3. DNA Structure:

Question 1

Describe DNA (9pts)

Answer 1

1. DNA is the store of genetic information
2. Double helix shape- complementary polynucleotide chains. It has minor and major grooves. The major groove is when the DNA helices are far apart and the minor grove is when they are close together. discovered by Rosalind Franklin.
3. The DNA polynucleotide strands are made up of nucleotides which are joined by 3-5 phosphodiester bonds.
4. DNA strand has a polarity due to the nature of the 3-5 phosphodiester bonds. It runs 5 prime to 3 prime.
5. DNA double helix strands are anti-parallel which means they run in opposite directions. Bases are on the inside of the helix whilst phosphate and sugars are on the outside.
6. DNA is an acid because the phosphate groups are protonated and can give up their protons.
7. DNA helix is held together by AT and CG base pairs
8. AT= 2 hydrogen bonds
   CG= 3 hydrogen bonds
9. The base pairs are the same size. The CG base pair is stronger due to having more hydrogen bonds.

Question 2

Describe the A form helix (7pts)

Answer 2

1. Polynucleotide strands coil around each other
2. Right handed helices
3. The helix has a clockwise orientation.
4. 11 bases per helical turn
5. Bases are in the inside of the helix whilst the sugar phosphate portions of the chains are on the outside of the helix.
6. Found during transcription of DNA when TRNA folds in an A form helix.
7. Found less commonly in nature

Question 3

Describe the B form helix (6pts)

Answer 3

1. Polynucleotide strands coil around each other
2. Right handed helices
3. The helix has a clockwise orientation
4. Bases are in the inside of the helix whilst the sugar phosphate portions of the chains are on the outside of the helix.
5. 10 bases per helical turn
6. B form DNA is found inside cells and nature

Question 4

Describe the Z form DNA (2pts)

Answer 4

1. left handed helix

2. can be detected in cells favoured by a high salt concentration

Question 5

Describe tetraplex DNA (4pts)

Answer 5

1. A four stranded DNA helix formed at telomeres
2. Requires G- rich DNA sequences
3. Formed in telomeres which are found at the end of chromosomes to protect them from degradation by nucleases.
4. Tetraplex is a component of the telomeres.

Question 6

Describe the Holiday 4 stranded junction (3pts)

Answer 6

1. Arise naturally in living cells through DNA strand exchange between 2 homologous chromosomes.
2. Important role in DNA repair. If one chromosome is damaged the good sequence on the other chromosome can be used through strand invasion to copy in the proper DNA sequence and repair the damage.
3. Holiday junction form continuously in cells.

Question 7

Describe DNA supercoiling in bacteria (5pts)

Answer 7

1. DNA supercoiling is when the helix is twisted and is coiled in space.
2. In bacteria the enzyme gyrase uses ATP to convert relaxed DNA into supercoiled DNA.
3. The enzyme TOPO IV, Topo I converts supercoiled DNA into relaxed DNA.
4. In bacteria the level of supercoiling reflects the balance between Gyrase and the DNA relaxing enzymes.
5. DNA supercoiling has energy stored in it as it facilitates the unwinding of the helix during DNA replication.
6. DNA supercoiled is smaller in size and more compact allowing it to fit inside the cell.

Question 8

Describe the levels of DNA structure (4pts)

Answer 8

1. Primary= Sequence of bases in DNA (DNA sequencing)
2. Secondary structure= helical structure which is the form of DNA e.g a form or b form (seen in xray’s)
3. Tertiary structure= DNA supercoiling (observed via electron microscopy)
4. Quaternary structure= Interlocked chromosomes during Mitosis

Question 9

Describe Sanger sequencing (3pts)

Answer 9

1. A DNA strand is copied with a DNA polymerase in the presence of inhibitors that arrest DNA synthesis
2. The DNA strands are separated by length on a polyacrylamide gel
3. If the DNA or incorporated inhibitor is radioactive or fluorescent the DNA bands can be visualised and the sequence of bases is read.

Question 10

Describe ECOLI Bacteria

Answer 10

1. E coli DNA is circular
2. E coli comprises 3x 10’6 base pairs
3. Bacterial DNA is supercoiled- the DNA ribbon is twisted in space. The supercoiling is caused by the enzyme gyrase.
4. E.coli chromosome is circular

Question 11

Describe DNA in eukaryotic cells (3pts)

Answer 11

1. Human DNA is organised into 23 pairs of chromosomes
2. DNA is complexed with histones and other proteins to form chromatin.
3. Nucleosomes are the building blocks of chromatin. They were first seen in electron microscopy studies and are beads on a string.

Question 12

Describe a nucleosome from stryer (2pts)

Answer 12

1. DNA double helix is wound across an octamer of histones.

2. Histone 1 binds to the outside of the core particle and to the linker DNA.

Question 13

Describe the chromatin theory (1pt)

Answer 13

DNA is condensed by higher order coiling and looping that would give sufficient compaction to allow it to fit within the nucleus

Question 14

Describe DNA damage (5pts)

Answer 14

1. DNA is chemically unstable.
2. Damage causes mutations in DNA:
3. Spontaneous- e.g loss of bases
4. Chemicals and radicles generated by oxidative metabolism- this changes the base structure
5. Radiation- Uv light produces thymine dimers which harm the DNA and Ionising radiation breaks chromosomes to cause leukaemia.

Question 15

Describe DNA repair ( 3 pts)

Answer 15

1. DNA damage must be sensed and continually repaired to maintain its cellular functions
2. Repair maintains genome stability
3. More than 100 different enzymes/ proteins are involved in the cell.
4. Many mechanisms use the undamaged strands of DNA (as the two strands are complementary) as templates to repair the damaged strands.