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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.
An Introduction to Kernel-Based Learning Algorithms
Published in Yu Hen Hu, Jenq-Neng Hwang, Handbook of Neural Network Signal Processing, 2018
Klaus-Robert Müller, Sebastian Mika, Koji Tsuda, Koji Schölkopf
In an attempt to further improve performance, we aimed to incorporate another piece of biological knowledge into the kernel, this time concerning the codon structure of the coding sequence. A codon is a triplet of adjacent nucleotides that codes for one amino acid. By definition, the difference between a true TIS and a pseudo-site is that downstream of a TIS, there is CDS (which shows codon structure), while upstream there is not. CDS and non-coding sequences show statistically different compositions. It is likely that the SVM exploits this difference for classification. We could hope to improve the kernel by reflecting the fact that CDS shifted by three nucleotides still looks like CDS. Therefore, we further modify the locality-improved kernel function to account for this translation invariance. In addition to counting matching nucleotides on corresponding positions, we also count matches that are shifted by three positions. We call this kernel codon-improved. Again, it can be shown to be a valid Mercer kernel function by explicitly deriving the monomial features.
Biomolecular Processing and Molecular Electronics
Published in Sergey Edward Lyshevski, Molecular Electronics, Circuits, and Processing Platforms, 2018
The hierarchy, coding, and protein synthesis may allow one to coherently examine and design the synthesis taxonomy. As documented, the genetic instructions from DNA are coded as codons that precisely specify particular amino acids and proteins. The genetic code is shared by all living organisms, from bacteria to humans. This paradigm results in the synthesis of extremely complex functional biosystems. There is a need for further development of engineering bioinformatics to study the synthesis and design taxonomy of complex devices and systems from biomolecules. Both nucleic acids and proteins are informational polymers assembled from linear sequences of nucleotides and amino acids, respectively. Messenger RNA (as the code carrier from the coding strand of a gene) is the intermediate step from DNA to proteins. Can one be able to utilize and apply this paradigm? Likely the answer is yes, but there are a great number of unsolved problems that may not be resolved in near future.
Optimized expression of large fragment DNA polymerase I from Geobacillus stearothermophilus in Escherichia coli expression system
Published in Preparative Biochemistry & Biotechnology, 2023
Eva Agustriana, Isa Nuryana, Fina Amreta Laksmi, Kartika Sari Dewi, Hans Wijaya, Nanik Rahmani, Danu Risqi Yudiargo, Astadewi Ismadara, Moch Irfan Hadi, Awan Purnawan, Apridah Cameliawati Djohan
In this study, the Bst DNA polymerase gene was synthesized and harbored in the plasmid pD451-SR. The gene was designed following the original sequence of the large-fragment DNA polymerase I gene from Geobacillus stearothermophilus with codon optimization. According to patent no CN106399299A[13], the sequence of the gene has a 1758 bp-nucleotide and encodes a 586 aa-protein with a predicted molecular weight of 67.8 kDa. The enzyme can be functional and thermostable in the temperature range between 25 °C and 75 °C with the optimum temperature at 65 °C[19]. A previous study has reported the full-length of the Bst DNA polymerase I gene consisted of 2648 bp with a predicted molecular weight of 98.6 kDa[20]. Belonging to DNA polymerase type I, Bst DNA polymerase with the complete sequence comprises three kinds of activity: (I) 5′→3′ exonuclease activity, (II) 5′→3′ DNA polymerase activity, and (III) 3′→5′ exonuclease activity[21]. Domains II and III are located in the C-terminus of Bst DNA polymerase and indicated as the large fragment which has no 5′→3′ proofreading exonuclease activity. The sequence gene of the large fragment excludes a 5′ terminal containing up to 876 bp in length, hence a predicted molecular weight of protein translated is decreased to be around 67 kDa[10,22,23]. Bst DNA polymerase used in this study was indicated to belong to the large fragment for sure.
Analysis of coronavirus envelope protein with cellular automata model
Published in International Journal of Parallel, Emergent and Distributed Systems, 2022
Raju Hazari, Parimal Pal Chaudhuri
Design of CA model for a physical system involves design of rule for each CA cell. A cell models the smallest component of the system so that the physical domain features of the component get represented in the binary bit pattern of its rule. Once the rule design step is complete, we can represent a 3NCA as a rule vector – a string of 3NCA rules ( 0–255). Figure 2(b) shows the rule vector for a 10 cell CA with the rules specified in Figure 2(a). The CA evolves at each time step through local interaction of each cell with its neighborhood. The design proceeds through a number of iterations to build a model that characterizes the system with efficient mapping of model parameters derived out of CA evolution to the physical domain features of the system. The string of 3NCA Rule Vector can be employed to model the biological strings: DNA, RNA, Codon string, and AA chain of a protein.
Extremozymes used in textile industry
Published in The Journal of The Textile Institute, 2022
Priyanka Kakkar, Neeraj Wadhwa
Native forms of extremozymes do not provide high product yield sufficient for industrial applications. Development of industrial enzymes with high yield and also cost effective is important for market. Heterologous expression of gene encoding extremozymes into the mesophilic host is a method to produce recombinants. Based on the knowledge of their genome, metabolism, doubling time and culture media the host is selected. E.coli is so far best known host for the expression of proteins but it has certain drawbacks as it is codon biased; produce inclusion bodies and LPS endotoxin. Other hosts include Bacillus subtilis, Saccharomyces cerevisiae, Trichoderma reesei can be used for protein expression. Depending on the system of different host, gene expression can be failed and codon harmonization algorithm is a useful tool to overcome codon bias and increase protein expression (Atalah et al., 2019).