The Physiology and Biochemistry of Prokaryotes

by White, David

• ISBN13: 9780195301687
• ISBN10: 0195301684
• Edition: 3rd
• Format: Hardcover
• Copyright: 2006-03-16
• Publisher: Oxford University Press

Summary

The third edition of The Physiology and Biochemistry of Prokaryotes covers the basic principles of prokaryotic physiology, biochemistry, and cell behavior. It presents microbial metabolism in the context of the chemical and physical problems that cells must solve in order to grow.

Author Biography

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.

Table of Contents

Boxed Material	x
Preface	xi
Symbols	xiii
Conversion Factors, Equations, and Units of Energy	xv
Definitions	xvii
Structure and Function	1	(52)
Phylogeny	3	(3)
Cell Structure	6	(38)
Summary	44	(9)
Study Questions	45	(8)
Growth and Cell Division	53	(30)
Measurement of Growth	53	(2)
Growth Physiology	55	(9)
Cell Division	64	(6)
Growth Yields	70	(1)
Growth Kinetics	71	(2)
Steady State Growth and Continuous Growth	73	(1)
Summary	74	(9)
Study Questions	75	(8)
Membrane Bioenergetics: The Proton Potential	83	(37)
The Chemiosmotic Theory	83	(1)
Electrochemical Energy	84	(6)
The Contributions of the ΔΨ and the ΔpH to the Overall Δp in Neutrophiles, Acidophiles, and Alkaliphiles	90	(1)
Ionophores	91	(2)
Measurement of the Δp	93	(1)
Use of the Δp to Do Work	94	(4)
Exergonic Reactions that Generate a Δp	98	(4)
Other Mechanisms for Creating a ΔΨ or a Δp	102	(10)
Halorhodopsin, a Light-Driven Chloride Pump	112	(1)
The Δp and ATP Synthesis in Alkaliphiles	112	(1)
Summary	112	(8)
Study Questions	114	(6)
Electron Transport	120	(29)
Aerobic and Anaerobic Respiration	121	(1)
The Electron Carriers	121	(4)
Organization of the Electron Carriers in Mitochondria	125	(3)
Organization of the Electron Carriers in Bacteria	128	(2)
Coupling Sites	130	(2)
How a Proton Potential Might Be Created at the Coupling Sites: Q Loops, Q Cycles, and Proton Pumps	132	(5)
Patterns of Electron Flow in Individual Bacterial Species	137	(7)
Summary	144	(5)
Study Questions	145	(4)
Photosynthesis	149	(24)
The Phototrophic Prokaryotes	149	(3)
The Purple Photosynthetic Bacteria	152	(5)
The Green Sulfur Bacteria (Chlorbiaceae)	157	(2)
Cyanobacteria and Chloroplasts	159	(2)
Efficiency of Photosynthesis	161	(1)
Photosynthetic Pigments	162	(6)
The Transfer of Energy from the Light-Harvesting Pigments to the Reaction Center	168	(1)
The Structure of Photosynthetic Membranes in Bacteria	169	(1)
Summary	169	(4)
Study Questions	170	(3)
The Regulation of Metabolic Pathways	173	(8)
Patterns of Regulation of Metabolic Pathways	173	(2)
Kinetics of Regulatory and Nonregulatory Enzymes	175	(3)
Conformational Changes in Regulatory Enzymes	178	(1)
Regulation by Covalent Modification	178	(1)
Summary	179	(2)
Study Questions	179	(2)
Bioenergetics in the Cytosol	181	(15)
High-Energy Molecules and Group Transfer Potential	181	(5)
The Central Role of Group Transfer Reactions in Biosynthesis	186	(2)
ATP Synthesis by Substrate Level Phosphorylation	188	(6)
Summary	194	(2)
Study Questions	195	(1)
Central Metabolic Pathways	196	(34)
Glycolysis	198	(6)
The Fate of NADH	204	(1)
Why Write NAD+ Instead of NAD, and NADH Instead of NADH2?	204	(1)
A Modified EMP Pathway in the Hyperthermophilic Archaeon Pyrococcus furiosus	204	(1)
The Pentose Phosphate Pathway	205	(5)
The Entner-Doudoroff Pathway	210	(3)
The Oxidation of Pyruvate to Acetyl-CoA: The Pyruvate Dehydrogenase Reaction	213	(1)
The Citric Acid Cycle	214	(5)
Carboxylations that Replenish Oxaloacetate: The Pyruvate and Phosphoenolpyruvate Carboxylases	219	(1)
Modification of the Citric Acid Cycle into a Reductive (Incomplete) Cycle During Fermentative Growth	220	(1)
Chemistry of Some of the Reactions in the Citric Acid Cycle	221	(2)
The Glyoxylate Cycle	223	(1)
Formation of Phosphoenolpyruvate	224	(1)
Formation of Pyruvate from Malate	225	(1)
Summary of the Relationships Between the Pathways	226	(1)
Summary	226	(4)
Study Questions	228	(2)
Metabolism of Lipids, Nucleotides, Amino Acids, and Hydrocarbons	230	(25)
Lipids	230	(8)
