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Sizing It Up! How Scientists Separate Proteins

Time Required Average (6-10 days)
Prerequisites Familiarity with how to use a micropipette is needed.
Material Availability This science fair project requires specialty items, including the Bio-Rad Size Exclusion Chromatography Kit and a sample of green fluorescent protein. See the Materials and Equipment list for details. It also requires a number of common molecular biology items, such as pipettes, micropipettes and tips, and a UV light—likely obtainable from your school laboratory.
Cost Very High (over $150)
Safety Adult supervision is recommended. Follow all safety instructions that come with the Bio-Rad kit(s).


Have you ever had to sort a jumble of objects into piles, based on their type? Maybe laundry, or a big load of dishes, or while organizing the garage or a closet? Scientists have to do something similar when they want to study or isolate just a single type of protein. For example, a botanist might discover an exotic plant that is poisonous when eaten, but that also has great antibiotic properties. To help develop a new antibiotic for human use, he or she would have to separate the different plant proteins, and research which ones are toxic and which ones help fight off infections. One way scientists do this is by sorting the proteins, based on their size, using a technique called size-exclusion chromatography. In this science fair project, you can try your hand at this biochemical sorting technique and use it to determine the relative size of the green fluorescent protein (GFP).


To determine the relative size of green fluorescent protein (GFP), using size-exclusion chromatography.

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Xiomara Fonseca, Tracy High School Senior

Kirk Brown, Tracy High School Biotechnology Teacher

Laurie Usinger, PhD, Bio-Rad

Edited by Sandra Slutz, PhD, Science Buddies

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Science Buddies Staff. "Sizing It Up! How Scientists Separate Proteins." Science Buddies, 28 July 2017, Accessed 16 Aug. 2018.

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Science Buddies Staff. (2017, July 28). Sizing It Up! How Scientists Separate Proteins. Retrieved from

Last edit date: 2017-07-28


Manufacturing a life-saving drug, studying how the APOE protein contributes to Alzheimer's in humans, researching the effects of a bacterial toxin—these are all real-life instances where a biologist or a biochemist would need to separate a mixture of proteins. How are proteins separated? There are several methods, but one of the simplest ways is size-exclusion chromatography, which uses the size of a protein as a physical means of sorting. Different proteins come in different sizes, much like a grapefruit, an orange, and a lime are all citrus, but you can tell them apart by size alone.

In size-exclusion chromatography, a protein mixture, suspended in a special liquid, is poured into a column. The column, as shown in Figure 1 below, contains a suspension of tiny beads with different-sized macroscopic pores. As the proteins travel through the column, they get tangled in the beads. The larger proteins can fit in fewer pores and thus, have a more direct and quicker path through the beads. In contrast, the smaller proteins can fit through more pores and take a more meandering path as they get caught in various holes and take a longer time to flow through the column. As time passes, the special liquid, called an eluate, drips out of the column and into tubes. The initial drips of eluate contain the larger proteins, which passed through quickly, while the later drips contain the smaller proteins. Changing the collection tube under the column every couple of minutes results in multiple tubes of protein—each tube containing proteins of a different sizes.

Protein mixture eluting through size-exclusion chromatography column

Figure 1. Size-exclusion chromatography columns contain beads with various-sized pores. The larger proteins, which fit in fewer pores, take a more direct path through the column and elute first. The smaller proteins are slower to elute as they meander in and out of pores.

In this science fair project, you'll use size-exclusion chromatography to approximate the size of green fluorescent protein (GFP). GFP, first isolated from the jellyfish Aequorea Victoria, glows green when exposed to blue light. Because of its fluorescent properties, it is often used in cellular and molecular biology to track the expression of genes and the location of other proteins. In such tracking studies, it is important to keep the size of GFP in mind—if it is too large, it might not be able to move into some cellular areas, thus skewing the results of the study. To determine the size of GFP, you'll used a protein size-exclusion chromatography kit from Bio-Rad, which is explained in the Materials and Equipment section, below. The kit contains two other proteins: hemoglobin and vitamin B12. You'll create a mixture of hemoglobin, vitamin B12, and GFP, then sort them with the chromatography column. Since hemoglobin is reddish-brown in color and vitamin B12 appears pink, you'll be able to tell which eluate samples contain each of these proteins. Using a UV light to make the GFP fluoresce, you'll determine which eluate samples contain GFP. From this information, you'll be able to determine the size of GFP, relative to the sizes of hemoglobin and vitamin B12.

