Every standard amino acid has five parts built around one central carbon, the alpha carbon. Attached to it are an amino group (-NH2), a carboxyl group (-COOH), a hydrogen atom, and a side chain called the R group. The first four are the same in every amino acid; the R group is what makes each one different.
- An alpha amino acid has an amino group, a carboxyl group, a hydrogen and an R group on one central carbon.
- The alpha carbon is the carbon directly bonded to the carboxyl group.
- Proteins are built from the same 20 standard amino acids, which differ only in their R groups.
- Every standard amino acid except glycine is chiral, and proteins use the L form.
- Glycine (C2H5NO2, 75.07) has a hydrogen as its R group; alanine (C3H7NO2, 89.09) has a methyl group.
- The amino and carboxyl groups join to form the peptide bond, releasing one water.
Four arms on one carbon
Picture a carbon atom holding four things at once, one in each direction. That is the whole plan of an amino acid. The carbon in the middle is the alpha carbon, and the four things it holds are an amino group, a carboxyl group, a hydrogen atom and a side chain.
Three of those four are identical from one amino acid to the next. Only the side chain, the R group, changes. Swap the R group and you have a different amino acid; keep it and you have the same one, whatever else happens.
So learning the parts of an amino acid is mostly learning one fixed frame and one variable slot. The rest of this page labels each part in turn and says what it does once amino acids start joining into chains.
- Alpha carbon at the center
- Amino group, -NH2
- Carboxyl group, -COOH
- Hydrogen, -H
- R group, the side chain that varies
The labeled structure
Written as a general formula, an alpha amino acid is H2N-CH(R)-COOH. Read left to right: the amino group, the alpha carbon carrying its hydrogen and its R group, then the carboxyl group.
| Part | Written as | Same in every amino acid? | What it does |
|---|---|---|---|
| Alpha carbon | C-alpha | Yes | The central atom every other part attaches to |
| Amino group | -NH2 | Yes (proline differs) | Forms the nitrogen end of a peptide bond |
| Carboxyl group | -COOH | Yes | Forms the carbon end of a peptide bond |
| Hydrogen | -H | Yes | Fills the fourth position on the alpha carbon |
| Side chain | -R | No | Sets size, charge and polarity, and names the amino acid |
The alpha carbon gets its name from its position: it is the carbon directly bonded to the carboxyl group. That is why these molecules are called alpha amino acids.
What is the alpha carbon?
The alpha carbon is the central carbon that anchors the other four parts. Every other part hangs from it, and when amino acids link into a chain, the alpha carbons become the points along the chain where side chains branch off.
Because it carries four different groups, the alpha carbon is usually a chiral center. A molecule with a chiral center has a mirror-image twin that cannot be laid over it exactly, the way a left hand cannot be laid over a right. The two forms are called L and D.
Proteins across living species are built from L-amino acids. Glycine is the one exception to chirality among the standard set: its R group is a second hydrogen, so two of its four groups are identical and it has no mirror-image partner.
The amino group and the carboxyl group
These two groups are the reason amino acids can build chains. The amino group, -NH2, is basic. The carboxyl group, -COOH, is acidic. Put one amino acid's carboxyl group next to another's amino group and they can react.
In that reaction the amino group attacks the carboxyl carbon, a molecule of water leaves, and an amide bond forms between them. When it joins amino acids, that amide bond is called the peptide bond. The amino acids on either side are now called residues.
Both groups also carry charge in water. At neutral pH the carboxyl group, with a pKa near 2, has lost its proton, and the amino group, with a pKa near 9, has gained one. A free amino acid at neutral pH therefore carries a positive and a negative charge at once, a form called a zwitterion.
Proline is the one standard amino acid that bends this rule. Its side chain loops back and bonds to its own amino nitrogen, forming a five-membered ring, so its nitrogen is a secondary amine.
The hydrogen
The hydrogen on the alpha carbon is the least discussed part, and it still matters. It is the fourth group that completes the carbon's set of four bonds.
In glycine, the R group is also a hydrogen. That is why glycine is the smallest standard amino acid and the only achiral one. PubChem lists glycine as C2H5NO2, molecular weight 75.07, under the systematic name 2-aminoacetic acid.
Compare alanine, where the R group is a methyl group, -CH3. PubChem lists it as C3H7NO2, molecular weight 89.09, named (2S)-2-aminopropanoic acid. The only difference between the two molecules is that one hydrogen has become a methyl group, which adds one carbon and two hydrogens and makes the alpha carbon chiral. The (2S) in alanine's name records which of the two mirror forms it is.
