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An Introduction to Agricultural Biochemistry PDF

490 Pages·1998·30.13 MB·English
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AN INTRODUCTION TO AGRICULTURAL BIOCHEMISTRY JOIN US ON THE INTERNET VIA WWW, GOPHER, FTP OR EMAIL: WWW: http://www.thomson.com GOPHER: gopher.thomson.com A service of ICDP FTP: ftp.thomson.com EMAIL: [email protected] AN INTRODUCTION TO AGRICULTURAL BIOCHEMISTRY J.M. Chesworth Honorary Lecturer in Agricultural Biochemistry and Nutrition Department of Agriculture University of Aberdeen, UK and Independent Consultant Mar Technical Services Huntly, UK T. Stuchbury Lecturer in Agricultural Biochemistry and Plant Physiology Department of Agriculture University of Aberdeen, UK and J.R. Scaife Lecturer in Agricultural Biochemistry and Nutrition Department of Agriculture University of Aberdeen, UK CHAPMAN & HALL London· Weinheim . New York· Tokyo· Melbourne· Madras Published by Chapman & Hall, 2-6 Boundary Row, London SEI SHN, UK Chapman & Hall, 2-6 Boundary Row, London SEI 8HN, UK Chapman & Hall GmbH, Pappelallee 3, 69469 Wcinheim, Gennany Chapman & Hall USA, 115 Fifth Avenue, New York, NY 10003, USA Chapman & Hall Japan, ITP-Japan, Kyowa Building, 3F, 2-2-1 Hirakawacho, Chiyoda-ku, Tokyo 102, Japan Chapman & Hall Australia, 102 Dodds Street, South Melbourne, Victoria 3205, Australia Chapman & Hall India, R. Seshadri, 32 Second Main Road, CIT East, Madras 600 035, India First edition 1998 © 1998 Chapman & Hall So/kover reprint of the hardcover 1st edition 1998 Typeset in 10/12 Palatino by Saxon Graphics Ltd, Derby ISBN-13: 978-0-412-64390-3 e-ISBN-13: 978-94-009-1441-4 DOl: 10.1 007/978-94-009-1441-4 Apart from any fair dealing for the purposes of research or private study, or criticism or review, as pennitted under the UK Copyright Designs and Patents Act, 1988, this publication may not be reproduced, stored, or transmitted, in any fonn or by any means, without the prior pennission in writing of the publishers, or in the case of reprographic reproduction only in accordance with the tenns of the licences issued by the Copyright Licensing Agency in the UK, or in accordance with the tenns of licences issued by the appropriate Reproduction Rights Organization outside the UK. Enquiries concerning reproduction outside the tenns stated here should be sent to the publishers at the London address printed on this page. The publisher makes no representation, express or implied, with regard to the accuracy of the infonnation contained in this book and cannot accept any legal responsibility or liabil ity for any errors or omissions that may be made. A catalogue record for this book is available from the British Library Library of Congress Catalog Card Number: 97-68949 i§ Printed on pennanent acid-free text paper, manufactured in accordance with ANSIINISO Z39.48-1992 and ANSIINISO Z39.48-l984 (Pennanence of Paper). CONTENTS Preface XVlll List of abbreviations xix PART ONE: THE CELL AND CELLULAR CONSTITUENTS 1 1 Cell structure and function 3 1.1 Introduction 3 1.2 Components of cells 3 1.2.1 Plasma membrane 3 1.2.2 Cytoplasm 4 1.2.3 The nucleoid and nucleus 6 1.2.4 Cell walls 6 1.2.5 Ribosomes 6 1.2.6 Endoplasmic reticulum 6 1.2.7 Vacuoles and specialized vesicles 7 1.2.8 Mitochondria 8 1.2.9 Chloroplasts 8 1.2.10 Cytoskeleton 8 1.3 Cell specialization and interaction 9 2 Water and solutions 11 2.1 Introduction 11 2.2 The ionization of water 12 2.2.1 The pH of water 12 2.3 What are acids and bases? 