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Lewin’s
CELLS Third edition
Lead Editors
George Plopper
Rensselaer Polytechnic Institute
David Sharp
Albert Einstein College of Medicine
Eric Sikorski
University of Tampa

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Library of Congress Cataloging-in-Publication Data

Lewin’s cells. — 3rd ed. / [edited by] George Plopper, David Sharp, Eric Sikorski.
p. ; cm.
Cells
Rev. ed. of: Lewin’s cells / lead editors, Lynne Cassimeris, Vishwanath R. Lingappa, George Plopper. 2nd ed. c2011.
Includes bibliographical references and index.
ISBN 978-1-284-02355-8
I. Plopper, George. II. Sharp, David, 1968- III. Sikorski, Eric. IV. Lewin, Benjamin. Cells. V. Title: Cells.
[DNLM: 1. Cells. 2. Cell Physiological Phenomena. 3. Eukaryotic Cells. QU 300]
571.6_dc23
2012050452
6048
Printed in the United States of America

17â•…16â•…15â•…14â•…13â•…â•…10â•…9â•…8â•…7â•…6â•…5â•…4â•…3â•…2â•…1

Brief contents
Part 1â•‡Introduction 1 Part 5â•‡ Cell division, apoptosis,
1 What is a cell?â•‡â•‡ 2 and cancer 631
Vishwanath R. Lingappa and Benjamin Lewin
14 Mitosisâ•‡â•‡632
2 Bioenergetics and cellular metabolismâ•‡â•‡ 31 Conly L. Rieder
Bianca Barquera
15 Cell cycle regulationâ•‡â•‡ 685
3 DNA replication, repair, and recombinationâ•‡â•‡ 59 Kathleen L. Gould and Susan L. Forsburg
Jocelyn E. Krebs
16 Apoptosisâ•‡â•‡725
4 Gene expression and regulationâ•‡â•‡ 103 Douglas R. Green
David G. Bear
17 Cancer: Principles and overviewâ•‡â•‡ 750
5 Protein structure and functionâ•‡â•‡ 169 Robert A. Weinberg
Stephen J. Smerdon
Part 6â•‡ Cell communication 777
Part 2â•‡ Membranes and 18 Principles of cell signalingâ•‡â•‡ 778
transport mechanisms 229 Elliott M. Ross and Melanie H. Cobb
6 Transport of ions and small molecules across 19 The extracellular matrix and cell
membranesâ•‡â•‡230 adhesionâ•‡â•‡831
Stephan E. Lehnart and Andrew R. Marks George Plopper
7 Membrane targeting of proteinsâ•‡â•‡ 301
D. Thomas Rutkowski and Vishwanath R. Lingappa Part 7â•‡ Prokaryotic and
8 Protein trafficking between membranesâ•‡â•‡ 354 plant cells 891
Vivek Malhotra, Graham Warren, and Ira Mellman 20 Prokaryotic cell biologyâ•‡â•‡ 892
Matthew Chapman and Jeff Errington
Part 3â•‡ The nucleus 401 21 Plant cell biologyâ•‡â•‡ 945
9 Nuclear structure and transportâ•‡â•‡ 402 Clive Lloyd
Charles N. Cole
10 Chromatin and chromosomesâ•‡â•‡ 451
Benjamin Lewin and Jocelyn E. Krebs
Part 4â•‡ The cytoskeleton 513

11 Microtubulesâ•‡â•‡514
Lynne Cassimeris
12 Actinâ•‡â•‡568
Enrique M. De La Cruz and E. Michael Ostap
13 Intermediate filamentsâ•‡â•‡604
Birgit Lane

Contents
Feature Boxesâ•‡â•‡xvii 1.16 Protein trafficking moves proteins through the

endoplasmic reticulum and Golgi apparatusâ•‡â•‡ 21
Prefaceâ•‡â•‡xviii
1.17 Protein folding and unfolding is an essential feature
Acknowledgmentsâ•‡â•‡xx of all cellsâ•‡â•‡ 22
1.18 The shape of a eukaryotic cell is determined by its
Contributorsâ•‡â•‡xxi
cytoskeletonâ•‡â•‡23
Abbreviationsâ•‡â•‡xxiii 1.19 Localization of cell structures is importantâ•‡â•‡ 25
1.20 Cellular functions are carried out by enzymes and
Part 1â•‡Introduction 1 enzyme pathways and are controlled by feedback
mechanismsâ•‡â•‡26
1.21 Signal transduction pathways execute predefined
1 What is a cell? . . . . . . . . . . . 2 responsesâ•‡â•‡26
Vishwanath R. Lingappa and Benjamin Lewin 1.22 Many enzymes and signaling pathways are organized as
1.1 Introductionâ•‡â•‡3 multiprotein complexes that function as machinesâ•‡â•‡ 27
1.2 Life began as a self-replicating structureâ•‡â•‡ 5 1.23 All organisms have cells that can grow and
divideâ•‡â•‡28
1.3 A prokaryotic cell consists of a single compartmentâ•‡â•‡ 7
1.24 Differentiation creates specialized cell types,
1.4 Prokaryotes are adapted for growth under many
including terminally differentiated cellsâ•‡â•‡ 29
diverse conditionsâ•‡â•‡8
Referencesâ•‡â•‡30
1.5 A eukaryotic cell contains many
membrane-delimited compartmentsâ•‡â•‡9
1.6 Membranes allow the cytoplasm to maintain 2 Bioenergetics and cellular
compartments with distinct environmentsâ•‡â•‡ 10
metabolism . . . . . . . . . . . . 31
1.7 The nucleus contains the genetic material and is
Bianca Barquera
surrounded by an envelopeâ•‡â•‡ 11
1.8 The plasma membrane allows a cell to maintain 2.1 Introductionâ•‡â•‡32
homeostasisâ•‡â•‡13 2.2 Chemical equilibrium and reaction kinetics are
1.9 Cells within cells: Organelles bounded by envelopes linkedâ•‡â•‡32
may have resulted from endosymbiosisâ•‡â•‡ 15 2.3 The steady state model is essential for
1.10 DNA is the cellular hereditary material, but there are understanding the net flow of reactants in linked
other forms of hereditary informationâ•‡â•‡ 16 reactionsâ•‡â•‡33
1.11 Cells require mechanisms to repair damage to 2.4 Thermodynamics is the systematic treatment of
DNAâ•‡â•‡17 energy changesâ•‡â•‡35
1.12 Mitochondria are energy factoriesâ•‡â•‡ 17 2.5 Standard free energy, the mass action ratio, and the
equilibrium constant characterize reaction rates in
1.13 Chloroplasts power plant cellsâ•‡â•‡ 18
metabolic pathwaysâ•‡â•‡38
1.14 Organelles require mechanisms for specific
2.6 Glycolysis is the best understood metabolic
localization of proteinsâ•‡â•‡ 19
pathwayâ•‡â•‡39
1.15 Proteins are transported to and through
2.7 Pyruvate metabolism by the pyruvate dehydrogenase
membranesâ•‡â•‡20
complex leads to oxidative respirationâ•‡â•‡ 42
vi

