BIO 1A03 Post-lab 4 Assignment

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Feb 20, 2024

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Post-Lab 4 Assignment 1. Include a screenshot of your results from the visual electrophoresis activity (your actual results and the ideal results must be visible in your screenshot. (1 mark) 2. Pertaining to Figure 4A-7 Why did the bands of DNA in lanes 2, 3, 4, and 5 migrate approximately the same distances when comparing Student A and Student B? How does this relate to the primer sets and DNA templates that were used during the PCR reaction? (2 marks) The reason why the bands traveled about the same distance is because of the size of fragments in the two DNA samples. If they traveled the same distance, they have the same DNA fragment sizes with similar quantities of DNA nucleotide bases. Since the primers used between the two student DNA contain the same DNA (different quantities), they target the same DNA template and amplify them. 3. Pertaining to Figure 4A-7: What would need to have been done during the gel electrophoresis procedure in order to separate all of the 100 bp ladder bands in the Figure 4A-7 and have them appear as individual bands in the 1.5% agarose gel? (1 mark) To have all of the 100bp ladder bands in Figure 4A-7 appear as individual bands in the 1.5% agarose, the gel would have to be run for a longer period of time. This will allow each 100bp to appear as single bands. 4. Pertaining to Figure 4A-7: Imagine that you repeat the DNA extraction, PCR, and gel electrophoresis experiment using Unknown Student A and B's DNA. After imaging the resulting gel, only the band representing the amylase gene fragment is present in Lane 2. You do not observe a band for the actin gene fragment in Lane 2, but you do observe an actin band in the samples in Lanes 3, 4, and 5. All

four lanes 2-5 have the amylase band. What could possibly explain why you do not see a band for actin in lane 2? (1 mark) One of the reasons that the amylase band was seen but the actin band wasn’t might be due to improper loading techniques. If the pipette contained air bubbles when pipetting lane two or the gel was punctured, it could have led to the actin gene fragment being lost in the gel. It could also be that the actin gene fragment wasnt loaded into the well or not enough of it was loaded to begin with. 5. What are the diploid amylase (AMY1A) gene copy numbers for Unknown Student A and Unknown Student B as calculated from your ImageJ and Excel analysis? Include the table from the excel file that you used to calculate their gene copy number. (2 marks) The AMY1A gene copies for Student A were 3 and were 7 for Student B 6. Attach the scatter plot figure showing the relationship between gene copy number and amylase enzyme concentration that you created using the data in Table 4A-3. Follow the formatting instructions given in this lab manual and in the Excel Tutorial #1 to create a publication quality figure. Don't forget to include a caption with your graph title, sample size, and correlation coefficient (r). (5 marks) Caption: Figure 2: This figure displays the relationship between amylase gene copy numbers and salivary amylase concentration in 21 individuals. (r = 0.67928201)

7. What can you determine from the r value about the relationship between gene copy number and amylase enzyme concentration? (1 mark) Looking at the r-value about the relationship between gene copy number and amylase enzyme concentration can see that there is a moderate positive relationship between these two variables. 8. Do Unknown Student A and Unknown Student B’s self-reported starch levels, AMY1A Gene copy numbers, and salivary amylase concentrations support an association between gene evolution, gene copy number, and amylase enzyme production? Please use Unknown Student A and Unknown Student B’s data to explain and support your choice for the presence or absence of an association. (2 marks) Yes it does. Overall between self reported starch levels (Moderate - Student A, High - B) There does seem to be a relationship between these variables. In Individuals where Self reported starch levels are high, Salivary Amylase concentrations aare also high as a result of an increase in amylase gene copy numbers. In indiviuals where self reported starch levels are moderate or low, Salivary amylase is moderate or low as a result of a moderate or low number of Amylase gene copy numbers. On average a trend between these variables suggest gene evolution between gene copy numbers and amylase enzyme production. 9. Submit your correctly formatted 100 bp ladder standard curve that you created in Excel. Follow the instructions in the tutorial 4 manual and Excel Tutorial #2 to complete your publication-quality figure. (5 marks) 10. What are the lengths of the DNA fragments, in base pairs, for the two bands that are seen in all of lanes 2 to 5 of Figure 4A-7? Show your calculations for both

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bands using the equation of the line generated from your 100bp standard curve. Which base pair value represents the amplified DNA that was targeted by the primers that were specific to a segment of an actin gene? Which base pair value represents the amplified DNA that was targeted by the primers that were specific to a segment of an amylase (AMY1A) gene? (4 marks) Y = 28067e^-0.087x ← This is the equation from my 100bp Standard Curve Actin Fragment Student A (53mm) Y = 28067e^-0.087(53) Y = 279.038 bp DNA Fragment Size ~ 279bp for Student A Actin Fragment Amylase Fragment Student A (63mm) Y = 28067e^-0.087(63) Y = 116.9036 DNA Fragment Size ~ 117bp for Student A Amylase Fragment Actin Fragment Student B (53mm) Y = 28067e^-0.087(53) Y = 279.038 bp DNA Fragment Size ~ 279bp for Student A Actin Fragment Amylase Fragment Student B (63mm) Y = 28067e^-0.087(63) Y = 116.9036 DNA Fragment Size ~ 117bp for Student B Amylase Fragment Grade: /24

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