Biochemical reactant reference species

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.)... 

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... 

Use of the third law is not the only way to get large molecules of biochemical reactants into tables of species properties. If apparent equilibrium constants and heats of reaction can be determined for a pathway of reactions from smaller molecules (for which Af G° and Af H° are known with respect to the elements) to form the large molecule, then the properties of the species of the large molecule can be determined relative to the elements in their reference states. This method has its problems in that it is very difficult to determine apparent equilibrium constants greater than about 10 to 10 and the number of reactions in the path may be large and some of the reactants may not be readily available in pure form. Thus it is fortunate that the third law method is available. 

A biochemical reactant is a sum of species. For example, ATP consists of an equilibrium mixture of the aqueous species ATP, HATP , HjATP, MgATP, etc. Similarly, phosphate refers to the equilibrium mixture of the aqueous species PO , HPO, H PO, HjPO, MgHPO, etc. Biochemical reactions are written using biochemical reactants in terms of an apparent equilibrium constant K, which is distinct from the standard equilibrium constant K. This subject is discussed in an lUPAC report (see Reference 1 below). 

The concepts involved in this approach are simple, but the equations become rather complicated. Biochemical reactions are written in terms of reactants like ATP that are made up of sums of species, and they are referred to as biochemical reactions to differentiate them from the underlying chemical reactions that are written in terms of species. The thermodynamics of biochemical reactions is independent of the properties of the enzymes that catalyze them. However, the fact that enzymes may couple reactions that might otherwise occur separately increases the number of constraints that have to be considered in thermodynamics. 

In this book, we follow the convention that the term species refers to a unique chemical compound, while a reactant is a biochemical compound that may be present as a number of related and rapidly inter-converting species. In a modern biochemistry textbook a reaction, such as the ATP hydrolysis reaction... 

Equilibrium compositions of systems of chemical reactions or systems of enzyme-catalyzed reactions can only be calculated by iterative methods, like the Newton-Raphson method, and so computer programs are required. These computer programs involve matrix operations for going back and forth between conservation matrices and stoichiometric number matrices. A more global view of biochemical equilibria can be obtained by specifying steady-state concentrations of coenzymes. These are referred to as calculations at the third level to distinguish them from the first level (chemical thermodynamic calculations in terms of species) and the second level (biochemical thermodynamic calculations at specified pH in terms of reactants). 

According to the peak current, the concentrations of the reactant can be quantified when the diffusivity is negligible. The potential at which the peak current occurs can be used to identify the reaction. Based on the half-cell potential of the electrochemical reactions, the identification for reactions or reactants is listed extensively in handbooks and references. Amperometric sensors can be used very effectively to carry out qualitative and quantitative analyses of chemical and biochemical species. 

---