Molecular Scissors: Restriction Enzymes 2009
Name: TEACHER'S NOTES Period: ____
Introduction:
In 1968, scientists Werner Arber and Hamilton Smith discovered a group of enzymes
(proteins that aid chemical reactions) in bacteria, which when added to any DNA result in
the hydrolysis (breakage) of the sugar-phosphate backbone between recognition sites
(specific nucleotide bases). This causes the double strand of DNA to break along the
recognition site and the DNA molecule becomes fragmented.
These “molecular scissors” are called restriction enzymes (RE)
How Restriction Enzymes work:
REs cut the DNA backbone at a very specific sequence, which is unique to each
different enzyme. Follow the example below to simulate the cutting action of the restriction
enzyme, HaeIII.
 HaeIII recognizes the following sequence:
“GGCC”
 The enzyme will cut between the middle G and C every time it “sees” it.
“GG” “CC”
 Use the DNA sequence below to answer the following questions.
ATGG|CCATTTCGGGCAATA
TACC |GGTAAAGCCCGTTAT
Questions:
1. On the DNA sequence above, draw a line where HaeIII would cut.
2. How many fragments of DNA would result from cutting this sequence with HaeIII?
2 fragments
3. DNA fragment size can be expressed as the number of base pairs (bp) in the
fragment. Indicate the size of the fragments.
Smaller fragment: 4 bp
Larger fragment: 15 bp
Modified from: Burke, M. 2009. Laboratory Handbook: From Phenotypes to Genotypes. School of
Biological Sciences. University of California, Irvine.
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Minority Science Programs – School of Biological Sciences – University of California, Irvine
Electrophoresis: Review 2009
Name: TEACHER'S NOTES Period: ____
Review:
The term electrophoresis means “to carry with electricity.” Gel electrophoresis
separates DNA fragments by size. The DNA is placed in wells created on a gel, electricity
is turned on, and the DNA fragments will move through the gel towards the positive
electrode. The smaller the fragment of DNA, the further it will move. We can use this
technique to separate DNA fragments created by restriction enzymes.
Questions:
1. Read the length (in base pairs) of the following fragments:
GGTAATT
(7 bp)
TTAG
(4 bp)
AAAGGCTAT
(9 bp)
2. Which fragment do you think would travel the furthest?
3. Which fragment would travel the least distance?
TTAG (4 bp)
AAAGGCTAT (9 bp)
4. Where do you think you would find the other fragment?
In between
5. Draw what you think a gel would look like after the above DNA had run through.
7 bp
2
4 bp
9 bp
Minority Science Programs – School of Biological Sciences – University of California, Irvine
Electrophoresis: Review 2009
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Minority Science Programs – School of Biological Sciences – University of California, Irvine