Module 2
DNA Files
Investigation 2.1 What is DNA?

Biotechnology – Extract DNA from Cells
(Recursos en
Español)
 DNA Gel Electrophoresis Simulation
 DNA Fingerprint and Forensics
Who Ate the Apple?
 Build a DNA Molecule (Recursos en
Español)
 Proteins to Proteomics
(Recursos en Español)
Investigation 2.2 DNA Gel Electrophoresis




Making an Agarose Gel
How to Use a Micropipette
Loading and Electrophoresis
Staining and Understanding Gel
Results
Module 2
DNA Files
Investigation 2.1 What is DNA?
Activity 1: Biotechnology
How Extract DNA from Cells
Objectives
1. Students will learn how to extract DNA from plant and animal cells.
Materials
salt solution (6g of salt to 94 ml
of water)
soap solution (1 part soap to 3
parts water)
Note: You can combine the soap
and salt solution to make buffer
solution. If you want students
to experiment with what is the
best method to extract DNA
from cells, having separate
bottles of salt and soap works
best.
91% alcohol (keep alcohol in the
freezer and on ice during the
experiment). Alcohol can be
purchased in drug stores.
test tubes
funnel
filter paper
glass rods (wooden sticks)
cauliflower, dry peas,
strawberries ( or other
fruit), liver (beef or chicken),
sweetbread (beef thymus
gland), wheat germ, cheek cells.
Mortar and pestle
blender
plastic baggies
Procedure
Cheek Cells
1. Pour approximately a teaspoon of water into a small Dixie
cup. If you have too much water, empty the cup.
2. Swish the water in your mouth vigorously for at least 30-45
seconds.
3. Place cell/ water mixture back into your Dixie cup.
4. Pour cell/water mixture to fill a test tube to approximately one inch
full.
5. Add 40 drops of soap solution and 40 drops of salt solution to your
test tube and gently mix with your wooden stick. Try not to create
soap bubbles!
6. Add cold alcohol down the sides of your test tube until you have twice
the amount of the cell/buffer mixture.
7. DNA will precipitate (come out of solution) and look like “white
mucous.”
8. Use your wooden stick or glass rod and twirl as you remove (loop) the
DNA.
Procedure
Beef/chicken liver and sweet bread (thymus gland)
1. Cut a piece of liver (2” x 2”). You do not need very
much.
2. Add approximately 40 drops of salt and 40 drops of
soap solution to your mortar and pestle. Note you may add more soap
solution if it is too dry.
3. Grind the mixture.
4. Use a funnel lined with filter paper and a test tube to filter your
cell/buffer mixture. Try not to break the filter paper as you squeeze.
If it is too dry add more soap solution.
5. Add cold alcohol down the sides of your test tube until you have twice
the amount of the cell/buffer mixture.
6. DNA will precipitate (come out of solution) and look like “white
mucous.”
7. Use your wooden stick or glass rod and twirl as you remove the DNA.
Procedure
Inquiry-based
1. Allow students to experiment with the DNA Extraction procedures.
Students can change the concentration of salt and/or soap solution.
2. Students can collaborate to see the procedure that yields the most
DNA extraction.
Instructor’s Notes:
 DNA is located on chromosomes.
 There are 46 chromosomes in each of our cells. Half (23
chromosomes) come from the father and half (23
chromosomes) come from the mother.

Chromosomes have banding patterns of dark and light
regions. The dark bands show regions where genes are located.

Only 2% of the DNA has genes (approximately
20,000-25,000 genes). Genes are the basic unit of heredity and
contain information to make proteins.

The rest (98%) of the DNA may help to regulate
when and how much proteins to make. Proteins control many of
the cell’s functions and make up most of the cell’s structure.

