DNA structure

Question 1

What is DNA present as in the nucleus?

Answer 1

Chromatin

Question 2

What is the structure of A-DNA?

Answer 2

• Right handed
• 11 base pair per turn
• Diameter of 2.3nm
• DNA is driven into A form when under dehydrating conditions
• Major and minor groove width very similar
• 20-25% shorter than B DNA

Question 3

What is the structure of B-DNA?

Answer 3

• Present in most of our cells
• 10 base pair per turn
• Most DNA present in our cells is B-form
• Right handed

Question 4

What is the structure of Z-DNA?

Answer 4

• Left handed
  
  • Repeats every other base pair
  • 12 base pair per turn
  • Conditions like alternating purine-pyrimidine sequence can promote the formation, negative DNA supercoiling

Question 5

How is the energy provided for the formation of major and minor grooves?

Answer 5

Hydrolysis of water

Question 6

Evidence of DNA structure from X-ray diffraction?

Answer 6

• There is a major groove which is wide and accessible to drugs and proteins
• Dark lines due to base pairs heavily diffracting light
• The cross confirmed a helical structure

Question 7

How is the DNA helix formed?

Answer 7

• Two antiparallel polynucleotide chains form a RH helix

Question 8

What is the diameter of the DNA?

Answer 8

2nm

Question 9

How many strands does tRNA have and what does it fold into?

Answer 9

Single stranded and folds into a A-form helix as its complementary to itself

Question 10

Examples of unusual DNA structure

Answer 10

Z DNA
Holiday junction
Tetraplex DNA

Question 11

What is the holiday junction ideal for?

Answer 11

○ Ideal for double strand break repair.

○ Homologous recombination

Question 12

Different levels of DNA strucutre

Answer 12

• Primary- sequence of bases
• Secondary- Helical structure
• Tertiary- DNA supercoiling
• Quaternary- interlocked chromosomes

Question 13

What does DNA gyrase with ATP cause?

Answer 13

Negative Supercoiling

Question 14

Structure of coli

Answer 14

• Circular and organised into 50 independently supercoiled domains

Question 15

How many base pairs does E coli DNA have?

Answer 15

3x10^6 basepairs

Question 16

What are nucleosomes?

Answer 16

Basic building block of chromatin

Question 17

How were nucleosomes first seen in an EM?

Answer 17

Seen as beads on strings

Question 18

How many bp are nucleosomes made up of?

Answer 18

146

Question 19

How many histones is it wrapped around?

Answer 19

8

Question 20

What is heterochromatin?

Answer 20

Chromatin is densely packed and not expressed

Question 21

What is euchromatin?

Answer 21

Chromatin is not densely packed and is expressed

Question 22

What does H1 protein do?

Answer 22

• H1 protein keeps the DNA in place which is wrapped around the hisones

Question 23

What damage is caused by mutations?

Answer 23

• Spontaneous like the hydrolysis of C to U
• Chemicals
	○ Change base structure
	○ Insert between bases
• Radiation
	○ UV light produces thymine dimers (cyclobutyl ring formed between adjacent thymines.)
	○ Ionising radiation
• Oxidative stress:
	○ Oxygen free radicals.

8-oxoguanine is how you detect stress

Question 24

What is the importance of DNA repair?

Answer 24

• Genome stability

* Other cancer prone families have DNA repair defects

Question 25

How can DNA be repaired?

Answer 25

• DNA photolyase 
• DNA photoreactivation:
	○ Photons cleave the C-C bond of cyclobutyl ring of thymine dimers
• Excision repair:
	○ Endonucleae enzyme cleaves the DNA backbone on 5' side of abnormal base
	○ RNA ligase reseals with correct base
	○ UvrA,UvrB recognises damage
	○ UvrC-incision
	○ UvrD-removes bases