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Introduction to Protein

Introduction to Protein. JL LO & HC Lee 2000 June-July. Gene & Protein. One gene, one protein ..talksprotein_3.ps Genotype & phenotype ..talksprotein_4.ps. What do proteins do?. Everything Structural and Functional Structural blood, muscle, bone, etc. Functional

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Introduction to Protein

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  1. Introduction to Protein JL LO & HC Lee 2000 June-July

  2. Gene & Protein • One gene, one protein • ..\talks\protein_3.ps • Genotype & phenotype • ..\talks\protein_4.ps

  3. What do proteins do? • Everything • Structural and Functional • Structural • blood, muscle, bone, etc. • Functional • metabolic, neural, reproduction Aberrant gene > malfunction protein > disease

  4. The Genetic Code I • 20 amino acids are coded by groups of three bases (triplets or CODONS) • Bases are: C, T, U (instead of A), G • 4x4x4 = 64 • 3 are stop codons • 61 code amino acids (with degeneracy)

  5. The Genetic Code II

  6. The Genetic Code III

  7. The Amino Acids • Single and 3-letter Codes • Aspartic Acid Asp D Glutamic Acid Glu E • Phenylanine Phe F Glycine Gly G • Alanine Ala A Cysteine Cys C • Histidine His H Isoleucine Ile I • Lysine Lys K Leucine Leu L • Methionine Met M Asparagine Asn N • Proline Pro P Glutamine Gln Q • Arginine Arg R Serine Ser S • Threonine Thr T Valine Val V • Tryptophan Trp W Tyrosine Tyr Y

  8. Alanine Grey - carbon White - hydrogen Blue – nitrogen Red – oxygen Alpha carbon Amine group Carboxylic acid group Side chain

  9. The CORN Law alpha Carbon cabOxylic acid group side chain (R) amiNe group

  10. Peptide Synthesis Two AminoAcids = 2 x (CORN) – > Dipeptide + Water (NCR) –CO2- + NH3+ –(CRO) = (N – C – R) – C=O | peptide bond H –N – (C – R – O) + H2O

  11. Polypeptide – chain of peptides

  12. Hydrophobic-Aliphatic Classification of Amino Acid Side Chains • Ala(A) • Val(V) • Leu(L) • Ile (I) • Mostly are bifurcated except Ala

  13. Hydrophobic-aromatic • Phe(F) • Tyr(Y) • Trp(W) • Non-polar

  14. Neutral-polar side chains • Ser(S) • Thr(T) • Cys(C) • Met(M) • Asn(N) • Gln(Q) • Possess hydroxyl group

  15. Acidic amino acids • Asp(D) • Glu(E) • Strongly polar nature • Catalytic • Metal ion binding ability

  16. Basic amino acids • His(H) • Lys(K) • Arg(R) • Frequently occurring in enzyme

  17. Conformationally important • Gly(G) • Pro(P) • G has no side chain • P is the most rigid one

  18. Peptide Geometry

  19. Peptide Torsion Angles • Three main chain torsion angle • ψ N - Calpha bond • Ψ C – Calpha bond • ω C – N bond 3D structure of peptide determined if all angles given

  20. Protein Conformation ..\talks\protein_6.ps..\talks\protein_7.ps Alpha-helices ..\..\proteins\1AEP_apolipophorin_III_1.gif Beta-sheets & coils ..\..\proteins\1FSC_fasciculin_1.gif 1IBA.pdb

  21. Structure of Alpha-Helix

  22. Properties of the Alpha-Helix • A pitch of 5.4 A • Have 3.6 amino acids residues per turn • 3.6/5.4=1.5 --- a rise per residue • Have negative Ψandψangles

  23. Distortion of Alpha-Helix • Buries against the other 2nd structure • Solvent • 310-helix

  24. Structure of Beta Sheet • Negative ψand Positive Ψ • Axial distance—3.5 A • Pitch – 7A

  25. Parallel & Anti-parallel Sheets

  26. More Examples • ..\..\proteins\1AVH_annexin_V_1.gif • ..\..\proteins\1ERB_pl_retinol_bp_1.gif • ..\..\proteins\1ADN_DNA_Repair_1.gif

  27. Tertiary Structure • ..\talks\protein_8.ps • More cartoons of Proteins • Go to-files

  28. THE END

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