2.8 Fatty acid oxidation is the major pathway of aerobic 3.17 Double-strand breaks are repaired by homologous
energy productionâ•‡â•‡43 and nonhomologous pathwaysâ•‡â•‡ 94
2.9 The Krebs cycle oxidizes acetyl-CoA and is a 3.18 HR is used for both repair and meiotic
metabolic hubâ•‡â•‡44 recombinationâ•‡â•‡96
2.10 Coupling of chemical reactions is a key feature of 3.19 Summaryâ•‡â•‡100
living organismsâ•‡â•‡46 Referencesâ•‡â•‡102
2.11 Oxidative phosphorylation is the final common
pathway converting electron energy to ATPâ•‡â•‡ 47
2.12 Photosynthesis completes the carbon cycle by
4 Gene expression and
converting CO2 to sugarâ•‡â•‡ 51 regulation . . . . . . . . . . . . 103
2.13 Nitrogen metabolism encompasses amino acid, David G. Bear
protein, and nucleic acid pathwaysâ•‡â•‡ 54
4.1 Introductionâ•‡â•‡104
2.14 The Cori cycle and the purine nucleotide cycle are
4.2 Genes are transcription unitsâ•‡â•‡ 107
specialized pathwaysâ•‡â•‡55
4.3 Transcription is a multistep process directed by
2.15 Metabolic viewpoints provide insight into cellular
DNA-dependent RNA polymeraseâ•‡â•‡ 109
regulation—only metabolically reversible reactions
are possible regulatory sitesâ•‡â•‡ 56 4.4 RNA polymerases are large multisubunit protein
complexesâ•‡â•‡112
2.16 Some new approachesâ•‡â•‡ 56
4.5 Promoters direct the initiation of transcriptionâ•‡â•‡ 116
2.17 Summaryâ•‡â•‡58
4.6 Activators and repressors regulate transcription
initiationâ•‡â•‡120
4.7 Transcriptional regulatory circuits control eukaryotic
3 DNA replication, repair, and cell growth, proliferation, and differentiationâ•‡â•‡ 126
recombination . . . . . . . . . . 59 4.8 The 5′ and 3′ ends of mature mRNAs are generated
by RNA processingâ•‡â•‡ 133
Jocelyn E. Krebs
4.9 Terminators direct the end of transcription
3.1 Introductionâ•‡â•‡60 elongationâ•‡â•‡137
3.2 DNA is the genetic materialâ•‡â•‡ 60 4.10 Introns in eukaryotic pre-mRNAs are removed by the
3.3 The structure of DNAâ•‡â•‡ 62 spliceosomeâ•‡â•‡140
3.4 DNA replication is semiconservative and 4.11 Alternative splicing generates protein diversityâ•‡â•‡ 144
bidirectionalâ•‡â•‡66 4.12 Translation is a three-stage process that decodes an
3.5 DNA polymerases replicate DNAâ•‡â•‡ 68 mRNA to synthesize a proteinâ•‡â•‡ 146
3.6 Helicases, single-strand binding proteins, and 4.13 Translation is catalyzed by the ribosomeâ•‡â•‡ 146
topoisomerases are required for replication fork 4.14 Translation is guided by a large number of protein
progressionâ•‡â•‡70 factors that regulate the interaction of
3.7 Priming is required to start DNA synthesisâ•‡â•‡ 71 aminoacylated tRNAs with the ribosomeâ•‡â•‡ 151
3.8 A sliding clamp ensures processive DNA replicationâ•‡â•‡ 72 4.15 Translation is controlled by the interaction of the 5′
3.9 Leading and lagging strand synthesis is and 3′ ends of the mRNA and by translational
coordinatedâ•‡â•‡74 repressor proteinsâ•‡â•‡156
3.10 Replication initiates at origins and is regulated by 4.16 Some mRNAs are translated at specific locations
the cell cycleâ•‡â•‡ 76 within the cytoplasmâ•‡â•‡ 159
3.11 Replicating the ends of a linear chromosomeâ•‡â•‡ 78 4.17 Sequence elements in the 5′ and 3′ untranslated
regions determine the stability of an mRNAâ•‡â•‡ 159
3.12 DNA is subject to damageâ•‡â•‡ 80
4.18 Noncoding RNAs are important regulators of gene
3.13 Direct repair can reverse some DNA damageâ•‡â•‡ 84
expressionâ•‡â•‡163
3.14 Mismatch repair corrects replication errorsâ•‡â•‡ 85
4.19 What’s next?â•‡â•‡166
3.15 Base excision repair replaces damaged basesâ•‡â•‡ 90
3.16 Nucleotide excision repair removes bulky DNA
lesionsâ•‡â•‡92
Contents vii

5 Protein structure and 6.4 Electrochemical gradients across the cell
membrane generate the membrane
function. . . . . . . . . . . . . . 169 potentialâ•‡â•‡235
Stephen J. Smerdon 6.5 K+ channels catalyze selective and rapid ion
5.1 Introductionâ•‡â•‡170 permeationâ•‡â•‡237
5.2 X-ray crystallography and structural biologyâ•‡â•‡ 171 6.6 Different K+ channels use a similar gate coupled to
different activating or inactivating
5.3 Nuclear magnetic resonanceâ•‡â•‡ 175
mechanismsâ•‡â•‡241
5.4 Electron microscopy of biomolecules and their
6.7 Voltage-dependent Na+ channels are activated by
complexesâ•‡â•‡180
membrane depolarization and translate electrical
5.5 Protein structure representations: a primerâ•‡â•‡ 183 signalsâ•‡â•‡246
5.6 Proteins are linear chains of amino acids: primary 6.8 Epithelial Na+ channels regulate Na+
structureâ•‡â•‡185 homeostasisâ•‡â•‡250
5.7 Secondary structure: the fundamental unit of 6.9 Plasma membrane Ca2+ channels activate
protein architectureâ•‡â•‡190 intracellular and intercellular signaling
5.8 Tertiary structure and the universe of protein processesâ•‡â•‡254
foldsâ•‡â•‡193 6.10 Cl− channels serve diverse biologic functionsâ•‡â•‡ 257
5.9 Modular architecture and repeating motifsâ•‡â•‡ 197 6.11 Selective water transport occurs through aquaporin
5.10 Quaternary structure and higher-order channelsâ•‡â•‡261
assembliesâ•‡â•‡201 6.12 Action potentials are electrical signals that depend
5.11 Enzymes are proteins that catalyze chemical on several types of ion channelsâ•‡â•‡ 264
reactionsâ•‡â•‡204 6.13 Cardiac and skeletal muscles are activated by
5.12 Posttranslational modifications and cofactorsâ•‡â•‡ 208 excitation-contraction couplingâ•‡â•‡267
5.13 Dynamics, flexibility, and conformational 6.14 Some glucose transporters are uniportersâ•‡â•‡ 271
changesâ•‡â•‡212 6.15 Symporters and antiporters mediate coupled
5.14 Protein–protein and protein–nucleic acid transportâ•‡â•‡273
interactionsâ•‡â•‡215 6.16 The transmembrane Na+ gradient is essential for the
5.15 Function without structure?â•‡â•‡ 220 function of many transportersâ•‡â•‡ 275
5.16 Structure and medicineâ•‡â•‡ 221 6.17 Some Na+ transporters regulate cytosolic or
5.17 What’s next? Structural biology in the extracellular pHâ•‡â•‡279
postgenomic eraâ•‡â•‡226 6.18 The Ca2+-ATPase pumps Ca2+ into intracellular storage
5.18 Summaryâ•‡â•‡227 compartmentsâ•‡â•‡282
Referencesâ•‡â•‡228 6.19 The Na+/K+-ATPase maintains the plasma membrane
Na+ and K+ gradientsâ•‡â•‡285
Part 2â•‡ Membranes and 6.20 The F1F0-ATP synthase couples H+ movement to ATP
synthesis or hydrolysisâ•‡â•‡ 289
transport mechanisms 229 6.21 H+-ATPases transport protons out of the
cytosolâ•‡â•‡290
6 Transport of ions and 6.22 What’s next?â•‡â•‡293
small molecules across 6.23 Summaryâ•‡â•‡294

6.24 Supplement: Derivation and application of the
membranes . . . . . . . . . . . 230 Nernst equationâ•‡â•‡295
Stephan E. Lehnart and Andrew R. Marks 6.25 Supplement: Most K+ channels undergo
6.1 Introductionâ•‡â•‡231 rectificationâ•‡â•‡297
6.2 Channels and carriers are the main types of 6.26 Supplement: Mutations in an anion channel cause
membrane transport proteinsâ•‡â•‡ 232 cystic fibrosisâ•‡â•‡298
6.3 Hydration of ions influences their flux through Referencesâ•‡â•‡300
transmembrane poresâ•‡â•‡234
viii Contents

7 Membrane targeting of 7.21 The ER synthesizes the major cellular
phospholipidsâ•‡â•‡335
proteins. . . . . . . . . . . . . . 301 7.22 Lipids must be moved from the ER to the membranes
D. Thomas Rutkowski and Vishwanath R. Lingappa of other organellesâ•‡â•‡ 337
7.1 Introductionâ•‡â•‡302 7.23 The two leaflets of a membrane often differ in lipid
7.2 Proteins enter the secretory pathway by compositionâ•‡â•‡338
translocation across the endoplasmic reticulum (ER) 7.24 The ER is morphologically and functionally
membrane (an overview)â•‡â•‡ 304 subdividedâ•‡â•‡339
7.3 Proteins use signal sequences to target the ER for 7.25 The ER is a dynamic organelleâ•‡â•‡ 341
translocationâ•‡â•‡306 7.26 Signal sequences are also used to target proteins to
7.4 Signal sequences are recognized by the signal other organellesâ•‡â•‡344
recognition particle (SRP)â•‡â•‡ 307 7.27 Import into mitochondria begins with signal
7.5 Interaction between SRP and its receptor allows sequence recognition at the outer membraneâ•‡â•‡ 344
proteins to dock at the ER membraneâ•‡â•‡ 308 7.28 Complexes in the inner and outer membranes
7.6 The translocon is an aqueous channel that conducts cooperate in mitochondrial protein importâ•‡â•‡ 345
proteinsâ•‡â•‡309 7.29 Proteins imported into chloroplasts must also cross
7.7 Translation is coupled to translocation for most two membranesâ•‡â•‡347
eukaryotic secretory and transmembrane 7.30 Proteins fold before they are imported into
proteinsâ•‡â•‡312 peroxisomesâ•‡â•‡349
7.8 Some proteins target and translocate 7.31 What’s next?â•‡â•‡350
posttranslationallyâ•‡â•‡314
7.9 ATP hydrolysis drives translocationâ•‡â•‡ 315
7.10 Transmembrane proteins move out of the
translocation channel and into the lipid
bilayerâ•‡â•‡318 8 Protein trafficking
7.11 Orientation of transmembrane proteins is
determined as they are integrated into the between membranes. . . . . 354
membraneâ•‡â•‡319 Vivek Malhotra, Graham Warren, and Ira Mellman
7.12 Signal sequences are removed by signal 8.1 Introductionâ•‡â•‡355
peptidaseâ•‡â•‡321 8.2 Overview of the exocytic pathwayâ•‡â•‡ 357
7.13 The lipid glycosylphosphatidylinositol (GPI) is 8.3 Overview of the endocytic pathwayâ•‡â•‡ 360
added to some translocated proteinsâ•‡â•‡ 322
8.4 Concepts in vesicle-mediated protein
7.14 Sugars are added to many translocating transportâ•‡â•‡364
proteinsâ•‡â•‡324
8.5 The concepts of signal-mediated and bulk flow
7.15 Chaperones assist folding of newly translocated protein transportâ•‡â•‡366
8.6 Coat protein II (COPII)–coated vesicles mediate
7.16 Protein disulfide isomerase ensures the formation of transport from the ER to the Golgi apparatusâ•‡â•‡ 367
the correct disulfide bonds as proteins foldâ•‡â•‡ 327
8.7 Resident proteins that escape from the ER are
7.17 The calnexin/calreticulin chaperoning system retrievedâ•‡â•‡369
recognizes carbohydrate modificationsâ•‡â•‡ 328
8.8 Coat protein I (COPI)–coated vesicles mediate
7.18 The assembly of proteins into complexes is retrograde transport from the Golgi apparatus
monitoredâ•‡â•‡329 to the ERâ•‡â•‡ 371
7.19 Terminally misfolded proteins in the ER are returned 8.9 There are two popular models for forward transport
to the cytosol for degradationâ•‡â•‡ 329 through the Golgi apparatusâ•‡â•‡ 372
7.20 Communication between the ER and nucleus 8.10 Retention of proteins in the Golgi apparatus
prevents the accumulation of unfolded proteins in depends on the membrane-spanning domainâ•‡â•‡ 374
the lumenâ•‡â•‡333
8.11 Rab GTPases and tethers are two types of proteins
that regulate vesicle targetingâ•‡â•‡ 374
Contents ix

