Karp's Cell and Molecular Biology: Concepts and Experiments. ISBN 1118886143, 978-1118886144
Karp's Cell and Molecular Biology: Concepts and Experiments. ISBN 1118886143, 978-1118886144
Experiments
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ISBN: 978‐1‐118‐88614‐4
BRV ISBN: 978‐1‐118‐30179‐1
10 9 8 7 6 5 4 3 2 1
PREFACE
skillfully designed the interior and front cover. John Sedat, and Joel Rosenbaum, for launching him in the direction
Janet Iwasa thanks Rob Savage, Dyche Mullins and Jack Szostak, that he went. He thanks his parents, Clifford and Adele Marshall for
for inspiring and guiding her along the path towards becoming a making him who he is. And he thanks his family, Jennifer and Wyeth,
biologist. Janet is particularly grateful for the support of her family, for continued inspiration and support.
PREFACE
Lipscomb University University of South Carolina University of Michigan‐Flint
MARGARET LYNCH DONNA RITCH COLLEEN TALBOT
Tufts University University of Wisconsin— California State Univerity,
CHARLES MALLERY Green Bay San Bernardino
University of Miami JOEL L. ROSENBAUM WILLIAM TERZAGHI
MICHAEL A. MCALEAR Yale University Wilkes University
Wesleyan University WOLFRAM SAENGER GISELLE THIBAUDEAU
ARDYTHE A. MCCRACKEN Freie Universitat Berlin Mississippi State University
University of Nevada—Reno SHIVENDRA V. SAHI JEFFREY L. TRAVIS
THOMAS MCKNIGHT Western Kentucky University University at Albany—SUNY
Texas A&M University JAMIE SANFORD PAUL TWIGG
JOANN MEERSCHAERT Ohio Northern University University of Nebraska‐Kearney
St. Cloud State University JOSHUA SANDQUIST NIGEL UNWIN
JOHN MENNINGER Grinnell College MRC Laboratory of Molecular Biology
University of Iowa PRASANNA SATPUTE‐KRISHNAN AJIT VARKI
KIRSTEN MONSEN National Institute of Health University of California—San Diego
Montclair State University INDER M. SAXENA JOSE VAZQUEZ
ANDREW NEWMAN University of Texas, Austin New York University
Cambridge University RANDY SCHEKMAN CLAIRE E. WALCZAK
MICHELLE MORITZ University of California—Berkeley Indiana University
University of California—San Francisco SANDRA SCHMID PAUL E. WANDA
ROBERT MORRIS The Scripps Research Institute Southern Illinois University,
Wheaton College TRINA SCHROER Edwardsville
ALAN NIGHORN Johns Hopkins University JENNIFER WATERS
University of Arizona TIM SCHUH Harvard University
ROBERT M. NISSEN St. Cloud State University CHRIS WATTERS
California State University, Los Angeles DAVID SCHULTZ Middlebury College
JONATHAN NUGENT University of Louisville ANDREW WEBBER
University of London ROD SCOTT Arizona State University
VERONICA C. NWOSU Wheaton College BEVERLY WENDLAND
North Carolina Central University KATIE SHANNON Johns Hopkins University
MIKE O’DONNELL University of North Carolina— GARY M. WESSEL
Rockefeller University Chapel Hill Brown University
GREG ODORIZZI JOEL B. SHEFFIELD ERIC V. WONG
University of Colorado, Boulder Temple University University of Louisville
LEOCADIA PALIULIS ERIC SHELDEN ANDREW WOOD
Bucknell University Washington State University Southern Illinois University
JAMES G. PATTON DENNIS SHEVLIN GARY YELLEN
Vanderbilt University College of New Jersey Harvard Medical School
HUGH R. B. PELHAM JEFF SINGER MASASUKE YOSHIDA
MRC Laboratory of Molecular Biology Portland State University Tokyo Institute of Technology
JONATHAN PINES ROGER D. SLOBODA DANIELA ZARNESCU
Wellcome/CRC Institute Dartmouth College University of Arizona
DEBRA PIRES HARRIETT E. SMITH‐SOMERVILLE JIANZHI ZHANG
University of California—Los Angeles University of Alabama University of Michigan
MITCH PRICE BRUCE STILLMAN ROBERT A. ZIMMERMAN
Pennsylvania State University Cold Spring Harbor Laboratory University of Massachusetts
1 Introduction to the Study of Cell and Hydrophobic Interactions and van der Waals Forces
