Pairing of Codon and Anticodon

The pairing of codons and anticodons required for insertion of the correct amino acid into the growing polypeptide chain is often referred to as decoding of fhe gene sequence. However, an equally important part of the decoding is the attachment of the correct amino acid to its corresponding cognate tRNA. This occurs in the cytoplasm and also in the nucleus. ... 

The amino acid codons represent a prescription for pairing between molecules of tRNA—with their attached amino acids—and molecules of mRNA. Functionally, the code works via antiparallel pairing of codon and anticodon in an RNA species. Translation into polypeptides is directed only by those triplet nucleotides which lie between the start and stop signals in an mRNA molecule. The corresponding complementary regions in DNA are the structural genes which are transcribed into mRNA by RNA polymerase. 

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. 

Note X and Y denote bases complementary to and capable of strong Watson-Crick base pairing with X andY respectively, Wobble bases—in the 3 position of codons and 5 position of anticodons—are shaded in pink. 

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.]... 

How does a cell read the code This question is dealt with in detail in Chapters 28 and 29. A key step is the positioning of each amino acid on the ribosome in proper sequence. This is accomplished by the pairing of codons of messenger RNA with the anticodons of the appropriate transfer RNA molecules as is indicated at the bottom of Fig. 5-30. Each tRNA carries the appropriate "activated" amino acid at its 3 end ready to be inserted into the growing peptide. 

The 3 terminal redundancy of the genetic code and its mechanistic basis were first appreciated by Francis Crick in 1966. He proposed that codons and anticodons interact in an antiparallel manner on the ribosome in such a way as to require strict Watson-Crick pairing (that is, A-U and G-C) in the first two positions of the codon but to allow other pairings in its 3 terminal position. Nonstandard base pairing between the 3 terminal position of the codon and the 5 terminal position of the anticodon alters the geometry between the paired bases Crick s proposal, labeled the wobble hypothesis, is now viewed as correctly describing the codon-anticodon interactions that underlie the translation of the genetic code. 

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. 

Distinguish carefully between the members of the following pairs of terms (a) nucleotide and nucleoside (b) introns and extrons (c) codons and anticodons. 

What are the rules that govern the recognition of a codon by the anticodon of a tRNA A simple hypothesis is that each of the bases of the codon forms a Watson-Crick type of base pair with a complementary base on the anticodon. The codon and anticodon would then be lined up in an antiparallel fashion. In the diagram in the margin, the prime denotes... 

Figure 30.21 16S rRNA monitors base-pairing between the codon and the anticodon. Adenine 1493, one of three universally conserved bases in 16S rRNA. forms hydrogen bonds with the bases in both the codon and the anticodon only if ifie codon and anticodon are correctly paired. [From J. M. Ogle and V. Ramakrishnan. Anna Rev. Biochem. 74 (2005) 129-177, Fig, 2a.J... 

The interactions between the third codon and anticodon nucleotides are less stringent. In fact, nontraditional base pairs (i.e., non-Watson-Crick) often occur. For example, tRNAs containing G in the 5 (or wobble ) position of the anticodon can pair with two different codons (i.e., G can interact with either C or U). The same is true for U, which can interact with A or G. When I is in the wobble position of an anticodon, a tRNA can base pair with three different codons, because I can interact with U or A or C. 

The pioneering molecular biologists recognized that, because amino acids cannot bind directly to the sets of three nucleotides that form their codons, adapters are required. The adapters were found to be tRNA molecules. Each tRNA molecule contains an anticodon and covalently binds a specific amino acid at its 3 -end (see Chapters 12 and 14). The anticodon of a tRNA molecule is a set of three nucleotides that can interact with a codon on mRNA (Fig. 15.2). To interact, the codon and anticodon must be complementary (i.e., they must be able to form base pairs in an antiparallel orientation). Thus, the anticodon of a tRNA serves as the link between an mRNA codon and the amino acid that the codon specifies. 

Polypeptide synthesis proceeds at peptidyl iP) and aminoacyl (.4) sites in the ribosome (Fig. 21-11). The synthesis in Fig. 21-11 shows initiation followed by sequential addition of Gly and lie. The 5 end of mRNA, located in the smaller subunit of the ribosome, is prepared to receive the tRNAs for Met and Gly (by matching of codon of mRNA and anticodon of tRNA). The tRNAs for Met and Gly pick up Met and Gly from the cytosol, enter the ribosome, and line up at the P and A sites, respectively, by base pairing of codons of mRNA and anticodons of tRNA (Fig. 21-1 la). The enzyme peptidyl transferase, contained in the large subunit of the ribosome, catalyzes the transfer and... 

The codon and anticodon are complementary, which means that a G-C-C codon on mRNA will match a C-G-G anticodon on tRNA. This is important because the C-G, G-C, G-C base pairs are capable of hydrogen bonding (see 138 and 139). This hydrogen bonding allows the tRNA to attach itself to... 

Figure 38-2. Recognition of the codon by the anticodon. One of the codons for phenylalanine is UULI. tRNA charged with phenyiaianine (Phe) has the com-piementary sequence AAA hence, it forms a base-pair compiex with the codon. The anticodon region typi-caiiy consists of a sequence of seven nucleotides vari-abie (N), modified purine ((Pu ),X,Y,Z,and two pyrimidines (Py) in the 3 to 5 direction.

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