scholarly journals The Transformation by Catalysis of Prebiotic Chemical Systems to Useful Biochemicals: A Perspective Based on IR Spectroscopy of the Primary Chemicals: I. The Synthesis of Peptides by the Condensation of Amino Acids

2020 ◽  
Vol 10 (3) ◽  
pp. 928 ◽  
Author(s):  
Ragnar Larsson ◽  
Abdul Malek
Keyword(s):  
Amino Acids ◽  
Hydrothermal Vents ◽  
Vibrational Energy ◽  
Cell Formation ◽  
Carbonyl Sulfide ◽  
Mean Value ◽  
Volcanic Gas ◽  
Chemical Systems ◽  
Subsequent Transformation ◽  
Prebiotic Chemical

It is now widely speculated that life originated at the “Black Smokers” of the undersea hydrothermal vents, where conditions exist for the formation of the primary ingredients and their subsequent transformation to higher biotic species such as amino acids, alcohols, etc. Any possible routes for the prebiotic oligomerization of simple compounds like amino acids, necessary for cell formation, has so far not been well understood. However, Leman et al. recently reported that under standard laboratory conditions carbonyl sulfide (COS) can “mediate” the oligomerization of simple amino acids in moderate yield. COS being a well-known volcanic gas points to its possible role in prebiotic peptide formation in the environment of the hydrothermal vents. Based on a previously developed and tested model for selective (vibrational) energy transfer (SET), we show that a COS-catalyzed condensation of α-amino-acids can lead to the formation of polypeptides. We also indicate that other agents can act as catalysts of the amino acid condensation, such as Fe(CN)63− and cyanamide (H2N-CN). This is related to the existence of vibrations with a frequency near to that of the critical vibration of the reactant, ρw (NH2). This wagging vibration occurs at 1048 ± 10 cm−1 (the mean value of Cu and Ni complexes) and, as the vibration of the presumed catalyst lies at 2079 cm−1, one notes that one quantum of the catalyst equals two quanta of the NH2 wagging: 2079/2 × 1048 = 0.9919. This is a good indication of a resonance.

scholarly journals The Transformation by Catalysis of Prebiotic Chemical Systems to Useful Biochemicals: A Perspective Based on IR Spectroscopy of the Primary Chemicals II. Catalysis and the Building of RNA

2020 ◽  
Vol 10 (14) ◽  
pp. 4712
Author(s):  
Ragnar Larsson ◽  
Abdul Malek ◽  
Ingemar Odenbrand
Keyword(s):  
Amino Acids ◽  
Energy Transfer ◽  
Ir Spectroscopy ◽  
Hydrogen Cyanide ◽  
Ribonucleic Acid ◽  
Carbonyl Sulfide ◽  
Catalyst System ◽  
Chemical Systems ◽  
Prebiotic Chemical

Having found that carbonyl sulfide (COS), works well as a catalyst in the transformation of amino acids to polypeptides, we have now tested COS as a catalyst also for the formation of substances that might be thought of as partners in the building of RNA. The model used was selective energy transfer (SET). This model implies that a certain number of vibrational quanta are donated from the catalyst system and a corresponding number of quanta of the reactant accept the energy thus transferred. In this way, we found that carbonyl sulfide, COS, was a perfect catalyst for combining, first, five molecules of formaldehyde to form one molecule of ribose, and next, five molecules of hydrogen cyanide, HCN, to form one molecule of adenine, one of the nucleobases of RNA. However, beyond this, we found that COS was a perfect catalyst for precisely all reactions, needed to build the RNA, ribonucleic acid.

scholarly journals Metabolite profiling during graft union formation reveals the reprogramming of primary metabolism and the induction of stilbene synthesis at the graft interface in grapevine

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Duyên Prodhomme ◽  
Josep Valls Fonayet ◽  
Cyril Hévin ◽  
Céline Franc ◽  
Ghislaine Hilbert ◽  
...  
Keyword(s):  
Amino Acids ◽  
Secondary Metabolism ◽  
Fruits And Vegetables ◽  
Cell Formation ◽  
Union Formation ◽  
Primary Metabolism ◽  
Graft Union ◽  
Primary And Secondary Metabolites ◽  
Primary And Secondary Metabolism ◽  
Graft Interface

