Worksheet 9 Protein Structure Learning Objective. This activity will help you dissect the multi-level structure of proteins. (10 points) Instructions. Answer the questions below. When you’re finished, upload your assignment into Blackboard as a .docx or .pdf (no .pages because I can’t view those). Drawings can be done in many different ways such as using the features in Word, using the Paint app on your computer and drawing with your mouse or touchpad, taking a picture of a hand-drawing and pasting that into the box below, or using a stylus/touch screen to draw in the structures. Pasted images taken from online will not be accepted. Part 1. Monomer: Amino Acid 1. Draw one generic amino acid molecule. Make the amino acid generic by having “R” as the side chain. 2. On your amino acid above, indicate the parts present in all amino acids by: ● ● ● Denoting the alpha carbon by placing an “α” as a subscript to that carbon Drawing a triangle around the amino group Drawing a circle around the carboxyl group 3. What type of bond is present between the atoms of your amino acid (in question 1)? Carbon bond 4. How many different amino acids can be incorporated during translation? 20 amino acids 5. What makes amino acids different from one another? The structure of the side chains are different. 6. List the categories of amino acids. 7. Identify one example (e.g., histidine) for each category of amino acids. (match a with a, etc.) a. non polar and neutral a. glycine b. polar and neutral b. asparagine c. acidic and polar c. glutamic d. basic and polar d. lysine Part 2. Primary Structure 8. Draw a string of three generic amino acids (include all of the atoms) with the amino end on the left and the carboxyl end on the right. This represents the backbone of the protein. 9. On your drawing above (for question 8), place boxes around each amino acid. 10. On your drawing above (for question 8), circle the bonds that connect each amino acid. 11.What type of bond connects each amino acid? Polar bonds 12. What is the name of the bond that connects each amino acid? Hydrogen bond Part 3. Secondary Structure 13. List the two major categories of secondary structure. 14. Draw a simple representation of each of the two major categories of secondary structure. a. B sheet a. b. a helix b. 15. Choose one kind of secondary structure. Draw a detailed representation of that secondary structure. Be sure to: ● ● Identify the individual atoms (e.g., Carbons, Hydrogens, Oxygens, Nitrogens) Orient/align the backbone atoms of non-adjacent atoms to allow for hydrogen interactions (see question 16-19 for further guidance). 16. Hydrogen interactions facilitate secondary structure. Define hydrogen interactions. Interaction involving a hydrogen atom located between a pair of other atoms having a high affinity for electrons. 17. What atoms do hydrogen interactions occur between? Nitrogen atoms. 18. Draw in at least three sets of hydrogen interactions to your drawing above (in question 15) with dotted lines (- - - -). 19. What part of the secondary structure do these hydrogen interactions (in question 15) occur between? (Select one) a. Backbone atoms b. Side chains/R groups Part 4. Tertiary Structure 20. How many polypeptide chains are present in the tertiary structure of a protein? 1 21. Tertiary structure is the irregular loops and folds of a polypeptide chain. Draw a representation of tertiary structure. 22. The irregular loops and folds of tertiary structure form because of interactions between which portions of the polypeptide chain? (Select one) a. Backbone atoms b. Side chains/R groups In the Table below, 23. List the different types of interactions that can occur at the level of tertiary protein structure. 24. Provide a description for each of these interactions as they apply to proteins. a. 23. Interaction name Hydrophobic interactions 24. Description Occur when two nonpolar side chains interact. b. Hydrogen interactions They form between polar groups. c. Salt bridges Made due to the attraction of positively charged side chains to negatively charged side chains. d. Sulfur-sulfur covalent bonds Only form between two cysteine amino acid residues. Part 5. Quaternary Structure Quaternary structure represents the three-dimensional (3D) structure of one functional protein. 25. The 3D quaternary structure is facilitated by interactions between which portions of the polypeptide chain? (Select one) a. Backbone atoms b. Side chains/R groups 26. List the different types of interactions that can occur at the level of quaternary protein structure. a. Hydrogen bonding b. van der Waals interactions c. Dipole interactions d. Ionic bonding 27. How many polypeptide chains are present in the quaternary structure of a protein? 2 28. When proteins have multiple polypeptide chains, what are the individual polypeptide chains called? Subunit 29. Find an example of a functional protein that is composed of multiple polypeptide chains (other than the example given in class). Provide the name of the protein below. Insulin 30. Draw a representation of the protein named above (in question 29). Be sure to decipher the different subunits.