GENETICS AND MOLECULAR BIOLOGY
CONTENTS 1 AN OVERVIEW OF CELL STRUCTURE AND FUNCTION CELL’S NEED FOR IMMENSE AMOUNTS OF INFORMATION RUDIMENTS OF PROKARYOTIC CELL STRUCTURE RUDIMENTS OF EUKARYOTIC CELL STRUCTURE PACKING DNA INTO CELLS MOVING MOLECULES INTO OR OUT OF CELLS DIFFUSION WITHIN THE SMALL VOLUME OF A CELL EXPONENTIALLY GROWING POPULATIONS COMPOSITION CHANGE IN GROWING CELLS AGE DISTRIBUTION IN POPULATIONS OF GROWING CELLS PROBLEMS REFERENCES 2 NUCLEIC ACID AND CHROMOSOME STRUCTURE THE REGULAR BACKBONE OF DNA GROOVES IN DNA AND HELICAL FORMS OF DNA DISSOCIATION AND REASSOCIATION OF BASE-PAIRED STRANDS READING SEQUENCE WITHOUT DISSOCIATING STRANDS ELECTROPHORETIC FRAGMENT SEPARATION BENT DNA SEQUENCES MEASUREMENT OF HELICAL PITCH TOPOLOGICAL CONSIDERATIONS IN DNA STRUCTURE GENERATING DNA WITH SUPERHELICAL TURNS MEASURING SUPERHELICAL TURNS DETERMINING LK, TW, AND WR IN HYPOTHETICAL STRUCTURES ALTERING LINKING NUMBER BIOLOGICAL SIGNIFICANCE OF SUPERHELICAL TURNS VII THE LINKING NUMBER PARADOX OF NUCLEOSOMES GENERAL CHROMOSOME STRUCTURE SOUTHERN TRANSFERS TO LOCATE NUCLEOSOMES ON GENES ARS ELEMENTS, CENTROMERES, AND TELOMERES 3 DNA SYNTHESIS A ENZYMOLOGY PROOFREADING, OKAZAKI FRAGMENTS, AND DNA LIGASE DETECTION AND BASIC PROPERTIES OF DNA POLYMERASES IN VITRO DNA REPLICATION ERROR AND DAMAGE CORRECTION B PHYSIOLOGICAL ASPECTS DNA REPLICATION AREAS IN CHROMOSOMES BIDIRECTIONAL REPLICATION FROM E COLI ORIGINS THE DNA ELONGATION RATE CONSTANCY OF THE E COLI DNA ELONGATION RATE REGULATING INITIATIONS GEL ELECTROPHORESIS ASSAY OF EUKARYOTIC REPLICATION ORIGINS HOW FAST COULD DNA BE REPLICATED? 4 RNA POLYMERASE AND RNA INITIATION MEASURING THE ACTIVITY OF RNA POLYMERASE CONCENTRATION OF FREE RNA POLYMERASE IN CELLS THE RNA POLYMERASE IN ESCHERICHIA COLI THREE RNA POLYMERASES IN EUKARYOTIC CELLS MULTIPLE BUT RELATED SUBUNITS IN POLYMERASES MULTIPLE SIGMA SUBUNITS THE STRUCTURE OF PROMOTERS ENHANCERS ENHANCER-BINDING PROTEINS DNA LOOPING IN REGULATING PROMOTER ACTIVITIES STEPS OF THE INITIATION PROCESS MEASUREMENT OF BINDING AND INITIATION RATES RELATING ABORTIVE INITIATIONS TO BINDING AND INITIATING ROLES OF AUXILIARY TRANSCRIPTION FACTORS MELTED DNA UNDER RNA POLYMERASE 5 TRANSCRIPTION, TERMINATION, AND RNA PROCESSING POLYMERASE ELONGATION RATE TRANSCRIPTION TERMINATION AT SPECIFIC SITES TERMINATION PROCESSING PROKARYOTIC RNAS AFTER SYNTHESIS S1 MAPPING TO LOCATE 5’ AND 3’ ENDS OF TRANSCRIPTS CAPS, SPLICES, EDITS, AND POLY-A TAILS ON EUKARYOTIC