From what we have described in this chapter so far, you may get the impression that in eukaryotes all regulation of gene expression is at the level of transcription. But is the amount of a protein in a cell really determined only by the amount of its mRNA? The answer is no. For example, a survey of genes and their expression in yeast cells showed that for about one-third of the genes, there was a clear correlation between mRNA and protein: more of one led to more of the other. But for two-thirds of the genes, there was no apparent relationship between the two: sometimes there was lots of mRNA and little or no protein, or lots of protein and little mRNA. The concentrations of these proteins must therefore have been determined by factors acting after the mRNA was made. Cells have two major ways to control the amount of a protein after transcription:

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REGULATION OF TRANSLATION There are a variety of ways in which the translation of mRNA can be regulated. One way, as we saw in the previous section, is to inhibit translation with siRNAs and miRNAs. A second way involves modification of the guanosine triphosphate cap on the 5′ end of the mRNA (see Key Concept 14.4). An mRNA that is capped with an unmodified GTP molecule is not translated. For example, stored mRNAs in the egg cells of the tobacco hornworm moth are capped with unmodified GTP molecules and are not translated. After the egg is fertilized, however, the caps are modified, allowing the mRNA to be translated to produce the proteins needed for early embryonic development.

In another system, repressor proteins directly block translation. For example, in mammalian cells the protein ferritin binds free iron ions (Fe²⁺). When iron is present in excess, ferritin synthesis rises dramatically, but the amount of ferritin mRNA remains constant, indicating that the increase in ferritin synthesis is due to an increased rate of mRNA translation. Indeed, when the iron level in the cell is low, a translational repressor protein binds to the 5′ noncoding region of ferritin mRNA and prevents its translation by blocking its attachment to a ribosome. When the iron level rises, some of the excess Fe²⁺ ions bind to the repressor and alter its three-dimensional structure, causing the repressor to detach from the mRNA and allowing translation to proceed (Figure 16.19). The binding site for the translational repressor on mRNA is a stem-and-loop region with sufficient three-dimensional structure for recognition by a protein or small molecule.

REGULATION OF PROTEIN LONGEVITY The protein content of a cell at any given time is a function of both protein synthesis and protein degradation. Certain proteins can be targeted for destruction in a chain of events that begins when an enzyme attaches a 76-amino acid protein called ubiquitin (so named because it is ubiquitous, or widespread) to a lysine residue of the protein to be destroyed. Other ubiquitins then attach to the primary one, forming a polyubiquitin chain. The protein–polyubiquitin complex then binds to a huge protein complex called a proteasome (from protease + soma, “body”) (Figure 16.20). Upon entering the proteasome, the polyubiquitin is removed and ATP energy is used to unfold the target protein. Three different proteases then digest the protein into small peptides and amino acids.

You may recall from Key Concept 11.2 that cyclins are proteins that regulate the activities of key enzymes at specific points in the cell cycle. Cyclins must be broken down at just the right time, and this is done by attaching ubiquitin to them and degrading them in the proteasomes. Viruses can hijack this system. For example, some strains of the human papillomavirus (HPV) add ubiquitin to the p53 and retinoblastoma proteins, targeting them for proteasomal degradation. These proteins normally inhibit the cell cycle, so the result of this HPV activity is unregulated cell division (cancer).