Chemistry of Life

Molecular genetics, biochemistry


Protein Translation

More YouTube Videos: From RNA to Protein Synthesis : Protein synthesis: an epic on the cellular level : Translation : Protein Translation

Coding instructions of nucleotide sequences in archival DNA, which have been transcribed and processed into mRNAs are translated into polypeptides and proteins at cytoplasmic ribosomes. Translation is the ultimate step in gene expression, in which archival genetic instructions are converted into sequences of amino acids in peptides, polypeptides, and proteins.

Analogous with transcription, translation incorporates initiation (usually cap-dependent activation-initiation in eukaryotes), elongation, and termination steps:

Initiation – Aminoacyl-tRNAs carrying specific amino acids pair with the corresponding mRNA codons at the ribosome. Here, base pairing (A-U, C-G) between triplet mRNA codons and complementary tRNA anticodons ensures the coded insertion of amino acids into a protein sequence (primary structure).

To initiate protein synthesis, a ribosome with bound initiator methionyl-tRNA must be assembled at the start codon of an mRNA. This process requires the coordinated activities of three translation initiation factors (IF) in prokaryotes and at least 12 translation initiation factors in eukaryotes (eIF). Most eukaryotic mRNAs require the cap-binding complex elF4F for efficient initiation of translation, which occurs as a result of ribosomal scanning from the capped 5' end of the mRNA to the initiation codon. Initiator tRNA, 40S, and 60S ribosomal subunits are assembled by eukaryotic initiation factors (eIFs) into an 80S ribosome at the initiation codon of mRNA.

The cap-binding complex eIF4F and the factors eIF4A and eIF4B are necessary for binding of 43S complexes (comprising a 40S subunit, eIF2/GTP/Met-tRNAi and eIF3) to the 5' end of capped mRNA yet are not sufficient to promote ribosomal scanning to the initiation codon. The cap-binding factor eIF1A enhances the ability of eIF1 to dissociate aberrantly assembled complexes from mRNA, and these factors synergistically mediate 48S complex assembly at the initiation codon. The joining of 48S complexes to 60S subunits to form 80S ribosomes requires eIF5B, which has an essential ribosome-dependent GTPase activity and hydrolysis of eIF2-bound GTP induced by eIF5. Initiation on a few mRNAs is cap-independent and occurs instead by internal ribosomal entry.

The factors eIF1A and eIF5B from eukaryotes show extensive amino acid sequence similarity to the factors IF1 and IF2 from prokaryotes. The physical interaction between the evolutionarily conserved factors eIF1A and eIF5B plays an important role in translation initiation, perhaps to direct or stabilize the binding of methionyl-tRNA to the ribosomal P site.[s] In eubacteria, base pairing between the 3' end of 16S rRNA and the ribosome-binding site of mRNA is required for efficient initiation of translation. A few cellular and viral mRNAs are translated by a cap and end-independent mechanism known as internal ribosomal entry. Ribosome shunting, or the ribosomal shunt initiation pathway is an alternate viral mechanism of translation initiation in which ribosomes bind to the mRNA in a normal cap-dependent mode, then jump upstream (5') of the initiator AUG codon.

Through the cap-dependent process:
1. The mRNA start codon forms an initiation complex with both the small ribosomal subunit and with initiator tRNA (carrying the amino acid methionine). In this step, the Met-tRNAi forms a base pair with the start codon at the P site – a second aminoacylated tRNA will subsequently bind to the adjacent A site during elongation.

The start codon is usually AUG, but prokaryotes may utilize alternative start codons, or insert N-Formylmethionine. The small subunit of the ribosome binds to 5' end of mRNA with the help of initiation factors (IF). Next, the large ribosomal subunit joins this complex to enable elongation.

2. Elongation – amino acids are added to the growing polypeptide chain as each tRNA delivers its amino acid, forming a complex with elongation factor (EF) and GTP. The amino acid is transferred from the tRNA to the mRNA, moving from the P site to the A site. Next, the peptidyl tRNA vacates the A site and moves to the P site, leaving the A site available for the next amino acid-carrying tRNA. Amino acids are joined by peptide bonds as carboxyl group are added to the 3' OH by an ester bond. The ribosome acts as an enzyme (ribozyme) in the formation of the peptide bond.

3. Termination – elongation of the polypeptide chain ceases when the ribosomal machine encounters a nonsense (stop) codon (UAA, UGA, or UAG). The newly assembled polypeptide is released from the ribosomal machine when the ribosome breaks into its large and small subunits, releasing both the polypeptide and its mRNA.

Each mRNA that codes for a specific polypeptide chain may be utilized hundreds of times before it is degraded (destroyed by nonstop decay) by the cell. Such degradation of proto-oncogene mRNA is essential for avoidance of unchecked proliferation and carcinogenesis. Some antibiotics act by disrupting prokaryotic translation.

~ cap-dependent translation initiation ~ internal ribosomal entry site ~ internal ribosomal entry ~ IRES ~ ribosome shunting ~ translation elongation ~ translation initiation ~ translation termination ~

Table  Comparisons of Eubacteria, Archaea, and Eukaryotes 

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. . . transcription begun 10/06/06