Add an appropriate buffer, and then hook the electrodes up to + and - output from a regulated power supply, and you will get a voltage between the two wires that causes a current to flow. Biological molecules carry electric charge, so they will move too, in an appropriate supporting medium.
Electrodes are made from thin platinum wire. Since the molecules are negatively charged, they move toward the cathode (red).
Gels
Two materials have traditionally been used for gels: polyacrylamide and agarose. Acrylamide is on the left, and its polymerized form is on the right.
Acrylamide is cross-linked into a mesh by the inclusion of a small amount of bis-acrylamide (technically, N,N' methylene-bisacrylamide).
You mix a solution of acrylamide and bis-acrylamide plus the appropriate buffer, then the reaction is started by addition of a small amount of TEMED and ammonium persulfate (5-20% is a range for acrylamide). The mixture is poured into a mold (glass plates separated by spacers, with something at the bottom to keep the liquid from running out.
Once it's set, the plug at the bottom is removed. Electrical continuity is maintained by wedging a piece of sponge into the bottom.
A gel mold contains two glass plates, one of which is notched. The "ears" of the notched plate have a tendency to get broken, so usually a set comes with an extra notched plate when you buy them.
The other material is agarose. This is a purified form of the agar that is used for bacteriological plates (petris dishes). Agar is a polysaccharide extracted from certain kinds of seaweed. Agar has been used to solidify desserts for a long time, it was introduced to Koch's laboratory by the wife of one of his assistants, who knew about it. He never publicly credited her with the idea.
[ It's amusing that the very first medium used for isolation of single colonies of bacteria was a potato, sliced through. Appropriate for a German laboratory, I think. ]
Biochemically agarose is a repeating polymer of dimers of galactose plus a galactose derivative.
Agar and agarose have the property that when mixed with water, boiled and then cooled, the material sets into a gel (like jello, but generally stiffer) at around 45°C. Once set, it can be heated a lot higher without losing its physical properties. The stiffness depends on the concentration of agarose used. 0.8-1.5% would be usual
Agarose gel electrophoresis also requires an appropriate buffer (e.g. Tris-acetate). This type of electrophoresis is extremely convenient. The gel is non-toxic, easily prepared by boiling, and the gel can be poured flat (see the picture above). You can't do this with polyacrylamide because oxygen inhibits the polymerization reaction.
Samples are loaded into wells under the surface of the buffer. The aqueous samples are made dense by addition of glycerol to 10% or so. Dyes (bromophenol blue and sometimes xylene cyanol) are also added into the samples, they move at characteristic rates and allow you to visualize the progress of the separation.
Separation in electrophoresis
For DNA at neutral pH, charge is carried by the phosphate groups, which contribute 1 or 2 negative charges (the average depends on the exact pH). This means that the charge to mass ratio is constant for DNA or RNA of different lengths.
The reason that DNA or RNA molecules of different sizes separate is the existence of a retarding force that is greater for larger molecules. Or maybe it's better to turn that around: we observe that the log of the distance traveled is inversely proportional to the length of the molecule, and infer the existence of a force that depends on length.
Samples for protein gels are typically prepared by boiling a protein mixture in the presence of a detergent SDS (sodium dodecyl sulfate). The hydrophobic part coats the protein and destroys its secondary structure. The evenly spaced sulfate groups impart negative charge. As with DNA, the charge to mass ratio is constant for polypeptides of different lengths. Separation occurs by means of the size-dependence of the retarding force.
Visualization
The classic method for visualizing protein gels is to stain with a blue dye (Coomassie brilliant blue). In this picture we can see a protein gel drying after the electrophoresis has been run. The blue spots are proteins.
DNA gels were often stained with a fluorescent dye such as ethidium bromide.
Ethidium is moderately mutagenic, so substitutes have been developed.
Alternatively if the material is radioactive, you just expose the dried (or even wet) gel to X-ray film. These days, they have fancy apparatus that records the emitted beta particles without the use of film. I remember the revolution caused by the introduction of automatic film processors.
Laemmli
To get the best resolution, you want the bands of protein or nucleic acid to be as thin as possible. Here is a gel with very nice resolution:
The thickness of the bands depends on how much of each protein is present in the sample.
To get a pretty gel (one with nice thin bands), for DNA or RNA the important thing is to have as little sample as possible and to run a thin gel (like 0.4 mm).
For protein gels, there is a trick, invented by Laemmli. There is a combination of two gels, one on top called the stacking gel, and a larger one below called the running gel The system has 3 different buffers. The upper and lower tank buffers contain glycine as the mobile anion and are at pH 8.8. The gels are
Stacking gel: 3% acrylamide, pH 6.8
Running gel: 5% - 20% acrylamide, pH 8.8
This system compresses a sample which might be almost a centimeter from top to bottom when first loaded, into a set of protein bands much less than one mm thick as they exit the stacking gel.
One last thing: a lab running protein gels will have a characteristic smell of sulfur. That's because a sulfhydryl reagent like beta-mercaptoethanol will be present in the samples to break disulfide bonds in the proteins. It's minimally dangerous in small quantities, but these days the safety police make you boil your samples in a fume hood.
