Cover
Microbial Biochemistry, 2nd Edition
ISBN 978-90-481-9436-0
Foreword
Contents
Abbreviations
Introduction
Chapter 1: Bacterial Growth
The Lag Phase
The Exponential Phase
Linear Growth
The Yield of Growth
Variation of the Growth Rate at Limiting Carbon Source Concentrations
Continuous Growth: The Chemostat
Advantages of the Continuous Exponential Culture
Diauxic Growth
Selected References
Bacterial Growth: Diauxie
Linear Growth
Continuous Growth: The Chemostat
Influence of Growth Rate on Cellular Constituents
Adaptive (Inducible) Enzymes: Prehistory
Chapter 2: The Outer Membrane of Gram-negative Bacteria and the Cytoplasmic Membrane
Chapter 3: Peptidoglycan Synthesis and Cell Division
Chapter 4: Cellular Permeability
Accumulation, Crypticity, and Selective Permeability
beta-Galactoside Permease
Accumulation in Induced Cells: Kinetics and Specificity
The Induced Synthesis of Galactoside Permease
Functional Significance of Galactoside Permease: Specific Crypticity
Functional Relationships of Permease: Induction
Genetic Relationships of Galactosidase and Galactoside Permease
Galactoside Permease as Protein
Periplasmic Binding Proteins and ATP Binding Cassettes
Phosphotransferases: The PTS System
TRAP Transporters
A Few Well-identified Cases of Specific Cellular Permeability
Amino Acid Permeases
Peptide Permeases
Porins
Iron Uptake
Conclusion
Selected References
beta-Galactoside Permease
Amino Acid Permeases
Periplasmic Proteins and ATP-Binding Cassettes
Phosphotransferase System
Peptide Permeaes
TRAP Transporters
Porins
Chapter 5: Allosteric Enzymes
Chapter 6: Glycolysis, Gluconeogenesis and Glycogen Synthesis
Chapter 7: The Pentose Phosphate and Entner-Doudoroff Pathways
The Pentose Phosphate Pathway
The Enzymes of the Oxidative Phase
Glucose 6-Phosphate Dehydrogenase
6-Phosphogluconolactonase
6-Phosphogluconate Dehydrogenase (Decarboxylating)
Ribose Phosphate Isomerase
The Enzymes of the Non-oxidative Phase
Regulation of the Pentose Phosphate Pathway
Chapter 8: The Tricarboxylic Acid Cycle and the Glyoxylate Bypass
The origin of acetyl CoA: The Pyruvate Dehydrogenase Complex
Overview of the Tricarboxylic Acid (TCA) Cycle
Organization of the Enzymes of the Tricarboxylic Acid Cycle
The Tricarboxylic Acid Cycle Is a Source of Biosynthetic Precursors
The Anaplerotic Glyoxylic Pathway Bypass
Chapter 9: ATP-Generating Processes: Respiration and Fermentation
Respiration
Fermentation
Acetone-Butanol Fermentation
The Stickland Reaction
Ornithine Fermentation
Glycine and Proline Degradation
Threonine Degradation
Glutamate Degradation
Lysine Degradation
Arginine Fermentation
Methionine Degradation
D-Selenocystine and D-Cysteine Degradation
Selected References
NADH-Ubiquinone Oxidoreductases
Erom Quinones to Oxygen
The Stickland Reaction
Arginîne and Ornithine Degradation
Threonine Degradation
Glycine Degradation
Proline Degradation
Glutamate Degradation
Lysine Degradation
Methionine gamma-Lyase
D-Selenocystine and D-Cysteine Degradation
Chapter 10: Biosynthesis of Lipids
Biosynthesis of Short Chain Fatty Acids
Biosynthesis of Long-Chain Fatty Acids
Regulation of Yeast Fatty Acid Synthesis at the Genetic Level
Regulation of Fatty Acid Synthesis in Bacteria
Biosynthesis of Triglycerides
Biosynthesis of Phosphoglycerides
Cyclopropane Fatty Acid Synthase (CFA Synthase)
Selected References
Short Chain Fatty Acid Synthesis
Fatty Acid Synthesis and Its Regulation
Cyclopropane Fatty Acid Synthetase
Chapter 11: Iron-Sulfur Proteins
Chapter 12: The Archaea
