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The Molecular Basis of the Informational System–The Replication of DNA–The Trancription to mRNA– Protein Biosynthesis
Published in Jean-Louis Burgot, Thermodynamics in Bioenergetics, 2019
The genetic code, which has just been precisely involved, is the relation between the arrangement of the bases of DNA (or of that which is its “transcript”) and the amino acids of a protein. A sequence of three bases, named codon, determine one amino acid. The codons of mRNA are sequentially read by molecules of tRNA. A molecule of tRNA brings a specific amino acid under an activated form up to the synthesis site. The carboxylic acid group is esterified by the 2’ and 3’rests of a ribose unit located at the end of the chain of tRNA. An aminoacyl-tRNA is built according to a reaction specifically catalyzed by an activation enzyme. The recognition site of the matrix on the tRNA is a sequence of three bases called anticodon. The Figures 145, 143 and 142 schematically represent the linkage between an amino acid and a tRNA and the linkage site of the amino acid and the anticodon.
Nanostructured Cellular Biomolecules and Their Transformation in Context of Bionanotechnology
Published in Anil Kumar Anal, Bionanotechnology, 2018
Protein synthesis initiates with the assembly of the translation complex. Ribosome identifies the initiation codon, which is usually AUG (codes for methionine), but GUG, UUG, or AUU may also be used. Among the two methionyl-tRNAMet molecule that translates AUG codons, initiator tRNA is used at the initiation codon. At the end of the initiation step, mRNA is positioned in such a way that the next codon can be translated during the elongation step, the initiator tRNA is attached to P site and A site of ribosome is ready to receive incoming aminoacyl-tRNA. During chain elongation process, tRNA with the correct aminoacyl-tRNA attach into the A site. The peptidyl transferase catalyzes a transfer of the amino acid from the P site to the amino acid at the A site with the formation of peptide bond such that the growing polypeptide chain is covalently attached to the tRNA in the A site, forming a peptidyl-tRNA. The first amino acid on the polypeptide has a free amino group, so it is called the N-terminal and the last amino acid has a free carboxylic group, so it is called the C-terminal. The mRNA shifts by one codon such that two tRNAs at the P and A site translocate. Following this, deaminoacylated tRNA is displaced from P to exit, E site and peptidyl-tRNA is displaced from A to P site. When one of the three stop codons (UAA, UAG, UGA) on the mRNA is reached, tRNA does not recognize these termination codons and release factor causing the hydrolysis of the peptidyl-tRNA releasing polypeptide chain (Moran et al. 2012).
Proteins and Proteomics
Published in Firdos Alam Khan, Biotechnology Fundamentals, 2020
Aminoacyl tRNA synthetase catalyzes the bonding between specific tRNAs and the amino acids that their anticodon sequences call for. The product of this reaction is an aminoacyl-tRNA molecule. This aminoacyl-tRNA travels inside the ribosome, where mRNA codons are matched through complementary base pairing to specific tRNA anticodons. The amino acids that the tRNAs carry are then used to assemble a protein. The rate of translation varies. It is significantly higher in prokaryotic cells, up to 17–21 amino acid residues per second, than in eukaryotic cells, up to 6–7 amino acid residues per second (Figure 3.5).
