Phenylalanine codons

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... 

The specific ribonucleotide sequence in mRNA forms a message that determines the order in which amino acid residues are to be joined. Each "word," or codon, along the mRNA chain consists of a sequence of three ribonucleotides that is specific for a given amino add. For example, the series UUC on mRNA is a codon directing incorporation of the amino acid phenylalanine into the growing protein. Of the 43 = 64 possible triplets of the four bases in RNA, 61 code for specific amino acids and 3 code for chain termination, fable 28.1 shows the meaning of each codon. 

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.

It has long been known that peptides of bacterial origin, such as N-formylat-ed oligopeptides, are potent activators of neutrophils. Bacterial protein biosynthesis is initiated by the codon AUG, which codes for polypeptide chains at the NH2 terminus to start with N-formylmethionine. However, very few mature bacterial proteins actually have this amino acid at the NH2 terminus because Af-formylmethionine is cleaved off by proteolytic processing. Sometimes just this amino acid is cleaved, but often several adjacent residues are also removed with it. These observations formed the basis for the chemical synthesis of a variety of N-formylated oligopeptides and an assessment of their ability to activate neutrophils in vitro. The most potent of these formylated peptides is TV-formylmethionyl-leucyl-phenylalanine (fMet-Leu-Phe). 

Figure 3.11. Structure of FcyRIIIA and FcyRIIIB. In FcyRIIIA, residue 203 is phenylalanine (Phe), which is followed by a hydrophobic transmembrane domain and a cytoplasmic domain. In FcyRIIIB, residue 203 is serine (Ser), which is followed by a stop codon. See text for details.

One of the groups of theories about the origin of the genetic code states that the code has to be the way it is, and is therefore universal, for stereochemical" reasons. In other words, phenylalanine, f. ex. must be represented by the triplets UUU and UUC because phenylalanine is somehow stereochemically related to these two codons 52,53,56,57) This seems likely, since steric fit is an essential property of the processes of replication, transcription and translation. That doesn t mean that one has conclusive evidence for such a statement. It only means that the theoreticians are groping in such a direction. 

Building on earlier work of Osawa and co-workers [55], Oliver and Kowal [52] tested the feasibility of introducing a noncoded amino acid at an unassigned codon in M. luteus. DNA templates were prepared which coded for 19-mer polypeptides containing either the unassigned codon AGA(Arg) or the termination codon TAG at position 13 under the control of a T7 RNA polymerase promoter. The corresponding tRNAs, produced as described in Sect. 2, were based on tRNA and acylated with phenylalanine. The tRNA was modified to prevent recognition by the alanine aminoacyl-tRNA synthetase and to increase translational efficiency. 

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). 

A set of coding rules are in action as in the translation process. First, a set of three adjacent nucleotides compose the code for each amino acid. A single amino acid can have several triplet codes or codons. Since there are four different nucleotides (or four different bases) in DNA and RNA, there exist 4 = 64 trinucleotide combinations. For instance, using U as a symbol for uracil, which is present in RNA, the triplet or code or codon UUU is specific for phenylalanine. 

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.

All the bases in the synthetic messenger RNA prepared by Nirenberg were U therefore, the codon is UUU. By referring to the codons in Table 27.4, we see that the UUU codes for phenylalanine. A polypeptide in which all the amino acid residues were phenylalanine was isolated in Nirenberg s experiment. 

Selective formation of microparticles from polynucleotides and lysine-rich proteinoids rich in individual radioactive amino acid has been studied and the focus of attention is on those homoanticodonic amino acids having one homogeneous codon (glycine, CCC lysine, UUU proline, GGG and phenylalanine, AAA)58). Precipitation of individual amino acid rich proteinoids with each of homopolyribonucleotides, with and without Mg2+, was tested58>. The results show that three (Lys-rich, Gly-rich,... 

Consult Table 18.2. The codon UUU translates to the amino acid phenylalanine. If a UUU sequence were to be mutated to UCU (the codon for serine), the protein produced would have a Ser residue in place of the Phe. Since UCU and UCC both code for Ser, a UCU UCC mutation would not lead to a change in the protein sequence. Thus, the advantage of a redundant code is that not all mutations cause disadvantageous changes in protein structure. 

This nine-base strand of m-RNA contains three codons UUC GGC, and, AUU, and calls for the amino acids phenylalanine, glycine, and, isoleucine in that order.7 Thus the order of the bases in DNA dictates a particular sequence in the m-RNA strand. When the m-RNA strand is complete, it leaves the nucleus and heads for the ribosomes in the cytoplasm. 

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. 

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