DNA + Interaction L1-2

Question 1

What are the different forms of DNA? (3)

Answer 1

A Form: Shorter, more compact. <70% humidity
B Form: Physiological structure of DNA, stable at high humidity
Z From: Longer, slim. Alternating C,G regions

Question 2

Describe Non-Specific interactions (3)

Answer 2

• Form only with the backbone of DNA
• Help to Stabilise Specific interactions
• Contribute to binding affinity

Question 3

What are the different types of binding in Non-Specific interactions? (3)

Answer 3

• Ionic, between P04 and positive Amino acids
• Van Der Waals
• Hydrogen bonds between polar groups on proteins and Oxygen of phosphate of groups

Question 4

Describe specific interactions (3)

Answer 4

• Form in major and minor grooves of DNA
• Interact with base pairs
• Sensitive to position and orientation

Question 5

How do interactions contribute to overall stability? (2)

Answer 5

• All interactions are weak but additively they can form relatively strong non-covalent bonds
• Addition of one H bond can make a large overall difference in stability

Question 6

Give examples of and describe DNA binding proteins motifs (2)

Answer 6

• Helix turn helix, positions interactions on groove, can change conformation of the DNA when bound.
  E.g Lamba repressor
• Zinc Fingers, Beta Sheet and helix, helix = interaction Sheet = scaffold.
  Three fingers wrap around major groove and give better stability between protein and DNA

Question 7

Explain how DNA is a flexible molecule (3)

Answer 7

• Free rotation through c3 and c5 bonds of deoxyribose
• Propeller twist as bases in double helix are not co-planar
• Dihedral angle bases don’t meet at 180 degrees