GEL ELECTROPHORESIS
1. What is Gel Electrophoresis?
 Gel electrophoresis is the separation of macromolecules like
DNA, RNA and proteins. DNA strands (or fragments) are
separated according to their size. Proteins are separated
according to their size and their charge (different proteins have
different charges). The DNA molecules are placed in a gel.
Because each of the DNA molecules are negatively charged, it
can be pulled through the gel by an electric field. Small DNA
molecules move more quickly through the gel than larger DNA
molecules. When the process is complete the larger DNA
molecules will be at the bottom and the smaller at the top with
the variation of the other sizes in order of its mass (large and
small) in between the largest and smallest DNA molecule.
2. What are the components of a gel electrophoresis chamber?
 The components of the gel electrophoresis consist of
 Agarose gel
 TBE buffer
 Electrophoresis chamber
 Power supply
 DNA samples
 DNA stains
3. What kinds of macromolecules can you “look at” with gel
electrophoresis? Do you need to use different techniques for
the different kinds of macromolecules?
 Nucleic Acid and Proteins are the 2 two macromolecules used in
gel electrophoresis.
Nucleic Acids
The direction of migration for nucleic acids in gel electrophoresis
tend to go from negative to positive electrodes, this is due to the
naturally-occurring negative charge carried by their sugar-phosphate
backbone.
Proteins
Proteins, unlike nucleic acids, can have varying charges and complex
shapes. Therefore they don’t migrate into the gel at similar rates, or at
all.
4. How do you visualize the macromolecules in the gel?
 That the macromolecules are stretched out and spread though
the sponge like gel and that they’re arranged in order by size,
due to the electricity, from smallest to largest.
5. What are real-life examples of what gel electrophoresis in used
in many ways such as genetic engineering, mechanically copying a
DNA sequence, determine the composition of DNA?
There are many ways gel electrophoresis are used for, such as
Illness, Family, Animals, and the most commonly thought of
Crime.
 Illness
Gel Electrophoresis helps scientists discover damaged
genes, including oncogenes. Certain diseases like sickle
cell anemia, Huntington’s disease and Duchenne muscular
dystrophy can be identified with the help of gel
electrophoresis. Viruses have been found to be identified
with it as well.
 Family
Gel Electrophoresis has been able to determine paternity
as well as established genetic links between larger groups
of people.
 Animals
Gel electrophoresis has many benefits to offer in fields
dealing with animals. This technique is used in zoos to help
reduce the negative impact of inbreeding. Taxonomists and
evolutionary biologists can learn more about evolutionary
relationships, identify species and document differences
between them. People who study animal behavior can use
DNA to glean information about kinship of animals and how
it impacts interaction with other animals.
 Crime
Scientist can use the gel electrophoresis technique to
examine tissue samples fond at crimes scenes. With the help
of the use of the many DNA databases that are now
available, such as CODIS, for example, DNA samples can be
compared with a suspects DNA from a crime scene and a
victims from another.
Important Terms to Remember
 Gel electrophoresis- is a technique used for? The separation of
deoxyribonucleic acid (DNA), ribonucleic acid (RNA), or protein
molecules using an electric current applied to a gel matrix.
 Macromolecule- A very large molecule, such as a polymer or
protein, consisting of many smaller structural units linked
together.
 DNA- deoxyribonucleic acid (DNA) is a nucleic acid that contains
the genetic instructions used in the development and functioning
of all known living organisms and some viruses.
 RNA- nucleic acid in all living cells: a nucleic acid containing
ribose found in all living cells, essential for protein synthesis
 Protein- organic compounds made of amino acids arranged in a
linear chain.
 Mass- a body of coherent matter, usually of indefinite shape and
often of considerable size.
 Nucleic acid- a macromolecule composed of chains of monomeric
nucleotides.
 Denature- to treat (a protein or the like) by chemical or physical
means so as to alter its original state.
 Protein ladders- are used for accurate protein sizing, monitoring
electrophoresis run and efficiency of protein transfer.
 Electrode- a conductor, not necessarily metallic, through which
a current enters or leaves a nonmetallic medium, as an
electrolytic cell, arc generator, vacuum tube, or gaseous
discharge tube.
 Agarose- a substance obtained from agar and used for
chromatographic separations.
Materials you will need:
 Electrophoresis chamber, gel form and comb
 Power supply that produces 50-150 volts
 Agar Agar granules
 Salt solution
 Commercial food colors
 Filter paper circles (cut out with whole punch)
 Tweezers
 Masking tape
 Water
DIRECTIONS
I. Construct the Gel Carrier
II. Cut the Gel Comb
III. Drill Holes for the Leads to the Power Supply
IV. Construct the Chamber Lid
V. Construct the Electrophoresis Chamber
VI. Place the Pegs in the Electrophoresis Chamber
VII. Wire the Electrophoresis Chamber
Problems Faced When Building
There wasn’t much difficulty building the gel electrophoresis
chamber. The main tasks I had trouble with was finding a reasonable
size contain that had all the specifications I needed, Finding an
appropriate energy source, and constructing custom parts I needed to
make in order for the chamber to work properly.
Results
After running the experiment several times the food coloring dyes,
which were the macromolecules in this case, successfully traveled
through the gel to show the density of their macromolecules in a
range of largest macromolecules to smallest. It appears from
running the test multiple times that blue has the smallest
macromolecules and then green very closely flows and yellow
follow with more dense macromolecules and then red with the
densest.