The Life-Supporting Properties of Water 37
36
Molecular Biology 1
2.4 Acids, Bases, and Buffers 38
1.1 The Discovery of Cells 2 2.5 The Nature of Biological Molecules 39
Microscopy 2
Functional Groups 40
Cell Theory 2
A Classification of Biological Molecules by Function 40
1.2 Basic Properties of Cells 3 2.6 Carbohydrates 42
Cells Are Highly Complex and Organized 3
The Structure of Simple Sugars 42
Cells Possess a Genetic Program and the Means
Stereoisomerism 42
to Use It 5
Linking Sugars Together 43
Cells Are Capable of Producing More of Themselves 5
Polysaccharides 44
Cells Acquire and Utilize Energy 5
Cells Carry Out a Variety of Chemical Reactions 6 2.7 Lipids 46
Cells Engage in Mechanical Activities 6 Fats 46
Cells Are Able to Respond to Stimuli 6 Steroids 47
Cells Are Capable of Self-Regulation 6 Phospholipids 47
Cells Evolve 7
2.8 Building Blocks of Proteins 48
1.3 Characteristics That Distinguish Prokaryotic The Structures of Amino Acids 49
and Eukaryotic Cells 8 The Properties of the Side Chains 50
1.4 Types of Prokaryotic Cells 13 2.9 Primary and Secondary Structures of Proteins 53
Domain Archaea and Domain Bacteria 13 Primary Structure 53
Prokaryotic Diversity 14 Secondary Structure 53
1.5 Types of Eukaryotic Cells 15 2.10 Tertiary Structure of Proteins 55
Cell Differentiation 15 Myoglobin: The First Globular Protein Whose Tertiary
Model Organisms 16 Structure Was Determined 56
1 .6 T HE HUM AN P E R S P E CTIVE: Tertiary Structure May Reveal Unexpected Similarities
The Prospect of Cell Replacement Therapy 17
between Proteins 56
Protein Domains 57
1.7 The Sizes of Cells and Their Components 21
Dynamic Changes within Proteins 58
1.8 Viruses and Viroids 23
2.11 Quaternary Structure of Proteins 58
1 .9 E X P E R IM E N TAL PAT HWAY S:
The Structure of Hemoglobin 59
The Origin of Eukaryotic Cells 26 Protein–Protein Interactions 59
3.12 Metabolic Regulation 109 4.11 The Diffusion of Ions through Membranes 143
Altering Enzyme Activity by Covalent Modification 109 4.12 EX P ERIMEN TAL PATHWAYS:
Altering Enzyme Activity by Allosteric Modulation 110 The Acetylcholine Receptor 147
CONTENTS
Other Roles for the Proton-Motive Force in Addition to ATP
Hydrolysis 152
Synthesis 193
Other Primary Ion Transport Systems 154
Using Light Energy to Actively Transport Ions 155 5.10 Peroxisomes 193
Secondary Active Transport (or Cotransport): Coupling 5.11 TH E H UMAN P ERSPECTI V E:
Transport to Existing Ion Gradients 155 Diseases that Result from Abnormal Mitochondrial or
4 .1 5 T HE HUM AN P E R S P E C TIVE: Peroxisomal Function 195
Defects in Ion Channels and Transporters as a Cause of Inherited
Disease 157
7.10 The Role of Cell-Adhesion Receptors in 8.10 Types of Vesicle Transport 280
Transmembrane Signaling 245 COPII-Coated Vesicles: Transporting Cargo from the ER to
the Golgi Complex 281
7.11 Tight Junctions: Sealing the Extracellular
COPI-Coated Vesicles: Transporting Escaped Proteins Back
Space 245
to the ER 284
7.12 Gap Junctions and Plasmodesmata: Mediating
8.11 Beyond the Golgi Complex: Sorting Proteins at
Intercellular Communication 247
the TGN 285
Gap Junctions 248
Sorting and Transport of Lysosomal Enzymes 285
Plasmodesmata 250
Sorting and Transport of Nonlysosomal Proteins 286
7. 13 E X P E R IM E N TAL PAT HWAYS:
8.12 TH E H UMAN P ERSPECTI V E:
The Role of Gap Junctions in Intercellular Communication 251
Disorders Resulting from Defects in Lysosomal Function 286
7.14 Cell Walls 254 8.13 Targeting Vesicles to a Particular
Compartment 288
8 Cytoplasmic Membrane Systems: 8.14 Exocytosis 290
Structure, Function, and Membrane 8.15 Lysosomes 291
Trafficking 257 8.16 Plant Cell Vacuoles 292
8.17 Endocytosis 293
8.1 An Overview of the Endomembrane System 258
Receptor-Mediated Endocytosis and the Role of
