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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
  • 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
  • virus structure
    • virion = virus particle
      • central core = genome: DNA or RNA
      • capsid = protein coat; determines shape
      • lipid/protein membrane on some animal viruses
  • virus classification
    • host kingdom
    • genome type (DNA or RNA)
    • strandedness (single or double)
    • virion shape
    • capsid symmetry
    • capsid size
    • +/- membrane
  • bacteriophage (“bacteria eater”)
    • reproduction
      • lytic cycle: virulent phages
        • infection, growth, lysis
      • lysogenic cycle: temperate phages
        • infection, incorporation, maintenance
  • 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
  • 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 + Met, Biotin


minimal + Met, Biotin, Thr, Leu



minimal + Thr, Leu

transduction viral transfer figure 13 10
transduction: viral transferFigure 13.10

generalized transduction

specialized transduction

  • 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

  • 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



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



an additional gene


on a


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
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



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
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
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 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,



in a




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