Determination Of Molecular Weight Of Unknown Protein Biology Essay


SDS Polyacrylamide Gel Electrophoresis ( SDS-PAGE ) is used to divide protein molecules based on size. By utilizing Na dodecyl sulfate ( SDS ) and a gel made from acrylamide, protein form, construction and charge no longer become factors as proteins migrate on to gels and protein sets are merely affected by size. Together with Western Blotting ( WB ) both common research lab techniques, they are used to further find the presence of a given protein. Using this cognition, this study will look at both techniques and besides discourse how both techniques can find the molecular weight of an unknown protein. Protein criterions and an unknown protein sample will be prepared for SDS-PAGE utilizing both a resolution and a stacker gel, and for WB analysis. The known protein criterions are identified and move as markers for the unknown sample. The unknown sample migrates to a similar distance as the ?- Galactosidase protein, every bit good as their Molecular Weights ( MW ) being really near together. It was concluded hence, that the unknown protein was ?- Galactosidase, but besides both techniques, SDS-PAGE and WB are utile tools when finding the molecular weights of terra incognitas, but besides placing them excessively. Both fluctuations of the same intent were successful, nevertheless, it can be said that the SDS-PAGE can give a more quantitative and definite result, based upon the consequences in this study.


SDS Polyacrylamide Gel Electrophoresis ( SDS-PAGE ) is the most normally used research lab technique to separate proteins. It involves using an electric current to a polyacrylamide gel matrix, leting the proteins to migrate through the matrix. However, in order for proteins to migrate onto the gel at a similar rate, or at all, the usage of the detergent SDS is required in order to denature the proteins, which do so in the presence of SDS. Proteins become negatively charged, as they bind to SDS, organizing a protein-detergent composite. Approximately 1.4 g of SDS becomes bound to per gm of protein, giving the denaturized proteins a similar charge to mass ratio. Therefore, since the denaturized proteins no longer have a complex third form, but form similar rod-like constructions and they all have a negative charge, differences in form and charge are no longer factors for separation in the gel. Consequently, the rate at which the SDS coated proteins migrate in the gel is strictly dependent on size.

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Previous surveies have involved utilizing SDS-PAGE to divide urinary proteins by MW ( 1 ) . The SDS-PAGE in this experiment was besides carried out following the process described by Laemmli, who carried out an experiment utilizing a stacking gel and SDS ( 2 ) . Laemmli ‘s system has shown to be the most popular discontinuous buffer system. SDS-PAGE involves the usage of discontinuous gels, dwelling of a resolution or dividing gel every bit good as a stacking gel. The deciding lower gel is where the proteins migrate to and divide into different sizes. The measure of acrylamide in the resolution gel defines how good the separation takes topographic point since higher concentrations of acrylamide restrict the mobility of proteins. The stacking upper gel is where the proteins are loaded and acts to concentrate big sample volumes, bring forthing better set declarations, compared to a gel with no stack. The difference in pH is one of the grounds why the proteins move from the stacking gel to the deciding gel, since the pH causes the molecules that were barricading the proteins traveling through the stack, to divide, hence liberating the proteins to travel down to the deciding gel. A molecular weight marker such as a known protein or criterion that produces sets of known size, migrates to the deciding gel, and is used to assist place unknown proteins ( 1 ) .

Western Blotting ( WB ) is a powerful and of import process which follows successful cataphoresis for the sensing of proteins, specifically those in low measures ( 3 ) . WB allows the transportation of proteins to a nitrocellulose membrane. Using the same rules as SDS-PAGE, an electric current is besides used, but is applied at 90 & A ; deg ; to the gel, leting the proteins to migrate out of the gel onto the membrane. WB can now get down to observe a mark protein in a sample by utilizing an antibody specific to that protein. Therefore, revolutionizing the immunological field, since prior to WB, the detached investigations in the gel were hard to entree with molecular investigations ( 3 ) .

Therefore in this experiment, it was sought to find the MW and individuality of the Unknown protein utilizing the two different techniques mentioned earlier, SDS-PAGE and Western Blotting.


SDS-PAGE Preparation

A 7.5 % deciding gel monomer solution was prepared uniting 4.85ml of Distilled Water ; 2.5ml of 1.5M Tris-HCL ( pH8.8 ) ; 100µl of 10 % ( w/v ) SDS stock and 2.5ml of 30 % Acrylamide/Bis. A comb is placed in the assembled gel sandwich and so carefully removed. 50µl of 10 % ammonium persulfate and 5µl of TEMED were added to the monomer solution and assorted good, avoiding aeration. The solution was so poured to within 1cm of the comb. The gel was overlain butyl alcohol and left to polymerize. These stairss to make a discontinuous buffer system are that of Laemmli ( 2 ) , and were already completed by staff. The readying of the 4 % stacking gel was performed by the pupils, and involved uniting 6.1ml of Distilled H2O ; 2.5ml of 0.5M Tris-HC1 ( pH 6.8 ) ; 100µl of 10 % SDS ; 1.3ml of 30 % Acrylamide/Bis ; 50µl of 10 % ammonium persulfate and 10µ of TEMED. After the butyl alcohol had been removed from the top of the gel and the gel had been washed, it was filled with stacking gel. The comb was inserted and left to polymerize for 45-60 proceedingss. After this clip, the comb was removed and the gel rinsed through with distilled H2O.

