Protein synthesis termination

Nonsense suppressors are produced by tethering a nonnatural amino acid to a stop (or nonsense ) anticodon in tRNA. As a result, the stop codon in an mRNA sequence is converted from a protein synthesis termination site to a site at which the nonnatural amino acid may specifically be inserted. DNA base substitutions that correspond to the stop anticodon of tRNA may thus be made in order to specifically incorporate nonnatural amino acids into proteins. 

As we can see from the figure, three codons are used as protein synthesis termination signals, while the other 61 specify the amino acids and the initiation signal. Between 61 codons and 20 amino acids there cannot be a one-to-one correspondence, and in fact some amino acids are specified by six codons, some by four, others by two, and only two amino acids are coded by a single codon. In technical terms, this is expressed by saying that the genetic code is degenerate. 

When protein synthesis terminates, the initiator amino acid, Methionine, will have a free amino group. This end of the protein is the N terminus and the last amino acid of the chain has a free carboxy or C terminus. Protein synthesis thus initiates with the amino terminus and proceeds towards the C terminus. Proteins synthesized on the rough ER are transported across a membrane aiad into the cisternal spaces between the sheets of the ER where they are packaged for export. 

Subsequent to protein synthesis termination a process of programmed cell death, apoptosis, ensues (Hughes etal, 1996). The details of this process remain to be clarified but there is evidence that ricin A and B chains are involved and that the mechanism is independent of that which inhibits protein synthesis (Battelli, 2004). 

The regions of the tRNA molecule teferred to in Chapter 35 (and illustrated in Figure 35-11) now become important. The thymidine-pseudouridine-cyti-dine (T PC) arm is involved in binding of the amino-acyl-tRNA to the ribosomal surface at the site of protein synthesis. The D arm is one of the sites important for the proper recognition of a given tRNA species by its proper aminoacyl-tRNA synthetase. The acceptor arm, located at the 3 -hydroxyl adenosyl terminal, is the site of attachment of the specific amino acid. 

LIKE TRANSCRIPTION, PROTEIN SYNTHESIS CAN BE DESCRIBED IN THREE PHASES INITIATION, ELONGATION, TERMINATION... 

Figure 38-9. Diagrammatic representation of the termination process of protein synthesis. The peptidyl-tRNAand aminoacyl-tRNA sites are indicated as P site and A site, respectively. The termination (stop) codon is indicated by the three vertical bars. Releasing factor RF1 binds to the stop codon. Releasing factor RF3, with bound GTP, binds to RFl. Flydrolysisofthe peptidyl-tRNA complex is shown by the entry of HjO. N and C indicate the amino and carboxyl terminal amino acids, respectively, and illustrate the polarity of protein synthesis.

Other antibiotics inhibit protein synthesis on all ribosomes (puromycin) or only on those of eukaryotic cells (cycloheximide). Puromycin (Figure 38—11) is a structural analog of tyrosinyl-tRNA. Puromycin is incorporated via the A site on the ribosome into the carboxyl terminal position of a peptide but causes the premature release of the polypeptide. Puromycin, as a tyrosinyl-tRNA analog, effectively inhibits protein synthesis in both prokaryotes and eukaryotes. Cycloheximide inhibits peptidyltransferase in the 60S ribosomal subunit in eukaryotes, presumably by binding to an rRNA component. 

Albumin (69 kDa) is the major protein of human plasma (3.4-4.7 g/dL) and makes up approximately 60% of the total plasma protein. About 40% of albumin is present in the plasma, and the other 60% is present in the extracellular space. The liver produces about 12 g of albumin per day, representing about 25% of total hepatic protein synthesis and half its secreted protein. Albumin is initially synthesized as a preproprotein. Its signal peptide is removed as it passes into the cisternae of the rough endoplasmic reticulum, and a hexapeptide at the resulting amino terminal is subsequently cleaved off farther along the secretory pathway. The synthesis of albumin is depressed in a variety of diseases, particularly those of the liver. The plasma of patients with liver disease often shows a decrease in the ratio of albumin to globulins (decreased albumin-globuhn ratio). The synthesis of albumin decreases rela-... 

Fig. 8.4 Outline of the main events in protein synthesis initiation, elongation, translocation and termination. AUG is an initiation codon on the mRNA it codes for Af-fomiylmelhionine and initiates the formation of the 70S rihosome. UAG is a termination codon it does not code for any amino acid and brings about termination of protein synthesis.

While the exact mechanism of action remains unclear, dacarbazine appears to inhibit DNA, RNA, and protein synthesis. Dacarbazine disappears rapidly from the plasma, with a terminal half-life of about 40 minutes. Dacarbazine has shown clinical benefit in the treatment of melanoma, Hodgkin s lymphoma, and soft tissue sarcomas. Side effects include myelosuppression, severe nausea and vomiting, and a flulike syndrome that starts about 7 days after treatment and lasts 1 to 3 weeks. 

Denileukin diftitox is a combination of the active sections of interleukin 2 and diphtheria toxin. It binds to high-affinity interleukin 2 receptors on the cancer cell (and other cells), and the toxin portion of the molecule inhibits protein synthesis to result in cell death. The pharmacokinetics of denileukin diftitox are best described by a two-compartment model, with an a half-life of 2 to 5 minutes and a terminal half-life of 70 to 80 minutes. Denileukin diftitox is used for the treatment of persistent or recurrent cutaneous T-cell lymphoma whose cells express the CD25 receptor. Side effects include vascular leak syndrome, fevers/chills, hypersensitivity reactions, hypotension, anorexia, diarrhea, and nausea and vomiting. 

Potter, M. D., and Nicchitta, C. V. (2002). Endoplasmic reticulum-bound ribosomes reside in stable association with the translocon following termination of protein synthesis. J. Biol. Chem. 277, 23314-23320. 

ALTERNATIVE START SITES If all of the above didn t provide enough diversity, some messages contain two AUG initiation codons separated by some intervening information. Protein synthesis can initiate at either site. This is useful for making proteins with or without NH2- terminal signal sequences. 

Finally, this section has focused almost entirely on axonal transport, but dendritic transport also occurs [25]. Since dendrites usually include postsynaptic regions while most axons terminate in presynaptic elements, the dendritic and axonal transport each receive a number of unique proteins. An added level of complexity for intraneuronal transport phenomena is the intriguing observation that mRNA is routed into dendrites where it is implicated in local protein synthesis at postsynaptic sites, but ribosomal components and mRNA are largely excluded from axonal domains [26]. Regulation of protein synthesis in dendritic compartments is an important mechanism is synaptic plasticity [27,28]. The importance of dendritic mRNA transport and local protein synthesis is underscored by the demonstration that the mutation associated with Fragile X syndrome affects a protein important for transport and localization of mRNA in dendrites [27, 29], Similar processes of mRNA transport have been described in glial cells [30]. 

In normal cells, the GDP/GTP-binding proteins, after protein synthesis, move to the cell membrane to which they become hooked by a hydrophobic farnesyl group. The y-subunit is anchored in the membrane by a post-translational modification of the C-terminal CAAX sequence (C - cystein, AA - aliphatic amino acids, X - methionine). This protein is first enzymatically farnesylated by a specific farnesyltransferase, then the AAX part is cleaved by specific proteases and finally the cystein residue is converted to a methyl ester. 

In A. vinelandii, C-terminal cleavage occurs in crude extracts after restoration of nickel and requires hours rather than minutes, as is the case in vivo. It does not require de novo protein synthesis and surprisingly is not redox or O2 sensitive. Also, it is not inhibited by well-established inhibitors of metallo- or serine protease families (Menon and Robson 1994). 

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