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 ΔΨ and the ΔpH to the Overall Δp in Neutrophiles, Acidophiles, and Alkaliphiles
4.4    Ionophores
4.5    Measurement of the Δp
4.6    Use of the Δp To Do Work
4.7    Exergonic Reactions That Generate a Δp
4.8    Other Mechanisms For Creating a ΔΨ or a Δp
4.9    Halorhodopsin, a Light-Driven Chloride Pump
4.10  The Δp 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 ΔpH
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

Box 1.1   Phylogeny
Box 1.2   Non-flagellar motility
Box 1.3   Historical Perspective: Christian Gram
Box 1.4   Tuberculosis
Box 1.5   Leprosy
Box 1.6   Cannulae and Hami: Cell Surface Structures of Archaea
Box 2.1   Transcriptional, Translational, and Post-Translational Regularion of Levls of rpoS
Box 3.1   Historical Perspective: The Discovery of DNA and Its Role,
Box 3.2   Historical Perspective: The Structure of DNA
Box 4.1   Historical Perspective: Oxidative Phosphorylation
Box 5.1   Historical Perspective: Cellular Respiration
Box 8.1   Historical Perspective: Energy Transfer in the Cytosol
Box 9.1   Historical Perspective: Cell-Free Yeast Fermentation and the Beginnings of Biochemistry
Box 9.2   Vitamins
Box 9.3   Historical Perspective: The Citric Acid Cycle
Box 12.1 Capsules As Virulence Factors
Box 16.1 Historical Perspective: The Morse Code
Box 18.1 SRP-Dependent Protein Translocation Across the Endoplasmic Reticulum Membrane in Eukaryotes
Box 21.1 Historical Perspective: Biofilms in the Ocean
Box 22.1 Early Discoveries of Prokaryotic Cell-Cell Communication
Box 23.1 Proteins Involved in Formation of the Spore Septum and Chromosome Partioning
Box 23.2 Sporulation-Specific Sigma Factors

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