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Amino Acids & Side Groups

Amino Acids & Side Groups. Polar Charged ACIDIC  negatively charged amino acids ASP & GLU    R group with a 2nd COOH that ionizes * above pH 7.0 Polar Charged BASIC  positively charged amino acids LYS, ARG, HIS R group with a 2nd amide * that protonates below pH 7.0 .

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Amino Acids & Side Groups

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  1. Amino Acids & Side Groups • Polar Charged • ACIDIC  negatively charged amino acids • ASP & GLU   R group with a 2nd COOH that ionizes* above pH 7.0 • Polar Charged • BASIC  positively charged amino acids • LYS, ARG, HIS • R group with a 2nd amide* that protonates below pH 7.0 

  2. Acidic Side Chains Basic Side Chains Acidic vs. Basic

  3. Polar Charged

  4. Amino Acids & Side Groups • Polar Uncharged • THR, TYR, ASN, GLN    (cys) • are soluble in water, i.e., hydrophilic  (attract H-bonds) • Contain hydroxyl or amino functional groups

  5. Polar UnchargedHydroxyl

  6. Polar Uncharged IIAmino Functional Groups

  7. Polar Uncharged Amino Acids

  8. Amino Acids & Side Groups • NON-POLAR (aliphatic) • Includes GLY, ALA, VAL, LEU, ILE, PRO • all contain only hydrocarbons groups   =   hydrophobicity • AROMATIC (hydrophobic non-polars)    • PHE & TRP     (TYR)    • all contain R groups with    ring structures* or Sulfur* • R groups with sulfur • MET,  CYS

  9. Non-PolarHydrocarbon R-Groups

  10. Non-PolarAromatic R-Groups

  11. Non-PolarSulfur R Groups

  12. Alpha Helix Beta-pleated sheets • The most common polypeptide helix • Stabilized by extensive hydrogen bonding • Hydrogen bonds extend up from the oxygen from the carbonyl group to the NH group of a peptide linkage • This was shown in class via the visuals • There are approximately 4 peptide bond links up stream between the atoms involved in the hydrogen bonds • Each turn of an alpha helix contains 3.6 amino acids. • Unlike the alpha helix, composed of two or more peptide chains • Polypeptide chains are joined by hydrogen bonds • When the hydrogen bonds are formed between the polypeptide chains they are termed interchains. • The polypeptide chains can run parallel to each other or anti-parallel • Recall the “ends” of a polypeptide chain • C-terminus • N-terminus/Amino-terminus Secondary Protein Structures

  13. Alpha Helix

  14. Beta-pleated sheets

  15. Beta-pleated Sheets and Alzheimer’s Disease • The amyloid protein, a class of fibrous proteins, is deposited in the brain. • Individuals, that have Alzheimer’s Disease, have the amyloid protein composed of twisted Beta-pleated sheet fibrils whose three-dimentional structure is virtually identical to that of silk fibrils • Silk • Contain Beta-pleated sheet protein structures

  16. Tertiary Structure • Interactions stabilizing Tertiary Structures • Four were mentioned in class • Disulfide Bonds • Hydrophobic interactions • Hydrogen bonds • Ionic interactions

  17. Disulfide Bonds • A disulfide bond is a covalent linkage formed by the sulfhydryl group (-SH) of two cysteine residues to form cystine • The folding of the polypeptide chain brings the cysteine residues near each other • Disulfide linkage contributes to the stability of the three-dimensional shape of the protein molecule • Disulfide bonds are found in proteins that are secreted by cells • Thought that these strong covalent bonds help stabilize the structure of proteins and help prevent them from becoming denatured in the extra-cellular environment

  18. Hydrophobic Interactions • Recall that amino acids with non-polar side chains tend to be located in the interior of the polypeptide • Here, they associate with other hydrophobic amino acids • Special Note • Proteins located in non-polar (lipid) environments such as the phopholipidbilayer, tend to be in an opposite form • Hydrophobic amino acids are located on the surface • Hydrophilic amino acids are located on the interior

  19. Ionic Interactions • Negatively charged groups interact with positively charged groups • Negatively charged groups • (-COO-) in the side chain of aspartate or glutamate • Positively charged groups • (-NH3+) in the side chain of lysine

  20. Dipole Moment • Dipole Moment is the measure of a molecule’s overall polarity • μ = Q * r • μ = Dipole Moment • Q = charge • r = distance between charges • Measured in debyes (\də-ˈbī\ )

  21. Van der Waals Forces • A weak attractive force between atoms or non-polar molecules caused by a temporary change in dipole moment • Arising from a brief shift of orbital electrons to one side of one atom or molecule, creating a similar shift in adjacent atoms or molecules.

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