Karp's cell biology / Janet Iwasa, Wallace Marshall. -- Global edition. -- Hoboken, New Jersey : John Wiley & Sons, Inc., [2016]. – (58.15/I96/global ed.)

Contents

1 Introduction to Cell Biology  1

1.1 The Discovery of Cells  2

1.2 Basic Properties-of Cells  3

1.3 Two Fundamentally Different Classes of Cells  8

1.4 Types of Prokaryotic Ceils  14

1.5 Types of Eukaryotic Cells  15

1.6 The Sizes of Cells and Their Components  18

1.7 Viruses  19

    THE HUMAN PERSPECTIVE  23

    EXPERIMENTAL PATHWAYS  27

2 The Structure and Functions of Biological Molecules  33

2.1 Covalent Bonds  34

2.2 Noncovalent Bonds  36

2.3 Acids, Bases and Buffers  39

2.4 The Nature of Biological Molecules  40

2.5 Carbohydrates  42

2.6 Lipids 47

2.7 Building Blocks of Proteins  49

2.8 Primary and Secondary Structures of Proteins  54

2.9 Tertiary Structure of Proteins  56

2.10 Quaternary Structure of Proteins  60

2.11 Protein Folding  61

2.12 Proteomics and Interactomics  64

2.13 Protein Engineering  67

2.14 Protein Adaptation and Evolution  69

2.15 Nucleic Acids  71

2.16 The Formation of Complex Macromolecular Structures  72

     THE HUMAN PERSPECTIVE  73

     EXPERIMENTAL PATHWAYS  79

3 Bioenergetics, Enzymes, and Metabolism  87

3.1 Bioenergetics  88

3.2 Free Energy  90

3.3 Coupling Endergonic and Exergonic Reactions  94

3.4 Equilibrium versus Steady-State Metabolism  94

3.5 Enzymes as Biological Catalysts  95

3.6 Mechanisms of Enzyme Catalysis  99

3.7 Enzyme Kinetics  103

3.8 Metabolism  106

3.9 Glycolysis and ATP Production  108

3.10 Reducing Power  112

3.11 Metabolic Regulation  113

3.12 Separating Catabolic and Anabolic Pathways  114

     THE HUMAN PERSPECTIVE  115

4 Genes, Chromosomes, and Genomes  123

4.1 The Concept of a Gone as a Unit of Inheritance  124

4.2 The Discovery of Chromosomes  125

4.3 Chromosomes: The Physical Carriers of the Genes  126

4.4 Genetic Analysis in Drosophila  127

4.5 The Structure of DNA  129

4.6 DNA Supercoiling  134

4.7 The Structure of the Genome  136

4.8 The Stability of the Genome  141

4.9 "Jumping Genes" and the Dynamic Nature of the Genome  143

4.10 Sequencing Genomes: The Footprints of Biological Evolution  146

4.11 Comparative Genomics: "If It's Conserved, It Must Be Important"  148

4.12 The Genetic Basis of "Being Human"  148

4.13 Genetic Variation within the Human Species Population  150

     THE HUMAN PERSPECTIVE  152

     EXPERIMENTAL PATHWAYS   157

5 The Path to Gene Expression  165

5.1 The Relationship between Genes, Proteins, and RNAs  166

5.2 The Role of RNA Polymerases in Transcription  169

5.3 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells  171

5.4 Synthesis and Processing of Eukaryotic, Ribosomal and Transfer RNAs  174

5.5 Synthesis and Structure of Eukaryotic Messenger RNAs  178

5.6 Split Genes: An Unexpected Finding  181

5.7 The Processing of Eukaryotic Messenger RNAs  184

5.8 Evolutionary Implications of Split Genes and RNA Splicing  189