Chapter 13: Methanogens and Methylotrophs
Chapter 14: Enzyme Induction in Catabolic Systems
The Specificity of Induction
De Novo Synthesis of beta-Galactosidase
Constitutive Mutants
Pleiotropy of the Constitutive Mutants
The Genetic Control and the Cytoplasmic Expression of Inducibility in the Synthesis of beta-Galactosidase in E. coli. The Lac R
Operators and Operons
Selected References
Chapter 15: Transcription: RNA Polymerase
The Synthesis of Messenger RNA: The Bacterial RNA Polymerase
Termination of Transcription in Prokaryotes
Yeast RNA Polymerases
Archaeal RNA Polymerases
Transcription Termination and PolyA Tails
Selected References
Trans-acting Transcription Factors
Eukaryotic RNA Polymerases
Termination of Transcription
Chapter 16: Negative Regulation
Induction Is Correlated with the Synthesis of a Specific Messenger
Isolation of the Lac Repressor
The lac Operator Is a DNA sequence
Direct Observation of Transcription Factor Dynamics in a Living Cell
Selected References
Messenger RNA
Isolation of Lac Repressor and lac Operator
Operators 02 and 03
Formation of Loop Structures in DNA
Quantifying lac Repressor Kinetics
Chapter 17: Enzyme Repression in Anabolic Pathways
Description of the Phenomenon
Isolation of Derepressed (Constitutive) Mutants in Biosynthetic Pathways. The Use of Structural Analogues
Replacement of Methionine by Selenomethionine in Proteins
Selected References
Chapter 18: Positive Regulation
The Promoter Region
Role of Cyclic AMP and of the CAP Protein in the Binding of RNA Polymerase to the Promoter Region
The Synthesis and Degradation of Cyclic AMP
How Does Glucose Exert Its Inhibitory Effect on E. coli beta-Galactosidase Synthesis?
Selected References
Chapter 19: The Ribosomes
The Components of E. coli Ribosomes
The Ribosomes of Eukaryotes and of Archaea
Mechanistic Aspects of Translation of Messenger RNA to Protein by Ribosomes
Selected References
General
Eukaryotic Ribosomes
Crystallography
Chapter 20: The Genetic Code, the Transfer RNAs and the Aminoacyl-tRNA-Synthetases
The Genetic Code
The Transfer RNAs
Selected References
Colinearity of Genes and Proteins
The Genetic Code
Selenocysteine and Pyrrolysine
Transfer RNAs
Aminoacyl-tRNA Synthetases
RNA-Dependent Cysteine Biosynthesis in Archaea
Chapter 21: Attenuation
Chapter 22: Riboswitches
Chapter 23: The Biological Fixation of Nitrogen
Chapter 24: How Biosynthetic Pathways have been Established
Chapter 25: The Aspartic Acid Family of Amino Acids: Biosynthesis
The Biosynthesis of Aspartic Acid and Asparagine
Biosynthesis of Lysine from Aspartate Semialdehyde in Bacteria
The Synthesis of Dipicolinic Acid, a Substance Present in the Spores of Gram-Positive Bacilli
The Reduction of Aspartate Semialdehyde to Homoserine, the Common Precursor of Methionine and Threonine
Biosynthesis of Methionine from Homoserine
S-Adenosylmethionine (SAM) Biosynthesis
Biosynthesis of Threonine from Homoserine
Biosynthetic Threonine Dehydratase
Isoleucine Biosynthesis
Summary of the Biosynthetic Pathway of the Aspartate Family of Amino Acids
Selected References
Chapter 26: Regulation of the Biosynthesis of the Amino Acids of the Aspartic Acid Family in Enterobacteriacea
Chapter 27: Other Patterns of Regulation of the Synthesis of Amino Acids of the Aspartate Family
Concerted Feedback Inhibition of Aspartokinase Activity in Rhodobacter capsulatus (Formerly Rhodopseudomonas capsulata)
Pseudomonads
Specific Reversal of a Particular Feedback Inhibition by Other Essential Metabolites. The Case of Rhodospirillum rubrum
