Fundamental Bacterial Genetics

ISBN-10: 0632044489

ISBN-13: 9780632044481

Edition: 2003

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A concise introduction to microbial genetics. The text focuses on one bacterial species, Escherichia coli, but draws examples from other microbial systems at appropriate points to support the fundamental concepts of molecular genetics.
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Book details

List price: $116.95
Copyright year: 2003
Publisher: John Wiley & Sons, Incorporated
Publication date: 10/10/2003
Binding: Paperback
Pages: 304
Size: 8.50" wide x 10.50" long x 1.00" tall
Weight: 2.134
Language: English

Introduction to the cell
The bacterial cell: a quick overview
How do cells grow?
What is genetics?
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 influence 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
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
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 modifiers
Chemicals that bind DNA bases: intercalators
Mutagens that physically damage the DNA: ultraviolet light and ionizing radiation
Mutator strains
Reverting mutations
Ames test
How have we exploited bacterial mutants?
DNA repair
Lesions that constitute DNA damage
Reverse, excise or tolerate?
Mechanisms that reverse DNA damage
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
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 specific for pyrimidine dimers
Mechanisms that tolerate DNA damage
Transdimer synthesis
Post replication/recombinational repair (PRR)
Introduction to the SOS regulon
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-specific recombination
A typical site-specific recombinational event
Bacteriophage [lambda]: a model for site-specific recombination
Other microbial examples of site-specific recombination
Illegitimate recombination
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
The structure of phage
The lifecycle of a bacteriophage
Lytic--lysogenic options
The [lambda] lifecycle
[lambda] adsorption
[lambda] DNA injection
Protecting the [lambda] genome in the bacterial cytoplasm
What happens to the [lambda] genome after it is stabilized?
[lambda] and the lytic--lysogenic decision
The [lambda] lysogenic pathway
The [lambda] lytic pathway
DNA replication during the [lambda] lytic pathway
Making [lambda] phage
Getting out of the cell--the [lambda] S and R proteins
Induction of [lambda] by the SOS system
Restriction and modification of DNA
The lifecycle of M13
M13 adsorption and injection
Protection of the M13 genome
M13 DNA replication
M13 phage production and release from the cell
The lifecycle of P1
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
The lifecycle of T4
T4 adsorption and injection
T4rII mutations and the nature of the genetic code
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
Natural plasmids
Origins of replication
Plasmid copy number
Setting the copy number
Plasmid incompatibility
Plasmid amplification
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
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
Natural competency
The process of natural transformation
The machinery of naturally transformable cells
Artificial transformation
Transformation as a genetic tool: gene mapping
Transformation as a molecular tool
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
Plasmids, bacteriophage, and transposons as tools
What is a cloning vector?
Why not use naturally occurring plasmids as vectors?
The importance of copy number
An example of how a cloning vector works--pBR322
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
Artificial chromosomes
Constructing phage vectors
Suicide vectors
Phage display vectors
Combining phage vectors and transposons
DNA cloning
Isolating DNA from cells
Plasmid DNA isolation
Chromosomal DNA isolation
Cutting DNA molecules
Type I restriction-modification systems
Type II restriction-modification systems
Type III restriction-modification systems
Restriction-modification 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 amplification--polymerase chain reaction
Adding novel DNA sequences to the ends of a PCR amplified sequence
Site-directed mutagenesis using PCR
Cloning and expressing a gene
DNA sequencing using dideoxy sequencing
DNA sequence searches
Bioinformatics and proteomics
Strategies for sequencing genomes
Bacterial genomes
Analyzing genomes
The E. coli K12 genome
Techniques for examining the proteome--SDS-PAGE and 2-D PAGE
Techniques for examining the proteome--microarray technology
Further reading
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