Efnisyfirlit

• Cover
• Title page
• Copyright
• Dedication
• ABOUT THE AUTHORS OF MOLECULAR BIOLOGY
• PREFACE
• LEARNING FROM THIS BOOK
• ACKNOWLEDGMENTS
• CONTENTS IN OVERVIEW
• CONTENTS IN FULL
• ABBREVIATIONS
• 1 Genomes and the flow of biological information
  • INTRODUCTION
  • 1.1 THE ROOTS OF BIOLOGY
  • 1.2 THE GENOME: A WORKING BLUEPRINT FOR LIFE
  • 1.3 BRINGING GENES TO LIFE: GENE EXPRESSION
  • 1.4 REGULATING GENE EXPRESSION
  • 1.5 CELLULAR INFRASTRUCTURE AND GENE EXPRESSION
  • 1.6 EXPRESSION OF THE GENOME
  • 1.7 EVOLUTION OF THE GENOME AND THE TREE OF LIFE
• 2 Biological molecules
  • INTRODUCTION
  • 2.1 ATOMS, MOLECULES, AND CHEMICAL BONDS
  • 2.2 LIFE IN AQUEOUS SOLUTION
  • 2.3 NON-COVALENT INTERACTIONS
  • 2.4 NUCLEOTIDES AND NUCLEIC ACIDS
  • 2.5 THE STRUCTURE OF DNA
  • 2.6 CHEMICAL PROPERTIES OF RNA
  • 2.7 RNA FOLDING AND STRUCTURE
  • 2.8 THE RNA WORLD AND ITS ROLE IN THE EVOLUTION OF MODERN-DAY LIFE
  • 2.9 FUNDAMENTALS OF PROTEIN STRUCTURE
  • 2.10 PROTEIN FOLDING
  • 2.11 PROTEIN FOLDS
  • 2.12 PROTEIN–DNA INTERACTIONS
  • 2.13 SUGARS AND CARBOHYDRATES
  • 2.14 LIPIDS
  • 2.15 CHEMICAL MODIFICATION IN BIOLOGICAL REGULATION
• 3 The chemical basis of life
  • INTRODUCTION
  • 3.1 THERMODYNAMIC RULES IN BIOLOGICAL SYSTEMS
  • 3.2 BINDING EQUILIBRIA AND KINETICS
  • 3.3 BINDING PROCESSES IN BIOLOGY
  • 3.4 ENZYME CATALYSIS
  • 3.5 ENZYME KINETICS
• 4 Chromosome structure and function
  • INTRODUCTION
  • 4.1 ORGANIZATION OF CHROMOSOMES
  • 4.2 THE CELL CYCLE AND CHROMOSOME DYNAMICS
  • 4.3 PACKAGING CHROMOSOMAL DNA
  • 4.4 VARIATION IN CHROMATIN STRUCTURE
  • 4.5 COVALENT MODIFICATIONS OF HISTONES
  • 4.6 NUCLEOSOME REMODELING COMPLEXES
  • 4.7 DNA METHYLATION
  • 4.8 ELEMENTS REQUIRED FOR CHROMOSOME FUNCTION
  • 4.9 THE CENTROMERE
  • 4.10 THE TELOMERE
  • 4.11 THE SEPARATION OF CHROMATIN DOMAINS BY BOUNDARY ELEMENTS
  • 4.12 CHROMOSOME ARCHITECTURE IN THE NUCLEUS
• 5 The cell cycle
  • INTRODUCTION
  • 5.1 STEPS IN THE EUKARYOTIC CELL CYCLE
  • 5.2 CYCLINS AND CDKS
  • 5.3 REGULATION OF CDK ACTIVITY
  • 5.4 CELL CYCLE REGULATION BY CDKS
  • 5.5 REGULATION OF PROTEOLYSIS BY CDKS
  • 5.6 CHECKPOINTS: INTRINSIC PATHWAYS THAT CAN HALT THE CELL CYCLE
  • 5.7 EXTRINSIC REGULATORS OF CELL CYCLE PROGRESSION
  • 5.8 THE CELL CYCLE AND CANCER
  • 5.9 THE BACTERIAL CELL CYCLE
• 6 DNA replication
  • INTRODUCTION
  • 6.1 OVERVIEW OF DNA REPLICATION
  • 6.2 DNA POLYMERASE: ITS MECHANISM OF ACTION
  • 6.3 INITIATION: ORIGIN BINDING AND UNWINDING
  • 6.4 INITIATION: PRIMING AND STRAND ELONGATION
  • 6.5 ELONGATION: FIDELITY OF DNA POLYMERASES
