The majority of genes carried in a cell’s DNA specify the amino acid sequence of proteins; the RNA molecules that are copied from these genes (which ultimately direct the synthesis of proteins) are called messenger RNA (mRNA) molecules. The final product of other genes, however, is the RNA molecule itself. These RNAs are known as noncoding RNAs because they do not code for protein. In a well-studied, single-celled eukaryote, the yeast Saccharomyces cerevisiae, over 1200 genes (more than 15% of the total) produce RNA as their final product. Humans may produce on the order of ten thousand noncoding RNAs. These RNAs, like proteins, serve as enzymatic, structural, and regulatory components for a wide variety of processes in the cell. In Chapter 5, we encountered one of them as the template carried by the enzyme telomerase. Although many of the noncoding RNAs are still mysterious, we shall see in this chapter that small nuclear RNA (snRNA) molecules direct the splicing of pre-mRNA to form mRNA, that ribosomal RNA (rRNA) molecules form the core of ribosomes, and that transfer RNA (tRNA) molecules form the adaptors that select amino acids and hold them in place on a ribosome for incorporation into protein. In Chapter 7, we shall see that microRNA (miRNA) molecules and small interfering RNA (siRNA) molecules serve as key regulators of eukaryotic gene expression, and that piwi-interacting RNAs (piRNAs) protect animal germ lines from transposons; we also discuss the long noncoding RNAs (lncRNAs), a diverse set of RNAs whose functions are just being discovered (Table 6–1).
Figure 6–10 Transcription of two genes as observed under the electron microscope. The micrograph shows many molecules of RNA polymerase simultaneously transcribing each of two adjacent genes. Molecules of RNA polymerase are visible as a series of dots along the DNA with the newly synthesized transcripts (fine threads) attached to them. The RNA molecules (ribosomal RNAs) shown in this example are not translated into protein but are instead used directly as components of ribosomes, the machines on which translation takes place. The particles at the 5ʹ end (the free end) of each rRNA transcript are believed to reflect the beginnings of ribosome assembly. From the relative lengths of the newly synthesized transcripts, it can be deduced that the RNA polymerase molecules are transcribing from left to right. (Courtesy of Ulrich Scheer.)
Each transcribed segment of DNA is called a transcription unit. In eukaryotes, a transcription unit typically carries the information of just one gene, and therefore codes for either a single RNA molecule or a single protein (or group of related proteins if the initial RNA transcript is spliced in more than one way to produce different mRNAs). In bacteria, a set of adjacent genes is often transcribed as a unit; the resulting mRNA molecule therefore carries the information for several distinct proteins.
Overall, RNA makes up a few percent of a cell’s dry weight, whereas proteins comprise about 50%. Most of the RNA in cells is rRNA; mRNA comprises only 3–5% of the total RNA in a typical mammalian cell. The mRNA population is made up of tens of thousands of different species, and there are on average only 10–15 molecules of each species of mRNA present in each cell.
Signals Encoded in DNA Tell RNA Polymerase Where to Start and Stop
To transcribe a gene accurately, RNA polymerase must recognize where on the genome to start and where to finish. The way in which RNA polymerases perform these tasks differs somewhat between bacteria and eukaryotes. Because the processes in bacteria are simpler, we discuss them first.