N-terminus vs C-terminus.
Every peptide chain has two different ends. The N-terminus carries a free amino group and the C-terminus a free carboxyl group, and sequences are always written from the first to the second. Here is how to tell them apart, why direction matters, and what caps such as Ac- and -NH2 do to each end.
Amino end and carboxyl end.
Amino acids join through peptide bonds, each formed between the carboxyl group of one amino acid and the amino group of the next. Every bond uses up one of each, so a linear chain is left with one free amino group at one end, the N-terminus (amino terminus), and one free carboxyl group at the other, the C-terminus (carboxyl terminus).
| N-terminus | C-terminus | |
|---|---|---|
| Also called | Amino terminus, N-terminal end | Carboxyl terminus, C-terminal end |
| Free group | Alpha-amino group (NH2) | Alpha-carboxyl group (COOH) |
| Charge near pH 7 | Mostly +1 (protonated) | About -1 (deprotonated) |
| Measured pKa in proteins | 7.7 on average | 3.3 on average |
| Place in a written sequence | Left, residue 1 | Right, the last residue |
| Common cap | Acetyl, written Ac- | Amide, written -NH2 |
| Made first by | Ribosomes, in cells | Solid-phase chemical synthesis |
Why sequences read N to C.
By convention, a sequence is written from the N-terminus on the left to the C-terminus on the right, and residues are numbered from the N-terminus, so residue 1 is always the amino end. The convention follows biology: ribosomes build proteins by adding each new amino acid to the C-terminal end of the growing chain, so the N-terminal residue is made first.
Chemical synthesis runs the other way. In solid-phase peptide synthesis, the standard method for research peptides, the C-terminal amino acid is anchored to a resin and the chain is extended one residue at a time toward the N-terminus. The written sequence stays N to C either way.
Direction is part of a peptide's identity. GHK (Gly-His-Lys) and KHG (Lys-His-Gly) contain the same three amino acids and have the same formula and mass, but they are different molecules. A mass result alone cannot tell them apart; tandem mass spectrometry can, because the fragments it produces depend on the order.
Ac- and -NH2.
Many peptides carry a cap on one or both ends. N-terminal acetylation (Ac-) adds an acetyl group, C2H2O or 42.04 g/mol, and removes the N-terminal positive charge. In cells it is one of the most common protein modifications: a proteomics study found 84% of the human protein N-termini it examined acetylated. C-terminal amidation (-NH2) replaces the terminal OH with NH2, lowering the mass by 0.98 g/mol and removing the negative charge. Many peptide hormones are amidated, and structure-activity data for 45 bioactive peptides found the amide required for the full activity of most of them.
| Compound | Written as | N-terminus | C-terminus |
|---|---|---|---|
| TB-500 | Ac-LKKTETQ | Acetylated | Free acid |
| SS-31 | D-Arg-Dmt-Lys-Phe-NH2 | Free amine | Amide |
| Ipamorelin | Aib-His-D-2-Nal-D-Phe-Lys-NH2 | Free amine | Amide |
| CJC-1295 (no DAC) | 29 residues ending in Arg-NH2 | Free amine | Amide |
| Tesamorelin | trans-3-hexenoyl-GHRH(1-44)-NH2 | Hexenoyl cap | Amide |
| MOTS-c | MRWQEMGYIFYPRKLR | Free amine | Free acid |
| BPC-157 | GEPPPGKPADDAGLV | Free amine | Free acid |
| GHK-Cu | Gly-His-Lys, with copper(II) | Free amine | Free acid |
Sequences as listed on each compound page.
What the ends add to net charge.
Near pH 7 an uncapped peptide carries about +1 at the N-terminus and -1 at the C-terminus, on top of its side-chain charges. Capping an end removes its charge. TB-500 shows the effect: with its acetyl cap, Ac-LKKTETQ has an estimated net charge of about 0 at pH 7, while the same sequence with a free N-terminus comes to about +1.0. Compare them in the calculator, capped and uncapped; the amino acid chart lists the pKa values behind the estimate.
Caps on the label.
Each Helion compound page lists its sequence with its caps, and every published lab report confirms identity by mass, which shifts with each cap. For a sequence of your own, the peptide molecular weight calculator applies both caps.
Specs and storage by compound.
Questions (8)
What is the N-terminus of a peptide?
The end of the chain with a free amino group. It is written first, on the left, and its residue is numbered 1.
What is the C-terminus of a peptide?
The end of the chain with a free carboxyl group. It is written last, on the right.
What is the difference between the N-terminus and the C-terminus?
The N-terminus has a free amino group and is mostly positively charged near pH 7; the C-terminus has a free carboxyl group and is negatively charged. Sequences run from N to C.
Which end of a peptide is made first?
In cells, the N-terminus: ribosomes add each new amino acid to the C-terminal end. In solid-phase chemical synthesis it is the reverse, and the C-terminal residue is attached to the resin first.
What does Ac- mean in a peptide sequence?
An acetylated N-terminus. The acetyl group adds 42.04 g/mol and removes the N-terminal positive charge, as in TB-500, Ac-LKKTETQ.
What does -NH2 mean at the end of a peptide sequence?
An amidated C-terminus: the terminal OH is replaced by NH2, which lowers the mass by 0.98 g/mol and removes the negative charge, as in SS-31, D-Arg-Dmt-Lys-Phe-NH2.
Is the N-terminus positive?
Usually. Its amino group has a measured pKa of about 7.7 in proteins, so near pH 7 it is mostly protonated and positive, unless it is acetylated.
Does reversing a sequence change its mass?
No. A reversed sequence has the same amino acids, formula and mass, but it is a different molecule; tandem mass spectrometry, which breaks the chain into fragments, can tell them apart.
Published studies (5)
- IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN). Nomenclature and symbolism for amino acids and peptides. Recommendations 1983
- A summary of the measured pK values of the ionizable groups in folded proteins
- Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans
- C-terminal amidated peptides: production by the in vitro enzymatic amidation of glycine-extended peptides and the importance of the amide to bioactivity
- Advances in Fmoc solid-phase peptide synthesis
Citations from PubMed for reference. They describe the compound in the literature, not any Helion lot, and nothing here is guidance on use.