Peptide Structure:
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.

C-Terminus C-Terminus
N- Terminus
N- Terminus

Gly Ser Val

* Secondary Structure:

* Intramolecular Hydrogen bonds cause three different motifs: * α-Helix * β-Sheet * Coil * α-Helix