scholarly journals Discovery of the elusive radical NCO and confirmation of H2NCO+ in space

2018 ◽  
Vol 612 ◽  
pp. L10 ◽  
Author(s):  
N. Marcelino ◽  
M. Agúndez ◽  
J. Cernicharo ◽  
E. Roueff ◽  
M. Tafalla
Keyword(s):  
Amino Acids ◽  
Column Density ◽  
Organic Molecules ◽  
Prebiotic Chemistry ◽  
Peptide Bond ◽  
Dense Core ◽  
Chemical Models

The isocyanate radical (NCO) is the simplest molecule containing the backbone of the peptide bond, C(=O)–N. This bond has a prebiotic interest since it links two amino acids to form large chains of proteins. It is also present in some organic molecules observed in space such as HNCO, NH2CHO, and CH3NCO. In this letter, we report the first detection in space of NCO towards the dense core L483. We also report the identification of the ion H2NCO+, which definitively confirms its presence in space, and observations of HNCO, HOCN, and HCNO in the same source. For NCO, we derive a column density of 2.2 × 1012 cm−2, which means that it is only ~5 times less abundant than HNCO. We find that H2NCO+, HOCN, and HCNO have abundances relative to HNCO of 1/400, 1/80, and 1/160, respectively. Both NCO and H2NCO+ are involved in the production of HNCO and several of its isomers. We have updated our previous chemical models involving NCO and the production of the CHNO isomers. Taking into account the uncertainties in the model, the observed abundances are reproduced relatively well. Indeed, the detection of NCO and H2NCO+ in L483 supports the chemical pathways to the formation of the detected CHNO isomers. Sensitive observations of NCO in sources in which other molecules containing the C(=O)–N subunit have been detected could help elucidate its role in prebiotic chemistry in space.

scholarly journals Extraterrestrial hexamethylenetetramine in meteorites—a precursor of prebiotic chemistry in the inner solar system

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Yasuhiro Oba ◽  
Yoshinori Takano ◽  
Hiroshi Naraoka ◽  
Yoshihiro Furukawa ◽  
Daniel P. Glavin ◽  
...  
Keyword(s):  
Amino Acids ◽  
Solar System ◽  
Experimental Evidence ◽  
Organic Compounds ◽  
Organic Molecules ◽  
Prebiotic Chemistry ◽  
Carbonaceous Chondrites ◽  
Astrophysical Interest ◽  
Extraction Processes ◽  
Extraterrestrial Materials

AbstractDespite extensive studies on the formation of organic molecules in various extraterrestrial environments, it still remains under debate when, where, and how such molecules were abiotically formed. A key molecule to solve the problem, hexamethylenetetramine (HMT) has not been confirmed in extraterrestrial materials despite extensive laboratory experimental evidence that it can be produced in interstellar or cometary environments. Here we report the first detection of HMT and functionalized HMT species in the carbonaceous chondrites Murchison, Murray, and Tagish Lake. While the part-per-billion level concentration of HMT in Murchison and Tagish Lake is comparable to other related soluble organic molecules like amino acids, these compounds may have eluded detection in previous studies due to the loss of HMT during the extraction processes. HMT, which can yield important molecules for prebiotic chemistry such as formaldehyde and ammonia upon degradation, is a likely precursor of meteoritic organic compounds of astrochemical and astrophysical interest.

scholarly journals The Case for Prebiotic Chemistry During the Hadean Eon

2019 ◽  
Author(s):  
Rainer Kühne
Keyword(s):  
Amino Acids ◽  
Nucleic Acids ◽  
Organic Molecules ◽  
Prebiotic Chemistry ◽  
Terrestrial Atmosphere ◽  
Cellular Life ◽  
Terrestrial Life

Geochemists disagree whether or not prebiotic chemistry has existed already during the Hadean Eon and whether the then terrestrial atmosphere has been strongly or weakly reduced. Here I argue that cellular life has existed already just after the end of the Hadean Eon and that terrestrial life has survived a number of cataclysms during the Earth's history. I argue that although organic molecules have been detected in meteorites that most organic molecules required for the formation of macromolecules must have been formed on Earth. Finally, I argue that the primitive terrestrial atmosphere during the Hadean Eon has been weakly reduced, so that amino acids and small nucleic acids could have been formed. I suggest that the first self-replicable macromolecules have been similar to viroids.

scholarly journals The Case for Prebiotic Chemistry During the Hadean Eon

2019 ◽  
Author(s):  
Rainer Kühne
Keyword(s):  
Amino Acids ◽  
Nucleic Acids ◽  
Organic Molecules ◽  
Prebiotic Chemistry ◽  
Terrestrial Atmosphere ◽  
Cellular Life ◽  
Terrestrial Life

Geochemists disagree whether or not prebiotic chemistry has existed already during the Hadean Eon and whether the then terrestrial atmosphere has been strongly or weakly reduced. Here I argue that cellular life has existed already just after the end of the Hadean Eon and that terrestrial life has survived a number of cataclysms during the Earth's history. I argue that although organic molecules have been detected in meteorites that most organic molecules required for the formation of macromolecules must have been formed on Earth. Finally, I argue that the primitive terrestrial atmosphere during the Hadean Eon has been weakly reduced, so that amino acids and small nucleic acids could have been formed. I suggest that the first self-replicable macromolecules have been similar to viroids.

