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Biochemistry and Molecular Biology... May 2021Ionization of amino acids (AA) is very important concept in biochemistry. We integrate the mathematical concept of probability with biochemically relevant process of AA...
Ionization of amino acids (AA) is very important concept in biochemistry. We integrate the mathematical concept of probability with biochemically relevant process of AA ionization. We visualize the ionization process with Mathematica software discussing intramolecular interactions between weakly acidic/basic functional groups and charge-pH variation of amino acids in water solution. The visualizations rely on the notion of probability of ionization of functional groups and demonstrate how the extent of ionization and charge varies with pH of the solution. The examples described include amino acids and weak diprotic acids and bases. The aim is to help students better appreciate the importance and consequences of AA ionization and correct some misconceptions.
Topics: Acids; Amino Acids; Biochemistry; Humans; Hydrogen-Ion Concentration; Mathematical Computing; Students
PubMed: 33096589
DOI: 10.1002/bmb.21470 -
Nature Chemistry Nov 2020Life is an out-of-equilibrium system sustained by a continuous supply of energy. In extant biology, the generation of the primary energy currency, adenosine...
Life is an out-of-equilibrium system sustained by a continuous supply of energy. In extant biology, the generation of the primary energy currency, adenosine 5'-triphosphate and its use in the synthesis of biomolecules require enzymes. Before their emergence, alternative energy sources, perhaps assisted by simple catalysts, must have mediated the activation of carboxylates and phosphates for condensation reactions. Here, we show that the chemical energy inherent to isonitriles can be harnessed to activate nucleoside phosphates and carboxylic acids through catalysis by acid and 4,5-dicyanoimidazole under mild aqueous conditions. Simultaneous activation of carboxylates and phosphates provides multiple pathways for the generation of reactive intermediates, including mixed carboxylic acid-phosphoric acid anhydrides, for the synthesis of peptidyl-RNAs, peptides, RNA oligomers and primordial phospholipids. Our results indicate that unified prebiotic activation chemistry could have enabled the joining of building blocks in aqueous solution from a common pool and enabled the progression of a system towards higher complexity, foreshadowing today's encapsulated peptide-nucleic acid system.
Topics: Catalysis; Origin of Life; Peptides; Phosphates; Phosphoric Acids; RNA
PubMed: 33093680
DOI: 10.1038/s41557-020-00564-3 -
Scientific Reports Aug 2022In recent years, there has been a continuous increase in the incidence of urolithiasis, especially in highly developed countries. Therefore, the question arises which...
In recent years, there has been a continuous increase in the incidence of urolithiasis, especially in highly developed countries. Therefore, the question arises which factors specific to these countries may be responsible for the increase in the incidence of this disease. In this article, we try to assess the effect of phosphoric acid, a component of various carbonated drinks, including Coca-Cola, on the nucleation and growth of struvite crystals, which are the main component of infectious urinary stones. The research was carried out in the environment of artificial urine with and without the presence of Proteus mirabilis bacteria. In the latter case, the activity of bacterial urease was simulated by adding an aqueous ammonia solution. The obtained results indicate that phosphoric acid present in artificial urine causes the nucleation of struvite to shift towards a lower pH, which means that struvite nucleates earlier in artificial urine compared to the control test. The amount of struvite formed is the greater the higher the concentration of phosphoric acid. At the same time, as the concentration of phosphoric acid increases, the growing struvite crystals are larger, which is disadvantageous because they are more difficult to remove from the urinary tract along with the urine. For the highest levels of phosphoric acid tested, large dendrites are formed, which are particularly undesirable as they can damage the epithelium of the urinary tract. The effect of phosphoric acid on the nucleation and growth of struvite is explained in base of chemical speciation analysis. This analysis indicates that the MgHCit and MgCit complexes have the main influence on the nucleation and growth of struvite in artificial urine in the presence of phosphoric acid. It should be keep in mind that all these effects of phosphoric acid are possible when the urinary tract is infected with urease-positive bacteria. In the absence of infection, phosphoric acid will not cause struvite to crystallize.
Topics: Carbonated Beverages; Crystallization; Humans; Magnesium Compounds; Phosphates; Phosphoric Acids; Proteus mirabilis; Struvite; Urease; Urine; Urolithiasis
PubMed: 35995826
DOI: 10.1038/s41598-022-18357-8 -
International Journal of Molecular... Nov 2022Among natural and synthetic polymers, main-chain phosphorus-containing polyacids (PCPAs) (polyphosphodiesters), stand in a unique position at the intersection of... (Review)
Review
Among natural and synthetic polymers, main-chain phosphorus-containing polyacids (PCPAs) (polyphosphodiesters), stand in a unique position at the intersection of chemistry, physics, biology and medicine. The structural similarity of polyphosphodiesters PCPAs to natural nucleic and teichoic acids, their biocompatibility, mimicking to biomolecules providing the 'stealth effect', high bone mineral affinity of polyphosphodiesters resulting in biomineralization at physiological conditions, and adjustable hydrolytic stability of polyphosphodiesters are the basis for various biomedical, industrial and household applications of this type of polymers. In the present review, we discuss the synthesis, properties and actual applications of polyphosphodiesters.
