Exploring the Genetics of Taste: SNP Analysis of the PTC Gene Using PCR EDVOTEK® WORKSHOP Introduction Explore the relationship between genotype and phenotype using Phenylthiocarbamide (PTC). Some think PTC tastes bitter, while others fi nd it tasteless. The ability to taste PTC has been linked to varia- tions in a taste receptor gene. In this workshop, you will learn to use PCR to distinguish between PTC alleles. Receive a fl ash drive/ entry in a T-shirt drawing.. Table of Contents Page Background Information 2 Experiment Overview 7 Experiment Procedures 8 Experiment Results and Analysis 12 Related Products 12 Exploring the Genetics of Taste Excerpts from Edvokit 345 SINGLE NUCLEOTIDE POLYMORPHISMS (SNPS) A G Single Nucleotide Polymorphisms (SNPs) are DNA sequence variations that occur in T C the genome sequence when a single nucleotide is altered. The genetic code is speci- C T fi ed by the four nucleotide letters: A (Adenine), C (Cytosine), T (Thymine), and G A (Guanine). SNP occurs when a single nucleotide, such as a T, replaces one of the other G C three nucleotides A, G, or C (Figure 1). Each person has many SNPs that together cre- G ate a unique DNA fi ngerprint profi le for that individual. 1 SNPs may fall within any region of the genome – the coding sequences of genes, the noncoding sequences of genes, or regions in-between genes (the intergenic regions). SNP When an SNP falls within a coding sequence, that alteration may not necessarily 2 change the amino acid sequence of the subsequent protein produced due to degen- eracy of the genetic code. On the other hand, SNPs that do not fall into a coding A G sequence may still affect that region of DNA in such a way by inducing gene splicing, C T transcription factor binding, or by altering the sequence of non-coding RNA. T T A Variations in our DNA sequences can affect many aspects of human physiology - how C A we develop diseases, respond to pathogens, process chemicals, drugs , and many G more. For example, sickle cell anaemia is caused by a single nucleotide mutation in the ß-globin chain of hemoglobin. This, in turn, causes the hydrophilic amino acid glutamic acid to be replaced with the hydrophobic amino acid valine, thus alter- ing the shape of the blood cells. Instead of having the usual disc-like shape that is Figure 1: Single Nucleotide fl exible, enabling them the pass even the smallest blood vessels, sickle cells are long Polymorphism (SNP) occurs “sickle-shaped” red blood cells that block the fl ow of blood through the blood ves- at a single base-pair location sels. Sickle cells can lead to various complications, including acute chest syndrome, (C/T). organ damage, gallstone, and stroke. 2 VISIT www.edvotek.com for complete experiment details & free student protocols. EDVOTEK® WORKSHOP Exploring the Genetics of Taste: SNP Analysis of the PTC Gene Using PCR THE BITTER TASTE AND THE BITTER COMPOUND PHENYLTHIOCARBAMIDE (PTC) Individuals vary greatly in their sensitivity to the bitter compound Phenylthiocarbamide (PTC). This is one of the best-known genetic traits in the human population and has been a popular teach- ing tool for genetic inheritance. In this experiment, we examine variable regions to distinguish differences in individuals by identifying two different forms (alleles) of a gene related to one’s ability to taste PTC (Figure 2). The famous European geneticist Professor Ed V. Otek, tested his rather large genet- ics class of students for the ability to taste PTC. He discovered that this gene has two alleles: the dominant allele (T), which confers the ability to taste PTC, and the recessive non-taster allele (t). A person inherits one copy of the gene from each of his / her parents. The combination of these different alleles within an individual is Figure 2: referred to as a genotype, which in turn dictates the phenotype: in this case, wheth- The structure of PTC. er an individual is a “taster” or “non taster.” PTC-tasters have one of two possible genotypes; either they are homozygous dominant and have two copies of the taster allele (TT), or they are heterozygous and have one taster allele and one non-taster allele (Tt). “Non-tasters” are homozygous recessive and have two copies of the non-taster allele (tt). Within the general population, about 70% of the people tested can taste PTC, whereas the other 30% cannot. THE PTC SENSITIVITY GENE – TAS2R38 Studies show that there is an inherited component that effects how people taste PTC. In 2003, more than 70 years after its original discovery, the gene responsible for PTC sensitivity, TAS2R38, was identifi ed. Analysis of SNPs within the coding region of TAS2R38 revealed that PTC taster and non-taster alleles differ in 3 amino acids. There are two common forms (or alleles) of the PTC gene: a dominant tasting allele and a recessive non-tasting allele. The