This point is illustrated by means of a generic reaction – the hydrolysis of adenosine 5′-triphosphate (ATP) to adenosine 5′-diphosphate (ADP) and phosphate (all reactions discussed in this chapter pertain to aqueous media), equation(1)

ATP+H2O=ADP+phosphate.ATP+H2O=ADP+phosphate. The apparent equilibrium constant K′ for this reaction is equation(2) K′=[ADP][phosphate]/[ATP].K′=[ADP][phosphate]/[ATP]. By convention the concentration of water has been omitted in the expression for K′. The concentrations used in Eq. (2) are total concentrations of the various ionic and metal bound forms of the reactants and products. For example equation(3) [ATP]=[ATP4−]+[HATP3−]+[H2ATP2−]+[H3−ATP]+[MgATP2−]+−[MgHATP]+[MgH2ATP]+[Mg2ATP],[ATP]=[ATP4−]+[HATP3−]+[H2ATP2−]+[H3ATP−]+[MgATP2−]+[MgHATP−]+[MgH2ATP]+[Mg2ATP], mTOR inhibitor equation(4) [ADP]=[ADP3−]+[HADP2−]+[H2−ADP]+[−MgADP]+[MgHADP],[ADP]=[ADP3−]+[HADP2−]+[H2ADP−]+[MgADP−]+[MgHADP],

equation(5) [phosphate]=[PO43−]+[HPO42−]+[H2PO4−]+[H3PO4] If calcium or other metal ions are present, one must also consider additional, analogous species such as CaATP2−. The essential point is that, because biochemical reactants such as ATP, ADP, BIBF 1120 chemical structure and phosphate exist in several different ionic and metal bound forms, there is a multiplicity of species that make up each of these reactants. This, in turn, leads to the aforementioned dependencies of thermodynamic quantities on pH and pX. Illustrations of these dependencies are shown in Figure 1. These surface plots were calculated by using the equilibrium constant for the chemical reference reaction equation(6) ATP4−+H2O=ADP3−+HPO42−+H+,and Linifanib (ABT-869) equilibrium constants for the pertinent H+ and Mg2+ binding constants: equation(7) ATP4−++H=HATP3−,ATP4−+H+=HATP3−,

equation(8) ATP4−+Mg2+=MgATP2−,ATP4−+Mg2+=MgATP2−, equation(9) HATP3−++H=H2ATP2−,HATP3−+H+=H2ATP2−, equation(10) HATP3−+Mg2+=MgHATP−,etc. It is important to recognize that the equilibrium constants K for reactions (6), (7), (8), (9) and (10) pertain to specific chemical species. Clearly, these chemical reactions must balance both the number of atoms and the charges. While equilibrium constants K depend on temperature and ionic strength they do not depend on pH or pX as do apparent equilibrium constants K′. Thus, it is important to maintain a clear distinction between K and K′ ( Alberty et al., 2011). The book Thermodynamics of Biochemical Reactions ( Alberty, 2003) contains a definitive treatment of transformed thermodynamic properties and many examples involving biochemical reactions. In 2002 IUPAC established a project to create standardized mechanisms for thermodynamic data communications using XML (Extensible Markup Language) technology. The aim is to enhance efficient information transfer all the way from measurement to publication to data-management systems and to scientific and engineering applications.