The Kinetics of Inhibition of the Action of Thrombin by the Fibrinopeptides Formed during the Clotting of Fibrinogen

1966 ◽  
Vol 16 (01/02) ◽  
pp. 277-295 ◽  
Author(s):  
A Silver ◽  
M Murray
Keyword(s):  
Amino Acids ◽  
Competitive Inhibition ◽  
Amorphous Material ◽  
Peptide Bond ◽  
Initial Reaction ◽  
Reaction Products ◽  
Coagulation Mechanism ◽  
Kinetics Of ◽  
Kinetics Of Inhibition ◽  
Burk Plot

SummaryVarious investigators have separated the coagulation products formed when fibrinogen is clotted with thrombin and identified fibrinopeptides A and B. Two other peaks are observed in the chromatogram of the products of coagulation, but these have mostly been dismissed by other workers. They have been identified by us as amino acids, smaller peptides and amorphous material (37). We have re-chromatographed these peaks and identified several amino acids. In a closed system of fibrinogen and thrombin, the only reaction products should be fibrin and peptide A and peptide B. This reasoning has come about because thrombin has been reported to be specific for the glycyl-arginyl peptide bond. It is suggested that thrombin also breaks other peptide linkages and the Peptide A and Peptide B are attacked by thrombin to yield proteolytic products. Thrombin is therefore probably not specific for the glycyl-arginyl bond but will react on other linkages as well.If the aforementioned is correct then the fibrinopeptides A and B would cause an inhibition with the coagulation mechanism itself. We have shown that an inhibition does occur. We suggest that there is an autoinhibition to the clotting mechanism that might be a control mechanism in the human body.The experiment was designed for coagulation to occur under controlled conditions of temperature and time. Purified reactants were used. We assembled an apparatus to record visually the speed of the initial reaction, the rate of the reaction, and the density of the final clot formed after a specific time.The figures we derived made available to us data whereby we could calculate and plot the information to show the mechanism and suggest that such an inhibition does exist and also further suggest that it might be competitive.In order to prove true competitive inhibition it is necessary to fulfill the criteria of the Lineweaver-Burk plot. This has been done. We have also satisfied other criteria of Dixon (29) and Bergman (31) that suggest true competitive inhibition.

scholarly journals Peculiarities of promiscuous l-threonine transaldolases for enantioselective synthesis of β-hydroxy-α-amino acids

2021 ◽  
Author(s):  
Shan Wang ◽  
Hai Deng
Keyword(s):  
Amino Acids ◽  
Organic Molecules ◽  
Stereoselective Synthesis ◽  
Enantioselective Synthesis ◽  
General Mechanism ◽  
Future Developments ◽  
Key Points ◽  
Biomaterial Science ◽  
One Step ◽  
Harsh Conditions

Abstract The introduction of β-hydroxy-α-amino acids (βHAAs) into organic molecules has received considerable attention as these molecules have often found widespread applications in bioorganic chemistry, medicinal chemistry and biomaterial science. Despite innovation of asymmetric synthesis of βHAAs, stereoselective synthesis to control the two chiral centres at Cα and Cβ positions is still challenging, with poor atomic economy and multi protection and deprotection steps. These syntheses are often operated under harsh conditions. Therefore, a biotransformation approach using biocatalysts is needed to selectively introduce these two chiral centres into structurally diverse molecules. Yet, there are few ways that enable one-step synthesis of βHAAs. One is to extend the substrate scope of the existing enzyme inventory. Threonine aldolases have been explored to produce βHAAs. However, the enzymes have poor controlled installation at Cβ position, often resulting in a mixture of diastereoisomers which are difficult to be separated. In this respect, l-threonine transaldolases (LTTAs) offer an excellent potential as the enzymes often provide controlled stereochemistry at Cα and Cβ positions. Another is to mine LTTA homologues and engineer the enzymes using directed evolution with the aim of finding engineered biocatalysts to accept broad substrates with enhanced conversion and stereoselectivity. Here, we review the development of LTTAs that incorporate various aldehyde acceptors to generate structurally diverse βHAAs and highlight areas for future developments. Key points • The general mechanism of the transaldolation reaction catalysed by LTTAs • Recent advances in LTTAs from different biosynthetic pathways • Applications of LTTAs as biocatalysts for production of βHAAs

scholarly journals Chiroptical activity of hydroxycarboxylic acids with implications for the origin of biological homochirality

