The Building Blocks of Life
Peptides are short polymers of amino acids linked by peptide (amide) bonds.
* What is an amino acid?
* An amino acid is a molecule containing… * an amine group * a carboxylic acid * α-carbon α-carbon a side chain (R-varies)
* There are 20 standard amino acids (standard meaning that they are directly coded for by DNA) * All except Proline are primary amines.
* All have a stereocenter with R-configuration at the alpha carbon * Except Cysteine, which has an S- configuration. * Except Glycine which is achiral (i.e. has no stereocenter).
* Amino acids have varying side chains (R), and thus are categorized by their side chains.
* Hydrophilic vs. Hydrophobic
* This property is determined by the polarity of the side chain. * “Like dissolves Like” * Polar - Hydrophilic * Non-Polar – Hydrophobic * Acidic vs. Non-acidic vs. Basic * This property is determined by comparison to water (pka=15.7)
* More acidic than water: Acidic * Lone pairs ready to accept a proton: Basic * Every thing else: Non-acidic
* What is a Peptide bond?
* A Peptide bond links two amino acids together. * Formed when the carboxyl group of one amino acid reacts with the amine group of another amino acid. * One molecule of water is released per bond formed.
* Peptide bonds provide stability.
* Torsional Strain: Cis vs. Trans
* Equilibrium favors Trans: The largest groups are furthest apart.
* Conjugation: Peptide bond
* Creates a Barrier to Rotation * Every conjugated atom and those directly bonded to them, stay Planar.
* This creates multiple flat areas (not all in the same plane) within the peptide molecule, stabilizing the Peptide structure.
* Peptide Structure is classified into four levels: * Primary Structure * Secondary Structure * Tertiary Structure * Quaternary Structure
* Primary Structure:
* Refers to the sequence in which the amino acids are bonded from N-terminus to C-terminus.
Gly Ser Val
* Secondary Structure:
* Intramolecular Hydrogen bonds cause three different motifs: * α-Helix * β-Sheet * Coil * α-Helix