| Titre : | Microbial Biochemistry Metabolic ,Principles Pathways ,and Applications : A Didactic Course for Master 1 Students in Biochemistry 2025-2026 |
| Autre titre: | : |
| Auteurs : | Halla Noureddine |
| Type de document : | texte imprimé |
| Langues: | Français |
| Note de contenu : |
Contents
Introduction Chapter 1: Introduction to Microbial Biochemistry: Fundamental Principles and Diversity 1.1 Defining Microbial Biochemistry: Scope and Significance 1.1.1 The Molecular Lens on Microbial Life 1.1.2 A Foundational Science for Biotechnology and Medicine 1.2 The Chemical Logic of Life: Anabolism, Catabolism, and Amphibolic Pathways 1.2.1 Metabolism: A Network of Ordered Reactions 1.2.1 Thermodynamic Foundations of Metabolism: 1.2.2 Catabolism: Harvesting Energy and Building Blocks 1.2.3 Anabolism: The Biosynthetic Enterprise: 1.2.4 Amphibolic Pathways: Dual Roles in Microbial Metabolism 1.2.5 Regulation of Metabolism 1.3 Bacterial Cell Structure: Organization, Composition, and Functional Complexity 1.3.1 Bacterial Diversity: Size, Shape, and Arrangements 1.3.1.1 Cell Shapes and Arrangements 1.3.1.2 Size Range 1.3.1.3 Determinants of Size and Shape 1.3.2 Cellular Organization in Prokaryotes 1.3.2.1 Chemical Composition and Dimensions 1.3.2.2 The Cytoplasm and Nucleoid 1.3.2.3 Ribosomes and Protein Synthesis 1.3.2.4 Inclusions and Microcompartments 1.3.2.5 The Prokaryotic Cytoskeleton 1.3.2.6 The Cell Envelope 1.3.2.7 Specialized Internal Structures 1.3.2.8 External Appendages 1.4 Nutrient Uptake, Environmental Constraints, and Growth in Microbes 1.4.1 Basic Nutrient Requirements 1.4.2 Transport Mechanisms Across the Plasma Membrane 1.4.2.1 Crossing the Barrier: Passive vs. Carrier-Mediated Transport 1.4.2.2 Active Transport: Concentrating Nutrients Against the Gradient 1.4.2.3 Group Translocation: The Phosphotransferase System (PTS) 1.4.3 Environmental Constraints and Adaptations 1.4.4 Growth Responses to Environmental Factors 1.4.5 Ecological and Applied Implications 1.5 Bacterial and Archaeal Growth 1.5.1 Life at the Limits 1.5.2 Reproductive Strategies 1.5.3 The Bacterial Cell Cycle 1.5.4 Archaeal Cell Cycles 1.5.5 Microbial Growth Curves 1.5.6 Mathematical Description of Growth 1.6 Metabolic Diversity of Prokaryotes 1.6.1 Classification by Carbon Source 1.6.2 Specialized Metabolic Groups 1.6.3 Ecological and Evolutionary Significance Chapter 2: Carbohydrate Catabolism in Microbes 2.1 Glucose as the Cornerstone of Microbial Metabolism 2.2 Glycolysis: The Embden-Meyerhof-Parnas (EMP) Pathway 2.2.1 Overview and Significance 2.2.2 The Preparatory Phase (Reactions 1-5) 2.1.3 The Payoff Phase (Reactions 6-10) 2.2.4 Stoichiometry, Energetics, and Regulation 2.2.5 Atypical Glycolytic Pathways in Extremophiles 2.3 Alternative Pathways for Hexose Catabolism 2.3.1 The Pentose Phosphate Pathway (PPP) 2.3.2 The Entner-Doudoroff (ED) Pathway 2.4 The Tricarboxylic Acid (TCA) Cycle 2.4.1 The Pyruvate Dehydrogenase Complex (PDC) 2.4.2 The Oxidative Decarboxylation of Acetyl-CoA 2.4.3 