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| Structure and Function | |
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| Phylogeny | |
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| Cell Structure | |
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| Summary | |
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| Study Questions | |
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| Reference and Notes | |
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| Growth and Cell Division | |
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| Measurement of Growth | |
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| Growth Physiology | |
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| Growth Yields | |
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| Growth Kinetics | |
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| Steady State Growth and Continuous Growth | |
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| Cell Division | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Chromosome Replication and Partitioning of Chromosomes | |
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| DNA Replication, Chromosome Separation, and Chromosome Partitioning | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Membrane Bioenergetics: The Proton Potential | |
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| The Chemiosmotic Theory | |
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| Electrochemical Energy | |
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| The Contributions of the ?? and the ?pH to the Overall ?p in Neutrophiles, Acidophiles, and Alkaliphiles | |
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| Ionophores | |
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| Measurement of the ?p | |
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| Use of the ?p To Do Work | |
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| Exergonic Reactions That Generate a ?p | |
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| Other Mechanisms For Creating a ?? or a ?p | |
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| Halorhodopsin, a Light-Driven Chloride Pump | |
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| The ?p and ATP Synthesis in Alkaliphiles | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Electron Transport | |
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| Aerobic and Anaerobic Respiration | |
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| The Electron Carriers | |
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| Organization of the Electron Carriers in Mitochondria | |
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| Organization of The Electron Carriers in Bacteria | |
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| Coupling Sites | |
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| How a Proton Potential Might Be Created at the Coupling Sites: Q Loops, Q Cycles, and Proton Pumps | |
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| Patterns of Electron Flow in Individual Bacterial Species | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Photosynthesis | |
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| The Phototrophic Prokaryotes | |
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| The Purple Photosynthetic Bacteria | |
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| The Green Sulfur Bacteria (Chlorobiaceae) | |
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| Cyanobacteria and Chloroplasts | |
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| Efficiency of Photosynthesis | |
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| Photosynthetic Pigments | |
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| The Transfer of Energy from the Light Harvesting Pigments to the Reaction Center | |
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| The Structure of Photosynthetic Membranes in Bacteria | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| The Regulation of Metabolic Pathways | |
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| Patterns of Regulation of Metabolic Pathways | |
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| Kinetics of Regulatory and Nonregulatory Enzymes | |
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| Conformational Changes in Regulatory Enzymes | |
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| Regulation by Covalent Modification | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Bioenergetics in the Cytosol | |
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| High-Energy Molecules and Group Transfer Potential | |
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| The Central Role of Group Transfer Reactions in Biosynthesis | |
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| ATP Synthesis by Substrate Level Phosphorylation | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Central Metabolic Pathways | |
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| Glycolysis | |
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| The Fate of NADH | |
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| Why Write NAD+ Instead of NAD, and NADH Instead of NADH2? | |
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| A Modified EMP Pathway in the Hyperthermophilic Archaeon Pyrococcus furiosus | |
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| The Pentose Phosphate Pathway | |
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| The Entner-Doudoroff Pathway | |
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| The Oxidation of Pyruvate to Acetyl-CoA: The Pyruvate Dehydrogenase Reaction | |
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| The Citric Acid Cycle | |
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| Carboxylations that Replenish Oxaloacetate: The Pyruvate and Phosphoenolpyruvate Carboxylases | |
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| Modification of the Citric Acid Cycle Into a Reductive (Incomplete) Cycle During Fermentative Growth | |
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| Chemistry of Some of the Reactions in the Citric Acid Cycle | |
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| The Glyoxylate Cycle | |
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| Formation of Phosphoenolpyruvate | |
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| Formation of Pyruvate from Malate | |
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| Summary of the Relationships Between the Pathways | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Metabolism of Lipids, Nucleotides, Amino Acids, and Hydrocarbons | |
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| Lipids | |
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| Nucleotides | |
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| Amino Acids | |
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| Aliphatic Hydrocarbons | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| RNA and Protein Synthesis | |
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| RNA Synthesis | |
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| Protein Synthesis | |
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| Cell Wall and Capsule Biosynthesis | |
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| Peptidoglycan | |
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| Lipopolysaccharide | |
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| Extracellular Polysaccharide Synthesis and Export in Gram Negative Bacteria | |
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| Levan and Dextran Synthesis | |
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| Glycogen Synthesis | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Inorganic Metabolism | |
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| Assimilation of Nitrate and Sulfate | |
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| Dissimilation of Nitraate and Sulfate | |
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| Nitrogen Fixation | |
