Codons, protein synthesis

Protein synthesis begins when the mRNA combines with a ribosome. There, tRNA molecules, which carry amino acids, align with mRNA, and a peptide bond forms between the amino acids. After the first tRNA detaches from the ribosome, the ribosome shifts to the next codon on the mRNA. Each time the ribosome shifts and the next tRNA aligns with the mRNA, a peptide bond joins the new amino acid to the growing polypeptide chain. After all the amino acids for a particular protein have been linked together by peptide bonds, the ribosome encounters a stop codon. Because there are no tRNAs to complement the termination codon, protein synthesis ends and the completed polypeptide chain is released from the ribosome. Then interactions between the amino acids in the chain form the protein into the three-dimensional structure that makes the polypeptide into a biologically active protein (see Figure 18.24). 

As described in the preceding sections protein synthesis involves transcription of the DNA to rtiRNA followed by translation of the mRNA as an amino acid sequence In addition to outlining the mechanics of transcription we have described the relationship among mRNA codons tRNA anticodons and ammo acids... 

Cellular protein biosynthesis involves the following steps. One strand of double-stranded DNA serves as a template strand for the synthesis of a complementary single-stranded messenger ribonucleic acid (mRNA) in a process called transcription. This mRNA in turn serves as a template to direct the synthesis of the protein in a process called translation. The codons of the mRNA are read sequentially by transfer RNA (tRNA) molecules, which bind specifically to the mRNA via triplets of nucleotides that are complementary to the particular codon, called an anticodon. Protein synthesis occurs on a ribosome, a complex consisting of more than 50 different proteins and several stmctural RNA molecules, which moves along the mRNA and mediates the binding of the tRNA molecules and the formation of the nascent peptide chain. The tRNA molecule carries an activated form of the specific amino acid to the ribosome where it is added to the end of the growing peptide chain. There is at least one tRNA for each amino acid. 

It has been known for some time that tetracyclines are accumulated by bacteria and prevent bacterial protein synthesis (Fig. 4). Furthermore, inhibition of protein synthesis is responsible for the bacteriostatic effect (85). Inhibition of protein synthesis results primarily from dismption of codon-anticodon interaction between tRNA and mRNA so that binding of aminoacyl-tRNA to the ribosomal acceptor (A) site is prevented (85). The precise mechanism is not understood. However, inhibition is likely to result from interaction of the tetracyclines with the 30S ribosomal subunit because these antibiotics are known to bind strongly to a single site on the 30S subunit (85). 

H Translation is the process by which mRNA directs protein synthesis. Each mRNA is divided into codons, ribonucleotide triplets that are recognized by small amino acid-carrying molecules of transfer RNA (tRNA), which deliver the appropriate amino acids needed for protein synthesis. 

The codon UAA stops protein synthesis. Why does the sequence UAA in the following stretch of mRNA not cause an) problems ... 

Anticodon (Section 28.5) A sequence of three bases on tRNA that reads the codons on mRNA and brings the correct amino acids into position for protein synthesis. 

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.

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.

The target of mupirocin is one of a group of enzymes which couple amino acids to their respective tRNAs for delivery to the ribosome and incorporation into protein. The particular enzyme inhibited by mupirocin is involved in producing isoleucyl-tRNA. The basis for the inhibition is a structural similarity between one end of the mupirocin molecule and isoleucine. Protein synthesis is halted when the ribosome encounters the isoleucine codon through depletion of the pool of isoleucyl-tRNA. 

Figure 7.5 Model of ferritin (and erythroid a-aminolaevulinate synthase) translation/ribosome binding regulation by IRP. In (a), with IRP not bound to the IRE (1) binding of the 43S preinitiation complex (consisting of the small ribosomal 40S subunit, GTP and Met-tRNAMet) to the mRNA is assisted by initiation factors associated with this complex, as well as additional eukaryotic initiation factors (elFs) that interact with the mRNA to facilitate 43S association. Subsequently (2), the 43S preinitiation complex moves along the 5 -UTR towards the AUG initiator codon, (3) GTP is hydrolysed, initiation factors are released and assembly of the 80S ribosome occurs. Protein synthesis from the open reading frame (ORF) can now proceed. In (b) With IRP bound to the IRE, access of the 43S preinitiation complex to the mRNA is sterically blocked. From Gray and Hentze, 1994, by permission of Oxford University Press.

Genetic code Sequence of nucleotides along the DNA and coded in triplets (codons) along the mRNA that determines the sequence of amino acids in protein synthesis. The DNA sequence of a gene can be used to predict the mRNA sequence, and subsequently to predict the amino acid sequence. 

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. 

Upon encountering a stop codon on the mRNA, the ribosome will halt incorporation of further amino acids into the polypeptide as there is no tRNA complementary to a stop codon (UAG, UGA, UAA). In order to liberate the polypeptide, the ester bond between the peptide and the tRNA residing in the P site has to be hydrolyzed — a reaction that is also catalyzed in the peptidyltransferase center. It is critical for protein synthesis that peptide release is tightly coupled to the presence of a stop codon in the decoding center to avoid premature termination resulting in shortened, nonfunctional proteins. Both functions, recognizing the stop codon and triggering... 

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

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