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Gerhard. Biochemical Pathways : An Atlas of Biochemistry and Molecular Biology. 2e. 2012.

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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
1.4.5 Plasmalogens
1.4.6 Sphingolipids
1.4.7 Steroids
1.4.8 Lipoproteins
1.5 Physico-Chemical Aspects of Biochemical Processess
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 CONTENTS
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
2.7 Genetic Code and the Flow of Information
2.7.1 From DNA to RNA
2.7.2 From Nucleic Acids to Proteins – The Genetic Code
2.7.3 Influence of Errors
2.8 Polymeric Carbohydrates
2.8.1 Polymeric Carbohydrates in Energy Storage
2.8.2 Polymeric Carbohydrates as Structural Elements
2.9 Glycosylated Proteins and Peptides
2.9.1 Glycoproteins
2.9.2 Proteoglycans
2.9.3 Peptidoglycans
2.10 Lipid Aggregates and Membranes
3 METABOLISM
3.1 Carbohydrate Metabolism and Citrate Cycle
3.1.1 Glycolysis and Gluconeogenesis
3.1.2 Polysaccharide Metabolism
3.1.3 Pyruvate Turnover and Acetyl-Coenzyme A
3.1.4 Di- and Oligosaccharides
3.1.5 Metabolism of Hexose Derivatives
3.1.6 Pentose Metabolism
3.1.7 Amino Sugars
3.1.8 Citrate Cycle
3.1.9 Glyoxylate Metabolism
3.2 Amino Acids and Derivatives
3.2.1 Nitrogen Fixation and Metabolism
3.2.2 Glutamate, Glutamine, Alanine, Aspartate, Asparagine and Ammonia Turnover
3.2.3 Proline and Hydroxyproline
3.2.4 Serine and Glycine
3.2.5 Lysine, Threonine, Methionine, Cysteine and Sulfur Metabolism
3.2.6 Leucine, Isoleucine and Valine
3.2.7 Phenylalanine, Tyrosine, Tryptophan and Derivatives
3.2.8 Histidine
3.2.9 Urea Cycle, Arginine and Associated Reactions
3.3 Tetrapyrroles
3.3.1 Pathways for the Biosynthesis of Tetrapyrroles
3.3.2 Heme and Cytochrome Biosynthesis
3.3.3 Linear Tetrapyrroles
3.3.4 Biosynthesis of Chlorophylls
3.3.5 Biosynthesis of Cobalamins
3.3.6 Siroheme Biosynthesis
3.4 Lipids and Glycolipids
3.4.1 Fatty Acids and Acyl-CoA
3.4.2 Triacylglycerols (Triglycerides)
3.4.3 Phospholipids
3.4.4 Glycolipids
3.5 Steroids and Isoprenoids
3.5.1 Cholesterol
3.5.2 Hopanoids, Steroids of Plants and Insects
3.5.3 Isoprenoids
3.5.4 Steroid Hormones
3.5.5 Gestagen
3.5.6 Androgens
3.5.7 Estrogens
3.5.8 Corticosteroids
3.5.9 Bile Acids
3.6 Nucleotides and Nucleosides
3.6.1 Purine Nucleotides and Nucleosides
3.6.2 Pyrimidine Nucleotides and Nucleosides
3.7 Cofactors and Vitamins
3.7.1 Retinol (Vitamin A)
3.7.2 Thiamin (Vitamin B1)
3.7.3 Riboflavin (Vitamin B2), FMN and FAD
3.7.4 Pyridoxine (Vitamin B6)
3.7.5 Cobalamin (Coenzyme B12, Vitamin B12)
3.7.6 Folate and Pterines
3.7.7 Pantothenate, Coenzyme A and Acyl Carrier Protein (ACP)
3.7.8 Biotin
3.7.9 Nicotinate, NAD+ and NADP+
3.7.10 Ascorbate (Vitamin C)
3.7.11 Calciferol (Vitamin D)
3.7.12 Tocopherol (Vitamin E)
3.7.13 Phylloquinone and Menaquinone (Vitamin K)
3.7.14 Other Compounds
3.8 Nucleic Acid Metabolism in Bacteria
3.8.1 Bacterial DNA Replication
3.8.2 Bacterial DNA Repair
3.8.3 Degradation of Nucleic Acids
3.9 Nucleic Acid Metabolism in Eukarya
3.9.1 Eukaryotic DNA Replication
3.9.2 Eukaryotic DNA Repair
3.10 Special Bacterial Metabolism and Biosynthesis of Antimicrobials
3.10.1 Bacterial Envelope
