Ch. 9 Topology Flashcards
Describe viral chromosomes. (4)
ss or ds
DNA or RNA
Contained in a capsid
Circular, Linear, or Segmented
Describe prokaryotic chromosomes. (4)
dsDNA (cells!)
NOT contained in a nucleus
Usually single
Usually circular
Describe eukaryotic chromosomes. (4)
dsDNA (cells!)
Contained in a nucleus
Usually linear
Often in pairs (homologs)
How do viral, prokaryotic, and eukaryotic chromosomes differ? (2)
size and structure
What is a feature ALL chromosomes have regardless of the type?
ALL are larger (longer) than the cells or viruses that carry them and MUST be packaged. (long but thin)
How is packaging generically performed; aka what do packaging methods avoid doing to DNA?
Packaging is performed in different ways that alter DNA structure WITHOUT breaking the DNA.
What is DNA topology?
The size and structure of DNA and how it is packaged.
What is supercoiling/supercoils?
DNA supercoiling is further coiling the DNA double helix. Supercoils are additional coils introduced into DNA double helix.
What are the two kinds of supercoils?
Overwinding (positive) of the double helix
Underwinding (negative) of the double helix
Where does supercoiling occur (2) and why?
It occurs in cells and viruses to create a reduced DNA footprint in the cell/capsid
What is relaxed DNA?
DNA structure when there is NO supercoiling present.
What does separation of supercoiled DNA cause?
Processes that separate DNA strands (replication, transcription, etc.) can cause excessive strain on the DNA that could cause breakage of DNA.
How is excessive coiling combated?
Specialized enzymes relieve excessive coiling and therefore prevent DNA breakage.
What do DNA topoisomerases do and how?
They produce supercoiling by breaking, winding, or unwinding the DNA helix and re-ligating the DNA strands.
How do you ADD a supercoil to a negative supercoil? Positive supercoil?
Negative SC: unwind
Positive SC: wind
How do REMOVE a supercoil from a negative supercoil? Positive supercoil?
Negative SC: wind
Positive SC: unwind
What does over or underwinding of the DNA helix cause?
It causes bending of the helix which leads to supercoils
What effect does bending have on DNA structure?
Puts strain on base pairs, which makes them easier to separate by enzymes like polymerases.
How is the supercoil observed structurally?
Observed by the DNA twisting around its central axis.
What is a linkage number?
Lk: how often one strand wraps around another; how supercoiling is quantified
What does increasing Lk correlate to? Decreasing Lk?
increasing Lk = positive supercoiling (200→202)
decreasing Lk = negative supercoiling (200→198)
What do Type I topoisomerases do?
break one strand and change Lk by one
What do Type II topoisomerases do?
break both strands and change Lk by two
Do topoisomerases only add supercoils?
No. They can add or remove.