Biochemical reactions thermodynamics

The energy for the fission of the covalent bond in organic contaminants is normally supplied thermally using thermodynamically accessible chemical or biochemical reactions, or by the introduction of catalysts to lower the activation energy of the reactions. There has been interest, however, in using electrical energy in a number of forms to carry out these reactions. A selection of processes for the destruction of contaminant is noted with some illustrative examples. 

The approximate kinetic formats discussed above face inherent difficulties to account for fundamental physicochemical properties of biochemical reactions, such as the Haldane relation discussed in Section III.C.4 a major drawback when aiming to formulate thermodynamically consistent models. 

Enzymes are biological molecules that catalyze biochemical reactions. The thermodynamics of biochemical enzymatic reactions are described in Exhibit 2.10. 

The thermodynamic principles described in Chapter 2 of this volume can be used to indicate whether or not a reaction can take place spontaneously. They do not, however, provide information about the rate at which a reaction will proceed. Most biochemical reactions proceed so slowly at physiological temperatures that catalysis is essential for the reactions to proceed at a satisfactory rate in the cell. 

Because cryosolvents must be used in studies of biochemical reactions in water, it is important to recall that the dielectric constant of a solution increases with decreasing temperature. Fink and Geeves describe the following steps (1) preliminary tests to identify possible cryosolvent(s) (2) determination of the effect of cosolvent on the catalytic properties (3) determination of the effect of cosolvent on the structural properties (4) determination of the effect of subzero temperature on the catalytic properties (5) determination of the effect of subzero temperature on the structural properties (6) detection of intermediates by initiating catalytic reaction at subzero temperature (7) kinetic, thermodynamic, and spectral characterization of detected intermediates (8) correlation of low-temperature findings with those under normal conditions and (9) structural studies on trapped intermediates. 

Whenever reporting equilibrium constants, detailed information concerning the reaction conditions should always be indicated. Alberty has also presented an important review of biochemical thermodynamics in which he discusses the apparent equilibrium constant for biochemical reactions (K ) in terms of sums of reactant species. 

Thermodynamic studies of systems at equilibrium permit one to gain insights regarding mechanisms of chemical and biochemical reactions. Thermodynamic consider-... 

AG, is directly associated with the direction in which a particular chemical reaction can proceed. If AG < 0 for a given set of conditions of a particular reaction, then the reaction will proceed spontaneously in the indicated direction until equilibrium is reached. Conversely, if AG is positive, then energy will be needed to shift the reaction further from its equilibrium condition. See Helmholtz Energy Endergonic Exergonic Enthalpy Entropy Thermodynamics Biochemical Thermodynamics... 

Biochemical reactions are basically the same as other chemical organic reactions with their thermodynamic and mechanistic characteristics, but they have the enzyme stage. Laws of thermodynamics, standard energy status and standard free energy change, reduction-oxidation (redox) and electrochemical potential equations are applicable to these reactions. Enzymes catalyse reactions and induce them to be much faster . Enzymes are classified by international... 

The field of theoretical molecular sciences ranges from fundamental physical questions relevant to the molecular concept, through the statics and dynamics of isolated molecules, aggregates and materials, molecular properties and interactions, and the role of molecules in the biological sciences. Therefore, it involves the physical basis for geometric and electronic structure, states of aggregation, physical and chemical transformations, thermodynamic and kinetic properties, as well as unusual properties such as extreme flexibility or strong relativistic or quantum-field effects, extreme conditions such as intense radiation fields or interaction with the continuum, and the specificity of biochemical reactions. 

Reaction 9.1 might seem to be thermodynamically favored, but in fact no kinetically easy route from triply bonded N2 to N03 exists, since the endothermic intermediate NO (Section 8.4.2) is likely to be involved. As written, reaction 9.2 has prohibitive energetics, but in practice the process is more complex than this. For example, the fact that free 02 is not formed, but is in effect consumed in other biochemical reactions, makes for a favorable energy balance. The limiting factor is again kinetics, as plausible intermediates such as hydrazine (H2N—NH2) are endergonic compounds. 

