What is an amino acid?

Twenty little building blocks, one shared design. Each has a central α-carbon carrying four things — an amino group, a carboxyl group, a hydrogen, and a side chain (R). String them together and you get a protein.

The α-carbon holds four groups

The α-carbon is carbon #2 — one carbon over from the carboxyl. Everything hangs off it:

• –NH₃⁺ — the amino group
• –COO⁻ — the carboxyl group
• –H — a hydrogen
• –R — the side chain that makes each amino acid unique

At body pH, it's a zwitterion

Look closely: the amino group is protonated (+) and the carboxyl is deprotonated (−) at the same time. That double-charged, net-zero form is a zwitterion — it's how amino acids actually exist in your cells (~pH 7), not the neutral form textbooks sometimes draw.

Twenty, and they share a look

Nature actually makes hundreds of amino acids — but only these 20 get built into your proteins. Same backbone every time; the twenty different R groups are the whole story from here on.

The α-carbon is a mirror trick

Four different groups on one carbon means it's a chiral center — the molecule and its mirror image can't be superimposed, like your left and right hands. These two alanines have the same atoms and bonds, yet they're not the same molecule.

D or L — set by glyceraldehyde

Chirality is named against one reference molecule, glyceraldehyde. From it we get two whole families:

• sugars are almost all D
• amino acids in proteins are almost all L

Life is picky — it committed to one mirror form and never looked back.

Your proteins are all L

Of the twenty, 19 are chiral (glycine is the lone exception) — and every single one your ribosome puts into a protein is the L form. The enzymes that build and read proteins are themselves L-handed, so they only fit L partners.

Same backbone, twenty personalities

Every amino acid is built on the exact same core — an α-carbon holding an amino group, a carboxyl group, and a hydrogen. Only the R group changes. That one swap decides everything: size, charge, and whether the residue loves water or runs from it.

Five families, twenty members

We sort all twenty by what the side chain is like:

• Nonpolar, aliphatic (7) — greasy, water-fearing
• Aromatic (3) — flat rings, mostly hydrophobic
• Polar, uncharged (5) — H-bond happily with water
• Acidic (2) — negative at pH 7
• Basic (3) — positive at pH 7

Amino acids are acids AND bases

Every amino acid has at least two ionizable groups — an α-carboxyl and an α-amino — so as pH changes it gains or loses protons. At physiological pH it's a zwitterion: + on one end, − on the other, net zero.

Each group has its own pKa

An ionizable group flips at its pKa: below the pKa it holds its proton, above the pKa it lets go.

• α-COOH: pKa ≈ 2 — lets go early, at low pH
• α-NH₃⁺: pKa ≈ 9–10 — holds on until high pH
• some R groups ionize too — Asp, Glu, Lys, Arg, His, Cys, Tyr

The isoelectric point, pI

The pI is the pH where the net charge is exactly zero. There the amino acid won't move in an electric field, and it's least soluble in water.

Amino acids link into a chain

A protein is just amino acids joined head to tail — here are eight. Each link is a peptide bond (highlighted in teal). Real proteins run dozens to thousands of residues long; that whole chain is a polypeptide, the raw material of every protein.

Direction matters: N → C

Every chain has a free amino end (the N-terminus) and a free carboxyl end (the C-terminus). By convention we always read and write a sequence from N to C.

Primary structure runs the show

The sequence is not just a label — it contains all the folding instructions. Those side chains, in that order, decide which parts bury, which twist into helices, which pair into sheets. Get the sequence, and (in principle) you get the whole protein.

The backbone starts to fold

Once the chain exists, the backbone can't help itself — it folds into regular, repeating local shapes, each one zipped up by hydrogen bonds between a backbone N–H and a backbone C=O. Two shapes dominate every protein: the α-helix and the β-sheet.

What holds the fold together

Five interactions lock the 3-D shape in place — the buried hydrophobic core does most of the work, and the other four hold the line.

Domains — proteins built from modules

A big protein rarely folds as one blob. It folds into domains — semi-independent modules, each ~100–200 residues, each with its own job (one binds DNA, another does the chemistry).

Two lifestyles: globular vs fibrous

Most proteins fold into one of two shapes for two very different jobs:

• Globular — compact, water-soluble balls that do the chemistry: enzymes, hemoglobin, antibodies.
• Fibrous — long, repetitive, insoluble strands that hold you together: collagen, keratin, silk.

Two oxygen carriers

Your body handles oxygen with two related globins. Myoglobin sits in muscle and stores O₂ — one chain, one heme, one O₂. Hemoglobin rides in the blood and transports O₂ — four chains, four hemes, four O₂. Each hemoglobin subunit is basically a myoglobin.

Heme — where oxygen binds

The real O₂ grabber is heme: a flat ring (a porphyrin) with an iron (Fe²⁺) at its center. The iron holds one O₂ — reversibly, so it can let go again in the tissues.

Cooperativity — teamwork

The four subunits talk to each other. Empty hemoglobin sits in a tense (T) state that binds O₂ poorly. But the moment one O₂ binds, all four subunits flip to the relaxed (R) state — and now the rest bind easily. One yes makes the next yes easier — that's what bends a plain curve into an S.

Denaturation — losing the shape

The fold is held by weak interactions, so it's fragile. Heat, a big swing in pH, or a chaotrope like urea snaps those bonds and the chain unravels — this is denaturation. The peptide backbone survives; the 3-D shape (and the function) is gone. That's a fried egg: heat unfolds its proteins for good.

Reversible — or not

Take the stress away and some small proteins refold on their own — proof that the sequence already holds all the folding instructions (Anfinsen's classic result).