The Cell

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.

Special Features

• Concise yet comprehensive - a broad range of material is presented in a unique four-part structure with sufficient depth to thoughtfully engage students without overwhelming them with details.
• Focuses on the molecular biology of cells as a unifying theme with topics such as developmental biology, the nervous system, the immune system, and plant biology being discussed as examples of more general principles.
• Extensive pedagogy supports students in identifying key points, comprehending illustrations, and learning cell biology in a broader context.
• Strong visual program clarifies content and allows students to visualize key concepts.

• New in-text learning objectives provide the framework for each chapter, encouraging students to focus their attention on key material and concepts.
• New Active Learning Guide, available on the companion site, is a chapter-by-chapter guide to help instructors create a dynamic learning environment with in-class exercises, clicker questions, and links to relevant media, animations, testing, and self-quizzing, all aligned with the new in-text learning objectives.
• New chapter on transcriptional regulation and epigenetics. (Ch. 9)
• Data Analysis Problems challenge students to read and interpret experimental results to foster their analytical skills.
• Molecular Medicine and Key Experiment boxes highlight the experimental nature of molecular and cellular biology and convey the excitement and medical relevance of research in this area, including topics such as splicing therapy for muscular dystrophy, the discovery of telomerase, the role of histone modifications, and mitochondrial replacement therapy.