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

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Presentation transcript:

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

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

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

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

The Genetic Code II

The Genetic Code III

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

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

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

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

Polypeptide – chain of peptides

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

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

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

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

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

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

Peptide Geometry

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

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

Structure of Alpha-Helix

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

Distortion of Alpha-Helix Buries against the other 2 nd structure Solvent helix

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

Parallel & Anti-parallel Sheets

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

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

THE END