Biochemical equilibria

Although effects of hydration are important in almost all biochemical equilibria, they are difficult to assess quantitatively. It is hard to know how many molecules of water are freed or immobilized in a given reaction. Charged groups in proteins are often hydrated. However, if they are buried in the interior of the protein, they may be solvated by polarizable protein side chain groups such as -OH or by backbone or side chain amide groups.57 58... 

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). 

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