BIO SCI 98 Chapter Notes - Chapter 5: Type I Topoisomerase, Linking Number, Phosphodiester Bond
19 Jun 2018
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Page 305-306, 312-314, 324, 398-402
DNA Supercoiling
-DNA is coiled in the form of a double helix
-Supercoiled DNA is a manifestation of structural strain
-If there is no coiling or bending = relaxed DNA
-Occurs in all chromosomal DNA, as well as viruses
-Tertiary structure
-Caused by underwinding of DNA → catalyzed by topoisomerases
-Highly regulated
-DNA topology: continuous deformations include conformational changes due to stretching,
thermal motion, or interaction with proteins/other molecules
-Topological properties of DNA can be changed by ligation or breakage of DNA strands
The Enzymes That Promote DNA Compaction
-DNA supercoiling influences DNA metabolism
-Replication, transcription, condensation during mitosis
-Catalyzed and facilitated by topoisomerases and SMC proteins
Topoisomerases Catalyze Changes in Linking Number of DNA
-Topoisomerases increase/decrease extent of DNA underwinding by changing the linking
number
-Type I topoisomerases break one of the two DNA strands, pass unbroken strand through
break, and ligate broken ends
-Change Lk in increments of 1
-Type II topoisomerases break both strands and change Lk in increments of 2
-DNA is never releases from enzyme during these transactions
-Activity can be seen with agarose gel electrophoresis
-More supercoiled DNA are more compact → travel faster
-E. coli has 4 topoisomerases
-Type I = Topo I and III → relax DNA by breaking singe strands
-Type I topoisomerase reaction
1) DNA binds to topoisomerase and one DNA strand is cleaved
2) Enzyme changes conformation
3) Unbroken DNA strand moves through break in first strand
4) DNA strand is ligated and released
-No ATP used
-Topoisomerase must both cleave DNA strand and ligate it again
-Cannot hydrolyze phosphodiester bond bc too high energy
-Nucleophile (Tyr res) attacks phosphodiester bond
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
Dna is coiled in the form of a double helix. Supercoiled dna is a manifestation of structural strain. If there is no coiling or bending = relaxed dna. Occurs in all chromosomal dna, as well as viruses. Caused by underwinding of dna catalyzed by topoisomerases. Dna topology: continuous deformations include conformational changes due to stretching, thermal motion, or interaction with proteins/other molecules. Topological properties of dna can be changed by ligation or breakage of dna strands. Catalyzed and facilitated by topoisomerases and smc proteins. Topoisomerases catalyze changes in linking number of dna. Topoisomerases increase/decrease extent of dna underwinding by changing the linking number. Type i topoisomerases break one of the two dna strands, pass unbroken strand through break, and ligate broken ends. Type ii topoisomerases break both strands and change lk in increments of 2. Dna is never releases from enzyme during these transactions. Activity can be seen with agarose gel electrophoresis. More supercoiled dna are more compact travel faster.
