Intro
o The pore size in polyacrylamide gels is controlled by the gel concentration and
the degree of polymer cross-linking.
o The electrophoretic mobility of the proteins is affected by the gel concentration.
o Higher percentage gels are more suitable for the separation of smaller
polypeptides.
o Polyacrylamide gels can also be prepared to have a gradient of gel concentrations.
Typically the top of the gel (under the sample wells) has a concentration of 5%
increasing linearly to 20% at the bottom.
o Gradient gels can be useful in separating protein mixtures that cover a large range
of molecular weights.
o It should be noted that acrylamide is a neurotoxin and can be absorbed through
the skin. However, in the polymerized polyacrylamide form it is non-toxic.
o Polyacrylamide gels are most often prepared between glass plates separated by
strips called spacers. As the liquid acrylamide mixture is poured between the
plates, air is displaced and polymerization proceeds more rapidly.
o Sodium dodecylsulfate (SDS) is a detergent which consists of a hydrocarbon
chain bonded to a highly negative charged sulfate group.
o Proteins which contain several polypeptide chains that are associated only by
noncovalent forces will be dissociated by SDS into separate, denatured
polypeptide chains.
o Proteins can contain covalent crosslinks known as disulfide bonds. These bonds
are formed between two cysteine amino acid residues that can be located in the
same or different polypeptide mercaptoethanol, can break disulfide bonds. This
allows SDS to completely dissociate and denature the protein.
o In most cases, SDS binds to proteins in a constant ration of 1.4 grams of SDS per
gram of protein. On average, the number of bound SDS molecules is half the
number of amino acid residues in the polypeptide.
o SDS denatures proteins are net negative and since the binding of the detergent is
proportional to the mass of the protein, the charge to mass ratio is constant.
o The proteins migrate through the gel towards the positive electrode at a rate that is
inversely proportional to their molecular weight. In other words, the smaller the
denatured polypeptide, the faster it migrates.
o After proteins are visualized by staining and destaining, their migration distance is
measured. The log10 of the molecular weights of the standard proteins are plotted
versus their migration distance. Taking the logarithm R1 allows the data to be
plotted as a straight line. The molecular weight of unknowns are then easily
calculated from the standard curve.
o The standard molecular weight markers are a mixture of proteins that give the
following denatured molecular weights: prestained 94,000; 67,000; 43,000;
30,000; 20,100; and 14,400. The denatured values have been rounded off for
convenience in graphical analysis.
Safety
o Gloves and goggles must be worn at all times.
o Unpolymerized acrylamide is a neurotoxin and should be handled with
extreme caution in a fume hood.
o Use a pipet pump to measure polyacrylamide gel components. Polymerized
acrylamide, such as precast gels, are safe but should still be handled with
gloves.
Procedures
o Bring a beaker of water, covered with aluminum foil, to a boil. Remove
from heat.
o Make sure the sample tubes A through E are tightly capped and well
labeled. The bottom of the tubes should be pushed through the foil and
immersed in the boiling water for 3 to 4 minutes. The tubes should be
kept suspended by the foil.
o Proceed to loading the gel while the samples are still warm.
o Open the pouch containing the gel cassette with scissors. Remove the
cassette and place it on the bench top with the front facing up.
o Some cassettes will have tape at the bottom of the front plate. Remove all
the tape to expose the bottom of the gel to allow electrical contact.
o Insert the Gel Cassette into the electrophoresis chamber.
o Remove the comb by placing your thumbs on the ridges, and pushing
(pressing) upwards, carefully and slowly.
o Place the gel cassette in the electrophoresis unit in the proper orientation.
Protein samples will not separate in the gel if the cassette is not oriented
correctly. Follow the directions accompanying the specific apparatus.
o Add diluted buffer, approx 125mL into inner chamber and 200mL into
outer chamber.
o Rinse each well by squirting electrophoresis buffer into the wells using a
transfer pipet.
o The gel is now ready for practice gel loading and/or samples.
o Place a fresh fine tip on the micropipette. Aspirate 10 μl of practice gel
loading solution.
o Place the lower portion of the fine pipet tip between the two glass plates,
below the surface of the electrode buffer, directly over a sample well. The
tip should be at an angle pointed towards the well. The tip should be
partially against the back plate of the gel cassette but the tip opening
should be over the sample well. Do not try to jam the pipet in between the
plates of the gel cassette.
o Eject all the sample by steadily pressing down on the plunger of the
automatic pipet. Do not release the plunger before all the sample is
ejected. Premature release of the plunger will cause buffer to mix with
sample in the micropipette tip. Release the pipet plunger after the sample
has been delivered and the pipet tip is out of the buffer.
o Before loading protein samples for the actual experiment, the practice gel
loading solution must be removed from the sample wells. Do this by
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filling a transfer pipet with buffer and squirting a stream into the sample
wells. This will displace the practice gel loading solution, which will be
diluted into the buffer and will not interfere with the experiment.
