Page 109 - Thermodynamics of Biochemical Reactions

Thernwdyanamics of Biochemical Reactions. Robert A. Alberty
Copyright 0 2003 John Wiley & Sons, Inc.
ISBN 0-471-22851-6

m 6.1 Calculation of Net Reactions Using Matrix
Multiplication
5s 6.2 Calculation of Pathways by Solving Linear
Equations
:& 6.3 Use of a Legendre Transform for Reactions
Involving Water as a Reactant
Calculations of Equilibrium Compositions for
Systems of Biochemical Reactions
6.5 Three Levels of Calculations of Compositions
for Systems of Biochemical Reactions
6.6 Consideration of Glycolysis at Specified [ATP],
[ADPI, [INADOXI, CNAD,,,I, and [Pi]
88i 6.7 Calculation of the Equilibrium Composition for
Glycolysis

Systems of biochemical reactions like glycolysis, the citric acid cycle, and larger
and smaller sequential and cyclic sets of enzyme-catalyzed reactions present
challenges to make calculations and to obtain an overview. The calculations of
equilibrium compositions for these systems of reactions are different from equilib-
rium calculations on chemical reactions because additional constraints, which
arise from the enzyme mechanisms, must be taken into account. These additional
constraints are taken into account when the stoichiometric number matrix is used
in the equilibrium calculation via the program equcalcrx, but they must be
explicitly written out when the conservation matrix is used with the program
equcalcc. The stoichiometric number matrix for a system of reactions can also be
used to calculate net reactions and pathways.
Since concentrations of ATP, ADP, NAD,,, and NAD,,, may be in steady
states, it is of interest to calculate equilibrium compositions that correspond with
these steady state concentrations. These calculations are referred to as level 3
equilibrium calculations because they are based on the introduction of [ATP],
[ADP], and the like, as natural variables by use of a Legendre transform.

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