The functional groups in proteins and peptides are a small, repeating set. The backbone holds amide (peptide) bonds plus one free amine and one free carboxyl at the ends. Side chains add hydroxyl, thiol, thioether, carboxyl, amine, carboxamide, guanidino, imidazole, phenol, indole and plain hydrocarbon groups.
- The backbone of a peptide is a repeating chain of amide (peptide) bonds with one free amine and one free carboxyl at the ends.
- IUPAC defines the side chain as carbon 3 onward; carbons 1 and 2 and nitrogen 2 form the backbone.
- Side-chain groups include hydroxyl, phenol, thiol, thioether, carboxyl, carboxamide, amine, guanidino, imidazole and indole.
- Two cysteine thiols can join through an S-S bond to form cystine.
- Lysine, arginine and histidine side chains can be protonated; aspartic, glutamic, cysteine and tyrosine side chains can be deprotonated.
What a functional group is
A chemist looking at a peptide for the first time does not read it atom by atom. She scans for familiar clusters: an -OH here, an -SH there, a nitrogen-rich ring near the end. Each cluster behaves in a predictable way wherever it turns up. Those clusters are functional groups.
A functional group is a specific arrangement of atoms that gives a molecule a particular kind of reactivity. A hydroxyl behaves like a hydroxyl whether it sits on serine or on a sugar. That is what makes the idea so handy for proteins. With twenty genetically coded amino acids and endless sequences, you cannot memorize every molecule, but you can learn about a dozen groups and predict a great deal about how a chain will dissolve, carry charge and react.
The groups fall into two places. The backbone repeats the same few groups along the whole chain. The side chains carry the variety. The IUPAC-IUB rules draw the line cleanly: carbon 1, carbon 2 and nitrogen 2 of each residue form the repeating main chain, and everything from carbon 3 onward is the side chain.
This page is organized by functional group. For the same ground organized amino acid by amino acid, see our guide to the R group in amino acids.
- Backbone: amide bonds
- Ends: free amine and carboxyl
- Hydroxyl: serine, threonine
- Thiol: cysteine
- Charged: lysine, arginine, aspartate
- Rings: histidine, tryptophan
Backbone groups: amide, amine and carboxyl
Every free amino acid carries an amine group and a carboxyl group on its alpha carbon. The IUPAC rules note that at pH 7 the usual form is R-CH(NH3+)-COO-, with the amine protonated and the carboxyl ionized, even though structures are often drawn uncharged.
When amino acids join, most of those groups are used up. The carboxyl of one residue and the amine of the next form an amide, which the IUPAC definition says may be called a peptide bond. A chain of fifty residues has forty-nine of them in a row, so the amide is by far the most common functional group in any protein.
Only the two ends escape. The N-terminal residue keeps a free amine and the C-terminal residue keeps a free carboxyl, unless something has been attached. The IUPAC text gives the usual changes: the N-terminal amine may be acetylated or formylated, and the C-terminal carboxyl may be converted to an amide, -CO-NH2. Those end groups can change a peptide's charge by one unit each, which is why sequence listings flag them. A sequence written without any note at the ends is normally read as a free amine at the start and a free carboxyl at the finish.
The backbone amide is uncharged, and it looks the same whichever two residues it joins. That uniformity is why a peptide's individual character comes almost entirely from its side chains and its two ends.
Side-chain groups at a glance
The side chains are where functional groups multiply. Reading the formulas in the IUPAC table of the twenty coded amino acids gives this map:
| Functional group | Amino acids | Formula fragment |
|---|---|---|
| Hydroxyl | Serine, threonine | HO-CH2-, CH3-CH(OH)- |
| Phenol (hydroxyl on a ring) | Tyrosine | 4-hydroxyphenyl |
| Thiol (mercapto) | Cysteine | HS-CH2- |
| Thioether (methylthio) | Methionine | CH3-S-[CH2]2- |
| Carboxyl | Aspartic acid, glutamic acid | HOOC-CH2-, HOOC-[CH2]2- |
| Carboxamide (carbamoyl) | Asparagine, glutamine | H2N-CO-CH2-, H2N-CO-[CH2]2- |
| Primary amine | Lysine | H2N-[CH2]4- |
| Guanidino | Arginine | H2N-C(=NH)-NH-[CH2]3- |
| Imidazole ring | Histidine | 1H-imidazol-4-yl |
| Indole ring | Tryptophan | 1H-indol-3-yl |
| Phenyl ring | Phenylalanine | C6H5-CH2- |
| Alkyl (hydrocarbon only) | Alanine, valine, leucine, isoleucine | CH3-, (CH3)2CH-, and so on |
Glycine has no side chain beyond a hydrogen. Proline is the odd one out: its side chain loops back and bonds to its own backbone nitrogen, making a pyrrolidine ring, so its amine is secondary rather than primary.
