Science Buddies: "Ask an Expert"

For my science fair project, I'm trying to see whether different flowers use the same molecule for pigment. I'm using electrophoresis, and I don't know which gel I should use. Please help!

Hi there!
The main physical difference in the two types of gels is the pore size i.e. the size of the gaps through which molecules will pass. Think of it as a filter with variable sizes of the outlet. Polyacrylamide has a finer pore size allowing you to separate molecules that are much more similar in size, better. Agarose is less 'selective' due to it's bigger pores and will let molecules of somewhat different sizes also travel together through it (although to different degrees). Further, for each type the actual pore size depends on the concentration of the polymer.

Since you will extract pigments from flowers, I think you could proceed with either one. Agarose is easier to obtain and safer to handle. Acrylamide is a respiratory irritant and requires very careful handling. Alternatively, you could also use thin layer chromatography to separate pigments and it may be easier than electrophoresis. As electrophoresis separates things based on both charge and mass, TLC is better for non-polar i.e. uncharged molecules (and many organic molecules including plant pigments are non-polar) as the separation occurs mainly by mass.

Let me know if you choose to give TLC a shot and need help with finding a protocol.
Good luck with the experiment and definitely write back if you have more questions or need more information.
MS

Thank you for your help! I'll definitely write back if I have any other questions or concerns.

You are very welcome!