To explore the consequences of coupling ATP hydrolysis under physiological conditions to a thermodynamically unfavorable biochemical reaction, consider the hypothetical transformation for which AG ° = 20 kJ/mol. 

It is important to realize that while thermodynamic information will tell us whether or not a reaction can take place it says nothing about the rate of the reaction. It will not even say whether a reaction will proceed at all within a given period of time. This has led to the occasional assertion that thermodynamics is not relevant to biochemistry. This is certainly not true it is important to understand energy relationships in biochemical reactions. At the same time, one should avoid the trap of assuming that thermodynamic calculations appropriate for equilibrium situations can always be applied directly to the steady state found in a living cell. 

We say that thermodynamics determines whether a process could occur, because thermodynamics tells us only whether the process is possible, not whether it actually does occur in a finite period of time. The rate at which a thermodynamically possible reaction occurs depends on the detailed mechanism of the process. For a biochemical pro-... 

In this chapter we discuss thermodynamic quantities. We then expand the discussion to show how the concept of free energy is used in predicting biochemical pathways, and we explore the central role of ATP in providing energy for biochemical reactions. 

Enthalpy is a function of state that is closely related to energy but is usually more pertinent for describing the thermodynamics of chemical or biochemical reactions. The change in enthalpy (AH) is related to the change in energy... 

In this chapter we discussed some principles of thermodynamics as they relate to biochemical reactions. The following points are of greatest importance. 

Thermodynamic applications that relate to biomolecular structure and biochemical reactions are also elaborated on in specific sections of subsequent chapters. 

In 1969 Wilhoit picked up where Burton had left off and compiled the standard thermodynamic properties AfG° and A H° of species involved in biochemical reactions. He recognized the problems involved in including species... 

This introductory chapter describes the thermodynamics of biochemical reactions in terms of equilibrium constants and apparent equilibrium constants and avoids references to other thermodynamic properties, which are introduced later. 

This is referred to as the extended Debye-Huckel equation. It is an approximation that gives a good fit of data at low ionic strengths (Goldberg and Tewari, 1991) when B= 1.6 L1/2 mol 1/2. Better fits can be obtained with more complicated equations with more parameters, but these parameters are not known for solutions involved in studying biochemical reactions. The way that thermodynamic properties vary with the ionic strength is discussed in more detail in Section 3.6. 

The equations and calculations described in this chapter are very useful, but so far we have not discussed thermodynamic properties other than equilibrium constants. The other properties introduced in the next three chapters provide a better understanding of the energetics and equilibria of reactions. We will consider the basic structure of thermodynamics in Chapter 2 and then to apply these ideas to chemical reactions in Chapter 3 and biochemical reactions in Chapter 4. 

When the pH is specified, we enter into a whole new world of thermodynamics because there is a complete set of new thermodynamic properties, called transformed properties, new fundamental equations, new Maxwell equations, new Gibbs-Helmholtz equations, and a new Gibbs-Duhem equation. These new equations are similar to those in chemical thermodynamics, which were discussed in the preceding chapter, but they deal with properties of reactants (sums of species) rather than species. The fundamental equations for transformed thermodynamic potentials include additional terms for hydrogen ions, and perhaps metal ions. The transformed thermodynamic properties of reactants in biochemical reactions are connected with the thermodynamic properties of species in chemical reactions by equations given here. 

The relationships between the thermodynamic properties of chemical reactions and the transformed thermodynamic properties of biochemical reactions have been treated in several reviews (Alberty, 1993a, 1994c, 1997b, 2001 e). Recommendations for Nomenclature and Tables in Biochemical Thermodynamics from an IUPAC-IUBMB Committee were published in 1994 and republished in 1996. This report is available on the Web http llwww.chem.qmw.ac.uhlimbmbl thermodl. 

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