The systematic names in the same table spell the groups out, which helps when a certificate or database uses the formal name. Cysteine is 2-amino-3-mercaptopropanoic acid, where mercapto means the thiol. Asparagine is 2-amino-3-carbamoylpropanoic acid, where carbamoyl means the side-chain amide. Arginine is 2-amino-5-guanidinopentanoic acid, and serine is 2-amino-3-hydroxypropanoic acid. Once you know the prefixes, a systematic name reads like a list of the groups on the molecule.
The alkyl and phenyl side chains deserve a word even though they do little chemistry. Groups made only of carbon and hydrogen do not ionize and do not hydrogen-bond, so a sequence full of leucine, isoleucine, valine and phenylalanine tends to resist water. That is a property of the functional groups too, just a quiet one, and it often decides whether a peptide dissolves easily in a plain aqueous buffer for a laboratory assay.
Which functional groups carry charge?
Some side-chain groups gain or lose a proton near neutral pH, and those set most of a peptide's charge. The IUPAC rules list the residues whose ionic form is worth naming. Arginine, histidine and lysine can be protonated, giving argininium, histidinium and lysinium residues. Aspartic, glutamic, cysteine and tyrosine residues can be deprotonated, giving aspartate, glutamate, cysteinate and tyrosinate residues.
In functional-group terms, the basic groups are the amine of lysine, the guanidino group of arginine and the imidazole of histidine. The acidic groups are the carboxyls of aspartic and glutamic acid, with the thiol of cysteine and the phenol of tyrosine giving up protons less readily. Our guide to acidic and basic amino acids goes into their pKa values and what they mean for net charge.
Counting these groups is the fastest way to estimate a peptide's behavior. A sequence heavy in lysine and arginine picks up many protons in acidic solution, which also means it shows high charge states in electrospray mass spectrometry. A sequence rich in aspartic and glutamic acid leans the other way.
Groups that take part in reactions
A few groups do more than carry charge. They form new bonds, and that matters both in nature and in synthesis.
Thiol. The cysteine -SH is the most reactive side chain in the standard set. The IUPAC text describes the classic reaction: hydrogen atoms are removed from the -SH groups of two cysteines, which join through an S-S bond to form cystine. In a peptide, that disulfide bond can hold a loop or tie two chains together.
Side-chain amine and carboxyl. Lysine's second amine and the second carboxyl of aspartic and glutamic acid can form amides of their own. The IUPAC definition of a peptide includes these isopeptide bonds, and our page on the Lys-Ala isopeptide bond shows one.
Hydroxyl. The hydroxyls of serine, threonine and tyrosine are sites where modifications attach. Gerber and colleagues, for example, made synthetic peptides carrying phosphorylation, methylation or acetylation to match natural modification states, including a phosphorylated serine in the protein separase.
Thioether. Methionine's sulfur carries no hydrogen, so it cannot join a disulfide the way cysteine does. It still makes the residue heavier and more sulfur-rich than its hydrocarbon neighbors, which a formula check will show.
Amines at the N-terminus and on lysine are also the usual handles for attaching tags to a peptide, a topic covered in our guide to labeled peptides.
Why do functional groups matter for testing?
Each group leaves a fingerprint in the analytical data. Charged groups decide which charge states appear in a mass spectrum; our guide to the m/z ratio shows how those states are read. Reactive groups decide which side products are possible, from an unformed disulfide to a modification sitting on the wrong residue. End groups decide whether the theoretical mass needs an amide or acetyl correction.
Knowing the groups in a sequence lets you read a certificate with sharper questions. If a peptide has two cysteines, has the disulfide formed? If it has a modified residue, is the modification included in the stated formula? If the C-terminus is amidated, does the theoretical mass include it? For our own lots, results appear only once the certificate for that lot is published on the certificate index.
FOR LABORATORY AND IN-VITRO RESEARCH USE ONLY. NOT FOR HUMAN OR ANIMAL CONSUMPTION.
Common questions
What is the most common functional group in a protein?
Which amino acid has a thiol group?
Which side chains contain an amide?
Do the functional groups change when amino acids join?
More science guides
Sources
- IUPAC-IUB JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, 3AA-1 and 3AA-2. Table 1: names, symbols, systematic names and formulas of the twenty genetically coded amino acids.
- IUPAC-IUB JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, 3AA-6 to 3AA-10. Ionization of functional groups: the predominant zwitterion form at pH 7.
- IUPAC-IUB JCBN, Nomenclature and Symbolism for Amino Acids and Peptides, 3AA-11 to 3AA-13. Definition of a peptide and peptide bond, amino-acid residues, N- and C-terminal residues, and how peptides are named.
- Gerber SA et al., Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS, PNAS 2003 (Europe PMC record). Synthetic peptides carrying phosphorylation, methylation and acetylation, including phosphorylated Ser-1126 of separase.
