Biochemical thermodynamics is complicated for several reasons: (1) Biochemical reactants consist of sums of species whenever a reactant has a pK within about two units of the pH of interest or binds metal ions reversibly. (2) Species of a biochemical reactant are often ions, and the activity coefficients of ions are functions of ionic strength. (3) Enzyme catalysis may introduce constraints in biochemical reactions in addition to balances of atoms of elements. (4) Metabolism is sufficiently complicated that it is important to find ways to obtain a more global view. (5) In biochemistry other kinds of work, such as electric work, elongation work, and surface work may be involved. When intensive variables like pH, pMg, oxygen partial pressures, and concentrations of coenzymes are specified, the Gibbs energy G no longer provides the criterion for spontaneous change and equilibrium, and so it is necessary to use Legendre transforms to define transformed Gibbs energies G' and further transformed Gibbs energies G'' that do. The logic used here is a continuation of the process described by Gibbs that introduced the enthalpy H, Helmholtz energy A, and the Gibbs energy G by use of Legendre transforms of the internal energy U.

In my NIH Project (5R01-GM48358-07) I am involved in developing new ways to treat the thermodynamics of systems of biochemical reactions and in producing new types of tables of thermodynamic properties of biochemical reactants, including proteins. Mathematica programs and data bases have been put on the web so that the apparent equilibrium constants and other thermodynamic properties of biochemical reactions can be calculated by simply typing in the reactions. It is important to understand that if the standard transformed Gibbs energy of a reactant or reaction can be expressed as a function of its natural variables (for example temperature and pH), all the other standard thermodynamic properties can be calculated by taking partial derivatives. These are calculations that have been facilitated by the development of mathematical programs for personal computers.

NIH Project 5-R01-GM48358-07 - Resources for the Thermodynamics of Biochemical Reactions

Alberty, R. A. Biochemical Reaction Equilibria from the Point of View of a Semigrand Partition Function, J. Chem. Phys., 114, 8270-8274 (2001).

Alberty, R. A. Effect of Temperature on Standard Transformed Gibbs Energies of Formation of Reactants at Specified pH and Ionic Strength and Apparent Equilibrium Constants of Biochemical Reactions, J. Phys. Chem. B, 105, 7865-7870 (2001).

Alberty, R. A. Systems of Biochemical Reactions from the Point of View of a Semigrand Partition Function, Biophys. Chem., 93, 1-10 (2001).

Alberty, R. A. Thermodynamics of Systems of Biochemical Reaction Systems, J. Theoret. Biology, 215, 491-501 (2002).

Alberty, R. A. Inverse Legendre Transform in Biochemical Thermodynamics: Applied to the Last Five Reactions of Glycolysis, J. Phys. Chem., B 106, 6594-6599 (2002).

Alberty, R. A. BasicBiochemData2, (2002)
http://www.mathsource.com/cgi-bin/msitem?0211-622.

Alberty, R. A. Standard Transformed Gibbs Energies of Coenzyme Derivatives as Functions of pH and Ionic Strength, Biophys. Chem., in press.

Alberty, R. A. Thermodynamics of Biochemical Reactions, Wiley (2003).

Alberty, R. A. Effect of Temperature on the Standard Transformed Thermodynamic Properties of Biochemical Reactions with Emphasis on the Maxwell Equations, J. Phys. Chem., in press.

Alberty, R. A. Fundamental Equation of Thermodynamics for Protein-Ligand Binding, Biophys. Chem., in press.