1. The structure and properties of amino acids determine the structure and properties of proteins and, therefore, their function. How do amino acids and peptide properties dictate protein structure and function? In your explanation, please include at least one representation and the key terms hydrophobicity, hydrogen bonding, electrostatic interactions, acid-base property.
2. Using your understanding of resonance and energetic favorability, explain why the predominant form of peptide bonds seen in proteins is trans, rigid and planar.
3. Keratins are a major class of structural proteins found in the hair, feathers, scales, nails and hooves of animals. They are designed to be unreactive and resistant to most forms of stress encountered by animals. One major group of keratins, α-keratins, are part of a broader family of proteins called intermediate filament (IF) proteins. These proteins have a structural feature exemplified by the α-keratins. While variations do exist, the most common arrangement for keratin is a coiled-coil of two α helices (see image to right). The amino acid sequence of each α-helix in the figure above is very regular and consists of quasi-repeating segments of 7 residues. Each coiled-coil is formed by the interaction of these α-helices with one another through side chain interactions. Using your knowledge of chemical interactions that stabilize polypeptides and amino acid structure, give a suitable explanation for how coiled-coil structures are stabilized in our bodies. Include a prediction and explanation of one amino acid that may be located at the junction between the helices.
4. Discuss any one disease involving the misfolding of a protein. What causes the protein to misfold? Describe the symptoms caused by the disorder and how misfolding of the protein is involved. Please provide diagrams and references to support your example.