2 \text{catechol} + O2 ->} \ldots\)
G) \(\ce{\text{enzyme} + \text{catechol} ->} \ldots\)
H) \(\ce{\text{enzyme} + \text{by-product} ->} \ldots\)

Official English text of the problem.

Answers

  • 3.1: Hydrogen peroxide, \(\ce{H2O2}\), SMILES OO. \[ \boxed{\ce{C6H6O2 + O2 -> C6H4O2 + H2O2}} \]

  • 3.2: \(\boxed{r_0=1.5\ \mu\mathrm{mol\,dm^{-3}\,min^{-1}}}\).

  • 3.3: \(\boxed{r=k_{\mathrm{catechol}}[\text{catechol}]}\), first order in catechol and zero order in oxygen over the investigated range, with \[ \boxed{k_{\mathrm{catechol}}=7.5\times10^{-4}\ \mathrm{min^{-1}}}. \]

  • 3.4: For assay duration \(\tau=2.0\ \mathrm{min}\), \[ \boxed{[E]=\frac{[\mathrm{DOPA}](K_{\mathrm M}+[S])}{k\tau[S]}}. \]

  • 3.5: \[ \boxed{k_{\mathrm{obs}}\approx4.2\times10^{-4}\ \mathrm{nmol\,dm^{-3}\,min^{-2}} =4.2\times10^{-13}\ \mathrm{mol\,dm^{-3}\,min^{-2}}}. \]

  • 3.6: Approximately \(70\ \mathrm{min}\), with \[ \boxed{t_{1/2}=\sqrt{\frac{[E]_0}{2k_{\mathrm{obs}}}}}. \]

  • 3.7: Writing \(C=[\text{catechol}]\), \(Q=[o\text{-quinone}]\), and \(C_0=C(0)\), a consistent rate equation is \[ \boxed{-\frac{d[E]}{dt}=k_I C Q \simeq k_I k_{\mathrm{catechol}}C_0^2t}, \qquad \boxed{k_{\mathrm{obs}}=\frac12 k_I k_{\mathrm{catechol}}C_0^2}. \]

  • 3.8: B — catechol + \(o\)-quinone. Catechol: Oc1ccccc1O; \(o\)-quinone: O=C1C=CC=CC1=O.

Solution

3.1 — Identification of the by-product and balanced reaction

The relevant molecules are catechol (benzene-1,2-diol), Oc1ccccc1O, with formula \(\ce{C6H6O2}\); dioxygen, O=O; and \(o\)-quinone (1,2-benzoquinone), O=C1C=CC=CC1=O, with formula \(\ce{C6H4O2}\).

During the first \(20.0\ \mathrm{min}\),

\[ -\Delta[\text{catechol}] =2.00-1.97 =0.030\ \mathrm{mmol\,dm^{-3}}, \]

\[ -\Delta[\ce{O2}] =0.200-0.170 =0.030\ \mathrm{mmol\,dm^{-3}}, \]

and

\[ \Delta[o\text{-quinone}] =30\ \mu\mathrm{mol\,dm^{-3}} =0.030\ \mathrm{mmol\,dm^{-3}}. \]

Thus catechol consumption, oxygen consumption, and quinone formation occur in a \(1:1:1\) molar ratio.

Converting one molecule of catechol into one molecule of quinone removes two hydrogen atoms. With one molecule of oxygen consumed, atom balance requires the remaining product to be hydrogen peroxide, \(\ce{H2O2}\), OO:

\[ \boxed{\ce{C6H6O2 + O2 -> C6H4O2 + H2O2}}. \]

Both sides contain six carbon atoms, six hydrogen atoms, and four oxygen atoms.

3.2 — Initial rate of quinone formation

The first interval gives the initial slope:

\[ r_0\simeq \frac{[\text{quinone}]_{20}-[\text{quinone}]_0}{20.0-0} =\frac{30-0}{20.0}. \]

Therefore,

\[ \boxed{r_0=1.5\ \mu\mathrm{mol\,dm^{-3}\,min^{-1}}}. \]

The next interval gives the same slope to the precision of the data.

3.3 — Rate law and catechol oxidation rate constant

Write the empirical rate law as

\[ r=k_{\mathrm{catechol}}[\text{catechol}]^a[\ce{O2}]^b. \]

Changing the oxygen concentration does not change the initial rate, so \(b=0\) over the investigated concentration range.

