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CONTENTS Page Preface Acknowledgments Symbols Conversion factors Definitions Chapter 1. STRUCTURE AND FUNCTION 1.1 Phylogeny 1.1.1 Archaea 1.2 Cell structure 1.2.1 Appendages 1.2.2 The glycocalyx 1.2.3 Cell walls 1.2.4 Periplasm 1.2.5 Cell membrane 1.2.6 Cytoplasm 1.2.7 Cytoskeleton 1.3. Summary 1.4 Study questions Chapter 2. GROWTH AND CELL DIVISION 2.1 Measurement of growth 2.1.1 Turbidity 2.1.2 Total cell counts 2.1.3 Viable cell counts 2.1.4 Dry weight and protein 2.2 Growth Physiology 2.2.1 Phase of population growth 2.2.2 Adaptive responses to nutrient limitation 2.2.3 Macromolecular composition as a function of growth rate 2.2.4 Diauxic growth 2.3 Cell Division 2.3.1 The period prior to septum formation 2.3.2 Cell division (cytokinesis) 2.3.3 Proteins required for septum formation and cell division 2.3.4 A model for the sequence of events in the assembly of proteins at the division site 2.3.5 Determining the site of septum formation; the nucleoid occlusion system and the Min system 2.3.6 Some differences with respect to the regulation of the site of septum formation in various bacteria 2.4 Growth Yields 2.5 Growth Kinetics 2.5.1 The equation for exponential growths 2.5.2 The relationship between the growth rate constant (k) and the nutrient concentraion (S) 2.6 Steady-state growth and continuous growth 2.6.1 The chemostat 2.7 Summary 2.8 Study questions Chapter 3. MEMBRANE BIOENERGETICS: THE PROTON POTENTIAL 3.1 Chemiosmotic theory 3.2 Electrochemical energy 3.2.1 The electrochemical energy of protons 3.2.2 Generating a ?? and a ?pH 3.3 Contributions of ?? and the ?pH to the overall ?p in neutrophiles, acidophiles, and alkaliphiles 3.4 Ionophores 3.4.1 The effect of uncouplers on respiration 3.5 Measurement of the ?p 3.5.1 Measurement of ?? 3.5.2 Measurement of ?pH 3.6 Use of the ?p to do work 3.6.1 Use of the ?p to drive solute uptake 3.6.2 The ATP synthase 3.7 Exergonic reactions that generate a ?p 3.7.1 Oxidation-reduction reactions as driving reactions 3.7.2 ATP hydrolysis as a driving reaction for creating a ?p 3.8 Other mechanisms for creating a ?? or a ?p 3.8.1 Sodium transport decarboxylases can create a sodium potential 3.8.2 Oxalate:formate exchange can create a ?p 3.8.3 End-product efflux as the driving reaction 3.8.4 Light absorbed by bacteriorhodopsin can drive the creation of a ?p 3.9 Halorhodopsin, a light-driven chloride pump 3.10 The ?p and ATP synthesis in alkaliphiles 3.11. Summary 3.12 Study questions Chapter 4. ELECTRON TRANSPORT 4.1 Aerobic and anaerobic respiration 4.2 The electron carriers 4.2.1 Flavoproteins 4.2.2 Quinones 4.2.3 Iron-sulfur proteins 4.2.4 Cytochromes 4.2.5 Standard electrode potentials of the electron carriers 4.3 Organization of the electron carriers in mitochondria 4.4 Organization of the electron carriers in bacteria 4.4.1 The different terminal oxidases 4.4.2 Bacterial electron transport chains are branched 4.5 Coupling sites 4.5.1 The identification of coupling sites 4.5.2 The actual number of ATPs that can be made per two electrons traveling through the coupling sites 4.6 Q loops, Q cycles, and proton pumps 4.6.1 The Q loop 4.6.2 The Q cycle 4.6.3 Pumps 4.7 Patterns of electron flow in individual bacterial species 4.7.1 Escherichia coli 4.7.2 Paracoccus denitrificans 4.7.3 Rhodobacter sphaeroides 4.7.4 Fumarate respiration in Wolinella succinogenes 4.8. Summary 4.9 Study questions Chapter 5. PHOTOSYNTHESIS 5.1 The phototrophic prokaryotes 5.1.1 Oxygenic