Thermodynamics biochemical species, thermodynamic tables

Chemical Thermodynamic Tables Including Biochemical Species... 

CHEMICAL THERMODYNAMIC TABLES INCLUDING BIOCHEMICAL SPECIES... 

When the standard thermodynamic properties of species are unknown for two reactants in a biochemical equation, the Af Gy (7=0) and Af 7/y (/=0) of the more basic species of this reactant can be assigned values of zero, so Af Gi for that reactant can be calculated under the experimental conditions. These assigned values become conventions of the thermodynamic table, like Af G (H ) = 0 and Af 7/ (H+) = 0 at each temperature. As described in the preceding section, this was done for adenosine in dilute aqueous solution (3) in 1992, but the determination of the thermodynamic properties of adenosine in dilute aqueous (4) made it possible to drop this convention for the ATP series. 

We emphasise that the next chapters refer only to the surface of Earth to which light and the atmosphere have access. This is a common restriction in the discussion of evolution but we shall have to examine also the geological and biochemical zones in (and beneath) the deep sea (in Chapter 11), where it appears that evolution could be taking a somewhat different and as yet less advanced route but based on the same principles. We emphasise that each chapter adds new uses of elements, of energy, of space, and of organisation with species variation as new chemotypes evolved. The thermodynamic characteristics of all cells are given in Table 4.11. 

A long time ago chemists realized that the most efficient way to store thermodynamic data on chemical reactions is by making tables of standard thermodynamic properties of species. The NBS Tables of Chemical Thermodynamic Properties (4) gives AfG°, Af// and Sm° for species at 298.15 K at xero ionic strength. Since the standard molar entropy is not available for many species of biochemical interest, the standard entropies of formation Af S" are used. This property of a species is calculated by using... 

Chapters 3-5 have described the calculation of various transformed thermodynamic properties of biochemical reactants and reactions from standard thermodynamic properties of species, but they have not discussed how these species properties were determined. Of course, some species properties came directly out of the National Bureau of Standard Tables (1) and CODATA Tables (2). One way to calculate standard thermodynamic properties of species not in the tables of chemical thermodynamic properties is to express the apparent equilibrium constant K in terms of the equilibrium constant K of a reference chemical reaction, that is a reference reaction written in terms of species, and binding polynomials of reactants, as described in Chapter 2. In order to do this the piiTs of the reactants in the pH range of interest must be known, and if metal ions are bound, the dissociation constants of the metal ion complexes must also be known. For the hydrolysis of adenosine triphosphate to adenosine diphosphate, the apparent equilibrium constant is given by... 

When the pH is specified, each biochemical half reaction makes an independent contribution to the apparent equilibrium constant K for the reaction written in terms of reactants rather than species. The studies of electochemical cells have played an important role in the development of biochemical thermodynamics, as indicated by the outstanding studies by W. Mansfield Clarke (1). The main source of tables of ° values for biochemical half reactions has been those of Segel (2). Although standard apparent reduction potentials ° can be measured for some half reactions of biochemical interest, their direct determination is usually not feasible because of the lack of reversibility of the electrode reactions. However, standard apparent reduction potentials can be calculated from for oxidoreductase reactions. Goldberg and coworkers (3) have compiled and evaluated the experimental determinations of apparent equilibrium constants and standard transformed enthalpies of oxidoreductase reactions, and their tables have made it possible to calculate ° values for about 60 half reactions as functions of pH and ionic strength at 298.15 K (4-8). 

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