ADVANCES IN GENETICS
CHAPTER 1 INTRODUCTION TO THE CELL THE BACTERIAL CELL: A QUICK OVERVIEW HOW DO CELLS GROW? WHAT IS GENETICS? SUMMARY CHAPTER 2 THE BACTERIAL DNA MOLECULE THE STRUCTURE OF DNA AND RNA DEOXYRIBONUCLEOSIDES AND DEOXYRIBONUCLEOTIDES DNA IS ONLY POLYMERIZED 5¢ TO 3¢ DOUBLE-STRANDED DNA SUPERCOILING DOUBLE-STRANDED DNA REPLICATION OF THE ESCHERICHIA COLI CHROMOSOME CONSTRAINTS THAT IN?UENCE DNA REPLICATION THE REPLICATION MACHINERY DNA POLYMERASES DNAG PRIMASE DNAA, DNAB, AND DNAC REPLICATION OF BOTH STRANDS THETA MODE REPLICATION MINIMIZING MISTAKES IN DNA REPLICATION THE DNA REPLICATION MACHINERY AS MOLECULAR TOOLS CHAPTER 3 MUTATIONS PHENOTYPE AND GENOTYPE CLASSES OF MUTATIONS POINT MUTATIONS AND THEIR CONSEQUENCES MEASURING MUTATIONS: RATE AND FREQUENCY SPONTANEOUS AND INDUCED MUTATIONS ERRORS DURING DNA REPLICATION: INCORPORATION ERRORS ERRORS DUE TO TAUTOMERISM FULL CONTENTS SPONTANEOUS ALTERATION BY DEPURINATION SPONTANEOUS ALTERATION BY DEAMINATION ALTERATIONS BY SPONTANEOUS GENETIC REARRANGEMENT ALTERATIONS CAUSED BY TRANSPOSITION INDUCED MUTATIONS CHEMICALS THAT MIMIC NORMAL DNA BASES: BASE ANALOGS CHEMICALS THAT REACT WITH DNA BASES: BASE MODI?ERS CHEMICALS THAT BIND DNA BASES: INTERCALATORS MUTAGENS THAT PHYSICALLY DAMAGE THE DNA: ULTRAVIOLET LIGHT AND IONIZING RADIATION MUTATOR STRAINS REVERTING MUTATIONS SUPPRESSION AMES TEST HOW HAVE WE EXPLOITED BACTERIAL MUTANTS? CHAPTER 4 DNA REPAIR LESIONS THAT CONSTITUTE DNA DAMAGE REVERSE, EXCISE OR TOLERATE? MECHANISMS THAT REVERSE DNA DAMAGE PHOTOREACTIVATION O6-METHYLGUANINE OR O4-METHYLTHYMINE METHYLTRANSFERASE MECHANISMS THAT EXCISE DNA DAMAGE UVRABC DIRECTED NUCLEOTIDE EXCISION REPAIR MUTHLS METHYL DIRECTED MISMATCH REPAIR VERY SHORT PATCH REPAIR GLYCOSYLASES URACIL-N-GLYCOSYLASE COUPLED WITH AP EXCISION REPAIR DEAMINATED BASES REMOVED BY DNA GLYCOSYLASE ALKYLATED BASES REMOVED BY DNA GLYCOSYLASE MUTM/MUTY: OXIDATIVE DAMAGE N-GLYCOSYLASES SPECI?C FOR PYRIMIDINE DIMERS MECHANISMS THAT TOLERATE DNA DAMAGE TRANSDIMER SYNTHESIS POST REPLICATION/RECOMBINATIONAL REPAIR (PRR) INTRODUCTION TO THE SOS REGULON CHAPTER 5 RECOMBINATION HOMOLOGOUS RECOMBINATION MODELS FOR HOMOLOGOUS RECOMBINATION THE HOLLIDAY OR DOUBLE-STRAND INVASION MODEL OF RECOMBINATION AN ALTERNATIVE TO THE HOLLIDAY MODEL: THE SINGLE-STRAND INVASION MODEL OF MESELSON AND RADDING FURTHER ENZYMATIC CONSIDERATIONS SITE-SPECI?C RECOMBINATION A TYPICAL SITE-SPECI?C RECOMBINATIONAL EVENT BACTERIOPHAGE L: A MODEL FOR SITE-SPECI?C RECOMBINATION OTHER MICROBIAL EXAMPLES OF SITE-SPECI?C RECOMBINATION FULL