Jeffrey T. Kushner Chem 504 Lesson Plan DNA, RNA & Protein Synthesis

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1 Jeffrey T. Kushner Chem 504 Lesson Plan DNA, RNA & Protein Synthesis Objective Students will be able to describe the bonding characteristics of the sugar-phosphate backbone of DNA & RNA. Students will be able to describe the bonding patterns of the nitrogen bases of DNA. Students will be able to compare and contrast DNA & RNA. Students will be able to extract DNA from onion cells. Students will be able to analyze an article on Protein Synthesis Students will be able to relate information about DNA to other nucleic acid processes. Overview (Setting) This lesson is designed for a college prep chemistry class with an extended lab period. (This lab period may coincide with the lecture period or it may follow at some other time.) Students are connecting knowledge learned in last years Biology course and now beginning to develop a more comprehensive and complete understanding of the chemical nature of metabolism. By the end of this lesson, students will be able to identify the structural characteristics of DNA and RNA, describe bonding patterns of DNA and RNA. This will build on their previous knowledge of protein synthesis and genetic roles of DNA and RNA. Pre-Class Activity Students will be shown the chemical structure of DNA. They will be asked to provide observations regarding the chemical structure and chemical nature of the molecule. ( Content Nucleic Acids Overview Notes (Introduction) DNA/RNA Standard To identify the building blocks of nucleic acids To describe DNA and RNA Organic Molecule--#4 Nucleic Acids DNA Deoxyribonucleic Acid Makes up genes Particular segment of DNA that determines a trait -double strand --RNA Ribonucleic Acid -Particular segment of DNA that has been copied to be used as a messenger or transfer molecule -single strand Large Complex Molecule made up of subunits Nucleotide (Kennesaw State University. 1999) DNA

2 Long Double Helix Twisted Ladder Sides Make up of sugar phosphate molecules Rungs Made up of nitrogen bases Adenine (A) -Thymine (T) Guanine (G) -Cytosine (C) FOR RNA Base pairs fit together to form pairs SPECIFIC PATTERN!!!!! A T (T-A) G C (C-G) -Sugar phosphate EX: A C G C T C A A C G C T T G C DNA DNA Double Helix T G C G A G T T G C G A A C G Traits (genes) are set by order of nitrogen bases

3 RNA Ribonucleic Acid Long Single strand Side Make up of sugar phosphate molecules Rung Made up of nitrogen bases Adenine (A) -Guanine (G) Cytosine (C) -**Uracil (U)** EX: A C G C U C A A C G C U U G C RNA (TRANSFER RNA trna) Rosenbaum, Katy ( Leja, Darryl, 1999 (

4 Structured Practice (Classwork) PIM 1. Initial Question a. Why do the nitrogen bases of DNA pair in a specific order? 2. Existing Information 3. Reflect and Organize 4. New Information Needed 5. Results 6. Community Knowledge Laboratory Activity Students will perform a DNA extraction. Using onion cells, students will breakdown the cell wall, lyses the cell membrane, and then isolate DNA using rubbing alcohol. Independent Practice Short Term Assignment: Due Tomorrow 1. Read Access Science Article Protein Synthesis. 2. Develop three investigation questions from reading. a. Investigation questions are questions that can not be answered from reading; they require further research and/or information to answer. Long Term Assignment: Due next Lab period 1. Students will complete the post-lab questions 2. Write a lab reflection paper.

5 ( PRE-CLASS Describe any features that you can from the following molecule.

6 Initial Question Why do the nitrogen base pairs of DNA bond in a specific pattern? The Penn Instructional Model Topic: Bonding of Nitrogen bases. Existing Information DNA/RNA Structure Nitrogen base names Bonding patterns Bond Types Results A bonding with T forms two nitrogen bonds. C bonding with G forms three nitrogen bonds. Bond lengths are uniform across helix. Purine bonds with Pyrimidine. Distance from sugar to sugar is uniform with a total of three rings falling between the sugar/phosphate backbone. Reflect And Organize What features bond A to T and C to G? How would the DNA molecule be affected if A bonded with C or G? What types of bonds hold the bases together? Peer Review What could happen if two purines or two pyrimidines did bond together? How is the structure of the overall double helix affected by this bond pattern? Are there any similarities in bonding that occur between the bases of DNA and the Model Accepted? New Information Needed? Structures of Nucleotides Structure of Double helix Bond lengths (??) Community Knowledge Nitrogen bases of DNA are paired as one purine with one pyrimidine. This bond pattern occurs for a few, vital reasons for the stable structure of DNA. When bonding a purine with a pyrimidine, a stable, uniform, bond length. Second, the specific binding pattern of A to T forms two nitrogen bonds; where as the bonding of C to G forms three nitrogen bonds.

