Translation involves a complex cellular organelle, the ribosome, which together with a number of accessory factors reads the code in a mRNA molecule and produces the appropriate polypeptide235. The ribosome is the site of polypeptide synthesis. It holds the various components (the mRNA, tRNAs, and accessory factors) in appropriate juxtaposition to one another to catalyze polypeptide synthesis. But perhaps we are getting ahead of ourselves. For one, what exactly is a tRNA?
The process of transcription is also used to generate other types of RNAs; these play structural, catalytic, and regulatory roles within the cell. Of these non-mRNAs, two are particularly important in the context of polypeptide synthesis. The first are molecules known as transfer RNAs (tRNAs). These small single stranded RNA molecules fold back on themselves to generate a compact L-shaped structure. In the bacterium E. coli, there are 87 genes that encode tRNAs (there are over 400 such tRNA encoding genes in human). For each amino acid and each codon there are one or more tRNAs. The only exception being the stop codons, for which there are no tRNAs. A tRNA specific for the amino acid phenylalanine would be written tRNAPhe. Two parts of the tRNA molecule are particularly important and functionally linked: the part that recognizes the codon on the mRNA (in the mRNA-ribosome complex) and the amino acid acceptor stem, which is where an amino acid is attached to the tRNA. Each specific type of tRNA can recognize a particular codon in an mRNA through base pairing interactions with what is known as the anti-codon. The rest of the tRNA molecule mediates interactions with protein catalysts (enzymes) known as amino acyl tRNA synthetases. There is a distinct amino acyl tRNA synthetase for each amino acid: there is a phenylalanine-tRNA synthetase and a proline-tRNA synthetase, etc. An amino acyl tRNA synthetase binds the appropriate tRNA and the appropriate amino acid and, through a reaction coupled to a thermodynamically favorable nucleotide triphosphate hydrolysis reaction, catalyzes the formation of a covalent bond between the amino acid acceptor stem of the tRNA and the amino acid, to form what is known as a charged or amino acyl-tRNA. The loop containing the anti-codon is located at the other end of the tRNA molecule. As we will see, in the course of polypeptide synthesis, the amino acid group attached to the tRNA’s acceptor stem will be transferred from the tRNA to the growing polypeptide.
Ribosomes: Ribosomes are composed of roughly equal amounts (by mass) of ribosomal (rRNAs) and ribosomal polypeptides. An active ribosome is composed of a small and a large ribosomal subunit. In the bacterium E. coli, the small subunit is composed of 21 different polypeptides and a 1542 nucleotide long rRNA molecule, while the large subunit is composed of 33 different polypeptides and two rRNAs, one 121 nucleotides long and the other 2904 nucleotides long236. It goes without saying (so why are we saying it?) that each ribosomal polypeptide and RNA is itself a gene product. The complete ribosome has a molecular weight of ~3 x 106 daltons. One of the rRNAs is an evolutionarily conserved catalyst, known as a ribozyme (in contrast to protein based catalysts, which are known as enzymes). This rRNA lies at the heart of the ribosome and catalyzes the transfer of an amino acid bound to a tRNA to the carboxylic acid end of the growing polypeptide chain. RNA based catalysis is a conserved feature of polypeptide synthesis and appears to represent an evolutionarily homologous trait.
The growing polypeptide chain is bound to a tRNA, known as the peptidyl tRNA. When a new aa-tRNA enters the ribosome’s active site (site A), the growing polypeptide is added to it, so that it becomes the peptidyl tRNA (with a newly added amino acid, the amino acid originally associated with incoming aa-tRNA). This attached polypeptide group is now one amino acid longer.
The cytoplasm of cells is packed with ribosomes. In a rapidly growing bacterial cell, ~25% of the total cell mass is ribosomes. Although structurally similar, there are characteristic differences between the ribosomes of bacteria, archaea, and eukaryotes. This is important from a practical perspective. For example, a number of antibiotics selectively inhibit polypeptide synthesis by bacterial, but not eukaryotic ribosomes. Both chloroplasts and mitochondria have ribosomes of the bacterial type. This is another piece of evidence that chloroplasts and mitochondria are descended from bacterial endosymbionts and a reason that translational blocking anti-bacterial antibiotics are mostly benign, since most of the ribosomes inside a eukaryotic cell are not effected by them.