CONTENTS ILLEGITIMATE RECOMBINATION CHAPTER 6 TRANSPOSITION THE STRUCTURE OF TRANSPOSONS THE FREQUENCY OF TRANSPOSITION THE TWO TYPES OF TRANSPOSITION REACTIONS THE TRANSPOSITION MACHINERY ACCESSORY PROTEINS ENCODED BY THE TRANSPOSON ACCESSORY PROTEINS ENCODED BY THE HOST NON-REPLICATIVE TRANSPOSITION REPLICATIVE TRANSPOSITION DOES THE FORMATION OF A COINTEGRATE PREDICT THE TRANSPOSITION MECHANISM? THE FATE OF THE DONOR SITE TARGET IMMUNITY TRANSPOSONS AS MOLECULAR TOOLS CHAPTER 7 BACTERIOPHAGE THE STRUCTURE OF PHAGE THE LIFECYCLE OF A BACTERIOPHAGE LYTIC–LYSOGENIC OPTIONS THE L LIFECYCLE L ADSORPTION L DNA INJECTION PROTECTING THE L GENOME IN THE BACTERIAL CYTOPLASM WHAT HAPPENS TO THE L GENOME AFTER IT IS STABILIZED? L AND THE LYTIC–LYSOGENIC DECISION THE L LYSOGENIC PATHWAY THE L LYTIC PATHWAY DNA REPLICATION DURING THE L LYTIC PATHWAY MAKING L PHAGE GETTING OUT OF THE CELL–THE L S AND R PROTEINS INDUCTION OF L BY THE SOS SYSTEM SUPERINFECTION RESTRICTION AND MODI?CATION OF DNA M13 ADSORPTION AND INJECTION PROTECTION OF THE M13 GENOME M13 DNA REPLICATION M13 PHAGE PRODUCTION AND RELEASE FROM THE CELL ADSORPTION, INJECTION, AND PROTECTION OF THE GENOME P1 DNA REPLICATION AND PHAGE ASSEMBLY THE LOCATION OF THE P1 PROPHAGE IN A LYSOGEN P1 TRANSDUCING PARTICLES T4 ADSORPTION AND INJECTION T4RII MUTATIONS AND THE NATURE OF THE GENETIC CODE FULL CONTENTS CHAPTER 8 TRANSDUCTION GENERALIZED TRANSDUCTION VS SPECIALIZED TRANSDUCTION P1 AS A MODEL FOR GENERALIZED TRANSDUCING PHAGE PACKAGING THE CHROMOSOME MOVING PIECES OF THE CHROMOSOME FROM ONE CELL TO ANOTHER IDENTIFYING TRANSDUCED BACTERIA: SELECTION VS SCREENING CARRYING OUT A TRANSDUCTION USES FOR TRANSDUCTION TWO-FACTOR CROSSES TO DETERMINE GENE LINKAGE MAPPING THE ORDER OF GENES – THREE-FACTOR CROSSES STRAIN CONSTRUCTION LOCALIZED MUTAGENESIS SPECIALIZED TRANSDUCING PHAGE MAKING MERODIPLOIDS WITH SPECIALIZED TRANSDUCING PHAGE MOVING MUTATIONS FROM PLASMIDS TO SPECIALIZED TRANSDUCING PHAGE TO THE CHROMOSOME CHAPTER 9 NATURAL PLASMIDS ORIGINS OF REPLICATION PLASMID COPY NUMBER SETTING THE COPY NUMBER PLASMID INCOMPATIBILITY PLASMID AMPLI?CATION OTHER GENES THAT CAN BE CARRIED BY PLASMIDS PLASMIDS CAN BE CIRCULAR OR LINEAR DNA BROAD HOST RANGE PLASMIDS MOVING PLASMIDS FROM CELL TO CELL CHAPTER 10 CONJUGATION THE F FACTOR THE R FACTORS THE CONJUGATION MACHINERY TRANSFER OF THE DNA SURFACE EXCLUSION F, HFR, OR F-PRIME FORMATION OF THE HFR TRANSFER OF DNA FROM AN HFR TO ANOTHER CELL FORMATION OF F-PRIMES TRANSFER OF F-PRIMES FROM ONE CELL TO ANOTHER GENETIC USES OF F-PRIMES GENETIC USES OF HFR