One: The Cell and Cellular Constituents.- 1 Cell structure and function.- 1.1 Introduction.- 1.2 Components of cells.- 1.2.1 Plasma membrane.- 1.2.2 Cytoplasm.- 1.2.3 The nucleoid and nucleus.- 1.2.4 Cell walls.- 1.2.5 Ribosomes.- 1.2.6 Endoplasmic reticulum.- 1.2.7 Vacuoles and specialized vesicles.- 1.2.8 Mitochondria.- 1.2.9 Chloroplasts.- 1.2.10 Cytoskeleton.- 1.3 Cell specialization and interaction.- 2 Water and solutions.- 2.1 Introduction.- 2.2 The ionization of water.- 2.2.1 The pH of water.- 2.3 What are acids and bases?.- 2.4 Biological systems, ionic strength and pH.- 2.4.1 Stabilization of pH by buffers.- 2.5 Colligative properties.- 2.5.1 Depression of freezing point.- 2.5.2 Osmotic pressure.- 2.5.3 Semipermeable membranes that allow some solutes to pass.- 3 The carbohydrates.- 3.1 Introduction.- 3.2 Structures of sugars.- 3.2.1 Optical isomers.- 3.3 Naming of sugars.- 3.4 Sugars with four carbon atoms, the tetroses.- 3.5 Sugars with five carbon atoms, the pentoses.- 3.5.1 Ring formation in sugars.- 3.5.2 Five- and six-membered rings.- 3.5.3 Ring formation is not permanent.- 3.6 Sugars with six carbon atoms, the hexoses.- 3.6.1 Glucose.- 3.6.2 Fructose.- 3.6.3 Other hexoses.- 3.7 Reducing and non-reducing sugars.- 3.8 Formation of sugar acetals.- 3.8.1 Formation of disaccharides.- 3.8.2 Sucrose.- 3.9 Polysaccharides.- 3.9.1 The storage carbohydrates - starch and glycogen.- 3.9.2 Structural polysaccharides in plants.- 3.9.3 Other polysaccharides and related compounds.- 4 Fatty acids and lipids.- 4.1 Introduction.- 4.2 Structure and occurrence of lipids.- 4.2.1 Fatty acids.- 4.2.2 Triacylglycerols and other acylglycerols.- 4.2.3 Glycerophospholipids.- 4.2.4 Glycosylglycerides.- 4.2.5 Sphingolipids.- 4.2.6 Terpenes and steroids.- 4.2.7 Waxes.- 5 Amino acids and proteins.- 5.1 Introduction.- 5.2 Amino acids.- 5.2.1 Structure of amino acids.- 5.3 Non-protein amino acids and related compounds.- 5.3.1 Canavanine.- 5.3.2 Selenium-containing amino acids.- 5.3.3 Mimosine.- 5.3.4 Lathyrogens.- 5.3.5 S-methyl cysteine sulphoxide (SMCO).- 5.3.6 Alkaloids.- 5.4 Phenolics.- 5.4.1 Lignin.- 5.4.2 Tannins.- 5.4.3 Flavonoids.- 5.5 Peptide bonds.- 5.6 Protein function and structure.- 5.6.1 Primary protein structure.- 5.6.2 Secondary protein structure.- 5.6.3 Tertiary structure.- 5.6.4 Quaternary structure.- 5.7 Properties of proteins.- 5.7.1 Ionic strength and presence of specific ions.- 5.7.2 Effect of pH.- 5.7.3 Denaturation.- 5.7.4 Effect of heat.- 5.8 Prions.- 6 Enzymes.- 6.1 Introduction.- 6.2 Types of reactions catalysed by enzymes.- 6.3 Mode of action of enzymes.- 6.4 Factors contributing to enzyme activity.- 6.4.1 Proximity of substrates at the active site.- 6.4.2 Environment.- 6.4.3 Acid-base catalysis.- 6.4.4 Effects on the stability of substrates and reaction intermediates.- 6.4.5 Formation of covalent enzyme-substrate intermediates.- 6.5 Factors affecting the rates of enzyme-catalysed reactions.- 6.5.1 Enzyme concentration.- 6.5.2 Substrate concentration.- 6.5.3 Temperature.- 6.5.4 pH.- 6.5.5 Presence of inhibitors.- 6.5.6 Presence of coenzymes.- 6.6 Allosteric enzymes.- 6.7 Molecular recognition.- 6.7.1 Receptors.