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AP Biology Names___Biomolecule Stations Per AP Biology Names____________________________________ Biomolecule Stations Per.______________ In this two-day activity, you will move through several different stations and learn about the four macromolecules in the biological world. Day 1: Modeling Carbohydrates and Lipids 1. Use the 3d-printed models to answer the questions for carbohydrates and lipids. NOTE: Blank corners indicate “carbon” atoms. Glucose Fructose Glycerol Acetic Acid Butyric Acid Caproic Acid Day 2: Modeling Proteins 1. Using the Amino Acid Sidechain list, organize the sidechains on the circular magnetic mat according to their name or properties. 2. Examine the side chains and their positions on the circle. Describe your observations on your answer sheet by answering questions #1-6 under Modeling Proteins. 3. Now you have explored the chemical properties and atomic composition of each sidechain, you are ready to predict how proteins spontaneously fold up into their 3D shapes. Answer questions #7-8 on your answer sheet. 4. Unwind the yellow tube. Notice the blue and red end caps. The blue end cap represents the N- terminus (the beginning) and the red end cap represents the C-terminus (the end) of the protein. 5. Select 15 metal U-shaped clips from your kit. Beginning at the N-terminus, place the 15 u-clips three inches apart on the tube. 6. Select methionine from the mat and place it on the clip closest to the blue end cap. Choose six hydrophobic sidechains, two acidic sidechains, two basic sidechains, two cysteine sidechains, and two other polar sidechains. Place them in any order you choose on your tubes u-clips. a. Side note: This sequence of amino acid sidechains that you determined is called the primary structure of your protein. As a general rule the final shape of a protein is determined by its primary structure. 7. Answer question #9 on your sheet. 8. Now begin to fold your protein according to the chemical properties of the sidechains. Remember all of these chemical properties affect the protein at the same time. a. Fold your protein so that all of the hydrophobic sidechains are buried on the inside of your protein where they will be hidden from polar water molecules. b. Fold your protein so the acidic and basic (charged) sidechains are on the outside surface of the protein and pair one negative sidechain with one positive sidechain so they come within one inch of each other and neutralize each other. This positive-negative pairing helps stabilize your protein. c. Continue to fold your protein applying these new properties: i. Make sure your polar sidechains are also on the outside of your protein where they can form a hydrogen bond with water. ii. Fold your protein so the two cysteine sidechains are positioned opposite each other on the inside of the protein where they can form a covalent disulfide bond that helps stabilize your protein. This is called a disulfide bridge. iii. Side note: this final shape of your protein is called the tertiary structure. 9. Answer questions #10-15 on your answer sheet. Day 1: Modeling Carbohydrates Answer Sheet 1. How many atoms of carbon are there in each molecule of glucose? Fructose? 2. Write the molecular formulas for glucose and fructose. 3. Compare the number of hydrogen atoms to the number of oxygen atoms in each sugar. What is the ratio? 4. Glucose and fructose are isomers of each other. Define “isomer” in your own words. 5. As a team, identify where the carbons, oxygens, and hydrogens are in the sucrose molecule (no need to write anything here). 6. What had to be removed to join glucose and fructose together, and what is the name of the reaction that joins monomers together to form a polymer? 7. Write the molecular formula for sucrose 8. What is the ratio of hydrogen to oxygen atoms in a sucrose molecule? 9. How many monosaccharides are needed to form a disaccharide molecule? Day 1: Modeling Lipids Answer Sheet 1. What are the formulas for glycerol? Butyric acid? Caproic acid? Acetic acid? 2. Are there any elements in the above molecules that are not in carbohydrates? If so, which? 3. How does the ratio of hydrogen to oxygen atoms compare in carbohydrates and the molecules you just built? 4. What combination of atoms is present in all three of the fatty acid molecules you just built? 5. What had to be removed to join the four molecules together? Draw how this could be done 6. Explain why the chemical process responsible for building a carbohydrate or lipid molecule is called dehydration (or condensation) synthesis? 7. Using the model, explain why saturated fats form solids at lower temperatures than unsaturated fats. Reference the model in your answer Day 2: Modeling Proteins Answer Sheet 1. Do you see similarities or patterns in the side chains? Explain what you observe. 2. Hydrophobic sidechains are composed primarily of _____________ atoms. 3. Acidic sidechains contain two __________________ atoms. This is called a carboxylic acid functional group. 4. Basic sidechains contain ____________________ atoms. This is called an amino functional group. 5. Hydrophilic sidechains have various combinations of what? 6. An exception to the observation in question #5 is what? 7. From your life experience with oil and water, which sidechains might position themselves on the interior of a protein where they are shielded from water? 8. From your experience with magnets or electricity, which sidechains might be attracted to each other? 9. Record the sequence of amino acids in your protein, starting with the N-terminus (blue end cap) 10. What happened as you continued to fold your protein and applied each new chemical property to your protein? 11. Were you able to fold your protein so that all the chemical properties were in effect at the same time? If not, do you have any ideas why you weren’t able to fold your protein in a way that allowed all of the chemical properties to be in effect simultaneously? 12. How many different proteins, 15 amino acids long, could you make given an unlimited number of each of the 20 amino acids? 13. In the space below, sketch the tertiary structure of your protein. 14. Which level of protein structure did you not do during this activity? 15. Sketch and label the two versions of the secondary structure of protein folding. Modeling Biomolecules: 2-day Activity 1. Day One a. Full Period b. Protein modeling 2. Day Two a. Full Period, 10-15 minutes per stations b. Modeling Carbohydrates c. Modeling Lipids .
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