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
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; Pi, 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 Pi . . . . . . . . (1)
and the expressions for the apparent equilibrium constant K ' and the apparent standard Gibbs energy change
. . . . . . . . (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
ATP4- + H2O = ADP3- + Pi2- + H+ . . . . . . . . (4)
leads to the equilibrium constant expression
. . . . . . . . (5)
where the equilibrium constant KATP4- is independent of pH. The 1976 Recommendations went on to show how
3. Corresponding New Recommendations
The new recommendation is that reaction 1 be should be written as
ATP + H2O = ADP + Pi . . . . . . . . (6)
where ATP refers to an equilibrium mixture of ATP4-, HATP3-, H2ATP2-, MgATP2-, 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
. . . . . . . . (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
Dr G 'o = - RT ln K ' . . . . . . . . (8)
The hydrolysis of ATP can also be described by means of a chemical equation such as
ATP4- + H2O = ADP3- + HPO42- + 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 HPO42-, rather than Pi2- is a move in the direction of showing that atoms and charge balance in equation 9. Strictly speaking ATP4- ought to be written C10H12O13N5P34-. 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 Kref. 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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