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Proteomics

Proteomics. BIOL 4900. Section 1 – Amino Acid Structure. Formation of Peptide bond. H 2 O. 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

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Proteomics

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  1. Proteomics BIOL 4900

  2. Section 1 – Amino Acid Structure

  3. Formation of Peptide bond H2O

  4. Section 2 – Polypeptide Diversity Insulin primary structure Primary Structure – linear sequence of amino acids in a polypeptide chain 20100 = 1.27 x 10130 possible combinations 9 x 1078 atoms estimated in universe

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

  6. Ramachandran Plot

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

  8. Anti parallel Parallel

  9. Helical Wheel

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

  11. Section 4 – Tertiary Structure

  12. X-ray Crystallography

  13. NMR

  14. Section 5 – Quaternary Structure

  15. Section 6 – Protein Stability

  16. Salt Bridges Metal Ions

  17. Section 7 – Membrane Proteins

  18. Section 8 - Glycoproteins

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

  20. Sugar derivatives Should be able to draw

  21. N-linked oligosaccharides

  22. O-linked oligosaccharides

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

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

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

  26. unsaturated saturated polysaturated even number of carbons 18:0 18:1cΔ9 18:2cΔ9, 12 18:2cΔ9, 12, 15 Δ9 double bond almost always cis ω-3 fatty acid

  27. Glycerophospholipids

  28. Lipid anchors for proteins • prenylated • fatty acylated • glycosylphatidylinositol

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

  30. 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

  31. GPI-Anchored Proteins

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