DNA Replication and Repair Flashcards
anti miRNA
singled stranded, chemicaly modified ASO bind to miRNA to block activity. miR-122 miRNA is therapy for HepC virus.
Components of a NT
nitrogenenous base attached on 1’ of ribose ring ribose phosphate group attached to 5’ carbon of ribose
Base Excision Repair
repairs those missed by NER, and that do not distort DNA
1) modified base recognized by DNA glysoylase which hydrlyzes glycosidic bond (base and sugar) to yield a-basic site.
2) AP site specific endonuclease cleaves Sugar phosphate backboke from 5’ to AP site
3) a different endonuclease cleaves Sp backbone from 3’ to AP site
4) DNA pol fills in gap and nick is sealed by ligase
Methylation of Adenine
this is done in bacterial cells and is used as an identifyer for DNA older strands
how are small RNAs delivered?
1) put them inside lipid nanoparticle with an external lipid layer that targets a particular region, where it is then take up in a lysocome and ssRNA comes in contact with mRNA 2) chemically modified so they do’t get degraded and have glycol-conjugate that is specific 3) virus expresses gene and makes RNA that folds back on itself.
how do Streomyces that make puromycin protect themselves?
they also make an enzyme that inactivates antibiotic in the bacteria itself. modifies the part of puromycin that is involved in the covalent attachment of polypeptide chain, rendering it inactive.
DNA Pol I vs DNA Pol III
1: distributive - dissociates easily replaces RNA primers Exonuclease 5’ to 3’ 3: processive both have Pol 5’ to 3’ and exonuclease 3’ to 5’
Cockayne syndrome
super hypersensitivity, premature aging, mutation in transcription NER
RNAi
endogenous gene silencing mechanism by siRNA and miRNA ds RNA induce translational inhibition or degradation of mRNA containing partially complimentary sequences.
When does Loss of Heterozygosity Occur?
Mis-regulation of HR use of other chromosomal homolog as template instead of sister chromatid
Nucleotide Excision Repair
Removes lesions that distort DNA structure \ block DNA and RNA pol movement ex: thymine dimers, DNA adducts Recognition of damage is by multi-protein complex, but all other steps are the same as BER
Rag Recombinase
initiates DS breaks in NHEJ to create antibody diversity
Steps NHEJ with Ku
1) Ku recognizes ds break and binds to protect form exonuclease 2) Ku recruits DNA-PKcs which autophosphorylates to attract ARTEMIS to remove DNA damage 3) polymerase fills in gap 4) Ligase 4 seals
Camptothecin
chemo drug targets topoisomerase
Dicer
ribonuclease of RNAse III that cleaves dsRNA into miRNA
How are DS breaks sensed?
PIKKs 1) ATM and ATR
How does BRCA1 promote HR?
phosphorylated by ATM and ATR to recruit to DS break. Depends on activated by CDK, when present, this pushes towards HR.
Dideoxyinosine
DDI inhibits DNA synthesis by the reverse transcriptase enzyme HIV medication Chain terminal mimic of nucleotide
What methods are for direct reversal of Damaged bases?
1) ssDNA break reversal by ligase
2) reversal of UV damage by photolyase
3) reversal of base alkylation (O6 methyltransferase MGMT)
what happens with imperfect match of miRNA?
transcriptional repression
Tat
The first protein synthesized in the human genome of HIV that leads to further expression of the viral genome. There is a tat mimic that fits nicely into the groove of HIV-TAR (tat activated region) to prevent replication of HIV
BER vs NER
BER targets damage that does not distort DNA NER targets damage that does distort DNA
BER: recognized by specific glycosylase
NER: recognized by multiprotein complex
Holliday Junction Resolution
can make two cuts Vertically: recombinants (DSBR) Horizontally: no recombinatns (synthesis dependent strand anneals)
Intercalation drugs
Actinomycin D
Doxorubicin
MGMT
is a direct reversal type of DNA repair that reverses base alkylation
removes added methyl group and adds it on itself Glioblatomas have MGMT silenced
How can RNAi be made in body?
make small RNA in vivo, purify the enzyme and let is up the RNA introduce it to cells to cleave mRNA in cell. Introduce gene that will express RNA that will naturally fold back on itself to generate siRNA or miRNA that will specifically target domain for degradation.
Cisplatin
alkylating agent drug that reacts with nitrogen in the bases to cause crosslinking. This causes too much damage in the cellular DNA when cells are dividing very rapidly and signals them to be sent into apoptosis. Chemotherapy drug.
Xeroderma Pigmentosum (XP)
sun hypersensitivity, pigmentation disorders mutation in Global Genome NER