Standard state, biological thermodynamic

In this chapter, we continue the discussion begun in the last chapter of applying thermodynamics to chemical processes. We will focus our discussion here on two examples of biological interest. The principles are the same — all of our thermodynamic relationships work. But biochemists have their own vocabulary, and sometimes apply unique conditions to their systems. For example, as we shall see, unusual standard states are sometimes chosen. There is nothing wrong with this, since the choice of standard states is completely arbitrary as long as we keep track of what is done. Standard states are usually chosen in a way that makes the results most useful. That is true in this case. 

Many biological processes involve hydrogen ions the standard state of an H+ solution is (by definition) a 1 mol L"1 solution, which would have a pH of nearly 0, a condition incompatible with most forms of life. Hence, it is convenient to define the biochemical standard state for solutes, in which all components except H+ are at 1 mol L-1, and H+ is present at 10 7mol L (i.e., pH 7). Biochemical standard-state free energy changes are symbolized by AG0, and the other thermodynamic parameters are indicated analogously (AH0, AS0, etc.). 

Carbon-centered radicals play an important role in organic synthesis, biological chemistry, and polymer chemistry. The radical chemistry observed in these areas can, to a good part, be rationalized by the thermodynamic stability of the open shell species involved. Challenges associated with the experimental determination of homolytic bond dissociation energies (BDEs) have lead to the widespread use of theoretically calculated values. These can be presented either directly as the enthalpy for the C-H bond dissociation reaction described in Equation 5.1, the gas-phase thermodynamic values at the standard state of 298.15K and 1 bar pressure being the most commonly reported values. 

The equations for the rate constant t and the equilibrium constant K were obtained under conditions corresponding to the biological standard state (pH = 7, p = 1 bar Section 7.2d). Thus the values of ArG calculated from the equation for K are ArG values which can differ significantly from ArG (pH — 1, p — 1 bar). Prebiotic conditions are more likely to be near pH = 7 than pH — 1 so we expect that the reaction will still be favorable (AT 3> 1) thermodynamically. 

Example 4.2 J Converting between thermodynamic and biological standard states... 

If the biological standard state is used in place of the thermodynamic standard state, we write eqn 4.10a in the same way. 

For example, H2P04 is written as Pi, ATP as ATP, and so on. We need to show hydrogen ions explicitly (because they account for differences between thermodynamic and biological standard states and for the role of pH) in such cases charges will not seem to be balanced. 

We saw in Section 4.2 that in biochemical work it is common to adopt the biological standard state (pH = 7, corresponding to neutral solution), rather than the thermodynamic standard state (pH = 0). To convert standard potentials to biological standard potentials, , we must first consider the variation of potential with pH. The two potentials differ when hydrogen ions are involved in the half-reaction, as in the fumaric acid/succinic acid couple fum/suc with fum = HOOCCH=CHCOOH and sue = HOOCCH2CH2COOH, which plays a role in the citric acid cycle (Case study 4.3) ... 

Up to this point, 1 have emphasised the application of thermodynamics to systems in the gas-phase. In solution, particularly in aqueous solutions where so much of biology occurs, the description of thermodynamic behaviour has to undergo some changes [1, Chap. 5 2, Chaps. 5, 6 and 7]. In particular, it is impossible to apply statistical thermodynamics, an alternative definition of standard state must be employed, and because the values of Ay.// and S° (and hence Af(j ) cannot be determined using the thermal properties of the species, they are relative, rather... 

It has been recommended [35,36] that AfG values calculated on the basis of a 0.001 m real concentration are more closely representative of the thermodynamic properties of biological systems than conventional A/7" values. This has been adopted here, and the values in this column are therefore 17,11 kJ more negative than those of the aqueous standard state. 

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