Biochemical standard state

In the term ΔG°(rxn), the " ° " symbol in dicates that we are dealing with a standard free energy change for the reaction. The value of ΔG° depends on the definition of a thermodynamic standard state. Since we need only concern ourselves with changes in free energy, we can define any reference state we please, and we may as well choose it to be the most reasonable or convenient for our purposes. In physical chemistry, the standard state is defined as follows
(1) Temperature T is specified
(2) Pressure P is 1 atm
(3) Activity of solutes in solution is 1 M (activity is roughly equivalent to concentration for dilute solutions)

Setting the activity to 1 simplifies the calculation of ΔG. The temperature can be any value, but must be specified. Usually 298 K (25°C) is chosen. The physical chemistry standard state is implicit in the designation ΔG°, which corresponds to the free energy change for the complete conversion of the pure reactants in their standard states into the pure products in their standard states.

In view of what we said above about choosing a convenient standard state, it makes sense to define a standard state more specifically tailored to biochemical applications. For instance, it is nonsensical to set the standard state for the activity of H⁺ to be 1 M (i.e. pH = 0), when most physiological processes take place in a buffered system held near pH = 7. The free energy change for biochemical standard state - symbolized as ΔG°′ - depends on a standard state, or a set of standard conditions, defined as follows:
(1) Activity of pure water is assigned a value of 1
(2) pH is assumed to be 7
(3) Hydrogen ion activity also assigned a value of 1
(4) Standard state of an ionizable substance is defined in terms of the total concentration of all of its forms

Water is the "standard" solvent, or medium, for biological systems. Setting its activity to 1 allows us to neglect the [H2O] term in Q. Since physiological pH is near neutrality, a standard state of pH 7 is reasonable. A hydrogen ion activity of would correspond to pH 0. As for water, setting the activity of H⁺ to 1 allows us to neglect the [H⁺] term in Q. There are many ionizable functional groups in biochemical systems. Many of these exist at pH 7 in significant amounts of more than one form. For example, phosphate in its H₂PO₄^– form has a pK_a of 7.2 at 25°C. This means that although in the biochemical standard state phosphate exits mostly as H₂PO₄^– and HPO₄^2–, we are able to treat it as one term in Q, ["phosphate"], meaning the sum of [H₂PO₄^– ] and [HPO₄^2– ] and whatever minor amounts of other forms may exist at pH 7.

Biochemical thermodynamics

Biochemical systems are generally open systems. Although processes occurring in living organisms and cells obey the laws of thermodynamics, and therefore spontaneously approach equilibrium, such systems are not at equilibrium. Rather, organisms and cells operate under nonequilibrium conditions, using input of free energy to maintain a steady state. The concept of a nonequilibrium steady state is an important one, and in order understand its implications, we must build on our knowledge of thermodynamics. A field of inquiry labeled nonequilibrium thermodynamics has developed to specifically address this situation.

The thermodynamic approach we have been taking, in discussing systems and processes, is in some ways most suited to description of equilibrium states. The paths for which we calculate entropy are reversible processes, processes that occur by infinitesimal displacements from equilibrium, and are therefore essentially always at equilibrium. We saw in the case of the Carnot cycle that the maximum possible efficiency for a heat engine is only attained when the cyclic process by which the engine operates is a fully reversible one. As noted already, biological systems are open, and definitely not at equilibrium - at least as long as they are actually living - and one might further expect a certain level of thermodynamic optimization to be characteristic of the organisms that have successfully colonized the planet. An analogy can indeed be drawn between the efficiency of a reversible (equilibrium) process in a closed system and the efficiency of open systems operating at a steady state.