The regulation of protein synthesis is an important part of the regulation of gene expression. Regulation of mRNA translation controls the levels of particular proteins that are synthesized upon demand, such as synthesis of the different chains of globin in hemoglobin, or the production of insulin from stored insulin mRNAs in response to blood glucose levels, to name a few. The control of the cell cycle and cell proliferation also involves regulation of protein synthesis, and malignant transformation of cells involves loss of certain translational regulatory controls. In fact, several translation initiation factors are over-expressed in certain cancers and play key roles in tumor development and progression. The process of protein synthesis and important examples of its regulation are now understood at the molecular level. We will discuss the mechanism and regulation of protein synthesis, elucidating this complex area of gene regulation with specific examples.

Many viruses compete with their infected host cell and often dominate the protein synthetic machinery to maintain viral production and thwart innate (intracellular) anti-viral responses. For many viruses, the inhibition of host cell protein synthesis is an important component of their ability to propagate and destroy the infected cell. The infected cell, in turn, responds by enacting antiviral activities that include the production of potent biological molecules such as β-interferon that function, in part, to inhibit protein synthesis. Finally, a large proportion of antibiotics currently in use or under development inhibit protein synthesis in bacteria but not animal cells by exploiting differences in the structure of prokaryotic and eukaryotic ribosomes.

Genetic Code


Since the genetic code is read in triplets (codons) comprising three of the four bases, there are 43 or 64 possible triplets encoding the 20 amino acids. All but 3 of these 64 codons specify amino acids. Since there are 61 codons specifying only 20 amino acids, the same amino acid may be encoded by more than one codon. The genetic code is therefore degenerate. The code is read by transfer RNAs (tRNAs), which are adapter molecules that decode the base sequence of an mRNA into the amino acid sequence of a protein. For each amino acid there is at least one corresponding tRNA which transports that amino acid to the ribosome and recognizes the particular codon(s) in the mRNA.
  1. Each amino acid is specified by a group of three nucleotides (codon)
  2. The genetic code is redundant (degenerate) - most amino acids have more than one codon (only methionine "start" AUG, and tryptophan UGC do not)
  3. "Stop" is encoded by UGA, UAG, UAA: no amino acid or tRNA.
tRNAtRNA secondary structure


tRNA 3D folded

tRNA Tertiary Structure

tRNAs Contain Modified Bases
— types and positions determine tRNA families
tRNA modified bases

Aminoacyl-tRNA Synthetases Couple Amino Acids To tRNAs

Synthetase facts:


tRNA Charging
translating ribosome

The active site (region of peptide synthesis) of the ribosome is at the interface of the small and large subunits

The active translating (elongating) ribosome is like a bead on a string


Ribosomes are complicated structures consisting of ribosomal RNAs and proteins that associate into a precise structure with multiple enzymatic activities. The ribosomes of prokaryotes, eukaryotes and organelles (such as mitochondria) all perform the same function and are structurally quite similar. In evolution, ribosomes from prokaryotes and eukaryotes are unrelated at the protein level, but are highly related at the rRNA level.

General Features in Common Between Eukaryotic and Prokaryotic Ribosomes

ribosome active site
tRNA base pairing

A tRNA (orange) is shown base pairing with part of mRNA (gold) on left and extending into the ribosome's peptidyltransferase center on right. Click To View Larger

The Functions Of Ribosomes In Translation Are Primarily Associated With rRNAs Rather Than rProteins.

The rRNAs: The Ribosome Has Three tRNA Binding Sites
3 binding sites on ribosome

A site – amino acyl site, contains new incoming AA-tRNA
P site – peptidyl site, contains growing peptide chain
E site – exit site, site at which AA discharged tRNA is removed

ribosome structure

Space-Filling Model Of Translating Ribosome

During protein synthesis, incoming tRNA (purple) carrying the next amino acid (blue sphere) enters the A site if its anticodon is complementary in sequence to the codon on mRNA.

The reaction (not shown) between A-site tRNA and P-site tRNA (orange) extends the peptide chain by one amino acid unit.

The amine from a new amino acid on the tRNA bound at the A site attacks a carbonyl at the end of the growing peptide chain, which is attached to the tRNA bound at the P site.

Some Antibiotics Block Ribosome Function

Specific segments of 16S & 23S rRNAs have been identified that correspond to the A and P sites.

antibioticsMany antibiotics act by binding or blocking rRNA activity within these enzymatic sites.


Protein synthesis can be divided into 6 stages:
  1. Amino acid activation: tRNA is charged by covalently linking it to its cognate amino acid (above).
  2. Formation of initiation complexes: association of mRNA, ribosomal subunits and initiation factors.
  3. Initiation of translation: assembly of stable ribosome complex at the initiation codon.
  4. Chain elongation: polypeptide synthesis by repetitive addition of amino acids to the nascent (growing) chain.
  5. Chain termination: release of nascent polypeptide.
  6. Ribosome dissociation: subunits separate before initiating new round of translation.


Initiating tRNA


  1. Translation generally initiates with a Met encoded by AUG (prokaryotes & eukaryotes).
  2. Special initiating tRNA carries Met to AUG codon.
    • In bacteria the initiating Met is modified, while attached to the tRNA, to contain an N-formyl group. It is referred to as N-formylMet (tRNAfmet).
    • The formyl group blocks acceptance of a growing peptide chain.
    • Elongating met-tRNA is distinct (tRNAmet), and the Met is not modified. The formyl group is always removed from bacterial proteins.
    • In eukaryotes the initiating Met is not modified (tRNAimet).
    • The initiating Met is removed from roughly half of bacterial proteins, and from some eukaryotic proteins

    Mechanism Of Translation Initiation

Initiation Complex Formation in Prokaryotes

Anti-association factors IF1 and IF3 bind the 30S subunit and prevent 50S subunit association. Eukaryotic initiation factors eIF1 and eIF3 are similar and they have the same functions. 30S subunit associates with tRNAfmet, GTP and IF2 to form a ternary complex. Association of ternary complex components, 30S ribosome and mRNA in prokaryotes takes place in any order. In eukaryotes it is highly ordered (as described later).

Initiation requires the assembly of the mRNA on the ribosome at the initiating AUG for translation


polycistronic mRNAs

The Shine-Delgarno Interaction Permits The Development Of Operons — Genetic Grouping Of Genes Of Related Function

A single mRNA can encode multiple proteins — polycistronic mRNA — of related function, and their translation can be temporally orchestrated when needed.

Eukaryotes initiate translation quite differently. In eukaryotes there is no such sequence or S/D interaction (at least routinely). In fact, the Shine Dalgarno sequence is specifically missing from the 3’ end of eukaryotic 18S rRNA.

elongation mechanism

Steps In Translation Elongation

release factor

Release factor has a 3-dimentional shape similar to that of tRNA



Translation is terminated at one of three stop codons (UAA, UAG & UGA).
The termination codon at the A site is recognized by the release factor instead of a tRNA.
The release factor binds the termination codon.
The peptide chain is then released followed by dissociation of the tRNA and the ribosome.