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Molecular Biology
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Molecular Biology
of the Gene
F I F T H
E D IT I O N
James D. Watson
Cold Spring Harbor
Laboratory
Tania A. Baker
Massachusetts Institute
of Technology
Stephen P. Bell
Massachusetts Institute
of Technology
Alexander Gann
Cold Spring Harbor
Laboratory Press
Michael Levine
University of California,
Berkeley
Richard Losick
Harvard University
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Benjamin
Cummings
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Benjamin Cummings
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ISBN 0-321-22368-3
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Preface
press, completion human genome longer
s the fifth editionofofthe is nogoes to
Molecular Biologysequence of the Gene
news. This was not something that could safely have been
A
anticipated when the first edition appeared in 1965; even when the
fourth edition came out in 1987, few if any foresaw how quickly we
would move into a world where whole genomes, not just individual
genes, could be visualized and compared. There has been a comparable leap in the elucidation of protein structures as well. Thus, in the
last few years, the structures of the huge molecular machines that
drive the basic processes discussed in this book-DNA transcription,
replication, protein synthesis, and so forth-have largely been solved
at the atomic level, and many details of their inner workings revealed.
The new edition of Molecular Biology of the Gene reflects these
advances, and many others besides. But when we sat down to plan
this latest version, we were all of a mind that much of the organization and scope of the original book should be retained. This was not a
matter of convenience-inevitably, in light of the dramatic changes
that had taken place since the last edition, the vast bulk of the text
had to be completely rewritten anyway, and all the art rendered
afresh. No, the reasoning was simply that, more than ever in this genomic era, there seemed a need for a book that explained what genes
are and how they work, and this was exactly what Molecular Biology
of the Gene had originally been designed to do.
Thus, we have resisted the temptation to become encyclopedic or to
delve into allied disciplines, such as cell biology. Also, we wanted the
new edition to retain a focus on principles and concepts, another feature of its predecessors. And so we illustrate our discussion sparingly
with experiments, which appear mainly in boxes. These considerations ensured the book did not become unwieldy. As stated by its author in the preface to the first edition: "Often I present a fact, and, because of lack of space, I cannot outline the experiments that
demonstrate its validity. Given the choice between deleting an
important principle or giving an experimental detail, I am inclined to
state the principle." The current incarnation of Molecular Biology of
the Gene adheres unapologetically to this philosophy.
An outline of this new edition will thus be familiar to anyone who
has used the book before. We begin (in Part 1 ) with a series of chapters
(modified in the current edition) that place the field of molecular
biology in context. These chapters summarize the history of genetics
and molecul_ar biology and also present the timeless chemical principles that determine the structure and function of macromolecules.
The text thereafter is organized to follow a familiar flow of topics. The
nature of the genetic material, its organization and its maintenance,
are discussed in Part 2 ; in addition to chapters on DNA structure,
replication, recombination, and repair, new to this part of the book is
a chapter on chromosomes, chromatin, and the nucleosome. This
addition reflects current appreciation of how the context in which
a given gene is found influences its function and regulation.
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The passage of information from gene to protein- so-called gene
expression - is covered in Part 3; and in Part 4 we describe the
regulation of that process. As well as chapters on the basic mechanisms of gene regulation, Part 4 has chapters on the regulation of
gene expression in animal development and in the evolution of
animal diversity. These chapters again conform to a tradition established by earlier editions: always there has been a chapter or two
linking basic mechanisms of molecular biology to pressing biological questions. In the current edition, these chapters investigate
perhaps the most striking revelation to come from comparing the
complete genome sequences of various animals: different animalsincluding humans-contain largely the same genes and so differences between those animals must result largely from changes in
how those genes are expressed.
New to the current edition is the final part-Part 5-comprising
chapters on experimental methods-the techniques of molecular
biology, genomics, and bioinformatics-and on the model organisms
whose study has revealed many of the underlying principles of
molecular biology.