- 6.7.2 Antibodies.- 7 Purines, pyrimidines and nucleic acids.- 7.1 Introduction.- 7.2 Purines and pyrimidines.- 7.3 Deoxyribonucleic acid (DNA).- 7.3.1 Chemical nature of DNA.- 7.3.2 The DNA double helix.- 7.3.3 Structure of DNA in prokaryotes and eukaryotes.- 7.3.4 Organelle DNA.- 7.4 Ribonucleic acid (RNA).- 7.4.1 Messenger RNA (mRNA).- 7.4.2 Transfer RNA (tRNA).- 7.4.3 Ribosomal RNA (rRNA).- 8 Vitamins and minerals.- 8.1 Vitamins in biochemistry.- 8.1.1 Introduction.- 8.1.2 Thiamin (vitamin B1).- 8.1.3 Riboflavin (vitamin B2).- 8.1.4 Nicotinic acid (niacin, formerly called vitamin B5).- 8.1.5 Pantothenic acid.- 8.1.6 Pyridoxine, pyridoxal and pyridoxamine (vitamin B6).- 8.1.7 Biotin.- 8.1.8 Folic acid.- 8.1.9 Vitamin B12.- 8.1.10 Vitamin C.- 8.1.11 Choline.- 8.1.12 Carnitine.- 8.1.13 Vitamin A.- 8.1.14 Vitamin D.- 8.1.15 Vitamin E.- 8.1.16 Vitamin K.- 8.2 Minerals in biochemistry.- 8.2.1 Introduction.- 8.2.2 Calcium.- 8.2.3 Phosphorus.- 8.2.4 Magnesium.- 8.2.5 Sodium, chloride and potassium.- 8.2.6 Sulphur and iron.- 8.2.7 Other elements with known biochemical functions.- 9 The composition of agricultural products.- 9.1 Introduction.- 9.1.1 Energy storage in animals and plants.- 9.2 The composition of animals.- 9.2.1 Body composition.- 9.2.2 Milk.- 9.3 Plant materials.- 9.4 Principal nutrients in plants and animals.- 9.4.1 Proteins.- 9.4.2 Lipids.- 9.4.3 Carbohydrates.- Two: Metabolism.- 10 Glycolysis.- 10.1 Introduction.- 10.2 Stage 1 - preparing glucose for splitting into two three-carbon units.- 10.2.1 Glucose phosphorylation.- 10.2.2 Fructose and its phosphates.- 10.2.3 Splitting of fructose-1,6-bisphosphate.- 10.3 Stage 2 - metabolism of the three-carbon compounds.- 10.3.1 First oxidation step.- 10.3.2 First energy released in the form of ATP.- 10.3.3 Formation of pyruvate.- 10.4 The entry of other sugars.- 10.4.1 Fructose.- 10.4.2 Galactose.- 10.4.3 The entry of glycogen.- 11 The tricarboxylic acid cycle.- 11.1 Introduction.- 11.2 The reactions of the TCA cycle.- 11.2.1 Production of acetyl-CoA.- 11.2.2 Reactions leading to the production of CO2.- 11.2.3 Reactions leading back to the formation of oxaloacetate.- 11.2.4 Overall reactions of the tricarboxylic acid cycle.- 11.3 Links with other metabolic pathways.- 11.4 Replenishment of TCA cycle intermediates.- 11.5 Conversion of propionate to glucose via the TCA cycle.- 11.6 Regulation of the TCA cycle.- 11.7 The glyoxylate cycle.- 12 Electron transport and oxidative phosphorylation.- 12.1 Introduction.- 12.2 The mitochondrion.- 12.3 Components of the electron transport chain.- 12.3.1 Flavoproteins.- 12.3.2 The iron-sulphur proteins.- 12.3.3 Ubiquinone.- 12.4 The electron transport chain complexes.- 12.4.1 Complex I - the NADH-dehydrogenase complex.- 12.4.2 Complex II - the succinate dehydrogenase complex.- 12.4.3 Complex III - the cytochrome b, c1 complex.- 12.4.4 Complex IV - cytochrome oxidase.- 12.5 Coupling of electron transport to ATP synthesis.- 12.6 The yield of ATP.- 12.7 NADH produced in the cytoplasm enters the electron transport chain via shuttle reactions.- 12.8 Regulation of oxidative phosphorylation by ADP/ATP supply.