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Amino Acids and Vitamin Production
Published in Debabrata Das, Soumya Pandit, Industrial Biotechnology, 2021
Amino acids are compounds that consist of carbon, hydrogen, oxygen, and nitrogen. They fill in as monomers or building squares and are made out of amino, carboxyl, hydrogen atoms, and a distinctive side chain, all attached to a carbon molecule, the alpha carbon. In an alpha-amino acid, the amino and carboxylate bunches are connected to a similar carbon particle, which is known as the alpha carbon. The different alpha-amino acids contrast depending on the side chain (R gathering) connected to their alpha carbon. All amino acids are known to be active optically except glycine. Optically active mixes can pivot the plane of captivated light either clockwise or counter-clockwise. Optically active aggravates that turn the plane of captured light clockwise are said to be dextrorotatory while those that pivot the plane of captivated light counter-clockwise are said to be levorotatory. Different types of amino acids are found in the body; however, 20 are required for the process of protein synthesis. They generally are of two types i.e. essential as well as non-essential amino acids. Amino acids that can be synthesized by our body and are not essential to be present or supplied through food are called non-essential amino acids such as alanine, arginine, asparagine, aspartic acid, cysteine, glutamic acid, glycine, proline, serine and tyrosine. Amino acids that cannot be synthesized in our body in sufficient quantity and need to be supplied through diet are called essential amino acids such as histidine, leucine, isoleucine etc. (Bender, 2012).
Thermodynamic and Transport Properties of Amino Acids in Aqueous Solution
Published in Miguel A. Esteso, Ana Cristina Faria Ribeiro, A. K. Haghi, Chemistry and Chemical Engineering for Sustainable Development, 2020
Carmen M. Romero, Miguel A. Esteso
Several classifications of amino acids have been proposed according to their characteristics such as polarity, side chain group, hydrophobicity and the locations of the principal functional groups as alpha- (α-), beta- (β-), gamma- (γ-) or delta- (δ-) amino acids. When amino acids have the amine group bound to the first (alpha-) carbon atom adjacent to the carboxylic group, they are called 2-, or α-amino acids. When the amine group is attached to the other terminal carbon atom, called the omega (ω) carbon atom, they are named α,ω-amino acids. The alpha carbon is a chiral carbon atom. The alpha-amino acids are the most common form found in nature, but only in the L-isomer with the exception of glycine that does not has a chiral carbon atom.1–3 According to the side chain, the amino acids can be divided into different categories, classified as aliphatic, hydrophobic, aromatic, polar or charged.
Introduction to the Biological System
Published in Ashutosh Kumar Dubey, Amartya Mukhopadhyay, Bikramjit Basu, Interdisciplinary Engineering Sciences, 2020
Ashutosh Kumar Dubey, Amartya Mukhopadhyay, Bikramjit Basu
Proteins are biological polymers made up of smaller units (monomers). The monomers are arranged in a linear manner and this arrangement is widely known as a polypeptide sequence. These monomers are known as amino acids. In general, amino acids consist of an acidic Carboxyl group (-COOH), a basic Amino group (-NH2), a hydrogen atom (H), and a variable “R” group. Each group is bonded to a central carbon (C) atom (also called alpha carbon). Two amino acids are linked together by a peptide bond (shown in Figure 8.1). The “R” group is specific to each amino acid which gives different identities to these protein monomers (Figure 8.1).
