Module Assignment Summer 2022 Introduction to Biochemistry and Molecular Biology BCMB 3100E 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 s Take Home Message 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 Learning Objectives 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 Part 1 Protein structure 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 Authored by Sarah Robinson Some questions adapted from cases by Paula Lemons b 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 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 In pure water how ordered disordered are the water molecules 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 Compare the movements and ordering of water in the first video pure water to this one What is close enough 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 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 the inside of the helix and the side chains green projecting outward D A space filling view of part C Here is a helpful article that discusses different ways to visualize protein structure https employees csbsju edu cschaller Principles 20Chem molecules 1 10 bio macromolecs htm a Why does there appear to be a hole in the ribbon model