DNA Structure

Question 1

Why does each DNA strand have polarity?

Answer 1

The polarity in DNA is due to the 3’ - 5’ bonds which causes polarity to run from 5’ to 3’.

Question 2

What causes DNA to be slightly acidic?

Answer 2

This is because the protonated phosphate group can give up their protons, and cause the formation of O(-).

Question 3

Describe the A form of DNA

Answer 3

A very compact DNA helix, where the coils are tightly paced together - Eg. tRNA

Question 4

Describe the B form of DNA

Answer 4

Less compact helix compared the A form DNA. Normal DNA present in eukaryotic cells.

Question 5

Describe the Z form of DNA.

Answer 5

It is the least compact helical form of DNA. It is detected in cells with a large concentration of salt, and requires a specific purine pyrimidine sequence to form.

Question 6

How can the forms of DNA change?

Answer 6

As DNA is not rigid and is conformationally mobile, the form of DNA can change depending on the base sequence and conditions. - Eg. Certain metal ions & DNA supercoils can change DNA from B to Z form.

Question 7

What is meant by the higher order of DNA?

Answer 7

Any assemblage of nucleosomes that assumes a reproducible conformation in 3D space.

Question 8

Describe the process of DNA supercoiling and relaxation in Bacteria.

Answer 8

• DNA Gyrase (topoisomerase enzyme) causes the circular DNA to supercoil, where the molecule relieves the helical stress by twisting around itself.
• Supercoiled DNA has energy stored in it as it formed by unwinding and reforming the helix
• Relaxation is dependent on ATP hydrolysis
• In E. coli the chromosome is organised into 50 supercoiled domains.

Question 9

Which DNA bases are purine (larger) ?

Answer 9

Adenine and Guanine

Question 10

Which DNA bases are pyrimidine (smaller) ?

Answer 10

Thymine and Cytosine

Question 11

Define mutagenic legions

Answer 11

A physical or chemical agent that permanently changes genetic material.

Question 12

What is chromatin?

Answer 12

A nucleoprotein complex formed when DNA is complexed with histones and other proteins. ONLY found in eukaryotes.

Question 13

Describe the formation of chromatin.

Answer 13

DNA wraps around histone octomers [(2A, 2B, 3,4)x2] with the negative phosphates being electrostatically attracted to the positive histone tails.

Question 14

Important enough of chromatin formation

Answer 14

It protects the core DNA from digestion as it is tightly packed with the histone octomers. BUT its not compact enough to fit in the nucleus.

Question 15

What is the structure of a nucleosome?

Answer 15

A small length of DNA (147bp) wrapped around 8 histones in a structure called “beads of a string”. They are the basic building blocks of chromatin.

Question 16

How can spontaneous mutation occur in damaged DNA?

Answer 16

• loss of bases

- hydrolysis of C to U

Question 17

How can chemicals & radicals generated by oxidative metabolism cause mutation in damaged DNA?

Answer 17

• changes base structure as DNA is chemically unstable

- insertion mutation

Question 18

How can radiation cause mutation in damaged DNA?

Answer 18

• UV light produce thymine dimers (mutagenic legions)

- ionising radiation break chromosomes and cause leukaemia (x rays)

Question 19

How is DNA repaired in cells?

Answer 19

• DNA is repaired by removal of the damaged bases followed by resynthesis of the excised region
• There are a number of mechanisms involved with DNA replications
• more than 100 enzymes are involved in repairing damaged DNA

Question 20

What is the importance of DNA repair?

Answer 20

• Maintains genome stability
• Patients with certain diseases have a defect in excision repair that deals with UV damage to DNA; very prone to skin cancer
• As repairing DNA is crucial for structure and function - damaging the DNA of cancerous cells could be treatment.

Question 21

Describe DNA Sequencing/ Sanger sequencing

Answer 21

• DNA is copied with DNA polymerase in presence of inhibitors - inhibit DNA synthesis at specific bases
• DNA strands separated by length on a polyacrymide gel
• Sequence reads 700 -1000 bases per read
• If DNA or incorporated inhibitors is radioactive/ fluorescent - DNA bonds can be visualised

Question 22

Describe the levels of DNA structure (primary, secondary, tertiary, quaternary, chromosomes)

Answer 22

• Primary - DNA sequencing
• Secondary - Helical structure ( A, B, Z form)
• Tertiary - DNA supercoiling
• Quaternary - High order coming and looping
• Chromosomes - Binary fission