Terms and Concepts

  • Size-exclusion chromatography
  • Eluate
  • Green fluorescent protein (GFP)
  • Hemoglobin
  • Vitamin B12
  • Kilodalton


  • How does size-exclusion chromatography work?
  • What are the sizes, in kilodaltons, of hemoglobin and vitamin B12?
  • From where does GFP come?
  • What other methods can be used to separate protein mixtures? What are their advantages and disadvantages?


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Materials and Equipment

Note: If you are carrying out this experiment in a school laboratory, which is recommended, some of the materials and equipment listed below may be more readily accessible. Note: Bio-Rad Kits are sold directly to schools. Please visit this page to learn how to purchase one.

Disclaimer: Science Buddies occasionally provides information (such as part numbers, supplier names, and supplier weblinks) to assist our users in locating specialty items for individual projects. The information is provided solely as a convenience to our users. We do our best to make sure that part numbers and descriptions are accurate when first listed. However, since part numbers do change as items are obsoleted or improved, please send us an email if you run across any parts that are no longer available. We also do our best to make sure that any listed supplier provides prompt, courteous service. Science Buddies does participate in affiliate programs with Home Science Tools,, Carolina Biological, and Jameco Electronics. Proceeds from the affiliate programs help support Science Buddies, a 501(c)(3) public charity. If you have any comments (positive or negative) related to purchases you've made for science fair projects from recommendations on our site, please let us know. Write to us at

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Experimental Procedure

Working with Biological Agents

For health and safety reasons, science fairs regulate what kinds of biological materials can be used in science fair projects. You should check with your science fair's Scientific Review Committee before starting this experiment to make sure your science fair project complies with all local rules. Many science fairs follow Intel® International Science and Engineering Fair (ISEF) regulations. For more information, visit these Science Buddies pages: Projects Involving Potentially Hazardous Biological Agents and Scientific Review Committee. You can also visit the webpage ISEF Rules & Guidelines directly.

Note: The Bio-Rad kit includes excellent detailed instructions, thus the procedure below is just an outline of the experiment. For step-by-step technical instructions, please consult the kit manuals.

Creating the Protein Mixture Sample

  1. If you need to create your own GFP sample:
    1. Follow the instructions that came with the pGLO Bacterial Transformation kit to put the GFP gene into bacteria (i.e. transform the bacteria).
    2. Then use the Green Fluorescent Protein Chromatography Kit and the instructions contained therein to grow the GFP expressing bacteria, and purify the protein, as shown in Figure 2, below.
Picture of plate with GFP bacteria and GFP columns.
Figure 2. You can use the Green Fluorescent Protein Chromatography Kit to grow bacteria expressing GFP (shown on the plate on the right) and then purify the protein from the bacteria (as shown in the columns on the left). (Photo courtesy of Bio-Rad Laboratories, Inc.)
  1. Once you have your GFP sample (either donated to you or created with the kits in step 1), combine 5 ul of the GFP protein sample with 10 ul of the hemoglobin/vitamin B12 mixture from the Size-exclusion Chromatography Kit. This new 15-ul mixture will be your protein mixture sample for the size-exclusion chromatography experiment.

Performing the Size-exclusion Chromatography and Analyzing the Results

  1. Carry out the size-exclusion chromatography, as instructed in the Bio-Rad kit's manual, using the GFP/ hemoglobin/vitamin B12 mixture as your protein sample.
  2. In the end, you should have 10 collection tubes from the columns. Note the color, in natural light, of each of these 10 tubes. Write your observations in your lab notebook.
  3. Based on your visual inspection and background reading, which tubes contain hemoglobin? Which collection tubes contain vitamin B12? Which tubes do you expect to contain GFP?
  4. Look at all 10 collection tubes in a dark room, using only a UV light. Tubes containing GFP will glow green under the UV light. Record which tubes contained GFP and the relative brightness (which corresponds to the relative quantity of GFP) in each tube. Do your observations match your expectations?
  5. Based on the results of the size-exclusion chromatography, what can you conclude about the size of GFP? Is it larger or smaller than hemoglobin? How about vitamin B12? Can you make any guesses about its size, in kilodaltons?

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  • Size-exclusion chromatography can only help you determine a relative size for GFP. Devise a way to get a better estimate, in daltons, of the size of GFP.
  • Try adding other proteins to the mixture and figuring out ways to isolate each one.
  • How does pH affect size-exclusion chromatography? Devise an experiment to find out.

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