Cell and molecular biololgy, concepts and experiments 6th ed g karp (wiley, 2010) 1

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Nobel Prizes Awarded for Research
in Cell and Molecular Biology Since 1958
Year

Recipient*

Prize

Area of Research

Pages in Text

2008

Francoise Barré-Sinoussi
Luc Montagnier
Harald zur Hausen
Martin Chalfie
Osamu Shimomura
Roger Tsien
Mario R. Capecchi
Martin J. Evans

Oliver Smithies
Andrew Z. Fire
Craig C. Mello
Roger D. Kornberg
Richard Axel
Linda B. Buck
Aaron Ciechanover
Avram Hershko
Irwin Rose
Peter Agre
Roderick MacKinnon
Sydney Brenner
John Sulston
H. Robert Horvitz
John B. Fenn
Koichi Tanaka
Kurt Wüthrich
Leland H. Hartwell
Tim Hunt
Paul Nurse
Arvid Carlsson
Paul Greengard
Eric Kandel
Günter Blobel
Robert Furchgott
Louis Ignarro
Ferid Murad
Jens C. Skou
Paul Boyer
John Walker

Stanley B. Prusiner
Rolf M. Zinkernagel
Peter C. Doherty
Edward B. Lewis
Christiane Nüsslein-Volhard
Eric Wieschaus
Alfred Gilman
Martin Rodbell
Kary Mullis
Michael Smith
Richard J. Roberts
Phillip A. Sharp

M & P**

Discovery of HIV

23

Chemistry

Role of HPV in cancer
Discovery and development
of GFP

654
267, 720

M&P

Development of techniques
for knockout mice

760

M&P

RNA Interference

449, 762

Chemistry
M&P

Transcription in eukaryotes
Olfactory receptors

427, 481
622

Chemistry

Ubiquitin and proteasomes

529

Chemistry

Structure of membrane
channels

Introduction of C. elegans
as a model organism
Apoptosis in C. elegans
Electrospray ionization in MS
MALDI in MS
NMR analysis of proteins
Control of the cell cycle

2007

2006

2004

2003
2002

2001

2000

1999
1998

1997

1996
1995

1994

1993

M&P

Chemistry

M&P

146, 148
17
643
740
740
56
564, 600

M&P

Synaptic transmission and
signal transduction

163
605

M&P
M&P

Protein trafficking
NO as intercellular
messenger

276
641

Chemistry

Naϩ/Kϩ-ATPase
Mechanism of ATP synthesis

153
195

M&P
M&P

Protein nature of prions
Recognition of virus-infected cells
by the immune system
Genetic control of
embryonic development

64
709

M&P

M&P
Chemistry
M&P

Structure and function of
GTP-binding (G) proteins
Polymerase chain reaction (PCR)
Site-directed mutagenesis (SDM)
Intervening sequences

EP12

610
751
760
438


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Year

Recipient*

Prize

Area of Research

1992

Edmond Fischer
Edwin Krebs
Erwin Neher
Bert Sakmann
J. Michael Bishop
Harold Varmus
Thomas R. Cech
Sidney Altman
Johann Deisenhofer
Robert Huber
Hartmut Michel
Susumu Tonegawa

M&P

Alteration of enzyme activity by
phosphorylation/dephosphorylation
Measurement of ion flux by
patch-clamp recording
Cellular genes capable of causing
malignant transformation
Ability of RNA to catalyze reactions

1991
1989

1988

1987
1986
1985
1984

1983
1982
1980

1978

1976
1975

1974

1972

Rita Levi-Montalcini
Stanley Cohen
Michael S. Brown
Joseph L. Goldstein
Georges Köhler
Cesar Milstein
Niels K. Jerne
Bruce Merrifield
Barbara McClintock
Aaron Klug
Paul Berg
Walter Gilbert

Frederick Sanger
Baruj Bennacerraf
Jean Dausset
George D. Snell
Werner Arber
Daniel Nathans
Hamilton O. Smith
Peter Mitchell
D. Carleton Gajdusek
David Baltimore
Renato Dulbecco
Howard M. Temin
Albert Claude
Christian de Duve
George E. Palade
Gerald Edelman
Rodney R. Porter
Christian B. Anfinsen

M&P
M&P
Chemistry

112, 614
147
677
469

Chemistry

Bacterial photosynthetic reaction
center

213

M&P

DNA rearrangements responsible
for antibody diversity
Factors that affect nerve outgrowth

696

M&P
M&P

372

Regulation of cholesterol metabolism
and endocytosis
Monoclonal antibodies

312

Antibody formation
Chemical synthesis of peptides
Mobile elements in the genome
Structure of nucleic acid-protein
complexes
Recombinant DNA technology

DNA sequencing technology

687
746
402
76

M&P

Major histocompatibility complex

699

M&P

Restriction endonuclease technology

746

Chemistry

Chemiosmotic mechanism of
oxidative phosphorylation
Prion-based diseases
Reverse transcriptase and tumor
virus activity

181

M&P

Structure and function of internal
components of cells

267

M&P

Immunoglobulin structure

693

Chemistry

Relationship between primary and
tertiary structure of proteins
Mechanism of hormone
action and cyclic AMP
Nerve impulse propagation
and transmission
Role of sugar nucleotides in
carbohydrate synthesis
Genetic structure of viruses

M&P

Chemistry
M&P
Chemistry
Chemistry

M&P
M&P

1971

Earl W. Sutherland

M&P

1970

Bernard Katz
Ulf von Euler
Luis F. Leloir

M&P

Max Delbrück
Alfred D. Hershey
Salvador E. Luria

M&P

1969

Pages in Text

Chemistry

763

748
753

64
676

62
614
160
280
22, 415


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Year

Recipient*

Prize

Area of Research

1968

H. Gobind Khorana
Marshall W. Nirenberg
Robert W. Holley
Peyton Rous
Francois Jacob
Andre M. Lwoff
Jacques L. Monod
Dorothy C. Hodgkin
John C. Eccles
Alan L. Hodgkin
Andrew F. Huxley
Francis H. C. Crick
James D. Watson
Maurice H. F. Wilkins
John C. Kendrew
Max F. Perutz
Melvin Calvin

M&P

Genetic code

M&P
M&P

Transfer RNA structure
Tumor viruses

Bacterial operons and messenger
RNA

F. MacFarlane Burnet
Peter B. Medawar
Arthur Kornberg
Severo Ochoa
George W. Beadle
Joshua Lederberg
Edward L. Tatum
Frederick Sanger

M&P

1966
1965

1964
1963

1962

1961
1960
1959
1958

Pages in Text
456
457

676
500, 421

Chemistry
M&P

X-ray structure of complex biological molecules
Ionic basis of nerve
membrane potentials

740
159

M&P

Three-dimensional structure
of DNA

386

Chemistry

M&P

Three-dimensional structure
of globular proteins
Biochemistry of CO2 assimilation
during photosynthesis
Clonal selection theory of
antibody formation

Synthesis of DNA and RNA

M&P

Gene expression

Chemistry

Primary structure of proteins

Chemistry

*In a few cases, corecipients whose research was in an area outside of cell and molecular biology have been omitted from this list.
**Medicine and Physiology

56
221
687
538, 456
420

54


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Page iii

6

th edition

Cell and
Molecular
Biology
Concepts
and

Experiments

Gerald Karp

John Wiley & Sons, Inc.


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ACQUISITIONS EDITOR
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Hilary Newman
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From Shigeo Takamori et al., courtesy of
Reinhard Jahn of the Max-Planck Institute for
Biophysical Chemistry, Cell 127:841, 2006.

