Viral & Prokaryotic Genetics “Simple” Model Systems.

Viral & Prokaryotic Genetics

“Simple” Model Systems

Experimental Model Systems for Genetics characteristics of good model

systemssmall genome size

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

bacteriophage: ~45,000 bplarge population size

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

bacteriophage: ~100 billion (1011) per liter

Experimental Model Systems for Genetics characteristics of good model

systemsshort generation time

E. coli:18-20 minutesO/N: 45 generations [1 => 1.76 x 1013]

bacteriophage: ~20 minutes

haploid genomegenotype => phenotype

viruses are smallTable 13.1

Viruses small resistant to inactivation by

alcoholdehydration

infectivity may decrease; can’t increase reproduction: obligate intracellular parasitesuses host nucleotides, amino acids, enzymes

hostsanimals, plants, fungi, protists, prokaryotes

Viruses virus structure

virion = virus particlecentral core = genome: DNA or RNA

capsid = protein coat; determines shape

lipid/protein membrane on some animal viruses

Viruses virus classification

host kingdomgenome type (DNA or RNA)strandedness (single or double)

virion shapecapsid symmetrycapsid size+/- membrane

Viruses bacteriophage (“bacteria eater”)reproduction

lytic cycle: virulent phagesinfection, growth, lysis

lysogenic cycle: temperate phagesinfection, incorporation, maintenance

bacteriophage life cyclesFigure 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 cycleFigure 13.3

mammalian influenza

virusFigure 13.4

HIV retrovirus structureFigure 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 recombinationFigure 13.7

minimal

minimal

minimal

complete

minimal + Met, Biotin, Thr, Leu

minimal + Met, Biotin

minimal + Thr, Leu

genetic recombination in bacteria

Figure 13.9

transformation: scavenging DNA

Figure 13.10

transduction: viral transferFigure 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) plasmidFigure 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

of a geneFigure 13.12

transpositionalinactivation

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

transpositionalinactivation

an additional gene hitchhiking on a TransposonFigure 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. coliFigure 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 repressorFigure 13.17

trp repressor is normally inactive;

trp operon is transcribedFigure 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

transcribedFigure 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 alsorequires

activation before genesare transcribed

induced lac operon alsorequires

activation before genesare transcribed

Figure 13.19

positive & negative regulation of the lac operon

Table 13.2

positive and negative regulation

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

in a healthy, well-nourishedculture

in a slow-growingnutrient-poorculture

lysis vs. lysogeny

Figure 13.20

map of the

entire Haemophil

us influenza

e chromosom

eFigure 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