Energetic Yield and Regulation 2.4.4 The Amphibolic Nature of the TCA Cycle 2.4.5 Anaplerotic Reactions 2.5 Variations on the TCA Cycle in Microbes 2.5.1 The Glyoxylate Cycle 2.5.2 Incomplete and Branched TCA Cycles 2.6 Oxidative Phosphorylation 2.6.1 ATP Synthase and the Chemiosmotic Mechanism 2.6.2 ATP Yield and the P/O Ratio 2.6.3 Flexibility and Regulation in Microbial ETCs 2.7 Fermentation: Anaerobic Catabolism and NAD⁺ Regeneration 2.7.1 The Biological Imperative of Fermentation 2.7.2 Lactic Acid Fermentation 2.7.3 Alcoholic Fermentation 2.7.4 Mixed-Acid and Butanediol Fermentations 2.7.5 Solventogenic Fermentations (ABE) 2.7.6 Amino Acid Fermentation: The Stickland Reaction Chapter 3: Lipid Catabolism in Microbes 3.1 Lipids as a High-Energy Microbial Fuel Source 3.2 Mobilization and Cellular Uptake of Fatty Acids 3.2.1 Extracellular Digestion: The Role of Microbial Lipases 3.2.2 Solubilization: The Action of Biosurfactants 3.2.3 Transport Across the Cell Envelope 3.2.4 Activation: The Acyl-CoA Synthetase Reaction 3.3 The Central Pathway: The Beta-Oxidation Spiral 3.3.1 Step 1: Dehydrogenation by Acyl-CoA Dehydrogenase 3.3.2 Step 2: Hydration by Enoyl-CoA Hydratase 3.3.3 Step 3: Dehydrogenation by L-β-Hydroxyacyl-CoA Dehydrogenase 3.3.4 Step 4: Thiolytic Cleavage by Thiolase 3.3.5 Energetics of Fatty Acid Oxidation: The Example of Palmitate (C16) 3.4 Catabolism of Non-Standard Fatty Acids 3.4.1 Oxidation of Unsaturated Fatty Acids 3.4.2 Oxidation of Odd-Chain Fatty Acids 3.5 Alternative Oxidation Pathways and Regulation 3.5.1 Alpha-Oxidation 3.5.2 Omega-Oxidation 3.5.3 Regulation of Fatty Acid Degradation in E. coli 3.6 Microbial Specificity and Lipid Diversity Chapter 4: Protein and Amino Acid Catabolism in Microbes 4.1 General Principles of Protein Degradation 4.1.1 The Dual Imperative: Extracellular Hydrolysis and Intracellular Turnover 4.1.1.1 Extracellular Proteases: A Strategy for Nutrient Acquisition 4.1.1.2 Intracellular Protein Turnover: Quality Control and Regulation 4.1.2 Mechanisms of Intracellular Proteolysis in Bacteria 4.1.2.1 ATP-Dependent Proteases: The Lon and Clp Families 4.1.2.2 The Bacterial Proteasome System in Select Species 4.2 Removal of Amino Acid Nitrogen: Deamination and Transamination 4.2.1 The Central Role of Transamination 4.2.1.1 The Ping-Pong Mechanism and the Role of Pyridoxal Phosphate (PLP) 4.2.2 Diverse Deamination Pathways 4.2.2.1 Oxidative Deamination: The Case of Glutamate Dehydrogenase 4.2.2.2 Non-Oxidative Deamination: Dehydratases and Desulfhydrases 4.3 Metabolic Fates of Amino Acid Carbon Skeletons 4.3.1 Integration into Central Metabolic Pathways: Glycolysis and the TCA Cycle 4.3.2 Glucogenic, Ketogenic, and Amphibolic Roles 4.4 Specialized Pathways for Anaerobic Amino Acid Catabolism 4.4.1 The Stickland Reaction: Coupled Fermentation in Proteolytic Clostridia 4.4.1.1 Mechanism and Donor-Acceptor Pairs 4.4.2 Fermentation of Specific Amino Acids 4.4.2.1 The Methylaspartate and Hydroxyglutarate Pathways for Glutamate 4.4.2.2 Catabolism