Phenylalanine genetic coding

Peptidic photoprobes can be based on the photoreactive amino acid p-benzoyl-L-phenylalanine inserted into a peptide in place of a natural aromatic residue by peptide synthesis [65] or by manipulation of the genetic code [66]. The use of p-benzoyl-L-phenylalanine for this purpose is not new, but the nature of peptide probes naturally offers opportunities for the location of linkage sites by proteomic analysis [67]. 

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. 

Although L-phenylalanine is a protein amino acid, and is known as a protein acid type of alkaloid precursor, its real role in biosynthesis (providing C and N atoms) only relates to carbon atoms. L-phenylalanine is a part of magic 20 (a term deployed by Crick in his discussion of the genetic code) and just for this reason should also be listed as a protein amino acid type of alkaloid precursor, although its duty in alkaloid synthesis is not the same as other protein amino acids. However, in relation to magic 20 it is necessary to observe that only part of these amino acids are well-known alkaloid precursors. They are formed from only two amino acid families Histidine and Aromatic and the Aspartate family . 

Nirenberg and Matthaei Reported that polyuridylic acid codes for phenylalanine and this opened the way to identification of genetic code. 

The genetic code refers to specific sequences of RNA bases (or DNA bases) that encode specific amino acids. Kach of these sequences is composed of a triplet of bases (three bases in a row). Hence, any mRNA molecule can be considered a continuous polymer of successive triplets. For example, the triplet UUU codes for phenylalanine, CAU encodes histidine, GAG encodes glutamate, AAA encodes lysine, and AUG codes for methionine. DNA is used for information storage, while mRNA is used for information transfer. 

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). 

Phenylalanine is one of the 10 essential amino acids that must be obtained from outside the body, as distinguished from the 11 nonessential amino acids that occur naturally within the body, including tyrosine. Exclusive of the nonessential amino add hydroxyproline, both sets comprise 20 common amino adds that are found in aU proteins, and they conform with, or are derived from, the common genetic code. It may be further noted that a large array of alkaloids are derived from phenylalanine and tyrosine, according to Cordell s Introduction to Alkaloids, as presented by Hoffman (1999, p. 145). 

Proteins are composed of chains of amino acids. In the genetic code of deoxyribonucleic acid (DNA), a codon or three-base sequence codes for the placement of each amino acid for example, the codon UUU places phenylalanine at that location in the protein and replacement of the third base with adenine results in the placement of leucine instead of phenylalanine. If a portion of the original code read. . . UUUACG. . . , deleting one of the uridine bases would cause that portion of the code to read. . . UUACG. .. the sequence UUA would then specify leucine. A point mutation changing one base might result in the formation of a different protein. 

D. S. King, L. Wang, P.G. Schultz, Addition of p-azido-L-phenylalanine to the genetic code of Escherichia coli.J. Am. Chem. Soc. 2002, 124, 9026-9027. 

The mutagen 5-bromouracil changes A-T pairs to G-C pairs or G-C pairs to A-T pairs. The mutation in (c) could be induced by 5-bromouracil. For example, the DNA sequence AAA, which codes for phenylalanine, could be changed to the sequence AAG, which codes for leucine. The other mutations could not arise from treatment with 5-bromouracil. Remember that the genetic code presented in the text is expressed in terms of RNA. The sequence UUU on RNA corresponds to the sequence AAA on the informational strand of DNA. Leucine is encoded by the sequence CUU on RNA, which corresponds to the sequence AAG on the informational strand of DNA. Remember also that, unless otherwise specified, nucleotide sequences are written in the 5 —> 3 direction. 

The years 1961-65 wimessed a cascade of discoveries in the relationship between information stored in DNA and the structure and biosynthesis of proteins. In 1961, Marshall W. Nirenberg (1927- ), National Institutes of Health (NIH) in Bethesda, added polyuridylic acid (a synthetic pseudo-RNA) to cell-free preparations of mRNA-depleted E. coli ribosomes, mixed with enzymes and 18 different amino acids. The ribosomes used polyuridylic add in place of their own mRNA and synthesized the polypeptide polyphenylalanine. The first entry into the genetic code was therefore UUU in RNA coding for phenylalanine in protein. 

