Bonds in Peptides

Hydrogen Bonds

• Also called Permanent dipole - Permanent dipole (PD-PD) bonds
• Require an H-bond donor (hydrogen bound to an electronegative atom – O, N, or S) and an H-bond acceptor (an electronegative atom – O, N, or S)
• Plays an important role in protein structure

Amino acid backbone:

Cysteine:

Methionine:

Hydrophobic Interactions

• Hydrophobic: Non-polar. Will repel polar solvents and functional groups.
• Hydrophilic: Polar/charged. Will interact with and attract polar solvents and functional groups.
• Hydrophobic amino acids will be arranged in the interior of proteins where they do not interact with the external aqueous environment.
• Hydrophilic amino acids will be arranged on the external surface of proteins where they interact with the external aqueous environment.
• Ambivalent amino acids are equally happy in a hydrophobic environment and a hydrophilic environment
• This arrangement works because water binds strongly to itself!

Electrostatic/Ionic interactions

• Bonds formed between oppositely charged molecules
• Electrons are completely transferred over from one valence shell to another
• In proteins this occurs between charged side chains
• The strongest type of non-covalent bonds

Arginine (+ve) ---- Aspartic Acid (-ve)

Van der Waals Forces

• Also referred to as Induced-Dipole – Induced-Dipole (ID – ID) bonds
• These types of interactions are weak on their own and require tight packing, but when many interactions are present in one area it can be quite strong.
• Can be found within folded proteins

Disulfide Bonds

• A covalent bond: electrons are shared between the two involved atoms.
• Two cysteine amino acids can form a disulfide bond
• The strongest type of bond found in proteins
• They aid in protein folding and maintaining structure

Cystine: