DNA Extraction from strawberries

DNA Extraction from strawberriesDNA Extraction from strawberriesThis assignment is worth 20 points.Although it will probably take you about an hour to prepare for the activity, including viewing the directions, the DNA extraction itself only takes about 10-15 minutes to complete.Also, please note that you will not receive any credit on this assignment if you do not submit all of the required photos as documentation of your completion of the activity. You will be prompted when it is time to take your first photo.In this activity, you will learn how you can easily extract real DNA from strawberries using common household items. A link to a very good instructional video is provided, along with detailed directions for completing the extraction.Learning outcomes• Understand that DNA is present in the cells of every living thing.• Use an extraction procedure to isolate DNA from the cells of a strawberry.• Determine how each of the ingredients in the protocol helps to extract DNA.• Extract a visible mass of DNA from strawberry tissue.• Examine the visual characteristics of a large amount of DNA precipitate.Required materialsImportant note: Be sure to first put your rubbing alcohol in the freezer so that it is ready to go. I suggest leaving it in the freezer overnight before using. It must be ice-cold. Don’t take it out of the freezer until prompted to do so.Figure A7-1: The required materials include fresh or frozen strawberries, dish soap or shampoo, salt, measuring spoons, a quart or gallon sized resealable bag, and 3 medium, clear, plastic or glass cups.You will need the following:• 2 ripe strawberries (fresh or frozen); if using fresh, be sure green leaves have been removed; if using frozen, be sure that they are fully defrosted before using• 1 resealable plastic bag (e.g. ziplock quart or gallon size); note that sandwich bags are too thin (they will tear)• 3 medium, clear, plastic or glass cups that can hold about a cup of liquid each; one cup will be used to mix the shampoo, salt, and water, and the other two will be used to collect the DNA extract• 2 teaspoons shampoo (without conditioner) or dish soap• Half teaspoon salt (either iodized or non-iodized)• Half cup tap water• 1 coffee filter• Ice-cold alcohol: it must be isopropyl alcohol (also known as rubbing alcohol; be sure that it is 70% or higher concentration); it must be used ice-cold directly from freezer• Popsicle stick, coffee stirrer, or flat or round wooden toothpick for spooling DNA• Digital camera for taking photos, and a way to transfer those photos to your computer for uploading with your assignment• A picture identification card (e.g. Pima school ID or driver’s license) to include in your photo documentationIntroductionAll living things are made of cells and each cell contains a full set of genetic instructions in the form of several long molecules of coiled DNA (deoxyribonucleic acid) called chromosomes. If the DNA molecules from each chromosome were uncoiled and laid end to end, each cell in a human would have a total of nearly 6 feet of DNA. This DNA is very neatly super-coiled into chromosomes and packaged into a compartment called the nucleus in every cell. In its strands lies the blueprint for life. The DNA molecule directs the synthesis of every protein and contains the genetic information that is passed on to new cells.In complex eukaryotic cells such as those from plants, animals, and fungi, most of the DNA is located in the cell nucleus (chloroplasts and mitochondria also carry some DNA). By contrast, in simpler cells called prokaryotes, including bacteria, DNA is not separated from the cytoplasm by a nuclear envelope.Although DNA is an incredibly small molecule, in large quantities it can be seen. In this activity, you will observe how DNA can be extracted from strawberries.One of the main reasons strawberries work so well is that they are soft and easy to pulverize. Also ripe strawberries produce enzymes that are already at work breaking down their cell walls. Most interestingly, commercial strawberries have enormous genomes. They have eight of each type of chromosome.There are three basic steps in DNA extraction. First, the cell must be broken open to release the nucleus, which contains the DNA. Second, the nucleus must also be opened to release the DNA. Third, once the DNA is released, it must be precipitated (aggregated together) out of solution. This is accomplished by adding ice-cold alcohol.Three main reagents are required to complete the extraction procedure, including salt, liquid detergent or shampoo, and alcohol.Both the cell and nuclear membranes are composed primarily of lipids. In order for the cell to be broken open, the lipid walls must be broken down. The manual grinding and addition of detergent solutions accomplish this task. Soap molecules mix with fats or lipids, causing structures made of lipids to fall apart.The addition of salt solution provides the DNA with a favorable environment by contributing positively charged atoms that neutralize the normal negative charge of the DNA, allowing the DNA to clump together. The white fibers you will see in your preparation are actually thousands of DNA strands wrapped around each other. An individual DNA strand is so small, it can only be imaged by the most sophisticated and specialized electron microscope.Alcohol is used to precipitate the DNA. In water, DNA is soluble. When it is in alcohol, it uncoils and precipitates out of solution.Scientists who study DNA and the gene sequences contained in the DNA molecules begin their study with an isolation procedure similar to the one you are performing today. They would follow up by additional purification steps to remove all the protein and contaminating materials (including enzymes that can attack and destroy DNA in storage unless removed). They would then use additional procedures to isolate the particular region of DNA that contains the genes (DNA segments) they are intending to study.YouTube instructional videoIn the following video, Dr. Eric Green and Dr. Carla Easter from the National Human Genome Research Institute (NHGRI) of the National Institutes of Health (NIH) demonstrate how to extract DNA from strawberries using everyday household items. You can easily do the same thing yourself at home. Closed captions are available and the written directions are provided just below the video window. Please be sure to read the written