Figure 6–76 Nonsense-mediated mRNA decay. As shown on the right, the failure to correctly splice a pre-mRNA often introduces a premature stop codon into the reading frame for the protein. These abnormal mRNAs are destroyed by the nonsense-mediated decay mechanism. To activate this mechanism, an mRNA molecule, bearing exon junction complexes (EJCs) to mark successfully completed splices, is first met by a ribosome that performs a “test” round of translation. As the mRNA passes through the tight channel of the ribosome, the EJCs are stripped off, and successful mRNAs are released to undergo multiple rounds of translation (left side). However, if an in-frame stop codon is encountered before the final EJC is reached (right side), the mRNA undergoes nonsense-mediated decay, which is triggered by the Upf proteins (green) that bind to each EJC. Note that this mechanism ensures that nonsense-mediated decay is triggered only when the premature stop codon is in the same reading frame as that of the normal protein. (Adapted from J. Lykke-Andersen et al., Cell 103:1121–1131, 2000. With permission from Elsevier.) premature termination codons. The surveillance system degrades the mRNAs produced from such rearranged genes, thereby avoiding the potential toxic effects of truncated proteins.
The nonsense-mediated surveillance pathway also plays an important role in mitigating the symptoms of many inherited human diseases. As we have seen, inherited diseases are usually caused by mutations that spoil the function of a key protein, such as hemoglobin or one of the blood-clotting factors. Approximately one-third of all genetic disorders in humans result from nonsense mutations or mutations (such as frameshift mutations or splice-site mutations) that place nonsense mutations into the gene’s reading frame. In individuals that carry one mutant and one functional gene, nonsense-mediated decay eliminates the aberrant mRNA and thereby prevents a potentially toxic protein from being made. Without this safeguard, individuals with one functional and one mutant “disease gene” would likely suffer much more severe symptoms.
Some Proteins Begin to Fold While Still Being Synthesized
The process of gene expression is not over when the genetic code has been used to create the sequence of amino acids that constitutes a protein. To be useful to the cell, this new polypeptide chain must fold up into its unique three-dimensional conformation, bind any small-molecule cofactors required for its activity, be appropriately modified by protein kinases or other protein-modifying enzymes, and assemble correctly with the other protein subunits with which it functions (Figure 6–77).
The information needed for all of the steps listed above is ultimately contained in the sequence of amino acids that the ribosome produces when it translates an mRNA molecule into a polypeptide chain. As discussed in Chapter 3, when a
Figure 6–77 Steps in the creation of a functional protein. As indicated, translation of an mRNA sequence into an amino acid sequence on the ribosome is not the end of the process of forming a protein. To function, the completed polypeptide chain must fold correctly into its three-dimensional conformation, bind any cofactors required, and assemble with its partner protein chains, if any. Noncovalent bond formation drives these changes. As indicated, many proteins also require covalent modifications of selected amino acids. Although the most frequent modifications are protein glycosylation and protein phosphorylation, over 200 different types of covalent modifications are known (see pp. 165–166).
protein folds into a compact structure, it buries most of its hydrophobic residues in an interior core. In addition, large numbers of noncovalent interactions form between various parts of the molecule. It is the sum of all of these energetically favorable arrangements that determines the final folding pattern of the polypeptide chain—as the conformation of lowest free energy (see pp. 114–115).