عنوان

Biological regulation and development :

(Number (ISBN

1468434179

(Number (ISBN

9781468434170

Number

b549532

Title Proper

Biological regulation and development :

General Material Designation

[Book]

Other Title Information

gene expression.

Place of Publication, Distribution, etc.

[Place of publication not identified]

Name of Publisher, Distributor, etc.

Springer

Date of Publication, Distribution, etc.

2012

Text of Note

1 Strategies of Genetic Regulation in Prokaryotes.- 1 Introduction.- 2 The Prokaryotic Chromosome and Its Genes.- 3 Gene Clustering and the Operon Concept.- 4 Regulatory Molecules and the Genes with Which They Interact.- 4.1 The Promoter.- 4.2 The Operator and Initiator Genes.- 4.3 Regulatory Proteins and the Small Molecules That Affect Their Activities.- 5 Induction and Repression.- 5.1 Induction.- 5.2 Repression.- 5.3 The Regulon.- 6 Autogenous Regulation.- 7 Integration of Regulatory Mechanisms.- 7.1 Catabolite Repression.- 7.2 Stringency.- 8 Translational Control.- 9 Conclusion.- References.- 2 Structure of Complex Operons.- 1 Evolution of the Operon Concept.- 2 Types of Complex Operons.- 2.1 Internal Promoters and Multiple Promoters.- 2.2 Antitermination and Antiattenuation.- 2.3 Divergent Transcription.- 2.4 Overlapping Transcription.- 3 Evolution of Complexity.- 4 Methodological Implications for Studies of Genome Organization.- 4.1 Use of the Cis/Trans Test.- 4.2 Cis-Acting Proteins.- References.- 3 Autogenous and Classical Regulation of Gene Expression: A General Theory and Experimental Evidence.- 1 Introduction.- 2 Repressors and Activators.- 2.1 Inducible Catabolic Systems.- 2.2 Repressible Biosynthetic Systems.- 2.3 Inducible Drug Resistance.- 2.4 Inducible Prophages.- 2.5 Other Systems.- 3 Inducible Systems.- 3.1 Criteria for Functional Effectiveness.- 3.2 Autogenous and Classical Regulation.- 3.3 Predictions.- 3.4 Arabinose.- 3.5 Other Activator-Controlled Inducible Catabolic Systems.- 3.6 Histidine Utilization.- 3.7 Other Repressor-Controlled Inducible Catabolic Systems.- 3.8 Inducible Biosynthetic Systems.- 3.9 Inducible Drug Resistance.- 3.10 Inducible Prophage Lambda.- 4 Repressible Systems.- 4.1 Criteria for Functional Effectiveness.- 4.2 Autogenous and Classical Regulation.- 4.3 Predictions.- 4.4 Tryptophan.- 4.5 Arginine.- 4.6 Histidine.- 4.7 Isoleucine-Valine.- 4.8 Repressible Drug Sensitivity.- 5 Autonomous Systems.- 5.1 Functional Implications and Predictions.- 5.2 Regulator of the Arabinose Operon.- 5.3 Regulator of DNA Replication.- 5.4 6-Phosphogluconate Dehydrogenase.- 5.5 T Antigen.- 5.6 Transcription Termination Factor Rho.- 5.7 RNA Polymerase.- 5.8 Histones.- 5.9 Unwinding Protein.- 5.10 Scaffolding Protein.- 6 Discussion.- References.- 4 Regulation of Enzyme Synthesis in the Bacteria: A Comparative and Evolutionary Study.- 1 Introduction.- 2 The Nature of the Evidence.- 2.1 Theories of Regulation of Enzyme Synthesis.- 2.2 Gene Arrangements.