Summary, Preamble, 1976 and New Recommendations

Summary
1 Preamble
2 Basic 1976 Recommendations on Symbols and Nomenclature
3 Corresponding New Recommendations
References for this Section

Chemical equations are written in terms of specific ionic and elemental species and balance elements and charge, whereas biochemical equations are written in terms of reactants that often consist of species in equilibrium with each other and do not balance elements that are assumed fixed, such as hydrogen at constant pH. Both kinds of reaction equations are needed in biochemistry. When the pH and the free concentrations of certain metal ions are specified, the apparent equilibrium constant K ' for a biochemical reaction is written in terms of sums of species and can be used to calculate a standard transformed Gibbs energy of reaction D_r G '^o. Transformed thermodynamic properties can be calculated directly from conventional thermodynamic properties of species. Calorimetry or the dependence of K ' on temperature can be used to obtain the standard transformed enthalpy of reaction D_r H '^o. Standard transformed Gibbs energies of formation D_f G '^o(i ) and standard transformed enthalpies of formation D_f H '^o(i ) for reactants (sums of species) can be calculated at various T, pH, pMg, and ionic strength (I ) if sufficient information about the chemical reactions involved is available. These quantities can also /be calculated from measurement of K ' for a number of reactions under the desired conditions. Tables can be used to calculate D_r G '^o and D_r H '^o for many more reactions.

1. Preamble

In 1976 an Interunion Commission on Biothermodynamics (IUPAC, IUB, IUPAB) published Recommendations for Measurement and Presentation of Biochemical Equilibrium Data (ref. 1). This report recommended symbols, units, and terminology for biochemical equilibrium data and standard conditions for equilibrium measurements. These recommendations have served biochemistry well, but subsequent developments indicate that new recommendations and an expanded nomenclature are needed. In 1985 the Interunion Commission on Biothermodynamics published Recommendations for the Presentation of Thermodynamic and Related Data in Biology (1985) (ref. 2).

Before discussing the new recommendations, some of the basic recommendations of 1976 are reviewed and the recommended changes in these basic matters are given.

2. Basic 1976 Recommendations on Symbols and Nomenclature

Note Abbreviations used in this document are: AMP, adenosine 5'-monophosphate; ADP, adenosine 5'-diphosphate; ATP, adenosine 5'-triphosphate; Glc, glucose; Glc-6-P, glucose 6-phosphate; P_i, orthophosphate. The designator (aq) is understood as being appended to all species that exist in aqueous solution.

In the 1976 Recommendations (ref. 1), the overall reaction for the hydrolysis of ATP to ADP was written as

total ATP + H₂O = total ADP + total P_i . . . . . . . . (1)

and the expressions for the apparent equilibrium constant K ' and the apparent standard Gibbs energy change DG^o' were written as

. . . . . . . . (2)

. . . . . . . . (3)

where these are equilibrium concentrations, recommended to be molar concentrations. The 1976 Recommendations further recommended that information about the experimental conditions could be indicated by writing K_c'(pH = x, etc.) and DG_c ^o'(pH = x, etc.), where the subscript c indicates that molar concentrations are used. The 1976 Recommendations pointed out that the hydrolysis of ATP can also be formulated in terms of particular species of reactants and products. For example, at high pH and in the absence of magnesium ion

ATP^4- + H₂O = ADP^3- + P_i^2- + H⁺ . . . . . . . . (4)

leads to the equilibrium constant expression

. . . . . . . . (5)

where the equilibrium constant K_ATP4- is independent of pH. The 1976 Recommendations went on to show how K ' is related to K_ATP4-.

3. Corresponding New Recommendations

The new recommendation is that reaction 1 be should be written as

ATP + H₂O = ADP + P_i . . . . . . . . (6)

where ATP refers to an equilibrium mixture of ATP^4-, HATP^3-, H₂ATP^2-, MgATP^2-, MgHATP^-, and Mg₂ATP at the specified pH and pMg. This is referred to as a biochemical equation to emphasize that it describes the reaction that occurs at specified pH and pMg. The apparent equilibrium constant K ' is made up of the equilibrium concentrations of the reactants relative to the standard state concentration c ^o, which is 1 M; note that M is an abbrevation for mol L^-1.

