Wood to Wheels 2012– Lesson Three
Jenn Coury
How Can Genetically Modified Foods be Detected with PCR?
Lesson Introduction

Title: How Can Genetically Modified Foods be Detected with PCR?

Lesson Overview: Using the Carolina lab Detecting Genetically Modified Foods with PCR, students
determine if soybeans and a food of their choice is genetically modified. Concepts covered include: the
relationship between genotype and phenotype, forensic identification of genes, methods for producing
transgenic crops, and the movement between in vitro (in lab) and in silico (on a computer)
computation. Students will have the opportunity to utilize several modern biological research methods
including: DNA extraction and purification, Polymerase chain reaction (PCR), Gel electrophoresis, and
bioinformatics.

Subject/ target grade: Scientific Inquiry , 12th

Duration: Approximately 12 hours. Seeds must be planted 2-3 weeks before the rest of the lab is
completed.

Setting: Laboratory & Classroom

Learning Objectives:
o Students will be able to determine if a plant has been genetically modified
o Students will be able to isolate DNA, amplify DNA by PCR, and interpret the results of gel
electrophoresis

Michigan Content Standards: relevant science standards that the lesson addresses.
Michigan Science High School Content Expectations:
B1.1 Scientific Inquiry
B1.1B Evaluate the uncertainties or validity of scientific conclusions using an understanding of sources of
measurement error, the challenges of controlling variables, accuracy of data analysis, logic of argument, logic of
experimental design, and/or the dependence on underlying assumptions.
B1.1C Conduct scientific investigations using appropriate tools and techniques (e.g., selecting an instrument that
measures the desired quantity—length, volume, weight, time interval, temperature—with the appropriate level
of precision).
B1.1D Identify patterns in data and relate them to theoretical models.
B1.1E Describe a reason for a given conclusion using evidence from an investigation.
B1.1f Predict what would happen if the variables, methods, or timing of an investigation were changed.
B1.1g Use empirical evidence to explain and critique the reasoning used to draw a scientific conclusion or
explanation.
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B1.1h Design and conduct a systematic scientific investigation that tests a hypothesis. Draw conclusions from data
presented in charts or tables.
B1.1i Distinguish between scientific explanations that are regarded as current scientific consensus and the emerging
questions that active researchers investigate.
B2.5 Living Organism Composition
B2.5A Recognize and explain that macromolecules such as lipids contain high energy bonds.
B4.2 DNA
B4.2B Recognize that every species has its own characteristic DNA sequence.
B4.2C Describe the structure and function of DNA.
B4.2D Predict the consequences that changes in the DNA composition of particular genes may have on an organism
(e.g., sickle cell anemia, other).
B4.2x DNA, RNA, and Protein Synthesis
B4.2f Demonstrate how the genetic information in DNA molecules provides instructions for assembling protein
molecules and that this is virtually the same mechanism for all life forms.
B4.2h Recognize that genetic engineering techniques provide great potential and responsibilities.
B4.r2i Explain how recombinant DNA technology allows scientists to analyze the structure and function of genes.
(recommended)
B4.r5x Recombinant DNA
B4.r5a Explain how recombinant DNA technology allows scientists to analyze the structure and function of genes.
(recommended)
B5.3 Natural Selection
B5.3f Demonstrate and explain how biotechnology can improve a population and species.
Next Generation Science Standards:
Eight practices of science and engineering
1. Asking questions (for science) and defining problems (for engineering)
2. Developing and using models
3. Planning and carrying out investigations
4. Analyzing and interpreting data
5. Using mathematics and computational thinking
6. Constructing explanations (for science) and designing solutions (for engineering)
7. Engaging in argument from evidence
8. Obtaining, evaluating, and communicating information
Performance Expectations
HS-LS1-1. Construct an explanation based on evidence for how the structure of DNA determines the structure of
proteins which carry out the essential functions of life through systems of specialized cells.
HS-ETS1-1. Analyze a major global challenge to specify qualitative and quantitative criteria and constraints for
solutions that account for societal needs and wants.
HS-ETS1-2. Design a solution to a complex real-world problem by breaking it down into smaller, more manageable
problems that can be solved through engineering.
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HS-ETS1-3. Evaluate a solution to a complex real-world problem based on prioritized criteria and trade-offs that
account for a range of constraints, including cost, safety, reliability, and aesthetics as well as possible social, cultural,
and environmental impacts.
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Lesson Background

The Guiding Question: How Can Genetically Modified Foods be Detected with PCR?

