Biochemistry of signal transduction and regulation.

Biochemistry of signal transduction and regulation.

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Bibliographic Details
Author / Creator:Krauss, Gerhard.
Edition:1st English ed.
Imprint:Weinheim ; New York : Wiley-VCH, 1999.
Description:xxii, 506 p. ; 25 cm.
Language:English
Subject:
Cellular signal transduction.
Cellular control mechanisms.
Cell Communication.
Gene Expression Regulation.
Signal Transduction.
Cellular control mechanisms.
Cellular signal transduction.
Format: Print Book
URL for this record:http://pi.lib.uchicago.edu/1001/cat/bib/4217314
Hidden Bibliographic Details
ISBN:3527297715
Table of Contents:
  • Preface
  • 1. The Regulation of Gene Expression
  • 1.1. Regulation of Gene Expression: How and Where? A Schematic Overview
  • 1.2. Protein-Nucleic Acid Interactions as a Basis for Specific Gene Regulation
  • 1.2.1. Structural Motifs of DNA-binding Proteins
  • 1.2.2. The Nature of the Specific Interactions in Protein-Nucleic Acid Complexes
  • 1.2.3. The Role of the DNA Conformation in Protein-DNA Interactions
  • 1.2.4. Structure of the Recognition Sequence and Quaternary Structure of DNA-binding Proteins
  • 1.3. The Principles of Transcription Regulation
  • 1.3.1. Elements of Transcription Regulation
  • 1.3.2. Functional Requirements for Repressors and Transcriptional Activators
  • 1.3.3. Mechanisms for the Control of the Activity of DNA-binding Proteins
  • 1.3.3.1. Binding of Effector Molecules
  • 1.3.3.2. Binding of Inhibitory Proteins
  • 1.3.3.3. Modification of Regulatory Proteins
  • 1.3.3.4. Changes in the Concentration of Regulatory DNA-binding Proteins
  • 1.4. Regulation of Transcription in Eucaryotes
  • 1.4.1. Overview of Transcription Initiation in Procaryotes
  • 1.4.2. The Basic Features of Eukaryotic Transcription
  • 1.4.3. The Eucaryotic Transcription Apparatus
  • 1.4.3.1. Structure of the Transcription Start Site and Regulatory Sequences
  • 1.4.3.2. Elementary Steps of Eucaryotic Transcription
  • 1.4.3.3. Formation of a Basal Transcription Apparatus from General Transcription Factors and RNA Polymerase
  • 1.4.3.4. Phosphorylation of RNA Polymerase II and the Onset of Transcription
  • 1.4.3.5. TFIIH--a Pivotal Regulatory Protein Complex
  • 1.4.4. Regulation of Eucaryotic Transcription by DNA-binding Proteins
  • 1.4.4.1. The Structure of Eucaryotic Transcriptional Activators
  • 1.4.4.2. Concerted Action of Transcriptional Activators and Coactivators in the Regulation of Transcription
  • 1.4.4.3. Interactions with the Transcription Apparatus
  • 1.4.5. Regulation of the Activity of Transcriptional Activators
  • 1.4.5.1. The Principal Pathways for the Regulation of Transcriptional Activators
  • 1.4.5.2. Phosphorylation of Transcriptional Activators
  • 1.4.5.3. Heterotypic Dimerization
  • 1.4.5.4. Regulation by Binding of Effector Molecules
  • 1.4.6. Specific Repression of Transcription
  • 1.4.7. Chromatin Structure and Transcription Activation
  • 1.4.7.1. Transcriptional Activity and Histone Acetylation
  • 1.4.7.2. Transcriptional Activity and Histone Methylation
  • 1.4.7.3. Enhanceosomes
  • 1.4.8. Methylation of DNA
  • 1.5. Post-transcriptional Regulation of Gene Expression
  • 1.5.1. Modifications at the 5' and 3' Ends of the Pre-mRNA
  • 1.5.2. Formation of Alternative mRNA by Alternative Polyadenylation and by Alternative Splicing
  • 1.5.3. Regulation via Transport and Splicing of Pre-mRNA
  • 1.5.4. Stability of the mRNA
