Part 1: Have Your DNA and Eat It Too! When isolated from a cell and stretched out, DNA looks like a twisted ladder. This shape is called a double helix. The sides of the DNA ladder are called the backbone and the steps (also called rungs) of the ladder are pairs of small chemicals called bases. There are four types of chemical bases in DNA: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). They form pairs in very specific ways: Adenine (A) always pairs with Thymine (T) and Cytosine (C) always pairs with Guanine (G). Purpose: To construct a model of DNA Materials: Masking tape and material from table below: Material Component White marshmallows DNA bases: Adenine, Cytosine, Guanine, Thymine 9 Toothpicks Hydrogen bonds Red Licorice Bits Deoxyribose Sugar cheerios Phosphate wire Sugar-phosphate bonding material 1. Create a 9 base DNA sequence and record it in your notebook. You will use this sequence to create a DNA strand that is nine bases long. You must use at least one of each base. You can choose any order with a few exceptions. You are NOT allowed to choose the following 3 bases in order: ATC, ATT, ACT, but any other order will do! In your notebook, record what base sequence you choose. 2. Gather your supplies. You will need 2 pieces of wire, 18 cheerios (phosphate), 18 pieces of red licorice bits (deoxyribose sugar) and 18 total nitrogenous bases (white marshmallows). 3. Create your bases. Using the 9 base sequence you chose in procedure 1, for each base, write the base letter (A,G, C or T) on each of 9 marshmallows. For example, if your 9 base sequence started out with the following bases: AGC, you would take 3 marshmallows and write an A on one, an G on the second and a C on the third. Do this for all 9 bases. 4. Assemble your DNA backbone. Using the first piece of wire, string on your phosphates and deoxyribose sugar; alternate between phosphate and deoxyribose sugar. This is one half of your DNA backbone. Use the second piece of wire and do the same with your remaining deoxyribose sugar and phosphate. You just constructed your DNA backbone. 5. Add your hydrogen bonds. Take your 9 toothpicks and insert them into ONE side of your backbone. Be sure to insert them into the deoxyribose sugar, NOT the phosphate! 6. Add your bases to your hydrogen bonds. Take the 9 marshmallows you labeled in step 3 and put them onto your 9 toothpicks. Make sure they are in the same order you have written down in your notebook. Label this side of your DNA, leading strand with masking tape. Make sure you know which end is the beginning end of your leading strand. 7. Complimentary base pair. Pair your bases with the correct complimentary base pair. With your remaining 9 marshmallows, write down the base that corresponds to each existing marshmallow that is on your DNA backbone. Then, slide each pair onto the correct toothpick. 8. Complete your DNA assembly. Insert your toothpicks (hydrogen bonds) onto the other DNA backbone. Make sure you affix the backbone so that it is anti-parallel to the existing backbone. 9. Create a double helix. Carefully twist your DNA molecule so that it looks like a double helix. 10. Get a stamp! Have your model checked by your teacher and get a stamp in your notebook! Good Job!
Conclusion: (answer these in your notebook) 1. What are the components of the DNA backbone? 2. To what molecule of the DNA backbone do the nitrogenous bases bond? 3. What are the names of the nitrogenous bases? 4. What is meant by complimentary base pairing? What bases are considered base pairs? 5. Why is the structure of DNA known as a double helix? 6. Draw and completely label your model of DNA showing the correct base pairings. Part 2: Have Your mrna and Eat It Too! A Model for Transcription (DNA RNA) Unlike DNA, RNA is single stranded. Like DNA, RNA has a sugar/phosphate backbone but the sugar is ribose. RNA has four types of nitrogenous bases: Adenine (A), Cytosine (C), Guanine (G), and Uracil (U), no Thymine! The bases form pairs in very specific ways: Adenine (A) always pairs with Uracil (U) and Cytosine (C) always pairs with Guanine (G). Purpose: To construct a model of mrna Materials: In addition to the materials in the chart below, you will need the model of DNA constructed in Part 1. Material Component White marshmallows mrna bases: Adenine, Cytosine, Guanine, Thymine 9 Toothpicks Bonds Black Licorice Bits Ribose Sugar cheerios Phosphate wire Sugar-phosphate bonding material 1. Gather your supplies. You will need 1 piece of wire, 9 pieces of black licorice (ribose sugar), 9 cheerios (phosphate), 9 toothpicks (bonds) and 9 marshmallows (nitrogenous bases). 2. Assemble your model of mrna. Using the wire, string on your phosphates and ribose sugar, alternating between phosphate and ribose. 3. Insert your bonds into each ribose sugar. (Insert each toothpick into the black licorice bits). 4. Next, break your hydrogen bonds on your DNA model to expose the nitrogenous bases. To do this, simply snap each toothpick in half, leaving one base on each side of the broken toothpick. 5. Next, using the leading strand of your exposed DNA bases as a guide (be sure you start from the beginning end), assemble the correct mrna bases onto the bonds of your mrna molecule, in the correct order. You will need to write the RNA base letter onto the marshmallow before you put it onto your mrna strand. For example, if your DNA sequence begins with AAT, you would write UUA on your 1 st 3 marshmallows and then put these marshmallows onto the toothpicks of your mrna model. Do this with all 9 of your marshmallows 6. Congratulations! You have just transcribed your DNA into mrna! Get your model checked by your teacher and get a stamp in your notebook!
