Gel Electrophoresis – Build Your Own Box Lab
Integrated Science 4
Name
Per
Introduction
Molecules can be separated by size using a process known as gel electrophoresis. The term
electrophoresis means to carry with electricity. The mixture of molecules is placed in a small well formed in an
agarose gel, which has a texture similar to that of gelatin. A buffer is then poured to cover the gel. When an
electric current is applied to the gel, the molecules move in the gel depending on their charge. The negatively
charged molecules move toward the positive electrode (red) and the positively charged molecules move toward
the negative electrode (black). Any molecules with no charge will not leave the well.
The gel acts as a strainer with tiny pores that allows the smallest molecules to move through it very quickly.
The larger the molecules, however, the more slowly they move through the gel. So the electrical charge causes
molecules to move depending on their charge and the gel slows down bigger molecules relative to smaller
molecules. This allows us to separate them.
In this experiment, you will analyze food dyes using agarose gel electrophoresis. The reference dyes are Blue 1,
Red 40, Yellow 5, and Yellow 6. The four dyes are similar (see Figure 1), and are all negatively charged at pH 8.
-
O3S
SO3-
SO3-
-
N
N+
N
OOC
-
N
N
N
OH
O3S
Yellow 5 (mass: 534.356 g/mol)
Blue 1 (mass: 792.844 g/mol)
SO3 -
OH
N
HO
N
-
O3S
SO3-
N
O
N
SO3-
Yellow 6 (mass: 452.363 g/mol)
Fig. 1. Reference dyes used in this experiment.
SO3Red 40 (mass: 496.416 g/mol)
Analysis Questions
1. Draw a sketch of your gel electrophoresis box and briefly describe the function of each component. Include
precise measurements of the distance travelled by each food dye in millimiters.
2. What two factors are used to separate molecules in gel electrophoresis?
3 What two factors control the distance the colored dye solutions migrated?
4. What force helps move the dyes through the gel?
5. What component of the electrophoresis system causes the molecules to separate by size? Explain.
6. Look at the structures of the dyes pictured here. Which of these dyes would migrate similarly to the dyes you
examined in this lab? Write your answer in terms of cause and effect.
OH OH
HO
O
HO
O-
O
OH O
HO
HO
O
OH
OH
O
OH O
HO
N+
HO
O
O
OH
OH
OH
Carminic acid
N
H
OH
O
Betanin (beetroot red)
OH
-
O3S
SO3-
SO3-
O
OH
N
N
O
N+
N
Fast green FCF
Citrus red 2
7. Use your data on distance travelled by each food dye molecule, and the provided data on
mass of each food dye molecule (on page 1) to write a mathematical formula that connects
these two variables. Show your work below.
8. Use your mathematical formula to predict how far a molecule of mass 600.000 g/mol
would travel in your gel electrophoresis box.
9. Calculate the mass of a molecule if it traveled 20 mm.
10. Describe a potential real world application of your mathematical formula.
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