Enzyme Kinetics

Rapid-Equilibrium Applications of Mathematica

Robert A. Alberty

• Publisher: Wiley
• Year: 2011
• Print ISBN: 9780470639320
• eBook ISBN: 9781118002155
• Edition: 1
• Topic: Biological Sciences
• Subtopic: Biochemistry
• Index: Biological Sciences

Rapid-Equilibrium Enzyme Kinetics helps readers emphasize the estimation of kinetic parameters with the minimum number of velocity measurements, thereby reducing the amount of laboratory work necessary, and allowing more time for the consideration of complicated mechanisms. The book systematically progresses through six levels of understanding the enzyme-catalyzed reaction, and includes a CD-ROM so that the reader may use the programs in the book to input their own experimental data.

Chapter 1

Biochemical Thermodynamics

1.1 Introduction

1.2 Chemical Thermodynamics

1.3 Transformed Thermodynamic Properties of Biochemical Reactants at a Specified pH

1.4 Calculation of the change in binding of hydrogen ions in a biochemical reaction at a specified pH by taking the derivative of logK′ or Δr G′° with respect to pH

1.5 Calculation of the standard transformed Gibbs energies of formation of biochemical reactants

1.6 Calculation of the standard transformed Gibbs energy of hydrolysis of ATP to ADP and the apparent equilibrium constant K′

1.7 Calculation of the change in the binding of hydrogen ions Δr NH in ATP + H2O = ADP + Pi at 298.15 K

1.8 Calculation of the change in the binding of hydrogen ions in a biochemical reaction at a specified pH without information on standard Gibbs energies of formation of species

1.9 Another way to consider the pH dependence of the apparent equilibrium constant

1.9.1 Distributions of species of inorganic phosphate as functions of pH

1.9.2 Distributions of species of ATP as functions of pH

1.9.3 Distributions of species of ADP as functions of pH

1.9.4 Calculations of the apparent equlibrium constant for ATP + H2O = ADP + Pi as a function of pH

1.10 Data on the thermodynamics of enzyme-catalyzed reactions in the literature and on the web

1.10.1 Experimental data on apparent equilibrium constants and heats of reactions

1.10.2 Data on thermodynamic properties of species obtained chemically or from experimental measurements of apparent equilibrium constants and heats of reaction of enzyme-catalyzed reactions

1.11 Discussion

1.1 Introduction

It is necessary to start a book on rapid-equilibrium enzyme kinetics with a chapter on biochemical thermodynamics for two reasons: (1) The complete rate equation for an enzyme-catalyzed reaction has to contain the biochemical thermodynamics of the reaction that is catalyzed. Setting the velocity in the complete rate equation equal to zero yields the Haldane relation for the apparent equilibrium constant K′ in terms of the kinetic parameters at the specified temperature, pH and ionic strength. (2) The equilibrim concentration of the enzyme-substrate complex in the rate-determining reaction is calculated with a set of independent biochemical reactions. When an independent set of reactions is at equilibrium, other reactions that are the sums or differences of the reactions in the independent set are also at equilibrium.

In chemical thermodynamics, reactions are written in terms of species, and chemical reactions must balance the various atoms and electric charges. But in biochemical thermodynamics, reactions are written in terms of reactants (sums of species like ATP), and all atoms are balanced except for hydrogen atoms because the pH is held constant. Electric charges are also not balanced in a biochemical reaction. Conceptually, hydrogen ions are added or removed during the reaction so that the pH is held constant. In practice a buffer is used to hold the pH approximately constant.

This book is about rapid-equilibrium rate equations because they are simpler than steady-state rate equations. This is not to say that all enzyme-catalyzed reactions involve a rate-determining reaction, but simply to say that rapid-equilibrium rate equations are the place to start in the investigation of rate equations. When the kinetic data for an enzyme-catalyzed r...

Table of contents

• Cover
• Half Title Page
• Title Page
• Copyright
• Preface
• Chapter 1: Biochemical Thermodynamics
• Chapter 2: A = P
• Chapter 3: Ordered A + B → Products
• Chapter 4: Random A + B → Products
• Chapter 5: A + B = P + Q
• Chapter 6: A + B + C → Products
• Chapter 7: Ordered O + mR → Products
• Chapter 8: Random O + mR → Products
• Chapter 9: Inhibition and activation of A → products
• Chapter 10: Modification of A → products
• Chapter 11: Inhibition, activation, and modification of A + B → products
• Chapter 12: Systems of Enzyme-Catalyzed Reactions
• References
• Index