Genome Sequence Variation Flashcards
Substitution
SNPs
Transition (purine –> purine) (pyrimidine–> pyrimidine)
Transversion (purine –> pyrimidine)
Indels
Insertion
Deletions
Inversion
create complement to genome
rotate 180°
Translocation
movement btwn diff chromosomes
Mutation Rate
gene mutation rate > DNA sequence mutation rate
- genes more nucleotides
Tautomeric Shifts
Alternate Base Pairing
- G now binds regular T
- C now binds regular A
Wobble
Alternate Base Pairing
- line up differently
Strand Slippage
Insertions + Deletions
- low sequence complexity
Unequal Crossing Over
Insertion + Deletions
- homologous pair don’t align properly
Deamination
Transition
C –> T/U (bp with A now)
Depurination
Transversion
- remove purine base
Base Analogs
Transition
T –> 5-Bromouracil (bp with G now)
Alkylating Agents
Transition
- ethylates G and T
- G –> ethylguanine (bp with T now)
Hydroylamine
Transition
C –> hydroxylamine-cytosine (bp with A now)
Oxidative Radicals
Transversion
G –> oxy-guanine (bp with A now)
Intercalating Agents
Insertions + Deletions
- molecules slide btwn bp
UV light
- bonds btwn adjacent thymine bases = thymine dimers
Mismatch Repair
- Search for methylation
- Nick and degrade
- Synthesize and ligate
Direct Repair
- specific enzymes to specific base modification
Base-Excision Repair
- Remove base
- Nick, Synthesize, Ligate
Nucleotide-Excision Repair
- Separate strands
- 2 nicks
- Synthesize and ligate
Transposons
- mobile elements in genome
1) Increase Genome size (noncoding DNA)
2) Disrupt Genes (insert in active)
3) Altered Expression (on regulatory sequence)
4) Genome Rearrangement
- direct orientation – deletion + duplication (same) translocation (diff)
- inverted orientation – inversion (same)
Duplicate Target Sequence
- transposase = staggered break
- insert TE
- gaps filled (terminal inverted sequence + flanking direct repeats)
Type II transposons
- DNA intermediates
- short inverted repeats at end
- replicative
- cut + paste
