Key facts
- Also called
- Carboxyl terminus, carboxy terminus, C-terminal end
- Chemical group
- Free alpha-carboxyl group of the last residue
- Position in sequence
- Written last (rightmost)
- Written as
- -OH (free acid) or -NH2 (amide)
- Acid vs amide mass
- Amide is 0.98 Da lighter
- Analytical relevance
- y-ion series in MS/MS; anchor point in SPPS
C-Terminus Definition
The C-terminus is the end of a peptide chain: the last amino acid residue, whose alpha-carboxyl group is not part of a peptide bond [1].
Every peptide bond uses up the carboxyl group of one residue and the amino group of the next. Follow a linear chain to its far end and you find one carboxyl group with nothing to bond to. The residue holding it is the C-terminal residue, and that free carboxyl group is what defines the C-terminus. The opposite end is the N-terminus.
In BPC-157 (GEPPPGKPADDAGLV) the C-terminal residue is valine; in KPV it is also valine; in MOTS-c it is arginine.
Why Is the C-Terminus Written Last?
It comes last because sequences are written N to C, the same order in which ribosomes build chains [1][2].
During translation, each new amino acid goes onto the carboxyl end of the growing chain, so the C-terminal residue is the last one added [2]. Chemical synthesis does it backwards. In solid-phase peptide synthesis, introduced by Merrifield in 1963, the C-terminal residue goes onto the solid support first, and the chain grows toward the N-terminus [3]. Pick the resin and linker, and you have decided whether the finished peptide comes off as a free acid or as an amide.
What Do -OH and -NH2 Mean at the End of a Sequence?
If a sequence ends in -OH, the C-terminus is a free carboxylic acid. If it ends in -NH2, the acid has been converted to a carboxamide.
| Form | Written | Group | Charge near pH 7 | Example |
|---|---|---|---|---|
| Free acid | -OH (or no suffix) | -COOH / -COO- | Negative | BPC-157, KPV, PT-141 (written -OH) |
| Amide | -NH2 | -CONH2 | Neutral | Sermorelin, ipamorelin, SS-31 |
| Ester | -OMe, -OEt, etc. | -COOR | Neutral | Synthetic intermediates |
On paper the change is one suffix. Chemically, you are looking at a different molecule. Replacing -OH with -NH2 lowers the monoisotopic mass by 0.98 Da and changes the formula by swapping one oxygen for one nitrogen and one hydrogen. Sermorelin is a good example. It is defined as GHRH (1-29) with an amidated C-terminus: YADAIFTNSYRKVLGQLSARKLLQDIMSR-NH2.
The acid and amide differ by less than 1 Da, which low-resolution mass data can easily blur. To avoid mislabeling, use high-resolution mass spectrometry or confirm the C-terminal form from synthesis records.
Charge and Chemistry at the C-Terminus
Near neutral pH, a free C-terminus is acidic and usually carries a negative charge. An amidated one carries no charge at all.
The terminal carboxyl group in a peptide typically has a pKa of roughly 2 to 3, so at pH 7 nearly all molecules carry it as -COO-. Amidation removes that negative charge, which shifts the peptide's net charge, isoelectric point and behavior in reversed-phase HPLC. Short peptides have few other charged groups to dilute the effect, so here the C-terminal form can visibly move the retention time.
Why Are So Many Peptides C-Terminally Amidated?
Plenty of natural peptide hormones and neuropeptides end in an amide. Synthetic analogues usually keep it so they match the natural structure.
Cells do it with an enzyme system that works on a precursor ending in glycine. The glycine is cleaved off, and its nitrogen stays behind as the C-terminal amide [4]. Reviews of neuropeptide biosynthesis describe this alpha-amidation as a common final processing step [4]. A lab that wants to study the natural molecule needs that amide in place, and that explains why so many synthetic analogue sequences end in -NH2. The ending belongs to the compound's identity, and to its PubChem formula.
There is also carboxypeptidase activity to think about. These enzymes strip amino acids off the C-terminus one at a time, so in vitro stability studies report the C-terminal form alongside the sequence.
