Protein synthesis chain termination

The final step in protein biosynthesis is chain termination. Natural mRNA molecules contain termination codons UAA, UGA, or UAG There are no tRNAs that have anticodons which are complementary to these codons. When the growing peptide chain encounters one of these termination codons, the peptidyl-tRNAis transferred to water instead of another aminoacyl-tRNA. The peptidyl-tRNA is hydrolyzed to free the completed protein and the tRNA. Chain termination completes protein synthesis. 

Energy requirements in protein synthesis are high. Four energy-rich phosphoric acid anhydride bonds are hydrolyzed for each amino acid residue. Amino acid activation uses up two energy-rich bonds per amino acid (ATP AMP + PP see p. 248), and two GTPs are consumed per elongation cycle. In addition, initiation and termination each require one GTP per chain. 

Zidovudine was the first drug of the class. It is a dideoxythymidine analog. It has to be phos-phorylated to the active triphosphate. This triphosphate is a competitive inhibitor of HIV reverse transcriptase. By incorporation into viral DNA it also acts as a chain-terminator of DNA synthesis. Mutations in viral reverse transcriptase are responsible for rapidly occurring resistance. Zidovudine slows disease progression and the occurrence of complications in AIDS patients. It is readily absorbed. However, first pass metabolism reduces its oral bioavailability with some 40%. It readily crosses the blood-brain barrier. Plasma protein binding is about 30%. Zidovudine is glucuronidated in the liver to an inactive metabolite. Its elimination half-life is 1 hour. 

The translation of the mRNA into proteins is the final step in the biological flow of information (see Fig. 6.1). Similar to other macromolecular polymerizations, protein synthesis can be divided into initiation, chain elongation, and termination. Critical players in this process are the aminoacyl transfer RNAs (tRNAs). These molecules form the interface between the mRNA and the growing polypeptide. Activation of tRNA involves the addition of an amino acid to its acceptor stem, a reaction catalyzed by an aminoacyl-tRNA synthetase. Each aminoacyl-tRNA synthetase is highly specific for one amino acid and its corresponding tRNA molecule. The anticodon loop of each aminoacyl-tRNA interacts... 

The ribosome can carry two aminoacyl-tRNAs simultaneously. In the chain elongation stage, the growing polypeptide is carried on one of these tRNAs. The chain is transferred to the second tRNA, which adds its amino acid to the growing peptide, and displaces the first tRNA. The ribosome then moves one codon along the mRNA to allow the next to be read. Termination of protein synthesis involves the release of the completed polypeptide, expulsion of the last tRNA, and dissociation of the ribosome from the mRNA. This is signaled by specific termination codons (UAA, UAG, or UGA) in the mRNA and requires the participation of various release factors. 

At one point or another during protein synthesis, several other proteins will be associated with the ribosome. These include factors that help in initiating the synthetic process, others that help in elongating the peptide chain, and yet others that play a role in terminating the synthesis of a peptide chain. Beyond this, there is also the mRNA to consider, as well as the aminoacylated tRNA molecules. Finally, since protein biosynthesis consumes energy, there is the hydrolysis of ATP and GTP to AMP and GDP, respectively, by the ribosome. 

The pathway of protein synthesis translates the three-letter alphabet of nucleotide sequences on mRNA into the twenty-letter alphabet of amino acids that constitute proteins. The mRNA is translated from its 5 -end to its 3 -end, producing a protein synthesized from its amino-terminal end to its carboxyl-terminal end. Prokaryotic mRNAs often have several coding regions, that is, they are polycistronic (see p. 420). Each coding region has its own initiation codon and produces a separate species of polypeptide. In contrast, each eukaryotic mRNA codes for only one polypeptide chain, that is, it is monocistronic. The process of translation is divided into three separate steps initiation, elongation, and termination. The polypeptide chains produced may be modified by posttranslational modification. Eukaryotic protein synthesis resembles that of prokaryotes in most details. [Note Individual differences are mentioned in the text.]... 

