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1. ElectrophoresisElectrophoresis

2. ElectrophoresisElectrophoresis
 Electrophoresis is a commonly used techniqueElectrophoresis is a commonly used technique
to separate proteins, lipoproteins, nucleic acid,to separate proteins, lipoproteins, nucleic acid,
particles, emulsion grains, or even bacteria onparticles, emulsion grains, or even bacteria on
the basis of their net charge in specifiedthe basis of their net charge in specified
buffered media.buffered media.
 Secara Istilah:Secara Istilah:
Pergerakan molekul - molekul yang bermuatanPergerakan molekul - molekul yang bermuatan
dibawah pengaruh medan listrikdibawah pengaruh medan listrik

3. Principles of SeparationPrinciples of Separation ::
1.1. Charge on the ProteinsCharge on the Proteins

4.  At the pI of a specific protein, the proteinAt the pI of a specific protein, the protein
molecule carries no net chargemolecule carries no net charge
and does not migrate in an electric field.and does not migrate in an electric field.
- At pH above the pI, the protein has a net- At pH above the pI, the protein has a net
negative charge and migratesnegative charge and migrates
towards the anode.towards the anode.
- At pH below the pI, the protein obtains a net- At pH below the pI, the protein obtains a net
positive charge on itspositive charge on its
surface and migrates towards the cathode.surface and migrates towards the cathode.

5. 2.2. Shape of the ProteinsShape of the Proteins

6. 3.3. Size of the ProteinsSize of the Proteins
SDS-PAGESDS-PAGE
SDS PAGESDS PAGE enables separation of proteins by sizeenables separation of proteins by size

7. SDSSDS
 If we want to separate manyIf we want to separate many
different protein moleculesdifferent protein molecules
of a variety of shapes andof a variety of shapes and
sizes, we first want to getsizes, we first want to get
them to be linear so that thethem to be linear so that the
proteins no longer have anyproteins no longer have any
secondary, tertiary orsecondary, tertiary or
quaternary structure (i.e. wequaternary structure (i.e. we
want them to have the samewant them to have the same
linear shape).linear shape).

8.  Analogy:Analogy:
Consider two proteins that are each 500 amino acidsConsider two proteins that are each 500 amino acids
long but one is shaped like a closed umbrella whilelong but one is shaped like a closed umbrella while
the other one looks like an open umbrella. If you triedthe other one looks like an open umbrella. If you tried
to run down the street with both of these moleculesto run down the street with both of these molecules
under your arms, which one would be more likely tounder your arms, which one would be more likely to
slow you down, even though they weigh exactly theslow you down, even though they weigh exactly the
same? This analogy helps point out that not only thesame? This analogy helps point out that not only the
mass but also the shape of an object will determinemass but also the shape of an object will determine
how well it can move through and environment. Sohow well it can move through and environment. So
we need a way to convert all proteins to the samewe need a way to convert all proteins to the same
shape - we use SDS.shape - we use SDS.

9. CellCell
Incubated with SDSIncubated with SDS
membranes will be dissolved, the proteins will bemembranes will be dissolved, the proteins will be
soluablized, all the proteins will be covered withsoluablized, all the proteins will be covered with
many negative chargesmany negative charges
- all proteins contain only primary structure- all proteins contain only primary structure
- all proteins have a large negative charge which means- all proteins have a large negative charge which means
they will all migrate towards the positve pole whenthey will all migrate towards the positve pole when
placed in an electric fieldplaced in an electric field

10. SDSSDS
 Sodium Dodecyl Sulphate (SDS) is an anionicSodium Dodecyl Sulphate (SDS) is an anionic
detergent that denatures proteins by wrapping thedetergent that denatures proteins by wrapping the
hydrophobic tail around the polypeptide backbone.hydrophobic tail around the polypeptide backbone.
 For almost all proteins, SDS binds at a ratio ofFor almost all proteins, SDS binds at a ratio of
approximately 1.4 g SDS per gram of protein, thusapproximately 1.4 g SDS per gram of protein, thus
conferring a net negative charge to the polypeptide inconferring a net negative charge to the polypeptide in
proportion to its length.proportion to its length.
 The SDS also disrupts hydrogen bonds, blocksThe SDS also disrupts hydrogen bonds, blocks
hydrophobic interactions, and substantially unfoldshydrophobic interactions, and substantially unfolds
the protein molecules, minimizing differences inthe protein molecules, minimizing differences in
molecular form by eliminating the tertiary andmolecular form by eliminating the tertiary and
secondary structures.secondary structures.

