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Translation (Protein Synthesis)

Translation is the process by which the nucleotide sequence of an mRNA is decoded by the ribosomal machinery to produce a specific sequence of amino acids - a polypeptide. It is the second step of gene expression, following transcription. - Biochemistry, Lippincott Illustrated Reviews, 8th ed.

Overview: The Central Dogma

DNA  →  (transcription)  →  mRNA  →  (translation)  →  Protein

After transcription and post-transcriptional processing (capping, poly-A tail addition, intron splicing), the mature mRNA travels from the nucleus to the cytoplasm, where ribosomes read its sequence and build the protein. - Histology: A Text and Atlas, 9th ed.

Key Molecular Players

1. mRNA and the Genetic Code

The mRNA carries the genetic message as a series of codons - triplets of three nucleotides. There are 4³ = 64 possible codons, encoding:

20 amino acids
3 stop codons: UAA, UAG, UGA
1 universal start codon: AUG (codes for methionine)

The code is degenerate - most amino acids are specified by more than one codon. Leucine and arginine each have 6 codons; only methionine and tryptophan have a single codon. - Thompson & Thompson Genetics and Genomics in Medicine, 9th ed.

The Complete Genetic Code:

First Base	U	C	A	G
U	Phe, Phe, Leu, Leu	Ser, Ser, Ser, Ser	Tyr, Tyr, Stop, Stop	Cys, Cys, Stop, Trp
C	Leu, Leu, Leu, Leu	Pro, Pro, Pro, Pro	His, His, Gln, Gln	Arg, Arg, Arg, Arg
A	Ile, Ile, Ile, Met	Thr, Thr, Thr, Thr	Asn, Asn, Lys, Lys	Ser, Ser, Arg, Arg
G	Val, Val, Val, Val	Ala, Ala, Ala, Ala	Asp, Asp, Glu, Glu	Gly, Gly, Gly, Gly

(Third base varies within each cell; Stop = UAA/UAG/UGA)

2. Transfer RNA (tRNA)

tRNA molecules are the adaptors that bridge the codon-amino acid relationship:

Each is 70-100 nucleotides long, folded into a cloverleaf structure
The 3' end carries a specific amino acid (attached by aminoacyl-tRNA synthetase) - a charged tRNA
The anticodon loop contains three bases that base-pair with the complementary mRNA codon
At least 50 tRNA species exist in humans; since some amino acids have multiple codons, one tRNA can recognize more than one codon via the wobble hypothesis (flexible pairing at the third/wobble position)
Biochemistry, Lippincott Illustrated Reviews, 8th ed.

3. Ribosomes

Ribosomes are macromolecular machines composed of ribosomal RNA (rRNA) and proteins:

Feature	Prokaryotic	Eukaryotic
Size	70S	80S
Small subunit	30S	40S
Large subunit	50S	60S

The ribosome has three tRNA-binding sites:

A site (Aminoacyl) - accepts incoming charged tRNA
P site (Peptidyl) - holds the tRNA linked to the growing polypeptide chain
E site (Exit) - holds the outgoing uncharged (empty) tRNA before it leaves

The small subunit ensures accurate codon-anticodon pairing; the large subunit catalyzes peptide bond formation. - Tietz Textbook of Laboratory Medicine, 7th ed.

The Three Stages of Translation

Ribosome translating mRNA - showing E, P, A sites, growing polypeptide chain, tRNA anticodon binding, and direction of synthesis

Stage 1 - Initiation

The goal is to assemble the ribosome around the start codon on mRNA.

In eukaryotes:

Initiation factor eIF-4E binds the 5' methylguanosine cap of the mRNA
Poly(A)-binding protein (PABP) binds the 3' poly-A tail
eIF-4G bridges eIF-4E and PABP, circularizing the mRNA
The pre-initiation complex forms: 40S small subunit + eIF-2 + Met-tRNA
This complex scans the mRNA 5'→3' until it finds the AUG start codon
The 60S large subunit joins, forming the complete 80S initiation complex
Translation elongation begins

Tietz Textbook of Laboratory Medicine, 7th ed.