The start of protein synthesis is signalled by specific codon-anticodon interactions. Termination is also signalled by a codon in the mRNA, although the stop signal is not recognized by tRNA, but by proteins that then trigger the hydrolysis of the completed polypeptide chain from the tRNA. Just how the secondary and tertiary structures of the proteins are achieved is not yet clear, but certainly the mechanism of protein synthesis, which we have outlined here, requires little modification to account for preferential formation of particular conformations. 

NONSENSE CODON A codon that does not specify any amino acid in protein synthesis, but instead specifies termination of a polypeptide chain the nonsense codons are UAA, UAG, and UGA. 

A protein tail, which is the same in all library members, is fused to the C-terminus of the ribosome display construct and serves as a spacer. This spacer has two main functions. First, it tethers the synthesized protein to the ribosome. Second, it keeps the structured part of the protein outside the ribosome and allows its folding and interaction with ligands, without clashing with the ribosomal tunnel. The ribosomal tunnel covers between 20 and 30 C-terminal amino acids of the nascent polypeptide chain during protein synthesis and can therefore prevent the folding of the protein (Malkin and Rich, 1967 Smith et al., 1978). 

Abrin exerts its toxic action in the same way as ricin. The abrin B-chain avidly binds to a variety of cell types, in particular reticuloendothehal cells which bear the appropriate mannose receptors. The abrin B-chain also binds to the galactosyl-terminated receptors on the cell membrane to allow the entry of the abrin A-chain. Once internalized, the abrin A-chain is transported from the cell membrane to the ribosomes, where it catalytically inactivates the 60S ribosomal subunit by removing adenine from positions 4 and 324 of 28S rRNA, thereby inhibiting protein synthesis and causing cell death (Stripe and Barbieri, 1986). 

Once protein synthesis is initiated, amino acids are added to the peptide chain corresponding to each triplet in the mRNA until the ribosome encounters a termination or stop codon, whereupon the polypeptide chain is released from the ribosome, and assumes its final configuration. A ribosome covers about 50 bases of an mRNA, which is usually hundreds of bases long. Thus, several ribosomes translate an mRNA consecutively and simultaneously at any instant as shown in Fig. 2.4. A group of ribosomes translating a message is called a polyribosome . 

Unspecific permeability is prevented in the translationally active translocon because the tunnel is occupied by the peptide chain being polymerized. Similarly, the pore is blocked by BiP proteins, prominent intraluminal chaperones, after dissociation of the ribosome from the complex (53). In fact, it has been argued that the BiP locks form a smaller barrier for uncharged polar molecules than for charged ones. Furthermore, the dissociation of ribosomes from translocon complexes is delayed after the termination of protein synthesis. When a nontranslating ribosome is associated with the translocon complex, they form a transitional low-selectivity channel between the cytosol and the ER lumen (5). 

The methionine residue found at the amino-terminal end of E. coli proteins is usually modified. In fact, protein synthesis in bacteria starts with H-formylmethionine (fMet). A special tRNA brings formylmethionine to the ribosome to initiate protein synthesis. This initiator tRNA (abbreviated as tRNAf) differs from the one that inserts methionine in internal positions (abbreviated as tRNA ). The subscript "f indicates that methionine attached to the initiator tRNA can be formylated, whereas it cannot be formyl-ated when attached to tRNA. In approximately one-half of E. coli proteins, N-formylmethionine is removed when the nascent chain is 10 amino acids long. 

Table 29.4). For example, the antibioticpuromycin inhibits protein synthesis by causing nascent prokaryotic polypeptide chains to be released before their synthesis is completed. Puromycin is an analog of the terminal aminoacyl-adenosine part of aminoacyl-tRNA (Figure 29.34). 

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. 

Termination of protein synthesis occurs when the polypeptidyl chain is transferred to a water molecule rather than an aminoacyl-tRNA. What molecule provides energy for this transfer ... 

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