We alluded to the explosion in the numbers of atomic structures
solved in the last few years. These include not only many of the
enzymes that mediate the basic processes of molecular biology, and
many of the proteins that regulate those processes, but the nucleosome as well. While it remains true that many of the basic concepts in
molecular biology can be understood without reliance on structural
detail- indeed it is one of the strengths of the field that this is the
case-nevertheless, many mechanistic insights come only from seeing
these details. Accordingly, where structures shed light on how
the molecules in question work, we present them; and we do so in a
consistent style throughout the book.
Each part opener includes a short text, outlining what will be
covered in the coming chapters, and a few photographs. These pictures, from the Cold Spring Harbor Laboratory Archive, were all taken
at the Laboratory on Long Island, the great majority at the Symposium
hosted there almost every summer since 1933. Captions identify who
is in each picture and when it was taken. We thank Clare Bunce and
the CSHL Archive for help with these.
Parts of the current edition grew out of an introductory course on molecular biology taught by one of us (RL) at Harvard University, and this
author is grateful to Steve Harrison and Jim Wang who contributed to
this course in past years and whose influence is reflected in Chapter 6
and elsewhere. We have shown sections of the manuscript to various
colleagues and their comments have been most valuable, greatly improving the accuracy and accessibility of the text and figures. Specifically we
thank: Jamie Cate, Richard Ebright. Mike Eisen, Chris Fromme, Ira Hall,
Adrian Krainer, Karolin Luger. Bill McGinnis, Matt Michael, Lily Mirels,
Nipam Patel, Craig Peterson, Mark Ptashne, Uttam RajBhandary, and
Bruce Stillman. In addition, Craig Hunter drafted the section on the
worm for Chapter 21. We also thank those who provided us with figures,
or the wherewithall to create them, including: Sean Carroll, Seth Darst,
Edward Egelman, Georg Halder, Stuart Kim, Bill McGinnis, Steve Paddock, Phoebe Rice, Matt Scott, Peter Sorger, Andrzej Stasiak, Tom Steitz,
Dan Voytas, and Steve West.
We are most grateful to Leemor Joshua-Tor who rendered all
the structure figures, often producing multiple versions and
patiently helping us see which best �()'fe��'gA(_� needed. We
are also grateful to those who provided their software1: Per Kraulis,
Robert Esnouf, Ethan Merritt, and Barry Honig. Coordinates were
obtained from the Protein Data Bank (www.rcsb.org/pdb/); and
citations to those who solved each structure are included in the
figure legends.
Our art program was developed and rendered by a talented and
enthusiastic team from the Dragonfly Media Group, led by Mike
Demaray and Craig Durant. Renate Hellmiss helped to develop some
of our initial sketches and provided early renderings of a number of
figures. The cover image was rendered by Torno Narashima from an
author concept sketch by Erica Beade (MBC Graphics).
We thank those at Cold Spring Harbor Laboratory Press who
handled development of this book. Jan Argentine, despite having to
enforce the deadlines, was throughout less cajoling than she was
tirelessly engaged in helping us solve the problems these presented.
Maryliz Dickerson kept organized the mass of material we generated
and Nora Rice helped coordinate author meetings and other aspects
of the project. Denise Weiss and Ed Atkeson produced the cover
design; and John Inglis, who initiated this collaboration, was on
hand with advice at critical points in the process. Most of all,
Kaaren Janssen, our editor, kept everything afloat with an energy,
enthusiasm, and activity far beyond anything we could reasonably have asked for; things simply would not have got to this point
without her.
We also wish to acknowledge the work of those at Benjamin Cummings who coordinated production of the book. Frank Ruggirello
oversaw the process carried out by Jim Smith, Kay Ueno. Corinne
Benson, Alexandra Fellowes, Jeanne Zalesky, and Donna Kalal. Ingrid
Mount at Elm Street Publishing Services coped cheerfully with the
many rounds of changes to art and text even very late in the process.
