Lecture 14a Flashcards
How do DNA pol III and I repair DNA?
3’ to 5’ exonuclease activity: incorrect bases are removed and correct ones are added.
How are DNA lesions repaired?
Direct reversal of damage.
Example 1: unlinking pyrimidine dimers –> UV light causes photodimer to form –> CPD photolyase enzyme breaks dimers when a certain wavelength of light present.
Example 2: Alkyltransferases reverse damage caused by alkylating agents. The enzyme adds takes off methyl on alkyl chain and adds it to its own active site –> enzyme can only be used once.
What is base excision repair?
Removal and replacement of one or more bases. Occurs after proofreading by DNA pol. Nonbulky damage to the DNA is recognized by one of several enzymes called DNA glycosylases that cleave the base–sugar bonds, releasing the incorrect base –> AP endonuclease cuts phosphate backbone –> dRpase removes stretch of DNA –> DNA pol adds nucleotides back –> DNA ligase.
What is nucleotide excision repair?
Repair to relieve replication and transcription blocks and repair the damage. Damage is recognized –> proteins assemble –> remove damaged strand (approx 30bp) –> replace cut DNA –> ligate
What are the two pathways for nucleotide excision repair?
Bulky areas or multiple damaged bases are recognized in
nontranscribed (GG-NER) or transcribed (TC-NER) regions of the genome.
In the GG-NER pathway, proteins binds to a lesion.
In the TC-NER pathway, proteins bind to RNA polymerase II complexes that are stalled at a lesion.
What is mismatch repair?
Recognition and repair of mismatched bases and small loops caused by the insertion and deletion of nucleotides in the course of replication.
Pathway: Recognition of damage by MutS protein –> new synthesized strand with incorrect base is cut by MutH protein –> remove nucleotide –> repair
How does mismatch repair tell the difference between the new and old strand?
Assumes that the old strand is unmethylated. If both strands are unmethylated then it looks for a free 3’ OH.
What is SOS repair?
Bypass of replication blocks by insertion of nonspecific bases. It is an emergency to prevent cell death in presence of major DNA damage.
Pathway: Pol III stalls at site of damage –> RecA protein and SSB bind to DNA and signal synthesis of pol V –> bypass pol replaces pol III –> bypass pol continues DNA synthesis –> bypass pol falls off and is replaced by pol III –> pol III DNA synthesis continues.
What are characteristic features of the bypass polymerase in SOS repair?
- Can tolerate unusually large adducts on bases
- Higher error rate because they lack 3’ to 5’ exonuclease activity
- Can only had a few nucleotides before falling off
What causes a double strand break?
X-ray or oxygen radical damage to the cell
How does double strand break repair occur in non-replicating cells?
Non-homologous end joining: proteins bind to broken ends –> trim back ends –> ligase joins 5’ P and 3’ OH. A few bases are lost in this process.
How does double strand break repair occur in replicating cells?
Uses homologous DNA (sister chromatid) as template. Mechanism is similar to crossing over in M1.
Pathway: proteins bind to broken ends and trim back 5’ ends –> strand invasion and D-loop formation with homologous DNA –> homologous DNA serves as DNA template for repairing both broken strands –> ligation.
