The RNA that is produced from transcription is actually not ready for its job in the cell. There are a few steps that the RNA needs to go through to get ready for its big debut. The amount of processing is much more extensive in eukaryotes rather than prokaryotes; we'll focus mostly on eukaryotic RNA processing.
The 5' end of almost all messenger RNAs (mRNAs), or the RNAs that will encode for proteins, contains a cap. This cap is a modified guanine nucleotide. This capping process helps to stabilize the RNA, assists with its transport to the cytoplasm, and also influences its translation.
The 3' end of the RNA is also modified by polyadenylation. A special enzyme called the poly-A polymerase adds a long chain of adenines to the 3' end of the RNA. Unlike other polymerases, the poly-A polymerase does not require a template, which means that the 3' poly A tail of an mRNA is not present in the initial gene. However, the poly-A tail is signaled by a short sequence at the end of the RNA. The poly-A tail is important for RNA transport as well as preventing its premature degradation.
The internal part of the RNA also undergoes modifications. Often, there are portions of the RNA that do not appear in the final RNA. Therefore, these regions will not be used for coding for the final protein. The regions of RNA that are removed from the immature RNA are called introns, while the regions that remain in the mature RNA are called exons.
The splicing reaction is catalyzed by a large complex called the spliceosome. This enzymatic complex consists of several RNAs and over 50 proteins. It is largely the RNAs in the complex that catalyze the reaction rather than the proteins.
Sometimes the RNA is spliced in an alternative fashion, meaning that some mature mRNAs may only contain a subset of exons. The splicing system allows the cell to shuffle different coding regions and domains. This process is called alternative splicing. This provides an evolutionary advantage, as the cell can try out different combinations without modifying the genome. One gene can therefore produce many different proteins. The converse of this situation is, however, that errors in the splicing reaction of particular RNAs can lead to disease states. Splicing is relatively rare in prokaryotes, but it does happen.
We've only focused on the splicing of eukaryotic mRNAs, but you should keep in mind that other types of RNAs also undergo modifications. In fact, mRNAs comprise a small percentage of the total RNA in the cell. We'll tell you more about those RNAs in the next section.
First though, here's a table to make your life a tiny bit easier.
|Gene organization along DNA||Organized into groups. Genes with a common function are often grouped together.||Scattered throughout the genome.|
|Promoter||Specific DNA sequence recognized by RNA polymerase||Loosely defined DNA sequence recognized by RNA polymerase and several accessory factors. The promoter includes regulatory regions that may be located far from the start of transcription.|
|Termination||Rho dependent or independent||Polyadenylation sequence signals proteins to release mRNA. RNA polymerase II falls off the DNA when an RNA-digesting enzyme reaches it.|
|RNA processing||Limited processing, splicing is relatively rare||5' cap and 3' poly-A tail on all mRNAs. Introns are removed leaving only exons.|