Structure of RNA

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RNA information is occasionally reverse transcribed into DNA, a process important in the life cycle of infectious retroviruses such as the human immunodeficiency virus (HIV), which causes the acquired immunodeficiency syndrome (AIDS). Reverse translation of protein sequence into nucleic acid sequence information, however, does not occur in nature.
RNA molecules are classified according to the roles they play in information transfer processes (Table 16.1). In prokaryotes, transcription and translation occur close together; in fact, ribosomes can begin translating a mRNA while it is still being synthesized. In eukaryotes, these processes are spatially separated: transcription occurs in the nucleus and translation in the cytoplasmic portions of the cell. Messenger RNAs (mRNA) serve as templates for the synthesis of protein; they carry information from the DNA to the cellular protein synthetic machinery. Here a number of other RNA species contribute to the synthesis of the peptide bond.
The molecules that transfer specific amino acids from soluble amino acid pools to ribosomes, and ensure the alignment of these amino acids in the proper sequence prior to peptide bond formation, are transfer RNAs (tRNA). All tRNA molecules are approximately the same size and shape. The assembly site, or factory, for peptide synthesis involves ribosomes. These complex subcellular particles contain three or four ribosomal RNA (rRNA) molecules and 70–80 ribosomal proteins.
Protein synthesis requires a close interdependent relationship between mRNA, the informational template, tRNA, the amino acid adaptor molecule, and rRNA, part of the synthetic machinery. In order for protein synthesis to occur at the correct time in a cell's life, the syntheses of mRNA, tRNA, and rRNA must be coordinated with the cell's response to the intra­ and extracellular environments.
All cellular RNA is synthesized on a DNA template and reflects a portion of the DNA base sequence. Therefore all RNA is associated with DNA at some time. Although DNA is the more prevalent genetic store of information, RNA can also carry genetic information. Genomic RNA is found in the RNA tumor viruses and the other small RNA viruses, such as poliovirus and reovirus.
16.2— Structure of RNA
RNA Is a Polymer of Ribonucleoside 5¢ ­Monophosphates
Chemically, RNA is similar to DNA. Although RNA is one of the more stable components within a cell, it is not as stable as DNA. The presence of the adjacent 2 ­
hydroxyl group makes the RNA phosphodiester bond more susceptible to chemical and enzymatic hydrolysis than its DNA counterpart. Some RNAs, such as bacterial mRNA, are synthesized, used, and degraded within minutes, whereas others, such as rRNA, are more stable metabolically.
RNA is an unbranched linear polymer of ribonucleoside monophosphates. The purines found in RNA are adenine and guanine; the pyrimidines are cytosine and uracil. Except for uracil, which replaces thymine, these are the same bases found in DNA.
A, C, G, and U nucleotides are incorporated into RNA during transcription. Many RNAs also contain modified nucleotides, which are synthesized after transcription. Modified nucleotides are especially characteristic of stable RNA species (i.e., tRNA and rRNA); however, some methylated nucleotides are also present in eukaryotic mRNA. For the most part, the functions of the modified nucleotides in RNA have not been identified. Where known, the function of nucleotide modification seems to involve ''fine tuning" rather than an indispensable role in the cell.
The 3 ,5 ­phosphodiester bonds of RNA form a chain or backbone from
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which the bases extend (Figure 16.1). Eukaryotic RNAs vary from approximately 65 nucleotides long to more than 200,000 nucleotides long. RNA sequences are complementary to the base sequences of specific portions of only one strand of DNA. Thus, unlike the base composition of DNA, molar ratios of A + U and G + C in RNA are not equal. All cellular RNA so far examined is linear and single stranded, but double­stranded RNA is present in some viral genomes.
Figure 16.1 Structure of the 3¢ ,5¢ ­phosphodiester bonds between ribonucleotides forming a single strand of RNA. The phosphate joins the 3 ­OH group of one ribose with the 5 ­OH group of the next ribose. This linkage produces a polyribonucleotide having a sugar–phosphate "backbone." The purine and pyrimidine bases extend away from the axis of the backbone and may pair with complementary bases to form double helical base paired regions.
Secondary Structure of RNA Involves Intramolecular Base Pairing
RNA, being single stranded rather than double stranded, does not usually form an extensive double helix. Rather, the structure in an RNA molecule arises from relatively short regions of intramolecular base pairing. Considerable helical structure exists in RNA even in the absence of extensive base pairing, for example, in the portions of an RNA that do not form intramolecular Watson–Crick base pairs. This helical structure is due to the strong base­stacking forces between A, G, and C residues. Base stacking is more important than simple hydrogen bonding in determining inter­ and intramolecular interactions. These forces act to restrict the possible conformations of an RNA molecule (Figure 16.2). RNA helical structures generally are of the "A type" with 11 nucleotides per turn in a double helix.
Double helical regions in RNA are often called "hairpins." There are considerable variations in the fine structural details of "hairpin" structures, including the length of base paired regions and the size and number of unpaired loops (Figure 16.3). Transfer RNAs are excellent examples of base stacking and hydrogen bonding in a single­stranded molecule (Figure 16.4a). About 60% of the bases are paired in four double helical stems. In addition, the unpaired regions have the capability to form base pairs with free bases in the same or other looped regions, thereby contributing to the molecule's tertiary structure. The anticodon region in tRNA is an unpaired, base­stacked, loop of seven nucleotides. The partial helix caused by base stacking in this loop binds, by specific base pairing, to a complementary codon in mRNA so that translation (peptide bond formation) can occur.
RNA Molecules Have Tertiary Structures
The actual functioning structures of RNA molecules are more complex than the base­stacked and hydrogen­bonded helices mentioned above. RNAs in vivo are
Figure 16.2 Helical structure of tRNA. Models indicating a helical structure due to (a) base stacking in the CCA terminus of tRNA and (b) the lack of an ordered helix when no stacking occurs in this non­base paired region. Redrawn from Sprinzl, M., and Cramer, F. Prog. Nucl. Res. Mol. Biol. 22:9, 1979.