directions, which include some hints and points of clarification, before attempting the extraction.YouTube Video: A demonstration of how to extract DNA from strawberries.Written directionsThe following written directions are provided courtesy of the National Human Genome Research Institute. The original version is located on their website (www.genome.gov/activities). I have altered their directions slightly by adding some additional hints and clarifying a few points of possible confusion or error (see bold printed items). I suggest using the written directions (below), in conjunction with the video above.1. Be sure that your strawberries are fully defrosted, if using frozen, or all of the green leaves are removed, if using fresh strawberries. This was not mentioned in the video.2. Put two strawberries into the plastic bag, seal it, and gently smash it for about two minutes by lightly pounding the bag with your fist. Completely crush the strawberries. This starts to break open the cells and release the DNA.3. In a medium, clear, plastic or glass cup, that can hold at least a cup of liquid, make your DNA extraction liquid: mix together 2 teaspoons of detergent, a half teaspoon of salt, and a half cup of water. Mix thoroughly.4. Pour all of the DNA extraction liquid into the bag with the crushed strawberries. This will further break open the cells.5. Reseal the bag and gently smash and mix for another minute (avoid making too many soap bubbles).6. This step is different than in the video: Pour the contents of the bag into a new medium, clear, plastic or glass cup that can hold about a cup of liquid. Don’t worry about the bubbles that are left behind in the bag. You actually don’t want them.7. Place the coffee filter inside a new medium, clear, plastic or glass cup of similar size, using one of your hands to hold it open and in place. If you have someone else to help you, have that person hold the filter instead. Then, pour the extract very slowly through the coffee filter, letting it drip into the new cup. Be careful to not let the extract flow over the sides of the filter. Let it drip for a few minutes.8. Gently squeeze the filter to get a little more liquid into the new cup, but don’t break the filter! If you happen to break the filter, or have extract escape over the sides, you can simply filter the extract again. In the next step, you will add alcohol to your filtered strawberry extract (what is in your new cup).9. Get your ice-cold rubbing alcohol from the freezer. Next, while holding the cup at an angle, slowly pour the ice-cold alcohol such that it drips onto the inside of the cup (rather than directly onto the strawberry liquid) and travels down slowly to the strawberry extract. They did not do this in the video, but probably should have. Make sure that the alcohol layer is about the same height as the strawberry layer. Do not mix or stir. You have just isolated the DNA from the rest of the material contained in the cells of the strawberry.10. Within a few seconds, watch for the development of a white cloudy substance (DNA) in the clear, top layer, directly above the strawberry layer.Documenting your resultsNow it is time to take the required documentation photos. Do so before you disturb the DNA clumps. See examples below. One photo must clearly show your container with DNA and strawberry extract (a clear layer with DNA clumps on top of a red layer of strawberry liquid) and a copy of your photo ID (e.g. Pima school ID or driver’s license) containing both your picture and your name. If you end up using your driver’s license, be sure to cover up your personal information, such as your driver’s license number, address, and signature. Your other photo must include both your container with DNA and YOU. Feel free to either take the picture yourself or have someone else take the photo.Figure A7-2: You need to obtain a picture showing your cup with DNA, along with your photo ID, as documentation of your completion of this part of the activity.Figure A7-3: You need to also obtain a picture of yourself with your cup of DNA as documentation of your completion of this part of the activity.After you have obtained your photos, and checked that they are of decent quality, you can pick up the DNA by spooling it on a toothpick, coffee stirrer, or Popsicle stick. Congratulations! That is DNA. If you want, you can preserve it by letting it dry on a small piece of wax paper. Note its web-like appearance when dry. The fibers are millions of DNA strands!Figure A7-4: Using a toothpick to spool the DNA out of the alcohol.End of the activity questionsAnswer the following questions in a computer document. They are based on the assignment introduction, directions, and YouTube video. You will be submitting your completed document in the Assignment 7 dropbox.Questions based on the procedure that YOU did:• 1. Did you use shampoo or dish soap? What was its specific brand name? If you used shampoo, did it have conditioner in it?• 2. What substance was used to precipitate the DNA out of solution: salt, shampoo or dish soap, or ice-cold alcohol?• 3. What substance caused the cells to lyse, or break open? shampoo or dish soap, or ice-cold alcoholQuestions based on the YouTube video:• 4. Why are strawberries a good choice for doing a DNA extraction?• 5. Do you need to use a metal hammer to forcefully pound the strawberry into a pulp, or will pounding with your fist be good enough?• 6. What does lysis mean?• 7. What is in the lysis solution?• 8. Why does the strawberry extract need to be filtered?• 9. What does precipitation mean in terms of this experiment?• 10. In what layer do we see the DNA — the top solution or the bottom solution?Your evaluation of the activity1. Did the activity help you to understand how DNA can be extracted, isolated, and viewed?2. Are the directions for the activity clear?3. What part of the activity was confusing?4. Include any suggestions you have to improve this activity.Thanks for your input.In order to get credit, submit your two documentation photos and your answers to the end of the activity questions (#1-10) in the Assignment 7 dropbox .Feel free to include the documentation photos in your computer document, or you can send them as separate file(s).Congratulations! You are now done with this activity!You will not receive any credit for this assignment if you do not submit all of the required photos

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