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Study Guide Test 3

Study Guide Test 3 - Watson Chapter 11 Transposable...

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Watson Chapter 11 Transposable Elements: DNA transposons Viral-like retrotransposons Poly-A retrotransposons DNA transposons require inverted repeat sequences (recombination sites), gene encoding transposase (possibly other things like resistance), target site duplication; includes P elements Viral-like retrotranposase have long terminal repeats (LTRs) in place of inverted repeat sequences for DNA. These tranposons encode for integrase and reverse transcriptase, needed for the RNA intermediate (“retro”). Same as DNA transposition except DNA forms element RNA to form cDNA from reverse transcription. This group includes the Ty elements (galactose helps transposition). RNA intermediate helps to get the retrotransposon out of the cell. Poly-A have no terminal inverted repeats; instead, they have a 5’UTR (untranslated) and the 3’UTR followed by a stretch of poly-a sequences. They carry ORF1 and ORF2 for reverse transcriptase and endonuclease activity. Uses RNA intermediate and reverse splicing to form LINE cDNA Autonomous transposons have everything needed to carry out transposition Nonautonomous transposons carry only terminal inverted repeats (cis acting sequences); cannot move on their own S & D between cut-and-paste and replicative Similarities: both from transpososome, 3’ OH attack phosophdiester bonds Differences: replicative is not excised from original position. Only 3’ OH ends created. At DNA transfer, 3’OH ends attach to new DNA but one side is still attached to old DNA. Replication fork to generate two copies of transposon DNA. In process of moving, replicative tranposon rearranges flanking chromosomal sequences. For some, site specific recombination occurs between two transposons. Cut-and-paste transposition / Replicative Watson Chapter 19 Altering Pattern-determining genes 1. Change in expression pattern a. Pax6 and ectopic eyes, antp and leg antennae 2. Changes in encoded regulatory proteins a. Ftz and Antp; one acquiring both proteins for repression and activation 3. Changes in target enhancers a. Changes in the target enhancers that are regulated by PDGs; variating affinities of target enhancers to binding sites
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Watson Chapter 9 DNA Damage: methylated Cs are hotspots for spontaneous mutations due to 5-methyl cytosine easily generating thymine (hard to repair) Spontaneous damage: hydrolysis and deamination Other Damage: Alkylation, Oxidation, Radiation, base analogs: 5-bromouracil intercalating agents: proflavin, acridine, ethidium Keto preferred over enol Mismatch repair system: MutS, the mismatch repair protein, scans DNA and makes kink at mismatch; recruits MutL and MutH (enzyme) which incises DNA upstream from mismatch. Pol III fills in the gap with the correct sequence and DNA ligase seals it.
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