Geoffrey M. Cooper
Each chapter contains:
· Data Analysis Problems
· Suggested Readings
· Animations and Videos
Preface
Part One: Fundamentals and Foundations
1. Introduction to Cells and Cell Research
1.1. The Origin and Evolution of Cells
- How did the first cell
arise?
- The evolution of metabolism
- Prokaryotes
- Prokaryotes
- The origin of eukaryotes
- The development of multicellular organisms
1.2. Experimental Models in Cell Biology
- E. coli
- Yeasts
- Caenorhabditis elegans and Drosophila melanogaster
-
Arabidopsis thaliana
- Vertebrates
- Animal cell culture
- Viruses
Key Experiment: HeLa Cells: The First Human Cell Line
Key Experiment: HeLa Cells: The First Human Cell Line
1.3. Tools of Cell Biology: Microscopy and Subcellular Fractionation
- Light microscopy
-
Fluorescence microscopy and GFP
- Following protein movements and interactions
- Sharpening the focus and seeing cells in three dimensions
- Super-resolution microscopy: breaking the diffraction barrier
- Electron microscopy
- Subcellular fractionation
2. Molecules and
Membranes
2.1. The Molecules of Cells
- Chemical bonds
- Carbohydrates
- Lipids
- Nucleic acids
- Proteins
Key Experiment: The Folding of Polypeptide Chains
2.2. Enzymes as Biological Catalysts
- The catalytic activity of enzymes
- Mechanisms of enzymatic
catalysis
- Coenzymes
- Regulation of enzyme activity
2.3. Cell Membranes
- Membrane lipids
- Membrane proteins
Key Experiment: The Structure of Cell Membranes
- Transport across cell membranes
3. Bioenergetics and Metabolism
3.1. Metabolic Energy and
ATP
- The laws of thermodynamics
- The role of ATP
3.2. Glycolysis and Oxidative Phosphorylation
- Glycolysis
- The citric acid cycle
- The citric acid cycle
- Electron transport and oxidative phosphorylation
- Chemiosmotic coupling
Key Experiment: The
Chemiosmotic Theory
3.3. Photosynthesis
- Electron transport
- ATP synthesis
- Synthesis of glucose
3.4. The Biosynthesis of Cell Constituents Carbohydrates
- Lipids
- Proteins
Key Experiment: Antimetabolites, Cancer, and AIDS
- Nucleic acids
4.
Fundamentals of Molecular Biology
4.1. Heredity, Genes, and DNA
- Genes and chromosomes
- Identification of DNA as the genetic material
- The structure of DNA
- Replication of DNA
4.2. Expression of Genetic Information
- The role of messenger RNA
- The genetic
code
- The genetic code
Key Experiment: The DNA Provirus Hypothesis
4.3. Recombinant DNA
- Restriction endonucleases
- Generation of recombinant DNA molecules
- DNA sequencing
- DNA sequencing - Expression of cloned genes
4.4. Detection of Nucleic Acids and
Proteins
- Amplification of DNA by the polymerase chain reaction
- Nucleic acid hybridization
- Antibodies as probes for proteins
4.5. Gene Function in Eukaryotes
- Gene transfer in plants and animals
- Mutagenesis of cloned DNAs
- Introducing mutations into cellular
genes
- Genome engineering by the CRISPR/Cas system
- Genome engineering by the CRISPR/Cas system
Key Experiment: RNA Interference
5. Genomics, Proteomics, and Systems Biology
5.1. Genomes and Transcriptomes
- The genomes of bacteria and yeast
- The genomes of
Caenorhabditis elegans, Drosophila melanogaster, and Arabidopsis thaliana
- The human genome
- The genomes of other vertebrates
Key Experiment: The Human Genome
- Next-generation sequencing and personal genomes
- Global analysis of gene expression
5.2. Proteomics
-
Identification of cell proteins
- Global analysis of protein localization
- Protein interactions
5.3. Systems Biology
- Systematic screens of gene function
- Regulation of gene expression
- Networks
- Synthetic biology
Molecular Medicine: Malaria and Synthetic
-
Biology
Part Two: The Flow of Genetic Information
6. Genes and Genomes
6.1. The Structure of Eukaryotic Genes
- Introns and exons
Key Experiment: The Discovery of Introns
- Roles of introns
6.2 Noncoding Sequences
- Noncoding RNAs
- Key
Experiment The ENCODE Project
