The Cell

by Cooper, Geoffrey M.; Hausman, Robert E.

• ISBN13: 9780878932146
• ISBN10: 0878932143
• Format: Hardcover
• Copyright: 2003-07-01
• Publisher: Sinauer Associates Inc

Summary

(ASM Press) Boston Univ., MA. Textbook for one-semester undergraduate course on cell and molecular biology. Covers evolution of cells and the fundamentals of molecular biology, genome organization and sequences, cell structure and function, and cell regulation. Abundant color illustrations. Previous edition: c2000. DNLM: Cytology.

Table of Contents

Preface	xv
Organization and Features of The Cell	xvii
Supplements to Accompany The Cell	xix
PART I Introduction
1 An Overview of Cells and Cell Research	3	(38)
THE ORIGIN AND EVOLUTION OF CELLS	4	(11)
The First Cell	4	(3)
The Evolution of Metabolism	7	(1)
Present-Day Prokaryotes	8	(1)
Eukaryotic Cells	9	(3)
The Development of Multicellular Organisms	12	(3)
CELLS AS EXPERIMENTAL MODELS	15	(5)
E. coli	15	(1)
Yeasts	16	(1)
Dictyostelium discoideum	17	(1)
Caenorhabditis elegans	17	(1)
Drosophile melanogaster	18	(1)
Arabidopsis thaliana	18	(1)
Vertebrates	19	(1)
TOOLS OF CELL BIOLOGY	20	(12)
Light Microscopy	21	(4)
Electron Microscopy	25	(3)
Subcellular Fractionation	28	(1)
Growth of Animal Cells in Culture	29	(5)
Culture of Plant Cells	34	(1)
Viruses	34
KEY EXPERIMENT Animal Cell Culture	32	(3)
MOLECULAR MEDICINE Viruses and Cancer	35	(2)
SUMMARY AND KEYTERMS	37	(1)
QUESTIONS	38	(1)
REFERENCES AND FURTHER READING	39	(2)
2 The Chemistry of Cells	41	(48)
THE MOLECULAR COMPOSITION OF CELLS	41	(15)
Carbohydrates	42	(2)
Lipids	44	(3)
Nucleic Acids	47	(3)
Proteins	50	(6)
THE CENTRAL ROLE OF ENZYMES AS BIOLOGICAL CATALYSTS	56	(7)
The Catalytic Activity of Enzymes	56	(1)
Mechanisms of Enzymatic Catalysis	57	(2)
Coenzymes	59	(2)
Regulation of Enzyme Activity	61	(2)
METABOLIC ENERGY	63	(11)
Free Energy and ATP	64	(2)
The Generation of ATP from Glucose	66	(5)
The Derivation of Energy from Other Organic Molecules	71	(1)
Photosynthesis	72	(2)
THE BIOSYNTHESIS OF CELL CONSTITUENTS	74	(6)
Carbohydrates	74	(1)
Lipids	75	(1)
Proteins	76	(3)
Nucleic Acids	79	(1)
CELL MEMBRANES	80
Membrane Lipids	80	(1)
Membrane Proteins	81	(2)
Transport across Cell Membranes	83
KEY EXPERIMENT The Folding of Polypeptide Chains	52	(27)
MOLECULAR MEDICINE Phenylketonuria	79	(6)
SUMMARY AND KEYTERMS	85	(2)
QUESTIONS	87	(1)
REFERENCES AND FURTHER READING	87	(2)
3 Fundamentals of Molecular Biology	89	(50)
HEREDITY, GENES, AND DNA	89	(7)
Genes and Chromosomes	90	(1)
Genes and Enzymes	91	(2)
Identification of DNA as the Genetic Material	93	(1)
The Structure of DNA	94	(1)
Replication of DNA	95	(1)
EXPRESSION OF GENETIC INFORMATION	96	(8)
Colinearity of Genes and Proteins	97	(1)
The Role of Messenger RNA	98	(1)
The Genetic Code	99	(1)
RNA Viruses and Reverse Transcription	100	(4)
RECOMBINANT DNA	104	(13)
Restriction Endonucleases	104	(3)