phototrophs 5.1.2 Anoxygenic phototrophs 5.2 The purple photosynthetic bacteria 5.2.1 Photosynthetic electron transport 5.2.2 A more detailed examination of the reaction center and what happens there 5.2.3 Source of electrons for growth 5.3 The green sulfur bacteria 5.3.1 Photosynthetic electron transport 5.4 Cyanobacteria and chloroplasts 5.4.1 Two light reactions 5.4.2 Photosynthetic electron transport 5.5 Efficiency of photosynthesis 5.5.1 ATP synthesis 5.5.2 ATP and NADPH synthesis 5.5.3 Carbohydrate synthesis and oxygen production 5.6 photosynthetic pigments 5.6.1 Light-harvesting pigments 5.6.2 Structures of the chlorophylls, bacteriochlorophylls, and carotenoids 5.7 The transfer of energy from the light-harvesting pigments to the reaction center 5.7.1 Mechanism of energy transfer 5.7.2 Evidence that energy absorbed by the light-harvesting pigments is transferred to the reaction center 5.8 The structure of photosynthetic membranes in bacteria 5.9. Summary 5.10 Study questions Chapter 6. THE REGULATION OF METABOLIC PATHWAYS 6.1 Patterns of regulation of metabolic pathways 6.1.1 Feedback inhibition by an end product of the pathway 6.1.2 Positive regulation 6.1.3 Regulatory enzymes catalyze irreversible reactions at branch points 6.2 Kinetics of regulatory and non-regulatory enzymes 6.2.1 Non-regulatory enzymes 6.2.2 Regulatory enzymes 6.3 Conformational changes in regulatory enzymes 6.4 Regulation by covalent modification 6.5. Summary 6.6 Study questions Chapter 7. BIOENERGETICS IN THE CYTOSOL 7.1 High energy molecules and group transfer potential 7.1.1 Group transfer potential 7.1.2 Adenosine triphosphate (ATP) 7.1.3 Phosphoenolpyruvic acid (PEP) 7.1.4 Acetyl derivatives of phosphate and coenzyme A 7.2 The central role of group transfer reactions in biosynthesis 7.2.1 How ATP can be used to form amide linkages, thioester bonds, and ester bonds 7.2.2 How ATP is used to form peptide bonds during protein synthesis 7.3 ATP synthesis by substrate level phosphorylation 7.3.1 1,3-bisphosphoglycerate 7.3.2 Acetyl-phosphate 7.3.3 Succinyl-CoA 7.3.4 Phosphoenolpyruvates 7.4. Summary 7.5 Study questions Chapter 8. CENTRAL METABOLIC PATHWAYS 8.1 Glycolysis 8.1.1 Glycolysis as an anabolic pathway 8.1.2 Regulation of glycolysis 8.1.3 The chemical bases for the isomerization and aldol cleavage reactions in glycolysis 8.1.4 Why are the glycolytic intermediates phosphorylated? 8.2 The fate of NADH 8.3 Why write NAD+ instead of NAD, and NADH instead of NADH2? 8.4 A modified EMP pathway in the hyperthermophilic archaeon Pyrococcus furiosus 8.5 The pentose phosphate pathway 8.5.1 The reactions of the pentose phosphate pathway 8.6 The Entner-Doudoroff pathway 8.6.1 The reactions of the Entner-Doudoroff pathway 8.6.2 Physiological role for the Entner-Doudoroff pathway 8.6.3 A partly non-phosphorylated Entner-Doudoroff pathway 8.7 The oxidation of pyruvate to acetyl-CoA: The pyruvate dehydrogenase reaction 8.7.1 Physiological control 8.8 The citric acid cycle 8.8.1 The reactions of the citric acid cycle 8.8.2 Regulation of the citric acid cycle 8.8.3 The citric acid cycle as an anabolic pathway 8.8.4 Distribution of the citric acid cycle 8.9 Carboxylations that replenish oxaloacetate: The pyruvate and 8.9.1 Regulatotion of PEP carboxylase phosphoenolpyruvate carboxylases 8.10 Modification of the citric acid cycle as a reductive (incomplete) cycle during fermentative growth 8.11 Chemistry of some of the reactions in the citric acid cycle 8.11.1 Acetyl-CoA condensation