  • 1.5.5. Regulation at the Level of Translation
  • 1.5.5.1. Regulation by binding of protein to the 5' end of the mRNA
  • 1.5.5.2. Regulation by Modification of Initiation Factors
  • 2. The Regulation of Enzyme Activity
  • 2.1. Enzymes as Catalysts
  • 2.2. Regulation of Enzymes by Effector Molecules
  • 2.3. Principal Features of Allosteric Regulation
  • 2.4. Regulation of Enzyme Activity by Binding of Inhibitor and Activator Proteins
  • 2.5. Regulation of Enzyme Activity by Phosphorylation
  • 2.5.1. Regulation of Glycogen Phosphorylase by Phosphorylation
  • 2.5.2. Regulation of Isocitrate Dehydrogenase (E. coli) by Phosphorylation
  • 2.6. Regulation via the Ubiquitin-Proteasome Pathway
  • 2.6.1. Components of the Ubiquitin System
  • 2.6.2. Degradation in the Proteasome
  • 2.6.3. Recognition of the Substrate in the Ubiquitin-Proteasome Degradation Pathway
  • 2.6.4. Regulatory Function of Ubiquitin Conjugation and the Targeted Degradation of Proteins
  • 2.7. Regulation of Proteins by Sumoylation
  • 3. Structure and Function of Signal Pathways
  • 3.1. General Function of Signal Pathways
  • 3.2. Structure of Signaling Pathways
  • 3.2.1. The Mechanisms of Intercellular Communication
  • 3.2.2. Principles of Intracellular Signal Transduction
  • 3.2.3. Components of Intracellular Signal Transduction
  • 3.2.4. Coupling of Proteins in Signaling Chains
  • 3.2.4.1. Coupling by Specific Protein-Protein Interactions
  • 3.2.4.2. Coupling by Protein Modules
  • 3.2.4.3. Coupling by Reversible Docking Sites
  • 3.2.4.4. Coupling by Colocalization
  • 3.2.4.5. Linearity, Branching and Crosstalk
  • 3.2.4.6. Variability and Specificity of Receptors and Signal Responses
  • 3.3. Extracellular Signaling Molecules
  • 3.3.1. The Chemical Nature of Hormones
  • 3.3.2. Hormone Analogs: Agonists and Antagonists
  • 3.3.3. Endocrine, Paracrine and Autocrine Signaling
  • 3.3.4. Direct Modification of Protein by Signaling Molecules
  • 3.4. Hormone Receptors
  • 3.4.1. Recognition of Hormones by Receptors
  • 3.4.2. The Interaction between Hormone and Receptor
  • 3.5. Signal Amplification
  • 3.6. Regulation of Inter- and Intracellular Signaling
  • 3.7. Membrane Anchoring and Signal Transduction
  • 3.7.1. Myristoylation
  • 3.7.2. Palmitoylation
  • 3.7.3. Farnesylation and Geranylation
  • 3.7.4. The Glycosyl-Phosphatidyl-Inositol Anchor (GPI Anchor)
  • 3.7.5. The Switch Function of Lipid Anchors
  • 4. Signaling by Nuclear Receptors
  • 4.1. Ligands of Nuclear Receptors
  • 4.2. Principles of Signaling by Nuclear Receptors
  • 4.3. Classification and Structure of Nuclear Receptors
  • 4.3.1. DNA-Binding Elements of Nuclear Receptors, HREs
  • 4.3.2. The DNA-Binding Domain of Nuclear Receptors
  • 4.3.3. HRE Recognition and Structure of the HRE-Receptor Complex
  • 4.3.4. Ligand-binding Domains
  • 4.3.5. Transactivating Elements of the Nuclear Receptors
  • 4.4. Mechanisms of Transcriptional Regulation by Nuclear Receptors
  • 4.5. Regulation and Variability of Signaling by Nuclear Receptors
  • 4.6. The Signaling Pathway of the Steroid Hormone Receptors
  • 4.7. Signaling by Retinoids, Vitamin D3, and the T3-Hormone
  • 4.7.1. Structure of the HREs of RXR Heterodimers
  • 4.7.2. Complexity of the Interaction between HRE, Receptor and Hormone
  • 5. G Protein-Coupled Signal Transmission Pathways
  • 5.1. Transmembrane Receptors: General Structure and Classification
  • 5.2. Structural Principles of Transmembrane Receptors
