1. Proteomics BIOL 4900

2. Section 1 – Amino Acid Structure

4. Formation of Peptide bond H2OH2O

5. Section 2 – Polypeptide Diversity Insulin primary structure Primary Structure – linear sequence of amino acids in a polypeptide chain 20 100 = 1.27 x 10 130 possible combinations 9 x 10 78 atoms estimated in universe

7. Section 3 – Secondary Structure Resonance prevents bond rotation of peptide bond

9. Ramachandran Plot

10. Pitch = 5.4 Å Turn = 3.4 aa C=O forms H bond With N-H of n+4 residue

12. Anti parallelParallel

14. Helical Wheel

15. All problems at end of chapter except 6, 13, and 19

16. Section 4 – Tertiary Structure

17. X-ray Crystallography

18. NMR

21. Section 5 – Quaternary Structure

22. Section 6 – Protein Stability

23. Salt Bridges Metal Ions

24. Section 7 – Membrane Proteins

28. Section 8 - Glycoproteins

29. Sialic acids are important for glycoproteins and glycolipids; recognition site of Influenza Viruses

30. Sugar derivatives Should be able to draw

31. N-linked oligosaccharides

32. O-linked oligosaccharides

33. Glycoproteins Carbohydrates can account for up to 70% of a protein by mass Half of all mammalian proteins are glycosylated

34. Biological Activity Define protein structure – Usually on surface – limit conformation; stabilize fold Recognition – Glycoconjugates Lectins – identify specific oligosaccharides Selectins – attachment of leukocytes – Blood groups

35. Section 9 – Lipid Classification Functions of lipids – essential component of biological membranes – Hydrocarbon chains serve as energy – intra- and intercellular signaling

36. saturated polysaturated unsaturated ω-3 fatty acid Δ 9 double bond almost always cis even number of carbons 18:0 18:1cΔ9 18:2cΔ9, 12 18:2cΔ9, 12, 15

38. Glycerophospholipids

40. Lipid anchors for proteins prenylated fatty acylated glycosylphatidylinositol

41. Occurs at CXXY If Y = Ala, Met, Ser; farnesylated If Y = Leu; Geranylgeranylated Prenylation

42. Fatty acylated Can add myristic acid or palmitic acid Myristoylation is very stable – amide linkage between α-amino of N-terminal G and myristic acid Palmiyolation can be undone by palmitoyl thioesterases – involved in protein signaling

43. GPI-Anchored Proteins