8.2 A Few Approaches to the Study of Coated Pits 294
Endomembranes 260 The Role of Phosphoinositides in the Regulation of
Insights Gained from Autoradiography 260 Coated Vesicles 296
Insights Gained from the Use of the Green Fluorescent 8.18 EX P ERIMEN TAL PATHWAYS:
Protein 260
Receptor‐Mediated Endocytosis 297
Insights Gained from the Analysis of Subcellular Fractions 262
Insights Gained from the Use 8.19 The Endocytic Pathway 300
of Cell-Free Systems 263 8.20 Phagocytosis 303
Insights Gained from the Study of Mutant Phenotypes 263
8.21 Posttranslational Uptake of Proteins by
8.3 The Endoplasmic Reticulum 265 Peroxisomes, Mitochondria, and
The Smooth Endoplasmic Reticulum 266 Chloroplasts 304
The Rough Endoplasmic Reticulum 267 Uptake of Proteins into Peroxisomes 304
8.4 Functions of the Rough Endoplasmic Uptake of Proteins into Mitochondria 304
Reticulum 268 Uptake of Proteins into Chloroplasts 306
Synthesis of Proteins on Membrane-Bound versus Free
Ribosomes 268
Synthesis of Secretory, Lysosomal, or Plant Vacuolar 9 The Cytoskeleton and
Proteins 268
Processing of Newly Synthesized Proteins in the Endoplasmic
Cell Motility 309
Reticulum 270
9.1 Overview of the Major Functions of the
Synthesis of Integral Membrane Proteins on ER-Bound
Ribosomes 270
Cytoskeleton 310
CONTENTS
Microtubules as Structural Supports and Organizers 313 10.1 The Concept of a Gene as a Unit of
Microtubules as Agents of Intracellular Motility 314 Inheritance 367
9.3 Motor Proteins: Kinesins and Dyneins 315 10.2 The Discovery of Chromosomes 368
Motor Proteins Traverse the Microtubular Cytoskeleton 315
Kinesins 316 10.3 Chromosomes as the Carriers of Genetic
Cytoplasmic Dynein 317 Information 369
9 .4 E X P E R IM E N TAL PAT HWAY: 10.4 Genetic Analysis in Drosophila 370
The Step Size of Kinesin 319 Crossing Over and Recombination 371
9.5 Microtubule-Organizing Centers (MTOCs) 321 Mutagenesis and Giant Chromosomes 371
Centrosomes 321 10.5 The Structure of DNA 373
Basal Bodies and Other MTOCs 322
The Watson-Crick Proposal 374
Microtubule Nucleation 322
The Importance of the
9.6 Microtubule Dynamics 323 Watson-Crick Proposal 375
The Dynamic Properties of Microtubules 323 10.6 EX P ERIMEN TAL PATHWAYS:
The Underlying Basis of The Chemical Nature of the Gene 377
Microtubule Dynamics 325
10.7 DNA Supercoiling 381
9.7 Structure and Function of Cilia and Flagella 327
Structure of Cilia and Flagella 329 10.8 The Complexity of the Genome 382
Growth by Intraflagellar Transport 331 DNA Denaturation 383
The Mechanism of Ciliary DNA Renaturation 384
and Flagellar Locomotion 331
10.9 TH E H UMAN P ERSPECTI V E:
9 .8 T HE HUM AN P E R S P E CTIVE: Diseases That Result from Expansion of Trinucleotide
The Role of Cilia in Development and Disease 333 Repeats 387
9.9 Intermediate Filaments 335 10.10 The Stability of the Genome: Duplication 389
Intermediate Filament Assembly and Disassembly 335
Whole-Genome Duplication (Polyploidization) 389
Types and Functions of Intermediate Filaments 336
Duplication and Modification of DNA Sequences 390
9.10 Actin 338 Evolution of Globin Genes 390
Actin Structure 338
10.11 The Dynamic Nature of the Genome: “Jumping
Actin Filament Assembly and Disassembly 339
Genes” 391
9.11 Myosin: The Molecular Motor of Actin 341 Transposons 392
Conventional (Type II) Myosins 341 The Role of Mobile Genetic Elements in Genome
Unconventional Myosins 341 Evolution 393
9.12 Muscle Organization and Contraction 344 10.12 Sequencing Genomes: The Footprints of
Organization of Sarcomeres 346 Biological Evolution 394
The Sliding Filament Model
10.13 Comparative Genomics: “If It’s Conserved, It
of Muscle Contraction 346
Must Be Important” 396
9.13 Actin-Binding Proteins 351
10.14 The Genetic Basis of “Being Human” 397
