Wobble codons

Amino acid Anticodon (3 5 ) Codon - wobble base (5 3 )... 

There may be no detectable effect because of the degeneracy of the code. This would be more likely if the changed base in the mRNA molecule were to be at the third nucleotide of a codon such mutations are often referred to as silent mutations. Because of wobble, the translation of a codon is least sensitive to a change at the third position. 

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. 

We now have clear evidence that selenium can be introduced specifically into proteins as selenocysteine and into a subset of tRNA species as mnm Se U or Se2U. The pathways and molecular mechanisms for insertion of selenium into these molecules have been well established in several model systems, the best studied being E. coli. The role for selenium in selenoproteins (i.e., the need for selenium over sulfur) is thought to be its ability to act as a more reactive nucleophile and perhaps a more rapid catalyst. However, a void in our knowledge exists for the specific need for selenium-modified tRNAs. Mutation of either selD or ybbB did not alter the growth characteristics of E. coli- however, no thorough analysis of the bacterial stress response has been carried out in any of these mutants. Clearly, further study is needed to better define the role for selenium in wobble codon usage for a subset of tRNA species. 

Figure 3 Cognate and near-cognate codon-anticodon interactions. The anticodon ioop of tRNA is shown as an example interacting with various codons on the mRNA. In correct, cognate codon-anticodon pairings, two Watson-Crick base pairs can be formed in the first two positions while the third position contains either a Watson-Crick or a wobble base pair.

Many amino acids are specified by more than one codon (redundancy). Frequently, a tRNA can translate more than one of these codons, sparing the ceE from making multiple tRNAs to carry the same amino acid. For instance, in Figure 1-4-6 the arg-tRNA shown can translate both the CGA and the CGG codons that specify arginine. This phenomenon is known as Wobble" and can be summarized as follows ... 

The third position of the codon does not always need to be paired with the anticodon (e.g., it is allowed to wobble in some cases). 

Answer E. Because of Wobble codons for the same amino acid often differ in the third base. Option B would be OK except that it is a stop codon. 

There are not 64 different tRNAs, one for each codon, but instead the tRNAs are capable of unconventional base pairing ( wobble ) with the codons during translation of the mRNA. 

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.

Wobble Allows Some tRNAs to Recognize More than One Codon... 

The wobble (or third) base of the codon contributes to specificity, but, because it pairs only loosely with its corresponding base in the anticodon, it permits rapid dissociation of the tRNA from its codon during protein synthesis. If all three bases of a codon engaged in strong Watson-Crick pairing with the three... 

TABLE 27-4 How the Wobble Base of the Anticodon Determines the Number of Codons a tRNA Can Recognize... 

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. 

The third position in each codon is much less specific than the first and second and is said to wobble. 

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... 

Wobble Nontraditional base-pairing between the 5-nucleotide (first nucleotide) of the anticodon with the 3 -nucleotide (last nucleotide) of the codon. I = inosine. 

The "wobble" hypothesis states that the first (5 ) base of the anticodon is not as spatially defined as the other two bases. Movement of that first base allows nontraditional base-pairing with the last (31) base of the codon, thus allowing a single tRNA to recognize more than one codon for a specific amino acid. 

Another pairing that occurs in tRNAs allows guanine to pair with uracil, e.g., G4 with U69. This was originally proposed to account for codon-anticodon interactions betweentRNA molecules and messenger RNA (Chapter 29). It is commonly called wobble pairing because the uracil must wobble away from its orientation in the normal Watson-Crick pair.27 37... 

The Code Was Deciphered with the Help of Synthetic Messengers The Code Is Highly Degenerate Wobble Introduces Ambiguity into Codon-Anticodon Interactions... 

Wobble Introduces Ambiguity into Codon-Anticodon Interactions... 

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. 

A careful comparison of the wobble rules with the genetic code indicates that the minimum number of tRNAs required to translate all 61 codons is 31. With the addition of tRNAjMet the total comes to 32. Most cells contain many more than this minimum number of tRNA types. 

Examples of standard (a) and wobble (b and c) base pairs formed between the first base in the anticodon and the third base in the codon. 

Crick, F. H. C., Codon-anticodon pairing The wobble hypothesis. J. Mol. Biol. 19 548-555, 1966. A classic paper. 

Explain why the use of GUG and UUG as initiation codons in place of AUG was not expected, even based on Crick s wobble hypothesis. 

Wobble. A proposed explanation for base-pairing that is not of the Watson-Crick type and that often occurs between the 3 base in the codon and the 5 base in the anticodon. 

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