Adenylate anhydride

Acidic proteinoid potentiates the active structure of lysine-rich proteinoid participating in forming microspheres in neutral buffer. Physical surface effects and providing micro condition in the microspheres could be surmised. Activation of amino acids generally requires acidic condition. Amino acids are activated by ATP and Mg2+ at pH 4-5 32 33). Aminoacyl adenylate anhydride and ester is formed preferentially from amino acid and adenylate imidazolide at pH 6.0J7). On the other hand, polycondensation of activated amino acids undergoes at pH values higher than 7. Peptides are formed from aminoacyl adenylate in basic buffer (the optimum pH is 10 for alanyl adenylate 40) from amino acid adenylate phosphoramidate and imidazole at pH 7.0 from N-(aminoacyl)-imidazole at pH 6-9 43). In this context, acidic and basic environments may be provided inside and/or on the surface of the microspheres composed of acidic and basic proteinoids in neutral buffer. Acidic micro condition suitable for the activation of amino acids and basic micro environment favorable for peptide formation from activated amino add may be provided. 

We can also get some information by comparing the modern biosynthetic pathways to the capabilities of prebiotic chemistry. Amino acids are usually activated in living organisms by reaction with ATP both through the ribosomal and non-ribosomal peptide synthesis pathways. Amino acyl fRNA synthetases bind ATP and free amino acids to cause the highly unfavorable adenylate anhydride formation to be close to equilibrium in the active site. 

In this scenario, the next key step was the discovery by early living organisms of alternative pathways to synthesize nucleoside triphosphates (stage 3 in Scheme 40), for instance by the introduction of an oxido-reduction metabolism. In the particular case of ATP, the increase in its concentration could have forced the chemical flux of the system to be reverted since the unstable adenylate anhydride was stabilized in the active site of the adenylate binding protein (E) allowing the activation of amino acids by ATP through the process that became predominant. 

Acyl CoA s, such as acetyl CoA, are the most common thioesters in nature. Coenzyme A, abbreviated CoA, is a thiol formed by a phosphoric anhydride linkage (0 = P—O—P=0) between phosphopantetheine and adenosine 3, 5 -bisphosphate. (The prefix "bis" means "two" and indicates that adenosine 3, 5 -bisphosphate has two phosphate groups, one on C3 and one on C5. ) Reaction of coenzyme A with an acyl phosphate or acyl adenylate... 

The following schemes represent the overall reaction of firefly bioluminescence (McElroy and DeLuca, 1978), where E is luciferase LH2 is D-luciferin PP is pyrophosphate AMP is adenosine phosphate LH2-AMP is D-luciferyl adenylate (an anhydride formed between the carboxyl group of luciferin and the phosphate group of AMP) and L is oxyluciferin. 

The mixed sulfuric phosphoric anhydride (PAdoPS or PAPS) of 3 -phospho-5 -adenylic acid is named as an acyl sulfate ... 

First, the amino acid is bound by the enzyme and reacts there with ATP to form diphosphate and an energy-rich mixed acid anhydride (aminoacyl adenylate). In the second step, the 3 -OH group (in other ligases it is the 2 -OH group) of the terminal ribose residue of the tRNA takes over the amino acid residue from the aminoacyl adenylate. In aminoacyl tRNAs, the carboxyl group of the amino acid is therefore esterified with the ribose residue of the terminal adenosine of the sequence. ..CCA-3. ... 

Figure 10.3 Enzymatic synthesis of poly(adenylic acid) in self-reproducing oleate liposomes (redrawn from Walde et al., 1994a). (a) The ADP penetrates (sluggishly) the liposome bilayer, (b) in the presence of polynucleotide phosphorylase, ADP is converted in poly(A), which remains entrapped in the liposome, (c) Polycondensation of ADP goes on simultaneously with the self-reproduction of liposomes (A is the membrane precursor, oleic anhydride, which, once added, induces the self-reproduction of liposomes S, surfactant, in this case oleate, which is the hydrolysis product of A on the bilayer E is polynucleotide phosphorylase).

The first step in the activation of a fatty acid— either for energy-yielding oxidation or for use in the synthesis of more complex lipids—is the formation of its thiol ester (see Fig. 17-5). The direct condensation of a fatty acid with coenzyme A is endergonic, but the formation of fatty acyl-CoA is made exergonic by stepwise removal of two phosphoiyl groups from ATP. First, adenylate (AMP) is transferred from ATP to the carboxyl group of the fatty acid, forming a mixed anhydride... 

This reaction occurs in two steps in the enzyme s active site. In step (Fig. 27-14) an enzyme-bound intermediate, aminoacyl adenylate (aminoacyl-AMP), forms when the carboxyl group of the amino acid reacts with the a-phosphoryl group of ATP to form an anhydride linkage, with displacement of pyrophosphate. In the sec-... 

The AG° values for the hydrolysis of any P - O - P bond of ATP, inorganic pyrophosphate, or any acyl CoA thiolester are all about -34 kj / mole, while the corresponding figure for the hydrolysis of a mixed carboxylic phosphate anhydride is about -55 kj / mole. Calculate the value of AG° for the following reaction describing the activation of fatty acids to the fatty acyl adenylate. 

