Peptide Sequence, Structure and Molecular Weight: A Plain-English Guide
For laboratory research use only. Not for human consumption.
Every research peptide is described by a short set of facts: its amino acid sequence, its molecular formula, its molecular weight and, often, one or more database identifiers. This guide explains what each of those terms means in general chemistry, so the descriptions you meet in papers, databases and product listings make sense. It covers chemistry and terminology only.
What a peptide is
A peptide is a chain of amino acids joined end to end. Each link is a peptide bond: an amide bond formed between the carboxyl group of one amino acid and the amino group of the next, with one molecule of water released as each bond forms.
Each amino acid within the chain is called a residue. A chain of two residues is a dipeptide, three a tripeptide, and so on.
There is no single agreed cut-off between a “peptide” and a “protein”. Many textbooks call chains of about 50 amino acids or more proteins or polypeptides, but the boundary is a convention rather than a rule, and other sources place it anywhere between about 50 and 100 residues.
The building blocks: amino acids and their codes
Proteins and most peptides are built from a standard set of 20 amino acids. Each has an official three-letter abbreviation and a one-letter code agreed by the IUPAC-IUB nomenclature commission. For example:
| Amino acid | Three-letter | One-letter |
|---|---|---|
| Glycine | Gly | G |
| Alanine | Ala | A |
| Lysine | Lys | K |
| Histidine | His | H |
| Proline | Pro | P |
Three-letter codes are easier to read; one-letter codes are compact, which is why long sequences in databases are usually written that way. Either form describes the same molecule.
Apart from glycine, the standard amino acids are chiral: they exist as two mirror-image forms, labelled L and D. The amino acids found in proteins are the L forms. Where a synthetic peptide contains a D-amino acid, that is normally shown explicitly in its name or sequence (for example with a “D-” prefix).
Reading a sequence
By convention, a peptide sequence is written from the N-terminus (the end with a free amino group) on the left to the C-terminus (the end with a free carboxyl group) on the right. So Gly-Ala and Ala-Gly are two different dipeptides, even though they contain the same two amino acids.
The order matters because it defines the molecule. Two peptides with the same amino acids in a different order have the same molecular formula and the same molecular weight, but they are different compounds. That is why molecular weight alone never identifies a peptide; the sequence does.
Beyond the chain: structural features you may see described
The sequence is the starting point, but descriptions often include extra structural detail.
- Terminal modifications. The ends of the chain can be chemically changed. Two common examples are N-terminal acetylation (written “Ac-” at the start of a sequence) and C-terminal amidation (written “-NH2” at the end). Each changes the molecular formula and the molecular weight.
- Disulfide bridges. Two cysteine residues can be linked through their sulfur atoms. This can join two parts of one chain or two separate chains.
- Cyclic peptides. Some peptides are closed into a ring instead of having two free ends.
- Non-standard residues. Synthetic peptides can include residues outside the standard 20, such as D-amino acids or other modified building blocks.
- Complexes and salt forms. A peptide may be supplied as a complex with a metal ion, or as a salt with a counter-ion. The counter-ion is not part of the peptide sequence, but it does contribute to the mass of the material.
When comparing two descriptions of “the same” peptide, these details are often where they differ.
Molecular formula and molecular weight
The molecular formula lists the atoms in one molecule, for example C4H8N2O3. The molecular weight (or molar mass) is the mass of one mole of the compound, given in grams per mole (g/mol). For a single molecule the same number is expressed in daltons (Da), where one dalton is one twelfth of the mass of a carbon-12 atom.
Working it out from the sequence
Because one water molecule is released for each peptide bond, you can estimate a peptide’s molecular weight like this:
molecular weight ≈ sum of the free amino acids − (number of peptide bonds × 18.015)
A peptide with n residues has n − 1 peptide bonds (for a simple linear chain).
Worked example: glycylglycine (Gly-Gly).
– Glycine: 75.07 g/mol. Two glycines: 150.14 g/mol.
– One peptide bond, so subtract one water: 150.14 − 18.015 = 132.12 g/mol.
– PubChem lists glycylglycine as C4H8N2O3 with a molecular weight of 132.12 g/mol, matching the calculation.
Worked example: glycylglycylglycine (Gly-Gly-Gly). Three glycines (225.21) minus two waters (36.03) gives about 189.18 g/mol. PubChem lists 189.17 g/mol; the small difference comes from rounding the inputs.
For real peptides, terminal modifications, disulfide bridges, metal complexes and counter-ions all change the figure, so a calculated value from the bare sequence is only a starting point.
Average mass and monoisotopic mass
You will often see two different masses listed for the same compound:
- Average molecular weight uses the natural mix of isotopes of each element. This is the figure used for weighing out material.
- Monoisotopic mass uses only the most abundant isotope of each element (for example carbon-12). This is the figure usually quoted in mass spectrometry.
For glycylglycine, PubChem gives an average molecular weight of 132.12 g/mol and a monoisotopic mass of 132.0535 Da. Neither figure is “wrong”; they answer different questions.
Identifiers: names, CAS numbers and PubChem CIDs
The same peptide can appear under a systematic name, a shorter common name, a code name and a sequence. Database identifiers exist so that people can be sure they mean the same compound.
- CAS Registry Number. Assigned by CAS, a division of the American Chemical Society, to a specific substance. Different salt forms or modified versions of a peptide can carry different CAS numbers.
- PubChem CID. A compound identifier in PubChem, the free public chemistry database maintained by the US National Center for Biotechnology Information (NCBI). A CID page lists the structure, molecular formula, computed masses and synonyms.
Quick reference
| Term | What it tells you |
|---|---|
| Sequence | Which amino acids, in which order (N- to C-terminus) |
| Modifications | Changes to the ends, bridges, rings or non-standard residues |
| Molecular formula | The atoms in one molecule |
| Average molecular weight | Mass per mole, natural isotope mix (g/mol) |
| Monoisotopic mass | Mass using the most abundant isotopes only (Da) |
| CAS number / PubChem CID | A database identifier for one specific substance |
Summary
A peptide’s identity is defined by its sequence and any modifications. The molecular formula and molecular weight follow from that structure, and identifiers such as CAS numbers and PubChem CIDs tie the description to one specific substance. Molecular weight on its own is never enough to tell two peptides apart.
For how lyophilised material is kept in the lab, see our storage and stability guide.
Related reading
- Storage and Stability of Lyophilised Peptides
- Lyophilised Powder vs Solution: What’s the Difference?
- Lab Equipment Checklist for Peptide Research
- Research materials
For laboratory research use only. Not for human consumption.