Module 8: Genome Changes

• what are the 3 ways a genome changes?

  1. errors during DNA replication
  2. spontaneous chemical changes in bases
  3. DNA damage (mutagens)
• when does a daughter cell that inherits mutations become a mutant?

  during DNA replication
• fill in the types of DNA repair

  A) photoreactivation

  B) base excision

  C) methyl mismatch

  D) recombination

  E) SOS

  
• what type of damage does photoreactivation repair?

  UV damage, forms dimers
• photoreactivation: photolyase protein binds and uses light energy to remove mutation
• what type of damage does base excision repair?

  incorrect base, prevents base pairing
• base excision repair:

  1. remove incorrect base and sugar phosphate backbone
  2. DNA polymerase builds correct base
• what type of damage does methyl mismatch repair?

  switched bases (most errors)
• what are the 3 methyl mismatch repair proteins and their purpose?

  1. MutS recognizes mismatch
  2. MutH recognizes methylated parent strand and degrades nonparent strand
  3. DNA polymerase 3 fills in gap
• what type of damage does recombination repair?

  large base errors
• what is the recombination repair mechanism?

  1. copy complementary region and regress replication fork
  2. remove damage and replace with copied strand
• what type of damage does SOS repair?

  severe damage and missing strand
• how does SOS repair function?

  1. stalls DNA polymerase and binds RecA
  2. forms umuCD complex to add random bases, error prone
• how is horizontal gene transfer different than vertical transfer?

  between individuals, not parent to offspring
• what are the 3 methods of horizontal gene transfer?

  1. conjugation: move DNA between 2 living cells
  2. transduction: virus moves DNA
  3. transformation: take up free DNA
• how is linear DNA incorporated in horizontal gene transfer?

  recombination repair mechanism lines up donor DNA and incorporates into genome
• what is the mechanism of transformation?

  1. free dsDNA in environment is taken up and processes to ssDNA
  2. rec-A mediated homologous recombination incorporates ssDNA into genome
• what are the mechanisms of transduction?

  1. transducing particle contains host DNA instead of viral genome and infects recipient cell
  2. homologous recombination of host DNA w/ recipient cell DNA
• what are the mechanisms of conjugation?

  1. pilus connects F+ cell (donor) and F- cell (recipient)
  2. simultaneous transfer of single strand from donor cell and replication in recipient
• integrated plasmids in conjugation can facilitate chromosome transfer
• what is the size of F-factor plasmid?

  99 kb, 1-2 copies per cell
• components of F-factor plasmid:

  • oriV
  • oriT
  • tra region
  • transposons and insertion elements
  • toxin-antitoxin system
• oriV: origin if replication where host replication machinery binds
• oriT: start site for transfer of single strand
• tra region: encodes transfer functions, proteins in conjugation
• core genome: common to all members of a species
• pan genome: found in some members of species
• how do you differentiate microbes with dynamic genomes?

  each has a signature: G and C ratio, preferred codons