Phenylalanine, anticodon

Among the 76 nucleotides of tRNA are two sets of three that are especially important The first is a group of three bases called the anticodon, which is comple mentary to the mRNA codon for the ammo acid being transferred Table 28 3 lists two mRNA codons for phenylalanine UUU and UUC (reading m the 5 3 direction) Because base pairing requires the mRNA and tRNA to be antiparallel the two anticodons are read m the 3 5 direction as AAA and AAG... 

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.

The base sequence and the tertiary structure of the yeast tRNA specific for phenylalanine (tRNA " ) is typical of all tRNAs. The molecule (see also p.86) contains a high proportion of unusual and modified components (shaded in dark green in Fig. 1). These include pseudouridine (T), dihydrouridine (D), thymidine (T), which otherwise only occurs in DNA, and many methylated nucleotides such as 7-methylguanidine (m G) and—in the anticodon—2 -0-methylguanidine (m G). Numerous base pairs, sometimes deviating from the usual pattern, stabilize the molecule s conformation (2). 

The actual information transfer is based on the interaction between the mRNA codons and another type of RNA, transfer RNA (tRNA see p. 82). tRNAs, of which there are numerous types, always provide the correct amino acid to the ribosome according to the sequence information in the mRNA. tRNAs are loaded with an amino acid residue at the 3 end. Approximately in the middle, they present the triplet that is complementary to each mRNA codon, known as the anticodon (GAA in the example shown). If the codon UUC appears on the mRNA, the anticodon binds a molecule of Phe-t-RNA to the mRNA (5) and thus brings the phenylalanine residue at the other end of the molecule into a position in which it can take over the growing polypeptide chain from the neighboring tRNA (6). 

Figure 5-30 Schematic cloverleaf structure of a phenylalanine-specific transfer RNA (tRNA he) of yeast. The dots represent pairs or triplets of hydrogen bonds. Nucleosides common to almost all tRNA molecules are circled. Other features common to most tRNA molecules are also marked. The manner in which the anticodon may be matched to a codon of mRNA is indicated at the bottom.

FIGURE 28.11 Phenylalanine tRNA from yeast, (a) A schematic drawing showing the sequence of bases. Transfer RNAs usually contain a number of modified bases ( gray circles). One of these is a modified guanosine (G ) in the anticodon. Hydrogen bonds, where present, are shown as dashed lines, (b) The structure of yeast tRNAphe as determined by X-ray crystallography. 

Figure 25-26 (a) Generalized representation of a tRNA molecule. Each segment represents a nucleotide, the actual number and sequence of nucleotides varies with the tRNA. There are regions of intrachain basepairing (dashed lines). The nucleotide at the long end has a ribose with a free 3 -OH. The nucleotide at the short end is phosphorylated at 5 -OH. The three nucleotides of the anticodon loop pair with the appropriate bases in mRNA. (b) Three-dimensional picture of a tRNA to show the manner in which the chain is coiled. An excellent review article on the determination of the structure of phenylalanine tRNA by x-ray diffraction has been published, J. L. Sussman and S.-H. Kim, Science 192, 853 (1976). 

When yeast phenylalanine tRNA is digested with a small amount of RNase (partial digest) such as T2 RNase, almost all of the cleavage sites are found in the anticodon loop. Explain this observation. 

Codons that specify the same amino acid are called synonyms. Most synonyms differ only in the third base of the codon for example GUU, GUC, GUA and GUG all code for valine. During protein synthesis, each codon is recognized by a triplet of bases, called an anticodon, in a specific tRNA molecule (see Topics G10 and H2). Each base in the codon base pairs with its complementary base in the anticodon. However, the pairing of the third base of a codon is less stringent than for the first two bases (i.e. there is some wobble base-pairing ) so that in some cases a single tRNA may base-pair with more than one codon. For example, phenylalanine tRNA, which has the anticodon GAA, recognizes both of the codons UUU and UUC. The third position of the codon is therefore also called the wobble position. 

The tRNA for proline, which has the anticodon GGG, hydrogen bonds to the CCC codon for proline in the mRNA and brings its attached proline amino acid into position for attachment to the growing protein chain. Then the tRNA for phenylalanine hydrogen bonds to the codon for phenylalanine in the mRNA and brings its attached phenylalanine into position for attachment to the proline. This process continues until a stop signal is reached. 

Fig. 20.8. Three-dimensional structure of phenylalanine specific tRNA from yeast. Watson-Crick type base pairs indicated by slabs, nonstandard base-base interactions that stabilize the tertiary structure are denoted a to h. Invariant and semi-invariant nucleotides are shaded, the four double helical regions are indicated by a a-(amino add) arm, Tarm, D arm, a.c. (anticodon arm [696]...

Many eucaryotic phenylalanine transfer ribonucleic acids (tRNA ) contain fluorescent components at the position adjacent to the 3 -end of an anticodon. A few related hypermodified nucleosides 1 have been isolated, their structure has been elucidated, and their chemical synthesis been performed. 

A mutation caused by the insertion of an extra base can be suppressed by a tRNA that contains a fourth base in its anticodon. For example, UUUC rather than UUU is read as the codon for phenylalanine by a tRNA that contains 3 -... 

Structure of a tRNA molecule. The tRNA is a roughly cloverleaf-shaped molecule containing an anticodon triplet on one "ieaf" and an amino acid attached covalently at its 3 end. The example shown is a yeast tRNA that codes for phenylalanine. The nucleotides not specifically identified are chemically modified analogs of the four standard nucleotides. 

Transfer-RNA molecules participate in protein synthesis according to the genetic code at the ribosomes in the cell. The results indicate that conformational changes of the transfer-RNA molecules are important for the interaction between codon and anticodon at the ribosomes, for example. Two distinct and invariant lifetimes of the ethidium label in the anticodon loop of the transfer-RNA for the aminoaeid phenylalanine in solution indicated two conformations 2S). 

Tricyclic hypermodified nucleosides are found in archaeal and eukaryotic tRNAs and are frequently observed at position 34 (wobble base) or position 37 (adjacent to the anticodon). Position 37 typically contains a hypermodified nucleoside such as N -threonylcarbamoyladenosine (t A), 2-methylthio-N -isopentenyl-ade-nosine (ms i A-37), or wybutosine (yW). yW and its derivatives occur at position 37 in archaeal and eukaryotic phenylalanine tRNA (tRNAphe). The modifications serve to maintain the correct translational reading frame via hydrophobic interactions, which reinforce codon—anticodon pairing and prevent incorrect Watson—Crick base-pairing. Studies have shown that unmodified tRNA leads to translational defects that have been implicated in different pathological states. ... 

FIGURE 27.28 Phenylalanine tRNA. (a) A schematic drawing showing the sequence of bases. RNAs usually contain modified bases (green boxes), slightly different from those in other RNAs. The anticodon for phenylalanine is shown in red, and the CCA triplet which bears the phenylalanine is in blue. (6) The experimentally determined structure for yeast phenylalanine tRNA. Complementary base-pairing is present in some regions, but not in others. 

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