Aspartic acid and glutamic acid are the acidic amino acids: their side chains lose a proton and turn negative at neutral pH. Lysine, arginine and histidine are the basic ones and can pick up a proton. Arginine is basic. Histidine is the odd one, mostly uncharged at pH 7.
- The acidic amino acids are aspartic acid and glutamic acid, with side-chain pKa values near 3.9 and 4.3.
- The basic amino acids are lysine, arginine and histidine; arginine's guanidino group has the highest listed pKa, 13.2.
- At pH 7 aspartate and glutamate are negative, lysine and arginine are positive, and histidine is mostly uncharged.
- Histidine's side-chain pKa of about 6 means roughly nine percent of its side chains are protonated at pH 7.
- An acetylated N-terminus or amidated C-terminus removes that end's charge from a peptide's net charge count.
Five side chains that hold a charge
Drop a pinch of salt in water and it splits into charged pieces. A few amino acids do something similar, only the charge stays stuck to one spot on the molecule. Five of the twenty that build proteins have a side chain that can gain or lose a proton, and so carry a plus or minus charge depending on how acidic the water around them is.
Two of them are acidic: aspartic acid and glutamic acid. Their side chains end in a carboxylic acid group, and at neutral pH that group has given up its proton and sits as a negatively charged carboxylate. Written in that charged form they are usually called aspartate and glutamate.
Three are basic: lysine, arginine and histidine. Their side chains contain nitrogen that can accept a proton and become positive. Lysine and arginine do this firmly at neutral pH. Histidine does it only partly, which is why it gets its own section below.
The polar amino acids guide covers all the water-loving side chains, charged and uncharged, and how hydropathy scales rank them. This page stays with the charged five: which way each one goes, how far, and why it matters when you read a peptide sequence or a lab report.
- Aspartic acid, about 3.9: negative at pH 7
- Glutamic acid, about 4.3: negative at pH 7
- Histidine, about 6.0: mostly neutral at pH 7
- Lysine, about 10.5: positive at pH 7
- Arginine, about 13.2: positive at pH 7
The pKa values behind each charge
Whether a group carries its proton comes down to one number, its pKa. When the pH of the solution is below the pKa, the group mostly keeps the proton. Above it, the group mostly loses it. At exactly the pKa, half the molecules have it and half do not.
Each free amino acid has at least two ionizable groups, the alpha-carboxyl and the alpha-amino group, and the charged five add a third on the side chain. The figures below are the ones PubChem carries from the Merck Index via the Hazardous Substances Data Bank. Other entries in the same records differ by a few tenths, and some were measured at a different temperature, so treat them as good working values rather than constants.
| Amino acid | Alpha-carboxyl | Alpha-amino | Side chain | Side chain at pH 7 |
|---|---|---|---|---|
| Aspartic acid (Asp, D) | 1.92 | 9.87 | 3.87 (carboxyl) | Negative |
| Glutamic acid (Glu, E) | 2.19 | 9.67 | 4.25 (carboxyl) | Negative |
| Lysine (Lys, K) | 2.18 | 8.95 | 10.53 (amine, at 38 °C) | Positive |
| Arginine (Arg, R) | 2.18 | 9.09 | 13.2 (guanidino) | Positive |
| Histidine (His, H) | 1.78 | 8.97 | 5.97 (imidazole) | Mostly neutral |
Read the side-chain column against pH 7 and the pattern falls out. The two carboxyls sit three pH units below neutral, so they are almost entirely deprotonated. The lysine amine and the arginine guanidino group sit three to six units above, so they are almost entirely protonated. Histidine sits one unit below, close enough to be partly charged and partly not.
Is arginine acidic or basic?
Basic, and the most strongly basic of the twenty. The name trips people up because every amino acid has an acid group in its backbone, and arginine is no exception. What makes it basic is the side chain: a guanidino group whose listed pKa of 13.2 is higher than any other side chain in the table.
A pKa that high means the group holds its proton across practically every pH a peptide solution will see in a laboratory. You would need a strongly alkaline solution to strip it. So in a sequence, every R counts as a positive charge, full stop.
Lysine is close behind. Its side chain amine, at 10.53, also stays protonated at neutral pH, and every K in a sequence usually counts as one positive charge. The practical difference between the two shows up mainly at high pH, where lysine starts to lose its charge well before arginine does.
The same question gets asked about histidine, and the answer there is less tidy. It is classed as basic because its imidazole ring can take a proton. At pH 7, though, it mostly has not.
Why is histidine a borderline case?