STRAINS —MAPPING GENES ON THE E COLI CHROMOSOME USING HFR CROSSES THE 50% RULE USING SEVERAL HFR STRAINS TO COVER THE CHROMOSOME MOBILIZATION OF NON-CONJUGATIBLE PLASMIDS BY R AND F CONJUGATION FROM PROKARYOTES TO EUKARYOTES FULL CONTENTS CHAPTER 11 TRANSFORMATION NATURAL COMPETENCY THE PROCESS OF NATURAL TRANSFORMATION THE MACHINERY OF NATURALLY TRANSFORMABLE CELLS ARTI?CIAL TRANSFORMATION TRANSFORMATION AS A GENETIC TOOL: GENE MAPPING TRANSFORMATION AS A MOLECULAR TOOL CHAPTER 12 GENE EXPRESSION AND REGULATION THE PLAYERS IN THE REGULATION GAME OPERONS AND REGULONS REPRESSION OF THE LAC OPERON ACTIVATION OF THE LAC OPERON BY CYCLIC AMP AND THE CAP PROTEIN REGULATION OF THE TRYPTOPHAN BIOSYNTHESIS OPERON BY ATTENUATION REGULATION OF THE HEAT-SHOCK REGULON BY AN ALTERNATE SIGMA FACTOR, MRNA STABILITY, AND PROTEOLYSIS REGULATION OF THE SOS REGULON BY PROTEOLYTIC CLEAVAGE OF THE REPRESSOR TWO-COMPONENT REGULATORY SYSTEMS: SIGNAL TRANSDUCTION AND THE CPS REGULON CHAPTER 13 PLASMIDS, BACTERIOPHAGE, AND TRANSPOSONS AS TOOLS WHAT IS A CLONING VECTOR? WHY NOT USE NATURALLY OCCURRING PLASMIDS AS VECTORS? THE IMPORTANCE OF COPY NUMBER MULTIPLE CLONING SITES DETERMINING WHICH PLASMIDS CONTAIN AN INSERT EXPRESSION VECTORS VECTORS FOR PURIFYING THE CLONED GENE PRODUCT VECTORS FOR LOCALIZING THE GENE PRODUCT VECTORS FOR STUDYING GENE EXPRESSION SHUTTLE VECTORS ARTI?CIAL CHROMOSOMES CONSTRUCTING PHAGE VECTORS SUICIDE VECTORS PHAGE DISPLAY VECTORS COMBINING PHAGE VECTORS AND TRANSPOSONS CHAPTER 14 DNA CLONING ISOLATING DNA FROM CELLS PLASMID DNA ISOLATION CHROMOSOMAL DNA ISOLATION CUTTING DNA MOLECULES TYPE I RESTRICTION–MODI?CATION SYSTEMS TYPE II RESTRICTION–MODI?CATION SYSTEMS TYPE III RESTRICTION–MODI?CATION SYSTEMS FULL CONTENTS RESTRICTION–MODI?CATION AS A MOLECULAR TOOL GENERATE DOUBLE-STRANDED BREAKS IN DNA BY SHEARING THE DNA JOINING DNA MOLECULES MANIPULATING THE ENDS OF MOLECULES VISUALIZING THE CLONING PROCESS CONSTRUCTING LIBRARIES OF CLONES DNA DETECTION —SOUTHERN BLOTTING DNA AMPLI?CATION —POLYMERASE CHAIN REACTION ADDING NOVEL DNA SEQUENCES TO THE ENDS OF A PCR AMPLI?ED SEQUENCE SITE-DIRECTED MUTAGENESIS USING PCR CLONING AND EXPRESSING A GENE DNA SEQUENCING USING DIDEOXY SEQUENCING DNA SEQUENCE SEARCHES CHAPTER 15 BIOINFORMATICS AND PROTEOMICS BIOINFORMATICS STRATEGIES FOR SEQUENCING GENOMES BACTERIAL GENOMES ANALYZING GENOMES THE E COLI K12 GENOME PROTEOMICS TECHNIQUES FOR EXAMINING THE PROTEOME —SDS-PAGE AND 2-D PAGE TECHNIQUES FOR EXAMINING THE PROTEOME —MICROARRAY TECHNOLOGY FULL CONTENTS CHAPTER ELEMENTS, IONS, AND TRACE