Cyber DNA Extraction and Gel Electrophoresis

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1 Cyber DNA Extraction and Gel Electrophoresis Contributors Adam Fleming Graduate Student Georgia Southern University, GA Cheri Alderman Partner Teacher Effingham High School, GA Intended Audience K Intended Audience Classroom Setting Requires special equipment Uses hands-on manipulatives Requires mathematical skills Can be performed individually Requires group work Requires more than one (45 min class) period Appropriate for special needs student Bioluminescence Page 1

2 Introduction Description Students will perform a virtual DNA extraction and gel electrophoresis. Abstract Students will practice DNA extraction and gel electrophoresis by performing a virtual version of these experiments on the University of Utah genetics teaching website. These labs will allow the students to work through a virtual gel electrophoresis and DNA extraction in order to prepare them to perform a real electrophoresis and DNA extraction in future labs. Core Themes Addressed The Cell Molecular Basis of Heredity Biological Evolution Interdependence of Organisms Matter, Energy, and Organization in Living Systems Other Molecular Techniques Keywords DNA, electrophoresis, DNA extraction Learning Objectives By completing this activity, students will be able to: 1. Identify the important aspects of DNA extraction 2. Identify the important aspects of gel electrophoresis National Science Education Standards Addressed Teaching Standard A: Science as inquiry Through conducting their own experiment, students are learning how to ask and answer valuable questions pertinent to the experiment at hand. Teaching Standard B: Physical Science DNA extraction and gel electrophoresis involve multiple biochemical reactions (e.g. lysis buffer, detergent, alcohol, etc.) Bioluminescence Page 2

3 Teaching Standard C: Life Science DNA extraction and gel electorphoresis involve understanding the basic components of the cell, molecular basis of heredity, and ultimately biological evolution. Teaching Standard E: Science and Technology This lab allows students to use a computer and website link to visualize the procedure of DNA extraction. Through doing so, students will achieve a connection between science and the use of technology. Teaching Standard F: Science in personal and social perspectives DNA extraction and gel electrophoresis are used very heavily in the field of forensic and investigative science. By gaining knowledge in the process, students will have a better perspective about how criminals are brought to justice, as well as, attributes to personal and community health. Bioluminescence Page 3

4 Teacher Handout Cyber DNA and Gel Electrophoresis Student Prior Knowledge Students should have the following prior knowledge before completing this activity: 1. Be familiar with the basics of DNA 2. Basic computer skills Teacher Background Information DNA extraction and gel electrophoresis are both routine molecular biology techniques used in research labs. DNA extraction utilizes the properties of cells and DNA in order to extract just the DNA from a suspension of cells. Extracted DNA can be used for several purposes including cloning and PCR. All DNA extraction techniques have 4 basic steps: lysis of the cells, removal of membrane lipids, removal of proteins, and finally precipitation of the DNA. Electrophoresis is a process that utilizes the porous nature of agarose and the charged nature of DNA in order to separate DNA fragments by size. The DNA can then be stained in the gel for visualization. The distance that DNA travels in the gel is a function of both the size of the DNA fragment and the length of time that the gel is exposed to an electrical field. These techniques can be used in conjunction to test for the presence of a known DNA sequence in an unknown organism. For example: the presence of an already identified bioluminescence gene in a newly discovered bioluminescent organism. Class Time This activity will require a minimum of one 90 minute class period 1. Cyber DNA Extraction 40 min 2. Cyber Gel Electrophoresis 40 min Teacher Preparation Time This lesson will require approximately 5 minutes of preparation time. 1. Prepare computers 5 min Bioluminescence Page 4

5 Materials and Equipment Per Class 1. Computers/laptops Methods DNA Extraction 1. Go to learn.genetics.utah.edu 2. Go to the virtual tabs section of the website 3. Click on the DNA extraction link 4. Start the virtual lab Gel Electrophoresis 1. Go to learn.genetics.utah.edu 2. Go to the virtual tabs section of the website 3. Click on the gel electrophoresis link 4. Start the virtual lab Tips/Suggestions Make sure the students know that the worksheet questions are meant to be filled out as they go through the virtual labs If some students finish early, there are many other interesting labs and lectures to be found on the Utah website References Adapted from learn.genetics.utah.edu, gel electrophoresis and DNA extraction, accessed 10/2/11 Answers to Student Worksheet Cyber-DNA extraction 1. Genetic testing, body identification, analysis of forensic evidence 2. Proteins and other cellular components 3. Cheek cells 4. Detergent and Protease K 5. Break down the proteins present in the cell 6. The salt causes the proteins and other cellular debris to clump together 7. The sample is centrifuged so the protein and cell debris clump at the bottom of the tube and the DNA stays in suspension Bioluminescence Page 5

