Transient kinetic isotope fractionation
{{Short description|Unusual processes that separate isotopes}}
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Transient kinetic isotope effects (or fractionation) occur when the reaction leading to isotope fractionation does not follow pure first-order kinetics (FOK) and therefore isotopic effects cannot be described with the classical equilibrium fractionation equations or with steady-state kinetic fractionation equations (also known as the Rayleigh equation).Mariotti A., J.C. Germon, P. Hubert, P. Kaiser, R. Letolle, A. Tardieux, P. Tardieux, (1981), Experimental determination of nitrogen kinetic isotope fractionation – Some principles – Illustration for the denitrification and nitrification processes, Plant and Soil 62(3), 413–430. In these instances, the general equations for biochemical isotope kinetics (GEBIK) and the general equations for biochemical isotope fractionation (GEBIF) can be used.
The GEBIK and GEBIF equations are the most generalized approach to describe isotopic effects in any chemical, catalytic reaction and biochemical reactions because they can describe isotopic effects in equilibrium reactions, kinetic chemical reactions and kinetic biochemical reactions.Maggi F. and W. J. Riley, (2010), Mathematical treatment of isotopologue and isotopomer speciation and fractionation in biochemical kinetics, Geochim. Cosmochim. Acta, {{doi|10.1016/j.gca.2009.12.021}} In the latter two cases, they can describe both stationary and non-stationary fractionation (i.e., variable and inverse fractionation). In general, isotopic effects depend on the number of reactants and on the number of combinations resulting from the number of substitutions in all reactants and products. Describing with accuracy isotopic effects, however, depends also on the specific rate law used to describe the chemical or biochemical reaction that produces isotopic effects. Normally, regardless of whether a reaction is purely chemical or whether it involves some enzyme of biological nature, the equations used to describe isotopic effects base on FOK. This approach systematically leads to isotopic effects that can be described by means of the Rayleigh equation. In this case, isotopic effects will always be expressed as a constant, hence will not be able to describe isotopic effects in reactions where fractionation and enrichment are variable or inverse during the course of a reaction. Most chemical reactions do not follow FOK; neither biochemical reactions can normally be described with FOK. To properly describe isotopic effects in chemical or biochemical reactions, different approaches must be employed such as the use of Michaelis–Menten reaction order (for chemical reactions) or coupled Michaelis–Menten and Monod reaction orders (for biochemical reactions). However, conversely to Michaelis–Menten kinetics, GEBIK and GEBIF equations are solved under the hypothesis of non-steady state. This characteristic allows GEBIK and GEBIF to capture transient isotopic effects.
Mathematical description of transient kinetic isotope effects
The GEBIK and GEBIF equations are introduced here below.
=Notation=
The GEBIK and GEBIF equations describe the dynamics of the following state variables
:; S : substrate concentration
:; P : product concentration
:; E : enzyme concentration
:; C : complex concentration
:; B : biomass concentration
Both S and P contain at least one isotopic expression of a tracer atom. For instance, if the carbon element is used as a tracer, both S and P contain at least one C atom, which may appear as
:
where is the number of tracer atoms within S, while is the number of isotopic substitutions in the same molecule. The condition must be satisfied. For example, the
Substrates and products appear in a chemical reaction with specific stoichiometric coefficients. When chemical reactions comprise combinations of reactants and products with various isotopic expressions, the stoichiometric coefficients are functions of the isotope substitution number. If and are the stoichiometric coefficient for substrate and product, a reaction takes the form
:
For example, in the reaction
For isotopomers, the substitution location is taken into account as and , where and indicate a different expressions of the same isotopologue . Isotopomers only exist when
:
where
Reactions of asymmetric isotopomers can be written using the partitioning coefficient {{mvar|u}} as
:
where
:
:
can be written as one reaction in which each isotopomer product is multiplied by its partition coefficient as
:
with
{{NumBlk|:|
For instance, consider the
:
In this case the reaction can be written as
:
with two substrates and two products without indication of the substitution location because all molecules are symmetric.
Biochemical kinetic reactions of type ({{EquationNote|1}}) are often catalytic reactions in which one or more substrates,
products,
{{NumBlk|:|
with the index
== Example ==
The reactions
:
:
:
:
can be written as
:
:
:
=Isotope mass balance=
The following isotope mass balances must hold
:
:
=General equations for biochemical isotope kinetics (GEBIK) =
To solve for the concentration of all components appearing in any general biochemical reaction as in ({{EquationNote|2}}), the Michaelis–Menten kinetics for an enzymatic reaction are coupled with the Monod kinetics for biomass dynamics. The most general case is to assume that the enzyme concentration is proportional to the biomass concentration and that the reaction is not in quasi-steady state. These hypotheses lead to the following system of equations
{{NumBlk|:|
x_{b_{ji}} [{k}_{2(i)} C_i -{k}_{1(i)} {E \overline{S}}_i]|{{EquationRef|3a}}}}
{{NumBlk|:|
{k}_{1(i)} {E\overline{S}}_i - [{k}_{2(i)} + {k}_{3(i)}] C_i|{{EquationRef|3b}}}}
{{NumBlk|:|
\sum_i u_{\gamma_{hi}} y_{d_{hi}} {k}_{3(i)} C_i|{{EquationRef|3c}}}}
{{NumBlk|:|
-\sum_i \frac{\ce{d} C_i}{\ce{d}t}|{{EquationRef|3d}}}}
{{NumBlk|:|
\sum_{\gamma_h} \frac{\ce{d}[{^{d_h}_{c_h}}\ce P^{\gamma_h}_h]}{\ce{d}t} - \mu B|{{EquationRef|3e}}}}
with
Microbial. 3, 371–394.
