• single, double stranded, ciruclar molecule
• haploid (one copy)
• variable and conserved regions

• replicate separately from chromosome
• small, closed, circular extrachromosomal DNA molecule
• each cell often has multiple copies

• promotor- RNA Pol. binds
• operator- repressor binding site
• coding region- structural genes
• terminator signals (strong and weak)

• no introns
• some overlap
• genes on both strands

• contains origin of replication, so
  • DNA sequence can replicate autonomously
• includes:
  • chromosomes
  • plasmids
  • bacteriophages

• no origin of replication
  • so cant replicate autonomously
• only replicates when recombined into replicon

• insertion sequences
• composite
• TnA type

1. helicase unwind DNA
2. DNA primase synthesizes short sequnce specific RNA primer
3. DNA Pol. III extends primers in 5-3 direction according to template
4. leading strand syn. continuously
5. lagging strand syn. discontinuously (Okazaki fragments)
6. DNA Pol. I excises RNA primers and fills in gaps

• physical- UV light
• chemical
  • covalent modifiers chemically alter bases
  • intercalators cause misreading

• transition (purine to purine or pyrimidine to pyrimidine)
• transversion (purine to pyrimidine)
• insertion (extra DNA)
• deletion (DNA removed)

• silent- no change in AA sequence
• missense- mutation results in change in AA sequence that may change function of protein
• nonsense- mutation causes change to stop codon that truncates protein (disrupt function)
• frameshift- change in reading frame caused by insertions, deletions
  • unless multiples of three, usually inserts stop codon
• null mutation- any mutation that destroys function of protein
• reversion- restores original sequence
• suppressor- second mutation restores original function

• proofreading (DNA Pol. remove errors during replication)
• direct DNA repair (enzyme repair of damaged base such as photlyase repair UV damage)
• exciesion repair (damaged DNA removed and repaired)
• recombinational repair
• SOS repair (global response to severe damage)
• error prone repair (last resort with no template available)

• mediated by recA protein
• cuts piece of DNA from sister chromosome to replaced damage section

• use recombination to replace large stretches of damaged DNA or many lesions

• homologous- foreign gene inserts at area of similar sequence
• heterologous- foreign gene inserts anywhere in genome

• site specific
• generalized
• transpositional

• mediated by RecA protein
• donor DNA contains sequence with homology to a section of recipient DNA

• introduction of DNA segment to specific site in replicon

• small mobile DNA elements move from site to site within or between replicons
• if inserted within gene, causes inactivation

• cannot replicate
• often encode virulence factors or antibiotic resistance
• small mobile DNA elements

• mainly in gram neg enteric bacteria
• def.- exchange of DNA from one bacterium to another through a conjugal bridge (sex pilus)

plasmid DNA

chromosomal genes

• one way transfer of F+ plasmid to recipient (F-)
  • F encodes sex pillus (traA) and has 60 genes
  • contains origin of replication (oriV)
• takes 10 minutes

DONOR will retain F+ (you get two F+ cells)

• donor is Hfr (high frequency recomb)
  • F plasmid integrated into crhom,.
• transfer requires 100 minutes
• recipient remains non-fertile
• some DNA makes it into recipient
  • if sufficiently homologous to recipient chromosome, it may be incorperated by recombination
  • if not incorporated, DNA will be lost (NOT A REPLICON)

• involves third mating type (F' cell)
  • F' has plasmid excised from Hfr chrom. that contains F plasmid plus extra genes adjacent to it in chromosome
• F' transfer both F plasmid and piece of chrom.

Both recipients become fertile and stably diploid for some chromosomal genes

• transfer resistance factors
• transfer virulence factors (toxin genes)
• molecular biol. (gene mapping)

• def.- uptake of naked DNA
• mainly happens in gram pos. bacteria
• ability of tranformation depends on presence of DNA binding protein (competence factor) on cell surface

doesnt occur naturally in gram negative (genetically engineered occurence)

• bacteriophage mediated DNA tranfer

• lytic phages- new viruses produced within the infected bacterium (virus usually burst the infected host to be relased)
• temperate phages- inserts its DNA into host bacterial chromsome (may or may not burst cell)

Describe lytic cycle

1. viral particles bind to host cell wall and injects DNA
2. viral DNA directs host machinery to produce viral proteins and viral DNA
3. viral proteins are assembled into coats and DNA is packaged
4. tail fibers and other components added to particles, so new particles are complete
5. host lyses, releasing infectious particles

1. viral particles bind to host cell wall and injects DNA
2. viral DNA integrats into bacterial chromosome
3. before binary fision, bacterial chromosome (with viral DNA) is replicated
4. following binary fision, each new cell has the viral DNA with bacterial chromosome

• dissemination of R factors
• phage conversion
  • allows production of toxins (ex: diptheria)
• molecular biology (maping bacterial genes)

• group of genes under control of a single promotoer and transcribed together
• results in long polycistronic message
• ex: enzymes in metabolic pathway often in operon group

• ex: lac operon
• inducible
• usually involves catabolic enzymes

When there is no lactose around, repressor binds to operator and prevents transcription. In presence of lactose, allolactose formed and binds to repressor. Repressor now cant bind to operator and transcription occurs.

• usually anabolic
• repressible
• ex: Trp operon (for Trp syn.)
• Repressor encoded not part of trp operon

At high Trp, Trp binds to repressor and activates it. Repressor bind to operator region, so no transcription. At low Trp, repressor is not active. This allows RNA Pol. to bind so transcription occurs.

• structural differences
• presence of modifying enzymes
• target absent

• mutation in target gene (struc, reg)
• acquire DNA encoding resistance genes

• alteration of ribosomal binding site
• mutation in gyrA preventing binding of DNA gyrase
• mutations in regulatory genes resulting in hyperproduction of enzymes that breakdown antibiotics

• encode a single gene (transposase)
• small
• contants terminal inverted nucleotide repeats

• encodes several genes
• insertion sequence on each end
• often encode virulence or resistance genes

• no insertion sequences
• terminal inverted repeats
• contain transposase, resolvase, other genes (ex: resistance genes)

• process
  • when they excise, it often takes a piece of DNA with them
  • phage head is packaged, both with phage and bacterial DNA
  • phage genome is often incomplete, soL
    • can infect another cell
    • no new phage produced
    • bacterial DNA may recombine with new chromosome

• chop up chromosome during infection
  • sometimes a piece of bacterial DNA co-packaged with phage DNA
  • when next cell is infected, DNA may recombine

1. inject phage genome
2. phage genome incorperates into bacterial chromosome
3. part of bacterial chromosome excised with phage
4. phage goes to new cell and injects its DNA with part of bacterial chromosomes
5. phage DNA incorperate into new host along with the DNA it took from old host bacterial chromosome