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Gel Electophoresis Simulation: Lab: Simulating Electrophoresis

The document describes a virtual lab simulation of electrophoresis. It involves separating DNA fragments of different lengths by applying an electric current to a gel. Smaller fragments will move faster through the gel than larger fragments. Students load DNA samples and standards into the gel wells and run an electric current to separate the fragments by size. They then stain the gel to view the separated DNA bands and compare them to the standards to estimate the fragment sizes. The document also describes a paper simulation modeling DNA fingerprinting to identify a suspect who ate stolen cheese based on matching their DNA to that found at the crime scene.

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Daniel Condreay
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573 views5 pages

Gel Electophoresis Simulation: Lab: Simulating Electrophoresis

The document describes a virtual lab simulation of electrophoresis. It involves separating DNA fragments of different lengths by applying an electric current to a gel. Smaller fragments will move faster through the gel than larger fragments. Students load DNA samples and standards into the gel wells and run an electric current to separate the fragments by size. They then stain the gel to view the separated DNA bands and compare them to the standards to estimate the fragment sizes. The document also describes a paper simulation modeling DNA fingerprinting to identify a suspect who ate stolen cheese based on matching their DNA to that found at the crime scene.

Uploaded by

Daniel Condreay
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
Available Formats
Download as PDF, TXT or read online on Scribd
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Lab: Simulating Electrophoresis

PART 1: Virtual Simulation

You will start by visiting the Gel Electophoresis Simulation to see how we would set up and run a sample of
DNA

Introduction:
After completing the introduction, write a description in your own words of how electrophoresis separates out
different lengths of DNA fragments:

The DNA’s molecules will travel throught the gel at different speeds, causing the DNA to be seperated from
each other.

STEP 1: Make the gel


Describe the process of making the gel below:
Put agarose into a flask. Next, add liquid buffer to the flask. Put plastic over the flask and place the flask in
the microwave. Then you pour the agarose mixture into the mold. Next you place the comb in one end of the
gel. Let the gel solidify and remove the comb.

STEP 2: Set up the gel apparatus


Describe the process of setting up the gel apparatus
Pour the buffer into the electrophoresis box. Place the gel into the electrophoresis box.

STEP 3: Load the DNA sample


Describe the process of loading the DNA sample
Using a clean pipet tip, use the micropipettor to suck some loading buffer, then add it to the DNA sample.
Next suck up the DNA into the pipet tip. Then eject the DNA into the first well of the gel. Next suck up some
of the standard DNA size. Then transfer the standard DNA size into the second well of the gel.

STEP 4:
Which ended is the negative and positive end? Which end is closest to the wells in your sample? Explain why
this is important.

The side with the DNA is the negative end and the side opposite of the DNA is the positive end. This is
important because the DNA will move towards the positive end due to the negative ions pushing it forward.

STEP 5:
What is the stain we use in this case and how does it allow us to see the DNA?
Ethidium Bromide allows us to see the DNA by fitting between the rungs of the DNA ladder.
Take a screenshot of your final stained gel including your estimated size measurements and paste it
below:

Part 2: Paper Simulation


Who Ate the Cheese?!

Objectives: In this simulation you will examine crime scene evidence to determine who is responsible for eating
the Principal's special imported Lindbergher Cheese (yes, the stinky cheese). You will model the process of
electrophoresis and DNA fingerprinting.

POLICE INCIDENT REPORT

Incident Data:
Incident type: Theft-------complaint status--------Pending DNA results
Processed by: Police Cheif Shoff---------Other Officers-------Li gase

Property:
Property code: rare cheese--------Owner’s name:----------Mr. Lesley
Name: Lindbergher-----------------Value:-------------------$12,000

Burglary Data:
Method of Entry:Unknown, no evidence of force on doors or windows.

Narrative: The cheese was allegedly stolen from the Principal’s office the night before homecoming. The
cheese was listed as a gift from the McCutcheon principal. Officer Li Gase dusted for fingerprints and found
none on the table or doors, the janitor claimed that they had been wiped clean earlier. The wheel of cheese
was on a platform in his office, and half of it had been eaten. We took pictures of the half eaten cheese and
sent it to the lab for further tests. Edna N. Zime, the lab technician said that saliva samples could be taken from
the teeth imprints of the cheese that was left behind.

Suspect Data:
Suspect Number: 1
Name: Mrs. Dubbah Elix
Description of Suspicion: She was seen entering the sitting room earlier in the evening. She is well known for
her love of cheese.

Suspect Number 2
Name: Electra Foresis
Description of Suspicion: Electra was recently involved in a expulsion with the McCutcheon principal that
sources say ended badly. Her motive may have been to sabotage the principal’s gift to the Mr. Lesely.

Suspect Number 3
Name: Ada Nine
Description of Suspicion: Ada was the janitor in charge of cleaning the office. She had access to the cheese.

Suspect Number 4
Name: Gene Tics
Description of Suspicion: Gene is the leader of the local Cheese-Makers Guild, he may not have wished for Mr.
Lesley to have cheese from anywhere but his own guild.

Crime Lab Data:


Crime lab investigator: R. Renee------------------Lab technician: N. Zime
List of Evidence received: Plastic bag with crumbs of cheese
List of Procecures used: DNA extraction, PCR, DNA restriction analysis

Narrative: After receiving the package with the plastic bag marked Crime Scene, the DNA was extracted.
Because the sample was so mall, the DNA was amplified using the polymerase chain reaction. We isolated the
DNA from the four suspects and compared them to the crime scene DNA using DNA restriction analysis.

Results: See attached DNA Results


DNA Evidence Evaluation
1. Retrieve your DNA samples from your teacher. Turn your paper strips (DNA sequences) so that the side
with the bases is facing you. The restriction enzyme cuts at every point it finds C C G G, always cutting
between the C and the G. Label the back of the slips with the suspect number so that you don't get them
confused after cutting. Use scissors to cut the DNA sequence at the C C G G points.

2. Count the number of base pairs (bp) in each piece of DNA that you created. Record the base pair number
on the back side of the DNA fragment.

3. Make an enlarged chart like the one shown. Your teacher will give you paper for this. Use a ruler to ensure
that the lengths are uniform.

4. Tape your DNA fragments to the chart, using the base pair numbers as a guideline for fragment placement.
Fragments will overlap each other.

5. Retrieve the crime scene DNA sequence from your teacher. Repeat the process above and add it to your
paper gel. Compare the crime scene DNA to the suspects and indicate on your chart, which suspect is guilty
of eating the cheese.

ANALYSIS:
1. On your chart, label the positive (+) and the negative (-) ends. Circle the suspect's DNA who matches
the DNA at the crime scene and write the name of the suspect. Insert a picture of your chart below:
For each of the following tasks performed in the activity, describe what they are actually simulating.
2. Cutting the DNA into fragments
This simulates collecting fingerprints at the crime scene.

3. Taping the DNA onto the large paper


This simulates the DNA going through the gel and being propelled forward by the negative ions of the
electricity.

For each word below, describe how it relates to DNA Fingerprinting:


4. Polymerase Chain Reaction
Makes it so we can see the DNA in the gel.

5. Gel Electrophoresis
Proppels the DNA forward, causing it to separate from each other.

6. Restriction Enzyme
Cuts the DNA specific points making it possible to match evidence from the crime scene.

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