- 2.3 The Experimental Approach.- 3 The Molecular Basis of Regulation of Gene Expression.- 3.1 Binding Domains.- 3.2 Origins of Regulatory Genes.- 4 The Biosynthesis of Aromatic Amino Acids.- 4.1 Aromatic Pathway Enzymes and Regulation in Escherichia coli.- 4.2 Aromatic Pathway Enzymes and Regulation in Bacillus.- 4.3 Aromatic Pathway Enzymes and Regulation in Other Genera.- 4.4 Genes and Enzymes of Tryptophan Biosynthesis.- 5 Catabolic Pathways.- 5.1 Induction and Repression.- 5.2 Catabolism of Aromatic Compounds.- 5.3 The ?-Ketoadipate Pathway.- 5.4 Meta Pathway Enzymes.- 5.5 Arrangements of Genes of Aromatic Pathway Enzymes.- 5.6 Plasmids and Regulation.- 6 Nitrogen Metabolism and Regulation.- 6.1 Glutamine Synthetase.- 6.2 Nitrogen Regulation in Fungi.- 7 Experimental Evolution.- 7.1 Growth on Novel Substrates.- 7.2 Amidase.- 7.3 Evolved ?-Galactosidase.- 7.4 Gene Duplications.- 7.5 New Metabolic Pathways.- 8 Discussion.- References.- 5 Importance of Symmetry and Conformational Flexibility in DNA Structure for Understanding Protein-DNA Interactions.- 1 Introduction.- 2 Symmetry in DNA Structure.- 3 Flexibility in DNA Structure-The Kink.- 4 Detailed Models for Drug-DNA Binding.- 4.1 Ethidium.- 4.2 Actinomycin.- 4.3 Irehdiamine.- 5 Nature of DNA Breathing.- 6 Organization of DNA in Chromatin.- 7 Active Form of DNA in Transcription, Replication, and Recombination.- 8 Operator-Repressor Interactions.- 9 Concluding Remarks.- References.- 6 Some Aspects of the Regulation of DNA Replication in Escherichia coli.- 1 Introduction.- 2 DNA Replication in Escherichia coli.- 3 Stoichiometry of DNA Replication.- 4 Regulation Is at the Level of Initiating Chromosome (or Replicon) Replication.- 5 The Replication Complex.- 6 The Destruction of the Replication Complex.- 7 Repair Replication (a Possible Example of Regulative Assembly).- 8 Regulation of the Quality of DNA Replication.- 9 RNA and the Initiation of Replication.- 10 Conclusion.- References.- 7 Genetic Control Signals in DNA.- 1 DNA Control Signals.- 1.1 Introduction.- 1.2 DNA Sequence.- 1.3 Sequence-Specific Protein-DNA Interactions.- 1.4 Genetics of Control Signals.- 1.5 DNA Sequence Analysis.- 1.6 Chemical Probes.- 1.7 General Information in DNA.- 2 Transcription Control Signals.- 2.1 The Transcription Unit.- 2.2 Development versus Maintenance.- 2.3 Control of Transcription.- 3 The Promoter and Its Regulation.- 3.1 The Promoter.- 3.2 Transcription Initiation.- 3.3 The RNA Polymerase.- 3.4 The Basic Promoter.- 3.5 Promoter Function-The Model.- 3.6 Energy-Information Coupling.- 3.7 Binding Energy and Kinetics.- 3.8 Justifying the Model.- 3.9 Promoter Strength.- 3.10 Promoter Activation.- 3.11 Repressors, Operators, and Negative Control.- 3.12 Promoters and Development.- 4 The Terminator and Its Function.- 4.1 Terminators and Rho Factor.- 4.2 Attenuators.- 4.3 Rho-Dependent and Rho-Independent Terminators.- 4.4 Reversing Initiation ... Somewhat.- 4.5 The Basic Terminator.- 4.6.

