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The Physiology and Biochemistry Prokaryotes is a textbook adopted for use in advanced undergraduate and beginning graduate-level biology courses that focus on the physiology and biochemistry of microorganisms. The text covers the basic principles of prokaryotic physiology, biochemistry, and cell behavior. It presents microbial metabolism within the context of the chemical and physiological problems that cells must solve in order to grow. The text is adopted because of its authoritative presentation of basic principles, coverage of recent advances from the field, clear illustrations, relevant examples and real-world applications. Course Issues: Key challenges and course issues include keeping current with the latest developments from the field; presenting/learning so much information in a single semester; training students to think like scientists; revealing the relevance of the material. Message: White provides the most current, authoritative, and relevant presentation of prokaryotic physiology and biochemistry.
David White is Professor Emeritus of Biology at Indiana University. He has taught numerous courses in the areas of microbiology, biochemistry, human biology, and biology.
James Drummond is Associate Professor of Molecular and Cellular Biochemistry at Indiana University.
Clay Fuqua is Professor of Biology and Associate Chair of Research at Indiana University.
Table of Contents
Chapter 1. Structure and Function 1.1 Phylogeny 1.2 Cell Structure 1.3 Summary Study Questions Reference and Notes
Chapter 2. Growth and Cell Division 2.1 Measurement of Growth 2.2 Growth Physiology 2.3 Growth Yields 2.4 Growth Kinetics 2.5 Steady State Growth and Continuous Growth 2.6 Cell Division 2.7 Summary Study Questions References and Notes
Chapter 3. Chromosome Replication and Partitioning of Chromosomes 3.1 DNA Replication, Chromosome Separation, and Chromosome Partitioning 3.2 Summary Study Questions References and Notes
Chapter 4. Membrane Bioenergetics: The Proton Potential 4.1 The Chemiosmotic Theory 4.2 Electrochemical Energy 4.3 The Contributions of the ?? and the ?pH to the Overall ?p in Neutrophiles, Acidophiles, and Alkaliphiles 4.4 Ionophores 4.5 Measurement of the ?p 4.6 Use of the ?p To Do Work 4.7 Exergonic Reactions That Generate a ?p 4.8 Other Mechanisms For Creating a ?? or a ?p 4.9 Halorhodopsin, a Light-Driven Chloride Pump 4.10 The ?p and ATP Synthesis in Alkaliphiles 4.11 Summary Study Questions References and Notes
Chapter 5. Electron Transport 5.1 Aerobic and Anaerobic Respiration 5.2 The Electron Carriers 5.3 Organization of the Electron Carriers in Mitochondria 5.4 Organization of The Electron Carriers in Bacteria 5.5 Coupling Sites 5.6 How a Proton Potential Might Be Created at the Coupling Sites: Q Loops, Q Cycles, and Proton Pumps 5.7 Patterns of Electron Flow in Individual Bacterial Species 5.8 Summary Study Questions References and Notes
Chapter 6. Photosynthesis 6.1 The Phototrophic Prokaryotes 6.2 The Purple Photosynthetic Bacteria 6.3 The Green Sulfur Bacteria (Chlorobiaceae) 6.4 Cyanobacteria and Chloroplasts 6.5 Efficiency of Photosynthesis 6.6 Photosynthetic Pigments 6.7 The Transfer of Energy from the Light Harvesting Pigments to the Reaction Center 6.8 The Structure of Photosynthetic Membranes in Bacteria 6.9 Summary Study Questions References and Notes
Chapter 7. The Regulation of Metabolic Pathways 7.1 Patterns of Regulation of Metabolic Pathways 7.2 Kinetics of Regulatory and Nonregulatory Enzymes 7.3 Conformational Changes in Regulatory Enzymes 7.4 Regulation by Covalent Modification 7.5 Summary Study Questions References and Notes
Chapter 8. Bioenergetics in the Cytosol 8.1 High-Energy Molecules and Group Transfer Potential 8.2 The Central Role of Group Transfer Reactions in Biosynthesis 8.3 ATP Synthesis by Substrate Level Phosphorylation 8.4 Summary Study Questions References and Notes
Chapter 9. Central Metabolic Pathways 9.1 Glycolysis 9.2 The Fate of NADH 9.3 Why Write NAD+ Instead of NAD, and NADH Instead of NADH2? 9.4 A Modified EMP Pathway in the Hyperthermophilic Archaeon Pyrococcus furiosus 9.5 The Pentose Phosphate Pathway 9.6 The Entner-Doudoroff Pathway 9.7 The Oxidation of Pyruvate to Acetyl-CoA: The Pyruvate Dehydrogenase Reaction 9.8 The Citric Acid Cycle 9.9 Carboxylations that Replenish Oxaloacetate: The Pyruvate and Phosphoenolpyruvate Carboxylases 9.10 Modification of the Citric Acid Cycle Into a Reductive (Incomplete) Cycle During Fermentative Growth 9.11 Chemistry of Some of the Reactions in the Citric Acid Cycle 9.12 The Glyoxylate Cycle 9.13 Formation of Phosphoenolpyruvate 9.14 Formation of Pyruvate from Malate 9.15. Summary of the Relationships Between the Pathways 9.16 Summary Study Questions References and Notes