Increasing catechol concentration from \(1.0\) to \(4.0\ \mathrm{mmol\,dm^{-3}}\) increases the rate from \(0.75\) to \(3.0\ \mu\mathrm{mol\,dm^{-3}\,min^{-1}}\), also by a factor of four. All the other measurements show the same proportionality. Hence \(a=1\), and

\[ \boxed{r=k_{\mathrm{catechol}}[\text{catechol}]}. \]

Converting the numerator and denominator to matching concentration units,

\[ k_{\mathrm{catechol}} =\frac{0.75\times10^{-3}\ \mathrm{mmol\,dm^{-3}\,min^{-1}}} {1.0\ \mathrm{mmol\,dm^{-3}}} =\boxed{7.5\times10^{-4}\ \mathrm{min^{-1}}}. \]

The zero order in oxygen applies while oxygen is available under the experimental conditions; it does not imply that oxidation can proceed without oxygen.

3.4 — Active-enzyme concentration from the assay

The assay substrate is L-tyrosine, N[C@@H](Cc1ccc(O)cc1)C(=O)O, and its measured product is L-DOPA, N[C@@H](Cc1ccc(O)c(O)c1)C(=O)O. These SMILES represent the neutral structures shown in the paper, with the \(S\) configuration of both L-amino acids.

Let \(\tau=2.0\ \mathrm{min}\) denote the assay duration, distinct from the inactivation time \(t\). The maximum product concentration is only \(2.0\ \mu\mathrm{mol\,dm^{-3}}\), compared with \(10.0\ \mathrm{mmol\,dm^{-3}}\) of substrate. Thus substrate depletion is at most

\[ \frac{2.0\times10^{-3}}{10.0}\times100\%=0.020\%, \]

and \([S]\) can be treated as constant.

Under the short-assay approximation that the sampled active-enzyme concentration remains effectively constant,

\[ \frac{[\mathrm{DOPA}]}{\tau} =r=\frac{k[E][S]}{K_{\mathrm M}+[S]}. \]

Rearranging gives

\[ \boxed{ [E]=\frac{[\mathrm{DOPA}]}{k\tau} \left(1+\frac{K_{\mathrm M}}{[S]}\right) }. \]

Numerically,

\[ [E] =[\mathrm{DOPA}] \frac{0.49+10.0}{250(2.0)(10.0)} =0.002098[\mathrm{DOPA}], \]

when both concentrations use the same units. Equivalently,

\[ \boxed{ \frac{[E]}{\mathrm{nmol\,dm^{-3}}} =2.098\, \frac{[\mathrm{DOPA}]}{\mu\mathrm{mol\,dm^{-3}}} }. \]

For the initial sample, this gives \(2.098(2.0)=4.196\ \mathrm{nmol\,dm^{-3}}\), agreeing with the stated \(4.2\ \mathrm{nmol\,dm^{-3}}\).

3.5 — Observed rate constant

From

\[ [E]=[E]_0-k_{\mathrm{obs}}t^2, \]

we obtain

\[ k_{\mathrm{obs}}=\frac{[E]_0-[E](t)}{t^2}. \]

At \(t=90.0\ \mathrm{min}\),

\[ [E](90)=2.098(0.38) =0.79724\ \mathrm{nmol\,dm^{-3}}. \]

Therefore,

\[ k_{\mathrm{obs}} =\frac{4.2-0.79724}{(90.0)^2} =4.2009\times10^{-4}\ \mathrm{nmol\,dm^{-3}\,min^{-2}}. \]

To sensible precision,

\[ \boxed{k_{\mathrm{obs}}\approx4.2\times10^{-4}\ \mathrm{nmol\,dm^{-3}\,min^{-2}}}. \]

A fit using all the measurements gives approximately \(4.20\times10^{-4}\) in the same units. Its units are concentration divided by time squared, as required by the parabolic equation.