Gut microbiota of cattle and horses and their use in the production of ethanol and lactic acid from timothy hay
Published in Biofuels, 2023
Alaa Emara Rabee, Mebarek Lamara, Suzanne L. Ishaq
Functional prediction of the metabolic pathways of fecal microbial communities in cows (CB) and horses (HB) was performed using PICRUSt2. The results revealed that the most enriched pathways were DNA repair and recombination, pentose phosphate, aminoacyl-tRNA biosynthesis, amino acid-related enzymes, starch and sucrose metabolism, and pyrimidine and purine metabolism (Figure 7). Principal components analysis (PCA) of PICRUSt2 functional prediction was created based on the relative abundance of metabolic pathways and was shown in Figure 8, which revealed that the samples of group CB and HB were clustered separately. Group CB showed significant (q < 0.05) higher relative abundances of genes related to carbohydrate metabolism, pentose phosphate pathway, glycerolipid metabolism, methane metabolism, starch and sucrose metabolism, nitrogen metabolism, pentose, and glucuronate interconversions, and fatty acid metabolism (Figure 7). Furthermore, the HB group showed significant (q < 0.05) higher relative abundances of genes related to translation proteins, translation factors, homologous recombination, DNA repair, and recombination proteins, D-Glutamine and D-glutamate metabolism, amino acid-related enzymes, D-Arginine and D-ornithine metabolism, bacterial secretion system, glutathione metabolism, purine metabolism, pyrimidine metabolism, lipopolysaccharide biosynthesis proteins, D-Alanine metabolism, lipid biosynthesis proteins, riboflavin metabolism, biosynthesis of unsaturated fatty acids, lipopolysaccharide biosynthesis (Figure 7).
Transcriptome analysis reveals that yeast extract inhibits synthesis of prodigiosin by Serratia marcescens SDSPY-136
Published in Preparative Biochemistry & Biotechnology, 2023
Junqing Wang, Tingting Zhang, Yang Liu, Shanshan Wang, Zerun Li, Ping Sun, Hui Xu
Various amino acids are involved in the synthesis of the intermediate of prodigiosin, to form its tripyrrole structure.[13,17] The A-ring of prodigiosin contains L-proline, B-ring contains L-serine and C-ring contains acetic acid and L-alanine.[13] We attempted to analyze the reactions involved in prodigiosin synthesis of amino acids. The gene encoding 1-pyrroline-5-carboxylate dehydrogenase (putA), which catalyzes glutamate to proline conversion, was upregulated in the TR group. Similar results were observed by Sun et al.[29] After proline generated L-1-pyrroline-3-hydroxy-5-carboxylate, dehydrogenase (E1.2.1.88) and proline dehydrogenase (putA) were up-regulated to generate L-erythro-4-hydroxyglutamate. So the proline did not react in the direction for the synthesis of prodigiosin (Figure 5). Key genes encoding molecules involved in serine metabolic pathways, including those for cystathionine beta-synthase (CBS), cystathionine synthase (CYSO), and cystathionine gamma-lyase (CTH; mccB) genes, were down-regulated, affecting the serine synthesis pathway. This affected serine as a precursor for 4-hydroxy-2,2′-bipyrrolid-5-methanol synthesis. The pyrrolid-β-ketothioester intermediate undergoes a condensation reaction with serine to form 4-hydroxy-2,2′-bipyrrolid-5-methanol.[13] In addition, tryptophan synthase (trpA, B; TRP), which regulates the synthesis of tryptophan from serine, was down-regulated (data not shown). Serine also produces L-methionine, as well as S-adenosyl methionine as an intermediate of prodigiosin synthesis (Figure 5). In addition to glyA, which produces the enzyme that synthesizes glycine from serine, the gene for serine ammonia-lyase (SDS) was up-regulated, which enhanced the conversion of serine to pyruvate, whereas other pathways in serine were inhibited. We predicted that 4-hydroxy-2,2′-bipyrrolid-5-methanol synthesis could not proceed because the limited amount of serine was consumed during upregulation of gene regulation. Genes that metabolize S-adenosyl methionine are enhanced in the polyamine production pathway, which is related to the action of transaminopropyl. Serratia marcescens requires S-adenosyl methionine and HBM to synthesize MBC in the presence of PIG-M. Two other amino acids, L-tyrosine and phenylalanine, are also involved in the TCA cycle; their pathways in carbon metabolism were found to be enhanced (Figure 5). The ribosome and aminoacyl-tRNA biosynthesis pathways are intimately connected to the pathways of these amino acids, and most relevant genes were enriched and significantly up-regulated under yeast extract conditions (Table S1). Structural molecular activity, rRNA binding, translation, and peptide metabolism showed the most significant enrichment in TR group, these were highly energy-consuming processes, which may also explain the reason for amino acid and carbon metabolism (Figure 3A).