Table of contents. Author's preface. Part 1: Structure and function of enzymes

Transcription

1 Author's preface xvii Part 1: Structure and function of enzymes 1 An introduction to enzymes 1.1 What are enzymes A brief history of enzymes The naming and classification of enzymes Why classify enzymes? The Enzyme Commission's system of classification The Enzyme Commission's recommendations on nomenclature The six main classes of enzymes 6 Summary of Chapter 1 12 Further reading 12 Problems 12 2 The structure of proteins 2.1 Introduction Amino acids, the building blocks of proteins Structure and classification of amino acids Stereochemistry of amino acids The basis of protein structure Levels of protein structure Bonds involved in the maintenance of protein structure The determination of primary structure The isolation of each polypeptide chain Determination of the amino acid composition of each polypeptide chain Determination of the amino acid sequence of each polypeptide chain 27 vii

2 viii Determination of the positions of disulphide bridges Some results of experimental investigation of primary structure Indirect determination of primary structure The determination of protein structure by X-ray crystallography The principles of X-ray crystallography Some results of X-ray crystallography The investigation of protein structure in solution 40 Summary of Chapter 2 41 Further reading 42 Problems 42 3 The biosynthesis and properties of proteins 3.1 The biosynthesis of proteins The central dogma of molecular genetics The double-helix structure of DNA The translation of genetic information into protein structure Modification of protein structure after translation Control of protein synthesis Sequence determination The properties of proteins Chemical properties of proteins Acid-base properties of proteins The solubility of globular proteins 61 Summary of Chapter 3 64 Further reading 65 Problems 65 4 Specificity of enzyme action 4.1 Types of specificity The active site The Fischer 'lock-and-key' hypothesis The Koshland 'induced-fit' hypothesis Hypotheses involving strain or transition-state stabilization Further comments on specificity 74 Summary of Chapter 4 74 Further reading 75 5 Monomeric and oligomeric enzymes 5.1 Monomeric enzymes Introduction The serine proteases Some other monomeric enzymes Oligomeric enzymes Introduction Lactate dehydrogenase Lactose synthase 81

3 ix Tryptophan synthase Pyruvate dehydrogenase 82 Summary of Chapter 5 84 Further reading 84 Part 2: Kinetic and chemical mechanisms of enzyme-catalysed reactions 6 An introduction to bioenergetics, catalysis and kinetics 6.1 Some concepts of bioenergetics The first and second laws of thermodynamics Enthalpy, entropy and free energy Free energy and chemical reactions Standard free energy Bioenergetics and the living cell Factors affecting the rates of chemical reactions The collision theory Activation energy and the transition-state theory Catalysis Kinetics of uncatalysed chemical reactions The Law of Mass Action and the order of reaction The use of initial velocity Kinetics of enzyme-catalysed reactions: an historical introduction Methods used for investigating the kinetics of enzyme-catalysed reactions Initial velocity studies Rapid-reaction techniques The nature of enzyme catalysis 103 Summary of Chapter Further reading 105 Problems Kinetics of single-substrate enzyme-catalysed reactions 7.1 The relationship between initial velocity and substrate concentration The Henri and Michaelis-Menten equations The Briggs-Haldane modification of the Michaelis-Menten equation The significance of the Michaelis-Menten equation Ill The Lineweaver-Burk plot The Eadie-Hofstee and Hanes plots The Eisenthal and Cornish-Bowden plot The Haldane relationship for reversible reactions Rapid-reaction kinetics Pre-steady-state kinetics Relaxation kinetics The King and Altman procedure 124 Summary of Chapter 7 126

4 x Further reading 126 Problems Enzyme inhibition 8.1 Introduction Reversible inhibition Competitive inhibition Uncompetitive inhibition Non-competitive inhibition Mixed inhibition Partial inhibition Substrate inhibition Allosteric inhibition Irreversible inhibition 149 Summary of Chapter Further reading 152 Problems Kinetics of multi-substrate enzyme-catalysed reactions 9.1 Examples of possible mechanisms Introduction Ping-pong bi-bi mechanism Random-order mechanism Compulsory-order mechanism Steady-state kinetics The general rate equation of Alberty Plots for mechanisms which follow the general rate equation The general rate equation of Dalziel Rate constants and the constants of Alberty and Dalziel Investigation of reaction mechanisms using steady-state methods The use of primary plots The use of inhibitors which compete with substrates for binding sites Investigation of reaction mechanisms using non-steady-state methods Isotope exchange at equilibrium Rapid-reaction studies 169 Summary of Chapter Further reading 170 Problems The investigation of active site structure 10.1 The identification of binding sites and catalytic sites Trapping the enzyme-substrate complex The use of substrate analogues Enzyme modification by chemical procedures affecting