Topics: Polymers; Acids; Polymerization
PubMed: 36499185
DOI: 10.3390/ijms232314857 -
Physiology (Bethesda, Md.) Dec 2005Acid/base transporters play a key role in establishing an acidic luminal environment for sperm maturation and storage in the male reproductive tract. Impairment of the... (Review)
Review
Acid/base transporters play a key role in establishing an acidic luminal environment for sperm maturation and storage in the male reproductive tract. Impairment of the acidification capacity of the epididymis, via either genetic mutations or exposure to environmental factors, may have profound consequences on male fertility.
Topics: Acid-Base Equilibrium; Acids; Animals; Genitalia, Male; Humans; Infertility, Male; Male; Membrane Transport Proteins
PubMed: 16287991
DOI: 10.1152/physiol.00036.2005 -
Yakugaku Zasshi : Journal of the... 2015To summarize our electroanalytical research in the biomedical field over the past 43 years, this review describes studies on specular reflection measurement, redox... (Review)
Review
To summarize our electroanalytical research in the biomedical field over the past 43 years, this review describes studies on specular reflection measurement, redox potential determination, amperometric acid sensing, HPLC with electrochemical detection, and potential oscillation across a liquid membrane. The specular reflection method was used for clarifying the adsorption of neurotransmitters and their related drugs onto a gold electrode and the interaction between dental alloys and compound iodine glycerin. A voltammetric screening test using a redox potential for the antioxidative effect of flavonoids was proposed. Amperometric acid sensing based on the measurement of the reduction prepeak current of 2-methyl-1,4-naphthoquinone (VK3) or 3,5-di-tert-buty1-1,2-benzoquinone (DBBQ) was applied to determine acid values of fats and oils, titrable acidity of coffee, and enzyme activity of lipase, free fatty acids (FFAs) in serum, short-chain fatty acids in feces, etc. The electrode reactions of phenothiazines, catechins, and cholesterol were applied to biomedical analysis using HPLC with electrochemical detection. A three-channel electrochemical detection system was utilized for the sensitive determination of redox compounds in Chinese herbal medicines. The behavior of barbituric acid derivatives was examined based on potential oscillation measurements.
Topics: Acids; Biomedical Research; Chromatography, High Pressure Liquid; Electrochemical Techniques; Electrodes; Humans; Oxidation-Reduction
PubMed: 25759051
DOI: 10.1248/yakushi.14-00223 -
Proceedings of the Japan Academy.... 2011This review focuses on the development of ruthenium and flavin catalysts for environmentally benign oxidation reactions based on mimicking the functions of cytochrome... (Review)
Review
This review focuses on the development of ruthenium and flavin catalysts for environmentally benign oxidation reactions based on mimicking the functions of cytochrome P-450 and flavoenzymes, and low valent transition-metal catalysts that replace conventional acids and bases. Several new concepts and new types of catalytic reactions based on these concepts are described. (Communicated by Ryoji Noyori, M.J.A.).
Topics: Acids; Alkalies; Biomimetics; Catalysis; Oxidation-Reduction; Salts; Transition Elements
PubMed: 21558760
DOI: 10.2183/pjab.87.242 -
Sheng Wu Gong Cheng Xue Bao = Chinese... May 2017Microbial fuel cells (MFCs) is a highly promising bioelectrochemical technology and uses microorganisms as catalyst to convert chemical energy directly to electrical... (Review)
Review
Microbial fuel cells (MFCs) is a highly promising bioelectrochemical technology and uses microorganisms as catalyst to convert chemical energy directly to electrical energy. Microorganisms in the anodic chamber of MFC oxidize the substrate and generate electrons. The electrons are absorbed by the anode and transported through an external circuit to the cathode for corresponding reduction. The flow of electrons is measured as current. This current is a linear measure of the activity of microorganisms. If a toxic event occurs, microbial activity will change, most likely decrease. Hence, fewer electrons are transported and current decreases as well. In this way, a microbial fuel cell-based biosensor provides a direct measure to detect toxicity for samples. This paper introduces the detection of antibiotics, heavy metals, organic pollutants and acid in MFCs. The existing problems and future application of MFCs are also analyzed.