Materials and Equipment Needed:
o Access to the internet and a projector
o Carolina Detecting Genetically Modified Food by PCR Lab (see page 3 for the contents of the kit)
 Student copies STUDENT LAB INSTRUCTIONS (pages 5-12)
 Student copies RESULTS AND DISCUSSION (pages 17-18)
 Needed but not included:
 Planting pot or flat
 Potting soil
 Soy or corn food products
 Micropipets and tips (1 μL to 1000 μL – Suggested 20 μL, 200 μL, and 1000 μL)
 Microcentrifuge tube racks (or Styrofoam with holes put in it)
 Microcentrifuge for 1.5-mL tube
 Thermal cycler (PCR) – I contacted a local university by emailing both the science
education professors and the head of the Biology Department to arrange running
the PCR in their lab. They actually ended up bringing the PCR to my school!
 Water bath or heating block
 Electrophoresis chambers
 Electrophoresis power supplies
 UV transilluminator (ethidium bromide staining) OR
 White light box (CarolinaBLU™ staining, optional)
 Camera or photo-documentary system (optional)
 Permanent markers
 Containers with cracked or crushed ice
 Vortexer (optional)
 Roundup® herbicide (optional)
o Paper Clip PCR Activity
 Student copies of the Paper Clip PCR Activity (pages 3-5)
 Small colored paper clips (blue, red, green, yellow and white)
 Each group will need about 25 paper clips of each color in a separate bag/cup,
and about 6 white paper clips

Safety precautions:
o Ethidium bromide is a carcinogen. It is therefore recommended that you use the CarolinaBLU
stain for gel electrophoresis if you are working with high school students.

Advanced Preparation:
o Order the Genetically Modified Foods by PCR to arrive no later than 1 month before performing
lab. If you receive GM plant tissue rather than GM/ Roundup Ready® seeds, you may also want
to see if you can find an alternative source of Roundup Ready® seeds (perhaps a local farmer) if
you want to test the phenotypes by spraying with Roundup® at the end.
o Part I. PLANT SOYBEAN SEEDS in the METHODS section (page 7) of Detecting Genetically
Modified Foods by PCR needs to be done 2-3 weeks before you plan on isolating the DNA and
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doing PCR. It will take this long for the first true leaves to develop. Be sure to familiarize
yourself with both the lesson plans and the STUDENT LAB INSTRUCTIONS (pages 5-12) of
Detecting Genetically Modified Foods by PCR. As stated in the lesson core, it is highly
recommended that you create an answer key that will match the students work. It has not
been included on purpose, as it is very important that as the instructor that you have a full
understanding of the procedure.

Background Information for Teachers:
o The entire Detecting Genetically Modified Food by PCR can be accessed online by clicking on the
Protocol button. In addition, there are a number of animations available by clicking on the
Resource button covering the following topics:
 Cutting & pasting: Explore the enzymes used to manipulate DNA.
 Transferring & storing: Find out about the mechanisms used to deliver foreign DNA into
a cell.
 Large-scale analysis: Learn about the techniques used to analyze the activity of
thousands of genes at a time.
 Sorting & sequencing: See the techniques used to sort DNA fragments, and determine
the sequence of DNA bases.
 Amplifying: Discover the mechanism used to make many copies of DNA.
 Model organisms: Meet some of the model organisms used in molecular biology
research.
All of the above, plus a video tutorial on Bioinformatics, is also included on the GM FOOD CDRom that is included with the Carolina kit.

Pre-teaching:
Students should have a working knowledge of DNA and protein synthesis.
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Lesson Core
Part I: Plant Soybean Seeds

