Proteins and peptides are polymers of amino acids linked by "peptide bonds", also called amide bonds. The amide bond results from the condensation of an amino and a carboxyl group, releasing water. The amide group is polar, with resonance giving partial double bond characteristics. This helps peptides be soluble even though the charges are lost during condensation.
Conventions: We always draw peptides with the amino acid retaining a free amino group on the left side and the amino acid retaining a free carboxyl group on the right side.
NCC-NCC-NCC...
The end with the free amino is called the "N-terminus" (avg. pKa ~ 8.6)
The end with the free carboxyl is called the "C-terminus" (avg. pKa ~ 3.6)
Each amino acid is called a "residue"
The number of amino acids is reflected in a general designation
An average residue has a mass of about 110 Daltons (18 Daltons less than an average amino acid).
Each peptide has a distinct sequence of the 20 amino acids; this is called the primary sequence. Unless specified, all of the residues are assumed to be in the L-conformation. Each peptide with a unique sequence will have a unique specific name.
glycylglycine: Gly-Gly
glycylserylglutamate: Gly-Ser-Glu
Solubility--the amount of a solute that a solvent will accommodate at a particular temperature.
Hydration stimulates solubility, and amino acid residues containing the following polar side-chains lead to hydration:
Negative interactions include hydrophobic groups (e.g. alkyl and aromatic). because these portions of the molecules do not favorably interact with water molecules, they exclude water from the cavity they occupy and cause long range disruption of the structure of water. Water will not accommodate a lot of hydrophobic groups and they act to decrease the solubility of a molecule.
Similar forces are also involved in intramolecular and intermolecular interactions