PRODUCTION SERVICES

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About the Author

G

erald C. Karp received a bachelor’s degree
from UCLA and a Ph.D. from the University
of Washington. He conducted postdoctoral
research at the University of Colorado Medical
Center before joining the faculty at the University of
Florida. Gerry is the author of numerous research articles
on the cell and molecular biology of early development.
His interests have included the synthesis of RNA in early
embryos, the movement of mesenchyme cells during

gastrulation, and cell determination in slime molds. For
13 years, he taught courses in molecular, cellular, and developmental biology at the University of Florida. During this
period, Gerry coauthored a text in developmental biology
with N. John Berrill and authored a text in cell and molecular biology. Finding it impossible to carry on life as both
full-time professor and author, Gerry gave up his faculty

position to concentrate on writing. He hopes to revise this
text every three years

About the Cover

A

molecular model of the membrane of a synaptic
vesicle. Within nerve cells, a synaptic vesicle
consists of a cellular membrane surrounding a
soluble compartment filled with neurotransmitter molecules. Vesicles of this type are assembled in the vicinity of a nerve cell’s nucleus and then transported to the tip of
the axon. There the vesicle awaits the arrival of a nerve
impulse that will induce it to fuse with the overlying plasma
membrane, releasing its contents into the narrow cleft that
separates the nerve cell from a neighboring cell. The threedimensional model of this membrane was constructed using
known structures of the various proteins along with information on their relative numbers obtained from the analysis of
purified synaptic vesicles. The image on the front cover
shows a synaptic vesicle that has been cut in half; the lipid
bilayer that forms the core of the vesicle membrane is shown

in green. The image on the back cover shows the surface
structure of an intact vesicle. Most of the proteins present in
this membrane are required for the interaction of the vesicle
with the plasma membrane. The large blue protein at the
lower right of the vesicle contains a ring of subunits that
rotates within the lipid bilayer as the protein pumps hydrogen
ions into the vesicle. The elevated concentration of hydrogen ions within the vesicle is subsequently used as an energy
source for the uptake of neurotransmitter molecules from the
surrounding cytosol. These images provide the most comprehensive model of any cellular membrane yet to be studied
and they reveal how much this membrane is dominated by

protein—both within the bilayer itself and on both membrane surfaces. (From Shigeo Takamori et al., courtesy of
Reinhard Jahn of the Max-Planck Institute for Biophysical
Chemistry, Cell 127:841, 2006.)


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To Patsy and Jenny


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Page vii

Preface to the Sixth Edition

B

efore I began work on the first edition of
this text, I drew up a number of basic guidelines regarding the type of book I planned

to write.

● I wanted a text suited for an introductory course in cell
and molecular biology that ran either a single semester or
1–2 quarters. I set out to draft a text of about 800 pages that
would not overwhelm or discourage students at this level.
● I wanted a text that elaborated on fundamental concepts,
such as the relationship between molecular structure and
function, the dynamic character of cellular organelles, the
use of chemical energy in running cellular activities and
ensuring accurate macromolecular biosynthesis, the observed
unity and diversity at the macromolecular and cellular levels,
and the mechanisms that regulate cellular activities.
● I wanted a text that was grounded in the experimental
approach. Cell and molecular biology is an experimental
science and, like most instructors, I believe students should
gain some knowledge of how we know what we know. With
this in mind, I decided to approach the experimental nature of
the subject in two ways. As I wrote each chapter, I included
enough experimental evidence to justify many of the conclusions that were being made. Along the way, I described the
salient features of key experimental approaches and research
methodologies. Chapters 8 and 9, for example, contain introductory sections on techniques that have proven most important in the analysis of cytomembranes and the cytoskeleton,
respectively. I included brief discussions of selected experiments
of major importance in the body of the chapters to reinforce
the experimental basis of our knowledge. I placed the more
detailed aspects of methodologies in a final “techniques chapter” because (1) I did not want to interrupt the flow of discussion of a subject with a large tangential section on technology
and (2) I realized that different instructors prefer to discuss a
particular technology in connection with different subjects.
For students and instructors who wanted to explore
the experimental approach in greater depth, I included an

Experimental Pathways at the end of most chapters. Each
of these narratives describes some of the key experimental
findings that have led to our current understanding of a
particular subject that is relevant to the chapter at hand.
Because the scope of the narrative is limited, the design
of the experiments can be considered in some detail. The
figures and tables provided in these sections are often those
that appeared in the original research article, which provides
the reader an opportunity to examine original data and to
realize that its analysis is not beyond their means. The
Experimental Pathways also illustrate the stepwise nature
of scientific discovery, showing how the result of one study
raises questions that provide the basis for subsequent studies.
● I wanted a text that was interesting and readable. To make
the text more relevant to undergraduate readers, particularly

premedical students, I included The Human Perspective.
These sections illustrate that virtually all human disorders
can be traced to disruption of activities at the cellular and
molecular level. Furthermore, they reveal the importance of
basic research as the pathway to understanding and eventually
treating most disorders. In Chapter 11, for example, The
Human Perspective describes how small synthetic siRNAs
may prove to be an important new tool in the treatment of
cancer and viral diseases, including AIDS. In this same chapter, the reader will learn how the action of such RNAs were
first revealed in studies on plants and nematodes. It becomes
evident that one can never predict the practical importance of
basic research in cell and molecular biology. I have also tried
to include relevant information about human biology and
clinical applications throughout the body of the text.

● I wanted a high-quality illustration program that helped
students visualize complex cellular and molecular processes.
To meet this goal, many of the illustrations have been
“stepped-out” so that information can be more easily broken
down into manageable parts. Events occurring at each step
are described in the figure legend and/or in the corresponding
text. I also sought to include a large number of micrographs
to enable students to see actual representations of most subjects being discussed. Included among the photographs are
many fluorescence micrographs that illustrate either the
dynamic properties of cells or provide a means to localize a
specific protein or nucleic acid sequence. Wherever possible, I
have tried to pair line art drawings with micrographs to help
students compare idealized and actual versions of a structure.

The most important changes in the sixth edition can be
delineated as follows:
● The references that have always appeared at the end of
each chapter in previous editions will now appear as a section at the end of the book.
● The body of information in cell and molecular biology
is continually changing, which provides much of the excitement we all feel about our selected field. Even though only
three years have passed since the publication of the fifth
edition, nearly every discussion in the text has been modified
to a greater or lesser degree. This has been done without
allowing the chapters to increase significantly in length.
● Every illustration in the fifth edition has been scrutinized
and many of those that were reutilized in the sixth edition
have been modified to some extent. Many of the drawings
from the fifth edition have been deleted to make room for
new pieces. Instructors have expressed particular approval
for figures that juxtapose line art and micrographs, and this

style of illustration has been expanded in the sixth edition.
Altogether, the sixth edition contains more than 60 new
micrographs and computer-derived images, all of which
were provided by the original source.

vii


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ACKNOWLEDGMENTS
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A
illustrations of the text.
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Book Companion Site (www.wiley.com/college/karp)
For the Student
●
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●

●

Quizzes for student self-testing.
Biology NewsFinder; Flash Cards; and Animations.
Answers to the end-of chapter Analytic Questions.
Additional reading resources provide students with an
extensive list of additional useful sources of information.
Experimental Pathways for Chapters 5, 6, 7, 9, 12, 13, and 15.

For the Instructor
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NEW Clinical Case Studies and accompanying
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Experimental Pathways Questions by Joel Piperberg,

Millersville University.

