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BISC Midterm 1
| Question | Answer |
|---|---|
| True or False (and why): Bacterial cells with error prone Pols are much more fit. | true, excess mutations in pol V homologs result in greater fitness |
| What is the reverse reaction of DNA Pol? | pyrophosphorlysis |
| What is the reaction of exonuclease? | DNAn -> DNAn-1 + dNMP |
| What is the direction and function of E. coli Pol I, Taq Pol? | 5'-3' "nick translation" |
| What is a transition base substitution mutation? | Purine-Purine or Pyrimidine-Pyrimidine |
| What is a transversion base substitution mutation? | Purine-Pyrimidine or Pyrimidine-Purine |
| What is the disfavored Enol Tautomer? | TG |
| What is the disfavored Imino Tautomer? | CA |
| What are the 3 activities of DNA Pol I? | Pol, 3'-5' exo, 5'-3' exo |
| What happens if the dNTP is incorrect? | If the hand receives an incorrect base, there will be an ugly space. the triphosphate leaves the enzyme and returns to solution. The game starts over. |
| What is the rate limiting step for the right nucleotide? | The conformational change to be read as correct |
| What is the rate limiting step for the wrong nucelotide? | The formation of the phosphodiester bond, the chemistry |
| True or False: there is direct competition between extending the mispair and proofreading the mispair. | True |
| What is the rate limiting step for Pol beta? | the chemistry for both correct and incorrect nucleotides |
| How does T4 proofread? | in order to bind dNTP, pol must translocate to the next template site and in order to proofread, the primer must move from the pol to exo site. |
| Which T4 variant has the highest exonuclease activity? | antimutator |
| Which T4 variant has the lowest exonuclease activity? | mutator |
| What are the 4 steps for post-replication mismatch repair? | 1. lesion scanning enzymes 2. nick DNA backbone 3. excise DNA lesion 4. fill and seal the gap |
| What happens if humans have an MMR defect? | familial colorectal cancer and genome instability |
| What are four purposes of MMR? | 1. major pathway for repair of pol generated mismatch 2. recombination barrier 3. pathogenic barrier 4. repair of IgV somatic hypermutation UG mismatches |
| What is the textbook model for E. coli MMR? | 1. MutS scans DNA looking for bulges 2. MutL/MutH bind hemi-methylated sequence and recognize unmethylated strand 3. MutH cleaves unmethylated DNA strand 4. exonuclease removes the stretch containing the mismatch 5. DNA Pol fills gap and ligase seals |
| Where does MutL-MutH stop on dsDNA? | GATC dam |
| What does UvrD helicase do? | unwinds dsDNA |
| What is MutL's function alone? | form complexes with MutH and UvrD |
| How does an exonuclease know to stop digesting ssDNA after the misincorporated base is removed? | exos digest a short (~50 nt) region of ssDNA to prevent premature ligation |
| How do eukaryotes recognize nascent DNA strand? | NOT methylation. nascent strand has nicks remaining from the replication process |
| What is EXO1 dependent MMR pathway? | 5’→3’ dsDNA-dependent ss exonuclease – initiates digestion of ssDNA at a strand break |
| What is EXO1 independent MMR pathway? | MLH1-PMS2 intrinsic endonuclease, activated by PCNA, followed by MLH-PMS strand-displacement, or maybe Pold-mediated strand displacement between 5’ & 3’ nicks flanking a mispair, acting in concert with human FEN1 flap endonuclease |
| What DNA ligase inhibits MMR? | CDC9 |
| What are the three R's | replication, recombination, repair |
| How can uracil be present in DNA? | deamination of cytosine or incorporation of uracil via DNA polymerase opposite adenosine |
| How is uracil removed from DNA? | base excision repair (BER) using uracil glycosylase (Ung) |
| What are Okazaki fragments? | short sections of DNA formed at the time of discontinuous synthesis of the lagging strand during replication of DNA. likely replication intermediates, not degradation products cause by the removal of uracil |
| What are 4 examples of DNA base damage? | 1. deamination of cytosine yielding uracil (foreign) 2. depurination or depyrimidation 3. deamination of 5 -methyl-cystosine to thymine (spy) 4. guanine mods |
| Which base pairs can uracil form? | UG or UA |
| What are the consequences of programmed deaminating C-U in bacteria? | regulation of nucleotide and nucleoside metabolism |
| What are the consequences of programmed deaminating C-U in humans? | immunological diversity, antagonize viral infection retrovirus, hepatitis |
| What are the consequences of spontaneous deaminating C-U in bacteria? | trigger BER and mutagenesis |
| What are the consequences of spontaneous deaminating C-U in humans? | disease, cancer |
| How does DNA glycosylase fix uracil mispair? | it flips it out, inspects it and then specifically removes a particular damaged base at the glycosidic bond to deoxyribose |
| What does a monofunctional glycosylase do? | cleave glycosidic linkage between base and sugar |
| What does a bifunctional glycosylase do? | cleave base-sugar linkage AND nick PDE backbone |
| What are the two mutation pathways for 8-oxodG with A? | Oxidize G in DNA: G to GO, GO pairs A. and Oxidize G in dNTP T to GO, GO pairs C |
| What is NER? | Nucleotide Excision Repair; a major DNA repair pathway |
| What is an effect of UV radiation? | crosslinks between pyrimidines bases (thymine dimer) |
| What does ionizing radiation (gamma- and X-rays) do to DNA? | creates double strand DNA breaks, leading to deletions, insertions, and chromosomal rearrangements |
| What does NER fix? | damaged bases, pyrimidine dimers, crosslinked molecules |
| What is the NER process? | 1. UvrA/B scan DNA for distortions 2. UvrB opens the helix and recruits UvrC 3. UvrC cleaves a single strand on both sides of the lesion 4. UvrD helicase removes the nicked DNA region and the gap is repaired by DNA Pol I |
| What can NER pathway defects cause? | Xeroderma pigmentosa, Cockaynes, Trichothiodystrophy |
| When does transcription coupled repair happen? | when RNA Pol encounters DNA damage |
| What are the NER protein analogs? | UvrA-XPC UvrB-XPB,XPD UvrC-XPF,XPG Uvr-None |
| What does Mfd translocase do? | mediates genome-wide TCR |
| What happens if stalling occurs at sites of DNA damage? | DNA synthesis is uncoupled, triggering DNA contortions, replication restart, and/or fork regression |
| what are the two options for complex replication-restart pathways? | branch migration to chicken foot and error-free copying to regressed fork flipping forward |
| Error Prone TLS is what? | translesion DNA synthesis |
| What is AID? | Activation Induced cytidine Deaminase, scans ssDNA slowly and deaminates haphazardly |
Created by:
javaughnr
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