Packet #9 Gene Action, part 2 (Biotechnology) Summer This Activity Packet belongs to: Activity

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1 Packet #9 Gene Action, part 2 (Biotechnology) Summer 2014 This Activity Packet belongs to: During this unit, you will complete work in the packet. When directed, write your answers on separate paper and turn it in. You will also turn in your packet when you take a test/quiz on this unit. You should expect a variety of quizzes: announced, unannounced, open-notes and closed-notes, mini quizzes (homework credit), pop quizzes (quiz/test credit). Packet page Activity Points Earned Avail. Biotechnology Web Lesson 15 DNA Biotechnology Notes Lab Testing for Sickle Cell gene (separate packet) Cracking Your Genetic Code (video) 10 Bioethics Discussion 10 Gene Action Test Review (Part 2) 20 Total 55 If this packet is LOST, please: drop it off at the BHS Science Dept. (rm 365) OR drop it off in Ms. Brunson s classroom (rm 351) OR call the Science Dept. at (617)

2 Biotechnology Web Lesson Part A: Gel Electrophoresis (5 pt) Go to the Genetic Science Learning Center Website: 1. In the Virtual Labs box, click on Gel Electrophoresis. 2. Answer the following questions: a. Electrophoresis is used to sort DNA by. b. What is placed into the holes at the end of the gel? c. By adding electric current, we can make the DNA d. Shorter strands of DNA move ( faster / slower ) than longer strands. 3. Place the steps in the correct order: a. Load DNA sample into the gel. b. Stain the gel and analyze results. c. Make the gel. d. Hook up the electrical current. e. Set up the gel apparatus. 4. In the Gel Electrophoresis Laboratory follow the steps to make your own gel, answer the questions as you go. a. What is agarose made from? b. Melted agarose is poured into a c. Buffer electric current in the electrophoresis box. d. In real life, loading samples into the gel wells takes e. The black end generates a charge, the red end a charge. f. The bubbles in the electrophoresis box are that your current is running. g. Staining the DNA will make it show up under a light. h. What are your estimates for the number of base pairs in the three bands? Part B: Applying what you learned DNA Fingerprinting! (5 pt) Introduction: 1. DNA is unique for everyone. The only exception is if a person has what? 2. What are DNA fingerprints used for? Part 1 It Takes a Lickin 3. What crime was committed? 4. What bodily fluid was removed from the crime scene to get DNA? Page 1

3 Part 2 DNA Fingerprinting at the NOVA Lab 5. What does a restriction enzyme do? 6. What is agarose gel? 7. What is electrophoresis? 8. Smaller fragments of DNA move ( further than / not as far as ) longer strands. (Select one.) 9. Why do you need to place a nylon membrane over the gel? 10. Probes attach themselves to 11. Which chemical in your virtual lab is radioactive? 12. Sketch your DNA fingerprint to the right (you don t have to draw all suspects) 13. Based on your DNA fingerprint, who licked the lollipop? More on next page Page 2

4 Part C. Gene Therapy A Case Study on Cystic Fibrosis Go to the Genetic Science Learning Center Website: 1. In the Human Health box, click on Gene Therapy. 2. In the top left box, choose the Interactive Explore Cystic Fibrosis: Case Study. Read each file and answer the questions below: Understanding the Problem (a and b) Is Cystic Fibrosis a Good Candidate for Gene Therapy? (c) Choosing a Vector for CF Gene Therapy (d and e) Before you can choose a vector, you will need to click on Gene Therapy at the top left to get back to the Gene Therapy page. Then, click on Gene Delivery: Tools of the Trade to learn about possible vectors. CF Gene Therapy Read World Challenges a. What causes CF at the DNA level? b. What causes CF at the cellular level? (In order words what causes the symptoms?) c. What makes CF a good candidate for gene therapy? d. What is a vector (scroll down)? Read the information about each vector type in the toolbox and fill in the table on the separate page. e. What vector should be used for CF? f. Write one sentence to summarize each of the four challenges for gene therapy. 1. Gene delivery and activation: 2. Immune response: 3. Disrupting important genes in target cells: 4. Commercial viability: If you finish early, you may use the internet to review DNA Replication, Transcription, and Translation (next page). Page 3

