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Building Protein Models This is an activity to help you understand primary and secondary structure of proteins. 1. Building the primary structure of a polypeptide. a. Using one pipe cleaner, construct a polypeptide using 8 plastic beads to represent amino acids. b. List the colors in order and the corresponding amino acids in the primary structure. Amino Acid Key Glycine Alanine Serine Cysteine Valine Leucine Lysine Proline Arginine Histidine Bead Color Black Orange White Dark blue Light blue Green Lavender Red Yellow Pink Amino Acid 1 2 3 4 5 6 7 8 c. Compare your primary structure to that of your neighbor. Is it exactly the same? d. Would both of these small polypeptides form the same shape and have the same function? 2. Secondary Structure - the - (Alpha) Helix a. Take another pipe cleaner. Select four pink beads and eight other beads. Build a primary structure starting and ending with pink beads. Space the beads evenly along the pipe cleaner. b. Twist the pipe cleaner into a coil so that all the pink beads are lined up. Imagine hydrogen bonds between the amino acids represented by the pink beads, holding the coil shape. Refer to the figure on the next page. QuickTime™ and a decompressor are needed to see this picture. 3. Constructing a ß- (beta) Pleated Sheet a. Take a pipe cleaner and bend it into a U. Be sure the ends are even with each other. b. Fold the arms of the pipe cleaner into pleats. Use the figure of the ß- pleated sheet above as an example. c. Use the short pieces of pipe cleaner to represent hydrogen bonds between the parallel arms of the polypeptide.