reactions 8.11.2 Decarboxlation reactions 8.12 The glyoxylate cycle 8.12.1 Regulation of the glyoxylate cycle 8.13 Formation of phosphoenolpyruvate 8.13.1 Formation of phosphoenolpyruvate from oxaloacetate 8.13.2 Formation of phosphoenolpyruvate from pyruvate 8.14 Formation of pyruvate from malate 8.15 Summary of the relationships between the pathways 8.16. Summary 8.17 Study questions Chapter 9. METABOLISM OF LIPIDS, NUCLEOTIDES, AMINO ACIDS, AND HYDROCARBONS 9.1 Lipids 9.1.1 Fatty acids 9.1.2 Phospholipid synthesis in bacteria 9.1.3 Synthesis of archaeal lipids 9.2 Nucleotides 9.2.1 Nomenclature and structures 9.2.2 The synthesis of the pyrimidine nucleotides 9.2.3 The synthesis of the purine nucleotides 9.2.4 The role of tetrahydrofolic acid 9.2.5 Synthesis of deoxyribonucleotides 9.3 Amino acids 9.3.1 Synthesis 9.3.2 Catabolism 9.4 Aliphatic hydrocarbons 9.4.1 Degradative pathways 9.5. Summary 9.6 Study questions Chapter 10. MACROMOLECULAR SYNTHESIS 10.1 DNA replication and partitioning 10.1.1 Semi-conservative replication 10.1.2 The topological problem 10.1.3 Creating the replication fork 10.1.4 Replicating the DNA 10.1.5 Termination 10.1.6 Chromosome separation and partitioning; some general principles 10.1.7 Chromosome partitioning in Bacillus subtilis 10.1.8 Chromosome partitioning in Caulobacter crescentus 10.1.9 Inhibitors of DNA replication 10.1.10 Repairing errors during replication 10.2 RNA synthesis 10.2.1 Initiation, chain elongation, and termination 10.2.2 Frequency of initiation 10.2.3 Role of topoisomerases 10.2.4 The sigma subunit 10.2.5 Regulation of transcription 10.2.6 Processing of ribosomal and transfer RNAs 10.2.7 Some antibiotic and other chemical inhibitors of transcription 10.3 Protein synthesis 10.3.1 Overview 10.3.2 Ribosomes 10.3.3 Charging of the tRNA (making the aminoacyl-tRNA) 10.3.4 Initiation 10.3.5 Chain elongation 10.3.6 Polysomes, coupled transcription and translation 10.3.7 Polycistronic messages 10.3.8 Polarity 10.3.9 Coupled translation 10.3.10 Folding of newly synthesized proteins: the role of chaperone proteins 10.3.11 Inhibitors 10.4 Summary 10.5 Study questions Chapter 11. CELL WALL AND CAPSULE BIOSYNTHESIS 11.1 Peptidoglycan 11.1.1 Structure 11.1.2 Synthesis 11.2 Lipopolysaccharide 11.2.1 Structure 11.2.2 Synthesis 11.3 Extracellular polysaccharide synthesis and export in gram- negative bacteria 11.3.1 Overview 11.3.2 Polysaccharide synthesis using undecaprenol-diphosphate intermediates 11.3.3 Synthesis of E. coli group II K1 antigen: A pathway that may use an undecaprenol monophosphate intermediate 11.3.4 Pathways not involving undecaprenol derivatives 11.3.5 Export of polysaccharides 11.4. Levan and dextran synthesis 11.5. Glycogen synthesis 11.6. Summary 11.7 Study questions Chapter 12. INORGANIC METABOLISM 12.1 Assimilation of nitrate and sulfate 12.2 Dissimilation of nitrate and sulfate 12.2.1 Dissimilatory nitrate reduction 12.2.2 Dissimilatory sulfate reduction 12.3 Nitrogen fixation 12.3.1 The nitrogen-fixing systems 12.3.1 The nitrogen-fixing pathway 12.4 Lithotrophy 12.4.1 The lithotrophs 12.5. Summary 12.6 Study questions Chapter 13. C1 METABOLISM 13.1 Carbon dioxide fixation systems 13.1.1 The Calvin cycle 13.1.2 The acetyl-CoA pathway 13.1.3 The acetyl-CoA pathway in Clostridium thermoaceticum 13.1.4 The acetyl-CoA pathway in methanogens 13.1.5 Methanogenesis from CO2 and H2 13.1.6 Methanogenesis from acetate 13.1.7 Incorporation of acetyl-CoA into cell carbon by methanogens 13.1.8 Using the acetyl-CoA