Coded amino acids

The addition of ammonia to the variety of acids derivable from either the breakdown of glucose, glycolysis, or of the pentose shunt reaction products, ribose and NADPH, and from the citrate cycle, gives the amino acids (see Table 4.7 and Figure 4.4) Polymerisation of amino acids in cells gives proteins. In some of the amino acids sulfur and selenium can be incorporated easily. We assume NH3 was present. (Note that Se is in a coded amino acid not in Table 4.7.) Some selective metal-binding properties can be seen in Table 4.7, but amino acid carboxylates can bind all. 

Allele One form of a genetic locus, distinguished from other forms (= alleles) by its particular nucleotide or its coded amino acid sequence. Single nucleotide polymorphisms are biallelic, i.e., one base pair is exchanged with just one other base pair. In such a case, only two different alleles exist in the population for such a gene locus. However, several different alleles may exist in the population if the locus is defined by more than one nucleotide (i.e., microsatelhtes, haplotypes). Thus,... 

To transcribe information from DNA to mRNA, one strand of the DNA is used as a template. This is called the anticoding, or template, strand and the sequence of mRNA is complementary to that of the template DNA strand (Fig. A2.8) (i.e., C->G, G->C, T->A, and A U note that T is replaced by U in mRNA). The other DNA strand, which has the same base sequence as the mRNA, is called the coding, or sense, strand. There are 64 (4 x 4 x 4) possible triplet codes of the four bases 61 are used for coding amino acids and three for termination signals. As there are 20 amino acids for the 61 codes, some triplets code for the same amino acid. A table of the genetic code is presented in Exhibit A2.2. 

Coenzymes are densely functionalized organic cofactors capable of catalyzing numerous diverse chemical reactions. Nature exploits the intrinsic chemical reactivity of these molecules to extend the chemical fimctionaUty of enzymes well beyond the reactivity of the coded amino acids. When these constituents are incorporated via covalent or non-covalent interactions into coenzyme-depen-dent enzymes, the inherent reactivity of the co enzyme is augmented and directed to effect chemical transformations with substrate and product selectivities, rates, and yields that are unachievable by either the protein or coenzyme alone. Thus, coenzymes play a critical role in the execution of a large number of essential metabolic processes. 

Site-directed mutagenesis allows one or more specific amino acids in a protein to be replaced with any of the other 20 coded amino acids that are normally present in proteins [3] and has been utilized extensively to study and modify the biophysical and biochemical characteristics of a wide variety of proteins. Despite its tremendous impact, conventional site-directed mutagenesis suffers from the strict constraint that substitutions are restricted to the 20 primary amino acids. While a tremendous amount of information has been obtained from such substitutions, there are many cases in which the incorporation of a noncoded amino acid could yield more detailed information or enable researchers to investigate or engineer proteins in novel ways. 

Recently, Jung et al. [42] developed two artificial neural network models to discriminate intestinal barrier-permeable heptapeptides identified by the peroral phage display experiments from randomly generated heptapeptides. There are two kinds of descriptors one is binary code of amino acid types (each position used 20 bits) and the other, which is called VHSE, is a property descriptor that characterizes the hydrophobic, steric, and electronic properties of 20 coded amino acids. Both types of descriptors produced statistically significant models and the predictive accuracy was about 70%. 

DNA triplet code RNA triplet code Amino acid specified... 

Though naturally occurring peptides based on coded amino acids have been widely used as drugs, there are problems with the use of peptides as therapeutic agents. The problems mainly arise from their rapid metabolism by proteolysis, and their interactions at multiple receptors. As a result, peptide researchers have sought modifications of peptide structures to create more stable and bioavailable molecules. P-27 ... 

Since the stereochemistry of the newly created quaternary carbon center was apparently determined in the second alkylation process, the core of this method should be applicable to the asymmetric alkylation of aldimine Schiffbase 42 derived from the corresponding a-amino adds. Indeed, di-alanine-, phenylalanine- and leucine-derived imines 42 (R1 = Me, CH2Ph, i-Bu) can be alkylated smoothly under similar conditions, affording the desired non-coded amino acid esters 43 with excellent asymmetric induction, as exemplified in Table 5.7 [19]. 

Code Amino acid Code Amino acid Code Amino acid Code Amino acid... 

Noncoded amino-acids Chemical synthesis is not limited to coded amino acids and potentially allows the generation of an infinite variety of nonnatural analogs. 

Jonsson, J., Eriksson, L., Hellberg, S., Sjostrom, M. and Wold, S. Multivariate Parametrizationof55 Coded andNon-Coded Amino Acids, QSAR, 1989,8,204-209. 

Szathmary E. The origin of the genetic code—amino acids as cofactors in an RNA world. Trends Genet. 1999 15 223-229. 

Acid hydrolysis yields 16 of the 20 coded amino acids tryptophan is destroyed, cysteine recovery is unreliable, and asparagine and glutamine are converted to aspartic acid and glutamic acid, respectively. Furthermore, some side groups, such as the hydroxyl in serine, promote the breakdown of the residue, whereas aliphatic amino acids, protected by stearic hindrance, require longer hydrolysis time. This variation in yield can be overcome by hydrolyzing samples for 24, 48, and 72 h and extrapolating the results to zero time point. 

Protein amino acids , alias the coded amino acids ... 

Coded amino acids is a better name for these twenty amino acids, rather than protein amino acids or primary protein amino acids (the term coded amino acids is increasingly used), because changes can occur to amino-acid residues after they have been laid in place in a polypeptide by ribosomal synthesis. Greenstein and... 

Table 1.1. The twenty coded amino acids (nineteen coded L-a-amino acids, and one coded L-a-imino acid) structures and definitionsa... 

So this three-letter system was introduced, more with the purpose of spacesaving nomenclature for peptides than to simplify the names of the amino acids. A one-letter system (thus, glycine is G) is more widely used now for peptides (but is never used to refer to individual amino acids in other contexts) and is restricted to naming peptides synthesised from the coded amino acids (Figure 1.3). 

Table 1.2. Post-translational changes to proteins the modified coded amino acids present in proteins, including crosslinking amino acids (secondary amino acids)... 

The aliphatic and aromatic coded amino acids may exist in a(3-dehydrogenated forms and the (3-hydroxy-a-amino acids may undergo post-translational dehydration, so as to introduce ot(3-dehydroamino acid residues, -NH-(C=CR1R2)-CO-, into polypeptides. 

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