Engage: How will the teacher introduce the question in a way that engages the students’ interest and
builds on their prior knowledge?
Follow the directions for “I. PLANT SOYBEAN SEEDS” in the METHODS section (page 7) of Detecting
Genetically Modified Foods by PCR. Remember that you have to plant your seeds 2-3 weeks before
you plan on isolating the DNA and doing PCR. Also, you may receive tissue from the Roundup Ready®
soybean plants, rather than seeds (I received tissue even though there was no mention of it online
when I ordered).
Inform the students that they will be in charge of caring for their plants for the next few weeks. Many
students have never taken care of a plant and this will be a new experience for them – help them along
the way. During these weeks you may also choose to have your students make both quantitative and
qualitative observations about the two types of soybeans in their science notebooks.
Building on prior knowledge: Questions that the teacher might ask to assess students’ prior
knowledge.
After planting,
Ask and discuss:
o What does genetically modified mean? (The genome of the organism has been altered, usually
so a specific trait is present)
o How do scientists transform a plant? (See slide 25 in PP from Lesson 1)
o What do you know about Roundup®? (See the INTRODUCTION section (page 5) of Detecting
Genetically Modified Foods by PCR)
o What do you think it means for a plant to be Roundup Ready®? (If students don’t know, ask
them if they know what Bt corn is – they may make the connection that Roundup Ready®
means the plants have a gene that makes them resistant to Roundup®)
o What differences do you expect between the wild-type and Roundup Ready® plants? (Accept
any answers the describe differences in the phenotype or genotypes of the plant.)
o How will you be able to observe these differences? (Possible student answers: observe,
measure, DNA fingerprint)
Tell the students:
You will be using a set of scientific techniques in the lab to determine if the soybean plants are
genetically modified or not. You will also have the opportunity to test a food product of your choice to
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see if it comes from Roundup Ready® seeds. Have the students read the INTRODUCTION (pg. 5) of
Detecting Genetically Modified Foods by PCR.
Use the Prezi Plant Transformation to show these techniques and review how a plant is transformed.
In their science notebooks, have the students answer:
o Describe the two important transgenes that have been widely introduced into crop plants.
 Bt gene: Crops can make a toxin that kills insects (so you don’t have to use insecticides)
 Glyphosphate-resistant gene: Crops are not killed by Roundup® (an herbicide used to kill
weeds)
o What is tubulin? A protein found in all plants
o Have the students write three hypotheses* regarding pheotypes. Which ones can you actually
test in the classroom? Just the wild-type
 If a wild-type soybean plant is sprayed with Roundup®, then the plant will X.
 If a Roundup Ready® soybean plant is sprayed with Roundup®, then the plant will X.
 If (food crop) is sprayed with Roundup®, then the plant will X.
*Note: Depending on the level of your students you may give them the above prompts or ask
them what they should be able to write hypotheses for.
o Have the students write two hypotheses for the genotypes. How will you test for these? DNA
Isolation, PRC, and Gel Electrophoresis
 If the DNA contains the 35S promoter (162bp) then the plant has been genetically
modified and is Roundup® Ready.
 Made the plant resistant to the herbicide
 If the DNA contains tubulin (187 bp), then the DNA came from a plant.
 Positive control for plant DNA.
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II. ISOLATE DNA FROM SOYBEAN AND FOOD PRODUCTS


Explore II: How will the teacher facilitate the students’ exploration of the problem and collection of
data. What questions will the teacher ask to guide students in exploration?
Elaboration II: How will the teacher facilitate the sharing of student explanations? What questions will
the teacher ask to clarify student thinking?
a) PRE-LAB: Have the students label their notebook as illustrated below. Then distribute a copy of the
LAB FLOW (pg 6) to each student of Detecting Genetically Modified Foods by PCR. As students read
through the instructions for II. ISOLATE DNA FROM SOYBEAN AND FOOD PRODUCTS (pages 8-9) of
Detecting Genetically Modified Foods by PCR they should fill in as much information as they can in
the correct columns. Remind the students to only record important information – in this case short
and sweet notes are ideal. They should cut out the pictures from the LAB FLOW and place them in
their notebook in order as they go. Step 3 is shown as an example below.
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NOTE: The students should number their steps according to the written directions and then match
the pictures. This way they can refer easily to text if they need to during the lab. Some of the
written steps have been combined into one picture, so there are more written steps then pictures.
This means some steps will share a picture.
It is highly recommended that you create an answer key that will match the students work. It has
not been included on purpose, as it is very important that as the instructor that you have a full
understanding of the procedure. While creating your answer key, you should use the same
instructions for II. ISOLATE DNA FROM SOYBEAN AND FOOD PRODUCTS (pages 8-9) of Detecting
Genetically Modified Foods by PCR as the students will, but a set of these directions with teacher
notes has also been included. These teacher notes are handwritten in the margins of the text and
should help you make important connections. In addition, refer to INFORMATION FOR
INSTRUCTOR (page 20-21) will have instructions specifically for the teacher.
After students have completed their procedure in their science notebook, discuss the procedure as
a class. Stress the importance of attention to detail and of following the directions as written.
Have students discuss and decide what foods they would like to be bring in to test for transgenes.
Foods should have either soy or corn as an ingredient (most soy and corn products WILL be
transgenic). Suggested foods include: corn and tortilla chips, artificial bacon bits, corn muffin mix,
granola and energy bars, protein powder, and pet food. Encourage students to brainstorm their
own list before sharing the above.
b) LAB: Follow the directions for II. ISOLATE DNA FROM SOYBEAN AND FOOD PRODUCTS (pages 8-9)
of Detecting Genetically Modified Foods by PCR. Be sure to have all lab material ready for the
students. Once again, INFORMATION FOR INSTRUCTOR (page 20-21) will help you with the set-up;
it includes materials per student team and how to make the boiling water bath.
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III. AMPLIFY DNA BY PCR


