1 Introduction to the Study of Cell and Molecular 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 Viruses and Viroids 26

1.5 Green Cells: Volvox, an Experiment in Multicellularity 35

1.6 Engineering Linkage: Tissue Engineering 36

2 The Chemical Basis of Life 39

2.1 Covalent Bonds 40

2.2 Engineering Linkage: Radionuclides for Imaging and Treatment 43

2.3 Noncovalent Bonds 44

2.4 Acids, Bases, and Buffers 48

2.5 The Nature of Biological Molecules 49

2.6 Green Cells: Chemical Fertilizers 52

2.7 Four Types of Biological Molecules 53

2.8 The Formation of Complex Macromolecular Structures 95

3 Bioenergetics, Enzymes, and Metabolism 99

3.1 Bioenergetics 100

3.2 Enzymes as Biological Catalysts 108

3.3 Metabolism 123

3.4 Green Cells: Regulation of Metabolism by the Light/Dark Cycle 134

3.5 Engineering Linkage: Using Metabolism to Image Tumors 135

4 The Structure and Function of the Plasma Membrane 137

4.1 Introduction to the Plasma Membrane 138

4.2 The Chemical Composition of Membranes 142

4.3 Membrane Proteins 148

4.4 Membrane Lipids and Membrane Fluidity 156

4.5 The Dynamic Nature of the Plasma Membrane 159

4.6 The Movement of Substances across Cell Membranes 166

4.7 Membrane Potentials and Nerve Impulses 189

4.8 Green Cells: Electrical Signaling in Plants 198

4.9 Engineering Linkage: Neurotechnology 199

5 Aerobic Respiration and the Mitochondrion 203

5.1 Mitochondrial Structure and Function 204

5.2 Aerobic Metabolism in the Mitochondrion 209

5.3 The Role of Mitochondria in the Formation of ATP 215

5.4 Engineering Linkage: Measuring Blood Oxygen 224

5.5 Establishment of a Proton-Motive Force 225

5.6 The Machinery for ATP Formation 226

5.7 Peroxisomes 233

5.8 Green Cells: Glyoxysomes 237

6 Photosynthesis and the Chloroplast 239

6.1 The Origin of Photosynthesis 240

6.2 Chloroplast Structure 241

6.3 An Overview of Photosynthetic Metabolism 243

6.4 The Absorption of Light 244

6.5 Green Cells: Chromoplasts 246

6.6 Photosynthetic Units and Reaction Centers 247

6.7 Photophosphorylation 255

6.8 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 256

6.9 Engineering Linkage: Photodynamic Therapy 264

7 Interactions Between Cells and Their Environment 267

7.1 Extracellular Interactions 268

7.2 Engineering Linkage: Organoids 277

7.3 Interactions of Cells with Extracellular Materials 278

7.4 Interactions of Cells with Other Cells 284

7.5 Tight Junctions: Sealing the Extracellular Space 294

7.6 Intercellular Communication 296

7.7 Cell Walls 303

7.8 Green Cells: Cell Walls and Plant Terrestrialization 306

8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking 307

8.1 An Overview of the Endomembrane System 308

8.2 A Few Approaches to the Study of Endomembranes 311

8.3 The Endoplasmic Reticulum 317

8.4 The Golgi Complex 330

8.5 Types of Vesicle Transport 335

8.6 Engineering Linkage: Extracellular Vesicles for Drug Delivery 347

8.7 Lysosomes 348

8.8 Green Cells: Plant Cell Vacuoles 350

8.9 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 351

8.10 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 363

9 The Cytoskeleton and Cell Motility 369

9.1 Overview of the Major Functions of the Cytoskeleton 370

9.2 Structure and Function of Microtubules 372

9.3 Green Cells: Why the Woodbine Twineth 376

9.4 Motor Proteins: Kinesins and Dyneins 377

9.5 Microtubule-Organizing Centers (MTOCs) 383

9.6 Structure and Function of Cilia and Flagella 390

9.7 Intermediate Filaments 398

9.8 Actin and Myosin 402

9.9 Muscle Organization and Contraction 410

9.10 Engineering Linkage: Muscle Biomechanics 416

9.11 Actin-Binding Proteins 417

9.12 Cellular Motility 420

9.13 The Bacterial Cytoskeleton 430

10 The Nature of the Gene and the Genome 433

10.1 The Concept of a Gene as a Unit of Inheritance 434

10.2 The Discovery of Chromosomes 435

10.3 Chromosomes as the Carriers of Genetic Information 436

10.4 The Chemical Nature of the Gene 441

10.5 The Complexity of the Genome 452

10.6 The Stability of the Genome 458

10.7 Sequencing Genomes: The Footprints of Biological Evolution 464

10.8 Engineering Linkage: Engineering Genomes 467

10.9 The Genetic Basis of “Being Human” 468

