Biology 2E- Zimmer Protein structure- amino acid kit Name: This activity will use a physical model to investigate protein shape and develop key concepts that govern how proteins fold into their final three-dimensional structure. Use your model to answer the questions below. Part A Formation of Peptide Bond 1. Examine the amino acids on the top row, circle the amine groups. 2. Draw a rectangle around the carboxyl groups. 3. What type of reaction occurs in the formation of a peptide bond? 4. Identify the amino acid in the top row. Part B - Primary structure The primary structure of a protein is determined by its amino acid sequence - the sequence of a certain polypeptide chain is shown below. Use it to answer the following questions. 1. How many amino acid monomers are in this polypeptide? Label a peptide bond and circle all of the R- groups (also called sidechains). 2. Label the N-end and the C-end. Using the chart to help you ( a.a. sidechain list ), what is the primary sequence (from N-to-C direction) of this polypeptide? Use 3-letter codes for each a.a. 3. How are the second and third amino acids (in the diagram above) represented differently on the Amino Acid Sidechain List? Why are there different ways to draw these sidechains? 4. In the diagram above, label the atoms in the backbone that could be involved in a hydrogen bond with another part of the polypeptide. Label one as partial positive and another as partial negative.
Part C Secondary structure The picture below is a section of a protein which is showing a type of local secondary structure known as an alpha helix. 5. What is the arrow pointing to? 6. Circle a hydrogen bond that pulls this structure together. 7. Why are the R-groups not shown in this picture? 8. What groups on the amino acids are always involved in these hydrogen bonds? 9. The alpha helix is not the only common type of secondary structure found in proteins. The diagram below shows a second type called a beta pleated sheet. Both of these folding patters can be found in larger proteins. What attractions do you think hold this shape together? Part D Tertiary structure 10. What type of bonding can you find in the tertiary structure? Show 1 example of each below:
Now it s time to create your own polypeptide: with your group, do the following: Before creating the primary structure for your polypeptide, organize your R-groups (sidechains). Place amino acid sidechain on the magnetic Chemical Properties Circle according to its chemical properties. You will need to consult the Amino Acid Sidechain List in your kit to find the name of each sidechain, so you can position it correctly on the circle. After each sidechain has been correctly positioned on the circle, look at the colored balls in each sidechain. Scientists established this CPK Coloring Scheme to make it easier to identify specific atoms in models of molecular structures. Carbon is Gray, Oxygen is Red, Nitrogen is Blue, Hydrogen is White, and Sulfur is Yellow. Answer the following questions about sidechains: 11. Hydrophobic sidechains are composed primarily of atoms. 12. Acidic sidechains contain two atoms. This is called a functional group. 13. Basic sidechains contain atoms. This is called an functional group. 14. Hydrophilic sidechains have various combinations of atoms. 15. From your experience with oil and water, which sidechains might position themselves on the interior of a protein, where they are shielded from water? 16. From your experience with chemistry, which sidechains might be attracted to each other? Take out your toober. Place a blue end cap on one end and the red end cap on the other end. The blue end cap represents the N-terminus (the beginning) of the protein, and the red end cap represents the C-terminus (the end) of the protein. 17. What are the N-terminus and the C-terminus referring to specifically? 18. What do the plastic clips represent on the amino acids? You will be using the following sidechains (1 methionine, 6 hydrophobic, 2 acidic, 2 basic, 2 cytosine, 2 other polar sidechains) to make your polypeptide. Select methionine from the chemical properties circle and place it on the clip closest to the N- terminus Choose the appropriate number of sidechains (from the bold list above). It doesn t matter which specific ones you choose as long as you have the correct number of each. Remove these 14 amino acids from the circle and make a pile. Mix your selected Sidechains together and place them in any order you choose on your mini-toober with equal spacing between each of them. 19. Why do they have equal spacing (what is the backbone of your polypeptide?
20. The sequence of amino acid Sidechains that you determined when placing them on the mini-toober is called the Primary Structure of your protein. List your primary sequence below (using 3 letter abbreviations and dashes). 21. Why is the primary structure important for your polypeptide? Does the order matter? Now you can begin to fold your 15-amino acid protein according to the chemical properties of its sidechains. All of these chemical properties will affect the protein at the same time! NOTE: You may need to use many hands working together to complete the folding of your polypeptide. The clips can twist if you need them to, but be careful not to drop the sidechains while you are folding. Also, as you continue to fold your protein to apply each new property listed below, you will probably find that some of the sidechains you previously positioned are no longer in place. For example, if you pair a negatively charged sidechain with a positively charged one, some of the hydrophobic sidechains may move to the outer surface of your protein. Find a shape in which all the properties apply. Start by folding your protein so that all of the hydrophobic sidechains (with yellow tape at base) are buried on the inside of your protein, making dispersion forces, where they will be hidden from polar water molecules. Next, fold your protein so the acidic and basic (charged) sidechains are on the outside surface of the protein and pair one negative sidechain (red) with one positive sidechain (blue) so that they come within one inch of each other and neutralize each other, making an ionic bond. This positivenegative pairing helps stabilize proteins. Continue to fold your protein making sure that your polar (white) sidechains are also on the outside surface of your protein where they can hydrogen bond with water. Last, fold your protein so that the two cysteine sidechains (green) are positioned opposite each other on the inside of the protein where they can form a covalent disulfide bond that helps stabilize your protein. The overall final shape of your polypeptide when it is folded is called the Tertiary Structure Compare your structure to the other groups polypeptides. Carefully remove clips, sidechains, and terminals--put into their respective bags. Roll up your toober. 22. How many water molecules would be produced from the making of this polypeptide? 23. What happened as you continued to fold your protein and applied each new chemical property to your protein? Did your protein look like the proteins other students folded? Explain.
24. To review, what types of attractions or bonds are involved in tertiary folding? What part of the polypeptide creates the folding from tertiary structure? 25. What would have happened to your protein shape if you had also included secondary structure? Why didn t we include this as part of the procedure? 26. Most real proteins are actually in the range of 300 amino acids long. How would this affect the complexity of the protein shape or potential shapes? 27. To create a protein with quaternary structure, what would we have to do in this activity?