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Cell Biology, 7th Edition International Student Version

ISBN: 978-1-118-65322-7
872 pages
July 2013, ©2013
Cell Biology, 7th Edition International Student Version (111865322X) cover image

Description

This Seventh Edition connects experimental material to key concepts of Cell Biology. The text offers streamlined information that reinforces a connection of key concepts to experimentation. Though the use paired art, and new science illustrations, readers benefit from a visual representation of experimental connections. Animations and video clips are tied to key illustrations with practice questions to provide a variety of ways to experience a key concept. This new edition offers an appropriate balance of concepts and experimentation. Experimental detail is offered when it helps to reinforce the concept being explained.
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Table of Contents

1 Introduction to Cell Biology 1

1.1 The Discovery of Cells 2

1.2 Basic Properties of Cells 3

Cells Are Highly Complex and Organized 3

Cells Possess a Generic Program and the Means to Use It 5

Cells Are Capable of Producing More of Themselves 5

Cells Acquire and Utilize Energy 5

Cells Carry Out a Variety of Chemical Reactions 6

Cells Engage in Mechanical Activities 6

Cells Are Able to Respond to Stimuli 6

Cells Are Capable of Self-Regulation 6

Cells Evolve 7

1.3 Two Fundamentally Different Classes of Cells 7

Characteristics That Distinguish Prokaryotic and Eukaryotic Cells 8

Types of Prokaryotic Cells 14

Types of Eukaryotic Cells: Cell Specialization 15

The Sizes of Cells and Their Components 17

Synthetic Biology 17

?? THE HUMAN PERSPECTIVE: The Prospect of Cell Replacement Therapy 20

1.4 Viruses 23

Viroids 26

?? EXPERIMENTAL PATHWAYS: The Origin of Eukaryotic Cells 26

2 The Structure and Functions of Biological Molecules 32

2.1 Covalent Bonds 33

Polar and Nonpolar Molecules 34

Ionizaton 34

2.2 Noncovalent Bonds 34

?? THE HUMAN PERSPECTIVE: Free Radicals as a Cause of Aging 35

Ionic Bonds: Attractions between Charged Atoms 35

Hydrogen Bonds 36

Hydrophobic Interactions and van der Waals Forces 36

The Life-Supporting Properties of Water 37

2.3 Acids, Bases, and Buffers 39

2.4 The Nature of Biological Molecules 40

Functional Groups 41

A Classification of Biological Molecules by Function 41

2.5 Four Types of Biological Molecules 42

Carbohydrates 43

?? THE HUMAN PERSPECTIVE: Diseases that Result from Expansion of Trinucleotide Repeats 138

