The Physiology and Biochemistry of Prokaryotes

Citation

White, D., Drummond, J. T., & Fuqua, C. (2011). The Physiology and Biochemistry of Prokaryotes (4th ed.). Oxford University Press.

Chapter Summary

The book has 23 chapters and is organised by physiological topic rather than by organism, a structure the publisher presents as a way to bring out general principles. Each section heading below keeps the book's chapter titles. The fourth edition adds two co-authors, Drummond and Fuqua, and the publisher lists three new chapters (RNA and protein synthesis, biofilms and structured multicellular assemblies, and cell-to-cell communication) and two unifying themes, energetics and molecular machinery.

Chapters 1–3: Structure and Function; Growth and Cell Division; Chromosome Replication and Partitioning of Chromosomes

The opening chapters set up the cell. Chapter 1 covers phylogeny and cell structure. Chapter 2 moves through the measurement of growth, growth physiology, yields and kinetics, steady-state and continuous growth, and cell division. Chapter 3 treats DNA replication, chromosome separation and chromosome partitioning.

Chapters 4–6: Membrane Bioenergetics: The Proton Potential; Electron Transport; Photosynthesis

The energetics block comes before the metabolic pathways. Chapter 4 begins with the chemiosmotic theory and the proton potential, including its measurement, the work it drives and the reactions that generate it. Chapter 5 turns to aerobic and anaerobic respiration and the organisation of electron carriers in mitochondria and bacteria. Chapter 6 covers phototrophic prokaryotes (purple bacteria, green sulfur bacteria, cyanobacteria), photosynthetic pigments and membrane structure.

Chapters 7–10: The Regulation of Metabolic Pathways; Bioenergetics in the Cytosol; Central Metabolic Pathways; Metabolism of Lipids, Nucleotides, Amino Acids, and Hydrocarbons

These chapters cover the chemistry of metabolism. Chapter 7 addresses enzyme regulation, kinetics and covalent modification. Chapter 8 deals with high-energy molecules, group transfer and substrate-level phosphorylation. Chapter 9 works through glycolysis, the pentose phosphate and Entner-Doudoroff pathways, pyruvate oxidation, the citric acid cycle and the glyoxylate cycle. Chapter 10 covers the metabolism of lipids, nucleotides, amino acids and aliphatic hydrocarbons.

Chapters 11–12: RNA and Protein Synthesis; Cell Wall and Capsule Biosynthesis

Chapter 11 has two sections, RNA synthesis and protein synthesis. Chapter 12 covers peptidoglycan, lipopolysaccharide, extracellular polysaccharide synthesis and export, levan and dextran synthesis, and glycogen synthesis.

Chapters 13–15: Inorganic Metabolism; C1 Metabolism; Fermentations

Chapter 13 covers assimilation and dissimilation of nitrate and sulfate, nitrogen fixation and lithotrophy. Chapter 14 covers carbon dioxide fixation systems and growth on C1 compounds by methylotrophs. Chapter 15 starts with oxygen toxicity and energy conservation by anaerobes, then treats electron sinks, the anaerobic food chain and individual fermentations, including propionate, acetate, lactate, mixed-acid and butyrate fermentations.

Chapters 16–18: Responses to Environmental Stress; Solute Transport; Protein Transport and Secretion

Chapter 16 addresses pH maintenance, osmotic pressure, the heat-shock response, DNA repair, the SOS response and oxidative stress. Chapter 17 covers solute uptake kinetics, energy-dependent transport and drug export. Chapter 18 covers the Sec system, the signal recognition particle, the TAT system, extracellular protein secretion and periplasmic folding.

Chapters 19–20: Responses to Environmental Cues; Chemotaxis, Photoresponses, Aerotaxis

Chapter 19 introduces two-component signalling systems and works through specific regulatory systems, such as the Nar, Ntr and Pho regulons and responses to osmotic pressure, catabolite repression and virulence factors. Chapter 20 develops a model of chemotaxis, then covers photoresponses and aerotaxis.

Chapters 21–23: Microbial Biofilms; Cell-Cell Communication Mechanisms; Bacterial Development

The final chapters deal with multicellular behaviour: the properties, formation, regulation and inhibition of biofilms (Chapter 21), diffusible and contact-dependent signalling (Chapter 22), and development in myxobacteria, Caulobacter and sporulation in Bacillus subtilis (Chapter 23).

