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Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233 Collagen pp. 233-240

Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233 Collagen pp. 233-240 Mb pp. 240-248 pp. 248-256 Bioinfo pp. 256-258 Stability pp. 258-262 Hydropathy pp. 263-266 Symmetry pp. 266-end Ch 9: pp. 276-278 pp. 278-283 Folding pp. 283-290 Chaperones pp. 290-306

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Sections in Voet to Study or Read Study Read Ch 8 : pp. 219-233 Collagen pp. 233-240

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  1. Sections in Voet to Study or Read StudyRead Ch 8: pp. 219-233 Collagen pp. 233-240 Mb pp. 240-248 pp. 248-256 Bioinfo pp. 256-258 Stability pp. 258-262 Hydropathy pp. 263-266 Symmetry pp. 266-end Ch 9: pp. 276-278 pp. 278-283 Folding pp. 283-290 Chaperones pp. 290-306 Prions pp. 306-312 Evolution pp. 312-end Suggested Problems Ch 9: 3, 4, 6, 12, 14

  2. Protein Explorer http://molvis.sdsc.edu/protexpl/frntdoor.htm Do the “1 hour tour” at this site. http://molvis.sdsc.edu/protexpl/qtour.htm It may take longer than 1 h.

  3. Table 8-6 Hydropathy Scale for Amino Acid Side Chains. Values below line are NEGATIVE!! Page 263

  4. Figure 8-60 Hydropathic index plot for bovine chymotrypsinogen. Page 263

  5. Figure 8-46abc Schematic diagrams of supersecondary structures Page 249

  6. Figure 8-46d Schematic diagrams of supersecondary structures. Page 249

  7. Figure 8-47a X-Ray structures of 4-helix bundle proteins.(a) E. coli cytochrome b562. Page 250

  8. Fibrous Proteins

  9. Figure 8-25 The microscopic organization of hair. Page 232

  10. Figure 8-26 The structure of a keratin. Page 232

  11. Figure 8-27a The two-stranded coiled coil. (a) View down the coil axis showing the interactions between the nonpolar edges of the a helices. Page 233

  12. Figure 8-27b The two-stranded coiled coil. (b) Side view in which the polypeptide back bone is represented by skeletal (left) and space-filling (right) forms. Page 233

  13. Exploring collagen http://www.rcsb.org/pdb/molecules/pdb4_1.html

  14. Figure 8-28 The amino acid sequence at the C-terminal end of the triple helical region of the bovine a1(I) collagen chain. Page 234

  15. Figure 8-29 The triple helix of collagen. Page 235

  16. Figure 8-30a X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (a) Ball and stick representation.

  17. Figure 8-30b X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (b) View along helix axis. Page 235

  18. Figure 8-30c X-Ray structure of the triple helical collagen model peptide (Pro-Hyp-Gly)10 in which the fifth Gly is replaced by Ala. (c) A schematic diagram. Page 236

  19. Figure 8-31 Electron micrograph of collagen fibrils from skin. Page 237

  20. Figure 8-32 Banded appearance of collagen fibrils. Page 237

  21. Figure 8-33 A biosynthetic pathway for cross-linking Lys, Hyl, and His side chains in collagen. Page 238

  22. Figure 8-34 Distorted structure in abnormal collagen. Page 239

  23. Globular Proteins

  24. Figure 8-35 X-Ray diffraction photograph of a single crystal of sperm whale myoglobin. Page 240

  25. Figure 8-39a Representations of the X-ray structure of sperm whale myoglobin. (a) The protein and its bound heme are drawn in stick form. Page 244

  26. Figure 8-39b Representations of the X-ray structure of sperm whale myoglobin. (b)A diagram in which the protein is represented by its computer-generated Ca backbone. Page 244

  27. Figure 8-39c Representations of the X-ray structure of sperm whale myoglobin. (c)A computer-generated cartoon drawing in an orientation similar to that of Part b. Page 244

  28. Figure 8-43a The H helix of sperm whale myoglobin. (a)A helical wheel representation in which the side chain positions about the a helix are projected down the helix axis onto a plane. Page 247

  29. Mb

  30. Cut-away view surface Stryer Fig. 3.45 Mb yellow = hydrophobic, blue=charged, white=others

  31. Stryer Fig. 3.46 Porin

  32. Porin

  33. Structural features of most globular proteins: 1. Very compact: e.g. Mb has room for only4 water molecules in its interior. 2. Most polar/charged R groups are on the surface and are hydrated. 3. Nearly all the hydrophobic R groups are on the interior. 4. Pro occurs at bends/loops/random structures and in sheets

  34. Chapter 9!!! Figure 9-1 Page 277

  35. Figure 9-2 Reductive denaturation and oxidative renaturation of RNase A. Page 277

  36. Figure 9-3 Plausible mechanism for the thiol- or enzyme-catalyzed disulfide interchange reaction in a protein. Page 278

  37. Figure 9-14b Reactions catalyzed by protein disulfide isomerase (PDI). (b) The oxidized PDI-dependent synthesis of disulfide bonds in proteins. Page 288

  38. Figure 9-4 Primary structure of porcine proinsulin. Page 278

  39. H-bond Fun Fact • 1984 survey of protein crystal data shows that “almost all groups capable of forming H-bonds do so.” (main chain amides, polar side chains)

  40. Many conformational states Fewer conformational states A “single” conformational state

  41. High energy Many conformational states Fewer conformational states A “single” conformational state Low energy

  42. Figure 9-11c Folding funnels. (c) Classic folding landscape. Page 285

  43. Figure 9-11d Folding funnels. (d) Rugged energy surface. Page 285

  44. “Ideal” “Real” ?

  45. Figure 9-12 Polypeptide backbone and disulfide bonds of native BPTI. Page 286

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