Oct 21 Flashcards
What N of Guanine and Adenine does methylation prefer?
N7 guanine and N3 of adenine
Nitrosourea, nitrosamine, ethylmethane sulfonate all do what?
Alkylating agents for DNA bases
What causes interstrand DNA crosslinking? (3)
UV, ionizating radiation, bifunctional alkylating agents
What is psoralen, and what does it do?
It is a natural compound from plants, it intercalates between bases and also is sensitive to light. When light activates it, it will join 2 pyrimidines, one from each strand of the same DNA molecule. Stalls DNA poly
How can psoralens be used for clinical therapies?
It is used for skin problems, so when shine light you cause interstrand crosslinking via pyrimidine bases and it prevents cell division
Alkylating and cross-linking agents can be used for chemotherapy. What does the platinum based one look like, what does it do?
Cis platin is Pt with 2 Cl and 2 NH3 on it. It alkylates mitochondrial DNA, so Cytochrome C activated and triggers apoptotic pathway
What are the 3 classes of DNA repair mechanisms?
Direct reversal, base excision and nucleotide excision
What does direct reversal repair do? Give examples
It is for very common and simple types of damage, like breaking pyrimidine dimer and removing methyl group
What is base excision repair (basic)
Base is removed, then repair occurs, it is specific for type of damaged base
What is nucleotide excision repair (basic)
It is when nucleotide(s) removed, then repair. It is for many types of damage
Is mismatch repair system in eu and/or prokaryotes?
It is in both
What is limitation of MMR system (direct repair)
It can’t repair misinsertions and short indels (insertions or deletions of many nuclotides)
What are the steps from DNA synthesis to error to repair for MMR system in E.coli?
- Dam methylase methylates adenines in the palindromic GATC on both strands of DNA.
2.The formed hemimethylated DNA duplex after replication, only the parental strands have methylated adenines in GATC sites.
3.MutS recognizes the mismatch and forms complex with MutL
4.The complex scans DNA bidirectionally and forms a loop of DNA.
5.MutH is recruited which cleaves unmethylated GATC sites (daughter strand)
6.MutS+L complex recruits helicase 2 (UvrD), it unwinds DNA and exonuclase degrades the cleaved strand which is flopping around, creates single strand gap
7.The single strand gap stablilized with single strand DNA binding protein (SSB), then filled in with DNA Pol 3 and sealed with ligase
Which exonuclase 5 to 3 or 3 to 5’ for which side the cleavage on the hemimethylated GATC?
When cleavage is on the 3’ side of the mismatch, a 5’ to 3’ exonuclease is recruited. When cleavage on 5’ side, then 3’ to 5’ exonuclase
Do eukaryotes have MMR system? What do we know about it?
It does have similar proteins to bacterial MutS and L, but it does not have MutH and Dam methylase homolog, and doesn’t use methylation to distinguish parental vs daughter strand