10.10 Green Cells: Gene Transfer by Agrobacterium tumefaciens 475

11 The Central Dogma: DNA to RNA to Protein 477

11.1 The Relationships among Genes, Proteins, and RNAs 478

11.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 483

11.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 487

11.4 Synthesis and Structure of Eukaryotic Messenger RNAs 491

11.5 Small Regulatory RNAs and RNA Silencing Pathways 507

11.6 Green Cells: Long-Range siRNA Movement 512

11.7 CRISPR and Other Noncoding RNAs 513

11.8 Encoding Genetic Information 514

11.9 Decoding the Codons: The Role of Transfer RNAs 517

11.10 Translating Genetic Information 520

11.11 Engineering Linkage: DNA Origami 534

12 Control of Gene Expression 537

12.1 Control of Gene Expression in Bacteria 538

12.2 Engineering Linkage: Building Digital Logic with Genes 542

12.3 Structure of the Nuclear Envelope 543

12.4 Chromosomes and Chromatin 550

12.5 The Nucleus as an Organized Organelle 567

12.6 An Overview of Gene Regulation in Eukaryotes 570

12.7 Transcriptional Control 571

12.8 Green Cells: The ABC Model and MADS Domain Transcription Factors 592

12.9 RNA Processing Control 593

12.10 Translational Control 594

12.11 Posttranslational Control: Determining Protein Stability 601

13 DNA Replication and Repair 605

13.1 DNA Replication 606

13.2 DNA Replication in Bacterial Cells 610

13.3 The Structure and Functions of DNA Polymerases 617

13.4 Replication in Viruses 621

13.5 Engineering Linkage: Storing Data in DNA 621

13.6 DNA Replication in Eukaryotic Cells 622

13.7 DNA Repair 628

13.8 Green Cells: Gamma Gardens 632

13.9 Between Replication and Repair 633

14 Cell Division 637

14.1 The Cell Cycle 638

14.2 M Phase: Mitosis and Cytokinesis 651

14.3 Engineering Linkage: The Role of Membrane Tension in Cell Division 672

14.4 Green Cells: Unique Aspects of Plant Cell Division 673

14.5 Meiosis 673

15 Cell Signaling and Signal Transduction: Communication between Cells 685

15.1 The Basic Elements of Cell Signaling Systems 686

15.2 A Survey of Extracellular Messengers and Their Receptors 689

15.3 G Protein-Coupled Receptors and Their Second Messengers 690

15.4 Engineering Linkage: Biosensors in Medicine and Biology 709

15.5 Protein-Tyrosine Phosphorylation as a Mechanism for Signal Transduction 710

15.6 Green Cells: Auxin Signaling 721

15.7 The Role of Calcium as an Intracellular Messenger 721

15.8 Convergence, Divergence, and Cross-Talk among Different Signaling Pathways 726

15.9 The Role of NO as an Intracellular Messenger 729

15.10 Apoptosis (Programmed Cell Death) 731

16 Cancer 737

16.1 Basic Properties of a Cancer Cell 738

16.2 The Causes of Cancer 741

16.3 Cancer: A Genetic Disorder 747

16.4 Engineering Linkage: Therapeutic Radiation 767

16.5 Green Cells: Plant-Based Chemotherapies 767

16.6 Strategies for Combating Cancer 768

17 The Immune Response 775

17.1 An Overview of the Immune Response 776

17.2 Green Cells: The Plant Immune System 780

17.3 The Clonal Selection Theory as It Applies to B Cells 781

17.4 T Lymphocytes: Activation and Mechanism of Action 787

17.5 Selected Topics on the Cellular and Molecular Basis of Immunity 790

17.6 Engineering Linkage: Adoptive T-cell Therapy 808

17.7 Signal Transduction Pathways in Lymphocyte Activation 809

18 Techniques in Cell and Molecular Biology 811

18.1 The Light Microscope 812

18.2 Transmission Electron Microscopy 822

18.3 Scanning Electron and Atomic Force Microscopy 828

18.4 The Use of Radioisotopes 830

18.5 Cell Culture 831

18.6 The Fractionation of a Cell’s Contents by Differential Centrifugation 833

18.7 Isolation, Purification, and Fractionation of Proteins 834

18.8 Determining the Structure of Proteins and Multisubunit Complexes 840

18.9 Fractionation of Nucleic Acids 842

18.10 Nucleic Acid Hybridization 845

18.11 Chemical Synthesis of DNA 846

18.12 Recombinant DNA Technology 847

18.13 Enzymatic Amplification of DNA by PCR 851

18.14 DNA Sequencing 853

18.15 DNA Libraries 855

18.16 DNA Transfer into Eukaryotic Cells and Mammalian Embryos 857

18.17 Gene Editing and Silencing 860

18.18 The Use of Antibodies 864

Additional Readings A-1

Glossary G-1

Index I-1

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