SAM Teacher s Guide Four Levels of Protein Structure Overview Students explore how protein folding creates distinct, functional proteins by examining each of the four different levels of protein structure. Students interpret how the sequence and properties of amino acids relate to how proteins fold. They identify the characteristic patterns of folding known as secondary structure, final folding of the entire protein chain (tertiary structure), and the coming together of more than one chain to form a functional unit (quaternary structure). Finally, students learn about how tertiary and quaternary structure relate to protein function. Learning Objectives Students will be able to: Recognize that a protein s three-dimensional shape allows it to perform a specific task. Identify the primary structure of a protein as a linear sequence of amino acids. Identify the unique side chains of amino acids that give them their properties. Explore how amino acids interact with water and how that affects the way proteins fold. Differentiate among the common secondary structures of a protein and identify the importance of hydrogen bonding in stabilizing these structures. Identify tertiary structure as the final folding pattern of a protein and infer that mistakes in folding are responsible for many human diseases. Explain that quaternary structure occurs when a protein is composed of more than one protein chain (subunit), and that the subunits come together to achieve the protein s function. Possible Student Pre/Misconceptions Proteins are a straight chain of amino acids that result from translation as seen in previous activities and units. The three-dimensional structure of proteins is less important than the amino acid sequence. Proteins are uniform throughout rather than having different parts for various functions. Models to Highlight and Possible Discussion Questions Page 1 Form and Function Model: Parvalbumin Highlight that the protein is made up of one long amino acid chain that is folded into a specific shape. Emphasize that representing a protein s structure in different styles and colors can illustrate the different, important aspects of its structure. Students will likely need help and feedback on choosing the views for the snapshots of this model. Link to other SAM activities: DNA to Proteins. Remind students that the sequence of amino acids is encoded in the sequence of nucleotides in DNA.
Possible Discussion Question: How might a mutation in DNA affect the primary structure of a protein? Page 2 Twenty Amino Acids Model: Twenty Rotatable Amino Acids Highlight that the backbone of all 20 amino acids is the same. It is the side chains that give each amino acid a different personality. The backbone connects to the backbones of other amino acids to form the peptide chain that makes up the protein. Emphasize that each amino acid has a side chain (or R group) that is different and that these side chains determine the polarity of the amino acid. Link to other SAM activities: Intermolecular Attractions and Chemical Bonds. The interactions between amino acids in a protein are affected by unequal sharing of electrons. Possible Discussion Question: What is the difference between polar and non-polar amino acids? What is the difference between a polar amino acid and one that is charged? Page 3 Secondary Structure Model: Protein Kinase Point out the use of the menu to change the way the model is drawn, which is essential for identifying the secondary structures. Highlight that alpha helices and beta sheets are present in the folded protein and ask how they can be identified. Possible Discussion Question: Why do you think different folding patterns happen? Page 4 The Glue in Secondary Structures Model: Protein G Highlight that helices and sheets are stabilized by hydrogen bonds between the backbone atoms common to all amino acids not the side chain atoms. Highlight the use the checkboxes and radio buttons to arrive at images that display different aspects of the secondary structures. Possible Discussion Question: Why are beta sheets and alpha helices common in proteins? Page 5 Water Helps Shape Proteins Model: Protein Folding in Water or Oil Review polarity and link to the importance of how proteins behave (folding, solubility) in water. Emphasize hydrophobic/hydrophilic interactions and how one protein can have regions of both. This will impact folding. Link to other SAM activities: Chemical Bonding. Polarity and electronegativity will influence the type of chemical bonds formed.
Possible Discussion Question: How do amino acids interactions with water affect the shape of the protein? Give students a mystery protein and a key with the 20 amino acids. Have students devise a folding pattern that makes sense based on their knowledge thus far of both proteins and chemical bonding/electronegativity. Page 6 Tertiary Structure Model: Lysozyme Note that tertiary structure is the coming together of distinct secondary structures. Emphasize that the stabilizing interactions between (not within) alpha helices and beta sheets (salt bridges, disulfide bonds, and additional side chain interactions) results in the protein having a very specific shape. Possible Discussion Questions: Why is the folded structure of a protein so important for its functionality? Can students think of any examples? Page 7 Protein Function Model: Alcohol Dehydrogenase Highlight how the folds of the protein come together from different parts of the chain to create this site, which will bind only with NAD or a molecule extremely similar to NAD. Highlight that all proteins are very specific in their recognition of partner molecules. Model: Can Proteins Take the Heat? Proteins are destabilized by heat because of the increased molecular motion. Relate the change in the egg whites to the destabilization and unfolding of the secondary and tertiary structures of the protein. Possible Discussion Questions: What are some specific jobs of proteins that require them to have a distinct 3D structure? (Possible answers: enzymes, roles in signal transduction, DNA synthesis, etc.) What types of situations may impact how a protein would function? Generate ideas about temperature, whether it is surrounded by water or oil, etc. Denaturation of proteins happens when proteins are heated, but it also happens when proteins are in acidic or basic environments. How do all of these things cause the same end result? What does denaturation look like at the molecular level?