of Branched-Chain Amino Acids (BCAAs) Chapter 5: Nucleic Acid Catabolism and Nucleotide Salvage in Microbes 5.1 Introduction: The Dual Mandate of Nucleic Acid Metabolism 5.1.1 The Centrality of Nucleotides in Microbial Life 5.1.2 Delineating Catabolism from Salvage: Two Strategies for Resource Management 5.1.3 The Initial Deconstruction: From Polymer to Monomer 5.2. The Complete Catabolism of Purine Nucleotides: From Ring to Waste 5.2.1 Overview of the Purine Degradation Pathway 5.2.2 The Initial Deamination Steps: Generating Hypoxanthine and Xanthine 5.2.3 Oxidation to Uric Acid: The Role of Xanthine Oxidase/Dehydrogenase 5.2.4 The Terminal Degradation Steps: From Uric Acid to Urea 5.2.5 Anaplerotic Connections: Replenishing Central Metabolism 5.3. The Catabolism of Pyrimidine Nucleotides: A Distinctive Pathway 5.3.1 Overview of the Pyrimidine Degradation Pathway 5.3.2 The Initial Reductive Step and Ring Cleavage 5.3.3 Breakdown of Uracil and Cytosine to Beta-Alanine 5.3.4 Breakdown of Thymine to Beta-Aminoisobutyric Acid 5.3.5 The Significance of End Products 5.4. Nucleotide Salvage Pathways: The Economics of Microbial Metabolism 5.4.1 The Biochemical Rationale for Salvage 5.4.2 Purine Salvage: Key Enzymes and Reactions 5.4.3 Pyrimidine Salvage: Parallel Mechanisms for Efficiency 5.4.4 Physiological and Ecological Significance of Salvage Pathways 5.5. Interconnections and Regulatory Integration: A Coordinated Network 5.5.1 Amphibolic Pathways and the Crossover Point 5.5.2 The Regulatory Cascade of Glutamine Synthetase (GS): A Master Switch for Nitrogen Metabolism 5.5.3 Specialization of Enzymes: The NAD+/NADP+ Paradigm 5.5.4 Case Study: Amino Acid Fermentation in Anaerobes (The Stickland Reaction) Chapter 6: Specialized Microbial Metabolism and Industrial Applications 6.1 Nitrogen Metabolism: A Cornerstone of Life 6.1.1 The Global Nitrogen Cycle 6.1.2 Nitrogen Fixation: The N2 Triple Bond Challenge 6.1.2.1 The Nitrogenase Complex 6.1.2.2 Energy Requirements 6.1.2.3 Oxygen Sensitivity and Protective Mechanisms 6.1.3 Ammonium Assimilation: The Gateways to Biomass 6.1.3.1 The Glutamate Dehydrogenase (GDH) Pathway 6.1.3.2 The Glutamine Synthetase (GS) / Glutamate Synthase (GOGAT) Pathway 6.1.3.3 Regulation of Glutamine Synthetase 6.1.4 Dissimilatory Nitrate Reduction (Denitrification) 6.1.5 Anammox (Anaerobic Ammonium Oxidation) 6.2 Catabolism of Other Inorganic Compounds (Chemolithotrophy) 6.2.1 Sulfur Oxidation: Harnessing the Power of Sulfur 6.2.2 Methane and Methanol Utilization (Methanotrophy and Methylotrophy) 6.2.3 Carbon Monoxide (CO) Utilization (Carboxydotrophy) 6.2.4 Oxidation of Iron and Hydrogen 6.3 Hydrocarbon Degradation: Breaking the Unbreakable 6.3.1 Aliphatic Hydrocarbon Degradation 6.3.2 Aromatic Hydrocarbon Degradation 6.4 Industrial Applications and Biotechnologies 6.4.1 Fermentation Products 6.4.2 Bioremediation: Cleaning up the Environment 6.4.3 Other Biotechnological Applications Conclusion References |
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