5 xi amino acid side chains Enzyme modification by treatment with proteases Enzyme modification by site-directed mutagenesis The effect of changing ph The investigation of the three-dimensional structures of active sites 187 Summary of Chapter Further reading 189 Problems The chemical nature of enzyme catalysis 11.1 An introduction to reaction mechanisms in organic chemistry Mechanisms of catalysis Acid-base catalysis Electrostatic catalysis Covalent catalysis Enzyme catalysis! Mechanisms of reactions catalysed by enzymes without cofactors Introduction Chymotrypsin Ribonuclease Lysozyme Triose phosphate isomerase Metal-activated enzymes and metalloenzymes Introduction Activation by alkali metal cations (Na + and K + ) Activation by alkaline earth metal cations (Ca 2+ and Mg 2+ ) Activation by transition metal cations (Cu, Zn, Mo, Fe and Co cations) The involvement of coenzymes in enzyme-catalysed reactions Introduction Nicotinamide nucleotides (NAD + and NADP + ) Flavin nucleotides (FMN and FAD) Adenosine phosphates (ATP, ADP and AMP) Coenzyme A (CoA.SH) Thiamine pyrophosphate (TPP) Pyridoxal phosphate Biotin Tetrahydrofolate Coenzyme B Summary of Chapter Further reading The binding of ligands to proteins 12.1 Introduction The binding of a ligand to a protein having a single ligand-binding site 223

6 xii 12.3 Cooperativity Positive homotropic cooperativity and the Hill equation The Adair equation for the binding of a ligand to a protein having two binding sites for that ligand General considerations Where there is no interaction between the binding sites Where there is positive homotropic cooperativity Where there is negative homotropic cooperativity The Adair equation for the binding of a ligand to a protein having three binding sites for that ligand The Adair equation for the binding of a ligand to a protein having four binding sites for that ligand Investigation of cooperative effects Measurement of the relationship between Y and [S] Measurement of the relationship between v 0 and [S o ] The Scatchard plot and equilibrium dialysis techniques The binding of oxygen to haemoglobin 237 Summary of Chapter Further reading 238 Problems Sigmoidal kinetics and allosteric enzymes 13.1 Introduction The Monod-Wyman-Changeux (MWC) model The MWC equation How the MWC model accounts for cooperative effects The MWC model and allosteric regulation The MWC model and the Hill equation The Koshland-Némethy-Filmer (KNF) model The KNF model for a dimeric protein The KNF model for any oligomeric enzyme The KNF model and allosteric regulation Differentiation between models for cooperative binding in proteins Sigmoidal kinetics in the absence of cooperative binding Ligand-binding evidence versus kinetic evidence The Ferdinand mechanism The Rabin and mnemonical mechanisms 251 Summary of Chapter Further reading 252 Problems The significance of sigmoidal behaviour 14.1 The physiological importance of cooperative oxygen-binding by haemoglobin Allosteric enzymes and metabolic regulation Introduction 258

7 xiii Characteristics of steady-state metabolic pathways Regulation of steady-state metabolic pathways by control of enzyme activity Allosteric enzymes and the amplification of metabolic regulation Other mechanisms of metabolic regulation Some examples of allosteric enzymes involved in metabolic regulation 269 Summary of Chapter Further reading 273 Part 3: Application of enzymology 15 Investigation of enzymes in biological preparations 15.1 Choice of preparation for the investigation of enzyme characteristics Enzyme assay Introduction Enzyme assay by kinetic determination of catalytic activity Coupled kinetic assays Radioimmunoassay (RIA) of enzymes Investigation of sub-cellular compartmentation of enzymes Enzyme histochemistry The use of centrifugation Some results of the investigation of enzyme compartmentation 291 Summary of Chapter Further reading 293 Problem Extraction and purification of enzymes 16.1 Extraction of enzymes Introduction The extraction of soluble enzymes The extraction of membrane-bound enzymes The nature of the extraction medium Purification of enzymes Preliminary purification procedures Further purification procedures Criteria of purity Determination of molecular weights of enzymes 308 Summary of Chapter Further reading : 310 Problem Enzymes as analytical reagents 17.1 The value of enzymes as analytical reagents 312

8 xiv 17.2 Principles of enzymatic analysis End-point methods Kinetic methods Immunoassay methods Handling enzymes and coenzymes 321 Summary of Chapter Further reading 323 Problems Instrumental techniques available for use in enzymatic analysis 18.1 Principles of the available detection techniques L L Introduction Manometry Spectrophotometry Spectrofluorimetry Electrochemical methods Enthalpimetry Radiochemical methods Dry-reagent techniques Automation in enzymatic analysis Introduction Fixed-time methods Fixed-concentration methods Methods involving continuous monitoring 337 Summary of Chapter Further reading Some applications of enzymatic analysis in medicine and industry 19.1 Applications in medicine 340 Q9.1.J! Assay of plasma enzymes Enzymes and inborn errors of metabolism Enzymes as reagents in clinical chemistry Applications in industry 349 Summary of Chapter Further reading Biotechnological applications of enzymes 20.1 Large-scale production and purification of enzymes Production of enzymes on an industrial scale Large-scale purification of enzymes Synthesis of artificial enzymes Immobilized enzymes Preparation of immobilized enzymes Properties of immobilized enzymes Applications of immobilized enzymes: general principles 20.3 Enzyme utilization in industry Introduction 365

9 Table of Contents xv Applications in food and drink industries Applications in other industries Enzymes and recombinant DNA technology Introduction Applications Enzymes and bioinformatics 379 Summary of Chapter Further reading 381 Problems 384 Answers to problems 386 Abbreviations 391 Index 393