FAKULTI SAINS DAN TEKNOLOGI

PUSAT BIOSAINS DAN BIOTEKNOLOGI

PRACTICAL BIOCHEMISTRY
(STBP2012)

EXPERIMENT 3 :
PURIFICATION & CHARACTERIZATION OF
α-LACTALBUMIN, A MILK PROTEIN

TARIKH AMALI : TUESDAY 29 JULY 2008 & 5 AUGUST

2008
GROUP NUMBER : 4

GROUP MEMBERS :
1) MUHAMMAD FAIZZUDDIN BIN JASMANI
A118634
2) ALIA FARHANA BT KASSIM
A117935

NAMA PENSYARAH :
Prof Dr. Othman Omar
Prof Dr. Zainon Mohd Ali
ASSOC. Prof. Dr. Hasidah Mohd. Sidek

QUESTIONS

CHROMATOGRAPHY

1. What is that mean by Void volume?

Void volume means the total space surrounding the gel particles in a packed volume
or the volume taken up by the liquids in the column. The
void volume also is the total volume of mobile phase between the injector and
detector flow cell including all extra column volumes. It can be determined by
injecting an unretained substance that measures dead volume plus extracolumn
volume. We used Vi or Vm as a symbols.

2. What is that mean by the elution volume?

Amount of solvent required to remove a particular analyte from a packed column
clarify what the elution volume is. The elution volume refers to the volume of eluent
(e.g. a buffer or a solvent) used in chromatography to remove one or more
compounds (e.g. an amino acid or an organic compound) from a chromatographic
bed. When eluting amino acids the volume of liquid used corresponds to a particular
amino acid, thus an identity of the amino acid can be established by referring to the
volume of buffer used. Used after the ion-exchange chromatography run has been
completed.

3. What is the size of suitable mesh for protein molecule with high molecular
weight, (100000 dalton )?
50 to 100 meshes.
4. What is that mean by the mobile phase and differentiate it with the stationary
phase in chromatography column.
Solvent poured on top of the loaded column, usually liquid and gas is termed as the
mobile phase. The solvent flows down the column, causing the components of the
mixture to distribute between the powdered adsorbent and the solvent, thus separating
the components of the mixture so that as the solvent flows out of the bottom of the
column, some components elute with early collections and other components elute
with late fractions. As a solute band progresses along a column, the solute molecules
are continually transferring from the mobile phase into the stationary phase and back
from the stationary phase into the mobile phase. This transfer process is not
instantaneous, because a finite time is required for the molecules to traverse by
diffusion through the mobile phase in order to reach, and enter the stationary phase.
So, those molecules close to the stationary phase will enter it almost immediately,
whereas those molecules some distance away from the stationary phase will find their
way to it a significant interval of time later. However, as the mobile phase is moving,
during this time interval while they are diffusing towards the stationary phase
boundary, they will be swept along the column and thus dispersed away from those
molecules that were close and entered it rapidly. As conclusion, molecule separated
they differ in the extent to which they are distributed between the mobile phase and
the stationary phase.

5. Define Rf and explain about the usage.

Rf stands for a retardation factor or also known as retention factor describes the ratio
of time spent in the stationary phase relative to time spent in the mobile phase which
being used in chromatography. Below is how to describe it mathematically using the
following ratio:

As example, if particular substance in an unknown mixture travels 2.5 cm and the

solvent front travels 5.0 cm, the retention factor would be 0.5. An Rf value will
 always be in the range 0 to 1: if the substance moves at all, it moves along the
direction the solvent ("mobile phase") does less, but cannot move further than the
solvent does. Rf values are only useful if they are between these two extremes. One
can choose a mobile phase with different characteristics (especially polarity) in order
to control how far the substance being investigated migrates. A Rf value is
characteristic for any given compound (provided that the same stationary and mobile
phases are used). It can provide corroborative evidence as to the identity of a
compound. If the identity of a compound is suspected but not yet proven, an authentic
sample of the compound, or standard, is spotted and run on a TLC plate side by side
(or on top of each other) with the compound in question. Note that this identity check
must be performed on a single plate, because it is difficult to duplicate all the factors
which influence Rf exactly from experiment to experiment.