Proteins regulate many of the cell’s activities.
Activity 2: DNA Gel Electrophoresis Simulation
Materials
food coloring (represent
filter paper (cut in rectangles)
DNA samples)
rubbing alcohol
mix equal parts of blue and red
water
mix equal parts of blue, red and
rulers
yellow (the primary colors)
Q-tips
beakers (or plastic containers)
foil
Other samples: leaves, berries, flowers, black felt pen, KoolAid –different flavors,
candy (Skittles or M&M’s)
Procedure
1. Draw a line across the bottom of 2 pieces of filter paper approximately 2
centimeters from the edge.
2. Use a different toothpick for each sample.
3. Make a spot (evenly spaced) of each sample across the bottom line of your
filter paper.
4. Place one of filter papers in alcohol and one in water.
5. Be sure the pencil line stays above the liquid.
NOTE: The solvent will separate the dyes present according to their molecular
size and give distinct banding patterns. The smaller size molecules in the dye
will travel farther and faster than the larger sized molecules. This is like what
happens in DNA gel electrophoresis. Instead of using solvents to separate the
different size molecules, we use electricity!
6. When the liquid reaches the top (approximately 1 ½ centimeters from the
top), remove the filter paper and draw a line to indicate how far the
molecules traveled.
7. You can repeat the procedure using other samples (leaves, berries, Skittles,
black felt pen.
DNA Gel Electrophoresis Simulation Student Worksheet
Name_____________________________________________________
Tape your filter paper here
1. Compare the banding patterns present on your filter paper from both the
alcohol and water solvents. Do you see any differences in the banding
patterns, sizes, colors? Explain what you see.
2. What color dye traveled the fastest? _____________________
3. What color dye traveled the slowest? _____________________
4. What is DNA gel electrophoresis?
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
_________________________________________________________
Activity 3: DNA Fingerprint and Forensics
Who ate the Apple?
Procedure
1. Handout “Who is Guilty?”
2. Transparency template for each student.
Problem: Someone ate Mrs. Phillips’ apple. The hungry thief left behind saliva
on the apple core. DNA saliva samples of the possible suspects have been
fingerprinted using DNA gel electrophoresis.
3. Match the known DNA saliva sample – the hungry thief- to see who ate
the apple.
Ashley
Abigail
Allen
Allison
Akeem
Armond
Allisha
Antonio
Arnold
Aaron
Addley
Ali
Adam
Who is Guilty?
Who ate the apple? ___________________________________
Activity 4: Build a DNA Molecule
Materials
Genetic Science Learning Center - handout
licorice (red and various colors)
marshmallows (gummy bears)
toothpicks
DNA paper template – Adapted from Access Excellence handout
color pencils
scissors
Procedure
Option 1:
Make a model of DNA using licorice and marshmallows (or gummy
bears).
Option 2:
1.