7 PIM INFORMATION SHEET Adapted from: Iowa State University. 2007

8 Extraction of DNA from an Onion Molecular biologists and biochemists are involved with research in finding out as much as possible about the DNA in plants and animals. Although DNA was discovered in the 1950 s, there still remains a lot to be known about it, especially how it is used to determine the physical traits that we all have, and how it regulates the workings of the body. We should always remember that DNA is just a chemical named deoxyribonucleic acid. Because it is a chemical, we can do reactions with it just like we can work with any other chemical. In this lab, we will use the chemical properties of DNA to extract it from the cells of onions. Experiment: Note: You should write all observations from this lab in the observation section on the third page of this lab. These observations will account for a large part of your grade, so be neat and complete! 1) Prepare a buffer solution by pouring the following into a clean 250 ml Erlenmeyer flask: ml of water (distilled water, if available) grams of sodium chloride (table salt) grams of baking soda (sodium hydrogen carbonate) ml of shampoo or liquid laundry detergent What buffer solutions are used for: This buffer solution is used in this lab for several reasons. First of all, the saltiness and acidity (ph) of the solution is very close to that in living things; as a result, the DNA will like to dissolve into this solution. Secondly, the detergent is added to help break down cell walls in the onion cells. Cell walls in living things are made of long polar molecules with a greasy end and a charged end. Because detergent is used to break apart greasy particles in your clothes, it will also work to tear apart the greasy molecules in cell walls. It will be important that these cell walls break down in this lab, because inside the cell is where the DNA is. 2) Chill the buffer solution by placing the flask in a larger beaker filled with crushed ice and water. Why we need to chill the buffer solution: As important as DNA molecules are to life, they are still extremely fragile, and break apart easily when removed from cells. To slow down the rate at which the DNA breaks up, we cool down the buffer solution to near freezing. Chemical reactions always take place slower in cold solutions than in warm ones, because there is a lot less energy around to make the reaction take place.

9 3) Dice an onion with a knife. Half an onion should be plenty for this lab. Use a mortar and pestle to mash the pieces of onion into a pulpy sludge. If you don t have a mortar and pestle, place the diced pieces of onion into a beaker or 125 ml flask and mash them with the blunt end of a test tube. Careful! Don t use too much force or the test tube and/or beaker will break! Why we need to mash the onion: What we want to do by mashing the onion is to either break the cell walls (releasing the DNA into the juice) or at the very least expose the cell walls so the detergent can break them down. 4) Place 10.0 ml of the vegetable mush/juice into a small, clean beaker or flask and mix in 20 ml of the chilled buffer solution. Stir vigorously with a stirring rod for three minutes. In this step, we re exposing the onion to the detergent solution. The detergent will break up the cell walls, releasing the onion DNA into the buffer solution. 5) Pour as much liquid as you can into a clean test tube. Let the test tube sit in a crushed ice/water bath for five minutes. In this time, the solids should settle to the bottom of the test tube, and the top should mainly be liquid. 6) Making sure to leave the pulp behind, strain the rest of the solution through a coffee filter or filter paper with a funnel and into another clean test tube. The test tube should be about half full when you have finished; if you have more, pour some out. The (hopefully) clear solution you have in this test tube consists of dissolved DNA fragments, as well as some other biochemical compounds such as RNA and some proteins. DNA is a very long molecule, but compared to the holes in a piece of filtering paper, the molecule is still small enough to pass through. 7) Obtain some ice-cold rubbing alcohol from an ice bath or a freezer. Using a drinking straw, gently add rubbing alcohol to the top until there is about an inch and a half sitting above the buffer solution. The best way to do this is to dip the drinking straw into the isopropanol bottle and then when it has filled to put your finger over the end. To add it to the test tube, slowly let it run down the side of the test tube into the DNA solution. Your goal is to have the rubbing alcohol stay on the top of the DNA solution, with as little mixing as possible. The rubbing alcohol is used to extract the DNA from the onion juice. The reason you want the rubbing alcohol to stay on top of the onion juice is because by doing that the liquid will form two distinct layers. Generally, molecules are attracted to the boundaries of two liquids - sometimes the concentration of large molecules can be much higher at the boundary between two liquids. That s what we re hoping for here... if the DNA is attracted to the surface, we can pull most of it out. However, if the alcohol and onion juice mixes too much, there will be too

