1. Lab 6: Molecular Biology Part A
A Process to DYE for
Lab 6: Molecular Biology
Part A

2. Gel- we use a gelatin Agarose Electro- using electricity
In these two labs (Part A and B) we will be using a separation technology called Gel electrophoresis.
Gel- we use a gelatin Agarose
Electro- using electricity
Phoresis- means ‘to carry across’

3. You are a lab technician mixing up a batch of stain (mixture of various dyes) for one of the researchers in your lab.
You had started making a large batch when you were interrupted during the procedure.
When you returned to the stain, you could not remember if you had added all of the components (geez- pay attention to your job, loser)…..
Rather than waste the whole batch of stain and start over, you will employ gel electrophoresis to determine if all of the dyes are present in the mixture.

4. You will load your gel into the electrophoresis container.
Next, you will cover your gel with an electrolyte buffer…this is a liquid that will conduct electricity.

5. Using a micro-pipette, you will load 10 micro-liters (µL) of each dye into a different well in the gel.

6. Questionable Mixture goes in the last lane
Orange G
Lane #4
Crystal Violet -
Lane #1
Malachite Green
Lane #3
Bromophenol Blue
Lane #5
Xylene Cyanol
Questionable Mixture goes in the last lane
Also, each dye’s molecules have a molecular weight….the heavier the molecules, the slower they will move across the gel and vise versa
Once you have loaded all the wells with the correct dyes, it will look like this…
You will have a positive electrode at one end and a negative at the other…
When you turn the electricity on, the molecules in the dye will begin to move across the gel….if the molecules have a negative charge, they will move toward the positive and vise versa. +

7. What about the well with the questionable mixture?
Since it’s mixed with dyes of different weights, some will move faster than others….
Also some of the dyes in the mixture might be negative, others positive…
So they will separate from each other and you’ll be able to see which dyes were put into the mixture…..

8. Next, write the purpose for this lab…..
So first, let’s hypothesize over what you think will happen with each dye when the electricity is turned on
First make a Table of Contents entry and write the title of this lab on the page you are using for Part A.
Next, write the purpose for this lab…..
Lab 6, Gel Electrophoresis Part A
Purpose: to understand the principles and practice of gel electrophoresis. Also, to demonstrate separation of molecules based on charge and size.

9. AND- Create your Data Collection table to fill in tomorrow…..
Underneath Purpose, write Dye Hypothesis: and create the following table:
Dye Names
Molecular Weight (MW)
Charge
Travel distance A
Malachite Green
329 B
Orange G
452 C
Bromophenol Blue
669 D
Crystal Violet
407 E
Xylene Cyanol
538
Using the pictures of the dye’s molecules, hypothesize if you think the charge of the molecule is neg. or pos. AND determine in order which dyes you think will travel farthest to shortest distance.
THEN after your filled in table….write Pre Lab Question: and write answers with complete sentences to the pre lab question.
AND- Create your Data Collection table to fill in tomorrow…..

10. Orange G
Malachite Green -
Bromophenol Blue
Xylene Cyanol
Crystal Violet

11. Pre Lab Question: Data:
Write a brief function for each of the parts used in gel electrophoresis:
a. Agarose gel
b. Electrophoresis buffer
c. Wells in the gel
d. Electric current
Data:
Dye Name
Dye Well #
Migration Distance (mm)
Migration Direction (+/-)
Dye Molecules “Speed” Rankings