week5_lecture_1 - Required readings for Week 5 WEAVER...

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Required readings for Week 5 WEAVER, MOLECULAR BIOLOGY 5 th Ed.: DNA damage & repair: Chapter 20, pp. 656- 674 (but skip “the role of chromatic remodeling in double-stranded break repair” section, pp. 666-667) DNA homologous recombination: Chapter 22 (but skip pp. 723-727) Assaying DNA-protein interactions: Chapter 5, pp. 108-114
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Lecture 1 this week - DNA damage and  repair  1 st  hour: recap, quiz (20 min), finish  Tetrahymena  experiments re: telomeres  (from last week), nucleotide excision  repair, base excision repair, mismatch  repair  Break  2 nd  hour: post-replication repair, the SOS  response, eukaryotic DNA repair
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RECAP REPLICONS Eukaryotic replicons – eukaryotic chromosomes have many replicons, many origins. Unidirectional vs. bidirectional origins E. coli ori C (3x13 bp + 5x9 bp, binds DnaA*ATP, recruits DnaB/C) Yeast ARSs ARG4 contains ARS stably maintained extra-chromosomal DNA Linker scanning mutagenesis to discover A, B 1 , B 2 , B 3 regions in ARS Plasmid incompatibility: Single copy vs. multi-copy plasmids DNA REPLICATION & E. coli CELL CYCLE - replication limiting factor is cell division - fast growth ---> replication starts before last replication cycle ends ROLLING CIRCLE REPLICATION: phages M13 & ϕ X174 REPLICATING LINEAR ENDS: T4 & T7 phages - concatemers Adenovirus - protein primer Parvovirus - hairpin loops, no free ends Telomeres - variable ends, rebuilt/extended after replication TELOMERASE: RNA-protein complex provides template for extension of DNA repeats at chromosome ends, GC-rich repeats in humans
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DNA “fidelity” 1. Replication accuracy 2. Damage correction mechanisms DNA REPLICATION VERY ACCURATE: * DNA pol III error rate ~7 X 10 -6 per division * with 3’ to 5’ exo proofreading, it is ~5 X 10 -9 per division * with repair mechanisms DNA REPAIR - MUTATION
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DNA DAMAGE: SINGLE BASE DNA DAMAGE: SINGLE BASE CHANGES CHANGES e.g., e.g., single replication single replication errors; cytosine errors; cytosine deamination to uracil deamination to uracil 1. Single base changes do 1.
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  • Spring '11
  • DAVIDSON
  • DNA

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