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1 Introduction and General Aspects 1.1 Organization of This Book 1.1.1 Conventions Used in This Book 1.1.2 Common Abbreviations 1.2 Carbohydrate Chemistry and Structure 1.2.1 Structure and Classification 1.2.2 Glycosidic Bonds 1.3 Amino Acid Chemistry and Structure 1.3.1 Structure and Classification 1.3.2 Peptide Bonds 1.4 Lipid Chemistry and Structure 1.4.1 Fatty Acids 1.4.2 Acylglycerols and Derivatives 1.4.3 Waxes 1.4.4 Glycerophospholipids (Phosphoglycerides) 1.4.5 Plasmalogens 1.4.6 Sphingolipids 1.4.7 Steroids 1.4.8 Lipoproteins 1.4.9 Lipid Aggregates and Membranes 1.5 Physico-Chemical Aspects of Biochemical Processes 1.5.1 Energetics of Chemical Reactions 1.5.2 Redox Reactions 1.5.3 Transport Through Membranes 1.5.4 Enzyme Kinetics 2 The Cell and its Components 2.1 Classification of Living Organisms 2.2 Structure of Cells 2.2.1 Prokaryotic Cells 2.2.2 General Characteristics of Eukaryotic Cells 2.2.3 Special Structures of Plant Cells 2.2.4 Special Structures of Animal Cells 2.3 Protein Structure and Function 2.3.1 Levels of Organization 2.3.2 Protein Function 2.4 Enzymes 2.4.1 Catalytic Mechanism 2.4.2 Isoenzymes 2.4.3 Multienzyme Complexes 2.4.4 Reaction Rate 2.4.5 Classification of Enzymes 2.5 Regulation of the Enzyme Activity 2.5.1 Regulation of the Quantity of Enzymes 2.5.2 Regulation of the Activity of Enzymes 2.5.3 Site of Regulation 2.6 Nucleic Acid Structure 2.6.1 Components of Nucleic Acids 2.6.2 Properties of RNA Chains 2.6.3 Properties of DNA Chains 2.6.4 Compaction Levels of DNA Chains 3 Carbohydrates and Citrate Cycle 3.1 Glycolysis and Gluconeogenesis 3.1.1 Glycolysis 3.1.2 Regulation Steps in Glycolysis 3.1.3 Gluconeogenesis 3.1.4 Resorption of Glucose 3.1.5 Response of Animal Organs to High and Low Glucose Levels 3.2 Polysaccharide Metabolism 3.2.1 Structures 3.2.2 Biosynthesis of Polysaccharides 3.2.3 Catabolism of Polysaccharides 3.2.4 Regulation of Glycogen Metabolism in Mammals 3.2.5 Medical Aspects 3.3 Pyruvate Turnover and Acetyl-Coenzyme A 3.3.1 Pyruvate Oxidation 3.3.2 Regulation of Pyruvate Deydrogenase Activity 3.3.3 Acetyl-Coenzyme A (Acetyl-CoA) 3.3.4 Anaplerotic Reactions 3.3.5 Initiation of Gluconeogenesis 3.3.6 Alcoholic Fermentation 3.4 Di- and Oligosaccharides 3.4.1 Sucrose 3.4.2 Lactose 3.4.3 Other Glycosides 3.5 Metabolism of Hexose Derivatives 3.5.1 Uronic Acids 3.5.2 Aldonic Acids 3.5.3 Entner-Doudoroff-Pathway 3.5.4 Inositol 3.5.5 Hexitols 3.5.6 Mannose and Deoxy Hexoses 3.6 Pentose Metabolism 3.6.1 Pentose Phosphate Cycle 3.6.2 Other Decarboxylation Reactions 3.6.3 Plant Cell Walls 3.6.4 Pentose Metabolism in Humans 3.7 Amino Sugars 3.7. Biosynthesis 3.7.2 Catabolism 3.8 Citrate Cycle 3.8.1 Reaction Sequence 3.8.2 Regulatory Mechanisms 3.8.3 Energy Balance 3.9 Glyoxylate Metabolism 3.9.1 Glyoxylate Cycle 3.9.2 Other Glyoxylate Reactions 4 Amino Acids and Derivatives 4.1 Nitrogen Fixation and Metabolism 4.2 Glutamate, Glutamine, Alanine, Aspartate, Asparagine and