Becker's World of the Cell 8th ed. - J. Hardin, et al., (Pearson, 2012) WW

914 Pages·2012·80.52 MB·English

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B E C K E R ’ S

World of the Cell

E I G H T H E D I T I O N

JEFF HARDIN

University of Wisconsin-Madison

GREGORY BERTONI

The Plant Cell

LEWIS J. KLEINSMITH

University of Michigan, Ann Arbor

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Library of Congress Cataloging-in-Publication Data
Hardin, Jeff.
Becker’s world of the cell / Jeff Hardin, Gregory Bertoni, Lewis J. Kleinsmith. — 8th ed.
p. ; cm.
World of the cell
Rev. ed. of: World of the cell / Wayne M. Becker . . . [et al.]. 7th ed.
Includes bibliographical references and index.
ISBN-13: 978-0-321-71602-6 (alk. paper)
ISBN-10: 0-321-71602-7 (alk. paper)
1. Cytology.
2. Molecular biology.
I. Bertoni, Gregory.
II. Kleinsmith, Lewis J.
III. Becker, Wayne M.
IV. World of the cell.
V. Title.
VI. Title: World of the cell.
[DNLM: 1. Cell Physiological Phenomena. 2. Molecular Biology. QU 375]
QH581.2.B43 2012
571.6—dc22
2010041983

ISBN-10: 0-321-71602-7; ISBN-13: 978-0-321-71602-6 (Student edition)
ISBN 10: 0-321-68962-3; ISBN 13: 978-0-321-68962-7 (Exam copy)
ISBN 10: 0-321-68963-1; ISBN 13: 978-0-321-68963-4 (Books a la Carte edition)

1 2 3 4 5 6 7 8 9 10—WBC—15 14 13 12 11

www.pearsonhighered.com

JEFF HARDIN is Professor and Chair of
the Zoology Department at the University
of Wisconsin-Madison. He is also faculty
director of the Biology Core Curriculum,
a four-semester honors biology sequence
for undergraduates. His research interests
center on how cells migrate and adhere to
one another to change the shape of
animal embryos. Dr. Hardin’s teaching is enhanced by his
extensive use of digital microscopy and his web-based teach-
ing materials, which are used on many campuses in the
United States and other countries. As part of his interest in
teaching biology, Dr. Hardin was a founding member of the
University of Wisconsin Teaching Academy. His teaching
awards include a Lily Teaching Fellowship and a National
Science Foundation Young Investigator Award. He is also on
the editorial board of CBE: Life Sciences Education, and
is a curator of WormClassroom, a digital initiative that
promotes the use of C. elegans in college classrooms and
laboratories.

GREGORY BERTONI has been active in
teaching, research, and scientific writing
for over 25 years. He earned a Ph.D. in
Cellular and Molecular Biology from the
University of Wisconsin-Madison, where
he taught students in introductory and
graduate-level biochemistry, sophomore
cell biology, and plant physiology. He
helped to develop a new course entitled
“Ways of Knowing” designed to introduce entering fresh-
men to a variety of academic fields as well as to the learning
process itself. His published research includes studies in bac-
terial pathogenesis, plant-microbe interactions, and plant
gene expression. Dr. Bertoni is a science editor for The Plant
Cell, a leading international research journal in plant cell
and molecular biology. He is also responsible for updating
the journal’s Teaching Tools in Plant Biology, an online
resource for biology instructors. He has been teaching biol-
ogy and medical microbiology at Columbus State Commu-
nity College in Columbus, Ohio for most of the past 10
years. In addition, Dr. Bertoni is a freelance scientific writer
who contributes to text- and web-based projects in biology,
physics, and microbiology and assists authors in preparing
manuscripts for publication.

iii

A B O U T T H E AU T H O R S

LEWIS J. KLEINSMITH is an Arthur F.
Thurnau Professor Emeritus of Molecu-
lar, Cellular, and Developmental Biology
at the University of Michigan, where he
has served on the faculty since receiving
his Ph.D. from Rockefeller University in
1968. His teaching experiences have
involved courses in introductory biology,
cell biology, and cancer biology, and his research interests
have included studies of growth control in cancer cells, the
role of protein phosphorylation in eukaryotic gene regula-
tion, and the control of gene expression during develop-
ment. Among his numerous publications, he is the author of
Principles of Cancer Biology as well as several award-winning
educational software programs. His honors include a
Guggenheim Fellowship, the Henry Russell Award, a Michi-
gan Distinguished Service Award, citations for outstanding
teaching from the Michigan Students Association, an NIH
Plain Language Award, and a Best Curriculum Innovation
Award from the EDUCOM Higher Education Software
Awards Competition.

