Recitation_4_handout_-_Simona

Recitation_4_handout_-_Simona - 7.05 Section 05 TA: Simona...

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7.05 – Section 05 03/05/2008 TA: Simona Tescu Email: tescu@mit.edu *adapted from Luke Thompson’s recitation handout 1/5 RECITATION #4 Covers lectures: 10, 11: DNA Replication, Sequencing and Transcription This week’s office hours: by appointment Solutions to this week’s handout will be posted online. Questions about exam I??? Overview of theory DNA Replication Semiconservative: each parental DNA strand will be replicated to a daughter strand Replication fork: Leading and Lagging strands (Okazaki fragments) Joining of the Okazaki fragments is performed by a DNA ligase: catalyzes the formation of a phosphodiester bond between the 3’ hydroxyl group at the end of one DNA chain and the 5’-phosphate group at the end of the other. Requires: Primer – synthesized by an RNA polymerase, called primase; it is base- paired to the template and has a free 3’-OH Helicase: unwinds the two strands, using ATP for energy Template (DNA-dependent DNA polymerase) Substrates: dATP, dCTP, dGTP, d T TP Mg 2+ : stabilizes the negative charges on phosphates, including the transition state Synthesis goes 5’ 3’ Proofreading goes 3’ 5’ 3’-OH attacks the 5’ α -phosphate of the incoming dNTP (first the incoming NTP base pairs to the template, and then the 3’-OH attacks the 5’ α -phosphate) Newly added dNTPs base-pair to the template (if not, mismatch will occur) Topoisomerases: break and reseal phosphodiester bonds Type I topoisomerase: catalyzes the relaxation of the supercoiled DNA, a thermodynamically favorable process Type II topoisomerase: utilizes free energy from ATP hydrolysis to add negative supercoils to DNA
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7.05 – Section 05 03/05/2008 TA: Simona Tescu Email: tescu@mit.edu *adapted from Luke Thompson’s recitation handout 2/5 DNA polymerases* Type exonuclease # of subunits processivity abundancy Cellular function I 5’ 3’ 3’ 5’ 1 Moderate ~20bp high Removes RNA primer, fills in short gaps II 3’ 5’ 1 Moderate ~10-100bp Medium DNA repair III core 3 Moderate ~100-200bp III Holoenzyme 3’ 5’ 10 High >5000bp Very low Chromosom replication Processivity – average number of nucleotides added before a polymerase dissociates. Questions
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This note was uploaded on 02/06/2009 for the course 7 7.05 taught by Professor Unknown during the Spring '09 term at MIT.

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Recitation_4_handout_-_Simona - 7.05 Section 05 TA: Simona...

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