DNA structure

Question 1

Describe the B form of DNA

Answer 1

This structure is the normal DNA in the nucleus
It has 10 base pairs per helical turn
The base pairs are on the inside and the sugar and phosphate are on the outside
Righ-handed turns

Question 2

Describe the A form of DNA

Answer 2

Morris Wilkins was able to produce the A form
Also a right-handed DNA helix
More tightly wound than B where the size of the major and minor groove is really close and more similarly sized

Question 3

Describe the Z form of DNA

Answer 3

A left-handed helix

Can be found inside cells but its function is not well established

Question 4

What is a nucleotide and how are they linked together?

Answer 4

Nucleotides are repeating base, sugar and phosphate units

They are linked together by 3’-5’ phosphate links

Question 5

Which bases are pyrimidine and which bases are purines?

Answer 5

Cytosine, thymine and uracil are pyrimidines
Adenine and guanine are purines
Pyrimidines consist of a six membered ring
Purines have two rings

Question 6

How many hydrogen bonds are there between each base pair?

Answer 6

There are three hydrogen bonds between cytosine and guanine

There are two hydrogen bonds between adenine and thymine

Question 7

What type of helix is tRNA folded in?

Answer 7

A-form

Question 8

List three unusual DNA structures

Answer 8

1. Left-handed or Z’ DNA formed by 5’…GCGCGCGCGC… or 5’…GTGTGTGTGTG
2. Four-stranded junction- Holliday junction
3. Tetraplex DNA: 4-stranded DNA helix formed at telomeres; involves G-rich DNA sequences

Question 9

How does a Holliday junction occur?

Answer 9

A Holliday junction arises naturally in living cells through DNA strand exchange between two homologous chromosomes
They have an important role in exchanging genetic information and DNA repair
(look up more)

Question 10

How do the structural levels of proteins apply to DNA?

Answer 10

Primary- the sequence of bases (determined through DNA sequencing
Secondary- the DNA’s helical structure (X-ray and chemistry)
Tertiary- DNA supercoiling formed naturally in bacteria (electron microscopy)
Quaternary- interlocked chromosomes

Question 11

Recall the steps of Sanger sequencing

Answer 11

A DNA strand is copied with a DNA polymerase in the presence of inhibitors that arrest DNA synthesis specifically at A, C, G or T
The DNA is denatured and then the strands are separated by length on a polyacrylamide gel
If the DNA or incorporated inhibitor is radioactive or fluorescent, the DNA bands can be visualised and the sequence read
(Between 770-1000 bases can be visualised per read)

Question 12

What causes DNA supercoiling in bacteria?

Answer 12

DNA gyrase

Question 13

What causes DNA relaxation in bacteria?

Answer 13

Topo IV and Topo I

Question 14

What does an E.coli chromosome look like

Answer 14

E.coli chromosome is circular and organised into ~50 independently supercoiled domains

Question 15

What is chromatin?

Answer 15

DNA is complexed with histones and other proteins to form a nucleoprotein complex called chromatin
Nucleosomes are the basic building blocks of chromatin

Question 16

List at least three ways mutations arise in DNA

Answer 16

1. Spontaneous e.g. loss of bases or hydrolysis of C to U Chemicals and radicals generated by oxidative metabolism:
2. Hydroxyl radicals can convert guanine to 8-oxoguanine; a lethal mutagenic base
3. Changes base structure
4. Insertion between bases (intercalators such as doxorubicin widely used as anticancer drugs)
5. Radiation
6. UV light produces thymine dimers
7. Ionising radiation (X-rays, gamma rays) break DNA chromosomes to cause leukaemia

Question 17

What happens if something breaks the DNA phosphodiester bonds

Answer 17

You get what is called a translocation where pieces from two different chromosomes are released and they can be linked together

Question 18

What happens to patients with xeroderma pigmentosum?

Answer 18

They have a defect in excision repair that deals with UV damage to DNA and so are very prone to skin cancer