. . . . . . . . (7)

The term c ^o arises in the derivation of this equilibrium constant expression from the fundamental equation of thermodynamics and makes the equilibrium constant dimensionless. The logarithm of K ' can only be taken if it is dimensionless (ref. 3). The standard state concentration used is an absolutely essential piece of information for the interpretation of the numerical value of an equilibrium constant. The apparent equilibrium constant K ' is a function of T, P, pH, pMg, and I (ionic strength). Various metal ions may be involved, but Mg²⁺ is used as an example. As described below,

D_r G '^o = - RT ln K ' . . . . . . . . (8)

where D_r G '^o is the standard transformed Gibbs energy of reaction. The important point is that when the pH, and sometimes the free concentrations of certain metal ions, are specified, the criterion of equilibrium is the transformed Gibbs energy G ' (ref. 4, 5). The reason for this name is discussed later in the section on transformed thermodynamic properties. Since the apparent equilibrium constant K ' yields the standard value (the change from the initial state with the separated reactants at c ^o to the final state with separated products at c ^o) of the change in the transformed Gibbs energy G ', the superscript ^o comes after the prime in D_r G '^o. The subscript r ( recommended in ref. 3) refers to a reaction and is not necessary, but it is useful in distinguishing the standard transformed Gibbs energy of reaction from the standard transformed Gibbs energy of formation D_f G '^o(i ) of reactant i, which is discussed below.

The hydrolysis of ATP can also be described by means of a chemical equation such as

ATP^4- + H₂O = ADP^3- + HPO₄^2- + H⁺ . . . . . . . . (9)

A chemical equation balances atoms and charge, but a biochemical equation does not balance H if the pH is specified or Mg if pMg is specified, and therefore does not balance charge. Equation 9 differs from equation 4 in one way that is significant but not of major importance. Writing HPO₄^2-, rather than P_i^2- is a move in the direction of showing that atoms and charge balance in equation 9. Strictly speaking ATP^4- ought to be written C₁₀H₁₂O₁₃N₅P₃^4-. That is not necessary or advocated here, but we will see later that the atomic composition of a biochemical species is used in calculating standard transformed thermodynamic properties. Chemical equation 9 leads to the following equilibrium constant expression

. . . . . . . . (10)

where c ^o = 1 M. The equilibrium constant K is a function of T, P, and I. This equilibrium constant expression does not completely describe the equilibrium that is reached except at high pH and in the absence of Mg²⁺. Chemical equations like equation 4 are useful in analyzing biochemical reactions and are often referred to as reference equations; thus, the corresponding equilibrium constants may be represented by K_ref. The effect of Mg²⁺ is discussed here, but this should be taken as only an example because the effects of other metal ions can be handled in the same manner.

1. Wadsö, I., Gutfreund, H., Privlov, P., Edsall, J. T., Jencks, W. P., Strong, G. T., and Biltonen, R. L. (1976) Recommendations for Measurement and Presentation of Biochemical Equilibrium Data, J. Biol. Chem. 251, 6879-6885; (1976) Q. Rev. Biophys. 9, 439-456.

2. Wadsö, I., and Biltonen, R. L.(1985) Recommendations for the Presentation of Thermodynamic Data and Related Data in Biology, Eur. J. Biochem. 153, 429-434.

3. Mills, I., Cvitas, T., Homann, K., Kallay, N., and Kuchitsu, K. (1988 and 1993) Quantities, Units and Symbols in Physical Chemistry, Blackwell Scientific Publications, Oxford.

4. Alberty, R. A. (1992) Biophys. Chem. 42, 117-131.

5. Alberty, R. A. (1992) Biophys. Chem. 43, 239-254.

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