5 DNA Review Websites Purpose: to review and expand your understanding of DNA: history of discovery, replication, transcription and translation. Go to the DNA Interactive website: 1. On the menu bar at the top of the webpage, click on CODE. 2. Choose Copying the Code from the menu at the bottom. a. Select Players from the top menu. Mouseover the film pictures and select Matthew Meselson. Select Models of DNA Replication and The Experiment to hear Meselson s explanation of semiconservative replication. b. Select Pieces of the Puzzle along the top menu Select The Central Dogma to review DNA and RNA structure. Select Models of DNA Replication to see conservative, semi-conservative, & dispersive models of replication. c. Click on Putting it Together along the top menu. First view Replication to view an animation of DNA being copied into new molecules of DNA. Next, choose Transcription to view an animation of DNA being copied into mrna. Finally, you can select Interactive to practice making an mrna strand. 3. Select Reading the Code from the bottom menu. a. Select Players from the top menu. Mouseover the film pictures and select Marshall Nirenberg. Watch the interview Breaking the Code to hear Nirenberg discuss decoding the first codon. b. Choose Pieces of the Puzzle along the top menu. Select The Genetic Code and Breaking the Code to view animations about the discovery of the genetic code. c. Click on Putting it Together along the top menu. Choose Translation to view an animation of mrna being translated into protein. Select Interactive to practice making a protein. 4. Select Controlling the Code from the bottom menu. a. Click on Putting it Together along the top menu. Choose Chromatin to view an animation of DNA packaging. 5. Select Finding the Structure from the bottom menu to learn about the history of DNA Discovery. a. Click on Players along the top menu. Choose Watson & Crick to hear interviews about finding the structure of DNA. b. Click on Pieces of the Puzzle along the top menu. Choose any of the pieces to learn about the different clues that went into finding the structure of DNA. MORE REVIEW WEBSITES: Go to: In the right column, choose Transcribe and Translate a Gene to do the interactive explore activity. Then, go back to the Molecules of Inheritance home page and choose What Makes a Firefly Glow to see an animation of protein synthesis. Go to: In this game, you will get to help a piece of DNA replicate semi-conservatively. You will be rewarded points for making two new sequences that are free of mutations, and you will receive bonus points for figuring out which organism s DNA you helped to replicated. Page 4

6 Notes on Biotechnology Making recombinant DNA to produce human proteins (like Growth Hormone) What is recombinant DNA? What do we need to make recombinant DNA? (See below in steps 1-4) Step #1 Isolate the gene of interest with restriction enzymes (see next page) Use #1 - To produce human proteins in bacteria (E.coli) Step #2 Vectors Mechanical Biological Step #3 Combine the gene of interest and the vector (plasmid) Step #4 Transfer the recombinant DNA to the host Page 5

7 DISCLAIMER restriction enzymes exist in nature, but scientists use them for purposes other than their natural purpose Figure 2: Restriction Enzymes EcoR I The enzyme EcoR I cuts a DNA strand when it encounters the nucleotide sequence CTTAAG. Circle the place(s) on the DNA strands where EcoR I would recognize and cut the DNA. Note: There may be more than one nucleotide sequence on each DNA strand. The first one has been done for you. Page 6

8 RFLP analysis Restriction Fragment Length Polymorphism How can we see the DNA fragments after they ve been cut up? Use #2 To identify people How do you analyze band fragment patterns on a gel? Describe your thought process on the family relatedness gel and the assault gel on the ppt. What happens if there is a mutation in the restriction site of a gene? Use #3 To identify human genetic diseases How can a single nucleotide make a difference? Wild-type allele (a restriction enzyme recognition site): = # of DNA fragments Mutant allele (restriction enzyme cannot recognize this sequence): = # of DNA fragments Page 7

9 In this gel, normal DNA is compared to Sickle Cell DNA. First the DNA is combined with the restriction enzyme MstI. What happens to the normal DNA (is it cut or not?): What happens to the sickle cell DNA (is it cut or not?): The Southern Hybridization tags the fragments of interest so it is easier to see. Can you tell the difference between the normal DNA and the sickle cell DNA? Use #5 Change characteristics What are transgenic organisms? Examples: Page 8

10 Lab: Testing for Sickle Cell Gene (Flow Chart) Page 9

11 Cracking your Genetic Code ( (You get two free blanks after that, I will start taking points off.) 1. What is genomics the study of? 2. What is a genome? 3. Describe the process used to get the DNA. 4. To obtain the first genome, it took years. 5. To obtain the first genome cost. 6. There are genes in pairs of chromosomes. 7. Genes code for. 8. How similar are human genomes? 9. There are how many differences in the spelling of genes between people? 10. It only takes letter variance to pre-dispose an individual to certain traits of diseases. 11. What did director of NIH find out about himself? 12. Finding out about your specific genome could be a teachable moment. Why? 13. Give an example of how finding out about your genetics could make you change your lifestyle for the worse. 14. APOE4 on chromosome 19 has been associated with what? 15. What other factors are needed to be taken into consideration besides knowing that you have APOE4? Page 10

12 16. Most genetic information is probabilistic. What does that mean? 17. If Elton found out she was predisposed to getting breast cancer, what things could she have done that she may not have done otherwise? 18. So far, scientists have found actionable genes. 19. The gene for Cystic Fibrosis is recessive. In order for someone to get this disease they must receive the abnormal gene from which parent? 20. Describe the role of the protein produced by the normal gene in a person who does not have the disease Cystic Fibrosis. 21. Describe the problem with the protein produced by the gene of a person who does have the disease Cystic Fibrosis. 22. What is melanoma? 23. What is the effect of the BRAF mutation on chromosome 7? 24. Genetic testing may develop into trying to produce the perfect child. Why is that probably not a possibility? 25. As an example, there are genes involved with height alone. 26. Scientists say, if you want a tall offspring. 27. How can genetic testing become an invasion of privacy? 28. Answer the following two reflection questions: a. What are some of the benefits and risks associated with genetic testing? b. Would you want to be tested even if there weren t an effective treatment you could take to prevent the disease? Do you think doctors should offer tests for genetic diseases before treatment is available? Why or why not? Page 11

