Synthesizing units (SUs) are generalized
enzymes that follow the rules of classic
enzyme kinetics with two modifications:
*product formation is not taken to be a function of
substrate
Substrate may refer to:
Physical layers
*Substrate (biology), the natural environment in which an organism lives, or the surface or medium on which an organism grows or is attached
** Substrate (locomotion), the surface over which an organism lo ...
concentrations but of substrate fluxes that arrive at the SUs
*the
dissociation rate The dissociation rate in chemistry, biochemistry, and pharmacology is the rate or speed at which a ligand dissociates from a protein, for instance, a receptor. It is an important factor in the binding affinity
In biochemistry and pharmacology, ...
of the substrate-SU complex to (unchanged) substrate and (unbounded) SU is assumed to be small.
Modifications of classic theory
Extension
The first modification is an extension of the classic theory; if arrival fluxes are taken proportional to substrate concentrations, the classic theory results. This extension allows application in spatially
heterogeneous environments (such as in living cells), and to treat
photons and
molecules
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioc ...
in the same framework (important in
photosynthesis
Photosynthesis is a process used by plants and other organisms to convert light energy into chemical energy that, through cellular respiration, can later be released to fuel the organism's activities. Some of this chemical energy is stored i ...
).
Simplification
The second modification allows a substantial simplification of the classic theory, and so application in complex
metabolic networks. The theory on synthesizing units
Kooijman, S. A. L. M. 1998. The Synthesizing Unit as model for the stoichiometric fusion and branching of metabolic fluxes. Biophys. Chem. 73: 179 - 188 (abstract)
/ref> is used in dynamic energy budget theory, where 4 basic modes are distinguished:
*the substrates can be substitutable or supplementary (= complementary); if the transformations A -> C and B -> C can occur, substrates A and B are said to be substitutable with respect to their transformation to C, if both are required to produce C they are said to be supplementary
*the processing of these substrates by SUs can be sequential or parallel; if in the transformation A + B -> C the binding of substrate A to the SU does not affect that of B, these substrates are processed simultaneously, if not these substrates are processed sequentially
Mixtures of the 4 basic modes can occur, especially if the substrates represent generalized compounds, rather than pure chemical compounds. A generalized compound is a mixture of chemical compounds that does not change in composition.
References
Sources
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Enzymes
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