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DNA 3R's
UCI SOM Lee
| Question | Answer |
|---|---|
| Helicase | MCM 2-7; opens the DNA helix; hexameric ring, uses ATP |
| Polymerase alpha | primer polymerase; lays down RNA primer for okazaki fragment binding |
| Polymerase beta | involved in BER |
| Polymerase gamma | mitochondrial DNA |
| Polymerase delta | lagging strand nuclear DNA |
| Polymerase epsilon | leading and lagging strand nuclear DNA |
| Polymerases with proofreading ability | gamma, delta, epsilon |
| Sliding clamp | PCNA |
| Clamp loader | RF-C |
| Single strand DNA binding protein | RPA |
| DNA ligase | Ligase I |
| DNA topoisomerase | Topo I and II |
| RNase H | removes all but one ribonucleotides |
| FEN1 | removes last ribonucleotide and several deoxynucleotides |
| Contributing factors to high fidelity DNA replication | polymerase, exonuclease proofreading, MMR |
| Are polymerization and editing activity located at the same site on the pol | NO |
| Do all DNA pols have 3’ to 5’ exonuclease activity | NO |
| DNA ligase action | seals 3’OH and 5’Phosphate |
| What does processivity mean | how many nucleotides are added in one attachement |
| Which enzyme is responsible for telomere length maintenance | telomerase |
| Human telomerase | hTERT-human telomere reverse transcriptase |
| What proteins recognize mispairs, small deletions, and small insertions in MMR | MSH heterodimer |
| What proteins make MMR cleavage | PMS2 |
| How are newly synthesized strands detected | lagging strand has gaps; leading strand I don’t have a clue |
| Examples of epigenetic change | hypermethylation of CpG island; post-translational modification of a histone; repair gene is transcriptionally silenced through epigenetic modification |
| 8-oxoG is repaired by | BER |
| BER steps | glycosylase cuts out the damaged base, AP endonuclease cleaves the deoxyribose phosphate backbone, AP lyase binds it all up |
| Y-family DNA pols | used for DNA synthesis when template is damaged; pol eta is in this family and it’s mutation leads to XPV |
| DNA topo I | introduces a single stranded break; attached to 3’ of DNA |
| DNA topo II | introduces a double stranded break; needed for daughter chromosome separation |
| Campothecin | drug that reversibly binds and stabilizes cleavable complexes formed between DNA and topo I; used in cancer treatment |
| Doxorubicin | inhibits topo II; widely used in breast cancer treatment; also known as adriamycin |
| Replication origin | discrete sit on chromosome where replication starts |
| Fusion of S and G1 cells results in | DNA synthesis inducement in G1 |
| Fusion of G2 and S cells results in | no change |
| Telomore DNA sequence | TTAGGG |
| Diseases caused by trinucleotide repeat expansion | fragile X syndrome, friedreich’s ataxia, myotonic dystrophy, spinocerebellar ataxia type B, huntington’s disease, kennedy’s disease |
| Huntington’s disease | expansion of CAG repeat |
| Spontaneous DNA damage | base loss (mostly purines), tautomeric shift (keto to enol or amino to imino), deamination, ROS damage (mostly in mitochondria, alkylation lesions |
| Environmentally induced DNA damage | UV damage (260 nm) eg thiamine dimmers (CPD) and 6-4PP, chemicals |
| 4 other types of DNA damage | replication errors, intra and inter strand crosslinks, DNA-protein crosslinks, strand breaks |
| types of DNA repair | photolyase, alkyltransferase, BER, DER, MMR |
| photolyase | reverses UV damage; not present in humans |
| alkyltransferase | removes methyl group from O6 position of guanine; the repair protein is AGT which is the same as MGMT |
| AGT | O6-alkylguanine-DNA alkyltransferase (used in alkyltransferase) |
| MGMT | O6-methylguanine-DNA methyltransferase (used in alkyltransferase) |
| O6-meG cell apoptosis process | requires MMR; MMR removes thymine which introduces a break in DNA; O6-meG also can bind to MutS which recruits ATR-ATRIP |
| BER short patch repair | dominant repair pathway; DNA pol beta fills one nucleotide |
| BER long patch repair | uses pol beta, delta and epsilon (2-10 bases), and PCNA. FEN1 removes DNA flap and ligase 1 seals the gap |
| 3 steps to BER | 1)N-glycosylase creates an AP site 2)AP endonuclease (APE) nicks at 5’ of AP site 3)extension by DNA pol |
| 3 genetic NER diseases | xenoderma pigmentosum, cockayne’s syndrome, trichothiodystrophy |
| xenoderma pigmentosum | light sensitivity, weird pigmentation, early skin cancer |
| cockayne’s syndrome | premature aging, dwarfism |
| trichothiodystrophy | premature aging, brittle hair, short, facial abnormalities |
| origins of DSB | IR, ROS, and replication of SSB |
| Rad 51-59 | basically facilitate in homology search |
| Rad 50 | process DNA at ends of a double stranded break |
| BRCA1 | deficient in breast cancer and interacts with Rad 50 |
| BRCA2 | breast cancer susceptibility gene and interacts with Rad 51` |
| DNA damage checkpoints | G1 checkpoint is leaving G1 and going to S, G2 checkpoint is leaving G2 and going into M, Metaphase checkpoint assures all chromosomes are attached to spindles |
| DNA damages repaired by BER | c deamination, 8-oxoguanine, single strand break |
| DNA damages repaired by NER | 6-4PP, bulky adduct, CPD (T-T dimmer) |
| DNA damages repaired by recombination repair | interstrand cross-link, double strand break |
| DNA damages repaired by MMR | A-G mismatch, T-C mismatch, insertion, deletion |
| Damages repaired by BER | x-rays, ROS, alkylating agents, spontaneous rxns |
| Damages repaired by NER | UV, polycyclic aromatic hydrocarbons |
| Damages repaired by recombination repair | x-rays, anti tumor agents |
| Damages repaired by MMR | replication errors |
| MMR subunits | MutSalpha (MSH2-6) recognizes the MM and interacts with PCNA; MLH1-PMS2 has endonuclease activity |
| MSH2-6 | recognizes a mismatch for MMR |
| PMS2-MLH1 | makes the cut in MMR |
| FAP and what gene is mutated | familial adenomatous polyposis; APC is mutated |
| Asbestos can lead to what | mesothelioma |
| Inhaling cigarette smoke can lead to what | G to T transversion |
| Futile DNA repair models | add extra DNA sequences when cell is not dividing |
| DNA translesion | DNA replication using a Y-family polymerase b/c there are too many mutations to use pol delta/epsilon |
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