- 13 Fatty acid oxidation and lipid breakdown.- 13.1 Introduction.- 13.2 ?-Oxidation.- 13.2.1 Mitochondrial ?-oxidation in animal tissues.- 13.2.2 The reactions of ?-oxidation.- 13.2.3 ?-Oxidation of odd-numbered acids.- 13.2.4 ?-Oxidation of unsaturated acids.- 13.2.5 ?-Oxidation in peroxisomes and glyoxisomes.- 13.2.6 The formation of ketone bodies.- 13.3 ?-Oxidation.- 13.4 ?-Oxidation.- 13.5 Peroxidation of fatty acids.- 13.5.1 Chemistry of lipid peroxidation.- 13.5.2 Prevention of fatty acid peroxidation.- 13.5.3 Detection and measurement of lipid peroxidation.- 13.5.4 Effects of peroxidation in living organisms.- 13.5.5 Lipoxygenase and cyclo-oxygenase.- 13.6 Breakdown of lipids.- 13.6.1 Triacylglycerol breakdown.- 13.6.2 Phospholipid breakdown.- 13.6.3 Breakdown of glycolipids.- 14 Breakdown of proteins and the oxidation of amino acids.- 14.1 Introduction.- 14.2 Breakdown of proteins.- 14.2.1 Digestion of proteins.- 14.2.2 Protein turnover.- 14.3 Breakdown of amino acids.- 14.3.1 Transamination reactions.- 14.3.2 Deamination.- 14.3.3 Oxidation of carbon skeletons of amino acids.- 14.3.4 The fate of ammonia.- 14.3.5 The urea cycle.- 14.3.6 The fate of urea in ruminants.- 14.4 Precursor functions of amino acids.- 15 The pentose phosphate pathway.- 15.1 Introduction.- 15.2 Oxidative reactions.- 15.3 Rearrangement reactions.- 15.4 Importance of the pathway.- 15.5 Regulation of the pathway.- 16 Fermentation pathways.- 16.1 Introduction.- 16.2 Anaerobic environments in agriculture.- 16.3 Lactate production.- 16.3.1 Muscle metabolism.- 16.3.2 Regeneration of glucose.- 16.4 Animal digestive systems.- 16.4.1 Acetate formation.- 16.4.2 Propionate formation.- 16.4.3 Butyrate synthesis.- 16.5 Soils.- 16.6 Waste treatment.- 16.7 Methane production.- 16.8 Dairy products.- 16.9 Meat.- 16.10 Fermentation in herbages.- 16.11 Ethanol production.- 17 Photosynthesis.- 17.1 Introduction.- 17.2 Chloroplasts.- 17.3 The light reactions.- 17.3.1 Photosynthetic pigments.- 17.3.2 Light absorption.- 17.3.3 Resonance energy transfer.- 17.3.4 The electron transport system.- 17.3.5 Photosystem I.- 17.3.6 Photosystem II.- 17.3.7 Cytochrome b-f complex.- 17.3.8 Plastocyanin.- 17.4 Integration of the electron transport system.- 17.5 ATP production.- 17.6 The dark reactions (Calvin cycle).- 17.7 Control of photosynthesis.- 17.8 Photorespiration.- 17.8.1 Factors affecting rates of photorespiration.- 17.9 Photosynthesis in C4 plants.- 17.10 Crassulacean acid metabolism.- 17.11 Herbicides and photosynthesis.- 18 Gluconeogenesis and carbohydrate synthesis.- 18.1 Introduction.- 18.1.1 Starting materials.- 18.1.2 Outline of the pathway.- 18.1.3 Differences between gluconeogenesis and glycolysis.- 18.2 Gluconeogenesis via pyruvate.- 18.2.1 The control of pyruvate production and use.- 18.3 The production of fructose-1,6-bisphosphate.- 18.4 The hydrolysis of fructose-1,6-bisphosphate.- 18.4.1 The control of phosphofructokinase and fructose-1,6-bisphosphatase.- 18.4.2 The fate of fructose-6-phosphate.- 18.5 The utilization of glucose-6-phosphate.- 18.6 Gluconeogenesis from propionate.- 18.7 The synthesis of complex carbohydrates.- 18.7.1 Disaccharides.- 18.7.2 Synthesis of polysaccharides.