An Introduction to Agricultural Biochemistry

490 Pages·1998·30.13 MB·English

by  J. M. Chesworth

AN INTRODUCTION
TO AGRICULTURAL
BIOCHEMISTRY
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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
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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
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i§
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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