Abstract Background Grafting with rootstocks is essential for the culture of many perennial fruit crops and is increasing being used in the production of annual fruits and vegetables. Our previous work based on microarrays showed that transcripts encoding enzymes of both primary and secondary metabolism were differentially expressed during graft union formation in both homo-grafts (a genotype grafted with itself) and hetero-grafts (two different genotypes grafted together). The aim of this study was to profile primary and secondary metabolites, and quantify the activity of phenylalanine ammonia lyase (PAL) and neutral invertase (NI) in the scion and rootstock tissues and the graft interface of homo and hetero-grafts of grapevine 1 month after grafting. Table-top grafting was done on over-wintering stems (canes) of grapevine and the graft interface tissues (containing some woody stem tissues and callus) were compared to the surrounding rootstock and scion tissues. The objective was to identify compounds involved in graft union formation and hetero-grafting responses. Results A total of 54 compounds from primary and secondary metabolism (19 amino acids, five primary and 30 secondary compounds metabolites) and the activity of two enzymes were measured. The graft interface was associated with an increase in the accumulation of the branched-chain amino acids, basic amino acids, certain stilbene compounds and higher PAL and NI activity in comparison to the surrounding woody stem tissues. Some amino acids and stilbenes were identified as being accumulated differently between the graft interfaces of the scion/rootstock combinations in a manner which was unrelated to their concentrations in the surrounding woody stem tissues. Conclusions This study revealed the modification of primary metabolism to support callus cell formation and the stimulation of stilbene synthesis at the graft interface, and how these processes are modified by hetero-grafting. Knowledge of the metabolites and/or enzymes required for successful graft union formation offer us the potential to identify markers that could be used by nurseries and researchers for selection and breeding purposes.

scholarly journals On the possible origin of protein homochirality, structure, and biochemical function

2019 ◽  
Vol 116 (52) ◽  
pp. 26571-26579 ◽  
Author(s):  
Jeffrey Skolnick ◽  
Hongyi Zhou ◽  
Mu Gao
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Ribosomal Proteins ◽  
Active Sites ◽  
Cell Formation ◽  
Binding Pocket ◽  
Nucleotide Biosynthesis ◽  
Native Proteins ◽  
Structural And Functional Properties ◽  
Biochemical Function

Living systems have chiral molecules, e.g., native proteins that almost entirely contain L-amino acids. How protein homochirality emerged from a background of equal numbers of L and D amino acids is among many questions about life’s origin. The origin of homochirality and its implications are explored in computer simulations examining the stability and structural and functional properties of an artificial library of compact proteins containing 1:1 (termed demi-chiral), 3:1, and 1:3 ratios of D:L and purely L or D amino acids generated without functional selection. Demi-chiral proteins have shorter secondary structures and fewer internal hydrogen bonds and are less stable than homochiral proteins. Selection for hydrogen bonding yields a preponderance of L or D amino acids. Demi-chiral proteins have native global folds, including similarity to early ribosomal proteins, similar small molecule ligand binding pocket geometries, and many constellations of L-chiral amino acids with a 1.0-Å RMSD to native enzyme active sites. For a representative subset containing 550 active site geometries matching 457 (2) 4-digit (3-digit) enzyme classification (E.C.) numbers, native active site amino acids were generated at random for 472 of 550 cases. This increases to 548 of 550 cases when similar residues are allowed. The most frequently generated sequences correspond to ancient enzymatic functions, e.g., glycolysis, replication, and nucleotide biosynthesis. Surprisingly, even without selection, demi-chiral proteins possess the requisite marginal biochemical function and structure of modern proteins, but were thermodynamically less stable. If demi-chiral proteins were present, they could engage in early metabolism, which created the feedback loop for transcription and cell formation.

Carbonaceous chondrites: tracers of the prebiotic chemical evolution of the Solar System

2005 ◽  
Vol 4 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Anja C. Andersen ◽  
Henning Haack
Keyword(s):  
Amino Acids ◽  
Solar System ◽  
Direct Result ◽  
Early Earth ◽  
Carbonaceous Chondrites ◽  
Subsequent Evolution ◽  
Prebiotic Chemical ◽  
Unique Source ◽  
Sugar Derivatives ◽  
Source Of Information

The astrobiological relevance of carbonaceous chondrites is reviewed. It is argued that the primitive meteorites called carbonaceous chondrites provide a unique source of information about the materials and conditions in the Solar System during the earliest phases of its history, and its subsequent evolution. Presolar dust grains extracted from the carbonaceous chondrites provide direct information on the previous generations of stars that provided the materials present for planet formation. The organic material found in carbonaceous chondrites consist of amino acids, carboxylic acids and sugar derivatives. Part of the amino acids found show L-enantiomeric excesses, which indicates that homochirality on Earth could be a direct result of input from meteoritic material to the early Earth.