= General equations for biochemical isotope fractionation (GEBIF) =
The isotopic composition of the components in a biochemical system can be defined in different ways depending on the definition of isotopic ratio. Three definitions are described here:
== Isotopic ratio – definition 1 ==
Isotopic ratio relative to each component in the system, each with its isotopic expression, with respect to the concentration of its most abundant isotopologue
:
:
== Isotopic ratio – definition 2 ==
Isotopic ratio relative to the mass of the tracer element in each component;
:
a_j} \sum_{\beta_j} \frac{(a_j-b_j) p}{^{b_j}M_{S_j}} \ {^{b_j}_{a_j}}S^{\beta_j}_j (t)
}
:
c_h} \sum_{\gamma_h} \frac{(c_h-d_h) p }{^{d_h}M_{P_h}} \ {^{d_h}_{c_h}}P^{\gamma_h}_h (t) }
where,
== Isotopic ratio – definition 3 ==
Isotopic ratio relative to the mass of the tracer element in the accumulated substrates and products
:
\sum_{b_j\neq a_j} \sum_{\beta_j} \frac{(a_j-b_j) p}{^{b_j}M_{S_j}} \ {^{b_j}_{a_j}}S^{\beta_j}_j (t) },
:
\sum_{d_h\neq c_h} \sum_{\gamma_h} \frac{(c_h-d_h) p }{^{d_h}M_{P_h}} \ {^{d_h}_{c_h}}P^{\gamma_h}_h (t) }.
== Isotopic composition ==
Regardless of the definition of the isotopic ratio, the isotopic composition of substrate and product are expressed as
{{NumBlk|:|
{{NumBlk|:|
where
== Fractionation factor ==
The isotopic ratio of the product can be used to define the instantaneous isotopic ratio
{{NumBlk|:|
and the time-dependent fractionation factor
{{NumBlk|:|
== Isotopic enrichment ==
The time-dependent isotopic enrichment is simply defined as
{{NumBlk|:|
Simplified forms of GEBIK and GEBIF
Under specific assumptions, the GEBIK and GEBIF equations become equivalent to the equation for steady-state kinetic isotope fractionation in both chemical and biochemical reactions. Here two mathematical treatments are proposed: (i) under biomass-free and enzyme-invariant (BFEI) hypothesis and (ii) under quasi-steady-state (QSS) hypothesis.
= BFEI hypothesis =
In instances where the biomass and enzyme concentrations are not appreciably changing in time, we can assume that biomass dynamics is negligible and that the total enzyme concentration is constant, and the GEBIK equations become
{{NumBlk|:|
{{NumBlk|:|
{{NumBlk|:|
{{NumBlk|:|
Eqs. ({{EquationNote|4}}) for isotopic compositions, Eq. ({{EquationNote|6}}) for the fractionation factor and Eq. ({{EquationNote|7}}) for the enrichment factor equally applies to the GEBIK equations under the BFEI hypothesis.
= QSS hypothesis =
If the quasi-steady-state hypothesis is assumed in addition to BFEI hypothesis, then the complex concentration can be assumed to be in a stationary (steady) state according to the Briggs–Haldane hypothesis, and the GEBIK equations become
{{NumBlk|:|
{{NumBlk|:|
1+ \displaystyle\sum_{p\neq i} \dfrac{\overline{S}_p}{K_p} \right) }|{{EquationRef|9a}}}}
which are written in a form similar to the classical Micaelis-Menten equations for any substrate and product. Here, the equations also show that the various isotopologue and isotopomer substrates appear as competing species. Eqs. ({{EquationNote|4}}) for isotopic compositions, Eq. ({{EquationNote|6}}) for the fractionation factor and Eq. ({{EquationNote|7}}) for the enrichment factor equally applies to the GEBIK equations under the BFEI and QSS hypothesis.
Example of application of GEBIK and GEBIF
An example is shown where GEBIK and GEBIF equations are used to describe the isotopic reactions of
:
:
:
These can be rewritten using the notation introduced before as.
:
:
:
The substrate
:
:
:
:
:
:
:
:
:
:
:
:
:
:
Example of application of GEBIK and GEBIF under BFEI and QSS hypotheses
The same reaction can be described with the GEBIK and GEBIF equations under the BFEI and QSS approximations as
:
:
:
:
:
:
:
:
:
where
See also
Notes
{{Notelist}}