What is a peptide bond?

An amide, made by condensation.

A peptide bond forms between the alpha-carboxyl group of one amino acid and the alpha-amino group of the next, giving an amide group (-CO-NH-) and releasing one molecule of water. Because each bond joins two residues, a linear chain of n amino acids has n - 1 peptide bonds: one in a dipeptide, two in a tripeptide such as GHK, three in a tetrapeptide such as SS-31.

The chain that results has a free amino group at one end and a free carboxyl group at the other, which is why sequences read from the N-terminus to the C-terminus. Peptide vs polypeptide vs protein covers the names for each chain length, and what are peptides? covers the molecules themselves.

Flat and partly double.

The peptide bond is not a plain single bond. The lone pair on the nitrogen is shared with the neighboring carbonyl, so the C-N bond takes on partial double-bond character. That shows in its length: about 1.32 angstroms, between a single C-N bond and a double C=N bond. As a result the atoms of the peptide group lie in one plane and the bond does not rotate freely, the fact Linus Pauling built on in his 1951 model of the alpha helix.

Bond lengths from a 2025 review of peptide bond geometry in IUCrJ.

Phi, psi and omega.

Because the peptide bond itself is rigid, a chain's shape comes from rotation around the two bonds on either side of each alpha carbon: phi, around the N-C-alpha bond, and psi, around the C-alpha-C bond. The peptide bond's own angle, omega, stays near 180 degrees. The Ramachandran plot, from a 1963 paper by Ramachandran and colleagues, maps which phi and psi combinations a residue can adopt without its atoms colliding.

Almost always trans.

A planar bond can sit in two forms, cis or trans. In proteins, trans dominates: a 1990 survey of protein structures found only 17 cis bonds among 31,005 peptide bonds not followed by proline, about 0.05%, against 99 of 1,534 bonds before a proline, about 6.5%. Proline's ring makes the two forms closer in energy, which is why X-Pro bonds are the main exception.

Strong, but slow to break.

Breaking a peptide bond with water, hydrolysis, releases energy, yet without a catalyst it is extremely slow: in neutral water at 25 °C the half-life is estimated at about 500 years. The reverse also holds: forming a peptide bond in dilute water is unfavorable, so cells and chemists both need activated building blocks to make one. In practice, peptides in a vial degrade far sooner through side-chain reactions such as deamidation and oxidation than through backbone hydrolysis; how long peptides last covers those.

Ribosomes and resin.

In cells, peptide bonds are made by the ribosome. Its peptidyl transferase center, where each new bond forms, is made of RNA: the 2000 crystal structure that showed this found no protein side-chain atom within about 18 angstroms of the reaction.

In the lab, peptides are built by solid-phase peptide synthesis, the method Bruce Merrifield introduced in 1963. The growing chain is anchored to a resin, and coupling reagents activate the carboxyl group of each incoming amino acid so it reacts with the free amino group of the chain. How peptides are made walks through the whole process.

Why HPLC reads at 214 nm.

Peptide bonds absorb ultraviolet light strongly below about 220 nm; the simple dipeptide Gly-Gly absorbs most near 193 nm. That is why HPLC purity, the headline number on a peptide lab report, is usually measured with UV detection at 210 to 220 nm, where every peptide bond in a chain contributes signal. At 214 nm one peptide bond absorbs with a molar extinction coefficient of about 923 M^-1 cm^-1. How peptides are tested explains the rest of a report.

Bonds you can check.

Every Helion compound page lists its sequence, and each published lab report confirms identity by mass and purity by HPLC. To see a chain's formula and mass from its sequence, use the peptide molecular weight calculator.

Specs and storage by compound.