3.10.2 Bacterial Protein Export across the Cytoplasmic Membrane
3.10.3 Protein Transport across the Outer Membrane of Gram-Negative Bacteria
3.10.4 Bacterial Transport Systems
3.10.5 Bacterial Fermentations
3.10.6 Anaerobic Respiration
3.10.7 Chemolithotrophy
3.10.8 Quinoenzymes, Alkane and Methane Oxidation
3.10.9 Antibiotics
3.11 Electron Transfer Reactions and Oxidative Phosphorylation
3.11.1 General Principles
3.11.2 Different types of electron transport chains
3.11.3 The Energetic Basis of the Oxidative Phosphorylation
3.11.4 Electron Transport System in Mitochondria and Bacteria
3.12 Photosynthesis
3.12.1 Light Reaction
3.12.2 Dark Reactions
3.13 Plant Secondary Metabolism
3.13.1 Phenolics
3.13.2 Terpenoids
3.13.3 Nitrogen-containing Secondary Metabolites
4 PROTEIN BIOSYNTHESIS, MODIFICATIONS AND DEGRADATION
4.1 Protein Synthesis in Bacteria
4.1.1 Bacterial Transcription
4.1.2 Regulation of Bacterial Gene Expression
4.1.3 Bacterial Protein Synthesis
4.1.4 Degradation of Nucleic Acids
4.2 Protein Biosynthesis in Eukarya
4.2.1 Eukaryotic Transcription
4.2.2 Regulation of Eukaryotic Transcription
4.2.3 Eukaryotic Translation
4.2.4 Translational Regulation
4.2.5 mRNA Degradation
4.3 Cell Cycle in Eukarya
4.3.1 Core Components of the Cell Cycle Machinery
4.3.2 Cell Cycle Regulation in Yeast
4.3.3 G1 to S Transition in Mammalian Cells
4.3.4 G2 to M Transition in Mammalian Cells
4.3.5 Mitosis in Mammalian Cells
4.3.6 Cell Cycle Checkpoints
4.4 Posttranslational Modification of Proteins
4.4.1 Protein Processing in the Endoplasmic Reticulum
4.4.2 Glycosylation Reactions in the Golgi Apparatus
4.4.3 Terminal Carbohydrate Structures of Glycoconjugates
4.5 Protein Folding, Transport / Targeting and Degradation
4.5.1 Folding of Proteins
4.5.2 Vesicular Transport and Secretion of Proteins
4.5.3 Protein Transport into the Nucleus
4.5.4 Protein Transport into Mitochondria
4.5.5 Protein Transport into Chloroplasts
4.5.6 Protein Degradation
4.5.7 Protein Degradation by the Ubiquitin-Proteasome System
5 VIRUSES
5.1 General Characteristics of Viruses
5.1.1 Genomic Characteristics of Viruses
5.1.2 Structure
5.2 DNA Viruses
5.2.1 Papillomavirus
5.3 RNA Viruses
5.3.1 Hepatitis C Virus
5.4 Retroviruses
5.4.1 Human Immunodeficiency Virus (HIV)
6 TRANSPORT
6.1 Transport Through Membranes
6.1.1 Systems of Eukaryotic Membrane Passage
6.1.2 Channels / Pores
6.1.3 Solute Carriers
6.1.4 Primary Active Transport Systems
6.1.5 Import by Endocytosis and Pinocytosis
6.1.6 The Cytoskeleton as Means for Intracellular Transport and Cellular Movements in Eukarya
6.2 Transport of Lipids in Plasma
6.2.1 Apolipoproteins (Apo)
6.2.2 Plasma Lipoprotein Metabolism
6.2.3 Lipid Transport Proteins
6.2.4 Lipoprotein Receptors
6.2.5 Lipid Metabolic Disorders
6.3 Oxygen Transport by Hemoglobin
6.3.1 Biosynthesis and Properties of Hemoglobin and Myoglobin
6.3.2 Oxygen Binding to Hemo- and Myoglobin
6.3.3 Hemoglobin Diseases in Humans
7 SIGNAL TRANSDUCTION AND CELLULAR COMMUNICATION
7.1 Intercellular Signal Transmission by Hormones
7.1.1 General Characteristics of Hormones
7.1.2 General Characteristics of Receptors
7.1.3 Insulin and Glucagon
7.1.4 Epinephrine and Norepinephrine (Catecholamines)
7.1.5 Hypothalamus-Anterior Pituitary Hormone System
