Biochemical reactions transformed properties

The field of theoretical molecular sciences ranges from fundamental physical questions relevant to the molecular concept, through the statics and dynamics of isolated molecules, aggregates and materials, molecular properties and interactions, and the role of molecules in the biological sciences. Therefore, it involves the physical basis for geometric and electronic structure, states of aggregation, physical and chemical transformations, thermodynamic and kinetic properties, as well as unusual properties such as extreme flexibility or strong relativistic or quantum-field effects, extreme conditions such as intense radiation fields or interaction with the continuum, and the specificity of biochemical reactions. 

Enzymes are proteins that act as biological catalysts. They facilitate chemical modification of substrate molecules by virtue of their specific binding properties, which arise from particular combinations of functional groups in the constituent amino acids at the so-called active site. In many cases, an essential cofactor, e.g. NAD+, PLP, or TPP, may also be bound to participate in the transformation. The involvement of enzymes in biochemical reactions has been a major theme throughout this book. The ability of enzymes to carry out quite complex chemical reactions, rapidly, at room temperature, and under essentially neutral conditions is viewed with envy by synthetic chemists, who are making rapid progress in harnessing this ability for their own uses. Several enzymes are currently of importance commercially, or for medical use, and... 

When the pH is specified, we enter into a whole new world of thermodynamics because there is a complete set of new thermodynamic properties, called transformed properties, new fundamental equations, new Maxwell equations, new Gibbs-Helmholtz equations, and a new Gibbs-Duhem equation. These new equations are similar to those in chemical thermodynamics, which were discussed in the preceding chapter, but they deal with properties of reactants (sums of species) rather than species. The fundamental equations for transformed thermodynamic potentials include additional terms for hydrogen ions, and perhaps metal ions. The transformed thermodynamic properties of reactants in biochemical reactions are connected with the thermodynamic properties of species in chemical reactions by equations given here. 

The relationships between the thermodynamic properties of chemical reactions and the transformed thermodynamic properties of biochemical reactions have been treated in several reviews (Alberty, 1993a, 1994c, 1997b, 2001 e). Recommendations for Nomenclature and Tables in Biochemical Thermodynamics from an IUPAC-IUBMB Committee were published in 1994 and republished in 1996. This report is available on the Web http llwww.chem.qmw.ac.uhlimbmbl thermodl. 

Statistical mechanics is often thought of as a way to predict the thermodynamic properties of molecules from their microscopic properties, but statistical mechnics is more than that because it provides a complementary way of looking at thermodynamics. The transformed Gibbs energy G for a biochemical reaction system at specified pH is given by... 

R. A. Alberty, Calculation of standard formation properties of species from standard transformed formation properties of reactants in biochemical reactions at specified pH, J. Phys. Chem.. 103, 261 265... 

Bioenergetics provides a quantitative description of the transformation of materials and energy in living systems. Most biochemical reactions occur in pathways, in which other reactions continuously add substrates and remove products. The rate of reactions depends on the properties of the enzymes (large proteins produced in cells) that catalyze the reaction. Substrates bind at the active sites of enzymes, where they are converted to products and later released. Enzymes are highly specific for given substrates and products. Inhibitors of enzymes decrease the rate of reaction. 

Four arsenic species common in natural samples are arsenate, arsenite, methanearsonic acid (MMAA) and dimethylarsinic acid (DMAA). These species possess different chemical properties which affect the mobility of arsenic in natural systems. For example, methanobacteriurn form trimethyl arsine from DMAA faster than fromMMAAor arsenate 3) and arsenate and MMAA are more strongly adsorbed than DMAA on alluvial soils ( ). Transformation between the different oxidation states and species of arsenic may occur as a result of chemical or biochemical reactions (J, 2, 7, 9). Inorganic chemical... 

The equations in the preceding sections are general, but now we will concentrate on the interpretation of measurements of apparent equilibrium constants at a single temperature because this is the situation for most studies of biochemical reactions. The effect of temperature will be treated in the next chapter. Since we will be considering experimental data, formation properties will be used. Equation 3.3-4 for the transformed chemical potential of a species can be written as... 

Two-dimensional Plots of Transformed Thermodynamic Properties of Biochemical Reactions... 

R. A. Alberty, Effect of temperature on the standard transformed thermodynamic properties of biochemical reactions with emphasis on the Maxwell equations, J. Phys. Chem. 107 B, 3631-3635 (2003). (Supporting Information is available.)... 

We have seen that calculating species properties from experimental values of K and A // ° is more complicated than calculating K and Ar ° from species values. Thermodynamic calculations can be made by alternate paths, and so there is more than one way to calculate species properties from experimental properties. This chapter emphasizes the concept of the inverse Legendre transform discussed by Callen (8). Biochemical reaction systems are described by transformed thermodynamic properties, and the inverse transform given in equation 6.2-1 provides the transformation from experimental reactant properties to calculated species properties. In this ehapter we first considered calculations of species properties at 298.15 K from measurements of K and Ar ° at 298.15 K. Then we considered the more difficult problem of calculating Af G°(298.15 K) and Af //°(298.15 K) from Ar G "(313.15 K) and Ar H (313.15 K). The programs developed here make it possible to go from Ar G and Ar H (F.pH,/) to Af G (298.15 K,/=0) and Af H (298.15 K,/=0) in one step. 

The calculation of Af G° and Af H° of species from experimental data on apparent equilibrium constants and transformed enthalpies of reaction is described in R. A. Alberty, Thermodynamics of Biochemical Reactions, Wiley, Hoboken, NJ (2003) and a number of places in the literature. That is not discussed here because this package is oriented toward the derivation of mathematical functions to calculate thermodynamic properties at specified T, pH, and ionic strength. There are two types of biochemical reactants in the database ... 

Enzymes are catalytically active proteins that are involved in every in vivo transformation. They enhance the rates of biochemical reactions by 10 to 10 2 by reduction of the free energy of activation. Two distinctive properties of enzymes are their high substrate specificity and the narrow range of conditions under which they are effective. They usually catalyze one reaction of a few substrates. Activities are dependent on pH, temperature, the presence of cofactors, as well as concentrations of substrates and products. Enzymes perform specific reactions because they possess cavities in which substrates are oriented white they are transformed (Figure 1). This process involves interaction of the substrate with amino acids of the enzyme. 

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