RNAS THE DISCOVERY AND ASSAY OF RNA SPLICING INVOLVEMENT OF THE U1 SNRNP PARTICLE IN SPLICING SPLICING REACTIONS AND COMPLEXES THE DISCOVERY OF SELF-SPLICING RNAS A COMMON MECHANISM FOR SPLICING REACTIONS OTHER RNA PROCESSING REACTIONS 6 PROTEIN STRUCTURE THE AMINO ACIDS THE PEPTIDE BOND ELECTROSTATIC FORCES THAT DETERMINE PROTEIN STRUCTURE HYDROGEN BONDS AND THE CHELATE EFFECT HYDROPHOBIC FORCES THERMODYNAMIC CONSIDERATIONS OF PROTEIN STRUCTURE STRUCTURES WITHIN PROTEINS THE ALPHA HELIX, BETA SHEET, AND BETA TURN CALCULATION OF PROTEIN TERTIARY STRUCTURE SECONDARY STRUCTURE PREDICTIONS STRUCTURES OF DNA-BINDING PROTEINS SALT EFFECTS ON PROTEIN-DNA INTERACTIONS LOCATING SPECIFIC RESIDUE-BASE INTERACTIONS 7 PROTEIN SYNTHESIS A CHEMICAL ASPECTS ACTIVATION OF AMINO ACIDS DURING PROTEIN SYNTHESIS FIDELITY OF AMINOACYLATION HOW SYNTHETASES IDENTIFY THE CORRECT TRNA MOLECULE DECODING THE MESSAGE BASE PAIRING BETWEEN RIBOSOMAL RNA AND MESSENGER EXPERIMENTAL SUPPORT FOR THE SHINE-DALGARNO HYPOTHESIS EUKARYOTIC TRANSLATION AND THE FIRST AUG TRICKING THE TRANSLATION MACHINERY INTO INITIATING PROTEIN ELONGATION PEPTIDE BOND FORMATION TRANSLOCATION TERMINATION, NONSENSE, AND SUPPRESSION CHAPERONES AND CATALYZED PROTEIN FOLDING RESOLUTION OF A PARADOX MESSENGER INSTABILITY PROTEIN ELONGATION RATES DIRECTING PROTEINS TO SPECIFIC CELLULAR SITES VERIFYING THE SIGNAL PEPTIDE MODEL THE SIGNAL RECOGNITION PARTICLE AND TRANSLOCATION EXPECTATIONS FOR RIBOSOME REGULATION PROPORTIONALITY OF RIBOSOME LEVELS AND GROWTH RATES REGULATION OF RIBOSOME SYNTHESIS BALANCING SYNTHESIS OF RIBOSOMAL COMPONENTS 8 GENETICS MUTATIONS POINT MUTATIONS, DELETIONS, INSERTIONS, AND DAMAGE CLASSICAL GENETICS OF CHROMOSOMES COMPLEMENTATION, CIS, TRANS, DOMINANT, AND RECESSIVE MECHANISM OF A TRANS DOMINANT NEGATIVE MUTATION GENETIC RECOMBINATION MAPPING BY RECOMBINATION FREQUENCIES MAPPING BY DELETIONS HETERODUPLEXES AND GENETIC RECOMBINATION BRANCH MIGRATION AND ISOMERIZATION ELEMENTS OF RECOMBINATION IN E COLI, RECA, RECBCD, AND CHI GENETIC SYSTEMS GROWING CELLS FOR GENETICS EXPERIMENTS TESTING PURIFIED CULTURES, SCORING ISOLATING AUXOTROPHS, USE OF MUTAGENS AND REPLICA PLATING GENETIC SELECTIONS MAPPING WITH GENERALIZED TRANSDUCING PHAGE PRINCIPLES OF BACTERIAL SEX ELEMENTS OF YEAST GENETICS ELEMENTS OF DROSOPHILA GENETICS ISOLATING MUTATIONS IN MUSCLE OR NERVE IN DROSOPHILA FATE MAPPING AND STUDY OF TISSUE-SPECIFIC GENE EXPRESSION 9 GENETIC ENGINEERING AND RECOMBINANT DNA THE ISOLATION OF