Worksheet 7 proteins

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Dec 6, 2023

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Student Name and UID : _______________________________________________________________ Worksheet 7: Proteins 1. Explore the effect of charge and hydrophobicity on the shape of a polypeptide. Use this link http://lab.concord.org/embeddable.html#interactives/samples/5-amino-acids.json KEY: Positive charge : Purple , Negative Charge : Pink Hydrophilic : Green Hydrophobic : Brown a. Set the first pull down to show charge and hydrophobicity and the second pull down as water . Click generate random protein , and then select random mix (last option). Run the simulation (arrow in center of playbar). What do you notice? (ie What type of amino acid are on the outside?) When you run it again, what is the same and what is different? Arginine and glutamine are on the end of the amino chains when charge, water and random mix are selected. When I run it again Leucine and threonine are on the ends of the chain. Theres a lot of different things going on but there are mostly hydrophobic bonds and some hydrophilic and 2 positive charges b. Now change the second pull down to oil . What changes? It changes to mostly all no charge and 2 each negative charge from lysine and arginine c. Now change the second pull down to vacuum . What changes? What type of interactions remain? Glutamine becomes hydrophilic and arginine has a negative charge d. Now instead of ‘random mix’, click Mostly hydrophobic and toggle between oil and water. What do you notice? Almost all hydrophobic bonds now and negative charges from glutamine and one hydrophilic from threonine e. Lastly click All hydrophilic and toggle between oil and water. What do you notice? Lysine has a positive charge with arginine and glutamine has negative charge and a good majority of bonds are hydrophobic but hydrophilic still present 2. What are the monomers (one subunit) of a polypeptide called? __________amino________ ____________acids ___  On the left half of the space below, draw a simple structure of a protein monomer with uncharged functional groups and R to denote the side chain. Circle and label the function groups and alpha carbon.  On the right half of the space, draw a similar structure with the two functional groups in their ionized (charged) forms. (At cellular pH both functional groups will be ionized. When we discuss whether this monomer is acidic/basic or polar/nonpolar then we are just referring to the variable side chains.) 3. After _______________dehydration_________ synthesis, a _________water_________ bond connects the two amino acids. Many subunits in a polymer make up the primary structure of a polypeptide . In the space below, draw a peptide dimer (2 amino acid connected by a bond, you can just use R for side chain again). Label the two ends of the dimer with N-terminus (to indicate amino group of the first amino acid) and C-terminus (to indicate carboxyl group of the last amino acid). 1

4. The interactions on the backbone (not the side chains) contribute to the ( circle one ): primary/secondary/ tertiary/quaternary structure of the protein. On your drawing for #3 indicated the partial charges on the atoms near the new covalent bond. For alpha-helix, these atoms of opposite partial charges that are four amino acids away are interacting to form ________hydrogen_____ bonds. 5. The interactions between side chains contribute to the primary/secondary/tertiary/quaternary ( circle one or more ) structure(s) of the protein. Tertiary 6. What happens when you denature a protein with heat or pH changes? Which bonds are most likely broken? Secondary and tertiary structures are altered but the peptide bonds of the primary structure between the amino acids are left intact. Weak hydrogen bonds break 7. Use what you have learned this semester about electronegativity, polarity, and functional groups to analyze the amino acid side chains ( shown in green here ). Below the special amino acids briefly indicated what special qualities they have. KNOW that O-C, C-N, N-H and H-O bonds are polar and C-C, or C-H are nonpolar . Determine and label the types of amino acids that are in Box A and Box B and then further characterize and label groups 1), 2) and 3) in Box B. Use the terms Polar (hydrophilic) or Non-polar (hydrophobic), Basic, Acidic, or Polar but Nonionizable . A group is nonpolar and group B 1) polar 2) polar 3) polar 2

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