1. Proteins and Polypeptides
Chapter 3
Proteins and Polypeptides
George Plopper

2. Figure 03.01_BTM: Creating a peptide bond between two amino acids.
Adapted from D. Voet and J. G. Voet. Biochemistry, Third edition. John Wiley & Sons, Ltd., Original figure adapted from R. E. Marsh and J. Donohue, Adv. Protein Chem. 22 (1967):

3. Figure 03.01_MID: Creating a peptide bond between two amino acids.
Adapted from C. K. Mathews, et al. Biochemistry: Third edition. Prentice Hall, 2000.

4. Figure 03.01_TOP: Creating a peptide bond between two amino acids.

5. Figure 01.14A: The 20 most common amino acids are classified into three classes based on the structure of their side chains.

6. Figure 01.14B: The 20 most common amino acids are classified into three classes based on the structure of their side chains.

7. Figure 01.14C: The 20 most common amino acids are classified into three classes based on the structure of their side chains.

8. Figure 01.14D: The 20 most common amino acids are classified into three classes based on the structure of their side chains.

9. Figure 01.14E: The 20 most common amino acids are classified into three classes based on the structure of their side chains.

10. Figure 03.02: The amino acid residue that supplies the hydrogen atom is designated the donor; the residue that binds the hydrogen atom is designated the acceptor.

11. Figure 03.03: By convention, the amino acid terminus (N-terminus) is drawn on the left and the carboxyl terminus (Cterminus) is on the right.

12. Figure 03.04: The Three Traits of Proteins.

13. Figure 03.05: Polypeptides may be proteins or protein subunits.

14. Figure 03.06A: Primary structure is the sequence of amino acids, reading from N terminus to C terminus.
Adapted from B. E. Tropp. Biochemistry: Concepts and Applications, First edition. Brooks/Cole Publishing Company, 1997.

15. Figure 3-6b

16. Figure 03.06B: Beta sheets are one of three types of secondary structure.
Adapted from B. E. Tropp. Biochemistry: Concepts and Applications, First edition. Brooks/Cole Publishing Company, 1997.

17. Figure 03.06C: The antiparallel beta sheet resmembles the parallel sheet, except the sequences are aligned with alternating structural polarity.
Adapted from B. E. Tropp. Biochemistry: Concepts and Applications, First edition. Brooks/Cole Publishing Company, 1997.

18. Figure 03.06G: Tertiary structure is the 3D orientation of secondary structres.
Adapted from B. E. Tropp. Biochemistry: Concepts and Applications, First edition. Brooks/Cole Publishing Company, 1997.

19. Figure 03.06H: Quaternary structure is the 3D orientation of tetrtiary structures (polypeptides). This protein has four different polypeptides (subunits).
Adapted from B. E. Tropp. Biochemistry: Concepts and Applications, First edition. Brooks/Cole Publishing Company, 1997.

20. iClicker time
Can glycine form hydrogen bonds with other amino acids? A. Yes, because it forms random coils between strands of beta sheets B. No, because it is nonpolar. C. Yes, because it is contains an alpha carbon. D. No, because it does not form disulfide bonds. E. Yes, because it contains a C=O bond and an N-H bond.

21. Figure 03.07A: This is a "space filling" or "van der Waals" representation of the protein ribonuclease A.
Structures from Protein Data Bank 1JVT. L. Vitagliano, et al., Proteins 46 (2002): Prepared by B. E. Tropp.

22. Figure 03.07B: This is a "stick model" using the same color scheme and with the same orientation of the same protein as in panel (a).
Structures from Protein Data Bank 1JVT. L. Vitagliano, et al., Proteins 46 (2002): Prepared by B. E. Tropp.

23. Figure 03.07C: This is a "ribbon model" with the same orientation of the protein as in panel (a). Alpha helices are red, antiparallel beta sheets are yellow.
Structures from Protein Data Bank 1JVT. L. Vitagliano, et al., Proteins 46 (2002): Prepared by B. E. Tropp.

24. Figure 03.08A: Alpha helices are represented by coiled ribbons, strands of beta sheets are represented by arrows pointed from N terminus to C terminus.

25. Figure 03.08B: Alpha helices are represented by coiled ribbons, strands of beta sheets are represented by arrows pointed from N terminus to C terminus.

26. Figure 03.08C: Alpha helices are represented by coiled ribbons, strands of beta sheets are represented by arrows pointed from N terminus to C terminus.

27. Figure 03.08D: Alpha helices are represented by coiled ribbons, strands of beta sheets are represented by arrows pointed from N terminus to C terminus.

28. Figure 03.09A: Chaperonins can bind to a polypeptide even as it is being synthesized by a ribosome, thereby helping prevent irrevesible misfolding.
Adapted from Young, J. C., et al., Nat. Rev. Mol. Cell Biol. 5 (2004):

29. Figure 03.09B: After the entire polypeptide has been synthesized, chaperonins assist its folding into a stable, functional shape (aka the "native" confirmation).
Adapted from Young, J. C., et al., Nat. Rev. Mol. Cell Biol. 5 (2004):

30. Figure 03.10: Dr. Anfinsen's experiment demonstrating spontaneous refolding of a denatured protein.
Adapted from L. A. Moran and K. G. Scrimgeour. Biochemistry, Second edition. Prentice Hall, 1994.

31. Figure 03. 11: Examples of domains in proteins
Figure 03.11: Examples of domains in proteins. Note that domains contain all three types of secondary structure.

32. Figure 03.12: Examples of the three structural classes of proteins.
Adapted from Hurley, J. H., J. Biol. Chem. 274 (1999): Structure from Protein Data Bank ID: 1TL7. Mou, T. C., et al., J. Biol. Chem. 280 (2005):

33. Figure 03.13A: The light and heavy chains interact to form binding sites at the tips of the short arms of the antibody.

34. Figure 03.13B: Each domain in the heavy and light chains is tinted a different color for easier identification.
Protein Data Bank ID: 1IGY. Harris, L. J., Skaletsky, E., and McPherson, A., J. Mol. Biol. 275 (1998):

35. Figure 03.14: Five classes of bonds that stabilize protein structure.

36. Figure 03.15: Seven different types of molecules can be covalently attached to amino acid side chains.

37. Figure 03. 16: Many proteins have more than one binding site
Figure 03.16: Many proteins have more than one binding site. Allosteric binding sites help control the shape and function of a protein.

38. Figure 03.17: Occupancy of an allosteric GTP binding site controls a G protein subunit's shape. Three different conformations of the subunit are overlaid for comparison.
Photo courtesy of Heidi E. Hamm and Will Oldham, Vanderbilt University Medical Center.

39. Figure 03.18: Proteasomes digest proteins in the cytosol.

40. Figure 03.19: Most membrane proteins and engulfed proteins are digested by lysosomes.

41. Figure 03.20: Extracellular proteins are digested by proteinases.