PLEASE HELP!!IDEA DUE THURSDAY!

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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Sun Nov 25, 2012 6:39 pm

Hi Pinkbear,

That’s great news. I’m glad your electrophoresis chamber works. You want to load a sample that’s as concentrated as possible, so look for an intense color similar to the food dye.

You will not be separating DNA at all, just plant pigments. So your problem will be "what pigments are found in different colored flowers," or "are the same plant pigments found in different colored flowers." or something similar. If you were compared different species of red flowers, your question would be, "do red flowers contain the same plant pigment.."

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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby pinkbear » Mon Nov 26, 2012 2:04 pm

Sorry, but isnt measuring the size of dna fragments measured in gel elctrophoresis? In my reasearch, it said the size of the dna fragments are what varied the bands of colors length from the origin. Im a little confused...?
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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Mon Nov 26, 2012 2:51 pm

Hi Pinkbear,

Sorry I did not include more detail. DNA is the molecule found in a cell nucleus that can vary in size and always has a negative charge. The traditional method to separate DNA fragments is by agarose gel electrophoresis. The gel module you are using was designed for this application.

http://en.wikipedia.org/wiki/Gel_electr ... leic_acids

However, electrophoresis is a general technique that can be used to separate any type of charged molecule.

http://en.wikipedia.org/wiki/Electrophoresis

You are purifying anthocyanins. Look at the structure of the anthocyanins in the link below. The ring structures are composed of carbon and hydrogen, the R groups are usually sugar molecules, which are composed of carbon, hydrogen, and oxygen and have a neutral charge. Notice that there is an oxygen with a positive charge in the molecule. The molecular weight is about 450 Daltons.

http://en.wikipedia.org/wiki/Anthocyanin

Here is the structure of DNA. Notice all of the phosphorus atoms on the molecule; these all have a negative charge and the molecule is much larger, up to several million Daltons.

http://en.wikipedia.org/wiki/DNA

As I recall, you did not want to do the DNA project because DNA is colorless and you would have to stain the DNA molecules with a DNA specific stain. Since you wanted to separate molecules that were already colored, you chose flower pigments. So you are using the same technique that is used for DNA separations, however, your basic application is different.

I see that your project deadline is coming soon, so you will need to revise whatever background information you have written and make sure your project board refers to plant pigments/anthocyanins and not to DNA. With your extraction protocol, I would not expect there would be any DNA at all in the samples. Since the anthocyanins are positively charged, not negatively charged like the DNA and food coloring, you will need to run the gel in the opposite direction compared to the food colors.

Does this help? If not, then post more questions. I want to make sure you understand all of the details before you put your project board together. You need to be able to explain the science behind your project to the science fair judges.

Donna Hardy
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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby pinkbear » Mon Nov 26, 2012 3:08 pm

So far since im basing my sfp on this http://www.usc.edu/CSSF/History/2009/Projects/J0403.pdf, this contains basically everything that im doing. For the reversing and putting the pigments opposite to were it was, im slighty confuzzled. When i ran the project i mixed a couple flower petals into the dye, and they still migrated to the negative end, and how is their a specefic distinction between the positive & negative ends? thanks
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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Mon Nov 26, 2012 4:20 pm

Hi Pinkbear,

This is helpful. Pansies get their purple color from anthocyanins, so this experiment should work for you also. There is no description of the polarity of the electrodes in the experiments described in the summary. If the pigments migrated towards the anode in your pilot experiment, then do go ahead and set up your next experiment the same way. I was basing my suggestion on my experience with protein electrophoresis, and I have never done the experiment that you are doing.

With proteins, if they have a net positive charge, then it is necessary to reverse the polarity of the electrophoresis module. However, it could be that the plant pigments have enough polarity that they will migrate towards the anode. You will verify what will happen with your results.

Go ahead and set up the experiment with the different colored geraniums petal extracts and let me know what happens. Will you be able to take a photograph of the gel as the colored bands migrate through the gel? If not, then measure the distance of each colored band from the origin every 15-20 minutes, if you can, in centimeters.


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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby pinkbear » Wed Nov 28, 2012 2:02 pm

ok so went through one trial, but the steel wire at the negative end (or whatever the pigments migrate to) got like, rusty! Um, what thhe heck happened,lol! anyway, since NOW im all out of steel wire were would you suggest i find some? also, since im trying to set up my board, i want to get the title out of the way. Would "The Molecular Migration of Plant Pigments" work? Thaaaaaaanks!
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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Thu Nov 29, 2012 10:27 am

Hi Pinkbear,

Your electrode corroded, and this can happen with inexpensive electrodes. Electrodes on regular laboratory equipment are made of platinum, but using this metal would have made the kit prohibitively expensive.

The electrode is probably made from a paper clip, so try to find some more paper clips that are the same size as the ones included in the kit. If you can find galvanized paper clips, they will be more resistant to corrosion. I recommend changing the electrodes for every run.

Are you using the bicarbonate buffer that is recommended? If there are any chloride ions in your sample or buffer, this would accelerate the corrosion.

It's good that you are working on your board. "Molecular Migration of Plant Pigments," is a nice title. I like the alliteration. You can add a subtitle with the research questions in smaller type, such as "how many plant pigments do geraniums contain?" of "how is geranium color related to plant pigments?"

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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Sun Dec 02, 2012 10:32 am

Hi Pinkbear.

How are your doing? Have you had a chance to repeat your experiment with new paper clips?

One of the good things about having unexpected results is that it gives you an opportunity to include more scientific information in your discussion and conclusion section. Here is a Science Buddies project on corrosion. There is helpful information in the discussion and references that explain the rusting process that you observed with your electrodes.

http://www.sciencebuddies.org/science-f ... background

The paper clip contains elemental iron, Fe. The Wikipedia article includes chemical equations for the oxidation of Fe to FeIII, or iron oxide.

http://en.wikipedia.org/wiki/Rust

The question is why did the electrode rust so quickly?

So, you have actually done two science experiments Let me know if you have any questions.


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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby pinkbear » Sun Dec 09, 2012 2:16 pm

hi, im wondering is my project including gel electrophoresis or molecular migration? Im just going to include my findings about the plant pigments. Thanks!
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Re: PLEASE HELP!!IDEA DUE THURSDAY!

Postby donnahardy2 » Sun Dec 09, 2012 6:57 pm

Hi Pinkbear,

In your project you used gel electrophoresis as a technique to separate the plant pigments, which are molecules. In gel electrophoresis, molecules migrate in an electrical field, based on charge and molecular weight.

Does this help?

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