Science Buddies: "Ask an Expert"

Hey! I know what I am trying to ask here is something that is already on the FAQ. Honestly, I'm struggling on finding an adequate research question for this Gel Electrophoresis Experiment. I was thinking of comparing the structure for fruits and veggies, but I can't seem to find the right data on it. If I may ask, is there anything that differentiates the DNA structure of fruits and vegetables(seen through gel electrophoresis)?

And if possible, can you recommend topics and questions to explore on Gel Electrophoresis?

And as for agarose powder, I can't seem to access that, is it fine if I use agar as in the powder you use for jelly?

Thankyou so much for reading this question! Hope you have a great day!

DNA structure is not drastically difference between different species. It's more about differences in sequence. I do not believe this would give you results readable by gel electrophoresis unless you are looking at a specific gene by PCR.

You would probably have more success looking at proteins, perhaps look at what makes the differences in color between certain vegetables and fruits.

Thanks for the reply,

if I may ask, how do we extract protein from vegetables and fruits? (this needs to be DIY if possible, or using school lab tools)
I discussed with my teacher just now, he told me to use different egg whites (through egg protein powder), is that acceptable?

"to what extent does the difference in protein powder impact the rate of gel electrophoresis?" Is my research question if I were to use protein powder.

If my idea is ok, do I just have to dilute the powder with water and put some droplets on my gel electrophoresis chamber?

Thank you for reading and have a great day

to add on my previous question, i would like to find out more about the plant samples.

"Use your gel electrophoresis chamber to determine if two different types of plants use the same molecule for pigment. To prepare your samples, take the flowers from a plant, grind up the flower, add a little bit of isopropyl alcohol, and continue grinding. Once the solids settle, pour the pigment-tinted alcohol into a separate container. Let most of the alcohol evaporate and then add a drop or two of your buffer solution to reconstitute the pigment."

How will the results look like? Will the difference be in terms of length or color?

Hey!

Today, I opened up the project about "Forensic Science: Building Your Own Tool for Identifying DNA" and I was thinking of making this my lab experiment. However, I wanted to make the experiment legit, so I ended up opening the "Make It Your Own" tab.

one of the choices intrigued me. It was "Use your gel electrophoresis chamber to determine if two different types of plants use the same molecule for pigment. To prepare your samples, take the flowers from a plant, grind up the flower, add a little bit of isopropyl alcohol, and continue grinding. Once the solids settle, pour the pigment-tinted alcohol into a separate container. Let most of the alcohol evaporate and then add a drop or two of your buffer solution to reconstitute the pigment."

I was wondering about which part of the substance will be inserted into the chamber? what does the term "use the same molecule for pigment" mean? (is it the isopropyl alcohol) do I have to grind the flower until it's completely liquified?

thankyou for reading and please answer ASAP!

Hello StrugglingStudent,

I've merged your most recent post in with the thread for your previous posts on the same topic. Keeping your similar posts together makes it easier for the expert who has been helping you to see that you have posted follow-up questions. Thank you for your patience!

Correlating to my previous question,

i grinded the flower and added some isoproply alcohol. However it isnt as liquified as water, and it kind of has a "sauce" like feel. Is this supposed to happen? i'll attatch the picture of it with this message. should i add some water?

Hi, I'm glad you've decided to work with gel electrophoresis, it can be fun!

Based on the protocol you posted, it sounds like you're trying to get the pigments suspended in the alcohol. They want you to have a liquidy solution, where the solids settle to the bottom. So I would put your flower goo in a clear glass (as skinny as possible) so you can see it from the side, and add a tablespoon of alcohol. Stir it, and let it sit. Look at it from the side, and see if you have an obvious liquid layer (it will be mostly clear, with no goop in it). If you don't, add another TEAspoon of alcohol, and repeat the process. Do this until you have a very small liquid layer - maybe a couple mm deep.

I'm suggesting you do it this way because you need very little liquid to load into your gel, and you want your pigments as concentrated as possible.

I hope this helps! Keep asking us questions as you go along.

