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Protein Chemistry Basics

Protein Chemistry Basics. Protein function Protein structure Primary Amino acids Linkage Protein conformation framework Dihedral angles Ramachandran plots Sequence similarity and variation. Protein Function in Cell. Enzymes Catalyze biological reactions Structural role Cell wall

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Protein Chemistry Basics

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  1. Protein ChemistryBasics • Protein function • Protein structure • Primary • Amino acids • Linkage • Protein conformation framework • Dihedral angles • Ramachandran plots • Sequence similarity and variation

  2. Protein Function in Cell • Enzymes • Catalyze biological reactions • Structural role • Cell wall • Cell membrane • Cytoplasm

  3. Protein Structure

  4. Protein Structure

  5. Model Molecule: Hemoglobin

  6. Hemoglobin: Background • Protein in red blood cells

  7. Red Blood Cell (Erythrocyte)

  8. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen

  9. Heme Groups in Hemoglobin

  10. Hemoglobin: Background • Protein in red blood cells • Composed of four subunits, each containing a heme group: a ring-like structure with a central iron atom that binds oxygen • Picks up oxygen in lungs, releases it in peripheral tissues (e.g. muscles)

  11. Hemoglobin – Quaternary Structure Two alpha subunits and two beta subunits (141 AA per alpha, 146 AA per beta)

  12. Hemoglobin – Tertiary Structure One beta subunit (8 alpha helices)

  13. Hemoglobin – Secondary Structure alpha helix

  14. β-Hairpin Motif • Simplest protein motif involving two beta strands [from Wikipedia] • adjacent in primary sequence • antiparallel • linked by a short loop • As isolated ribbon or part of betasheet • a special case of a turn • direction of protein backbone reverses • flanking secondary structure elements interact (hydrogen bonds) CS 882 course project

  15. Types of Turns • β-turn (most common) • donor and acceptor residues of hydrogen bonds are separated by 3 residues (ii +3 H-bonding) • δ-turn • ii +1 H-bonding • γ-turn • ii +2 H-bonding • α-turn • ii +4 H-bonding • π-turn • ii +5 H-bonding • ω-loop • a longer loop with no internal hydrogen bonding CS 882 course project

  16. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding

  17. Hydrogen Bonding • Involves three atoms: • Donor electronegative atom (D) (Nitrogen or Oxygen in proteins) • Hydrogen bound to donor (H) • Acceptor electronegative atom (A) in close proximity D – H A

  18. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation

  19. δ- δ+ δ- D – H A D-H Interaction • Polarization due to electron withdrawal from the hydrogen to D giving D partial negative charge and the H a partial positive charge • Proximity of the Acceptor A causes further charge separation • Result: • Closer approach of A to H • Higher interaction energy than a simple van der Waals interaction

  20. Hydrogen Bonding And Secondary Structure beta-sheet alpha-helix

  21. Structure Stabilizing Interactions • Noncovalent • Van der Waals forces (transient, weak electrical attraction of one atom for another) • Hydrophobic (clustering of nonpolar groups) • Hydrogen bonding • Covalent • Disulfide bonds

  22. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond

  23. Disulfide Bridge

  24. Disulfide Bonds • Side chain of cysteine contains highly reactive thiol group • Two thiol groups form a disulfide bond • Contribute to the stability of the folded state by linking distant parts of the polypeptide chain

  25. Disulfide Bridge – Linking Distant Amino Acids

  26. Hemoglobin – Primary Structure NH2-Val-His-Leu-Thr-Pro-Glu-Glu- Lys-Ser-Ala-Val-Thr-Ala-Leu-Trp- Gly-Lys-Val-Asn-Val-Asp-Glu-Val- Gly-Gly-Glu-….. beta subunit amino acid sequence

  27. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds

  28. Protein Structure - Primary • Protein: chain of amino acids joined by peptide bonds • Amino Acid • Central carbon (Cα) attached to: • Hydrogen (H) • Amino group (-NH2) • Carboxyl group (-COOH) • Side chain (R)

  29. General Amino Acid Structure H H2N COOH Cα R

  30. General Amino Acid Structure At pH 7.0 H +H3N COO- Cα R

  31. General Amino Acid Structure

  32. Amino Acids • Chiral

  33. Chirality: Glyceraldehyde D-glyderaldehyde L-glyderaldehyde

  34. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain

  35. 20 Naturally-occurring Amino Acids

  36. Amino Acids • Chiral • 20 naturally occuring; distinguishing side chain • Classification: • Non-polar (hydrophobic) • Charged polar • Uncharged polar

  37. Alanine: Nonpolar

  38. Serine: Uncharged Polar

  39. Aspartic AcidCharged Polar

  40. GlycineNonpolar (special case)

  41. Peptide Bond • Joins amino acids

  42. Peptide Bond Formation

  43. Peptide Chain

  44. Peptide Bond • Joins amino acids • 40% double bond character • Caused by resonance

  45. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length

  46. Peptide Bond Lengths

  47. Peptide bond • Joins amino acids • 40% double bond character • Caused by resonance • Results in shorter bond length • Double bond disallows rotation

  48. Protein Conformation Framework • Bond rotation determines protein folding, 3D structure

  49. Bond Rotation Determines Protein Folding

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