After the samples are loaded, carefully snap the cover all the way down
onto the electrode terminals.
Set the power supply at 200 volts for 35 minutes.
After the electrophoresis is finished, turn off power, unplug the unit,
disconnect the leads and remove the cover.
After electrophoresis, carefully open the gel cassette and allow the gel to
remain on one of the plates.
Submerge the gel and plate in a small tray with 100ml of fixative solution.
(Use enough solution to cover the gel.)
Lay the cassette down and remove the front place by placing a spatula or
finger at the top edge, near the sample wells, and lifting it away from the
larger back plate. In most cases, the gel will stay on the back plate. If it
partially pulls away with the front plate, let it fall onto the back plate.
Slide the gel into a staining tray. If the gel sticks to the plate, pipet some
of prepared staining solution onto the gel and gently nudge the gel off the
plate.
Gently float a sheet of Protein InstaStain® with the stain side (blue) in the
liquid. Cover the gel to prevent evaporation.
Gently agitate on a rocking platform for 1-3 hours or overnight.
After staining, Protein bands will appear medium to dark blue against a
light background and will be ready for excellent photographic results. No
destaining is required. If the gel is too dark, destain in several changes
of fresh destain solution until the appearance and contrast of the protein
bands against the background improves.
The gel should be stored in a mixture of 50ml of distilled water containing
6ml of acetic acid and 3ml of glycerol overnight.
For permanent storage, the gel can be dried between two sheets of
cellophane (saran wrap) stretched in an embroidery hoop. Air dry the gel
for several days until the gel is paper thin. Cut the “extra” saran wrap
surrounding the dried gel. Place the dried gel overnight between two
heavy books to avoid curling. Tape it into a laboratory book.
Post Lab Questions
1. The migration rate of glutamate dehydrogenase is very similar to the migration
rate of b-amylase during SDS polyacrylamide gel electrophoresis. Yet the native
molecular weight of glutamate dehydrogenase is 330 kDa and that of β-amylase is
206 kDa. Explain.
Glutamate dehydrogenase is a hexamer with a molecular weight of 300,000 (+/- 2000), βamylase is a tetramer with a molecular weight of 206,000. Upon denaturation with SDS
and 2-mercaptoethanol, 6 subunits of approx. 50,000 will be generated from glutamate
dehydrogenerase. Likewise, the native β-amylase, which has 4 subunits, will yield a
protein band of approx. 50,000
2. Many genes have been cloned and sequenced. The precise amino acid sequence
of a polypeptide can be determined from the DNA sequence and the molecular
weight can be calculated. Can a reasonable estimate of the native molecular weight
of a protein be determined from the sequence of their structural genes? Why?
The native molecular weight of a subunit can be determined by this method, however
often proteins are aggregates of polypeptide chains. Approximately 1% of protein mass
consists of carbohydrate and the structure and mass of the oligosaccharide cannot be
anticipated by DNA sequencing. Also, DNA does not yield information on enzyme
cofactors.
3. lgG contains 2 small and 2 large polypeptide chains. A preparation of lgG was
incubated with SDS, heated and submitted to SDS polyacrylamide gel
electrophoresis. One major band near the top of the gel was observed after staining.
Explain.
Disulfide links are still intact. SDS does not cause the cleavage of covalent bonds.
4. Glutamate dehydrogenase can have a native molecular weight of 2 x 106 in
concentrated solutions. Upon the addition of NADH and glutamate, the native
molecular weight is 330,000. Explain these phenomena.
Concentrated solutions of the protein tend to polymerize, forming chains of
approximately 6 enzyme molecules. The substrates NADH and glutamate are bound,
causing conformational changes in the protein and disaggregation to the 330,000
molecular weight enzyme.
5. A purified, active preparation of carbonic anhydrase was submitted to native
polyacrylamide gel electrophoresis at alkaline pH. Three major bands were
observed after staining. The same preparation of protein was denatured and
submitted to SDS-polyacrylamide gel electrophoresis. One band was observed after
staining. Explain these results.
Carbonic anhydrase has 3 major isoenzymic forms, differing in amino acid sequence and
net charge but all having similar molecular weights.
6. A glycoprotein consisting of a single polypeptide chain and over 40% (by weight)
of N-acetylglucosamine, mannose and sialic acid was found to have a native
molecular weight of 75,000 by several analytical methods. However, analysis by
SDS polyacrylamide gel electrophoresis gave molecular weight of 100,000. Explain.
SDS-polyacrylamide gel electrophoresis gives anomaious molecular weight values for
proteins having high percentages of carbohydrate. These proteins tend to bind less SDS
than normal, which tends to decrease the charge to mass ratio.
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