8.12 Soluble N-ethymaleimide-sensitive factor attachment 9.13 Cytoplasmic receptors recognize nuclear localization
protein receptor (SNARE) proteins likely mediate sequences (NLSs) and mediate nuclear protein
fusion of vesicles with target membranesâ•‡â•‡ 377 importâ•‡â•‡423
8.13 Endocytosis is often mediated by clathrin-coated 9.14 Export of proteins from the nucleus is also
vesiclesâ•‡â•‡380 receptor-mediatedâ•‡â•‡425
8.14 Adaptor complexes link clathrin and transmembrane 9.15 The Ran GTPase controls the directionality and
cargo proteinsâ•‡â•‡383 irreversibility of nuclear transportâ•‡â•‡ 427
8.15 Some receptors recycle from early endosomes, 9.16 Multiple models have been proposed for the mechanism
whereas others are degraded in lysosomesâ•‡â•‡ 386 of movement through nuclear pore complexesâ•‡â•‡ 429
8.16 Early endosomes become late endosomes and 9.17 Nuclear transport can be regulatedâ•‡â•‡ 431
lysosomes by maturationâ•‡â•‡ 388 9.18 Multiple classes of RNA are exported from the
8.17 Sorting of lysosomal proteins occurs in the nucleusâ•‡â•‡432
trans-Golgi network (TGN)â•‡â•‡ 390 9.19 Ribosomal subunits are assembled in the nucleolus
8.18 Polarized epithelial cells transport proteins to apical and exported by multiple receptorsâ•‡â•‡ 434
and basolateral membranesâ•‡â•‡ 393 9.20 tRNAs are exported by a dedicated exportin and can
8.19 Some cells store proteins for later secretionâ•‡â•‡ 395 also use other receptorsâ•‡â•‡ 435
8.20 Some proteins are secreted without entering the 9.21 mRNAs are exported from the nucleus as
ER–Golgi pathwayâ•‡â•‡397 RNA-protein complexesâ•‡â•‡437
8.21 What’s next?â•‡â•‡398 9.22 hnRNPs move from sites of processing to nuclear
8.22 Summaryâ•‡â•‡398 pore complexesâ•‡â•‡439
Referencesâ•‡â•‡399 9.23 mRNA export requires several novel factorsâ•‡â•‡ 440
9.24 U snRNAs are exported, modified, assembled into
Part 3â•‡ The nucleus 401 9.25

complexes, and imported back into the nucleusâ•‡â•‡ 444
Precursors to microRNAs are partially processed in
the nucleus, exported, and further processed in the
9 Nuclear structure and cytoplasmâ•‡â•‡444
transport. . . . . . . . . . . . . 402 9.26 What’s next?â•‡â•‡446
Charles N. Cole 9.27 Summaryâ•‡â•‡448
9.2 Nuclei vary in appearance according to cell type and
organismâ•‡â•‡405 10 Chromatin and
9.3 Chromosomes occupy distinct territoriesâ•‡â•‡ 406 chromosomes. . . . . . . . . . 451
9.4 The nucleus contains subcompartments that are not Benjamin Lewin and Jocelyn E. Krebs
membrane-boundedâ•‡â•‡407
9.5 Some processes occur at distinct nuclear sites and
may reflect an underlying structureâ•‡â•‡ 409 10.2 Chromatin is divided into euchromatin and
heterochromatinâ•‡â•‡453
9.6 The nucleus is bounded by the nuclear envelopeâ•‡â•‡ 411
10.3 Chromosomes have banding patternsâ•‡â•‡ 455
9.7 The nuclear lamina underlies the nuclear envelopeâ•‡â•‡ 412
10.4 Eukaryotic DNA has loops and domains attached to a
9.8 Large molecules are actively transported between
scaffoldâ•‡â•‡456
the nucleus and cytoplasmâ•‡â•‡ 414
10.5 Specific sequences attach DNA to an interphase
9.9 Nuclear pore complexes are symmetrical channelsâ•‡â•‡ 415
matrix or a metaphase scaffoldâ•‡â•‡ 457
9.10 Nuclear pore complexes are constructed from
10.6 The eukaryotic chromosome is a segregation
nucleoporinsâ•‡â•‡418
deviceâ•‡â•‡458
9.11 Proteins are selectively transported into the nucleus
10.7 Point centromeres have short DNA sequences in
through nuclear poresâ•‡â•‡ 421
Saccharomyces cerevisiaeâ•‡â•‡460
9.12 Nuclear localization sequences target proteins to
10.8 The centromere binds a protein complexâ•‡â•‡ 461
the nucleusâ•‡â•‡422
x Contents

10.9 Regional centromeres contain repetitive DNAâ•‡â•‡ 461 11.5 Microtubule assembly and disassembly proceed by a
10.10 Telomeres are replicated by a special mechanismâ•‡â•‡ 463 unique process termed dynamic instabilityâ•‡â•‡ 524
10.11 Lampbrush chromosomes are extendedâ•‡â•‡ 465 11.6 A cap of GTP-tubulin subunits regulates the
transitions of dynamic instabilityâ•‡â•‡ 526
10.12 Polytene chromosomes form bandsâ•‡â•‡ 466
11.7 Cells use microtubule-organizing centers to nucleate
10.13 Polytene chromosomes expand at sites of gene
microtubule assemblyâ•‡â•‡528
expressionâ•‡â•‡467
11.8 Microtubule dynamics in cellsâ•‡â•‡ 531
10.14 The nucleosome is the subunit of all
chromatinâ•‡â•‡470 11.9 Why do cells have dynamic microtubules?â•‡â•‡ 534
10.15 DNA is coiled in arrays of nucleosomesâ•‡â•‡ 472 11.10 Cells use several classes of proteins to regulate the
stability of their microtubulesâ•‡â•‡ 536
10.16 Nucleosomes have a common structureâ•‡â•‡ 473
11.11 Introduction to microtubule-based motor
10.17 Organization of the histone octamerâ•‡â•‡ 476
10.18 Histone variants produce alternative
11.12 How motor proteins workâ•‡â•‡ 543
nucleosomesâ•‡â•‡478
11.13 How cargoes are loaded onto the right motorâ•‡â•‡ 549
10.19 The path of nucleosomes in the chromatin fiberâ•‡â•‡ 479
11.14 Microtubule dynamics and motors combine to
10.20 Replication of chromatin requires assembly of
generate the asymmetric organization of cellsâ•‡â•‡ 550
nucleosomesâ•‡â•‡481
11.15 Interactions between microtubules and actin
10.21 Do nucleosomes lie at specific positions?â•‡â•‡ 484
filamentsâ•‡â•‡555
10.22 Domains of nuclease sensitivity define regions that
11.16 Cilia and flagella are motile structuresâ•‡â•‡ 557
contain active genesâ•‡â•‡ 487
10.23 Histone octamers are displaced and reassembled
during transcriptionâ•‡â•‡489 11.18 Summaryâ•‡â•‡563
10.24 Chromatin remodeling is an active processâ•‡â•‡ 493 11.19 Supplement: What if tubulin did not hydrolyze
GTP?â•‡â•‡564
10.25 Histones are covalently modifiedâ•‡â•‡ 496
11.20 Supplement: Fluorescence recovery after
10.26 Heterochromatin propagates from a nucleation
photobleachingâ•‡â•‡553
eventâ•‡â•‡500
11.21 Supplement: Tubulin synthesis and
10.27 Heterochromatin depends on interactions with
modification 565
histonesâ•‡â•‡501
10.28 X chromosomes undergo global changesâ•‡â•‡ 504
10.29 Chromosome condensation is caused by
condensinsâ•‡â•‡506 12 Actin. . . . . . . . . . . . . . . . 568
10.30 What’s next?â•‡â•‡509 Enrique M. De La Cruz and E. Michael Ostap
10.31 Summaryâ•‡â•‡509 12.1 Introductionâ•‡â•‡569
Referencesâ•‡â•‡512 12.2 Actin is a ubiquitously expressed cytoskeletal
proteinâ•‡â•‡570
12.3 Actin monomers bind ATP and ADPâ•‡â•‡ 570
Part 4â•‡ The cytoskeleton 513 12.4 Actin filaments are structurally polarized
polymersâ•‡â•‡571
11 Microtubules . . . . . . . . . . 514 12.5 Actin polymerization is a multistep and dynamic
Lynne Cassimeris processâ•‡â•‡572
12.6 Actin subunits hydrolyze ATP after
polymerizationâ•‡â•‡575
11.2 Microtubules are polar polymers of α- and
12.7 Actin binding proteins regulate actin polymerization
β-tubulinâ•‡â•‡517
and organizationâ•‡â•‡577
11.3 General functions of microtubulesâ•‡â•‡ 519
12.8 Actin monomer binding proteins influence
11.4 Purified tubulin subunits assemble into polymerizationâ•‡â•‡578
microtubulesâ•‡â•‡522
Contents xi

