Solution Manual for Cell and Molecular Biology: Concepts and Experiments 7th Edition Gerald Karp

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Solution Manual for Cell and Molecular Biology: Concepts and Experiments, 7th Edition, Gerald Karp,,

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Table of Contents

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

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

1.4 Viruses 23

Viroids 26

2 The Chemical Basis of Life 32

2.1 Covalent Bonds 33

Polar and Nonpolar Molecules 34

Ionizaton 34

2.2 Noncovalent Bonds 34

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

Lipids 47

Proteins 50

Nucleic Acids 77

2.6 The Formation of Complex Macromolecular Structures 79

The Assembly of Tobacco Mosaic Virus Particles and Ribosomal Subunits 79

3 Bioenergetics,Enzymes, and Metabolism 86

3.1 Bioenergetics 87

The Laws of Thermodynamics and the Concept of Entropy 87

Free Energy 89

3.2 Enzymes as Biological Catalysts 94

The Properties of Enzymes 95

Overcoming the Activation Energy Barrier 96

The Active Site 97

Mechanisms of Enzyme Catalysis 99

Enzyme Kinetics 102

3.3 Metabolism 108

An Overview of Metabolism 108

Oxidation and Reduction: A Matter of Electrons 109

The Capture and Utilization of Energy 110

Metabolic Regulation 115

4 The Structure and Function of the Plasma Membrane 120

4.1 An Overview of Membrane Functions 121

4.2 A Brief History of Studies on Plasma Membrane Structure 123

4.3 The Chemical Composition of Membranes 125

Membrane Lipids 125

The Asymmetry of Membrane Lipids 128

Membrane Carbohydrates 129

4.4 The Structure and Functions of Membrane Proteins 130

Integral Membrane Proteins 130

Studying the Structure and Properties of Integral Membrane Proteins 132Peripheral Membrane Proteins 137

Lipid-Anchored Membrane Proteins 137

4.5 Membrane Lipids and Membrane Fluidity 138

The Importance of Membrane Fluidity 139

Maintaining Membrane Fluidity 139

Lipid Rafts 139

4.6 The Dynamic Nature of the Plasma Membrane 140

The Diffusion of Membrane Proteins after Cell Fusion 141

Restrictions on Protein and Lipid Mobility 142

The Red Blood Cell: An Example of Plasma Membrane Structure 145

4.7 The Movement of Substances Across Cell Membranes 147

The Energetics of Solute Movement 147

Diffusion of Substances through Membranes 149

Facilitated Diffusion 156

Active Transport 157

4.8 Membrane Potentials and Nerve Impulses 164

The Resting Potential 164

The Action Potential 165

Propagation of Action Potentials as an Impulse 167

Neurotransmission: Jumping the Synaptic Cleft 168

5 Aerobic Respiration and the Mitochondrion 178

5.1 Mitochondrial Structure and Function 179

Mitochondrial Membranes 180

The Mitochondrial Matrix 182

5.2 Oxidative Metabolism in the Mitochondrion 183

The Tricarboxylic Acid (TCA) Cycle 185

The Importance of Reduced Coenzymes in the Formation of ATP 186

5.3 The Role of Mitochondria in the Formation of ATP 189

OxidationReduction Potentials 189

Electron Transport 190

Types of Electron Carriers 191

5.4 Translocation of Protons and the Establishment of a Proton-Motive Force 198

5.5 The Machinery for ATP Formation 199

The Structure of ATP Synthase 200

The Basis of ATP Formation According to the Binding Change Mechanism 201

Other Roles for the Proton-Motive Force in Addition to ATP Synthesis 205

5.6 Peroxisomes 206

6 Photosynthesis and the Chloroplast 211

6.1 Chloroplast Structure and Function 213

6.2 An Overview of Photosynthetic Metabolism 214

6.3 The Absorption of Light 216

Photosynthetic Pigments 216

6.4 Photosynthetic Units and Reaction Centers 218

Oxygen Formation: Coordinating the Action of Two Different Photosynthetic Systems 218