WAYNE M. BECKER taught cell biology
at the University of Wisconsin-Madison
for 30 years until his retirement. His
interest in textbook writing grew out of
notes, outlines, and problem sets that he
assembled for his students, culminating
in Energy and the Living Cell, a paperback
text on bioenergetics published in 1977,
and The World of the Cell, the first edition
of which appeared in 1986. He earned all his degrees at the
University of Wisconsin-Madison. All three degrees are in
biochemistry, an orientation that is readily discernible in his
textbooks. His research interests were in plant molecular
biology, focused specifically on the regulation of the expres-
sion of genes that encode enzymes of the photorespiratory
pathway. His honors include a Chancellor’s Award for
Distinguished Teaching, Guggenheim and Fulbright Fellow-
ships, and a Visiting Scholar Award from the Royal Society
of London. This text builds on his foundation, and is
inspired by his legacy.

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“B

cause we enjoy interacting with biology under-
grads and think that they should have biology
textbooks that are clearly written, make the subject matter
relevant to the reader, and help them appreciate not only
how much we already know about biology—cell biology, in
our case—but also how much more remains to be investi-
gated and discovered.” That’s how any of the authors of this
text would likely respond if asked why we’ve invested so
much time in writing and revising The World of the Cell.
Each of us has an extensive history of teaching undergrad-
uate courses in cell biology and related areas, and each of
us treasures our contact with students as one of the most
rewarding aspects of being a faculty member.
As we reflect on the changes we’ve seen in our courses
over the years, we realize that the past several decades
have seen an explosive growth in our understanding of the
properties and functions of living cells. This enormous
profusion of information presents us with a daunting
challenge as we confront the task of keeping Becker’s
World of the Cell up to date while simultaneously ensuring
that it remains both manageable in length and readily
comprehensible to students encountering the field of cell
and molecular biology for the first time. This eighth edi-
tion represents our most recent attempt to rise to that
challenge. As with the previous editions, each of us has
brought our own teaching and writing experience to the
venture in ways that we have found mutually beneficial—a
view that we hope our readers will share.
One major objective for this edition has been to
update the content of the text, especially in areas where the
pace of research is especially brisk and recent findings are
particularly significant. At the same time, we have
remained committed to the three central goals that have
characterized each preceding edition. As always, our pri-
mary goal is to introduce students to the fundamental
principles that guide cellular organization and function.
Second, we think it is important for students to understand
some of the critical scientific evidence that has led to the
formulation of these central concepts. And finally, we have
sought to accomplish these goals in a book of manageable
length that can be easily read and understood by beginning
cell biology students—and that still fits in their backpacks!
To accomplish this third goal, we have necessarily been
selective both in the types of examples chosen to illustrate
key concepts and in the quantity of scientific evidence
included. We have, in other words, attempted to remain
faithful to the overall purpose of each previous edition: to
present the essential principles, processes, and methodol-

ogy of molecular and cell biology as lucidly as possible. We
have also given careful attention to accuracy, consistency,
vocabulary, and readability to minimize confusion and
maximize understanding for our readers.

What’s New in This Edition

The eighth edition retains the clear writing style from
previous editions, and adds new emphasis on modern
genetic/genomic/proteomic approaches to cell biology:

■ New, up-to-date information has been added on the
tools that modern cell biologists use, including model
organisms, bioinformatics, and genomics/proteomics.
This discussion in Chapter 1 better establishes the
modern, 21st century approach to cell biology while
retaining the classical emphasis from previous editions.

■ Major reorganization of the cell cycle and
apoptosis material, including moving apoptosis from
Chapter 14 to Chapter 19 to better match conven-
tional course syllabi.

■ New discussions of modern genetic and molecular
technologies, such as nanotechnology, biolumines-
cence, X-ray crystallographic data, and genetic
engineering of animals and transgenic plants.

■ Content updates have been added throughout
the book highlighting the most recent advances
in the understanding of cell biology (see Content
Highlights of the Eighth Edition).

■ New, In-text media callouts that link chapter content
to multimedia resources, such as learning activities, 3D
molecular structure tutorials, videos, and animations,
that are available on www.thecellplace.com

■ New online videos, 3D structure tutorials,
animations, and activities have been added to
The Cell Place (www.thecellplace.com) to enhance
student learning through dynamic visualization.

■ New Pearson E-text and Pearson Custom Library
options are available.