Some Other Cases
Conclusion
Selected References
Chapter 28: Biosynthesis of the Amino Acids of the Glutamic Acid Family and Its Regulation
The Biosynthesis of Glutamine
Biosynthesis of Glutamine: Cumulative Feedback Inhibition
Biosynthesis of Glutamine: The Covalent Modification of Glutamine Synthetase
Glutamine Synthetase Structure
Reversible Adenylylation of the Glutamine Synthetase
Regulation of Glutamine Synthetase Activity by Covalent Adenylylation
The Regulation of the Synthesis of Glutamine Synthetase also Involves the Two Forms of PII and UTase/UR
Glutamine Synthetase in Other Microorganisms
The Biosynthesis of Glutamate
Glutamate Dehydrogenase
Glutamate Synthase
Biosynthesis of Proline
The Biosynthesis of Arginine and Polyamines
Nitric Oxide Synthase in Bacteria
The Biosynthesis of Lysine in Yeasts and Molds
Selected References
Glutamine Synthetase Activity and Its Regulation by Covalent Modification: Structure
Glutamine Synthetase: Regulation of Gene Expression
The Levels of Glutamine Synthetase Are also Regulated by Oxidation Followed by Proteolytic Degradation
Glutamate Synthase
Proline Biosynthesis
Arginine Biosynthesis and Regulation
The Arginine Repressor
The Methionine Salvage Pathway
Nitric Oxide Synthase
Aminoadipic Acid Pathway
Chapter 29: Biosynthesis of Amino Acids Derived from Phosphoglyceric Acid and Pyruvic Acid
Biosynthesis of Glycine and Serine
Biosynthesis of Cysteine
O-Acetylation of Serine
Cysteine Synthesis in Methanogens
Allosteric Regulation of Cysteine Synthesis
Regulation of Cysteine Synthesis at the Genetic Level
Biosynthesis of Alanine
Biosynthesis of Valine
Biosynthesis of Leucine
Isoleucine Synthesis from Pyruvate
Regulation of Valine, Isoleucine and Leucine Biosynthesis
Selected References
Serine Biosynthesis
Serine Hydroxymethylase
Sulfite Reductase
Cysteine Synthesis in Methanogens
Valine and Leucine
Isoleucine Synthesis from Pyruvate
Aspartate-beta-Decarboxylase
Chapter 30: Selenocysteine and Selenoproteins
Chapter 31: Biosynthesis of Aromatic Amino Acids and Its Regulation
The Common Pathway (Shikimic Pathway)
Formation of Shikimic Acid
Formation of Chorismic Acid
Physiological Aspects of the Regulation of the Common Pathway
Characteristics of the Common Pathway in Several Organisms
Biosynthesis of Phenylalanine and Tyrosine from Chorismic Acid
The tyrR Regulon
Regulation of the pheA Gene by Attenuation
Other Organisms: The Arogenate Pathway of Phenylalanine and Tyrosine Biosynthesis
Aspartate as a Presursor of Aromatic Amino Acids
The Biosynthesis of Tryptophan from Chorismic Acid
Anthranilate Synthase-Anthranilate Phosphoribosyltransferase
Phosphoribosylanthranilate Isomerase-Indoleglycerophosphate Synthase
Tryptophan Synthase
Regulation of Tryptophan Biosynthesis at the Genetic Level: The Tryptophan Repressor
A Unitary Model for Induction and Repression
Isolation of the Trp Repressor
Enterochelin (Enterobactin) Biosynthesis
Selected References
The Common Pathway
Biosynthesis of Phenylalanine and Tyrosine
DKFP Pathway: Aspartate as a Precursor of Aromatic Amino Acids
TyrR
Tryptophan Synthesis
Tryptophan Repressor: Functional Aspects
Enterochelin
Chapter 32: The Biosynthesis of Histidine and Its Regulation
Regulation of Histidine Biosynthesis at the Genetic Level
Synthesis of Diphthamide, a Modified Histidine, by Archaea
Selected References
Chapter 33: The Biosynthesis of Nucleotides
Chapter 34: The Biosynthesis of Deoxyribonucleotides
