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BIOL 308 - Lecture 6 Which type of RNA is
very flexible around the secondary and
tertiary structures?
Small RNA TERM 2
What is Uracil?
DEFINITION 2 Demethylated thymine TERM 3
DNA functions in replication and transcription
depend on it's ___________. When the helix
becomes locally uncoiled, what happens?
DEFINITION 3 Topological state-Base pairing is interrupted, molecule exhibits super coiling TERM 4
What is a "relaxed
molecule"?
DEFINITION 4 Circular DNA without any super helical turn TERM 5
Besides DNA packaging, what is another use
for super coils?
DEFINITION 5 Reduce the stress induced by twisting of the double helix
Strain is released mainly by writhing into
superhelical turns -- this in result is
energetically cheaper than just untwisting it.
Think of the shoelace TERM 7
How often does a supercoil occur in a DNA
molecule?
DEFINITION 7 Every 10 bp TERM 8
Formation of a positive supercoil.
DEFINITION 8 Protein pushes --> infront of protein two strands wrap around eachother more than once every 10 bp --> turns are smaller TERM 9
When does positive supercoiling occur?
DEFINITION 9 When B-DNA is twisting incredibly tightly around its axis TERM 10
Describe negative supercoiling.
DEFINITION 10 Protein pushes --> two strands become wrapped around eachother less than once every 10 bp --> turns are longer
What is the linking #? What is the equation?
-total# of times one strand of closed ds DNA encircles the other strandL = T + WL is constant in unbroken duplex DNA, so any change in T must be met with an equal and opposite change in supercoiling TERM 17
How do you change L?
DEFINITION 17 Break one or both strands of DNA --> wind them tighter/looser --> rejoin ends TERM 18
Most cell DNA are _______ supercoiled.
DEFINITION 18 -negatively TERM 19
How does a cell regulate supercoiling?
DEFINITION 19 Use topoisomerases ex. ProkaryotesTOPO I - nicking-closing enzyme that makes a cut in one strand (relaxing -ve super coil). Does not use ATP and changes L in steps of one.TOPO II
- relax positive super coil; use ATP, makes a ds cut, passes a duplex DNA through it and reseals the cut. Changes L In steps of two. TERM 20
In the previous example, Prokaryotes were
discussed in relation to topoisomerases. How
about with Eukaryotes?
DEFINITION 20 Topo I - similar to bacterialTopo II - relaxes only supercoiled DNA --> cannot induce super coils