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| Lithotrophy | |
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| Summary | |
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| Study Questions | |
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| Reference and Notes | |
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| C1 Metabolism | |
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| Carbon Dioxide Fixation Systems | |
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| Growth on C1 Compounds Other than CO2: The Methylotrophs | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Fermentations | |
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| Oxygen Toxicity | |
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| Energy Conservation by Anaerobic Bacteria | |
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| Electron Sinks | |
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| The Anaerobic Food Chain | |
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| How to Balance a Fermentation | |
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| Propionate Fermentation via the Acrylate Pathway | |
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| Propionate Fermentation via the Succinate-Propionate Pathway | |
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| Acetate Fermentation ( Acetogenesis) | |
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| Lactate Fermentation | |
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| Mixed-Acid and Butanediol Fermentation | |
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| Butyrate Fermentation | |
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| Ruminococcus albus | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Responses to Environmental Stress | |
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| Maintaining a ?pH | |
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| Osmotic Pressure and Osmotic Potential | |
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| Heat-Shock Response (HSR) | |
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| Repairing Damaged DNA | |
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| The SOS Response | |
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| Oxidative Stress | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Solute Transport | |
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| The Use of Proteoliposomes to Study Solute Transport | |
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| Kinetics of Solute Uptake | |
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| Energy-Dependent Transport | |
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| How to Determine the Source of Energy for Transport | |
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| Drug-Export Systems | |
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| Bacterial Transport Systems in Summary | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Protein Transport and Secretion | |
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| The Sec System | |
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| The Translocation of Membrane-Bound Proteins | |
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| The E. coli SRP | |
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| Protein Translocation of Folded Proteins: The TAT System | |
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| Extracellular Protein Secretion | |
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| Folding of Periplasmic Proteins | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Responses to Environmental Cues | |
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| Introduction to Two-Component Signaling Systems | |
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| Responses by Facultative Anaerobes to Anaerobiosis | |
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| Response to Nitrate and Nitrite: The Nar Regulatory System | |
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| Response to Nitrogen Supply: The Ntr Regulon | |
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| Response to Inorganic Phosphate Supply: The Pho Regulon | |
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| Effect of Oxygen and Light on the Expression of Photosynthetic Genes in the Purple Photosynthetic Bacterium Rhodobacter capsulatus | |
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| Response to Osmotic Pressure and Temperature: Regulation of Porin Synthesis | |
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| Response to Potassium Ion and External Osmolarity: Stimulation of Transcription of the kdpABC Operson by a Two-Component Regulatory System | |
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| Acetyl Phosphate Is a Possible Global Signal in Certain Two-Component Systems | |
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| Response to Carbon Sources: Catabolite Repression, Inducer Expulsion, Permease Synthesis | |
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| Virulence Factors: Synthesis in Response to Temperature, pH, Nutrient Osmolarity, and Quorum Sensors | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Chemotaxis, Photoresponses, Aerotaxis | |
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| Bacteria Measure Changes in Concentration Over Time | |
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| Tumbling | |
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| Adaptation | |
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| Proteins Required for Chemotaxis | |
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| A Model for Chemotaxis | |
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| Mechanism of Repellent Action | |
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| Chemotaxis That Does Not Use MCPs: The Phosphotransferase System Is Involved In Chemotaxis Toward PTS Sugars | |
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| Chemotaxis That Is Not Identical With The Model Proposed For The Enteric Bacteria | |
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| Photoresponses | |
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| Halobacteria | |
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| Photosynthetic Bacteria | |
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| Aerotaxis | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Microbial Biofilms - Structured Multicellular Assemblies | |
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| Bacterial Multicellular Structures | |
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| Prevalence and Importance of Biofilms | |
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| Properties of Biofilms | |
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| Progression of Biofilm Formation and Dissolution | |
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| Regulation of Biofilm Formation | |
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| Inhibition of Biofilm Formation | |
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| Evolutionary Processes in Biofilms | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Cell-Cell Communication Mechanisms | |
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| Diversity of Diffusible Signal Molecules Produced by Bacteria | |
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| Specific Signaling Systems | |
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| Cell-Cell Signaling that Requires Contact | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |
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| Bacterial Development | |
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| Myxobacteria | |
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| Caulobacter | |
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| Sporulation in Bacillus subtilis | |
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| Summary | |
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| Study Questions | |
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| References and Notes | |