06a: DNA Repair Flashcards
The major methylated bases in prokaryotes are (X). The modified bases are called (Y).
X = adenine and cytosine
Y = N6-methyladenine and N4-methylcytosine
Why is bacterial DNA methylated?
Protection mechanism (methylated DNA won’t be cleaved by bacteria’s own restriction endonucleases)
T/F: methylation in bacteria is maintain after replication, as it is in eukaryotes.
True
Methylation of (X) residues in the sequence (Y) in bacteria is involved in mismatch error repair.
X = adenine
Y = GATC
The major methylated bases in eukaryotes are (X). The modified bases are called (Y).
X = cytosine
Y = 5’-methylcytosine
(X)% of cytosine in eukaryotic DNA is methylated.
X = 3-5
5’-methylcytosine in (prokaryotes/eukaryotes) is usually found nearby which other base(s) or in which sequence?
Eukaryotes;
Musically found 5’ to a G (so in CG sequence)
T/F: methylation in eukaryotes is heritable.
True
(During/after) replication, (X) carries out methylation of daughter strand.
After;
X = maintenance methylase
T/F: Methylation of DNA mainly occurs after fertilization.
False - methylation sites can be selected during gametogenesis
(Methylated/unmethylated) promoter is expressed.
Unmethylated
At 6 weeks of age, (X)-globin gene expressed and (Y)- globin gene not expressed. Does this change?
X = epsilon Y = gamma
Yes! Reversed at 12 weeks of age
Inactivity of methylated genes (can/can’t) be reversed. If can’t, why not? If can, how?
Can; by 5-azacytidine
5-azacytidine functional and structural importance.
Reverses methylation of genes.
Cytidine analog with N at 5’ position (that can’t be methylated)
What can 5-azacytidine be treatment for?
Beta-thalassemia
When would 5-azacytidine be introduced to the cell for it to carry out function effectively?
During replication of DNA (so it can be incorporated into daughter strands)
List some causes of DNA mutation.
- Replication mistakes
- ROS
- Chemical damage
- Radiation
- Deamination of cytosine/5-methylcytosine
Deamination of 5-methylcytosine converts it to which base?
Thymine
Deamination of 5-methylcytosine will cause a (X) mutation. A (Y) bp will become a (Z) bp.
X = transition point mutation
Y = GC Z = AT
What’s especially dangerous about a 5-methylcytosine deamination?
Thymine isn’t seen as abnormal base by repair enzymes
What defines a transition point mutation?
Purine-pyrimidine changes to a different purine-pyrimidine
What defines a transverse point mutation?
Purine-pyrimidine changes to pyrimidine-purine
Which mutations can shift the reading frame of DNA?
Insertion or deletion mutations
Exposure to UV light can result in (X) of which bases?
X = intra-strand dimerization of adjacent thymine a
Give example of direct base repair in DNA.
Repair of O6-alkylguanine
Base modification is found (more/less/about the same) in purines than in pyrimidines.
More
Why is O6-alkylguanine problematic?
High probability of base pairing with thymine (so GC pair becomes GT then AT)
(X) repair of O6-methylguanine is carried out by (Y) in prok and (Z) in euk.
X = direct
Y = Z = O6-methylguanine DNA methyltransferase (MGMT)
How does MGMT work?
Direct repair of O6-methylguanine by transferring the methyl from damaged base to itself (self-alkylation)
MGMT acts (before/during/after) replication.
Before
Which repair mechanism used to correct intra-strand thymine dimers in prok?
NT excision repair
Does NT excision repair require ATP hydrolysis?
Yes
List steps in prok NT excision repair.
- UvAB complex scans/finds damage and bends DNA
- UvrA leaves and UvrC binds
- Endonuclease cuts damaged strand 5’ THEN 3’ to damage
- Helicase removes damaged pieces
- DNA pol 1 replaces DNA and ligase seals Nick
What are the categories of excision repair in prok?
- NT excision repair
2. Base excision repair
Which enzymes carry out base excision repair?
DNA-N-glycolases
Can uracil be found in DNA?
Yes - damage situation (if cytosine is deaminated)
If deamination of cytosine isn’t repaired over time, what (transition/transversion) mutation can occur?
Transition;
GC goes to AT
Which repair mechanism is used in cases of deaminated cytosine? Which enzyme used?
Base excision repair by uracil DNA-N-glycosylase
Which repair mechanism leaves an apyrimidinic or apurinic site?
Base excision repair (glycosylase removes base, but not entire backbone)
In base excision repair, is an endonuclease necessary? Why/why not?
Yes - apyrimidinic or apurinic endonuclease cuts backbone 5’ to damage
Nick translation is part of which prokaryotic repair mechanism?
Base excision repair
What repair pathways are found in eukaryotes?
2 major BER pathways (short and long patch)
List, in order, the key players in base excision repair in prok.
- DNA-N-glycosylase
- Abasic endonuclease
- DNA pol 1
- DNA ligase
Mismatch repair in prok is carried out by:
MutHLS system
(X) is a motor protein that’s involved in (Y) repair.
X = MutHLS Y = mismatch
The parent and daughter strands can be distinguished during (X) repair because:
X = mismatch
Parent strand is methylated and MutHLS pulls strands, scanning for the methylation to distinguish the two
What sequence is MutHLS searching for to identify parent strand?
Methylated Adenine in GATC sequence
Do any prokaryotic repair mechanisms use exonucleases?
Yes - mismatch repair
Which polymerase involved in mismatch repair?
DNA polymerase 3
MutH, a(n) (X), has what function?
X = endonuclease
In mismatch repair, cuts backbone 5’ to G in GATC sequence of daughter strand
Does mismatch repair occur in humans?
Yes - just different enzymes