Biodegradation of diisopropyl ether, ethyl tert-butyl ether, and other fuel oxygenates by Mycolicibacterium sp. strain CH28
Published in Bioremediation Journal, 2022
Ingrid Zsilinszky, Balázs Fehér, István Kiss, Attila Komóczi, Péter Gyula, Zsolt Szabó
Our comprehensive review of the literature failed to find any studies investigating the degradation pathway of DIPE. Biodegradation of MTBE, ETBE, dimethyl ether, diethyl ether, and aralkyl ethers was described to proceed through an O-dealkylation reaction (Bernhardt et al. 1988; Resnick and Gibson 1993; Chauvaux et al. 2001; Kim and Engesser 2005). In general, the monooxygenases being responsible for this reaction catalyze the incorporation of an oxygen atom to the alpha carbon atom of the ether bond. This process results in the formation of an unstable hemiacetal structure which spontaneously decomposes to an alcohol and a carbonyl compound (White, Russell, and Tidswell 1996). Accordingly, O-dealkylation of DIPE leads to the simultaneous formation of 2-propanol and acetone followed by the conversion of 2-propanol to acetone by a secondary alcohol dehydrogenase. This is in great agreement with our findings, since we have managed to detect 2-propanol and acetone as degradation intermediates. Considering our results and the literature discussed, we propose the upper pathway of DIPE degradation in strain CH28 yielding acetone as the major intermediate (Figure 7).
Numerical investigation of the role of osteopontin on the mechanical strength of biological composites
Published in Computer Methods in Biomechanics and Biomedical Engineering, 2019
The MD simulations involve several main stages explained below. Firstly, the atomistic system was subjected to energy minimisation (EM) simulation via the steepest descent method. To obtain a system with 310 K temperature and 1 bar pressure, equilibrium simulation was then performed for 200 ps. The simulation was conducted in the canonical ensemble (NVT) for the first 100 ps, and in the isothermal-isobaric ensemble (NPT) for the subsequent 100 ps. Then, it was continued with MD simulation without any forces applied on the osteopontin peptide. The atomistic model after the MD simulation performed for 4 ns was then used as the initial model for subsequent steered molecular dynamics (SMD) simulation. The alpha carbon in the peptide C-terminal end was subjected to load. The spring constant and velocity employed in the SMD simulation are 1000 kJ·mol−1·nm−2 and 0.01 nm·ps−1. The author notes that the spring constant and velocity could have some effects. The effects of spring constant and velocity could be explored in future work. As shown in Figure 1, to investigate the behaviour in the thickness direction, the osteopontin peptide was moved in the direction normal to surface (thickness direction). Besides, to investigate the behaviour in the interface direction, the osteopontin peptide was moved in the direction tangential to surface (interface direction). To visualise and analyse the atomistic results, the Visual Molecular Dynamics (VMD) software (Humphrey et al. 1996) was employed.
Consequences of ligand derivatization on the electronic properties of polyoxovanadate-alkoxide clusters
Published in Journal of Coordination Chemistry, 2019
Bradley E. Schurr, Olaf Nachtigall, Lauren E. VanGelder, Justine Drappeau, William W. Brennessel, Ellen M. Matson
Pleased with the improvements observed in the electrochemical stability and solubility of POV-alkoxides bearing ether-functionalized TRIS ligands [32], we sought to extend our synthetic routes to incorporate a variety of polar functional groups at the surface of the hexavanadate cluster. We anticipated that the generation of these derivatized coordination complexes would provide our research group with a better understanding of the physicochemical consequences of ligand modification. Specifically, we hypothesized that by targeting a series of ligand substitutions varying in polarity we would create an opportunity to improve the solubility of the clusters, while simultaneously tuning the redox properties of these systems in a controlled and predictable fashion. Our intuition was founded in work reported by Thompson and Sanford describing the consequences of ligand susbtitutions on the solubility and electrochemical profiles of chromium(III) and vanadium(III) acetylacetone complexes [34]. By varying the functional group at the alpha-carbon of metal acetylacetonate species with progressively more polar moieties, the authors note not only a dramatic improvement in the solubility of their complexes in acetontrile (0.002–1.92 M), but also modest shifts in E1/2 for the redox couples of each molecule [34]. As such, we targeted a series of organo-functionalized POV-alkoxide clusters possessing a similar range of substitutions at the tertiary-carbon of the tris(hydroxymethyl)methane (TRISR) ligand.