6 8. The DNA is solution at the top of the tube 9. When the isopropyl alcohol is added to the solution the DNA come out of solution 10. DNA must be stored in the freezer Virtual Gel Electrophoresis 1. Gel electrophoresis is used to separate different sized strands of DNA or protein 2. The filter is the agarose gel 3. The electric current is what makes the DNA move 4. Positive end 5. False 6. The gel is stained in order to visualize the DNA 7. Buffer is added to allow for electrical charge to flow through the gel 8. The comb is used to make the wells 9. True 10. Loading buffer is used to better visualize the DNA 11. The standard is used as a reference to measure the unknown sample by 12. False 13. False 14. We know the current is running because there are bubbles moving inside the gel box 15. Rungs; UV bps, 3500 bps, 1500 bps Bioluminescence Page 6

7 Student Handout Cyber DNA Extraction and Gel Electrophoresis Introduction Gel electrophoresis is a scientific technique that uses the molecular properties of DNA and agarose to separate different strands of DNA by size. It involves making the buffer and agarose, setting up the agarose, loading the DNA samples, separating DNA via electrophoresis, and staining the gel to see the DNA banding pattern. DNA extraction is a procedure that uses the chemical properties of DNA to collect useable DNA for subsequent molecular analysis. There are three basic steps in a DNA extraction: 1. Lysing the cells open to expose the DNA within. This is commonly achieved by grinding the sample or using a lysis buffer. 2. Removing membrane lipids by adding a detergent. 3. Removing proteins by adding a protease (optional but almost always done). 4. Precipitating the DNA with an alcohol usually an ice-cold alcohol such as ethanol or isopropyl alcohol. Since DNA is insoluble in these alcohols, it will stick together, creating a pellet when placed in a centrifuge. Student Background Knowledge 1. Be familiar with the basics of DNA 2. Basic computer skills Vocabulary Gel electrophoresis: The process of separating different lengths of DNA strands using a gel medium and an electrical current DNA Extraction: The process by which DNA is purified from cells by utilizing the chemical properties of cells and DNA Bioluminescence Page 7

8 Materials Checklist Computers with internet access Procedure DNA Extraction 1. Go to learn.genetics.utah.edu 2. Go to the virtual tabs section of the website 3. Click on the DNA extraction link 4. Start the virtual lab Gel Electrophoresis 1. Go to learn.genetics.utah.edu 2. Go to the virtual tabs section of the website 3. Click on the gel electrophoresis link 4. Start the virtual lab Bioluminescence Page 8

9 Student Worksheet Cyber- DNA Extraction Questions (to be answered when going through the virtual program) 1. What are 2 reasons that explain why scientists isolate DNA? 2. Name 1 thing we have to separate DNA from? 3. What type of cell did we use to extract DNA? 4. What are the two things that the Lysis solution contains? 5. What does proteinase K do? 6. What does the salt solution do? 7. Why do we centrifuge the sample? 8. After centrifugation, what floats to the top of the 1.5 ml tube? Bioluminescence Page 9

10 9. What happens to the DNA when we add isopropyl alcohol? 10. To store DNA, where do you have to store it? Questions: Virtual Gel Electrophoresis 1. What is gel electrophoresis used for? 2. What is the filter that sorts the DNA? 3. What makes the DNA move? 4. DNA migrates to the end of the gel. 5. True or False: Long strands of DNA migrate farther than short strands of DNA. 6. Why do we stain the gel? 7. Why do we add buffer into the gel mix? 8. What is the gel comb used for? 9. True or False: buffer keeps the gel from drying out. 10. Why do add the loading buffer to the DNA sample? 11. Why do we also run a standard? 12. True or False: the red wire will generate a negative charge. 13. True or False: because DNA is negatively charged, it will migrate to the negative pole. Bioluminescence Page 10

11 14. How do we know that the current is running in the gel box? 15. Ethidium bromide fits between the of the DNA ladder and shows up under light. 16. Write down your DNA estimates below. (largest (1) to smallest (3)) bp= base pair 1 bp 2 bp 3 bp Bioluminescence Page 11