Contents

1. Introduction

2. Sources of Experimental Data

3. Calculation of Standard Thermodynamic Properties of Species from Apparent Equilibrium Constants and Heats of Biochemical Reactions

4. Calculation of Standard Transformed Thermodynamic Properties of Reactants and Reactions at Specified pH

5. Further Transformed Thermodynamic Properties

6. Maxwell Relations

7. Use of Mathematica®

8. Statistical Mechanics of Systems of Biochemical Reactions

9. Names of Enzymes

10. Acknowledgement

3. Calculation of Standard Thermodynamic Properties of Species from Apparent Equilibrium Constants and Heats of Biochemical Reactions

These calculations are described in the references given above, but some general comments are needed. Early calculations of properties of species of biochemical reactants were made by Burton (1953), Wilhoit (1969), Thauer (1977), and Miller Smith-Magowan (1990), and Larson, Tewari, and Goldberg (1992); but the developments in 1992 provided a better understanding of the process, new nomenclature, and computer programs. This is not the place to discuss the required equations that are given in Alberty, Thermodynamics of Biochemical Reactions (2003), but the current status of the data base that is being produced can be described. The standard thermodynamic properties of species of 131 biochemical reactants are given in computer readable form in Mathematica^® (Wolfram Research, Inc., 100 Trade Center Drive, Champaign, IL 61801-7237).

R. A. Alberty, BasicBiochemData2, (2003)

http://www.mathsource.com/cgi-bin/msitem?0211-622 .

This is a Mathematica package that includes data on species and computer programs for using these data to calculate standard transformed Gibbs energies of formation of reactants (sums of species) and biochemical reactions. Other thermodynamic properties at 298.15 K and specified pH and ionic strength can also be calculated. The apparent equilibrium constant of any biochemical reaction involving these reactants can be calculated at 298.15 K, pHs in the range 5-9, and ionic strengths in the range zero to about 0.35 M. For about 70 of these reactants these properties can be calculated in approximately the range 273.15 K and 313.15 K because the standard enthalpies of formation are known for the species involved. This data base contains enough information to calculate the apparent equilibrium constants of all the reactions in glycolysis and the citric acid cycle and many more chemical reactions. It is of interest to note that three proteins are included in this data base. It is possible to include the properties of the reaction site of a protein when the pKs of neighboring groups are known. When metal ions like Mg²⁺ affect apparent equilibrium constants and heats of reaction, these effects can also be included by using the Legendre transform G’ = G – n_c(H) µ(H⁺) – n_c(Mg) µ(Mg²⁺), where n_c(Mg) is the total amount of magnesium atoms in the system and µ(Mg²⁺) is the chemical potential of magnesium ions at the specified temperature, pMg, and ionic strength.

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