Explore III: How will the teacher facilitate the students’ exploration of the problem and collection of
data. What questions will the teacher ask to guide students in exploration?
Elaboration III: How will the teacher facilitate the sharing of student explanations? What questions will
the teacher ask to clarify student thinking?
a) PRE-LAB Online: Have students complete the PCR Virtual Lab online. If you do not have access to a
computer lab, you may also do this activity as a class on a projector. As they work through the PCR
Virtual Lab, have them record the answers to the following questions in their science notebooks.
1) What are primers? Short nucleotide sequences that attach the beginning and the end of the
DNA sequence you would like to amplify in PCR
2) What is DNA polymerase? What is special about the DNA polymerase used in PCR? An enzyme
that copies DNA, it is from a bacteria that lives in a hot springs so it does not break down in the
hot temperatures
3) What are nucleotides? Building blocks of DNA – A, T, C, G
4) What happens at 94°C? Break apart DNA – Denature
5) What happens at 60°C? Primer sticks to the spot the polymerase will start – Anneal
6) What happens at 72°C? New nucleotides attach – Extension
7) After 30 cycles how many copies of the sequence do you have? Over one billion!
b) PRE-LAB Model: Have students complete the Explore section of Paper Clip PCR. In this activity four
different colored paper clips represent the four bases that make up the nucleotides of DNA.
Students will model the process of amplifying DNA in PCR using the paperclips. After completing
the activity, students should record the answers to the following answers in their science
notebooks. The first two questions and answers are in the activity itself.
1) How many nucleotides is our desired PCR Product?
2) What are the DNA Sequences of our PCR Product? (Hint: The top and bottom sequences should
pair with each other.)
PCR Product top strand:
PCR Product bottom strand:
3) Describe the three main steps in PCR:
a. Denature: Separate DNA strands with heat - 94°C
b. Anneal: Primers attach - 60°C
c. Extend: DNA Polymerase (an enzyme) builds the new DNA - 72°C
4) Describe the goal of PCR in one sentence. PCR amplifies a specific DNA sequence.
c) PRE-LAB Notebook: Have the students label their notebook as illustrated below (same as Part II)
and locate their copy of the LAB FLOW (pg 6) of Detecting Genetically Modified Foods by PCR. As
students read through the instructions for III. AMPLIFY DNA BY PCR (pages 10-11) of Detecting
Genetically Modified Foods by PCR they should fill in as much information as they can in the correct
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columns. Remind the students to only record important information – in this case short and sweet
notes are ideal. They should cut out the pictures from the LAB FLOW and place them in their
notebook in order as they go.
NOTE: The students should number their steps according to the written directions and then match
the pictures. This way they can refer easily to text if they need to during the lab. Some of the
written numbered steps have multiple parts that are lettered. Students should include ALL steps,
numbered and lettered. Some steps have been combined into one picture, so there are more
written steps then pictures. This means some steps will share a picture.
It is highly recommended that you create an answer key that will match the students work. It has
not been included on purpose, as it is very important that as the instructor that you have a full
understanding of the procedure. While creating your answer key, you should use the same
instructions for III. AMPLIFY DNA BY PCR (pages 10-11) of Detecting Genetically Modified Foods by
PCR as the students will, but a set of these directions with teacher notes has also been included.
These teacher notes are handwritten in the margins of the text and should help you make
important connections. In addition, refer to INFORMATION FOR INSTRUCTOR (page 21-22) will
have instructions specifically for the teacher.
After students have completed their procedure in their science notebook, discuss the procedure as
a class. Stress the importance of attention to detail and of following the directions as written.
Make connections between what the students will be doing in lab and what they saw in the online
and model activities. You may also use the following graph to show the steps of PCR:
Make sure the students understand the purpose of performing each of the PCR reactions and have
them record in their science notebooks.
a) Tubulin: present in all plants, + control for DNA
b) Wild-type soybean: - control, no GM gene, the 35S promoter is absent
c) Roundup Ready® soybean: GM gene, the 35S promoter is present
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d) LAB: Follow the directions for III. AMPLIFY DNA BY PCR (pages 10-11) of Detecting Genetically
Modified Foods by PCR. Be sure to have all lab material ready for the students. Once again,
INFORMATION FOR INSTRUCTOR (page 21-23) will help you with the set-up.
NOTE: If you are visiting a college to perform your PCR be sure to have all of your logistics in order
and set expectations with the students for the visit. This is a great opportunity to collaborate with
a scientist and have the students see a real science lab.
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IV. ANALYZE PCR PRODUCTS BY GEL ELECTROPHORESIS