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Jana Bocková ◽  
Nykola C. Jones ◽  
Uwe J. Meierhenrich ◽  
Søren V. Hoffmann ◽  
Cornelia Meinert
Keyword(s):  
Amino Acids ◽  
Lactic Acid ◽  
Organic Molecules ◽  
Building Blocks ◽  
Aliphatic Chain ◽  
Monocarboxylic Acids ◽  
Hydroxycarboxylic Acids ◽  
Polarised Light ◽  
Suitable Target ◽  
Anisotropy Spectra

AbstractCircularly polarised light (CPL) interacting with interstellar organic molecules might have imparted chiral bias and hence preluded prebiotic evolution of biomolecular homochirality. The l-enrichment of extra-terrestrial amino acids in meteorites, as opposed to no detectable excess in monocarboxylic acids and amines, has previously been attributed to their intrinsic interaction with stellar CPL revealed by substantial differences in their chiroptical signals. Recent analyses of meteoritic hydroxycarboxylic acids (HCAs) – potential co-building blocks of ancestral proto-peptides – indicated a chiral bias toward the l-enantiomer of lactic acid. Here we report on novel anisotropy spectra of several HCAs using a synchrotron radiation electronic circular dichroism spectrophotometer to support the re-evaluation of chiral biomarkers of extra-terrestrial origin in the context of absolute photochirogenesis. We found that irradiation by CPL which would yield l-excess in amino acids would also yield l-excess in aliphatic chain HCAs, including lactic acid and mandelic acid, in the examined conditions. Only tartaric acid would show “unnatural” d-enrichment, which makes it a suitable target compound for further assessing the relevance of the CPL scenario.

scholarly journals Simple and efficient modifications of well known techniques for reliable growth of high-quality crystals of small bioorganic molecules

2014 ◽  
Vol 47 (4) ◽  
pp. 1435-1442 ◽  
Author(s):  
Denis A. Rychkov ◽  
Sergey G. Arkhipov ◽  
Elena V. Boldyreva
Keyword(s):  
Amino Acids ◽  
Secondary School ◽  
Organic Molecules ◽  
Poor Quality ◽  
Chemical Degradation ◽  
School Level ◽  
Chemistry Curriculum ◽  
High Quality ◽  
Small Organic Molecules ◽  
Secondary School Level

A number of modifications to traditional techniques are suggested in order to overcome problems that frequently arise when growing crystals from solution. These improvements, and their combination, help to avoid problems such as poor nucleation, the spontaneous precipitation of many poor-quality small powder-like crystals, crystals adhering to the crystallization vessel or to each other, and chemical degradation of the solution. The proposed techniques can be used to crystallize desirable metastable polymorphs reliably. None of the suggested methods demands the usage of any special or expensive equipment, or specific skills, and they can be implemented in the chemistry curriculum even at secondary school level. Examples are given for the crystallization of small organic molecules such as carboxylic acids, amino acids, pharmaceuticals etc., but the same techniques are applicable to other classes of compound.

Absorption of L-alanine and other dissolved nutrients by the spines of Paracentrotus lividus (Echinoidea)

1977 ◽  
Vol 57 (4) ◽  
pp. 1031-1045 ◽  
Author(s):  
M. E. de Burgh ◽  
A. B. West ◽  
F. Jeal
Keyword(s):  
Amino Acids ◽  
Organic Molecules ◽  
Marine Invertebrates ◽  
Analytical Techniques ◽  
Paracentrotus Lividus ◽  
Direct Absorption ◽  
Dissolved Nutrients ◽  
Recent Developments ◽  
Modern Analytical

The possibility that marine invertebrates might obtain part of their nutritional requirements by direct absorption of dissolved molecules through the epidermis has recently received considerable attention. This revival of interest in a field which had been virtually abandoned since the early part of the century was led by the findings of Stephens & Schinske (1957, 1958, 1961). Modern analytical techniques have revealed that the amount of dissolved nutrients in coastal waters is much greater than was formerly realized; total amino acids have been recorded in concentrations of up to 10-4 mole/litre in south-east Alaskan waters (Schell, 1974) and 7 x 10-5 mole/litre off Helgoland (Bohling, 1970). Direct absorption of amino acids has been conclusively established in several phyla (see reviews by Stephens, 1968,1972), and one of the major aims of current research is to show that dissolved organic molecules taken up from available concentrations could be of nutritional significance. Recent developments concerning the possible roles of uptake in marine ecosystems have been reviewed by West, de Burgh & Jeal (1977).

