RNA molecules for appropriate gene expression (Section 5.3).^50 Typical nucleases include the exonucle-
ases, which bind to unprotected RNA termini and degrade RNA in either the 3- or 5-direction (5and 3-
exonucleases). There are also endonucleases, which cut in the center of an RNA molecule, often leaving an
exposed tail for further degradation by the exonucleases. After splicing, eukaryotic introns are released as lar-
iat molecules, which would be resistant to degradation and recycling were it not for a debranching enzyme,
which is a specialized nuclease that specifically cuts the 2–5linkage that joins the branch-site to the first
nucleotide of an intron. The resultant “linearized” intron can then be degraded by standard nucleases.
While some nucleases diffuse freely throughout a cellular compartment, many of them act in a highly
regulated manner, as part of macromolecular machines such as the exosome. Processed mRNA molecules
are specifically degraded through a carefully orchestrated pathway involving decapping of the 5-end and
loss of the 3-poly A tail that normally protect mRNA molecules from degradation. Within the exosome, a
complex of 3→ 5 exonucleases degrade these unprotected mRNAs. This and other exonucleolytic
machinery also degrade mRNAs that have been improperly capped, adenylated or exported, thus provid-
ing a form of mRNA quality control.^50
7.2.5.2 Nonsense-Mediated Decay and RNA Quality Control. Transcription, splicing, and other
processes involved in RNA synthesis are highly imperfect. Mistakes in these pathways, together with aber-
rant transcripts from mutated genes and invading viruses lead to deleterious RNA molecules, which, if
unchecked, would result in aberrant protein expression in the cell. A major mechanism for destroying
these unwanted messages is nonsense-mediated decay (NMD).^51 This pathway is based upon the fact that
aberrant transcripts commonly contain stop codons (or “nonsense codons”) at inappropriate positions within
the RNA sequence. During the process of NMD, RNAs containing these premature stop codonsare iden-
tified and targeted for rapid degradation by exonucleases. Defects in the complex process of NMD have
now been linked to numerous important human disorders.
A second important pathway for RNA quality controlis enforced by the ADAR family of enzymes, which
recognize and target duplex RNA molecules that are either produced endogenously or result from viral infec-
tion. ADAR enzymes recognize long RNA duplexes and, as in transversional editing, the paired adenosines
are converted into inosines. When employed as a form of quality control, this base transversion can result in
transcript destabilization and susceptibility to degradation. In a similar (or perhaps related) process, the RNA
interference (RNAi)machinery also targets RNA duplexes and marks them for destruction (Section 7.5.3).^42
7.3 RNAs in the Protein Factory: Translation
In modern organisms, proteins are the dominant macromolecular building materials for cellular function.
However, all proteins are the product of a factory that must receive the encoded instructions, gather the
amino acid starting materials, and stitch them together in the proper order. But the ribosome is not a mere
assembly line for protein synthesis. It is sensitively regulated to produce the correct quantity of protein, to
detect problems that arise during synthesis, and to rapidly dispose of defective products. Despite the diver-
sity of life, all organisms utilize similar ribosomal factories to build proteins and modulate the required
levels of gene expression.
7.3.1 Messenger RNA and the Genetic Code
For protein synthesis, the encoded instructions are contained in messenger RNA (mRNA), which is read
like a tape by ribosomes. An mRNA sequence is translated into protein through the genetic code, which
has the same basic format for all forms of life on earth (Figure 7.25). The code consists of nucleotide triplets
(codons) that specify the identity and sequential position of amino acids in a protein.46,52For example, the
sequence 5-AAA-3codes for the amino acid lysine. Each amino acid (and the tRNA to which it is
appended) is specified by several different codons (synonyms), which differ primarily in the identity of the
third position. For example, CCU, CCC, CCA, and CCG all encode the amino acid proline. The ribosome
RNA Structure and Function 273