Biogen Idec Community Laboratory
Activity Overview
Our Genes, Our Selves
DNA Testing: Should your patient take the Medicine?
Summary:
Students simulate a DNA test to investigate if a patient should take a medicine to
treat lymphoma. In this model, students run a restriction digest and gel
electrophoresis to determine if the patient sample has a working or faulty
enzyme, the key indicator in whether or not the patient can take the medicine.
Key Concepts and Process Skills:
1. To become comfortable in a laboratory setting.
2. Lymphoma is a type of cancer of the blood.
3. In some situation, a genetic disorder can help make decisions about the
treatment of a patient.
4. A protein digest can be used to cut strands of DNA into small fragments at
specific places along the strand of DNA.
5. Gel electrophoresis is a procedure that separates DNA based on size and
help determine if an individual has a particular gene.
California Standards Correlation:
1.Cell Biology
1c. Students know the nucleus is the repository for genetic information in plant
and animal cells.
2b. Genetics
2b. Students know sexual reproduction produces offspring that inherit half their
genes from each parent.
2c. Students know an inherited trait can be determined by one or more genes.
2d. Students know plant and animal cells contain many thousands of different
genes and typically have two copies of every gene. The two copies (or alleles) of
the gene may or may not be identical, and one may be dominant in determining
the phenotype while the other is recessive.
2e. Students know DNA (deoxyribonucleic acid) is the genetic material of living
organisms and is located in the chromosomes of each cell.
7. Investigation and Experimentation
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7a. Use appropriate tools and technology to perform tests, collect data, and
display data.
7c. Communicate the logical connection among hypotheses, science concepts,
tests conducted, data collected, and conclusions drawn from scientific
evidence.
7d. Construct models and diagrams to communicate knowledge.
7e. Communicate steps and results from investigation orally and in written
reports.
Key Vocabulary
Agarose- The main ingredient of the gel that the DNA migrates through during
gel electrophoresis. The agarose is made of a chain of sugar molecules that
come from seaweed.
Buffer- A liquid that fills the gel electrophoresis box around the agarose gel. The
buffer provides ions to carry a current and helps maintain the pH level.
Cancer- A disease that is caused by some body cells that begins to grow
uncontrollably and damage the parts of the body around them.
DNA- Deoxyribonucleic Acid. The genetic information that carries information
from parent to offspring.
Enzyme- A type of protein that speeds up chemical reaction in a living thing.
Evidence- Information or data helpful in forming a conclusion.
Gel electrophoresis- A technique used to separate DNA pieces, or fragments,
based on size.
Genes- A segment of DNA that codes for a specific protein.
Genetic Disorder- An abnormal condition that a person inherits through their
genes.
Lymphoma- A type of blood cancer that affect white blood cells called Blymphocytes (also known as B-cells)
Micropipet- A tool used for making very precise and accurate measurements of
small volume or fluid.
Picofuge- A device used to quickly spin a microcentrifuge tube to help get all of
the liquid or solid inside of the tube to collect at the very bottom.
Protein- Large organic molecules that are produced by information from the
DNA code.
Restriction digest- The process in which DNA is exposed to restriction enzymes
(molecular scissors), causing it to be cut into fragments at specific places along
the DNA strand.
Simulation- An experience that mimics a real life situation or scenario.
μl (say microliter)- a very small volume ( 1/1000th of a milliliter)
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Advance Preparation (Optional)
The following tasks should be completed before students arrive at the
Community Lab
1.) Introduction of vocabulary
2.) Introduction of equipment (use provided diagram and descriptions)
3.) Cancer overview
4.) DNA overview
5.) Flash Animation Gel Electrophoresis and on-line lab.
Teaching Summary
Equipment Practice
1. Micropipette practice
Introduction of Gel Electrophoresis
2. Watch and discuss Flash Animation Gel Electrophoresis by GSLC.
Introduction to the DNA Testing
3. Explanation of background information.
4. Equipment demonstration and explanations
Doing the lab
5. Students simulate the DNA testing by running a restriction digest and gel
electrophoresis.
6. Students analyze individual data and record onto a class data table.
7. Students complete analysis questions.
Follow-up
8. Discussion of analysis and the conclusions made.
9. Summary of major points and concepts of the lab.
Teaching Detail
Equipment Practice
1. Micropipette practice
Introduction:
Have the students read through the introduction of micropipet practice. Explain
that a micropipet is a very useful tool to scientists to measure very small volumes
of liquid.
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Micropipet Demonstration:
Demonstrate how to use a micropipette and ask the students to watch closely, as
that the correct use will be critical to getting good results in the experiment.
Micropipet step by step with students
1. Have each student hold a micropipet. Remind them that the selection of the
correct micropipet is very important.
2. Select the correct measurement. Use one hand to turn the volume
adjustment until the correct numbers are in view.
