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. 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) The Genetic Code I

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 HIsoleucine Ile I Lysine Lys K LeucineLeu L Methionine Met M Asparagine Asn N Proline ProP GlutamineGln Q Arginine Arg RSerineSerS Threonine Thr T Valine Val V Tryptophan Trp W Tyrosine Tyr Y

8. Alanine G rey - carbon W hite - hydrogen B lue – nitrogen R ed – oxygen Carboxylic acid group Amine groupAlpha carbon Side chain

9. The CORN Law alpha C arbon cab O xylic acid group side chain (R) ami Ne group

10. Two AminoAcids = 2 x (CORN) – > Dipeptide + Water (NCR) – CO 2 - + N H 3 + – (CRO) = (N – C – R ) – C =O | peptide bond H – N – (C – R – O ) + H 2 O Peptide Synthesis

11. Polypeptide – chain of peptides

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

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 - C alpha bond Ψ  C – C alpha bond ω  C – N bond 3D structure of peptide determined if all angles given

20. Protein Conformation..\talks\protein_6.ps..\talks\protein_6.ps..\talks\protein_7.ps..\talks\protein_7.ps Alpha-helices..\..\proteins\1AEP_apolipophorin_III_1.gif Beta-sheets & coils..\..\proteins\1FSC_fasciculin_1.gif..\..\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 2 nd structure Solvent 3 10 -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