01. Molecular Structures — Nucleic Acid Conformations and Supercoiling

Question 1

Describe circular DNA.

Answer 1

• Double-stranded closed structure
• Present in prokaryotes, and certain organelles
• Support the endosymbiont theory

Question 2

Compare circular and linear DNA in terms of primary, secondary, and tertiary structures.

Answer 2

1. Sugar-phosphate chain.
2. Double-helical structure (H-bonds, stacking)
3. Protein complexes — supercoiling.

Question 3

Why does supercoiling occur?

Answer 3

• Generally, supercoiling is meant to relieve torsion from under or overwound DNA.
• Underwound DNA will negatively supercoil, and overwound DNA will positively supercoil. (Coils are in the opposite direction).
• Supercoiling helps condense/pack DNA and save space
• Uncoiling occurs for transcription/replication.
• One supercoil per ever 10 bp opened.

Question 4

What is the difference between positive and negative supercoiling? (for B-DNA)

Answer 4

• Positive supercoils
  
  • happens in front of an opening
  • relieves overwinding
  • supercoils are left-handed to offset overwound right-handed helix
  • less chance of protein interaction
• Negative supercoils
  
  • happens behind opening
  • relieves underwinding
  • supercoils are right-handed to offset the underwound loss of right-handed turns
  • store energy that assists in strand separation; untwisting is favoured, good for protein interactions

Question 5

Define twisting, writhing, and linking numbers.

Answer 5

• Twisting (T) = The number of turns in dsDNA; how many times one strand crosses over the other.
  
  • T = total # of bp ÷ # of bp/turn
  • positive if right-handed, negative if left
• Writhing (W) = the number of superhelical turns (how many times the duplex dsDNA crosses over itself)
  
  • negative supercoils = W < 0
  • positive supercoils = W >0
  • relaxed dsDNA = W = 0
• Linking (L) = total # of times one strand encircles the other
  
  • L = T+W

Question 6

What are topoisomerases?

Answer 6

• Enzymes that recognize + regulate supercoiling.

Question 7

Describe prokaryotic topoisomerases.

Answer 7

• Type |
  
  • single strand cut
  • untwists, or relaxes negative supercoils / generates positive supercoiling
  • example: reverse gyrase generates positive supercoils with ATP
• Type II
  
  • double strand cut
  • relaxes positive supercoiling / introduces negative supercoiling
  • Example: gyrase

Question 8

Describe eukaryotic topoisomerases.

Answer 8

• Function as a cleavage complex: TOPcc
• TOP1/TOP1mt — type | action, relaxes both kinds of supercoil
• TOP2a/TOP2b — type II action, relaxes both kind of supercoiled DNA, but no supercoil introduction
• TOP3a/TOP3b — type I action, only relaxes hyper negative supercoiling.