Wobble base

Fig. 8. Non-Watson-Crick base pairs occurring in double-stranded RNA where — represents the site of attachment to the sugar (a) A—U reverse-Watson-Crick (b) G—C reverse-Watson-Crick (c) A—U Hoogsteen (d) A—U reverse-Hoogsteen (e) G—U wobble and (f) G—U reverse-wobble.

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. 

All of the uniaxial fatigue data reported to date have been generated using a fatigue testing machine built by MRC that is based on the principal of a wobble plate. The machine has positions for 30 specimens and is capable of operation at controlled... 

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. 

Clearly, the results emerging suggested that at least two nucleotides were modified, the absolute sequence position within the tRNA had yet to be established. Ching etalP showed that a Se U residue was present in the wobble position of the tRNA " from C. sticklandii. This study confirmed a notion that the modification probably affects the translation efficiency of certain transcripts, based on the level of modification by selenium. The authors speculated that the modification to seleno-tRNA (GAG) allowed for more efficient use of this tRNA species as compared to the tRNA (GAA). Even today, no definitive data exist to show that this modification alters the translation efficiency in these bacterial model systems. Nonetheless, these studies had established the chemical forms of Se U and mnm Se U, and established that they were derived from modifications to nucleotides that first required sulfur (S U and mnm S U), the mechanism by which selenium was inserted into the tRNA would not be definitively answered until many years later. 

Watson-Crick wobble base pair mismatch mismatch mismatch... 

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.

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. 

I I I I I Watson-Crick pairs G-U wobble base pair /WWW exon... 

Murphy, F. V., 4th Ramakrishnan, V. Structure of a purine-purine wobble base pair in the decoding center of the ribosome. Nat. Struct. Mol. Biol. 2004,11, 1251-1252. 

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. 

Wobble Base pairing rules used for position... 

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.

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. 

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. 

Crick or wobble (GU) base pairing in the stems. This requires certain relationships in the sequences of the DNA in the genes that encode these molecules as discussed in Section E,3. Because of the base-pairing requirements, some of the bases in the stems protrude as bulges and fail to form pairs. Often, it is possible to find more than one reasonable structure, each having some bases unpaired.328... 

While tRNAs consist largely of loops and stems containing Watson-Crick base pairs, they also contain Hoogsteen pairs, wobble pairs, and triplets such as the following. 

Selenium is found to a minor extent wherever sulfur exists in nature. This includes the sulfur-containing modified bases of tRNA molecules. In addition to a small amount of nonspecific incorporation of Se into all S-containing bases there are, at least in bacteria, specific Se-containing tRNAs. In E. coli one of these is specific for lysine and one for glutamate. One of the modified bases has been identified as 5-methyl-amino-methyl-2-selenouridine.570 It is present at the first position of the anticodon, the "wobble" position.571... 

---