Nucleotides	238	(5)
Amino Acids	243	(5)
Aliphatic Hydrocarbons	248	(3)
Summary	251	(4)
Study Questions	253	(2)
Macromolecular Synthesis	255	(63)
DNA Replication, Chromosome Separation, and Chromosome Partitioning	255	(25)
RNA Synthesis	280	(13)
Protein Synthesis	293	(13)
Summary	306	(12)
Study Questions	308	(10)
Cell Wall and Capsule Biosynthesis	318	(18)
Peptidoglycan	318	(5)
Lipopolysaccharide	323	(5)
Extracellular Polysaccharide Synthesis and Export in Gram-Negative Bacteria	328	(5)
Levan and Dextran Synthesis	333	(1)
Glycogen Synthesis	333	(1)
Summary	333	(3)
Study Questions	334	(2)
Inorganic Metabolism	336	(23)
Assimilation of Nitrate and Sulfate	336	(2)
Dissimilation of Nitrate and Sulfate	338	(3)
Nitrogen Fixation	341	(4)
Lithotrophy	345	(10)
Summary	355	(4)
Study Questions	356	(3)
C1 Metabolism	359	(24)
Carbon Dioxide Fixation Systems	359	(16)
Growth on C1 Compounds Other than CO2: The Methylotrophs	375	(3)
Summary	378	(5)
Study Questions	380	(3)
Fermentations	383	(21)
Oxygen Toxicity	383	(1)
Energy Conservation by Anaerobic Bacteria	384	(2)
Electron Sinks	386	(1)
The Anaerobic Food Chain	386	(1)
How to Balance a Fermentation	387	(1)
Propionate Fermentation via the Acrylate Pathway	388	(1)
Propionate Fermentation via the Succinate-Propionate Pathway	389	(2)
Acetate Fermentation (Acetogenesis)	391	(1)
Lactate Fermentation	392	(2)
Mixed-Acid and Butanediol Fermentation	394	(3)
Butyrate Fermentation	397	(3)
Ruminococcus albus	400	(1)
Summary	401	(3)
Study Questions	402	(2)
Homeostasis	404	(13)
Maintaining a ΔpH	404	(3)
Osmotic Pressure and Osmotic Potential	407	(6)
Summary	413	(4)
Study Questions	414	(3)
Solute Transport	417	(21)
The Use of Proteoliposomes to Study Solute Transport	417	(1)
Kinetics of Solute Uptake	418	(1)
Energy-Dependent Transport	419	(10)
How to Determine the Source of Energy for Transport	429	(1)
Drug-Export Systems	430	(1)
Bacterial Transport Systems in Summary	431	(1)
Summary	431	(7)
Study Questions	434	(4)
Protein Transport	438	(29)
The Sec System	439	(4)
The Translocation of Membrane-Bound Proteins	443	(2)
The E. coli SRP	445	(1)
Protein Translocation of Folded Proteins; the Tat System	445	(2)
Extracellular Protein Secretion	447	(10)
Folding of Periplasmic Proteins	457	(2)
Summary	459	(8)
Study Questions	460	(7)
Microbial Development and Physiological Adaptation: Varied Responses to Environmental Cues and Intercellular Signals	467	(132)
Introduction to Two-Component Signaling Systems	469	(5)
Responses by Facultative Anaerobes to Anaerobiosis	474	(6)
Response to Nitrate and Nitrite: The Nar Regulatory System	480	(4)
Response to Nitrogen Supply: The Ntr Regulon	484	(5)
Response to Inorganic Phosphate Supply: The Pho Regulon	489	(2)
Effect of Oxygen and Light on the Expression of Photosynthetic Genes in the Purple Photosynthetic Bacterium Rhodobacter capsulatus	491	(1)
Response to Osmotic Pressure and Temperature: Regulation of Porin Synthesis	492	(2)
Response to Potassium Ion and External Osmolarity: Stimulation of Transcription of the kdpABC Operon by a Two-Component Regulatory System	494	(1)
Acetyl-Phosphate Is a Possible Global Signal in Certain Two-Component Systems	494	(2)
Response to Carbon Sources: Catabolite Repression, Inducer Expulsion, Permease Synthesis	496	(6)
Virulence Factors: Synthesis in Response to Temperature, pH, Nutrient, Osmolarity, and Quorum Sensors	502	(7)
Chemotaxis	509	(10)
Photoresponses	519	(3)
Aerotaxis	522	(1)
Introduction to Bacterial Development and to Quorum Sensing	522	(1)
Myxobacteria	523	(11)
Caulobacter Development: Control of DNA Replication and Cell Cycle Genes	534	(5)
Sporulation in Bacillus subtilis	539	(11)
Competence in Bacillus subtilis	550	(2)
Bioluminescence	552	(9)
Systems Similar to LuxR/LuxI in Nonluminescent Bacteria	561	(3)
Biofilms	564	(6)
Summary	570	(29)
Study Questions	572	(27)
How Bacteria Respond to Environmental Stress	599	(18)
Heat-Shock Response	599	(4)
Repairing Damaged DNA	603	(5)
The SOS Response	608	(3)
Oxidative Stress	611	(2)
Summary	613	(4)
Study Questions	614	(3)
Index	617