Other Amino Acid Syntheses

Kinetic studies on reducing gas mixtures showed that the concentration of ammonia falls during the reaction, while that of HCN first rises and then stays almost constant. The amino acid concentration increases steadily as the reaction time increases, while the aldehyde concentration remains constant. 

Glycine and the other amino acids are probably formed via the Strecker-cyano-hydrin synthesis (which has been known for more than 150 years) from aldehyde, HCN and ammonia, with subsequent hydrolysis (Strecker, 1850,1854 Miller, 1953). 

It is also possible that reactions involving free radicals take place the formation of such radicals has been clearly demonstrated during electrical discharges. 

Abelson (1956) carried out experiments using atmospheres containing CO2, (CO), N2, (NH3), H2 and H2O and detected small amounts of simple amino acids, the formation of which was prevented by adding oxygen. Many of the Miller-Urey experiments involved various energy sources and were carried out in the liquid and solid states as well as on gas mixtures. 

Although the Miller-Urey experiments of 1953 are of only historic interest today, they do mark the beginning of prebiotic chemistry and modern biogenesis research. 

New experiments using weakly reducing or neutral gas atmospheres were conceived and carried out more than 20 years after Miller s first successes (Schlesinger and Miller, 1983). Comparisons of a series of simulated prebiotic atmospheres containing CH4, CO and CO2 as carbon sources, using electrical discharges at 298 K, led to the following results  

Mixtures of (a) CH4 + H2 + N2 + NH3, (b) CH4 + H2 + N2, with the molar ratio of H2 to CH4 varying between 0 and 4 the amino acid yields (with respect to the amount of carbon) varied between 1.2 and 4.7%, almost independent of the H2/CH4 ratio and the amount of NH3 in the reaction mixture. 

After 2 days, the yield approached 60% of the maximum when CH4 was used and 80% using CO. 

The results so far available, and the models derived from them, indicate the following a reducing atmosphere is more favourable for amino acid synthesis. If, however, the partial pressure of methane on the primeval Earth was either zero or very low, a relatively high H2/CO or H2/CO2 ratio still allowed good rates of amino acid synthesis. It is, however, still an open question as to whether these concepts are realistic, because of the possibility that hydrogen could have escaped into space. It is arguable that in certain areas on the young Earth (and under unknown conditions), 

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Attenuation. A major mechanism of feedback repression, known as attenuation, depends not upon a repressor protein but upon control of premature termination. It was first worked out in detail by Yanofsky et al. for the trp operon of E. coli and related bacteria.184 186 Accumulation of tryptophan in the cell represses the trp biosynthetic operon by the action of accumulating tryptophanyl-tRNATlP, which specifically induces termination in the trp operon. Other specific "charged" arnino-acyl-tRNA molecules induce termination at other amino acid synthesis operons. 

The amino acids are required for protein synthesis. Some must be supplied in the diet (the essential amino acids) since they cannot be synthesized in the body. The remainder are nonessential amino acids that are supplied in the diet but can be formed from metabolic intermediates by transamination, using the amino nitrogen from other amino acids. After deamination, amino nitrogen is excreted as urea, and the carbon skeletons that remain after transamination (1) are oxidized to CO2 via the citric acid cycle, (2) form glucose (gluconeogenesis), or (3) form ketone bodies. 

Aminotransferase (transaminase) reactions form pymvate from alanine, oxaloacetate from aspartate, and a-ketoglutarate from glutamate. Because these reactions are reversible, the cycle also serves as a source of carbon skeletons for the synthesis of these amino acids. Other amino acids contribute to gluconeogenesis because their carbon skeletons give rise to citric acid cycle... 

By contrast, the cytoplasmic decarboxylation of dopa to dopamine by the enzyme dopa decarboxylase is about 100 times more rapid (Am 4x 10 " M) than its synthesis and indeed it is difficult to detect endogenous dopa in the CNS. This enzyme, which requires pyridoxal phosphate (vitamin B6) as co-factor, can decarboxylate other amino acids (e.g. tryptophan and tyrosine) and in view of its low substrate specificity is known as a general L-aromatic amino-acid decarboxylase. 

Interaction of Ni11 ions with amino acids is also important for asymmetric synthesis of amino acids. A convenient large-scale asymmetric synthesis of enantiometrically pure trans-cinnamyl-glycine and -o-alanine via reaction of cinnamyl halides with Ni11 complexes of a chiral Schiff base of glycine and alanine has been elaborated.1711 Similar procedures have been applied to other amino acids as well.1712... 