Generation of Recombinant DNA Molecules	107	(1)
Vectors for Recombinant DNA	108	(3)
DNA Sequencing	111	(2)
Expression of Cloned Genes	113	(2)
Amplification of DNA by the Polymerase Chain Reaction	115	(2)
DETECTION OF NUCLEIC ACIDS AND PROTEINS	117	(6)
Nucleic Acid Hybridization	117	(2)
Detection of Small Amounts of DNA or RNA by PCR	119	(2)
Antibodies as Probes for Proteins 119 Probes for Screening Recombinant DNA Libraries	121	(2)
GENE FUNCTION IN EUKARYOTES	123
Genetic Analysis in Yeasts	123	(2)
Gene Transfer in Plants and Animals	125	(3)
Mutagenesis of Cloned DNAs	128	(1)
Introducing Mutations into Cellular Genes	128
KEY EXPERIMENT The DNA Provirus Hypothesis	102	(3)
MOLECULAR MEDICINE HIV and AIDS	105	(27)
SUMMARY AND KEY TERMS	132	(2)
QUESTIONS	134	(1)
REFERENCES AND FURTHER READING	135	(4)
PART II The Flow of Genetic Information
4 The Organization and Sequences of Cellular Genomes	139	(40)
THE COMPLEXITY OF EUKARYOTIC GENOMES	139	(2)
Introns and Exons	141	(4)
Repetitive DNA Sequences	145	(3)
Gene Duplication and Pseudogenes	148	(1)
The Composition of Higher Eukaryotic Genomes	149	(1)
CHROMOSOMES AND CHROMATIN	150	(8)
Chromatin	150	(4)
Centromeres	154	(3)
Telomeres	157	(1)
THE SEQUENCES OF COMPLETE GENOMES	158
Prokaryotic Genomes	159	(2)
The Yeast Genome	161	(2)
The Genomes of Caenorhabditis elegans and Drosophile melanogaster	163	(2)
Plant Genomes	165	(2)
The Human Genome	167
KEY EXPERIMENT The Discovery of introns	142	(28)
KEY EXPERIMENT The Human Genome	170	(3)
SUMMARY AND KEYTERMS	173	(2)
QUESTIONS	175	(1)
REFERENCES AND FURTHER READING	175	(4)
5 Replication, Maintenance, and Rearrangements of Genomic DNA	179	(52)
DNA REPLICATION	179	(13)
DNA Polymerases	180	(2)
The Replication Fork	182	(6)
The Fidelity of Replication	188	(1)
Origins and the Initiation of Replication	189	(2)
Telomeres and Telomerase: Replicating the Ends of Chromosomes	191	(1)
DNA REPAIR	192	(12)
Direct Reversal of DNA Damage	194	(3)
Excision Repair	197	(4)
Error-Prone Repair	201	(1)
Recombinational Repair	202	(2)
RECOMBINATION BETWEEN HOMOLOGOUS DNA SEQUENCES	204	(7)
DNA Molecules Recombine by Breaking and Rejoining	205	(2)
Models of Homologous Recombination	207	(2)
Enzymes Involved in Homologous Recombination	209	(2)
DNA REARRANGEMENTS	211	(7)
Site-Specific Recombination	211	(5)
Transposition via DNA Intermediates	216	(4)
Transposition via RNA Intermediates	220	(5)
Gene Amplification	225
KEY EXPERIMENT Rearrangement of Immunoglobulin Genes	218
MOLECULAR MEDICINE Colon Cancer and DNA Repair	203	(24)
SUMMARY AND KEYTERMS	227	(1)
QUESTIONS	228	(1)
REFERENCES AND FURTHER READING	229	(2)
6 RNA Synthesis and Processing	231	(50)
TRANSCRIPTION IN PROKARYOTES	231	(8)
RNA Polymerase and Transcription	232	(4)
Repressors and Negative Control of Transcription	236	(2)
Positive Control of Transcription	238	(1)
EUKARYOTIC RNA POLYMERASES AND GENERAL TRANSCRIPTION FACTORS	239	(5)
