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The Bioinformatics / Molecular Evolution Lab

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The purpose of the Bioinformatics/Molecular Evolution lab is to explore a particular protein given to us by its amino acid sequence. By entering this protein into the Entrez Protein Database in the National Center for Biotechnology Information, and using tools within this database such as Jpred, SMART, and Protoparm, the given protein could be fully analyzed. This experiment was very successful as our particular protein could be identified, and the tools within the NCBI database allowed us to fully analyze both chemical and physical aspects of this protein.
Bioinformatics combines both aspects of biology and key components of computer science. When it comes to DNA, the smaller molecules that make up DNA, along with the sequence of these …show more content…

In addition, it has many cofactor binding sites such as Mg and Zn and interacts non-covalently with metal ions.5
This particular protein of interest is made up of 524 amino acids. When further analyzing this protein, the Jpred results displayed in Figure 2 give a further understanding of the secondary structure of this protein. It is apparent that the secondary structure of alkaline phosphatase, tissue non-specific isozyme isoform 1-precursor contains primarily alpha helices, yet also contains a few beta sheets. The figure displays the alpha helices by long, red tube like figures and the beta sheets as green arrows. Because this figure contains many more long red tubes than green arrows, it is apparent that the secondary structure contains mostly alpha helices. What results in the secondary structure of a protein is the regular pattern of hydrogen bonding between the N-H from the peptide and the C=O groups of the amino acids. These two structures that result in the hydrogen bonding are found relatively close to one another within the linear sequence. Within this regular pattern of hydrogen bonding is where the alpha helices and beta sheets are found. What primarily makes up the secondary structure of our studied protein, alkaline phosphatase, tissue non-specific isozyme isoform 1-precursor, are alpha helices. Alpha helices are rod-like structures that are stabilized as a result of the hydrogen bonds between the N-H and the C=O groups found among the main

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