Amino Acids/Proteins
Amino Acids:
The building blocks of proteins. A protein is a polymer of amino acids.
Generic Amino Acids- (Stereochemistry...)
They can be classified by the nature of their side chain groups (R) into:
| Category | Amino Acids |
| Acidic | Aspartate (Aspartic Acid, Asp, D); Glutamate (Glutamic Acid, Glu, E) |
| Basic | Arginine (Arg, R); Histidine (His, H); Lysine (Lys, K) |
| Uncharged Polar (Hydrophilic) |
Asparagine (Asn, N); Glutamine (Gln, Q); Cysteine (Cys, C); Serine(Ser, S); Threonine (Thr, T); Tyrosine (Tyr, Y) |
| Uncharged Nonpolar (Hydrophobic) |
Alanine (Ala, A); Isoleucine (Ile, I); Leucine (Leu, L); Phenylalanine (Phe, F); Proline (Pro, P); Tryptophan (Trp, W); Valine (Val, V); Methionine (Met, M); Glycine (Gly, G) |
Proline
Ionization Curves:
As we discussed earlier are actually plots of the Henderson-Hasselbach equation, and are used to visualize the ionization changes that occur over a range of pH values.
Such a plot can be used to determine the net charge on an amino acid, such as aspartic acid, at any pH value.
The Peptide Bond:
Attaches amino acids together to form a peptide. The peptide bond is repeated many times to create polypeptide chains which comprise the basic structure of all proteins.
Formation of a Peptide Bond:
i.e. Representative Peptide:
Primary Structure (10):
A particular linear sequence of amino acids unique to each protein. All share the following characteristics:
1) Amino acids in the interior of the polypeptide chain no longer posses ionizable amino or carboxyl groups. These amino acids are referred to as residues. Therefore, for a large protein, charge and polarity are determined by the side chains on the residues.
2) The end of the peptide with the free amino group, the amino terminus or N-terminus, is the beginning of the chain and is depicted on the left.
3) The end with the free carboxyl group, the carboxy terminus or C-terminus, is drawn on the right.
Secondary Structure (20):
Rotation about the two bonds attached to the a carbon allow the peptide to fold into certain three-dimensional arrangements. The two most common:
a-Helix:
-A spiral arrangement (R groups extending outward) with ~3.6 amino acid residues per turn.
-Stabilized by intrachain H-bonds.
-Most amino acids fit well into the a-helix, with one exception Proline, known as a "helix breaker".
-Right-handed or Left-handed helix'
b-Sheet:
-Flat, extended arrangement.
-Interchain H-bonding.
-Parallel (same direction) or Antiparallel (opposite direction).
Tertiary Structure (30):
- The entire conformation of a complete polypeptide chain.
-Hydrophobic effect.
-Like Attracts Like...
Quaternary Structure (40):
-Assembly of two or more polypeptides, each having its own 20 and 30 structure, into a complete, functional protein.
Clinical Correlate:
-One of the polypeptide chains making up the 40 structure of hemoglobinS undergoes a mutation.
-Glutamic Acid (Polar) to Valine (Nonpolar, Hydrophobic)
-Hydrophobic Effect.....
-Abnormal hydrophobic patch on the surface of the polypeptide. This patch mediates the aggregation of HbS molecules into long rod-like structures ("sickle" cells)