scholarly journals Vitamin E and stress

1967 ◽  
Vol 21 (1) ◽  
pp. 103-114 ◽  
Author(s):  
A. T. Diplock ◽  
J. Bunyan ◽  
D. Mchale ◽  
J. Green
Keyword(s):  
Amino Acids ◽  
Vitamin E ◽  
Muscular Dystrophy ◽  
Selenium Deficiency ◽  
Mean Value ◽  
Exudative Diathesis ◽  
High Incidence ◽  
Sulphur Amino Acids ◽  
Deficiency Diseases

1. The metabolism of small amounts of [5-Me-14C]D-α-tocopherol and [5-Me-3H]D-α- tocopherol has been studied in the vitamin E-deficient chick. Small doses of the labelled tocopherol were given to chicks, which were then subjected to stress by giving them diets formulated to produce encephalomalacia, exudative diathesis or muscular dystrophy.2. Tocopherol concentrations in the cerebella and brains of chicks with incipient encephalomacia were the same as those in normal chicks in which the dietary fat stress was absent.3. α-Tocopherol delayed the onset of encephalomalacia by a mean value of 3.5 days when its concentration in the cerebellum was about 2 × 10−7g/g of lipid. This concentration is considerably below the usual effective concentrations of antioxidants in vitro.4. Selenium deficiency, under conditions leading to a high incidence of exudative diathesis, was not associated with lowered tocopherol levels and did not result in detectable destruction of tocopherol.5. Nor was there any destruction of tocopherol or significant effect on its metabolism in the processes leading to muscular dystrophy: on the contrary, the affected muscles of dystrophic chicks, which had received a diet deficient in sulphur amino acids, contained significantly more tocopherol than muscles from control birds.6. These results do not support the hypothesis that lipid peroxidation is a causative process in the aetiology of vitamin E-deficiency diseases in the chick. The relationships between unsaturated lipid, Se, sulphur amino acids and tocopherol in the chick require further exploration.

scholarly journals Hereditary high concentration of glutathione in canine erythrocytes associated with high accumulation of glutamate, glutamine, and aspartate

Blood ◽  
1982 ◽  
Vol 59 (5) ◽  
pp. 883-889 ◽  
Author(s):  
Y Maede ◽  
N Kasai ◽  
N Taniguchi
Keyword(s):  
Amino Acids ◽  
Feedback Inhibition ◽  
Clinical Signs ◽  
Mean Value ◽  
Glutathione Metabolism ◽  
High Concentration ◽  
Normal Range ◽  
High Accumulation ◽  
The Mean ◽  
Cysteine Synthetase

We have found a dog family in which there were five cases of increased red cell glutathione corresponding to four to five times the normal concentration without any clinical signs. In the present study, we mainly examined the concentrations of free amino acids in the erythrocytes, plasma, and urine of two of the dogs, and we demonstrated that the concentrations of glutamate, aspartate, and glutamine in their erythrocytes increases to 92, 63, and 13 times the mean value in the normal blood, respectively. There were no changes observed in the other amino acids as compared to normal, although the glycine and histidine in the erythrocyte showed slight increases. The concentrations of amino acids in the plasma and urine of the dogs were almost equal to normal ones. The activities of some of the enzymes involved in the glutathione metabolism in the erythrocytes from the two dogs were all within the normal range. The increased level of glutathione could be explained by the fact that the feedback inhibition of gamma-glutamyl cysteine synthetase by glutathione was released by the high levels of glutamate in the erythrocytes.

scholarly journals C-skeleton in the genetic code from a basic series 5 → 0, guiding valences and other numeral features in the code

2021 ◽  
Vol 9 (12) ◽  
Author(s):  
Åsa Wohlin
Keyword(s):  
Amino Acids ◽  
Genetic Code ◽  
Base Pair ◽  
Mean Value ◽  
Atomic Mass ◽  
Side Chain ◽  
Mass Analysis ◽  
Guiding Principle ◽  
Basic Series