Hello again, I'm realizing I didn't answer all of your questions from above. I also just realized that you're using white flowers, and that isn't going to work for this experiment.
You should take a look at this website:
https://www.gardeningknowhow.com/orname ... e-from.htm

But on a basic level, plants make different molecules (the pigments) in their flowers which absorb different colors of light. All light that isn't absorbed is reflected, and looks a certain color to our eyes. However, white flowers appear white because they are reflecting all of the light; they don't contain the pigments you're looking for in your experiment.

So, you'll need to start over with BRIGHTLY colored flowers. You'll want to do this with at least 2 different colored flowers, ground up separately and loaded into different wells, so you can compare the bands you get - that's the idea behind the experiment.

Another point: when you grind your flowers, you're trying to free the pigment molecules and get them dissolved into the alcohol. So the alcohol you collect needs to be colored - otherwise you haven't extracted the molecules you want for this experiment. So if you don't get great results with isopropyl alcohol, try methanol (your science teacher should be able to get you some, if you can't find it at the store). From what I can tell, methanol is a good solvent for these molecules (but not water).


You can look up the pigments mentioned in the article, and look at their structure (wikipedia is easiest for this). Then you can even make a hypothesis - based on their structure, which do you think will move most easily through the 'net' formed by your gel? Molecules that slip easily through the gel will end up farther down the gel.


I hope this helps!

Hey, thanks for the reply

i'm kinda confused with my results cause the flower pigments didnt move although the chamber was working just fine and the electrodes are correct.

I was wondering whether this was due to the fact that anthocyanins are positively charged.... and im quite confused of what research question i should make for this project. I know you guys can't help me that much on this, but i was wondering on how this project "electrophoresis of flower pigments" is significant towards real life (the correlation) and what will i be comparing (the effect of .... on....)

would it be better if i tested the 4 types of anthocyanins as mentioned in this website
http://www.biologydiscussion.com/plants ... nins/25272
through electrophoresis?

thankyou and please reply asap because my experiment paper is due tomorrow.....

This may be too late, sorry about that. I would say that its definitely worth a try to switch your electrodes and see if your pigments move, as anthocyanins can apparently be cations. However, if nothing left the well in the wrong direction (started moving toward the negative electrode) this may not be a charge issue.
Can you send me your complete protocol? Including the answers to:
What flowers are you using?
Are you sure your pigments are staying in the well and not dispersing into the buffer?
How long did you let the gel run, at what voltage?
What are you using as your buffer?

As far as the relevance of this, and actually doing an experiment instead of just an observation, that partly depends on how long you have to complete the experiment (or is the whole thing due today? The things that come to mind first for me are more long term; eg how does x additive given to a plant affect pigmentation levels... and the additives could be of scientific interest. So let me know your timeline, and we'll figure something out.
Sorry I didn't get this yesterday!

What flowers are you using?
purple roses and the magnolia champaca flower (yellow) (you can search these up)
Are you sure your pigments are staying in the well and not dispersing into the buffer?
unfortunately they are dispersing into the buffer, so i didnt know what to do, ended up using food dye. However, the food dye didnt move much either.....
How long did you let the gel run, at what voltage?
i added 10-9volt batteries :')
What are you using as your buffer?
baking soda + deionized water (ph 7 water)

i'm feeling kinda hopeless now cause the assignment was supposed to be due last night, but here i am now, 4 am, still typing :')

Good grief, I'm sorry I missed your reply; I'm frustrated because I had it tagged to tell me if replies were posted...
Anyway, it sucks that this has been such a problematic project.
It sounds like the protocol for using flowers needed to include mixing your pigments with something that would make them sink (glycerol is what is frequently used).
When you used the food coloring, did bubbles form in your buffer near the electrodes? If not, the batteries may have needed replacing.
Anyway, this is beside the point if you've already turned it in. But don't be too discouraged; this is how real science goes. Sometimes experiments fail over and over, and you have to keep looking for ways to tweak it.
If you're still writing, let me know if you have questions about how to write this up.