Tertiary Structure of DNA Flashcards
Where is the DNA double helix stored? (for prokaryotes and eukaryotes)
The DNA double helix is packaged into different chromosomes.
In prokaryotes these are often closed, circular stretches of DNA
In eukaryotes, these are more often linear stretches of DNA.
How is DNA compacted into chromosomes?
Through being in the tertiary structure.
What is the length of an E.coli chromosome (in linear form) relative to the length of an E.coli cell?
1.7mm chromsome relative to a cell which is 2 microns.
What is the first stage of DNA compaction?
DNA supercoiling.
Why does DNA need compacting?
Because DNA molecules tend to be very large and have to packed into a very small volume (eg. eukaryotic nucleus).
What is DNA supercoiling?
When the axis of the DNA double helix is coiled in on itself and forms a new helix, superhelix normally called a super coil.
How is supercoiling induced?
By the seperation of the two DNA strands the strain caused this results in supercoiling.
What structures can supercoiling occur in?
Only in closed structures - bacterial chromosomes and plasmids are circular so therefore closed.
Eukaryotic DNA are also closed as they form loops and their ends are held together by proteins.
What does an greater number of supercoils cause?
Increased torsion
What would cause a untwisting to release supercoils?
A break in either of the strands.
What is an open or closed molecule with no supercoils called?
Relaxed.
What are the two ways DNA can be supercoiled?
Negatively and positvely
Which way is most naturally occurring DNA supercoiled?
Negatively.
What is negatively supercoiled DNA said to be?
Underwound
Which way does negatively supercoiling twist DNA?
In the opposite direction to the turns of a right handed helix.
How can torsional stress of a negatively supercoiled DNA be released?
By loosening the winding of the duplex and limited disruption of the base pairs.
(This is important for DNA replication and DNA transcription).
Which enzymes introduce and remove supercoils?
Topoisomerases
What do type I topoisomerases do?
They incrementally relax supercoiled DNA (eukaryotic and prokaryotic)
What do type II topoisomerases do?
Introduce supercoils (prokaryotic).
Requires ATP hydrolysis to occur.
However the energy stored in supercoiling fuels transcription and replication.
What is positive supercoiling?
When the DNA is coiled in the same direction as duplex helical turns and is termed as overwound.
What are the effects of underwinding (negative supercoiling)?
The strands are somewhat easier to separate.
In principle underwinding should facilitate strand separation every 10 base pairs. However hydrogen bonding between base pairs generally would prevent this over a short distance. Strand separation is a greater problem in longer DNAs.
What is DNA wound around in the eukaryotic nucleus?
The DNA is wound around nucleosomes which are made up of proteins called histones. The nucleosomes assemble the DNA into 30nm threads.
Describe the structure of a nucleosome.
Contains a protein core made up of 8 histones.
How are the nucleosomes linked together?
By linker DNA.
What happens to nucleosomes and DNA when in the presence of nuclease?
(Nuclease breaks down DNA)
The nuclease enzyme breaks down the linker DNA in between the nucleosomes (nucleosome core particles). The nuclease can only digest the linker DNA not the DNA wound around the nucleosome.
This results in the separation of one nucleosome core particle, which then can be separated from the DNA by addition of a high salt concentration.
