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X-Nuclei MRI and Energy Metabolism
Published in Guillaume Madelin, X-Nuclei Magnetic Resonance Imaging, 2022
Physical and chemical properties of ATP. Structurally, ATP is an RNA nucleotide that bears a chain of three phosphates: One sugar: the ribose. The ribose is a 5-carbon sugar that lies at the center of the ATP molecule.One nitrogen base: the adenine. The adenine base consists of linked rings of carbon and nitrogen atoms and is attached to one side of the ribose.Three phosphate groups. The three phosphate groups, in order of closest to furthest from the ribose sugar, are labeled α, β, and γ and are key to the activity of ATP.
Fundamentals of biology and thermodynamics
Published in Mohammad E. Khosroshahi, Applications of Biophotonics and Nanobiomaterials in Biomedical Engineering, 2017
These are biopolymers, or large biomolecules, which exist in two forms—as DNA (deoxyribonucleic acid) and RNA (ribonucleic acid), and are made from monomers known as nucleotides. Each nucleotide has three components: a 5-carbon sugar, a phosphate group (tetrahedral PO4), and a nitrogen-containing ring, which could be either purine or pyrimidine. The four bases composing DNA are adenine (A), guanine (G), thymine (T), and cytosine (C). In the case of RNA, (T) is replaced by uracil (U). If the sugar is deoxyribose, the polymer is DNA. If the sugar is ribose, the polymer is RNA. When all three components are combined, they form a nucleic acid. Nucleotides are also known as phosphate nucleotides.
Subsurface Processes
Published in Stephen M. Testa, Geological Aspects of Hazardous Waste Management, 2020
Enzymes are proteins, and proteins consist of long chains of the 20 common amino acids which are connected in precise ways so that even their shape must be correct in order to catalyze a specific reaction. The amino-acid sequence determines the protein structure and composition. How the cell determines this sequence is the role of the cell as a coding device. The code, called the genetic code, is stored in a sequence of several purine and pyrimidine bases attached to a sugar and linked by phosphate groups. In deoxyribonucleic acid (DNA), the sugar is deoxyribose. In ribonucleic acid (RNA), the sugar is ribose. The coding mechanism is the sequencing of bases in the DNA (and in RNA for some bacteria). Each amino acid is coded for by a three-base sequence on the DNA strand. Each DNA strand is bonded to another strand of complimentary DNA into a double-helix structure through the unique pairing of the purine and pyrimidine bases. When replicating, the helix opens, and complimentary DNA strands are built along each strand to form two identical sets of DNA. When translating the information contained in the base sequences, the DNA opens and the sequence is read by building a similarly complimentary RNA strand that then builds the proteins according to its newly produced coded base sequences. There are various base sequences for recognizing when to start and stop specific translations. The series of bases which code for a specific protein is called a gene. The genes are arranged into groups called chromosomes. The genetic code is, therefore, a code only for enzymes and other proteins. These proteins then control and carry out all other reactions needed by the organism.
Lyotropic isotropic to columnar phase transition in RNA solutions
Published in Liquid Crystals, 2022
RNA is generally found in organisms as a single-stranded chain of nucleotides. RNA is a linear polymer of nucleotides linked by a ribose-phosphate backbone. Polymerization of nucleotides occurs in a condensation reaction in which phosphodiester bonds are formed. RNA helices intrinsically resist bend or twist deformations. Generally, RNA is fairly rigid and posses high flexibility. Some RNA are also moderately flexible. RNA is an important precursor to DNA. The self-assembly of RNA NTP (rNTPs) is a template of the RNA world and the origins of life. RNA contains a Ribose sugar, which has two hydroxyl groups make the RNA less stable in solution because of their propensity for hydrolysis [1]. RNA has a higher tilt of its bases as well as a shorter rise for the base pairs [1]. The three most commonly studied of RNA are messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA), which are present in all organism.
Structural variations on Salmonella biofilm by exposition to river water
Published in International Journal of Environmental Health Research, 2021
Contreras-Soto Mb, Medrano-Félix Ja, Sañudo-Barajas Ja, Vélez-de la Rocha R, Ibarra-Rodríguez Jr, Martínez-Urtaza J, Chaidez C, Castro-del Campo N
The presence of ribose, was detected in all strains and in all conditions, being higher in planktonic bacteria, where Typhimurium 14028 and Infantis Cli S-304 were the strains that had the greatest amount of this compound. The 5-carbon sugar ribose is an important component of nucleotides and is found in RNA; it is known that within the biofilm formation there are cells in the planktonic state and cells segmented to the exopolysaccharide matrix; this might explain the detection of ribose as a component of biofilms in this study. Interestingly, diverse studies demonstrated that D-ribose inhibited AI-2 (autoinducer 2) that induced biofilm growth and co-aggregation in Gram negative and Gram positive bacteria (Jang et al. 2013; Lee et al. 2015; Cho et al. 2016; Sintim and Gürsoy 2016; Liu L et al. 2017). There is no information about the role of ribose in Salmonella biofilms; however, the literature shows ribose as a biofilm inhibiting agent; therefore, these findings open an important source of opportunities to expand scientific search for knowledge about biofilm formation and composition in Salmonella and other enterobacterias.
The effect of NADPH oxidase inhibitor diphenyleneiodonium (DPI) and glutathione (GSH) on Isatis cappadocica, under Arsenic (As) toxicity
Published in International Journal of Phytoremediation, 2021
Zahra Souri, Naser Karimi, Parvaiz Ahmad
Exposure to As triggers the overproduction of ROS thereby inducing the oxidative stress through stimulating the ROS-producing enzymes e.g., NADPH oxidases, and inhibiting the mechanisms involved in biosynthesis of molecules regulating the redox homeostasis (Flora 2011; Gupta et al.2013; Janků et al.2019; Mishra et al.2019). On the other hand, the main source of ROS involved and the mechanisms implicated in GSH mediated alleviation under As stress are broadly unexplored (Gupta et al.2013; Mishra et al.2019). During As toxicity, oxidative stress triggered through the overproduction of ROS and disturbances of antioxidative responses have been demonstrated as a key function in plant cells (Lin et al.2008; Sharma 2012; Gupta et al.2013). Greater activity of NADPH oxidase stimulates the production of O2− and H2O2 (Figure 8), and consequently oxidative stress that is suggested to be primarily responsible for oxidative toxicity (Figure 8). Due to disruption of cellular redox balance and NADPH/NADP+ ratio, the use of DPI as an inhibitor of NADPH oxidase disrupts many biochemical pathways dependent on NADP such as pentose phosphate pathway and consequently reducing the GSH levels (Figure 8). The pentose phosphate pathway produces ribulose 5-phosphate, a precursor to ribose and deoxy ribose required for RNA and DNA synthesis (Noctor et al.2006). Moreover, the oxidized glutathione (GSSG) is recovered by NADPH from the pentose phosphate pathway (Figure 8). It has also been reported that, NADPH is crucial for key antioxidative functions like GR activity, an important enzyme in the AsA-GSH cycle to protect the stress mediated oxidative stress (Gill et al.2013; Corpas and Barroso 2014). Optimal concentrations of GSH are required for several biochemical pathways and the recycling of GSSG and GSH form an essential factor for improving the chelating capacity in hyperaccumulator plants. Upon As exposure, GSH content drops as a consequence of its incorporation into PC biosynthesis and it has been noted that As is detoxified by complexation with PC and/or vacuolar sequestration (Karimi et al.2009; Guo et al.2012; Souri et al.2017).