Viral

1
Viral Prokaryotic Genetics

• Simple Model Systems

2
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

3
Experimental Model Systems for Genetics

• characteristics of good model systems
• short generation time
• E. coli18-20 minutes
• O/N 45 generations 1 gt 1.76 x 1013
• l bacteriophage 20 minutes
• haploid genome
• genotype gt phenotype

4
viruses are smallTable 13.1
5
Viruses

• small
• resistant to inactivation by
• alcohol
• dehydration
• infectivity may decrease cant increase
• reproduction obligate intracellular parasites
• uses host nucleotides, amino acids, enzymes
• hosts
• animals, plants, fungi, protists, prokaryotes

6
Viruses

• virus structure
• virion virus particle
• central core genome DNA or RNA
• capsid protein coat determines shape
• lipid/protein membrane on some animal viruses

7
Viruses

• virus classification
• host kingdom
• genome type (DNA or RNA)
• strandedness (single or double)
• virion shape
• capsid symmetry
• capsid size
• /- membrane

8
Viruses

• bacteriophage (bacteria eater)
• reproduction
• lytic cycle virulent phages
• infection, growth, lysis
• lysogenic cycle temperate phages
• infection, incorporation, maintenance

9
bacteriophage l life cyclesFigure 13.2
10
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

11
bacteriophage lytic life cycleFigure 13.3
12
mammalian influenza virusFigure 13.4
13
HIV retrovirus structureFigure 13.5
14
Laboratory Propagation of BacteriaFigure 13.6
15
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

16
bacteria exhibit genetic recombinationFigure 13.7
minimal
complete
minimal Met, Biotin
minimal Met, Biotin, Thr, Leu
minimal
minimal
minimal Thr, Leu
17
genetic recombination in bacteriaFigure 13.9
18
transformation scavenging DNAFigure 13.10
19
transduction viral transferFigure 13.10
generalized transduction
specialized transduction
20
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

21
conjugation programmed genetic exchange
programmed by the chromosome or by an F
(fertility) plasmid Figure 13.11
22
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

23
of a geneFigure 13.12
transpositional
inactivation
24
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 gt plasmid gt new cell gt
  chromosome
• may transfer an antibiotic resistance gene from
  one cell to another

25
of a gene
transpositional
inactivation
an additional gene hitchhiking on a
Transposon Figure 13.12
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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

27
alternate regulatory mechanismsFigure 13.14
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Regulation of Gene Expression

• transcriptional regulation of gene expression
• the E. coli lac operon is inducible

29
enzyme induction in bacteria Figure 13.13
30
the lac operon of E. coliFigure 13.16
31
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

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a repressor protein blocks transcription lac
repressor blocks transcription Figures 13.15,
13.17
promoter
gene
33
Regulation of Gene Expression

• regulation of lac operon expression
• lac repressor (lac I gene product) blocks
  transcription
• lac inducer inactivates lac repressor

34
lac inducer inactivates the lac repressorFigure
13.17
35
trp repressor is normally inactive trp operon
is transcribedFigure 13.18
36
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

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trp co-repressor activates trp repressor trp
operon is not transcribedFigure 13.18
38
positive and negative regulation

• both lac and trp operons are negatively regulated
• 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

39
induced lac operon alsorequiresactivation
before genesare transcribed induced lac operon
alsorequiresactivation before genesare
transcribed Figure 13.19
40
positive negative regulation of the lac
operonTable 13.2
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positive and negative regulation in ?
bacteriophage

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

42
lysis vs. lysogenyFigure 13.20
in a healthy, well-nourished culture
in a slow-growing nutrient-poor culture
43
map of the entire Haemophilus influenzae
chromosomeFigure 13.21
44
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

45
How many genes does it take?Figure 13.22