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Free «Biochemistry» Essay Sample

This research is about ways in which statistical proteomes can easily lose active editing domain naturally. This is revealed by the editing mechanism involving the aminoacyl – tRNA synthetases (aaRSs) together with its inactive form of the hydrolytic active sites. Mycoplasma mobile is a form of leucyl – tRNA sythetase (LeuRS) has its unique form of the amino acid editing domain called the CPI. This CPI domain is normally present in the isoleucyl, the leucyl – t RNA, and in the valyl – tRNA synthetases. This CPI domain is found in the synthetic core of the Rossmann ATP – binding fold. This domain is commonly in its hydrolytic nature. The fusion process occurs when the primary form of structure of the Rossmann fold ends up splitting into two sections. Therefore, the study was practical by obtaining a LeuRS hybrid form of a chimera through the utilization of the Myoplamsa mobile compound LeuRS. The study was chiefly done to investigate the evolution process that the protein fusions, as well as other proteins, undergo. This is the fusion of the CPI editing site onto to the domain of the RossMann fold site.



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The study reveals that the aaRSs class I modular construction and its adaptation can attract and further accommodate additional groups of stringent forms of amino acids. This is possible in the presence, and effects of the CPI domain dependant distal on to the amino acids at the synthetic core. Therefore, in the process of trying to find a more effective form of synthesizing protein, there is also a subsequent increase in the specificity of the CPI domain in the synthetic site. Eventually, this process leads to an increase in the hydrolytic editing sites.

The current research is attempting to establish why the leucyl-tRNA has diminished its CP1 domain through the evolution of genome, which causes impaired editing. This action eventually leads to the diverse impairment editing of the gene on study. A portion of the aaRS cannot completely distinguish amid isosteric or partially covering amino acid substrates. It possesses a hydrolytic editing area, which has been made during development to the synthelase’s antique synthetic center. The editing part eradicates errors to maintain the soaring loyalty necessary for protein fusion.

Objectives Statement

The chief objective of this study is to evaluate the evolutionary inferences of adding the domain of aaRS CPI, which eventually leads to the development of fidelity through a series of multiple enzymatic chemical mechanisms. The researcher wished to establish if fidelity resulted from the fusion of the CP1 domains namely cognate and noncognate bacteria to the core of the aminoacyclation canon. The study also established the influence of the domain insertions on the synthetic site.

Experimental Techniques

Many experimental procedures were used in this study. For instance, the procedure involving the design and the construction of the hybrid form of the compound LeuRSs. This involves the mutagenesis process involving the polymerase chain reaction, PCR. The process further involves the introduction of the SpeI restriction endonuclease site of (A_CTAGT) into the p14bLiMmLeuRS (19) form of plasmid. This plasmid is said to encode the wild type gene of MmLeuRS at the recognized sites that encodes for the domain of the CPI fusion at the exact regions of Glu229 and the one of Gly232 positions.

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There was a second major experimental procedure used in the purification of the hybrid MnLeuRS. This involves the utilization of the wild type of the MnLeuRs together with the hybrid protein that consists of six histidines. These two compounds were synthesized recombinant in the present of an E. coli. Later on, a process of purification using the FPLC HisTrap HP column was performed. Subsequently, there was purification of the MonoQ 5/50 GL column through the utilization of both the high, and the low salt buffers. This involved the utilization of a 20mM of TRIS – HCL at the Ph value of 8.2 together with a 5mM NaCl. Additionally, there was a 1Mm of NaCl and a 20Mm TRIS – HCL with a pH of 8.2. The next step involves the purification of the ion exchange and, later on, purification on the size exclusion of the Superdex – 200 columns. This process involved the use of a 100 Mm of NaCl together with a 10 mM of TRIS – HCL, 20 Mm of NaH2PO4 in a 5% concentration of glycerol. This procedure was done to ensure the complete removal of the compounds LeuRS, ValRS, and compound IleRS from the E. coli bacterial cell.

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The next procedure involves the rapid quench kinetics. This is a multiple form of turn over kinetics reaction process. It involves the use of an approximately 5Mm of proteins together with the Myoplasma mobile tRNA Leu UAA of 12.5 mM transcript together with a 50 mM of the Leucine. There was also the involvement of a 2mM of tRNA Leu and a 10 Mm wild form or the hybrid type that was complexed together with leucyl – adenylate. These components were then fitted together into a single equation, which is exponential to be utilized in the measure of the Ktrans.

Additionally, there was also the transcription and the misaminoacylation of the compound Myoplasma mobile tRNA through the in vitro method. This step also involved the utilization of a charged form of isoleucine and/or methionine. There is further application of the E. Coli LeuRS as an editing defective mutant.