4.5 The Stability of the Genome 140

Whole-Genome Duplication (Polyploidization) 140

Duplication and Modification of DNA Sequences 141

“Jumping Genes” and the Dynamic Nature of the Genome 142

4.6 Sequencing Genomes: The Footprints of Biological Evolution 145

Comparative Genomics: “If It’s Conserved, It Must Be Important” 147

The Genetic Basis of “Being Human” 148

Genetic Variation Within the Human Species Population 150

?? THE HUMAN PERSPECTIVE: Application of Genomic Analyses to Medicine 151

?? EXPERIMENTAL PATHWAYS: The Chemical Nature of the Gene 154

5 The Path to Gene Expression 160

5.1 The Relationship between Genes, Proteins, and RNAs 161

An Overview of the Flow of Information through the Cell 162

5.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 163

Transcription in Bacteria 166

Transcription and RNA Processing in Eukaryotic Cells 167

5.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 169

Synthesizing the rRNA Precursor 170

Processing the rRNA Precursor 171

Synthesis and Processing of the 5S rRNA 174

Transfer RNAs 174

5.4 Synthesis and Processing of Eukaryotic Messenger RNAs 175

The Machinery for mRNA Transcription 175

Split Genes: An Unexpected Finding 178

The Processing of Eukaryotic Messenger RNAs 182

Evolutionary Implications of Split Genes and RNA Splicing 188

Creating New Ribozymes in the Laboratory 188

5.5 Small Regulatory RNAs and RNA Silencing Pathways 189

?? THE HUMAN PERSPECTIVE: Clinical Applications of RNA Interference 192

MicroRNAs: Small RNAs that Regulate Gene Expression 193

piRNAs: A Class of Small RNAs that Function in Germ Cells 194

Other Noncoding RNAs 195

5.6 Encoding Genetic Information 195

The Properties of the Genetic Code 195

5.7 Decoding the Codons: The Role of Transfer RNAs 198

The Structure of tRNAs 199

5.8 Translating Genetic Information 202

Initiation 202

Elongation 205

Termination 208

mRNA Surveillance and Quality Control 208

Polyribosomes 209

?? EXPERIMENTAL PATHWAYS: The Role of RNA as a Catalyst 211

6 Controlling Gene Expression 217

6.1 Control of Gene Expression in Bacteria 218

Organization of Bacterial Genomes 218

The Bacterial Operon 218

Riboswitches 221

6.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus 222

The Nuclear Envelope 222

Chromosomes and Chromatin 227

?? THE HUMAN PERSPECTIVE: Chromosomal Aberrations and Human Disorders 238

Epigenetics: There’s More to Inheritance than DNA 243

The Nucleus as an Organized Organelle 244

6.3 An Overview of Gene Regulation in Eukaryotes 246

6.4 Transcriptional Control 248

The Role of Transcription Factors in Regulating Gene Expression 251

The Structure of Transcription Factors 253

DNA Sites Involved in Regulating Transcription 256

Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators 259

Transcriptional Repression 264

6.5 RNA Processing Control 267

6.6 Translational Control 270

Initiation of Translation 270

Cytoplasmic Localization of mRNAs 271

The Control of mRNA Stability 272

The Role of MicroRNAs in Translational Control 273

6.7 Posttranslational Control: Determining Protein Stability 275

7 Replicating and Repairing DNA 279

7.1 DNA Replication 280

Semiconservative Replication 280

Replication in Bacterial Cells 283

The Structure and Functions of DNA Polymerases 288

Replication in Eukaryotic Cells 292

7.2 DNA Repair 298

Nucleotide Excision Repair 299

Base Excision Repair 300

Mismatch Repair 301

Double-Strand Breakage Repair 301

7.3 Between Replication and Repair 302

?? THE HUMAN PERSPECTIVE: The Consequences of DNA Repair Deficiencies 303

8 Cellular Membranes 306

8.1 An Overview of Membrane Functions 307

8.2 A Brief History of Studies on Plasma Membrane Structure 309

8.3 The Chemical Composition of Membranes 311

Membrane Lipids 311

The Asymmetry of Membrane Lipids 314

Membrane Carbohydrates 315

8.4 The Structure and Functions of Membrane Proteins 316

Integral Membrane Proteins 316

Studying the Structure and Properties of Integral Membrane Proteins 318

Peripheral Membrane Proteins 323

Lipid-Anchored Membrane Proteins 323

8.5 Membrane Lipids and Membrane Fluidity 324

The Importance of Membrane Fluidity 325

Maintaining Membrane Fluidity 325

Lipid Rafts 325

8.6 The Dynamic Nature of the Plasma Membrane 326

The Diffusion of Membrane Proteins after Cell Fusion 327

Restrictions on Protein and Lipid Mobility 328

The Red Blood Cell: An Example of Plasma Membrane Structure 331

8.7 The Movement of Substances Across Cell Membranes 333

The Energetics of Solute Movement 333

Diffusion of Substances through Membranes 335

Facilitated Diffusion 342

Active Transport 343

?? THE HUMAN PERSPECTIVE: Defects in Ion Channels and Transporters as a Cause of Inherited Disease 348

8.8 Membrane Potentials and Nerve Impulses 350

The Resting Potential 350

The Action Potential 351

Propagation of Action Potentials as an Impulse 353

Neurotransmission: Jumping the Synaptic Cleft 354

?? EXPERIMENTAL PATHWAYS: The Acetylcholine Receptor 357

9 Mitochondrial Structure and Function 364

9.1 Mitochondrial Structure and Function 365

Mitochondrial Membranes 366

The Mitochondrial Matrix 368

9.2 Oxidative Metabolism in the Mitochondrion 369

The Tricarboxylic Acid (TCA) Cycle 371

The Importance of Reduced Coenzymes in the Formation of ATP 372

?? THE HUMAN PERSPECTIVE: The Role of Anaerobic and Aerobic Metabolism in Exercise 374