Ammonia Turnover 4.2.1 Glutamine Metabolism 4.2.2 Glutamate Metabolism 4.2.3 Alanine Metabolism 4.2.4 Aspartate and Asparagine Metabolism 4.2.5 Transamination Reactions 4.3 Proline and Hydroxyproline 4.4 Serine and Glycine 4.4.1 Serine Metabolism 4.4.2 Glycine Metabolism 4.5 Lysine, Threonine, Methionine, Cysteine and Sulfur Metabolism 4.5.1 Common Steps of Biosynthesis and Their Regulation 4.5.2 Lysine Metabolism 4.5.3 Threonine Metabolism 4.5.4 Methionine Metabolism 4.5.5 Cysteine Metabolism 4.5.6 Sulfur Metabolism 4.5.7 Glutathione Metabolism 4.5.8 Reactive Oxygen Species, Damage and Protection Mechanisms 4.6 Leucine, Isoleucine and Valine 4.6.1 Biosynthetic Reactions 4.6.2 Degradation of Branched-Chain Amino Acids 4.7 Phenylalanine, Tyrosine, Tryptophan and Derivatives 4.7.1 Biosynthesis of Aromatic Amino Acids 4.7.2 Biosynthesis of Quinone Cofactors 4.7.3 Derivatives and Degradation of Aromatic Amino Acids 4.7.4 Catecholamines 4.7.5 Thyroid Hormones 4.7.6 Aromatic Compounds in Plants 4.8 Histidine 4.8.1 Biosynthesis 4.8.2 Interconversions and Degradation 4.9 Urea cycle, Arginine and Associated Reactions 4.9.1 Urea Cycle 4.9.2 Phosphagens (Phosphocreatine and Phosphoarginine) 4.9.3 Polyamines 5 Tetrapyrroles 5.1 Steps to Protoporphyrin IX 5.2 Hemoglobin, Myoglobin and Cytochromes 5.2.1 Heme Biosynthesis 5.2.2 Biosynthesis and Properties of Hemoglobin and Myoglobin 5.2.3 Oxygen Binding to Hemo- and Myoglobin 5.2.4 Cytochromes and Other Heme Derivatives 5.3 Bile Pigments and Bilins 5.3.1 Hemoglobin Oxidation and Bile Pigments 5.3.2 Bilins 5.4 Chlorophylls 6 Lipids 6.1 Fatty Acids and Acyl-CoA 6.1.1 Biosynthesis of Fatty Acids 6.1.2 Regulation of Fatty Acid Synthesis 6.1.3 Fatty Acid Desaturation and Chain Elongation 6.1.4 Transport and Activation of Fatty Acids 6.1.5 Fatty Acid Oxidation 6.1.6 Energy Yield of the Fatty Acid Oxidation 6.1.7 Ketone Bodies 6.2 Triacylglycerols (Triglycerides) 6.2.1 Biosynthesis of Triacylglycerols (Lipogenesis) 6.2.2 Mobilization of Triacylglycerols (Lipolysis) 6.3 Phospholipids 6.3.1 Occurrence of Phospholipids 6.3.2 Glycerophospholipids 6.3.3 Ether Lipids 6.3.4 Sphingophospholipids 6.3.5 Choline, Betaine, Sarcosine 7 Steroids 7.1 Cholesterol 7.1.1 Biosynthesis 7.1.2 Turnover of Cholesterol 7.1.3 Function of Cholesterol in Membranes 7.1.4 Regulation of Cholesterol Synthesis 7.1.5 Cholesterol Homeostasis 7.2 Hopanoids, Steroids of Plants and Insects 7.2.1 Hopanoids 7.2.2 Phyto- and Mycosterols 7.2.3 Ecdysone 7.3 Isoprenoids 7.3.1 Terpenes 7.3.2 All-trans Metabolites 7.3.3 Poly-cis Metabolites 7.3.4 Isoprenoid Side Chains 7.4 Steroid Hormones 7.4.1 Biosynthesis 7.4.2 Activation and Regulation of Steroid Hormones 7.4.3 Transport of Steroid Hormones 7.4.4 Degradation of Steroids 7.5 Gestagen 7.5.1 Biosynthesis of Progesterone 7.5.2 Gestagen Function, Transport and Degradation 7.6 Androgens 7.6.1 Biosynthesis 7.6.2 Transport and Degradation 7.6.3 Biological Function of Androgens 7.6.4 Medical Aspects 7.7 Estrogens 7.7.1 Biosynthesis 7.7.2 