Killing Weeds by Inhibiting Electron Transport 225

6.5 Photophosphorylation 225

Noncyclic Versus Cyclic Photophosphorylation 226

6.6 Carbon Dioxide Fixation and the Synthesis of Carbohydrate 226

Carbohydrate Synthesis in C3 Plants 226

Carbohydrate Synthesis in C4 Plants 231

Carbohydrate Synthesis in CAM Plants 232

7 Interactions Between Cells and Their Environment 235

7.1 The Extracellular Space 236

The Extracellular Matrix 236

7.2 Interactions of Cells with Extracellular Materials 244

Integrins 244

Focal Adhesions and Hemidesmosomes: Anchoring Cells to Their Substratum 247

7.3 Interactions of Cells with Other Cells 250

Selectins 251

The Immunoglobulin Superfamily 252

Cadherins 253

Adhesion in Inflammation and Metastasis 255

Adherens Junctions and Desmosomes: Anchoring Cells to Other Cells 257

The Role of Cell-Adhesion Receptors in Transmembrane Signaling 259

7.4 Tight Junctions: Sealing The Extracellular Space 260

7.5 Gap Junctions and Plasmodesmata: Mediating Intercellular Communication 262

Plasmodesmata 265

7.6 Cell Walls 266

8 Cytoplasmic Membrane Systems: Structure, Function, and Membrane Trafficking 270

8.1 An Overview of the Endomembrane System 271

8.2 A Few Approaches to the Study of Endomembranes 273

Insights Gained from Autoradiography 273

Insights Gained from the Use of the Green Fluorescent Protein 273

Insights Gained from the Biochemical Analysis of Subcellular Fractions 275

Insights Gained from the Use of Cell-Free Systems 276

Insights Gained from the Study of Mutant Phenotypes 277

8.3 The Endoplasmic Reticulum 279

The Smooth Endoplasmic Reticulum 280

Functions of the Rough Endoplasmic Reticulum 280

From the ER to the Golgi Complex: The First Step in Vesicular Transport 289

8.4 The Golgi Complex 290

Glycosylation in the Golgi Complex 292

The Movement of Materials through the Golgi Complex 292

8.5 Types of Vesicle Transport and Their Functions 295

COPII-Coated Vesicles: Transporting Cargo from the ER to the Golgi Complex 296

COPI-Coated Vesicles: Transporting Escaped Proteins Back to the ER 298

Beyond the Golgi Complex: Sorting Proteins at the TGN 298

Targeting Vesicles to a Particular Compartment 300

8.6 Lysosomes 303

Autophagy 304

8.7 Plant Cell Vacuoles 307

8.8 The Endocytic Pathway: Moving Membrane and Materials into the Cell Interior 308

Endocytosis 308

Phagocytosis 315

8.9 Posttranslational Uptake of Proteins by Peroxisomes, Mitochondria, and Chloroplasts 316

Uptake of Proteins into Peroxisomes 316

Uptake of Proteins into Mitochondria 316

Uptake of Proteins into Chloroplasts 318

9 The Cytoskeleton and Cell Motility 324

9.1 Overview of the Major Functions of the Cytoskeleton 325

9.2 The Study of the Cytoskeleton 326

The Use of Live-Cell Fluorescence Imaging 326

The Use of In Vitro and In Vivo Single-Molecule Assays 327

The Use of Fluorescence Imaging Techniques to Monitor the Dynamics of the Cytoskeleton 329