14 2.4 Biological systems, ionic strength and pH 14 2.4.1 Stabilization of pH by buffers 14 2.5 Colligative properties 15 2.5.1 Depression of freezing point 16 2.5.2 Osmotic pressure 16 2.5.3 Semipermeable membranes that allow some solutes to pass 17 3 The carbohydrates 19 3.1 Introduction 19 3.2 Structures of sugars 20 3.2.1 Optical isomers 20 3.3 Naming of sugars 20 3.4 Sugars with four carbon atoms, the tetroses 20 vi Contents 3.5 Sugars with five carbon atoms, the pentoses 21 3.5.1 Ring formation in sugars 22 3.5.2 Five-and six-membered rings 23 3.5.3 Ring formation is not permanent 23 3.6 Sugars with six carbon atoms, the hexoses 23 3.6.1 Glucose 23 3.6.2 Fructose 23 3.6.3 Other hexoses 23 3.7 Reducing and non-reducing sugars 24 3.8 Formation of sugar acetals 24 3.8.1 Formation of disaccharides 25 3.8.2 Sucrose 25 3.9 Polysaccharides 26 3.9.1 The storage carbohydrates - starch and glycogen 26 3.9.2 Structural polysaccharides in plants 29 3.9.3 Other polysaccharides and related compounds 32 4 Fatty acids and lipids 35 4.1 Introduction 35 4.2 Structure and occurrence of lipids 35 4.2.1 Fatty acids 35 4.2.2 Triacylglycerols and other acylglycerols 39 4.2.3 Glycerophospholipids 42 4.2.4 Glycosylglycerides 43 4.2.5 Sphingolipids 44 4.2.6 Terpenes and steroids 45 4.2.7 Waxes 47 5 Amino acids and proteins 51 5.1 Introduction 51 5.2 Amino acids 52 5.2.1 Structure of amino acids 52 5.3 Non-protein amino acids and related compounds 52 5.3.1 Canavanine 52 5.3.2 Selenium-containing amino acids 52 5.3.3 Mimosine 54 5.3.4 Lathyrogens 55 5.3.5 S-methyl cysteine sulphoxide (SMCO) 55 5.3.6 Alkaloids 55 5.4 Phenolics 57 5.4.1 Lignin 57 5.4.2 Tannins 57 5.4.3 Flavonoids 58 5.5 Peptide bonds 59 5.6 Protein function and structure 61 5.6.1 Primary protein structure 62 5.6.2 Secondary protein structure 62 5.6.3 Tertiary structure 63 Contents vii 5.6.4 Quaternary structure 64 5.7 Properties of proteins 66 5.7.1 Ionic strength and presence of specific ions 67 5.7.2 Effect of pH 68 5.7.3 Denaturation 68 5.7.4 Effect of heat 69 5.8 Prions 69 6 Enzymes 71 6.1 Introduction 71 6.2 Types of reactions catalysed by enzymes 71 6.3 Mode of action of enzymes 72 6.4 Factors contributing to enzyme activity 73 6.4.1 Proximity of substrates at the active site 73 6.4.2 Environment 74 6.4.3 Acid-base catalysis 74 6.4.4 Effects on the stability of substrates and reaction intermediates 74 6.4.5 Formation of covalent enzyme-substrate intermediates 74 6.5 Factors affecting the rates of enzyme-catalysed reactions 76 6.5.1 Enzyme concentration 76 6.5.2 Substrate concentration 76 6.5.3 Temperature 79 6.5.4 pH 79 6.5.5 Presence of inhibitors 81 6.5.6 Presence of coenzymes 84 6.6 Allosteric enzymes 90 6.7 Molecular recognition 91 6.7.1 Receptors 91 6.7.2 Antibodies 91 7 Purines, pyrimidines and nucleic acids 95 7.1 Introduction 95 7.2 Purines and pyrimidines 95 7.3 Deoxyribonucleic acid (DNA) 96 7.3.1 Chemical nature of DNA 96 7.3.2 The DNA double helix 98 7.3.3 Structure of DNA in prokaryotes and eukaryotes 98 7.3.4 Organelle DNA 100 7.4 Ribonucleic acid (RNA) 100 7.4.1 Messenger RNA (mRNA) 101 7.4.2 Transfer RNA (tRNA) 101 7.4.3 Ribosomal RNA (rRNA) 102 8 Vitamins and minerals 105 8.1 Vitamins in biochemistry 105 8.1.1 Introduction 105 8.1.2 Thiamin (vitamin B1) 106 8.1.3 Riboflavin (vitamin B 108 2) viii Contents 8.1.4 Nicotinic acid (niacin, formerly called vitamin B5) 108 8.1.5 Pantothenic acid 112 8.1.6 Pyridoxine, pyridoxal and pyridoxamine (vitamin B6) 112 8.1.7 Biotin 114 8.1.8 Folic acid 114 8.1.9 Vitamin B12 115 8.1.10 Vitamin C 117 8.1.11 Choline 118 8.1.12 Carnitine 119 8.1.13 Vitamin A 119 8.1.14 Vitamin 0 121 8.1.15 Vitamin E 124 8.1.16 Vitamin K 126 8.2 Minerals in biochemistry 127 8.2.1 Introduction 127 8.2.2 Calcium 127 8.2.3 Phosphorus 128 8.2.4 Magnesium 128 8.2.5 Sodium, chloride and potassium 129 8.2.6 Sulphur and iron 129 8.2.7 Other elements with known biochemical functions 130 9 The composition of agricultural products 133 9.1 Introduction 133 9.1.1 Energy storage in animals and plants 133 92 The composition of animals 134 9.2.1 Body composition 134 9.2.2 Milk 134 9.3 Plant materials 134 9.4 Principal nutrients in plants and animals 00 9.4.1 Proteins 00 9.4.2 Lipids 00 9.4.3 Carbohydrates 00 PART TWO: METABOLISM 139 10 Glycolysis 141 