LESSON PHYSICAL PROPERTIES AND DNA

PHYSICAL PROPERTIES AND DNA TIP: This activity can be done with student-made green detergent instead of store-purchased detergent (www.beyondbenign.org/ K12education/ msgc/10%20 Shampoozled. doc). DESCRIPTION: Students extract DNA from living plant tissues in order to measure, observe, and think about various properties of two objects. BACKGROUND INFORMATION: Deoxyribonucleic acid (DNA) is a molecule that encodes the genetic instructions used in the development and functioning of all known living organisms. Every living thing contains DNA. DNA isolation is one of the most basic and essential techniques in the study of DNA. The extraction of DNA from cells and its purification are of primary importance to the field of biotechnology and forensics. Extraction and purification of DNA are the first steps in the analysis and manipulation of DNA that allow scientists to detect genetic disorders, produce DNA fingerprints of individuals, and even create genetically engineered organisms that can produce beneficial products such as insulin, antibiotics, and hormones. DNA can be extracted from many types of cells. The first step is to lyse or break open the cell. This can be done by grinding a piece of tissue in a blender. After the cells have broken open, a salt solution such as NaCl and a detergent solution containing the compound SDS (sodiumdodecyl sulfate) is added. These solutions break down and emulsify the fat and proteins that make up a cell membrane. Finally, ethanol is added because DNA is soluble in water. The alcohol causes DNA to precipitate, or settle out of the solution, leaving behind all the cellular components that aren t soluble in alcohol. The DNA can be spooled (wound) on a stirring rod and pulled from the solution at this point. Strawberries, bacteria, humans all living things have genes, and all of these genes are made of DNA. That s why scientists can take a gene from one living thing and put it into another. For example, they can put human genes into bacteria to make new medicines. The procedure for DNA extraction is really a procedure for nucleic acid extraction, so there will be a mix of DNA and RNA (ribonucleic acid) in the white stringy stuff. However, much of the RNA is cut by ribonucleases (enzymes that cut RNA) that are released when the cells are broken open. Each cell contains 6 feet of DNA, only one-millionth of an inch wide. To fit all this DNA into a cell, it must be packed efficiently with histone proteins. This is what makes DNA clump together. The salt helps precipitate the DNA. (DNA is normally dissolved in water).

OBJECTIVES: Students learn techniques for the extraction of nucleic acids and think about what future experiments could be designed based on what they have learned about measuring several properties of matter. Students are exposed to the difference between correlation and causation. COMMON CORE STANDARDS: CCSS: 10.RST 2: Follow precisely a multistep procedure when carrying out experiments. 10.RST 7: Integrate quantitative or technical information expressed in words in a text with a version of that information expressed visually (e.g. graph, model, table). 10.SL 1: Engage effectively in a range of collaborative discussions with diverse partners NGSCS: LS3.A: DNA = instructions for special characteristics LS3.A: Each cell has the same genetic content, but expressed differently PS1.B: Reactions are collisions of molecules, atom rearrangement, affinity binding PS3.B: Systems move toward stable states NGSCS Cross-Cutting Concepts: 1. Patterns: Empirical evidence is needed to identify patterns 2. Cause and Effect: Empirical evidence is required to differentiate between cause and correlation and make claims about specific causes and effects 3. Scale, Proportion, and Quantity: The significance of a phenomenon is dependent on the scale, proportion, and quantity at which it occurs. TIME: 55 MINUTES: THINK-PAIR-SHARE (5 MINUTES); STATION A (20 MINUTES); STA- TION B (20 MINUTES); DISCUSSION (10 MINUTES). MATERIALS: Access to sink and water STATION A: Observation, Conductivity, Density, Environmental Impact 4 energy balls to share among the class (can be purchased www.teachersource.com) Mass weighing scales Graduated cylinder (at least 100 ml and can fit a strawberry inside it) (1 per group) Rolls of paper towels (1 per group) Rulers (1 per group) Strawberries (2 per group) Data Table 1 (one per student) Data Table 2 (one per student)

