Thermodynamics in Biochemistry

Chapter 1 Cells, Biomolecules, and Water 3 Chapter 2 Thermodynamics in Biochemistry 29... 

The free energy function dominates most discussions of thermodynamics in biochemistry. Not only does the sign of AG determine the direction in which a reaction proceeds, but the magnitude of AG indicates just how far the reaction must proceed before the system comes to equilibrium. This is because the standard free energy change AG° has a simple relationship to the equilibrium constant. We elaborate on... 

Bray, TI. G., and White, K. Kinetics and Thermodynamics in Biochemistry. London Churchill, 1967. 

The intended audience of the second volume entitled Chemical Thermodynamics Advanced Applications is the advanced student or research scientist. We have used it, independently of the first volume, as the text for an advanced topics graduate level course in chemical thermodynamics. It can also serve as an introduction to thermodynamic studies involving more specialized disciplines, including geology, chemical separations, and biochemistry, for the research scientist in or outside of those disciplines. We hope it will be especially helpful for non-thermodynamicists who might be unfamiliar with the power and utility of thermodynamics in diverse applications. Given the more advanced nature of the material covered here, problems are only provided at the end of the chapters in this volume. Taken together, the two volumes make an excellent reference source for chemical thermodynamics. 

Hill, T. L., 1960, An Introduction to Statistical Thermodynamics, Addison-Wesley, Reading, Mass. Hill, T. L., 1985, Cooperativity Theory in Biochemistry, Steady State and Equilibrium Systems, Springer-Verlag, New York. 

It is important to appreciate that this principle of coupling-in-series underlies all biochemical pathways or processes, e.g. glycolysis, generation of ATP in the mitochondrion, protein synthesis from amino acids or a signal transduction pathway. Indeed, despite the fundamental importance of signalling pathways in biochemistry, a thermodynamic analysis of such a pathway has never been done, but the principles outlined above must apply even to signalling pathways. 

DilP recently discussed the merits and limitations of models that assume thermodynamic additivity and independence (of energy types, of neighbor interactions, of conformational freedom, of monomer contact pairing frequencies, etc.). He states that biological molecules may achieve stability in the face of thermal uncertainty, as polymers do, by compounding many small interactions this summing can stump modelers because application of the additivity principle leads to accumulated error. Entropies and free energy may not be additive to describe weak interactions that are ensembles of states. He concludes that additivity principles appear to be few and limited in scope in biochemistry. 

Table 6-5 gives thermodynamic dissociation constants and values of AG 0 and AH 0 for a number of acids of interest in biochemistry. Some of these values were used in obtaining the values of AGf° for the ions of Table 6-4. The data of Table 6-5 can also be used in evaluation of Gibbs energy changes for reactions of ionic forms not given in Table 6-4.

Thermodynamics is useful in biochemistry for predicting whether a given reaction can occur and, if so, how much work a cell can obtain from the process. 

In chapter 2, thermodynamics is presented in a way that is most relevant to the consideration of biochemical phenomena. We chose to present the rather difficult topic of thermodynamics in the beginning of the text because thermodynamics is an important consideration in all aspects of biochemistry. The central role of ATP as the main carrier of free energy in biochemical systems is emphasized. 

Baker D, Agard DA (1994) Kinetics versus thermodynamics in protein folding, Biochemistry, 33 7505-7509... 

K. D. Wittrup. Secretion effidency in Saccharomyces cerevisiae of bovine pancreatic trypsin inhibitor mutants lacking disulfide bonds is correlated with thermodynamic stability. Biochemistry (1998) 37(5) 1264-73. 

Jolicoeur, Carmel, Thermodynamic Flow Methods in Biochemistry ... 

Thermodynamic Flow Methods in Biochemistry Calorimetry, Densimetry and Dilatometry... 

Falzon, L., and Davidson V. L., 1996, Intramolecular electron transfer in trimethylamine dehydrogenase A thermodynamic analysis, Biochemistry 35 12111912118. 

The conservation matrix A is useful in chemical thermodynamics, but biochemistry takes a more global view. When the pH is specified, hydrogen ions are not conserved, and so the second row and the second column in coiunat3 are deleted. 

---