The search for regularities in the background for the genetic code and its codon assignments is here further developed, earlier shown to have many correlations with numeral series of integers 5 →0 with different exponents. The atomic mass analysis here counts on 20 + 4 double-coded amino acids, here including Ile AUA as such. A central finding here is that the C-skeleton seems to build on an hierarchical development of the mentioned basic series giving top numbers equal to those returning in side-chain divisions and on first three levels those of C-atoms in base-pair domains. It can very elementary explain the 3/2-division in the weight series. A few main results from earlier articles are shortly recapitulated, since it’s shown here that an x­3-series times 15 (x = integers 5 → 0) joins those earlier aspects and add new ones. It’s found also that atoms with valences 4 + 3 relative those with 2 + 1 make up a 3 to 1-division in both base-pair groups of codon domains, strengthening the earlier observation of valences as one important guiding principle in the relation between codons and domains of amino acids; valences of the atoms which in themselves make up a basic series 5 → 0 in the code when phosphorus P is included. Finally, fundamental factors in the code are gathered, where step 4 →3 seems reign at bottom of the code and number 7, exactly mean value of all atoms.

Studies on the Chemical Composition of Muscle Tissue

1961 ◽  
Vol 38 (4) ◽  
pp. 707-728
Author(s):  
JAMES D. ROBERTSON
Keyword(s):  
Amino Acids ◽  
Adenosine Triphosphate ◽  
Sea Water ◽  
Osmotic Coefficients ◽  
Muscle Cells ◽  
Mean Value ◽  
Soluble Phosphate ◽  
Nitrogenous Compounds ◽  
Whole Muscle ◽  
Hexose Phosphates

1. Comprehensive analyses have been made of the muscle and plasma for inorganic ions, organic phosphates, soluble carbohydrates, amino acids and nitrogenous bases. 2. Compared with a total of 1108 mg. ions/kg. water in the plasma, the muscle had 1045, of which 515 were mg. ions (Na, K, Ca, Mg, Cl, SO4, lactate, HCO3, inorganic and arginine phosphates, adenosine triphosphate, hexose phosphates, etc.), and the remainder amino acids (405 mM.) and the nitrogenous compounds trimethylamine oxide (59 mM.) and betaine (66 mM.). 3. Measurements of the apparent extracellular spaces in the muscle following injections of inulin, sucrose and sodium thiosulphate have led to the conclusion that the inulin space or permeation, 12.1%±0.69 (S.E.) of the total muscle water, is the best indication of total extracellular fluid in the muscle. The copper space, 4.11±0.37, represents a maximum value for the blood space (that filled with haemocyanin), leaving 8.0% as the volume occupied by interstitial fluid. 4. Intracellular concentrations of potassium and chloride do not conform to values expected on the basis of a Donnan equilibrium with plasma: [Ki]/[Ko] = 21.9, [Clo]/[Cli] = 9.9. 5. Mean values in mg. ions/kg. water for the whole muscle concentrations of phosphate ions are inorganic phosphate 18.3, arginine phosphate 71.0, adenosine triphosphate 11.6, remaining acid-soluble phosphate, chiefly hexose phosphates, 14.4, total 115.2. 6. Total non-protein amino acids of muscle from measurements of α-amino N are 339-551 mM., mean 476. These are chiefly glycine, proline, arginine, taurine, alanine and glutamine. Most of the arginine is combined as arginine phosphate. 7. Direct measurements of osmolality of the plasma using Krogh-Baldes thermocouples give a mean value of 100.4±0.34 (N = 9), taking sea water as 100. Measurements of the juice expressed from muscle with a tissue-press give a mean value compared with plasma (100) of 102.0±0.70 if done within 1.5 hr. of removing the muscle, 101.7±0.87 for seven estimations done within an hour; the latter result is not significantly different from the plasma values. Delay in measurement leads to higher values (plus 5-8% on plasma), owing to the breakdown of labile compounds. 8. Compared with whole muscle on a water-content basis, the concentrations of ions in the muscle-juice are Na 76%, K 74%, Ca 10%, Mg 40%, Cl 100%, total acid-soluble P 78%. This is interpreted as showing binding by proteins of fractions of all these ions except chloride. If the juice is corrected for its extracellular component, approximate percentages of ions bound inside the muscle cells are Na 82%, K 26%, Ca 100%, Mg 64% and P 22% all the cellular chloride is free. 9. A final osmotic balance sheet for Nephrops muscle cells, in which consideration has been given to such factors as binding of ions, osmotic coefficients of ions and probable ideal behaviour of the nitrogenous compounds, shows that about 92% of the total osmotic concentration (in milliosmoles) has been accounted for. 10. Increasing the concentration of potassium and calcium in sea water leads to increases in the values of these ions in both plasma and muscle.

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