Explore IV: How will the teacher facilitate the students’ exploration of the problem and collection of
data. What questions will the teacher ask to guide students in exploration?
Elaboration IV: How will the teacher facilitate the sharing of student explanations? What questions will
the teacher ask to clarify student thinking?
a) PRE-LAB Online: Have students complete the Gel Electrophoresis Virtual Lab online. If you do not
have access to a computer lab, you may also do this activity as a class on a projector. As they work
through the Gel Electrophoresis Virtual Lab, have them record the answers to the following
questions in their science notebooks.
1) Why is buffer added to the gel? To allow the current to flow
2) What are the holes (wells) from the comb used for? To load the DNA
3) What is the purpose of the DNA size standard? To have a known to compare to
4) Which fragments will move the farthest? The shortest? Small, big (get stuck)
5) What are the lengths of the three bands shown in the gel? How were you able to determine the
lengths? 6000, 3000, 1500. By estimating using the DNA Size Standards ladder.
b) PRE-LAB Notebook: Have the students label their notebook as illustrated below (same as Part II &
II) and locate their copy of the LAB FLOW (pg 6) of Detecting Genetically Modified Foods by PCR. As
students read through the instructions for IV. ANALYZE PCR PRODUCTS BY GEL ELECTROPHORESIS
(pages 11-12) of Detecting Genetically Modified Foods by PCR they should fill in as much
information as they can in the correct columns. Remind the students to only record important
information – in this case short and sweet notes are ideal. They should cut out the pictures from
the LAB FLOW and place them in their notebook in order as they go.
NOTE: The students should number their steps according to the written directions and then match
the pictures. This way they can refer easily to text if they need to during the lab. Some steps have
been combined into one picture, so there are more written steps then pictures. This means some
steps will share a picture.
It is highly recommended that you create an answer key that will match the students work. It has
not been included on purpose, as it is very important that as the instructor that you have a full
understanding of the procedure. While creating your answer key, you should use the same
instructions for IV. ANALYZE PCR PRODUCTS BY GEL ELECTROPHORESIS (pages 11-12) of Detecting
Genetically Modified Foods by PCR as the students will, but a set of these directions with teacher
notes has also been included. These teacher notes are handwritten in the margins of the text and
should help you make important connections. In addition, refer to INFORMATION FOR
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INSTRUCTOR (page 22-23) will have instructions specifically for the teacher. The figure with
number 7 in the student directions does not seem to match the written directions, as each group is
testing Wild-type OR Roundup Ready® (not both) and one food product. I would suggest giving the
students the illustration below of how to load their gels. This assumes two groups are sharing one
gel with no less than 11 wells. The marker is placed in the middle it is closer to all of the samples.
The wild-type and Roundup Ready® are placed on either side so they can be more easily compared.
GROUP 1
Food
Wild-type Soy
tubulin
35S
tubulin
35S
Well 1
Well 2
Well 3
Well 4
Marker
pBR322/BstNI
Well 5
GROUP 2
Roundup Ready®
Food
tubulin
35S
tubulin
35S
Well 6
Well 7
Well 8
Well 9
After students have completed their procedure in their science notebook, discuss the procedure as
a class. Stress the importance of attention to detail and of following the directions as written.
Make connections between what the students will be doing in lab and what they saw in the online
activities. If possible demonstrate loading a gel, reminding them that the tip of the pipette will be
in the liquid buffer (not in the gel) and the once the DNA is dispensed it will fall into the well (the
dye helps with visualization.
c) LAB: Follow the directions for IV. ANALYZE PCR PRODUCTS BY GEL ELECTROPHORESIS (pages 11-12)
of Detecting Genetically Modified Foods by PCR. Be sure to have all lab material ready for the
students. Once again, INFORMATION FOR INSTRUCTOR (page 21-23) will help you with the set-up.
You will pour the gels ahead of time for the students.
Below is a digital photograph of the gel I ran as a trial. The food product I chose (FP) was fritos.
The fritos did not show the 35S promoter (well 1) or tubulin (well 3). This may be because all of
the DNA was destroyed during the processing of the corn into fritos. The Roundup Ready® tissue
showed the 35S promoter with a length of 162bp (well 2, faint) and the tubulin with a length of
187bp (well 4). The ladder (well 5) showed the top four bands – the 121bp band was never visible.