Eukaryotic RNA Polymerases	239	(1)
General Transcription Factors and Initiation of Transcription by RNA Polymerase II	240	(3)
Transcription by RNA Polymerases I and III	243	(1)
REGULATION OF TRANSCRIPTION IN EUKARYOTES	244	(17)
cis-Acting Regulatory Sequences: Promoters and Enhancers	245	(4)
Transcriptional Regulatory Proteins	249	(3)
Structure and Function of Transcriptional Activators	252	(2)
Eukaryotic Repressors	254	(2)
Relationship of Chromatin Structure to Transcription	256	(3)
Regulation of Transcription by Noncoding RNAs	259	(1)
DNA Methylation	260	(1)
RNA PROCESSING AND TURNOVER	261
Processing of Ribosomal and Transfer RNAs	262	(2)
Processing of mRNA in Eukaryotes	264	(2)
Splicing Mechanisms	266	(6)
Alternative Splicing	272	(1)
RNA Editing	273	(1)
RNA Degradation	274
KEY EXPERIMENT Isolation of a Eukaryotic Transcription Factor	251	(17)
KEY EXPERIMENT The Discovery of snRNPs	268	(8)
SUMMARY AND KEYTERMS	276	(2)
QUESTIONS	278	(1)
REFERENCES AND FURTHER READING	279	(2)
7 Protein Synthesis, Processing, and Regulation	281	(42)
TRANSLATION OF mRNA	281	(17)
Transfer RNAs	282	(1)
The Ribosome	283	(6)
The Organization of mRNAs and the Initiation of Translation	289	(1)
The Process of Translation	290	(6)
Regulation of Translation	296	(2)
PROTEIN FOLDING AND PROCESSING	298	(11)
Chaperones and Protein Folding	298	(5)
Enzymes and Protein Folding	303	(1)
Protein Cleavage	303	(2)
Glycosylation	305	(2)
Attachment of Lipids	307	(2)
REGULATION OF PROTEIN FUNCTION	309
Regulation by Small Molecules	310	(1)
Protein Phosphorylation	311	(2)
Protein-Protein Interactions	313	(1)
PROTEIN DEGRADATION	313	(1)
The Ubiquitin-Proteasome Pathway	313	(2)
Lysosomal Proteolysis	315
KEY EXPERIMENT Catalytic Role of Ribosomal RNA	288	(4)
MOLECULAR MEDICINE Antibiotics and Protein Synthesis	292	(24)
SUMMARY AND KEYTERMS	316	(2)
QUESTIONS	318	(1)
REFERENCES AND FURTHER READING	318	(5)
PART III Cell Structure and Function
8 The Nucleus	323	(32)
THE NUCLEAR ENVELOPE AND TRAFFIC BETWEEN THE NUCLEUS AND CYTOPLASM	323	(12)
Structure of the Nuclear Envelope	324	(2)
The Nuclear Pore Complex	326	(2)
Selective Transport of Proteins to and from the Nucleus	328	(4)
Regulation of Nuclear Protein Import	332	(2)
Transport of RNAs	334	(1)
INTERNAL ORGANIZATION OF THE NUCLEUS	335	(4)
Chromosomes and Higher-Order Chromatin Structure	335	(2)
Functional Domains within the Nucleus	337	(2)
THE NUCLEOLUS	339	(6)
Ribosomal RNA Genes and the Organization of the Nucleolus	339	(3)
Transcription and Processing of rRNA	342	(2)
Ribosome Assembly	344	(1)
THE NUCLEUS DURING MITOSIS	345
Dissolution of the Nuclear Envelope	345	(3)
Chromosome Condensation	348	(1)
Re-formation of the Interphase Nucleus	349
KEY EXPERIMENT Identification of Nuclear Localization Signals	330	(10)
MOLECULAR MEDICINE Nuclear Lamina Diseases	340	(11)
SUMMARY AND KEYTERMS	351	(1)