5.9 Creating New Ribozymes in the Laboratory  191

5.10 Small Regulatory RNAs and RNA Silencing Pathway  191

5.11 Small RNAs: miRNAs and piRNAs  193

5.12 CRISPR and other Noncoding RNAs  195

5.13 Encoding Genetic Information  196

5.14 Decoding the Codons: The Role of Transfer RNAs  198

5.15 Translating Genetic Information: Initiation  201

5.16 Translating Genetic Information: Elongation and Termination  205

5.17 mRNA Surveillance and Quality Control  208

5.18 Polyribosomes  209

     THE HUMAN PERSPECTIVE  210

     EXPERIMENTAL PATHWAYS  212

6 Controlling Gene Expression  220

6.1 Control of Gene Expression in Bacteria  221

6.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus  225

6.3 Chromosomes and Chromatin  230

6.4 Heterochromatin and Euchromatin  234

6.5 The Structure of a Mitotic Chromosome  238

6.6 Epigenetics: There's More to Inheritance than DNA  243

6.7 The Nucleus as an Organized Organelle  244

6.8 An Overview of Gene Regulation in Eukaryotes  247

6.9 Transcriptional Control  248

6.10 The Role of Transcription Factors in Regulating Gene Expression  252

6.11 The Structure of Transcription Factors  253

6.12 DNA Sites Involved in Regulating Transcription  256

6.13 The Glucocorticoid Receptor: An Example of Transcriptional Activation  258

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

6.15 Transcriptional Activation from Paused Polymerases  263

6.16 Transcriptional Repression  264

6.17 RNA Processing Control  267

6.18 Translational Control  269

6.19 The Role of MicroRNAs in Translational Control  273

6.20 Posttranslational Control: Determining Protein Stability 274

     THE HUMAN PERSPECTIVE  275

7 DNA Replication and Repair  282

7.1 DNA Replication  283

7.2 DNA Replication in Bacterial Cells  286

7.3 The Machinery Operating at the Replication Fork  291

7.4 The Structure and Functions of DNA Polymerases  293

7.5 Replication in Viruses  296

7.6 DNA Replication in Eukaryotic Cells  296

7.7 Chromatin Structure and Replication  300

7.8 DNA Repair  302

7.9 Between Replication and Repair  305

    THE HUMAN PERSPECTIVE  306

8 Cellular Membrane  311

8.1 Introduction to the Plasma Membrane  312

8.2 The Chemical Composition of Membranes  315

8.3 Membrane Carbohydrates  319

8.4 The Structure and Functions of Membrane Proteins  320

8.5 Studying the Structure and Properties of Integral Membrane Proteins  323

8.6 Membrane Lipids and Membrane Fluidity  327

8.7 The Dynamic Nature of the Plasma Membrane  329

8.8 The Red Blood Cell: An Example of Plasma Membrane Structure  334

8.9 The Movement of Substances across Cell Membranes  336

8.10 Diffusion through the Lipid Bilayer  338

8.11 The Diffusion of Ions, through Membranes  340

8.12 Facilitated Diffusion  345

8.13 Active Transport  346

8.14 Membrane Potentials  350

8.15 Propagation of Action Potentials as an Impulse  353

8.16 Neurotransmission: Jumping the Synaptic Cleft  354

     THE HUMAN PERSPECTIVE  357

     EXPERIMENTAL PATHWAYS  359

