Viral prokaryotic genetics
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Viral & Prokaryotic Genetics. “Simple” Model Systems. Experimental Model Systems for Genetics. characteristics of good model systems small genome size E. coli : ~4 million base pairs (bp) l bacteriophage: ~45,000 bp large population size E. coli : ~one billion (10 9 ) per liter

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Viral prokaryotic genetics

Viral & Prokaryotic Genetics

“Simple” Model Systems


Experimental model systems for genetics
Experimental Model Systems for Genetics

  • characteristics of good model systems

    • small genome size

      • E. coli: ~4 million base pairs (bp)

      • l bacteriophage: ~45,000 bp

    • large population size

      • E. coli: ~one billion (109) per liter

      • l bacteriophage: ~100 billion (1011) per liter


Experimental model systems for genetics1
Experimental Model Systems for Genetics

  • characteristics of good model systems

    • short generation time

      • E. coli:18-20 minutes

        • O/N: 45 generations [1 => 1.76 x 1013]

      • l bacteriophage: ~20 minutes

    • haploid genome

      • genotype => phenotype



Viruses
Viruses

  • small

  • resistant to inactivation by

    • alcohol

    • dehydration

  • infectivity may decrease; can’t increase

  • reproduction: obligate intracellular parasites

    • uses host nucleotides, amino acids, enzymes

  • hosts

    • animals, plants, fungi, protists, prokaryotes


Viruses1
Viruses

  • virus structure

    • virion = virus particle

      • central core = genome: DNA or RNA

      • capsid = protein coat; determines shape

      • lipid/protein membrane on some animal viruses


Viruses2
Viruses

  • virus classification

    • host kingdom

    • genome type (DNA or RNA)

    • strandedness (single or double)

    • virion shape

    • capsid symmetry

    • capsid size

    • +/- membrane


Viruses3
Viruses

  • bacteriophage (“bacteria eater”)

    • reproduction

      • lytic cycle: virulent phages

        • infection, growth, lysis

      • lysogenic cycle: temperate phages

        • infection, incorporation, maintenance


Bacteriophage l life cycles figure 13 2
bacteriophage l life cyclesFigure 13.2


Viruses4
Viruses

  • expression of bacteriophage genes during lytic infection

    • early genes - immediate

    • middle genes

      • depends on early genes

      • replicates viral DNA

    • late genes

      • packages DNA

      • prepares for lysis



Mammalian influenza virus figure 13 4
mammalian influenza virusFigure 13.4




Prokaryotes
Prokaryotes

  • bacteria reproduce by binary fission

    • reproduction produces clones of identical cells

    • research requires growth of pure cultures

  • auxotrophic bacteria with different requirements can undergo recombination


Bacteria exhibit genetic recombination figure 13 7
bacteria exhibit genetic recombinationFigure 13.7

minimal

minimal + Met, Biotin

complete

minimal + Met, Biotin, Thr, Leu

minimal

minimal

minimal + Thr, Leu



Transformation scavenging dna figure 13 10
transformation: scavenging DNAFigure 13.10


Transduction viral transfer figure 13 10
transduction: viral transferFigure 13.10

generalized transduction

specialized transduction


Prokaryotes1
Prokaryotes

  • recombination exchanges new DNA with existing DNA

    • three mechanisms can provide new DNA

      • transformation - takes up DNA from the environment

      • transduction - viral transfer from one cell to another

      • conjugation - genetically programmed transfer from donor cell to recipient cell


Conjugation programmed genetic exchange
conjugation: programmed genetic exchange

programmed by the chromosome

or by an

F (fertility) plasmid

Figure 13.11


Prokaryotes2
Prokaryotes

  • Plasmids provide additional genes

    • small circular DNAs with their own ORIs

    • most carry a few genes that aid their hosts

      • metabolic factors carry genes for unusual biochemical functions

      • F factors carry genes for conjugation

      • Resistance (R) factors carry genes that inactivate antibiotics and genes for their own transfer


Of a gene figure 13 12
of a geneFigure 13.12

transpositional

inactivation


Transposable elements
Transposable Elements

  • mobile genetic elements

    • move from one location to another on a DNA molecule

    • may move into a gene - inactivating it

    • may move chromosome => plasmid => new cell => chromosome

    • may transfer an antibiotic resistance gene from one cell to another


Of a gene
of a gene

transpositional

inactivation

an additional gene

hitchhiking

on a

Transposon

Figure 13.12


Regulation of gene expression
Regulation of Gene Expression

  • transcriptional regulation of gene expression

    • saves energy

      • constitutive genes are always expressed

      • regulated genes are expressed only when they are needed



Regulation of gene expression1
Regulation of Gene Expression

  • transcriptional regulation of gene expression

    • the E. colilac operon is inducible


Enzyme induction in bacteria figure 13 13
enzyme induction in bacteria Figure 13.13


The lac operon of e coli figure 13 16
the lac operon of E. coliFigure 13.16


Regulation of gene expression2
Regulation of Gene Expression

  • regulation of lac operon expression

    • the lac operon encodes catabolic enzymes

      • the substrate (lactose) comes and goes

      • the cell does not need a catabolic pathway if there is no substrate

    • the lac operon is inducible

      • expressed only when lactose is present

      • allolactose is the inducer


A repressor protein blocks transcription lac repressor blocks transcription figures 13 15 13 17
a repressor protein blocks transcriptionlac repressor blocks transcription Figures 13.15, 13.17

promoter

gene


Regulation of gene expression3
Regulation of Gene Expression

  • regulation of lac operon expression

    • lac repressor (lac I gene product) blocks transcription

    • lac inducer inactivates lac repressor


Lac inducer inactivates the lac repressor figure 13 17
lac inducer inactivates the lac repressorFigure 13.17


Trp repressor is normally inactive trp operon is transcribed figure 13 18
trp repressor is normally inactive; trp operon is transcribedFigure 13.18


Regulation of gene expression4
Regulation of Gene Expression

  • regulation of trp operon expression

    • the trp operon encodes anabolic enzymes

      • the product is normally needed

      • the cell needs an anabolic pathway except when the amount of product is adequate

    • the trp operon is repressible

      • trp repressor is normally inactive

      • trp co-repressor activates trp repressor when the amount of tryptophan is adequate


Trp co repressor activates trp repressor trp operon is not transcribed figure 13 18
trp co-repressor activates trp repressor; trp operon is not transcribedFigure 13.18


Positive and negative regulation
positive and negative regulation

  • both lac and trp operons are negativelyregulated

    • each is regulated by a repressor

  • lac operon is also positively regulated

    • after lac repressor is inactivated by the inducer, transcription must be stimulated by a positive regulator


inducedlac operon alsorequiresactivation before genesare transcribedinducedlac operon alsorequiresactivation before genesare transcribed Figure 13.19


Positive negative regulation of the lac operon table 13 2
positive & negative regulation ofthe lac operonTable 13.2


Positive and negative regulation in bacteriophage
positive and negative regulation in  bacteriophage

  • the “decision” between lysis & lysogeny depends on a competition between two repressors


Lysis vs lysogeny figure 13 20
lysis vs. lysogenyFigure 13.20

in a healthy,

well-nourished

culture

in a

slow-growing

nutrient-poor

culture


Map of the entire haemophilus influenzae chromosome figure 13 21
map of the entire Haemophilus influenzae chromosomeFigure 13.21


New tools for discovery
new tools for discovery

  • genome sequencing reveals previously unknown details about prokaryotic metabolism

  • functional genomics identifies the genes without a known function

  • comparative genomics reveals new information by finding similarities and differences among sequenced genomes



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