10 much alcohol throughout the whole liquid, and the DNA won t be attracted to the surface, making it much harder to pull any out of the tube. 8) Very gently insert a coffee stirrer or glass rod through the upper alcohol layer in the test tube into the DNA containing buffer solution. While disturbing the solution as little as possible, leave the glass rod or stirrer in one place and rotate it in one direction, like you would spin a globe; with luck the DNA fragments will wind onto the stick in the same way that thread winds onto a spool. DNA spools onto the stick or glass rod because the exposed ends have polar chemical groups on them. Glass and wood are also polar, so the ends of the DNA are attracted to the stirrer. By winding the stirrer, you are basically just reeling in the DNA molecules. 9) After twirling the stick for about 60 seconds, pull the stirrer up through the alcohol layer. You should see the DNA adhere to the end of the stick and appear as a transparent, viscous sludge at its tip. The molecule that you have collected on this stick consists of the entire genetic code for the making of an onion. When you pull the DNA through the nonpolar alcohol layer, it clumps together because it would rather be attached to polar materials such as the stick or even itself. Remember, like dissolves like, meaning that polar compounds will tend to want to stay in polar environments while nonpolar compounds will want to stay in nonpolar environments. In this case, DNA, a polar compound, sticks to itself simply because it prefers a polar environment (itself) to a nonpolar environment (the rubbing alcohol). 10) Clean up: The waste left over from this lab should consist of a soapy onion paste, a soapy onion liquid, 10 ml of isopropanol solution, and a large amount of onion goo. All solutions can go down the sink, while the onion goo should be wrapped in a paper towel and thrown in the garbage. The collected DNA is a totally safe compound, and can be thrown away or saved to show your parents and friends if you like. Observations: Use the space here and on the back of this sheet to write down any observations that you have about this lab.

11 Postlab Questions: 1) Did you get a large amount of DNA in this experiment? If so, why do you think your group did so well? If not, what do you think went wrong? 2) Based on what you know of chemistry, what improvements do you think we could have done on this lab? (There is no right or wrong answer for this question, so use your creativity and intelligence for an answer). 3) Do you think this method would work well for other foods? Why or why not (explain your reasoning)?

12 Lab Reflection Essay Write a four paragraph essay reflecting on the lab procedure, lab observations, your knowledge of the lab, and ways you could have improved this lab experience. Use the outline below as a guide for 4 paragraphs. Lab Overview Describe/summarize the procedure What was performed during the lab? What materials were used? What role did each group member have? Lab Observations Overview Describe what was observed. Describe how the observations indicate what was being studied What do the observations tell you? How are the observations used to prove/disprove the objective of the lab? Lab Content Connection Describe the lecture principles to the lab What was occurring during the lab How do the lecture/pogil activities tie in with the lab principles being studied. What is the Chemistry behind the lab? Lab Improvement Describe was the lab could have been performed better. How could the lab notebook detail more precise information? How could observations during the lab be improved? What would you change? What improvements could you make? Lab notebook writing? Organization?

13 Lab Reflection Essay Rubric Category Introduction First paragraph is catch. Thesis is evident and to the point regarding lab. First paragraph is weak. Thesis is mixed among many sentences and hard to piece A catchy beginning was attempted by confusing. Thesis is not entirely No attempt made to catch readers attention. Thesis is not apparent. Accuracy of Facts Organization Focus on Assigned Topic Mechanics All facts presented accurately and related to lab. Essay is well organized. Four paragraphs evident. Essay follows logical order with clear transitions. Entire essay discusses lab. Allows reader to fully understand lab topic. The essay has few, if any spelling, punctuation, capitalization, grammar, or usage errors. together. Almost all facts present are accurate. Only occasionally related to lab. Essay is pretty well organized. Four paragraphs evident. Essay is mostly logical with one idea out of place. Most of essay is related to lab. Essay wanders around one point, but comes back into main focus. The essay has three or less mechanical errors. Student Class apparent. Most facts presented are (70%) accurate. Evidence is suggested regarding lab. Essay is hard to follow. Paragraphs unclear. Essay does not follow logical order. Some of the essay is related to topic, but reader does not learn much about the topic. The essay has five or less mechanical errors. Several factual errors made in essay. No effort to relate to lab. Ideas seem to be randomly arranged. No effort at paragraph organization. No attempt has been made to relate lab. The essay has more than five mechanical errors. Total Points Grade

14 Sample Student Investigation Questions. 1. What chemical process allows DNA to form mrna? 2. What features of mrna allow it to interact with a trna? 3. What happens if the mrna sequence differs from the DNA sequence? a. By one added base? b. By one deleted base? c. By more than one base?

15 REFERENCES DNA Quest. (accessed: 8/6/07) DNA Molecule. Iowa State University (accessed 8/6/07) Extraction of DNA from Onion Cells. Cavlcade Publishing, (accessed: 8/6/07) Nucleic Acids. Chemistry; A Project of the American Chemical Society. Freeman. New York, Garrett, R. H., and Grisham, C.M. Principles of Biochemistry with a Human Focus, updated Third Edition. Brooks/Cole. Belmont, CA, Leja, Darryl, (accessed 8/6/07) McMurry, John., and Casellion, Mary, E. Metabolism Fundamentals of General, Organic, and Biological Chemistry; Fourth Edition. Pearson Education, Inc. New Jersey Cambell, Neil. Metabolism. Biology, Third Edition. The Benjamin/Cummings Publishing Company, Inc Rosenbaum, Katy (accessed: 8/6/05) Smith, Andri.; Hermes, Matthew. Cisplatin and DNA. Kennesaw State University (accessed: 8/6/07)