Text of Note

Polymerase-Terminator DNA Interactions.- 4.7 RNA Structure and Braking.- 4.8 Terminator DNA Melting.- 4.9 RNA Elimination.- 4.10 Concerted Process.- 4.11 Rho-Dependent Termination.- 4.12 Translation and Transcript Termination.- 4.13 Terminator Strength.- 5 Terminator Regulation.- 5.1 Regulation and Rho Factor.- 5.2 The trp Attenuator.- 5.3 Control by Antitermination.- 6 Concluding Remarks.- 6.1 Transcription Regulatory Mechanisms.- 6.2 Adaptive Response versus Development.- 6.3 A Problem in Genetic Design.- References.- 8 On the Molecular Bases of the Specificity of Interaction of Transcriptional Proteins with Genome DNA.- 1 Introduction.- 2 Molecular Bases of Protein-Nucleic Acid Interactions.- 2.1 Protein Structures and Functional Groups.- 2.2 Nucleic Acid Conformations and Functional Groups.- 3 The Problem of the Other Sites.- 3.1 Informational Aspects of Regulation.- 3.2 Thermodynamic Aspects of Recognition.- 3.3 Methods for Studying Specific and Nonspecific Binding of Proteins to Nucleic Acids and Definitions of Interaction Parameters.- 4 The Lactose Operon of Escherichia coli.- 4.1 lac Repressor-Operator-Inducer-DNA Interactions.- 4.2 Repression of the Lactose Operon as an Integrated Control System.- 4.3 In Vivo Determination of the Thermodynamic Parameters of the lac System.- 4.4 Kinetics of Intracellular Repressor Transport.- 4.5 Other Components of the Lactose Operon.- 5 Extension to Other Transcription Regulatory Systems.- 5.1 Prokaryotic Control Systems.- 5.2 Eukaryotic Control Systems.- References.- 9 Genetic Signals and Nucleotide Sequences in Messenger RNA.- 1 Introduction.- 2 Ribosome Recognition of Initiation Signals.- 2.1 A Bit of History.- 2.2 A Look at Today's Catalog of Ribosome-Binding Sites.- 2.3 mRNA and rRNA Pair during Initiation.- 2.4 Proteins as Determinants in Initiation.- 2.5 RNA versus Proteins in Species Specificity.- 2.6 mRNA Structure and Initiation.- 2.7 Translational Control at the Molecular Level.- 2.8 The Why and Wherefore of Translational Restarts.- 2.9 Mutations in Ribosome-Binding Sites.- 2.10 Perspectives and Problems.- 3 Sequences Directing Elongation of Polypeptide Chains.- 3.1 Selective Codon Usage in Bacteriophage Messengers.- 3.2 Overlapping Genes and Signals in Messenger RNA.- 4 RNA * RNA Interactions in Ribosome Function.- 5 Are Eukaryotic Messengers Different?.- References.- 10 The Role of tRNA in Regulation.- 1 Introduction.- 1.1 Biosynthesis of tRNA.- 1.2 tRNA in Protein Synthesis.- 2 tRNA as a Regulatory Molecule.- 2.1 Stringent Control.- 2.2 Operon-Specific Control.- 3 tRNA as a Target for Regulation.- 3.1 tRNA-Dependent Modulation of Translation: An Evolutionary Equilibrium.- 3.2 tRNA-Dependent Modulation of Translation: A Developmental Regulation.- 4 tRNA Has Other Functions.- 5 Concluding Remarks.- References.- 11 Suppression.- 1 Introduction.- 2 A Short Synopsis of Suppression.- 2.1 How It Started.- 2.2 The Problem of Nomenclature.- 2.3 Nonsense Suppression.- 2.4 Missense Suppression.- 2.5 Frameshift Suppression.- 2.6 Ribosomal Suppression.- 2.7 Polarity Suppression.- 3 Some Topics in Molecular Biology Influenced by Analysis of Genetic Suppression.- 3.1 Phasing of Messenger RNA.- 3.2 UAG, UAA, and UGA in Polypeptide Chain Termination.- 3.3 Effect of tRNA Modification on Codon Specificity.- 3.4 How Specific Is Codon * Anticodon Interaction?.- 3.5 Other Errors in Translation.- 3.6 Polarity and the Coupling of Transcription to Translation in Bacteria.- 3.7 Genetics of tRNA.- 3.8 Biosynthesis of tRNAs.- 3.9 tRNA Structure-Function Relationships: Mischarging Suppressor tRNAs.- 4 Nonsense Mutations in the Escherichia coli lacI Gene.- 4.1 Suppression of Nonsense Mutations Generates Altered lac Repressor Molecules.- 5 Current Developments in Eukaryotic Suppression.- 5.1 tRNA-Mediated Suppression in Yeast.- 5.2 The Search for Nonsense Mutations and Their Suppressors in Drosophila and Mammalian Cells.- 6 Outlook.- References.- 12 Regulation of the Protein-Synthesizing Machinery-Ribosomes, tRNA, Factors, and So On.- 1 Introduction.- 2 The Concepts and Elements.- 2.1 Characteristics of Control at the Operon Level.- 2.2 Transcription and the Regulation of the Protein-Synthesizing System.- 2.3 Relations between the Major Synthetic Activities.- 2.4 Parameters Characterizing Steady States of Growth.- 3. Patterns and Frequencies of Transcription.- 3.1 Protein Synthesis at Medium and High Growth Rates.- 3.2 Protein Synthesis at Low Growth Rates.- 3.3 The Amino Acids-Substrates and Effectors.- 3.4 Transcription and Translation Frequencies.- 3.5 Synopsis.- 4 The Role of ppGpp in Regulation of the Protein-Synthesizing System.- 4.1 ppGpp Concentrations.- 4.2 The Relaxed Syndrome.- 4.3 Ribosome and Protein Synthesis during Shift-Down Transients.- 4.4 The Low Efficiency of Ribosomes at Low Growth Rates.- 4.5 Synopsis.- 5 Ribosome Synthesis during the Cell Cycle.- 6 Afterthoughts.- References.

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