9.3 The Role of Mitochondria in the Formation of ATP 375

Oxidation–Reduction Potentials 375

Electron Transport 376

Types of Electron Carriers 377

9.4 Translocation of Protons and the Establishment of a Proton-Motive Force 384

9.5 The Machinery for ATP Formation 385

The Structure of ATP Synthase 386

The Basis of ATP Formation According to the Binding Change Mechanism 387

Other Roles for the Proton-Motive Force in Addition to ATP Synthesis 391

9.6 Peroxisomes 392

?? THE HUMAN PERSPECTIVE: Diseases that Result from Abnormal Mitochondrial or Peroxisomal Function 393

10 Chloroplast Structure and Function 397

10.1 Chloroplast Structure and Function 399

10.2 An Overview of Photosynthetic Metabolism 400

10.3 The Absorption of Light 402

Photosynthetic Pigments 402

10.4 Photosynthetic Units and Reaction Centers 404

Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems 404

Killing Weeds by Inhibiting Electron Transport 411

10.5 Photophosphorylation 411

Noncyclic Versus Cyclic Photophosphorylation 412

10.6 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 412

Carbohydrate Synthesis in C3 Plants 412

Carbohydrate Synthesis in C4 Plants 417

Carbohydrate Synthesis in CAM Plants 418

11 The Extracellular Matrix and Cell Interactions 421

11.1 The Extracellular Space 422

The Extracellular Matrix 422

11.2 Interactions of Cells with Extracellular Materials 430

Integrins 430

Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum 433

11.3 Interactions of Cells with Other Cells 436

Selectins 437

The Immunoglobulin Superfamily 438

Cadherins 439

?? THE HUMAN PERSPECTIVE: The Role of Cell Adhesion in Inflammation and Metastasis 441

Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells 443

The Role of Cell-Adhesion Receptors in Transmembrane Signaling 445

11.4 Tight Junctions: Sealing The Extracellular Space 446

11.5 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication 448

Plasmodesmata 451

11.6 Cell Walls 452

12 Cellular Organelles and Membrane Trafficking 456

12.1 An Overview of the Endomembrane System 457

12.2 A Few Approaches to the Study of Endomembranes 459

Insights Gained from Autoradiography 459

Insights Gained from the Use of the Green Fluorescent Protein 459

Insights Gained from the Biochemical Analysis of Subcellular Fractions 461

Insights Gained from the Use of Cell-Free Systems 462

Insights Gained from the Study of Mutant Phenotypes 463

12.3 The Endoplasmic Reticulum 465

The Smooth Endoplasmic Reticulum 466

Functions of the Rough Endoplasmic Reticulum 466

From the ER to the Golgi Complex: The First Step in Vesicular Transport 475

12.4 The Golgi Complex 476

Glycosylation in the Golgi Complex 478

The Movement of Materials through the Golgi Complex 478

12.5 Types of Vesicle Transport and Their Functions 481

COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex 482

COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER 484

Beyond the Golgi Complex: Sorting Proteins at the TGN 484

Targeting Vesicles to a Particular Compartment 486

12.6 Lysosomes 489

Autophagy 490

?? THE HUMAN PERSPECTIVE: Disorders Resulting from Defects in Lysosomal Function 492

12.7 Plant Cell Vacuoles 493

12.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 494

Endocytosis 494

Phagocytosis 501

12.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 502

Uptake of Proteins into Peroxisomes 502

Uptake of Proteins into Mitochondria 502

Uptake of Proteins into Chloroplasts 504

?? EXPERIMENTAL PATHWAYS: Receptor-Mediated Endocytosis 505

13 The Cytoskeleton 510

13.1 Overview of the Major Functions of the Cytoskeleton 511

13.2 The Study of the Cytoskeleton 512

The Use of Live-Cell Fluorescence Imaging 512

The Use of In Vitro and In Vivo Single-Molecule Assays 513

The Use of Fluorescence Imaging Techniques to Monitor the Dynamics of the Cytoskeleton 515

