AP Biology 12
Molecular Biology
Lab 6B: Virtual Electrophoresis
Learning Intentions
o How does gel electrophoresis separate DNA fragments?
o How can you use a standard curve to determine the size of unknown DNA fragments?
Background
From University of Utah: http://learn.genetics.utah.edu/content/labs/gel/
From Campbell Website: Activity: Gel Electrophoresis of DNA
Activity: Analyzing DNA Fragments Using Gel Electrophoresis
Investigation: How Can Gel Electrophoresis Be Used to Analyze DNA?
Answers to Investigation Questions
1. What is the relationship of migration distance to fragment size?
The smaller the DNA fragment, the farther it migrates across the gel.
2. Approximately how many base pairs are there in the fragment circled in red at left?
Migration Distance: 23.8 ± 0.2 mm (notice that I can’t help proper sigfigs and uncertainty)
Using the graph, this corresponds to a fragment length of 3000-4000 base pairs.
3. Which lane shows a digest with BamHI only?
BamHI would make cuts at the three BamHI restriction sites, producing DNA fragments of
2kB, 6kB, and 12kB (4kb + 8kb). Therefore, Gel lane III shows the digest with BamHI only.
4. Which lane shows a digest with EcoRI only?
EcoRI would make cuts at the one EcoRI restriction site, producing only one DNA
fragment of 20kb in length (2kb + 4kb + 8kb + 6kb). Therefore, Gel lane II shows the
digest with EcoRI only.
5. Which lane shows the fragments produced when the plasmid was incubated with both
EcoRI and BamHI?
EcoRI and BamHI would make cuts at the one EcoRI and the three BamHI restriction sites,
producing five DNA fragments at 2kb, 4kb, 6kb, and 8kb in length. Therefore, Gel lane IV
shows the digest with EcoRI and BamHI.
6. A segment of DNA has two restriction sites--I and II. When incubated with restriction
enzymes I and II, three fragments will be formed – a, b, and c. Which of the gels produced
by electrophoresis would represent the separation and identity of these fragments?
Out of the three fragments produced, b is the smallest, c is the longest, and a is in the
middle. Since the smaller the fragment, the farther it migrates across the gel, b will move
the farthest, followed by a, and finally c. The only gel that has the fragments in this order
is gel "B."