Question 1

How many amino acids are there and how are they classified?

Accepted Answer

There are 20 standard amino acids encoded by the genetic code. They are usually grouped by the chemistry of their side chain: nonpolar (aliphatic) such as glycine, alanine, valine, leucine, isoleucine, proline, and methionine; aromatic such as phenylalanine, tryptophan, and tyrosine; polar uncharged such as serine, threonine, cysteine, asparagine, and glutamine; acidic (negatively charged at pH 7) which are aspartate and glutamate; and basic (positively charged at pH 7) which are lysine, arginine, and histidine. The side chain determines nearly everything about how the residue behaves in a protein.

Question 2

Which amino acids have ionizable side chains?

Accepted Answer

Seven of the 20 have a side chain that gains or loses a proton in the normal pH range: aspartate (pKa about 3.65), glutamate (4.25), histidine (6.0), cysteine (8.18), tyrosine (10.07), lysine (10.53), and arginine (12.48). These are the only side chains that contribute to a protein's net charge, so they are the ones that matter for calculating charge at a given pH and for finding the isoelectric point. Histidine is especially important in enzymes because its pKa near 6 means it can act as both an acid and a base at physiological pH.

Question 3

What is the isoelectric point (pI) of an amino acid?

Accepted Answer

The isoelectric point is the pH at which the amino acid carries no net electrical charge, existing as a zwitterion. You find it by averaging the two pKa values that flank the neutral form. For an amino acid with no ionizable side chain, that is simply the average of the carboxyl and amino pKa values, giving a pI near 6. For an acidic amino acid you average the two lowest pKa values, and for a basic one you average the two highest, which is why aspartate has a pI of 2.77 while arginine has a pI of 10.76.

Question 4

Which amino acids are essential?

Accepted Answer

Nine amino acids are essential, meaning the human body cannot synthesize them and they must come from the diet: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, and valine. Six more are considered conditionally essential, meaning the body normally makes enough but may not during illness, stress, or rapid growth: arginine, cysteine, glutamine, glycine, proline, and tyrosine. The remaining five, alanine, asparagine, aspartate, glutamate, and serine, are non-essential.

Question 5

What does the hydropathy value mean?

Accepted Answer

The hydropathy index, from the Kyte-Doolittle scale, measures how water-repelling or water-attracting a side chain is. Positive values mean hydrophobic, with isoleucine highest at 4.5, and negative values mean hydrophilic, with arginine lowest at -4.5. Hydrophobic residues tend to be buried in a protein's core or embedded in a membrane, while hydrophilic residues sit on the surface in contact with water. This is why stretches of strongly positive hydropathy in a sequence often indicate a transmembrane helix.

Amino acid	Side-chain pKa	Charge at pH 7	Why it matters
Aspartate (D)	3.65	Negative	Deprotonated well below pH 7
Glutamate (E)	4.25	Negative	Deprotonated well below pH 7
Histidine (H)	6.00	Slightly positive	Only side chain that buffers near physiological pH; common in enzyme active sites
Cysteine (C)	8.18	Neutral (protonated)	Forms disulfide bonds when oxidized
Tyrosine (Y)	10.07	Neutral (protonated)	Absorbs at 280 nm, used to quantify protein
Lysine (K)	10.53	Positive	Protonated far above pH 7
Arginine (R)	12.48	Positive	Most basic side chain; essentially always positive

Amino Acid Chart — All 20

How to read this chart

The seven ionizable side chains

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