Term
| What are the steps of homologous recombination? |
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Definition
1. Formation of ss or ds breaks in the DNA.
2. Alignment of homologous DNA (requires nearly identicle nucleotide sequence for ~100 bp).
3. Strand invasion and formation of Holliday Junction
4. Branch migration - movement of the Holliday Junction along the DNA molecules.
5. Resolution - cleavage of Holliday Junction at either the invading strand (non-recombinant, patch, non-cross over) or the other strand (recombinant, splice, or crossover) |
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Term
| What are 3 sources of DNA breaks in homologous recombination in prokaryotes? |
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Definition
1. Ionizing radiation
2. DNA replication errors
3. Linear DNA that enters the bacteria during phage-mediated transduction or cell-cell conjugation.
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Term
What are sources of DNA breaks in homologous recombination in eukaryotes?
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Definition
Mitotic - ionizing radiation, damaging agents, DNA replication errors, transponson movement, and immunoglobulin synth.
Meiotic - Spo11 induces double strand breaks to initiate recombination during protracted prophase. |
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Term
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Definition
| induces double strand breaks to initiate recombination during protracted prophase |
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Term
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Definition
| generation of ssDNA with 3' overhangs and recruits RecA |
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Term
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Definition
| Stabilization of ssDNA, strand exchange and assembles Holliday Junction |
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Term
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Definition
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Term
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Definition
| makes the nicks for resolution |
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Term
| Where are "hotspots" for mediating disease causing recombination errors? |
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Definition
| Tandemly repeated DNA and interspersed repetitive DNA. |
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Term
| What is transpositional recombination? |
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Definition
| Movement of certain sections of DNA to randomly different positions in the genome. Present in all organisms. |
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Term
| What percent of human genome is transposon related DNA sequence? What percent DNA and RNA transposons? |
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Definition
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Term
| What are the 2 classes of transposable elements and how do they work? |
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Definition
DNA transposons - "cut and paste"; jumping genes; mediated by transposonase
RNA transposon - "copy and paste"; selfish genes; reverse transcription of RNA of the transposon into complementary DNA |
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Term
| What are the 2 types of RNA transposons and what percent of the human genome do they make up? |
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Definition
Viral-like [Long Terminal Rpt (LTR)] retrotransposon - 11%
Poly-A (non LTR) retrotransposon - 31% |
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Term
| List the steps of DNA transposons. |
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Definition
1. Transposon is transcribed; Transposase is made in the cytoplasm and moves to the nucleus.
2. Cuts original transposon DNA
3. Cuts the target DNA in a sequence independent manner
4. Ligates the transposon in the new site. |
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Term
| List the steps of Viral-like Transposons. |
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Definition
1. Transposon is transcribed; integrase and RT are made in the cytoplasm
2. mRNA of the transposon, integrase and RT form a complex in the cytoplasm
3. mRNA is reverse transcribed to cDNA and the cDNA is processed at the ends by integrase
4. cDNA and the proteins move into the nucleus, integrase cuts the target DNA in random site and ligases the cDNA |
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Term
| List the steps of Poly-A retrotransposon. |
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Definition
1. Transposon is transcribed, RNA binding protein and endonuclease/RT protein are made in the cytoplasm
2. Proteins immediately bind mRNA that it was synthesized from
3. RNA - protein complex moves to nucleus
4. Endonuclease breaks DNA in random site
5. Poly(A) of the transposon mRNA forms a bp with T in the DNA
6. mRNA of the transposon is reverse transcribed using the 3' end of the cut DNA as the primer and mRNA as the template
7. Transposon is integrated by a mechanism not clearly understood |
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Term
| Poly-A retrotransposons give rise to processed pseudogenes. What are pseudogenes? |
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Definition
| DNA sequences similar to normal genes but non-functional; |
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Term
| What identifies a pseudogene? |
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Definition
1. Lack of promoter
2. Lack of introns
3. Missing 5' ends
4. Having DNA-encoded poly(A) region in the 3' end
5. Errors in the open reading frame
6. The two ends have target site duplication |
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Term
Conservative site specific recombination (CSSR)
What enzyme mediates the recombination? |
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Definition
Similar to transponsonal recombination, but cutting and insertion sites are sequence dependent. Takes place at 2 recombination sites that are directional in nature. The product depends on the relative direction of the 2 participating sites.
Recombinase |
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Term
Illegitimate Recombination or
Non-Homologous End Joining (NHEJ) |
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Definition
Break ends are directly ligated without need for a template; microhomologies with just 1-2 complementary bp is used to join the ends;
Primary mechanism of ds break repair in eukaryotes and humans |
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