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Reading Guide: Pratt and Cornely, Chapter 4 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 all 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 secondary 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. How is it different than a motif? 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. Which is the most common? 21. How are proteins denatured? 22. Most of the time, all the information required for a protein to fold is contained in _____. 23. Name two types of covalent modification that might occur in protein processing. 24. Typically, when a protein is misfolded, what two possible fates awaits it? What third possibility leads to diseases such as Alzheimer’s disease? 25. What secondary structure is most common in amyloid fiber formation? 26. What is a prion, and how does it act as an infectious agent? 27. A protein composed of 3 identical subunits is called a _____. A protein of 2 different subunits is called a _____. 28. What are the advantages of quaternary structure? 29. Why does a larger protein move down a gel filtration column faster than a small protein? 30. What types of solid phases are used in ion exchange chromatography? 31. Use data from table 4.1 to estimate the pI of an Asp-Val dipeptide and a Lys-Cys dipeptide. 32. Why is the detergent SDS added to a protein mixture in gel electrophoresis? 33. Summarize five typical steps in the standard approach to sequencing a protein. 34. What information about a protein can be gathered from x-ray crystallography?