The end of the protein-coding message is signaled by the presence of one of three stop codons (UAA, UAG, or UGA) (see Figure 6–48). These are not recognized by a tRNA and do not specify an amino acid, but instead signal to the ribosome to stop translation. Proteins known as release factors bind to any ribosome with a stop codon positioned in the A site, forcing the peptidyl transferase in the ribosome to catalyze the addition of a water molecule instead of an amino acid to the peptidyl-tRNA (Figure 6–72). This reaction frees the carboxyl end of the growing polypeptide chain from its attachment to a tRNA molecule, and since only this etc.
attachment normally holds the growing polypeptide to the ribosome, the com pleted protein chain is immediately released into the cytoplasm. The ribosome then releases its bound mRNA molecule and separates into the large and small subunits. These subunits can then assemble on this or another mRNA molecule to begin a new round of protein synthesis.
Figure 6–71 Structure of a typical bacterial mRNA molecule. Unlike eukaryotic ribosomes, which typically require a capped 5ʹ end on the mRNA, prokaryotic ribosomes initiate translation at ribosome-binding sites (Shine–Dalgarno sequences), which can be located anywhere along an mRNA molecule. This property of their ribosomes permits bacteria to synthesize more than one type of protein from a single mRNA molecule.
During translation, the nascent polypeptide moves through a large, water-filled tunnel (approximately 10 nm × 1.5 nm) in the large subunit of the ribosome. The walls of this tunnel, made primarily of 23S rRNA, are a patchwork of tiny hydrophobic surfaces embedded in a more extensive hydrophilic surface. This structure is not complementary to any peptide, and thus provides a “Teflon” coating through which a polypeptide chain can easily slide. The dimensions of the tunnel suggest that nascent proteins are largely unstructured as they pass through the ribosome, although some α-helical regions of the protein can form before leaving the ribosome tunnel. As it leaves the ribosome, a newly synthesized protein must fold into its proper three-dimensional conformation to be useful to the cell. Later in this chapter we discuss how this folding occurs. First, however, we describe several additional aspects of the translation process itself.
The synthesis of most protein molecules takes between 20 seconds and several minutes. During this very short period, however, it is usual for multiple initiations to take place on each mRNA molecule being translated. As soon as the preceding ribosome has translated enough of the nucleotide sequence to move out of the way, the 5ʹ end of the mRNA is threaded into a new ribosome. The mRNA molecules being translated are therefore usually found in the form of polyribosomes (or polysomes): large cytoplasmic assemblies made up of several ribosomes spaced as close as 80 nucleotides apart along a single mRNA molecule (Figure 6–73). These multiple initiations allow the cell to make many more protein molecules in a given time than would be possible if each protein had to be completed before the next could start.
Both bacteria and eukaryotes use polysomes, and both employ additional strategies to speed up the overall rate of protein synthesis. Because bacterial mRNA does not need to be processed and is accessible to ribosomes while it is being made, ribosomes can attach to the free end of a bacterial mRNA molecule and start translating it even before the transcription of that RNA is complete, following closely behind the RNA polymerase as it moves along DNA. In eukaryotes, as we have seen, the 5ʹand 3ʹ ends of the mRNA interact (see Figure 6–73A); therefore, as soon as a ribosome dissociates, its two subunits are in an optimal position to reinitiate translation on the same mRNA molecule.
There Are Minor Variations in the Standard Genetic Code