Recommendations for terminology and databases for biochemical thermodynamics

Abstract

Chemical equations are normally written in terms of specific ionic and elemental species and balance atoms of elements and electric charge. However, in a biochemical context it is usually better to write them with ionic reactants expressed as totals of species in equilibrium with each other. This implies that atoms of elements assumed to be at fixed concentrations, such as hydrogen at a specified pH, should not be balanced in a biochemical equation used for thermodynamic analysis. However, both kinds of equations are needed in biochemistry. The apparent equilibrium constant K′ for a biochemical reaction is written in terms of such sums of species and can be used to calculate standard transformed Gibbs energies of reaction Δ r G′°. This property for a biochemical reaction can be calculated from the standard transformed Gibbs energies of formation Δ f G i ′° of reactants, which can be calculated from the standard Gibbs energies of formation of species Δ f G j ° and measured apparent equilibrium constants of enzyme-catalyzed reactions. Tables of Δ r G′° of reactions and Δ f G i ′° of reactants as functions of pH and temperature are available on the web, as are functions for calculating these properties. Biochemical thermodynamics is also important in enzyme kinetics because apparent equilibrium constant K′ can be calculated from experimentally determined kinetic parameters when initial velocities have been determined for both forward and reverse reactions. Specific recommendations are made for reporting experimental results in the literature.