DNA THE BIOLOGY OF RESTRICTION ENZYMES CUTTING DNA WITH RESTRICTION ENZYMES ISOLATION OF DNA FRAGMENTS JOINING DNA FRAGMENTS VECTORS: SELECTION AND AUTONOMOUS DNA REPLICATION PLASMID VECTORS A PHAGE VECTOR FOR BACTERIA VECTORS FOR HIGHER CELLS PUTTING DNA BACK INTO CELLS CLONING FROM RNA PLAQUE AND COLONY HYBRIDIZATION FOR CLONE IDENTIFICATION WALKING ALONG A CHROMOSOME TO CLONE A GENE ARREST OF TRANSLATION TO ASSAY FOR DNA OF A GENE CHEMICAL DNA SEQUENCING ENZYMATIC DNA SEQUENCING 10 ADVANCED GENETIC ENGINEERING FINDING CLONES FROM A KNOWN AMINO ACID SEQUENCE FINDING CLONES USING ANTIBODIES AGAINST A PROTEIN SOUTHERN, NORTHERN, AND WESTERN TRANSFERS POLYMERASE CHAIN REACTION ISOLATION OF RARE SEQUENCES UTILIZING PCR PHYSICAL AND GENETIC MAPS OF CHROMOSOMES CHROMOSOME MAPPING DNA FINGERPRINTING—FORENSICS MEGABASE SEQUENCING FOOTPRINTING, PREMODIFICATION AND MISSING CONTACT PROBING ANTISENSE RNA: SELECTIVE GENE INACTIVATION HYPERSYNTHESIS OF PROTEINS ALTERING CLONED DNA BY IN VITRO MUTAGENESIS MUTAGENESIS WITH CHEMICALLY SYNTHESIZED DNA 11 REPRESSION AND THE LAC OPERON BACKGROUND OF THE LAC OPERON THE ROLE OF INDUCER ANALOGS IN THE STUDY OF THE LAC OPERON PROVING LAC REPRESSOR IS A PROTEIN AN ASSAY FOR LAC REPRESSOR THE DIFFICULTY OF DETECTING WILD-TYPE LAC REPRESSOR DETECTION AND PURIFICATION OF LAC REPRESSOR REPRESSOR BINDS TO DNA: THE OPERATOR IS DNA THE MIGRATION RETARDATION ASSAY AND DNA LOOPING THE ISOLATION AND STRUCTURE OF OPERATOR IN VIVO AFFINITY OF REPRESSOR FOR OPERATOR THE DNA-BINDING DOMAIN OF LAC REPRESSOR A MECHANISM FOR INDUCTION 12 INDUCTION, REPRESSION, AND THE ARABAD OPERON THE SUGAR ARABINOSE AND ARABINOSE METABOLISM GENETICS OF THE ARABINOSE SYSTEM DETECTION AND ISOLATION OF ARAC PROTEIN REPRESSION BY ARAC REGULATING ARAC SYNTHESIS BINDING SITES OF THE ARA REGULATORY PROTEINS DNA LOOPING AND REPRESSION OF ARABAD IN VIVO FOOTPRINTING DEMONSTRATION OF LOOPING HOW ARAC PROTEIN LOOPS AND UNLOOPS WHY LOOPING IS BIOLOGICALLY SENSIBLE WHY POSITIVE REGULATORS ARE A GOOD IDEA 13 ATTENUATION AND THE TRP OPERON THE AROMATIC AMINO ACID SYNTHETIC PATHWAY AND ITS REGULATION RAPID INDUCTION CAPABILITIES OF THE TRP OPERON THE SERENDIPITOUS DISCOVERY OF TRP ENZYME HYPERSYNTHESIS EARLY EXPLORATIONS OF THE HYPERSYNTHESIS TRP MULTIPLE SECONDARY STRUCTURES IN TRP LEADER RNA COUPLING TRANSLATION TO TERMINATION RNA SECONDARY STRUCTURE AND THE ATTENUATION MECHANISM OTHER ATTENUATED SYSTEMS: OPERONS, BACILLUS SUBTILIS AND HIV 14 LAMBDA PHAGE GENES AND