Michele Sordi, while part of the Benjamin Cummings team, helped
bring us all together in the first place.
And finally we gratefully acknowledge our families and friends
who, throughout this period, provided such strong support, despite
having to put up with our frequent absences and distractions.
James D. Watson
Tania A. Baker
Stephen P. Bell
Alexander Gann
Michael Levine
Richard Losick
1 Per Kraulis granted permission to use MolScript (Kraulis P. }. 1991. MOLSCRIPT: A
program to produce both detailed and schematic plots of protein structures. Journal of
Applied Crystallography 24: 946-950). Robert Esnouf gave permission to use BobScript
(Esnouf R.M. 1997. Journal of Molecular Graphics 15: 132-134). In addition, Ethan
Merritt gave us use of Raster3D (Merritt E.A. and Bacon D.J. 1997. Raster3D: Photorealistic Molecular Graphics. Methods in Enzymology 277: 505-524), and Barry Honig
granted permission to use GRASP (Nicolls A., Sharp K.A., and Honig B. 1991. Protein
folding and association: Insights from the interfacial and thermodynamic properties of
hydrocarbons. Proteins 11: 281-296).
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About the Authors
JAMES D. WATSON was Director of Cold Spring Harbor Laboratory
from 1968 to 1993 and is now its President. He spent his undergraduate
years at the University of Chicago and received his Ph.D. in 1950 from
Indiana University. Between 1950 and 1953, he did postdoctoral research
in Copenhagen and Cambridge, England. While at Cambridge, he began
the collaboration that resulted in the elucidation of the double-helical
structure of DNA in 1953. (For this discovery, Watson, Francis Crick, and
Maurice Wilkins were awarded the Nobel Prize in 1962.) Later in 1953,
he went to the California Institute of Technology. He moved to Harvard in
1955, where he taught and did research on RNA synthesis and protein
synthesis until 1976. He was the first Director of the National Center for
Genome Research of the National Institutes of Health from 1989 to 1992.
Dr. Watson was sole author of the first, second, and third editions of Molecular Biology of the Gene, and a co-author of the fourth edition. These
were published in 1965, 1970, 1976, and 1987 respectively. Watson has
also been involved in two other textbooks: he was one of the original authors of Molecular Biology of the Cell, and is also an author of
Recombinant DNA: a Short Course.
TANIA A. BAKER is the Whitehead Professor of Biology at the Massachusetts Institute of Technology and an Investigator of the Howard
Hughes Medical Institute. She received a B.S. in biochemistry from the
University of Wisconsin, Madison, and a Ph.D. in biochemistry from
Stanford University in 1988. Her graduate research was carried out in
the laboratory of Professor Arthur Kornberg and focused on mechanisms of initiation of DNA replication. She did postdoctoral research
in the laboratory of Dr. Kiyoshi Mizuuchi at the National Institutes of
Health, studying the mechanism and regulation of DNA transposition.
Her current research explores mechanisms and regulation of genetic recombination, enzyme-catalyzed protein unfolding, and ATP-dependent
protein degradation. Professor Baker received the 2001 Eli Lilly
Research Award from the American Society of Microbiology and the
2000 MIT School of Science Teaching Prize for Undergraduate
Education. She is co-author (with Arthur Kornberg) of the book DNA
Replication, Second Edition.
STEPHEN P. BELL is a Professor of Biology at the Massachusetts
Institute of Technology and an Assistant Investigator of the Howard
Hughes Medical Institute. He received B.A. degrees from the Department
of Biochemistry, Molecular Biology, and Cell Biology and the Integrated
Sciences Program at Northwestern University and a Ph.D. in biochemistry at the University of California, Berkeley in 1991. His graduate research was carried out in the laboratory of Dr. Robert Tjian and focused
on eukaryotic transcription. He did postdoctoral research in the laboratory of Dr. Bruce Stillman at Cold Spring Harbor Laboratory, working on
the initiation of eukaryotic DNA replication. His current research focuses on the mechanisms controlling the duplication of eukaryotic chromosomes. Professor Bell received the 2001 ASBMB-Schering Plough
Scientific Achievement Award and the Everett Moore Baker Memorial
Award for Excellence in Undergraduate Teaching at MIT in 1998.
