IMAT Biology · Molecular Biology and Gene Expression

The Genetic Code and Protein Synthesis

The mRNA is read three bases at a time; each codon is matched by a tRNA anticodon on the ribosome, which joins the amino acids into a polypeptide.

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Why this matters

The 2024 ministry paper asked three definitions here (translation twice, the anticodon once), and the 2023 paper asked what share of all codons are stop codons. Older papers built a DNA template from tRNA anticodons (2018), counted uracils in anticodons (2017) and asked which nucleic acid takes no direct part in translation (2016).

Concept 1 of 5: Codons: why the code uses triplets, and the start and stop codons

Four bases must spell 20 amino acids. Pairs of bases give only 16 words, not enough. Triplets give 64, more than enough, so most amino acids get several codons and three codons are left to mean 'stop'.

Definition

A codon is a group of three mRNA bases that stands for one amino acid or for stop.

There are $4^3 = 64$ codons: 61 code for the 20 amino acids and 3 are stop codons (UAA, UAG, UGA).
AUG is the start codon; it also codes for methionine inside a chain.
Codons are read in order from the start codon, in one reading frame, 5′→3′ along the mRNA.
A stop codon has no matching tRNA and adds no amino acid, so a polypeptide has one amino acid fewer than the codons from start to stop.

Number of possible codons

\text{codons} = 4^{\,n}, \qquad 4^3 = 64 = 61 \text{ (amino acids)} + 3 \text{ (stop)}

$n$ number of bases per codon
$4$ number of different bases in mRNA (A, U, G, C)

Worked example

(a) Show why a code of two-base codons could not specify all 20 amino acids. (b) The coding part of an mRNA, from the first base of AUG to the last base of the stop codon, is 1203 nucleotides long. How many amino acids are in the polypeptide?

Practice this conceptself-check · 4 quick reps

Stop codons code for no amino acid and have no tRNA

At a stop codon a protein release factor, not a tRNA, binds the ribosome. So count stop codons when finding mRNA length, but not when counting amino acids.

Concept 2 of 5: Properties of the genetic code: degenerate, unambiguous, universal

Because there are more codons than amino acids, most amino acids have several codons, usually differing only in the third base. But each codon has only one meaning, and almost every organism uses the same dictionary, which is why a human gene can be read by a bacterium.

Definition

Six properties of the code, each tested by name:

Triplet, degenerate (redundant), unambiguous, non-overlapping, nearly universal, with fixed start and stop signals.
Degeneracy mostly lies in the third base of the codon, which also pairs loosely with the anticodon (the wobble position).
Known exceptions to universality are small, for example human mitochondria read UGA as tryptophan instead of stop.
Universality is what makes gene transfer between species possible; that technology belongs to the biotechnology chapter.

Property	Meaning	Example
Triplet	three bases make one codon	AUG is one codon
Degenerate	most amino acids have more than one codon	glycine: GGU, GGC, GGA and GGG
Unambiguous	each codon has only one meaning	GGU always means glycine
Non-overlapping	each base belongs to one codon, read codon after codon with no gaps	AUGGCC is read AUG, then GCC
Nearly universal	the same codons mean the same in almost all organisms	bacteria can make human insulin from the human gene

Practice this conceptself-check · 3 quick reps

Degenerate is not the same as ambiguous

Degenerate means one amino acid has several codons. Ambiguous would mean one codon has several amino acids, which never happens. The code is degenerate but unambiguous.

Concept 3 of 5: mRNA, tRNA and rRNA: structure and job of each

Three kinds of RNA share the work. mRNA carries the message, tRNA carries the amino acids and reads the message, and rRNA with proteins forms the machine that joins the amino acids. All three are single strands made by transcription, but tRNA and rRNA fold back on themselves.

Definition

All three are single polynucleotide strands of ribonucleotides (ribose; A, U, G, C), made by transcription.

A codon is on the mRNA; the matching anticodon is three bases on a tRNA.
tRNA and rRNA fold into shapes held by hydrogen bonds between their own bases.
DNA is used directly in transcription but not in translation; tRNA is used directly in translation but not in transcription.

RNA	Structure	Job
mRNA (messenger)	one linear strand of codons; in eukaryotes with a cap and a poly-A tail	carries the gene's message from DNA to the ribosome
tRNA (transfer)	one strand of about 75 to 90 nucleotides folded into a cloverleaf, with an anticodon loop; the amino acid binds the 3′ end	brings one kind of amino acid and pairs its anticodon with the codon
rRNA (ribosomal)	long strands folded and combined with proteins into the two ribosome subunits	forms the ribosome; the rRNA of the large subunit makes the peptide bonds

Practice this conceptself-check · 3 quick reps

Codons are on mRNA; anticodons are on tRNA

rRNA has no anticodons, and mRNA has no anticodons. A codon is a triplet of the message; an anticodon is the complementary triplet on the tRNA that reads it.

Concept 4 of 5: From DNA to mRNA codons to tRNA anticodons

Each step is a complement. The mRNA is the complement of the template strand, and the anticodon is the complement of the mRNA codon. Two complements bring you back to the template's letters, with U in place of T.

Definition

Lined up base by base:

Codon (mRNA, 5′→3′) = complement of the template strand.
Anticodon (tRNA, written 3′→5′ under the codon) = complement of the codon.
So the anticodons read like the template strand, with U for T, and the codons read like the coding strand, with U for T.
To find the template DNA from anticodons, keep the letters and change U to T.