  • 6.6 ELONGATION: COORDINATING LEADING AND LAGGING STRAND SYNTHESIS AT THE FORK
  • 6.7 TERMINATION OF DNA REPLICATION
  • 6.8 REGULATION OF THE INITIATION OF REPLICATION IN E. COLI
  • 6.9 REGULATION OF THE INITIATION OF REPLICATION IN EUKARYOTES
  • 6.10 THE END-REPLICATION PROBLEM AND TELOMERASE
  • 6.11 REPLICATING THROUGH CHROMATIN IN EUKARYOTES
• 7 Chromosome segregation
  • INTRODUCTION
  • 7.1 THE STAGES OF MITOSIS
  • 7.2 CHROMOSOME CONDENSATION AND COHESION
  • 7.3 THE MITOTIC SPINDLE
  • 7.4 PROMETAPHASE AND METAPHASE
  • 7.5 ANAPHASE: AN IRREVERSIBLE STEP IN CHROMOSOME SEGREGATION
  • 7.6 THE COMPLETION OF MITOSIS AND CYTOKINESIS
  • 7.7 MEIOSIS: GENERATING HAPLOID GAMETES FROM DIPLOID CELLS
  • 7.8 CHROMOSOME SEGREGATION IN BACTERIA
• 8 Transcription
  • INTRODUCTION
  • 8.1 OVERVIEW OF TRANSCRIPTION
  • 8.2 RNA POLYMERASE CORE ENZYME
  • 8.3 PROMOTER RECOGNITION IN BACTERIA AND EUKARYOTES
  • 8.4 INITIATION OF TRANSCRIPTION AND TRANSITION TO AN ELONGATING COMPLEX
  • 8.5 TRANSCRIPTION ELONGATION
  • 8.6 TRANSCRIPTION TERMINATION
• 9 Regulation of transcription
  • INTRODUCTION
  • 9.1 PRINCIPLES OF TRANSCRIPTION REGULATION
  • 9.2 DNA-BINDING DOMAINS IN PROTEINS THAT REGULATE TRANSCRIPTION
  • 9.3 MECHANISMS FOR REGULATING TRANSCRIPTION INITIATION IN BACTERIA
  • 9.4 COMPETITION BETWEEN CI AND CRO AND CONTROL OF THE FATE OF BACTERIOPHAGE LAMBDA
  • 9.5 REGULATION OF TRANSCRIPTION TERMINATION IN BACTERIA
  • 9.6 REGULATION OF TRANSCRIPTION INITIATION AND ELONGATION IN EUKARYOTES
  • 9.7 COMBINATORIAL REGULATION OF EUKARYOTIC TRANSCRIPTION
  • 9.8 THE ROLE OF SIGNALING CASCADES IN THE REGULATION OF TRANSCRIPTION
  • 9.9 GENE SILENCING
• 10 RNA processing
  • INTRODUCTION
  • 10.1 OVERVIEW OF RNA PROCESSING
  • 10.2 tRNA AND rRNA PROCESSING
  • 10.3 tRNA AND rRNA NUCLEOTIDE MODIFICATIONS
  • 10.4 mRNA CAPPING AND POLYADENYLATION
  • 10.5 RNA SPLICING
  • 10.6 EUKARYOTIC mRNA SPLICING BY THE SPLICEOSOME
  • 10.7 EXON DEFINITION AND ALTERNATIVE SPLICING
  • 10.8 RNA EDITING
  • 10.9 DEGRADATION OF NORMAL RNAs
  • 10.10 DEGRADATION OF FOREIGN AND DEFECTIVE RNAs
  • 10.11 RNA-BINDING DOMAINS IN PROTEINS
• 11 Translation
  • INTRODUCTION
  • 11.1 OVERVIEW OF TRANSLATION
  • 11.2 tRNA AND THE GENETIC CODE
  • 11.3 AMINOACYL-tRNA SYNTHETASES
  • 11.4 STRUCTURE OF THE RIBOSOME
  • 11.5 THE TRANSLATION CYCLE: THE RIBOSOME IN ACTION
  • 11.6 PROTEIN FACTORS CRITICAL TO THE TRANSLATION CYCLE
  • 11.7 TRANSLATION INITIATION: SHARED FEATURES IN BACTERIA AND EUKARYOTES
  • 11.8 BACTERIAL TRANSLATION INITIATION
  • 11.9 EUKARYOTIC TRANSLATION INITIATION
