Different Types of RNA Exhibit Various Conformations Related to Their Functions

As noted earlier, the primary structure of RNA is generally similar to that of DNA with two exceptions: the sugar component of RNA, ribose, has a hydroxyl group at the 2' position (see Figure 2-14b), and thymine in DNA is replaced by uracil in RNA. The hydroxyl group on C2 of ribose makes RNA more chemically labile than DNA and provides a chemically reactive group that takes part in RNA-mediated catalysis. As a result of this lability, RNA is cleaved into mononucleotides by alkaline solution, whereas DNA is not. Like DNA, RNA is a long polynucleotide that can be double-stranded or single-stranded, linear or circular. It can also participate in a hybrid helix composed of one RNA strand and one DNA strand. As noted above, RNA-RNA and RNA-DNA double helices have a compact conformation like the A form of DNA (see Figure 4-4b).

Unlike DNA, which exists primarily as a very long double helix, most cellular RNAs are single-stranded and exhibit a variety of conformations (Figure 4-8). Differences in the sizes and conformations of the various types of RNA permit them to carry out specific functions in a cell. The simplest secondary structures in single-stranded RNAs are formed by pairing of complementary bases. "Hairpins" are formed by pairing of bases within «5-10 nucleotides of each other, and "stem-loops" by pairing of bases that are separated by >10 to several hundred nucleotides. These simple folds can cooperate to form more complicated tertiary structures, one of which is termed a "pseudoknot."

As discussed in detail later, tRNA molecules adopt a well-defined three-dimensional architecture in solution that is crucial in protein synthesis. Larger rRNA molecules also have locally well-defined three-dimensional structures, with more flexible links in between. Secondary and tertiary structures also have been recognized in mRNA, particularly near the ends of molecules. Clearly, then, RNA molecules are like proteins in that they have structured domains connected by less structured, flexible stretches.

The folded domains of RNA molecules not only are structurally analogous to the a helices and p strands found in proteins, but in some cases also have catalytic capacities. Such catalytic RNAs are called ribozymes. Although ri-bozymes usually are associated with proteins that stabilize the ribozyme structure, it is the RNA that acts as a catalyst. Some ribozymes can catalyze splicing, a remarkable process in which an internal RNA sequence is cut and removed, and the two resulting chains then ligated. This process occurs during formation of the majority of functional mRNA molecules in eukaryotic cells, and also occurs in bacteria and ar-chaea. Remarkably, some RNAs carry out self-splicing, with the catalytic activity residing in the sequence that is removed. The mechanisms of splicing and self-splicing are discussed in detail in Chapter 12. As noted later in this chapter, rRNA

► FIGURE 4-8 RNA secondary and tertiary structures. (a) Stem-loops, hairpins, and other secondary structures can form by base pairing between distant complementary segments of an RNA molecule. In stem-loops, the single-stranded loop between the base-paired helical stem may be hundreds or even thousands of nucleotides long, whereas in hairpins, the short turn may contain as few as four nucleotides. (b) Pseudoknots, one type of RNA tertiary structure, are formed by interaction of secondary loops through base pairing between complementary bases (green and blue). Only base-paired bases are shown. A secondary structure diagram is shown at right. [Part (b) adapted from P J. A. Michiels et al., 2001, J. Mol. Biol. 310:1109.]

(a) Secondary structure

(a) Secondary structure

Double-helical stem region

Stem-loop

Double-helical stem region

Stem-loop

(b) Tertiary structure

(b) Tertiary structure

plays a catalytic role in the formation of peptide bonds during protein synthesis.

In this chapter, we focus on the functions of mRNA, tRNA, and rRNA in gene expression. In later chapters we will encounter other RNAs, often associated with proteins, that participate in other cell functions.

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