We have seen in this chapter that RNA can carry genetic information in mRNAs, and we saw in Chapter 5 that the genomes of some viruses are composed solely of RNA. We have also seen that complementary base-pairing and other types of hydrogen bonds can occur between nucleotides in the same chain of RNA, causing an RNA molecule to fold up in a unique way determined by its nucleotide sequence (see, for example, Figures 6–50 and 6–67). Comparisons of many RNA structures have revealed conserved motifs, short structural elements that are used over and over again as parts of larger structures (Figure 6–89).
Protein catalysts require a surface with unique contours and chemical properties on which a given set of substrates can react (discussed in Chapter 3). In exactly the same way, an RNA molecule with an appropriately folded shape can serve as a catalyst (Figure 6–90). Like some proteins, many of these ribozymes work by positioning metal ions at their active sites. This feature gives them a wider range of catalytic activities than provided by the limited chemical groups of a polynucleotide chain.
Much of our inference about the RNA world has come from experiments in which large pools of RNA molecules of random nucleotide sequences are generated in the laboratory. Those rare RNA molecules with a property specified by the experimenter are then selected out and studied (Figure 6–91). Such experiments have created RNAs that can catalyze a wide variety of biochemical reactions (Table 6–5), with reaction rate enhancements only a few orders of magnitude lower than
Figure 6–89 Some common elements of RNA structure. Conventional, complementary base-pairing interactions are indicated by red “rungs” in double-helical portions of the RNA.
Figure 6–90 A ribozyme. This simple RNA molecule catalyzes the cleavage of a second RNA at a specific site. This ribozyme is found embedded in larger RNA genomes—called viroids—which infect plants. The cleavage, which occurs in nature at a distant location on the same RNA molecule that contains the ribozyme, is a step in the replication of the viroid genome. Although not shown in the figure, the reaction requires a magnesium ion positioned at the active site. (Adapted from T.R. Cech and O.C. Uhlenbeck, Nature 372:39–40, 1994. With permission from Macmillan Publishers Ltd.)
Figure 6–91 In vitro selection of a synthetic ribozyme. Beginning with a large pool of nucleic acid molecules synthesized in the laboratory, those rare RNA molecules that possess a specified catalytic activity can be isolated and studied. Although a specific example (that of an autophosphorylating ribozyme) is shown, variations of this procedure have been used to generate many of the ribozymes listed in Table 6–5. During the autophosphorylation step, the RNA molecules are kept sufficiently dilute to prevent the “cross”phosphorylation of additional RNA molecules. In reality, several repetitions of this procedure are necessary to select the very rare RNA molecules with this catalytic activity. Thus, the material initially eluted from the column is converted back into DNA, amplified many fold (using reverse transcriptase and PCR, as explained in Chapter 8), transcribed back into RNA, and subjected to repeated rounds of selection. (Adapted from J.R. Lorsch and
J.W. Szostak, Nature 371:31–36, 1994. With permission from Macmillan Publishers Ltd.) those of the “fastest” protein enzymes. Given these findings, it is not clear why protein catalysts greatly outnumber ribozymes in modern cells. Experiments have shown, however, that RNA molecules may have more difficulty than proteins in binding to flexible, hydrophobic substrates. In any case, the availability of 20 types of amino acids presumably provides proteins with a greater number of catalytic strategies.