A Database of Biochemical Thermodynamic Quantities – Glycolysis, the Tricarboxylic Acid Cycle & the Pentose Phosphate Pathway
This web base bio-thermodynamic database can be used to obtain formation properties and dissociation constants (provided as pK’s) for reference species associated with biochemical reactants at specified temperature and ionic strength; and to obtain reaction properties (including free energies and enthalpies) for associated reactions.
Experimental data: experimental conditions, experimental results, notes and strategies applied in calculations, reference information, etc.
Tables & Results
- Table 1 – Reactions with standard reaction enthalpies ΔrH0 estimated for I = 0.
- Table 2 – Reactant database. Dissociation pK and ΔdH are reported for T = 298.15 K and I = 0.1 M. Unless indicated, values are obtained from NIST database.
- Table 3 – Values of ΔfGi0 (at T = 298.15 K, I = 0 M) used in this study and that were taken from Table 3.2 of Alberty.
- Table 4 – Optimal reaction free energies for reference chemical reactions( ΔrG0, T = 298.15 K, I = 0 M) and for biochemical reactions (ΔrG’0) at physiological condition (T = 310.15 K, I = 0.18 M, pH = 7, [Mg2+] = 0.8 mM, [K+] = 140 mM, [Na+] = 10 mM, [Ca2+] = 0.0001 mM). ΔrG0 of fimal four entries (PDH, IDH2, AKGDH, and SDH) are calculated from Alberty’s database (Alberty) and used as model constraints for which there are no equilibrium data in the raw-data database. Since the ΔfGi0 values for CoQ and CoQH2 are not predicted here, these values are set to 0 and -88.60 kJ/mol, respectively (from Alberty) to computed ΔrG0 for the SDH reaction.
- Table 5 – Optimal predicted ΔfGi0 for reference species (T = 298.15 K, I = 0 M).