- Repetitive sequences
- Gene duplication and pseudogenes
6.3. Chromosomes and Chromatin
- Chromatin
- Centromeres
- Telomeres
7. Replication, Maintenance, and Rearrangements of Genomic DNA
7.1. DNA Replication
- DNA
polymerases
- The replication fork
- The fidelity of replication
- Origins and the initiation of replication
- Telomeres and telomerase: Maintaining the ends of chromosomes
Key Experiment: Telomerase Is a Reverse
- Transcriptase
7.2. DNA Repair
- Direct reversal of
DNA damage
- Excision repair
Molecular Medicine: Colon Cancer and DNA Repair
- Translesion DNA synthesis
- Repair of double-strand breaks
7.3. DNA Rearrangements and Gene
- Amplification
- Antibody genes
- Gene amplification
8. RNA Synthesis and
Processing
8.1. Transcription in Bacteria
- RNA polymerase
- Bacterial promoters
- Elongation and termination
8.2. Eukaryotic RNA Polymerases and General Transcription Factors
- Eukaryotic RNA polymerases
- General transcription factors and initiation of transcription
by RNA polymerase II
- Transcription by RNA polymerases I and III
8.3. RNA Processing and Turnover
- Processing of ribosomal and transfer RNAs
- Processing of mRNA in eukaryotes
- Processing of mRNA in eukaryotes
Key Experiment: The Discovery of snRNPs
- Alternative
splicing
Molecular Medicine: Splicing Therapy for Duchenne
- Muscular Dystrophy
- RNA editing
- RNA degradation
9. Transcriptional Regulation and Epigenetics (NEW!)
9.1. Gene Regulation in E. coli
- The lac repressor
- Positive control of transcription
9.2.
Transcription Factors in Eukaryotes
- cis-acting regulatory sequences: promoters and enhancers
- Transcription factor binding sites
- Transcriptional regulatory proteins
Key Experiment: Isolation of a Eukaryotic
- Transcription Factor
- Regulation of elongation
9.3.
Chromatin and Epigenetics
- Histone modifications
Key Experiment: The Role of Histone
- Modification
- Chromatin remodeling factors
- Histones and epigenetic inheritance
- DNA methylation
- Noncoding RNAs
10. Protein Synthesis, Processing, and
Regulation
10.1. Translation of mRNA
- Transfer RNAs
- The ribosome
- The organization of mRNAs and the initiation of translation
- The process of translation
- Regulation of translation
10.2. Protein Folding and Processing
- Chaperones and protein folding
-
Protein misfolding diseases
Molecular Medicine: Alzheimer's Disease
- Enzymes that catalyze protein folding
- Protein cleavage
- Attachment of carbohydrates and lipids
10.3. Regulation of Protein Function and Stability
- Regulation by small molecules
- Protein
phosphorylation and other modifications
Key Experiment: The Discovery of Tyrosine
- Kinases
- Protein-protein interactions
- Protein degradation
Part Three: Cell Structure and Function
11. The Nucleus
11.1. The Nuclear Envelope and Traffic between the
Nucleus and the Cytoplasm
- Structure of the nuclear envelope
- The nuclear pore complex
Molecular Medicine: Nuclear Lamina Diseases
- Selective transport of proteins to and from the nucleus
Key Experiment: Identification of Nuclear
- Localization Signals
- Localization
Signals - Transport of RNAs
- Regulation of nuclear protein import
11.2. The Organization of Chromatin
- Chromosome territories
- Chromatin localization and transcriptional activity
- Replication and transcription factories
11.3. Nuclear Bodies
- The nucleolus and
rRNA
- Polycomb bodies: Centers of transcriptional repression
- Cajal bodies and speckles: Processing and storage of snRNPs
12. Protein Sorting and Transport
12.1. The Endoplasmic Reticulum
- The endoplasmic reticulum and protein secretion
- Targeting proteins to the
endoplasmic reticulum
Key Experiment: The Signal Hypothesis
- Insertion of proteins into the ER membrane
- Insertion of proteins into the ER membrane
- Quality control in the ER
- The smooth ER and lipid synthesis
- Export of proteins and lipids from the ER
12.2. The
Golgi Apparatus
- Organization of the Golgi