2.
3.
4.
Give each students a nucleotide template to color as follow:
Phosphate red
Sugar (leave white)
Adenine –blue
Thymine – green
Guanine- yellow
Cytosine- orange
Color and cut out paper nucleotide templates.
Students can work in groups
Use tape to assemble DNA molecule
Taylor, Tish . “Discovering DNA Structure.” Access Excellence. 1994 Woodrow Wilson Biology Institute.
http://www.accessexcellence.org/AE/AEPC/WWC/1994/discovering_dna.html
Activity 5: Central Dogma
DNA – RNA - Protein
Materials
DNA ACTIVITY CARDs: TAC, ATC, etc. Print template cards
and laminate.
Activity 5: Proteins and Proteomics
Central Dogma
DNA----------RNA-------------- Protein
Materials
Genetic Science Learning Center - handout
licorice (red and various colors)
marshmallows (gummy bears)
round shapes (or Post-It paper)
toothpicks
scissors
Procedure
Option 1:
1. Follow procedure in the Genetics Science Learning Center
Reading DNA http://learn.genetics.utah.edu/units/basics/print-andgo/reading_DNA.cfm
Option 2:
1. Print amino acid cards (or write amino acids on 3X5 card). You may need to
write an amino acid several times depending on the protein you build.
2. Print DNA, m-RNA, and t-RNA cards.
3. Distribute cards so that each student has a card.
4. TAC is the START codon. ACT is the STOP codon. Have students with the
DNA cards line up (or place on the table top or floor) between the start and
stop codons.
5. Students with the m-RNA cards position themselves (or place on the table
top or floor) complimentary to the DNA.
6. t-RNA cards pick up the correct amino acids and position themselves along
the m-RNA.
7. Demonstrate alternative splicing. Remove one or two of the exons in the mRNA message. Now, what proteins are made?
What is Proteomics?
Proteomics is the study of all the proteins in an organism. There are approximately
20,000 – 30,000 genes that code for over 100,000 proteins in the human body.
How are proteins encoded, how do they interact with one another, what function do
they serve in biological pathways, how are proteins expressed in various cells and
at different times in the life cycle of organisms are just of the few questions
scientists are studying.
Procedure
1. Handout amino acid codon – Genetics Learning -Utah.
2. Use the following DNA sequences to assemble amino acids. You can
abbreviate the amino acid. Remember the start and stop codons!
DNA sequence #1
TAC AGG TCA GGC GTC AAA TTG ATC CCG ATT
Protein
_________________________________________________
DNA sequence #2
TCA GTC TAC TAT GGC TAG CCT AAT GCG CCG ATC AAA
Protein
_________________________________________________
DNA sequence #3
TTA TAC GGC ATG TTA GGC CGC CCC GGA TTA GGT ACT TTA
Protein
_________________________________________________
Alternative Splicing Student Worksheet
Name ____________________________________________________
How can approximately 25,000 genes in our DNA code for over 100,000
proteins?
One answer is alternative splicing. More than one protein can be made
from one gene.
Procedure
1. Squares 1-6 represent exons. Exons are the parts of a gene that become
translated into proteins. Use coloring pencils to color the squares 1-6.
2. Using your color pencils, make the following proteins.
 alternative splicing m-RNA 1 - exon 1, 3, 6
 alternative splicing m-RNA 2 – exon 1, 2, 4, 5, 6
 alternative splicing m-RNA 3 – exon 2, 3, 5, 6
m-RNA exons
1
2
3
4
5
6
m-RNA 1
1
3
6
m-RNA 2
1
2
4
5
m-RNA 3
2
3
5
6
6
Investigation 2.2 DNA Gel Electrophoresis
Lab procedures adapted with permission from General Biology for Non-majors Lab Manual,
Phillips, M., McGraw- Hill, 2009.
Purpose
To introduce students to the theory and methods used to perform agarose gel
electrophoresis. What is electrophoresis? Electrophoresis uses electricity to
separate molecules according to size. It is one of the most important procedures
used in studying DNA.
Case Scenario
Scenario adapted from BIOTECH Project, University of Arizona, “Mystery of the Stolen
Cat Food.” http://biotech.bio5.org/content/activities#DNAFingerprinting
Mystery of the Stolen Cat Food
Fluffy is my white haired cat. She sometimes likes to have her meals on the back
porch, so I put her dish of cat food outside. Recently, she’s been whining and
complaining because she’s hungry. After doing a little detective work, I realized
that another white haired cat has been eating Fluffy’s food. However, there are 2
other white haired cats in my neighborhood and I can’t tell which cat is eating
Fluffy’s food. You are going to help me figure out which cat is the criminal!
Materials
BioRad electrophoresis equipment and food color dyes.
DNA Electrophoresis
1. Balance
2. Small weigh boat and scoop
3. Power supply
4. Plastic electrophoresis box with tray
5. Comb
6. Masking tape
7. Micropipette
8. Box of tips
9. 1 large beaker for discarding used tips.
10. 250 mLflask
11. 50 mL graduated cylinder
12. Rulers
13. Agarose (BioRad)
14. TAE Buffer (BioRad)
15. Practice gels and practice loading dye (loading dye – ½ glycerin, ½ water, 1-3
drops of blue food coloring).
16. Crime scene food color samples (DNA), mixed with glycerin. Prepare samples
ahead of class.
 One sample of each food color: ½ glycerin, ½ water, 1-3 drops of food
coloring: red, yellow, blue, green, and mystery mix.
Tube #1 - saliva from food (mystery mix)
Tube #2 - Fluffy (red)
Tube #3 - white cat #1 (yellow)
Tube #4 - white cat #2 (blue)
Tube #5 - white cat #3 (mystery mix)
Making an agarose gel
Prepare a 1.0% agaorse gel: Weigh 0.4 g of agarose and place it in a 250
mL flask with 40 mL of 1X TAE buffer solution. Note: you can prepare
agarose gel of 0.8% by placing 0.32 g of agaorse and place it in a flask with
40 mL of TAE buffer.

Note gels may be prepared ahead of time.

Cover flask with saran wrap and heat in microwave for one minute (agarose
should boil)
Use gloves to remove flask
Swirl gently to be sure all of the agarose is dissolved.
Wait until it cools enough so it feels warm to the touch but will not burn.
(temp of baby’s milk bottle).



Preparing Gel Tray
Prepare Gel Tray: Use masking tape to tape each end of the gel tray. Be sure the
tape fits tightly. You may want to tape twice around.
 Insert comb.
 Pour dissolved agarose into the tray, avoid creating bubbles.
 If any bubbles appear, use a plastic pipette to move them to the side and out of the
way.


