Wolberger_DNA Flashcards
T/F. Most DNA in humans is A-DNA form.
False, B-DNA.
type of linkage between deoxyribonucleotides
phosphodiester
direction of nucleic acids
5’ - 3’
be able to draw nucleotides and their basepairing faces
do it
form of DNA produced when DNA fibers maintained at a lower humidity
A-DNA
what stabilizes helix?
base stacking and base pair hydrogen bonding
distance between bp (B-DNA)
3.4A
how many base pairs per turn (B-DNA)
10.5 bp
what is helix diameter (B-DNA)
20A
what is conformation of sugar pucker on B-DNA
C2’ - endo
T/F. Major groove is deep but narrow, and minor groove is shallow, on A-DNA.
True
T/F. A-DNA helix is overwound compared with B-DNA.
False, helix is underwound at 11bp/turn and is also wider at 23A
What makes Z-DNA crazy?
Left handed helix, DNA sequence must be alternating purine-pyrimidine
T/F. In A and B DNA, all bases are in the anti orientation.
True, and this is a key difference from Z-DNA, which has some bases anti- and some syn-
why does syn- conformation suck for pyrimidines?
you get steric crashing between the sugar and oxygen
what nucleotide forms quadruplex DNA?
Guanine bases, called G-quartets
T/F. DNA binding proteins typically recognize binding sites from functional groups exposed in the major groove.
True
What secondary structural motif is common to many DNA binding proteins?
An alpha helix, which is inserted into DNA major groove
what is supercoiling
topological deformation of DNA, found in closed loops and regions of linear DNA with constrained ends
negative supercoiling
DNA is partially unwound
positive supercoiling
DNA is overwound
T/F. Supercoiling makes it more energetically favorable to melt out (unwind) local stretches of DNA.
False in general - True for negative supercoiling, but false for positive supercoiling (why you need topoisomerases)
how to calculate DNA twist
number of helical turns in DNA, twist = #bp/10.5 (ex. 21 bp, twist = +2
how to calculate writhe (supercoiling)
if writhe is negative, DNA is negatively supercoiled. Writhe = linking number - twist
linking number
integer to describe how many times a nucleotide strand winds around the other. For relaxed 21 bp DNA, linking number = 2