- 19 Synthesis of fatty acids and lipids.- 19.1 Introduction.- 19.2 Tissue and subcellular location of fatty acid synthesis.- 19.3 Source of the primary substrate - acetate.- 19.4 Production of malonyl-CoA.- 19.4.1 Animals.- 19.4.2 Plants.- 19.4.3 Bacteria.- 19.5 Synthesis of long-chain saturated fatty acids from acetyl-CoA and malonyl-CoA.- 19.5.1 Acyl carrier protein and its function.- 19.5.2 The reactions of fatty acid synthesis.- 19.5.3 Chain length specificity of fatty acid synthetases.- 19.5.4 Synthesis of branched-chain fatty acids.- 19.5.5 Release of fatty acids from fatty acid synthetase.- 19.6 Fatty acid elongation.- 19.7 Formation of unsaturated fatty acids.- 19.7.1 Desaturation of fatty acids in animals.- 19.7.2 Desaturation of fatty acids in plants.- 19.7.3 Essential fatty acids.- 19.8 Synthesis of triacylglycerols.- 19.8.1 The 2-monoacylglycerol pathway.- 19.8.2 The glycerol-3-phosphate pathway.- 19.8.3 Triacylglycerol synthesis in plants.- 19.9 Phospholipids.- 19.10 Glycolipid synthesis.- 19.11 Synthesis of sphingolipids.- 19.12 Biosynthesis of terpenes and sterols.- 19.12.1 Synthesis of mevalonic acid.- 19.12.2 Conversion of mevalonic acid to squalene.- 20 Synthesis of amino acids.- 20.1 Introduction.- 20.2 Assimilation of nitrate.- 20.3 Nitrogen fixation.- 20.3.1 Molecular biology of nitrogen fixation.- 20.4 Assimilation of ammonia.- 20.5 Biosynthesis of amino acids.- 20.5.1 Aromatic amino acids and related compounds.- 20.5.2 Branched-chain aliphatic amino acids.- 20.6 Nutritional role of amino acids.- 20.7 Herbicides and amino acid biosynthesis.- 21 The synthesis of nucleic acids and proteins.- 21.1 Introduction.- 21.2 Synthesis of purine and pyrimidine nucleotides.- 21.3 Replication of DNA.- 21.3.1 DNA synthesis in viruses.- 21.3.2 Accuracy of DNA synthesis.- 21.4 Synthesis of RNA.- 21.5 The genetic code.- 21.6 Protein synthesis.- 21.6.1 Amino acid activation.- 21.6.2 Initiation.- 21.6.3 Elongation.- 21.6.4 Termination.- 21.6.5 Post-translational modification of proteins.- 21.6.6 Location of protein synthesis.- 21.7 Regulation of protein synthesis.- 21.7.1 Regulation in prokaryotes.- 21.7.2 Regulation in eukaryotes.- 21.8 Protein synthesis in chloroplasts and mitochondria.- 21.9 Genetic engineering.- 21.9.1 Enzymes used in DNA manipulation.- 21.9.2 Isolation and synthesis of DNA.- 21.9.3 Gene cloning.- 21.9.4 Screening techniques.- 21.9.5 Restriction fragment length polymorphism (RFLP).- 21.9.6 AntisenseRNA.- 21.9.7 Vectors and methods for insertion of DNA into cells.- 21.9.8 Site-specific mutagenesis (oligonucleotide-directed mutagenesis).- 22 Compartments, membranes and regulation.- 22.1 Cell compartments.- 22.2 Lipids and membranes.- 22.3 Transport across membranes.- 22.3.1 Membrane transport mechanisms.- 22.3.2 Other functions of membranes.- 22.4 Principles of metabolic regulation.- 22.4.1 Allosteric regulation.- 22.4.2 Covalent modification.- 22.4.3 Changes in the amount of enzyme.- 22.4.4 Coordinated regulation of pathways.- 22.4.5 Coordination of metabolism in different tissues.- Three: Strategies for Processing of Nutrients in Plants.- 23 Seeds and germination.