Transport and Degradation 7.7.3 Biological Function of Estrogens 7.7.4 Medical Aspects 7.8 Corticosteroids 7.8.1 Biosynthesis 7.8.2 Transport and Degradation 7.8.3 Biological Function 7.8.4 Medical Aspects 7.9 Bile Acids 7.9.1 Occurence 7.9.2 Biosynthesis 7.9.3 Regulation of Biosynthesis 7.9.4 Medical Aspects 8 Nucleotides and Nucleosides 8.1 Purine Nucleotides and Nucleosides 8.1.1 Biosynthesis of Inosine 5´-Phosphate 8.1.2 Interconversions of Purine Ribonucleotides 8.1.3 ATP and Conservation of Energy 8.1.4 Ribonucleotide Reduction to Deoxyribonucleotides 8.1.5 Interconversions and Degradation of Purine Deoxyribonucleotides 8.1.6 Catabolism of Bases 8.1.7 Medical Aspects 8.2 Pyrimidine Nucleotides and Nucleosides 8.2.1 Biosynthesis of Uridine 5´-Phosphate 8.2.2 Interconversions of Pyrimidine Ribonucleotides 8.2.3 Ribonucleotide Reduction and Interconversions of Pyrimidine Deoxyribonucleotides 8.2.4 Catabolism of Bases 8.2.5 Medical Aspects Medical Aspects 9 Cofactors and Vitamins 9.1 Retinol (Vitamin A) 9.1.1 Biosynthesis and Interconversions 9.1.2 Biochemical Function 9.2 Thiamin (Vitamin B1) 9.2.1 Biosynthesis 9.2.2 Biochemical Function 9.3 Riboflavin (Vitamin B2), FMN and FAD 9.3.1 Biosynthesis and Interconversions 9.3.2 Biochemical Function 9.4 Pyridoxine (Vitamin B6) 9.4.1 Biosynthesis and Interconversions 9.4.2 Biochemical Function 9.5 Cobalamin (Coenzyme B12, Vitamin B12) 9.5.1 Biosynthesis of the Coenzyme and Reduction of the Vitamin 9.5.2 Biochemical Function 9.5.3 Siroheme and Coenzyme 430 9.6 Folate and Pterines 9.6.1 Tetrahydrofolate/Folylpolyglutamate 9.6.2 General Reactions of the C1 Metabolism 9.6.3 Tetrahydrobiopterin 9.6.4 Molybdenum and Tungsten Cofactors 9.6.5 Methanopterin 9.7 Pantothenate, Coenzyme A and Acyl Carrier Protein (ACP) 9.7.1 Biosynthesis and Interconversions 9.7.2 Biochemical Function 9.8 Biotin 9.8.1 Biosynthesis and Interconversions 9.8.2 Biochemical Function 9.9 Nicotinate, NAD+ and NADP+ 9.9.1 Biosynthesis and Degradation of NAD+ and NADP+ 9.9.2 Mechanism of the Redox Reactions, Stereospecificity 9.9.3 Biochemical Function of the Nicotinamide Coenzymes 9.10 Ascorbate (Vitamin C) 9.10.1 Biosynthesis and Interconversions 9.10.2 Biochemical Function 9.11 Calciferol (Vitamin D) 9.11.1 Biosynthesis and Interconversions 9.11.2 Biochemical Function 9.12 Tocopherol (Vitamin E) 9.13 Phylloquinone and Menaquinone (Vitamin K) 9.14 Other Compounds 9.14.1 Lipoate 9.14.2 Essential Fatty Acids ('Vitamin F') 9.14.3 Essential Amino Acids 10 Nucleic Acid Metabolism and Protein Synthesis in Bacteria 10.1 Genetic Code and Information Transfer 10.1.1 From DNA to RNA 10.1.2 From Nucleic Acids to Proteins — The Genetic Code 10.1.3 Influence of Errors 10.2 Bacterial DNA Replication 10.2.1 Cell Cycle and Replication 10.2.2 Initiation of Replication 10.2.3 Elongation and Termination 10.2.4 Fidelity of Replication 10.3 Bacterial DNA Repair 10.3.1 DNA Damage 10.3.2 Direct Reversal of Damage 10.3.3 Excision Repair Systems 10.3.4 Mismatch Repair 10.3.5 