  • 5.2.1. The Extracellular Domain of Transmembrane Receptors
  • 5.2.2. The Transmembrane Domain
  • 5.2.3. The Intracellular Domain of Membrane Receptors
  • 5.2.4. Regulation of Receptor Activity
  • 5.3. G Protein-Coupled Receptors
  • 5.3.1. Structure of G Protein-Coupled Receptors
  • 5.3.2. Ligand Binding
  • 5.3.3. Mechanism of Signal Transmission
  • 5.3.4. Switching Off and Desensitization of 7-Helix Transmembrane Receptors
  • 5.3.5. Dimerization of GPCRs
  • 5.4. Regulatory GTPases
  • 5.4.1. The GTPase Superfamily: General Functions and Mechanism
  • 5.4.2. Inhibition of GTPases by GTP Analogs
  • 5.4.3. The G-domain as Common Structural Element of the GTPases
  • 5.4.4. The Different GTPase Families
  • 5.5. The Heterotrimeric G Proteins
  • 5.5.1. Classification of the Heterotrimeric G Proteins
  • 5.5.2. Toxins as Tools in the Characterization of Heterotrimeric G Proteins
  • 5.5.3. The Functional Cycle of Heterotrimeric G Proteins
  • 5.5.4. Structural and Mechanistic Aspects of the Switch Function of G Proteins
  • 5.5.5. Structure and Function of the [beta gamma]-Complex
  • 5.5.6. Membrane Association of the G Proteins
  • 5.5.7. Regulators of G Proteins: Phosducin and RGS Proteins
  • 5.6. Effector Molecules of G Proteins
  • 5.6.1. Adenylyl Cyclase and cAMP as Second Messenger
  • 5.6.2. Phospholipase C
  • 6. Intracellular Messenger Substances: Second Messengers
  • 6.1. General Functions of Intracellular Messenger Substances
  • 6.2. cAMP
  • 6.3. cGMP
  • 6.4. Metabolism of Inositol Phospholipids and Inositol Phosphates
  • 6.5. Inositol 1,4,5-Triphosphate and Release of Ca[superscript 2+]
  • 6.5.1. Release of Ca[superscript 2+] from Ca[superscript 2+] Storage
  • 6.5.2. Influx of Ca[superscript 2+] from the Extracellular Region
  • 6.5.3. Removal and Storage of Ca[superscript 2+]
  • 6.5.4. Temporal and Spatial Changes in Ca[superscript 2+] Concentration
  • 6.6. Phosphatidyl Inositol Phosphates and PI3-Kinase
  • 6.6.1. PI3-Kinases
  • 6.6.2. The Messenger Substance PtdIns(3,4,5)P[subscript 3]
  • 6.6.3. Akt Kinase and PtdIns(3,4,5)P[subscript 3] Signaling
  • 6.6.4. Functions of PtIns(4,5)P[subscript 2]
  • 6.7. Ca[superscript 2+] as a Signal Molecule
  • 6.7.1. Calmodulin as a Ca[superscript 2+] Receptor
  • 6.7.2. Target Proteins of Ca[superscript 2+]/Calmodulin
  • 6.7.3. Other Ca[superscript 2+] Receptors
  • 6.8. Diacylglycerol as a Signal Molecule
  • 6.9. Other Lipid Messengers
  • 6.10. The NO Signaling Molecule
  • 6.10.1. Reactivity and Stability of NO
  • 6.10.2. Synthesis of NO
  • 6.10.3. Physiological Functions and Attack Points of NO
  • 7. Ser/Thr-specific Protein Kinases and Protein Phosphatases
  • 7.1. Classification, Structure and Characteristics of Protein Kinases
  • 7.1.1. General Classification and Function of Protein Kinases
  • 7.1.2. Classification of Ser/Thr-specific Protein Kinases
  • 7.2. Structure and Regulation of Protein Kinases
  • 7.2.1. Main Structural Elements of Protein Kinases
  • 7.2.2. Substrate Binding and Recognition
  • 7.2.3. Control of Protein Kinase Activity
  • 7.3. Protein Kinase A
  • 7.3.1. Structure and Substrate Specificity of Protein Kinase A
  • 7.3.2. Regulation of Protein Kinase A
  • 7.4. Protein Kinase C
  • 7.4.1. Characterization and Classification
  • 7.4.2. Structure and Activation of Protein Kinase C
  • 7.4.3. Regulation of Protein Kinase C
  • 7.4.4. Functions and Substrates of Protein Kinase C
  • 7.5. Ca[superscript 2+]/Calmodulin-dependent Protein Kinases
  • 7.5.1. Importance and General Function