12.9 Nucleating proteins control cellular actin 13.10 Interacting proteins facilitate secondary functions
polymerizationâ•‡â•‡579 of intermediate filamentsâ•‡â•‡ 624
12.10 Capping proteins regulate the length of actin 13.11 Intermediate filament genes are represented
filamentsâ•‡â•‡580 through metazoan evolutionâ•‡â•‡ 626
12.11 Severing and depolymerizing proteins regulate actin 13.12 What’s next?â•‡â•‡628
filament dynamicsâ•‡â•‡581 13.13 Summaryâ•‡â•‡629
12.12 Cross-linking proteins organize actin filaments into Referencesâ•‡â•‡630
bundles and orthogonal networksâ•‡â•‡ 582
12.13 Actin and actin binding proteins work together to
drive cell migrationâ•‡â•‡ 584 Part 5â•‡ Cell division,
12.14
12.15
Small G proteins regulate actin polymerizationâ•‡â•‡ 586
Myosins are actin-based molecular motors with
apoptosis, and cancer 631
essential roles in many cellular processesâ•‡â•‡ 587
12.16 Myosins have three structural domainsâ•‡â•‡ 590 14 Mitosis. . . . . . . . . . . . . . . 632
12.17 ATP hydrolysis by myosin is a multistep Conly L. Rieder
reactionâ•‡â•‡594 14.1 Introductionâ•‡â•‡633
12.18 Myosin motors have kinetic properties suited for 14.2 Mitosis is divided into stagesâ•‡â•‡ 636
their cellular rolesâ•‡â•‡ 595 14.3 Mitosis requires the formation of a new apparatus
12.19 Myosins take nanometer steps and generate called the spindleâ•‡â•‡ 638
piconewton forcesâ•‡â•‡596 14.4 Spindle formation and function depend on the
12.20 Myosins are regulated by multiple mechanismsâ•‡â•‡ 597 dynamic behavior of microtubules and their
12.21 Myosin-II functions in muscle contractionâ•‡â•‡ 598 associated motor proteinsâ•‡â•‡ 641
12.22 What’s next?â•‡â•‡602 14.5 Centrosomes are microtubule-organizing
12.23 Summaryâ•‡â•‡602 centersâ•‡â•‡643
Referencesâ•‡â•‡603 14.6 Centrosomes reproduce about the time the DNA is
replicatedâ•‡â•‡644
14.7 Spindles begin to form as separating asters
13 Intermediate filaments . . . . 604 interactâ•‡â•‡647
Birgit Lane 14.8 Spindles require chromosomes for stabilization but
13.1 Introductionâ•‡â•‡605 can “self-organize” without centrosomesâ•‡â•‡ 649
13.2 Similarities in structure define the intermediate 14.9 The centromere is a specialized region on the
filament familyâ•‡â•‡606 chromosome that contains the kinetochoresâ•‡â•‡ 651
13.3 Intermediate filament subunits assemble with high 14.10 Kinetochores form at the onset of prometaphase and
affinity into strain-resistant structuresâ•‡â•‡ 608 contain microtubule motor proteinsâ•‡â•‡ 652
13.4 Two-thirds of all intermediate filament proteins are 14.11 Kinetochores capture and stabilize their associated
keratinsâ•‡â•‡611 microtubulesâ•‡â•‡654
13.5 Mutations in keratins cause epithelial cell 14.12 Mistakes in kinetochore attachment are
fragilityâ•‡â•‡615 correctedâ•‡â•‡658
13.6 Intermediate filament proteins of nerve, muscle, 14.13 Kinetochore fibers must both shorten and elongate
and connective tissue often show overlapping to allow chromosomes to moveâ•‡â•‡ 662
expressionâ•‡â•‡617 14.14 Congression involves pulling forces that act on the
13.7 Lamin intermediate filaments reinforce the nuclear kinetochoresâ•‡â•‡663
envelopeâ•‡â•‡619 14.15 Congression is also regulated by forces that act
13.8 Even the divergent lens filament proteins are along the chromosome arms and the activity of
conserved in evolutionâ•‡â•‡ 621 sister kinetochoresâ•‡â•‡665
13.9 Posttranslational modifications regulate and 14.16 Kinetochores control the metaphase-to-anaphase
remodel intermediate filament networksâ•‡â•‡ 621 transitionâ•‡â•‡667
xii Contents

14.17 The force to move a chromosome toward a pole is 16 Apoptosis. . . . . . . . . . . . . 725
produced by two mechanismsâ•‡â•‡ 669
Douglas R. Green
14.18 Anaphase has two phasesâ•‡â•‡ 670
14.19 Changes occur during telophase that lead the cell
out of the mitotic stateâ•‡â•‡ 673 16.2 Caspases orchestrate apoptosis by cleaving specific
substratesâ•‡â•‡728
14.20 During cytokinesis, the cytoplasm is partitioned to
form two new daughter cellsâ•‡â•‡ 674 16.3 Executioner caspases are activated by cleavage,
whereas initiator caspases are activated by
14.21 Formation of the contractile ring requires the
dimerizationâ•‡â•‡729
spindle and stem bodiesâ•‡â•‡ 677
16.4 Some inhibitors of apoptosis proteins block
14.22 The contractile ring cleaves the cell in twoâ•‡â•‡ 680
caspasesâ•‡â•‡730
14.23 The segregation of nonnuclear organelles during
16.5 Some caspases have functions in
cytokinesis is based on chanceâ•‡â•‡ 682
inflammationâ•‡â•‡731
16.6 The death receptor pathway of apoptosis transmits
14.25 Summaryâ•‡â•‡683 external signalsâ•‡â•‡732
Referencesâ•‡â•‡684 16.7 Apoptosis signaling by TNFR1 is complexâ•‡â•‡ 734
16.8 Mitochondrial pathway of apoptosisâ•‡â•‡ 735
15 Cell cycle regulation . . . . . 685 16.9 Bcl-2 family proteins mediate and regulate MOMP
Kathleen L. Gould and Susan L. Forsburg and apoptosisâ•‡â•‡736
16.10 Multidomain Bcl-2 proteins Bax and Bak are required
for MOMPâ•‡â•‡737
15.2 Several experimental systems are used for cell cycle
16.11 Activation of Bax and Bak are controlled by other
researchâ•‡â•‡688
Bcl-2 family proteinsâ•‡â•‡ 738
15.3 A cycle of cyclin-dependent kinase activities
16.12 Cytochrome c, released upon MOMP, induces caspase
regulates cell proliferationâ•‡â•‡ 692
activationâ•‡â•‡739
15.4 CDK-cyclin complexes are regulated in several
16.13 Some proteins released upon MOMP block IAPsâ•‡â•‡ 740
waysâ•‡â•‡694
16.14 The death receptor pathway of apoptosis can engage
15.5 Cells may withdraw from the cell cycleâ•‡â•‡ 696
MOMP through the cleavage of the BH3-only protein
15.6 Entry into cell cycle is tightly regulatedâ•‡â•‡ 698 Bidâ•‡â•‡740
15.7 DNA replication requires the ordered assembly of 16.15 MOMP can cause caspase-independent cell
protein complexesâ•‡â•‡700 deathâ•‡â•‡741
15.8 Mitosis is orchestrated by several protein 16.16 Mitochondrial permeability transition can cause
kinasesâ•‡â•‡703 MOMPâ•‡â•‡742
15.9 Sister chromatids are held together until 16.17 Many discoveries about apoptosis were made in
anaphaseâ•‡â•‡706 nematodesâ•‡â•‡742
15.10 Exit from mitosis requires more than cyclin 16.18 Apoptosis in insects has features distinct from
proteolysisâ•‡â•‡708 mammals and nematodesâ•‡â•‡ 743
15.11 Events of the cell cycle are coordinatedâ•‡â•‡ 711 16.19 Clearance of apoptotic cells requires cellular
15.12 Checkpoint controls coordinate different cell cycle interactionâ•‡â•‡744
eventsâ•‡â•‡712 16.20 Apoptosis plays a role in diseases such as viral
15.13 DNA replication and DNA damage checkpoints infection and cancerâ•‡â•‡ 746
monitor defects in DNA metabolismâ•‡â•‡ 714 16.21 Apoptotic cells are gone but not forgottenâ•‡â•‡ 747
15.14 The SAC monitors defects in chromosome- 16.22 What’s next?â•‡â•‡748
microtubule attachmentâ•‡â•‡718
15.15 Cell cycle deregulation can lead to cancerâ•‡â•‡ 721
Contents xiii