Wait approximately 20-30 minutes until the gel sets (appears opaque). Be
careful not to move or jar gel while it is solidifying.
Rinse the flask immediately with warm tap water then rinse flask 3 times
with distilled water. Swirl around each time.
How to Use a Micropipette Practice
Practice micropipetting: Your instructor will demonstrate the proper use of
the micropipette.
 While the gel is solidifying, practice micropipetting 10 µL of practice loading
dye. Remember, you are using very small amounts; 1 L is equal to 1 millionth
of a Liter. See the 1 L flask for comparison.
 ALWAYS put a plastic tip on the micropipette.
Push the pipette into the plastic tip.
 Hold the micropipette so your thumb is on top of
the dispensing knob or plunger. (shake hands with
the pipette).
 ALWAYS keep micropipette vertically (up) when
there is fluid in it. Never allow fluid to run back
into the pipette by laying it down filled.
 Use your thumb to control the speed of the
plunger. ALWAYS release (lift your thumb up)
SLOWLY.
 The micropipette has two stops. Press to the first stop. Push down harder
to the second stop. SLOWLY release (lift your thumb up).
 Hold the micropipette in one hand vertically about eye level and bring your
sample tube to the same level.
 Press to the first stop and do not release. Insert the pipette tip just under
the surface of the solution. SLOWLY, release (let your thumb up).
Filling the sample well: Use the sample provided to practice
loading a sample gel.
To fill the sample well:
 Press to the first stop and continue to press to the second stop to fill
the well with sample fluid. DO NOT RELEASE until you remove the tip
from the well. SLOWLY release. If you do not keep plunger down until
you remove the tip from the well, you will suck liquid back into the tip.
 Eject the used tip in a beaker.
 ALWAYS change tips for each new sample you need to pipette.
Loading DNA Sample
1. Gently remove tape and comb from gel tray and place the tray in the
electrophoresis box. Be sure the wells are at the negative end. The
DNA samples will run to the positive end.
2. Measure 250 mL of buffer (1x TAE). Pour prepared running buffer
solution (approximately 250 mL) into the gel box reservoirs to cover the
gel. The gel should be completely covered about 1 mm in depth. Do not
overload. Be sure no air is trapped underneath the gel tray.
Loading samples
3. Press to the first stop. Insert the pipette tip just under the surface of
the DNA sample. SLOWLY, release (let your thumb up).
Fill your well by pressing down to the first stop. Then, continue to press to
the second stop to release all the fluid. DO NOT RELEASE until you remove
the tip from the well, then SLOWLY release.
Electrophoresis
4. Avoid shock by making sure the table top is dry. Do not turn the power
on until it is dry.
5. Connect the top of the box with voltage cables. The negative cable is
black and the positive cable is red. Be sure the wells are at the
negative end.
6. Plug power supply into the outlet. Turn on Power. Turn voltage to 100
volts and run for approximately 25-30 minutes. Look through the
apparatus to see migration.
7. Turn off Power supply.
8. Disconnect leads from power supply.
Student Name____________________________________________
DNA Electrophoresis Student Worksheet
1. What is electrophoresis?
_________________________________________________________
_________________________________________________________
2. Use color pencils to draw the gel results.
3. Which cat ate Fluffy’s food? __________________________
Websites/References
DNA Extraction Virtual and Electrophoresis Lab Learn Genetics University
of Utah
http://learn.genetics.utah.edu/units/biotech/index.cfm
Biotech Project-The Univerisity of Arizona
http://biotech.bio5.org/content/activities#DNAFingerprinting
Human Genome Project Information – Image Gallery
http://www.ornl.gov/sci/techresources/Human_Genome/education/images.s
html
DNA Replication image – scroll down to image (many images available)
http://genomics.energy.gov/gallery/basic_genomics/gallery-01.html
Fingerprint E.coli
http://reconstructors.rice.edu/extra/cdc/
Cracking the Code of Life – go to Sequence Yourself
http://www.pbs.org/wgbh/nova/genome/
Putting DNA to Work -Science Museum of the National Academy of
Sciences
http://www.koshland-science-museum.org/exhibitdna/index.jsp
Proteomics and Cancer Fact sheet
http://www.cancer.gov/cancertopics/factsheet/proteomicsqa
Access Excellence http://www.accessexcellence.org/
DNA Interactive. Cold Springs Harbor laboratory 2003. 10 April 2007.
http://www.dnai.org/
Learn.Genetics. The Biotechniques Virtual Laboratory. University of Utah
2007.
10 April 2007.
http://learn.genetics.utah.edu/units/biotech/index.cfm
Taylor, Tish . “Discovering DNA Structure.” Access Excellence. 1994
Woodrow Wilson Biology Institute.
http://www.accessexcellence.org/AE/AEPC/WWC/1994/discovering_
dna.html