Nucleic Acid Structure:- Many RNAs Have More Complex Three-Dimensional Structures

Messenger RNA is only one of several classes of cellular RNA. Transfer RNAs serve as adapter molecules in protein synthesis; covalently linked to an amino acid at one end, they pair with the mRNA in such a way that amino acids are joined to a growing polypeptide in the correct sequence. Ribosomal RNAs are components of ribosomes. There is also a wide variety of special-function RNAs, including some (called ribozymes) that have enzymatic activity. All the RNAs are considered in de tail in Chapter 26. The diverse and often complex functions of these RNAs reflect a diversity of structure much richer than that observed in DNA molecules. The product of transcription of DNA is always single-stranded RNA. The single strand tends to assume a right-handed helical conformation dominated by base stacking interactions (Fig. 8–25), which are stronger between two purines than between a purine and pyrimidine or between two pyrimidines. The purine-purine interaction is so strong that a pyrimidine separating two purines is often displaced from the stacking pattern so that the purines can interact. Any self-complementary sequences in the molecule produce more complex structures. RNA can base-pair with complementary regions of either RNA or DNA. Base pairing matches the pat tern for DNA: G pairs with C and A pairs with U (or with the occasional T residue in some RNAs). One difference is that base pairing between G and U residues—unusual in DNA—is fairly common in RNA (see Fig. 8–27). The paired strands in RNA or RNA-DNA duplexes are antiparallel, as in DNA.

RNA has no simple, regular secondary structure that serves as a reference point, as does the double he lix for DNA. The three-dimensional structures of many RNAs, like those of proteins, are complex and unique. Weak interactions, especially base-stacking interactions, play a major role in stabilizing RNA structures, just as they do in DNA. Where complementary sequences are present, the predominant double-stranded structure is an A-form right-handed double helix. Z-form helices have been made in the laboratory (under very high-salt or high-temperature conditions). The B form of RNA has not been observed. Breaks in the regular A-form he lix caused by mismatched or unmatched bases in one or both strands are common and result in bulges or in ternal loops (Fig. 8–26). Hairpin loops form between nearby self-complementary sequences. The potential for base-paired helical structures in many RNAs is extensive (Fig. 8–27), and the resulting hairpins are the most common type of secondary structure in RNA. Specific

FIGURE 8–25 Typical right-handed stacking pattern of single stranded RNA. The bases are shown in gray, the phosphate atoms in yellow, and the riboses and phosphate oxygens in green. Green is used to represent RNA strands in succeeding chapters, just as blue is used for DNA.

FIGURE 8–26 Secondary structure of RNAs. (a)Bulge, internal loop, and hairpin loop. (b)The paired regions generally have an A-form right-handed helix, as shown for a hairpin.

FIGURE 8–27 Base-paired helical structures in an RNA. Shown here is the possible secondary structure of the M1 RNA component of the enzyme RNase P of E.coli, with many hairpins. RNase P, which also contains a protein component (not shown), functions in the processing of transfer RNAs (see Fig. 26–23). The two brackets indicate additional complementary sequences that may be paired in the three-dimensional structure. The blue dots indicate non-Watson Crick GUU base pairs (boxed inset). Note that GUU base pairs are allowed only when presynthesized strands of RNA fold up or anneal with each other. There are no RNA polymerases (the enzymes that synthesize RNAs on a DNA template) that insert a U opposite a template G, or vice versa, during RNA synthesis.

short base sequences (such as UUCG) are often found at the ends of RNA hairpins and are known to form par ticularly tight and stable loops. Such sequences may act as starting points for the folding of an RNA molecule into its precise three-dimensional structure. Important additional structural contributions are made by hydro gen bonds that are not part of standard Watson-Crick base pairs. For example, the 2-hydroxyl group of ribose can hydrogen-bond with other groups. Some of these properties are evident in the structure of the phenyl alanine transfer RNA of yeast—the tRNA responsible for inserting Phe residues into polypeptides—and in two RNA enzymes, or ribozymes, whose functions, like those of protein enzymes, depend on their three-dimensional structures (Fig. 8–28). The analysis of RNA structure and the relationship between structure and function is an emerging field of inquiry that has many of the same complexities as the analysis of protein structure. The importance of understanding RNA structure grows as we become increasingly aware of the large number of functional roles for RNA molecules.

FIGURE 8–28 Three-dimensional structure in RNA. (a) Three-dimensional structure of phenylalanine tRNA of yeast (PDB ID 1TRA). Some unusual base-pairing patterns found in this tRNA are shown. Note also the involvement of the oxygen of a ribose phosphodiester bond in one hydrogen-bonding arrangement, and a ribose 2-hydroxyl group in another (both in red). (b) A hammerhead ribozyme (so named because the secondary structure at the active site looks like the head of a hammer), derived from certain plant viruses (derived from PDB ID 1MME). Ribozymes, or RNA enzymes, catalyze a variety of reactions, primarily in RNA metabolism and protein synthesis. The com plex three-dimensional structures of these RNAs reflect the complexity inherent in catalysis, as described for protein enzymes in Chapter 6. (c) A segment of mRNA known as an intron, from the ciliated protozoan Tetrahymena thermophila (derived from PDB ID 1GRZ). This intron (a ribozyme) catalyzes its own excision from between exons in an mRNA strand.

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مواضيع ذات صلة

Nucleic Acid Structure:- Messenger RNAs Code for Polypeptide Chains

Nucleic Acid Structure:- Certain DNA Sequences Adopt Unusual Structures

Nucleic Acid Structure:- DNA Can Occur in Different Three-Dimensional Forms

Nucleic Acid Structure:- DNA Is a Double Helix

Nucleic Acid Structure:- DNA Molecules Have Distinctive Base Compositions

Nucleic Acid Structure:- DNA Stores Genetic Information

Carbohydrates as Informational Molecules: The Sugar Code:- Lectin-Carbohydrate Interactions Are Very Strong and Highly Specific

Carbohydrates as Informational Molecules: The Sugar Code:- Lectins Are Proteins That Read the Sugar Code and Mediate Many Biological Processes

Polysaccharides:- Glycolipids and Lipopolysaccharides Are Membrane Components

Polysaccharides: - Glycoproteins Have Covalently Attached Oligosaccharides

Polysaccharides:- Proteoglycans Are Glycosaminoglycan-Containing Macromolecules of the Cell Surface and Extracellular Matrix

Polysaccharides:- Glycosaminoglycans Are Heteropolysaccharides of the Extracellular Matrix