Double-Strand Repair and Recombination 10.3.6 SOS Response (Damage Tolerance Mechanism) 10.4 Bacterial Transcription 10.4.1 RNA Polymerase 10.4.2 Transcription 10.4.3 Products of Transcription 10.4.4 Fidelity of Transcription 10.4.5 Inhibitors of Transcription 10.5 Regulation of Bacterial Transcription 10.5.1 Regulation at the Initiation Step 10.5.2 Regulation of Elongation 10.5.3 Modification of Transcription Termination 10.5.4 Integration of Metabolism by Stimulons 10.6 Bacterial Protein Synthesis 10.6.1 Components of the Bacterial Translation System 10.6.2 Aminoacylation of tRNAs 10.6.3 Polypeptide Synthesis 10.6.4 Fidelity of Translation 10.6.5 Selenocysteine 10.7 Degradation of Nucleic Acids 10.7.1 Exodeoxyribonucleases (Exo-DNases) 10.7.2 Endodeoxyribonucleases (Endo-DNases) 10.7.3 Ribonucleases (RNases) 11 Nucleic Acid Metabolism, Protein Synthesis and Cell Cycle in Eukarya 11.1 Eukaryotic DNA Replication 11.1.1 Cell Cycle and DNA Replication 11.1.2 Initiation of Replication 11.1.3 DNA Polymerases 11.1.4 Replication Forks 11.1.5 Telomeres 11.1.6 Fidelity of Replication 11.2 Eukaryotic DNA Repair 11.2.1 DNA Damage and Principles of Repair 11.2.2 Direct Reversal of Damage 11.2.3 Excision Repair System 11.2.4 Mismatch Repair 11.2.5 Double-Strand Repair and Recombination 11.2.6 DNA Repair and Human Diseases 11.3 Eukaryotic Transcription 11.3.1 RNA Polymerases 11.3.2 mRNA Transcription by RNA Pol II 11.3.3 Processing of mRNA 11.3.4 snRNA Transcription 11.3.5 rRNA Transcription by RNA Pol I 11.3.6 Processing of rRNA 11.3.7 tRNA Transcription by RNA Pol III 11.3.8 Modification/Processing of tRNAs 11.3.9 5 S rRNA Transcription by RNA Pol III 11.3.10 Inhibitors of Transcription 11.4 Regulation of Eukaryotic Transcription 11.4.1 Structure of Core Promoter DNA Elements 11.4.2 Structure of Specific Transcription Factors 11.4.3 Modulation of the Transcription Rate 11.5 Eukaryotic Protein Synthesis 11.5.1 Components of the Translation System 11.5.2 Polypeptide Synthesis 11.5.3 Posttranslational Protein Processing 11.5.4 Translational Regulation 11.5.5 mRNA Degradation 11.6 Cell Cycle in Eukarya 11.6.1 Cyclins and Cyclin-Dependent Kinases 11.6.2 Regulation of G1 to S Phase Transition in Yeast 11.6.3 Control of the Pre-Replication Complex Assembly in Yeast 11.6.4 Regulation of the G1 to S Phase Transition in Mammals — The Role of the Rb Protein 11.6.5 Regulatory Mechanisms During M Phase (Mitosis) 11.6.6 Cell Cycle Checkpoints 11.6.7 Protein Degradation 12 Viruses 12.1 General Characteristics of Viruses 12.1.1 Genomic Characteristics 12.1.2 Structure 12.2 DNA Viruses 12.2.1 Bacteriophage  12.3 RNA Viruses 12.3.1 Tobacco Mosaic Virus 12.4 Retroviruses 12.4.1 Human Immunodeficiency Virus (HIV) 13 Glycosylated Proteins and Lipids 13.1 Glycosylated Proteins and Peptides 13.1.1 Glycoproteins 13.1.2 Proteoglycans 13.1.3 Peptidoglycans 13.1.4 Glycoprotein Degradation Diseases and Mucopolysaccharidoses 13.1.5 Repeating Units of Glycosaminoglycans as Components of Proteoglycans 