Anticodon loop

The anticodon region consists of seven nucleotides, and it recognizes the three-letter codon in mRNA (Figure 38-2). The sequence read from the 3 to 5 direction in that anticodon loop consists of a variable base-modified purine-XYZ-pyrimidine-pyrimidine-5h Note that this direction of reading the anticodon is 3 " to 5 whereas the genetic code in Table 38—1 is read 5 to 3 since the codon and the anticodon loop of the mRNA and tRNA molecules, respectively, are antipar-allel in their complementarity just like all other inter-molecular interactions between nucleic acid strands. 

Each tRNA has a different sequence at the anticodon loop that is complementary to the codon sequence in the RNA. The recognition structure that is formed is analogous to double-stranded, antiparallel DNA. If the codon (in the RNA) is GCA (written 5 to 3 ), the anticodon loop in the tRNA would have the sequence UGC (again written to 5 to 3 )-... 

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. 

How, in turn, does the synthetase recognize its specific tRNA From extensive mutagenesis studies, it appears that the aminoacyl-tRNA synthetases recognize particular regions of the tRNA molecule, most often in their anticodon loops and/or in their acceptor stems. 

The wyebutine base at position 37 in the anticodon loop of tRNAphehas also been used as a fluorescence probe/194-2001 The wyebutine base, like ethidium, exhibits a reduced fluorescence lifetime when exposed to aqueous... 

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).

Many specificity elements for tRNA are also the result of interactions with the three bases of the anticodon loop C34 (and U34), U35, and G36 are each bound within separate pockets of the anticodon-binding domain." Although it is likely that in free tRNA , like most other free tRNAs, anticodon bases are normally stacked with one another, binding by GlnRS disrupts this base stacking, allowing each base to be recognized by... 

We know fhat the anticodon is a triplet of bases occupying the anticodon loop in the tRNA structure. By Watson-Crick base-pairing, this anticodon can recognize the... 

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... 

On each of the tRNA molecules, one of the single-stranded loops contains a trinucleotide sequence that is complementary to the triplet codon sequence used in the genetic code to specify a particular amino acid. This loop on the tRNA is known as the anticodon loop, and it is used to match the tRNA with a complementary codon on the mRNA. In this way the amino acids carried by the tRNA molecules can be aligned in the proper sequence for polymerization into a functional protein. 

N 130 "Loop Formation in Polynucleotide Chains. II. Flexibility of the Anticodon Loop of fRNAphe "... 

I A 14-nucleotide I intron (shown in purple) in the anticodon loop is removed by I splicing. 

An intron (see below) must be removed from the anticodon loop, and sequences at both the 5 - and the 3 -ends of the molecule must be trimmed. Other posttranscriptional modifications include addition of a -CCA sequence by nucleotidyltransferase)to the 3 -terminal end of tRNAs, and modification oTbases at specific positions to produce "unusual bases (see p. 290). 

The anticodon loop of one of the tRNA Gly molecules from E. coli is as follows. Identify the anticodon, reading from 3 to 5. This tRNA recognizes two different Gly codons. What are they Write them from 5 to 3. ... 

Anticoagulation systems in blood 634 Anticodon 231 Anticodon loop in tRNA... 

The ribosomal translocation process is quite complex. As the tRNAs move from A to P to E sites on the 16S RNA platform, the mRNA must also move in discrete single-codon steps. Tire acceptor stems of the tRNAs in the A and P sites must react at the appropriate times in the peptidyltransferase center. Study of protection from chemical probes suggests that tRNAs sometimes lie with the anticodon loop in the A site of the small ribosomal subunit, while the acceptor stem is in the P site of the large subunit (an A/P site as illustrated in Fig. 29-12B). Each aminoacyl-tRNA enters as a complex with EF-Tu and may initially bind with its anticodon in the A site and the acceptor stem with attached EF-Tu in a transient T site, the composite state being A/T. After loss of EF-Tu the acceptor stem can move into the A site to give an A/A state. The peptidyltransferase reaction itself necessarily involves movement at the acceptor stems by 0.1 nm or more. However, additional movement of 1 nm is needed to move the two tRNAs into states A/P and P/E, respectively. Movement of the mRNA then moves the... 

A suppressor of frame-shift mutations in Salmonella is a tRNA containing at the anticodon position the nucleotide quartet CCCC instead of the usual CCC triplet anticodon.442 443 It has eight unpaired bases in the anticodon loop instead of the usual seven. Other frame-shift repressor tRNAs have been identified in E. cob, 444 Salmonella, and yeast.445 Not all suppressor genes encode tRNAs. For example, a UGA suppressor from E. coli is a mutant 16S rRNA from which C1054 has been deleted.446 A general nonsense suppressor in yeast is homologous to yeast elongation factor EF-la as well as to E. coli EF-Tu.447... 

Figure 25-26 (a) Generalized representation of a tRNA molecule. Each segment represents a nucleotide, the actual number and sequence of nucleotides varies with the tRNA. There are regions of intrachain basepairing (dashed lines). The nucleotide at the long end has a ribose with a free 3 -OH. The nucleotide at the short end is phosphorylated at 5 -OH. The three nucleotides of the anticodon loop pair with the appropriate bases in mRNA. (b) Three-dimensional picture of a tRNA to show the manner in which the chain is coiled. An excellent review article on the determination of the structure of phenylalanine tRNA by x-ray diffraction has been published, J. L. Sussman and S.-H. Kim, Science 192, 853 (1976). 

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