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The Physiology and Biochemistry of Prokaryotes

Fourth Edition

David White, James Drummond, and Clay Fuqua

Publication Date - 02 December 2011

ISBN: 9780195393040

656 pages
7 x 10 inches

In Stock

The most current, authoritative, and relevant presentation of prokaryotic physiology and biochemistry


The Physiology and Biochemistry of Prokaryotes covers the basic principles of prokaryotic physiology, biochemistry, and cell behavior. The fourth edition features comprehensive updates that integrate the latest developments in the field, including genomics, microbial diversity, systems biology, cell-to-cell signaling, and biofilms. The book also presents microbial metabolism in the context of the chemical and physical problems that cells must solve in order to grow.

Written in a clear, straightforward manner, the fourth edition adds two new coauthors, Jim Drummond and Clay Fuqua, each a highly respected scholar in his field. The text is organized by topic rather than by organism; this innovative structure will help you to better understand the general principles of physiology and metabolism. Each chapter ends with a summary, thought-provoking study questions, and an extensive list of references to outside research literature that you can access for more information and detailed explanations of material in the text.

New to this Edition

  • New coauthors Jim Drummond and Clay Fuqua each contribute chapters that make this edition the most authoritative and current book in the discipline
  • Three new chapters cover RNA and protein synthesis, microbial films, structured multicellular assemblies, and cell-to-cell communication mechanisms
  • Comprehensive revisions update the text with the latest research in the discipline
  • A new thematic emphasis introduces two themes: A comprehensive energetics perspective and Molecular machinery will be described throughout the text to help create a unifying narrative across biological principles

About the Author(s)

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.

Previous Publication Date(s)

March 2006
September 1999
January 1995

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

Related Title

Microbial Physiology and Biochemistry Laboratory