The molar ellipticity of these dendrimers was found to increase proportional to the number of chiral end groups. This is to be expected, in the absence of interactions between the terminal tryptophane moieties. No higher-generation dendrimers of this type have been reported. Other amino-acid-containing chiral dendrimers have been described by Meijer et al. who attached various amino acid derivatives to the periphery of poly(propylene imine) dendrimers (see Sect. 3) and more recently by Liskamp et al. (modification of polyamide dendra) [22] and Ritter et al. (synthesis of grafted polymerizable dendrimers containing L-aspartic acid components) [23]. 

Moser et al. (1968) (one of the co-authors was Clifford Matthews) reported a peptide synthesis using the HCN trimer aminomalonitrile, after pre-treatment in the form of a mild hydrolysis. IR spectra showed the typical nitrile bands (2,200 cm ) and imino-keto bands (1,650 cm ). Acid hydrolysis gave only glycine, while alkaline cleavage of the polymer afforded other amino acids, such as arginine, aspartic acid, threonine etc. The formation of the polymer could have occurred according to the scheme shown in Fig. 4.9. 

The amino acid composition of storage proteins differs from that of the complete sprout [12, 13]. At least in the case of oilseed rape, alfalfa (Medicago sativa L.) and Camelina sativa, amino acids in the sprout are used mainly, either directly or indirectly, for the synthesis of the Rubisco proteins. Computer analysis shows that the amino acid composition of cruciferin and napin is completely different to the amino acid composition of Rubisco. This indicates that amino acids released from the seed storage proteins must be converted into other amino acids prior to Rubisco synthesis. 

The other nine amino acids are essential and must be taken from the diet. Notice that some of the amino acids require other amino acids for their synthesis. Exam questions usually center on whether or not an amino acid is essential and the metabolites that serve as precursors for specific amino acids. 

The first example of a dynamic flux analysis was a study performed in the 1960s [269]. In the yeast Candida utilis, the authors determined metabolic fluxes via the amino acid synthesis network by applying a pulse with 15N-labeled ammonia and chasing the label with unlabeled ammonia. Differential equations were then used to calculate the isotope abundance of intermediates in these pathways, with unknown rate values fitted to experimental data. In this way, the authors could show that only glutamic acid and glutamine-amide receive their nitrogen atoms directly from ammonia, to then pass it on to the other amino acids. 

However, the revision of many naturally occurring amino acids is under progress. For limitation of other amino acids various methods such as ion chromatography, amino acid analysis, HPEC, and CZE are available and have to be tested case by case. In addition, tests for other non-amino acid related substances have to be developed. Possibly substances of different origin (production by synthesis, by fermentation, or by protein hydrolysis) may need different methods. In addition, a test for enantiomeric purity has to be included. 

The synthesis in many extant organisms of these two amide residues from their respective precursors glutamate and aspartate esterified to tRNA (the indirect aminoacylation pathways described in Sections 5.14.3 and 5.14.4) and that of other amino acid residues, such as selenocysteine (which is also synthesized from a precursor esterified on a tRNA °) support the model of prebiotic metabolism taking place at the surface of solid particles, " analogous to ancestral RNAs. 

Hi) Synthesis of S-prenylated peptides Various syntheses of S-prenylated peptides " have relied on the assembly of the peptide backbone on the solid phase, using standard protocols, and subsequent S-prenylation in solution. As a consequence, any final deprotection steps of other amino acids after the S-prenylation cannot be performed under strongly acidic conditions due to the acid lability of the prenyl group. The prenylation reactions themselves can he carried out under basic or mildly acidic conditions. Typical synthesis problems that arise during the S-alkylation are (1) incomplete conversion because of solubility problems, (2) oxidation of the thiol group to disulfides under basic conditions, (3) formation of the sulfonium... 

The citric acid cycle is at the heart of aerobic cellular metabolism, or respiration. This is true of both prokaryotic and eukaryotic organisms, of plants and animals, of organisms large and small. Here is the main point. On the one hand, the small molecule products of catabolism of carbohydrates, lipids, and amino acids feed into the citric acid cycle. There they are converted to the ultimate end products of catabolism, carbon dioxide and water. On the other hand, the molecules of the citric acid cycle are intermediates for carbohydrate, lipid, and amino acid synthesis. Thus, the citric acid cycle is said to be amphibolic, involved in both catabolism and anabolism. It is a sink for the products of degradation of carbohydrates, lipids, and proteins and a source of building blocks for them as well. 