17 Cancer: Principles and 18.6 Signals are sorted and integrated in signaling
pathways and networksâ•‡â•‡ 784
overview . . . . . . . . . . . . . 750 18.7 Cellular signaling pathways can be thought of as
Robert A. Weinberg biochemical logic circuitsâ•‡â•‡ 786
17.1 Tumors are masses of cells derived from a single 18.8 Scaffolds increase signaling efficiency and enhance
cellâ•‡â•‡751 spatial organization of signalingâ•‡â•‡ 788
17.2 Cancer cells have a number of phenotypic 18.9 Independent, modular domains specify
characteristicsâ•‡â•‡752 protein-protein interactionsâ•‡â•‡789
17.3 Cancer cells arise after DNA damageâ•‡â•‡ 755 18.10 Cellular signaling is remarkably adaptiveâ•‡â•‡ 791
17.4 Cancer cells are created when certain genes are 18.11 Signaling proteins are frequently expressed as
mutatedâ•‡â•‡756 multiple speciesâ•‡â•‡794
17.5 Cellular genomes harbor a number of 18.12 Activating and deactivating reactions are separate
proto-oncogenesâ•‡â•‡758 and independently controlledâ•‡â•‡ 795
17.6 Elimination of tumor-suppressor activity requires 18.13 Cellular signaling uses both allostery and covalent
two mutationsâ•‡â•‡759 modificationâ•‡â•‡795
17.7 Genesis of tumors is a complex processâ•‡â•‡ 761 18.14 Second messengers provide readily diffusible
17.8 Cell growth and proliferation are activated by pathways for information transferâ•‡â•‡ 796
growth factorsâ•‡â•‡764 18.15 Ca2+ signaling serves diverse purposes in all
17.9 Cells are subject to growth inhibition and may exit eukaryotic cellsâ•‡â•‡798
from the cell cycleâ•‡â•‡ 766 18.16 Lipids and lipid-derived compounds are signaling
17.10 Tumor suppressors block inappropriate entry into moleculesâ•‡â•‡799
the cell cycleâ•‡â•‡ 768 18.17 PI 3-kinase regulates both cell shape and the
17.11 Mutation of DNA repair and maintenance genes can activation of essential growth and metabolic
increase the overall mutation rateâ•‡â•‡ 769 functionsâ•‡â•‡801
17.12 Cancer cells may achieve immortalityâ•‡â•‡ 771 18.18 Signaling through ion channel receptors is very
fastâ•‡â•‡802
17.13 Access to vital supplies is provided by
angiogenesisâ•‡â•‡772 18.19 Nuclear receptors regulate transcriptionâ•‡â•‡ 804
17.14 Cancer cells may invade new locations in the 18.20 G protein-signaling modules are widely used and
bodyâ•‡â•‡773 highly adaptableâ•‡â•‡805
17.15 What’s next?â•‡â•‡774 18.21 Heterotrimeric G proteins regulate a wide variety of
effectorsâ•‡â•‡808
18.22 Heterotrimeric G proteins are controlled by a
regulatory GTPase cycleâ•‡â•‡ 808
18.23 Small, monomeric GTP-binding proteins are multiuse
Part 6â•‡Cell switchesâ•‡â•‡810
18.24 Protein phosphorylation/dephosphorylation is a
communication 777 major regulatory mechanism in the cellâ•‡â•‡ 811
18.25 Two-component protein phosphorylation systems
18 Principles of cell signaling. . 778 are signaling relaysâ•‡â•‡ 814
Elliott M. Ross and Melanie H. Cobb 18.26 Pharmacologic inhibitors of protein kinases may be
18.1 Introductionâ•‡â•‡779 used to understand and treat diseaseâ•‡â•‡ 815
18.2 Cellular signaling is primarily chemicalâ•‡â•‡ 780 18.27 Phosphoprotein phosphatases reverse the actions of
18.3 Receptors sense diverse stimuli but initiate a limited kinases and are independently regulatedâ•‡â•‡ 815
repertoire of cellular signalsâ•‡â•‡ 780 18.28 Covalent modification by ubiquitin and
18.4 Receptors are catalysts and amplifiersâ•‡â•‡ 782 ubiquitin-like proteins is another way of regulating
protein functionâ•‡â•‡818
18.5 Ligand binding changes receptor
conformationâ•‡â•‡782
18.29 Wnt pathway regulates cell fate during development
and other processes in the adultâ•‡â•‡ 820
xiv Contents

18.30 Diverse signaling mechanisms are regulated by 19.21 Calcium-dependent cadherins mediate adhesion
protein-tyrosine kinasesâ•‡â•‡820 between cellsâ•‡â•‡882
18.31 Src family protein kinases cooperate with receptor 19.22 Calcium-independent neural cell adhesion molecules
protein-tyrosine kinasesâ•‡â•‡822 mediate adhesion between neural cellsâ•‡â•‡ 885
18.32 MAPKs are central to many signaling pathwaysâ•‡â•‡ 823 19.23 Selectins control adhesion of circulating
18.33 Cyclin-dependent protein kinases control the cell immune cellsâ•‡â•‡887
cycleâ•‡â•‡824 19.24 What’s next?â•‡â•‡888
18.34 Diverse receptors recruit protein-tyrosine kinases to 19.25 Summaryâ•‡â•‡888
the plasma membraneâ•‡â•‡ 825 Referencesâ•‡â•‡889
Referencesâ•‡â•‡829 Part 7â•‡ Prokaryotic and
plant cells 891
19 The extracellular matrix
and cell adhesion . . . . . . . 831 20 Prokaryotic cell biology.....892
George Plopper Matthew Chapman and Jeff Errington
19.1 Introductionâ•‡â•‡832 20.1 Introductionâ•‡â•‡893
19.2 Collagen provides structural support to tissuesâ•‡â•‡ 835 20.2 Molecular phylogeny techniques are used to
understand microbial evolutionâ•‡â•‡ 895
19.3 Fibronectins connect cells to collagenous
matricesâ•‡â•‡839 20.3 Prokaryotic life-styles are diverseâ•‡â•‡ 897
19.4 Elastic fibers impart flexibility to tissuesâ•‡â•‡ 841 20.4 Archaea are prokaryotes with similarities to
eukaryotic cellsâ•‡â•‡899
19.5 Laminins provide an adhesive substrate for cellsâ•‡â•‡ 844
20.5 Most prokaryotes produce a polysaccharide-rich
19.6 Matricellular proteins regulate cell–ECM layer called the capsuleâ•‡â•‡ 901
interactionsâ•‡â•‡846
20.6 The bacterial cell wall contains a cross-linked
19.7 Proteoglycans provide hydration to tissuesâ•‡â•‡ 848 meshwork of peptidoglycanâ•‡â•‡ 903
19.8 HA is a GAG enriched in connective tissuesâ•‡â•‡ 851 20.7 The cell envelope of gram-positive bacteria has
19.9 HSPGs are cell surface coreceptorsâ•‡â•‡ 853 unique featuresâ•‡â•‡907
19.10 Basal lamina is a specialized ECMâ•‡â•‡ 855 20.8 Gram-negative bacteria have an outer membrane
19.11 Proteases degrade ECM componentsâ•‡â•‡ 857 and a periplasmic spaceâ•‡â•‡ 909
19.12 Most integrins are receptors for ECM proteinsâ•‡â•‡ 860 20.9 The cytoplasmic membrane is a selective barrier for
19.13 Integrin receptors participate in cell signalingâ•‡â•‡ 863 secretionâ•‡â•‡912
19.14 Integrins and ECM molecules play key roles in 20.10 Prokaryotes have several secretion pathwaysâ•‡â•‡ 913
developmentâ•‡â•‡867 20.11 Pili and flagella are appendages on the cell surface
19.15 Tight junctions form selectively permeable barriers of most prokaryotesâ•‡â•‡ 915
between cellsâ•‡â•‡870 20.12 Prokaryotic genomes contain chromosomes and
19.16 Septate junctions in invertebrates are similar to mobile DNA elementsâ•‡â•‡ 919
tight junctionsâ•‡â•‡873 20.13 The bacterial nucleoid and cytoplasm are highly
19.17 Adherens junctions link adjacent cellsâ•‡â•‡ 875 orderedâ•‡â•‡921
19.18 Desmosomes are intermediate filament-based cell 20.14 Bacterial chromosomes are replicated in specialized
adhesion complexesâ•‡â•‡877 replication factoriesâ•‡â•‡923
19.19 Hemidesmosomes attach epithelial cells to the basal 20.15 Prokaryotic chromosome segregation occurs in the
laminaâ•‡â•‡878 absence of a mitotic spindleâ•‡â•‡ 925
19.20 Gap junctions allow direct transfer of molecules 20.16 Prokaryotic cell division involves formation of a
between adjacent cellsâ•‡â•‡ 880 complex cytokinetic ringâ•‡â•‡ 927
20.17 Prokaryotes respond to stress with complex
developmental changesâ•‡â•‡931
Contents xv