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Acknowledgments

T

here are many people at John Wiley & Sons who
have made important contributions to this text. I
continue to be grateful to Geraldine Osnato
whose work and support over two editions is not
forgotten. Ably taking her place in this edition was Merillat

Staat who served as the editor on the project with the guidance
of Kevin Witt. Thanks also go to Merillat for directing the
development of the diverse supplements that are offered with
this text. I am particularly indebted to the Wiley production

staff, who are simply the best. Jeanine Furino, the Production


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ACKNOWLEDGMENTS

Editor, served as the central nervous system, coordinating the
information arriving from compositors, copyeditors, proofreaders, illustrators, photo editors, designers, and dummiers,
as well as the constant barrage of text changes ordered by the
author. Always calm, organized, and meticulous, she made
sure everything was done correctly. Hilary Newman and
Anna Melhorn were responsible for the photo and line-art
programs respectively. It has been my good fortune to work
with Hilary on all six editions of this text. Hilary is skillful
and perseverant, and I have utmost confidence in her ability
to obtain any image requested. It was also a great pleasure
working with Anna for the fourth time. The book has a
complex illustration program and Anna did a superb job in
coordinating all the many facets required to guide it to completion. The elegant design of the book and cover is due to the

ix

efforts of Madelyn Lesure, whose talents are evident. Thanks

to Alissa Etrheim who served as editorial assistant for most of
the project but moved to the wilds of Alaska just before publication. Thanks also to Claire Walczak for all of her help in
revising Chapter 9 and contributing a section on fluorescence
imaging techniques and the accompanying artwork. A special
thanks is owed Laura Ierardi who skillfully laid out the pages
for each chapter.
I am especially thankful to the many biologists who have
contributed micrographs for use in this book; more than any
other element, these images bring the study of cell biology to
life on the printed page. Finally, I would like to apologize in
advance for any errors that may occur in the text, and express
my heartfelt embarrassment. I am grateful for the constructive criticism and sound advice from the following reviewers:

CHARLES MALLERY

JAMES BARBER

University of Miami

Imperial College of Science—Wolfson Laboratories

Northwestern University

MICHAEL A. MCALEAR

JOHN D. BELL

KENNETH J. BALAZOVICH

Wesleyan University

Brigham Young University

University of Michigan

JOANN MEERSCHAERT

WENDY A. BICKMORE

MARTIN BOOTMAN

Saint Cloud State University

Medical Research Council, United Kingdom

Babraham Institute

JOHN MENNINGER
University of Iowa

ASHOK BIDWAI

RICHARD E. DEARBORN

Sixth edition reviewers:
RAVI ALLADA

Albany College of Pharmacy

KIRSTEN MONSEN

LINDA DEVEAUX

Montclair State University

Idaho State University

ALAN NIGHORN

BENJAMIN GLICK

University of Arizona

The University of Chicago

CHARLES PUTNAM

REGINALD HALABY

The University of Arizona

West Virginia University

DANIEL BRANTON
Harvard University

THOMAS R. BREEN
Southern Illinois University

SHARON K. BULLOCK

Virginia Commonwealth University

Montclair State University

DAVID REISMAN

MICHAEL HAMPSEY

University of South Carolina

University of Medicine and Dentistry of
New Jersey

SHIVENDRA V. SAHI
Western Kentucky University

MICHAEL HARRINGTON

ERIC SHELDEN

University of Alberta

Washington State University

MARCIA HARRISON

PAUL TWIGG

Marshall University

University of Nebraska-Kearney

R. SCOTT HAWLEY

CLAIRE E. WALCZAK

Royal Children’s Hospitals—
The Murdoch Institute

American Cancer Society Research Professor

Indiana University

DENNIS O. CLEGG

MARK HENS

PAUL E. WANDA

University of California—Santa Barbara

University of North Carolina, Greensboro

Southern Illinois University, Edwardsville

ORNA COHEN-FIX

JEN-CHIH HSIEH

ANDREW WOOD

State University of New York at Stony Brook

Southern Illinois University

National Institute of Health, Laboratory of
Molecular and Cellular Biology

MICHAEL G. JONZ

JIANZHI ZHANG

RONALD H. COOPER

University of Ottawa

University of Michigan

ROLAND KAUNAS

RODERICK A. CAPALDI
University of Oregon

GORDON G. CARMICHAEL
University of Connecticut Health Center

RATNA CHAKRABARTI
University of Central Florida

K. H. ANDY CHOO

University of California—Los Angeles

PHILIPPA D. DARBRE
University of Reading

REBECCA KELLUM

Thanks are still owed to the
following reviewers of the previous
four editions:
LINDA AMOS

University of Kentucky

MRC Laboratory of Molecular Biology

Research Institute of Molecular Pathology

KIM KIRBY

KARL AUFDERHEIDE

SUSAN DESIMONE

University of Guelph

Texas A&M University

Middlebury College

FAITH LIEBL

GERALD T. BABCOCK

DAVID DOE

Southern Illinois University, Edwardsville

Michigan State University

Westfield State College

JON LOWRANCE

WILLIAM E. BALCH

ROBERT S. DOTSON

Lipscomb University

The Scripps Research Institute

Tulane University

Texas A&M University

TOM KELLER
Florida State University

ROGER W. DAVENPORT
University of Maryland

BARRY J. DICKSON


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ACKNOWLEDGMENTS

JENNIFER A. DOUDNA

MARGARET LYNCH

KATIE SHANNON

Yale University

Tufts University

University of North Carolina—Chapel Hill

MICHAEL EDIDIN

CHARLES MALLERY

JOEL B. SHEFFIELD

Johns Hopkins University

University of Miami

Temple University

EVAN E. EICHLER

ARDYTHE A. MCCRACKEN

DENNIS SHEVLIN

University of Washington

University of Nevada—Reno

College of New Jersey

ARRI EISEN

THOMAS MCKNIGHT

HARRIETT E. SMITH-SOMERVILLE

Emory University

Texas A&M University

University of Alabama

ROBERT FILLINGAME

MICHELLE MORITZ

BRUCE STILLMAN

University of Wisconsin Medical School

University of California—San Francisco

Cold Springs Harbor Laboratory

JACEK GAERTIG

ANDREW NEWMAN

ADRIANA STOICA

University of Georgia

Cambridge University

Georgetown University

REGINALD HALABY

ALAN NIGHORN

COLLEEN TALBOT

Montclair State University

University of Arizona

California State Univerity, San Bernardino

REBECCA HEALD

JONATHAN NUGENT

GISELLE THIBAUDEAU

University of California—Berkeley

University of London

Mississippi State University

ROBERT HELLING

MIKE O’DONNELL

JEFFREY L. TRAVIS

University of Michigan

Rockefeller University

University at Albany—SUNY

ARTHUR HORWICH

JAMES PATTON

PAUL TWIGG

Yale University School of Medicine

Vanderbilt University

University of Nebraska—Kearney

JOEL A. HUBERMAN

HUGH R. B. PELHAM

NIGEL UNWIN

Roswell Park Cancer Institute

MRC Laboratory of Molecular Biology

MRC Laboratory of Molecular Biology

GREGORY D. D. HURST

JONATHAN PINES

AJIT VARKI

University College London

Wellcome/CRC Institute

University of California—San Diego

KEN JACOBSON

DEBRA PIRES

JOSE VAZQUEZ

University of North Carolina

University of California—Los Angeles

New York University

MARIE JANICKE

MITCH PRICE

JENNIFER WATERS

University at Buffalo—SUNY

Pennsylvania State University

Harvard University

HAIG H. KAZAZIAN, JR.

DAVID REISMAN

CHRIS WATTERS

University of Pennsylvania

University of South Carolina

Middlebury College

LAURA R. KELLER

DONNA RITCH

ANDREW WEBBER

Florida State University

University of Wisconsin—Green Bay

Arizona State University

NEMAT O. KEYHANI

JOEL L. ROSENBAUM

BEVERLY WENDLAND

University of Florida

Yale University

Johns Hopkins University

NANCY KLECKNER

WOLFRAM SAENGER

GARY M. WESSEL

Harvard University

Freie Universitat Berlin

Brown University

WERNER KÜHLBRANDT

RANDY SCHEKMAN

ERIC V. WONG

Max-Planck-Institut für Biophysik

University of California—Berkeley

University of Louisville

JAMES LAKE

SANDRA SCHMID

GARY YELLEN

University of California—Los Angeles

The Scripps Research Institute

Harvard Medical School

ROBERT C. LIDDINGTON

TRINA SCHROER

MASASUKE YOSHIDA

Burnham Institute

Johns Hopkins University

Tokyo Institute of Technology

VISHWANATH R. LINGAPPA

DAVID SCHULTZ

ROBERT A. ZIMMERMAN

University of California—San Francisco

University of Louisville

University of Massachusetts

JEANNETTE M. LOUTSCH

ROD SCOTT

Arkansas State University

Wheaton College


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To the Student

A

t the time I began college, biology would have
been at the bottom of a list of potential majors.
I enrolled in a physical anthropology course to
fulfill the life science requirement by the easiest
possible route. During that course, I learned for the first time
about chromosomes, mitosis, and genetic recombination, and
I became fascinated by the intricate activities that could take
place in such a small volume of cellular space. The next
semester, I took Introductory Biology and began to seriously
consider becoming a cell biologist. I am burdening you with
this personal trivia so you will understand why I wrote this
book and to warn you of possible repercussions.
Even though many years have passed, I still find cell biology the most fascinating subject to explore, and I still love
spending the day reading about the latest findings by colleagues
in the field. Thus, for me, writing a text on cell biology provides
a reason and an opportunity to keep abreast with what is going
on throughout the field. My primary goal in writing this text is
to help generate an appreciation in students for the activities in
which the giant molecules and minuscule structures that inhabit the cellular world of life are engaged. Another goal is to provide the reader with an insight into the types of questions that
cell and molecular biologists ask and the experimental
approaches they use to seek answers. As you read the text, think
like a researcher; consider the evidence that is presented, think
of alternate explanations, plan experiments that could lead to
new hypotheses.
You might begin this approach by looking at one of the
many electron micrographs that fill the pages of this text. To
take this photograph, you would be sitting in a small, pitchblack room in front of a large metallic instrument whose column rises several meters above your head. You are looking