- 23.1 Seeds and plant development.- 23.2 Seeds as food and agricultural commodities.- 23.3 Seed composition.- 23.3.1 Seed carbohydrates.- 23.3.2 Seed lipids.- 23.3.3 Seed proteins.- 23.3.4 Seed minerals.- 23.4 Germination.- 23.4.1 Starch breakdown.- 23.4.2 Beer and whisky production.- 23.4.3 Protein breakdown.- 23.4.4 Lipid breakdown.- 24 Vegetative growth of plants.- 24.1 Introduction.- 24.2 Composition of shoots.- 24.2.1 Plant cell walls.- 24.3 Important shoot crops and their products.- 24.3.1 Temperate grasses.- 24.3.2 Tropical grasses.- 24.3.3 Forage legumes.- 24.3.4 Brassicas.- 24.3.5 Straws.- 24.3.6 Hay.- 24.3.7 Silage.- 24.3.8 Wood.- 24.4 Important root and tuber crops.- 24.4.1 Root crops.- 24.4.2 Tubers.- 25 Reproductive growth.- 25.1 Flowering.- 25.2 Fruit development and composition.- 25.3 Fruit ripening.- 25.3.1 Changes in colour.- 25.3.2 Changes in texture.- 25.3.3 Changes in flavour.- 25.3.4 Respiration in ripening fruit.- 25.4 Seed development.- 25.4.1 Starch biosynthesis.- 25.4.2 Protein synthesis.- 25.4.3 Biosynthesis of fats.- 26 Plant nutrition.- 26.1 Introduction.- 26.2 Biochemical functions of major plant nutrients.- 26.2.1 Nitrogen.- 26.2.2 Sulphur.- 26.2.3 Phosphorus.- 26.2.4 Potassium.- 26.2.5 Calcium.- 26.2.6 Magnesium.- 26.3 Trace elements - micronutrients.- 26.4 Toxic effects of minerals.- 26.5 Interaction between carbon and nitrogen metabolism.- 26.5.1 Carbon assimilation.- 26.5.2 Nitrogen assimilation.- 26.5.3 Senescence and nutrient cycling.- 27 Regulation of plant growth and development.- 27.1 Introduction.- 27.2 Responses to light.- 27.2.1 Effects on photosynthesis.- 27.2.2 Phytochrome-mediated responses.- 27.2.3 Other responses to light.- 27.3 Responses to temperature.- 27.3.1 Photosynthesis.- 27.3.2 Vernalization.- 27.4 Responses to atmosphere.- 27.5 Responses to stress.- 27.5.1 Temperature stress.- 27.5.2 Water stress.- 27.5.3 Salt stress.- 27.6 Nature of plant hormones.- 27.7 Auxins.- 27.7.1 Biochemistry of auxins.- 27.7.2 Synthetic auxins.- 27.7.3 Sites of synthesis and transport of auxins.- 27.7.4 Physiological activities and applications of auxins.- 27.8 Gibberellins.- 27.8.1 Biochemistry of gibberellins.- 27.8.2 Sites of synthesis and transport of gibberellins.- 27.8.3 Physiological activities and applications of gibberellins.- 27.8.4 Growth retardants.- 27.9 Cytokinins.- 27.9.1 Biochemistry of cytokinins.- 27.9.2 Sites of synthesis and transport of cytokinins.- 27.9.3 Physiological activities and applications of cytokinins.- 27.10 Abscisic acid (ABA).- 27.10.1 Biochemistry of abscisic acid.- 27.10.2 Sites of synthesis and transport of abscisic acid.- 27.10.3 Physiological activities and applications of abscisic acid.- 27.11 Ethylene.- 27.11.1 Biochemistry of ethylene.- 27.11.2 Sites of synthesis and transport of ethylene.- 27.11.3 Methods of modulating the effects of ethylene on plants.- 27.11.4 Physiological activities and applications of ethylene.- 27.12 Miscellaneous plant growth regulators.- 27.12.1 Morphactins.- 27.12.2 Maleic hydrazide.- 27.12.3 Glyphosine.- Four: Strategies for Processing of Nutrients in Animals.- 28 Digestion and absorption in ruminants and non-ruminants.