Wolberger_DNA

Question 1

T/F. Most DNA in humans is A-DNA form.

Answer 1

False, B-DNA.

Question 2

type of linkage between deoxyribonucleotides

Answer 2

phosphodiester

Question 3

direction of nucleic acids

Answer 3

5’ - 3’

Question 4

be able to draw nucleotides and their basepairing faces

Answer 4

do it

Question 5

form of DNA produced when DNA fibers maintained at a lower humidity

Answer 5

A-DNA

Question 6

what stabilizes helix?

Answer 6

base stacking and base pair hydrogen bonding

Question 7

distance between bp (B-DNA)

Answer 7

3.4A

Question 8

how many base pairs per turn (B-DNA)

Answer 8

10.5 bp

Question 9

what is helix diameter (B-DNA)

Answer 9

20A

Question 10

what is conformation of sugar pucker on B-DNA

Answer 10

C2’ - endo

Question 11

T/F. Major groove is deep but narrow, and minor groove is shallow, on A-DNA.

Answer 11

True

Question 12

T/F. A-DNA helix is overwound compared with B-DNA.

Answer 12

False, helix is underwound at 11bp/turn and is also wider at 23A

Question 13

What makes Z-DNA crazy?

Answer 13

Left handed helix, DNA sequence must be alternating purine-pyrimidine

Question 14

T/F. In A and B DNA, all bases are in the anti orientation.

Answer 14

True, and this is a key difference from Z-DNA, which has some bases anti- and some syn-

Question 15

why does syn- conformation suck for pyrimidines?

Answer 15

you get steric crashing between the sugar and oxygen

Question 16

what nucleotide forms quadruplex DNA?

Answer 16

Guanine bases, called G-quartets

Question 17

T/F. DNA binding proteins typically recognize binding sites from functional groups exposed in the major groove.

Answer 17

True

Question 18

What secondary structural motif is common to many DNA binding proteins?

Answer 18

An alpha helix, which is inserted into DNA major groove

Question 19

what is supercoiling

Answer 19

topological deformation of DNA, found in closed loops and regions of linear DNA with constrained ends

Question 20

negative supercoiling

Answer 20

DNA is partially unwound

Question 21

positive supercoiling

Answer 21

DNA is overwound

Question 22

T/F. Supercoiling makes it more energetically favorable to melt out (unwind) local stretches of DNA.

Answer 22

False in general - True for negative supercoiling, but false for positive supercoiling (why you need topoisomerases)

Question 23

how to calculate DNA twist

Answer 23

number of helical turns in DNA, twist = #bp/10.5 (ex. 21 bp, twist = +2

Question 24

how to calculate writhe (supercoiling)

Answer 24

if writhe is negative, DNA is negatively supercoiled. Writhe = linking number - twist

Question 25

linking number

Answer 25

integer to describe how many times a nucleotide strand winds around the other. For relaxed 21 bp DNA, linking number = 2