13 Genetic Disorders Ethical Questions The following questions should be answered after watching Cracking the Code. Your aunt has just been diagnosed with a rare form of cancer caused by a defective gene. Individuals with this form of the gene are 80% more likely to contract this type of cancer. Eight in ten people with this defective gene contract this form of cancer. In the population as a whole, only one in ten people contract this type of cancer. Because defective genes are inherited, your family doctor has told you that you are at high risk. A test is available that can determine if you carry a defective copy of the gene. It will NOT tell you if you will actually GET cancer, but will tell you the LIKELIHOOD that you might contract this rare form of cancer. BEFORE ANSWERING THE QUESTIONS THAT FOLLOW, PLEASE COMPLETE THE FOLLOWING TABLE. POSSIBLE REASONS TO GET TESTED POSSIBLE REASONS TO NOT GET TESTED Question 1. Should you agree to be tested? Why or why not? Question 2. If you decide to be tested, WHEN will you get tested? Explain. If time permits: Question 3. You were tested and found to carry a defective copy of this gene. You marry and have a child. At what point will you share this information with them? Will you have your child tested? When? Page 12

14 Bioethics Group Discussion With our knowledge of the human genome, with sequencing technology, and with a much better understanding of the chemistry that takes place in our bodies, come a lot of new, ethical questions. Here are a few that may become issues, if they are not already, in the next twenty years. Think about each of the questions below. You may feel very strongly about how to answer, and you may feel completely conflicted. Wherever your opinion lies is fine you certainly will not be graded based on your answers. All I ask is that you back up your reasoning with as many facts as you can, and that you appreciate that we all have different opinions. Put your answer to each question on a separate notecard give a few sentences for each question, and write without talking to anyone. Once everyone is done writing their opinions, we will break into groups. Within each group, you ll take on one of the following roles: 1. recorder 2. facilitator 3. reporter (there may be two of these) The recorder s job is to take notes on the discussion, recording each person s comments, ideas, opinions, and questions. The facilitator will manage the group s discussion, encouraging everyone to offer input. The reporter will read off, to the whole class, what the group discussed. EVERYONE, regardless of his or her role, needs to contribute to the conversation within the group. Once all groups have had the time to discuss, we ll share our responses to the questions as a class. Questions: 1. How do you feel about parents giving human growth hormone to their shorter-than-average children? Do you think this should be allowed? Why or why not? 2. Genetically modified foods currently grow in crop fields. Do you have concerns about the safety of this (ecologically)? If you do, do you think that the benefits (such as providing more nutritious food to hungry populations) outweigh the drawbacks? Explain your reasoning. 3. Should parents be allowed to choose fertilized eggs that carry the traits they want in their offspring? For instance, should parents be allowed to select for the sex of their babies? Should they be able to select for embryos without life-threatening diseases (such as Tay Sachs)? Why or why not? 4. Should parents be allowed to sequence their kids genomes? Let s say we determine the gene for alcoholism, or for heart disease as a parent, would you want to know the fate of your child? Why or why not? 5. Assume a family has a history of Huntington s disease. Huntington s is a dominant disorder (if one parent has it, there s a fifty percent chance it will get passed on to offspring), and is incurable. It involves the degeneration (breakdown) of neurons in the brain, and eventually leads to death. Should parents of children under the age of 18 be permitted to have their children tested? Why or why not? 6. Assume that a couple has prenatal testing done and they find out that their child will be born with a deadly spinal disorder that will cause paralysis or possible death. At the very least, this will require numerous operations throughout the child s life, assuming the child lives. Should insurance companies be allowed to charge higher premiums for this child? Why or why not? Page 13

15 Gene Action Test Review Questions Format of Exam: This test will be composed of multiple choice and short essay to test your knowledge and understanding of DNA and biotechnology. Don t forget your notecard! This is worth 2 points on your exam! Review sheets: You will need to create your own study sheet by answering the questions below. Write the question into your answer and number your answers please put them in order. Please type your answers. Turn this in right before you take the test OR earn half credit. Content of Exam: You will be tested on information from in-class activities, laboratory experiments, homework assignments, articles, notes, and readings. You should also know how to apply the concepts learned in this unit to new examples. Biotechnology: 1. What is the Human Genome Project? ( Cracking Your Genetic Code ) 2. What is recombinant DNA and what can we use it for? 3. What do restriction enzymes do? 4. What are the steps to producing recombinant DNA? What role does each of the following play: gene of interest, restriction enzymes, plasmid, and bacteria? 5. How does gel electrophoresis work? 6. What is DNA fingerprinting? a. What is the process? b. How can it be used in crime scene analysis and to determine paternity? Page 14