REGULATORY CIRCUITRY A THE STRUCTURE AND BIOLOGY OF LAMBDA THE PHYSICAL STRUCTURE OF LAMBDA THE GENETIC STRUCTURE OF LAMBDA LYSOGENY AND IMMUNITY LAMBDA’S RELATIVES AND LAMBDA HYBRIDS B CHRONOLOGY OF A LYTIC INFECTIVE CYCLE LAMBDA ADSORPTION TO CELLS EARLY TRANSCRIPTION OF GENES N AND CRO N PROTEIN AND ANTITERMINATION OF EARLY GENE TRANSCRIPTION THE ROLE OF CRO PROTEIN INITIATING DNA SYNTHESIS WITH THE O AND P PROTEINS PROTEINS KIL, ?, ?, AND EXO Q PROTEIN AND LATE PROTEN SYNTHESIS LYSIS C THE LYSOGENIC INFECTIVE CYCLE AND INDUCTION OF LYSO- GENS CHRONOLOGY OF BECOMING A LYSOGEN SITE FOR CRO REPRESSION AND CI ACTIVATION COOPERATIVITY IN REPRESSOR BINDING AND ITS MEASUREMENT THE NEED FOR AND THE REALIZATION OF HAIR-TRIGGER INDUCTION INDUCTION FROM THE LYSOGENIC STATE ENTROPY, A BASIS FOR LAMBDA REPRESSOR INACTIVATION 15 XENOPUS 5S RNA SYNTHESIS BIOLOGY OF 5S RNA SYNTHESIS IN XENOPUS IN VITRO 5S RNA SYNTHESIS TFIIIA BINDING TO THE MIDDLE OF ITS GENE AS WELL AS TO RNA SWITCHING FROM OOCYTE TO SOMATIC 5S SYNTHESIS STRUCTURE AND FUNCTION OF TFIIIA 16 REGULATION OF MATING TYPE IN YEAST THE YEAST CELL CYCLE MATING TYPE CONVERSION IN SACCHAROMYCES CEREVISIAE CLONING THE MATING TYPE LOCI IN YEAST TRANSFER OF MATING TYPE GENE COPIES TO AN EXPRESSION SITE STRUCTURE OF THE MATING TYPE LOCI THE EXPRESSION AND RECOMBINATION PARADOXES SILENCING HML AND HMR ISOLATION OF ?2 PROTEIN STERILE MUTANTS, MEMBRANE RECEPTORS AND G FACTORS DNA CLEAVAGE AT THE MAT LOCUS DNA STRAND INHERITANCE AND SWITCHING IN FISSION YEAST 17 GENES REGULATING DEVELOPMENT GENERAL CONSIDERATIONS ON SIGNALING OUTLINE OF EARLY DROSOPHILA DEVELOPMENT CLASSICAL EMBRYOLOGY USING GENETICS TO BEGIN STUDY OF DEVELOPMENTAL SYSTEMS CLONING DEVELOPMENTAL GENES ENHANCER TRAPS FOR DETECTING AND CLONING DEVELOPMENTAL GENES EXPRESSION PATTERNS OF DEVELOPMENTAL GENES SIMILARITIES AMONG DEVELOPMENTAL GENES OVERALL MODEL OF DROSOPHILA EARLY DEVELOPMENT 18 LAMBDA PHAGE INTEGRATION AND EXCISION MAPPING INTEGRATED LAMBDA SIMULTANEOUS DELETION OF CHROMOSOMAL AND LAMBDA DNA DNA HETERODUPLEXES PROVE THAT LAMBDA INTEGRATES GENE ORDER PERMUTATION AND THE CAMPBELL MODEL ISOLATION OF INTEGRATION-DEFECTIVE MUTANTS ISOLATION OF EXCISION-DEFICIENT MUTANTS PROPERTIES OF THE INT AND XIS GENE PRODUCTS INCORRECT EXCISION AND GAL AND BIO TRANSDUCING PHAGE TRANSDUCING PHAGE CARRYING GENES OTHER THAN GAL AND BIO USE OF TRANSDUCING PHAGE TO STUDY INTEGRATION AND EXCISION DEMONSTRATING XIS IS UNSTABLE INHIBITION BY A DOWNSTREAM