Lab 1B AssignmentBIOL3212 –Biochemistry LabTA: John DonlanAmy Wu 1.
The ALPI gene encodes for a protein called alkalinephosphatase and is most prominently expressed in cells of the small intestinal(terminal ilium), with a small amount of expression present in transverse coloncells. ALPI specifically encodes for the intestinal alkaline phosphatase whichis a digestive enzyme that is necessary for maintaining intestinal homeostasisand protection from pathogens. It is also involved in the successfulfunctioning of the gut mucosal defense system and may possibly aid in the removalof endotoxins. The ALPI gene is located on chromosome 2 and is 4,634 base pairsin length. Consisting of 11 exons, the gene is located on the positive (+) DNAstrand.
Although EcoRI cut sites can be seen when the gene is zoomed out, theydo not fall on the gene and thus there are no EcoRI cut sites present on theALPI specifically. The protein itself is expected to be 528 amino acids inlength. Three vertebrate species that were located in the “comparison” track includethe wallaby, panda and killer whale. I was drawn to these three organisms dueto the vast differences in ecological niches that each one occupies.
Being fromthe Australasian region myself, I was drawn to those organisms that are commonlyfound in this environment. Killer whales (Orcas) have long-been studied in NewZealand and I had the chance to do this in high school during my work with amarine conservation group. 2. 3. The Homosapiens erb-b2 receptor tyrosine kinase 2 gene (gene symbol: ERBB2), alsocommonly referred to as HER2 encodes fora member of the epidermal growth factor (EGF) receptor family of receptortyrosine kinases. Although unable to bind itself to growth factors due to alack of ligand-binding domains, this receptor is able to bind to other ligand-boundEGF receptors which enhance kinase-mediated activation of downstream signaling pathways.
Located on chromosome 17, the ERBB2 gene consists of 31 exons, and is locatedon the positive (+) strand of DNA. The protein itself is expected to be 1055amino acids in length. From the ERBB2 gene expression bar graph, it can be seenthat there is huge variation in terms of the cell types that express the gene. Thisis to be expected as kinase pathways are numerous within the body.
The highestmedian expression is shown to be in the skin (sun exposed, lower leg), howeverother significant sites of expression include the breast (mammary tissue), thebladder, the mucosa of the esophagus. In order to find this gene in the genomebrowser, I first searched “HER2” which unfortunately did not provide me with aRefSeq link, however, did provide me with the alternate name “ERBB2”. Uponentering this in the search bar, the RefSeq link was able to be retrieved. Ichose to search for this gene as I was researching the effects of itsoverexpression over the summer when working at the Zhao Lab at Dana FarberCancer Institute. The Zhao Lab is involved heavily in the research of breastcancer brain metastases, especially in cases of HER2 positive breast cancer.
Manyreports illustrate that the overexpression/amplification of ERBB2 result incancers, particularly in those of the breast and ovaries.