  • 11.10 TRANSLATION ELONGATION: DECODING, PEPTIDE BOND FORMATION, AND TRANSLOCATION
  • 11.11 TRANSLATION TERMINATION, RECYCLING, AND REINITIATION
  • 11.12 RIBOSOME RESCUE IN BACTERIA AND EUKARYOTES
  • 11.13 RECODING: PROGRAMMED STOP CODON READ-THROUGH AND FRAMESHIFTING
  • 11.14 ANTIBIOTICS THAT TARGET THE RIBOSOME
• 12 Regulation of translation
  • INTRODUCTION
  • 12.1 GLOBAL REGULATION OF TRANSLATION INITIATION IN BACTERIA AND EUKARYOTES
  • 12.2 REGULATION OF TRANSLATION INITIATION BY CIS-ACTING SEQUENCES IN THE 5' UNTRANSLATED REGION IN BACTERIA AND EUKARYOTES
  • 12.3 REGULATION OF TRANSLATION INITIATION THROUGH CIS-ACTING SEQUENCES IN THE 3' UTR IN EUKARYOTES
  • 12.4 REGULATION OF TRANSLATION ELONGATION IN BACTERIA AND EUKARYOTES
  • 12.5 VIRAL CORRUPTION OF THE TRANSLATIONAL MACHINERY
• 13 Regulatory RNAs
  • INTRODUCTION
  • 13.1 OVERVIEW OF REGULATORY RNAs
  • 13.2 BACTERIAL BASE-PAIRING sRNAs
  • 13.3 EUKARYOTIC sRNAS: miRNAS, siRNAs, AND piRNAs
  • 13.4 PROCESSING OF EUKARYOTIC sRNAs
  • 13.5 LOADING OF ARGONAUTE FAMILY PROTEINS WITH EUKARYOTIC sRNAs
  • 13.6 GENE SILENCING BY SMALL EUKARYOTIC RNAs
  • 13.7 VIRAL DEFENSE BY THE CRISPR SYSTEMS IN BACTERIA AND ARCHAEA
  • 13.8 RNA-MEDIATED REGULATION IN CIS
  • 13.9 PROTEIN-BINDING REGULATORY RNAs
  • 13.10 LONG INTERGENIC NON-CODING RNAs
• 14 Protein modification and targeting
  • INTRODUCTION
  • 14.1 CHAPERONE-ASSISTED PROTEIN FOLDING
  • 14.2 TARGETING OF PROTEINS THROUGHOUT THE CELL
  • 14.3 POST-TRANSLATIONAL CLEAVAGE OF THE POLYPEPTIDE CHAIN
  • 14.4 COVALENT REARRANGEMENTS YIELD A FLUORESCENT PROTEIN
  • 14.5 LIPID MODIFICATION OF PROTEINS
  • 14.6 GLYCOSYLATION OF PROTEINS
  • 14.7 PROTEIN PHOSPHORYLATION, ACETYLATION, AND METHYLATION
  • 14.8 PROTEIN MODIFICATION BY NUCLEOTIDES
  • 14.9 DIRECT CHEMICAL MODIFICATION OF PROTEINS
  • 14.10 UBIQUITINATION AND SUMOYLATION OF PROTEINS
  • 14.11 PROTEIN DEGRADATION
• 15 Cellular responses to DNA damage
  • INTRODUCTION
  • 15.1 TYPES OF DNA DAMAGE
  • 15.2 POST-REPLICATION MISMATCH REPAIR
  • 15.3 REPAIR OF DNA DAMAGE BY DIRECT REVERSAL
  • 15.4 REPAIR OF DNA DAMAGE BY BASE EXCISION REPAIR
  • 15.5 NUCLEOTIDE EXCISION REPAIR OF BULKY LESIONS
  • 15.6 TRANSLESION DNA SYNTHESIS
  • 15.7 THE DNA DAMAGE RESPONSE
  • 15.8 THE DNA DAMAGE RESPONSE IN BACTERIA
  • 15.9 THE DNA DAMAGE RESPONSE IN EUKARYOTES
  • 15.10 DNA DAMAGE AND CELL DEATH IN MAMMALIAN CELLS
• 16 Repair of DNA double-strand breaks and homologous recombination
  • INTRODUCTION
  • 16.1 AN OVERVIEW OF DNA DOUBLE-STRAND BREAK REPAIR AND HOMOLOGOUS RECOMBINATION