13.3 Microtubules 516

Structure and Composition 516

Microtubule-Associated Proteins 517

Microtubules as Structural Supports and Organizers 518

Microtubules as Agents of Intracellular Motility 519

Motor Proteins that Traverse the Microtubular Cytoskeleton 520

Microtubule-Organizing Centers (MTOCs) 525

The Dynamic Properties of Microtubules 527

Cilia and Flagella: Structure and Function 531

?? THE HUMAN PERSPECTIVE: The Role of Cilia in Development and Disease 535

13.4 Intermediate Filaments 540

Intermediate Filament Assembly and Disassembly 540

Types and Functions of Intermediate Filaments 542

13.5 Microfilaments 542

Microfilament Assembly and Disassembly 544

Myosin: The Molecular Motor of Actin Filaments 546

13.6 Muscle Contractility 550

The Sliding Filament Model of Muscle Contraction 552

13.7 Nonmuscle Motility 557

Actin-Binding Proteins 558

Examples of Nonmuscle Motility and Contractility 560

14 Cell Division 572

14.1 The Cell Cycle 573

Cell Cycles in Vivo 574

Control of the Cell Cycle 574

14.2 M Phase: Mitosis and Cytokinesis 581

Prophase 583

Prometaphase 588

Metaphase 590

Anaphase 592

Telophase 597

Motor Proteins Required for Mitotic Movements 597

Cytokinesis 597

14.3 Meiosis 602

The Stages of Meiosis 603

?? THE HUMAN PERSPECTIVE: Meiotic Nondisjunction and Its Consequences 608

Genetic Recombination During Meiosis 610

?? EXPERIMENTAL PATHWAYS: The Discovery and Characterization of MPF 611

15 Cell Signaling Pathways 617

15.1 The Basic Elements of Cell Signaling Systems 618

15.2 A Survey of Extracellular Messengers and Their Receptors 621

15.3 G Protein-Coupled Receptors and Their Second Messengers 621

Signal Transduction by G Protein-Coupled Receptors 622

?? THE HUMAN PERSPECTIVE: Disorders Associated with G Protein-Coupled Receptors 625

Second Messengers 627

The Specificity of G Protein-Coupled Responses 630

Regulation of Blood Glucose Levels 631

The Role of GPCRs in Sensory Perception 634

15.4 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction 636

The Ras-MAP Kinase Pathway 640

Signaling by the Insulin Receptor 644

?? THE HUMAN PERSPECTIVE: Signaling Pathways and Human Longevity 647

Signaling Pathways in Plants 648

15.5 The Role of Calcium as an Intracellular Messenger 648

Regulating Calcium Concentrations in Plant Cells 652

15.6 Convergence, Divergence, and Cross-Talk Among Different Signaling Pathways 653

Examples of Convergence, Divergence, and Cross-Talk Among Signaling Pathways 654

15.7 The Role of NO as an Intercellular Messenger 655

15.8 Apoptosis (Programmed Cell Death) 656

The Extrinsic Pathway of Apoptosis 658

The Intrinsic Pathway of Apoptosis 659

16 Cancer 664

16.1 Basic Properties of a Cancer Cell 665

16.2 The Causes of Cancer 667

16.3 The Genetics of Cancer 669

Tumor-Suppressor Genes and Oncogenes: Brakes and Accelerators 671

The Cancer Genome 683

Gene-Expression Analysis 685

16.4 New Strategies for Combating Cancer 687

Immunotherapy 688

Inhibiting the Activity of Cancer-Promoting Proteins 689

Inhibiting the Formation of New Blood Vessels (Angiogenesis) 692

?? EXPERIMENTAL PATHWAYS: The Discovery of Oncogenes 694

17 Immunity 699

17.1 An Overview of the Immune Response 700

Innate Immune Responses 700

Adaptive Immune Responses 703

17.2 The Clonal Selection Theory as It Applies to B Cells 704

Vaccination 706

17.3 T Lymphocytes: Activation and Mechanism of Action 707

17.4 Selected Topics on the Cellular and Molecular Basis of Immunity 710

The Modular Structure of Antibodies 710

DNA Rearrangements that Produce Genes Encoding B- and T-Cell Antigen Receptors 713

