1. Packet #9
Supplement

2. 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
BASIC  positively charged amino acids
LYS, ARG, HIS
R group with a 2nd amide* that protonates below pH 7.0 

3. Acidic Side Chains
Basic Side Chains
Acidic vs. Basic

4. Polar Charged

5. 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

6. Polar Uncharged Hydroxyl

7. Polar Uncharged II Amino Functional Groups

8. Polar Uncharged Amino Acids

9. 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

10. Non-Polar Hydrocarbon R-Groups

11. Non-Polar Aromatic R-Groups

12. Non-Polar Sulfur R Groups

13. Secondary Protein Structures
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

14. Alpha Helix

15. Beta-pleated sheets

16. 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

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

18. 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

20. 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

21. 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

24. 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\ )

25. 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.