DNA structure

Question 1

What is DNA present as in the nucleus?

Answer 1

Chromatin.

Question 2

What can damage DNA? (2 things)

Answer 2

DNA can be damaged by radiation and chemcials.

Question 3

Describe the structure of DNA.

Answer 3

• DNA has a double helix structure which is made up of two complementary polynucleotide chains that run anti-parallel to each other.
• Each nucleotide is joined together by phosphodiester bonds to form a polynucleotide chain.
• The two strands are held together by hydrogen bonds between the complemantary base pairs.
• One strand runs from 5’-3’ and the other from 3’-5’.
• The helix consists of minor and major groves that can be receptors for drugs.

DNA is acidic becasue of the negatively charged phosphates that loose a proton.

This allows histones (proteins) with a positive charge to associate with DNA.

Question 4

Where does the major groove occur?

Answer 4

The major grove occurs where the backbones are far apart.

Question 5

Where does the minor grove occur?

Answer 5

The minor grove occurs where the backbones are closer together.

Question 6

Is DNA - protein binding interaction easier on the major or minor groove and why?

Answer 6

• Proteins like transcription factors that can bind to specific sequences in double-stranded DNA usually make contacts to the sides of the bases exposed in the major groove.
• This is because the edges of the bases are more accessible in major grooves.

Question 7

What are the 3 forms of DNA?

Answer 7

There are 2 helical forms (form A and B) and 1 form (form Z) which is mostly a laboratory anomaly.

Question 8

Give information on A - DNA.

Answer 8

1. It has a fatter and more compact helix compared to B - DNA (which is the most common form of DNA).
2. It has right handed turns.
3. It has 11 base pairs per helical turn.
4. It has a diameter of 2.3nm.
5. The width of the major and minor grooves are very similar in size.
6. It is 20-25% shorter than B - DNA.
7. DNA is driven into A - form when under dehydrating conditions.
8. It is found in RNA and tRNA.

Question 9

Give information on B - DNA.

Answer 9

1. It has right handed turns.
2. This form is present in most of our cells.
3. It consists of 10 base pairs per helical turn.
4. It is 2nm (or 20 angstrom) in diameter.

Question 10

Give information on Z - DNA.

Answer 10

1. It has left handed turns.
2. It runs from 3’-5’ (compared to the normal 5’-3’). Hence it coils the other way compared to A and B.
3. It repeats every other base pair.
4. It consists of 12 base pairs per helical turn.
5. Formation of this structure is generally unfavourable, although certain conditions can promote it; such as alternating purine–pyrimidine sequence, negative DNA supercoiling or high salt and some cations.

Question 11

What does the X-ray diffravtion photograph tell us about the structure of DNA?

Answer 11

Question 12

How many hydrogen bonds form between C and G base pairs? What is the distance between them?

Answer 12

• C and G make 3 hydrogen bonds.
• The distance between this base pair is 1.08nm.

Question 13

How many hydrogen bonds form between A and T base pairs? What is the distance between them?

Answer 13

• A and T base pairs form 2 hydrogen bonds.
• The distance between this base pair is 1.11nm.

Question 14

What are the functions of holliday junctions?

Answer 14

• The Holliday junction is a key intermediate in homologous recombination, a biological process that increases genetic diversity by shifting genes between two chromosomes.
• They are also involved in the repair of double-strand breaks (Double-strand breaks are where both strands in the double helix are severed, are particularly hazardous to the cell because they can lead to genome rearrangements).

Question 15

When does a Holliday junction form?

Answer 15

Holliday junction, cross-shaped structure that forms during the process of genetic recombination, when two double-stranded DNA molecules become separated into four strands in order to exchange segments of genetic information.

Question 16

What are the four levels of DNA structure?

Answer 16

1. Primary structure:- Sequence of bases (DNA sequencing).
2. Secondary structure:- Helical structure (Deciding if its an A, B or Z form). Can be identified using X-ray crystallography and by chemistry.
3. Tertiary structure:- DNA helix is coiled and compacted to enable it to go to the nucleus ( called DNA supercoiling). DNA supercoiling is caused by the enzyme DNA gyrase. It is an active process and needs ATP. Length of all DNA in chromosome is about 2m (over 6 feet) so this is an important property. Supercoiling can be seen through electron microscopy.
4. Quaternary structure:- Before chromosome segregate in metaphase the chromosomes when they are replicated can be tangled so the two daughter chromosomes can be tangled together. If they are pulled apart you can break a gene so the cell has sophisticated methods of untangling the DNA. If you don’t have proteins that can untangle chromosomes it causes interlocked chromosomes that can lead to improper cell division.

Question 17

Which enzyme caused DNA supercoiling? What else is needed for it to happen?

Answer 17

• DNA gyrase causes negetive DNA supercoiling.
• It is an active process and needs ATP.

Question 18

What are the two types of supercoiling?

Answer 18

1. Positive supercoiling - Positive means left handed or clockwise supercoiling.
2. Negetive supercoiling - Negetive means right handed or anti-clockwise supercoiling.

Question 19

How many base pairs does Escherichia coli DNA have?

Answer 19

It has 3x10^6 base pairs.

Question 20

Describe eukaryotic DNA.

Answer 20

• Humans have 3 billion basepairs of DNA.
• This DNA is organised into 23 pairs of linear chromosomes.
• The DNA is complexed with histones and made into a fibre called chromatin.
• The DNA double helix is wound around 8 histone subunits.

Question 21

What is a nucleosome?

Answer 21

Nucleosome is a structural unit of a eukaryotic chromosome, consisting of a length of DNA coiled around a core of 8 histones.

Question 22

How were nucleosomes first seen in an electron microscope?

Answer 22

Nucleosomes were seen as ‘beads on a string’.

Question 23

Describe the structure of nucleosomes.

Answer 23

1. It consist of 8 histones (two molecules of each of 2A, 2B, 3 and 4) present in the middle of DNA.
2. These histones are positively charged amino acids.
3. They interact with the negetive charges of the phosphates in the DNA.
4. These electrostatic interactions allow the DNA to be stored along the outside of these 8 histones.

Question 24

What is the function of Histone 1?

Answer 24

1. Histone 1 sits on top of the structure, keeping in place the DNA that has wrapped around the nucleosome.
2. The H1 protein binds to the “linker DNA” (approximately 20-80 nucleotides in length) region between nucleosomes, helping stabilize the zig-zagged 30 nm chromatin fiber.

Question 25

What are the differences between heterochromatin and euchromatin?

Answer 25

Question 26

What damage does mutations cause in DNA?

Answer 26

1. Sponataneous - e.g. loss of bases, or hydrolysis of C to U.
2. Chemicals - change base structure, insertion between bases.
3. Radiation - UV light produces thymine dimers, ionizing radiation breaks DNA chromosomes to cause leukemia.

Question 27

What is the importance of DNA repair?

Answer 27

1. It maintains genome stabillity.
2. 50-100 differen enzymes / proteins are present in the cell to check that there is no damage to the DNA. They can repair the DNA if damage is found.

Question 28

What is a disease caused due to failed repair mechanisms?

Answer 28

• Xeroderma pigmentosum is a disease that causes defect in excision repair that deals with the UV damage to DNA.
• These patients are prone to skin cancer.