BIOC0001 PRACTICALS EXAM QUESTIONS AND
ANSWERS WITH COMPLETE SOLUTIONS VERIFIED
LATEST UPDATE
How many base pairs long is a typical gene?
~10^4bp.
What is supercoiling? What is its purpose?
The twisting of a DS DNA helix around itself allowing it to be packaged efficiently into a
cell.
Why might two sections of DNA which are the same length travel at different rates
during gel electrophoresis?
Some of the DNA, but not all, becomes relaxed during laboratory preparation (the state
of a circular, non-supercoiled plasmid). Some of the DNA remains supercoiled and so is
more compact meaning it migrates faster than its equally sized linear or relaxed
counterpart.
How are restriction endonucleases made?
They are made naturally by bacteria as a defence against viral infection.
What are all restriction sites recognised by restriction endonucleases known as?
Palindromic.
Why are all restriction sites palindromic?
It allows the restriction endonuclease to cut both strands at the same point.
,What is the gel used in gel electrophoresis? Why?
Agarose.
What type of molecule is agarose?
Polysaccharide.
Describe the movement of DNA fragments in agarose gel electrophoresis.
They move towards the anode (positive end) of the gel by moving through pores in the
gel. The larger the fragment, the more drag it will experience whilst moving through the
gel and so the slower it will move.
What chemical is used to visualise DNA and how does it work?
Ethidium bromide which intercalates (inserts) between bases and will fluoresce a pink-
orange colour when illuminated with UV light (300nm).
What wavelength is the UV light used to show the ethidium bromide?
300nm.
What does a restriction map of a DNA fragment show?
The positions of the different target sites for various restriction endonucleases.
Draw the locations of three restriction sites P, Q and R on a 9kb plasmid given the
following information:
- Digestion with enzyme P gives a single 9kb piece of DNA.
- Double digest with enzymes P and Q gives two fragments of 2kb and 7kb in
length.
- Double digest with enzymes P and R gives two fragments of 3kb and 6kb in
length.
, - Double digest with enzymes Q and R gives two fragments of 1kb and 8kb in
length.
Describe how the lengths of DNA fragments on a gel electropheresis digest are
estimated? How is a graph used here?
The fragment migrations are compared against the migrations of fragments of known
length. To do this, a standard curve of logbp (x) vs distance migrated/mm (y) must be
plotted using the reference results. A line of best fit should then be drawn through the
points and this then used to calculate the length of the DNA fragments of the practical
digest by reading from the y-value representing the distance a specific DNA fragment
migrated across to the LOB and then down to the relevant fragment length.
Why do fragments of the same length migrate together in distinct bands?
Because the agarose gel restricts random diffusion.
What are agarose vs polyacrylamide gels used for?
Agarose gel is used for a gel electrophoresis of larger DNA molecules between 200-
20,000bp. Polyacrylamide gel on the other hand is used for gel electrophoresis of
smaller DNA molecules between 10-2000bp.
When hybridising a digest with probes, why is a blot used?
Because probes don't readily diffuse in the gel used in the gel electrophoresis.
How long was the recognition sequence of the restriction endonuclease Alu 1?
What was the recognition sequence?
4 bases long - AG/CT.
How long was the recognition sequence of the restriction endonuclease Taq 1?
What was the recognition sequence?
ANSWERS WITH COMPLETE SOLUTIONS VERIFIED
LATEST UPDATE
How many base pairs long is a typical gene?
~10^4bp.
What is supercoiling? What is its purpose?
The twisting of a DS DNA helix around itself allowing it to be packaged efficiently into a
cell.
Why might two sections of DNA which are the same length travel at different rates
during gel electrophoresis?
Some of the DNA, but not all, becomes relaxed during laboratory preparation (the state
of a circular, non-supercoiled plasmid). Some of the DNA remains supercoiled and so is
more compact meaning it migrates faster than its equally sized linear or relaxed
counterpart.
How are restriction endonucleases made?
They are made naturally by bacteria as a defence against viral infection.
What are all restriction sites recognised by restriction endonucleases known as?
Palindromic.
Why are all restriction sites palindromic?
It allows the restriction endonuclease to cut both strands at the same point.
,What is the gel used in gel electrophoresis? Why?
Agarose.
What type of molecule is agarose?
Polysaccharide.
Describe the movement of DNA fragments in agarose gel electrophoresis.
They move towards the anode (positive end) of the gel by moving through pores in the
gel. The larger the fragment, the more drag it will experience whilst moving through the
gel and so the slower it will move.
What chemical is used to visualise DNA and how does it work?
Ethidium bromide which intercalates (inserts) between bases and will fluoresce a pink-
orange colour when illuminated with UV light (300nm).
What wavelength is the UV light used to show the ethidium bromide?
300nm.
What does a restriction map of a DNA fragment show?
The positions of the different target sites for various restriction endonucleases.
Draw the locations of three restriction sites P, Q and R on a 9kb plasmid given the
following information:
- Digestion with enzyme P gives a single 9kb piece of DNA.
- Double digest with enzymes P and Q gives two fragments of 2kb and 7kb in
length.
- Double digest with enzymes P and R gives two fragments of 3kb and 6kb in
length.
, - Double digest with enzymes Q and R gives two fragments of 1kb and 8kb in
length.
Describe how the lengths of DNA fragments on a gel electropheresis digest are
estimated? How is a graph used here?
The fragment migrations are compared against the migrations of fragments of known
length. To do this, a standard curve of logbp (x) vs distance migrated/mm (y) must be
plotted using the reference results. A line of best fit should then be drawn through the
points and this then used to calculate the length of the DNA fragments of the practical
digest by reading from the y-value representing the distance a specific DNA fragment
migrated across to the LOB and then down to the relevant fragment length.
Why do fragments of the same length migrate together in distinct bands?
Because the agarose gel restricts random diffusion.
What are agarose vs polyacrylamide gels used for?
Agarose gel is used for a gel electrophoresis of larger DNA molecules between 200-
20,000bp. Polyacrylamide gel on the other hand is used for gel electrophoresis of
smaller DNA molecules between 10-2000bp.
When hybridising a digest with probes, why is a blot used?
Because probes don't readily diffuse in the gel used in the gel electrophoresis.
How long was the recognition sequence of the restriction endonuclease Alu 1?
What was the recognition sequence?
4 bases long - AG/CT.
How long was the recognition sequence of the restriction endonuclease Taq 1?
What was the recognition sequence?
