Why are the results of gel electrophoresis measured in kDa?

Question

Gel electrophoresis measures the movement of proteins, which is a function of their size - so why are results expressed in kDa, which is a unit of mass? How would the results account for proteins with different charges and/or sizes moving different distances? Or am I misunderstanding the point?

Answer 1

No, you're not misunderstanding anything - your point is absolutely correct.  What you're missing in your post is an indication that you understand polyacrylamide gel electrophoresis of proteins in the presence of sodium dodecyl sulfate (SDS-PAGE) and that there are different types of gel electrophoresis for the analysis of proteins.

In the olden days, 40 or 50 years ago, the migration of proteins during electrophoresis was indeed a function of charge as well as size.  For some applications, that's still the case, and when performing isoelectric focusing, proteins migrate according to charge alone.  This changed with the introduction of SDS-PAGE.

In SDS-PAGE, the combination of a reducing agent to break disulfide bonds and the detergent, sodium dodecyl sulfate (SDS), denatures proteins - in theory, completely.  In addition to deaturing proteins, SDS has two key properties - it is highly charged, and the amount of it that binds to a denatured protein is proportional to the mass of that protein.  As a result, the charge-to-mass ratios of SDS-bound proteins are identical.  This removes the variable of charge, and the differences in mobility of the proteins during electrophoresis thus become a function solely of their mass.  Given that the shape of the proteins is considered to be the same under these conditions - linear, basically - their size is proportional to their mass.  As a practical matter, it's been shown empirically that proteins migrate according to their mass in SDS-PAGE.

That's kind of a long answer, but the key point is that under the conditions used during SDS-PAGE, all proteins have an identical charge-to-mass ratio.

Answer 2

In addition to Zeep's answer, frequently when you run an SDS-PAGE gel, you also run a set of molecular weight markers.  These markers contain a series of control proteins of various known molecular weights to which you can compare your protein(s) of interest.  There are some exceptions where a protein does not run as expected on an SDS-PAGE gel, but these are rare and it is usually adequate to compare your protein(s) to the molecular weight markers.

Answer 3

"Electrophoresis" refers to the electromotive force (EMF) that is used to move the molecules through the gel matrix. By placing the molecules in wells in the gel and applying an electric current, the molecules will move through the matrix at different rates, usually determined by mass, toward the positive anode if negatively charged or toward the negative cathode if positively charged [2].