Page 8 Quaternary Structure Model: Homodimer (Alcohol Dehydrogenase) and Heterotrimer (G Protein) Some proteins achieve their function by acting as a complex of multiple subunits (quaternary structure). Highlight that the unique surface of each protein enables it to perform its specific function. Possible Discussion Questions: How do proteins differ? Highlight the differences at primary, secondary, tertiary, quaternary structure. Why is the folded structure of a protein so important for its functionality? Demonstration/Laboratory Ideas: Construct chains or amino acids and physically show folding patterns using beads, children s toys, etc. Use Toobers (inexpensive flexible foam rods) for showing folding and how distant parts of a protein come together to form a binding site or other specialty area. For more information and clear ideas on how to use them, see http://www.umass.edu/molvis/toobers. Use molecular model kits to focus in on bonding within a protein. Use oil and water demonstration to review hydrophobic/ hydrophilic interactions. Link back to the importance of water in living systems (cell membrane review). Use an overhead projector and Petri dish to demonstrate that acid can cause denaturation of egg white proteins. Relate this demonstration to what happens in digestion in the stomach.
Connections to Other SAM Activities The focus of this activity is for students to understand the primary, secondary, tertiary and quaternary structures of proteins. This activity is supported by many activities that deal with the attractions between atoms and molecules. First, Electrostatics focuses on the attraction of positive and negative charges. This will play a role in understanding salt bridges, hydrogen bonding and intermolecular attractions. The Intermolecular Attractions activity highlights hydrogen bonding, which plays a role in stabilizing the alpha helices and beta sheets within proteins. In addition, this activity discusses the forces of attraction that are at work on the intramolecular level of proteins as well as the intermolecular level (in the quaternary structure of proteins). Chemical Bonds allows students to make connections between the polar and non-polar nature of bonds and how one part of a molecule could be partially positive or negative due to the uneven sharing of electrons. The Solubility activity highlights the tendencies of globular proteins that have hydrophobic and/or hydrophilic regions and how they will behave, particularly in water. Molecular Geometry explains the specific orientation of atoms within larger molecules. Finally, Proteins and Nucleic Acids introduces the structure and function of amino acids and protein molecules while DNA to Proteins explains where proteins originate. This activity supports three other SAM activities. First, Molecular Recognition builds on student understanding of why structure is so important in protein function. This activity also supports Diffusion, Osmosis, and Active Transport and Cellular Respiration because there are references in both of these activities to larger scale protein complexes.
Activity Answer Guide *Sample snapshots: Other snapshots may answer the questions. Page 1: 1. Use the Do It Yourself controls above to create a view that shows how the protein is folded. Use the text tool end of the folded chain. to label each Page 2: 1. Label the ball and stick amino acid models as indicated in the What to do section. 2. Use the link above to open and explore the 20 rotatable 3D amino acids. Then select the Sidechain color scheme. The atoms that are colored gray are the same in every amino acid. What are they called? 2. Create a view that you think best shows the primary structure of parvalbumin. Use the text tool to explain why you chose this way of representing primary structure. (b) 3. On the page of 3D amino acids, find glutamine and histidine. Use the different color schemes to select the true statement(s) below. (More than one statement may be true.) (a)(c)
Page 3: 1. Take a snapshot of an alpha helix that shows how it folds. Page 4: 1. Hydrogen bonds stabilizing an alpha helix. Use the arrow tool to point out the hydrogen bonds. There are many alpha helices in the protein. They are easy to recognize using the cartoon or string of beads representations. 2. Hydrogen bonds stabilizing a beta sheet. Use the arrow tool to point out the hydrogen bonds. 2. Take a snapshot of a beta sheet that shows how much space it occupies within the protein. Hint. 3. Hydrogen bonds stabilizing alpha helices and beta sheets form between the atoms of which part(s) of the amino acids involved? (c) There are two beta sheets in the protein, the one above (encompassing approximately amino acids 29-59) and from about 92-105. Students can find the beta sheets using the cartoon representation, then change to spacefill to show the amount of space occupied by the sheet. This exemplifies the advantages of two different representations.
