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Proteins and Amino Acids

Proteins and Amino Acids

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Proteins and Amino Acids

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  1. Proteins and Amino Acids

  2. Biological Functions of Proteins • Facilitate biochemical reactions • Structural support • Storage and Transport • Immune protection • Generate movement • Transmission of nerve impulses • Control growth and differentiation

  3. Key Properties of Proteins • Linear polymers of amino acids • Contains a wide range of functional groups • Forms complex assemblies of more than one polypeptide chain • Versatile structure – some are rigid while others are flexible

  4. Globular and Fibrous Proteins • Globular protein • Usually water soluble, compact, roughly spherical • Hydrophobic interior, hydrophilic surface • Globular proteins include enzymes,carrier and regulatory proteins • Fibrous protein • Provide mechanical support • Often assembled into large cables or threads • α-Keratins: major components of hair and nails • Collagen: major component of tendons, skin, bones and teeth

  5. General Structure of Proteins • Twenty common a-amino acids have carboxyl and amino groups bonded to the α-carbon atom • A hydrogen atom and a side chain (R) are also attached to the α-carbon atom

  6. Zwitterions • Under normal cellular conditions amino acids are zwitterions (dipolar ions): Amino group = -NH3+ Carboxyl group = -COO-

  7. Stereochemistry of amino acids • 19 of the 20 common amino acids have a chiral a-carbon atom (Gly does not) • Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each) • Mirror image pairs of amino acids are designated L (levo) and D (dextro) • Proteins are assembled from L-amino acids (a few D-amino acids occur in nature)

  8. Amino acid side chains • Nine non-polar aa • Six polar uncharged aa • Five charged aa • Three basic aa • Two acidic aa • Two aa with sulfur groups • Four ring-forming aa • Three have aromatic rings

  9. Hydropathy • Relative hydrophobicity of the amino acid • The larger the hydropathy, the greater the tendency of an amino acid to prefer a hydrophobic environment • Hydropathyaffects protein folding: hydrophobic side chains tend to be in the interiorhydrophilic residues tend to be on the surface

  10. Acid-base chemistry of amino acids

  11. Isoelectric point • pH at which the amino acid bears zero net charge

  12. Titration curve of Histidine

  13. Polymer of amino acid • Peptide bond - linkage between amino acids is a secondary amide bond • Formed by condensation of the α-carboxyl of one amino acid with the α-amino of another amino acid (loss of H2O molecule)

  14. Resonance Structure of the peptide bond

  15. Trans and Cis configuration of peptide bond • Usually in the trans configuration

  16. Dihedral Angle

  17. Dihedral angle of proteins • The phi angle is the angle around the -N-Cα- bond • The psi angle is the angle around the -Cα-C- bond • The omega angle is the angle around the -C1-N- bond (i.e. the peptide bond)

  18. Levels of Protein Structure

  19. Primary structure >2CQG:A|PDBID|CHAIN|SEQUENCEGSSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDSGPSSG

  20. Secondary Structure

  21. Alpha-helix

  22. Right-handed and Left-handed α-Helix

  23. Right-handed and Left-handed α-Helix

  24. Beta-sheet

  25. Determining 2o structure: Ramanchandran Plot

  26. Supersecondary structure: Motifs • Secondary structures often group together to form a specific geometric arrangements known as motifs • Since motifs contain more than one secondary structural element, these are referred to as super secondary structures

  27. Domains • stable, independently folding, compact structural units within a protein, formed by segments of the polypeptide chain, with relative independent structure and function distinguishable from other regions and stabilized through the same kind of linkages than the tertiary level • Often each domain has a separate function to perform for the protein, such as: • Bind a small ligand • Spanning the plasma membrane (transmembraneproteins) • Contain the catalytic site (enzymes) • DNA-binding (in transcription factors) • Providing a surface to bind specifically to another protein • In some (but not all) cases, each domain in a protein is encoded by a separate exon in the gene encoding that protein.

  28. Tertiary Structure • Forces holding the tertiary (and higher order) structure together • Salt bridge • Covalent bond (disulfide bridges) • Hydrophobic interaction • Hydrogen bonding

  29. Quaternary Structure

  30. Protein Folding