13.2 Glycolipids 13.2.1 Glycosphingolipids 13.2.2 Glycoglycerolipids 13.2.3 Glycosylphosphopolyprenols 13.3 Protein Processing in the Endoplasmic Reticulum 13.3.1 Protein Synthesis and Import Into the Endoplasmic Reticulum (ER) 13.3.2 Location of the ER Proteins 13.3.3 Synthesis of Dolichol-Bound Oligosaccharides and N-Glycosylation 13.3.4 Formation of Lipid-Anchored Proteins in the ER 13.3.5 Acylation of Proteins 13.4 Glycosylation Reactions in the Golgi Apparatus 13.4.1 Formation of Glycoproteins 13.4.2 Formation of Proteoglycans 13.4.3 Formation of Glycolipids 13.5 Terminal Carbohydrate Structures of Glycoconjugates 13.5.1 Blood Groups 14 Protein Folding, Transport and Degradation 14.1 Folding of Proteins 14.1.1 Protein Folding in Bacteria 14.1.2 Protein Folding in the Eukaryotic Cytosol 14.1.3 Protein Folding in the Eukaryotic Endoplasmic Reticulum 14.2 Vesicular Transport and Secretion of Proteins 14.2.1 Pathways of Transport 14.2.2 Transport Vesicles 14.3 Protein Transport Into the Nucleus 14.3.1 Targeting Mechanism 14.3.2 Transport Mechanism 14.4 Protein Transport Into Mitochondria 14.4.1 Targeting Mechanism 14.4.2 Transport Mechanism 14.5 Protein Transport Into Chloroplasts 14.5.1 Targeting Mechanism 14.5.2 Transport Mechanism 14.6 Protein Degradation 14.6.1 Classification of Peptidases 14.6.2 Reaction Mechanism of Serine Peptidases 14.6.3 Reaction Mechanism of Cysteine Peptidases 14.6.4 Reaction Mechanism of Aspartate Peptidases 14.6.5 Reaction Mechanism of Metallopeptidases 14.6.6 Peptidase Inhibitors 14.6.7 Protein Degradation by the Ubiquitin (Ub) System 15 Special Bacterial Metabolism, Antibiotics 15.1 Bacterial Envelope 15.2 Bacterial Protein Export 15.3 Bacterial Transport Systems 15.3.1 Types of Active Transport 15.4 Bacterial Fermentations 15.5 Anaerobic Respiration 15.5.1 Redox Reactions and Electron Transport 15.5.2 Methanogenesis 15.5.3 Acetogenesis by CO2 Fixation 15.6 Chemolithotrophy 15.7 Alkane and Methane Oxidation, Quinoenzymes 15.8 Antibiotics 15.8.1 Penicillin and Cephalosporin 15.8.2 Streptomycin 15.8.3 Erythromycin 15.8.4 Tetracycline 16 Oxidative Phosphorylation and Photosynthesis 16.1 Oxidative Phosphorylation 16.1.1 Energy Balance and Reaction Yield 16.1.2 Electron Transport System in Mitochondria 16.1.3 Bacterial Electron Transport Systems 16.1.4 H+ Transporting ATP Synthase 16.1.5 Redox Potentials in the Respiratory Chain 16.2 Photosynthesis 16.2.1 Light Reaction 16.2.2 Dark Reactions 17 Cellular Communication 17.1 Intercellular Signal Transmission by Hormones 17.1.1 General Characteristics of Hormones 17.1.2 General Characteristics of Receptors 17.1.3 Insulin and Glucagon 17.1.4 Epinephrine and Norepinephrine (Catecholamines) 17.1.5 Hypothalamus-Anterior Pituitary Hormone System 17.1.6 Placental Hormones 17.1.7 Hormones Regulating the Extracellular Ca++, Mg++ and Phosphate Concentrations 17.1.8 Hormones Regulating the Na+ Concentration and the Water Balance 17.1.9 Hormones of the Gastrointestinal Tract 17.2 Nerve Conduction and