4. Place a snapshot here that illustrates your answer to the previous question. to other polar molecules. The opposite charges on the polar molecules attract each other. There is less attraction between non-polar molecules and water because there is no opposing charge on the non-polar molecules to attract the water. 5. Which solvent(s) leads to folding of the protein? (c) 6. Where do the amino acids with polar side chains end up when the protein chain folds? (c) This image shows a backbone trace of the protein with the hydrogen bonds (purple dotted lines) stabilizing the alpha helix and beta sheet. The side chains are omitted for clarity of view. Page 5: Page 6: 1. Show an interaction that stabilizes two alpha helices to each other. Use the annotation tool to label the type of interaction you are showing. 1. Is water a polar or non-polar molecule? Explain your answer by writing about the bonds in water. The bonds in water are polar covalent bonds. The oxygen pulls the electrons more strongly than the hydrogens do, so the oxygen is slightly negative while the hydrogens are slightly positive. Because the electrons are not evenly shared across the molecule, the molecule is polar. 2. Which type of amino acid is hydrophobic? (b) 3. Which of the following correctly describe the interactions of the amino acids with water? (Check ALL that apply.) (b)(c) 4. Use your knowledge of positive and negative charge to explain why polar molecules attract each other better than nonpolar molecules. Because polar molecules have charge differences on their surfaces, they are attracted
2. Create a view that shows both the amino acids at the surface and those that fold into the inside of the protein. Use the annotation tools to label the part that is more attracted to water. Page 8: 1. Does TNF have the quaternary level of structure? Make sure to try different color schemes on the model of TNF above. (a) 2. Explain your answer to the previous question: TNF is made up of three protein chains. This can be seen using the color by subunits selection next to the image of TNF. Page 9: 1. The "primary structure" of a protein refers to: (c) 2. What part of an amino acid has properties (shape, charge) that are different from other amino acids? Page 7: 1. On the left is a different small molecule than NAD. Why wouldn t this molecule bind to alcohol dehydrogenase in place of NAD? (Choose the BEST answer below.) (d) 2. What would you expect to happen to the function of proteins at very high temperatures? (b) 3. Explain your answer to the previous question. If the protein unfolds, it will lose its shape and will be unable to perform its function(s). Proteins are folded into specific shapes that allow them to do their jobs. (a) 3. The protein shown at right has folded in water. Which of the following statements about it is FALSE? (c) 4. Which of the following do hydrogen bonds help to stabilize? (Check ALL that apply.) (b)(c)(d) 5. Select the two correct choices: A protein with quaternary structure (a)(d) 6. Why do defects in protein folding cause disease? Protein folding patterns play a major role in the protein's functionality. If there are defects in the folding the protein may not be able to do its job, such as bonding to the correct substrate.
SAM HOMEWORK QUESTIONS Four Levels of Protein Structure Directions: After completing the unit, answer the following questions to review. 1. Below is a picture of a folded protein. A protein is a chain of amino acids. Use an arrow to label the amino acid units shown in this picture. 2. Which part of an amino acid gives it its unique personality? 3. Identify and describe the secondary structure indicated by the arrow in the picture to the left. Be specific. What keeps this secondary structure in this particular shape? 4. The way a protein is folded determines its functionality. How might the exposure of a protein to higher than normal temperatures affect its function? 5. A particular protein has both hydrophobic (water-fearing) and hydrophilic (waterloving) regions. If this protein folded spontaneously in water, which regions would be on the inside and which on the outside? Why?
SAM HOMEWORK QUESTIONS Four Levels of Protein Structure With Suggested Answers for Teachers Directions: After completing the unit, answer the following questions to review. 1. Below is a picture of a folded protein. A protein is a chain of amino acids. Use an arrow to label the amino acid units shown in this picture. Sample arrow shown. Each arrow should point to one of the beads, which represent the amino acids in the protein. 2. Which part of an amino acid gives it its unique personality? All amino acids have a part that is unique, called the side chain or R group. 3. Identify and describe the secondary structure indicated by the arrow in the picture to the left. Be specific. What keeps this secondary structure in this particular shape? Picture shows an alpha helix (pink) connected by a loop (white) to a beta sheet (yellow). (Students may not have color version but should be able to identify the alpha helix by the shape.) The arrow points to the alpha helix. An alpha helix is shaped like a long spiral. It is held in this shape by hydrogen bonds that form between the atoms of peptide backbone. 4. The way a protein is folded determines its functionality. How might the exposure of a protein to higher than normal temperatures affect its function? Higher temperatures can cause proteins to denature or unfold. This can alter the shape, and thus, the functionality of a protein. 5. A particular protein has both hydrophobic (water-fearing) and hydrophilic (waterloving) regions. If this protein folded spontaneously in water, which regions would be on the inside and which on the outside? Why? Surrounding water molecules attract polar amino acids to the outside of the protein because they are hydrophilic. Non-polar amino acids are hydrophobic less attracted to the polar water molecule and they tend to move into the interior of the folded protein, forming its core.