through a pair of binoculars at a vivid, bright green screen. The
parts of the cell you are examining appear dark and colorless
against the bright green background. They are dark because
they’ve been stained with heavy metal atoms that deflect a fraction of the electrons within a beam that is being focused on the
viewing screen by large electromagnetic lenses in the wall of the
column. The electrons that strike the screen are accelerated
through the evacuated space of the column by a force of tens of
thousands of volts. One of your hands may be gripping a knob
that controls the magnifying power of the lenses. A simple turn
of this knob can switch the image in front of your eyes from
that of a whole field of cells to a tiny part of a cell, such as a few
ribosomes or a small portion of a single membrane. By turning
other knobs, you can watch different parts of the specimen
glide across the screen, giving you the sensation that you’re
driving around inside a cell. Once you have found a structure of
interest, you can turn a handle that lifts the screen out of view,
allowing the electron beam to strike a piece of film and produce
a photographic image of the specimen.
Because the study of cell function requires the use of considerable instrumentation, such as the electron microscope just

described, the investigator is physically removed from the
subject being studied. To a large degree, cells are like tiny black
boxes. We have developed many ways to probe the boxes, but
we are always groping in an area that cannot be fully illuminated. A discovery is made or a new technique is developed and a
new thin beam of light penetrates the box. With further work,
our understanding of the structure or process is broadened, but
we are always left with additional questions. We generate more
complete and sophisticated constructions, but we can never be
sure how closely our views approach reality. In this regard, the
study of cell and molecular biology can be compared to the study

of an elephant as conducted by six blind men in an old Indian
fable. The six travel to a nearby palace to learn about the nature
of elephants. When they arrive, each approaches the elephant
and begins to touch it. The first blind man touches the side of
the elephant and concludes that an elephant is smooth like a
wall. The second touches the trunk and decides that an elephant is round like a snake. The other members of the group
touch the tusk, leg, ear, and tail of the elephant, and each forms
his impression of the animal based on his own limited experiences. Cell biologists are limited in a similar manner as to what
they can learn by using a particular technique or experimental
approach. Although each new piece of information adds to the
preexisting body of knowledge to provide a better concept of
the activity being studied, the total picture remains uncertain.
Before closing these introductory comments, let me take
the liberty of offering the reader some advice: Don’t accept
everything you read as being true. There are several reasons for
urging such skepticism. Undoubtedly, there are errors in this
text that reflect the author’s ignorance or misinterpretation of
some aspect of the scientific literature. But, more importantly,
we should consider the nature of biological research. Biology
is an empirical science; nothing is ever proved. We compile
data concerning a particular cell organelle, metabolic reaction,
intracellular movement, etc., and draw some type of conclusion.
Some conclusions rest on more solid evidence than others. Even
if there is a consensus of agreement concerning the “facts”
regarding a particular phenomenon, there are often several possible interpretations of the data. Hypotheses are put forth and
generally stimulate further research, thereby leading to a reevaluation of the original proposal. Most hypotheses that remain
valid undergo a sort of evolution and, when presented in the
text, should not be considered wholly correct or incorrect.
Cell biology is a rapidly moving field and some of the
best hypotheses often generate considerable controversy. Even

though this is a textbook where one expects to find material
that is well tested, there are many places where new ideas are
presented. These ideas are often described as models. I’ve
included such models because they convey the current thinking in the field, even if they are speculative. Moreover, they
reinforce the idea that cell biologists operate at the frontier of
science, a boundary between the unknown and known (or
thought to be known). Remain skeptical.

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Brief Contents
1
2
3
4
5
6
7
8
9
10

11
12
13
14
15
16
17
18

Introduction to the Study of Cell and Molecular Biology 1
The Chemical Basis of Life

Bioenergetics, Enzymes, and Metabolism 85
The Structure and Function of the Plasma Membrane 117
Aerobic Respiration and the Mitochondrion 173
Photosynthesis and the Chloroplast 206
Interactions Between Cells and Their Environment 230
Cytoplasmic Membrane Systems: Structure, Function, and Membrane
Trafficking 264
The Cytoskeleton and Cell Motility 318
The Nature of the Gene and the Genome 379
Gene Expression: From Transcription to Translation 419
The Cell Nucleus and the Control of Gene Expression

475

DNA Replication and Repair 533
Cellular Reproduction 560
Cell Signaling and Signal Transduction: Communication Between Cells 605
Cancer 650

The Immune Response 682
Techniques in Cell and Molecular Biology 715

Glossary G-1
Additional Readings A-1
Index I-1

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31


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Contents
● TH E H U M A N P E R S P E CT I V E : Protein Misfolding Can Have
Deadly Consequences 64
Nucleic Acids 74

1 Introduction to the Study of Cell
and Molecular Biology 1
1.1

THE DISCOVERY OF CELLS 2

1.2

BASIC PROPERTIES OF CELLS 3

2.6

Cells Are Highly Complex and Organized 3
Cells Possess a Genetic Program and the Means to Use It 5
Cells Are Capable of Producing More of Themselves 5
Cells Acquire and Utilize Energy 5
Cells Carry Out a Variety of Chemical Reactions 5
Cells Engage in Mechanical Activities 6
Cells Are Able to Respond to Stimuli 6
Cells Are Capable of Self-Regulation 6
Cells Evolve 6

1.3

1.4

2

VIRUSES 21
Viroids 24
● E X P E R I M E N TA L PAT H W AY S : The Origin of Eukaryotic
Cells 25

The Chemical Basis of Life

2.1

2.2

● E X P E R I M E NTA L PATH W AY S : Chaperones: Helping
Proteins Reach Their Proper Folded State 78

3

Bioenergetics, Enzymes,
and Metabolism 84
3.1

COVALENT BONDS 32
Polar and Nonpolar Molecules 33
Ionization 33
NONCOVALENT BONDS 33
Ionic Bonds: Attractions Between Charged Atoms 33
● T H E H U M A N P E R S P E CT I V E : Free Radicals as a Cause
of Aging 34
Hydrogen Bonds 35
Hydrophobic Interactions and van der Waals Forces 36
The Life-Supporting Properties of Water 36
ACIDS, BASES, AND BUFFERS 38

2.4

THE NATURE OF BIOLOGICAL MOLECULES 39
Functional Groups 40
A Classification of Biological Molecules by Function 40

FOUR TYPES OF BIOLOGICAL MOLECULES 41
Carbohydrates
Lipids 46
Proteins 49

42

BIOENERGETICS 85
The Laws of Thermodynamics and the Concept
of Entropy 85
Free Energy 87

3.2

ENZYMES AS BIOLOGICAL CATALYSTS 92
The Properties of Enzymes 93
Overcoming the Activation Energy Barrier 94
The Active Site 95
Mechanisms of Enzyme Catalysis 97
Enzyme Kinetics 100
● TH E H U M A N P E R S P E CT I V E : The Growing Problem
of Antibiotic Resistance 104

