Biochemical reactant

Tables of Standard Transformed Thermodynamic Properties at 298.15 K for Biochemical Reactants at Specified pH and Ionic Strength... 

From now on we will assume that Af G-0 and Af H)° of biochemical reactants made up of single species have been calculated using equations 4.4-10 and 4.4-12 and that AfG ° and AfH-° of biochemical reactants with more than one species have been calculated using equations 4.5-1 and 4.5-3. 

THERMODYNAMIC PROPERTIES AT 298.15 K FOR BIOCHEMICAL REACTANTS AT SPECIFIED pH AND IONIC STRENGTH... 

Table 4.2 provides AfG° and AfH° for species of 131 biochemical reactants at 298.15 K in dilute aqueous solutions at zero ionic strength. These values are available in the package BasicBiochemData2 (Alberty, 2002d), which is the first item in the second part of this book. These values can be used to calculate ArG-° and Af//-° for biochemical reactants at desired pHs in the range 5 to 9 and desired ionic strengths in the range 0 to about 0.35 M, as described in this chapter. 

These last two plots have shown the importance of determinations of acid dissociation constants of biochemical reactants. In the next chapter we will see that it is also important to know the pKs of acid groups when heats of reaction are determined calorimetrically. 

In Chapter 4 the effects of temperature on Af G ° and AfH ° and on ArG ° and ArH ° are discussed on the basis of the assumption that A,H° at zero ionic strength is independent of temperature. Therefore the effects of heat capacities of species were not treated. When a biochemical reactant contains two or more species, the standard transformed molar heat capacity of the pseudoisomer group is given by (Alberty, 1983a)... 

The semigrand partition function F corresponds with a system of enzyme-catalyzed reactions in contact with a reservoir of hydrogen ions at a specified pH. The semigrand partition function can be written for an aqueous solution of a biochemical reactant at specified pH or a system involving many biochemical reations. The other thermodynamic properties of the system can be calculated from F. 

Table 3 Standard Transformed Enthalpies of Formation (in kJ mol-1) of Biochemical Reactants at pH 7 and Ionic Strengths of 0, 0.10, and 0.25 M.

Reactants and reactions in biochemistry 2.2.1 An example of a biochemical reactant... 

Based on our exploration of a biochemical reactant in the previous section, we now recognize that the familiar biochemical reaction... 

The previous section illustrated how to calculate apparent equilibrium properties for biochemical reactions expressed in terms of biochemical reactants that are sums... 

This chapter has presented the basics of how thermodynamics are treated for biochemical systems, with an emphasis on the impact of pH and ion binding on apparent equilibria and Gibbs free energy functions. This field owes much to the work of Robert Alberty an extensive study of the field is presented in Alberty s text, Thermodynamics of Biochemical Systems [4], In our study of the theory and simulation of biochemical systems, we will usually be concerned with biochemical reactants such as ATP and ADP, although the detailed breakdown of these reactants into individual species will be important for many applications. 

The derivation of the Michaelis-Menten equation in the previous section differs from the standard treatment of the subject found in most textbooks in that the quasi-steady approximation is justified based on the argument that the catalytic cycle kinetics is rapid compared to the overall biochemical reactant kinetics. In... 

Previous chapters have introduced methods for simulating the kinetics of relatively simple chemical systems, such as the phosphorylation-dephosphorylation system of Section 5.1 or the model of glycolysis illustrated in Section 3.1.4.2. However, the essential fact that biochemical reactants in solution exist as sums of rapidly interconverting species, as described in Chapter 2, is not explicitly taken into account in these simple models. As a result, influences of the binding of hydrogen and metal ions to reactants on thermodynamic driving forces and reactions kinetics are not taken into account in these simulations. 

Since a great deal of information is available regarding the thermodynamic and ion-binding properties of biochemical reactants [4, 5], it is possible to construct simulations of biochemical systems that properly incorporate these data. Specifically, realistic simulations of biochemical systems require combining the following concepts into the simulations. 

The strategy for determining the differential equations for biochemical reactants, pH, and binding ions is to express the equations for reactants based on the stoichiometry of the reference reactions and to determine the kinetics of pH and binding ions based on mass balance. 

However, the differential equations for the pH, [Mg2+], and [K+] (and concentrations of any other binding ions) are not as straightforward to determine as the equations for the biochemical reactants. 

Charges for all of the references species in Table 6.1 are indicated using superscripts, even when the charge is zero. This notation distinguishes biochemical reactants (for example ACCOA) from references species (for example ACCOA0). 

We have chosen to use C032- as a reference species in reaction numbers 1, 4, and 5. Therefore the apparent thermodynamic properties of these reactions will be calculated in terms of the biochemical reactant XCO2. (See Section 2.6 for a discussion on the treatment of CO2 in biochemical reactions.)... 

Figure 6.2 Illustration of the reactions of pyruvate dehydrogenase and the TCA cycle. The abbreviations for the biochemical reactants are listed in Table 6.1 and the stoichiometries of the 11 biochemical reference reactions are listed in Table 6.2.

Introducing the chemical potential (or free energy) and the thermodynamic constraint provides a solid physical chemistry foundation for the constraint-based analysis approach to metabolic systems analysis. Treatment of the network thermodynamics not only improves the accuracy of the predictions on the steady state fluxes, but can also be used to make predictions on the steady state concentrations of metabolites. To see this, we substitute the relation between reaction Gibbs free energy (ArG ) of the th reaction and the concentrations of biochemical reactants... 

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