Page 223 - Thermodynamics of Biochemical Reactions

BasicBiochemData2 223

calcGeflsplequat-, ~Hc-, ionstr-, 21-, nH1-1 :=
Module[{energy, trGereactant),(*This program uses CviAfGiIO=-RTlnK' to calculate the
standard Gibba energy of formation of the species of a reactant that does not have a
pK in the range 4 to 10. The equation is of the form pyruvate+atp-x-
adp==-8.31451*.29815*Log[K11, where K' is the apparent equilibrium constant at 298.15
K, pHc, and ionic strength is. The reactant has charge number zl and hydrogen atom
number nH1. The output is the species vector without the standard enthalpy of
formation. *)
energy = Solve[equat, x] /. pH -> pHc /. is -> ionstr;
trGereactant = energy[[l,l,Z]l;
gefl = trGereactant - nH1*8.31451*0.29815*Log[lO]*pHc +
(2.91482*(zlA2 - nH1)*ionstrA0.5)/
(1 + 1.6*ionstrA0.5); {{gefl, -, zl, nH1})1

calcGefZsgCequat-, pHc-, ionstr-, 21-, nHl-, pKO-1 :=
Module[(energy, trGereactant, pKe, trgefpHiS,gefl, gefZ},(*This program uses Evils.
fGi'O=-RTlnK' to calculate the standard Gibbs energies of formation of the two species
of a reactant for which the pK at zero ionic strength is pKO. The equation is of the
form pyruvate+atp-x-adp==-8.31451*.29815*LogIK11, where K' is the apparent equilibrium
constant at 298.15 K, pHc, and ionic strength is. The more basic form of the reactant
has charge number zl and hydrogen atom number nH1. The output is the species matrix
without the standard enthalpies of formation.*)
energy = SolveCequat, XI /. pH -> pHc /. is -> ionstr;
trGereactant = energyl[l,l,Z]l;
pKe = pKO + (0.510651*ionstrA0.5*2*zl)/
(1 + 1.6*ionstrA0.5); trgefpHis =
trGereactant + 8.31451*0.29815*Log[l + 10A(pKe - pHc)];
gefl = trgefpHis - nH1*8.31451*0.29815*Log[lOl*pHc +
(2.91482*(zlA2 - nH1)*ionstrA0.5)/
(1 + 1.6*ionstrA0.5);
gef2 = gefl + 8.31451*0.29815*L0gIlO~~-pK0)1;
({gefl, _, zl, nHl1, Cgef2, _, zl + 1, nH1 + 1111

calcGef3sp[equat-, pHc-, ionstr-, zl-, nHl-, pKlO-,
pK20-1 := Module[{energy, trGereactant, pKe, trgefpHis,
gefl, gef2, gef3, pKle, pKZe},(*This program uses xviAfGitO=-RTlnK1 to calculate
the standard Gibbs energies of formation of the three Species of a reactant for which
the pKs at zero ionic strength is pKlO and pK20. The equation is of the form
gyruvate+atp-x-adp==-8.31451*.29815*Log[K'], where K' is the apparent equilibrium
constant at 298.15 K, ~Hc, and ionic strength is. The more basic form of the reactant
has charge number zl and hydrogen atom number nH1. The output is the species matrix
without the standard enthalpies of formation of the three species.*)
energy = Solvelequat, x] /. pH -> pHc /. is -> ionstr;
trGereactant = energy"l,l,2]1;
pKle = pKlO + (0.510651*ionstrA0.5*2*zl~/
(I + 1.6*ionstrA0.5);
pK2e = pK20 + (0.510651*ionstrA0.5*(2*zl + 2))/
(1 + 1.6*ionstrA0.5); trgefpHis =
trGereactant + 8.31451*0.29815*
LOg[l + 10"(pKle - pHC) + 10"(pKle + pK2e - 2*pHc)l;
gefl = trgefpHis - nH1*8.31451*0.29815*Log[lOl*pHc +
(2.91482*(zlA2 - nH1)*ionstrA0.5)/
(1 + 1.6*ionstrA0.5);
gef2 = gefl + 8.31451*0.29815*L0g[10"(-pK10)1:
gef3 = gef2 + 8.31151*0.29815*L0gClO~~-pK20~1;
{{gefl, _, zl, nH1). {gef2, -, zl + 1, nH1 + 11,
(gef3, -, zl + 2, nH1 + 2111
The following example is concerned with biochemical reaction EC 1.1.1.37. If the standard Gibbs energies of formation of
both coA and acetyl coA are unknown, the convention can be adopted that the standard Gibbs energy of formation of RS- is
zero. The standard Gibbs energy of formatin of RSH can be calculated using the pK at zero ionic strength.