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               234                                                                                   Protein Synthesis


               to selenocysteine by the enzyme selenocysteine synthase,  10Sa RNA) to remove the resulting partially synthesized
               which uses selenophosphate as a donor. Elongation  proteins and free the ribosomal subunits. The 5 - and

               factor Tu does not bind Sec–tRNA Sec  as it does other  3 -ends of this molecule resemble alanyl–tRNA, while

               elongator AA–tRNAs; instead, a unique protein SELB  the central portion encodes a peptide “tag.” Alanyl–tRNA
               transports Sec-tRNA Sec  to the ribosomal A-site. SELB is  synthetase aminoacylates the tmRNA, which is then
               specific for Sec–tRNA Sec , rejecting other AA–tRNAs  transported to the stalled elongation complex by EF-Tu.
               including Ser–tRNA Sec . The final novel feature of seleno-  After attaching alanine to the end of the growing nascent
               cysteine insertion is the mechanism of mRNA recognition.  polypeptide, the ribosome switches from the truncated
               The UGA triplet can be used in the same organism as  mRNA to the tmRNA in a mechanism called trans-
               either a selenocysteine or a stop codon. The sequence  translation. The ribosome adds 10 additional amino acids
               context determines its recognition as a selenocysteine  totheendoftheproteinaccordingtothetmRNAsequence.
               codon. The ternary complex SELB:GTP:Sec–tRNA Sec  The resulting tagged protein is released and degraded, as

               recognizes a stem-loop structure immediately 3 (down-  the tag is a recognition signal for several proteases.
               stream) from a UGA codon that is read as selenocysteine.
               This structural feature of the mRNA is specifically
                                                                 F. mRNA Surveillance
               bound by the carboxyl-terminal portion of SELB, while
               other regions of the protein are highly homologous  Eukaryotes use a surveillance mechanism to identify
               to EF-Tu as expected. Insertion of selenocysteine into  mRNAs with mutations (typically premature termination
               polypeptides therefore requires formation of a quaternary  codons) or processing errors (such as incorrect splicing).
               SELB:GTP:Sec–tRNA  Sec :mRNA complex. This is in  Once detected, the aberrant messages are degraded
               contrast to all other elongation steps in protein synthesis,  to prevent the synthesis of truncated proteins. Recent
               which proceed through ternary complexes.          evidence suggests that these mRNAs must be at least
                                                                 partially translated to determine whether a stop codon is in
                                                                 its proper context. In mammalian systems, the translating
               D. Degradation of Incomplete Polypeptides
                                                                 ribosome is proposed to measure the distance between
               One consequence of the necessary accuracy in protein syn-  the final splicing junction and the termination signal—if
               thesis is the release of peptidyl–tRNA molecules repre-  they are within 50 nucleotides of one another, termination
               senting incomplete translation products. These products  is allowed to proceed. If they are further apart, either
               can be the result of ribosome stalling, a premature stop  because of a misplaced stop codon within the mRNA
               codon that is not suppressed, or detection by the ribosome  reading frame or a splicing error, the mRNA is targeted
               of noncognate tRNA present in the decoding center. It has  for rapid degradation. How the ribosome recognizes this
               been estimated that this “drop-off” might result in a trun-  distance is not yet known. This mRNA surveillance is also
               cated polypeptide chain approximately 10% as often as the  called nonsense-mediated decay because the majority of
               full-length protein. Not only is this a waste of amino acids  mutational errors result in premature termination codons.
               resulting in useless products but also tRNA molecules are
               sequestered and unavailable for translation of other genes.
                                                                 G. Accuracy Mechanisms
                 The incomplete peptidyl–tRNAs are substrates in bac-
               teria and yeast for the enzyme peptidyl–tRNA hydrolase,  Despite the types of translational errors described above,
               which cleaves the ester bond between the tRNA and its  mRNA-directed protein synthesis is remarkably accurate.
               attached polypeptide. Peptidyl–tRNA hydrolase therefore  How is it that the ribosome and translational factors are
               removes the useless (and potentially harmful) protein frag-  able to achieve such faithful transmission of genetic in-
               ments and recycles the tRNAs. Interestingly, although the  formation? One way to describe the specificity of cog-
               initiatortRNA(fMet–tRNA  fMet )mimicsapeptidyl–tRNA  nate over noncognate AA–tRNAs is termed the “kinetic
               by virtue of its N-formyl group, peptidyl–tRNA hydrolase  proofreading” mechanism. One can imagine that selec-
               does not recognize the initiator as a substrate. The hydro-  tion of an EF-Tu:GTP:AA–tRNA ternary complex by the
               lase bypasses fMet–tRNA fMet  because of the presence of  ribosome during elongation can be considered a “scan-
               structural features unique to fMet–tRNA fMet .    ning” step. Depending on the codon–anticodon interac-
                                                                 tion, the AA–tRNA will either bind irreversibly in the ri-
                                                                 bosomal A-site (in the case of the cognate AA–tRNA), or
               E. A Dual-Function RNA
                                                                 dissociate from the ribosome before or after GTP hydrol-
               A particular challenge arises when an mRNA lacks in-  ysis (noncognate AA–tRNA). In this model, the rate of
               frame stop codons due to deletion or degradation. Bacteria  EF-Tu-triggered GTP hydrolysis is the same for cognate
               use a unique tRNA–mRNA hybrid (tmRNA, also called  and noncognate substrates. However, because the cognate
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