DNA damage and repair Flashcards
What is alkylation
Electrophillic substances attack negative charges on DNA and bind to them, adding carbon containing alkyl groups. This can cause replication stalling.
What is intercalation
The insertion of molecules inbetween the planar bases of DNA. Example is ethidium bromide which distorts DNA and disrupts replication
What is UV damage to DNA replication
UV damage creates thymine dimers which contain cyclobutane rings and distort DNA
What are the two types of DNA subsitution
Transition is a base substitution of the same size (A - G or C - T). Transversion is a base substitution of different size (purine to pyrimidine).
What are tautomeric shifts
A spontaneous shift in protons and double bond arrangement when adenine goes from an amino acid to an emino acid and can bind with cytosine instead of thymine.
What is deamination
Deamination of adenine to hypoxanthine allows base pairing with cytosine instead of thymine.
Describe DNA photolyase
A direct DNA repair system activated by UV (also caused by UV) by an enzyme called photoautolyase. Its a direct repair system meaning no synthesis of DNA is required
Describe DNA repair system that repairs O6 methyl guanine
O6 methylguanine methyl transferase removes O6, This is a suicide enzyme so needs to be constantly grown in the cell. This is a direct repair system so no DNA synthesis is required.
Describe the Base Excision Repair system
Removal of specific bases. DNA glycosylases breaks the glycosidic bonds in the damaged bases to remove them. This creates an apurinic or apyyrimidine site (AP site, sugar no base). DNA phosphodiesterase removes AP sugar and then DNA pol I (5’ exonuclease) and ligase repairs gap.
Describe the Nucleotide excision repair system
Carried out by uvrABC excinuclease. UVR AB recognises distortion (UVR A not needed anymore). UVR C nicks each side of distortion. DNA unwound by UVR D helicase. Repaired by DNA pol I (5’ exonuclease) and ligase repairs the gaps.
Describe key differences between base excision repair (BER) and nucleotide excision repair. (NER)
NER is not as precise as BER but can repair bulky damage where as BER can’t. BER uses glycosidases for more specific repairs. NER can repair nucleotides (do BER job) if needed.
Explain why DNA sometimes contains uracil
Uracil arises in DNA from either spontaneous deamination thinking it was a cytosine or misincorporation by DNA pol III thinking it was a thymine.
Why is it important for DNA to remove uracil?
The cell cant distinguish whether uracil arose from deamination or misincorporation, and therefore unsure if parent strand was a adenine or guanine. Could result in mutation
Desribe DNA repair system that is responsible for removal of Uracil
Base-excision repair is used and uracil N-glycosylase is a specific enzyme used to remove uracil. Base excision repair flips out uracil creating an AP site. AP endonuclease recognises AP site and cleaves it. DNA phosphodiestase removes AP sugar creating a gap. DNA pol I (5’ exonuclease) removes a few more bases and ligase fills gaps.
Describe Mismatch repair and how it figures out which is the non-template strand?
Mismatch repair scans DNA and removes replication errors (missed by DNA pol III). It repairs damage and sits next to DNA pol III. Mismatch repair recognises which is the non-template strand because DNA is methylated on adenine every GATC (250nt) which identifies a parent strand.