11. · SDS are attached to the protein· SDS are attached to the protein
in a constant ratio, Proteins nowin a constant ratio, Proteins now
have identical charge density.have identical charge density.

12. PAGEPAGE
 If the proteins are denatured and put into an electricIf the proteins are denatured and put into an electric
field, they will all move towards the positive pole atfield, they will all move towards the positive pole at
the same rate, with no separation by size. So we needthe same rate, with no separation by size. So we need
to put the proteins into an environment that will allowto put the proteins into an environment that will allow
different sized proteins to move at different rates. Thedifferent sized proteins to move at different rates. The
environment of choice is polyacrylamide, which is aenvironment of choice is polyacrylamide, which is a
polymer of acrylamide monomers. When thispolymer of acrylamide monomers. When this
polymer is formed, it turns into a gel and we will usepolymer is formed, it turns into a gel and we will use
electricity to pull the proteins through the gel so theelectricity to pull the proteins through the gel so the
entire process is called polyacrylamide gelentire process is called polyacrylamide gel
electrophoresis (electrophoresis (PAGEPAGE).).

13. PAGEPAGE
This cartoon shows a slab of polyacrylamide (dark gray) with tunnelsThis cartoon shows a slab of polyacrylamide (dark gray) with tunnels
(different sized red rings with shading to depict depth) exposed on the(different sized red rings with shading to depict depth) exposed on the
edge. Notice that there are many different sizes of tunnels scatterededge. Notice that there are many different sizes of tunnels scattered
randomly throughout the gel.randomly throughout the gel.

14.  Analogy:Analogy:
Think of the gel as a tiny forrest with manyThink of the gel as a tiny forrest with many
branches and twigs througout the forrest butbranches and twigs througout the forrest but
they form tunnels of different sizes. If we letthey form tunnels of different sizes. If we let
children and adults run through this forrest atchildren and adults run through this forrest at
the same time, who will be able to get throughthe same time, who will be able to get through
faster? The children of course. Why? Becausefaster? The children of course. Why? Because
of their small size, they are more easily able toof their small size, they are more easily able to
move through the forrest. Likewize, smallmove through the forrest. Likewize, small
molecules can manuver through themolecules can manuver through the
polyacrylamide forrest faster than bigpolyacrylamide forrest faster than big
molecules.molecules.

15.  An electric filed is established with the positive poleAn electric filed is established with the positive pole
(red plus) at the far end and the negative pole (black(red plus) at the far end and the negative pole (black
minus) at the closer end. Since all the proteins haveminus) at the closer end. Since all the proteins have
strong negative charges, they will all move in thestrong negative charges, they will all move in the
direction the arrow is pointing (run to red).direction the arrow is pointing (run to red).

16. There are two types of buffer systems used in proteinThere are two types of buffer systems used in protein
gel electrophoresis: continuous and discontinuousgel electrophoresis: continuous and discontinuous..
 A continuous system uses only one buffer forA continuous system uses only one buffer for
the tanks and the gel.the tanks and the gel.
 In a discontinuous system, a nonrestrictiveIn a discontinuous system, a nonrestrictive
large-pore gel called a stacking gel is layeredlarge-pore gel called a stacking gel is layered
on top of a separating (resolving) gel. The twoon top of a separating (resolving) gel. The two
gel layers are each made with a differentgel layers are each made with a different
buffer, and the tank buffers differ from the gelbuffer, and the tank buffers differ from the gel
buffers.buffers.

17. SDS-PAGE has a number of uses,SDS-PAGE has a number of uses,
which include:which include:
 Establishing protein sizeEstablishing protein size
 Protein identificationProtein identification
 Determining sample purityDetermining sample purity
 Identifying disulfide bondsIdentifying disulfide bonds
 Quantifying proteinsQuantifying proteins
 Blotting applicationsBlotting applications

18. Procedure:Procedure:
1.1. The separating gel.The separating gel.
Prepare the separating gel solution except ammonium persulfatePrepare the separating gel solution except ammonium persulfate
and TEMED in a vacuum flask. De-aerate for 1 min. underand TEMED in a vacuum flask. De-aerate for 1 min. under
vacuum. After adding the ammonium persulfate andvacuum. After adding the ammonium persulfate and
TEMED mix the solution gently.TEMED mix the solution gently.
With a pipet fill the separating gel solution between the glassWith a pipet fill the separating gel solution between the glass
plate sandwich along the edge of one of the spacers, untilplate sandwich along the edge of one of the spacers, until
the height of the solution is 1.0 cm below the comb.the height of the solution is 1.0 cm below the comb.
Immediately overlay the solution with water saturated 2-Immediately overlay the solution with water saturated 2-
butanol or isopropanol to exclude air and to obtain an evenbutanol or isopropanol to exclude air and to obtain an even
interface between the gels.interface between the gels.
Allow the gel to polymerize for 45 min. The gel isAllow the gel to polymerize for 45 min. The gel is
polymerized when a sharp interface is visible below thepolymerized when a sharp interface is visible below the
overlay.overlay.

