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Electrophoresis is also called 'cataphoresis'. A fluid-soaked membrane may be used instead of a fluid or (fluid-soaked) gel; this is membrane electrophoresis (...gel electrophoresis, in the case of the gel).

I will refrain from making the lamentable observation that "electrophoresis is chromatography with potential".

Cf. electroosmosis.

The mechanism of electrophoresis is rather a brilliant idea, in my opinion. It works under the principle that all biological molecules (fats, proteins, nucleic acids, etc.) will carry some inherent charge, whether it's positive or negative. Therefore, each molecule will be capable of moving through an ionic gradient, its rate depending on the total charge of the molecule.

The typical setup is simplistic: the medium into which the gradient will be induced is placed in a chamber which has an anode (+) at one end and a cathode (-) at the other. (The charged ends should not be live at this point.) The medium is then inoculated with a sample of the molecules with which you are experimenting. There may be a label introduced directly into the medium prior to inoculation with the sample (eg. ethidium bromide); added to the sample itself or inherent in the sample (eg. radioactivity or fluorescence); or added after the procedure is finished (also works with ethidium bromide). The label will serve to indicate movement from the start point through the ion gradient, and is used to indicate size, amount, or charge of the molecule.

There are some inherent differences between fluid, gel, and membrane electrophoresis. Fluid electrophoresis seems to be most effective in measuring the charge of the molecule by its rate of movement through the charge gradient. (If anyone knows any other uses for this, please let me know. I can't think of any, and am not experienced with it.) Membrane electrophoresis is similar to gel electrophoresis, but may be more effective with smaller quantities of sample or when later removing the desired portion of the sample. The basic principle of gel electrophoresis (and membrane electrophoresis) is that the molecule is now forced to not only move through the ion gradient, but figure out how to get around the fibers (cellulose or other fibers in membrane, usually agarose or polyacrylamide polysaccharides in gel). This allows for separation not only as to charge, but as to size and shape. Smaller, linear molecules will move more quickly than larger, circular or globular molecules. Thus, gel or membrane electrophoresis would be effective in determining, say, the length of a piece of DNA or the size of a protein.

(I seem to have neglected capillary electrophoresis, which is more involved with analytical chemistry than biochemistry in my experience, but BelDion seems to have covered that nicely.)

Electrophoresis is a favoured method by many in the biochemistry, molecular biology, and genetics fields for its efficiency and effectiveness. In fact, many genomes have been at least partially mapped using the Sanger or dideoxynucleotide method of DNA sequencing, which involves oodles of electrophoresis.

See also: two-dimensional electrophoresis or 2D electrophoresis, SDS-PAGE

Gel Electrophoresis
(Or, Why I Stopped Wanting To Be a Biologist When I Grew Up)

It all started innocently enough. I had just begun my senior year as a biology major at a West Texas college, and I had just completed a research project on the germination requirements of poppy mallow seeds. The research had been hard, yes, and often sheer drudgery, definitely, but in the end, it had been fun. Yes, between the seed-collecting field trips in which my blistering skin threatened to turn me into a melanoma farm before my 30th birthday and the hours upon hours of blindingly dull lab work staring through a microscope at itty-bitty plant embryos, in a sick, masochistic way, I'd actually had fun. After all, the field trips were kind of cool, in a rattlesnake-ridden way, and the little seeds were kinda pretty, especially in comparison with the fungus cultures that somebody in the lab was growing on piles of horse poop.

So, a few days before the semester began, poor doomed fool that I was, I wandered blithely into my supervising professor's office and said, "Hey, Dr. Amos, I was thinking ... I have a pretty light course load this semester, so do you think I could maybe do another research project before I graduate?"

"Why, yes." She smiled in a way that seems more and more sinister each time I remember it. "I have a project you could do. Why don't you run a series of electrophoretic protein analyses comparing your white and purple populations of Callirhoe involucrata? Some people have suggested the two are really subspecies instead of varieties. And besides, all the big schools are using electrophoresis these days. You want to be ready for graduate school, don't you?"

Of course I did. So I went out with my ice cooler and little plastic bags in which I would place one leaf from 30 different plants in each population. I drove 15 miles outside the city limits to a bucolic roadside site where one wildflower population was supposed to be and ... discovered that the highway department, in a rare fit of productivity, had graded the shoulder. Where the plants had once been was now nothing but smooth caliche and gravel.

I should have taken this as a cosmic sign that my new project was doomed from the start. But I didn't. I persevered, found other sites, collected my leaves, and took them back to the university.

Once I was back in the lab, Denise, one of the graduate students, showed me how to electrophorese with all the grace and skill of a fighter pilot showing the village idiot how to fly.

"It's really easy, once you get the hang of it. It's just like cooking," she told me brightly.

She neglected to tell me that she'd taken all her cooking classes at the Mafia Poisoning and Assassination College.

