This page was produced as an assignment for Genetics 677, an undergraduate course at UW - Madison.
What is Gene Ontology?
Gene Ontology (GO) refers to an ongoing project and collaboration of a hoard of scientists that are trying to classify and compare gene functions and products across species [1]. That is, it is an effort to create a unified database of all gene functions in all organisms and how they are interconnected. In the context of the pah gene, GO would try to create a system of pathways that illustrates the bigger picture of how Phe catabolism fits into metabolism and functioning as a whole.
There are three categories by which GO defines a gene or gene product (in this case, the PAH protein): biological process, molecular function, and cellular components. Biological process refers to the overall goal of the protein's activity. Examples of broad biological processes would be metabolism, respiration, or development. Molecular function generally describes what a protein is capable of. Many times these can line up with certain domains that a protein has (for example, Iron binding, or amino acid binding sites). Cellular components refer to where in the cell the protein is in its active state. This could be in the nucleus, secreted into the blood, or in any of the organelles inside the cell.
There are three categories by which GO defines a gene or gene product (in this case, the PAH protein): biological process, molecular function, and cellular components. Biological process refers to the overall goal of the protein's activity. Examples of broad biological processes would be metabolism, respiration, or development. Molecular function generally describes what a protein is capable of. Many times these can line up with certain domains that a protein has (for example, Iron binding, or amino acid binding sites). Cellular components refer to where in the cell the protein is in its active state. This could be in the nucleus, secreted into the blood, or in any of the organelles inside the cell.
Ontology of the pah gene
Using the GO database, the pah gene was returned with information regarding 6 different biological processes, 3 different molecular functions, and 1 cellular component.
Biological Processes
Small molecule metabolic Neurotransmitter biosynthetic L-phenylalanine catabolic process Cellular nitrogen compound metabolic process Cellular amino acid biosynthetic process Catecholamine biosynthetic process |
Molecular Functions
Amino acid binding Iron ion binding Phenylalanine 4-monooxygenase activity |
Cellular Components
Cytosol |
|
Analysis and Discussion
Most of the biological processes and molecular functions are not surprising; the molecular functions closely and clearly reflect the domains that the PAH protein possesses. Likewise, the overall biological processes mainly re-emphasize what is already known about the gene: it is involved in catabolizing the amino acid phenylalanine into another amino acid, tyrosine, which is an important molecule in the makeup of neurotransmitters. Catecholamines are other hormones that are tyrosine derivatives [2].
Overall, pah is a well-researched gene that is involved in many pathways in the body and is involved in many different activities. While it may not be directly responsible for synthesis of products such neurotransmitters or catecholamines, the fact that it is necessary for the production of tyrosine makes it indirectly involved and/or responsible for many more processes than it would have been if tyrosine were not the end-product.
Overall, pah is a well-researched gene that is involved in many pathways in the body and is involved in many different activities. While it may not be directly responsible for synthesis of products such neurotransmitters or catecholamines, the fact that it is necessary for the production of tyrosine makes it indirectly involved and/or responsible for many more processes than it would have been if tyrosine were not the end-product.
References
1. The Gene Ontology Consortium. Gene ontology: tool for the unification of biology. Nat. Genet.. May 2000;25(1):25-9. http://www.geneontology.org/
2."Catecholamines - Blood: MedlinePlus Medical Encyclopedia." U.S. National Library of Medicine, 1 Feb. 2011. Web. 20 Mar. 2013. <http://www.nlm.nih.gov/medlineplus/ency/article/003561.htm>.
2."Catecholamines - Blood: MedlinePlus Medical Encyclopedia." U.S. National Library of Medicine, 1 Feb. 2011. Web. 20 Mar. 2013. <http://www.nlm.nih.gov/medlineplus/ency/article/003561.htm>.