3.3

31

2.3

2.5

The Assembly of Tobacco Mosaic Virus Particles
and Ribosomal Subunits 76

TWO FUNDAMENTALLY DIFFERENT CLASSES OF CELLS 7
Characteristics That Distinguish Prokaryotic and
Eukaryotic Cells 8
Types of Prokaryotic Cells 12
Types of Eukaryotic Cells: Cell Specialization 15
The Sizes of Cells and Their Components 16
Synthetic Biology 18
● T H E H U M A N P E R S P E CT I V E : The Prospect of Cell
Replacement Therapy 19

THE FORMATION OF COMPLEX MACROMOLECULAR
STRUCTURES 76

METABOLISM 105
An Overview of Metabolism 105
Oxidation and Reduction: A Matter
of Electrons 106
The Capture and Utilization of Energy 107
Metabolic Regulation 112

4

The Structure of Function
of the Plasma Membrane 117
4.1

AN OVERVIEW OF MEMBRANE FUNCTIONS 118

4.2

A BRIEF HISTORY OF STUDIES ON PLASMA MEMBRANE
STRUCTURE 119

4.3

THE CHEMICAL COMPOSITION OF MEMBRANES 122
Membrane Lipids 122
The Asymmetry of Membrane Lipids 125
Membrane Carbohydrates 126

4.4

THE STRUCTURE AND FUNCTIONS OF MEMBRANE
PROTEINS 127
Integral Membrane Proteins 128
Studying the Structure and Properties of Integral Membrane
Proteins 128
Peripheral Membrane Proteins 132
Lipid-Anchored Membrane Proteins 133

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4.5

4.6

MEMBRANE LIPIDS AND MEMBRANE FLUIDITY 133
The Importance of Membrane Fluidity 134
Maintaining Membrane Fluidity 135
Lipid Rafts 135
THE DYNAMIC NATURE OF THE PLASMA MEMBRANE 136
The Diffusion of Membrane Proteins after Cell Fusion 136
Restrictions on Protein and Lipid Mobility 137
The Red Blood Cell: An Example of Plasma Membrane
Structure 140

4.7

6

Photosynthesis and the Chloroplast 206

6.1

CHLOROPLAST STRUCTURE AND FUNCTION 208

6.2

AN OVERVIEW OF PHOTOSYNTHETIC METABOLISM 209

6.3

THE ABSORPTION OF LIGHT 211
Photosynthetic Pigments 211

6.4

PHOTOSYNTHETIC UNITS AND REACTION CENTERS 213
Oxygen Formation: Coordinating the Action of Two
Different Photosynthetic Systems 213
Killing Weeds by Inhibiting Electron Transport 220

THE MOVEMENT OF SUBSTANCES ACROSS CELL MEMBRANES 143
The Energetics of Solute Movement 143
Diffusion of Substances through Membranes 144
Facilitated Diffusion 151
Active Transport 152

6.5
6.6

● T H E H U M A N P E R S P E CT I V E : Defects in Ion

Channels and Transporters as a Cause of Inherited
Disease 156

4.8

● E X P E R I M E N TA L PAT H W AY S :
The Acetylcholine Receptor

Interactions Between Cells
and Their Environment 230
7.1
7.2

INTERACTIONS OF CELLS WITH EXTRACELLULAR MATERIALS 239
Integrins 239
Focal Adhesions and Hemidesmosomes: Anchoring Cells
to Their Substratum 242

MITOCHONDRIAL STRUCTURE AND FUNCTION 174

7.3

INTERACTIONS OF CELLS WITH OTHER CELLS 245

Mitochondrial Membranes 175
The Mitochondrial Matrix 176

Selectins 245
● TH E H U M A N P E R S P E CTI V E : The Role of Cell Adhesion
in Inflammation and Metastasis 247

OXIDATIVE METABOLISM IN THE MITOCHONDRION 177
The Tricarboxylic Acid (TCA) Cycle 180
The Importance of Reduced Coenzymes in the Formation
of ATP 181

5.3

182

● T H E H U M A N P E R S P E CT I V E : The Role of Anaerobic and
Aerobic Metabolism in Exercise 183
Electron Transport 185
Types of Electron Carriers 185

5.4
5.5

5.6

The Immunoglobulin Superfamily 249
Cadherins 249
Adherens Junctions and Desmosomes: Anchoring Cells
to Other Cells 250
The Role of Cell-Adhesion Receptors in Transmembrane
Signaling 253

THE ROLE OF MITOCHONDRIA IN THE FORMATION OF ATP 182
Oxidation–Reduction Potentials

THE EXTRACELLULAR SPACE 231
The Extracellular Matrix 232

166

Aerobic Respiration
and the Mitochondrion 173

5.2

CARBON DIOXIDE FIXATION AND THE SYNTHESIS
OF CARBOHYDRATE 221

7

5

5.1

220

Carbohydrate Synthesis in C3 Plants 221
Carbohydrate Synthesis in C4 Plants 226
Carbohydrate Synthesis in CAM Plants 227

MEMBRANE POTENTIALS AND NERVE IMPULSES 159
The Resting Potential 159
The Action Potential 160
Propagation of Action Potentials as an Impulse 162
Neurotransmission: Jumping the Synaptic Cleft 163

PHOTOPHOSPHORYLATION 220
Noncyclic Versus Cyclic Photophosphorylation

TRANSLOCATION OF PROTONS AND THE ESTABLISHMENT
OF A PROTON-MOTIVE FORCE 191
THE MACHINERY FOR ATP FORMATION 192
The Structure of ATP Synthase 193
The Basis of ATP Formation According to the Binding
Change Mechanism 195
Other Roles for the Proton-Motive Force in Addition to
ATP Synthesis 199
PEROXISOMES 200
● T H E H U M A N P E R S P E CT I V E : Diseases that Result
from Abnormal Mitochrondrial or Peroxisomal
Function 201

7.4

TIGHT JUNCTIONS: SEALING THE EXTRACELLULAR SPACE 254

7.5

GAP JUNCTIONS AND PLASMODESMATA: MEDIATING
INTERCELLULAR COMMUNICATION 256
Plasmodesmata 258

7.6

CELL WALLS 260

8

Cytoplasmic Membrane Systems:
Structure, Function, and Membrane
Trafficking 264
8.1

AN OVERVIEW OF THE ENDOMEMBRANE SYSTEM 265

8.2

A FEW APPROACHES TO THE STUDY OF ENDOMEMBRANES 267
Insights Gained from Autoradiography 267
Insights Gained from the Use
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Microtubule-Organizing Centers (MTOCs) 333
The Dynamic Properties of Microtubules 335

Cilia and Flagella: Structure and Function 339

Insights Gained from the Biochemical Analysis
of Subcellular Fractions 269
Insights Gained from the Use of Cell-Free Systems 270
Insights Gained from the Study of Mutant
Phenotypes 271

8.3

THE ENDOPLASMIC RETICULUM 273

8.5

8.6

● TH E H U M A N P E R S P E CT I V E : The Role of Cilia
in Development and Disease 340

9.4

INTERMEDIATE FILAMENTS 347
Intermediate Filament Assembly and Disassembly 348
Types and Functions of Intermediate Filaments 349

9.5

Glycosylation in the Golgi Complex 284
The Movement of Materials through the Golgi
Complex 287

MICROFILAMENTS 351
Microfilament Assembly and Disassembly 352
Myosin: The Molecular Motor of Actin Filaments 354

9.6

MUSCLE CONTRACTILITY 359
The Sliding Filament Model of Muscle Contraction 360

TYPES OF VESICLE TRANSPORT AND THEIR FUNCTIONS 288

9.7

NONMUSCLE MOTILITY 365

The Smooth Endoplasmic Reticulum 273
Functions of the Rough Endoplasmic Reticulum 273
From the ER to the Golgi Complex: The First Step in
Vesicular Transport 283

