Page 196 - Thermodynamics of Biochemical Reactions

I 1.0 Introduction

The objective of this package is to give the basic thermodynamic data on a large number of species involved in
biochemical reactions at 298.15 K, 1 bar, and zero ionic strength and show how to use these data to calculate apparent
equilibrium constants K of biochemical reactions at desired pHs and ionic strengths. Programs are given for making all of
these calculations and more. The apparent equilibrium constant is related to the standard transformed Gibbs energy of
reaction A, G'"and to the standard transformed Gibbs energies of the reactants A, G;'" by (ref. 1-3)
A, G = v, 'Af G, = - RT In IC (1)
The v, ' are the stoichiometric numbers of reactants in the biochemical equation (positive for reactants on the right side of the
equation and negative for reactants on the left side). The prime is needed on the stoichiometric numbers to distinguish them
from the stoichiomeric numbers in the underlying chemical reactions. The standard transformed enthalpy of reaction
A, H ''I (heat of reaction) is related to the standard transformed enthalpies offormation Af Hi ''I of the reactants by
Ar H'" = v,'A~ H, "' (2)
These thermodynamic properties are functions of the pH and ionic strength, and they can be calculated from the standard
Gibbs energies of formation Af Go and standard enthalpies of formation Af H" of the species involved. The Af G; "' values of
131 reactants as functions of pH and ionic strength and the Af H, lo values of 69 reactants are calculated using the Mntherrzat-
icu programs calcdGmat and calcdHmat (ref. 4). These functions make it possible to calculate values of these properties at
298.15 K and at pHs in the range 5 to 9 and ionic strengths in the range 0 to 0.35 M.
The following tables are given and can be printed out:
table1 gives standard transformed Gibbs energies of formation of 131 reactants at pH 7 and ionic strengths of 0, 0.10, and
0.25 M.
table2 gives standard transformed Gibbs energies of formation of 131 reactants at ionic strength 0.25 M and pH values 015,
6, 7, 8, and 9.
table3 gives standard transformed enthalpies of formation of 69 reactants at pH 7 and ionic strengths of 0, 0.10, and 0.25 M.
table4 gives standard transformed enthalpies of formation of 69 reactants at ionic strength 0.25 M and pH values of 5, 6, 7, 8,
and 9.
These tables can be used to calculate A, G'" and A, H'" at pH 7 and ionic strengths of 0, 0.10, and 0.25 M or at ionic strength
0.25 M and pHs of 5, 6, 7, 8, and 9 for any reaction for which all the reactants are in these tables. They can also be used to
calculate standard apparent reduction potentials. The species data can be used to calculate average bindings of hydrogen ions
by reactants. Mathernaticu programs for carrying out these calculations are provided.
The basic thermodynamic data comes from classical thermodynamic tables and from experimental measurements of
K and Ar H'" at a particular pH and ionic strength together with measurements of acid dissociation constants. Some biochemi-
cal reactants consist of a single species, but others are sums of species; for example, ATP is made up of the species ATP4-,
HATP3- , and H2 ATP2- in the pH range 4 to 10 in the absence of metal ions that are bound reversibly. Therefore, the basic
thermodynamic data on biochemical reactions includes the standard Gibbs energies of formation A, Go and the standard
enthalpies of formation Af H" of species at zero ionic strength.
The basic data stored for each species is a list of ( A, Go , A, H" , zi , NHi ), where zi is the charge number, and
NH1 is the number of hydrogen atoms in the species. When a reactant is made up of more than one species, the basic data is
represented by a matrix with a row for each species. The values of the standard transformed Gibbs energies of formation
Af G'" and standard transformed enthalpies of formation Af H'" of these species are functions of pH and ionic strength, where
the effects of ionic strength are calculated using the extended Debye-Huckel equation and the effects of pH are calculated
using the number of hydrogen atoms in the species. These functions for reactants are calculated using the Mntiiemntica
programs calcdGmat and calcdHmat.
This data base is set up in such a way that typing the name of a reactant, say atp (lower case letters are used because
capital letters are used for Mnthenzatica operations) yields the function of pH and ionic strength for Af G'" and typing the
name atph yields the function of pH and ionic strength for Af H'" . These functions can be evaluated at a specific pH and

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