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Basic Knowledge

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Kinetics of Enzyme-Modifier Interactions

Abstract

This introductory chapter contains a collection of concepts that serve as support for the following parts of this book. Understanding microscopic reversibility and the fundamentals of linked functions are necessary instruments for interpreting allosteric interactions between substrates and modifiers. The basic theories of enzyme kinetics are approached from the consideration that all enzyme-catalyzed reactions are reversible and that mechanisms are determined by the ensemble of kinetic barriers that preside over the quasi-equilibrium and steady-state assumptions. Emphasis is given to initial rates and their precise determination as an essential starting point in kinetic data analysis. Lying in-between, practical tools, brief refreshing of useful methods and some constructive criticism.

The key to a knowledge of enzymes is the study of reaction

velocities, not of equilibria.

J.B.S. Haldane, Enzymes, Reprint 1965, M.I.T. Press, p. 3

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Notes

  1. 1.

    Also available at http://www.chem.qmul.ac.uk/iubmb/kinetics/.

  2. 2.

    http://enzyme.expasy.org.

  3. 3.

    http://www.brenda-enzymes.org.

  4. 4.

    http://merops.sanger.ac.uk.

  5. 5.

    Since 1991 International Union of Biochemistry and Molecular Biology (IUBMB).

  6. 6.

    http://virtualrat.org/software/kapattern.

  7. 7.

    http://www.biokin.com/king-altman.

  8. 8.

    http://www.mathworks.com/ .

  9. 9.

    http://www.kintek-corp.com/KGExplorer/.

  10. 10.

    http://www.biokin.com/.

  11. 11.

    As per December 2014.

  12. 12.

    The notion of operational definition has been introduced in 1927 by P.W. Bridgman referring to the definition of something, like a variable or an object, through the operations needed to measure it. In enzyme kinetics, operational definitions are for instance the Michaelis constant and competitive inhibition. Such definitions have acknowledged practical value because they are traceable to measurements without making assumptions on the underlying mechanisms.

  13. 13.

    In the context of enzyme kinetics the term apparent applies to a parameter, such as the limiting rate and the Michaelis constant, in the form it is measured at particular reactant concentrations.

  14. 14.

    I wish I could pronounce correctly the name of this valuable scientist.

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Author information

Authors and Affiliations

  1. Department of Biochemistry, University of Zurich, Zurich, Switzerland

    Antonio Baici

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  1. Antonio Baici
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Appendices

Appendix 1

1.1.1 Derivation of Kinetic Parameters Using Mathematical Software

Redirected from Sect. 1.4. The following example (Fig. 1.21) demonstrates the derivation of k cat,S and K m,S using Maple. Mathematical software is a helpful alternative to paper and pencil in rearranging and extracting information from rate equations. A more cumbersome example is discussed in Sect. 2.5, Eq. (2.57), where the apparent Michaelis constant of the general modifier mechanism depends on modifier concentration.

Fig. 1.21
figure 29

Derivation of equations in Sect. 1.4 using Maple

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Appendix 2

1.2.1 List of Symbols

Table 4
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Table 5
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Baici, A. (2015). Basic Knowledge. In: Kinetics of Enzyme-Modifier Interactions. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1402-5_1

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