Term
| What is the difference between a transversion and a transition? |
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Definition
transversion: pyrimidine - pyrimidine , purine - purine mix ups
transitions: pyrimidines- purines mixups |
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Term
| What is a DNA micro satellite? |
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Definition
| a "hotspot" for a mutattion to occur: if there are long repeating sequences of CA |
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Term
| If a mutation isn't going to be permanent, when does it have to be found by? |
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Definition
| before the second round of replication |
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Term
| how does mismatch repair affect mutation rate in E. coli cells? |
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Definition
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Term
| What is the mismatch repair system in bacteria ? How does it work ? |
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Definition
| MutS recognizes dimers from the distortion in the DNA backbone. Must binds to it, and it induces a conformational change in the MutS. MutS has ATPase activity that is required for mismatch repair. MutS recruits MutLwhich recruits MutH. MutH nicks one strand near the mismatch. It then eats from the nick to past the mismatch. Ligase then fills it in. |
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Term
| what does MutS use as a cofactor? |
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Definition
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Term
| How does the mismatch repair system recognize the newly synthesized DNA? |
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Definition
| MutH can only recognize the "hemimethylated" DNA, which is the newly synthesized DNA since Dam methyltransferase hasn't had a chance to catch up to DNA polymerase and methylate it. Then MutH nicks it |
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Term
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Definition
| it's a test that tests mutagens on bacteria to see if they will grow even if they are under unfavorable conditions. (see if chemical will revert growth conditions) |
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Term
| How do bases get deaminated? What is the result ? |
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Definition
| When water is added to the bases, cytosine loses it amine group, guanine loses its purine group (depurination), when 5-methylcytosine is added to water, then it loses it amine group. |
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Term
| Why does DNA have thymine instead of uracil? |
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Definition
| If DNA had uracil instead of thymine, then the deamination of cytosine would yield a base that would be natural and the repair systems wouldn't work. |
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Term
| how does gamma radiation and x rays affect DNA? |
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Definition
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Term
| What does photo reactivation fix? |
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Definition
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Term
| Which enzymes fix double stranded breaks in E. coli? |
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Definition
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Term
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Definition
| uses energy from light to fix thymine dimers |
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Term
| Sometimes DNA gets methylated from UV radiation. How does it get fixed? |
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Definition
| methyl transferase will come and remove the methyl group from the base. |
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Term
| Give an example of coupling reaction and mutagenic base repair |
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Definition
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Term
| Which enzyme is involved in base excision repair? |
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Definition
| DNA glycosylase.....cuts out bases that have flipped to the outside on minor groove by hydrolyzing glycosidic bond |
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Term
| Why is oxoG so mutagenic? |
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Definition
| It can pair with both adenine and cytosine |
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Term
| if oxoG pairs with A during replication, what mutation has occurred? |
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Definition
| It was a G:C to a A:T....so a transversion |
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Term
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Definition
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Term
| what does a fail-safe glycosylase do? |
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Definition
| it identifies the replication product of oxoG (daughter strand) and removes the A base pair, replaces it with C |
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Term
| How does nucleotide excision work? |
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Definition
| Recognizes distortions to the shape of double helix (thymine dimmer or by the presence of a bulky chemical adduct). Cuts out the section and uses DNApolymerases to fill in the gap. |
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Term
| True or false: RNA polymerase is a damage sensitive protein |
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Definition
| YES TRUE. because mechanisms of repair are more efficient when they are on the template strand for transcription. |
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Term
| What does TFIIH do in transcription-coupled repair? |
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Definition
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Term
| How does nucleotide excision work? |
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Definition
| Recognizes distortions to the shape of double helix (thymine dimmer or by the presence of a bulky chemical adduct). Cuts out the section and uses DNApolymerases to fill in the gap. |
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Term
| True or false: RNA polymerase is a damage sensitive protein |
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Definition
| YES TRUE. because mechanisms of repair are more efficient when they are on the template strand for transcription. |
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Term
| What does TFIIH do in transcription-coupled repair? |
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Definition
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Term
| what is the mechanism for double strand break repair? |
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Definition
| there are two ways: one uses homologous recombination with the non damaged sister strand of DNA as the template---introduces no mutations. The other way is to use NHEJ, which sticks two ends of chromosomes together |
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Term
| why do eukaryotes use NHEJ rather than prokaryotes? |
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Definition
| we have more introns to spare |
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Term
| In eukaryotes, which type of polymerase is able to carry out translesion repair? |
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Definition
| Y family---it is able to incorporate nucleotides from template and without a template (SOS response) |
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Term
| in e. coli, what is the name of the polymerase that can do translesion repair? |
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Definition
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Term
| Which type of translesion polymerase is better for fixing thymine dimers? Why? |
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Definition