- Protein glycosylation within the Golgi
- Lipid and polysaccharide metabolism in the Golgi
- Protein sorting and export from the Golgi apparatus
12.3. The Mechanism of Vesicular Transport
- Cargo selection, coat proteins, and
vesicle budding
- Vesicle fusion
12.4. Lysosomes
- Lysosomal acid hydrolases
Molecular Medicine: Gaucher Disease
- Endocytosis and lysosome formation
- Autophagy
13. Mitochondria, Chloroplasts, and Peroxisomes
13.1. Mitochondria
- Organization and function
of mitochondria
- The genetic system of mitochondria
- Protein import and mitochondrial assembly
Molecular Medicine: Mitochondrial Replacement Therapy
- Mitochondrial lipids
- Transport of metabolites across the inner membrane
13.2. Chloroplasts and Other Plastids
- The
structure and function of chloroplasts
- The chloroplast genome
- Import and sorting of chloroplast proteins
- Other plastids
13.3. Peroxisomes
- Functions of peroxisomes
- Peroxisome assembly
Molecular Medicine: Peroxisome Biogenesis Disorders
14. The Cytoskeleton
and Cell Movement
14.1. Structure and Organization of Actin Filaments
- Assembly and organization of actin filaments
- Association of actin filaments with the plasma membrane
- Microvilli
- Cell surface protrusions and cell movement
14.2. Myosin Motors
- Muscle
contraction
- Contractile assemblies of actin and myosin in nonmuscle cells
- Unconventional myosins
14.3. Microtubules
- Structure and dynamic organization of microtubules
- Assembly of microtubules
- MAPs and the organization of microtubules
14.4. Microtubule Motors and
Movement
Key Experiment: The Isolation of Kinesin
- Microtubule motor proteins
- Cargo transport and intracellular organization
- Cilia and flagella
- Microtubules during mitosis
14.5. Intermediate Filaments
- Intermediate filament proteins
- Assembly of intermediate
filaments
- Intracellular organization of intermediate filaments
Key Experiment: Function of Intermediate Filaments
15. The Plasma Membrane
15.1. Structure of the Plasma Membrane
- The lipid bilayer
- Plasma membrane proteins
- Plasma membrane domains
15.2.
Transport of Small Molecules
- Facilitated diffusion and carrier proteins
- Facilitated diffusion and carrier proteins
- Active transport driven by ATP hydrolysis
- Active transport driven by ion gradients
Molecular Medicine: Cystic Fibrosis
15.3.
Endocytosis
Phagocytosis
- Clathrin-mediated endocytosis
Key Experiment: The LDL Receptor
- Transport to lysosomes and receptor recycling
16. Cell Walls, the Extracellular Matrix, and Cell Interactions
16.1. Cell Walls
- Bacterial cell walls
- Eukaryotic cell
walls
16.2. The Extracellular Matrix and Cell-Matrix
- Interactions
- Matrix structural proteins
- Matrix polysaccharides
- Adhesion proteins
- Cell-matrix interactions
Key Experiment: The Characterization of Integrin
16.3. Cell-Cell Interactions
- Adhesion
junctions
- Tight junctions
- Gap junctions
- Plasmodesmata
Molecular Medicine: Gap Junction Diseases
Part Four: Cell Regulation
17. Cell Signaling
17.1. Signaling Molecules and Their Receptors
- Modes of cell-cell signaling
- Steroid hormones and
the nuclear receptor superfamily
- Signaling by other small molecules
- Peptide hormones and growth factors
17.2. G Proteins and Cyclic AMP
17.2
Key Experiment: G Protein-Coupled Receptors and Odor Detection
- The cAMP pathway: Second messengers and protein
phosphorylation
17.3. Tyrosine Kinases and Signaling by the MAP Kinase and PI 3-Kinase Pathways
- Receptor tyrosine kinases
- Nonreceptor tyrosine kinases
- MAP kinase pathways
Molecular Medicine: Cancer: Signal Transduction and the ras Oncogenes
- The PI 3-kinase/Akt and
mTOR pathways
17.4. Receptors Coupled to Transcription Factors
- The TGF-B/Smad pathway
- NF-kB signaling
- The Wnt and Notch pathways
17.5. Signaling Dynamics and Networks
- Feedback loops and signaling dynamics
- Networks and crosstalk
18. The Cell
Cycle
18.1. The Eukaryotic Cell Cycle
