1. Amino Acids & Side Groups Polar Charged ◦ ACIDIC negatively charged amino acids  ASP & GLU R group with a 2nd COOH that ionizes* above pH 7.02nd COOH that ionizes* Polar Charged ◦ BASIC positively charged amino acids  LYS, ARG, HIS  R group with a 2nd amide* that protonates below pH 7.0 with a 2nd amide*

2. Acidic vs. Basic Acidic Side ChainsBasic Side Chains

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 groupshydroxylamino functional groups

5. Polar Uncharged Hydroxyl

6. Polar Uncharged II Amino 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 = hydrophobicityhydrocarbons groups AROMATIC (hydrophobic non-polars) ◦ PHE & TRP (TYR)  all contain R groups with ring structures* or Sulfur* ring structures Sulfur R groups with sulfur ◦ MET, CYS

9. Non-Polar Hydrocarbon R-Groups

10. Non-Polar Aromatic R-Groups

11. Non-Polar Sulfur R Groups

12. Secondary Protein Structures Alpha HelixBeta-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

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

19. 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 phopholipid bilayer, tend to be in an opposite form Hydrophobic amino acids are located on the surface Hydrophilic amino acids are located on the interior

20. 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  (-NH 3 + ) in the side chain of lysine

23. 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 (\d ə - ˈ b ī \ )

24. 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.