Even though the 121bp band was missing in the ladder, the 35S promoter and tubulin band both
show up below the 383bp band in the ladder as expected. The bands were visible immediately after
the 40 minutes of destaining. The photograph was taken about 6 hours later, after the gel was
placed in just enough water to cover the gel. When I left the gel like this overnight, the 162bp and
187bp bands became too faint to see.
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V. BIOINFORMATICS
 Explore V: How will the teacher facilitate the students’ exploration of the problem and collection of
data. What questions will the teacher ask to guide students in exploration?
 Elaboration V: How will the teacher facilitate the sharing of student explanations? What questions will
the teacher ask to clarify student thinking?
This section should be completed before students are asked to analyze the gels.
As of August, 2012, the online and print directions for this were not up to date with the current BLAST
website. In addition, I found the directions to not be entirely clear and had to watch the video tutorial
that came with the Carolina kit on CD (the online link is no longer active) to arrive at the correct
answers. Also, for a high school classroom, Part II seems to go beyond our scope. To address these
issues, I’ve included BIOINFORMATION (pages 13-16) of Detecting Genetically Modified Foods by PCR
with updated handwritten notes and images. Be sure to walk through the directions and try the
activity online ahead of time so you are familiar with how BLAST works. You may choose to have your
students work individually or walk through this as a class with a projector. The directions below are
written for doing I. USE BLAST TO FIND DNA SEQUENCES IN DATABASES (ELECTRONIC PCR) for each of
the sets of primers (35S promoter and tubulin) as a class.
Read the introduction to BIOINFORMATICS (pg. 13) of Detecting Genetically Modified Foods by PCR
together as a class.
When finished, ask:
o What is bioinformatics? Using computers to identify nucleotide sequences
o What does in silico mean? Experiments done on a computer
o What does in vitro mean? Experiments done in lab
BIOINFORMATICS: I. USE BLAST TO FIND DNA SEQUENCES IN DATABASES (ELECTRONIC PCR)
Ask:
o What is the purpose of PCR and gel electrophoresis? To amplify the desired DNA and confirm its
presence. The gel separates fragments of different sizes, allowing you to identify differences
between samples.
In the science notebooks, have students answer the following questions and then discuss their
predictions.
o Do you expect all samples to have the same band for tubulin? Why or why not? Yes, tubulin is
present in all plants and will a specific length.
o Do you expect all samples to have the same pattern of banding on the gel? Why or why not?
No, the GM plants (Roundup Ready®) should show the band for the 35S promoter. The wildtype will not have this band. The food products will vary depending on if they are GM or not.
Explain:
o PCR uses primers which anneal to the beginning (forward primer) and end (reverse primer) of
the desired sequence producing the desired product. Therefore each fragment will have its
own characteristic length. The 35S promoter is known to be 162 bp in length. Tubulin is 187bp
in length. Therefore, they will show as distinct bands on the gel. BLAST (Basic Local Alignment
Search Tool) allows scientists to make predictions. When a set of primer sequence is entered
into BLAST, it will identify the length of the product and search a database to identify the
organisms whose genome contains the sequence of the product.
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Follow the directions given with this lesson (not online), defaulting to the handwritten notes if
something is crossed off. BLAST will allow the students to determine the length of the product. Based
on your explanation above and the directions in 4c. and 4d. students should then be able to determine
that the first primer set is from the 35S promoter (162bp) and the second primer set is tubulin (187bp
according to Carolina’s key, 184 according to BLAST). You may want to have them to have them
sketch what this would look like on the gel (the 35S promoter should be closer to the well).
The following figures are referenced in the set of directions with handwritten teacher notes. They are
screenshots with expected results. The video does a good job of explaining the 35S promoter, it is
worth a watch. However the video does not demonstrate tubulin, and I was unable to get BLAST to
predict a length of 187. I therefore included my screenshots of my 184 calculations for tubulin.
Figure 1: Initiate a Blast Search
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Figure 2a: Results of the BLAST search 2a
35S Promoter (Set #1)
Tubulin (Set#2)
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Figure 3d: Alignments
35S Promoter (Set #1)
Tubulin (Set#2)