9 Mitochondrion and Aerobic Respiration  368

9.1 Mitochondrial Structure and Function  369

9.2 Oxidative Metabolism in the Mitochondrion  372

9.3 The Role of Mitochondria in the Formation of ATP  377

9.4 Electron-Transport Complexes  381

9.5 Translocation of Protons and the Establishment of a Proton-Motive Force  385

9.6 The Machinery for ATP Formation  386

9.7 The Binding Change Mechanism of ATP Formation  388

9.8 Using the Proton Gradient  391

9.9 Peroxisomes  392

    THE HUMAN PERSPECTIVE  394

10 Chloroplast and Photosynthesis  401

10.1 The Origin of Photosynthesis  402

10.2 Chloroplast Structure and Function  403

10.3 An Overview of Photosynthetic Metabolism  404

10.4 The Absorption of Light  405

10.5 Photosynthetic Units and Reaction Centers  407

10.6 The Operations of Photosystem II and Photosystem I  409

10.7 An Overview of Photosynthetic Electron, Transport  413

10.8 Photophosphorylation  415

10.9 Carbon Dioxide Fixation and the Carbohydrate Synthesis  415

10.10 Carbohydrate Synthesis in C4 and CAM Plants  420

      THE HUMAN PERSPECTIVE  421

11 The Extracellular Matrix and Cell Interactions  426

11.1 Overview of Extracellular Interactions  427

11.2 The Extracellular Space  428

11.3 Components of the Extracellular Matrix  430

11.4 Dynamic Properties of the Extracellular Matrix  435

11.5 Interactions of Cells with Extracellular Materials  436

11.6 Anchoring Cells to Their Substratum  438

11.7 Interactions of Cells with Other Cells  441

11.8 Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells  445

11.9 The Role of Cell-Adhesion Receptors in Transmembrane Signaling  447

11.10 Tight Junctions: Sealing the Extracellular Space  447

11.11 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication  449

11.12 Cell Walls  453

      THE HUMAN PERSPECTIVE  455

      EXPERIMENTAL PATHWAYS  457

12 Cellular Organelles and Membrane Trafficking  463

12.1 An Overview of the Endomembrane System  464

12.2 A Few Approaches to the Study of Endomembranes  466

12.3 The Endoplasmic Reticulum  472

12.4 Functions of the Rough Endoplasmic Reticulum  473

12.5 Membrane Biosynthesis in the Endoplasmic Reticulum  477

12.6 Glycosylation in the Rough Endoplasmic Reticulum  479

12.7 Mechanisms That Ensure the Destruction of Misfolded Proteins  481

12.8 ER to Golgi Vesicular Transport  482

12.9 The Golgi Complex  482

12.10 Types of Vesicle Transport and Their Functions  487

12.11 Beyond the Golgi Complex: Sorting Proteins at the TGN  491

12.12 Targeting Vesicles to a Particular Compartment  493

12.13 Exocytosis  496

12.14 Lysosomes  496

12.15 Plant Cell Vacuoles  498

12.16 Endocytosis 498

12.17 The Endocytic Pathway  502

12.18 Phagocytosis  505

12.19 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts  505

      THE HUMAN PERSPECTIVE  508

      EXPERIMENTAL PATHWAYS  510

13 The Cytoskeleton  517

13.1 Overview of the Major Functions of the Cytoskeleton  518                       13.2 Microtubules: Structure and Function  520