20.18 Some prokaryotic life cycles include obligatory 21.11 The large forces of turgor pressure are resisted by
developmental changesâ•‡â•‡935 the strength of cellulose microfibrils in the cell
20.19 Some prokaryotes and eukaryotes have wallâ•‡â•‡966
endosymbiotic relationshipsâ•‡â•‡936 21.12 The cell wall must be loosened and reorganized to
20.20 Prokaryotes can colonize and cause disease in allow growthâ•‡â•‡968
higher organismsâ•‡â•‡938 21.13 Cellulose is synthesized at the plasma membrane,
20.21 Biofilms are highly organized communities of not preassembled and secreted like other wall
microbesâ•‡â•‡940 componentsâ•‡â•‡969
20.22 What’s next?â•‡â•‡942 21.14 Cortical microtubules organize components in the
cell wallâ•‡â•‡971
21.15 Cortical microtubules are highly dynamic and can
change their orientationâ•‡â•‡ 973
21.16 A dispersed Golgi system delivers vesicles to the cell
21 Plant cell biology . . . . . . . 945 surface for growthâ•‡â•‡ 976
Clive Lloyd 21.17 Actin filaments form a network for delivering
21.1 Introductionâ•‡â•‡946 materials around the cellâ•‡â•‡ 978
21.2 How plants growâ•‡â•‡ 947 21.18 Differentiation of xylem cells requires extensive
specializationâ•‡â•‡980
21.3 The meristem provides new growth modules in a
repetitive mannerâ•‡â•‡948 21.19 Specialized plant cells elongate by tip growthâ•‡â•‡ 982
21.4 The plane in which a cell divides is important for 21.20 Plants contain unique organelles called
tissue organizationâ•‡â•‡950 plastidsâ•‡â•‡986
21.5 Cytoplasmic structures predict the plane of cell 21.21 Chloroplasts manufacture food from atmospheric
division before mitosis beginsâ•‡â•‡ 953 CO2â•‡â•‡988
21.6 Plant mitosis occurs without centrosomesâ•‡â•‡ 956 21.22 Polarized flow of the hormone auxin coordinates
growthâ•‡â•‡990
21.7 The cytokinetic apparatus builds a new wall in the
plane anticipated by the preprophase bandâ•‡â•‡ 958 21.23 What’s next?â•‡â•‡991
21.8 Secretion during cytokinesis forms the cell 21.24 Summaryâ•‡â•‡993
plateâ•‡â•‡961 Referencesâ•‡â•‡995
21.9 Plasmodesmata are intercellular channels that
connect plant cellsâ•‡â•‡ 962 Glossaryâ•‡â•‡997
21.10 Cell expansion is driven by swelling of the Indexâ•‡â•‡1027
vacuoleâ•‡â•‡964
xvi Contents

Feature Boxes
Historical Perspectives
2.1â•‡ Diabetes and Metabolismâ•… 57 15.1â•‡ Discovering S Phaseâ•… 687

5.3â•‡ Levinthal’s Paradoxâ•… 193 19.1â•‡A Brief History of Research on the Extracellular
5.5â•‡ Origins of Enzyme Catalysisâ•… 206 Matrixâ•…834
5.8â•‡Sickle-cell Anemia and the Origins of Molecular 20.1â•‡ Bacteria Guide Human Health and Developmentâ•… 893
Medicineâ•…222 21.1â•‡ The Plane of Cell Divisionâ•… 959
Medical applications
â•⁄ 3.1â•‡ Xeroderma Pigmentosum (XP)â•… 86 13.1â•‡ Using Networks to Identify Diseasesâ•… 623
â•⁄ 9.1â•‡Manipulation and Inhibition of Nuclear Transport by 14.1â•‡ Mitosis as a Pharmacologic Targetâ•… 660
Animal Virusesâ•…442 18.1â•‡Treating Chronic Myelogenous Leukemia with Tyrosine
10.1â•‡ Chromosome Painting and Spectral Karyotypingâ•… 468 Kinase Inhibitorsâ•… 816
Methods and Techniques
4.1â•‡ Gene Expression Profilingâ•… 128 â•⁄5.7â•‡Binding Equilibriaâ•… 216

5.1â•‡ Crystals and Diffractionâ•… 173 11.1â•‡Motility Assays for Microtubule-Based Motor
5.2â•‡ Nuclear Magnetic Resonanceâ•… 176 Proteinsâ•…544
5.4â•‡ Measuring Enzyme Activityâ•… 205 12.1â•‡Two Models for How Polymer Assembly Can Generate
Forceâ•…585
5.6â•‡ Molecular Dynamicsâ•… 213
xvii

Preface
Eighty years ago, the cellular world opened up. The elec- Perhaps most exciting is the combination of structural
tron microscope granted us, for the first time, a detailed and mechanistic information with developments in genet-
perspective of basic cellular structures, and the ultracentri- ics, biochemistry, and physiology—the primary vision of
fuge allowed us to biochemically isolate and characterize the emerging field of systems biology. Most cell biologists
fractions of cytoplasmic and nuclear material. Geneticists today recognize that only a comprehensive approach to
could investigate the relationship between the ever-Â� research, from the nuclear pore complex to the extracel-
shifting chromosomal structure and the molecular mecha- lular matrix, will begin to lift the veil from the cellular
nisms of genetic inheritance—an effort that culminated processes underlying cystic fibrosis, epilepsy, and cancer.
with the triumphant revelation of the structures of DNA Any cell biology textbook must provide a current per-
and RNA and a translation of the genetic code. spective of the structure, function, and regulation of bio-
But we have come a long way from there. We have logical systems, but in today’s world it is imperative that
perfected our understanding of genes themselves, adjust- we also present the subject in the context of biochemistry
ing our definition from “determinants of a genetic pheno- and molecular biology, genomics, histology and pathology,
type,” to “protein-encoding segments of DNA,” and now, and physiology. Thoroughly revised and updated, Lewin’s
more precisely, “units of genomic information Â�required for CELLS, Third Edition turns a new and sharper lens on the
the transcription of functional messenger RNA or noncod- fundamental units of life.
ing RNA.” So far, the complete genomes of over 4,000 or-
ganisms have been published, revealing the sequences
of over 100 million genetic loci. And we are still learn- Audience
ing about the proteins these mRNAs produce. The RSCB
This third edition, expanded and updated from the sec-
Protein Data Bank (PDB) was established in 1971 as an
ond, is geared for advanced undergraduate and graduate
international repository for structural data, but it did not
students taking a first course in cell biology. A key objec-
truly begin to grow until the early 1990s. Now, in 2013,
tive in developing this book was to present the concepts
it holds more than 90,000 structures and is expanding
and mechanisms underlying cell structure and function,
at the rate of about 7,000 structures per year. For now,
gleaned from decades of research, in a format that pro-
X-ray crystallography and nuclear magnetic resonance
vides students with the information necessary for a solid
are the only techniques available for the determination of
foundation in cell biology, without overwhelming them
macromolecular structures at high resolution. Important
with too much detail. The major goal of the team of lead
advances in other methods, however—including visual-
editors and 29 expert authors has been to incorporate the
ization of fluorescently tagged proteins in living cells and
current research in the field, thoroughly cover each topic,
new types of electron microscopy—are describing cellular
and provide ample illustrations of cellular processes at the
structures and processes in ever-increasing detail.
molecular level—but without being unwieldy.
What this all means is that the scope of biological
questions that can be asked has been fundamentally
changed. The new field of structural genomics has enabled
us to relate increased structural resolution to functional
Key Features
changes, providing powerful insights at deeper levels of Lewin’s CELLS, Third Edition covers the structure, organiza-
understanding. With our growing ability to process huge tion, growth, regulation, movement, and interactions of
data sets, complete characterizations of cellular structures cells with an emphasis on those in the eukaryotic Â�domain.
such as the nuclear pore complex and the centrosome, These topics are presented in 21 chapters grouped into
which are constructed from hundreds of proteins, may seven parts, beginning with the definition of a cell, pro-
soon be attainable. viding background on basic cellular processes, continuing
xviii