  • 16.2 DOUBLE-STRAND BREAK REPAIR BY NHEJ
  • 16.3 HOMOLOGY-DIRECTED REPAIR OF DOUBLE-STRAND BREAKS
  • 16.4 GENERATION OF SINGLE-STRANDED DNA BY HELICASES AND NUCLEASES
  • 16.5 THE MECHANISM OF DNA STRAND PAIRING AND EXCHANGE
  • 16.6 GENE CONVERSION THROUGH HOMOLOGY-DIRECTED REPAIR
  • 16.7 HOMOLOGOUS RECOMBINATION
  • 16.8 REPAIR OF DAMAGED REPLICATION FORKS BY HOMOLOGY-DIRECTED REPAIR
  • 16.9 CHROMOSOME REARRANGEMENTS DURING ABERRANT RECOMBINATION AND REPAIR
• 17 Mobile DNA
  • INTRODUCTION
  • 17.1 TRANSPOSABLE ELEMENTS: OVERVIEW
  • 17.2 AN OVERVIEW OF DNA-ONLY TRANSPOSONS
  • 17.3 THE MECHANISM OF DNA-ONLY CUT-AND-PASTE TRANSPOSITION
  • 17.4 DNA CUT-AND-PASTE TRANSPOSITION IN ADAPTIVE IMMUNITY
  • 17.5 RETROTRANSPOSONS
  • 17.6 LTR RETROTRANSPOSONS
  • 17.7 NON-LTR RETROTRANSPOSONS: LINEs, SINEs, AND GROUP II MOBILE INTRONS
  • 17.8 TRANSPOSABLE ELEMENTS IN THE HUMAN GENOME
  • 17.9 CONTROL OF TRANSPOSITION
  • 17.10 CSSR: OVERVIEW
  • 17.11 CSSR SYSTEMS THAT CONTROL GENE EXPRESSION
  • 17.12 CSSR CONVERSION OF DNA DIMERS TO MONOMERS
  • 17.13 BACTERIOPHAGE LAMBDA INTEGRATION AND EXCISION
• 18 Genomics and genetic variation
  • INTRODUCTION
  • 18.1 GENOME SEQUENCES AND SEQUENCING PROJECTS
  • 18.2 FINDING FUNCTIONS IN A GENOME
  • 18.3 FUNCTIONAL GENOMICS
  • 18.4 HIGH-THROUGHPUT GENOME-WIDE -OMICS PROJECTS
  • 18.5 THE EVOLVING GENOME: EVOLUTIONARY FORCES
  • 18.6 THE EVOLVING GENOME: MECHANISMS OF VARIATION
  • 18.7 GENE DUPLICATION AND DIVERGENCE OF GENE FUNCTION
  • 18.8 REORGANIZATION OF CHROMOSOMES
  • 18.9 EPIGENETICS AND IMPRINTING
  • 18.10 HUMAN GENOME VARIATION
  • 18.11 HUMAN GENETIC DISEASES: FINDING DISEASE LOCI
  • 18.12 HUMAN GENETICS: IMPACTS AND IMPLICATIONS
• 19 Tools and techniques in molecular biology
  • INTRODUCTION
  • 19.1 MODEL ORGANISMS
  • 19.2 CULTURED CELLS AND VIRUSES
  • 19.3 AMPLIFICATION OF DNA AND RNA SEQUENCES
  • 19.4 DNA CLONING
  • 19.5 UNDIRECTED GENOME MANIPULATION
  • 19.6 DIRECTED GENOME MANIPULATION
  • 19.7 DETECTION OF BIOLOGICAL MOLECULES
  • 19.8 SEPARATION AND ISOLATION OF BIOLOGICAL MOLECULES
  • 19.9 IDENTIFYING THE COMPOSITION OF BIOLOGICAL MOLECULES
  • 19.10 OBTAINING AND ANALYZING SEQUENCES ON A GENOMIC SCALE
  • 19.11 DETECTION OF SPECIFIC DNA SEQUENCES
  • 19.12 DETECTION OF SPECIFIC RNA MOLECULES
  • 19.13 DETECTION OF SPECIFIC PROTEINS
  • 19.14 DETECTION OF INTERACTIONS BETWEEN MOLECULES
  • 19.15 GENOME-WIDE DETECTION OF INTERACTIONS BETWEEN MOLECULES
  • 19.16 IMAGING CELLS AND MOLECULES
  • 19.17 MOLECULAR STRUCTURE DETERMINATION
• GLOSSARY
• INDEX

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