QUESTIONS	352	(1)
REFERENCES AND FURTHER READING	353	(2)
9 Protein Sorting and Transport: The Endoplasmic Reticulum, Golgi Apparatus, and Lysosomes	355	(44)
THE ENDOPLASMIC RETICULUM	355	(19)
The Endoplasmic Reticulum and Protein Secretion	356	(1)
Targeting Proteins to the Endoplasmic Reticulum	357	(5)
Insertion of Proteins into the ER Membrane	362	(4)
Protein Folding and Processing in the ER	366	(3)
The Smooth ER and Lipid Synthesis	369	(3)
Export of Proteins and Lipids from the ER	372	(2)
THE GOLGI APPARATUS	374	(8)
Organization of the Golgi	375	(2)
Protein Glycosylation within the Golgi	377	(2)
Lipid and Polysaccharide Metabolism in the Golgi	379	(1)
Protein Sorting and Export from the Golgi Apparatus	380	(2)
THE MECHANISM OF VESICULAR TRANSPORT	382
Experimental Approaches to Under standing Vesicular Transport	383	(2)
Coat Proteins, Cargo Selection, and Vesicle Budding	385	(2)
Vesicle Fusion	387	(2)
LYSOSOMES	389	(1)
Lysosomal Acid Hydrolases	389	(1)
Endocytosis and Lysosome Formation	390	(3)
Phagocytosis and Autophagy	393
KEY EXPERIMENT The Signal Hypothesis	360	(32)
MOLECULAR MEDICINE Gaucher's Disease	392	(2)
SUMMARY AND KEYTERMS	394	(2)
QUESTIONS	396	(1)
REFERENCES AND FURTHER READING	396	(3)
10 Bioenergetics and Metabolism: Mitochondria, Chloroplasts, and Peroxisomes	399	(36)
MITOCHONDRIA	399	(9)
Organization and Function of Mitochondria	400	(1)
The Genetic System of Mitochondria	401	(2)
Protein Import and Mitochondrial Assembly	403	(5)
THE MECHANISM OF OXIDATIVE PHOSPHORYLATION	408	(7)
The Electron Transport Chain	408	(2)
Chemiosmotic Coupling	410	(4)
Transport of Metabolites across the Inner Membrane	414	(1)
CHLOROPLASTS AND OTHER PLASTIDS	415	(7)
The Structure and Function of Chloroplasts	415	(2)
The Chloroplast Genome	417	(1)
Import and Sorting of Chloroplast Proteins	418	(2)
Other Plastids	420	(2)
PHOTOSYNTHESIS	422
Electron Flow through Photosystems I and II	422	(3)
Cyclic Electron Flow	425	(1)
ATP Synthesis	426	(1)
PEROXISOMES	426	(1)
Functions of Peroxisomes	427	(2)
Peroxisome Assembly	429
KEY EXPERIMENT The Chemiosmotic Theory	412
MOLECULAR MEDICINE Diseases of Mitochondria: Leber's Hereditary Optic Neuropathy	406	(24)
SUMMARY AND KEYTERMS	430	(2)
QUESTIONS	432	(1)
REFERENCES AND FURTHER READING	433	(2)
11 The Cytoskeleton and Cell Movement	435	(48)
STRUCTURE AND ORGANIZATION OF ACTIN FILAMENTS	435	(12)
Assembly and Disassembly of Actin Filaments	436	(4)
Organization of Actin Filaments	440	(2)
Association of Actin Filaments with the Plasma Membrane	442	(3)
Protrusions of the Cell Surface	445	(2)
ACTIN, MYOSIN, AND CELL MOVEMENT	447	(8)
Muscle Contraction	447	(4)
Contractile Assemblies of Actin and
Myosin in Nonmuscle Cells	451	(2)
Unconventional Myosins	453	(1)
Cell Migration and Crawling	454	(1)
INTERMEDIATE FILAMENTS	455	(7)
Intermediate Filament Proteins	455	(1)
Assembly of Intermediate Filaments	456	(1)