MINERALS THAT MAKE UP LIVING SYSTEMS ELEMENTS IONS TRACE MINERALS OXYGEN SODIUM MANGANESE CARBON POTASSIUM IRON NITROGEN MAGNESIUM COBALT HYDROGEN CALCIUM COPPER PHOSPHORUS CHLORIDE ZINC SULFUR ALUMINUM IODINE NICKEL CHROMIUM SELENIUM BORON VANADIUM MOLYBDENUM SILICON TIN FLUORINE MACROMOLECULES AND TO PRODUCE ENERGY FOR THIS SYNTHESIS DNA IS ALSO USED TO TRANS- MIT INFORMATION FROM ONE GENERATION TO THE NEXT RNA HAS A VERY SIMILAR COMPOSITION TO DNA THE TWO MAJOR DIFFERENCES BETWEEN DNA AND RNA ARE IN THE SUGAR USED IN THE SUGAR–PHOSPHATE BACKBONE (RIBOSE FOR RNA AND DEOXYRIBOSE FOR DNA) AND IN ONE OF THE BASES (URACIL FOR RNA AND THYMINE FOR DNA) IN ESCHERICHIA COLI, DNA EXISTS AS A DOUBLE-STRANDED MOLECULE CHAPTER 2 DESCRIBES IN DETAIL BOTH THE STRUCTURE AND REPLICATION OF DNA THE RNA IN THE CELL HAS AT LEAST FOUR DIFFERENT FUNCTIONS 1 MESSENGER RNA (MRNA) IS USED TO DIRECT THE SYNTHESIS OF SPECI?C PROTEINS 2 TRANSFER RNA (TRNA) IS USED AS AN ADAPTER MOLECULE BETWEEN THE MRNA AND THE AMINO ACIDS IN THE PROCESS OF MAKING THE PROTEINS 3 RIBOSOMAL RNA (RRNA) IS A STRUCTURAL COMPONENT OF A LARGE COMPLEX OF PROTEINS AND RNA KNOWN AS THE RIBOSOME THE RIBOSOME IS RESPONSIBLE FOR BINDING TO THE MRNA AND DIRECTING THE SYNTHESIS OF PROTEINS 4 THE FOURTH CLASS OF RNA IS A CATCH-ALL CLASS THERE ARE SMALL, STABLE RNAS WHOSE FUNCTIONS REMAIN A MYSTERY SOME SMALL, STABLE RNAS HAVE BEEN SHOWN TO BE IN- VOLVED IN REGULATING EXPRESSION OF SPECI?C REGIONS OF THE DNA OTHER SMALL, STABLE RNAS HAVE BEEN SHOWN TO BE PART OF LARGE COMPLEXES THAT PLAY A SPECI?C ROLE IN THE CELL IN GENERAL, RNA IS USED TO CONVEY INFORMATION FROM THE DNA INTO PROTEINS PROTEINS ARE COMPOSED OF AMINO ACIDS MOST PROTEINS ARE MADE FROM A UNIQUE COMBINATION OF 20 DIFFERENT AMINO ACIDS (FIG 1 2) THE ORDER IN WHICH AMINO ACIDS APPEAR IN A PROTEIN ARE SPECI?ED BY THE MRNA USED TO DIRECT SYNTHESIS OF THE PROTEIN ALL AMINO ACIDS HAVE A COMMON CORE OF REPEATING AMINO–CARBON–CARBOXYL GROUPS, WITH VARYING SIDE CHAINS ON THE CENTRAL CARBON PROTEINS, THEREFORE, HAVE A REPEATING BACKBONE WITH AN AMINO TERMINUS AND CARBOXYL TERMINUS THE AMINO ACIDS CAN BE GROUPED TOGETHER AND DESCRIBED BY PHYSICAL PROPERTIES SUCH AS CHARGE (ACID OR BASIC), SIZE, INTERACTIONS WITH WATER (HYDROPHOBIC —WATER “HATING” OR HYDROPHILIC —WATER “LOVING”), A SPECI?C ELEMENT (SULFUR CONTAINING) OR STRUCTURE THEY CONTAIN (AROMATIC RINGS) THE TYPES OF AMINO ACIDS USED TO MAKE UP A PROTEIN SPECIFY WHAT THE PROTEIN IS CAPABLE OF PROTEINS PERFORM MANY DUTIES IN THE CELL, INCLUDING FUNCTIONING AS STRUC- TURAL AND MOTOR