Spontaneous mutations:DNA replication (base tautomerization and isertions or deletions)
- Tautomerization-bases are changed by gaining additional hydrogens, they change to a different base.
- Insertions-slippage on the synthesized strand
- Deletion-slippage on the template strand.
Spontaneous mutations: Depurination and Depyrimidization
- Depurination- apurinic sites are formed
- Depyrimidization- apyrimidic sites are formed
- This happens through cleavage of the base
Induced Mutations:Base Analogs
A chemical mutagen- changes the base to another type of base that doesn't pair normally
Induced Mutations:DNA-modifying agents
Chemical mutagen-alters bases in the DNA causing them to mispair
Induced Mutations:Itercalating agents
Chemical mutagen- distorts DNA to induce single nucleotide insertions and deletions.
Induced Mutations:UV light
Physical mutagen-results in thymine dimers.
Characterize the following mutations: Forward
- Forward-wild type > mutant
- Reverse- mutant > wild type
- Suppressor- reversion involving second mutation at a different site than O.G. mutation.
Describe the following types of point mutations, along with what they change:
- Silent- Codon for A.A. > Different codon for same A.A.
- Missense: Codon for A.A. > Codon for different A.A.
- Nonsense- Sense codon > Stop codon
- Frameshift- Insertion or deletion of 1 or more BPs
Explain what a conditional mutation is:
A mutation expressed only under certain environmental conditions.
Distinguish between a prototrph and auxotrophic mutant
- Auxotrophic mutant-One that is unable to make an essential molecule.
- Arises from a mutation in a prototroph
- Has a conditional phenotype
Describe the effects of the following non-coding sequence mutations: Operator, promoter, tRNA and rRNA
- Operator-Repressor doesn't bind
- Promoter- RNA poly doesn't bind
- tRNA and rRNA-disrupts translation
Describe how the following methods detect or select for mutations: Replica Plating
Used for screening and detection of auxotrophs. Get a replica block and grow it on a bunch of different mediums.
Describe how the following methods detect or select for mutations: Ames Test
- Grow bacteria with mutagen, w/out mutagen, and w/ mutagen in liver extract. See what happens!
- Uses His residue
- Uses Auxotrophic Salmonella
Discuss the following DNA repair mechanisms: Excision repair: Nucleotide and base
- Nucleotide-UvrABC repair enzyme comes in and removes damaged nucleotides. It is filled by DNA poly I and sealed w/ Ligase
- Base-Uses DNA glyosylases ro remove unnatural bases. AP endonucleases recognize damaged DNA and nick the backbone at damage. DNA poly removes, and then fills in gap. Ligase seals.
Discuss the following DNA repair mechanisms: Direct repair photoreactivation and removal of alkyl groups
- Photoreactivation-uses light to split apart thymine dimers.Photolyase
- Alkyl groups- removed by Alkyltransferase or Methylgaunine Methyltransferase
Discuss the following DNA repair mechanisms: Mismatch repair
Mismatch correction enzyme scans new strands of DNA, removes them and replaced by DNA poly I and sealed by ligase. Old DNA is methylated, new isn't.
Discuss the following DNA repair mechanisms:Recombinational repair
- Repairs both DNA strands.
- Involves recombination with an undamaged molecule
- RecA catalyzes recombination.
- Grabs DNA from sister DNA.
Discuss the following DNA repair mechanisms:SOS response
- Used to repair excessive damage that halts replication
- RecA protein initiates recombination repair
- RecA acts as protease, destroying repressor protein (increasing production of excision repair enzymes)
- Life or death situation
Distinguish between vertical gene transfer vs horizontal gene transfer
- Vertical- Parents to progeny, in eukary this introduces genetic variation. Prokary do no do this.
- Horizontal- genes from independent mature organisms are transferred to one another. Creates a stable recombinant having both donor and recipient.
During HGT, it is the Donor DNA
During HGT it is the DNA in the recipient
During HGT it is a partially diploid cell. Caused by exogenote genes being the same as those present in the recipient.
Identify the 4 outcomes of HGT
- Population of stable recombinant
- 1-Integration of exogenote
- 2-Exogenote self replicates (plasmid)
- No stable recombinant
- 3-Exogenote cannot self replicate
- 4-Host restriction (host cuts it up)
Briefly characterize the following recombination mechanism: Homologous recombination
A reciprocal change between a pair of DNA molecules with same nucleotide sequence.
Briefly characterize the following recombination mechanism:site specific recombination
Viral genomes integrated into hosts