- 28.1 Introduction.- 28.2 Structure of the digestive tract.- 28.3 Carbohydrate digestion in monogastric animals.- 28.4 Carbohydrate digestion in ruminants.- 28.5 Absorption and utilization of glucose.- 28.6 Digestion of lipids in monogastric animals.- 28.6.1 Digestion in the stomach.- 28.6.2 Digestion in the small intestine.- 28.7 Absorption of lipid from the small intestine.- 28.7.1 Glycerides and fatty acids.- 28.7.2 Phospholipids.- 28.7.3 Cholesterol.- 28.7.4 Chylomicron formation.- 28.8 Uptake of absorbed lipid by body tissue.- 28.9 Digestion of lipids in ruminant animals.- 28.10 Lipid digestion in poultry.- 28.11 Digestion of proteins in monogastric animals.- 28.11.1 Digestion in the stomach.- 28.11.2 Digestion in the small intestine.- 28.12 Digestion of protein in ruminants.- 28.13 Inhibitors of digestive enzymes.- 29 Maintenance.- 29.1 Introduction.- 29.2 Body temperature and heat production.- 29.3 Biochemical production of heat.- 29.3.1 Background heat production from the maintenance of ion gradients in cells.- 29.3.2 Background heat production from protein turnover.- 29.3.3 Background heat production from other metabolic events.- 29.3.4 Heat production from muscular activity.- 29.3.5 Heat production from uncoupled phosphorylation.- 30 Regulation and manipulation of growth and development in animals.- 30.1 Introduction.- 30.1.1 General principles.- 30.2 Rates and patterns of growth.- 30.3 Muscle growth.- 30.3.1 Cellular growth as a component of muscular growth.- 30.3.2 Protein accretion as a component of growth.- 30.3.3 Control of protein synthesis.- 30.4 Growth of collagen.- 30.5 Growth of bone.- 30.5.1 Calcification of bone.- 30.6 Growth of adipose tissue.- 30.6.1 Growth in adipose tissue cell number.- 30.6.2 Deposition of fat within adipocytes.- 30.7 Manipulation of growth.- 30.7.1 Growth hormone and insulin-like growth factors.- 30.7.2 Oestrogens and androgens.- 30.7.3 The ?-agonists.- 30.7.4 Glucocorticoids.- 30.7.5 Thyroid hormones.- 30.7.6 Antibiotics.- 31 Lactation and its manipulation.- 31.1 Introduction.- 31.2 Origins of the components of milk..- 31.3 The origin of lactose.- 31.4 Milk proteins.- 31.4.1 The origin of milk proteins.- 31.4.2 Amino acid supply to the mammary gland.- 31.4.3 Protein synthesis.- 31.5 The fats.- 31.5.1 Synthesis de novo.- 31.5.2 Uptake of fatty acids from blood.- 31.5.3 Modifications to fatty acids in the mammary gland.- 31.6 The supply of energy in the mammary gland.- 31.7 Metabolism in lactation..- 31.7.1 Endocrine control of lactation.- 31.8 Manipulation of lactation.- 31.8.1 Dietary manipulation of lactation.- 31.8.2 Manipulation of milk production by exogenous hormones.- 32 Muscle and meat.- 32.1 Introduction.- 32.2 Biochemistry of muscular contraction.- 32.2.1 Structure of thick filaments.- 32.2.2 Structure of thin filaments.- 32.2.3 Mechanism of muscle movement.- 32.2.4 Control of muscle movement.- 32.3 Energy provision in muscle tissue.- 32.3.1 Myoglobin.- 32.4 Changes in muscle after death.- 32.4.1 Enzymes leading to the degeneration of myofibrils.- 32.4.2 The role of myoglobin.- 32.4.3 Conditioning.- 32.4.4 Cold shortening.- 32.4.5 Effects of stress pre-slaughter.