COMPONENTS, ENZYMES, SIGNALING MOLECULES, AND REGULATORY MOLE- CULES SOME PROTEINS PERFORM ONLY ONE FUNCTION WHILE OTHERS ARE MULTIFUNCTIONAL LIPIDS ARE AN UNUSUAL GROUP OF MOLECULES THAT, IN BACTERIA, ARE USED TO MAKE THE MEMBRANES THAT SURROUND A CELL ONE TYPE OF LIPID, KNOWN AS A FATTY ACID, IS COMPOSED CHAPTER ELEMENTS PHOSPHATE PYRIMIDINES PURINES RIBOSE DEOXYRIBOSE AMINO ACIDS FATTY ACIDS GLYCEROL OTHER COMPONENTS SUGARS NUCLEIC ACIDS PROTEINS LIPIDS CARBOHYDRATES OR POLYSACCHARIDES FIG 1 1 THREE LEVELS OF ORGANIZATION DESCRIBE THE COMPOUNDS THAT MAKE UP LIVING ORGANISMS OF LONG CHAINS OF CARBON MOLECULES ATTACHED TO A SMALLER HEAD GROUP (FIG 1 3A) THE SMALL HEAD GROUP IS KNOWN AS THE POLAR HEAD GROUP THE FATTY ACID CHAINS ARE EXTREMELY HYDROPHOBIC AND LINE UP WITH THE LONG CHAINS OF CARBONS NEAR EACH OTHER BECAUSE OF THE PROPERTIES OF THE FATTY ACID CHAINS, MEMBRANES ARE DOUBLE-SIDED (FIG 1 3B) ONE SIDE OF A MEMBRANE IS KNOWN AS A LEA?ET THE POLAR HEAD GROUPS FACE THE OUTSIDE SURFACES OF THE MEMBRANES BECAUSE THE POLAR HEAD GROUPS ARE WATER SOLUBLE OTHER CHEMICAL GROUPS CAN BE ADDED TO THE HEAD GROUPS OF THE LIPIDS BUT, IN GENERAL, INTRODUCTION TO THE CELL ASPARTATE ASP GLUTAMATE GLU NEGATIVELY CHARGED R GROUPS NH FIG 1 2 THE 20 COMMON AMINO ACIDS USED TO MAKE PROTEINS OTHER CHEMICAL GROUPS CANNOT BE ADDED TO THE FATTY ACIDS IF THE FATTY ACIDS CONTAIN ONLY SINGLE BONDS, THEY ARE KNOWN AS SATURATED FATTY ACIDS SATURATED FATTY ACIDS ARE ?EXIBLE AND CAN BE TIGHTLY PACKED IF THE FATTY ACIDS CONTAIN ANY DOUBLE BONDS THEY ARE KNOWN AS UNSATURATED FATTY ACIDS (FIG 1 3C) UNSATURATED FATTY ACIDS HAVE A KINK IN THEM AND CANNOT BE PACKED AS CLOSELY MEMBRANES USUALLY CONTAIN A MIXTURE OF FATTY ACIDS TO MAINTAIN THE RIGHT PACKING DENSITY AND ?UIDITY CARBOHYDRATES ARE COMPOSED OF SIMPLE SUGARS (FIG 1 4) THEY CAN BE USED AS: 1 AN IMMEDIATE SOURCE OF ENERGY; 2 A STORED SOURCE OF ENERGY; 3 STRUCTURAL COMPONENTS OF THE CELL IN BACTERIA, CARBOHYDRATES THAT ARE USED AS IMMEDIATE SOURCES OF ENERGY ARE THE SIMPLE CARBOHY- DRATES SUCH AS GLUCOSE, LACTOSE, AND GALACTOSE FREQUENTLY, THE CARBOHYDRATES THAT A BACTERIUM UTILIZES AS ENERGY SOURCES CAN BE USED TO DISTINGUISH ONE SPECIES OF BACTERIA FROM ANOTHER ENERGY IS USUALLY STORED IN A CARBOHY- DRATE THAT IS A LONG POLYMER OF GLUCOSE KNOWN AS GLYCOGEN STRUCTURALLY, CARBOHYDRATES ARE USED TO MAKE A PROTECTIVE COVERING FOR THE OUTSIDE OF THE THE COMPOSITION OF AN AVERAGE E COLI CELL COMPONENT NO OF DIFFERENT SPECIES % OF CELL WATER NUCLEIC ACIDS DNA LIPIDS LIPOPOLYSACCHARIDE PEPTIDOGLYCAN GLYCOGEN POLYAMINES