■ New PowerPoint Lecture Tools, including pre-made
lecture outlines containing all of the figures and
photos and embedded animations, and 5–10 personal
response system (PRS) clicker questions per chapter.

v

P R E FAC E

VIDEOS www.thecellplace.com
Spindle formation
during mitosis

Content Highlights of
the Eighth Edition

Updated material and new information has been added
throughout the book. Topics that have been altered,
updated, or added include the following:

CHAPTER 1: Added a new box essay and figure
describing the use of model organisms in cell biology
research. Updated discussions of nanotechnology, new
types of light and electron microscopes, advances in
gene and genome sequencing, new “-omics” fields, and
bioinformatic tools at NCBI (PubMed, GenBank,
OMIM). Introduced “in silico” research as an extension
of traditional in vivo and in vitro research.

CHAPTER 2: Described how viral self-assembly can be
used in nanotechnology and biomedicine; described
electronegativity in relation to polarity and solubility of
biomolecules; and introduced soaps and detergents as
amphipathic molecules.

CHAPTER 3: Streamlined discussion of protein function;
improved discussion of peptide bond geometry;
introduced CASP—the worldwide test of protein
structure modeling programs; added miRNA and siRNA
to the discussion of RNA; introduced lipid rafts earlier.

CHAPTER 4: Added discussions of the important
functions of what had been called “junk” DNA, how
mitochondrial DNA analysis is used to trace genetic
lineages and the origin of modern humans, construction
of an artificial ribosome in vitro, and how prions cause
chronic wasting disease in deer and elk. Presented new
results of X-ALD gene therapy clinical trial.

CHAPTER 5: Discussion of bioluminescence now
includes luciferase, GFP, and YFP as tools for cell
biologists; new figure added to show localization of
YFP protein fusion by fluorescence microscopy.
Strengths in discussions of bioenergetics and
thermodynamics have been retained.

CHAPTER 6: Updated discussion on induced fit; added
new figures showing formation of lysozyme active site
after protein folding and the changes in the active site
of carboxypeptidase following substrate binding; added
description of aspirin as an irreversible inhibitor of
cyclooxygenase; described cryophilic microorganisms
such as Listeria.

CHAPTER 7: Added a new paragraph and figure
describing the common glycolipids MGDG and
DGDG; included a more extensive description of lipid
raft composition, formation, and proteomics; added
descriptions of how antimicrobial peptides disrupt cell
membranes, described membrane receptors for nutrients
and for the gaseous hormone ethylene; updated roles of
caveolae in human physiology and disease.

CHAPTER 8: Added description of aquaporin
discovery by Agre and colleagues; added new figure
showing structures of bacterial porin and human
aquaporin. Updated discussion of all five subclasses of
P-type ATPases; added discussion of how the
Na+/glucose symporter can affect the treatment of
cholera; introduced additional members of the human
glucose transporter family; described use of bacteri-
orhodopsin in biomolecular electronics.

CHAPTER 9: Added new discussion clarifying
resonance stabilization and electron delocalization;
expanded discussion of anaerobic respiration; described
role of unusual microorganisms in geochemical cycling
of nutrients and global biomass production; noted how
oxidative stress and free radicals can damage cells.

CHAPTER 10: Included more emphasis on cellular
locations of biochemical processes and on similarities
between bacterial and eukaryotic respiration; clarified
difference between internal and external electron
acceptors; introduced pyruvate symporter. In response
to reviewer requests, added figure and extensive
description of b-oxidation of fatty acids.

CHAPTER 11: Added new paragraph describing newly
discovered quantum effects during photosynthetic light
harvesting; emphasized similarities between mitochon-
drial and chloroplast electron transport; introduced
pioneering work of van Niel in the 1930s using
photosynthetic bacteria. Added an analogy for a
potential energy barrier by comparing the thylakoid
membrane to a hydroelectric dam, clarified
nomenclature of photosystems I and II.

CHAPTER 12: Added new paragraph describing
mechanism of action and clinical uses of botulinum
toxin. Added new material on N-glycosylation and
secretion involving interleukin-31 and p53 and new
micrographs showing exocytosis and phagocytosis.
Added new paragraph describing reactive oxygen
species and their detoxification in the peroxisome;
included a more detailed description of the reaction
mechanism of P-450 monooxygenases.