9.14 Cellular Motility 353
9 .1 5 E X P E R IM E N TAL PAT HWAY:
10.15 Genetic Variation within the Human Species
Population 398
Studying Actin‐Based Motility without Cells 358
DNA Sequence Variation 398
9.16 Actin-dependent Processes During Structural Variation 399
Development 361 Copy Number Variation 399
Axonal Outgrowth 361
10.16 TH E H UMAN PERSPECTI V E:
9.17 The Bacterial Cytoskeleton 362 Application of Genomic Analyses to Medicine 400
11.1 The Relationship between Genes, Proteins, Initiation of Translation in Prokaryotes 442
and RNAs 405 Initiation of Translation in Eukaryotes 443
Evidence That DNA Is the Genetic Material 405 The Role of the Ribosome 444
An Overview of the Flow of Information through the Cell 406
11.17 Translating Genetic Information: Elongation
11.2 The Role of RNA Polymerases in and Termination 445
Transcription 408 Elongation Step 1: Aminoacyl-tRNA Selection 445
11.3 An Overview of Transcription in Both Prokaryotic Elongation Step 2: Peptide Bond Formation 445
and Eukaryotic Cells 410 Elongation Step 3: Translocation 446
Elongation Step 4: Releasing the Deacylated tRNA 447
Transcription in Bacteria 410
Termination 448
Transcription and RNA Processing in Eukaryotic Cells 411
11.4 Synthesis and Processing of Eukaryotic 11.18 mRNA Surveillance and Quality Control 448
11.13 CRISPR and other Noncoding RNAs 435 12.7 Epigenetics: There’s More to Inheritance than
CRISPR: Noncoding RNA in Bacteria 435
DNA 480
Other Noncoding RNAs 436 12.8 The Nucleus as an Organized Organelle 480
11.14 Encoding Genetic Information 436 12.9 An Overview of Gene Regulation in
The Properties of the Genetic Code 436 Eukaryotes 483
Identifying the Codons 437 12.10 Profiling Gene Activity 485
11.15 Decoding the Codons: The Role of Transfer DNA Microarrays 485
RNAs 439 RNA Sequencing 487
CONTENTS
The Eukaryotic Replication Fork 528
The Zinc-Finger Motif 490
Replication and Nuclear Structure 530
The Helix–Loop–Helix (HLH) Motif 490
The Leucine Zipper Motif 491 13.7 Chromatin Structure and Replication 530
12.13 DNA Sites Involved in Regulating 13.8 DNA Repair 531
Transcription 492 Nucleotide Excision Repair 532
12.14 An Example of Transcriptional Activation: Base Excision Repair 532
The Glucocorticoid Receptor 494 Mismatch Repair 534
Double-Strand Breakage Repair 534
12.15 Transcriptional Activation: The Role of
Enhancers, Promoters, and Coactivators 495 13.9 Between Replication and Repair 535
Coactivators That Interact with the Basal Transcription 13.10 TH E H UMAN PERSPECTI V E:
Machinery 496 Consequences of DNA Repair Deficiencies 536
Coactivators That Alter Chromatin Structure 496
Cytokinesis in Plant Cells: Formation of the Cell Plate 570 Information 610
14.12 Overview of Meiosis 571 15.12 Signaling by the Insulin Receptor 611
The Insulin Receptor Is a Protein-Tyrosine Kinase 611
14.13 The Stages of Meiosis 574
Insulin Receptor Substrates 1 and 2 611
14. 14 T HE HUM AN P E R S P E CT IVE:
Glucose Transport 612
Meiotic Nondisjunction and Its Consequences 577
Diabetes Mellitus 613
14.15 Genetic Recombination during Meiosis 579 15.13 Signaling Pathways in Plants 613
15.14 The Role of Calcium as an Intracellular
15 Cell Signaling and Signal Messenger 613
Transduction: Communication IP3 and Voltage-Gated Ca2+ Channels 613
Visualizing Cytoplasmic Ca2+ Concentration in Living
between Cells 582 Cells 614
Ca2+-Binding Proteins 615
15.1 The Basic Elements of Cell Signaling
Regulating Calcium Concentrations in Plant Cells 617
Systems 583
15.15 Convergence, Divergence, and Cross-Talk
15.2 A Survey of Extracellular Messengers and Their
among Different Signaling Pathways 617
Receptors 586
15.16 The Role of NO as an Intercellular
15.3 Signal Transduction by G Protein-Coupled Messenger 619
Receptors 587 NO as an Activator of Guanylyl Cyclase 620
