Molecular Biology of the Gene

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 in1953, 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 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 ASBMBÐSchering Plough Scientific Achievement Award, and the Everett Moore Baker Memorial Award for Excellence in Undergraduate Teaching at MIT in 1998. 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 at the Center for Integrative Genomics. He received his B.A. from the Department of Genetics at U.C. Berkeley, and his Ph.D. with Alan Garen in the Department of Molecular Biophysics and Biochemistry from Yale Universityin 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 these two species should be italicized and Ciona (sea squirt) embryos. He holds the F. Williams Chair in Genetics and Development at U.C. 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.

I. CHEMISTRY AND GENETICS.

1. The Mendelian View of the World.


Mendel's Discoveries.

Chromosomal Theory of Heredity.

Gene Linkage and Crossing Over.

Chromosome Mapping.

The Origin of Genetic Variability Through Mutations.

Early Speculations about What Genes Are and How They Act.

Preliminary Attempts to Find a Gene-Protein Relationship. 2. Nucleic Acids Convey Genetic Information.


Avery's Bombshell: DNA Can Carry Genetic Specificity.

The Double Helix.

The Genetic Information within DNA is Conveyed by the Sequence of its Four Nucleotide Building Blocks.

The Central Dogma.

Establishing the Direction of Protein Synthesis.

The Era of Genomics. 3. The Importance of Weak Chemical Interactions.


Characteristics of Chemical Bonds.

The Concept of Free Energy.

Weak Bonds in Biological Systems. 4. The Importance of High-Energy Bonds.


Molecules that Donate Energy Are Thermodynamically Unstable.

Enzymes Lower Activation Energies in Biochemical Reactions.

Free Energy in Biomolecules.

High-Energy Bonds in Biosynthetic Reactions.

Activation of Precursors in Group Transfer Reactions. 5. Weak and Strong Bonds Determine Macromolecular Structure.


Higher-Order Structures Determined by Intra- and Intermolecular Interactions.

The Specific Conformation of a Protein Results from its Pattern of Hydrogen Bonds.

Most Proteins Are Modular, Containing Two or Three Domains.

Weak Bonds Correctly Position Proteins Along DNA and RNA Molecules.

Allostery: Regulation of a Protein's Function by Changing its Shape. II. MAINTENANCE OF THE GENOME.

6. The Structures of DNA and RNA.


DNA Structure.

DNA Topology.

RNA Structure. 7. Chromosomes, Chromatin, and the Nucleosome.


Chromosome Sequence and Diversity.

Chromosome Duplication and Segregation.

The Nucleosome.

Higher-Order Chromatin Structure.

Regulation of Chromatin Structure.

Nucleosome Assembly. 8.The Replication of DNA.


The Chemistry of DNA Synthesis.

The Mechanism of DNA Polymerase.

The Replication Fork.

The Specialization of DNA Polymerases.

DNA Synthesis at the Replication Fork.

Initiation of DNA Replication.

Binding and Unwinding: Origin Selection and Activation by the Initiator Protein.

Finishing Replication. 9. The Mutability and Repair of DNA.


Replication Errors and Their Repair.

DNA Damage.

Repair of DNA Damage. 10. Homologous Recombination at the Molecular Level.


Models for Homologous Recombination.

Homologous Recombination Protein Machines.

Homologous Recombination in Eukaryotes.

Mating-Type Switching.

Genetic Consequences of the Mechanism of Homologous Recombination. 11. Site-Specific Recombination and Transposition of DNA.


Conservative Site-Specific Recombination.

Biological Roles of Site-specific Recombination.

Transposition.

Examples of Transposable Elements and their Regulation.

V(D)J Recombination. III. EXPRESSION OF THE GENOME.

12. Mechanisms of Transcription.


RNA Polymerases and the Transcription Cycle.

The Transcription Cycle in Bacteria.

Transcription in Eukaryotes. 13. RNA Splicing.


The Chemistry of Splicing.

The Spliceosome Machinery.

Splicing Pathways.

Alternative Splicing.

Exon Shuffling.

RNA Editing.

mRNA Transport. 14. Translation 411.


Messenger RNA.

Transfer RNA.

Attachment of Amino Acids to tRNA.

The Ribosome.

Initiation of Translation.

Translation Elongation.

Termination of Translation.

Translation-Dependent Regulation of mRNA and Protein Stability. 15. The Genetic Code.


The Code Is Degenerate.

Three Rules Govern the Genetic Code.

Suppressor Mutations Can Reside in the Same or a Different Gene.

The Code Is Nearly Universal. IV. REGULATION.

16. Gene Regulation in Prokaryotes.


Principles of Transcriptional Regulation.

Regulation of Transcription Initiation: Examples from Bacteria.

Examples of Gene Regulation at Steps after Transcription Initiation.

The Case of Phage λ: Layers of Regulation. 17. Gene Regulation in Eukaryotes.


Conserved Mechanisms of Transcriptional Regulation from Yeast to Mammals.

Recruitment of Protein Complexes to Genes by Eukaryotic Activators.

Signal Integration and Combinatorial Control.

Transcriptional Repressors.

Signal Transduction and the Control of Transcriptional Regulators.

Gene “Silencing” by Modification of Histones and DNA.

Eukaryotic Gene Regulation at Steps after Transcription Initiation.

RNAs in Gene Regulation. 18. Gene Regulation During Development.


Three Strategies by Which Cells Are Instructed to Express Specific Sets of Genes During Development.

Examples of the Three Strategies for Establishing Differential Gene Expression.

The Molecular Biology of Drosophila Embryogenesis. 19. Comparative Genomics and the Evolution of Animal Diversity.


Most Animals Have Essentially the Same Genes.

Three Ways Gene Expression Is Changed During Evolution.

Experimental Manipulations that Alter Animal Morphology.

Morphological Changes in Crustaceans and Insects.

Genome Evolution and Human Origins. V. METHODS.
20. Techniques of Molecular Biology.


Introduction.

Nucleic Acids.

Proteins. 21. Model Organisms.


Bacteriophage.

Bacteria.

Baker's Yeast, Saccharomyces cerevisiae.

The Nematode Worm, Caenorhabditis elegans.

The Fruit Fly, Drosophila melanogaster.

The House Mouse, Mus musculus.