GK12 Gel Electrophoresis Lesson Plan
Topic:
Using Gel electrophoresis to separate and analyze DNA fragments
National Science Education Standards:
Science and Technology Standards
a. Abilities of technological design.
b. Understanding about science and technology
NSTA Standards:
5 General Skills of Teaching a- Vary their teaching actions, strategies, and methods to promote
the development of multiple students skills and levels of understanding. c- Successfully organize
and engage students in collaborative learning using different students group learning strategies.
e- Understand and build effectively upon the prior beliefs, knowledge, experiences, and interest
of students. (www.blueplanetbiomes.org)
MS Science Frameworks:
Life Science Biology I 1. Apply inquiry-based and problem-solving processes and skills to
scientific investigations.
a. Conduct a scientific investigation demonstrating safe procedures and proper care of
laboratory equipment. (Safety rules and symbols)
b. Formulate questions that can be answered through research and experimental design.
c. Apply the components of scientific processes and methods in classroom and laboratory
investigations (e.g., hypotheses, experimental design, observations, data analyses, interpretations,
theory development).
e. Analyze procedures, data, and conclusions to determine the scientific validity of
research.
f. Recognize and analyze alternative explanations for experimental results and to make
predictions based on observations and prior knowledge.
g. Communicate and defend a scientific argument in oral, written, and graphic form.
Physical Science 2. Describe the biochemical basis of life and explain how energy flows within
and between the living systems.
e. Examine the life processes to conclude the role enzymes play in regulating biochemical
reactions. Enzyme structure, Enzyme function, including enzyme-substrate specificity and
factors that affect enzyme function (pH and temperature).
Life Science Biology II 3. Investigate and discuss the molecular basis of heredity.
d. Assess the potential implications of DNA technology with respect to its impact on
society. Modern DNA technologies (e.g., polymerase chain reaction (PCR), gene splicing, gel
electrophoresis, transformation, recombinant DNA) in agriculture, medicine and forensics.
Genetics 3. Apply the principles of heredity to demonstrate genetic understandings.
d. Distinguish and explain the applications of various tools and techniques used in DNA
manipulation. Steps in genetic engineering experiments, Use of restriction enzymes, Role of
vectors in genetic research, and Use of transformation techniques.
g. Research genomics (human and other organisms.) and predict benefits and medical
advances that may result from the use of genome projects.
Objectives:
 Students will utilize lab safety and aseptic techniques.
 Students will use the scientific method to predict the results of the
experiment.
 Students will perform current research techniques by performing gel
electrophoresis.
 Students will distinguish between different DNA fragment sizes.
 Students will explain the uses of the different dyes and molecular weight
markers used for the experiment.
 Students will make observations on the migration of the dyes and DNA
fragments.
 Students will explore the properties of DNA that allow for electrophoresis to
be performed.
Classroom Procedure:
Engage
First, ask the students to discuss their knowledge of gel electrophoresis. Second, ask the students
to discuss where they may have seen or heard of the term gel electrophoresis. Third, show the
students Power Point pictures of genotypes and DNA bands on a gel and ask the students to
make observations on whether the two samples are identical, similar, or different.
Materials: projector, computer, PowerPoint lecture
Time: 5 min
Classroom arrangement: students sit in their desks in the classroom (they can be in the lab
provided the lab has a projector screen setup)
Explore
Bring the students into the lab and explain safety procedures, demonstrate how to put on and take
off disposable gloves, and proper usage of pipettors. Let the students practice putting on sterile
pipette tips, loading a practice sample (i.e. water), and ejecting the used tip a few times. To test
their accuracy they can pipette water into a weigh dish several times to be sure they are pipetting
the same amount each time.
Materials: safety glasses, gloves, pipettors, pipette tips, water, scale
Time: 10 min
Classroom arrangement: groups of 4-5 students in the lab
Elaborate
Students will go to the lab and conduct the gel electrophoresis experiment to separate the DNA
fragments. Have the students load their samples into the wells and connect the gel to a power
source to run for an hour. Allow students to answer questions from the lab worksheet with their
lab groups. Assist as necessary.
