Dail W. Mullins

Experimental studies related to the origin of the genetic code and the process of protein synthesis - A review

A survey is presented of the literature on the experimental evidence for the genetic code assignments and the chemical reactions involved in the process of protein synthesis. In view of the enormous number of theoretical models that have been advanced to explain the origin of the genetic code, attention is confined to experimental studies. Since genetic coding has significance only within the context of protein synthesis, it is believed that the problem of the origin of the code must be dealt with in terms of the origin of the process of protein synthesis. It is contended that the answers must lie in the nature of the molecules, amino acids and nucleotides, the affinities they might have for one another, and the effect that those affinities must have on the chemical reactions that are related to primitive protein synthesis. The survey establishes that for the bulk of amino acids, there is a direct and significant correlation between the hydrophobicity rank of the amino acids and the hydrophobicity rank of their anticodonic dinucleotides.

Hydrolytic properties of phenylalanyl- and N-acetylphenylalanyl adenylate anhydrides

We have used a novel spectrophotometric method to study the hydrolysis of N-acetylphenylalanyl adenylate anhydride (AcPhe-AMP) and phenylalanyl-adenylate anhydride (Phe-AMP) at low concentrations (10−5 M), 25 °C, constant buffer concentration (0.05 M), and as a function of pH. While Phe-AMP is susceptible principally to attack by OH−, with two different rates depending on whether the α-amino group of the amino acid is protonated or not, the AcPhe-AMP is susceptible to acid decomposition as well. At pHs 4–8, the Phe-AMP hydrolyzes faster than the AcPhe-AMP, but at pH less than 4 or pH greater than 8, the blocked form hydrolyzes faster. Both forms are also attacked by H2O, and at the same rate. Moreover, the hydrolysis of Phe-AMP is shown to be greatly catalyzed by carbonate, although the AcPhe-AMP is not subject to such catalysis. The rate laws for the various mechanisms and the activation energies for the hydrolyses at pH 7.1 are given.

Rationalization of some genetic anticodonic assignments

The genetic code appears to be a logic matrix in which, generally speaking, there is a correlation between the hydrophobicities of amino acids and their anticodonic nucleotides. There are several exceptions to this generality, however, and using previous data on hydrophobicity and binding constants, coupled with new data on reaction rates, we rationalize several of the anticodonic assignments.

Complexes of polyadenylic acid and the methyl esters of amino acids

This report includes studies of the binding of the methyl esters of a series of amino acids to polyadenylic acid. The principal data were obtained using proton NMR; however, some additional data were obtained through the study of insoluble complexes and through ultraviolet spectroscopy. The binding constants are in the order Phe>Ile⩾Leu>Val>Gly, and show a direct correlation with the hydrophobicities of the amino acids. In most cases they are essentially double the binding constants found by Reuben and Polk (1980) for monomeric AMP. All of these amino acids, except Gly, have A as the middle letter of their anticodons, and Phe is the only one with XAA as its only anticodon. It has the anticodon richest in A and has the highest binding constant for A. These results, coupled with other data, continue to support a model of the origin of the code which is based on weak, but selective affinities between amino acids and their anticodons.

Chirally selective, intramolecular interaction observed in an aminoacyl adenylate anhydride

All earthly creatures use only L-amino acids in template directed protein synthesis. The reason for this exclusive use of the L-isomer is not yet apparent, although recent experiments by Usher and his colleagues have shown some stereoselctivity in the aminoacylation of di- and polynucleotides [1–3]. We have separately reported on intramolecular interactions between hydrophobic amino acid side chains and the adenine ring in aminoacyl adenylates [4]. There was a preferential association of Phe > Leu = Ile > Val with the adenine in these studies, but we made no attempts to address the question of D, L selectivity. Recently, in1H NMR studies of N-acetylphenylalanyl adenylate anhydride, we noticed evidence that both D- and L-isomers of the amino acid were present and, furthermore, that one isomer seemed to be associating with the adenine ring more strongly than the other. Using HPLC, we have separated the two diastereoisomers and have enzymatically determined that the isomer which associates more strongly is the biologically important one, the L-isomer. We present those studies here and discuss the evolutionary significance of this finding.

The case for the anticode

The present paper will focus on the developments in our lab related to the origin of the code since the Israel meeting (1,2). Principally these items are: (a) a new set of correlations (3) which include ranked hydrophobicities of amino acids and dinucleotides; (b) binding constants (4) of Phe for the four mononucleotides; and (c) binding constants (5) of Phe, Leu, Ile, Val, and Gly for polyadenylic acid (poly A). The data continue to support a model for the origin of the code based on relationships between amino acids and their anticodons.

Aminoacyl-nucleotide reactions - Studies related to the origin of the genetic code and protein synthesis

In the present paper, we report on the effect of pH and carbonate on the hydrolysis rate constants of N-blocked and free aminoacyl adenylate anhydrides. Whereas the hydrolysis of free aminoacyly adenylates seems principally catalyzed by OH−, the hydrolysis of the N-blocked species is also catalyzed by H+, giving this compound a U-shaped hydrolysis vs. pH curve. Furthermore, at pHs<8, carbonate has an extreme catalytic effect on the hydrolysis of free aminoacyl-AMP anhydride, but essentially no effect on the hydrolysis of N-blocked aminoacyl-AMP anhydride. Furthermore, the N-blocked aminoacyl-AMP anhydride is a very efficient generator of peptides using free glycine as acceptor. The possible significance of the observations to prebiological peptide synthesis is discussed.

Isolated Microsystems in Evolution

This chapter is concerned with the subject of isolated microsystems and their importance in the evolution of the living state from purely chemical systems. We have chosen to discuss this particular topic for two main reasons. First, although the subject of the role of microsystems in evolution has been previously examined by several authors, a brief review of the available literature has revealed that certain basic concepts relative to this topic have not been, for the most part, adequately developed. Second, Professor A. I. Oparin (1), the man whose work we honor here, and his colleagues have spent a considerable amount of time and effort in exploring the many facets of one particular type of chemical microsystem, namely, coacervate droplets. Their studies, coupled with those of Professor S. W. Fox (2), and his co-workers on proteinoid microspheres, have served to emphasize the great importance of isolated microenvironments with regard to the appearance and evolution of living systems.

Summary of Evidence for an Anticodonic Basis for the Origin of the Genetic Code

This article summarizes the data available from our own laboratory and others supporting the hypothesis that the genetic code origin was based on relationships (probably affinities) between amino acids and their anticodon nucleotides. Selective activation seems to follow from selective affinity and consequently, incorporation of amino acids into peptides can also be selective. We believe that these selectivities in affinity and activation, coupled with the base pairing specificities, allowed the origin of the code and the process of translation.

Phosphate Production and Analysis in the Non-Enzymatic Activation of Amino Acids by ATP when Using Hydroxylamine as a Trapping Agent

Abstract Phosphate Production, Hydroxylamine, ATP Saygin and Decker [6, 7] have reported that the formation of hydroxamic acids in solutions containing ATP, MgCl2, hydroxylamine and an acidic acceptor (acetic acid or amino acids) is not accompanied by the release of inorganic phosphate from ATP. Using an ion exchange chromatography method developed by Lowenstein [8] to separate the various components of such reaction mixtures, we now show that inorganic phosphate, as well as some pyrophosphate, is produced during incubation at 50 °C. Evidence is also presented to indicate that the failure of Saygin and Decker [6, 7] to detect phosphate is due to a total inhibition of their phosphate assay system by ATP.