Evaluate and Lesson Closure: How will the teacher connect the student explanations and bring out the
big scientific idea. What questions will the teacher ask to bring the big scientific idea of the lesson?
What questions will the teacher ask to assess mastery of the learning objectives?
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Have the students complete RESULTS AND DISCUSSION (page 17-18) of Detecting Genetically Modified
Foods by PCR in their science notebooks. You may want to encourage students to work in small groups
and come to a consensus.
It is highly recommended that you create an answer key that will match the students work. Although
an answer key is provided (pages 25-26), it is very important that as the instructor that you have a full
understanding of the procedure. A set of these directions with teacher notes has also been included.
These teacher notes are handwritten in the margins of the text and should help you make important
connections.
o Question I corresponds to II. ISOLATE DNA FROM SOYBEAN AND FOOD PRODUCTS
o Question 2 corresponds to III. AMPLIFY DNA BY PCR
o Questions 3 & 4 correspond to IV. ANALYZE PCR PRODUCTS BY GEL ELECTROPHORESIS &
V. BIOINFORMATICS
Lesson Extension
 Assessment Options:
o Have students type a final copy of their answers to RESULTS AND DISCUSSION (page 17-18) of
Detecting Genetically Modified Foods by PCR. For number four, I provided them with photos of
the gels (you may have to artificially darken the bands for copying) and asked them to create a
chart similar to #3. We then worked as a class to label all of the wells and distinguish bands. I
also added a question about the scientific inquiry process. The modified pages are titled
“Results and Discussion Assessment.”
o Have each group pick one person who is responsible for presenting the answer to each
question (#1-4). Rearrange the groups so that all the Question 1 students are now together,
etc. After they have had time to compare answers, have each Question group report out to the
class.
o Have the students write an explanation/conclusion (using their rubric) for any of the
hypotheses from Part I.
 If a wild-type soybean plant is sprayed with Roundup®, then the plant will X.
 If a Roundup Ready® soybean plant is sprayed with Roundup®, then the plant will X.
 If (food crop) is sprayed with Roundup®, then the plant will X.
 If the DNA contains the 35S promoter (162bp) then the plant has been genetically
modified and is Roundup® Ready.
 If the DNA contains tubulin (187 bp), then the DNA came from a plant.
If you were able to grow both the wild-type and Roundup Ready® you can now test these
predictions and your evidence from PCR.
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Lesson Enrichments (optional)
These activities are designed to tie the science of genetically modified foods into the social implications of
tinkering with nature. They could be implemented informally as discussions, or could be assessed formally if a
rubric was developed.
1) Watch a portion of Food, Inc. Consider Monsanto’s role in genetically modified organisms.
Watch Chapter 8: From Seed to Supermarket of Food, Inc. Have students discuss and present their
thoughts on the Socratic Discussion Focus Question (below) or any of the Deepening Questions from
the Food Inc. Discussion Guide (pages 71-77).
Should companies be able to own the DNA contained in plant seeds? After viewing this film
chapter, ask students to name some of the issues raised about genetically modified organisms.
Ask them whether they think companies should be able to own the genetic material contained
in plant seeds. What might be arguments for each side?
Needed: Copy of Food Inc & student copies of pages 71-77 of the Food Inc. Discussion Guide.
Note: Monsanto is the reason Carolina could not include GM soybean seeds. Will elicit a good debate.
2) Read an excerpt from Michael Pollan’s Botany of Desire. Consider the implications of the New
Leaf Potato.
Watch Chapter 4: Control from movie Botany of Desire OR read the corresponding section from the
book Botany of Desire. Have students discuss and present their thoughts on any of the Questions
below from the PBS Viewer’s Guide for The Botany of Desire.
