Page 205 - Thermodynamics of Biochemical Reactions

BasicB ioc hemData2 205

Clear[acetaldehyde, acetate, acetone, acetylcoA, acetylphos, aconitatecis, adenine,
adenosine, adp, alanine, ammonia, amp, arabinose, asparaginel, aspartate, atp, bpg,
butanoln, butyrate, citrate, citrateiso, COA, coAglutathione, c02g, coatot, coag,
cog, creatine, creatinine, cysteineb. cystinel, cytochromecox, cytochromecred,
dihydroxyacetonephos, ethanol, ethylacetate, fadox, fadred, fadenzox, fadenzred,
ferredoxinox, ferredoxinred, fmnox, fmnred, formate, fructose, fructose6phos.
fructosel6phos, fumarate, galactose, galactoselphos, glucose, glucoselphos,
glucose6phosr glutamate, glutamine, glutathioneox, glutathionered, glyceraldehydeghos,
glycerol, glycero13phosr glycine, glycolate, glycylglycine, glyoxylate, haag, h2g,
h20, h202ap, hydroxypropionateb, hypoxanthine, indole, ketoglutarate, lactate,
lactose, leucineisol, leucinel, lyxose, malate, maltose, mannitolD, mannose,
methaneaq, methaneg, methanol, methioninel, methylamineion, nlag, n2g, nadox,
nadred, nadpox, nadpred, o2ag, 02g, oxalate, oxaloacetate, oxalosuccinate, palmitate,
pep, pg2, pg3, phenylalaninel, pi, ppi, gropanol2, propanoln, pyruvate, retinal,
retinol, ribose, riboselphos, ribose5phos, ribulose, serinel, sorbose, succinate,
succinylcoA, sucrose, thioredoxinox, thioredoxinred, tryptophanel, tyrosinel,
ubiguinoneox, ubiguinonered, urate, urea, uricacid, valinel, xylose, xylulose];
Evaluate[listfnpHis] = Map[calcdGmat, listspeciesdata] ;

The following shows an example of a function of pH and ionic strength for a reactant that gives the standard transformed
Gibbs energy of formation.

0.5 0.5 -PH
-0.403393 (-2838.18 + (29.1482 is )/(1 + 1.6 is ) - 34.7056 Log[lO I
-2.47897 Log [E
0.5 0.5 -PH
-0.403393 (-2811.48 + (11.6593 is )/(1 + 1.6 is ) - 32.2266 Log[lO
E I) +
0.5 0.5 -PH
-0.403393 (-2768.1 - (11.6593 is )/(1 + 1.6 is ) - 29.7477 Log[lO
E ])I

The value of the standard transformed Gibbs energy of formation of ATP at pH 7 and ionic strength 0.25 M can be calcu-
lated in kJ/mol as follows:

atp/.pH->7/.is->.25

-2292.5

The values at pHs 6,7, and 8 and at ionic strengths 0 and 0.25 M can also be calculated.

atp/.pH->{6,7,8l/.is->{0,.251

{[-2366.43, -2363.76}, [-2292.61, -2292.51, {-2220.96, -2223.44))