In prokaryotes, the 30S subunit binds directly at the Shine-Dalgarno sequence (a purine-rich region ~10 bases upstream of AUG), placing AUG in the P site directly.

Stage 2 - Elongation

Amino acids are added one at a time, reading the mRNA 5'→3'. Each cycle has three steps:

Aminoacyl-tRNA binding (A site entry)
- A charged tRNA with the matching anticodon enters the A site (assisted by elongation factor EF-Tu·GTP in prokaryotes; eEF-1·GTP in eukaryotes)
- GTP hydrolysis confirms correct codon-anticodon pairing
Transpeptidation (Peptide bond formation)
- The peptidyl transferase activity of the large subunit rRNA (a ribozyme) transfers the growing peptide chain from the P-site tRNA to the amino acid on the A-site tRNA
- A new peptide bond forms; the chain grows by one amino acid
Translocation
- The ribosome moves exactly 3 nucleotides (one codon) in the 5'→3' direction (powered by EF-G·GTP in prokaryotes; eEF-2·GTP in eukaryotes)
- The tRNA in A site shifts to P site; the now-empty P-site tRNA moves to E site and exits
- The A site is free for the next aminoacyl-tRNA

This cycle repeats for every codon, building the polypeptide from the N-terminus to the C-terminus.

Biochemistry, Lippincott Illustrated Reviews, 8th ed.

Stage 3 - Termination

When a stop codon (UAA, UAG, or UGA) enters the A site:

No tRNA matches a stop codon
Release factors (RF-1/RF-2 in prokaryotes; single eRF in eukaryotes) recognize the stop codon
Release factors trigger hydrolysis of the bond between the peptide and the P-site tRNA
The completed polypeptide is released
The ribosomal subunits, mRNA, and tRNA dissociate and are recycled
Biochemistry, Lippincott Illustrated Reviews, 8th ed.

After Translation - Post-Translational Events

Once released, the polypeptide undergoes further processing:

Protein folding - spontaneous or chaperone-assisted, into native 3D conformation
Cleavage of the N-terminal signal peptide (for secreted/membrane proteins)
Phosphorylation (serine, threonine, tyrosine) - regulates activity
Glycosylation - on asparagine, serine, threonine residues (secreted/membrane proteins)
Disulfide bond formation (via cysteine cross-linking)
Acetylation of the N-terminus (prevents degradation)

These modifications mean the proteome (total protein diversity) far exceeds the number of genes - estimated 250,000 to several million distinct protein forms in human cells. - Tietz Textbook of Laboratory Medicine, 7th ed.

Efficiency: Polysomes

A single mRNA is not translated by just one ribosome. Multiple ribosomes can bind the same mRNA simultaneously (spaced ~80 nucleotides apart), forming a polyribosome (polysome). This maximises the number of protein copies produced from a single mRNA molecule. - Histology: A Text and Atlas, 9th ed.

Antibiotics That Inhibit Translation

The structural difference between prokaryotic (70S) and eukaryotic (80S) ribosomes is clinically exploited:

Antibiotic	Target	Mechanism
Aminoglycosides (streptomycin)	30S	Misreading of mRNA codons
Tetracyclines	30S	Block aminoacyl-tRNA entry to A site
Macrolides (erythromycin)	50S	Block translocation
Lincosamides (clindamycin)	50S	Block peptidyl transferase
Chloramphenicol	50S	Inhibits peptidyl transferase

Histology: A Text and Atlas, 9th ed.; Biochemistry, Lippincott Illustrated Reviews, 8th ed.

Summary Flowchart

mRNA (5' cap → AUG → codons → UAA/UAG/UGA → poly-A tail 3')
         ↓
    Ribosome assembles at AUG (Initiation)
         ↓
    tRNA delivers amino acids, peptide bonds form (Elongation)
         ↓
    Stop codon → release factor → polypeptide released (Termination)
         ↓
    Post-translational modifications → Functional protein

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