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BISC110/S11: Lab 6 Taster SNP1: Difference between revisions
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BISC110/S11: Lab 6 Taster SNP1 (view source)
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(New page: {{Template:BISC110/S11}} <div style="padding: 10px; width: 725px; border: 5px solid #9966ff;"> =='''Introduction'''== In the 1930’s Arthur Fox, a chemist at Dupont, synthesized phenylth...) |
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In the 1930’s Arthur Fox, a chemist at Dupont, synthesized phenylthiocarbamide (PTC). While transferring the compound to a bottle he generated a cloud of PTC dust which elicited a dramatic response in his lab mate. Although Fox tasted nothing, his colleague, C. R. Noller, complained that the dust was intensely bitter. (Arthur L. Fox’s original 1932 paper, ''The Relationship Between Chemical Constitution and Health'', can be read at the web site of the journal, [http://www.pnas.org/content/18/1/115.full.pdf+html?sid=ef417f77-b941-4e61-ba96-a412c980cd43 ''The Proceedings of the National Academy of Science'']). | In the 1930’s Arthur Fox, a chemist at Dupont, synthesized phenylthiocarbamide (PTC). While transferring the compound to a bottle he generated a cloud of PTC dust which elicited a dramatic response in his lab mate. Although Fox tasted nothing, his colleague, C. R. Noller, complained that the dust was intensely bitter. (Arthur L. Fox’s original 1932 paper, ''The Relationship Between Chemical Constitution and Health'', can be read at the web site of the journal, [http://www.pnas.org/content/18/1/115.full.pdf+html?sid=ef417f77-b941-4e61-ba96-a412c980cd43 ''The Proceedings of the National Academy of Science'']). | ||
Since Fox's serendipitous discovery, variation in the ability to taste PTC (and other related bitter compounds such as those found in broccoli!) has become one of the most studied of human genetic traits. On the surface, PTC sensitivity appears to be inherited as a simple Mendelian trait with two alleles, T for taster and t for nontaster; in reality its inheritance is much more complicated. Today we know that PTC sensitivity is mediated by the PTC gene (aka TAS2R38) that encodes a bitter taste receptor (a heteromeric G-protein coupled receptor to be exact) which is found on the surface of cells of the tongue. Kim et. al.(2003), published a ground-breaking paper entitled, ''Positional Cloning of the Human Quantitative Trait Locus Underlying Taste Sensitivity to Phenylthiocarbamide'', in the journal ''Science'', which can be downloaded in PDF form through the Wellesley College Library's on-line subscription to | Since Fox's serendipitous discovery, variation in the ability to taste PTC (and other related bitter compounds such as those found in broccoli!) has become one of the most studied of human genetic traits. On the surface, PTC sensitivity appears to be inherited as a simple Mendelian trait with two alleles, T for taster and t for nontaster; in reality its inheritance is much more complicated. Today we know that PTC sensitivity is mediated by the PTC gene (aka TAS2R38) that encodes a bitter taste receptor (a heteromeric G-protein coupled receptor to be exact) which is found on the surface of cells of the tongue. Kim et. al.(2003), published a ground-breaking paper entitled, ''Positional Cloning of the Human Quantitative Trait Locus Underlying Taste Sensitivity to Phenylthiocarbamide'', in the journal ''Science'', which can be downloaded in PDF form through the Wellesley College Library's on-line subscription to [http://0-www.sciencemag.org.luna.wellesley.edu/cgi/reprint/299/5610/1221.pdf ''Science'']. To learn even more about the PTC gene, check out the [http://chemse.oxfordjournals.org/cgi/content/full/31/7/599 review article by Kim and Drayna (2006)] and another [http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=16636110 review by S. Wooding (2006)]. You should also view the video [http://www.pbs.org/wgbh/nova/sciencenow/0404/01.html “The Science of Picky Eaters”].<br><br> | ||
Additional studies of the PTC gene in humans across the globe have revealed that there are two common alleles, taster and nontaster; however, there are at least five other rare alleles that affect the taster phenotype. These different forms of the gene code for proteins that vary in their ability to bind bitter compounds such as PTC. The two common alleles of the PTC gene differ by three single nucleotide polymorphisms (SNPs) which are shown below. SNPs ( | Additional studies of the PTC gene in humans across the globe have revealed that there are two common alleles, taster and nontaster; however, there are at least five other rare alleles that affect the taster phenotype. These different forms of the gene code for proteins that vary in their ability to bind bitter compounds such as PTC. The two common alleles of the PTC gene differ by three single nucleotide polymorphisms (SNPs) which are shown below. SNPs (pronounced “snips”) represent the simplest type of genetic variation between individuals. A SNP refers to a specific location in the genome where different people have been shown to have a different nucleotide. If more than one percent of the population has a different base at a particular location, that location is considered a SNP. If less than one percent of the population has a different base, it is considered a mutation. <br><br> | ||
<center>'''Polymorphic Sites in the PTC Taster Gene''' | <center>'''Polymorphic Sites in the PTC Taster Gene''' | ||
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The common nontaster allele (or haplotype) has a G at nucleotide position 145 (G145), T at position 785 (T785) and A at position 886 (A886). This nontaster allele produces a polypeptide with alanine, valine and isoleucine at these sites and therefore is referred to as the AVI allele. The common taster allele has C145, C785, and G886, produces a polypeptide with proline, alanine, and valine at these sites, and is referred to as the PAV allele.<br> | The common nontaster allele (or haplotype) has a G at nucleotide position 145 (G145), T at position 785 (T785) and A at position 886 (A886). This nontaster allele produces a polypeptide with alanine, valine and isoleucine at these sites and therefore is referred to as the AVI allele. The common taster allele has C145, C785, and G886, produces a polypeptide with proline, alanine, and valine at these sites, and is referred to as the PAV allele.<br> | ||
The SNP at position 785 is useful for determining your PTC genotype since the taster sequence in this region forms a Fnu4H1 restriction site while replacing C785 with T785 in the nontaster allele eliminates this restriction site. (A restriction site is a specific DNA sequence that is recognized and cleaved by a specific restriction enzyme or endonuclease.) There are two other Fnu4H1 restriction sites within the PTC gene, but we will use primers specifically designed to bind to regions flanking the one polymorphic Fnu4H1 site while excluding the other two. Using these primers in a polymerase chain reaction (PCR) generates a 303 base pair (bp) fragment. Restriction digestion of this PCR product with Fnu4H1 will yield one 303 bp fragment for the nontaster allele and two shorter fragments (65 bp and 239 bp) for the taster allele. Visit the following web site to learn more about PCR and see an animation of how it works | The SNP at position 785 is useful for determining your PTC genotype since the taster sequence in this region forms a Fnu4H1 restriction site while replacing C785 with T785 in the nontaster allele eliminates this restriction site. (A restriction site is a specific DNA sequence that is recognized and cleaved by a specific restriction enzyme or endonuclease.) There are two other Fnu4H1 restriction sites within the PTC gene, but we will use primers specifically designed to bind to regions flanking the one polymorphic Fnu4H1 site while excluding the other two. Using these primers in a polymerase chain reaction (PCR) generates a 303 base pair (bp) fragment. Restriction digestion of this PCR product with Fnu4H1 will yield one 303 bp fragment for the nontaster allele and two shorter fragments (65 bp and 239 bp) for the taster allele. Visit the following [dnalc.org//ddnalc/resources/pcr.html web site] to learn more about PCR and see an animation of how it works.<br><br> | ||
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