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Bio/CS 251 Bioinformatics Homework 2 KEY 1/26/07 25 points Due Date: Wednesday, 1/31/06 at 5 pm to Dr. James, 255 SC 1. Organic molecules that contain hydroxyl groups (-OH) are called alcohols. Would you expect such molecules to be hydrophobic or hydrophilic? Why? Hydrophilic. The Oxygen atom attracts electrons much more forcefully than does a Hydrogen atom. In this way, oxygen is a strongly electronegative atom. As a result the O-H bond is said to be polarized, such that one of the atoms has a partial negative charge, and the other a partial positive charge. Molecules, such at water, that have an asymmetric distribution of charge are said to be polar. Polar molecules of biological importance contain one or more electronegative atoms, usually O, N, S, and/or P. 2. Write the “one-letter” amino acid sequence that corresponds to the peptide shown below (write the appropriate one-letter symbol below each 3-letter symbol): His – Ala – Val – Glu – Ala – Asn – Ile – Cys – Glu – Asp – Ala – Tyr H A V E A N I C E D A Y ! 3. Examine the chemical structures of the amino acid R groups shown in Figure 2.6, Higgs and Attwood. What atom(s) is/are found in the R groups that are in the hydrophilic amino acids that generally is/are absent in the nonpolar group of amino acids? (List all polar chemical groups found in hydrophilic amino acids) 4. -C=O - SH - NH3+ - C = NH2+ - NH2 -C=O | O- - OH -C=O | NH2 The following amino acids are internal residues in a polypeptide chain and are located such that they can interact with each other as indicated. Which amino acid pairs in (a) could produce ionic interactions? Which amino acid pairs in (b) could form H-bonds? Which amino acid pairs in (c) could produce hydrophobic interactions? For each of your answer choices in (a), (b), and (c), draw the interactions that would occur between the appropriate atoms. (a) (b) (c) 1) Leu…..His Cys…..Cys Arg…..Thr 2) Asn….Gln Ala…..Pro Ile…..Ile 3) Arg….Asp Tyr….Glu Val….Leu 4) Cys….Met Gly…Ala Pro….Phe An –helical segment consists of 180 amino acid residues. How many turns are there in this segment, and how long is it? 5. At 3.6 aa per turn, 180/3.6 = 50 turns x 0.54 nm per turn = 27 nm long = (pitch) 2.7 x 10-8 meters (1 nanometer = 1 x 10-9 meters) 6. Examine the following two peptide sequences, each of which is part of a larger protein, and answer the questions that follow. A - Val – Gly – Ile – Met – Ile – Leu – Leu – Phe – Ala – Gly – Val – Met – Ile – Cys – Val – Ile – Leu – Trp B – Glu – Ala – Tyr – Leu – Thr – Phe – Gln – Val – Asp – Met – Asn – Ile – Ser - a) Which peptide is likely to be found in the interior of a protein? Why? Peptide A is likely to be found in a protein’s interior, shielded from water molecules, because this peptide is uniformly hydrophobic. This hydrophobic peptide could also be found in a lipid bilayer, e.g., the cell membrane. b) Which peptide could form an amphipathic -sheet? Why? Where in the protein would this peptide most likely be found. Why? Peptide B could form an amphipathic -sheet, because the peptide alternates hydrophilic with hydrophobic aa’s every other residue. This could easily form one strand of a -sheet in which all of the hydrophilic residues would be on one face of the sheet, with all of the hydrophobic residues on the other face. An amphipathic -sheet would most likely be found on the surface of a protein, with the hydrophilic residues facing outward into the aqueous environment, and the hydrophobic residues facing inward away from water. c) Draw the -sheet structure formed by this peptide, showing the peptide backbone, with correct orientation of peptide bonds, and showing each of the R-groups Glu Tyr Ala Thr Leu Gln Phe Asp Val Asn Met Ser Ile …compact image courtesy of Chris Husko, ’06 (thanks, Chris!) d) Which peptide is most likely to span a membrane? Why? Is this membrane-spanning peptide most likely to form an -helix or -sheet? Explain. Peptide A is hydrophobic and therefore would be more stable within the hydrophobic interior of a lipid bilayer than Peptide B. Although it could form a -sheet, it is very common for hydrophobic membrane-spanning domains to fold into an -helix.