pathway to oxidize acetate to CO2 anaerobically 13.1.9 The reductive tricarboxylic acid pathway (reductive citric acid cycle) 13.2 Growth on C1 compounds other than CO2: The methylotrophs 13.2.1 Growth on methane 13.3. Summary 13.4 Study questions Chapter 14. FERMENTATIONS 14.1 Oxygen toxicity 14.2 Energy conservation by anaerobic bacteria 14.3 Electron sinks 14.4 The anaerobic food chain 14.4.1 Interspecies hydrogen transfer 14.5 How to balance a fermentation 14.6 Propionate fermentation using the acrylate pathway 14.6.1 The fermentation pathway of C. propionicum 14.7 Propionate fermentation using the succinate-propionate pathway 14.7.1 The PEP carytransphosphorylase of propionibacteria and its physiological significance 14.8 Acetate fermentation (acetogenesis) 14.9 Lactate fermentation 14.10 Mixed acid and butanediol fermentations 14.11 Butyrate fermentation 14.11.1 Butyrate and butanol-acetone fermentation in C. acetobutylicum 14.12 Ruminococcus albus 14.13 Summary 14.14 Study questions Chapter 15. HOMEOSTASIS 15.1 Maintaining a ?pH 15.1 Neutrophiles, acidophiles, alkaliphiles 15.1.2 Demonstrating pH homeostasis 15.1.3 The mechanism of pH homeostasis 15.2 Osmotic pressure and osmotic potential 15.2.1 Osmotic pressure 15.2.2 Osmotic potential 15.2.3 Turgor pressure and its importance for growth 15.2.4 Adaptation to high osmolarity media 15.2.5 Adaptation to low osmolarity media 15.2.6 Conceptual problems 15.2.7 What is the nature of the signal sensed by the osmosensors? 15.3 Summary 15.4 Study questions Chapter 16. SOLUTE TRANSPORT 16.1 Reconstitution into proteoliposomes 16.2 Kinetics of solute uptake 16.2.1 Transporter-mediated uptake 16.2.2 Uptake in the absence of a transporter 16.3 Energy-dependent transport 16.3.1 Secondary transport 16.3.2 Evidence for solute/proton or solute/sodium symport 16.3.3 Primary transport driven by ATP 16.4 How to determine the source of energy for transport 16.5 Drug-export systems 16.6 A summary of bacterial transport systems 16.7. Summary 16.8 Study questions Chapter 17. PROTEIN EXPORT AND SECRETION 17.1 The Sec system 17.1.1 The components 17.1.2 A model for protein export 17.2 The translocation of membrane-bound proteins 17.3. The E. coli SRP 17.3.1 SRP-dependent translocation across the endoplasmic reticulum (ER) membrane in eukaryotes: comparison to prokaryotes 17.4. Protein translocation of folded proteins; the TAT system 17.5 Extracellular protein secretion 17.5.1 The type I pathway 17.5.2 The type III pathway 17.5.3 The type II pathway 17.5.4 The type V pathway: autotransporters 17.5.5 The chaperone/usher pathway 17.5.6 The type IV pathway 17.6 Folding of periplasmic proteins 17.7. Summary 17.8 Study questions Chapter 18. MICROBIAL DEVELOPMENT AND PHYSIOLOGICAL ADAPTATION; VARIED RESPONSES TO ENVIRONMENTAL CUES AND INTERCELLULAR SIGNALS 18.1 An introduction to two-component signaling systems 18.1.1 Components of two-component signaling systems 18.1.2 Signal transduction in two-component systems 18.1.3 Amino acid sequences define histidine kinases and response regulator proteins 18.2 Responses by facultative anaerobes to anaerobiosis 18.2.1 Metabolic changes accompanying shift to anaerobiosis 18.2.2 Regulatory systems that govern gene expression accompanying the shift to anaerobiosis 18.3 Response to nitrate and nitrite: The Nar regulatory system 18.3.1 Pathway of nitrate reduction 18.3.2 The enzymes involved 18.3.3 The Nar system and gene regulation; and overview 18.3.4 The roles of NarX and NarQ 18.3.5 The regulatory role of IHF (integration host factor) 18.3.6 Some biochemical and genetic evidence for roles of NarX, NarQ, NarL, NarP 18.4 Response to nitrogen supply: the Ntr regulon 18.4.1 A model for the regulation of the Ntr regulon 18.4.2 Regulatory role of IHF (integration host factor) 18.4.3 Effect of PII-UMP and PII on glutamine synthetase activity 18.5 Response to inorganic phosphate supply: The Pho regulon 18. 