Lecture 5: DNA Coils and Chromosomes

Question 1

Compare the structures of chromosomes in prokaryotes and eukaryotes.

Answer 1

Prokaryotes - circular DNA

Eukaryotes - linear DNA

Question 2

How can bacterial, phage and plasmid DNA be visualised?

Answer 2

Bacterial, phage and plasmid DNA can be visualized by electron microscopy - the lysed cells are treated with heavy metals which shadow the DNA from the electron beam.

Question 3

How many chromosomes are there in the nucleus of a normal human somatic cell?

Answer 3

46 (the diploid number for humans)

Question 4

What is the first stage of DNA compaction?

Answer 4

DNA supercoiling

Question 5

Why is DNA compaction necessary?

Answer 5

DNA molecules are very long and have to fit in a very small space, such as the eukaryotic nucleus.

Question 6

What is supercoiling?

Answer 6

When the axis of the DNA double helix (the line you would draw straight through the centre of the DNA double helix) is coiled on itself, this forms a superhelix of a supercoil. It is a helix whose strands are made up of a smaller helix, like a old-fashioned phone cord.

Separating the strands of a helix can induce supercoiling. This is shown when an elastic band is twisted and then the strands pulled apart. The elastic band develops strain ahead of the continuing parting and writhes and supercoils.

Question 7

When and by whom was supercoiling discovered?

Answer 7

Jerome Vinograd first detected supercoiling in small, circular viral DNAs in 1965.

Question 8

What are two other terms for supercoiling?

Answer 8

Supertwisting and superhelicity

Question 9

What characteristic of a chromosome is necessary for supercoiling?

Answer 9

A closed structure is required for supercoiling. Bacterial chromosomes are circular, so hence closed.

Eukaryotic chromosomes form large loops with ends held together by proteins.

Question 10

Relate supercoiling to torsion.

Answer 10

Supercoiling creates torsion in the DNA molecule. The greater the degree of supercoiling, the greater the torsion.
Removal of one turn induces structural strain (turn is a spiral in the helix of DNA just in the normal double helix). The strain is generally accommodated by formation of a supercoil.

Question 11

How can the torsion caused by supercoiling be relieved?

Answer 11

Either of the strands can be cut to relieve the torsion caused by supercoiling as this allows the molecule to untwist, releasing the supercoils.

Question 12

What term is used to describe an open or closed structure which is not supercoiled?

Answer 12

Relaxed

Question 13

What are positive and negative supercoiling?

Answer 13

Positive supercoiling twists the DNA in the same direction of the turns of the intrinsic helical turns, e.g. the right handed double helix.

Negative supercoiling twists the DNA in the opposite way from the turns of the right handed double helix.

Question 14

What is another term for a) positively and b) negatively supercoiled DNA?

Answer 14

a) Overwound DNA

b) Underwound DNA

Question 15

Is most naturally occurring DNA positively or negatively supercoiled?

Answer 15

Negatively

Question 16

What is the implication of most naturally occurring DNA being negatively supercoiled?

Answer 16

As mostly naturally occurring DNA is negatively supercoiled, this means that the supercoils twist the DNA in the opposite direction to the right handed helix.

This means that the torsional stress can be relieved by loosening the winding of the double helix of the DNA and limited disruption of the the base pairing is required. This is important for DNA replication and transcription.

DNA underwinding makes it easier to separate strands.

In principle, each turn of underwinding should facilitate strand separation over about 10 base pairs, as shown. However, the hydrogen-bonded base pairs would generally prevent strand separation over such a short distance and the effect becomes important only for longer DNAs and higher levels of DNA underwinding.

Question 17

What causes supercoiling?

Answer 17

Supercoils are introduced and removed by enzymes called topoisomerases.

Supercoiling is introduced by Type 2 topoisomerases (prokaryotes only). This requires energy from ATP hydrolysis and this energy is stored in the supercoils and fuels transcription and replication.

Supercoiling is removed by Type 1 topoisomerases (prokaryotes and eukaryotes), through incremental relaxation of the DNA.

Question 18

What is Lk?

Answer 18

The link number

Question 19

What are nucleosomes?

Answer 19

Nucleosomes have a protein core of 8 basic proteins called histones and in eukaryotic cells, the DNA wraps around these nucleosomes, which assemble the DNA into 30 nm threads.

Question 20

How many times can a length of 146 nucleotides wrap around the histone core?

Answer 20

This length of 146 nucleotide pairs is sufficient to wrap 1.65 times around the histone core.

Question 21

In what way is DNA wrapped around nucleosomes protected?

Answer 21

The DNA wrapped around nucleosomes is protected from degradation by nucleases, which can only attack the linker DNA between the nucleosomes.