Translation anticodons

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. 

Most of the aforementioned efforts are based on the nonsense suppression methodology as the method for peptide altering [100]. In this approach, a nonsense codon is introduced into the enzyme-coding mRNA in the site that has to be altered. Simultaneously, the tRNA-noncoded amino acid hybrids are prepared with nonsense anticodons. Finally, the translation of modified mRNA is performed in vivo [101] or in vitro [102]. 

There are 64 different three-letter codons, but we don t have to have 64 different tRNA molecules. Some of the anticodon loops of some of the tRNAs can recognize (bind to) more than one condon in the mRNA. The anticodon loops of the various tRNAs may also contain modified bases that can read (pair with) multiple normal bases in the RNA. This turns out to be the reason for the wobble hypothesis, in which the first two letters of a codon are more significant than the last letter. Look in a codon table and you ll see that changing the last base in a codon often doesn t change the identity of the amino acid. A tRNA that could recognize any base in codon position 3 would translate all four codons as the same amino acid. If you ve actually bothered to look over a codon table, you realize that it s not quite so simple. Some amino acids have single codons (such as AUG for Met), some amino acids have only two codons, and some have four. 

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).

The anticodon sequence in tRNA is antiparallel and complementary to the codon translated in mRNA. 

These experiments make it clear that removing competition with release factors leads to more efficient incorporation of the desired amino acid. Unfortunately, the technology to incorporate nonstandard nucleotides into mRNAs coding for full-length proteins is not yet available. Alternatives that have been tested include using (i) a 4-nucleotide codon-anticodon pair, dubbed frame-shift suppression (Sect. 6.1), (ii) a rare codon, and (iii) cell-free extracts from organisms that are either deficient in a release factor (Sect. 5.1) or unable to translate one or more codons (Sect. 6.2). 

Cysteine and tyrosine are described as conditionally essential (see text). Selenocysteine is not always included in lists of amino acids but it obeys the definition of an amino acid, it is present in the diet, is present in some mammalian proteins, and it is incorporated directly into these proteins as selenocysteine during the normal process of translation there is a specific tRNA for this amino acid the anticodon is AGU. 

There is one separate tRNA for each amino acid and one separate specific synthetase. The enzyme must bind not only the correct amino acid but also the correct tRNA, so that each synthetase has specific recognition sites for both. Transfer RNAs contain a three-base sequence that is an anticodon, which binds to its complementary codon on messenger RNA. The importance of the synthetase in relation to fidelity of translating the information in messenger RNA is indicated by the fact that, once an amino acid is bound to tRNA, its identity as an amino acid is dictated by the anticodon site on the transfer RNA and not by the amino acid itself. (The enzyme can be considered as a dictionary, since it provides a cross-reference between the nucleic acid and amino acid languages.)... 

A tRNA molecule is specific for a particular amino acid, though there may be several different forms for each amino acid. Although relatively small, the polynucleotide chain may show several loops or arms because of base pairing along the chain. One arm always ends in the sequence cytosine-cytosine-adenosine. The 3 -hydroxyl of this terminal adenosine unit is used to attach the amino acid via an ester linkage. However, it is now a section of the nucleotide sequence that identifies the tRNA-amino acid combination, and not the amino acid itself. A loop in the RNA molecule contains a specific sequence of bases, termed an anticodon, and this sequence allows the tRNA to bind to a complementary sequence of bases, a codon, on mRNA. The synthesis of a protein from the message carried in mRNA is called translation, and a simplified representation of the process as characterized in the bacterium Escherichia coli is shown below. 

The mRNA is bound to the smaller 30S subunit of the bacterial ribosome. The mRNA is a transcription of one of the genes of DNA, and carries the information as a series of three-base codons. The message is read (translated) in the 5 to 3 direction along the mRNA molecule. The aminoacyl-tRNA anticodon (UAC) allows binding via hydrogen bonding to the appropriate codon (AUG) on mRNA. In prokaryotes, the first amino acid encoded in the sequence is A-formylmethionine (fMet). Although the codon for initiation (A-formylmethionine) is the same as... 

Protein synthesis means translation into a peptide chain of a genetic message first copied (transcribed) into m-RNA (p. 274). Amino acid (AA) assembly occurs at the ribosome. Delivery of amino acids to m-RNA involves different transfer RNA molecules (t-RNA), each of which binds a specific AA. Each t-RNA bears an anticodon nucleobase triplet that is complementary to a particular m-RNA coding unit (codon, consisting of 3 nucleobases. 

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... 

When a mutation introduces a termination codon in the interior of a gene, translation is prematurely halted and the incomplete polypeptide is usually inactive. These are called nonsense mutations. The gene can be restored to normal function if a second mutation either (1) converts the misplaced termination codon to a codon specifying an amino acid or (2) suppresses the effects of the termination codon. Such restorative mutations are called nonsense suppressors they generally involve mutations in tRNA genes to produce altered (suppressor) tRNAs that can recognize the termination codon and insert an amino acid at that position. Most known suppressor tRNAs have single base substitutions in their anticodons. 

Terms in bold are defined aminoacyl-tRNA 1035 aminoacyl-tRNA synthetases 1035 translation 1035 codon 1035 reading frame 1036 initiation codon 1038 termination codons 1038 open reading frame (ORF) 1039 anticodon 1039 wobble 1041... 

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