5.1 The signal transduction pathway 18.6 Effect of oxygen and light on the expression of photosynthetic genes 18.6.1 Response to oxygen 18.6.2 Response to light 18.7 Response to osmotic pressure and temperature: Regulation of porin synthesis 18.7.1 Regulation of expression of ompF and ompC by a two- component system, EnvZ/OmpR 18.7.2 Repression of transcription of ompF and ompC by IHF (integration host factor) 18.7.3 Inhibition of translation of ompF mRNA by micF RNA, an antisense RNA 18.8 Response to potassium ion: Regulation of transcription of the kdpABC operon 18.9 Acetyl-phosphate as a possible global signal 18.9.1 Changing the intracellular levels of acetyl phosphate to investigate its possible role 18.9.2 A regulatory role for OmpR-P and acetyl phosphate in the repression of transcription of flagellar biosynthesis genes in E. coli. 18.10 Response to carbon sources: catabolite repression, inducer expulsion, permease synthesis 18.10.1 Catabolite repression in E. coli that does not involve c-AMP or CRP: The Cra system 18.10.2 Catabolite repression in gram-positive bacteria via the Ccpa system 18.10.3 Two mechanisms leading to the prevention by glucose of the intracellular accumulation of other sugars in some gram-positive bacteria; uncoupling from the proton gradient, and inducer expulsion. 18.10.4 Response to carbon source: Induction of a permease for dicarboxylic acids in Rhizobium meliloti 18.11 Regulation of virulence genes: Temperature, pH, nutrient, osmolarity, quorum-sensors 18.11.1 ToxR and cholera 18.11.2 The PhoP/PhoQ two-component regulatory system 18.11.3 PmrA/PmrB: A two-component system that interacts with the PhoP/PhoQ system 18.11.4 The bvg genes and pertussis 18.11.5 Virulence genes and bacillary dysentery 18.11.6 Virulence gene expression in Staphylococcus: Stimulation of a two-component system by a peptide pheromone 18.11.7 Virulence gene expression in Agrobacterium tumefaciens; stimulation of a two-component system by phenolic plant exudates 18.12 Chemotaxis 18.12.1 Bacteria measure changes in concentration over time 18.12.2 Tumbling 18.12.3 Adaptation 18.12.4 Proteins required for chemotaxis 18.12.5 A model for chemotaxis 18.12.6 Mechanism of repellent action 18.12.7 Chemotaxis that does not use MCPs: The phosphotransferase system (PTS) is involved in chemotaxis towards PTS sugars 18.12.8 Chemotaxis that is not identical with the model proposed for the enteric bacteria 18.13 Photoresponses 18.3.1 Halobacteria 18.3.2 Photosynthetic bacteria 18.14 Aerotaxis 18.15 An introduction to bacterial development 18.5.1 Quorum sensing 18.16 Myxobacteria 18.16.1 Life cycle 18.16.2 Intercellular signaling and gliding motility 18.16.3 Intercellular signaling and multicellular development 18.16.4 A-signal identity and generation 18.16.5 C-signal identity and generation 18.16.6 Preventing developmental gene expression during growth: SasN 18.16.7 The frz genes regulate reversal of motility and cell movements into the aggregates 18.16.8 Che3 and Che4 are also important for development 18.16.9 The mglA locus appears to coordinate motility between