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Table 11.5 Pairing Combinations at the Third
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Codon Position
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Number-one Base in tRNA (5 End) G C A U I Number-three Base in mRNA (3 End) U or C G U A or G A, U, or C
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(table 11.6; cf. table 11.4). Because mitochondrial transfer RNAs for unmixed families of codons have a U in the rst (wobble) position of the anticodon, apparently, given the structure of the mitochondrial transfer RNAs, the U can pair with U, C,A, or G. Presumably, evolutionary pressure has minimized the number of transfer RNA genes in the DNA of the mitochondrion, in keeping with its small size. Reduction from thirty-two to twenty-four is a 25% savings. (Recent evidence suggests that mammalian mitochondria may need only twenty-two transfer RNAs.) It has also been found that yeast mitochondria read the CUX family as threonine rather than as leucine (tables 11.4 and 11.6) and the terminator UGA (opal) as tryptophan rather than as termination. However, there appear to be differences among different groups of organisms reading the CUX family. Human and Neurospora mitochondria appear to read the CUX codons as leucine, just as cellular systems do. Of the groups so far analyzed, only yeast reads the CUX family as threonine. Similarly, human and Drosophila mitochondria read AGA and AGG as stop signals rather than as arginine (table 11.7). In 1985, it was discovered that Paramecium species read the UAA and UAG stop codons as glutamine within the cell. In addition, a prokaryote (Mycoplasma capricolum) reads UGA as tryptophan. We do not yet know how general this nding is:scientists have scrutinized the genetic code of very few species.We can thus conclude that the genetic code seems to have universal tendencies among prokaryotes, eukaryotes, and viruses. Mitochondria, however, read the code slightly differently: different wobble rules apply, and mitochondria and cells read at least one terminator and one unmixed family of codons differently.Also, the mitochondrial discrepancies are not universal among all types of mitochondria. Further work, involving the sequencing of more mitochondrial DNAs, should elucidate the pattern of discrepancies among the mitochondria of diverse species.We also now know that not every organism reads all codons in the same way. Ciliated protozoa and a mycoplasma read some stop signals as coding for amino acids. Nuclear variants are known in the following codons: CUG, AUA, UAA, UAG, UGA, CGG, and AGA. Mitochondrial variants are known in CUX,AUA, UAA, UAG,AAA, UGA, CGX,AGA, and AGG. One other type of variation of codon reading occurs: site-speci c variation, in which the interpretation of a codon depends on its speci c location.We are already familiar with the fact that GUG and, rarely, UUG can serve as prokaryotic initiation codons.This means that they are recognized by tRNAMet. However, they are not recognized by f tRNAMet (i.e., GUG and UUG are not misread internally in m messenger RNAs). In some cases, two of the termination codons (UGA and UAG, but not UAA) are misinterpreted as codons for amino acids.That is, termination will not occur at the normal place,resulting in a longer-than-usual protein. In some cases, these read-through proteins are vital the
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Tamarin: Principles of Genetics, Seventh Edition
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III. Molecular Genetics
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11. Gene Expression: Translation
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H N H Guanine O N HC N C N C N H H C C N H N C
H C CH N C O HC N C N CH Cytosine Inosine To ribose sugar N C O C N H H
H N C N
H C CH N C O Cytosine To ribose sugar
To ribose sugar
To ribose sugar
O C N H Guanine O N HC N C N C NH H C C N H
H C CH N C O Uracil
H N C N To ribose sugar H Inosine O N HC N C N CH C C N H C N
N CH N Adenine To ribose sugar
To ribose sugar
To ribose sugar
O C N H Inosine O N Figure 11.33 C C C N N CH H
H C CH N C O Uracil To ribose sugar
Base-pairing possibilities for guanine and inosine in the third (3 ) position of a codon. In the wobble position, guanine can form base pairs with both cytosine and uracil. Inosine, in the wobble position, can pair with cytosine, adenine, and uracil.
HC N
To ribose sugar
organism depends on their existence. For example, in the phage Q , the coat-protein gene is read through about 2% of the time.Without this small number of read-through proteins, the phage coat cannot be constructed properly. One last example of site-speci c variation involves the amino acid selenocysteine (cysteine with a selenium atom replacing the sulfur; see g. 11.1). Although many proteins have unusual amino acids, almost all are due to posttranslational modi cations of normal amino acids.
However, the amino acid selenocysteine is inserted directly into some proteins,such as formate dehydrogenase in E. coli, which has selenium in its active site. Selenocysteine is inserted into the protein by a novel transfer RNA that recognizes the termination codon, UGA, if that codon is involved in a particular stem-loop secondary structure in the messenger RNA. The selenocysteine transfer RNA is originally charged with a serine that is then modi ed to a selenocysteine. In addition to the
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