Like DNA, RNA is a linear polymer made of four different types of nucleotide subunits linked together by phosphodiester bonds (see Figure 6–4). It differs from DNA chemically in two respects: (1) the nucleotides in RNA are ribonucleotides— that is, they contain the sugar ribose (hence the name ribonucleic acid) rather than deoxyribose; (2) although, like DNA, RNA contains the bases adenine (A), guanine (G), and cytosine (C), it contains the base uracil (U) instead of the thymine (T) in DNA (Figure 6–5). Since U, like T, can base-pair by hydrogen-bonding with A (Figure 6–6), the complementary base-pairing properties described for DNA in Chapters 4 and 5 apply also to RNA (in RNA, G pairs with C, and A pairs with U). We also find other types of base pairs in RNA: for example, G occasionally pairs with U.
Although these chemical differences are slight, DNA and RNA differ quite dramatically in overall structure. Whereas DNA always occurs in cells as a double-stranded helix, RNA is single-stranded. An RNA chain can therefore fold up into a particular shape, just as a polypeptide chain folds up to form the final shape of a protein (Figure 6–7). As we see later in this chapter, the ability to fold into complex three-dimensional shapes allows some RNA molecules to have precise structural and catalytic functions.
Transcription Produces RNA Complementary to One Strand of DNA
The RNA in a cell is made by DNA transcription, a process that has certain similarities to the process of DNA replication discussed in Chapter 5. Transcription begins with the opening and unwinding of a small portion of the DNA double helix to expose the bases on each DNA strand. One of the two strands of the DNA double helix then acts as a template for the synthesis of an RNA molecule. As in DNA replication, the nucleotide sequence of the RNA chain is determined by the complementary base-pairing between incoming nucleotides and the DNA
Figure 6–4 A short length of RNA. The phosphodiester chemical linkage between nucleotides in RNA is the same as that in DNA.
Figure 6–5 The chemical structure of RNA. (A) RNA contains the sugar ribose, which differs from deoxyribose, the sugar used in DNA, by the presence of an additional –OH group. (B) RNA contains the base uracil, which differs from thymine, the equivalent base in DNA, by the absence of a –CH3 group.
Figure 6–6 Uracil forms base pairs with adenine. The absence of a methyl group in U has no effect on base-pairing; thus, U-A base pairs closely resemble T-A base pairs (see Figure 4–4).
template. When a good match is made (A with T, U with A, G with C, and C with G), the incoming ribonucleotide is covalently linked to the growing RNA chain in an enzymatically catalyzed reaction. The RNA chain produced by transcription— the transcript—is therefore elongated one nucleotide at a time, and it has a nucleotide sequence that is exactly complementary to the strand of DNA used as the template (Figure 6–8).
Transcription, however, differs from DNA replication in several crucial ways. Unlike a newly formed DNA strand, the RNA strand does not remain hydrogen-bonded to the DNA template strand. Instead, just behind the region where the ribonucleotides are being added, the RNA chain is displaced and the DNA helix re-forms. Thus, the RNA molecules produced by transcription are released from the DNA template as single strands. In addition, because they are copied from only a limited region of the DNA, RNA molecules are much shorter than DNA molecules. A DNA molecule in a human chromosome can be up to 250 million nucleotide-pairs long; in contrast, most RNAs are no more than a few thousand nucleotides long, and many are considerably shorter.