scholarly journals Isolation, purification and structure of exochelin MS, the extracellular siderophore from Mycobacterium smegmatis

1995 ◽  
Vol 305 (1) ◽  
pp. 187-196 ◽  
Author(s):  
G J Sharman ◽  
D H Williams ◽  
D F Ewing ◽  
C Ratledge
Keyword(s):  
Amino Acids ◽  
Mycobacterium Smegmatis ◽  
Methyl Esters ◽  
Three Dimensional ◽  
Iron Chelation ◽  
Peptide Bond ◽  
Exchange Chromatography ◽  
Peptide Bonds ◽  
Hydrolysis Of ◽  
Gallium Complex

The extracellular siderophore from Mycobacterium smegmatis, exochelin MS, was isolated from iron-deficiently grown cultures and purified to > 98% by a combination of ion-exchange chromatography and h.p.l.c. The material is unextractable into organic solvents, is basic (pI = 9.3-9.5), has a lambda max at 420 nm and a probable Ks for Fe3+ of between 10(25) and 10(30). Its structure has been determined by examination of desferri- and ferri-exochelin and its gallium complex. The methods used were electrospray-m.s. and one- and two-dimensional (NOESY, DQF-COSY and TOCSY) 1H n.m.r. The constituent amino acids were examined by chiral g.l.c analysis of N-trifluoroacetyl isopropyl and N-pentafluoropropionyl methyl esters after hydrolysis, and reductive HI hydrolysis, of the siderophore. The exochelin is a formylated pentapeptide: N-(delta-N-formyl,delta N-hydroxy-R-ornithyl) -beta-alaninyl-delta N-hydroxy-R-ornithinyl-R-allo-threoninyl-delta N-hydroxy-S-ornithine. The linkages involving the three ornithine residues are via their delta N(OH) and alpha-CO groups leaving three free alpha-NH2 groups. Although there are two peptide bonds, these involve the three R (D)-amino acids. Thus the molecule has no conventional peptide bond, and this suggests that it will be resistant to peptidase hydrolysis. The co-ordination centre with Fe3+ is hexadenate in an octahedral structure involving the three hydroxamic acid groups. Molecular modelling shows it to have similar features to other ferric trihydroxamate siderophores whose three-dimensional structures have been established. The molecule is shown to have little flexibility around the iron chelation centre, although the terminal (Orn-3) residue, which is not involved in iron binding except at its delta N atom, has more motional freedom.

scholarly journals The rate-limiting step of protein synthesis in vivo and in vitro and the distribution of growing peptides between the puromycinlabile and puromycin-non-labile sites on polyribosomes

1971 ◽  
Vol 122 (3) ◽  
pp. 267-276 ◽  
Author(s):  
D. C. N. Earl ◽  
Susan T. Hindley
Keyword(s):  
Amino Acids ◽  
Protein Synthesis ◽  
Donor Site ◽  
Peptide Bond ◽  
Rate Limiting Step ◽  
Limiting Step ◽  
Donor And Acceptor ◽  
Rate Limiting

1. At 3 min after an intravenous injection of radioactive amino acids into the rat, the bulk of radioactivity associated with liver polyribosomes can be interpreted as growing peptides. 2. In an attempt to identify the rate-limiting step of protein synthesis in vivo and in vitro, use was made of the action of puromycin at 0°C, in releasing growing peptides only from the donor site, to study the distribution of growing peptides between the donor and acceptor sites. 3. Evidence is presented that all growing peptides in a population of liver polyribosomes labelled in vivo are similarly distributed between the donor and acceptor sites, and that the proportion released by puromycin is not an artifact of methodology. 4. The proportion released by puromycin is about 50% for both liver and muscle polyribosomes labelled in vivo, suggesting that neither the availability nor binding of aminoacyl-tRNA nor peptide bond synthesis nor translocation can limit the rate of protein synthesis in vivo. Attempts to alter this by starvation, hypophysectomy, growth hormone, alloxan, insulin and partial hepatectomy were unsuccessful. 5. Growing peptides on liver polyribosomes labelled in a cell-free system in vitro or by incubating hemidiaphragms in vitro were largely in the donor site, suggesting that either the availability or binding of aminoacyl-tRNA, or peptide bond synthesis, must be rate limiting in vitro and that the rate-limiting step differs from that in vivo. 6. Neither in vivo nor in the hemidiaphragm system in vitro was a correlation found between the proportion of growing peptides in the donor site and changes in the rate of incorporation of radioactivity into protein. This could indicate that the intracellular concentration of amino acids or aminoacyl-tRNA limits the rate of protein synthesis and that the increased incorporation results from a rise to a higher but still suboptimum concentration.

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