Thermodynamics of systems of biochemical reactions

When a reaction system described in terms of species is in a certain state, the Gibbs energy G provides the means for determining whether each reaction will go to the right or the left, and the equilibrium composition of the whole system can be calculated using G. When the pH is specified, a system of biochemical reactions is described in terms of reactants, like ATP (a sum of species), and the transformed Gibbs energy G' provides the means for determining whether each reaction will go to the right or the left. The equilibrium composition of the whole system can be calculated using G'. Since metabolism is complicated, the thermodynamics of systems of reactions like glycolysis and the citric acid cycle can also be considered at specified concentrations of coenzymes like ATP, ADP, NAD(ox), and NAD(red). This is of interest because coenzymes tend to be in steady states because they are involved in many reactions. When the concentrations of coenzymes are constant, the further transformed Gibbs energy G" provides the means for calculating whether each reaction will go to the right or the left, and the equilibrium composition of the whole system can be calculated using G". Under these conditions, a metabolic reaction system can be reconceptualized in terms of sums of reactants; for example, glycolysis can be represented by C(6)=2C(3), where C(6) is the sum of the reactants with six carbon atoms and C(3) is the sum of the reactants with three carbon atoms. These calculations can also be described by use of semigrand partition functions. Semigrand partition functions have the advantage of containing all the thermodynamic information on a series of reactions at specified pH or at specified pH and specified concentrations of coenzymes.