- Phases of the cell cycle
- Regulation of the cell cycle by cell growth and extracellular signals
- Cell cycle checkpoints
18.2. Regulators of Cell Cycle Progression
- Protein kinases and cell cycle regulation
Key Experiment: The
Discovery of MPF
Key Experiment: The Identification of Cyclin
- Families of cyclins and cyclin-dependent kinases
- Growth factors and the regulation of G1 Cdk's
- S phase and regulation of DNA replication
- DNA damage checkpoints
18.3. The Events of M Phase
- Stages of
mitosis
- Entry into mitosis
- The spindle assembly checkpoint and progression to anaphase
- Cytokinesis
19. Cell Renewal and Cell Death
19.1. Stem Cells and the Maintenance of Adult Tissues
- Proliferation of differentiated cells
- Stem cells
- Medical
applications of adult stem cells
19.2. Pluripotent Stem Cells, Cellular Reprogramming, and Regenerative Medicine
- Embryonic stem cells
Key Experiment: Culture of Embryonic
- Stem Cells
- Somatic cell nuclear transfer
- Induced pluripotent stem cells
-
Transdifferentiation of somatic cells
19.3. Programmed Cell Death
- The events of apoptosis
Key Experiment: Identification of Genes Required for Programmed Cell Death
- Caspases: The executioners of apoptosis
- Central regulators of apoptosis: The Bcl-2 family
- Signaling
pathways that regulate apoptosis
- Alternative pathways of programmed cell death
20. Cancer
20.1. The Development and Causes of Cancer
- Types of cancer
- The development of cancer
- Properties of cancer cells
- Causes of cancer
20.2. Oncogenes
- Retroviral
oncogenes
- Proto-oncogenes
Key Experiment: The Discovery of Proto-Oncogenes
- Oncogenes in human cancer
- Functions of oncogene products
20.3. Tumor Suppressor Genes
- Identification of tumor suppressor genes
- Functions of tumor suppressor gene products
- Cancer
genomics
20.4. Molecular Approaches to Cancer Treatment
- Prevention and early detection
- Oncogene-targeted drugs
Molecular Medicine: Imatinib: Cancer Treatment
- Targeted against the bcr/abl Oncogene
- Immunotherapy
Answers to Questions
Glossary
Illustration
Credits
Index
Instructor Resources: Ancillary Resource Center (ARC) www.oup-arc.com
Instructor's Manual
- Active Learning Guide with in-class exercises, clicker questions, and links to relevant media, animations, testing, and self-quizzing NEW
- Data
Analysis Problems with over 70 real-world analysis exercises
- Chapter outlines, reviews, and key terms
PowerPoint Slides
- All figures and photographs from the text
Test Bank
- Over 1300 multiple choice, fill-in-the-blank, true-or-false, and short answer questions
-
Includes all chapter quiz questions from the text
Computerized Test Bank
- The entire test file provided in Blackboard's Diploma software
Student Resources:
Companion Website www.oup.com/us/cooper8e
Videos
- A collection of
online videos - referenced throughout the text - helps students visualize complex cellular and molecular structures and processes
Animations
- Narrated animations help students grasp key concepts and processes
Micrographs
- Interactive illustrating cellular structures
Additional Resources:
Dashboard for The Cell, 8/e register-ca.dashboard.oup.com
- An interactive site offering a full e-book, built in colour-coded gradebook that allows instructors to track student progress, and a wealth of study
resources and auto-graded quizzes beyond what is provided in the text and on the companion site.
- Can be purchased separately or in a package
- Full interactive e-book
- All Student Resources (see full list above)
- Chapter Quizzes: Two assignable quizzes available for each
chapter
-- Multiple choice quizzes test student comprehension of material covered in each chapter
-- Essay questions challenge students to synthesize and apply what they have learned
E-Book ISBN 9781605357713
Geoffrey M. Cooper is Professor of Biology at Boston University.
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