Exam 3 review
DNA Structure, supercoiling, RNA structure, and DNA Damage
1) DNA supercoiling
o DNA is not just a simple double helix in the cell
o Even though we draw DNA as a smooth double helix, it’s actually twisted and
coiled in on itself.
o DNA can twist, coil, loop, and fold.
▪ This extra twisting is called supercoiling.
o Why supercoiling exists:
▪ Each human cell contains ~2 meters of DNA packed into a
microscopic nucleus.
▪ Because humans have ~32 trillion cells, DNA must be extremely
compacted.
▪ Supercoiling helps condense DNA so it fits inside cells.
▪ In bacteria like E.coli, DNA forms supercoiled domains.
o Supercoiling is the overwinding or underwinding of the DNA double helix.
This changes the # of base pairs per turn of the helix.
o Normal DNA structure :
▪ DNA normally has 10.5 base pairs per turn, which is considered
relaxed DNA. Supercoiling changes this number.
o Types of Supercoiling:
▪ Negative supercoiling : DNA is underwound.
• Less twisting
• DNA becomes more extended
• More than 10.5 base pairs per turn.
• For every 10.5 base pairs, there is less than one full twist.
• Most organisms (including humans and E.coli) have negatively
supercoiled DNA.
o This is because it makes it easier to separate strands.
o helps with replication and transcription.
▪ Positive supercoiling : DNA is overwound.
• More twisting
• DNA becomes more compact
• Less than 10.5 base pairs per turn.
• For every 10.5 base pairs there is more than one twist.
o Supercoiling during DNA processes
, ▪ Positive supercoiling commonly occurs
• Ahead of replication forms
• Ahead of transcription machinery
o This is because when enzymes move along DNA and
separate strands, they push twisting ahead of them,
which builds up positive supercoiling.
o Twist and Writhe:
▪ Twist (T) = # of times the 2 DNA strands twist around each other
▪ Writhe (W) = how many times the DNA helix crosses over itself.
• This produces looped supercoils.
o Linking # (L)
▪ L= T+ W, where L= linking number.
▪ Without cutting DNA, the linking number stays constant. But twist and
writhe can convert into each other.
• EX: DNA can reduce twist by increasing writhe.
o Topoisomerases = enzymes that control supercoiling.
▪ Topoisomerase II (DNA gyrase)
• Introduces negative supercoils.
• Mechanism :
o Cuts both DNA strands
o Passes another segment of DNA through the break
o Reseals the DNA
▪ Topoisomerase I
• Relieves supercoiling by relaxing DNA
• Mechanism:
o Cuts only one DNA strand
o Allows twisting
o Rejoins the strand.
o Supercoiling in DNA replication
▪ Replication requires opening DNA strands, but when replication
machinery moves forwards, positive supercoiling builds up ahead.
This can block replication.
▪ Solution : DNA gyrase introduces negative supercoils
• This relieves the tension so replication continues.
o Supercoiling in transcription
▪ RNA polymerase must open DNA and read the gene, and this causes
positive supercoiling ahead and negative supercoiling behind.
DNA Structure, supercoiling, RNA structure, and DNA Damage
1) DNA supercoiling
o DNA is not just a simple double helix in the cell
o Even though we draw DNA as a smooth double helix, it’s actually twisted and
coiled in on itself.
o DNA can twist, coil, loop, and fold.
▪ This extra twisting is called supercoiling.
o Why supercoiling exists:
▪ Each human cell contains ~2 meters of DNA packed into a
microscopic nucleus.
▪ Because humans have ~32 trillion cells, DNA must be extremely
compacted.
▪ Supercoiling helps condense DNA so it fits inside cells.
▪ In bacteria like E.coli, DNA forms supercoiled domains.
o Supercoiling is the overwinding or underwinding of the DNA double helix.
This changes the # of base pairs per turn of the helix.
o Normal DNA structure :
▪ DNA normally has 10.5 base pairs per turn, which is considered
relaxed DNA. Supercoiling changes this number.
o Types of Supercoiling:
▪ Negative supercoiling : DNA is underwound.
• Less twisting
• DNA becomes more extended
• More than 10.5 base pairs per turn.
• For every 10.5 base pairs, there is less than one full twist.
• Most organisms (including humans and E.coli) have negatively
supercoiled DNA.
o This is because it makes it easier to separate strands.
o helps with replication and transcription.
▪ Positive supercoiling : DNA is overwound.
• More twisting
• DNA becomes more compact
• Less than 10.5 base pairs per turn.
• For every 10.5 base pairs there is more than one twist.
o Supercoiling during DNA processes
, ▪ Positive supercoiling commonly occurs
• Ahead of replication forms
• Ahead of transcription machinery
o This is because when enzymes move along DNA and
separate strands, they push twisting ahead of them,
which builds up positive supercoiling.
o Twist and Writhe:
▪ Twist (T) = # of times the 2 DNA strands twist around each other
▪ Writhe (W) = how many times the DNA helix crosses over itself.
• This produces looped supercoils.
o Linking # (L)
▪ L= T+ W, where L= linking number.
▪ Without cutting DNA, the linking number stays constant. But twist and
writhe can convert into each other.
• EX: DNA can reduce twist by increasing writhe.
o Topoisomerases = enzymes that control supercoiling.
▪ Topoisomerase II (DNA gyrase)
• Introduces negative supercoils.
• Mechanism :
o Cuts both DNA strands
o Passes another segment of DNA through the break
o Reseals the DNA
▪ Topoisomerase I
• Relieves supercoiling by relaxing DNA
• Mechanism:
o Cuts only one DNA strand
o Allows twisting
o Rejoins the strand.
o Supercoiling in DNA replication
▪ Replication requires opening DNA strands, but when replication
machinery moves forwards, positive supercoiling builds up ahead.
This can block replication.
▪ Solution : DNA gyrase introduces negative supercoils
• This relieves the tension so replication continues.
o Supercoiling in transcription
▪ RNA polymerase must open DNA and read the gene, and this causes
positive supercoiling ahead and negative supercoiling behind.
