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UGA BCMB 3100 - End of Module 1 Assignment: Insulin

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Authored by Sarah Robinson Some questions adapted from cases by Paula Lemons End of Module 1 Assignment: Insulin Honor Statement: This assignment adheres to the standards of UGA’s Culture of Honesty policy. The answers to these questions are my own words and all external sources have been cited. (You do not need to use proper citation formatting, just copy and paste the link.) Life works because of proteins; when proteins don’t work, disease typically occurs. Protein function is dictated by protein structure. Protein structure can be explained through basic chemistry that you learned in gen chem, e.g., hydrogen bonding. Biological structures like proteins arise because of the electrostatic properties of molecules. Biological structures also form because life takes place in water. In other words, the chemical structure of living things is due to both enthalpic and entropic forces. 1) Learn about insulin’s structure and function. 2) State whether an alpha helix has an internal pore and where the side chains are located in an alpha helix. 3) Describe in detail the secondary, tertiary, and quaternary structure of Insulin. 4) Visualize proteins with different models. Explore the crystal structure of Insulin. 5) Describe how non-covalent interactions give rise to tertiary and quaternary structure. 6) Determine the non-covalent interactions that can occur between amino acid side chains 7) Explain the hydrophobic effect including the role of water, entropy, and van der Waals interactions. 8) Identify the different types of non-covalent interactions in a given biological molecule. 9) Explain why the energies of formation are different for different non-covalent interactions. 10) Explain the contributions of enthalpy and entropy to protein folding. 11) Explain the role of enthalpy and entropy in determining the spontaneity of a reaction. Please type your answers so that they are visibly different from the question text. 1. Read the following article about insulin: http://pdb101.rcsb.org/motm/14. Answer the following questions related to the reading. a. Briefly, what is the function of Insulin? Insulin is a hormone that helps regulate glucose levels in the blood. Insulin is released from the pancreas in response to high blood glucose levels after eating food or drinking a beverage. It spreads throughout the body and binds to insulin receptors on the surface of muscle, fat, and liver cells. It informs these organs to uptake the excess glucose from the blood and stores it in the form of glycogen or fat. b. The majority of the amino acids located in the center of the protein are ____, while the majority of the amino acids located on the surface of insulin are______. Highlight your answer a. Polar ; nonpolar Introduction to Biochemistry and Molecular Biology Module Assignment BCMB 3100E Summer 2022 s Take-Home Message Learning Objectives Part 1 – Protein structureb. Nonpolar ; polar c. How and why do the types of amino acid you answered for question 1b end up in the interior of the protein? To answer that question, we need to incorporate the hydrophobic effect, water, entropy, and van der Waals interactions. Start by viewing this video of pure water: https://www.youtube.com/watch?v=t5ZFoU0S5iE&feature=youtu.be As you watch it, consider these questions: • what type of non-covalent interaction occurs between water molecules? • does a water molecule stay bound to its neighboring water molecules? • how often are bonds broken and formed? • In pure water, how ordered/disordered are the water molecules? Watch this next video of a benzene in water: https://www.youtube.com/watch?v=vgbAY0Go_8A This would the same thing as the side chain of phenylalanine in water. You may need to play it several times. As you watch it, consider these questions: • What type of non-covalent interaction occurs between two benzenes? Is that the same type of interaction that occurs between two water molecules? • How close are the water molecules to the benzene? • What interaction, if any, is occurring between the benzene ring and the water molecules? are they close enough? • Compare the movements and ordering of water in the first video (pure water) to this one. What is different? Why? Here is a static image from the video: Use your own words to explain how the types of amino acids you answered for 1b end up in the interior of the protein. Be sure to discuss the hydrophobic effect, water, entropy and van der Waals interactions. Incorporate what you learned from the videos above and also refer back to the AK lecture videos or textbook section 2.4. Nonpolar amino acids have no polarity and do not interact with water. In contrast, water is highly polar and forms hydrogen bonds, and interacts with polar amino acids. When non-polar amino acids encounter an aqueous environment, water molecules tend to surround the non-polar substance. This is not favorable because it limits the water molecule’s ability to interact with other water molecules. In essence, the entropy of the system decreases. As a result, the non-polar amino acids will aggregate together in the interior of the protein furthest away from the aqueous environment. The non-polar amino acids are held together by van der Waals interactions. This process, known as the hydrophobic effect, is favorable because it releases trapped water molecules and allows them to once again form hydrogen bonds with other water molecules and in turn increase the entropy of the system.d. What types of secondary structure does Insulin have? To determine this, go to this link https://www.rcsb.org/structure/1TRZ and explore the “3D view” and “Sequence tabs” The secondary structures of insulin includes alpha-helices, beta-sheet, and beta-turn (also called reverse turn). e. Looking back at the article about insulin, http://pdb101.rcsb.org/motm/14, How many subunits does Insulin have? How are they held together? Insulin has two subunits (-subunit and -subunit) held together by three disulfide bonds. 2. Let’s explore protein structure in more detail, before we learn more about protein folding. Figure 4.11 The structure of the alpha helix. (A) A ribbon depiction shows the α-carbon atoms and side chains (green). (B) A side view of a ball-and-stick version depicts the hydrogen bonds (dashed lines) between NH and CO groups. (C) An end view shows the coiled backbone as


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