on to the components of cells and the regulation of cell For the student
functions, and ending with cell diversity. Plant cells and
The Navigate Companion Website we have developed
prokaryotic cells are covered in separate chapters to em-
exclusively for the third edition of this text, go.jblearning
phasize their diversity while highlighting the properties
.com/Cells3eCW, offers a variety of resources to enhance
shared by all cells.
understanding of cell biology. Students will find chapter
summaries and study quizzes that help them to review the
Design key concepts, as well as an interactive glossary, flashcards,
The design of Lewin’s CELLS, Third Edition is specifically and crosswords to aid with memorization of key terms.
intended to enhance pedagogy. Chapters are divided into The site also contains a selection of interactive figures,
sections with declarative titles that emphasize the main animations, and videos, visual aids that are Â�essential to
points. Each section begins with a set of Key Concepts understanding the dynamic nature of cells. The interactive
that enable readers to grasp the important ideas at the outÂ�- figures include diagrams and micrographs with labels that
set. To stimulate students’ interest in future work, chapters can be turned on and off as well as short videos with labels
include a section called What’s Next? that Â�describes some showing the progression of key processes. For those stu-
of the interesting questions that researchers are tackling. dents who wish to explore topics in cell biology in greater
Key review articles have been listed for students interested depth, a list of important research papers and reviews is
in the experiments that led to the current understand- also provided for every chapter in the book, along with
ing of each topic, and additional references to original links to related sites on the website.
research papers and reviews are available on this book’s Access to this site is free with every new, printed copy
Student Companion Website. Each chapter in Lewin’s of the text; it is also available for purchase separately.
CELLS, Third Edition includes Concept and Reasoning Visit go.jblearning.com/Cells3eCW to purchase standalone
Checks, allowing students to test their understanding Â�access to the Navigate Companion Website.
of the material just presented. Pedagogy has also been
enhanced by adding special feature boxes to highlight
Medical Applications, Historical Perspectives, and For the instructor
Methods and Techniques used to study cell processes. Compatible with Windows and Macintosh platforms, the
The artists, in collaboration with the authors and Instructor’s Media CD provides instructors with the follow-
editors, have developed the illustrations to be as self-Â� ing traditional ancillaries:
explanatory as possible, with such features as label boxes • The PowerPoint Image Bank provides the il-
that lead the reader through a figure. Liberal use of well- lustrations, photographs, and tables (to which
labeled micrographs and molecular structures helps stu- Jones & Bartlett Learning holds the copyright or
dents to recognize cellular components and understand has permission to reproduce digitally) inserted into
relationships between structure and function. Whenever PowerPoint slides. Instructors can quickly and eas-
possible, the schematic figures take into account the rela- ily copy individual images or tables into their exist-
tive sizes of molecules. Colors and molecular shapes, the ing lecture slides.
latter based on atomic structures where known, are used • The PowerPoint Lecture Outline Slides presen-
in a consistent manner throughout the book. tation package provides lecture notes and images
for each chapter of Lewin’s CELLS, Third Edition.
Instructors with the Microsoft PowerPoint soft-
Supplements to the Text ware can customize the outlines, art, and order of
presentation.
Jones & Bartlett Learning offers an impressive array of
• The Instructor’s Media CD also contains more than
ancillaries to assist instructors and students in teaching
350 interactive figures, animations, and videos.
and mastering the concepts in this text. Additional infor-
A Test Bank is also available through your Jones & Bartlett
mation and review copies of any of the following items
Learning sales representative. The questions are presented
are available through your Jones & Bartlett Learning
in straight text files that are compatible with most learning
sales representative or by going to go.jblearning.com
management systems.
/Cells3e.
George Plopper
David Sharp
Eric Sikorski
Preface xix

Acknowledgments
We thank the many scientists who provided advice infor-

mally throughout the development of this edition of Lewin’s
CELLS and the following scientific advisors who read Â�portions
of the text and made many valuable suggestions:
Stephen Adam Northwestern University Feinberg School Frank McCormick University of California, San Francisco, CA
of Medicine, Chicago, IL Akira Nagafuchi Kumamoto University, Kumamoto City,
Tobias Baskin University of Massachusetts, Amherst, MA Japan
Harris Bernstein National Institutes of Health, Bethesda, MD Roel Nusse Stanford University, Palo Alto, CA
Fred Chang Columbia University, New York, NY Andrew Osborne Harvard Medical School, Boston, MA
Amy Chow City of Hope, Duarte, CA Erin O’Shea Harvard University, Cambridge, MA
Louis DeFelice Vanderbilt University, Nashville, TN Marcus Peter University of Chicago, Chicago, IL
Paola Deprez Institute of Microbiology–ETH, Zurich, Suzanne Pfeffer Stanford University, Stanford, CA
Switzerland Tom Rapoport Harvard Medical School, Boston, MA
Arshad Desai University of California, San Diego, CA Ulrich Rodeck Thomas Jefferson University,
Paul De Weer University of Pennsylvania, Philadelphia, PA Philadelphia, PA
Biff Forbush Yale University, New Haven, CT Michael Rossi University of New Haven, West Haven, CT
Joseph Gall Carnegie Institution, Baltimore, MD Michael Roth University of Texas Southwestern Medical
Emily Gillett Harvard Medical School, Boston, MA Center, Dallas, TX
Rebecca Heald University of California, Berkeley, CA Robert Seiser Roosevelt University, Schaumburg, IL
Alistair Hetherington Bristol University, Bristol, United Kingdom Lucy Shapiro Stanford University, Palo Alto, CA
Harald Herrmann German Cancer Research Center, Thomas Shea University of Massachusetts, Lowell, MA
Heidelberg, Germany David Siderovski University of North Carolina, Chapel Hill, NC
Philip Hinds Tufts Medical Center, Boston, MA Mark Solomon Yale University, New Haven, CT
Jer-Yuan Hsu University of California, San Diego, CA Chris Staiger Purdue University, West Lafayette, IN
Martin Humphries University of Manchester, Manchester, Margaret A. Titus University of Minnesota, Minneapolis, MN
United Kingdom Heather True Washington University, St. Louis, MO
James Kadonaga University of California, San Diego, CA Livingston
Randall King Harvard Medical School, Boston, MA Van De Water Albany Medical Center, NY
Cindy Knall University of Alaska, Anchorage, AK Miguel Vicente-
Roberto Kolter Harvard Medical School, Boston, MA Manzanares University of Virginia, Charlottesville, VA
Susan LaFlamme Albany Medical Center, NY Patrick Viollier Case Western Reserve University,
Francene Lemoine Northwestern State University, Cleveland, OH
Natchitoches, LA Claire Walczak Indiana University, Bloomington, IN
Rudolf Leube Johannes Gutenberg University, Mainz, Junying Yuan Harvard Medical School, Boston, MA
Germany Gary Zieve Stony Brook University, Stony Brook, NY
Vivek Malhotra University of California, San Diego, CA Sally Zigmond University of Pennsylvania, Philadelphia, PA
We are also grateful to all the scientists who made

this book possible by providing essential micrographs
and other images and to the journal and book publishers
for permission to reproduce them. The credits are in the
figure legends.
We welcome suggestions for revisions or corrections,
which can be sent to us at info@jbpub.com.
xx

Contributors
Lead Editors of the microtubule cytoskeleton in cell division, migration,

and morphogenesis.
George Plopper is a Professor of Biology at Rensselaer Eric Sikorski is an Assistant Professor of Biology at the
Polytechnic Institute. He studies signal transduction and University of Tampa. He currently studies the effects of
cellular behavior induced by extracellular matrix binding beta-hydroxy-beta-methylbutyrate (HMB) on skeletal
and is author of the textbook Principles of Cell Biology. muscle damage and recovery after high-intensity resis-
David Sharp is a Professor of Physiology and Biophysics at tance training.
the Albert Einstein College of Medicine. He studies the role
Authors David G. Bear is Professor of Cell Biology and Physiology