Standard Sample and Unknown Protein Sample Preparation

2 tubings incorporating pre-stained protein criterions assorted with sample buffer ( 0.01M phosphate ( pH 7.2 ) incorporating 1 % SDS, 10 % glycerin, 0.002 % bromophenol blue and 0.01M mercaptoethanol ) in one, and pre-stained Unknown protein sample assorted with the same sample buffer in the other were given and 10µl of each sample were removed and placed in separate micro extractor tubings. The tubings were incubated in a boiling H2O bath for 3 proceedingss and so the contents of the tubing incorporating the protein samples was added to 1 good, whilst the contents of the tubing incorporating the unknown protein was added to another well. The gels were run at 200V, until the bromophenol bluish set was 1cm from the underside of the gel, which took approx. 55 proceedingss. After the cataphoresis was complete, the run alonging membrane was removed from the sandwich and the glass home bases were lifted off from the gel. The gels were measured and so placed in transportation buffer for 10 proceedingss. The proteins criterions and their molecular weights were identified, calculated and given to the pupils.

Western Blotting

Nitrocellulose paper, scotch-brite fiber tablets and filter paper, were cut to the size of the gel, and the latter two were saturated with transportation buffer. The cellulose nitrate should be touched to the buffer and allowed to wet by capillary action. The Trans-Blot cell assembly was set up by puting a fiber tablet onto the gray side of the gel holder, followed by a concentrated piece of filter paper ; the pre-equilibrated SDS gel and the nitrocellulose sheet. Air bubbles were removed before and after a farther piece of concentrated filter paper was placed on top of the cellulose nitrate. Finally, a concentrated fiber tablet was placed on top of the filter paper. The gel holder was firmly closed and placed in the half-filled Trans-Blot armored combat vehicle so that the gray panel of the holder was in the cathode side of the armored combat vehicle. The buffer armored combat vehicle was so filled to the underside of the anode disc before electroblotting at 30V and 400mA, took topographic point overnight at room temperature.

Probing the Membrane

At the following session, membranes were placed in the staining bath and were covered with ~20mls of Blocking solution for 10 proceedingss. Then, this was poured off and 5ml of Antibody solution was added to the membrane and it was incubated for 30 proceedingss at room temperature. The membrane was so washed three times in 10ml TTBS, before adding 5ml of anti-mouse IGG Alkaline Phosphatase Conjugate, and incubated at room temperature for a farther 30 proceedingss. The membrane was washed as earlier, prior to 10ml of coloring material development solution was added to the membrane and incubated at room temperature in the dark. After 5-20 proceedingss, colour development should be complete, and as a consequence the membrane should be rinsed with distilled H2O to halt the reaction. The membrane should be placed on filter paper to dry before analyzing it.



Following SDS-PAGE, and the remotion of the gel, protein criterions were identified and the known Molecular Weights ( Fig. 1 ) , measured in kilo Daltons ( kDa ) , were calculated and given to the category. The six standard proteins ( Table 1 ) were identified as: Myosin ( 200 kDa ) , a motor protein found in eucaryotic tissues, and plays a cardinal function in musculus contraction in the striated and smooth musculus cells along with actin ; ?-Galactosidase ( 116 kDa ) a hydrolase enzyme, which catalyses the hydrolysis of ?-galactosides into monosaccharoses and an indispensable homo organic structure enzyme which is besides produced in E.coli ; Phosphorylase ? ( 97 kDa ) a contractile protein found in coney musculus ; Albumin – Bovine ( 66 kDa ) or Bovine Serum Albumin ( BSA ) is a serum albumen protein, which has many maps in research lab techniques, such as ELISAs, Immunoblots and Immunohistochemistry, every bit good as being normally used to find the measure of other proteins, by comparing an unknown measure of protein to cognize sums of BSA ; Albumin – Chicken Egg ( 45 kDa ) is a H2O soluble protein, but the best known signifier of albumen is egg white ; and Carbonic Anhydarse ( 29 kDa ) is an enzyme which catalyses the rapid transition of CO2 into hydrogen carbonate and protons and is responsible for the passenger car of CO2 out of tissues. Table 1 besides shows the computation of MW into log10, based upon kDa weights, and non Da weights. The distance the protein bands travelled on the gel were measured in centimeters ( centimeter ) ( Table 1 ) , every bit good as the distance the Unknown protein migrated on the gel, which was 1.1cm. Protein criterions measured the undermentioned distances: Myosin – 0.4cm ; ?-Galactosidase – 1.0cm ; Phosphorylase ? – 1.3cm ; Bovine Albumin – 1.8cm ; Chicken Albumin – 2.3cm and carbonaceous Anhydrase – 3.8cm.

