Genetics of Amylase: Analyzing Chewing Starch Results

EXERCISE NINE: GENETICS AND CHEWING THE STARCH WORKSHEET Name Section Date Salivary Amylase Assay Results (8 points) Fill out the table with readings from the standard curve done by the instructor, and the reading from your sample. Table One. Amylase Assay Results Units/mL Absorbance (405 nm) 0 0 59.7 0.14 119.4 0.25 179.1 0.41 238.8 0.53 298.5 0.6 358.2 0.79 417.9 0.96 477.6 1.13 Your Sample Ex. 9 Chewing the Starch Worksheet- 1

PASTE IN THE STANDARD CURVE FOR AMYLASE FROM AN EXCEL SHEET YOU CONSTRUCT. RESIZE TO BE FIT WITHIN THIS BOX (No greater than~7” X 7”) Figure One. Standard Curve fore Amylase Assay What is the formula for the regression line? _____________________ What is the r 2 value for the line? __________ What does the r2 value tell you about this line? X in the regression line is the amount of amylase while Y is the absorbance. Rearrange the formula: X = ___________. What is the concentration of amylase in your sample based the formula? _____ Ex. 9 Chewing the Starch Worksheet- 2

PASTE IN THE CALIBRATION CURVE FOR AMYLASE ACTIVITY VERSUS COPY NUMBER FROM YOUR INSTRUCTOR’S EXCEL SHEET. RESIZE TO BE FIT WITHIN THIS BOX (No greater than~7” X 7”) Figure Two. Calibration Curve for Amylase Copy Number What is the formula for the regression line? _____________________ What is the r 2 value for the line? __________. What does the r2 value tell you about this line? X in the regression line is copy number while Y is the units. Rearrange the formula: X = ___________. What is the copy number for amylase in your sample based the formula? _____* *No one has a copy number of zero. If your number is less than 1, put in 1. Ex. 9 Chewing the Starch Worksheet- 3

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PASTE IN THE HISTOGRAM GRAPH FOR AMYLASE FROM YOUR INSTRUCTOR’S EXCEL SHEET. RESIZE TO BE FIT WITHIN THIS BOX (No greater than~5” X ”) Figure Three. Class Amylase Copy Number Distribution What is the range of copy numbers in the class? What is the sample size? What is the mean copy number for the class? What is the most common copy number? Ex. 9 Chewing the Starch Worksheet- 4

Salivary Amylase Assay Analysis (8 points) Population Data Figure Two from the reading is on the checklist. It shows amylase gene distributions for different populations. Write a short answer addressing the following points. Which population does your class distribution most resemble? Does this fit with the self-assessed heritage of your class? If it does not what is a possible reason? Individual Data The reading discussed the possible physiological effects of having low (1-3) or high copy ( 4 or greater) numbers of the amylase gene. Write a short answer addressing the following points. Do you fall into a low or high copy number group? What health advice applies to you based on your copy number and the information in the reading? Amylase Genetics The amylase genes are close together on chromosome one. Since they are close together, the genes on one chromosome are rarely affected by recombination in Prophase I of Meiosis. For genes like this, each chromosome has a haplotype which, in this case, is the simply the number of amylase genes on one chromosome. Using shorthand, the haplotype for one chromosome could be AMY 5 and for the other chromosome, AMY 6. The genotype would be AMY 5/AMY 6. Figure Four below shows common haplotypes found in a European population. The most common haplotypes have an odd number of AMY1 genes. Ex. 9 Chewing the Starch Worksheet- 5

Figure Four. Common Amylase Haplotypes in a European Population. Modified from Figure One from Usher et al (Usher et al., 2015, Structural Forms of the Human Amylase Locus and their Relationships to SNPs, haplotypes, and obesity, Nat Genet 47(8): 921-925). The figure above shows that for AMY 1 there are haplotypes that have 1, 2, 3, 4, 5, or 7 copies. Of course, each person has two copies of the chromosome which carries the amylase gene. A person with a TOTAL copy number of 6 could have a haplotype of 3,3 since this adds up to 6. But they could also be 4,2. Can you use these numbers to come up with what your haplotype might be? _________ (Put in Yes or No) If Yes, what are your possible haplotypes? My total copy number is _____. My haplotype(s) could be If NO, what type of haplotype copy numbers would you need? My total copy number is _____. To get this number I would need a chromosome that was ____ and a chromosome that was _____. Using a Punnett Square to Predict Possible Offspring. A Punnett Square is a simple way to use genotypes to predict the possible offspring from a genetic cross. See the Amoeba Sisters video for an example of a monohybrid cross. For the AMY1 locus, the haplotypes act like a single allele since recombination (crossing over) rarely separates these during meiosis. Your instructor will help you pick two parents to do a Punnett Square cross. Ex. 9 Chewing the Starch Worksheet- 6

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What are the genotypes of the parents? _________ X ________ Draw out the Punnett Square for this cross. We can classify salivary amylase phenotypes into low (2-3), medium (4-6) and high groups (7+) So your possible offspring can be categorized both for total number of AMY1 genes and which group they are in. List the possible offspring from your cross, there total number of AMY1 genes and which group they fall into. Is it possible to have offspring that are higher or lower than the parents? _________ (Put in Yes, No or Maybe) Explain why or why not? Ex. 9 Chewing the Starch Worksheet- 7

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