and Assistant Dean for Admissions at the University of
Vishwanath R. Lingappa is Senior Scientist at Bioconformatics New Mexico School of Medicine and is Professor and Chair
Laboratory, CPMC Research Institute; Chief Technology of Chemistry and Chemical Biology at the University of
Officer at Prosetta Corporation; and Emeritus Professor of New Mexico. His research interests focus on the assembly
Physiology at the University of California, San Francisco. and intracellular trafficking of messenger RNA ribonu-
His research is in protein biogenesis. He practices inter- cleoprotein complexes in striated muscle cells, muscular
nal medicine as a volunteer physician at San Francisco dystrophies, and muscle cell cancers.
General Hospital and has coauthored textbooks of physi- Stephen J. Smerdon is joint head of the Division of
ology and pathophysiology. Molecular Structure at the MRC National Institute for
Benjamin Lewin founded the journal Cell in 1974 and was Medical Research, UK, where he works on the structural
Editor until 1999. He also founded the Cell Press journals biology of a variety of cell signaling pathways, particu-
Neuron, Immunity, and Molecular Cell. In 2000, he founded larly the regulation of DNA-damage complex assembly
Virtual Text, which was acquired by Jones and Bartlett by phosphorylation-dependent mechanisms.
Publishers in 2005. He is the original author of Genes and Stephan E. Lehnart is a Professor of Translational Cardiology
Essential Genes. at the Center of Molecular Cardiology of the University
Raymond Ochs is a Professor of Pharmaceutical Sciences Medical Center Göttingen and an Adjunct Associate
at St. John’s University in New York. His research con- Professor at the University of Maryland Biotechnology
cerns regulation of intermediary metabolism and control Institute. His major research interests are membrane trans-
by Â�intracellular calcium ion. port mechanisms that control intracellular calcium cycling
Blanca Barquera is an Associate Professor of Biology at in the heart and other organs that contribute significantly
Rensselaer Polytechnic Institute. Her research focuses on to disease processes.
sodium bioenergetics in pathogenic bacteria, mechanistic Andrew R. Marks is the Clyde and Helen Wu Professor
enzymology of respiratory proteins and ion transporters, of Medicine and Chair and Professor of the Department
membrane proteins, and bacterial physiology. of Physiology and Cellular Biophysics at Columbia
Jocelyn E. Krebs is an Associate Professor of Biological University. He works on how macromolecular signaling
Sciences at the University of Alaska, Anchorage. Her lab complexes regulate ion channel function in muscle and
studies DNA repair and transcription in the context of nonmuscle systems. He is a member of the Institute of
chromatin structure in the yeast Saccharomyces cerevisiae Medicine of the National Academy of Sciences, American
and the role of chromatin remodeling during vertebrate Academy of Arts and Sciences, and the National Academy
development in the frog Xenopus laevis. of Sciences.
xxi

D. Thomas Rutkowski is an Assistant Professor in the State Department of Health. He is also a Professor in the
Department of Anatomy and Cell Biology at the University Department of Biomedical Sciences, State University of
of Iowa Carver College of Medicine. His lab studies how New York at Albany. Dr. Rieder has spent over 30 years
cells adapt to chronic protein misfolding stress in normal researching how cells divide.
physiology and disease. Kathleen L. Gould is Professor and Vice-Chair of Cell and
Vivek Malhotra is the Chair of Cell and Developmental Developmental Biology at Vanderbilt University School
Biology at CRG in Barcelona, Spain. His laboratory has of Medicine and an Investigator of the Howard Hughes
long been involved in the mechanism of protein secretion Medical Institute. Her laboratory studies the mecha-
and Golgi organization. nism and regulation of cytokinesis in the fission yeast
Graham Warren is the Scientific Director of the Max F. Schizosaccharomyces pombe.
Perutz Laboratories, Vienna, Austria, and his laboratory Susan L. Forsburg is a Professor in Molecular and
studies the structure, function, and biogenesis of the Golgi Computational Biology at the University of Southern
apparatus. California. Her laboratory studies DNA replication and
Ira Mellman is Vice President of Research Oncology at genome dynamics in the fission yeast Schizosaccharomyces
Genentech, Inc., in San Francisco, California. His research pombe.
focuses on the cell biology of the immune response (spe- Douglas R. Green is the Chair of Immunology at St. Jude
cifically the role of dendritic cells in T-cell stimulation) and Children’s Research Hospital in Memphis, TN. His labora-
on the signals that control the formation and function of tory studies the process of apoptosis and related forms of
epithelial cells. cell death.
Charles N. Cole is a Professor of Biochemistry and of Robert A. Weinberg is the Daniel K. Ludwig and American
Genetics at Dartmouth Medical School. His interests have Cancer Society Professor for Cancer Research at the
included nuclear transport, regulation of cellular transfor- Massachusetts Institute of Technology and a found-
mation and immortalization, RNA metabolism, microR- ing member of the Whitehead Institute for Biomedical
NAs, and breast cancer. Research. His research is focused on the molecular mecha-
Pamela A. Silver is a Professor of Systems Biology at Harvard nisms that control cell proliferation and the formation of
Medical School. Her interests have included nuclear trans- tumors.
port, organization of the genome, RNA dynamics, and Elliott M. Ross is a Professor in the Graduate Programs
synthetic biology. in Molecular Biophysics and Cell Regulation and the
Lynne Cassimeris is a Professor in the Department of Department of Pharmacology at the University of Texas
Biological Sciences at Lehigh University in Bethlehem, PA. Southwestern Medical Center in Dallas. His group studies
She studies microtubule assembly dynamics and mitosis. information processing in G-protein signaling networks.
Enrique M. De La Cruz is an Associate Professor of Molecular Melanie H. Cobb is a Professor in Pharmacology and the
Biophysics and Biochemistry at Yale University. His labora- Graduate Programs in Cell Regulation and Cancer Biology
tory uses biochemical and biophysical techniques to inves- at the University of Texas Southwestern Medical Center
tigate the mechanisms of actin- and myosin-based motility. at Dallas. Her group studies regulation and function of
His work also focuses on motor properties of RNA helicases. protein kinases with an emphasis on MAPK pathways
and WNKs.
E. Michael Ostap is a Professor of Physiology at the
University of Pennsylvania School of Medicine and is a Matthew Chapman is an Associate Professor at the University
member of the Pennsylvania Muscle Institute. His labo- of Michigan and the 2009 recipient of the university’s
ratory uses cell biological, biochemical, and biophysical Class of 1923 Teaching Award. His lab studies the function
techniques to investigate the mechanisms of cell motility. and biogenesis of bacterial amyloid fibers.
His work is currently focused on the study of unconven- Jeff Errington is Director of the Institute for Cell and
tional myosins. Molecular Biosciences at Newcastle University, Newcastle-
Birgit Lane is Executive Director of the Institute of Medical upon-Tyne, UK. He works on the cell cycle and cell mor-
Biology in Singapore. She studies intermediate filaments, phogenesis of bacteria.
particularly keratins, and the part they play in normal tis- Clive Lloyd is a Project Leader at The John Innes Centre,
sue resilience and in human diseases. Norwich, UK. He studies the role of the cytoskeleton in
Conly L. Rieder is a Senior Research Scientist and Chief of plant growth and development.
the Wadsworth Center’s Laboratory of Cell Regulation.
The Wadsworth Center is a research arm of the New York
xxii Contributors

Abbreviations
A Adenine or adenosine Units
ADP Adenosine diphosphate Å Angstrom
AMP Adenosine monophosphate D or Da Dalton
cAMP Cyclic AMP g Gram
ATP Adenosine triphosphate h or hr Hour
ATPase Adenosine triphosphatase M Molar concentration
bp Base pair(s) m Meter
C Cytidine or cytosine m or min Minute
cDNA Complementary DNA N Newton
CDP Cytidine diphosphate S Svedberg unit
CMP Cytidine monophosphate s or sec Second
CTP Cytidine triphosphate v Volt
DNA Deoxyribonucleic acid
DNAase Deoxyribonuclease Amino acids
G Guanine or guanosine A Ala Alanine
GDP Guanosine diphosphate C Cys Cysteine
GlcNAc N-Acetyl-d-glucosamine D Asp Aspartic acid
GMP Guanosine monophosphate E Glu Glutamic acid
GTP Guanosine triphosphate F Phe Phenylalanine
ΔG Free energy change G Gly Glycine
kb Kilobases or kilobase pairs H His Histidine
Mb Megabases or megabase pairs I Ile Isoleucine
mRNA Messenger RNA K Lys Lysine
MW Molecular weight L Leu Leucine
Pi Inorganic phosphate M Met Methionine
PPi Inorganic pyrophosphate N Asn Asparagine
RNA Ribonucleic acid P Pro Proline
RNAase Ribonuclease Q Gln Glutamine
rRNA Ribosomal RNA R Arg Arginine
tRNA Transfer RNA S Ser Serine
T Thymine or thymidine T Thr Threonine
U Uracil V Val Valine
UDP Uridine diphosphate W Trp Tryptophan
UMP Uridine monophosphate Y Tyr Tyrosine
UTP Uridine triphosphate
Prefix
(Abbreviation) Multiple
mega (M) 106
kilo (k) 103
deci (d) 10–1
centi (c) 10–2
milli (m) 10–3
micro (µ) 10–6
nano (n) 10–9
pico (p) 10–12
xxiii

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Lewin's CELLS

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CELLS Third edition

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Library of Congress Cataloging-in-Publication Data

Printed in the United States of America

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Part 4â•‡ The cytoskeleton 513

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Feature Boxesâ•‡â•‡xvii 1.16 Protein trafficking moves proteins through the

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small molecules across 6.23 Summaryâ•‡â•‡294

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Part 3â•‡ The nucleus 401 9.25

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2.1â•‡ Diabetes and Metabolismâ•… 57 15.1â•‡ Discovering S Phaseâ•… 687

Methods and Techniques

4.1â•‡ Gene Expression Profilingâ•… 128 â•⁄5.7â•‡Binding Equilibriaâ•… 216

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We thank the many scientists who provided advice infor-

We are also grateful to all the scientists who made

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Lead Editors of the microtubule cytoskeleton in cell division, migration,

Authors David G. Bear is Professor of Cell Biology and Physiology

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