8.4

THE GOLGI COMPLEX 284

Actin-Binding Proteins 365
Examples of Nonmuscle Motility and Contractility 367

COPII-Coated Vesicles: Transporting Cargo from the ER
to the Golgi Complex 289

COPI-Coated Vesicles: Transporting Escaped Proteins Back
to the ER 291
Beyond the Golgi Complex: Sorting Proteins
at the TGN 292
Targeting Vesicles to a Particular Compartment 294

10

10.1

THE CONCEPT OF A GENE AS A UNIT OF INHERITANCE 380

LYSOSOMES 297

10.2

CHROMOSOMES: THE PHYSICAL CARRIERS
OF THE GENES 381

The Nature of the Gene
and the Genome 379

● T H E H U M A N P E R S P E CT I V E : Disorders Resulting from
Defects in Lysosomal Function 299

8.7

PLANT CELL VACUOLES 301

8.8

THE ENDOCYTIC PATHWAY: MOVING MEMBRANE AND MATERIALS
INTO THE CELL INTERIOR 301
Endocytosis 302
Phagocytosis 308

8.9

The Discovery of Chromosomes 381
Chromosomes as the Carriers of Genetic Information 382
Genetic Analysis in Drosophila 383
Crossing Over and Recombination 383
Mutagenesis and Giant Chromosomes 385

10.3

10.4

9.2

THE STUDY OF THE CYTOSKELETON 320
The Use of Live-Cell Fluorescence Imaging 320
The Use of In Vitro and In Vivo Single-Molecule
Assays 322
The Use of Florescence Imaging Techniques to Monitor
the Dynamics of the Cytoskeleton 323

9.3

MICROTUBULES 324

Microtubule-Associated Proteins 325
Microtubules as Structural Supports and Organizers 326
Motor Proteins that Traverse the Microtubular
Cytoskeleton 328

393

● TH E H U M A N P E R S P E CT I V E : Diseases that Result from
Expansion of Trinucleotide Repeats 396

10.5

THE STABILITY OF THE GENOME 399
Whole-Genome Duplication (Polyploidization) 399
Duplication and Modification of DNA Sequences 400
“Jumping Genes” and the Dynamic Nature
of the Genome 402

10.6

SEQUENCING GENOMES: THE FOOTPRINTS
OF BIOLOGICAL EVOLUTION 405

The Cytoskeleton and Cell Motility 318
OVERVIEW OF THE MAJOR FUNCTIONS
OF THE CYTOSKELETON 319

THE STRUCTURE OF THE GENOME 393
The Complexity of the Genome

● E X P E R I M E N TA L PAT H W AY S : Receptor-Mediated
Endocytosis 312

9.1

THE CHEMICAL NATURE OF THE GENE 386
The Structure of DNA 386
The Watson-Crick Proposal 387
DNA Supercoiling 390

POSTTRANSLATIONAL UPTAKE OF PROTEINS BY PEROXISOMES,
MITOCHONDRIA, AND CHLOROPLASTS 309
Uptake of Proteins into Peroxisomes 309
Uptake of Proteins into Mitochondria 309
Uptake of Proteins into Chloroplasts 311

9

xv

Comparative Genomics: “If It’s Conserved, It Must
Be Important 406
The Genetic Basis of “Being Human” 407
Genetic Variation Within the Human Species
Population 408
● TH E H U M A N P E R S P E CT I V E : Application of Genomic
Analyses to Medicine 410
● E X P E R I M E NTA L PATH W AY S :
The Chemical Nature of the Gene

413


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11 Gene Expression: From Transcription

Epigenetics: There’s More to Inheritance
than DNA 496
The Nucleus as an Organized Organelle 497

to Translation 419
11.1

THE RELATIONSHIP BETWEEN GENES AND PROTEINS 420
An Overview of the Flow of Information through
the Cell 421

11.2

AN OVERVIEW OF TRANSCRIPTION IN BOTH PROKARYOTIC
AND EUKARYOTIC CELLS 422

11.5

12.4

TRANSCRIPTIONAL-LEVEL CONTROL 505
The Role of Transcription Factors in Regulating Gene
Expression 508
The Structure of Transcription Factors 509
DNA Sites Involved in Regulating
Transcription 511
Transcriptional Activation: The Role of Enhancers,
Promoters, and Coactivators 514
Transcriptional Repression 519

12.5

PROCESSING-LEVEL CONTROL 522

The Machinery for mRNA Transcription 435
Split Genes: An Unexpected Finding 437
The Processing of Eukaryotic Messenger RNAs 440
Evolutionary Implications of Split Genes and RNA
Splicing 447
Creating New Ribozymes in the Laboratory 448

12.6

TRANSLATIONAL-LEVEL CONTROL 524
Cytoplasmic Localization of mRNAs 524
The Control of mRNA Translation 525
The Control of mRNA Stability 526
The Role of MicroRNAs
in Translational-Level Control 527

SMALL REGULATORY RNAs AND RNA SILENCING PATHWAYS 448

12.7

POSTRANSLATIONAL CONTROL:
DETERMINING PROTEIN STABILITY 529

SYNTHESIS AND PROCESSING OF RIBOSOMAL
AND TRANSFER RNAs 428

SYNTHESIS AND PROCESSING OF MESSENGER RNAs

434

MicroRNAs: Small RNAs that Regulate
Gene Expression 452
piRNAs: A Class of Small RNAs
that Function in Germ Cells 454
Other Noncoding RNAs 454

13
13.1

ENCODING GENETIC INFORMATION 455
DECODING THE CODONS: THE ROLE OF TRANSFER RNAs

457

13.2

The Structure of tRNAs 457

11.8

Initiation 461
Elongation 464
Termination 466
mRNA Surveillance and Quality Control 466
Polyribosomes 467

12

The Cell Nucleus and the Control
of Gene Expression 475
12.1

481

● T H E H U M A N P E R S P E CT I V E : Chromosomal Aberrations
and Human Disorders 491

DNA REPLICATION 534

DNA REPAIR 552

● TH E H U M A N P E R S P E CTI V E : The Consequences
of DNA Repair Deficiencies 556

13.3

14
14.1

BETWEEN REPLICATION AND REPAIR 557

Cellular Reproduction 560
THE CELL CYCLE 561
Cell Cycles in Vivo 562
Control of the Cell Cycle 562

THE NUCLEUS OF A EUKARYOTIC CELL 476
The Nuclear Envelope 476
Chromosomes and Chromatin

DNA Replication and Repair 533

Nucleotide Excision Repair 553
Base Excision Repair 554
Mismatch Repair 554
Double-Strand Breakage Repair 555

TRANSLATING GENETIC INFORMATION 461

● E X P E R I M E N TA L PAT H W AY S : The Role of RNA
as a Catalyst 469

503

Semiconservative Replication 534
Replication in Bacterial Cells 537
The Structure and Functions of DNA
Polymerases 542
Replication in Eukaryotic Cells 546

The Properties of the Genetic Code 455

11.7

500

CONTROL OF GENE EXPRESSION IN EUKARYOTES

● T H E H U M A N P E R S P E CT I V E : Clinical Applications of
RNA Interference 451

11.6

499

12.3

Synthesizing the rRNA Precursor 429
Processing the rRNA Precursor 430

Synthesis and Processing of the 5S rRNA 432
Transfer RNAs 433

11.4

CONTROL OF GENE EXPRESSION IN BACTERIA
The Bacterial Operon
Riboswitches 503

Transcription in Bacteria 425
Transcription and RNA Processing in
Eukaryotic Cells 426

11.3

12.2

14.2

M PHASE: MITOSIS AND CYTOKINESIS 569
Prophase 571
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Metaphase 578
Anaphase 579
Telophase 585
Forces Required for Mitotic Movements
Cytokinesis 585

14.3

16.4

585

The Stages of Meiosis 591
● T H E H U M A N P E R S P E CT I V E : Meiotic Nondisjunction and
Its Consequences 596
Genetic Recombination During Meiosis 597

17
17.1

Cell Signaling and Signal Transduction:
Communication Between Cells 605

676

The Immune Response

682

AN OVERVIEW OF THE IMMUNE RESPONSE 683
Innate Immune Responses 684
Adaptive Immune Responses 686

