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Introduction to Protein

Explore the world of proteins, from genotype to phenotype and beyond. Learn about the genetic code, amino acids, peptide synthesis, and protein conformation. Delve into the structural and functional aspects of proteins and discover their vital roles in various biological processes. From alpha-helices to beta-sheets, unravel the intricate dance of protein structures. Uncover the secrets of protein tertiary structures and their significance in the complex web of life.

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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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