Thermodynamic biological

In solid-state chemical physics, surface phenomena and surface characterization have long been of considerable interest to scientists working in physics, chemistry, thermodynamics, biology, astrophysics, and other fields. 

Ecosystems are open systems. Their boundaries are permeable, permitting energy and matter to cross them. Effects of environmental constraints and influences on the system play an important role in the regulation and maintenance of the system s spatio-temporal as well as trophic organization and functioning. Indeed, ecosystems operate outside the realm of classical thermodynamics. Biological, chemical, and some physical processes inside of ecosystems are nonlinear. Stationary states of ecosystems are non-equilibrium states far from thermostatic equilibrium. In the course of time, entropy does not tend to a maximum value, or entropy production to a minimum. Entropy decreases when the order of organization and structure of the ecosystem increases. Entropy production is counterbalanced by export of entropy out of the system. 

Thermodynamically, biological oxidation of organic substrates is comparable to nonbiological oxidations, such as the burning of wood. The total free energy released is the same, whether the source is a biological substance, such as glucose, or the oxidation of a compound in a wood fire, calorimeter, or cell. 

Wadsd I 1994 MIcrocalorlmetry of aqueous and biological systems Solution Calorimetry, Experimental Thermodynamics vol IV, ed K N Marsh and PAG O Hare (Oxford Blackwell)... 

Benzinger T H 1971 Thermodynamics, chemical reactions and molecular biology Nature 229 100-2... 

Besides yielding qualitative information, these biologically and pharmaceutically motivated applications of SMD can also yield quantitative information about the binding potential of the ligand-receptor complex. A first advance in the reconstruction of the thermodynamic potential from SMD data by discounting irreversible work was made by Balsera et al. (1997) as outlined in Sect. Reconstruction of the potential of mean force below. 

Syntheses of sterically modified biopolymers can clearly yield insights into the presuppositions and possibilities of biological self-organization processes of biopolymers far beyond general thermodynamic and kinetic descriptions of natural systems. 

Enzymatic Catalysis. Enzymes are biological catalysts. They increase the rate of a chemical reaction without undergoing permanent change and without affecting the reaction equiUbrium. The thermodynamic approach to the study of a chemical reaction calculates the equiUbrium concentrations using the thermodynamic properties of the substrates and products. This approach gives no information about the rate at which the equiUbrium is reached. The kinetic approach is concerned with the reaction rates and the factors that determine these, eg, pH, temperature, and presence of a catalyst. Therefore, the kinetic approach is essentially an experimental investigation. 

StiJl, D. R., F. F. Westnim, Jr., and G. C. Sinke, The Chemical Thermodynamics of Organic Compounds, John Wiley and Sons, New York, 1969. Stuper, A. J., W. E. Brugger, and P. C. Jurs, Computer Assisted Studies of Chemical Structur e and Biological Function, John Wiley and Sons, New York, 1979. 

Many thermodynamic quantities can be calculated from the set of normal mode frequencies. In calculating these quantities, one must always be aware that the harmonic approximation may not provide an adequate physical model of a biological molecule under physiological conditions. 

PS Brereton, FJM Verhagen, ZH Zhou, MWW Adams. Effect of iron-sulfur cluster environment m modulating the thermodynamic properties and biological function of ferredoxm from Pyrococcus furiosus. Biochemistry 37 7351-7362, 1998. 

The thermodynamic stability of a protein in its native state is small and depends on the differences in entropy and enthalpy between the native state and the unfolded state. From the biological point of view it is important that this free energy difference is small because cells must be able to degrade proteins as well as synthesize them, and the functions of many proteins require structural flexibility. 

Privalov, P. L., and Makhatadze, G. I., 1993. Contributions of hydration to protein folding thermodynamics. II. The entropy and Gibbs energy of hydration. y(9wra z/ of Molecular Biology 232 660-679. 

---