Biochemical reactions calculations

Initially, most theoretical methods calculated the properties of molecules in the gas phase as isolated species, but chemical reactions are most often carried out in solution. Biochemical reactions normally take place in water. Consequently, there is increasing interest in methods for including solvents in the calculations. In the simplest approach, solvents are treated as a continuum, whose average properties are included in the calculation. Explicit inclusion of solvent molecules in the calculation greatly expands the size of the problem, but newer approaches do this for at least those solvent molecules next to the dissolved species of interest. The detailed structures and properties of these solvent molecules affect their direct interaction with the dissolved species. Reactions at catalytic surfaces present an additional challenge, as the theoretical techniques must be able to handle the reactants and the atoms in the surface, as well as possible solvent species. The first concrete examples of computationally based rational catalyst design have begun to appear in publications and to have impact in industry. 

S. L. Bell and B. 0. Palsson, Expa A program for calculating extreme pathways in biochemical reaction networks. Bioinformatics 21(8), 1739 1740 (2005). 

With the advent of PM3, biochemical reactions, for example, those involved in the Embden—Meyerhof pathway, can be studied. Until now, systems such as glucose-6—phosphate were either poorly represented, or were prohibitively slow to calculate. 

During fermentation, the enhanced absorption rate of oxygen increases the bulk concentration and, as a consequence, the production rate of cells can be increased as well. To predict this effect, the enhanced transfer rate has to be incorporated into the differential mass balance equations of fermentation processes studied. If you know the mathematical expression of the biochemical reactions and their dependence on oxygen concentration as well as the enhanced absorption rates due to the dispersed organic phase,you can calculate the fermentation exactly after solving the equation system obtained. 

It is important to realize that while thermodynamic information will tell us whether or not a reaction can take place it says nothing about the rate of the reaction. It will not even say whether a reaction will proceed at all within a given period of time. This has led to the occasional assertion that thermodynamics is not relevant to biochemistry. This is certainly not true it is important to understand energy relationships in biochemical reactions. At the same time, one should avoid the trap of assuming that thermodynamic calculations appropriate for equilibrium situations can always be applied directly to the steady state found in a living cell. 

The equations and calculations described in this chapter are very useful, but so far we have not discussed thermodynamic properties other than equilibrium constants. The other properties introduced in the next three chapters provide a better understanding of the energetics and equilibria of reactions. We will consider the basic structure of thermodynamics in Chapter 2 and then to apply these ideas to chemical reactions in Chapter 3 and biochemical reactions in Chapter 4. 

Goldberg and Akers (2001) have also published a Mathematica package for calculations on biochemical reactions. 

Proteins that are reactants in biochemical reactions are also be included in BasicBiochemData2 examples included are cytochrome c, ferrodoxin, and thioredoxin. Later in Chapter 7 it is shown that the effect of pH on a biochemical reaction involving a protein can be calculated if the pKs of groups in the reactive site of the protein can be determined. 

Calculation of the Binding of Hydrogen Ions by Reactants and the Changes in Binding of Hydrogen Ions in Biochemical Reactions... 

Calculation of the Change in Binding of Magnesium Ions in a Biochemical Reaction... 

Thus, in making calculations, we rewrite equation 4.2-4 for a biochemical reaction as... 

CALCULATION OF THE BINDING OF HYDROGEN IONS BY REACTANTS AND THE CHANGES IN BINDING OF HYDROGEN IONS IN BIOCHEMICAL REACTIONS... 

CALCULATION OF THE CHANGE IN BINDING OF MAGNESIUM IONS IN A BIOCHEMICAL REACTION... 

The change in binding of magnesium ions in a biochemical reaction can also be calculated from the acid dissociation and magnesium complex ion dissociation constants using... 

K and went on to calculate A,G ° and AfH ° at pH 7 and ionic strength 0.25 M for the corresponding reactants. This made it possible to calculate apparent equilibrium constants for six biochemical reactions at 283.15 and... 

II 6.4 Calculations of Equilibrium Compositions for Systems of Biochemical Reactions... 

Systems of biochemical reactions like glycolysis, the citric acid cycle, and larger and smaller sequential and cyclic sets of enzyme-catalyzed reactions present challenges to make calculations and to obtain an overview. The calculations of equilibrium compositions for these systems of reactions are different from equilibrium calculations on chemical reactions because additional constraints, which arise from the enzyme mechanisms, must be taken into account. These additional constraints are taken into account when the stoichiometric number matrix is used in the equilibrium calculation via the program equcalcrx, but they must be explicitly written out when the conservation matrix is used with the program equcalcc. The stoichiometric number matrix for a system of reactions can also be used to calculate net reactions and pathways. 

This calculation can be made for chemical reactions, biochemical reactions at specified pH, or at steady state concentrations of reactants like ATP and ADP, as is discussed in Section 6.6. The advantage of the matrix formulation of this calculation is that very large matrices can be handled. 

CALCULATIONS OF EQUILIBRIUM COMPOSITIONS FOR SYSTEMS OF BIOCHEMICAL REACTIONS... 

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