  • 7.5.2. Structure and Autoregulation of CaM Kinase II
  • 7.6. Ser/Thr-specific Protein Phosphatases
  • 7.6.1. Structure and Classification of Ser/Thr Protein Phosphatases
  • 7.6.2. Regulation of Ser/Thr Protein Phosphatases
  • 7.6.3. Protein Phosphatase I, PPI
  • 7.6.4. Protein Phosphatase 2A, PP2A
  • 7.6.5. Protein Phosphatase 2B, Calcineurin
  • 7.7. Regulation of Protein Phosphorylation by Subcellular Localization
  • 8. Signal Transmission via Transmembrane Receptors with Tyrosine-Specific Protein Kinase Activity
  • 8.1. Structure and Function of Receptor Tyrosine Kinases
  • 8.1.1. General Structure and Classification
  • 8.1.2. Ligand Binding and Activation
  • 8.1.3. Structure and Activation of the Tyrosine Kinase Domain
  • 8.1.4. Effector Proteins of the Receptor Tyrosine Kinases
  • 8.1.5. Attenuation and Termination of RTK Signaling
  • 8.2. Protein Modules as Coupling Elements of Signal Proteins
  • 8.2.1. SH2 Domains
  • 8.2.2. Phosphotyrosine-binding Domain (PTB Domain)
  • 8.2.3. SH3 Domains
  • 8.2.4. Membrane-targeting Domains: Pleckstrin Homology (PH) Domains and FYVE Domains
  • 8.2.5. Phosphoserine/Threonine-binding Domains
  • 8.2.6. PDZ Domains
  • 8.3. Nonreceptor Tyrosine-specific Protein Kinases
  • 8.3.1. Structure and General Function of Nonreceptor Tyrosine Kinases
  • 8.3.2. Src Tyrosine Kinase and Abl Tyrosine Kinase
  • 8.4. Protein Tyrosine Phosphatases
  • 8.4.1. Structure and Classification of Protein Tyrosine Phosphatases
  • 8.4.2. Cooperation of Protein Tyrosine Phosphatases and Protein Tyrosine Kinases
  • 8.4.3. Regulation of Protein Tyrosine Phosphatases
  • 8.5. Adaptor Molecules of Intracellular Signal Transduction
  • 9. Signal Transmission via Ras Proteins
  • 9.1. The Ras Superfamily of Monomeric GTPases
  • 9.2. General Importance of Ras Protein
  • 9.3. Structure and Biochemical Properties of Ras Protein
  • 9.3.1. Structure of the GTP- and GDP-bound Forms of Ras Protein
  • 9.3.2. GTP Hydrolysis: Mechanism and Stimulation by GAP Proteins
  • 9.3.3. Structure and Biochemical Properties of Transforming Mutants of Ras Protein
  • 9.4. Membrane Localization of Ras Protein
  • 9.5. GTPase-activating Protein (GAP) in Ras Signal Transduction
  • 9.6. Guanine Nucleotide Exchange Factors (GEFs) in Signal Transduction via Ras Proteins
  • 9.6.1. General Function of GEFs
  • 9.6.2. Structure and Activation of GEFs
  • 9.7. Raf Kinase as an Effector of Signal Transduction by Ras Proteins
  • 9.7.1. Structure of Raf Kinase
  • 9.7.2. Interaction of Raf Kinase with Ras Protein
  • 9.7.3. Mechanism of Activation and Regulation of Raf Kinase
  • 9.8. Reception and Transmission of Multiple Signals by Ras Protein
  • 10. Intracellular Signal Transduction: the Protein Cascades of the MAP Kinase Pathways
  • 10.1. Components of MAPK Pathways
  • 10.2. The Major MAPK Pathways of Mammals
  • 10.2.1. The ERK Pathway
  • 10.2.2. The JNK/SAPK, p38 and ERK5 MAPK Pathways
  • 11. Membrane Receptors with Associated Tyrosine Kinase Activity
  • 11.1. Cytokines and Cytokine Receptors
  • 11.2. Structure and Activation of Cytokine Receptors
  • 11.2.1. Activation of Cytoplasmic Tyrosine Kinases
  • 11.2.2. The Jak-Stat Pathway
  • 11.2.2.1. The Janus Kinases
  • 11.2.2.2. The Stat Proteins
  • 11.3. T and B Cell Antigen Receptors
  • 11.3.1. Receptor Structure
  • 11.3.2. Intracellular Signal Molecules of the T and B Cell Antigen Receptors
  • 11.4. Signal Transduction via Integrins
  • 12. Other Receptor Classes
