Pipe Cleaner Proteins. Essential question: How does the structure of proteins relate to their function in the cell?

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1 Pipe Cleaner Proteins GPS: SB1 Students will analyze the nature of the relationships between structures and functions in living cells. Essential question: How does the structure of proteins relate to their function in the cell? Materials per student: 12 pipe cleaners Black pipe cleaners cut into short (4 cm) strands to represent hydrogen bonds Assorted beads with holes large enough for pipe cleaners to fit through (*Note: materials available at most craft stores) Pre-Activity Discussion: All living organisms contain proteins. They make up over 50% of the dry weight of cells and have many different functions including structural support, transport of substances through the cell, signaling from one cell to another, movement, storage, and defense against foreign substances. All of the many thousands of proteins known are composed of 20 amino acids. These amino acids are connected into long polymers called polypeptides. Proteins are actually polypeptides folded into many different formations. The simplest formation is called the primary structure and consists of a unique sequence of amino acids in a long polypeptide chain (hundreds or thousands of amino acids long). The order of amino acids in a protein is controlled by our DNA. For example, sickle-cell anemia, an inherited blood disorder, is caused by a substitution of one amino acid for another in the primary structure of hemoglobin, the protein that carries oxygen through our blood. Secondary Structure refers to coiled or folded polypeptides. The main types of secondary structures are the alpha helix and the beta pleated sheet. Hydrogen bonds hold these structures together along the backbone of the polypeptide. Tertiary structures result when the side chains of amino acids in a polypeptide chain interact folding further into a specialized structure. Quaternary Structure involves the folding of two or more polypeptide chains into a functioning protein, such as hemoglobin which is composed of four subunits with a heme group containing iron at the center of each subunit. The study of folding of proteins is an on-going science and there are many factors that influence the shape and function of a protein including ph, temperature, and salt concentration. A change in the protein s environment may denature the protein changing its structure (example: heating the white of an egg).

2 Procedure: 1. Students should select 12 pipe cleaners and enough beads to cover them, leaving a slight space between each bead to represent the peptide bond between each amino acid. No more than twenty different beads should be used since there are only 20 amino acids. Students may align the beads in any pattern they wish. They now have 12 polypeptide chains. These models represent the primary structure of a protein.

3 2. For the secondary structure have students fold two of the primary chains in a zigzag pattern to represent pleated sheet structures. Attach these pleated sheets together by using short pipe cleaners to represent hydrogen bonds between amino acids on the parallel strands. 3. Repeat step #2 so that each student has four sets of pleated sheets. 4. With the remaining four polypeptide chains, make alpha helices by winding the chains around a pencil. 5. To make the tertiary structures, have students take one set of pleated sheets and one alpha helix and then fold them together. 6. To make the quaternary structure, have students link four of the tertiary structures together. Explain that if this were hemoglobin, there would be a heme group in the center of each subunit with iron in the middle that binds to oxygen, carrying oxygen through the blood. However, hemoglobin subunits are made up mostly of alpha helical secondary structures. References: Biology, Campbell and Reece, Pearson Education, Inc., 2002

4 Pipe Cleaner Proteins Student Work Sheet Essential question: How does the structure of proteins relate to their function in the cell? 1. After the class discussion on protein structure, take 12 pipe cleaners and place beads representing amino acids (no more than 20 different kinds) in any order you wish on the pipe cleaners, leaving a slight space between the beads to represent peptide bonds between amino acids. What protein structure does this represent? 2. Draw a diagram of your model here using the attached sheet of abbreviations to label your amino acids: 3. Now take two of your chains and bend them in a zigzag pattern. Use the short, black pipe cleaner pieces to link them together. This secondary protein structure is called a. 4. Draw a diagram of your model of step #3 here: 5. Repeat step #3 three more times. Now you should have four sets. 6. Take your remaining four polypeptide chains and wind them around a pencil to make the second type of secondary structure. It is called an.

5 7. Combine one set of structures from step #3 with one of the structures in step #6 and fold them together. Now you have what type of protein structure? 8. Draw a diagram of your structure in step #7: 9. Repeat step #7 three more times until you have four structures. Link these together with your short pieces of black pipe cleaners. You now have what type of protein structure?. 10. Draw a picture of this structure : 11. How is the structure in step #10 similar to hemoglobin? What changes would you make to make it more like hemoglobin? 12. What blood disorder may result from the substitution of only one amino acid in the primary structure of hemoglobin? 13. What are some physical and chemical changes that may affect the structure of a protein? 14. What happens when a protein is denatured? 15. How do you think the structure of a protein and its function are related?

6 List of Amino Acids and Abbreviations 1. Glycine (Gly) 2. Alanine (Ala) 3. Valine (Val) 4. Leucine (Leu) 5. Isoleucine(Ile) 6. Methionine (Met) 7. Phenylalanine (Phe) 8. Tryptophan (Trp) 9. Proline (Pro) 10. Serine (Ser) 11. Threonine (Thr) 12. Cysteine (Cys) 13. Tyrosine (Tyr) 14. Asparagine (Asn) 15. Glutamine (Gln) 16. Aspartic Acid (Asp) 17. Glutamic Acid (Glu) 18. Lysine (Lys) 19. Arginine (Arg) 20. Histidine (His)

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