Receptors 587 Inhibiting Phosphodiesterase 620
G Proteins 588
Termination of the Response 589
15.17 Apoptosis (Programmed Cell Death) 621
Bacterial Toxins 590 The Extrinsic Pathway of Apoptosis 622
The Intrinsic Pathway of Apoptosis 623
15. 4 E X P E R IM E N TAL PAT HWAYS:
Necroptosis 624
The Discovery and Characterization of GTP‐Binding
Signaling Cell Survival 624
Proteins 590
15. 5 T HE HUM AN P E R S P E CT IV E:
Disorders Associated with G Protein‐Coupled Receptors 594 16 Cancer 627
15.6 Second Messengers 595
16.1 Basic Properties of a Cancer Cell 628
The Discovery of Cyclic AMP 595
Phosphatidylinositol-Derived Second Messengers 596 16.2 The Causes of Cancer 631
Phospholipase C 597 16.3 EX P ERIMEN TAL PATHWAYS:
15.7 The Specificity of G Protein-Coupled The Discovery of Oncogenes 632
CONTENTS
Oncogenes That Encode Products
That Affect Apoptosis 648 18.1 The Light Microscope 693
Resolution 694
16.10 The Mutator Phenotype: Mutant Genes
Visibility 695
Involved in DNA Repair 649
18.2 Bright-Field and Phase-Contrast Microscopy 695
16.11 MicroRNAs: A New Player in the Genetics of
Cancer 649 Bright-Field Light Microscopy 695
Phase-Contrast Microscopy 695
16.12 The Cancer Genome 649
18.3 Fluorescence Microscopy (and Related
16.13 Gene-Expression Analysis 651 Fluorescence-Based Techniques) 696
16.14 Strategies for Combating Cancer 654 Laser Scanning Confocal Microscopy 699
16.15 Immunotherapy 654 Super-Resolution Fluorescence Microscopy 699
Light Sheet Fluorescence Microscopy 700
16.16 Inhibiting the Activity of Cancer-Promoting
Proteins 656 18.4 Transmission Electron Microscopy 701
16.17 The Concept of a Cancer Stem Cell 658 18.5 Specimen Preparation for Electron
16.18 Inhibiting the Formation of New Blood Vessels Microscopy 703
(Angiogenesis) 659 Cryofixation and the Use of Frozen Specimens 703
Negative Staining 705
Shadow Casting 705
17 The Immune Response 661 Freeze-Fracture Replication and Freeze Etching 705
17.1 An Overview of the Immune Response 662 18.6 Scanning Electron Microscopy 707
Innate Immune Responses 663 18.7 Atomic Force Microscopy 708
Adaptive Immune Responses 665
18.8 The Use of Radioisotopes 709
17.2 The Clonal Selection Theory as It Applies to B
Cells 666 18.9 Cell Culture 710
1 7 .3 T HE HUM AN P E R S P E CTIVE: 18.10 The Fractionation of a Cell’s Contents by
Autoimmune Diseases 668 Differential Centrifugation 711
17.4 Vaccination 671 18.11 Purification and Characterization of Proteins by
1 7 .5 E X P E R IM E N TAL PAT HWAY S: Liquid Column Chromatography 712
The Role of the Major Histocompatibility Complex in Antigen Ion-Exchange Chromatography 712
Presentation 672 Gel Filtration Chromatography 712
17.6 T Lymphocytes: Activation and Mechanism of Affinity Chromatography 713
Action 675 18.12 Determining Protein–Protein Interactions 714
17.7 The Modular Structure of Antibodies 678 18.13 Characterization of Proteins by Polyacrylamide
17.8 DNA Rearrangements That Produce Genes Gel Electrophoresis 715
Encoding B- and T-Cell Antigen Receptors 681 SDS–PAGE 716
17.9 Membrane-Bound Antigen Receptor Two-Dimensional Gel Electrophoresis 716
Complexes 683 18.14 Characterization of Proteins by
17.10 The Major Histocompatibility Complex 684 Spectrometry 716
17.11 Distinguishing Self from Nonself 686 18.15 Characterization of Proteins by Mass
17.12 Lymphocytes Are Activated by Cell-Surface Spectrometry 716
Signals 689 18.16 Determining the Structure of Proteins and
Activation of Helper T Cells by Professional APCs 689 Multisubunit Complexes 717
Activation of B Cells by TH Cells 689 18.17 Fractionation of Nucleic Acids 719
17.13 Signal Transduction Pathways in Lymphocyte Separation of DNAs by Gel Electrophoresis 719
Activation 689 Separation of Nucleic Acids by Ultracentrifugation 719