4. Genetically Modified Organisms (GMOs) enable farmers to grow crops with fewer pesticides.
However, critics argue that when we eat GMOs we do not know exactly what we're putting into
our mouths or what the long-term effects might be. In your opinion, are GMOs a net plus or a
net minus for our U.S. food system? What about food systems in malnourished countries? Is
the conclusion always the same? Why or why not?
5. Is spraying chemical insecticides onto crops different than putting natural insecticides
directly into plants' genes, as the New Leaf potato did? Why or why not?
6. Is there a difference between the apple research and crossbreeding being done at the Cornell
University lab in Geneva, New York, and Monsanto's genetic engineering efforts like the New
Leaf potato? How are they similar or different?
7. A scientist in the film suggests that BT potatoes offer benefits solely to the farmer and not to
the consumer. What if prices could be lowered significantly or calories per serving increased
dramatically? Would GMO products then be more acceptable to you? To the general public?
Why or why not?
Needed: Copy of Botany of Desire (movie or book) and student copies of questions 4-7 above.
Note: May appeal to your “readers” as Botany of Desire is not considered a “science” book.
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3) Learn more about a genetically modified food that interests you with your own research.
Choose a genetically modified food that interests you (Bt corn, Round-up Ready® soy, etc). Research
and present your GM crop. Some questions to begin your research are:
 How was the food genetically engineered?
 Why was the food genetically engineered?
 What are the benefits and disadvantages of the GM food?
 Are there any current social issues regarding the food?
Needed: Internet access
Note: Encourages students to be curious and make connections to their everyday lives.
4) Research current issues in the news concerning genetically modified foods.
Find a recent article concerning a current issue regarding genetically modified foods. Present the issue
to the class. Some questions to begin your research are:
 What is the claim of the article?
 What is the evidence presented?
 What is your confidence in the evidence? (Consider the sources)
 What evidence can you find that refutes the claim? (Site your sources)
Needed: Internet access
Note: Encourages students to make connections between science and its social implications. Topics will
always be changing.
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Resources:
Center for Ecoliteracy. (2009). Food, Inc. Discussion Guide. Retrieved from
http://www.ecoliteracy.org/sites/default/files/uploads/foodinc_discussion_guide.pdf
Connecticut’s Biobus. (2012). Paper Clip PCR. Retrieved from
http://www.ctbiobus.org/download/paperclip.pdf
Dolan DNA Learning Center. (2012). Detecting Genetically Modified Foods with PCR: Interactive Instruction
Manual. Retrieved from http://bioinformatics.dnalc.org/gmo/animation/gmo.html
Dolan DNA Learning Center. (2006). Detecting Genetically Foods with PCR: Instruction Manual. Retrieved
fromhttp://www.carolina.com/text/teacherresources/instructions/biotech/detecting_genetically_mod
ified_foods_by_pcr.pdf
Donovan, J. (2012). Building Better Bioenergy Trees. Michigan Tech Research Magazine. Retrieved from
http://www.mtu.edu/research/archives/magazine/2012/stories/bioenergy-trees/
Genetic Science Learning Center. (2012). Gel Electrophoresis Virtual Lab.Learn.Genetics. Retrieved from
http://learn.genetics.utah.edu/content/labs/gel/
Genetic Science Learning Center. (2012). PCR Virtual Lab.Learn.Genetics. Retrieved from
http://learn.genetics.utah.edu/content/labs/pcr/
Hu, W. et. al. (1999). Repression of lignin biosynthesis promotes cellulose accumulation and growth in
transgenic trees. Nature Biotechnology 17: 808-812. Retrieved from
http://www.dfrc.wisc.edu/dfrcwebpdfs/1999-Hu-NBT-17-808.pdf.
PBS. (2012). The Botany of Desire Viewers Guide. Retrieved from
http://www.pbs.org/thebotanyofdesire/viewers-guide.php
Watson, J.D., Gilman, J.W., Witkowsi, J., & Zoller, M. (1992). Recombinant DNA. New York: Scientific American
Books.
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