Conclusions: (answer these questions in your notebook) 1. What are 3 major differences between the RNA model you constructed and the DNA model you constructed previously? 2. What are 2 similarities between the RNA model you constructed and the DNA model you constructed previously? 3. Draw and completely label your model of RNA. 4. What is the difference between introns and exons? 5. On your completed model of RNA, assume the 5 th -8 th base was an intron, what would the remaining RNA molecule look like? Draw the remaining RNA molecule after the introns are spliced out, with only the exons remaining. Part 3: Translation - mrna Protein The four nitrogenous bases in mrna (A,C, G and U) create a code. Cells read this mrna code to make proteins, the building blocks of all organisms. Reading the mrna copy to string together the small molecules (amino acids) that make up a polypeptide is called translation. Cells read DNA in small portions (genes) to create a protein. To do this, the cell must first make a copy of the gene s code to send to the proteinbuilding organelle, the ribosome. This process is called transcription (completed in Part B). This copy, mrna, is a recipe for assembling a polypeptide. Polypeptides are built from small molecules (monomers) called amino acids. The mrna travels from the nucleus to the ribosome and the appropriate amino acids are assembled into a polypeptide chain the primary structure of a protein. This process is called Translation. Purpose: To simulate translation. Work with the group at your table for this task. Materials: Previously made model of mrna Rectangle cut outs Tape Colored pencils 1. Begin to create your polypeptide. At your table, join all of your mrna to make a long mrna strand. (27 bases long if there are 3 in your group, 18 bases long if there are 2 in your group.) In your notebook, record the bases that are present in your new, long strand of mrna. 2. Assemble a start and a stop codon. Each group of two or three must complete this step as a group! At the beginning and the end of your new, long strand of mrna, attach a start and a stop codon. To do this:
cut out and label a rectangle to represent a start codon and a rectangle to represent a stop codon Place them at the beginning and end of your long strand. 3. Use your new model of mrna (created in Step 1) and the amino acid rectangle cut-outs to create a polypeptide chain. To do this: cut out a rectangle and label it with the correct amino acid that is coded for by the first codon from your mrna molecule. Repeat this process for the remaining codons in your mrna molecule. Color each amino acid a unique color. For example, color all the lysine red, all the alanine blue. 4. Bond your polypeptide. Tape your amino acids together in the correct order as coded for in your mrna strand. Don t forget to bond your start and stop codons at the beginning and the end of your new, polypeptide. Tape the polypeptide into your notebook. 5. Get your polypeptide checked. Get a stamp in your composition book. Congratulations! You made a protein! Analysis: (Answer these in your composition book): 1. Write down all the bases in your long mrna strand. Delete the 5 th base (remove it, cross it out), how does the resulting amino acid sequence change? Record the new polypeptide from this change. 2. Again, using your original bases sequence you wrote down in #1, except this time delete the 3 rd codon (remove it, cross it out), how does the resulting amino acid sequence change? Record the new polypeptide from this change. 3. Again, using your original bases sequence you wrote down in #1, except this time substitute the 5 th base with a different base (you choose which base), how does the resulting amino acid sequence change? Record the new polypeptide from this change. 4. Give an example of one other alteration in your mrna that will affect the final amino acid sequence. 5. Some changes have no effect on the final amino acid sequence. Give an example. Conclusion: (Answer these in your composition book) 1. What enzyme adds nitrogenous bases to mrna? 2. In what part of the cell does transcription take place? 3. In your own words, describe transcription. 4. What is the protein-building organelle? 5. What kind of RNA brings the amino acid to the ribosome? 6. What kind of RNA contains the anticodon? 7. In what part of the cell does translation take place? 8. In your own words, describe translation. 9. What does the tape on your amino acid sequence represent?