Lecture 17: DNA Topology and Topoisomerases

Question 1

How many histone types are there in a nucleosome

Answer 1

1. H1 - “linker histone”
   a. 1 per nucleosome
2. H2A -
   a. 2 per nucleosome
3. H2B
   a. 2 per nucleosome
4. H3
   a. 2 per nucleosome
5. H4
   a. 2 per nucleosome

Question 2

What are closed domains of DNA?

Answer 2

DNA where the ends are concealed. May be due to:

a. being circular
b. or proteins concealing the end

Question 3

What is meant be linking number and how is it calculated?

Answer 3

Linking number (LK): Equal to the number of times the two DNA strands revolve around each other

LK of normal DNA = LK^0

LK^0 = N/H

N = no. of bp in DNA (section)
H = bp per turn of helix (usually 10.5)

Question 4

What is negative and positive supercoiling?

Answer 4

Negative supercoiling: Removal of twists

Positive supercoiling: addition of twists

Question 5

What is DNA supercoiling like in vivo

Answer 5

1. DNA molecules can be bound by
   proteins to dorm local “looped domains”
2. Each loop is constrained separately,
   allowing individualised levels of
   supercoiling

Question 6

What is meant by superhelical density (sigma)

Answer 6

Superhelical density/sigma = deltaLK/LK^0

usually ~-0.02 to -0.05

Energy is required to maintain supercoils, which is why its usually negative

Question 7

What are the two types of topoisomerase and what do they do?

Answer 7

1. Type 1 topoisomerase
   a. Removes negative supercoils
   b. Alters LK by -1
2. Type 2 topoisomerase
   a. Energy required to introduce
   supercoils
   b. Introduces negative supercoils,
   requiring ATP (DNA gyrase in bacteria)
   c. DNA gyrase in E. coli: alpha2beta2,
   alpha gene = gyrA, beta gene = gyrB
   d. Target for antibiotics:
   i. nalidixic acid targets gyrA
   ii. novobiocin targets gyrB