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Proteins and Amino Acids

Proteins and Amino Acids. Biological Functions of Proteins. Facilitate biochemical reactions Structural support Storage and Transport Immune protection Generate movement Transmission of nerve impulses Control growth and differentiation. Key Properties of Proteins.

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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

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