TRNA anticodon

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... 

Figure 1 Schematic drawing of the morphology of the ribosome. The ribosomal subunits are labeled, as are the approximate locations of their respective functional centers. The drawing is a transparent view from the solvent side of the small subunit. Transfer RNAs are shown in different binding states with the arrow indicating their direction of movement through the ribosome. The tRNA anticodon ends are oriented towards the viewer, whereas the 3-ends of the tRNAs are oriented towards the peptidyl transferase region on the large subunit. The letters h and b denote the head and body regions on the 30S subunit, respectively.

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... 

The ribosome is both the site of protein synthesis and an active participant in the process. The eukaryotic ribosome is constructed from two subunits the smaller 40S subunit and the larger 60S subunit. Basically, the 40S subunit binds the mRNA and monitors the recognihon between the mRNA codon and tRNA anticodon. The 60S subunit has the binding sites for aminoacyl-tRNAs and catalyzes the formation of peptide bonds. Remarkably, the catalytic entity for peptide bond formahon in the 60S subunit is the RNA component, not the protein component. Therefore, the 60S subunit acts as a ribozyme. 

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... 

The illustration shows the ligase responsible for the activation of aspartate. Each subunit of the dimeric enzyme (protein parts shown in orange) binds one molecule of tRNA (blue). The active centers can be located by the bound ATP (green). They are associated with the 3 end of the tRNA. Another domain in the protein (upper left) is responsible for recognition of the tRNA anticodon. 

Figure 12-1. Codon-anticodon base pairing. Special wobble base-pairing rules apply to the third (3 ) position of the codon. The first (S ) position of the tRNA anticodon is frequently inosine (I) to provide this flexibility in hydrogen bonding.

FIGURE 27-8 Pairing relationship of codon and anticodon, (a) Alignment of the two RNAs is antiparallel. The tRNA is shown in the traditional cloverleaf configuration, (b) Three different codon pairing relationships are possible when the tRNA anticodon contains inosinate. 

The first two bases of an mRNA codon always form strong Watson-Criclc base pairs with the corresponding bases of the tRNA anticodon and confer most of the coding specificity. 

P, and A, described later in the text the tRNA anticodons are in orange. Proteins appear as blue wormlike structures the rRNA as a blended space-filling representation designed to highlight surface features, with the bases in white and the backbone in green. The structure on the right is the 30S subunit... 

Binding of the tRNA anticodon to the mRNA codon follows the rules of complementary and antiparallel binding, that is, the mRNA codon is "read" 5 ->3 by an anticodon pairing in the "flipped" (3 —>5 ) orientation (Figure 31.9). [Note When writing the sequences of bolh codons and anticodons, the nucleotide sequence must ALWAYS be listed in the 5 —>3 order.]... 

As the mRJSlA leaves the cell nucleus in which it was created and enters the cytoplasm, it binds with specialized structures called ribosomes, as shown in Figure 13.36. Ribosomes are microscopic complexes of rRNA and proteins, and they are the site where proteins are built. As the mRNA is scrolled sequentially over the ribosome, the anticodon end of a free tRNA molecule binds to an mRNA codon. In this manner, tRNA molecules and their tag-along amino acids are placed adjacent to one another along the mRNA strand. The amino acids then chemically bond with one another, forming a long polypeptide chain that breaks away from the tRNA as it forms. This process continues until a stop mRNA codon, for which there are no tRNA anticodons, is encountered. At this point, the primary structure of a new protein has been built. 

Figure 25-28 Peptide-bond formation in protein biosynthesis showing how the amino-acid sequence is determined by complementary basepairing between messenger RNA and transfer RNA, The peptide chain is bound to tRNA, which is associated with mRNA through three bases in mRNA (codon) and three bases in tRNA (anticodon). In the diagram, the next codon A-A-G codes for lysine. Hence, Lys-tRNA associates with mRNA by codon-anticodon base-pairing and, under enzyme control, couples to the end of the peptide chain.

Table 6.1 shows the relationship between the codon sequence in mRNA and its corresponding amino acid in the new protein. Because there are 64 (43) different anticodon combinations and only 20 encoded amino acids, some different anticodon sequences encode for the same amino acid. Generally, all the anticodons matching a given amino acid will have the same first two nucleotides. Exceptions are arginine, serine, and isoleucine. For example, the codon for proline will always start with CC, but the arginine codon may start with either AG or CG. The 3 end of the tRNA anticodon pairs with the 5 end of the mRNA codon. In other words, the codon and anticodon align and bind in an antiparallel fashion. 

In translocation, the peptidyl-tRNA is shifted from the A site to the P site on the ribosome. What happens to the peptidyl-tRNA anticodon-codon interaction ... 

The redundancy in the genetic code is settled on the tRNA anticodon side. For each codon on the mRNA, the first two nucleotides (counting from the... 

During translation, the anticodon (on tRNA) and the codon (on mRNA) are arranged in the form of a short antiparallel double helix of the Watson-Crick type so that the base in 3 -position of the codon forms a base pair with the base in S -position of the anticodon. Because the number of tRNA s (and the number of anticodons) is limited, the same tRNA anticodon has to base-pair with several of the possible mRNA codons which differ in their 3 -position. Nature solves this problem by allowing nonstandard (wobble) base pairs ... 

Base on the tRNA anticodon in S -position Bases recognized on the mRNA codon ... 

Impairs proper aminoacyl tRNA anticodon-codon pairing —> misreading —> aberrant product [antibacterial]... 

Several different codons can code for the same amino acid. The corresponding anticodon follows the slash mark after each codon. The mRNA codons are written with the 5 end on the left and the 3 end on the right, and the tRNA anticodons have the 3 end on the left and the 5 end on the right. 

C represents a segment of the template strand of a molecule of DNA. Draw (a) the coding strand (b) the mRNA that is synthesized from C during transcription (c) the tRNA anticodons that are complementary to the mRNA codons (d) the amino acids (use one-letter codes) that form the peptide that C codes for. 

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