After the discovery of three-letter codons, researchers were anxious to answer the next question Which triplets of bases (codons) code for which amino acids In 1961, Marshall Nirenberg and his coworkers at the National Institutes of Health (NIH) in Bethesda, Maryland, attempted to break the code in a very ingenious way. They made a synthetic molecule of mRNA consisting of uracil bases only. Thus, this mRNA contained only one codon, the triplet UUU. They incubated this synthetic mRNA with ribosomes, amino acids, tRNAs, and the appropriate enzymes for protein synthesis. The exciting result of this experiment was that a polypeptide that consisted only of phenylalanine was synthesized. Thus, the first word of the genetic code had been deciphered UUU phenylalanine. 

Several important features of the three-nucleotide genetic coding system are illustrated in Table 1.1. First, the code is redundant but lacks ambiguity. For example, both TTC and TTT code for phenylalanine, thus the code is redundant however, neither TTC or TTT code for any other amino acid, thus the code is not ambiguous. 

Nevertheless, current knowledge of biochemical systems and synthetic techniques may allow us to explore them from a slightly different perspective. Namely, what would life look like with an expanded genetic code—that is, with additional amino acids added into the proteins of life. Indeed, over the past few years chemists have been able to utilize native biochemical systems as well as evolved tRNA molecules (which we will discuss in Chapter 25) to load many unique amino acids into proteins of interest at any specific point desired in a number of different cells, including those of yeast, some mammals, and bacteria like E. coli. Some of the unnatural amino acids are shown below. They include ones with unique metals (like selenium), reactive functional groups (such as a ketone and an azide) that can be used for additional chemistry, and a boronic acid that can be used to bind certain sugars covalently. These synthetic amino acids are all derivatives of phenylalanine, but many other amino acid parent structures can be used as well. 

Table 61.1 The genetic code is composed of triplets of three bases. For example, UUU codes for the amino acid phenylalanine and UCU...

The next question is which of the 64 triplets code for which amino acid In 1961, Marshall Nirenberg provided a simple experimental approach to the problem based on the observation that synthetic polynucleotides direct polypeptide synthesis in much the same manner as do natural mRNAs. Nirenberg incubated ribosomes, amino acids, tRNAs, and appropriate protein-synthesizing enzymes. With only these components, there was no polypeptide synthesis. However, when he added synthetic polyuridylic acid (poly U), a polypeptide of high molecular weight was synthesized. Even more important, the synthetic polypeptide contained only phenylalanine. With this discovery, the first element of the genetic code was deciphered the triplet UUU codes for phenylalanine. 

The property of polynucleotide phosphorylase to synthesize a polyribonucleotide with a composition proportional to the amounts of NDP s present was crucial to its use in elucidating the genetic code. When UDP alone was present, the homopolymer poly U was obtained, the very homopolymer used by Nirenberg and Heinrich Matthei in their classic experiment. Having obtained polyphenylalanine as the polypeptide product of translation, they concluded that U—U—U would code for the amino acid phenylalanine, were the genetic code based on nucleotide triplets. 

The genetic code consists of a series of three nucleotides (triplet) in mRNA, called a codon. Each codon specifies an amino acid and its sequence in a protein. Early work on protein synthesis showed that repeating triplets of uracil, UUU, produced a polypeptide that contained only phenylalanine. Therefore, a sequence of —UUU UUU UUU— codes for three phenylalanines. 

A genetic disease is the result of a defective enzyme caused by a mutation in its genetic code. For example, phenylketonuria (PKU) results when DNA cannot direct the synthesis of the enzyme phenylalanine hydroxylase, required for the conversion of phenylalanine to tyrosine. In an attempt to break down the phenylalanine, other enzymes in the cells convert it to phenylpyruvate. If phenylalanine and phenylpyruvate accumulate in the blood of an infant, it can lead to severe brain damage and mental retardation. If PKU is detected in a newborn baby, a diet is prescribed that eliminates all the foods that contain phenylalanine. Preventing the buildup of the phenylpyruvate ensures normal growth and development. 

Furter, R., Expansion of the genetic code site-directed p-fluoro-phenylalanine incorporation in Escherichia coli, Protein ScL, 7, 2, 419,1998. 

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