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Zachary Feldman 12 September 2013 BSCI 111a Problem Set- Amino Acids and Protein Structure 3. Alanine forms L and D isomers because all four of its alpha carbons bonds are different. Glycine, however, does not have a chiral alpha carbon. Since there are two identical hydrogen atoms bonded to its alpha carbon, mirror images of the molecule are exactly the same. 5. Hydrogen bonds between oxygens in backbone carbonyl groups and amino hydrogens in the next rung of the helix stabilize the structure. The collective effect of hydrogen bonds between every rung of the helix makes the structure quite stable. R groups project outwards from the helix backbone, so the exposed surface of the protein consists almost entirely of amino acid side chains. 9. Hydrogen bonds form in the plane of the sheet between the carbonyl oxygens and amino hydrogens of adjacent strands. The R groups are oriented perpendicularly to the sheet, and they alternate pointing to one side or the other. The vertical orientation of the R groups causes the alpha carbons other bonds to form the base of a tetrahedron, and the alternation of R group position produces a pleated three-dimensional structure. 1. Hydrophilic groups orient themselves on the outside surface of the protein, and hydrophobic groups orient themselves towards its interior. 2. A trio of aspartate, histidine, and serine residues in the active site is responsible for the enzymes function. Aspartate attracts positively charged residues on substrate proteins, and contributes to the enzymes specificity. Electrostatic interactions between serine and histidine in

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the active site cause the oxygen in serines R group to become highly nucleophilic, enabling the enzyme to cleave peptide bonds. 5. Trypsin has three alpha helices. 6. Trypsin has two beta sheets. 7. The sheets are mostly connected by direct turns, but there are a small number of intervening sequences. 1. Hemoglobin is composed of two pairs of identical polypeptide chains for a total of four. 2. In sickle cell anemia, a single hydrophilic glutamic acid residue is replaced with a valine residue in the betaglobin subunit. While mutated hemoglobin behaves normally under oxygenated conditions, its hydrophobic valine residue causes problems when oxygen levels decrease. In low oxygen, another hydrophobic area of the protein is exposed, and the valine from one betaglobin is able to approach and form hydrophobic interactions with this section in a different molecule. As a result, the molecules form long chains held together by the entropydriven aggregation of hydrophobic residue sequences. 1. Original titer = (diluted titer) / (dilution factor) = (colonies per L * 10L / 1mL) / (dilution factor) Original titer = [(132 colonies per quadrant) * (4 quadrants / L) * (10L / mL)] / (1*10-6) = 5.28*109 cells per mL 1a. The experimental effect in the Larson et al. paper is the decrease in hand flora levels caused by hand washing with antimicrobial soap relative to plain soap. The results of this experiment, however, indicate that antimicrobial soap does not offer any significant improvement over plain soap. Since microbe growth is itself a biological process, it would be a source of intrinsic variation in this experiment. The varying lifestyles of the subjects would also be a source of

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intrinsic variation, especially considering the length of this study. The scope of this study simulates regular household use of either antibacterial or plain hand soap for a year in order to gauge their relative long-term effectiveness. 1b.