shape of the receptor protein determines how strongly it can bind to PTC. Since all people have two copies of every gene, combinations of the alleles determine whether someone fi nds PTC intensely bitter, some- what bitter, or tasteless. As discussed earlier, there are 3 positions within the gene that control the ability to taste PTC (as shown in table below). Nucleotide Change in Nucleotide Change in Codon Change in Amino Acid Table I - Relation- Position (Nontaster > Taster) (Nontaster > Taster) (Nontaster > Taster) ship of Variations 145 G > C GCA > CCA Alanine > Proline at Specifi c loca- tions in TAS2R38 785 T > C GTT > GCT Valine > Alanine gene and Ability to Taste PCR. 886 A > G ATC > GTC Valine > Isoleucine RESTRICTION ENZYME DIGESTION Restriction enzymes are endonucleases which catalyze the cleavage of the phosphate bonds within both strands of DNA. The distinguishing feature of restriction enzymes is that they only cut at very specifi c sequences of bases. A single base change in the recognition results in the inability of the restriction enzyme to cut the DNA at that sequence location. Differences in the sequence of DNA at that specifi c location can be quickly identifi ed using restriction enzyme digestion. A restriction enzyme requires a specifi c double-stranded recognition sequence of nucleotide bases to cut DNA. Recognition sites are usually 4 to 8 base pairs in length. Cleavage occurs within or near the site. Recognition sites are frequently symmetrical, i.e., both DNA strands in the site have the same base sequence when read 5’ to 3’. Such sequences are called palindromes. CONTACT US? CALL 1.800.EDVOTEK • Fax 202-370-1501 • email [email protected] 3 Exploring the Genetics of Taste: SNP Analysis of the PTC Gene Using PCR EDVOTEK® WORKSHOP Homozygous Taster (TT) Heterozygous Taster (Tt) Non-Taster (tt) Extraction of DNA Extraction of DNA Extraction of DNA from Buccal cells from Buccal cells from Buccal cells PCR Amplification of PCR Amplification of PCR Amplification of PTC region PTC region PTC region GGCGGCCACT GGCGGGCACT GGCGGGCACT PCR Product 221 bp PCR Product 221 bp PCR Product 221 bp Hae III Restriction Digest Hae III Restriction Digest Hae III Restriction Digest GGCGG CCACT GGCGG CCACT GGCGGGCACT Figure 3: Agarose Gel Electrophoresis Agarose Gel Electrophoresis Agarose Gel Electrophoresis Determining PTC Genotype 44 bp Fragment 44 bp Fragment 221 bp Fragment 177 bp Fragment 177 bp Fragment (remains uncut) 221 bp Fragment Lane 1 Lane 2 Lane 3 (TT) (Tt) (tt) PTC TASTER: Homozygous Taster (TT) = sizes of 177 & 44 bp Heterozygous Taster (Tt) = 1 allele remains uncut at 221bp while 221 bp Fragment the other allele cuts and generates fragments of 177 bp and 44 bp. 177 bp Fragment PTC NON-TASTER: 44 bp Fragment Homozygous recessive (tt) = remains uncut at 221 bp Consider the recognition site and cleavage pattern of EcoRI and HaeIII below. The cleavage positions are indicat- ed by arrows. Digestion with EcoRI produces asymmetric “sticky ends”, whereas HaeIII restriction enzyme cleav- age produces “blunt’ ends. Cleavage pattern of EcoRI: ↓ 5’-GAATTC-3’ Eco RI 5’-G AATTC-3’ 3’-CTTAAG-5’ Digestion 3’-CTTAA G-5’ ↑ Cleavage pattern of HaeIII: 5’-GG CC-3’ 5’-GG and CC-3’ 3’-CC GG-5’ 3’-CC and GG-5’ In the example of the PTC gene, HaeIII only cuts the taster allele (5’-GGCGGCCACT-3’). The polymorphism present in the non- taster allele (5’-GGCGGGCACT-3’) changes a single base change in the restriction enzyme recognition site, so HaeIII can not digest non-taster DNA. THE POLYMERASE CHAIN REACTION (PCR) The PCR reaction is a DNA amplifi cation technique that revolutionized almost all aspects of biological research. The procedure was invented by Dr. Kary Mullis while at Cetus Corporation in 1984. Dr. Mullis was awarded a Nobel Prize for his work in 1994. PCR amplifi cation can produce millions of copies from a small quantity of DNA. The enormous utility of PCR is based on its procedural simplicity and specifi city. Since the fi rst application of PCR to diagnose sickle cell anemia, a large number of amplifi cations have successfully been developed. PCR has made amplifi cation of DNA an effective alternative to cloning. It is currently routinely used in forensics, paternity/kinship testing, and the identifi cation of human remains. 4 VISIT www.edvotek.com for complete experiment details & free student protocols. EDVOTEK® WORKSHOP Exploring the Genetics of Taste: SNP Analysis of the PTC Gene Using PCR In preparation for PCR amplifi cation, a set of two DNA “primers” are designed to target a specifi c region of the genomic sequence containing the gene of interest. The primers are two synthetic oligonucleotides typically 15-30 base pairs in length that are synthesized so that they correspond to the start and end of a specifi c region of the DNA sequence to be amplifi ed.