Discussion section1

Discussion section1 - strand passage (5-linked phospho Tyr)...

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Discussion section 04/11/08 Sharon, Kwan-I, Wu Email: k9wu@ucsd.edu
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Central Dogma DNA --------> RNA ------> Protein 1. DNA, RNA, and proteins are all polymers 2. Enzymes carry out polymerization transcription translation
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The “bases” in DNA Purines are attached at their N9 position to the 1’ carbon atom of sugar Pyrimidines are attached at their N1 position to the 1’ carbon atom of sugar
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DNA and RNA Deoxyribonucleic acid Ribonucleic acid Nucleotide is the sugar, base, & phosphate Nucleoside is the base & sugar w/o phosphate
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DNA has “directionality” DNA synthesis occurs in the 5’-->3’ direction
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DNA structure=> double helix “Antiparallel” 3.4nm 10bp/turn
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Three forms of DNA
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Forces stabilizing the DNA helix 1. Base pairing Watson-and-Crick/ non- Watson-and-Crick 1. Base stacking 2. Ion interactions (ex. Mg2+)
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(http://users.ugent.be/~avierstr/principles/pcrsteps.gif)
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Superhelix topology Twist + Writhe = Linking number
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topoisomerases type I: one strand only is cut, then repaired type II: both strands are cut, then repaired (multimeric enzymes, ATP hydrolysis)
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Mechanism of type 1A topoisomerase relaxes only negative supercoils by 
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Unformatted text preview: strand passage (5-linked phospho Tyr) Mechanism of type 1B topoisomerase relaxes both negative and positive supercoils by controlled rotation(3-linked phospho Tyr) Mechanism of type II topoisomerase-both strands are cleaved at staggered positions (sticky end)-relaxes positive and negative supercoils-can de-catenate two dsDNA circles DNA Experimental Tools Spectroscopy Staining Purification Fractionation Hybridization spectroscopic absorbance OD 260/280 ratio High GC content, Higher Tm High AT content, Lower Tm staining EtBr Bind to ds DNA by intercalation(slipping in between the stacked bases) Purification:density centrifugation Fractionation: by electrophoretic mobility Large fragments Small fragments Gel Electrophoresis: agarose: 150bp - 30kb polyacrylamide: < 500bp Hybridization Southern blotting: DNA/DNA Northern blotting: DNA/RNA Western blotting: protein/protein Southern blotting DNA Fingerprinting microarrays...
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This note was uploaded on 10/30/2010 for the course CHEM 114C taught by Professor Alexanderhoffmann during the Spring '08 term at UCSD.

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Discussion section1 - strand passage (5-linked phospho Tyr)...

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