Page 56 - Thermodynamics of Biochemical Reactions

50 Chapter 3 Chemical Equilibrium in Aqueous Solutions

only C, and C, organic molecules and ions. Cox et al. (1989) list a number of
species on which there is international agreement.
As discussed in Chapter 1, Burton (1957) used equilibrium constants for
enzyme-catalyzed reactions to calculate standard Gibbs energies of formation for
species of biochemical interest. Wilhoit (1969) and Thauer (1977) considerably
extended Burton's table. Goldberg (1984) and Goldberg and Tewari (1989) have
calculated AsGj and ASHY for more species of biochemical interest from measure-
ments of apparent equilibrium constants and enthalpies of enzyme-catalyzed
reactions. When the standard Gibbs energies of formation for all the species in a
system are known, the equilibrium composition can be calculated by use of a
computer program that minimizes the Gibbs energy. This was illustrated for the
hydrolysis of ATP, which involves 17 species (Alberty, 1991).
In making thermodynamic tables of properties of species in biochemical
reactions, there are cases where it is not possible to calculate A, Gi.' and As HL with
respect to the elements because equilibrium constants and heats of reaction have
not been measured for reactions connecting the species with the elements. In these
cases it is possible to assign A,GP = AfHi = Cim(i) = 0 for one species and to
calculate AfG;, A,H:, and Cbm(i) for other species on the basis of this convention.
Alberty and Goldberg (1992) applied this convention to adenosine because at that
time it was not possible to connect ATP4- with the elements in their reference
states. They showed that values of AfGP and AfHY calculated in this way can be
used to calculate equilibrium constants and enthalpies of reaction. But, of course,
A,GP and A,HY calculated in this way cannot be used to calculate equilibrium
constants and enthalpies for reactions that form adenosine from the elements.
More recently Boerio-Goates et al. (2001) have determined the enthalpy of
combustion of adenosine (cr), its third law entropy, and its solubility in water at
298.15K. This makes it possible to calculate A,H"(adenosine, aq) and A,G'
(adenosine, aq) at 298.15K. They have recalculated A,H' and A,G" for all of the
species in the ATP series. This does not change the values of equilibrium
constants and enthalpies of reaction calculated from the previous table (Alberty
and Goldberg, 1992). An essential part of any table is a list of the conventions.
Using values of standard formation properties from tables based on different
conventions will lead to incorrect results.
The most basic data on thermodynamic properties of species at a certain
temperature include A,GP(Z = 0) and A,HP(I = 0), the charge number i, and the
number NH(i) of hydrogen atoms in the species. The number of hydrogen atoms
in a species is not used in this chapter but in the next chapter. A database in
computer readable form is presented in the Mathenzatica package BasicBiochem-
Data2, which is the first item in the second part of this book. The basic data on
the species of 131 reactants are given in section 2 of this package. The data for
each reactant is in the form of a matrix with a row for each species of the reactant:
namesp = (((A,GL, A,H;, zl, NH(l)], (AfGi, ASH;, z2, NH(2)$, . . .j (3.8-1)
The first entry is for the species with the fewest hydrogen atoms. Only species of
interest in the range pH 5 to 9 are included. No complex ions are included in this
table. The advantage of this table is that, with Mathematicu in a personal
computer, it is not necessary to copy these numbers to make a calculation.
Programs for making these calculations are also included in the package.
The sources of the data are described in Alberty (1998b, d, and other articles).
The complications of dissolved carbon dioxide are discussed in Section 8.7.
Reactions involving NAD,,, NAD,,,, NADP,,, and NADP,,, are discussed in
Chapter 9.
This data file and programs (Alberty, 2001) for using it are available on the
web at http:llww~.n.latlz.sourc.e. cornlcgi-binlnisitemP0211-622. It can be read using
MathReader, which is free from Wolfram Research, Inc. (100 Trade Center Drive,
Champaign, IL 61820-7237): tzttpllwivw.~vo~fLum.coin. BasicBiochemData2 is
available in two forms at MathSource: a package that can be downloaded using