Lecture 31 DNA Repair

- does not use ATP
- covalently attaches to DNA phosphate ---> creates single strand break
- allows rotation of the double helix to solve winding problem

- uses 2 ATP
- produces double stranded breaks in G segment to allow T segment passage.
- blocked by etoposide

UV, X-rays
- Both of these are very energetic and tend to break biological molecules

Mismatched base pairs

Reactive oxygen species (H2O2 , O2-)

Ethyl-methane sulfonate (EMS), ethidium bromide

- Adjacent pyrimidine rings form covalent bonds with each other
- which leads to error in replication
- Structure distortion
■ XP disease - Nucleotide excision repair not functioning properly

- loss of purine from a nucleotide
- from hydrolysis of Nglycosidic bond
- base leaves the AP site

- loss of an amine group
- from hydrolytic attack of bond joining amine group to a base
- C goes to U

Spontaneous loss of purines - depurination
- DNA of each human cell loses 5000 purines (A and G) every day
- Most common
Deamination
- About 100 cytosines are converted to uracil via deamination

- can eliminate the H-acceptor group of guanine
- changes the base pairing from GC to AT

- binds to DNA between base pairs
● Can be used to identify where DNA is after electrophoresis
- a DNA intercalating agent

- cell cycle checkpoint activation
- transcriptional program activation (fixes domain involved in transcription)
DNA Repair (damage is too much - discard damaged areas)

DNA photolyase
- Photoreactive repair
Demethylation
- Catalyzed by methyltransferase (suicidal enzyme)

- Abnormal bases
- No helicase needed
1. AP endonuclease and phosphodiesterase remove sugar phosphate
2. DNA polymerase adds new nucleotides
3. DNA ligase seals nick
- Depurination and deamination (needs glycosylase before endonuclease)

- uses nuclease and DNA helicase to produce large single stranded break
- DNA polymerase and ligase used to fill gap
- Pyrimidine dimers

- small vs big chunk repair
- repairs depurination and deanimation vs repairs pyrimidine dimers

- Removes mismatched pairs from new strand but not parent strand
- New strand may be identified as it is unmethylated when created

- MMR
- Scans for mismatched pairs

- MMR
- looks for GATC sequence close by in order to distinguish new standand old strand

- MMR
- Hydrolyzes phosphodiester linkage

Homologous recombination and Nonhomologous end joining

- Deanimation converts methyl c to thymine
- enzyme (glycosylase) that repairs that is not efficient

- Loss of nucleotides due to degradation from ends
- End joining
- Deletion of DNA sequence
- Quick but not accurate
- Gene deletion/inactivation
- No template needed

- Loss of nucleotides due to degradation from ends
- End processing and homologous recombination
- Damage repaired accurately using information from sister chromatid
- Allows for gene manipulation in genome = gene replacement