STATION B: DNA Extraction Strawberries Zip-lock bags Funnels Coffee filters 270mL (at least) of detergent Salt Meat tenderizer original unseasoned OR pineapple juice (to cut histone proteins) Test tubes Test tube racks 1 L of rubbing alcohol (70-95% isopropyl) in an icebath or refrigerator Glass beakers (at least 150 ml) Wooden stirring rods PREP: Need to have a garden that will provide at least 2 strawberries per group. Ripeness may affect the experiment- the riper the better. If strawberries are not an option, consider using green peas, spinach, kiwi, or broccoli. Chill 1 L of rubbing alcohol in the fridge or in an ice bath. ACTIVITY: 1. Start with a Think-Pair-Share activity: Ask students to individually think about the following question: How many different metrics can you think of to measure something? (one minute). Possible answers: Mass, weight, how much light goes through, light absorption, sweetness, volume, surface area, boiling point the possibilities are endless here. Have students form groups of four to discuss (two minutes). Discuss as a class (two minutes). 2. Introduce students to the activity and start Station A. There will be one Station A per group. 3. Once students are done with Station A, have students read and follow the procedure for Station B (the Station B s should be set up already)

DISCUSSION: 1. Discuss the cell compartments, organelles, histone proteins, nuclear envelope, cell wall, then talk about how can we get the DNA. What steps may have broken open certain parts? 2. If we see in an experiment that there is more DNA when size of the fruit increases, is this correlation or causation? 3. Do you think the number of seeds in any fruit correlates with the amount of DNA? 4. Does the amount of DNA organisms contain correlate to its complexity? 5. What do scientists do with DNA after they have isolated it? TEACHER TIPS: If you want to save the DNA, you can transfer it to a small container filled with alcohol. You can discuss simple DNA organisms that are used frequently for experiments like C. Elegans (we know its whole genome and entire fate map) If any students are done early, ask them to calculate the number of miles of DNA in a human body give them the following: the human body contains about 100 trillion cells, each of which contains six feet of DNA. (Answer: over a billion miles of DNA- farther than the distance from the earth to the sun). Why use detergent and meat tenderizer? See links below: http://learn.genetics.utah.edu/content/labs/extraction/howto/detergent/ http://learn.genetics.utah.edu/content/labs/extraction/howto/enzyme/ Other types of foods that you can use besides strawberries are spinach, broccoli, green peas. (If you want to use these hardier food sources, replace the mashing in a ziplock baggie step with a blender using ½ cup [100mL] of food and 1 cup of cold water blended on high for 15 seconds.) REFERENCES: Borquez, Christopher. How to Extract DNA from Anything Living. Multimedia Educational Resource for Learning and Online Teaching, California State University. 30 Jun 2005. Web. 21 Oct 2014. <http://www.merlot.org/merlot/viewassignment.htm?id=91954>. Do-It-Yourself Strawberry DNA. The Tech Museum of Innovation, Department of Genetics, Stanford University School of Medicine. 2013. Web. 21 Oct 2014. <http://genetics.thetech. org/online-exhibits/do-it-yourself-strawberry-dna>. Massengale, Cheryl. Extract DNA from Anything Living. Biology Junction. 2010. Web. 21 Oct 2014. <http://www.biologyjunction.com/extracting_dna.htm>. Packed Up Properties. Beyond Benign: Green Chemistry Education. 2010. Web. 21 Oct 2014. <http://www.beyondbenign.org/k12education/middleschool.html>.

