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Bioinformatics - Assignment Example

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Subject: Health sciences and medicine, Assignment   Topic:  Bioinformatics; CW1 – Database Coursework Date: 26th October 2012 Partial DNA sequence for a gene that your company is interested in: CGGCGCCGCGAGCTTCTCCTCTCCTCACGACCGAGGCAGAGCAGTCATTATGGCGAACCTTGGCTGCTGGATGCTGGTTCTCTTTGTGGCCACATGGAGTGACCTGGGCCTCTGCAAGAAGCGCCCGAAGCCTGGAGGATGGAACACTGGGGGCAGCCGATACCCGGGGCAGGGCAGCCCTGGAGGCAACCGCTACCCACCTCAGGGCGGTGGTGGCTGGGGGCAGCCTCATGGTGGTGG A short report telling them what data is publicly available for this gene…
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Download file to see previous pages Homo sapiens [Humans] Most of the query results were from Homo sapiens (human) thereby providing a likelihood that the partial DNA sequence could have probably originated from humans. c. In trying to find the function of a gene it can be useful to see how widely distributed amongst species. For example is it limited to bacteria? From the BLAST output what can you say about the distribution of the gene amongst different species? The prion protein gene is not limited to humans and related species (primates); Sumatran orungatan (Pongo abelii) and Macaca fascicularis are also primates. Albeit the gene we obtained was from a primate, prion gene can also be found in other mammals, such as sheep and cattle. 2) Using the secondary databases find out as much as you can about the functional and structural properties of the gene. Why is this gene significant? What does it do? What does it look like? Where is it found within the organism? Are there any related genes? Accession CAA58442 Amino acid sequence of prion protein [Human] MANLGCWMLVLFVATWSDLGLCKKRPKPGGWNTGGSRYPGQGSPGGNRYPPQGGGGWGQPHGGGWGQPHGGGWGQPHGGGWGQGGGTHSQWNKPSKPKTNMKHMAGAAAAGAVVGGLGGYMLGSAMSRPIIHFGSDYEDRYYRENMHRYPNQVYYRPMDEYSNQNNFVHDCVNITIKQHTVTTTTKGENFTETDVKMMERVVEQMCITQYERESQAYYQRGSSMVLFSSPPVILLISFLIFLIVG The gene exists as a single copy and encodes a membrane glycosylphosphatidylinositol-anchored glycoprotein. It is located on chromosome 20. This protein of molecular weight – 26884.3 has a primary structure made up of 245 amino acids and a theoretical pI (Isoelectric point) of 9.13 (Gasteiger et al., 2005). Monomeric form (C) of the gene product is alpha-helical in structure albeit misfolding of this protein gives rise to a protease resistant form (PRPN (Sc) and is usually anchored on the cell membrane via a lipid anchor. The protein is of importance due to its implication in the etiology of human and livestock disease where its malformation may lead to neuronal degeneration. . Figure 1: NMR solution structure of the human prion protein (Zahn et al., 2000) The gene is involved in synaptic plasticity and neuronal development; it may also play roles in the uptake of iron and homeostasis. Related genes i). RNA-binding protein FUS isoform 1 [Homo sapiens] ii). TATA-binding protein-associated factor 2N isoform 1 [Homo sapiens] iii). Chain A, Mouse Prion Protein (121-231) Containing The Substitution F175a iv). Single-stranded DNA-binding protein [Arthrobacter sp. Rue61a] v). Hypothetical conserved protein [Oceanobacillus iheyensis HTE831] vi). Translation initiation factor IF-2 [Corynebacterium glutamicum R] 3) Is this protein related to any diseases? What are they? What causes them? Are there any mutations of the gene associated with diseases? The misfolding of the prion protein results to a variant of prion protein (PrPc) associated with various neurodegenerative diseases collectively termed transmissible spongiform encephalopathies (TSEs) or prion-related diseases (Taylor et al., 2009; Prusiner, 1998). Upon misfolding of the prion protein, there is a significantly large increase in the ?-sheet content of the protein. This causes the proteins to aggregate into large macromolecules. Prion proteins associated diseases include bovine spongiform encep ...Download file to see next pagesRead More
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