Lecture 2B - DNA Supercoiling Flashcards
what DNA can be easily topologically constrained?
circular DNA, unlike linear DNA because it has free ends;
how long do the supercoils happen at?
10 bases
what are topoisomers?
circular DNA that is covalently closed but have the same length and different linking numbers
what topoisomer moves the shortest to farthest: supercoil, circular, linear
circular, linear, supercoil
what is cccDNA?
covalently closed circular DNA
what is the linking number?
it is the number of times one strand would pass through another strand for both strands to be separated.
what is twist?
number of times one strand wraps around another; it can be determined by dividing total bp by 10.5 b/c that’s how much per twist
what is writhe?
number of times helix crosses over itself
what is Lk0?
linking number of relaxed cccDNA at physiological conditions; there are no nicks or cuts so no writhes
what do topoisomerase 1 do?
can break a phosphodiester bond to relieve the stress, the nick is then repaired; change linking number by 1 by making single strand breaks
are most DNA negatively or positively supercoiled?
negatively because it can provide energy for separating the strands using the stored energy
The energy in the strand is measured using ___.
linking difference which is shown by the equation ; Lk0 < 0 is negatively supercoiled, lk0 > 0 is positively supercoiled
what is the mech of topoisomerase type 1?
tyrosine attacks phosphodiester bond of target DNA and cleaves it, enzyme changes from closed to open conformation, unbroken strand then moves over, then 3-OH from broken end attacks the phosphotyrosine bond to reform the helix
what is topoisomerase type 2 and mech?
changes linking number by 2; makes double strand breaks before resealing it; uses ATP; DNA wraps around enzyme then double strand break, strand crosses over, resealing
what is DNA gyrase?
type 2 topoisomerase that can induce negative supercoiling