Membrane-Bound Antigen Receptor Complexes 716

The Major Histocompatibility Complex 716

Distinguishing Self from Nonself 721

Lymphocytes Are Activated by Cell-Surface Signals 722

Signal Transduction Pathways in Lymphocyte Activation 723

?? THE HUMAN PERSPECTIVE: Autoimmune Diseases 724

?? EXPERIMENTAL PATHWAYS: The Role of the Major Histocompatibility Complex in Antigen Presentation 727

18 Methods in Cell Biology 732

18.1 The Light Microscope 733

Resolution 733

Visibility 734

Preparation of Specimens for Bright-Field Light Microscopy 735

Phase-Contrast Microscopy 735

Fluorescence Microscopy (and Related Fluorescence-Based Techniques) 736

Video Microscopy and Image Processing 738

Laser Scanning Confocal Microscopy 739

Super-Resolution Fluorescence Microscopy 740

18.2 Transmission Electron Microscopy 740

Specimen Preparation for Electron Microscopy 742

18.3 Scanning Electron and Atomic Force Microscopy 746

Atomic Force Microscopy 748

18.4 The Use of Radioisotopes 748

18.5 Cell Culture 749

18.6 The Fractionation of a Cell’s Contents by Differential Centrifugation 752

18.7 Isolation, Purification, and Fractionation of Proteins 752

Selective Precipitation 752

Liquid Column Chromatography 753

Polyacrylamide Gel Electrophoresis 756

Protein Measurement and Analysis 757

18.8 Determining the Structure of Proteins and Multisubunit Complexes 758

18.9 Fractionation of Nucleic Acids 760

Separation of DNAs by Gel Electrophoresis 760

Separation of Nucleic Acids by Ultracentrifugation 760

18.10 Nucleic Acid Hybridization 762

18.11 Chemical Synthesis of DNA 764

18.12 Recombinant DNA Technology 764

Restriction Endonucleases 764

Formation of Recombinant DNAs 766

DNA Cloning 766

18.13 Enzymatic Amplification of DNA by PCR 769

Applications of PCR 770

18.14 DNA Sequencing 771

18.15 DNA Libraries 773

Genomic Libraries 773

cDNA Libraries 774

18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 775

18.17 Determining Eukaryotic Gene Function by Gene Elimination or Silencing 778

In Vitro Mutagenesis 778

Knockout Mice 778

RNA Interference 780

18.18 The Use of Antibodies 780

Glossary G-1

Additional Readings A-1

Index I-1

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New to This Edition

The text has been completely updated to reflect the most recent advances in cellular and molecular biology.

"Cell Flix" - Video clips and animations that are tied to paired art in the text. An icon invites students to further their understanding by going to WileyPLUS and viewing a related video, or animation and then answering a set of test your knowledge questions.

"Question Pathways" - Includes 3 tiers of question types: experimental, critical and animation questions. Instructors have asked for more question types involving experimentation, clinical applications and critical thinking. This is the area where students need more practice. Karp builds on its reputation for experimental coverage by providing experiment based questions in WileyPlus. These critical thinking questions are written by Sarah Chavez of Washington University , and they address the experimental discussions, methods and pathways found in every chapter. Instructors can now offer more practice or assignments dealing with experimentation in WileyPlus.

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The Wiley Advantage

  • Offers an appropriate balance of concepts and experimentation.
  • Experimental detail is offered when it helps to reinforce the concept being explained.
  • Strong illustration program includes stepped-out art to break down complex processes into steps.
  • Illustrations are paired with micrographs to help students compare the real (micrograph) with the ideal (illustration).
  • Human aspects of cell biology are integral to this text, with “Human Perspective” essays throughout.
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