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Lec 08 Origins of Variation.docx

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Biology 1001A

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Lecture 08: Origins of Variation Mechanism of proofreading and likely result of proofreading defects 1. Polymerization activity of DNA polymerase adds DNA nucleotides to new chain in 5’ > 3’ direction using complementary base pairing rules 2. DNA polymerase adds mispaired nucleotide 3. DNA polymerase recognizes the mismatched base pair; enzyme reverses, using its 3’ > 5’ exonuclease to remove the misparired nucleotide from the strand 4. DNA polymerase resumes its polymerization activity in the forward direction, extending the new chain in the 3’ > 5’ direction - In bacteria, proofreading has reduced error from 1 mistake for every 1,000 to 10,000 nucleotides assembled to 1 mistake for every 1 million nucleotides assembled Mechanism of mismatch repair 1. Repair enzymes move along DNA, scanning for distortions in double helix due to a mispaired base; enzymes break the backbone of the new strand on each side of the mismatch 2. Enzymes remove several to many bases, leaving gap in DNA 3. DNA polymerase fills in gap with 5’ > 3’ polymerizing activity, using template strand as guide 4. DNA ligase seals the nick left after gap filling to complete the repair Differences among insertion sequences, transposons and retrotransposons - Transposable elements (TEs): mobile elements - Transposition: mechanism of movement of TEs; occurs at a low frequency as 1. cut-and-paste process: TE leaves original location and transposes to a new location 2. copy-and-paste process: copy of TE transposes to a new location, leaving original TE behind (TE remains at original spot and copy integrates into target site) - Two major types of bacterial TEs 1. Insertion sequences (IS): simpler; inverted repeat, central sequence, inverted repeat 2. Transposons: IS element, central sequence (possibly including host genes), IS element - Two classes of eukaryotic TEs: 1. Transposons: very similar to bacterial transposons and their transposition processes 2. Retrotransposons: DNA element integrated into chromosomal DNA; named so because transposition occurs via an intermediate RNA copy of the TE a. Retrotransposon is transcribed into complementary RNA copy b. Reverse transcriptase (encoded by a gene in retrotransposon) uses RNA as template to make DNA copy of retrotransposon c. DNA copy is then inserted into DNA at a new location (original is left in place) Implications of insertion of mobile elements into DNA - TEs inserted into chromosomes be
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