● E X P E R I M E N TA L PAT H W AY S : The Discovery and
Characterization of MPF 599

15

NEW STRATEGIES FOR COMBATING CANCER 671
Immunotherapy 672
Inhibiting the Activity of Cancer-Promoting Proteins 673
Inhibiting the Formation of New Blood Vessels
(Angiogenesis) 675
● E X P E R I M E NTA L PATH W AY S :
The Discovery of Oncogenes

MEIOSIS 590

xvii

17.2

THE CLONAL SELECTION THEORY AS IT APPLIES
TO B CELLS 687
Vaccination

689

15.1

THE BASIC ELEMENTS OF CELL SIGNALING SYSTEMS 606

17.3

T LYMPHOCYTES: ACTIVATION AND MECHANISM OF ACTION 690

15.2

A SURVEY OF EXTRACELLULAR MESSENGERS
AND THEIR RECEPTORS 608

17.4

SELECTED TOPICS ON THE CELLULAR AND MOLECULAR BASIS
OF IMMUNITY 693

15.3

G PROTEIN-COUPLED RECEPTORS
AND THEIR SECOND MESSENGERS 609

The Modular Structure of Antibodies 693
DNA Rearrangement of Genes Encoding B- and T-Cell
Antigen Receptors 696
Membrane-Bound Antigen Receptor Complexes 699
The Major Histocompatibility Complex 699

Distinguishing Self from Nonself 704
Lymphocytes Are Activated by Cell-Surface Signals 704
Signal Transduction Pathways Used
in Lymphocyte Activation 706

Signal Transduction by G Protein-Coupled Receptors 610
● T H E H U M A N P E R S P E CT I V E : Disorders Associated with G
Protein-Coupled Receptors 612
Second Messengers 614
The Specificity of G Protein-Coupled Responses 618
Regulation of Blood Glucose Levels 618
The Role of GPCRs in Sensory Perception 622

15.4

● TH E H U M A N P E R S P E CT I V E : Autoimmune
Diseases 707

PROTEIN-TYROSINE PHOSPHORYLATION AS A MECHANISM
FOR SIGNAL TRANSDUCTION 623

● E X P E R I M E NTA L PATH W AY S : The Role of the Major
Histocompatibility Complex in Antigen
Presentation 709

The Ras-MAP Kinase Pathway 627
Signaling by the Insulin Receptor 631
Signaling Pathways in Plants 633

15.5

THE ROLE OF CALCIUM AS AN INTRACELLULAR MESSENGER 634
Regulating Calcium Concentrations in Plant Cells 638

15.6

CONVERGENCE, DIVERGENCE, AND CROSSTALK AMONG DIFFERENT
SIGNALING PATHWAYS 638

18

Techniques in Cell and Molecular
Biology 715
18.1

THE LIGHT MICROSCOPE 716
Resolution 716
Visibility 717
Preparation of Specimens for Bright-Field Light
Microscopy 718
Phase-Contrast Microscopy 718
Fluorescence Microscopy (and Related Fluorescence-Based
Techniques) 719
Video Microscopy and Image Processing 721
Laser Scanning Confocal Microscopy 721
Super-Resolution Fluorescence Microscopy 722

18.2

TRANSMISSION ELECTRON MICROSCOPY 722

Specimen Preparation for Electron Microscopy 724

18.3

SCANNING ELECTRON AND ATOMIC FORCE MICROSCOPY 729

Examples of Convergence, Divergence, and Crosstalk
Among Signaling Pathways 639

15.7

THE ROLE OF NO AS AN INTERCELLULAR MESSENGER 640

15.8

APOPTOSIS (PROGRAMMED CELL DEATH) 642
The Extrinsic Pathway of Apoptosis 643
The Intrinsic Pathway of Apoptosis 644

16

Cancer

650

16.1

BASIC PROPERTIES OF A CANCER CELL 651

16.2

THE CAUSES OF CANCER 653

16.3

THE GENETICS OF CANCER 654
Tumor-Suppressor Genes and Oncogenes: Brakes
and Accelerators 656
The Cancer Genome 667
Gene-Expression Analysis 669

Atomic Force Microscopy

730

18.4

THE USE OF RADIOISOTOPES 730

18.5

CELL CULTURE 731


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18.7

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CONTENTS

THE FRACTIONATION OF A CELL’S CONTENTS
BY DIFFERENTIAL CENTRIFUGATION 733

18.14 ENZYMATIC AMPLIFICATION OF DNA BY PCR 751

ISOLATION, PURIFICATION,
AND FRACTIONATION OF PROTEINS 734

18.15 DNA SEQUENCING 753

Selective Precipitation 734
Liquid Column Chromatography 735
Polyacrylamide Gel Electrophoresis 737
Protein Measurement and Analysis 739

18.8
18.9

DETERMINING THE STRUCTURE OF PROTEINS
AND MULTISUBUNIT COMPLEXES 740
PURIFICATION OF NUCLEIC ACIDS 742

18.10 FRACTIONATION OF NUCLEIC ACIDS 742
Separation of DNAs by Gel Electrophoresis 742
Separation of Nucleic Acids
by Ultracentrifugation 743

18.11 NUCLEIC ACID HYBRIDIZATION 745

Applications of PCR

18.16 DNA LIBRARIES 755
Genomic Libraries 755
cDNA Libraries 756

18.17 DNA TRANSFER INTO EUKARYOTIC CELLS
AND MAMMALIAN EMBRYOS 757
18.18 DETERMINING EUKARYOTIC GENE FUNCTION
BY GENE ELIMINATION OR SILENCING 760
In Vitro Mutagenesis 760
Knockout Mice 760
RNA Interference 762

18.19 THE USE OF ANTIBODIES 763

Glossary G-1

18.12 CHEMICAL SYNTHESIS OF DNA 746

Additional Readings A-1

18.13 RECOMBINANT DNA TECHNOLOGY 746

Restriction Endonucleases 746
Formation of Recombinant DNAs
DNA Cloning 748

752

Index I-1
748


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1
Introduction to the Study
of Cell and Molecular Biology

C

The Discovery of Cells
1.2 Basic Properties of Cells
1.3 Two Fundamentally
Different Classes of Cells
1.4 Viruses
1.1

The Human Perspective:

The Prospect

of Cell Replacement Therapy
Experimental Pathways:

of Eukaryotic Cells

The Origin

ells, and the structures they comprise, are too small to be directly seen,
heard, or touched. In spite of this tremendous handicap, cells are the
subject of hundreds of thousands of publications each year, with virtually
every aspect of their minuscule structure coming under scrutiny. In many ways, the
study of cell and molecular biology stands as a tribute to human curiosity for seeking
to discover, and to human creative intelligence for devising the complex instruments
and elaborate techniques by which these discoveries can be made. This is not to
imply that cell and molecular biologists have a monopoly on these noble traits. At
one end of the scientific spectrum, astronomers are searching the outer fringes of the
universe for black holes and whirling pulsars whose properties seem unimaginable
when compared to those of Earth. At the other end of the spectrum, nuclear physicists
are focusing their attention on subatomic particles that have equally inconceivable
properties. Clearly, our universe consists of worlds within worlds, all aspects of which
make for fascinating study.
As will be apparent throughout this book, cell and molecular biology is reductionist;
that is, it is based on the view that knowledge of the parts of the whole can explain
the character of the whole. When viewed in this way, our feeling for the wonder and

An example of the role of technological innovation in the field of cell biology. This light
micrograph shows a cell lying on a microscopic bed of synthetic posts. The flexible posts
serve as sensors to measure mechanical forces exerted by the cell. The red-stained elements
are bundles of actin filaments within the cell that generate forces during cell locomotion.
When the cell moves, it pulls on the attached posts, which report the amount of strain they
are experiencing. The cell nucleus is stained green. (FROM J. L. TAN ET AL., PROC. NAT’L. ACAD. SCI.
U.S.A., 100 (4), 2003; COURTESY

OF

CHRISTOPHER S. CHEN, THE JOHNS HOPKINS UNIVERSITY.)

