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 structure of DNA. It is also shown on page 245 of Purves. The structures of the amino acids are on pg. 49 of Purves. There's also a link here to an image of the pKa's of the amino acids.
   
   • a) At pH 7.0, which of the following amino acid side chains would most likely form an ionic bond with a molecule such as DNA? Phenylalanine Arginine Aspartic Acid

   • b)With which part of the DNA molecule will it bind?

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