Reading Guide: Pratt and Cornely, Chapter 4, pp 87-103.
1. “Proteins are the workhorses of the cell.” What do they do?
2. What is a protein? What is a polypeptide?
3. What is meant by an “L” amino acid? What physical characteristics do all the standard amino
acids share?
4. How are hydrophobic amino acids similar to each other?
5. Which category do Pratt and Cornely list Histidine as? Which other category could it be in?
6. name the 4 amino acids that are charged at almost ally physiological conditions. Which are
acidic? Which are basic?
7. Given the following one letter abbreviations, give the name and structure (with
stereochemistry) for each amino acid: L, M, H, G, K, D. (Be able to do this for all 20 standard
amino acids.)
8. Draw the structure of MSG (monosodium glutamate.) What is its role in taste perception.
9. Assuming all conventions, draw the oligopeptide: WACPR. What is its net charge at pH 7?
What is its net charge at pH 8.4? (Use Table 4.1 for pKa values.)
10. Describe the four levels of protein structure.
11. Draw a structure for the peptide bond that explains why it has limited rotation.
12. Polypeptides form structures that minimize bad interactions and maximize good interactions.
List a few interactions that contribute to or detract from polypeptide stability.
13. Describe the alpha helix structure.
14. Draw a parallel beta sheet between two oligonucleotides that are five alanine residues long.
How is an antiparallel sheet different in h-bonding?
15. What is an irregular secondary structure? What is a loop?
16. Define a protein domain.
17. Why is the interior of a globular protein often regular in its secondary structure, while the
outside is often irregular?
18. Is it possible to have a charged amino acid in the protein core? If so, how does it exist?
19. How much more stable is a folded protein than an unfolded protein? What is the major factor
in tertiary structure protein stabilization?
20. List three types of cross-linking observed in proteins.