Materials:
Each gel electrophoresis kit needs:
• Five 9 V batteries connected in series
• Two alligator clips with one red wire and one black wire
• Small Tupperware with two holes on either end
• Two wires bent through holes in Tupperware and connected to alligator clips
Additional Supplies:
• 1X TAE buffer (Tris base, Acetic acid, EDTA) or 1x TBE buffer (Tris base, Borate,
EDTA)
• Agarose
• Loading Dye
• Ethidium Bromide
• Safety glasses
• UV light
• Surgical gloves
• DNA
• Erlenmeyer flask
• Microwave
• Make copies of activity sheets for each student
• Set up lab for experiment. Note: Preparation of the gels before lab to allow for
solidification time and lecturing while the gel is hooked up the electric current saves
valuable time.
Time: 1 hour 15 min
Classroom Arrangement: have the students divide into groups of 4-5 students and go to lab
Explain
Through the Power Point presentation, explain the actual processes scientists use to isolate,
amplify, and analyze DNA samples to detect if the samples came from the same person. Lecture
the students on the principles of gel electrophoresis and how it is used research. More
specifically, discuss what gel electrophoresis is, how gel electrophoresis works, the specific
components used in the experiment, uses of gel electrophoresis, and why safety procedures are
necessary. After this portion of the lecture, involve the students in a discussion of what they
learned. Lecture students on current research and how gel electrophoresis is used in that research.
I used a lecture based on my graduate student research involving the exploration of histones in
Histoplasma capsulatum. The lecture entailed a detailed description of Histoplasma capsulatum
(a dimorphic fungus), the disease it causes, symptoms and treatment, how and why it is studied
in my lab, and current and future research applications. The conclusion of the lecture emphasized
specifically how gel electrophoresis is used to isolate DNA fragments from Histoplasma
capsulatum, leading up to the explain portion of the lesson plan. After this portion of the lecture,
involve the students in a discussion of what they learned.
Materials: projector, computer, PowerPoint lecture
Time: 15 min
Classroom arrangement: students return to their desks in the classroom (they can stay in the
lab provided the lab has a projector screen setup)
Evaluate
Discuss the answers to the lab questions as a class. Students will turn in completed activity
sheet. To be more interactive, posters with statements that could either be the correct or incorrect
answers to the questions can be placed around the classroom. The students can place Post-it
notes on the posters stating whether they agree or disagree with the statement and why.
Materials: student worksheets, posters, Post-it notes
Time: 15 min
Classroom Arrangement: have the students post their answers on the posters around the
classroom and return to their seats for discussion.
References:
1. Davis, Bridgette, Sherry Herron, and Parker Nelson. “Make it happen with
electrophoresis.” National Science Teachers Association Conference March 19, 2009.
2. “DNA gel electrophoresis.” BURST Training Session November 29, 2005.
Lesson Plan Rubric
Feature
Teaching
Goals and
Objectives
Unacceptable=1
Inappropriate for
procedures,
assessments, and
age.
Marginal=2
Age
appropriate
but only
address
concrete
operational
levels
Mastery=3
Aligned with
procedures and
assessments. Age
appropriate.
Address all
cognitive levels;
address the needs,
interests and
abilities of a
diverse group of
students; relate to
state and national
standards
Inquiry
Plans do not
include student
inquiry.
Divergent,
Inquirybased
questions are
planned to
engage
students in
discussion.
Divergent
questions are
planned as wells
as a studentcentered inquiry
which requires
students to
collect, interpret,
and reflect on
data.
Cooperative
Learning and
Small Group
Work
Plans do not
include work in
small groups
Plans include
student
participation
in small
group work
but the
activity is
poorly
planned.