7.1.6 Placental Hormones
7.1.7 Hormones Regulating the Extracellular Ca++, Mg++ and Phosphate Concentrations
7.1.8 Hormones Regulating the Na+ Concentration and the Water Balance
7.1.9 Hormones of the Gastrointestinal Tract
7.2 Nerve Conduction and Synaptic Transmission
7.2.1 Membrane Potential
7.2.2 Conduction of the Action Potential along the Axon
7.2.3 Transmitter Gated Signalling at the Synapse
7.2.4 Voltage Gated Signalling at the Synapse
7.2.5 Postsynaptic Receptors
7.2.6 Axonal Transport
7.3 Principles of Intracellular Communication
7.4 Receptors Coupled to Heterotrimeric G-Proteins
7.4.1 Mechanism of Heterotrimeric G-Protein Action
7.4.2 cAMP Metabolism, Activation of Adenylate Cyclase and Protein Kinase A
7.4.3 Activation of Phospholipase C and Protein Kinase C
7.4.4 Metabolic Role of Inositol Phosphates and Ca++
7.4.5 Muscle Contraction
7.4.6 Visual Process
7.4.7 Olfactory and Gustatory Processes
7.4.8 Arachidonate Metabolism and Eicosanoids
7.5 Receptors Acting Through Tyrosine Kinases
7.5.1 Regulatory Factors for Cell Growth and Function
7.5.2 Components of the Signal Cascades
7.5.3 Receptor Tyrosine Kinases
7.5.4. Tyrosine Kinase-Associated Receptors (TKaR)
7.6 Programmed Cell Death (Apoptosis)
7.7 Receptors for Steroid and Thyroid Hormones, for Retinoids and Vitamin D
7.8 Cyclic GMP Dependent Pathways and Effects of Nitric Oxide (NO)
7.8.1 Membrane Bound Guanylate Cyclases
7.8.2 Soluble Guanylate Cyclases and Their Activation by Nitric Oxide (NO)
7.8.3 Protein Kinase G
8 IMMUNE SYSTEM
8.1 Components of the Immune System
8.1.1 Innate, Non Adaptive Immune System
8.1.2 Specific, Adaptive Immune System
8.1.3 Development and Maturation of the Cellular Components
8.1.4 Antigen Receptor of B Lymphocytes, Antibodies
8.1.5 Complement System
8.1.6 Antigen Receptor of T Lymphocytes
8.1.7 Antigen Presentation by MHC Molecules
8.1.8 Cytokines, Chemokines and Receptors
8.2 Generation of a Specific Immune Response
8.2.1 Activation of T Cells
8.2.2 CD4+ T Effector Cells, Regulation of the Immune Response
8.2.3 Activation of B Cells
8.2.4 Lymphocyte Circulation and Generation of Cellular and Humoral Immune Responses in Lymphoid Tissue
8.2.5 Cellular Cytotoxicity and Apoptosis
8.2.6 Interactions between the Immune System and the Neuroendocrine System
8.2.7 Immunological Tolerance
8.2.8 Induction of Specific Immune Responses against Pathogens
8.3 Pathologic Immune responses
8.3.1 IgE-Mediated Hypersensitivity of the Immediate Type
8.3.2 Autoimmunity
8.4 Adhesion of Leukocytes
9 BLOOD COAGULATION AND FIBRINOLYSIS
9.1 Hemostasis
9.2 Initial Reactions
9.2.1 Reactions Initiated by the Tissue Factor
9.2.2 Contact Activation
9.2.3 Generation of Binding Surfaces
9.3 Coagulation Propagation and Control
9.3.1 Requirements for Protease Activity
9.3.2 Pathways Leading to Thrombin
9.3.3 Key Events
9.3.4 Controlled Propagation
9.3.5 Generation of Fibrin
9.4 Platelets (Thrombocytes)
9.5 Fibrinolysis
9.5.1 Pathways of Plasminogen Activation
9.5.2 Control of Fibrinolysis
10 BIOCHEMICAL NETWORKS, BIOINFORMATICS AND SYSTEMS BIOLOGY
10.1 Systems Biology and Networks
10.2 Modeling of Metabolic Fluxes
10.3 Biochemical Pathways Information Resources
10.3.1 Overview
10.3.2 Detailed Description of Some Databases