In the absence of tRNA, the enzymes will, with a few exceptions, activate amino acids to the attack of nucleophiles, and ATP to the attack of pyrophosphate.43 6 This is done by forming a tightly bound complex with the aminoacyl adenylate, the mixed anhydride of the amino acid, and AMP. (The chemistry of activation is discussed in Chapter 2, section D2c.)... 

The structure of firefly luciferin has been confirmed by total synthesis. The firefly emits a ycllow-grccn luminescence, and luciferin in this case is a benzthiazole derivative. Activation of the firefly luciferin involves the elimination of pyrophosphate from ATP widi the formation of an add anhydride linkage between the carboxyl group of luciferin and the phosphate group of adenylic acid forming luciferyl-adenylate. 

Following structure-activity studies, the adenylate is thought to be stabilized within a cleft formed between the two subdomains of the activation domain [41,58], The rate is thus related to the formation, presence, and stability of this mixed anhydride with respect to PPi, and at high MgATP2 concentrations, with respect to ATP in the formation of diadenosine tetraphosphate (A2P4). Thus a high rate of the amino acid-dependent isotope exchange does not necessarily reflect the efficiency of adenylate formation, and certainly not the efficiency of incorporation of an amino acid into peptidyl intermediates or the final product. 

Among activated forms of amino acids, mixed anhydrides with inorganic phosphate or phosphate esters require a special discussion because they are universally involved in peptide biosynthesis through the ribosomal and non-ribosomal pathways. These mixed anhydrides have stimulated studies in prebiotic chemistry very early in the history of this field. Amino acyl adenylates 18c have been shown to polymerize in solution [159,160] and in the presence of clays [139]. However, their participation as major activated amino acid species to the prebiotic formation of peptides from amino acids is unlikely for at least two reasons. Firstly, amino acid adenylates that have a significant lifetime in aqueous solution become very unstable as soon as either CO2 or bicarbonate is present at millimolar concentration [137]. Lacey and coworkers [161] were therefore conduced to consider that CO2 was absent in the primitive atmosphere for aminoacyl adenylate to have a sufficient lifetime and then to allow for the emergence of the modern process of amino acid activation and of the translation apparatus. But this proposition is unlikely, as shown by the analysis of geological records in favor of CO2 contents in the atmosphere higher than present levels [128]. It is also in contradiction with most studies of the evolution of the atmosphere of telluric planets [30,32], Secondly, there is no prebiotic pathway available for adenylate formation and ATP proved to be inefficient in this reaction [162]. 

Alternatively, the difference in free energy between NCAs and adenylates, which is approximately of 5 kj mol 1 would have allowed the presence of small but substantial amounts of phosphate mixed anhydrides (possibly adenylates) of amino acids at equilibrium. 

Several systems based on the potentialities of amino acid-phosphoric acid mixed anhydrides have been devised to check the idea that the genetic code developed from an early pathway of RNA-dependent peptide synthesis in an RNA world [168]. RNA sequences have thus been selected that are capable of self-aminoacylation using amino acid adenylates, catalyzing a reaction chemically similar to the aminoacylation of fRNA by the protein aminoacyl fRNA synthetases [169]. 

In addition to the reaction of mercaptopropionic acid, mixed anhydrides were also formed and identified starting from leucine and phenylalanine in the presence of Ca2+ ions, showing that RNAs can replace protein aminoa-cyl fRNA synthetase catalysts for amino acid activation. The formation of a detectable amount of aminoacyl S -phosphalc polynucleotide seems to be in contradiction with the instability predicted for aminoacyl adenylates (Table 1), however it can be explained by the low pH value increasing their stability and the fact that the selected RNA structures are likely to stabilize the mixed anhydride moiety of the covalent conjugate by favorable intramolecular interactions induced by folding. 

Amino acyl adenylates are obtained in the reaction of adenosine 5-phosphate (ASP) with free amino acids in aqueous pyridine, mediated by DCC. The linkage is an anhydride between the amino acid carboxyl group and the phosphate in A5P." ... 

A.7.1 Esterification of Acids using Carbodiimides. The formation of anhydrides from carboxylic acids, thiocarboxylic acids, sulfonic acids and phosphorous acids are discussed in Section 2.4.S.2. In this section only special cases of anhydride formation are described. Mixed anhydrides of amino acids and adenylic acid are produced from the corresponding acids using DCC as the condensation agent. ° Mixed anhydrides not containing amino acids, such as butyryl adenate, adenosine 5 -phosphosulfate and p-nitrophenyl-thymidine-5-phosphate are also obtained. 

Paul Berg showed that the activation of a fatty acid is accomplished in two steps. First, the fatty acid reacts with ATP to form an acyl adenylate. In this mixed anhydride, the carboxyl group of a fatty acid is bonded to the phosphoryl group of AMP. The other two phosphoryl groups of the ATP substrate are released as pyrophosphate. The sulfhydryl group of CoA then attacks the acyl adenylate, which is tightly bound to the enzyme, to form acyl CoA and AMP. 

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