13.3 Motor Proteins: Kinesins and Dyneins  524

13.4 Microtubule-Organizing Centers (MTOCs)  527

13.5 Microtubule Dynamics  530

13.6 Cilia and Flagella: Structure and Function  534

13.7 Intermediate Filaments  541

13.8 Microfilaments  544

13.9 Myosin: The Molecular Motor of Actin Filaments  547

13.10 Muscle Contractility  552

13.11 Nonmuscle Motility  557

13.12 Cellular Motility  560

13.13 Actin-Dependent Processes During Development  564

13.14 The Bacterial Cytoskeleton  567

      THE HUMAN PERSPECTIVE  568

      EXPERIMENTAL PATHWAYS  569

14 Cell Division  578

14.1 The Cell Cycle  579

14.2 Regulation of the Cell Cycle  581

14.3 Control of the Cell Cycle: The Role of Protein Kinases  582

14.4 Control of the Cell Cycle: Checkpoints, Cdk Inhibitors, and Cellular Responses  586

14.5 M Phase: Mitosis and Cytokinesis  588

14.6 Prophase  588

14.7 Prometaphase  594

14.8 Metaphase  596

14.9 Anaphase  598

14.10 Telophase and Cytokinesis  603

14.11 Meiosis  608

14.12 The Stages of Meiosis  610

14.13 Genetic Recombination during Meiosis  613

      THE HUMAN PERSPECTIVE  615

      EXPERIMENTAL PATHWAYS  616

15 Cell Signaling Pathways  624

15.1 The Basic Elements of Cell Signaling Systems  625

15.2 A Survey of Extracellular Messengers and Their Receptors  628

15.3 Signal Transduction by G Protein-Coupled Receptors  629

15.4 Second Messengers  632

15.5 The Specificity of G Protein-Coupled Responses  636

15.6 Regulation of Blood Glucose Levels  636

15.7 The Role of GPCRs in Sensory Perception  640

15.8 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction  641

15.9 The Ras-MAP Kinase Pathway  645

15.10 Signaling by the Insulin Receptor  648

15.11 Signaling Pathways in Plants  651

15.12 The Role of Calcium as an Intracellular Messenger  651

15.13 Convergence, Divergence, and Cross-Talk among Different Signaling Pathways  655

15.14 The Role of NO as an Intercellular Messenger  657

15.15 Apoptosis (Programmed Cell Death)  659

      THE HUMAN PERSPECTIVE  663

      EXPERIMENTAL PATHWAYS  665

16 Cancer  673

16.1 Basic Properties of a Cancer Cell  674

16.2 The Causes of Cancer  677

16.3 The Genetics of Cancer  678

16.4 An Overview of Tumor-Suppressor Genes and Oncogenes  680

16.5 Tumor-Suppressor Genes: The RB Gene  681

16.6 Tumor-Suppressor Genes: The TP53 Gene  684

16.7 Other Tumor-Suppressor Genes  687

16.8 Oncogenes  688

16.9 The Mutator Phenotype: Mutant Genes Involved in DNA Repair  691

16.10 MicroRNAs: A New Player in the Genetics of Cancer  691

16.11 The Cancer Genome  691

16.12 Gene-Expression Analysis  694

16.13 Strategies for Combating Cancer  696

16.14 Immunotherapy  696

16.15 Inhibiting the Activity of Cancer-Promoting Proteins  698

16.16 The Concept of a Cancer Stem Cell  701

16.17 Inhibiting the Formation of New Blood Vessels (Angiogenesis)  701

      EXPERIMENTAL PATHWAYS  702

17 Immunity  709

17.1 An Overview of the immune Response  710

17.2 The Clonal Selection Theory as It Applies to Cells  714

17.3 Vaccination  715

17.4 T Lymphocytes: Activation and Mechanism of Action  717

17.5 The Modular Structure of Antibodies  720

17.6 DNA Rearrangements That Produce Genes Encoding B- and T-Cell Antigen Receptors  723

17.7 Membrane-Bound Antigen Receptor Complexes  725

17.8 The Major Histocompatibility Complex  726

17.9 Distinguishing Self from Nonself  730

17.10 Lymphocytes Are activated by Cell-Surface Signals  731

17.11 Signal Transduction Pathways in Lymphocyte Activation  732

      THE HUMAN PERSPECTIVE  733

      EXPERIMENTAL PATHWAYS  736

18 Techniques in Cell and Molecular Biology  742

18.1 The Light Microscope  743

18.2 Bright-Field and Phase-Contrast Microscopy  745

18.3 Fluorescence Microscopy (and Related Fluorescence-Based Techniques)  746

18.4 Transmission Electron Microscopy  752

18.5 Specimen Preparation for Electron Microscopy  753

18.6 Scanning Electron Microscopy  757

18.7 Atomic Force Microscopy  758

18.8 The Use of Radioisotopes  759

18.9 Cell Culture  760

18.10 The Fractionation of a Cell's Contents by Differential Centrifugation  762

18.11 Purification and Characterization of Proteins by Liquid Column Chromatography  762

18.12 Determining Protein-Protein Interactions  764

18.13 Characterization of Proteins by Polyacrylamide Gel Electrophoresis  766

18.14 Characterization of Proteins by Spectrometry  767

18.15 Characterization of Proteins by Mass Spectrometry  767

18.16 Determining the Structure of Proteins and Multisubunit Complexes  768

18.17 Fractionation of Nucleic Acids  770

18.18 Nucleic Acid Hybridization  773

18.19 Chemical Synthesis of DNA  774

18.20 Recombinant DNA Technology  774

18.21 Enzymatic Amplification of DNA by PCR  778

18.22 DNA Sequencing  780

18.23 DNA Libraries  782

18.24 DNA Transfer into Eukaryotic Cells and Mammalian Embryos  783

18.25 Gene Editing and Silencing  786

18.26 The Use of Antibodies  789

Glossary  G-1

Additional Reading  A-1

Index  I-1