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Tables of Contents for The Physiology and Biochemistry of Prokaryotes
Chapter/Section Title
Page #
Page Count
Preface
xi
Acknowledgments
xv
Symbols
xvii
Conversion factors, equations, and units of energy
xix
Definitions
xxi
Structure and function
1
36
Phylogeny
1
4
Cell structure
5
24
Summary
29
8
Growth and cell division
37
29
Measurement of growth
37
2
Growth physiology
39
14
Growth kinetics
53
2
Steady-state growth and continuous growth
55
1
Summary
56
10
Membrane bioenergetics: The proton potential
66
37
Chemiosmotic theory
66
1
Electrochemical energy
67
6
The contributions of Δψ and the ΔpH to the overall Δp in neutrophiles, acidophiles, and alkaliphiles
73
1
Ionophores
73
2
Measurement of the Δp
75
2
Use of the Δp to do work
77
4
Exergonic reactions that generate a Δp.
81
4
Other mechanisms for creating a ψ or a Δp
85
10
Halorhodopsin, a light-driven chloride pump
95
1
The Δp and ATP synthesis in alkaliphiles
95
1
Summary
95
8
Electron transport
103
29
Aerobic and anaerobic respiration
104
1
The electron carriers
104
5
Organization of the electron carriers in mitochondria
109
1
Organization of the electron carriers in bacteria
109
3
Coupling sites
112
2
Q loops, Q cycles, and proton pumps
114
6
Patterns of electron flow in individual bacterial species
120
7
Summary
127
5
Photosynthesis
132
25
The phototrophic prokaryotes
132
3
The purple photosynthetic bacteria
135
5
The green sulfur bacteria
140
2
Cyanobacteria and chloroplasts
142
2
Efficiency of photosynthesis
144
1
Photosynthetic pigments
145
6
The transfer of energy from the light-harvesting pigments to the reaction center
151
1
The structure of photosynthetic membranes in bacteria
152
1
Summary
152
5
The regulation of metabolic pathways
157
8
Patterns of regulation of metabolic pathways
157
2
Kinetics of regulatory and nonregulatory enzymes
159
3
Conformational changes in regulatory enzymes
162
1
Regulation by covalent modification
163
1
Summary
163
2
Bioenergetics in the cytosol
165
15
High-energy molecules and group transfer potential
165
5
The central role of group transfer reactions in biosynthesis
170
1
ATP synthesis by substrate-level phosphorylation
171
7
Summary
178
2
Central metabolic pathways
180
32
Glycolysis
182
5
The fate of NADH
187
1
Why write NAD+ instead of NAD, and NADH instead of NADH2?
187
1
A modified EMP pathway in the hyperthermophilic archaeon Pyrococcus furiosus
187
1
The pentose phospate pathway
188
5
The Entner-Doudoroff pathway
193
2
The oxidation of pyruvate to acetyl-CoA: The pyruvate dehydrogenase reaction
195
2
The citric acid cycle
197
3
Carboxylations that replenish oxaloacetate: The pyruvate and phosphoenolpyruvate carboxylases
200
1
Modification of the citric acid cycle into a reductive (incomplete) cycle during fermentative growth
201
1
Chemistry of some of the reactions in the citric acid cycle
202
2
The glyoxylate cycle
204
1
Formation of phosphoenolpyruvate
204
2
Formation of pyruvate from malate
206
1
Summary of the relationships between the pathways
206
1
Summary
207
5
Metabolism of lipids, nucleotides, amino acids, and hydrocarbons
212
27
Lipids
212
8
Nucleotides
220
6
Amino acids
226
6
Aliphatic hydrocarbons
232
2
Summary
234
5
Macromolecular synthesis
239
56
DNA replication and partitioning
239
22
RNA synthesis
261
13
Protein synthesis
274
10
Summary
284
11
Cell wall and capsule biosynthesis
295
19
Peptidoglycan
295
5
Lipopolysaccharide
300
4
Extracellular polysaccharide synthesis and export in gram-negative bacteria
304
6
Levan and dextran synthesis
310
1
Glycogen synthesis
311
1
Summary
311
3
Inorganic metabolism
314
24
Assimilation of nitrate and sulfate
314
2
Dissimilation of nitrate and sulfate
316
3
Nitrogen fixation
319
4
Lithotrophy
323
10
Summary
333
5
C1 metabolism
338
25
Carbon dioxide fixation systems
338
16
Growth on C1 compounds other than CO2: The methylotrophs
354
5
Summary
359
4
Fermentations
363
21
Oxygen toxicity
363
1
Energy conservation by anaerobic bacteria
364
2
Electron sinks
366
1
The anaerobic food chain
366
1
How to balance a fermentation
367
1
Propionate fermentation using the acrylate pathway
368
1
Propionate fermentation using the succinate-propionate pathway
369
3
Acetate fermentation (acetogenesis)
372
1
Lactate fermentation
372
2
Mixed acid and butanediol fermentation
374
3
Butyrate fermentation
377
4
Ruminococcus albus
381
1
Summary
382
2
Homeostasis
384
14
Maintaining a ΔpH
384
4
Osmotic pressure and osmotic potential
388
5
Summary
393
5
Solute transport
398
19
Reconstitution into proteoliposomes
398
1
Kinetics of solute uptake
399
1
Energy-dependent transport
400
10
How to determine the source of energy for transport
410
1
A summary of bacterial transport systems
411
1
Summary
412
5
Protein export and secretion
417
17
The Sec system
417
5
The translocation of membrane-bound proteins
422
1
The E. coli SRP
422
2
Extracellular protein secretion
424
5
Summary
429
5
Adaptive and developmental changes
434
100
An introduction to two-component signaling systems
435
4
Responses by facultative anaerobes to anaerobiosis
439
7
Response to nitrate and nitrite: The Nar regulatory system
446
3
Response to attractants and repellents: Chemotaxis
449
9
Photoresponses
458
3
Aerotaxis
461
1
Effect of oxygen and light on the expression of photosynthetic genes in the purple photosynthetic bacterium Rhodobacter capsulatus
461
2
Response to nitrogen supply: The Ntr regulon
463
6
Response to inorganic phoshate supply: The Pho regulon
469
1
Response to osmotic pressure and temperature: Regulation of porin synthesis
470
3
Response to potassium ion: Regulation of the kdp FABC operon
473
1
Acetyl phosphate as a possible global signal in certain two-component systems
473
2
Response to carbon source: Catabolite repression
475
6
Response to carbon source: Induction of a permease for dicarboxylic acids in Rhizobium meliloti
481
1
Initiation of sporulation in Bacillus subtilis: Response to carbon supply or nitrogen supply
481
6
Quorum sensing by B. subtilis
487
2
The initiation of DNA replication in Caulobacter and the regulation of transcription of cell cycle genes
489
2
Intercellular signaling in myxobacteria
491
5
Virulence factors: Synthesis in response to temperature, pH, nutrient, osmolarity
496
8
Quorum sensing using acylated homoserine lactones
504
9
Summary
513
21
How bacteria respond to environmental stress
534
15
Heat-shock response
534
3
Repairing damaged DNA
537
4
The SOS response
541
3
Oxidative stress
544
1
Summary
545
4
Index
549