3.6 — First half-life

The measured DOPA concentration is proportional to active-enzyme concentration. It falls from \(2.0\) to \(1.00\ \mu\mathrm{mol\,dm^{-3}}\) at \(t=70.0\ \mathrm{min}\), so the experimental first half-life is approximately

\[ \boxed{t_{1/2}\approx70\ \mathrm{min}}. \]

In general, substituting \([E](t_{1/2})=[E]_0/2\) gives

\[ \frac{[E]_0}{2}=[E]_0-k_{\mathrm{obs}}t_{1/2}^2. \]

Thus,

\[ \boxed{t_{1/2}=\sqrt{\frac{[E]_0}{2k_{\mathrm{obs}}}}}. \]

Using the coefficient from 3.5 gives

\[ t_{1/2} =\sqrt{\frac{4.2}{2(4.2\times10^{-4})}} =70.7\ \mathrm{min}, \]

consistent with about \(70\ \mathrm{min}\) from the rounded experimental data.

3.7 — Rate equation for enzyme inactivation

Let

\[ C=[\text{catechol}],\qquad Q=[o\text{-quinone}],\qquad C_0=C(0). \]

First, differentiating the observed parabola gives

\[ r_I\equiv-\frac{d[E]}{dt}=2k_{\mathrm{obs}}t. \]

Thus the enzyme-loss rate increases approximately linearly with time.

Next, the half-life data show that

\[ C_0t_{1/2}\approx 140\ \mathrm{mmol\,dm^{-3}\,min}. \]

For example, \(1.0(140)=4.0(35)=8.0(17.5)=10.0(14)=140\); the \(6.0\) entry gives \(138\), consistent with rounding. Therefore,

\[ t_{1/2}\propto C_0^{-1}. \]

At the fixed initial enzyme concentration, the relation from 3.6 then requires

\[ k_{\mathrm{obs}}\propto t_{1/2}^{-2}\propto C_0^2. \]

Writing \(k_{\mathrm{obs}}=aC_0^2\), the directly inferred time-dependent rate equation is

\[ \boxed{r_I=2aC_0^2t}. \]

To express this in terms of reacting species, use quinone formation:

\[ \frac{dQ}{dt}=k_{\mathrm{catechol}}C. \]

For the approximate parabolic model, take \(C\simeq C_0\). This is reasonable over the reported experiment: independent catechol oxidation changes its concentration by only about \(6.5\%\) in \(90\ \mathrm{min}\). With initially negligible quinone,

\[ Q(t)\simeq k_{\mathrm{catechol}}C_0t. \]

A rate law first order in both catechol and quinone therefore gives

\[ r_I=k_I C Q \simeq k_I k_{\mathrm{catechol}}C_0^2t, \]

which has exactly the required time and initial-catechol dependences. Consequently, a consistent rate equation is

\[ \boxed{-\frac{d[E]}{dt}=k_I[\text{catechol}][o\text{-quinone}]}. \]

Integrating under the same approximations,

\[ \boxed{ [E](t)\simeq[E]_0 -\frac12 k_I k_{\mathrm{catechol}}C_0^2t^2 }, \]

so that

\[ \boxed{k_{\mathrm{obs}}=\frac12 k_I k_{\mathrm{catechol}}C_0^2}. \]

Here \(k_I\) is defined for the rate of active-enzyme loss, including any fixed yield of inactivation per slow reaction event. Its fitted value is

\[ k_I =\frac{2(4.2\times10^{-13})} {(7.5\times10^{-4})(2.00\times10^{-3})^2} \approx2.8\times10^{-4}\ \mathrm{dm^3\,mol^{-1}\,min^{-1}}. \]

This model accounts for the observations through slow generation of an inactivating species from catechol and quinone, followed by rapid reaction with the enzyme. Oxygen is needed to generate quinone; quinone and hydrogen peroxide without catechol do not provide this route. The enzyme concentration does not appear in the limiting rate while sufficient active enzyme remains to capture the generated species.

3.8 — Reactants of the rate-determining step

The rate law derived above is proportional to catechol concentration multiplied by quinone concentration. The corresponding listed reactants are therefore

\[ \boxed{\text{B: catechol + }o\text{-quinone}}. \]

Catechol is Oc1ccccc1O, and \(o\)-quinone is O=C1C=CC=CC1=O.

Quinone accumulates approximately linearly with time, so its slow reaction with the nearly constant catechol concentration generates the inactivating species at an increasing rate. This produces the observed quadratic loss of active enzyme.

The solution was checked against the official solution.