CHAPTER 13: Reorganized discussion of squid giant
axon and the basic membrane potential measuring
technique: how membrane potential is measured in
neurons is now discussed prior to what contributes to
the membrane potential. Updated depiction of voltage-
gated channels to reflect X-ray crystallographic data.
Changed terminology from “terminal bulb” to “synaptic
bouton,” which is more common among neurobiolo-
gists. Updated the discussion of neurotransmitters to
include endocannabinoids, and created a new table
showing chemical structure of selected neurotransmit-
ters. Now mention “kiss-and-run” exocytosis as an
additional mechanism of neurotransmitter release.

vi
Preface

CHAPTER 14: Added a discussion of co-receptors, a
section on how Wnts and Hedgehogs feed into G
protein signaling, a new table on hormones, a section
on nuclear hormone receptors, and added PTEN to the
discussion of insulin signaling. Reorganized content
between Chapter 14 and Chapter 19 to streamline
discussion: apoptosis and discussion of C. elegans has
been moved out of this chapter.

CHAPTER 15: Katanins are now discussed in the
microtubule section. Added significant new information
on formins in the actin section, and much more coverage
of Rho GTPases, including RhoGEFs, GAPs, and GDIs.

CHAPTER 16: Added new information and a new part
of a figure on hair cells, as well as significant new text
on intraflagellar transport (IFT) and ciliopathies to Box
16A. Updated the figure on focal contacts and the
leading edge to provide an integrated view of actin
polymerization at the leading edge.

CHAPTER 17: Added further description of apical-basal
polarity in epithelia, and the epithelial-mesenchymal
transition (EMT), and there is now more emphasis on
the dynamic nature of cell adhesion. Added new infor-
mation on the Par3/Par6/aPKC polarity complex and
on the dystrophin/dystroglycan complex. Also updated
discussion of claudins to include paracellular transport
and human diseases associated with claudins. Added
text about kindlins to the focal adhesion discussion and
updated treatment of integrin-linked kinase (ILK).

CHAPTER 18: Added new information on NTF2 in the
Ran/importin/exportin section. Updated section on
nuclear bodies to be more explicit about types and
functions of nuclear bodies (Cajal, GEMs, speckles,
etc.). Added a new figure describing the percentage of
various types of DNA in the human genome.

CHAPTER 19: Added new information on spindle
midzones, as well as new material and a new figure on
myosin and Rho during cytokinesis. Added new
material on ATR and checkpoint kinases in the cell
cycle control section. Reorganized content between
Chapter 14 and Chapter 19 to streamline discussion:
much of the Ras discussion and Akt/PI3K has been
moved out of this chapter. Apoptosis was removed from
Chapter 14, and is now in Chapter 19. In addition, the
apoptosis figure was redrawn to show a more accurate
depiction of the apoptosome based on cryoEM data.

CHAPTER 20: Added substantially more discussion
and a new figure on knockout mice. The section on
genetic engineering has been reworked, and there is
now better balance between genetic engineering of
animals and transgenic plants. A new figure showing
pronuclear injection in mice was added. Updated the
section on screening of bacterial clones to reflect the
“modern” way of doing this by restriction digests and

sequencing. The section on gene conversion was short-
ened to accommodate more modern material.

CHAPTER 21: Added information on regulatory role of
the C terminus of RNA pol II. Added a discussion of
electrophoretic mobility shift assays (EMSAs) as a
technique, while the historical method of R loop
detection was streamlined and supplemented with an
improved schematic diagram.

CHAPTER 22: Added a new figure showing the results
of experiments with microsomes, demonstrating that
cotranslational import is required for cleavage of the
signal sequence. Added a brief discussion of operons in
eukaryotes.

CHAPTER 23: Added further discussion and a new
figure regarding the Dolly cloning method. Substantially
increased the discussion of embryonic stem (ES) cells and
induced pluripotent stem cells (iPS cells), including a new
figure. Added two new figures on methylation of DNA
and chromatin/histone remodeling, increased coverage of
epigenetics, and added discussion of Prader-Willi and
Angelman syndromes. Added a box on the yeast
two-hybrid system, updated the discussion of the struc-
ture of the lac repressor/operon to reflect crystallographic
data. Revised and expanded the discussion of Hox genes
(including a new figure). Added discussion of
SUMOylation in the post-translational control section.

CHAPTER 24: Added discussion on how cancers evade
destruction by the immune system, and how the tumor
microenvironment influences tumor growth, invasion,
and metastasis. More discussion of the ability of cancer
cells to evade apoptosis and of the Rho family in triggering
the enhanced cell motility that leads to invasion and
metastasis. Added more discussion on how polycyclic
aromatic hydrocarbons in tobacco cause unique muta-
tions in the p53 gene, and added information about the
typical mutation patterns in cancer cells obtained from
genome sequencing studies. Added information about the
role of microRNAs and histone methylation in cancer
epigenetics, and more information about cancer vaccines.

