Molecular Biology: Principles of Genome Function
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- LÍF644M Sameindaerfðafræði
Lýsing:
The biological world operates on a multitude of scales - from molecules to cells to tissues to organisms to ecosystems. Throughout all these levels runs a common thread: the communication and onward passage of information - from cell to cell, from organism to organism and, ultimately, from generation to generation. But how does this information - no more than a static repository of data - come alive to govern the processes that constitute life? The answer lies in the concerted action of molecular components which cooperate through a series of carefully-regulated processes to bring the information in our genome to life.
These components and processes lie at the heart of one of the most fascinating subjects to engage the minds of scientists today: molecular biology. Molecular Biology: Principles of Genome Function offers a fresh, distinctive approach to the teaching of molecular biology. It is an approach that reflects the challenge of teaching a subject that is in many ways unrecognizable from the molecular biology of the 20th century - a discipline in which our understanding has advanced immeasurably, but about which many questions remain to be answered.
It is written with several guiding themes in mind: - A focus on key principles provides a robust conceptual framework on which students can build a solid understanding of the discipline; - An emphasis on the commonalities that exist between the three kingdoms of life, and the discussion of differences between the three kingdoms where such differences offer instructive insights into molecular processes and components, gives students an accurate depiction of our current understanding of the conserved nature of molecular biology, and the differences that underpin biological diversity; - An integrated approach demonstrates how certain molecular phenomena have diverse impacts on genome function by presenting them as themes that recur throughout the book, rather than as artificially separated topics At heart, molecular biology is an experimental science, and a central element to the understanding of molecular biology is an appreciation of the approaches taken to yield the information from which concepts and principles are deduced.
Yet there is also the challenge of introducing the experimental evidence in a way that students can readily comprehend. Molecular Biology responds to this challenge with Experimental Approach panels, which branch off from the text in a clearly-signposted way. These panels describe pieces of research that have been undertaken, and which have been particularly valuable in elucidating different aspects of molecular biology.
Each panel is carefully cross-referenced to the discussion of key molecular biology tools and techniques, which are presented in a dedicated chapter at the end of the book. Beyond this, Molecular Biology further enriches the learning experience with full-colour, custom-drawn artwork; end-of-chapter questions and summaries; relevant suggested further readings grouped by topic; and an extensive glossary of key terms.
Annað
- Höfundar: Nancy Craig, Rachel Green, Carol Greider, Gisela Storz, Cynthia Wolberger
- Útgáfa:3
- Útgáfudagur: 2021-02-25
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- Format:ePub
- ISBN 13: 9780192522795
- Print ISBN: 9780198788652
- ISBN 10: 0192522795
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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