Plans include
student
participation in
small group work
in an effective
and well-planned
manner.
Exemplary=4
Follows the 5E
learning cycle.
Activities and
assessments are
aligned, age
appropriate, address
all cognitive levels,
address the needs,
interests and abilities
of a diverse group of
students, include
enrichment for special
needs students; and
relate to state and
national standards
Follows the 5E
learning cycle.
Divergent questions
are planned as well as
a student-centered
inquiry which requires
students to collect,
interpret, and reflect
on data. Students are
required to report
results and conclusions
as well as identify new
problems for
investigation.
Follows the 5E
learning cycle. Plans
include student
participation in small
group work in an
effective and wellplanned manner. In
addition plans include
job descriptions for
each student.
Name:__________________________
Date:___________
Gel Electrophoresis Lab
Problem: How are DNA fragments visualized and separated on an agarose gel?
Hypothesis:
Procedure:
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Measure 100 ml of 1XTAE buffer and place in Erlenmeyer flask.
Add 0.7 g of agarose to Erlenmeyer flask with 1XTAE buffer.
Microwave the flask for 1 min or until the agarose is dissolved.
Cool the flask by swirling it under running water from the sink.
Ask me to add 10 ul of Ethidium Bromide to the flask. Note: EVERY STEP AFTER THIS YOU
MUST BE WEARING GLOVES BECAUSE ETHIDIUM BROMIDE CAUSES CANCER!!!!!
Pour the agarose mixture into the Tupperware container. Make sure the bottom of the
container is completely covered.
Use the comb to rake out any bubbles.
Place the comb 1/3 of the length of the Tupperware and secure with tape and clips.
Make sure the teeth of the comb do not go all the way to the bottom of the container.
Allow the gel to set for approximately 20 min.
Add 2 ul of Loading dye to the samples I have provided you.
When the gel is solidified, use a plastic knife to cut off the excess gel.
Pour 1XTAE solution into the Tupperware container until it completely covers the
agarose gel.
Load the DNA samples into the wells. To do this set the pipetor to 10 ul to suck up the
samples. BE CAREFUL not to puncture the bottom of the agarose well.
Record the names of the samples and what wells you put them in.
Hook up the electrodes being sure that the positive electrode is on the opposite end of
the wells.
Run the gel for approximately 30 min.
Visualize the gel using a UV light. CAUTION: YOU MUST WEAR SAFETY GLASSES WHILE
VIEWING GEL UNDER UV LIGHT.
Draw a sketch of your results in the space provided in your lab worksheet.
Answer the questions in the back of the packet.
Apparatus:
Assemble five 9V batteries according to diagram below. Attach the black alligator clip to the negative
electrode and the red alligator clip to the positive electrode.
Set up the gel apparatus according to the picture below.
- Electrode
Comb held up by
tape
+ Electrode
Use this DNA ladder (ie Molecular Weight Marker) to determine the fragment sizes of your DNA.
Results:
Record which samples were put in what lanes in the table below.
Lane
Sample Name
1
2
3
4
5
Draw a sketch of the agarose gel in the space provided below:
Record the fragment sizes of each sample in the table below using the provided molecular weight
marker.
Lane
Fragment Size (in kb)
1
2
3
4
5
Questions:
1. How does the process of gel electrophoresis separate DNA fragments?
2. What is the purpose of the agarose gel?
3. What is the purpose of adding blue “tracking” dye to the DNA samples?
4. Explain why DNA has an overall negative charge.
5. Why is the fact that DNA has a negative charge so important in the gel electrophoresis process?
6. Explain how an agarose gel can separate DNA fragments of different lengths.
7. What is the purpose of ethidium bromide in gel electrophoresis?
8. Why is a molecular weight marker used when running the fragments through the gel?
9. On the gel picture below,
(a) circle the smallest fragment produced by a restriction enzyme and label it “smallest.”
(b) circle the largest fragment produced by a restriction enzyme and label it “largest.”