ELEMENT IN VITRO ASSAY OF INTEGRATION AND EXCISION HOST PROTEINS INVOLVED IN INTEGRATION AND EXCISION STRUCTURE OF THE ATT REGIONS STRUCTURE OF THE INTASOME HOLLIDAY STRUCTURES AND BRANCH MIGRATION IN INTEGRATION 19 TRANSPOSABLE GENETIC ELEMENTS IS ELEMENTS IN BACTERIA STRUCTURE AND PROPERTIES OF IS ELEMENTS DISCOVERY OF TN ELEMENTS STRUCTURE AND PROPERTIES OF TN ELEMENTS INVERTING DNA SEGMENTS BY RECOMBINATION, FLAGELLIN SYNTHESIS MU PHAGE AS A GIANT TRANSPOSABLE ELEMENT AN INVERTIBLE SEGMENT OF MU PHAGE IN VITRO TRANSPOSITION, THREADING OR GLOBAL TOPOLOGY? RETROTRANSPOSONS IN HIGHER CELLS AN RNA TRANSPOSITION INTERMEDIATE P ELEMENTS AND TRANSFORMATION P ELEMENT HOPPING BY CHROMOSOME RESCUE 20 GENERATING GENETIC DIVERSITY: ANTIBODIES THE BASIC ADAPTIVE IMMUNE RESPONSE TELLING THE DIFFERENCE BETWEEN FOREIGN AND SELF THE NUMBER OF DIFFERENT ANTIBODIES PRODUCED MYELOMAS AND MONOCLONAL ANTIBODIES THE STRUCTURE OF ANTIBODIES MANY COPIES OF V GENES AND ONLY A FEW C GENES THE J REGIONS THE D REGIONS IN H CHAINS INDUCED MUTATIONS AND ANTIBODY DIVERSITY CLASS SWITCHING OF HEAVY CHAINS ENHANCERS AND EXPRESSION OF IMMUNOGLOBULIN GENES THE AIDS VIRUS ENGINEERING ANTIBODY SYNTHESIS IN BACTERIA ASSAYING FOR SEQUENCE REQUIREMENTS OF GENE REARRANGEMENTS CLONING THE RECOMBINASE 21 BIOLOGICAL ASSEMBLY, RIBOSOMES AND LAMBDA PHAGE A RIBOSOME ASSEMBLY RNASE AND RIBOSOMES THE GLOBAL STRUCTURE OF RIBOSOMES ASSEMBLY OF RIBOSOMES EXPERIMENTS WITH IN VITRO RIBOSOME ASSEMBLY DETERMINING DETAILS OF LOCAL RIBOSOMAL STRUCTURE B LAMBDA PHAGE ASSEMBLY GENERAL ASPECTS THE GEOMETRY OF CAPSIDS THE STRUCTURE OF THE LAMBDA PARTICLE THE HEAD ASSEMBLY SEQUENCE AND HOST PROTEINS PACKAGING THE DNA AND FORMATION OF THE COS ENDS FORMATION OF THE TAIL IN VITRO PACKAGING 22 CHEMOTAXIS ASSAYING CHEMOTAXIS FUNDAMENTAL PROPERTIES OF CHEMOTAXIS GENETICS OF MOTILITY AND CHEMOTAXIS HOW CELLS SWIM THE MECHANISM OF CHEMOTAXIS THE ENERGY FOR CHEMOTAXIS ADAPTATION METHYLATION AND ADAPTATION PHOSPHORYLATION AND THE RAPID RESPONSE 23 ONCOGENESIS, MOLECULAR ASPECTS BACTERIALLY INDUCED TUMORS IN PLANTS TRANSFORMATION AND ONCOGENESIS BY DAMAGING THE CHROMOSOME IDENTIFYING A NUCLEOTIDE CHANGE CAUSING CANCER RETROVIRUSES AND CANCER CELLULAR COUNTERPARTS OF RETROVIRAL ONCOGENES IDENTIFICATION OF THE SRC AND SIS GENE PRODUCTS DNA TUMOR VIRUSES RECESSIVE ONCOGENIC MUTATIONS, TUMOR SUPPRESSORS THE RAS-FOS-JUN PATHWAY DIRECTIONS FOR FUTURE RESEARCH IN MOLECULAR BIOLOGY HINTS AND SOLUTIONS TO ODD-NUMBERED PROBLEMS