Large Molecules Problems

  1. Glycophorin is a major transmembrane protein of erythrocytes (red blood cells). It has a single peptide backbone. Consider the distribution of amino acids with neutral, acidic, or basic R groups (side chains) along the peptide backbone of glycophorin:
    • a) List the amino acids you would expect to predominate in the portion of the protein embedded in the membrane. Why?

    • b) List the amino acids you would expect to find at the surfaces of the membrane. Why?

  2. After discovering a new species of bacteria in a Yellowstone National Park hot spring (temperature 95-100C) you take it back to lab and analyze its DNA . You discover that it has many more G-C bonds than A-T bonds. Can you come up with theory that explains this?

  3. Ionic bonds between positively and negatively charged amino acid side chains, sometimes called salt bridges, often stabilize protein 3ostructures.
    • a) Given the salt bridge:

      Over what range of pH will this salt bridge be stable? (Assume that the side chains must be at least 50% charged in order for the salt bridge to be stable.)

    • b) Given this salt bridge:

      Over what range of pH will this salt bridge be stable?
    • c) Which type of salt bridge is more likely to be found in enzymes inside human cells?
      Why?

  4. This links to an image of the