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.
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.
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.
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 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 CD-Rom that is included with the Carolina kit.
· Pre-teaching:
Students should have a working knowledge of DNA and protein synthesis.
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 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.
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.
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.