1


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Chapter 1 INTRODUCTION TO THE STUDY OF CELL AND MOLECULAR BIOLOGY

mystery of life may be replaced by the need to explain everything in terms of the workings of the “machinery” of the living system. To the degree to which this occurs, it is hoped
that this loss can be replaced by an equally strong appreciation
for the beauty and complexity of the mechanisms underlying

cellular activity. ■

1.1 THE DISCOVERY OF CELLS
Because of their small size, cells can only be observed with the
aid of a microscope, an instrument that provides a magnified
image of a tiny object. We do not know when humans first discovered the remarkable ability of curved-glass surfaces to bend
light and form images. Spectacles were first made in Europe in
the thirteenth century, and the first compound (double-lens)
light microscopes were constructed by the end of the sixteenth
century. By the mid-1600s, a handful of pioneering scientists
had used their handmade microscopes to uncover a world that
would never have been revealed to the naked eye. The discovery of cells (Figure 1.1a) is generally credited to Robert Hooke,
an English microscopist who, at age 27, was awarded the position of curator of the Royal Society of London, England’s foremost scientific academy. One of the many questions Hooke
attempted to answer was why stoppers made of cork (part of
the bark of trees) were so well suited to holding air in a bottle.
As he wrote in 1665: “I took a good clear piece of cork, and
with a Pen-knife sharpen’d as keen as a Razor, I cut a piece of
it off, and . . . then examining it with a Microscope, me thought
I could perceive it to appear a little porous . . . much like a
Honeycomb.” Hooke called the pores cells because they reminded him of the cells inhabited by monks living in a
monastery. In actual fact, Hooke had observed the empty cell
walls of dead plant tissue, walls that had originally been produced by the living cells they surrounded.
Meanwhile, Anton van Leeuwenhoek, a Dutchman who
earned a living selling clothes and buttons, was spending his
spare time grinding lenses and constructing simple microscopes of remarkable quality (Figure 1.1b). For 50 years,
Leeuwenhoek sent letters to the Royal Society of London describing his microscopic observations—along with a rambling
discourse on his daily habits and the state of his health.
Leeuwenhoek was the first to examine a drop of pond water
under the microscope and, to his amazement, observe the
teeming microscopic “animalcules” that darted back and forth

before his eyes. He was also the first to describe various forms
of bacteria, which he obtained from water in which pepper
had been soaked and from scrapings of his teeth. His initial
letters to the Royal Society describing this previously unseen
world were met with such skepticism that the society dispatched its curator, Robert Hooke, to confirm the observations. Hooke did just that, and Leeuwenhoek was soon a
worldwide celebrity, receiving visits in Holland from Peter the
Great of Russia and the queen of England.
It wasn’t until the 1830s that the widespread importance
of cells was realized. In 1838, Matthias Schleiden, a German
lawyer turned botanist, concluded that, despite differences in

(a)

(b)

FIGURE 1.1 The discovery of cells. (a) One of Robert Hooke’s more
ornate compound (double-lens) microscopes. (Inset) Hooke’s drawing
of a thin slice of cork, showing the honeycomb-like network of “cells.”
(b) Single-lens microscope used by Anton van Leeuwenhoek to observe
bacteria and other microorganisms. The biconvex lens, which was capable of magnifying an object approximately 270 times and providing a
resolution of approximately 1.35 ␮m, was held between two metal
plates. (FROM THE GRANGER COLLECTION; (INSET AND FIGURE 1-1B)
CORBIS BETTMANN)

the structure of various tissues, plants were made of cells and
that the plant embryo arose from a single cell. In 1839,
Theodor Schwann, a German zoologist and colleague of
Schleiden’s, published a comprehensive report on the cellular
basis of animal life. Schwann concluded that the cells of plants
and animals are similar structures and proposed these two

tenets of the cell theory:
■
■

All organisms are composed of one or more cells.
The cell is the structural unit of life.

Schleiden and Schwann’s ideas on the origin of cells proved
to be less insightful; both agreed that cells could arise from
noncellular materials. Given the prominence that these two


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1.2 BASIC PROPERTIES OF CELLS

scientists held in the scientific world, it took a number of years
before observations by other biologists were accepted as
demonstrating that cells did not arise in this manner any more
than organisms arose by spontaneous generation. By 1855,
Rudolf Virchow, a German pathologist, had made a convincing case for the third tenet of the cell theory:
■

Cells can arise only by division from a preexisting cell.

1.2 BASIC PROPERTIES OF CELLS
Just as plants and animals are alive, so too are cells. Life, in
fact, is the most basic property of cells, and cells are the smallest units to exhibit this property. Unlike the parts of a cell,
which simply deteriorate if isolated, whole cells can be removed from a plant or animal and cultured in a laboratory
where they will grow and reproduce for extended periods of
time. If mistreated, they may die. Death can also be considered one of the most basic properties of life, because only a living entity faces this prospect. Remarkably, cells within the
body generally die “by their own hand”—the victims of an internal program that causes cells that are no longer needed or
cells that pose a risk of becoming cancerous to eliminate
themselves.
The first culture of human cells was begun by George and
Martha Gey of Johns Hopkins University in 1951. The cells
were obtained from a malignant tumor and named HeLa cells
after the donor, Henrietta Lacks. HeLa cells—descended by
cell division from this first cell sample—are still being grown

FIGURE 1.2 HeLa cells, such as the ones pictured here, were the first
human cells to be kept in culture for long periods of time and are still in
use today. Unlike normal cells, which have a finite lifetime in culture,
these cancerous HeLa cells can be cultured indefinitely as long as conditions are favorable to support cell growth and division. (TORSTEN
WITTMANN/PHOTO RESEARCHERS INC.)

3

in laboratories around the world today (Figure 1.2). Because
they are so much simpler to study than cells situated within
the body, cells grown in vitro (i.e., in culture, outside the
body) have become an essential tool of cell and molecular
biologists. In fact, much of the information that will be discussed in this book has been obtained using cells grown in
laboratory cultures.

We will begin our exploration of cells by examining a few
of their most fundamental properties.

Cells Are Highly Complex and Organized
Complexity is a property that is evident when encountered,
but difficult to describe. For the present, we can think of complexity in terms of order and consistency. The more complex a
structure, the greater the number of parts that must be in their
proper place, the less tolerance of errors in the nature and interactions of the parts, and the more regulation or control that
must be exerted to maintain the system. Cellular activities can
be remarkably precise. DNA duplication, for example, occurs
with an error rate of less than one mistake every ten million
nucleotides incorporated—and most of these are quickly corrected by an elaborate repair mechanism that recognizes the
defect.
During the course of this book, we will have occasion to
consider the complexity of life at several different levels. We
will discuss the organization of atoms into small-sized molecules; the organization of these molecules into giant polymers;
and the organization of different types of polymeric molecules
into complexes, which in turn are organized into subcellular
organelles and finally into cells. As will be apparent, there is a
great deal of consistency at every level. Each type of cell has a
consistent appearance when viewed under a high-powered
electron microscope; that is, its organelles have a particular
shape and location, from one individual of a species to another.
Similarly, each type of organelle has a consistent composition
of macromolecules, which are arranged in a predictable pattern.
Consider the cells lining your intestine that are responsible for
removing nutrients from your digestive tract (Figure 1.3).
The epithelial cells that line the intestine are tightly connected to each other like bricks in a wall. The apical ends of
these cells, which face the intestinal channel, have long
processes (microvilli) that facilitate absorption of nutrients.

The microvilli are able to project outward from the apical cell
surface because they contain an internal skeleton made of
filaments, which in turn are composed of protein (actin)
monomers polymerized in a characteristic array. At their basal
ends, intestinal cells have large numbers of mitochondria that
provide the energy required to fuel various membrane transport processes. Each mitochondrion is composed of a defined
pattern of internal membranes, which in turn are composed of
a consistent array of proteins, including an electrically powered ATP-synthesizing machine that projects from the inner
membrane like a ball on a stick. Each of these various levels of
organization is illustrated in the insets of Figure 1.3.
Fortunately for cell and molecular biologists, evolution
has moved rather slowly at the levels of biological organiza-