DNA Repair Flashcards
Give 3 examples of exogenous causes of mutations in DNA
UV
Cosmic radiation
Pollutants
Give 3 examples of endogenous causes of mutations in DNA
ROS as byproduct of normal metabolism
Alkylation- addition of methyl group
Hydrolysis
What are two consequences of DNA damage?
- Block replication or transcription- cell cycle arrest. Cell becomes senescent
- Cancer
What happens when there is hydrolysis of the glycosidic bond?
Complete loss of base. Called depurination or depyrimidination
Example of a common deamination damage to the base
When cytosine is deaminated, it becomes Uracil.
Especially in CpG sites, cytosine is methylated in vivo (5 methylcytosine). Deamination of this methylated cytosine turns it into a thymine.
Example of a common alkylation damage to the base
Guanine is frequently methylated (o6-methylguanine). Instead of a GC base pair, you now have an AT base pair
Example of Direct reversal repair
Photolyase- fixes TT dimers caused by UV radiation
Methylguanine methyltransferase (MGMT): reverses o6-methylguanine back to guanine)
What type of excision repair is involved in repairing DNA that has not induced a conformational change?
Base excision repair (BER)
What enzyme is responsible for excising the glycosidic bond in base excision repair?
Glycosylase
After glycosylase excises the glycosidic bond, what site on the DNA is exposed?
AP site (apurinic/apyrimidinic site, also known as abasic site)
What type of excision repair is involved in damages that cause conformational changes in the DNA structure?
Nucleotide excision repair (NER)
What protein is responsible for recognizing the local bending resulting from UV mediated pyrimidine dimerization?
XPC
What are the two ways NER machinery recognizes damage?
Global Genome NER
Transcription-Coupled NEr
Where does global genome NER recognize damage?
Anywhere in the genome
Where does transcription-coupled NER recognize damage?
Within region of active transcription
Defects in global genome NER cause ______.
Cancer
e.g. Xeroderma pigmentosum (XP)
Defects in transcription-coupled NER result in ______.
CNS disorder
e.g. Cockayne syndrome
Xeroderma pigmentosum is a result of a defect in which NER mechanism?
global genome NER
Cockayne syndrome is a result of a defect in which NER mechanism?
Transcription coupled NER
What protein complex carries out the remaining steps of NER following recognition?
TFIIH
What proteins within the TFIIH protein complex are involved in the local unwinding of DNA?
XPB and XPD
What type of repair is involved when the is a mis-incorporation of bases?
Mismatch repair
What two groups of protein are the main players in mismatch repair?
MutS Homolog (MSH): 1,2
MutL Homolog (MLH)/ PMS in Eukaryotes: 1,2, and 6
Which class of proteins recognize mispaired nucleotides?
MSH (which form dimers)
MSH proteins recruit _____.
MLH/PMS proteins (which are dimerized)
MLH proteins recruit _____.
Helicases
How do MMR proteins differentiate the newly synthesized strand from the mother strand in e. coli?
mother strand is heavily methylated
How do MMR proteins differentiate the newly synthesized strand from the mother strand in eukaryotes?
Frequent occurrence of nicks is recognized
Easy in lagging stand
Leading strand- marked by transient presence of ribonucleotides
Mutations in MMR genes give rise to _______.
Hereditary nonpolyposis colorectal cancer (HNPCC), also known as (Taylor) Lynch Syndrome
What type of repair occurs when the cell doesn’t have the means to repair?
DNA bypass
What nucleotide sequence does pol eta add (DNA bypass repair)?
AA
Briefly describe the steps that occur to repair DNA when there is a lesion in front of the replication fork
Translesion repair
PCNA interacts with pol eta and pol iota and moves them towards fork
Pol eta adds AA
Pol iota then extends this new strand
Explain DNA damage response
Cell recognizes damage and enters cell cycle arrest
ATM and ATR recognize breaks in DNA
Chk1 and Chk 2 initiate repair, arrest, or apoptosis