19. separating gelseparating gel 10 %10 % 15 %15 %
 rangerange 16-70 kD16-70 kD 12-45 k12-45 k
 waterwater 1600 µl1600 µl 939 µl939 µl
 1.5 M Tris pH 8.81.5 M Tris pH 8.8 1000 µl1000 µl 1000 µl1000 µl
 30% Acrylamide30% Acrylamide 1333 µl1333 µl 2000 µl2000 µl
 10% SDS10% SDS 40 µl40 µl 40 µl40 µl
 20% Ammonium20% Ammonium
persulfatepersulfate 14 µl14 µl 14 µl14 µl
 TEMEDTEMED 7 µl7 µl 7 µl7 µl

20. 2. The stacking gel.2. The stacking gel.
 Prepare the stacking gel just before using the gel, toPrepare the stacking gel just before using the gel, to
maintain the ion discontinuities at the interfacemaintain the ion discontinuities at the interface
between the two gels. Mix the ingredients and de-between the two gels. Mix the ingredients and de-
aerate before adding the ammonium persulfate andaerate before adding the ammonium persulfate and
TEMED.TEMED.
 Remove the solution from the top of the gel, rinseRemove the solution from the top of the gel, rinse
with water and dry the area above the gel carefullywith water and dry the area above the gel carefully
with filter paper. Fill the stacking gel solution on topwith filter paper. Fill the stacking gel solution on top
of the separating gel. Place the well forming comb inof the separating gel. Place the well forming comb in
position, being careful not to trap air bubbles underposition, being careful not to trap air bubbles under
the teeth. Visible polymerization of the gel shouldthe teeth. Visible polymerization of the gel should
occur within 20 min.occur within 20 min.

21. stacking gelstacking gel
 waterwater 1475 µl1475 µl
 0.5 M Tris pH 6.80.5 M Tris pH 6.8 625 µl625 µl
 30% Acrylamide30% Acrylamide 335 µl335 µl
 10% SDS10% SDS 25 µl25 µl

 20% Ammonium persulfate20% Ammonium persulfate 10 µl10 µl
 TEMEDTEMED 3 µl3 µl

22. 3. Sample Preparation3. Sample Preparation
 2* Sample buffer:2* Sample buffer:
 0.5 M Tris pH 6.80.5 M Tris pH 6.8 2.4 ml2.4 ml
 10 % (w/v) SDS10 % (w/v) SDS 4.0 ml4.0 ml
 0.2 % Bromophenolblue(w/v in water)0.2 % Bromophenolblue(w/v in water) 0.60.6
mlml
 GlycerolGlycerol 2.0 ml2.0 ml

23.  Prepare the 2* SDS-reducing sample buffer byPrepare the 2* SDS-reducing sample buffer by
adding 100 µl 2-mercaptoethanol to each 0.9adding 100 µl 2-mercaptoethanol to each 0.9
ml 2* Sample buffer. Dilute the sample (10 µl)ml 2* Sample buffer. Dilute the sample (10 µl)
with an equal volume of 2* SDS-reducingwith an equal volume of 2* SDS-reducing
sample buffer. Heat the samples withsample buffer. Heat the samples with
cytoplasmic proteins for 3 min at 95°C.cytoplasmic proteins for 3 min at 95°C.
Hydrophobic (membrane) proteins areHydrophobic (membrane) proteins are
incubate 15 min at 37°C ( or 10 min at 60°C)incubate 15 min at 37°C ( or 10 min at 60°C)
to avoid aggregation.to avoid aggregation.

24. 4.4. ElectrophoresisElectrophoresis
 Dilute the 5* running buffer with 4 volumes ofDilute the 5* running buffer with 4 volumes of
waterwater
 5 * Running buffer5 * Running buffer (for 1 liter)(for 1 liter)
 TrisTris 15 g15 g
 GlycineGlycine 72 g72 g
 SDSSDS 5 g5 g

25.  Assemble the electrophoresis cell, removeAssemble the electrophoresis cell, remove
tubing, clamps and comb. Fill the upper andtubing, clamps and comb. Fill the upper and
lower reservoir with electrode buffer. Load thelower reservoir with electrode buffer. Load the
samples into the wells in the stacking gel.samples into the wells in the stacking gel.
Connect the electrophoresis unit to the powerConnect the electrophoresis unit to the power
supply. The lower electrode is the anode (+)supply. The lower electrode is the anode (+)
and the upper is the cathode (-). Start with aand the upper is the cathode (-). Start with a
low voltage (70 volt) and increase to a higherlow voltage (70 volt) and increase to a higher
(200 volt) when the samples entered the(200 volt) when the samples entered the
stacking gel, continue the electrophoresis untilstacking gel, continue the electrophoresis until
the blue dye has reached the bottom of the gel.the blue dye has reached the bottom of the gel.

