Cheap Electrophoresis – Using Food Coloring
Introduction
A forensic scientist sits in her lab with three DNA samples in front of her. One sample is the DNA left
behind at the crime scene by the criminal; the other two samples are DNA from possible suspects. How will
she determine if either of the suspects' DNA matches the crime scene DNA? The scientist knows she can use
an enzyme to cut each DNA sample at a particular sequence of nucleotides; this will leave behind several
different pieces of DNA. The exact number of pieces and their sizes will be unique to each individual. This
means that there will be an exact match in the pattern of different-sized pieces of DNA between one of the
suspects and the DNA left at the crime scene, but not to any other suspects' DNA. The only problem left is,
how will she "see" and "measure" the different pieces of DNA in each sample? You might have seen such a
scene on the television show CSI. The answer is gel electrophoresis!
Gel electrophoresis is a technique used to separate and view macromolecules. Macromolecules are "large"
molecules, such as DNA, RNA, and proteins. During gel electrophoresis, the macromolecules (DNA in the
forensics example above) are loaded into a gel. Then a current is applied across the gel. The result is a
separation of the macromolecules, based on mass. In order to "see" the macromolecules in the gel, scientists
add either dyes, which stain the area of the gel that contains the macromolecules, or chemicals that bind the
macromolecules and fluoresce when the gel is exposed to ultraviolet light.
So how does gel electrophoresis work? It is based on the principal that nucleic acids, like DNA and RNA,
are negatively charged. This means that if you put nucleic acids in an electric field, they will migrate away
from the negative end of the field and toward the positive end. The nucleic acids are placed inside the gel for
two main reasons. One, the gel is a way of holding them to know where they are. Two, the migration needs
to occur in a manner that allows for the separation of different-sized pieces of DNA or RNA. The gel has
many microscopic holes through which the nucleic acids wiggle as they migrate within the electric field. The
smaller the nucleic acid sequence, the easier it is for it to wiggle through the holes. So, smaller pieces of
DNA and RNA "run" through the gel faster than larger pieces. Returning to our forensic science example,
this means that the individual pieces of DNA in each sample are sorted within the gel—the larger pieces
appear at the top of the chamber and the smaller pieces appear at the bottom of the chamber. The scientist
compares the pattern of the pieces of the crime scene DNA to the pattern of the suspects' DNA and looks to
see if there is an exact match.
Protein gel electrophoresis works similarly, except that proteins are not always negatively charged. In order
to force the proteins to migrate toward the positive end of the electric field, the proteins are denatured,
forced to unfold, in the presence of a chemical that coats the protein in negative charges. The amount of
coating is relative to the size of the protein, which means that the total negative charge is greater in larger
proteins. Using this technique, proteins, like nucleic acids, can be separated based on mass.
Gel electrophoresis is a common technique in laboratories and has many uses, including the forensics
example above. The most common uses are:
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Sorting pools of macromolecules to determine how many different macromolecules are in a sample.
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Determining the exact size of a macromolecule. This can be done by running a mixture of molecules
of known sizes, called a ladder, in the same gel as the macromolecule you want to measure. Then
you can determine which known molecule in the ladder is closest in migration pattern to the unknown
molecule; thus, approximate size.
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Purifying a single type of macromolecule.
For example, a scientist may want to learn more about the proteins that a bacteria releases into the
environment. To do this, the scientist collects the liquid media the bacteria grows in and runs a sample of the
media in a gel to look at how many proteins are in there. Perhaps the scientist wants to know the identity of
one of the proteins. Based on size, the scientist may be able to guess what some of those proteins are; to
check if he's right, the scientist can take advantage of the fact that the protein is now "trapped" in the gel. By
cutting out the region of the gel containing the protein that's the size he's interested in, and using other
techniques to separate the gel from the protein, he can purify the protein and use that pure sample for further
experimentation.
The equipment for gel electrophoresis is fairly simple. There is a chamber to hold the actual gel. The
chamber has both positive and negative electrodes to which you connect a power source in order to create
the electric field. The gel is immersed in a buffer solution, which provides ions to carry the current and keeps
the pH fairly constant. The sample is loaded into wells in the gel.
Figure 1. This gel electrophoresis chamber is connected to a power supply by black and red leads.
The red lead is attached to the positive electrode; the samples will run toward the positive electrode
when the power is turned on. (Photo by Jeffrey M. Vinocur, April 21, 2006.)
In this project you'll build your own gel electrophoresis chamber. Once it is built, you'll be able to examine
different food coloring dyes and explore some of the following questions. How many different
macromolecules make up each food coloring dye? Is there only one per color? Which color runs through the
gel fastest? You might be surprised by the results!
Terms, Concepts and Questions to Start Background Research
Before starting this project you will need to familiarize yourself with the following terms:
Use the internet and materials above to define the following terms.
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Gel electrophoresis
Macromolecule
DNA
RNA
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Protein
Mass
Nucleic acid
Denature
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DNA, RNA, and protein
ladders
Electrode
Agarose
Questions
1.
What is gel electrophoresis?
2.
What are the components of a gel electrophoresis chamber?
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?
4.
How do you visualize the macromolecules in the gel?
5.
What are real-life examples of what gel electrophoresis is used for?
6.
What characteristics of the molecules influence their separation during the electrophoresis?
Bibliography
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This website provides a simple animated walkthrough of gel electrophoresis and is an excellent
starting point.
The University of Utah, Genetic Science Learning Center. (2008). Gel Electrophoresis. Retrieved
March 4, 2008 from http://learn.genetics.utah.edu/units/biotech/gel/
These two references give slightly more involved and technical explanations about how gel
electrophoresis works.
o Bowen, R.A., Austgen, L., and Rouge, M. (2000). Gel Electrophoresis of DNA and RNA.
Retrieved March 4, 2008 from
http://www.vivo.colostate.edu/hbooks/genetics/biotech/gels/index.html
o Wikipedia contributors. (2008, March 3). Gel Electrophoresis. Wikipedia: The Free
Encyclopedia. Retrieved March 4, 2008 from
http://en.wikipedia.org/w/index.php?title=Gel_electrophoresis&oldid=195457494
Adapted from http://www.sciencebuddies.org/science-fairprojects/project_ideas/BioChem_p028.shtml?fave=no&isb=cmlkOjY3NTg1MjQsc2lkOjAscDoxLGl
hOkJpb0NoZW0&from=TSW