Topics: Acids; Anti-Bacterial Agents; Bioelectric Energy Sources; Biosensing Techniques; Electricity; Electrodes; Metals, Heavy; Oxidation-Reduction
PubMed: 28876027
DOI: 10.13345/j.cjb.160354 -
PloS One Apr 2010Hydrogen production by fermenting bacteria such as Escherichia coli offers a potential source of hydrogen biofuel. Because H(2) production involves consumption of 2H(+),...
BACKGROUND
Hydrogen production by fermenting bacteria such as Escherichia coli offers a potential source of hydrogen biofuel. Because H(2) production involves consumption of 2H(+), hydrogenase expression is likely to involve pH response and regulation. Hydrogenase consumption of protons in E. coli has been implicated in acid resistance, the ability to survive exposure to acid levels (pH 2-2.5) that are three pH units lower than the pH limit of growth (pH 5-6). Enhanced survival in acid enables a larger infective inoculum to pass through the stomach and colonize the intestine. Most acid resistance mechanisms have been defined using aerobic cultures, but the use of anaerobic cultures will reveal novel acid resistance mechanisms.
METHODS AND PRINCIPAL FINDINGS
We analyzed the pH regulation of bacterial hydrogenases in live cultures of E. coli K-12 W3110. During anaerobic growth in the range of pH 5 to 6.5, E. coli expresses three hydrogenase isoenzymes that reversibly oxidize H(2) to 2H(+). Anoxic conditions were used to determine which of the hydrogenase complexes contribute to acid resistance, measured as the survival of cultures grown at pH 5.5 without aeration and exposed for 2 hours at pH 2 or at pH 2.5. Survival of all strains in extreme acid was significantly lower in low oxygen than for aerated cultures. Deletion of hyc (Hyd-3) decreased anoxic acid survival 3-fold at pH 2.5, and 20-fold at pH 2, but had no effect on acid survival with aeration. Deletion of hyb (Hyd-2) did not significantly affect acid survival. The pH-dependence of H(2) production and consumption was tested using a H(2)-specific Clark-type electrode. Hyd-3-dependent H(2) production was increased 70-fold from pH 6.5 to 5.5, whereas Hyd-2-dependent H(2) consumption was maximal at alkaline pH. H(2) production, was unaffected by a shift in external or internal pH. H(2) production was associated with hycE expression levels as a function of external pH.
CONCLUSIONS
Anaerobic growing cultures of E. coli generate H(2) via Hyd-3 at low external pH, and consume H(2) via Hyd-2 at high external pH. Hyd-3 proton conversion to H(2) is required for acid resistance in anaerobic cultures of E. coli.
Topics: Acids; Anaerobiosis; Biofuels; Escherichia coli; Escherichia coli Proteins; Fermentation; Hydrogen; Hydrogen-Ion Concentration; Hydrogenase; Protons
PubMed: 20405029
DOI: 10.1371/journal.pone.0010132 -
Molecules (Basel, Switzerland) Apr 2022Marine fish collagen has attracted considerable attention due to its characteristics, including its biodegradability, biocompatibility, and weak antigenicity, and is...
Marine fish collagen has attracted considerable attention due to its characteristics, including its biodegradability, biocompatibility, and weak antigenicity, and is considered a safer material compared to collagen from terrestrial animals. The aim of this study was to extract and characterize collagen from the skin of lizardfish ( Bloch, 1795) with three different acids. The yields of acetic acid-extracted collagen (AESkC), lactic acid-extracted collagen (LESkC), and citric acid-extracted collagen (CESkC) were 11.73 ± 1.14%, 11.63 ± 1.10%, and 11.39 ± 1.05% (based on wet weight), respectively. All extracted collagens were categorized as type I collagen with mainly alpha chains (α and α) detected and γ and β chains to some extent. Fourier transform infrared (FTIR) spectra showed an intact triple-helical structure in the AESkC, LESkC, and CESkC. UV-vis spectra and X-ray diffraction further demonstrated the similarity of the extracted collagens to previously reported fish skin collagens. AESkC ( = 40.24 °C) had higher thermostability compared to LESkC ( = 38.72 °C) and CESkC ( = 36.74 °C). All samples were highly soluble in acidic pH and low concentrations of NaCl (0-20 g/L). Under field emission scanning electron microscopy (FESEM) observation, we noted the loose, fibrous, and porous structures of the collagens. The results suggest that the lizardfish skin collagens could be a potential alternative source of collagen, especially the AESkC due to its greater thermostability characteristic.
Topics: Acids; Animals; Collagen; Fish Proteins; Fishes; Skin; Solubility
PubMed: 35458650
DOI: 10.3390/molecules27082452