Biochem 285 FA23 Class Activity #1

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Jan 9, 2024

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Biochem 285 FA23 E. Mearls Class Activity #1 Your Name: Keerti, Nusaiba, Devanshee, Arin Please select: I worked on this assignment independently – I worked on this assignment with (please list the names of your group members): Instructions: - You can work independently or with a group (indicate this below) - Your assignment must be turned into the Canvas “Class Activity #1” assignment by this coming Sunday at 11:59pm. - Each member of a group can turn in the same assignment, but every member of the group must submit separately to Canvas. - Answers are credited based on the depth of explanation. If you are unsure of an answer, you can still earn credit by explaining what you do know and why you are unsure of the answer. Part I: Bonds and Molecular Interactions (8 points): Three amino acid side chains are found close together in a protein (as shown): A. Identify the category that each one of these amino acids belongs in and explain why you chose that category. If you cannot determine the category for an amino acid, indicate this and then explain why you are unable to determine the category (3pts). 1. Basic: The amino acid’s side chain contains a protonated amino group with a plus one positive charge. At physiological pH of 7, amino groups tend to accept hydrogens from their environment, a behavior that gives them a basic character. Hydrogen acceptors are classified as bases according to Lowry Bronsted Theory.

2. Acidic: The amino acid’s side chain has a carboxyl group. At typical cellular pH, carboxyl groups tend to release their protons (H+) and assume a negative charge. This behavior gives the side chain an acidic character because acids are proton donors. 3. Cysteine can be both nonpolar and polar. Based on its environment, the characterization of polar and nonpolar changes. In a basic cellular environment, the amino acid’s sulfhydryl group will release a proton, leaving a thiolate anion in its place. The presence of an anion creates a permanent electron dense region that can participate in dipole- dipole and ionic bonds; thus giving the amino acid a polar character. At the typical cellular pH; however, cysteine’s sulfhydryl will remain protonated. Since the electronegativity difference between sulfur and hydrogen is less than 0.5 and the rest of the side chain contains nonpolar carbon-hydrogen bonds, at the typical cellular pH, cysteine has nonpolar character. B. Identify the strongest bond type that can occur between any of these amino acid side chains and indicate the atoms involved. Explain why it is the strongest (2pts). The strongest bond type that can occur in this peptide section is an ionic bond. This bond would form between the H+ of amino acid 1’s side chain, and the O- of amino acid 2’s side chain. Ionic bonds involve the interaction of two permanent, full charges. The permanence of the charge and the presence of a full charge makes ionic bonds significantly stronger in character than London dispersion forces, hydrogen bonds, and dipole-dipole interactions. Covalent bonds cannot form between the side chains of the amino acids present. C. If the pH were to drop very low (pH = 1), how would the amino acids in this image be affected? Which bond would be strongest under these conditions? (3pts) pH changes the protonation state of the acidic and basic categories. If the pH were to drop very low, the carboxyl in amino acid two’s side chain would become protonated to help reduce the concentration of H+ in the cell. Amino acid one would remain in its protonated form to prevent further increasing the concentration of hydrogen cations in the cell. The side chain in amino acid three would be unaffected, for it is thermodynamically unfavorable for a sulfhydryl group to release its proton in a H+ dense environment. Under these conditions, the strongest bond type that could occur between the R chains is a hydrogen bond between the carboxylic acid of amino acid 2 and the amino group of amino acid 1. Part II – Protein Structure (8pts) Below are two Ramachandran plots for the amino acids Glycine and Proline.

A. What does a Ramachandran plot tell you (2pts)? A Ramachandran plot tells us the arrangement of where amino acids can be in a protein and where each atom lines up. It is a plot of the phi and psi (torsion angles) of an amino acid and a simplified way to visualize its secondary conformation. B. If you look at the plots, glycine appears to be able to occupy a greater range of phi and psi angles compared to proline. Why do you think that is (2pts)? Glycine only has hydrogen in its side chain while proline has a covalently bonded ring structure. Glycine occupies a greater range of torsion angles because there is minimal steric hindrance in the side chain hence can have more possible phi and psi angles compared to proline which has a constrained side chain. C. Both plots have significant white space. What does that white space represent? The white space indicates psi and phi angle combinations that do not exist. If a combination of angles is not possible due to steric clashing, then there will be no black dots on a Ramachandran plot. D. Does the data above support the idea that proline can be part of an α-helix? Explain your answer (2pts).

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The data above shows that there is a possibility that proline exists as a part of an α-helix. In Proline’s Ramachandran plot, there is a significant lobe in the center of the plot just to the left of the y-axis. Rotation combinations at this specific location are typically associated with right handed alpha helices. Part III: Domains, subunits, and protein models (Adapted from an Exam question, 8pts): The protein below is made from 6 identical dimers. Use both images below to answer the following questions. A. Determine the total number of subunits in the protein. Explain how you determined this (2pts). There are 12 total subunits in the protein. According to the context of the question, the protein depicted above contains 6 identical dimers. A dimer is a protein composed of two polypeptide chain subunits. A subunit is defined as a polypeptide chain that can form a stable folded structure by itself, therefore, if you multiply the number of dimers by the number of polypeptides in each, you will get twelve subunits. B. Determine the total number of domains in each subunit. Explain how you determined this (2pts). There are three domains in each subunit. The upper most image contains a simplified representation of the primary structure of each subunit in the protein. In this simplified representation, there are three color coded sections which correspond to areas in the bottom most image with unique conformations. C. True or false: The bottom most image is a ribbon model. Explain your reasoning (2pts). This statement is false. The bottom most image does not use symbols such as coiled and flat ribbons to represent different secondary structures such as alpha helices and beta pleated sheets.

D. True or false: The bottom most image shows the quaternary structure of the protein. Explain your reasoning (2pts). This statement is true. Quaternary structure is the assemblage of one or more polypeptide chains into a functional protein. The bottom image illustrates a protein with more than one polypeptide subunit and highlights their relative positions to one another.

Biochem 285 FA23 Class Activity #1

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