Which part makes each amino acid different?
The R group makes each amino acid different. It is the variable part, and it is the part that gives each amino acid its identity and behavior. Proteins in all living species are built from the same set of 20 standard amino acids, which means 20 different R groups on the same frame.
Side chains are usually sorted into four groups by their chemistry:
- Nonpolar, such as alanine and leucine
- Polar but uncharged, such as serine and threonine
- Negatively charged, aspartic acid and glutamic acid
- Positively charged, histidine, lysine and arginine
Our guide to the R group in amino acids goes through the side chains in detail, and acidic and basic amino acids covers the charged ones.
Adding up the parts: a worked example
The parts also explain the arithmetic behind a molecular formula. Take glycine and alanine from the PubChem records above and join them into the dipeptide glycyl-alanine.
Glycine's carboxyl group reacts with alanine's amino group. The carboxyl gives up an -OH and the amino group gives up an -H, which leave together as one water molecule, H2O. Everything else stays.
| Step | Formula | Molecular weight |
|---|---|---|
| Glycine | C2H5NO2 | 75.07 |
| Alanine | C3H7NO2 | 89.09 |
| Sum | C5H12N2O4 | 164.16 |
| Minus one water | H2O | 18.02 |
| Glycyl-alanine | C5H10N2O3 | about 146.14 |
The same subtraction repeats for every bond in a longer chain: a peptide with n residues has n minus 1 peptide bonds and has lost n minus 1 waters. That is the arithmetic a laboratory runs when it predicts the mass a mass spectrometer should report for a known sequence.
Common labeling mistakes
A few errors turn up again and again on hand-drawn structures.
The first is labeling the wrong carbon as alpha. In an amino acid with a long side chain, such as lysine, there are several carbons, and only the one bonded directly to the carboxyl group is the alpha carbon. The others belong to the R group.
The second is drawing proline like the others. Proline's side chain closes into a ring on its own nitrogen, so its amino group is part of that ring and carries one hydrogen fewer. A diagram that gives proline a free -NH2 is wrong.
The third is forgetting charge. The neutral formula H2N-CH(R)-COOH is how amino acids are usually drawn, but in water at neutral pH the groups sit as -NH3+ and -COO-. Both drawings describe the same molecule; they describe it in different conditions, and a labeled diagram should say which one it shows.
What happens to the parts in a peptide?
In a peptide, the parts split into two jobs: backbone and side chain. The amino group, alpha carbon and carboxyl carbon of each residue become the repeating backbone of the chain. The R groups hang off that backbone, one per residue.
Most of the amino and carboxyl groups are used up in peptide bonds. Only two survive in their free form: the amino group on the first residue, called the N-terminus, and the carboxyl group on the last, called the C-terminus. That is why a peptide of any length has exactly one of each, unless its ends have been capped.
The backbone geometry that results is covered in our guide to the polypeptide backbone, and how single amino acids act as building blocks for larger molecules is in amino acids as monomers.
For laboratory work, the same parts explain how a peptide's mass is calculated: add up the residues and account for one water lost per peptide bond.
FOR LABORATORY AND IN-VITRO RESEARCH USE ONLY. NOT FOR HUMAN OR ANIMAL CONSUMPTION.
Common questions
What are the main parts of an amino acid?
Which part of an amino acid makes each one different?
Why is it called the alpha carbon?
Which parts of an amino acid form the peptide bond?
More science guides
Sources
- LibreTexts Biology, Fundamentals of Biochemistry (Jakubowski and Flatt), 3.1 Amino Acids and Peptides. The four groups on the alpha carbon, L-amino acids in proteins, glycine's achirality, zwitterions and pKa values near 2 and 9, proline's ring, residues and peptide bond formation.
- LibreTexts Chemistry, 18.3 Amino Acids (Saint Francis University, Chem 114). Definition of the alpha carbon, the set of 20 amino acids, L and D forms, and the four side-chain classes.
- PubChem Compound Summary for CID 750, Glycine. Formula C2H5NO2, molecular weight 75.07, IUPAC name 2-aminoacetic acid.
- PubChem Compound Summary for CID 5950, L-Alanine. Formula C3H7NO2, molecular weight 89.09, IUPAC name (2S)-2-aminopropanoic acid.