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ALEXANDER GANN is Editorial Director of Cold Spring Harbor
Laboratory Press, and a faculty member of the Watson School of Biological Sciences at Cold Spring Harbor Laboratory. He received his
B.Sc in microbiology from University College London and a Ph.D. in
molecular biology from The University of Edinburgh in 1989. His
graduate research was carried out in the laboratory of Noreen Murray
and focused on DNA recognition by restriction enzymes. He did
postdoctoral research in the laboratory of Mark Ptashne at Harvard,
working on transcriptional regulation, and that of Jeremy Brockes
at the Ludwig Institute of Cancer Research at University College
London, where he .worked on newt limb regeneration. He was a Lecturer at Lancaster University, England, from 1996 to 1999, before
moving to Cold Spring Harbor Laboratory. He is co-author (with
Mark Ptashne) of the book Genes & Signals (2002).
MICHAEL LEVINE is a Professor of Molecular and Cell Biology at the
University of California, Berkeley, and is also Co-Director of the Center
for Integrative Genomics. He received his B.A. from the Department of
Genetics at the University of California, Berkeley, and his Ph.D. with
Alan Garen in the Department of Molecular Biophysics and Biochemistry from Yale University in 1981. As a postdoctoral fellow with Walter
Gehring and Gerry Rubin from 1982 - 1984, he studied the molecular
genetics of Drosophila development. Professor Levine's research group
currently studies the gene networks responsible for the gastrulation of
the Drosophila and Ciona (sea squirt) embryos. He holds the F. Williams
Chair in Genetics and Development at the University of California,
Berkeley. He was awarded the Monsanto Prize in Molecular Biology
from the National Academy of Sciences in 1996, and was elected to the
American Academy of Arts and Sciences in 1996 and the National
Academy of Sciences in 1998.
RICHARD M. LOSICK is the Maria Moors Cabot Professor of Biology,
a Harvard College Professor, and a Howard Hughes Medical Institute
Professor in the Faculty of Arts & Sciences at Harvard University. He
received his A.B. in chemistry at Princeton University and his Ph.D. in
biochemistry at the Massachusetts Institute of Technology. Upon completion of his graduate work, Professor Losick was named a Junior
Fellow of the Harvard Society of Fellows when he began his studies on
RNA polymerase and the regulation of gene transcription in bacteria.
Professor Losick is a past Chairman of the Departments of Cellular and
Developmental Biology and Molecular and Cellular Biology at Harvard
University. He received the Camille and Henry Dreyfuss Teacher-Scholar
Award, is a member of the National Academy of Sciences, a Fellow of
the American Academy of Arts and Sciences, a Fellow of the American
Association for the Advancement of Science, a Fellow of the American
Academy of Microbiology, and a former Visiting Scholar of the Phi Beta
Kappa Society.
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Brief Contents
PAR T 1
PART 2
PART 3 CHEMISTRY AND GENETICS
1
2
l
The Mendelian View of the World 5
Nucleic Acids Convey Genetic Information 19
41
55
3 The Importance of Weak Chemical Interactions
4 The Importance of High-Energy Bonds
s Weak and Strong Bonds Determine
Macromolecular Structure
MAINTENANCE OF THE GENOME
6
69
93
The Structures of DNA and RNA 97
129
181
235
259
7 Chromosomes, Chromatin, and the Nucleosome
o The Replication of DNA
9 The Mutability and Repair of DNA
to Homologous Recombination at the Molecular Level
11 Site-Specific Recombination and Transposition of DNA
EXPRESSION OF THE GENOME 343
12 Mechanisms of Transcription
293
347
379
411
13 RNA Splicing
14 Translation
15 The Genetic Code
461
ix
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