The Formation of Deoxyribonucleoside Diphosphates from Ribose Nucleoside Diphosphates
The Ribosenucleoside Diphosphate (NDP) Reductase System of E. coli
Regulation of the Activity of Ribonucleoside Diphosphate Reductase
dCMP Deaminase and Thymidylate Synthase
dUTPase
The Ribonucleoside Phosphate Reductase of Other Organisms
A Ribonucleotide Triphosphate Reductase Reaction in E. coli Grown Under Anaerobic Conditions
The Synthesis of Deoxyribonucleoside Triphosphates from the Diphosphates
Organization of DNA Precursor Synthesis in Eukaryotic Cells
Selected References
Thioredoxin and Glutaredoxin
Ribonucleoside Diphosphate and Triphosphate Reductases
Thymidylate Kinases
Nucleoside Diphosphate Kinase
Chapter 35: Biosynthesis of Some Water-Soluble Vitamins and of Their Coenzyme Forms
Biosynthesis of Thiamin and Cocarboxylase
Control of Thiamin Biosynthesis
Biosynthesis of Riboflavin
Biosynthesis of Nicotinamide, NAD+ and NADP+
Regulation of the Biosynthesis of Nicotinamide and Its Derivatives
NAD+ and the ADP-Ribosylation of Proteins
Biosynthesis of Para-Aminobenzoic Acid, of Folic Acid and Its Derivatives
Biosynthesis of Vitamin B6 Pyridoxine, and of Its Derivatives, Pyridoxal, Pyridoxamine and Pyridoxal Phosphate
Biosynthesis of Biotin, Biotin CO2, and Biocytin
The Biotin Operon and Its Repressor
Biosynthesis of Lipoic Acid
Biosynthesis of Pantothenate and Coenzyme A
The Biosynthesis of Inositol
Biosynthesis of Pyrroloquinoline Quinone
Selected References
Thiamin
Riboflavin
Pyridoxal Phosphate
Chapter 36: Biosynthesis of Carotene, Vitamin A, Sterols, Ubiquinones and Menaquinones
Synthesis of the Common Precursor
The Non-mevalonate Pathway of Isoprenoid Precursor (Dimethylallyl Pyrophosphate) Biosynthesis
Synthesis of beta-Carotene, Carotenoids and Vitamin A
Synthesis of Sterols
The Biosynthesis of Ubiquinones and Menaquinones
Selected References
Chapter 37: Biosynthesis of the Tetrapyrrole Ring System
Synthesis of Protoporphyrin
Synthesis of Heme from Protoporphyrin
Heme Biosynthesis in Archaea
Synthesis of Chlorophyll from Protoporphyrin
Biosynthesis of the Phycobilin Chromophores. Chromatic Adaptation
A Type of Chromatic Adaptation Under Conditions of Sulfur Starvation
Selected References
The Tetrapyrroles
ALA Synthesis
Heme Biosynthesis in Archaea
Phycobilins
Complementary Chromatic Adaptation
The Effect of Sulfur Starvation on Chromatic Adaptation
Chapter 38: Biosynthesis of Cobalamins Including Vitamin B12
Chapter 39: Interactions Between Proteins and DNA
Chapter 40: Evolution of Biosynthetic Pathways
Principles of Protein Evolution
Two Theories for the Evolution of Biosynthetic Pathways
The Methionine and Cysteine Biosynthetic Pathways
The Threonine, Isoleucine, Cysteine and Tryptophan Biosynthetic Pathways
The Evolutionary Pathway Leading to the Three Isofunctional Aspartokinases in Escherichia coli
Transmembrane Facilitators
DNA-Binding Regulator Proteins
Selected References
Two Books
Two Different Theories on the Evolution of Biosynthetic Pathways
Common Origin of Cystathionine-gamma-Synthase and Cystathionase
Common Origin of Threonine Synthase, Threonine Dehydratase, D-Serine Dehydratase, and the B Chain of Tryptophan Synthase
Comparison of arg Genes with Homologous and Analogous Enzymes
Evolution of the E. coli Aspartokinases and Homoserine Dehydrogenases
Structural and Evolutionary Relationships Between E. coli Aspartokinase-Homoserine Dehydrogenases and Monofunctional Homoserine
Superfamily of Transmembrane Facilitators
DNA-Binding Regulator Proteins
Index