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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 (109) per liter
l bacteriophage: ~100 billion (1011) per
liter
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 are small
Table 13.1
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
Viruses
 virus structure
 virion = virus particle
central core = genome: DNA or RNA
capsid = protein coat; determines shape
lipid/protein membrane on some animal
viruses
Viruses
 virus classification
 host kingdom
 genome type (DNA or RNA)
 strandedness (single or double)
 virion shape
 capsid symmetry
 capsid size
 +/- membrane
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
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
bacteriophage lytic life cycle
Figure 13.3
mammalian
influenza virus
Figure 13.4
HIV retrovirus structure
Figure 13.5
Laboratory Propagation of Bacteria
Figure 13.6
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
minimal
minimal + Met, Biotin
minimal + Thr, Leu
complete
minimal
minimal +
Met, Biotin,
Thr, Leu
minimal
genetic recombination in bacteria
Figure 13.9
transformation: scavenging DNA
Figure 13.10
transduction: viral transfer
Figure 13.10
generalized transduction
specialized transduction
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
programmed by
the
chromosome
or by an
F (fertility)
plasmid
Figure 13.11
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
transpositional
inactivation
of a gene
Figure 13.12
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
transpositional
inactivation
of a gene
an additional gene
hitchhiking
on a
Transposon
Figure 13.12
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
alternate regulatory mechanisms
Figure 13.14
Regulation of Gene Expression
• transcriptional regulation of gene expression
– the E. coli lac operon is inducible
enzyme
induction in bacteria Figure 13.13
the lac operon of E. coli
Figure 13.16
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
promoter
gene
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
trp repressor is
normally inactive;
trp operon is
transcribed
Figure 13.18
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
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
induced lac operon also
requires
activation before genes
are transcribed
induced lac operon also
requires
activation before genes
are transcribed
Figure 13.19
positive & negative regulation of the lac operon
Table 13.2
positive and negative regulation
in l bacteriophage
• the “decision” between lysis & lysogeny
depends on a competition between two
repressors
lysis vs. lysogeny
Figure 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
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
How many genes
does it take…?
Figure 13.22