First, she showed me how to grind up the leaves. She put a little bit of leaf in the bottom of a pestle that was nestled in a tray of crushed ice, added some sand, then poured in a milliliter of an evil elixir that contained 2-mercaptoethanol. 2-mercaptoethanol, which helps break down the plant tissue into its constituent proteins, is a chemical that is a close cousin to the aromatic that gives skunk spray its odor, and 2-merc definitely shows the relationship. Unfortunately, 2-merc is also, and in itty-bitty quantities, a liver poison, a nerve poison, and a potent carcinogen. A single drop, carelessly spilled on one's skin, will be absorbed by the epidermis like an alcoholic imbibing a can of furniture polish. Even looking at a bottle of 2-merc probably causes as much bad luck as breaking a mirror with a black cat on Friday the 13th.

Holding her breath, Denise took a mortar and ground everything up into a green, gelatinous goo. The goo was put into a tiny vial and put into the deep freeze for later use. She then left me to spend the next eight hours grinding up the rest of the leaves, during which I had an allergic skin reaction to the powder in my rubber gloves that left me with Dermatitis of the Gods.

The next day, she showed me how to make the starch gel. This gel would serve as the medium through which the various denatured proteins would travel once an electric current is applied to the gel. Small proteins can travel easily between the sticky starch particles, but large proteins get bogged down, so the proteins will separate out according to size.

Making the starch gel was, in fact, very much like making slightly toxic Jell-o. She mixed a quarter-cup of powdered potato starch with a chemical solution in a big Erlenmeyer flask and had me boil it over an open Bunsen burner flame. The lab's emergency shower came in handy when I caught my barbecue mitts on fire.

Once the starch was boiling in big, sticky blops, she stuck a vacuum hose over the top to suck out all the dissolved gases so bubbles wouldn't form in the gel when it cooled. Then she poured the starch out into a little plexiglass tray and popped it in the glass-fronted fridge in the corner to cool.

Once the gel had set to an opaque white, she took out the vials of green goo and showed me how to cut wicks from filter paper while they thawed. Then we got out the gel and cut a one-inch strip near one end. We soaked a wick in each vial, then stuck the wicks between the strip and the rest of the gel at even intervals. Then the gel tray went into one of the electrophoresis pans that resided in the refrigerator. Denise put a plastic sack full of ice on the gel so that it wouldn't heat up and burst into flames during the night. Yes, Virginia, Jello will burn, especially if it has 250 volts running through it for twelve hours. We hooked the electrophoresis tray up to its power source, turned on the juice, and left.

The next day, Denise showed me how to make the dyes to stain the proteins. This process was my second cosmic warning: every other bottle had a skull-and-crossbones on it. I found out I was going to become close friends with arsenic and cyanide. I was not a happy camper.

She showed me how to cut the gel into thin slices with the aid of high-G piano wire strung on a hacksaw blade. Then she bathed each slice in a separate dye and left the slice & dye trays in a dark cupboard. After the slices had time to soak up the dye, she took the slices out and preserved them in a fixing solution that was mostly made of methanol and acetone, more liquids that don't do a body good. She showed me how to wrap and store the preserved slices so that the protein patterns could be analyzed and compared.

And then she left me to do the other 29 gels all by myself.

It was ... a very useful learning experience. I'm pleased I went through it.

Electrophoresis is used extensively in revealing genetic variation in enzymes and other proteins. In the case where all individuals in the samples reveal an enzyme with the same electrophoretic mobility it is called monomorphism. A hypothetical gel showing the stained bands can be seen below.


    __   __   __   __   __

all five bands display identical electrophoretic mobility (they are the same enzyme)

That shows how electrophoresis works in a more simple scenario in which the individuals are homozygous for an allele represented by the migrating enzyme, however, often you must take into account the presence of heterozygous individuals. Allozymes are enzymes that have differing eletrophoretic mobilites resulting from allelic differences at a single locus. For example, consider a hypothetical allele which exists in two forms; one associated with a rapidly migrating enzyme and the other associated with a more slowly migrating enzyme. When tested using gel electrophoresis, the results yielded will show three possible outcomes; homozygous for the rapidly migrating enzyme, homozygous for the slowly migrating enzyme and heterozygous for both rapid and slow enzymes. This means that in homozygous individuals only one band will appear in the gel, representing either rapid or slow enzymes, and in heterozygous individuals two bands will appear, once stained, to represent both rapid and slow enzymes.

Monomeric Polymorphism
     __    __         __               
     __          __   __     __         
                                         R= rapid   
     R/S   R/R  S/S   R/S    S/S         S= slow

In the above example the enzyme itself is monomeric, meaning it consists of only one polypeptide chain, so the heterozygous individual will show the two possibilities of a rapid enzyme and slow enzyme; each enzyme representing a single allele. However, if the enzyme were a dimer, molecularly consisting of two polypeptide chains, three possibilities arise; enzymes containing two rapidly migrating polypeptides, two slowly migrating polypeptides, and both rapidly and slowly migrating polypeptides. The rapidly migrating (rapid + rapid) and slowly migrating (slow + slow) homodimers behave in a similar manner as in the case of a monodimer, but the heterodimer (rapid + slow) will typically have an intermediate electrophoretic mobility. In the case of multimeric (consisting of multiple polypeptide chains) enzymes the outcome becomes increasingly complex.

Dimeric Polymorphism
  __                  __              
  __        __                          RR= rapidly migrating homodimer   
            __                  __      SS= slowly migrating homodimer
                                        RS= heterodimer (rapidly + slowly migrating)
RR/RS      RS/SS     RR/RR    SS/SS          

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