Understanding Protein Structure: Peptide Bonds, Secondary Structures, and Hydrogen Bonding, Lecture notes of English

Download Understanding Protein Structure: Peptide Bonds, Secondary Structures, and Hydrogen Bonding and more Lecture notes English in PDF only on Docsity! Scott Seiple AP Biology Lesson Plan Lesson: Primary and Secondary Structure of Proteins Purpose: 1. To understand how amino acids can react to form peptides through peptide bonds. 2. Students will be able to understand how amino acids can form secondary structures through hydrogen bonds. Objective: Students will be able identify peptide bonds in proteins and describe the overall reaction between amino acids that create peptide bonds. Students will be able to describe how hydrogen bonding can form the secondary structure of proteins. Students will be able to describe alpha-helices and beta-sheets structure and formation. Materials: 1. 3 models of α-helix 2. Protein structure guided inquiry exercise Procedure: 1. Attendance and administrative stuff. Break students into lab groups. (5 min) 2. Review basic functions of proteins and the structure of amino acids. 3. Distribute POGIL to students. Ask students to complete the first page of the exercise. (10 min) a. Monitor progress/provide guidance during completion of exercise. 4. Review answers to Primary Structure POGIL. (5 min) 5. Students should work on the Secondary Structure second of the POGIL. (20 min) a. Three groups will start on the alpha-helix section of the exercise while three groups will start on the beta-pleated-sheet section of the exercise. b. After 10 minutes, groups will switch. c. Group progress is monitored throughout the completion of the exercise. 6. Wrap-up. Go over the answer to the last question of the POGIL. Collect group sheets. Inform students that full answers will be discussed during class the next period. Assign HW. Read p. 71-80 in Campbell and Reece. Answer 6, 11, 13 on p. 86 in Campbell and Reece (2 min) Assessment: Immediate: Group answers to POGIL exercise Next day: Answers to HW problems Later: Unit test In proteins, an extended chain of amino acids can fold back and come close enough to one another to form hydrogen bonds. When this happens repeatedly a sheet of amino acids joined by peptide bonds is formed. This is called a β-sheet or a β-pleated sheet. It’s called a pleated sheet because proteins are, just like all structures, three-dimensional, and the three dimensional arrangement of the a β-sheet has a pleated arrangement to it. A 3-D image of a pleated sheet can be seen below. http://student.ccbcmd.edu/~gkaiser/biotutorials/proteins/images/betasheet.jpg A parallel pleated sheet has amino acids in an arrangement so that the nitrogen terminus of both amino acids is on the same end of the sheet while an antiparallel pleated sheet is arranged in a method so that the nitrogen terminus of the amino acid are on the opposite side the sheet. Which of the two arrangements (parallel or antiparallel) from the previous exercise will form the stronger sheet? Explain. Now, look at one of the three peptide models set up around the room (they are all the same). Using grammatically correct sentences, describe the structures that you see. This is another secondary structure found in proteins called an α-helix. Look carefully at the alpha-helix. Are there any forces that can be found that might cause the helix to maintain this specific structure? What are they? Again, using grammatically correct English, describe the origins of the forces that make would cause peptide chain to form. Be specific. For example describe exactly which atoms are participating in α-Helices almost always rotate in a clockwise or right-handed direction. Explain why it is virtually impossible to have an alpha helix that rotates in counterclockwise or left-handed direction. α-helices and β-pleated sheets are examples of secondary protein structures. Secondary protein structures are units that make up common structural motifs found within proteins, but they are not the overall structure of the protein. For example, β-sheets are often found in proteins, but the entire structure of the protein is not a simple β-sheet. Secondary structures of proteins are often determined by one particular type of bonding. What type of bonding is this? Introduction to Protein Structure Proteins are composed of extended chains of chemically bonded amino acids. All proteins are said to have at least three levels of organization: primary, secondary, tertiary. Some proteins have an even higher level of organization called the quarternary structure. In this exercise, you will investigate the primary and secondary structure of proteins. Primary Protein Structure and the Peptide Bond Look at the two amino acids below. These two amino acids will react with one another in such a way as to produce chemical bond between the two amino acids and water. This kind of reaction is called a dehydration or condensation reaction. N C C R 1 O O H H H H N C C O O H H H H R 2 1. Circle an area between the two molecules that can easily give off a water molecule. The –OH bond from the amino acid on the left and an H bonded to nitrogen should be circled. 2. In the space below show the dipeptide that results when the two amino acids react with one another. Circle the peptide bond (the new bond that you formed). N C C R 1 O H H H N C C O H H R 2 O H 3. Now show the tripeptide that will form when a third amino acid reacts with your new dipeptide. Circle the peptide bonds. N C C R 1 O H H H N C C O H H R 2 N C C R 3 O O H H H The covalent sequential arrangement of amino acids joined by peptide bonds in a protein is called the primary structure of the protein. For example, if a protein has the following amino acid sequence, Ala-Tyr-Thr-Glu-Phe-Glu-Met-Leu-Ile, that sequence makes up the primary structure of that protein. 4. How are peptide bonds related to the primary structure of proteins? The particular order of amino acids joined by peptide bonds determines the structure of the proteins 5. The end of a protein containing an amino acid with a free -NH2 or –NH3 + is called the N- terminus of the protein while the end of an amino acid with a free –COOH or –COO- group is called the C-terminus. By convention, proteins are always said to start with the C-terminus N-terminus