the A- and S-motility systems 18.16.10 Chemotaxis 18.17 The initiation of DNA replication in Caulobacter and the regulation of cell cycle genes 18.17.1 The Caulobacter life cycle 18.17.2 Ctra, a global regulator of gene expression 18.18 Sporulation in Bacillus subtilis 18.18.1 Stages in sporulation 18.18.2 Genes involved in formation of the spore septum and chromosome partitioning 18.18.3 Phosphorelay system for initiation of sporulation 18.18.5 Choosing the pole for the asymmetric division 18.18.4 Does quorum sensing play a role in the initiation of sporulation? 18.18.6 Sporulation is a last resort 18.19 Competence in Bacillus subtilis 18.19.1 The model 18.19.2 Quorum sensing 18.20 Bioluminescence 18.20.1 A brief survey of bioluminescent systems 18.20.2 Biochemistry of bacterial bioluminescence 18.20.3 Intercellular signaling, quorum sensing, and the lux genes 18.21 LuxR/LuxI-like systems in non-luminescent bacteria 18.21.1 The Rhizobiaceae 18.21.2 Pseudomonas aeruginosa 18.21.3 Erwinia carotovora subsp. Carotovora 18.21.4 Vibrio cholerae 18.22 Biofilms 18.22.1 Abiotic surfaces 18.22.2 Biotic surfaces 18.22.3 Advantages to living in a biofilm 18.22.4 Biofilms are organized communities 18.22.5 How biofilms form 18.22.6 Adaptive changes in biofilms 18.22.7 Quorum sensing in biofilms 18.23 Summary 18.24 Study questions Chapter 19. HOW BACTERIA RESPOND TO ENVIRONMENTAL STRESS 19.1 Heat-shock response 19.1.1 Heat-shock proteins 19.1.2 The ?32 (RpoH) regulon 19.1.3 The ?E (?24) regulon 19.1.4. The ?S (RpoS) regulon 19.1.5 Cpx system 19.1.6 Functions of E. coli heat-shock proteins 19.2 Repairing damaged DNA 19.2.1 Kinds of DNA damage 19.2.2 Repairing uv-damaged DNA by photoreactivation 19.2.3 Repairing damaged DNA via excision (nucleotie excission repair) 19.2.4 Repairing damaged DNA by recombination (post-replication repair) 19.2.5 Repair of deaminated bases (base-excision repair) 19.2.6 The GO system and protection from 8-oxoguanine (7,8- dihydro-8-oxoguanine 19.3 The SOS response 19.3.1 SOS mutagenesis 19.3.2 Regulation of the SOS response 19.4 Oxidative stress 19.4.1 Toxic forms of oxygen 19.4.2 Proteins made in response to oxidative stress 19.4.3 Transcriptional regulation of genes induced by oxidative stress 19.5 Summary 19.6 Study questions BOXES 1.1. Phylogeny 1.2. Non-flagellar Motility 1.3. Historical Perspective: Christian Gram 1.4. Tuberculosis 1.5. Leprosy 2.1. Transcriptional, Translational, Post-Translational Regulation Of Levels Of Rpos 3.1. Historical Perspective: Oxidative Phosphorylation 4.1. Historical Perspective: Cellular Respiration 7.1. Historical Perspective: Energy Transfer in the Cytosol 8.1. Vitamins 8.2. Historical Perspective: Cell-Free Yeast Fermentation and the Beginnings of Biochemistry 8.3. Historical Perspective: The Citric Acid Cycle 10.1. Historical Perspective: The Discovery of DNA and Its Role, 10.2. Historical Perspective: The Structure of DNA 17.1. Srp-Dependent Protein Translocation Across The Endoplasmic Reticulum (Er) Membrane In Eukaryotes 18.1. Sporulation Specific Sigma Factors 18.2. Proteins Involved In Formation Of The Spore Septum And Chromosome Partitioning 18.3. Activation of the two-component regulatory system by CSF and ComX 18.4. The Biochemistry of Bacterial Luminescence 19.1. Historical Perspective: The Morse Code Index
Library of Congress Subject Headings for this publication:
Prokaryotes -- Physiology.
Microbial metabolism.
Bacteria -- metabolism.
Archaea -- physiology.
Prokaryotic Cells -- physiology.