Chapter 10. Metabolism of Lipids, Nucleotides, Amino Acids, and Hydrocarbons 10.1 Lipids 10.2 Nucleotides 10.3 Amino Acids 10.4 Aliphatic Hydrocarbons 10.5 Summary Study Questions References and Notes
Chapter 11. RNA and Protein Synthesis 11.1 RNA Synthesis 11.2 Protein Synthesis
Chapter 12. Cell Wall and Capsule Biosynthesis 12.1 Peptidoglycan 12.2 Lipopolysaccharide 12.3 Extracellular Polysaccharide Synthesis and Export in Gram Negative Bacteria 12.4 Levan and Dextran Synthesis 12.5 Glycogen Synthesis 12.6 Summary Study Questions References and Notes
Chapter 13. Inorganic Metabolism 13.1 Assimilation of Nitrate and Sulfate 13.2 Dissimilation of Nitraate and Sulfate 13.3 Nitrogen Fixation 13.4 Lithotrophy 13.5 Summary Study Questions Reference and Notes
Chapter 14. C1 Metabolism 14.1 Carbon Dioxide Fixation Systems 14.2 Growth on C1 Compounds Other than CO2: The Methylotrophs 14.3 Summary Study Questions References and Notes
Chapter 15. Fermentations 15.1 Oxygen Toxicity 15.2 Energy Conservation by Anaerobic Bacteria 15.3 Electron Sinks 15.4 The Anaerobic Food Chain 15.5 How to Balance a Fermentation 15.6 Propionate Fermentation via the Acrylate Pathway 15.7 Propionate Fermentation via the Succinate-Propionate Pathway 15.8 Acetate Fermentation ( Acetogenesis) 15.9 Lactate Fermentation 15.10 Mixed-Acid and Butanediol Fermentation 15.11 Butyrate Fermentation 15.12 Ruminococcus albus 15.13 Summary Study Questions References and Notes
Chapter 16. Responses to Environmental Stress 16.1 Maintaining a ?pH 16.2 Osmotic Pressure and Osmotic Potential 16.3 Heat-Shock Response (HSR) 16.4 Repairing Damaged DNA 16.5 The SOS Response 16.6 Oxidative Stress 16.7 Summary Study Questions References and Notes
Chapter 17. Solute Transport 17.1 The Use of Proteoliposomes to Study Solute Transport 17.2 Kinetics of Solute Uptake 17.3 Energy-Dependent Transport 17.4 How to Determine the Source of Energy for Transport 17.5 Drug-Export Systems 17.6 Bacterial Transport Systems in Summary 17.7 Summary Study Questions References and Notes
Chapter 18. Protein Transport and Secretion 18.1 The Sec System 18.2 The Translocation of Membrane-Bound Proteins 18.3 The E. coli SRP 18.4 Protein Translocation of Folded Proteins: The TAT System 18.5 Extracellular Protein Secretion 18.6 Folding of Periplasmic Proteins 18.7 Summary Study Questions References and Notes
Chapter 19. Responses to Environmental Cues 19.1 Introduction to Two-Component Signaling Systems 19.2 Responses by Facultative Anaerobes to Anaerobiosis 19.3 Response to Nitrate and Nitrite: The Nar Regulatory System 19.4 Response to Nitrogen Supply: The Ntr Regulon 19.5 Response to Inorganic Phosphate Supply: The Pho Regulon 19.6 Effect of Oxygen and Light on the Expression of Photosynthetic Genes in the Purple Photosynthetic Bacterium Rhodobacter capsulatus 19.7 Response to Osmotic Pressure and Temperature: Regulation of Porin Synthesis 19.8 Response to Potassium Ion and External Osmolarity: Stimulation of Transcription of the kdpABC Operson by a Two-Component Regulatory System 19.9 Acetyl Phosphate Is a Possible Global Signal in Certain Two-Component Systems 19.10. Response to Carbon Sources: Catabolite Repression, Inducer Expulsion, Permease Synthesis 19.11. Virulence Factors: Synthesis in Response to Temperature, pH, Nutrient Osmolarity, and Quorum Sensors 19.12. Summary Study Questions References and Notes
Chapter 20. Chemotaxis, Photoresponses, Aerotaxis 20.1 Bacteria Measure Changes in Concentration Over Time 20.2 Tumbling 20.3 Adaptation 20.4 Proteins Required for Chemotaxis 20.5 A Model for Chemotaxis 20.6 Mechanism of Repellent Action 20.7 Chemotaxis That Does Not Use MCPs: The Phosphotransferase System Is Involved In Chemotaxis Toward PTS Sugars 20.8 Chemotaxis That Is Not Identical With The Model Proposed For The Enteric Bacteria 20.9 Photoresponses 20.10 Halobacteria 20.11 Photosynthetic Bacteria 20.12 Aerotaxis 20.13 Summary Study Questions References and Notes
Chapter 21. Microbial Biofilms - Structured Multicellular Assemblies 21.1 Bacterial Multicellular Structures 21.2 Prevalence and Importance of Biofilms 21.3 Properties of Biofilms 21.4 Progression of Biofilm Formation and Dissolution 21.5 Regulation of Biofilm Formation 21.6 Inhibition of Biofilm Formation 21.7 Evolutionary Processes in Biofilms 21.8 Summary Study Questions References and Notes
Chapter 22. Cell-Cell Communication Mechanisms 22.1 Diversity of Diffusible Signal Molecules Produced by Bacteria 22.2 Specific Signaling Systems 22.3 Cell-Cell Signaling that Requires Contact 22.4 Summary Study Questions References and Notes
Chapter 23. Bacterial Development 23.1 Myxobacteria 23.2 Caulobacter 23.3 Sporulation in Bacillus subtilis 23.4 Summary Study Questions References and Notes