STATION WORKSHEETS/INSTRUCTIONS STATION A Exploring Physical Properties: Observation, Conductivity, Density, Environmental Impact 1. Observations: Color: Describe the natural color of the material Odor: Sniff the item (without touching it to your nose). Describe any smell the material has State of Matter: Is the material a liquid, a solid, or a gas? Mark your findings on Data Table 1. 2. Conductivity: the ability of a substance to allow the flow of energy or electricity Pick up the energy ball. Touch a finger to one metal tab. Pick up the strawberry and hold it to the other tab on the energy ball. If the light flashes and the ball makes a sound, the object carries an electrical current. If the ball doesn t light up or make sound, the object does not carry a current. Repeat the process with the paper towel roll to determine if it is conductive or not. Mark your findings on Data Table 1. 3. Environmental Impacts Read the information in the chart below. In your Data Table 1, give each material a ratio of to + or mark them with separate colors to indicated positive or negative qualities. MATERIAL AIR QUALITY WATER QUALITY LAND QUALITY BIODIVERSITY STRAWBERRY PAPER + Strawberry plant produces oxygen + no chemical pollutants to create them Typically shipped from thousands of miles away Chlorine released 4th largest emissions of greenhouse gas + Strawberries can be sustainably watered Requires lots of water to make it Sometimes releases water with chlorine in it + 100% Compostable + Degrades quickly + Renewable resource + Replant trees + Renewable resource + 45% recycled back into paper + Forests can be sustainably managed + Does not bioaccumulate in plants & animals + Attracts insects to the garden Could become infected by a plant pathogen like a fungus that can spread Removal of trees lessens animal habitat + Forests can be sustainably managed

DATA TABLE 1 STRAWBERRY PAPER TOWEL ROLL CONDUCTIVITY (YES/NO) COLOR ODOR STATE OF MATTER IMPACT ON ENVIRONMENT DENSITY Strawberry 1. Using the balance, find the mass. Note the mass in Data Table 2. 2. Pour 40 ml of water in the graduated cylinder. 3. Carefully drop the strawberry piece into the cylinder of water. 4. Determine the amount the water level increased. For example, if the water is at 50 ml, it increased 10 ml. This is your volume. Note the volume in Data Table 2. 5. D=M/V (density = mass divided by volume). Calculate and note in Data Table 2. 6. Pour the water out of the graduated cylinder into the sink. 7. Dry off the materials. Paper Towel Roll 1. Use the balance to find the mass of the paper towel roll. Record in Data Table 2. 2. Use a ruler to calculate the volume of the paper towel roll (πr2h). 3. Calculate the density using the formula. STRAWBERRY PAPER TOWEL ROLL MASS VOLUME DENSITY

STATION B Make a Prediction! Make a prediction! (e.g. If we used commercial detergent instead of our handmade green detergent, more DNA would have shown up). Get approval from your teacher after writing a prediction. Do you think any of your observations from Station A may influence how much DNA there is? 1. Put at least two strawberries in a plastic bag and push out all the extra air. Seal it tightly. 2. With your fingers, squeeze and smash the strawberry mixture for 2 minutes. 3. Pour the strawberry mixture from the bag into the funnel through the coffee filter. Let it drip into the test tube until there is no liquid left in the funnel. This separates the cells from each other, so you now have a really thin strawberry-cell soup. 4. Estimate how much strawberry soup you have and add about 1/6 of that amount of liquid detergent (about 30ml or 2 tablespoons). Swirl to mix. 5. Let the mixture sit for 5-10 minutes. 6. Add a pinch of enzymes (meat tenderizer/pineapple juice) to each test tube and stir gently. Be careful! If you stir too hard, you ll break up the DNA, making it harder to see. 7. Get the rubbing alcohol from the ice bath or refrigerator and pour 100mL into an easypouring beaker. 8. Tilt the test tube and very slowly pour the cold rubbing alcohol down the side. The alcohol should form a layer on top of the strawberry liquid. Pour until you have about the same amount of alcohol in the tube as strawberry mixture. (Don t let the alcohol and strawberry liquid mix. The DNA collects between the two layers!) 9. Alcohol is less dense than water, so it floats on top forming two separate layers. 10. All of the grease and the protein that we broke up in the first two steps move to the bottom, watery layer. 11. DNA will rise into the alcohol layer from the bottom layer. 12. Dip the stirring rod into the test tube where the alcohol and strawberry layers meet. Slowly turning the stirring rod will spool (wrap) the DNA around the rod so it can be removed from the liquid. Pull up the rod. The whitish, stringy stuff is DNA containing strawberry genes! (If you don t see DNA after the DNA extraction, you may have a solution that is too watery. If your soup after filtration is see-through, make sure to remove some water so that the cell soup is opaque.)