What Is a Peptide? Amino Acids, Peptide Bonds and Structure

Published September 30, 2026 · ROVIQ Research

A peptide is a chain of amino acids. That one sentence carries most of the chemistry a researcher needs to read a peptide's name, its sequence and its Certificate of Analysis. This guide covers what peptides are made of, how the links between amino acids form, how peptides differ from proteins, how sequences are written, and how research peptides are made and checked. It is chemistry only: it says nothing about what any peptide does in a living organism.

The building blocks: amino acids

An amino acid has a central carbon atom (the alpha carbon) carrying four groups: an amino group, a carboxyl group, a hydrogen atom, and a side chain. The side chain is what makes each amino acid different. It can be as small as a single hydrogen atom, as in glycine, or a larger group that is acidic, basic, polar or water-repelling. Proteins are built mainly from twenty standard amino acids, and each has a standard name, a three-letter symbol and a one-letter symbol (IUPAC-IUB JCBN, 1984).

The peptide bond

Two amino acids join when the carboxyl group of one reacts with the amino group of the other. The reaction releases one molecule of water, and the link it forms is an amide bond, called a peptide bond in this context. Each amino acid built into a chain this way is called a residue.

The peptide bond is not freely rotating. In their 1951 models of protein structure, Pauling, Corey and Branson built the polypeptide chain from planar amide groups (Pauling et al., 1951). That planarity is why a peptide backbone is described as a series of rigid flat units joined at the alpha carbons, with rotation possible only around the bonds on either side of each unit.

A chain has two different ends. One carries a free amino group, the N-terminus, and the other a free carboxyl group, the C-terminus. By convention, sequences are written from the N-terminus on the left to the C-terminus on the right (IUPAC-IUB JCBN, 1984).

Peptides and proteins

Chains are named by how many residues they contain: a dipeptide has two, a tripeptide three, and an oligopeptide a few. Longer chains are polypeptides. There is no sharp chemical boundary between a peptide and a protein. By a common convention, chains of up to about 50 amino acids are called peptides and longer chains proteins, though usage varies. Proteins also usually fold into a defined three-dimensional shape, which most short peptides lack.

How sequences are written

A peptide's sequence lists its residues from the N-terminus to the C-terminus, using the three-letter or one-letter symbols (IUPAC-IUB JCBN, 1984). Two examples from this site:

• GHK is the tripeptide Gly-His-Lys: glycine, histidine and lysine. GHK-Cu is that tripeptide with a bound copper ion (see GHK-Cu Research).
• Selank is the seven-residue peptide Thr-Lys-Pro-Arg-Pro-Gly-Pro, written TKPRPGP in one-letter symbols (see Selank and Semax Research).

Some names describe the length rather than the sequence. BPC-157, for example, is described in the literature as a pentadecapeptide: a peptide of fifteen residues (see BPC-157 & TB-500).

How research peptides are made

Most synthetic peptides are made by solid-phase peptide synthesis (SPPS). Its inventor, R. Bruce Merrifield, received the 1984 Nobel Prize in Chemistry for it (Merrifield, 1985). The first amino acid is attached to an insoluble resin support, and the chain is built one residue at a time. After each coupling step, excess reagents are washed away while the growing chain stays anchored to the resin. When the sequence is complete, the peptide is cut from the resin. Today the Fmoc version of SPPS is the method of choice for peptide synthesis (Behrendt et al., 2016).

Synthesis is not perfect. A step that fails can leave a chain with a residue missing (a deletion sequence) or an extra one, and side reactions can leave other structural relatives of the target (D'Hondt et al., 2014). So the crude product is purified, most often by reversed-phase HPLC (Mant et al., 2007). Purified peptides are commonly isolated together with counter-ions, such as trifluoroacetate, left over from synthesis and purification (D'Hondt et al., 2014). The glossary explains why that matters on a COA. The final product is then usually freeze-dried into a powder for storage (see Lyophilized Peptide Stability).

How a peptide's identity and purity are checked

Two measurements answer two different questions. Mass spectrometry measures the mass of what is in the sample and compares it with the mass expected from the sequence, which confirms identity. HPLC separates the sample into its components and reports what share of the detected material is the target peptide, which is purity. A Certificate of Analysis typically reports both. How to Read a Peptide COA and How to Read an HPLC Chromatogram walk through each one.