Figure 1 shows the SDS-PAGE for both the criterions and the unknown. The migration of the terra incognita was found to be similar to ?-Galactosidase. Figure 1 allows us to gauge the molecular weight similar to that of ?-Galactosidase, at 116 kDa, whereas Graph 1 allows a more quantitative analysis. It shows that the log10 MW of the unknown protein was about 2.03. Removing log10, it can be calculated that the MW of the unknown protein was hence, 107.2 kDa. This MW is really near to that of ?-Galactosidase, and hence, ?-Galactosidase must be the Unknown protein.

Western Blotting

The transportation of proteins from the polyacrylamide gel to the nitrocellulose membrane after SDS- PAGE analysis can be seen in Figure 2. The bluish sets seen are the protein bands that have been transferred. The Western Blot involved membrane blocking, in order to cut down non-specific protein interactions between the membrane and the antibody. This was done by puting the membrane in BSA. The membrane was so incubated with the primary antibody, which is specific for the protein of involvement, and we now know that that protein was ?-Galactosidase. The membrane was rinsed to take any unbound primary antibody and so incubated with the secondary antibody, which binds to the primary antibody. The secondary antibody is modified in such a manner, that it will convey about a reaction and give coloring material, leting for ocular designation of protein. Figure 2 shows the dark coloring material production and when analysed against the bluish sets, it is clear that the unknown antibody had been identified and hence the protein had been identified, due to the migration distance, which was similar to ?-Galactosidase.

Table 1:

Identified Protein Standards and their Molecular Weights

Protein Standards


( kDa )

Log10 MW


Migrated ( centimeter )









Phosphorylase ?




Albumin – Bovine




Albumin – Chicken Egg




Carbonaceous Anhydrase




Table shows the known molecular weight ( kDa ) , computation of log10 molecular weights of the identified criterion proteins ( n=6 ) , and the distance protein bands migrated on the gel ( centimeter ) which were measured before the Western Blot process.


SDS-PAGE image of Protein Standards and Unknown Protein

200 kDa

116 kDa

66 kDa

97 kDa

45 kDa

29 kDa







SDS-PAGE was run at 200V for approx. 55 proceedingss as the bromophenol bluish set was 1cm off from the underside of the gel ( 7.5 % Separating Gel and 4 % Stacking Gel ) . Lane 1 shows sets for the Unknown Protein and Lane 2 is the marker lane, demoing all sets of the Protein Standards. Molecular Weights ( kDa ) are highlighted on the side of the pointers. Both samples were incubated in a boiling H2O bath for 3 proceedingss, so as to denature the proteins and organize the SDS composites, so that they could migrate onto the gel. The Unknown protein set migrated to a similar point to the 2nd criterion protein, at approx. 116 kDa, therefore the unknown protein must be ?-Galactosidase.


Log10 MW and Migration Distance of Protein Standards

Myosin –


?-Galactosidase –


Phosphorylase ? –


Albumin – Bovine –


Albumin – Chicken Egg – 2.3cm

Carbonaceous Anhydrase – 3.8cm

The graph shows the consequences of the SDS-PAGE. The chart at the side represents each of the Standards separately. The Log10 MW of Standards is shown against the Distance Migrated on the polyacrylamide gel leting the MW of the unknown protein to be calculated. The distance travelled of the unknown protein was 1.1cm, hence, the log10 MW is about 2.03. This is really similar to the log10 MW for ?-Galactosidase, which is 2.06. Again, bespeaking that the unknown protein is ?-Galactosidase.


Western Blot Analysis of Standard and Unknown Sample Separated by SDS-PAGE




The Western Blot was prepared with 5ml of a primary and secondary antibody – 5ml of anti-mouse IGG Alkaline Phosphatase Conjugate. Colour development occurred in about 20 proceedingss. Lane 2 shows the reaction of the 2nd antibody to give a alteration in coloring material, and Lane 1 contains the proteins from the gel which transferred on the nitrocellulose membrane, and act as MW markers.


In this experiment, it was concluded that the unknown sample was ?- Galactosidase. This protein is a hydrolase enzyme, which catalyses the hydrolysis of ?-galactosides into monosaccharoses and is an indispensable homo organic structure enzyme. In E. coli, ?-galactosidase is produced by activation of the lac operon, as the lacZ cistron.

The SDS-PAGE technique highlighted the standard proteins really good, doing any comparison really easy. Using the SDS-PAGE technique gave more of a definite consequence, as the MW of the terra incognita could be measured and read off the graph, whereas in the WB, it was a batch more hard to specify what the coloring material alteration represented. Merely after several comparings and careful analysis of the western smudge, could it be said that the antibody for the protein, ?-galactosidase, was in fact the right one.

Although the right consequence was identified, utilizing the two techniques ; the experiment could be improved with more pattern, and besides possibly making more than one gel, or western smudge. Equally good as this, the gel could hold been run more easy and carefully, as there were some handling mistakes.


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