How the C-Terminus Is Used in Analysis
Tandem mass spectrometry uses the C-terminus as the anchor for the y-ion series, the counterpart to the b ions that carry the N-terminus.
Under the standard fragment nomenclature, backbone fragments that keep the C-terminus are named x, y and z ions [5]. A y-ion ladder confirms the sequence from the C-terminal side, and its mass offsets show whether the terminus is an acid or an amide [5]. Put it together with the b ions and you have two independent readings of one chain. See Mass Spectrometry and LC-MS for how the data are produced.
On a Certificate of Analysis, the C-terminal form should be stated in the sequence line and reflected in the expected mass. If a document gives the sequence but never says -OH or -NH2, ask which form you actually received.
C-Terminus vs Carboxyl Side Chains
The C-terminus is one specific carboxyl group. Do not confuse it with the carboxyl groups on aspartic acid and glutamic acid side chains.
Those Asp and Glu side-chain carboxyls can form bonds as well. Glutathione shows how: its glutamate links to cysteine through the side-chain gamma carboxyl, not the alpha carboxyl, while the true C-terminus is the carboxyl of glycine at the other end [6]. See Glutathione and Understanding Peptide Sequences to see how links like this are written.
FAQFrequently asked questions
What is the C-terminus of a peptide?
It is the end of the chain, where the last amino acid keeps a free carboxyl group. In any sequence it is written last. Every other residue uses its alpha-carboxyl group in a peptide bond, so the C-terminal residue is the only one whose alpha-carboxyl group remains free unless it is modified.
What does -NH2 mean at the end of a peptide sequence?
It means the C-terminal carboxyl group has been turned into an amide (-CONH2). That amide is uncharged, about 0.98 Da lighter than the free acid, and has a different formula. Because it is part of the compound's identity, sermorelin, ipamorelin and SS-31 are all written with -NH2.
Is the C-terminus positive or negative?
Near neutral pH a free C-terminus is usually negative, because its carboxyl group typically has a pKa of roughly 2 to 3 and is ionized to -COO-. An amidated C-terminus carries no charge. That one difference shifts net charge, isoelectric point and HPLC retention.
What is the difference between the C-terminus and the N-terminus?
The N-terminus is the start of the chain, with a free amino group, and the C-terminus is the end, with a free carboxyl group. Sequences run from N to C. Ribosomes build chains from the N-terminus, while solid-phase synthesis builds them from the C-terminus anchored to a resin.
Why are some synthetic peptides amidated at the C-terminus?
Many natural peptide hormones and neuropeptides end in an amide made by enzymatic processing of a glycine-extended precursor. Synthetic analogues often keep the amide so the laboratory compound matches the natural structure. The chemist sets this during synthesis by choosing the resin and linker.
How can you tell whether a peptide ends in an acid or an amide?
Start with the written sequence and look for -OH or -NH2. Then compare the measured mass with the calculated mass for each form. The two differ by 0.98 Da, so high-resolution mass spectrometry or y-ion fragment data are the most reliable way to confirm which C-terminal form is present.
REFScientific references
-
IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983. Eur J Biochem. 1984;138(1):9-37. PubMed 6692818
nomenclature standard -
Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 4th ed. New York: Garland Science; 2002. From RNA to Protein. NCBI Bookshelf NBK26829. Source
textbook (NCBI Bookshelf) -
Merrifield RB. Solid phase peptide synthesis. I. The synthesis of a tetrapeptide. J Am Chem Soc. 1963;85(14):2149-2154. doi:10.1021/ja00897a025 (not indexed in PubMed; verified via Crossref).
original chemistry method paper -
Eipper BA, Stoffers DA, Mains RE. The biosynthesis of neuropeptides: peptide alpha-amidation. Annu Rev Neurosci. 1992;15:57-85. PubMed 1575450
review -
Roepstorff P, Fohlman J. Proposal for a common nomenclature for sequence ions in mass spectra of peptides. Biomed Mass Spectrom. 1984;11(11):601. PubMed 6525415
nomenclature proposal (mass spectrometry)
Research Library: Peptide Fundamentals
Research Library
Research Library: Peptide Fundamentals
Peptides