Bio285 F19 Problem Set 1 Francis Peptide Bonds Question 1 Draw two amino acids sitting side by side unbonded, then draw them with a peptide bond connecting them. What type of reaction is this? What is a product of the reaction? Amino Acid Chemistry Question 2 A. Consider the structure of Tyrosine. Draw it. Is it considered a polar or non-polar amino acid? Why is its classification a bit ambiguous (it is sometimes classified as non-polar)? (hint: discuss the chemistry of the R group) B. Draw another amino acid. Label its functional groups. Say something about the chemistry of its R group (categorization, types of interactions it would make in different levels of structure, etc).Bio285 F19 Problem Set 1 Francis Secondary Structure Question 3 A. Remembering that the amino acid chains projecting from each polypeptide backbone in a beta sheet point alternately above and below the plan of the sheet, consider the following protein sequence: Leu-Lys-Val-Asp-Ile-Ser-Leu-Arg-Leu-Lys-Ile-Arg-Phe-Glu. Do you find anything remarkable about the arrangement of the amino acids in this sequence when incorporated into a beta sheet? Can you make any predictions as to how this Beta sheet might be arranged in a protein? B. Although alpha helices are common components of polypeptide chains, they need to be of a certain minimum length. To find out how chain length affects alpha helix formation, you measure the circular dichroism (a measure of helicity) for a series of peptides of increasing lengths. Why is there essentially no helix formation until the chain is at least six amino acids long? Protein Folding Question 4 A. What are the two termini of a polypeptide chain? What functional groups are on either end? B. What are the four weak (noncovalent) interactions that determine the conformation of a protein?Bio285 F19 Problem Set 1 Francis C. Name and briefly define the four levels of protein structure, and name the kinds of bonds that are important for holding that level of structure together. Question 5 A. Himalayan rabbits have a mutation in their gene for tyrosinase (the enzyme that makes melanin which is responsible for their black hair). In the experiment shown above, the rabbit’s back was shaved and it wore a cold pack as the hair re-grew. Hint: Think about the effect of heat (thermal energy) on protein folding and if you had a mutation in a protein that caused it to be less stably folded… i. What might explain these results? ii. Can you provide an explanation for why there are certain body parts of the rabbit that are black (without the use of the cold pack)?Bio285 F19 Problem Set 1 Francis B. Urea is used to denature proteins (and interestingly, in some proteins, if you dilute out the urea, the proteins can fold back together by themselves – suggesting they don’t need chaperones to fold). It is a molecule that disrupts the hydrogen-bonded network of water molecules. Why might high concentrations of urea unfold proteins? The structure of urea is shown here. Question 6 A. α-1-Antitrypsin Deficiency disease is caused by a single codon change, resulting in a substitution of a lysine for a glutamic acid. Consider the chemistry of these two different amino acid residues. Why would such a change be particularly detrimental to the proper folding of the polypeptide given the knowledge that the arginine was forming an ionic bond (electrostatic interaction) with the glutamic acid?Bio285 F19 Problem Set 1 Francis B. You are studying how your protein of interest, which we’ll call “BIO285”, interacts with its binding partner protein, which we’ll call “Studyin”. You hypothesize that BIO285 is making an important ionic bond with Studyin, so you decide to test you’re your hypothesis by changing one of the amino acids on the binding surface of BIO285 from a polar charged amino acid to a hydrophobic amino acid to see if this disrupts the interaction. However, when you try to purify the mutant BIO285 (to test binding interactions in vitro), your mutant BIO285 precipitates in solution (clumps up). You do a few experiments that suggest the overall structure of the protein is still intact (this is important – this means that the protein is not unfolding or mis-folding). Provide a molecular explanation for this behavior. Unfolded/misfolding proteins Question 7 A. What characteristic of the prion form of PrP makes it transmissible? B. Does PrP misfolding directly affect how proteins other than PrP fold? C. In the case of the unfolded protein response, name three ways in which cells respond to an unfolded protein emergency and why these processes are needed in the unfolded protein