Synaptic Transmission 17.2.1 Membrane Potential 17.2.2 Conduction of the Action Potential Along the Axon 17.2.3 Transmitter Gated Signalling at the Synapse 17.2.4 Voltage Gated Signalling at the Synapse 17.2.5 Postsynaptic Receptors 17.2.6 Axonal Transport 17.3 Principles of Intracellular Communication 17.4 Receptors Coupled to Heterotrimeric G-Proteins 17.4.1 Mechanism of Heterotrimeric G-Protein Action 17.4.2 cAMP Metabolism, Activation of Adenylate Cyclase and Protein Kinase A 17.4.3 Activation of Phospholipase C and Protein Kinase C 17.4.4 Metabolic Role of Inositol Phosphates and Ca++ 17.4.5 Muscle Contraction 17.4.6 Visual Process 17.4.7 Olfactory and Gustatory Processes 17.4.8 Arachidonate Metabolism and Eicosanoids 17.5 Receptors Acting Through Tyrosine Kinases 17.5.1 Regulatory Factors for Cell Growth and Function 17.5.2 Components of the Signal Cascades 17.5.3 Receptor Tyrosine Kinases 17.5.4 Tyrosine Kinase Associated Receptors 17.6 Receptors for Steroid and Thyroid Hormones, for Retinoids and Vitamin D 17.7 Cyclic GMP Dependent Reactions and Effects of Nitric Oxide (NO) 17.7.1 Membrane Bound Guanylate Cyclases 17.7.2 Soluble Guanylate Cyclases and Their Activation by Nitric Oxide 17.7.3 Protein Kinase G (PKG) 18 Eukaryotic Transport 18.1 Systems of Eukaryotic Membrane Passage 18.1.1 Channels and Transporters 18.1.2 Import by Endocytosis and Pinocytosis 18.1.3 The Cytoskeleton as Means for Intracellular Transport and Cellular Movements in Eukarya 18.2 Plasma Lipoproteins 18.2.1 Apolipoproteins (Apo) 18.2.2 Plasma Lipoprotein Metabolism 18.2.3 Lipid Transport Proteins 18.2.4 Lipoprotein Receptors 18.2.5 Lipid Metabolic Disorders 19 Antimicrobial Defense Systems 19.1 Immune System 19.1.1 Cells of the Non Adaptive Immune Defense System 19.1.2 Development and Maturation of the Cellular Components 19.1.3 Antigen Recognition by B Lymphocytes 19.1.4 Antigen Recognition by T Lymphocytes 19.1.5 Antigen Presentation by MHC Molecules 19.1.6 Cytokines and Cytokine Receptors 19.1.7 Regulation of the Immune Response 19.1.8 IgE Mediated Hypersensitivity of the Immediate Type 19.2 Complement System 19.2.1 Activation of the Complement Pathways 19.2.2 Formation of the Membrane Attack Complex (MAC), Lysis of Pathogens and Cells 19.2.3 Other Effects of the Complement System 19.2.4 Control Mechanism of the Complement System 19.2.5 Medical Aspects 19.3 Adhesion of Leucocytes 20 Blood Coagulation and Fibrinolysis 20.1 Hemostasis 20.2 Initial Reactions 20.2.1 Reactions Initiated at the Tissue Factor 20.2.2 Contact Activation 20.2.3 Generation of Binding Surfaces 20.3 Coagulation Propagation and Control 20.3.1 Requirements for Protease Activity 20.3.2 Pathways Leading to Thrombin 20.3.3 Key Events 20.3.4 Controlled Propagation 20.3.5 Generation of Fibrin 20.4 Platelets (Thrombocytes) 20.5 Fibrinolysis 20.5.1 Pathways of Plasminogen Activation 20.5.2 Control of Fibrinolysis 21 Further Information 21.1 Electronic Storage of Biochemical Information 21.2 Printed Sources 22 Index |