DNA modification and repair Flashcards
Major methylated bases in prokaryotes
N6-methyladenine and N4-methylcytosine
Goal of methylation in bacteria
Protect DNA from cleavage by endonucleases
Methylated base in eukaryotes
5’ methylcytosine
Where is methylated cytosine usually found?
C residues 5’ to G, i.e. 5’- CG -3’
When are methylation sites selected?
During gametogenesis and embryogenesis during periods of demethylation and de novo methylation.
Which protein carries out methylation during DNA synthesis?
Maintenance methylase
How does methylation control gene expression via promoters?
Methylated promoters are not expressed. This is how temporal expression of globin genes is controlled.
5-azacytidine
Cytidine analog that can be metabolized into dCTP and incorporated into DNA structure. It can reverse methylation.
Methylation of which residue is involved in mismatch error correction.
Methylation of A in the sequence 5’–GATC–3’
What does deamination of 5-methylcytosine do to the base?
It becomes thymine
Point mutation
Change in a single base pair
Transition mutation
Purine-pyrimidine base pair is changed to a different base pair. For example, CG to TA.
Transverse mutation
Purine-pyrimidine base pair is switched to pyrimidine-purine base pair. For example, CG to GC
Intercalating agents
Fit between adjacent base pairs of the double helix. Examples include ethidium bromide and doxorubicin.
Which mutations will shift the reading frame?
Deletion or insertion mutations
What mutation does UV light typically cause?
Intrastrand dimerization of adjacent thymines. Either a cyclobutane or 6-4 photoproduct
Which oxidized base is the most abundant from ROS-related oxidation of DNA?
8-oxoguanine
Which base can 8-oxoguanine mispair with?
Adenine
Methylation or ethylation agents typically cause modifications of which bases?
Purines, for example O6-alkylguanine.
Which base does O6-alkylguanine have a high probability of being paired with?
Thymine
MGMT
Directly repairs O6-alkylguanine in prokaryotes and eukaryotes. Self-alkylates to restore guanine.
Which DNA polymerase is involved in NER in prokaryotes?
DNA pol I
Repair proteins involved in NER in prokaryotes
UvrA, UvrB, and UvrC
Which complex cuts both sides of the dimer in pk NER?
UvrBC complex. Cuts at 3’ end, then 5’ end.
Two mechanisms of NER in eukaryotes
Global genome and transcription coupled
Which proteins are involved in NER in eukaryotes?
XP proteins, named after xeroderma pigmentosum
Which type of mutation affects mainly pyrimidines?
Ultraviolent radiation
Which type of mutation is caused by O6-alkylguanine
GC to AT. This is a transition mutation.
Base excision repair protein
DNA-N-glycosylase
Deamination of cytosine will turn it into?
Uracil
DNA polymerase involved in prokaryotic base excision repair
DNA pol I
Two mechanisms of BER in eukaryotes
Short patch (similar to prokaryotes) and long patch
Which proteins does long patch BER involve?
DNA pol delta, epsilon; FEN-1; PCNA
Which subunit proofreads for mistakes during DNA replication in eukaryotes?
DNA pol III ε subunit
MutHLS
Prokaryotic mismatch repair system
Which sequence is unmethylated in the daughter strand and clues MutHLS in on which base is mismatched?
GATC
Which polymerase fills in the DNA for mismatch repair?
DNA pol III