Intracellular Organization of Intermediate Filaments	457	(2)
Functions of Keratins and Neurofilaments: Diseases of the Skin and Nervous System	459	(3)
MICROTUBULES	462	(6)
Structure, Assembly, and Dynamic Instability of Microtubules	462	(4)
The Centrosome, Centrioles, and Microtubule Organization 463 Reorganization of Microtubules during Mitosis	466	(1)
Stabilization of Microtubules and Cell Polarity	467	(1)
MICROTUBULE MOTORS AND MOVEMENTS	468
Identification of Microtubule Motor Proteins	468	(4)
Organelle Transport and Intracellular Organization	472	(2)
Separation of Mitotic Chromosomes	474	(1)
Cilia and Flagella	474
KEY EXPERIMENT Expression of Mutant Keratin Causes Abnormal Skin Development	460	(10)
KEY EXPERIMENT The Isolation of Kinesin	470	(8)
SUMMARY AND KEYTERMS	478	(2)
QUESTIONS	480	(1)
REFERENCES AND FURTHER READING	481	(2)
12 The Cell Surface	483	(58)
STRUCTURE OF THE PLASMA MEMBRANE	483	(10)
The Phospholipid Bilayer	483	(3)
Membrane Proteins	486	(4)
Mobility of Membrane Proteins	490	(2)
The Glycocalyx	492	(1)
TRANSPORT OF SMALL MOLECULES	493	(17)
Passive Diffusion	494	(1)
Facilitated Diffusion and Carrier Proteins	494	(2)
Ion Channels	496	(7)
Active Transport Driven by ATP Hydrolysis	503	(4)
Active Transport Driven by Ion Gradients	507	(3)
ENDOCYTOSIS	510	(8)
Phagocytosis	510	(1)
Receptor-Mediated Endocytosis	511	(4)
Protein Trafficking in Endocytosis	515	(3)
CELL WALLS AND THE EXTRACELLULAR MATRIX	518	(10)
Bacterial Cell Walls	518	(1)
Plant Cell Walls	519	(3)
The Extracellular Matrix	522	(6)
CELL-CELL INTERACTIONS	528
Cell Adhesion Proteins	528	(3)
Tight Junctions	531	(1)
Gap Junctions	532	(1)
Plant Cell adhesion and Plasmodesmata	532
KEY EXPERIMENT The LDL Receptor	512
MOLECULAR MEDICINE Cystic Fibrosis	509	(24)
SUMMARY AND KEY TERMS	533	(2)
QUESTIONS	535	(1)
REFERNCES AND FURTHER READING	536	(5)
PART IV Cell Regulation
13 Cell Signaling	541	(50)
SIGNALING MOLECULES AND THEIR RECEPTORS	541	(9)
Modes of Cell-Cell Signaling	542	(1)
Steroid Hormones and the Nuclear
Receptor Superfamily	543	(2)
Nitric Oxide and Carbon Monoxide	545	(1)
Neurotransmitters	546	(1)
Peptide Hormones and Growth Factors	546	(2)
Eicosanoids	548	(1)
Plant Hormones	549	(1)
FUNCTIONS OF CELL SURFACE RECEPTORS	550	(8)
G Protein-Coupled Receptors	551	(2)
Receptor Protein-Tyrosine Kinases	553	(4)
Cytokine Receptors and Nonreceptor Protein-Tyrosine Kinases	557	(1)
Receptors Linked to Other Enzymatic Activities	557	(1)
PATHWAYS OF INTRACELLULAR SIGNAL TRANSDUCTION	558	(13)
The cAMP Pathway: Second Messengers and Protein Phosphorylation	559	(2)
Cyclic GMP	561	(1)
Phospholipids and Cat+	562	(3)
Ras, Raf, and the MAP Kinase Pathway	565	(5)
The JAK/STAT Pathway	570	(1)
SIGNAL TRANSDUCTION AND THE CYTOSKELETON	571	(4)
Integrins and Signal Transduction	571	(3)
Regulation of the Actin Cytoskeleton	574	(1)
SIGNALING IN DEVELOPMENT AND DIFFERENTIATION	575	(4)