10.1 Introduction 141 10.2 Stage 1 - preparing glucose for splittil)g into two three-carbon units 141 10.2.1 Glucose phosphorylation 141 10.2.2 Fructose and its phosphates 143 10.2.3 Splitting of fructose-1,6-bisphosphate 143 10.3 Stage 2 - metabolism of the three-carbon compounds 143 10.3.1 First oxidation step 143 10.3.2 First energy released in the form of ATP 145 10.3.3 Formation of pyruvate 145 10.4 The entry of other sugars 145 10.4.1 Fructose 146 Contents ix 10.4.2 Galactose 146 10.4.3 The entry of glycogen 146 11 The tricarboxylic acid cycle 149 11.1 Introduction 149 11.2 The reactions of the TCA cycle 149 11.2.1 Production of acetyl-CoA 149 11.2.2 Reactions leading to the production of CO 150 2 11.2.3 Reactions leading back to the formation of oxaloacetate 150 11.2.4 Overall reactions of the tricarboxylic acid cycle 153 11.3 Links with other metabolic pathways 153 11.4 Replenishment of TCA cycle intermediates 155 11.5 Conversion of propionate to glucose via the TCA cycle 155 11.6 Regulation of the TCA cycle 155 11.7 The glyoxylate cycle 156 12 Electron transport and oxidative phosphorylation 161 12.1 Introduction 161 12.2 The mitochondrion 163 12.3 Components of the electron transport chain 163 12.3.1 Flavoproteins 163 12.3.2 The iron-sulphur proteins 164 12.3.3 Ubiquinone 164 12.4 The electron transport chain complexes 164 12.4.1 Complex I - the NADH-dehydrogenase complex 164 12.4.2 Complex II - the succinate dehydrogenase complex 164 12.4.3 Complex III - the cytochrome b, c complex 165 1 12.4.4 Complex IV - cytochrome oxidase 165 12.5 Coupling of electron transport to ATP synthesis 166 12.6 The yield of ATP 168 12.7 NADH produced in the cytoplasm enters the electron transport chain via 169 shuttle reactions 12.8 Regulation of oxidative phosphorylation by ADP/ATP supply 169 13 Fatty acid oxidation and lipid breakdown 173 13.1 Introduction 173 13.2 j3-0xidation 174 13.2.1 Mitochondrialj3-oxidation in animal tissues 174 13.2.2 The reactions of j3-oxidation 176 13.2.3 j3-0xidation of odd-numbered acids 176 13.2.4 j3-0xidation of unsaturated acids 178 13.2.5 j3-0xidation in peroxisomes and glyoxisomes 179 13.2.6 The formation of ketone bodies 181 13.3 a-Oxidation 182 13.4 w-Oxidation 183 13.5 Peroxidation of fatty acids 183 13.5.1 Chemistry of lipid peroxidation 184 13.5.2 Prevention of fatty acid peroxidation 185 x Contents 13.5.3 Detection and measurement of lipid peroxidation 185 13.5.4 Effects of peroxidation in living organisms 186 13.5.5 Lipoxygenase and cyclo-oxygenase 188 13.6 Breakdown of lipids 189 13.6.1 Triacylglycerol breakdown 190 13.6.2 Phospholipid breakdown 191 13.6.3 Breakdown of glycolipids 192 14 Breakdown of proteins and the oxidation of amino acids 193 14.1 Introduction 193 14.2 Breakdown of proteins 194 14.2.1 Digestion of proteins 194 14.2.2 Protein turnover 194 14.3 Breakdown of amino acids 194 14.3.1 Transamination reactions 194 14.3.2 Deamination 195 14.3.3 Oxidation of carbon skeletons of amino acids 195 14.3.4 The fate of ammonia 197 14.3.5 The urea cycle 197 14.3.6 The fate of urea in ruminants 199 14.4 Precursor functions of amino acids 199 15 The pentose phosphate pathway 201 15.1 Introduction 201 15.2 Oxidative reactions 201 15.3 Rearrangement reactions 201 15.4 Importance of the pathway 205 15.5 Regulation of the pathway 206 16 Fermentation pathways 207 16.1 Introduction 207 16.2 Anaerobic environments in agriculture 207 16.3 Lactate production 207 16.3.1 Muscle metabolism 208 16.3.2 Regeneration of glucose 208 16.4 Animal digestive systems 208 16.4.1 Acetate formation 209 16.4.2 Propionate formation 209 16.4.3 Butyrate synthesis 210 16.5 Soils 210 16.6 Waste treatment 211 16.7 Methane production 213 16.8 Dairy products 213 16.9 Meat 213 16.10 Fermentation in herbages 214 16.11 Ethanol production 214 17 Photosynthesis 217 17.1 Introduction 217

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