APPENDIX: Added mention of photoconvertible and
photoswitchable fluorophores. Added a section on
various techniques for superresolution microscopy.
Streamlined discussion of correlative microscopy.
Updated figure on the fluorescence microscope to more
accurately reflect modern epifluorescence systems.

Techniques and Methods
Throughout the text, we have tried to explain not only
what we know about cells but also how we know what we
know. Toward that end, we have included descriptions of
experimental techniques and findings in every chapter,
almost always in the context of the questions they address
and in anticipation of the answers they provide. For exam-
ple, polyacrylamide gel electrophoresis is introduced not

Preface
vii

in a chapter that simply catalogues a variety of methods
for studying cells but in Chapter 7, where it becomes
important to our understanding of how membrane pro-
teins can be separated from one another. Similarly, equi-
librium density centrifugation is described in Chapter 12,
where it is essential to our understanding of how lyso-
somes were originally distinguished from mitochondria
and subsequently from peroxisomes as well.
To help readers locate techniques out of context, an
alphabetical Guide to Techniques and Methods appears
on the inside of the front cover, with references to chap-
ters, pages, tables, figures, and boxed essays, as appropri-
ate. To enhance its usefulness, the Guide to Techniques
and Methods includes references not just to laboratory
techniques but also to the mathematical determination of
values such as ΔG (free energy change) and ΔE0¿ (standard
reduction potential), bioinformatics techniques such as
BLAST searching, and even to clinical procedures such as
the treatment of methanol poisoning.
Microscopy is the only exception to our general
approach of introducing techniques in context. The tech-
niques of light and electron microscopy are so pervasively
relevant to contemporary cell biology that they warrant
special consideration as a self-contained unit, which is
included as an Appendix entitled Visualizing Cells and
Molecules. This Appendix gives students ready access to
detailed information on a variety of microscopy tech-
niques, including cutting-edge uses of light microscopy
for imaging and manipulating molecular processes.

Building on the Strengths
of Previous Editions

We have retained and built upon the strengths of prior
editions in four key areas:

1. The chapter organization focuses on main
concepts.

■ Each chapter is divided into sections that
begin with a concept statement heading, which
summarizes the material and helps students
focus on the main points to study and review.

■ Chapters are written and organized in ways that
allow instructors to assign the chapters and
chapter sections in different sequences to
make the book adaptable to a wide variety of
course plans.

■ Each chapter culminates with a bulleted Summary
of Key Points that briefly describes the main points
covered in each section of the chapter.

■ Each Summary of Key Points is followed by a
Making Connections paragraph that highlights
some of the interrelationships that connect the
content of the current chapter to topics covered
elsewhere in the book.

2. The illustrations teach concepts at an appropriate
level of detail.

■ Many of the more complex figures incorporate
minicaptions to help students grasp concepts more
quickly by drawing their focus into the body of an
illustration rather than depending solely on a sep-
arate figure legend to describe what is taking place.

■ Overview figures outline complicated structures or
processes in broad strokes and are followed by text
and figures that present supporting details.

■ Carefully selected micrographs are usually accom-
panied by scale bars to indicate magnification.

3. Important terminology is highlighted and defined
in several ways.

■ Boldface type is used to highlight the most impor-
tant terms in each chapter, all of which are defined
in the Glossary.

■ Italics are employed to identify additional tech-
nical terms that are less important than boldfaced
terms but significant in their own right. Occasion-
ally, italics are also used to highlight important
phrases or sentences.

■ The Glossary includes definitions and page refer-
ences for all bold-faced key terms and acronyms in
every chapter—more than 1500 terms in all, a veri-
table “dictionary of cell biology” in its own right.

4. Each chapter helps students learn the process of
science, not just facts.

■ Text discussions emphasize the experimental
evidence that underlies our understanding of cell
structure and function, to remind readers that
advances in cell biology, as in all branches of
science, come not from lecturers in their classrooms
or textbook authors at their computers but from
researchers in their laboratories.

■ The inclusion of a Problem Set at the end of each
chapter reflects our conviction that we learn
science not just by reading or hearing about it, but
by working with it. The problems are designed to
emphasize understanding and application, rather
than rote recall. Many of the problems are class-
tested, having been selected from problem sets and
exams we have used in our own courses.

■ To maximize the usefulness of the problem sets,
detailed answers for all problems are available for
students in a Solutions Manual that is available for
purchase separately.

■ Each chapter contains one or more Boxed Essays to
aid students in their understanding of particularly
important or intriguing aspects of cell biology.

viii
Preface