| Pol Eta, has a more open pocket |
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Term
| What is the difference between the polymerase switching and the gap filling model ? |
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Definition
| polymerase switching is the when the replicative polymerase comes to the mutation site, falls off, and the translesion polymerase hops on. the gap filling model is when the replicative polymerase just jumps ahead |
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Term
| Does the Holliday model start with a single or double strand break? |
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Definition
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Term
| Why does the "Double Strand Break Repair" introduce ssDNA 3' ends? |
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Definition
| so that both can invade the other whole chromosome |
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Term
| What is the RecBCD pathway? |
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Definition
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Term
| Which enzyme involed in the RecBCD pathway has the ability to be a helices and a nuclease? |
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Definition
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Term
| which sequence elements control RecBCD? |
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Definition
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Term
| What is the difference between RecB and RecD subunits? |
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Definition
| they both are helicases and use ATP hydrolysis, however Rec B has a 3 to 5 helices and has a multimulctional nuclease domain |
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Term
| Which subunit of RecBCD leads the complex ? |
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Definition
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Term
| What does the C subunit of RecBCD do? |
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Definition
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Term
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Definition
| strand invasion and pairing homologous DNAs |
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Term
| Which enzyme breaks double stranded broken DNA into single strands to prepare for homologous recombination?? |
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Definition
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Term
| how does the RecBCD pathway work? |
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Definition
| RecBCD is gliding along the DSB and is cutting both strands into little pieces. Then it encounters the X sequence, and stops for moment. Then it continues on at the rate half as fast as it was moving before and then it starts chopping more on theater strand. |
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Term
| In the Holliday model, how many nicks in how many DNA strands initiates the homologous recombination? |
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Definition
| 2 nicks, in two identical DNA strands but in two different DNA duplexes |
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Term
| how many nucleotides long are X sites? |
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Definition
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Term
| There is 1 RecA for every _________ nucleotides of sand. |
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Definition
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Term
| What are the two binding sites of RecA? |
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Definition
Primary: binding the ssDNA
Secondary: binding the dsDNA, while scanning for complementary sequence. Doesn’t need a specific sequence to bind |
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Term
| In the DSB model, When the ssDNA actually invade ? |
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Definition
| when a complementary sequence is found. RecA catalyzes the H bond between the two sequences |
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Term
| Which model of DNA homologous recombination uses a Polymerase and ligase? |
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Definition
| ---NOT holliday model, so the DSB method |
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Term
| What does the RuvAB complex do? |
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Definition
| initiates the branch migration!! |
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Term
| What does RuvA do? What is it? |
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Definition
| it is a DNA binding protein that recognizes the crossover sites regardless of specific sequence |
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Term
| How many RuvB molecules does RuvA recruit to the Holliday site? What is RuvB? |
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Definition
| it is an ATPase, that catalyzes the actual migration |
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Term
| What is special about the resolving of the DSB model ? |
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Definition
| depending on how it is cut, (by RuvC) two different products can be formed. either non-crossover (identical to parents) or splice products |
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Term
| How many sites are there for cutting per Holliday junction? |
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Definition
| 2: each one has a crossover and parental strand[image] |
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Term
| What happens if the Holliday junctions are cleaved in the same way? |
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Definition
| then patch recombination results (like parent, no crossing over occurs) |
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Term
| What happens if the Holliday junction are cleaved in different ways? |
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Definition
| Then splice recombination products results |
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Term
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Definition
| introduces double-strand breaks, cut-sites are located most commonly in chromosomal regions that are not tightly packed with nucleosomes such as promoters (hotspots for recombination) |
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Term
| How does SPO11 cut the DNA? |
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Definition
| Tyrosine side chain attacks the phosphate backbone to cut DNA, and generate covalent complex between protein and DNA. |
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Term
| WHat are the benefits of the eukaryotic covalent complex formation in homologous recombination? |
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Definition
| The bond energy that it takes to break the chromosme into two is stored within the protein-DNA linkage. So that same energy is reharnessed when the cleavage reaction is reversed. |
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Term
| What is the MRX enzyme complex? |
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Definition
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Term
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Definition
| bacterial RecA homolog in eukaryote and play a role for meiotic recombination |
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Term
| When are Rad51 and Dmc1 expressed? |
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Definition
| Rad51 expresses both mitotically and meiotically, but Dmc1 is expressed in only meiosis |
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Term
| What's the difference between SPO11 and HO? |
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Definition
| Spo11 keeps DNA covalently linked, HO hydrolyzes the DNA |
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Term
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Definition
| endonuclease involved in homolgous recombination in yeast |
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