  • 12.1. Receptors with Intrinsic Ser/Thr Kinase Activity: the TGF[beta] Receptor and the Smad Proteins
  • 12.1.1. TGF[beta] Receptor
  • 12.1.2. Smad Proteins
  • 12.2. Receptor Regulation by Intramembrane Proteolysis
  • 12.3. Signal Transduction via the Two-Component Pathway
  • 13. Regulation of the Cell Cycle
  • 13.1. Overview of the Cell Cycle
  • 13.1.1. Principles of Cell Cycle Control
  • 13.1.2. Intrinsic Control Mechanisms
  • 13.1.3. External Control Mechanisms
  • 13.1.4. Critical Cell Cycle Events and Cell Cycle Transitions
  • 13.2. Key Elements of the Cell Cycle Apparatus
  • 13.2.1. Cyclin-dependent Protein Kinases, CDKs
  • 13.2.2. Structure of CDKs and Regulation by Phosphorylation
  • 13.2.3. Cyclins
  • 13.2.4. Regulation of Cyclin Concentration
  • 13.2.5. Structural Basis for CDK Activation
  • 13.2.6. Inhibitors of CDKs: the CKIs
  • 13.2.7. Substrates of CDKs
  • 13.2.8. Multiple Regulation of CDKs
  • 13.3. Regulation of the Cell Cycle by Proteolysis
  • 13.3.1. Targeted Proteolysis by the SCF Complex
  • 13.3.2. Proteolysis during Mitosis: the Anaphase-promoting Complex/Cyclosome
  • 13.4. The G[subscript 1]/S Phase Transition
  • 13.4.1. Function of the D-type Cyclins
  • 13.4.2. Function of pRb in the Cell Cycle
  • 13.5. Cell Cycle Control of DNA Replication
  • 13.6. The G[subscript 2]/M Transition and Cdc25 Phosphatase
  • 13.7. Summary of Cell Cycle Progression
  • 13.8. The DNA Damage Checkpoints
  • 14. Malfunction of Signaling Pathways and Tumorigenesis: Oncogenes and Tumor Suppressor Genes
  • 14.1. General Aspects of Tumor Formation
  • 14.1.1. Characteristics of Tumor Cells
  • 14.1.2. Genetic Changes in Tumor Cells
  • 14.1.3. Epigenetic Changes in Tumor Cells
  • 14.1.4. Causes of Oncogenic Mutations
  • 14.1.5. DNA Repair, DNA Damage Checkpoints, and Tumor Formation
  • 14.1.6. Cell Division and Tumor Formation
  • 14.2. Cell Division Activity, Errors in Function of Signal Proteins, and Tumor Formation
  • 14.2.1. The Fate of a Cell: Quiescence, Division, or Death
  • 14.3. Definition and General Function of Oncogenes and Tumor Suppressor Genes
  • 14.3.1. Oncogenes and Proto-Oncogenes
  • 14.3.2. Mechanisms of Activation of Proto-Oncogenes
  • 14.3.3. Examples of the Functions of Oncogenes
  • 14.4. Tumor Suppressor Genes: General Functions
  • 14.5. DNA Repair, DNA Integrity and Tumor Suppression
  • 14.6. The Retinoblastoma Protein pRb in Cancer
  • 14.7. The p16[superscript INK4a] Gene Locus and ARF
  • 14.8. The Tumor Suppressor Protein p53
  • 14.8.1. Structure and Biochemical Properties of the p53 Protein
  • 14.8.2. Sequence-Specific DNA Binding of p53
  • 14.8.3. Genes Regulated by p53
  • 14.8.4. Activation, Regulation and Modulation of the Function of p53
  • 14.8.5. Overview of p53 Regulation
  • 14.8.6. The MDM2-p53 Network and Cancer
  • 14.9. The Tumor Suppressor APC and Wnt/[beta]-Catenin Signaling
  • 15. Apoptosis
  • 15.1. Basic Functions of Apoptosis
  • 15.2. Overview of Apoptosis
  • 15.3. Caspases: Death by Proteolysis
  • 15.4. The Family of Bcl-2 Proteins: Gatekeepers of Apoptosis
  • 15.5. The Mitochondrial Pathway of Apoptosis
  • 15.6. Death Receptor-triggered Apoptosis
  • 15.6.1. The Fas/CD95 Signaling Pathway
  • 15.6.2. Tumor Necrosis Factor-Receptor 1 and Apoptosis
  • 15.7. Links of Apoptosis and Cellular Signaling Pathways
  • 15.7.1. P13-Kinase/Akt Kinase and Apoptosis
  • 15.7.2. The Protein p53 and Apoptosis
  • Index
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