Finally, there was the step of pyrophosphate exchange; this assay involved the Kmax and the Kcat in the activation of the amino acids methionine, leucine, valine, and isoleucine. The component of pyrophosphate and ATP were then separated using the thin layer chromatography. This procedure terminated by the quantization of the components through the phosphorimaging process.

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The compound leucyl – tRNA sythetase ended up losing its function. This eventually led to the enhancement of the fidelity between the cognate, and the non – cognate CPI domains of the bacteria to the core of the aminoacylation canonical. This occurred when the mobile LeuRS was to fuse the CPI domains to the catalytic form of class I aaRS core. This led to the reconstruction of the additional part of the hydrolytic editing that was involved to increase the chances of fidelity by the proteins components synthesis process. There was the formation of the hybrid form of the myoplasma mobile LeuRS with a CPI domain from the bacterial E. Coli LeuRS (MmLeuRS/CPI Leu) together with the ValRS (MnLeuRS/CPI Val) CPI domains. There was the retention of the beta strand linkers on each case that appeared to possess a native CPI domain. Similarly, there was a fusion of the N – and the C – terminals of the beta strand present in the CPI domain to the Rossmann fold of the component myoplasma mobile LeuRS at the positions of Glu 229 and Gly 232.

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In the process, a more advanced form of the protein synthesis evolved. There was further an additional of the fidelity of the proteome. The step involving the CPI domain editing led to the addition of a hydrolytic sieve. This additional sieve’s function was to correct as well as clear any form of the aaRS aminoacylation errors that might have occurred during the process. The results of the IleuRS reveals that the CPI domain is further linked to the tRNA – dependant activity of the pre-transfer editing. Moreover, the removal of the CPI domain shows that it can further influence the activity of the pre-transfer editing of the synthetic core.

The process of editing of the CPI domain further influences the stability of the adenylate and the hydrolysis process during the synthesis of the active sites. Specificity and fidelity of the component aaRSs are found to be greatly dependant on the fine synthetic cores of the enzymes. This is because these sites are involved in the binding and the activation of the amino acids at the ATP–dependant aminoacylation process to obtain the tRNA. This majorly occurs when the CPI domain fuses, and then leads to the splitting of the Rossmann fold, which is composed of the class I aaRS catalytic cores of the components of LeuRS, the IleRS, and the component ValRS. The process of the insertion of the LeuRS CPI editing domain mainly leads to a significant enhancement of specificity at the site of the active form of synthetic aminoacylation. Therefore, the fusion of the two forms of proteins eventually led to the subsequent second form of a mechanism. This mechanism later led to the reduction of the errors and mistakes that occurs during the process of obtaining the hydrolytic editing sites (Mascarenhas, et al., 2008).

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Future studies ought to utilize the form of human LeuRS enzyme. This is because this enzyme is capable of retaining the CPI domain by actively increasing the presence of amino acids discrimination at the site of synthetic of hybrid myoplasma mobile LeuRS. This event is contrasting with the study because it eventually leads to a decrease in the fidelity of the myoplasma mobile LeuRS wild type.

The chemical reactions with structures, especially for enzymes in catalyzed reactions took place during the study. For instance, the enzymatic equations involved in the kinetics experimental procedure with the tRNA, and the enzymes responsible, eventually leads to the formation of AMP.

The table below shows the multiple and single turnover kinetic measurements during the process of tRNA aminoacylation with Leucine.


  k1 (s-1) k2 (s-1)

ktrans (s-1)


MmLeuRS 18.5 ± 3.4 2.1 ± 0.11

15.2 ± 2.1


MmLeuRS/CP1Leu 9.7 ± 1 1.37 ± 0.12

12.6 ± 3.7


MmLeuRS/CP1Ile 10.6 ± 0.13 1.67 ± 0.13

14.8 ± 1.1


MmLeuRS/CP1Val 10.7 ± 0.23 0.42 ± 0.05

10.5 ± 1.1


This table describes the methods applied in Hellmann and Martinis procedures. These forms of kinetic constants can further be defined in a more understandable and simplified reactions equations as follows;

                                                 (k1)…                                            (k2)

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Enz + Leu + ATP + tRNA Leu   →   Enz • Leu–tRNALeu •AMP    →    Enz + Leu–tRNALeu + AMP

                                               (k trans)

Enz•Leu–AMP + tRNALeu       →        Enz. Leu–tRNALeu•AMP

The research reveals that the CPI domain can greatly affect the outcome of the amino acids at the synthetic sites during its insertion. The additional process of the CPI domain evolution leads to the formation of various multiple mechanisms, which eventually leads to the CPI fidelity. Future studies should use the form of human LeuRS enzyme because it can retain the CPI domain by actively increasing the availability of amino acids discrimination at the site of synthetic of hybrid myoplasma mobile LeuRS


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