Class Activity #2_FA23_student copy

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Jan 9, 2024

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Biochem 285 FA23 E. Mearls Class Activity #2 Total points = 24 Your Name: I worked on this assignment with: Part I – Protein folding (Former exam question) 8pts The model images below represent the interaction between two protein subunits. Use these images and your knowledge of protein folding to answer the questions below. A) Name the predominant secondary structure you see and name the model (A, B, or C) that helped you make this determination. Explain your choices (2pts). B) Assuming this protein is in an aqueous solution, describe the distribution of amino acid R groups in the final 3-D structure of this protein (in other words, where would you expect to non- polar, polar, or charged amino acids in this structure?) (2pts). C) Use your knowledge of the hydrophobic effect to explain why the amino acid R groups are arranged in this way. In your answer, be sure to explain how this leads to thermodynamic favorability and spontaneous protein folding (4pts). 1

Part II – 2D gels (Multiple Choice Exam question Fall 2022) Which, if any, of these statements correctly describes how proteins move in a 2D gel? For each statement, explain why you think it is correct or incorrect (8pts). A) Proteins will become more negatively charged as they move towards the (+) electrode (2pts) B) Proteins will separate based only on size during the first step and based only on charge in the second step (2pts) C) Proteins will always migrate toward the (-) electrode in the first step, and the (+) electrode in the second step (2pts) D) Most proteins will experience deprotonation of their acidic and/or basic amino acid side chains as they move towards the (+) electrode in the first step (2pts) 2

Part III – Analyzing Proteins (8pts) Native-PAGE and reducing SDS-PAGE techniques are often used to learn about protein structure. You have purified your favorite protein, Mex1, and want to use these techniques learn more about the structure of this protein. Answer the questions below about the technique and about the “preliminary data” for Mex1 shown below: Use the two gels below to answer the following questions: A) Does Mex1 have quaternary structure? Explain your reasoning and point to specific parts of the data to support your conclusion (2pts). B) Can you predict how many subunits the functional protein has based on the data? (2pts) C) Can you determine whether Mex1 has disulfide bonds? If so, how? If not, why not? (4pts) 3

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