UMass Amherst BIOLOGY 285 - Problem Set 1 (5 pages)

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Problem Set 1



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Problem Set 1

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Pages:
5
School:
University of Massachusetts Amherst
Course:
Biology 285 - Cellular & Molecular Biology
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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 LysIle 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 hydrogenbonded network of water molecules Why might high concentrations of urea unfold proteins The structure of urea is shown here Question 6 A 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 response


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