26. Detection of Proteins in GelsDetection of Proteins in Gels
 Dye staining with Coomassie Brilliant BlueDye staining with Coomassie Brilliant Blue
R250R250
 Staining solution (5/5/1):Staining solution (5/5/1):
 Coomassie Brilliant Blue R-250Coomassie Brilliant Blue R-250 0.1 %0.1 %
(w/v)(w/v)
 MethanolMethanol 45.5 % (v/v)45.5 % (v/v)
 Acetic acidAcetic acid 9.0 % (v/v)9.0 % (v/v)

27. • Filter the solution before use. Soak the gel inFilter the solution before use. Soak the gel in
an excess of staining solution for 1 hour.an excess of staining solution for 1 hour.
Destain with destain solution, with a KleenexDestain with destain solution, with a Kleenex
Tissue (to absorb the CCB-R250) until theTissue (to absorb the CCB-R250) until the
background is clear.background is clear.
 Destain solution:Destain solution:
 MethanolMethanol 5.0 % (v/v)5.0 % (v/v)
 Acetic acidAcetic acid 7.0 % (v/v)7.0 % (v/v)

28. • Staining with Coomassie Brilliant Blue G-Staining with Coomassie Brilliant Blue G-
250.250.
• Fixation for at least 1 h in 12 % (W/V) TCAFixation for at least 1 h in 12 % (W/V) TCA
• Staining solution:Staining solution:
• Coomassie Brilliant BlueCoomassie Brilliant Blue
• G-250G-250 0.1 % (w/v)0.1 % (w/v)
• Phosphoric acidPhosphoric acid 2.0 % (w/v)2.0 % (w/v)
• Ammonium sulfateAmmonium sulfate 6.0 % (w/v)6.0 % (w/v)

29.  The staining solution should be prepared in theThe staining solution should be prepared in the
following sequence: only after completefollowing sequence: only after complete
solubilization of the ammonium sulfate in thesolubilization of the ammonium sulfate in the
acid the aliquot volume of a stock solution ofacid the aliquot volume of a stock solution of
CBB G-250 (1 g/ 20 ml water) should beCBB G-250 (1 g/ 20 ml water) should be
added. The staining solution should never beadded. The staining solution should never be
passed through a filter. The staining solutionpassed through a filter. The staining solution
should be shaken prior to use for evenshould be shaken prior to use for even
distribution of the colloidal particles.distribution of the colloidal particles.
Stain until the bands are clearly visible (2Stain until the bands are clearly visible (2
hours or o/n). Destain with destain solution.hours or o/n). Destain with destain solution.

30. This shows a top view of an SDS PAGE after theThis shows a top view of an SDS PAGE after the
current has been on for a while (positive pole atcurrent has been on for a while (positive pole at
the bottom) and then turned off. The gel (gray box)the bottom) and then turned off. The gel (gray box)
has five numbered lanes where five differenthas five numbered lanes where five different
samples of proteins (many copies of each kind ofsamples of proteins (many copies of each kind of
protein) were applied to the gel. (Lane 1, molecularprotein) were applied to the gel. (Lane 1, molecular
weight standards of known sizes; Lane 2, a mixtureweight standards of known sizes; Lane 2, a mixture
of three proteins of different sizes with a being theof three proteins of different sizes with a being the
biggest and c being the smallest protein; Lane 3,biggest and c being the smallest protein; Lane 3,
protein a by itself; Lane 4, protein b by itself; Laneprotein a by itself; Lane 4, protein b by itself; Lane
5 protein c by itself.) Notice that each group of the5 protein c by itself.) Notice that each group of the
three proteinsthree proteins migrated the same distance inmigrated the same distance in
the gel whether they were with other proteinsthe gel whether they were with other proteins
(lane 2) or not (lanes 3-5). The molecular(lane 2) or not (lanes 3-5). The molecular
weight standards are used to measure theweight standards are used to measure the
relative sizes of the unknow proteins (a, b,relative sizes of the unknow proteins (a, b,
and c).and c).

31. THANK YOUTHANK YOU