The Receptor Tyrosine Kinase/Ras/Raf/ERK Pathway in Drosophile and C. elegans	575	(2)
Hedgehog and Wnt	577	(1)
Notch Signaling	578	(1)
REGULATION OF PROGRAMMED CELL DEATH	579
Caspases and Apoptosis	580	(2)
Cell Death Receptors and Caspase Activation	582	(1)
Signaling Cell Survival	582
KEY EXPERIMENT The Src Protein-Tyrosine Kinase	554	(18)
MOLECULAR MEDICINE Cancer: Signal Transduction, and the ras Oncogenes	572	(12)
SUMMARY AND KEYTERMS	584	(3)
QUESTIONS	587	(1)
REFERENCES AND FURTHER READING	587	(4)
14 The Cell Cycle	591	(40)
THE EUKARYOTIC CELL CYCLE	591	(8)
Phases of the Cell Cycle	592	(2)
Regulation of the Cell Cycle by Cell Growth and Extracellular Signals	594	(2)
Cell Cycle Checkpoints	596	(2)
Restricting DNA Replication to Once per Cell Cycle	598	(1)
REGULATORS OF CELL CYCLE PROGRESSION	599	(9)
MPF: A Dimer of Cdc2 and Cyclin	599	(4)
Families of Cyclins and Cyclin Dependent Kinases	603	(2)
Growth Factors and the D-Type Cyclins	605	(1)
Inhibitors of Cell Cycle Progression	606	(2)
THE EVENTS OF M PHASE	608	(7)
Stages of Mitosis	608	(3)
MPF and Progression to Metaphase	611	(2)
Proteolysis and the Inactivation of MPF: Anaphase and Telophase	613	(1)
Cytokinesis	614	(1)
MEIOSIS AND FERTILIZATION	615	(6)
The Process of Meiosis	615	(3)
Regulation of Oocyte Meiosis	618	(2)
Fertilization	620	(1)
STEM CELLS AND THE MAINTENANCE OF ADULT TISSUES	621
Proliferation of Differentiated Cells	621	(1)
Stem Cells	622	(2)
Medical Applications of Stem Cells	624
KEY EXPERIMENT The Discovery of MPF	600	(22)
KEY EXPERIMENT Culture of Embryonic Stem Cells	622	(3)
SUMMARY AND KEYTERMS	625	(3)
QUESTIONS	628	(1)
REFERENCES AND FURTHER READING	628	(3)
15 Cancer	631	(44)
THE DEVELOPMENT AND CAUSES OF CANCER	631	(9)
Types of Cancer	631	(2)
The Development of Cancer	633	(1)
Causes of Cancer	634	(2)
Properties of Cancer Cells	636	(4)
Transformation of Cells in Culture	640	(1)
TUMOR VIRUSES	640	(4)
Hepatitis B and C Viruses	641	(1)
SV40 and Polyomavirus	641	(1)
Papillomaviruses	642	(1)
Adenoviruses	642	(1)
Herpesviruses	643	(1)
Retroviruses	644	(1)
ONCOGENES	644	(13)
Retroviral Oncogenes	645	(1)
Proto-Oncogenes	646	(3)
Oncogenes in Human Cancer	649	(4)
Functions of Oncogene Products	653	(4)
TUMOR SUPPRESSOR GENES	657	(7)
Identification of Tumor Suppressor Genes	657	(3)
Functions of Tumor Suppressor Gene Products	660	(3)
Roles of Oncogenes and Tumor Suppressor Genes in Tumor Development	663	(1)
APPLICATIONS OF MOLECULAR BIOLOGY TO CANCER PREVENTION AND TREATMENT	664
Prevention and Early Detection	664	(1)
Molecular Diagnosis	665	(1)
Treatment	666
KEY EXPERIMENT The Discovery of Proto-Oncogenes	648	(19)
MOLECULAR MEDICINE STI-571: Cancer Treatment Targeted against the bci/abl Oncogene	667	(2)
SUMMARYAND KEYTERMS	669	(2)
QUESTIONS	671	(1)
REFERENCES AND FURTHER READING	671	(4)
Answers to Questions	675	(6)
Glossary	681	(18)
Index	699