Key Concepts

Chapters 1–6: cell, growth and energy

• Proton potential: the electrochemical gradient across the membrane that links respiration and photosynthesis to ATP synthesis, transport and other work.
• Chemiosmotic theory: the explanation of how electron transport builds that gradient.
• Growth physiology and kinetics: how growth is measured and how yield and rate are described.

Chapters 7–15: metabolism

• Regulation of metabolic pathways: enzyme kinetics, conformational change and covalent modification as control points.
• Group transfer potential: a way to compare high-energy molecules in biosynthesis.
• Central pathways: glycolysis and its variants, the citric acid cycle and the glyoxylate cycle.
• Lithotrophy and C1 metabolism: energy and carbon from inorganic and one-carbon compounds.
• Fermentation balance: how electron sinks and the anaerobic food chain constrain fermentations.

Chapters 16–23: response, transport and behaviour

• Stress responses: heat shock, the SOS response and oxidative stress.
• Two-component signalling: the signalling systems that link environmental conditions to changes in gene expression.
• Chemotaxis: the sensory and adaptation machinery behind directed movement.
• Biofilms and cell-cell communication: multicellular assemblies and signalling between cells.
• Bacterial development: differentiation in Caulobacter, myxobacteria and sporulating Bacillus.

Critical Analysis

Strengths

• Topic-based organisation. The publisher says the topic-based structure helps readers understand general principles of physiology and metabolism, and the book presents metabolism in terms of the chemical and physical problems cells must solve in order to grow.
• Energetics first. Chapters 4–6 introduce the proton potential before the pathway chapters, so later metabolism can be read in the light of how cells conserve energy.
• Wide coverage of regulation and behaviour. Five chapters (19–23) cover signalling, chemotaxis, biofilms, cell-cell communication and development, the topics that show how cells sense their surroundings and act on what they sense.
• Built-in study aids. The publisher notes that each chapter ends with a summary, study questions and an extensive list of references to the research literature.

Limitations

• Biochemistry-heavy. The section lists are detailed (Chapter 9 alone has sixteen numbered sections, among them the chemistry of citric acid cycle reactions), so readers need a solid biochemistry background.
• Genetics only in part. The contents list replication, partitioning, RNA and protein synthesis, but no chapters on bacterial genetic analysis, horizontal gene transfer or genomics as such; those are better pursued in a dedicated bacterial genetics text.
• Dated. Published in 2011, it does not reflect later work on topics such as biofilms and cell-cell signalling, which the publisher singles out as new to this edition.
• Not a survey of diversity. Because organisation is by topic, there is no organism-by-organism tour. Readers who want one will need a general microbiology text.

Where It Fits in the Course

This is the advanced physiology and biochemistry text in the microbiology list. Money's Microbiology: A Very Short Introduction is the brief orientation, and OpenStax Microbiology and Tortora et al.'s Microbiology: An Introduction are one-semester introductory texts with a strong health focus. Madigan et al.'s Brock Biology of Microorganisms is the general textbook that covers cell structure, metabolism, genetics, diversity and ecology; a reader would usually work through a text like that first.

White, Drummond and Fuqua then go deeper into the physiology and biochemistry of cells, taking the metabolism and regulation chapters of a general text to research level. It complements Henkin and Peters's Snyder and Champness Molecular Genetics of Bacteria, an advanced textbook on bacterial genetic analysis and molecular genetics. Read together, the two cover how bacteria work and how their genes are studied and regulated.

How to Use This Book

The book is aimed at advanced undergraduate and graduate students in microbiology, biochemistry or related fields, and at researchers who need a systematic account of prokaryotic physiology. A general microbiology course and a biochemistry course are the practical prerequisites.

A practical plan:

• Core: Chapters 1–2 for the cell and growth, then Chapters 4–9 for energetics and central metabolism, which the later chapters assume.
• Choose by interest: Chapters 10–15 for biosynthesis, inorganic and C1 metabolism and fermentations. Chapters 16–20 for stress, transport and sensing. Chapters 21–23 for multicellular behaviour.
• Use the end-of-chapter material. Work the study questions after each chapter, and follow the reference lists into the primary literature on topics of particular interest.