It was snbseqnently discovered that the first enzyme in the pathway for isoleucine synthesis, which is threonine deaminase, was inhibited by isoleucine in an extract of E. coli. No other amino acid caused inhibition of the enzyme. Threonine deaminase is, in fact, the rate-limiting enzyme in the pathway for isoleucine synthesis, so that this was interpreted as a feedback control mechanism (Fignre 3.13(a)). Similarly it was shown that the hrst enzyme in the pathway for cytidine triphosphate synthesis, which is aspartate transcarbamoylase, was inhibited by cytidine triphosphate (Fignre 3.13(b)). Since the chemical structures of isoleucine and threonine, or cytidine triphosphate and aspartate, are completely different, the qnestion arose, how does isolencine or cytidine triphosphate inhibit its respective enzyme The answer was provided in 1963, by Monod, Changenx Jacob. 

The synthesis of arginine from citrulline. The latter is produced from other amino acids in the small intestine and then released into the blood. The kidney takes up citrulline and converts it to arginine, which is then released into the blood for use by other tissues (Figure 8.18). Since arginine is a precursor for a number of important compounds, and aids wound healing, this is a significant biochemical role of the kidney. 

In contrast to the inherent limitations of synthesis in solution, solid-phase peptide synthesis provides a key method for the generation of many large and complex peptides. The application of phosphorylated amino acids to solid-phase methodology has been the subject of particular interest in consideration of the synthetic potential of this approach for the rapid and routine preparation of complex phosphopeptides. Unlike other amino acids, the generation of Ser(F)- and Thr(P)-peptides is complicated due to the sensitivity of these residues to harsh acid or base conditions and the selection of suitable phosphate derivatives that are compatible with solid-phase peptide synthesis. 

Point mutations that give altered sterol profiles have been generated in A. thaliana and S. cerevisiae LSs. Matsuda and co-workers used a yeast expression system to select for spontaneous mutations in A. thaliana CS that restored sterol-independent growth to an LS-deficient mutant of yeast [67]. In this way they were able to identify a mutation from isoleucine to valine (at Ile481) that allowed synthesis of the sterols lanosterol and parkeol. Further studies have identified a number of other amino acid residues in A. thaliana CS and... 

The chemotactic peptides are also active in the stimulation of release of O and in the release of lysosomal contents Directed locomotion by PMNs is stimulated by a family of tri-, tetra-, and dipeptides which have in common formylated methionine as the first amino acid. Since formylated methionine is the initiator to which other amino acids are added in the synthesis of bacterial protein, small peptides which commence with formylated methionine are likely to be liberated proteolytically at sites of bacterial infection, possibly explaining their great potency as chematoxins. Using superoxide-dependent chemiluminescence (see below) as a measure of synthesis of O , Hatch et al. showed a hierarchy of potency of FMLP > FMP > FMV > FMA. Becker et al. measured the formation of O in suspensions of rabbit PMNs and found that the hierarchy of potency was the same for stimulation of the formation of O7 as it was for stimulation of release of lysosomal enzymes, namely... 

Eugene Kennedy and Albert Lehninger showed in 1948 that, in eulcaiyotes, the entire set of reactions of the citric acid cycle takes place in mitochondria. Isolated mitochondria were found to contain not only all the enzymes and coenzymes required for the citric acid cycle, but also all the enzymes and proteins necessaiy for the last stage of respiration—electron transfer and ATP synthesis by oxidative phosphoiylation. As we shall see in later chapters, mitochondria also contain the enzymes for the oxidation of fatty acids and some amino acids to acetyl-CoA, and the oxidative degradation of other amino acids to a-ketoglutarate, succinyl-CoA, or oxaloacetate. Thus, in nonphotosynthetic eulcaiyotes, the mitochondrion is the site of most energy-yielding... 

Alanine and Glutamine in the Blood Normal human blood plasma contains all the amino acids required for the synthesis of body proteins, but not in equal concentrations. Alanine and glutamine are present in much higher concentrations than any other amino acids. Suggest why. 

Amino Acids Amino acids that enter the liver follow several important metabolic routes (Fig. 23-14). (1) They are precursors for protein synthesis, a process discussed in Chapter 27. The liver constantly renews its own proteins, which have a relatively high turnover rate (average half-life of only a few days), and is also the site of biosynthesis of most plasma proteins. (2) Alternatively amino acids pass in the bloodstream to other organs, to be used in the synthesis of tissue proteins. (3) Other amino acids are precursors in the biosynthesis of nucleotides, hormones, and other nitrogenous compounds in the liver and other tissues. 

This equation is not intended to imply a mechanism for peptide synthesis. The equilibrium position for this reaction in an aqueous solution favors the free amino acids rather than the peptide. Therefore, both biological and laboratory syntheses of peptides usually do not involve a simple splitting out of water. Since the dipeptide of Eq. 2-11 still contains reactive carboxyl and amino groups, other amino acid units can be joined by additional peptide linkages to form polypeptides. These range from short-chain oligomers to polymers of from 50 to several thousand amino acid units, the proteins.75-77... 

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