11. You are searching for a gene that traces its ancestry to an ancient gene in fish. Evolutionarily older fish, like the coelacanth, have only one copy of this gene. More modern fish, like a three-spine stickleback, have three. Modern humans and mammals have no homologous sequence.
A. Name the gel-based assay that would allow you to see the number of copies of this gene each of your sample organisms has.
The gel-based assay you can use to determine the number of copies of this gene is called PCR (Polymerase Chain Reaction). Here is how you can use PCR to identify the number of copies of the gene in your sample organisms:
1. Collect samples from the organisms you want to study. In this case, you would need samples from ancient fish like the coelacanth, modern fish like the three-spine stickleback, and modern humans or mammals.
2. Extract the DNA from the samples. This can be done using various DNA extraction techniques depending on the source of the sample.
3. Design primers specific to the gene you are interested in. Primers are short DNA sequences that bind to specific regions on the DNA molecule, allowing PCR to amplify the gene in question. In this case, you would design primers that specifically target the gene with multiple copies in modern fish.
4. Set up a PCR reaction by combining the extracted DNA, primers, nucleotides (building blocks of DNA), and a DNA polymerase enzyme. The DNA polymerase enzyme will amplify the target gene using the primers as a guide.
5. Run the PCR reaction in a thermal cycler. The thermal cycler repeatedly heats and cools the reaction mixture to facilitate the different steps of PCR amplification.
6. Analyze the PCR products on an agarose gel. Agarose gel electrophoresis is a technique that separates DNA fragments based on their size. By comparing the sizes of the PCR products, you can determine the number of copies of the gene in each sample organism.
7. Visualize the results by staining the DNA with a fluorescent dye or using other detection methods. This will allow you to see the bands on the gel corresponding to the PCR products.
8. Compare the banding pattern of the different samples. Based on the number and size of the bands, you can determine the number of copies of the gene present in each organism. For example, the coelacanth should show one band indicating a single copy while the three-spine stickleback should show three bands indicating three copies of the gene.
By using the PCR technique and analyzing the results on an agarose gel, you will be able to see the number of copies of this gene in each of your sample organisms.