the anticodon
/ AN-tee-koh-don /
If a codon on the mRNA is a written word, the anticodon is the key cut to fit that exact lock. It is the three-base stretch on a transfer RNA that pairs with a matching codon, and it is how the right tRNA — and thus the right amino acid — is selected at the ribosome.
The anticodon sits in a loop at one tip of the folded tRNA, three bases exposed and ready to pair. Reading happens by ordinary base-pairing, but with the two strands running antiparallel, so the alignment is flipped: the anticodon's first base lines up against the codon's third base, and vice versa. So a codon written 5'-AUG-3' is read by an anticodon written 3'-UAC-5' (often listed in the other direction as 5'-CAU-3'). Getting this orientation right is the only reliable way to predict which tRNA reads which codon. The first two pairings are strict; the third is the loose 'wobble' position, which is why one anticodon can sometimes read several related codons.
The anticodon is one of the two ends that make the tRNA an adapter — it is the end that speaks the language of nucleic acids. But here is the subtlety that trips people up: the anticodon does not, by itself, guarantee the correct amino acid arrives. The ribosome trusts the anticodon completely and asks no questions about the cargo. The match between an anticodon and its proper amino acid is enforced earlier and elsewhere, by the charging enzyme. The anticodon decides which codon is read; it does not decide what the tRNA is carrying.
To read the mRNA codon 5'-GCA-3' (alanine), the matching tRNA presents the anticodon 3'-CGU-5'. Pairing antiparallel: codon G-C-A against anticodon C-G-U, base by base. This tRNA arrives charged with alanine.
The anticodon pairs antiparallel with the codon, so write the directions carefully.
Anticodons pair antiparallel with codons, so the simple-looking 'complement' must be flipped end-for-end. Forgetting this is the single most common mistake when matching codons to anticodons by hand.