9.3 Microtubules 330

Structure and Composition 330

Microtubule-Associated Proteins 331

Microtubules as Structural Supports and Organizers 332

Microtubules as Agents of Intracellular Motility 333

Motor Proteins that Traverse the Microtubular Cytoskeleton 334

Microtubule-Organizing Centers (MTOCs) 339

The Dynamic Properties of Microtubules 341

Cilia and Flagella: Structure and Function 345

9.4 Intermediate Filaments 354

Intermediate Filament Assembly and Disassembly 354

Types and Functions of Intermediate Filaments 356

9.5 Microfilaments 356

Microfilament Assembly and Disassembly 358

Myosin: The Molecular Motor of Actin Filaments 360

9.6 Muscle Contractility 364

The Sliding Filament Model of Muscle Contraction 366

9.7 Nonmuscle Motility 371

Actin-Binding Proteins 372

Examples of Nonmuscle Motility and Contractility 374

10 The Nature of the Gene and the Genome 386

10.1 The Concept of a Gene as a Unit of Inheritance 387

10.2 Chromosomes: The Physical Carriers of the Genes 388

The Discovery of Chromosomes 388

Chromosomes as the Carriers of Genetic Information 389

Genetic Analysis in Drosophila 390

Crossing Over and Recombination 390

Mutagenesis and Giant Chromosomes 392

10.3 The Chemical Nature of the Gene 393

The Structure of DNA 393

The Watson-Crick Proposal 394

DNA Supercoiling 397

10.4 The Structure of the Genome 398

The Complexity of the Genome 399

10.5 The Stability of the Genome 406

Whole-Genome Duplication (Polyploidization) 406

Duplication and Modification of DNA Sequences 407

Jumping Genes and the Dynamic Nature of the Genome 408

10.6 Sequencing Genomes: The Footprints of Biological Evolution 411

Comparative Genomics: If Its Conserved, It Must Be Important 413

The Genetic Basis of Being Human 414

Genetic Variation Within the Human Species Population 416

11 Gene Expression: From Transcription to Translation 426

11.1 The Relationship between Genes, Proteins, and RNAs 427

An Overview of the Flow of Information through the Cell 428

11.2 An Overview of Transcription in Both Prokaryotic and Eukaryotic Cells 429

Transcription in Bacteria 432

Transcription and RNA Processing in Eukaryotic Cells 433

11.3 Synthesis and Processing of Eukaryotic Ribosomal and Transfer RNAs 435

Synthesizing the rRNA Precursor 436

Processing the rRNA Precursor 437

Synthesis and Processing of the 5S rRNA 440

Transfer RNAs 440

11.4 Synthesis and Processing of Eukaryotic Messenger RNAs 441

The Machinery for mRNA Transcription 441

Split Genes: An Unexpected Finding 444

The Processing of Eukaryotic Messenger RNAs 448

Evolutionary Implications of Split Genes and RNA Splicing 454

Creating New Ribozymes in the Laboratory 454

11.5 Small Regulatory RNAs and RNA Silencing Pathways 455

MicroRNAs: Small RNAs that Regulate Gene Expression 459

piRNAs: A Class of Small RNAs that Function in Germ Cells 460

Other Noncoding RNAs 461

11.6 Encoding Genetic Information 461

The Properties of the Genetic Code 461

11.7 Decoding the Codons: The Role of Transfer RNAs 464

The Structure of tRNAs 465

11.8 Translating Genetic Information 468

Initiation 468

Elongation 471

Termination 474

mRNA Surveillance and Quality Control 474

Polyribosomes 475

12 Control of Gene Expression 483

12.1 Control of Gene Expression in Bacteria 484

Organization of Bacterial Genomes 484

The Bacterial Operon 484

Riboswitches 487

12.2 Control of Gene Expression in Eukaryotes: Structure and Function of the Cell Nucleus 488

The Nuclear Envelope 488

Chromosomes and Chromatin 493

Epigenetics: Theres More to Inheritance than DNA 509

The Nucleus as an Organized Organelle 510

12.3 An Overview of Gene Regulation in Eukaryotes 512

12.4 Transcriptional Control 514

The Role of Transcription Factors in Regulating Gene Expression 517

The Structure of Transcription Factors 519

DNA Sites Involved in Regulating Transcription 522

Transcriptional Activation: The Role of Enhancers, Promoters, and Coactivators 525

Transcriptional Repression 530

12.5 RNA Processing Control 533

12.6 Translational Control 536

Initiation of Translation 536

Cytoplasmic Localization of mRNAs 537

The Control of mRNA Stability 538

The Role of MicroRNAs in Translational Control 539

12.7 Posttranslational Control: Determining Protein Stability 541

13 DNA Replication and Repair 545

13.1 DNA Replication 546

Semiconservative Replication 546

Replication in Bacterial Cells 549

The Structure and Functions of DNA Polymerases 554

Replication in Eukaryotic Cells 558

13.2 DNA Repair 564

Nucleotide Excision Repair 565

Base Excision Repair 566

Mismatch Repair 567

Double-Strand Breakage Repair 567

13.3 Between Replication and Repair 568

14 Cellular Reproduction 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

Genetic Recombination During Meiosis 610

15 Cell Signaling and Signal Transduction: Communication Between Cells 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

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

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

17 The Immune Response 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

18 Techniques in Cell and Molecular 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 Cells 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