Anticodons and the template strand

\text{anticodon} = \text{complement of the codon} = \text{template strand with } T \rightarrow U

Worked example

A template strand reads 3′-TAC GGA CTT-5′. Write the mRNA codons, the anticodons that read them, and the amino acids. Use: AUG = Met, CCU = Pro, GAA = Glu.

Practice this conceptself-check · 3 quick reps

Anticodons match the template strand, not the coding strand

Two complements cancel out: template → mRNA → anticodon brings you back to the template sequence, with U for T. An option that matches the coding strand describes the mRNA, not the anticodons.

Concept 5 of 5: Translation on the ribosome: initiation, elongation, termination

The ribosome slides along the mRNA one codon at a time. At each codon the right tRNA arrives with its amino acid, the ribosome moves the growing chain onto that amino acid, and the empty tRNA leaves. A stop codon ends the process.

Definition

Translation is the synthesis of a polypeptide from the information in mRNA.

It happens in the cytoplasm on ribosomes, free or on the rough ER, in prokaryotes and eukaryotes alike.
Ribosomes: 70S (30S + 50S subunits) in prokaryotes, 80S (40S + 60S) in the eukaryotic cytoplasm.
The mRNA is read 5′→3′; the chain grows from its amino (N) end to its carboxyl (C) end.
Each amino acid is joined to its tRNA by an aminoacyl-tRNA synthetase, using ATP; elongation uses GTP.
Several ribosomes can read one mRNA at once (a polysome).

Stage	What happens
Initiation	the small subunit binds the mRNA and finds AUG; the initiator tRNA carrying methionine pairs with it in the P site; the large subunit joins
Elongation	a charged tRNA enters the A site; the rRNA forms a peptide bond, passing the chain onto the new amino acid; the ribosome moves one codon along and the empty tRNA leaves from the E site
Termination	a stop codon reaches the A site; a release factor (a protein) binds; the polypeptide is freed and the subunits separate
After translation	the chain folds; proteins for secretion, made on the rough ER, are modified in the Golgi apparatus

Practice this conceptself-check · 3 quick reps

Translation is in the cytoplasm, in every kind of cell

Capping, splicing and transcription happen in the eukaryotic nucleus, but translation happens on ribosomes in the cytoplasm. It is not special to eukaryotes: bacteria translate on their own 70S ribosomes.

Summary — formulas & gotchas at a glance

A revision cheat-sheet for the formulas and gotchas above. Click any concept name to jump back to its full explanation.

Formulas (2)

Codons: why the code uses triplets, and the start and stop codons
Number of possible codons
$\text{codons} = 4^{\,n}, \qquad 4^3 = 64 = 61 \text{ (amino acids)} + 3 \text{ (stop)}$
From DNA to mRNA codons to tRNA anticodons
Anticodons and the template strand
$\text{anticodon} = \text{complement of the codon} = \text{template strand with } T \rightarrow U$

Reference tables (3)

Properties of the genetic code: degenerate, unambiguous, universal5 rows

Property	Meaning	Example
Triplet	three bases make one codon	AUG is one codon
Degenerate	most amino acids have more than one codon	glycine: GGU, GGC, GGA and GGG
Unambiguous	each codon has only one meaning	GGU always means glycine
Non-overlapping	each base belongs to one codon, read codon after codon with no gaps	AUGGCC is read AUG, then GCC
Nearly universal	the same codons mean the same in almost all organisms	bacteria can make human insulin from the human gene

mRNA, tRNA and rRNA: structure and job of each3 rows

RNA	Structure	Job
mRNA (messenger)	one linear strand of codons; in eukaryotes with a cap and a poly-A tail	carries the gene's message from DNA to the ribosome
tRNA (transfer)	one strand of about 75 to 90 nucleotides folded into a cloverleaf, with an anticodon loop; the amino acid binds the 3′ end	brings one kind of amino acid and pairs its anticodon with the codon
rRNA (ribosomal)	long strands folded and combined with proteins into the two ribosome subunits	forms the ribosome; the rRNA of the large subunit makes the peptide bonds

Translation on the ribosome: initiation, elongation, termination4 rows

Stage	What happens
Initiation	the small subunit binds the mRNA and finds AUG; the initiator tRNA carrying methionine pairs with it in the P site; the large subunit joins
Elongation	a charged tRNA enters the A site; the rRNA forms a peptide bond, passing the chain onto the new amino acid; the ribosome moves one codon along and the empty tRNA leaves from the E site
Termination	a stop codon reaches the A site; a release factor (a protein) binds; the polypeptide is freed and the subunits separate
After translation	the chain folds; proteins for secretion, made on the rough ER, are modified in the Golgi apparatus

Watch out for (5)

Stop codons code for no amino acid and have no tRNA
→ Codons: why the code uses triplets, and the start and stop codons
Degenerate is not the same as ambiguous
→ Properties of the genetic code: degenerate, unambiguous, universal
Codons are on mRNA; anticodons are on tRNA
→ mRNA, tRNA and rRNA: structure and job of each
Anticodons match the template strand, not the coding strand
→ From DNA to mRNA codons to tRNA anticodons
Translation is in the cytoplasm, in every kind of cell
→ Translation on the ribosome: initiation, elongation, termination

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