Lecture 2

Question 1

function of major groove

Answer 1

*

Question 2

base pairs per turn of b dna

Answer 2

10

Question 3

relative dif between each form of dna

Answer 3

groove size, diameter, rise, pitch, handednes

Question 4

interactions stabilizing dsdna duplex

Answer 4

hydrophobic, van der waals

Question 5

chargaffs rule

Answer 5

[A]=[T] and [G]=[C]

Question 6

lactam vs lactim

Answer 6

*

Question 7

lactam/lactim dominates at pH 7

Answer 7

lactam (99.99%)

Question 8

if 0.01% lactim form, how many bases out of 3 B bp are in the lactim form

Answer 8

600,000

Question 9

increased/decreased ionic strength causes denaturation

Answer 9

decreased ionic strength

Question 10

how does pH effect denaturation

Answer 10

*

Question 11

left handed superhelix is positive/negative supercoiling

Answer 11

negative supercoiling

Question 12

predominant supercoil orientation

Answer 12

left handed superhelix (negative supercoil)

Question 13

define negative supercoiling

Answer 13

deficit of helical turns

Question 14

Lk, linking number

Answer 14

*

Question 15

specific linking difference

Answer 15

*

Question 16

writhing number Wr

Answer 16

*

Question 17

twisting number Tw

Answer 17

*

Question 18

omege protein has type 1/2 topoisomerase activity?

Answer 18

type 1

Question 19

DNA gyrase has type 1/2 topoisomerase activity?

Answer 19

type 2

Question 20

negative supercoiling refers to high/low energy structure

Answer 20

high energy

Question 21

purpose of negative supercoiling

Answer 21

facilitate replication and transcription

Question 22

eukaryotic topoisomerase 3 is this type?

Answer 22

type 2

Question 23

region around histone core is negative/positve supercoil

Answer 23

negative

Question 24

region unbond to histone core is negative/positive sueprcoil

Answer 24

positive

Question 25

dna form with lowest pitch

Answer 25

DNA A

Question 26

dna denatured by increased/decreased ionic strength

Answer 26

decreased

Question 27

chemical reagents that denature dna

Answer 27

urea and formamide

Question 28

stabilization of a h bond

Answer 28

4 kj / mol

Question 29

stacking interactions GC vs AT

Answer 29

GC stacking is stronger than AT

Question 30

renaturation process

Answer 30

step 1, nucleation, is second order. once nucleation site is found the strands zip up quickly in a first order reaction

Question 31

hyperchromic effect

Answer 31

ds DNA absorbs less light at 260nm than the two constituent ss DNA

Question 32

carbon of purine that binds to sugar

Answer 32

9

Question 33

carbon of pyrimidine that binds to sugar

Answer 33

1