With a side-chain pKa of 5.97, histidine is the only one of the five whose charge changes inside the ordinary working range of a lab buffer. The arithmetic is short. At pH 7, one unit above the pKa, the ratio of uncharged to charged imidazole is ten to the power of one, about ten to one. Roughly nine percent of the side chains carry a proton and the rest do not.
Drop the pH to 6 and it is close to half and half. Drop it to 5 and most of the histidines are positive. So the same peptide can carry a different net charge in two buffers that look almost identical on paper.
That sensitivity is the reason histidine turns up so often in discussions of buffering and of metal binding. A group that can take or give a proton near neutral pH is useful in chemistry for exactly the reason it is awkward in a sequence count: it does not sit still. When you tally the charge on a peptide at pH 7, count each histidine as roughly zero and note that the figure moves if the pH moves.
Isoelectric points, computed from the table
The isoelectric point, or pI, is the pH at which a molecule carries no net charge. For a free amino acid with three ionizable groups, it is the average of the two pKa values on either side of the neutral form. Using the PubChem figures above:
- Aspartic acid: (1.92 + 3.87) / 2 = about 2.9
- Glutamic acid: (2.19 + 4.25) / 2 = about 3.2
- Histidine: (5.97 + 8.97) / 2 = about 7.5
- Lysine: (8.95 + 10.53) / 2 = about 9.7
- Arginine: (9.09 + 13.2) / 2 = about 11.1
These are our calculations from the listed constants, and they inherit whatever spread those constants have. The ranking is what matters: the two acidic residues sit at the bottom, arginine at the top, histidine near neutral.
For a peptide the pI depends on every ionizable group in the chain, including the two ends, and the side-chain pKa values shift once the residue sits inside a chain rather than floating free. Software estimates a peptide pI from the sequence. Treat the output as an estimate for the same reason.
Counting the charge on a short peptide
For a quick estimate at pH 7, give each free N-terminal amine +1, each free C-terminal carboxyl −1, each K and R +1, each D and E −1, and each H about zero. Capped ends change the count: an acetylated N-terminus loses its +1 and an amidated C-terminus loses its −1.
Two small examples from this catalog:
| Peptide | Ends | Side chains | Estimated net charge |
|---|---|---|---|
| KPV (Lys-Pro-Val) | +1 and −1 | K +1 | +1 |
| GHK (Gly-His-Lys) | +1 and −1 | H about 0, K +1 | About +1 |
Both come out mildly positive. That is the sort of thing a lab wants to know before it picks a container or a chromatography method, because charged peptides stick to some surfaces more than others and separate differently on ion-exchange and reversed-phase columns.
The estimate ignores counterions. A basic peptide purified by reversed-phase HPLC is usually isolated as a salt, with an anion such as trifluoroacetate or acetate paired to each positive charge. Those counterions add weight to the powder without adding peptide, which is one reason net peptide content on a certificate sits below the labeled mass.
Where this shows up in a lab report
A certificate of analysis rarely talks about charge directly, but charge sits behind several of its lines. Mass spectrometry by electrospray ionizes peptides by adding protons, and basic residues are where many of those protons land, so a peptide rich in lysine and arginine often shows several charge states in its spectrum. The reported mass is the neutral mass worked back from those peaks.
Acidic residues matter for stability. Aspartic acid in particular is a known weak point in a backbone, and the R group guide covers how side chains become the sites where peptides degrade. For the broader question of what these building blocks are for inside a cell, see what amino acids do. The guide to reading a peptide COA walks through the certificate fields themselves.
FOR LABORATORY AND IN-VITRO RESEARCH USE ONLY. NOT FOR HUMAN OR ANIMAL CONSUMPTION.
Common questions
Which amino acids are acidic?
Is arginine acidic or basic?
Why is histidine sometimes called basic and sometimes neutral?
Do pKa values change inside a peptide?
More science guides
Sources
- PubChem, L-Aspartic acid, dissociation constants. pK1 1.92, pK2 3.87 and pK3 9.87 as listed from the Merck Index.
- PubChem, L-Glutamic acid, dissociation constants. pK1 2.19, pK2 4.25 and pK3 9.67.
- PubChem, L-Lysine, dissociation constants. pK1 2.18, pK2 8.95 and pK3 10.53 at 38 degrees C.
- PubChem, L-Arginine, dissociation constants. pK1 2.18, pK2 9.09 and pK3 13.2.
- PubChem, L-Histidine, dissociation constants. pK1 1.78, pK2 5.97 and pK3 8.97.
- National Human Genome Research Institute, Talking Glossary: Amino Acids. Twenty amino acids build proteins, linked in chains called polypeptides.
