Figure 6–21 A comparison of the structures of prokaryotic and eukaryotic mRNA molecules. (A) The 5ʹ and 3ʹ ends of a bacterial mRNA are the unmodified ends of the chain synthesized by the RNA polymerase, which initiates and terminates transcription at those points, respectively. The corresponding ends of a eukaryotic mRNA are formed by adding a 5ʹ cap and by cleavage of the pre-mRNA transcript near the 3ʹ end and the addition of a poly-A tail, respectively. The figure also illustrates another difference between the prokaryotic and eukaryotic mRNAs: bacterial mRNAs can contain the instructions for several different proteins, whereas eukaryotic mRNAs nearly always contain the information for only a single protein. (B) The structure of the cap at the 5ʹ end of eukaryotic mRNA molecules. Note the unusual 5ʹ-to-5ʹ linkage of the 7-methyl G to the remainder of the RNA. Many eukaryotic mRNAs carry an additional modification: methylation of the 2ʹ-hydroxyl group of the ribose sugar at the 5ʹ end of the primary transcript (see Figure 6–23).
into protein. RNA splicing joins together the different portions of a protein-coding sequence, and it provides eukaryotes with the ability to synthesize several different proteins from the same gene.
A simple strategy has evolved to couple all of the above RNA processing steps to transcription elongation. As discussed previously, a key step in transcription initiation by RNA polymerase II is the phosphorylation of the RNA polymerase II tail, also called the CTD (C-terminal domain). This phosphorylation, which proceeds gradually as the RNA polymerase initiates transcription and moves along the DNA, not only helps dissociate the RNA polymerase II from other proteins present at the start point of transcription, but also allows a new set of proteins to associate with the RNA polymerase tail that function in transcription elongation and RNA processing. As discussed next, some of these processing proteins are thought to “hop” from the polymerase tail onto the nascent RNA molecule to begin processing it as it emerges from the RNA polymerase. Thus, we can view RNA polymerase II in its elongation mode as an RNA factory that not only moves along the DNA synthesizing an RNA molecule, but also processes the RNA that it produces (Figure 6–22). Fully extended, the CTD is nearly 10 times longer than the remainder of RNA polymerase. As a flexible protein domain, it serves as a scaffold or tether, holding a variety of proteins close by so that they can rapidly act when needed. This strategy, which greatly speeds up the overall rate of a series of consecutive reactions, is one that is commonly utilized in the cell (see Figures 4–58 and 16–18).
RNA Capping Is the First Modification of Eukaryotic Pre-mRNAs
As soon as RNA polymerase II has produced about 25 nucleotides of RNA, the 5ʹ end of the new RNA molecule is modified by addition of a cap that consists of a modified guanine nucleotide (see Figure 6–21B). Three enzymes, acting in succession, perform the capping reaction: one (a phosphatase) removes a phosphate from the 5ʹ end of the nascent RNA, another (a guanyl transferase) adds a GMP in