Synthesis from coded amino acids

Synthesis of amino acids starting from coded amino acids other than glycine... 

A potentially general method of identifying a probe is, first, to purify a protein of interest by chromatography (qv) or electrophoresis. Then a partial amino acid sequence of the protein is deterrnined chemically (see Amino acids). The amino acid sequence is used to predict likely short DNA sequences which direct the synthesis of the protein sequence. Because the genetic code uses redundant codons to direct the synthesis of some amino acids, the predicted probe is unlikely to be unique. The least redundant sequence of 25—30 nucleotides is synthesized chemically as a mixture. The mixed probe is used to screen the Hbrary and the identified clones further screened, either with another probe reverse-translated from the known amino acid sequence or by directly sequencing the clones. Whereas not all recombinant clones encode the protein of interest, reiterative screening allows identification of the correct DNA recombinant. 

Now we will return briefly to Sections 3.8-3.11 and 4.6-4.8 where we considered the general problem of multiple flows, here of H, C, N, O, S and P. We observe immediately that all the products are from the same small molecule environmental sources and are required to be formed in relatively fixed amounts using the same source of energy and a series of intermediates. Controlling all the processes to bring about optimum cellular production are feedbacks between them and linked with the code which generates proteins, and here we note particularly enzymes, i.e. catalysts. The catalysts are made from the amino acids, the synthesis of which they themselves manage, while the amino acids control the catalysts so as to maintain a restricted balanced set of reaction pathways in an autocatalytic assembly. It is also the feedback controls on both the DNA (RNA) from the same units used in the... 

Table 17-3. Synthesis of D-amino acids from a-keto acids by E. coli cells harboring pFADA which codes for four enzyme genes alanine racemase, L-alanine dehydrogenase, formate dehydrogenase, and D-amino acid aminotransferase.

Nitrogen is the one element above all others that we associate with growth. As pointed out in Chapter 14, it is a constituent of proteins, enzymes, chlorophyll, deoxyribonucleic acids that make up the genetic code, amino acids and many intermediates invplved in the synthesis of plant substances. It is characteristically present in comparatively large amounts in the growing tips of plants, hut it can move about readily from one part of the plant to another to meet the primary needs at the time. 

Protein synthesis occurs in vivo in two steps. In the first step the polymerizing enzyme RNA-nucleotidyl transferase (RNA polymerase) catalyzes the formation of messenger RNA (m-RNA) from ribonucleotides at the site of the stored information (in the cell nucleus). DNA is the template. Messenger RNA contains the genetic code (amino acid code). Thus, m-RNA is complementary to the strand of DNA used as a template, i.e., cytosine corresponds to guanine, and vice versa uridine corresponds to adenine, and adenine corresponds to thymine (see also Chapter 29),... 

The cell must possess the machinery necessary to translate information accurately and efficiently from the nucleotide sequence of an mRNA into the sequence of amino acids of the corresponding specific protein. Clarification of our understanding of this process, which is termed translation, awaited deciphering of the genetic code. It was realized early that mRNA molecules themselves have no affinity for amino acids and, therefore, that the translation of the information in the mRNA nucleotide sequence into the amino acid sequence of a protein requires an intermediate adapter molecule. This adapter molecule must recognize a specific nucleotide sequence on the one hand as well as a specific amino acid on the other. With such an adapter molecule, the cell can direct a specific amino acid into the proper sequential position of a protein during its synthesis as dictated by the nucleotide sequence of the specific mRNA. In fact, the functional groups of the amino acids do not themselves actually come into contact with the mRNA template. 

A number of essential organic molecules is required and represents more than 15 % of the cell. They are all made from the elements, H, C, N, O, P, S and Se, all of which except phosphorus are in coded form in amino acids. From their simple inorganic forms in the environment they give rise to all DNA (RNA), lipids, saccharides and proteins, and all small molecules participating in their synthesis. 

Now, this tentative description of the development of a correlation, later to become information from bases to the synthesis of proteins, by no means solves the problem of the origin of this code nor does it bring into focus the fact that the very proteins which were produced are responsible for the synthesis of the basic metabolic units, formaldehyde and acetic acid and then the amino acids and bases and finally the polymers by catalysts which are the polymers themselves. We do state, however, that the set of reactions quite probably give the most kinetically stable products. Now, the amounts of the different amino acids, lipids, saccharides... 

Figure 10 Alteration of the genetic code for incorporation of non-natural amino acids, (a) In nonsense suppression, the stop codon UAG is decoded by a non-natural tRNA with the anticodon CUA. In vivo decoding of the UAG codon by this tRNA is in competition with termination of protein synthesis by release factor 1 (RFl). Purified in vitro translation systems allow omission of RF1 from the reaction mixture, (b) A new codon-anticodon pair can be created using four-base codons such as GGGU. Crystal structures of these codon-anticodon complexes in the ribosomal decoding center revealed that the C in the third anticodon position interacts with both the third and fourth codon position (purple line) while the extra A in the anticodon loop does not contact the codon.(c) Non-natural base pairs also allow creation of new codon-anticodon pairs. Shown here is the interaction of the base Y with either base X or (hydrogen bonds are indicated by red dashes).

Translation of the information encoded in DNA, expressed as a particular nucleotide sequence, into a protein, expressed as an amino acid sequence, depends on the genetic code. In this code, sequences of three nucleotides (termed a codon) represent one of the 20 amino acids that compose the protein molecule. Because there are 64 codons which can be constructed for the four different bases, and only 20 different amino acids that are coded for, several amino acids may be coded for by more than one codon. There are also three codons, called stop codons, that terminate the transfer of information. Furthermore, although all cells contain the same complement of genes, certain cells (for example, the neurons) have specialized genes that encode specific proteins for the synthesis of specific transmitters. The expression of such genes is under the control of regulatory proteins called transcription factors which control the transcription of mRNAs from the genes they control. 

The ultimate purpose of DNA expression is protein synthesis. mRNAs serve as the intermediate carrier of the DNA genetic information for protein synthesis. The DNA message is carried in the form of base sequences that are transferred to RNA, also in terms of base sequences, and finally these are transferred into amino acid sequences through a translation process based on the genetic code. This process of information from the RNA to the protein is called translation. 

As is well known, the first stage in synthesizing proteins is transcription of genetic code from DNA to messenger RNA (mRNA), a process that depends on RNA polymerase (transcriptase). A strand of nucleotides in RNA mirrors the order of nucleotides in DNA, thus containing information in a certain sequence in which amino acids must be bound to form the corresponding protein. Protein synthesis takes place on ribosomes, which can be represented as certain machines in which proteins and various amino acids are assembled. 

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 . 

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