3. Attach a pipette tip by pressing firmly.
4. Depress the control button until there is some resistance, the first stop.
5. Hold the micropipet vertically upright and submerge the top into the liquid
while still holding the control button at the first stop.
6. Slowly allow the control button to return to its original position. If you do not
do this very slowly, the volume will not be accurate.
7. Wait a few second to ensure all liquid has been drawn up into the pipet tip.
8. Withdraw the micropipet from the liquid.
9. Align the micropipet tip with the side wall of the well or tube and slowly
depress the control button to the first stop and then keep pressing to the
second stop.
10. Keep the control button depressed and slowly withdraw the micropipet tip
from the well or tube.
11. Allow the control button to go back to its original position.
12. Discard the tip into a proper container by depressing the ejection button.
Prelab: Micropipet Practice
As a class, read through the procedures and explain where each piece of
equipment or material can be found. Be sure that students understand that
they will be measuring colored water with the micropipet into the same
collection tube each time and that they total volume in the end will determine if
the measurements were correct.
Discuss micropipet practice
When students have completed the practice, discuss difficulties that the
students had and ways to correct for any errors to assure that they get the most
accurate measurements in the clinical trial lab.
Introduction of Gel Electrophoresis
2. Watch and discuss Flash Animation Gel Electrophoresis by GSLC.
On the large screen, show the flash animation of gel electrophoresis by Genetic
Science Learning center at http://gslc.genetics.utah.edu/units/biotech/gel/ .
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There are two parts to the interactive animation. Part 1 is a tutorial on how gel
electrophoresis works and part 2 allows the students to interactively run a gel.
Part 1 is essential in explaining the concepts for the day. Part 2 is great and very
valuable if you got an early start with the students.
Introduction to the DNA Testing
3. Explanation of background information.
Ask the students to imagine the following: You work for a company that
develops therapies to treat patients with cancer. The company must first
determine if the therapy will help treat the cancer in the patient. If they give
the medicine to a patients with a particular condition, it could cause bad
side effects.
Explain to the students that what they will be doing is a simulation of an actually
DNA Testing.
Have students read through the introduction and important terms and concepts.
Stop between each paragraph to help explain concepts and to answer any
questions.
4. Equipment demonstration and explanations
Discuss overall procedure, the big idea.
Talk through the entire list of materials one by one and explain where each can
be found and if there is any specific safety or precautionary issues that might be
associated with each.
Point out any steps that student tend to get confused or stumped.
Reinforce that the buffer solution is very carcinogenic and should not be
handled. If they need to, ask the instructor first.
Doing the lab
5. Students simulate the DNA testing by running a restriction digest and gel
electrophoresis.
6. Students analyze individual data and record onto a class data table.
If the students run the gel correctly, they should determine that about ____% of
the patients have a faulty enzyme and can not take the medicine.
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7. Students complete analysis questions.
Follow-up
8. Discussion of analysis and the conclusions made.
1. Should your patient take the cancer medicine? Why or Why not? Use specific
evidence from your experiment to answer the question. Hint: The DNA of
patients who have the working enzyme gene, TPMT, will have been digested
by the restriction enzymes, Hind III and Nhe1.
Each student answer will probably differ. It is important they compare the
quantitative data, length of bands, to explain their answer.
2. How certain are you of whether or not your patient should take the medicine?
If the side effects of a patient taking CancerKiller with faulty TPMT were
lethal, do you think the test that you ran would be sufficient to determine if
your patient should take the medicine? Explain your answer.
This answer can vary by students but is important in getting them to think
about how many tests might need to be done in order to make a confident
decision to follow through with a procedure. When a person’s well-being is on
the line, a lot of consideration must be made.
3. From a business point of view, do you think that there are enough patients
who are able to take CancerKiller to mass-produce and market this medicine?
Use specific evidence from the class data to answer your question.
??????????
Extend Equipment Questions:
1. What could be the cause of faint bands or no visible bands at all?
This could be caused by not enough DNA being put into the well, if the DNA
went too far and went completely off the gel, or if the DNA was degraded.
2. 2. What causes the DNA to travel through the gel?
DNA has a negative charge. When the power supplies are turned on, the
negatively charged DNA is attracted to the red positive lead.
3. Why do smaller DNA fragments travel further down the gel?
All of the DNA fragments are being attracted toward the positive lead. The
smaller fragments can move faster through the gel matrix and therefore have
moved farther through the gel in a given amount of time than a larger piece.
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4. A group found that the TMPT control sample formed a large band very close
to the well and did not travel through the agarose. What could have been the
source of this error?
This could be an indication of a failed restriction digest. If the enzymes do not
break the DNA into the appropriate pieces, that DNA will be too large to move
through the gel matrix.
9. Summary of major points and concepts of the lab.
-Scientist use technology and equipment as a way to solve problems. They are a
tool in the work they do.
-Specific genetic information can be determined by running a test like a gel
electrophoresis to determine if someone is a candidate for taking a medicine or
therapy.
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