Electrophoresis

1. Define the isoelectric point for protein.

Isoelectric point means the pH at which a particular molecule or surface carries no net
electrical charge. The pI value can also affect the solubility of a molecule at a given
pH. Such molecules have minimum solubility in water or salt solutions at the pH
which corresponds to their pI and often precipitate out of solution. Biological
amphoteric molecules such as proteins contain both acidic and basic functional
groups. Amino acids which make up proteins may be positive, negative, neutral or
polar in nature, and together give a protein its overall charge. At a pH below their pI,
proteins carry a net positive charge; above their pI they carry a net negative charge.
Proteins can thus be separated according to their isoelectric point (overall charge) on
a polyacrylamide gel using a technique called isoelectric focusing, which utilizes a
pH gradient to separate proteins. Calculation for isoelecric point for protein:
2. Explains about effects of the increases of the acrylamide concentration from
7.5% to 15% against sample migration.

The amount of acrylamide used can be inversely related with The size of the pores
created in the gel. As example, a 7.5% polyacrylamide gel will have larger pores in
the gel than a 15% polyacrylamide gel. To resolve large proteins we are typically used
gels with a low percentage of acrylamide and high percentage gels are used to resolve
small proteins.

3. SDS-PAGE’s method is used to determine the molecular weight of protein. What

is the function of the chemical reagent during the process of the method?

A) β-mercaptoethanol

β-mercaptoethanol acts as disulfide bond reducing agent and assist in protein

denaturation by reducing all the disulfide bonds.

B) SDS

SDS is a detergents that disrupts the secondary, tertiary, and quaternary structure

to produce linear polypeptide chains coated with negatively charged SDS

molecules. It binds to hydrophobic regions of the denatured protein chain.

4) What is the function of methanol/ethanol in staining solution?

Methanol in staining solution functions as to reduce the size of pores in the gel and to
eliminate SDS from protein. It also decolorizes gel after treatment process with the
gel. The background color of the gel is cleared by methanol so that the bands can be
observed.
PRACTICAL 3 : GEL FILTRATION CHROMATOGAPHY

METHODS :
A) The Preparation of Sephadex G-75 Column (well-prepared)
1. A small of glass wool which was wetted with water was placed in the bottom of the
glass column (25 x 1.5cm). Then, column was mounted at a stand using two finger
clamps and then the exit is closed. Water is added to the column until glass wool is
covered and make sure there are no air bubbles trapped.

2. The prepared Sephadex G-75 is balanced with 0.02M Tris Buffer pH 7.0. Then, the
slurry is stirred and poured inside the column.

3. After the Sephadex is packed, the flow rate was adjusted into 1.0mL/min and the
column must be make sure is not dry.

4. Successful separation will be achieved if the flow rate is constant, surface of the
Sephadex is flat and always cover with buffer.

B) Isolation of α-lactalbumin

1. Height and diameter of the column are determined for calculating volume of the
column. The void value is determined and the Vo value of the column used was recorded.

2. Whey milk sample is saturated 2x with freeze dry methods. About 10mL of whey
supernatant is then dissolved in 5mL of 0.02M Tris buffer pH 7.0.
• These for us to get the amount of protein that we needed for the other steps
3. Then, opened he stopcock to allow flow of the buffer until the buffer head is same
level with the top of the column. Carefully (slowly and around the inside of the walls of
the column) poured the 1.0mL of sample (2x saturated) on the top of the column without
disturbing the gel surface.

4. The fraction is collected right after loading the sample and test tubes are used to collect
2.0mL of every fraction.

5. After the entire sample entered the gel, 5mL of Tris buffer is added carefully without
disturbing the gel surface. After all the buffer entered the gel, the whole top of the column
is filled in with the buffer and the column lid which is connected to the volumetric flask
containing the same buffer is attached.

6. The fraction was continued collect and the absorbance at 280nm of every fraction was
read using quartz cuvette and Tris buffer was used as blank. All readings obtained are
recorded and sample is diluted when the readings exceed 1.0

7. The fraction were collected until absorbance readings at 280nm show no protein eluted

8. After that, a graph of readings at 280nm is plotted against elution volume. The Vo
volume is marked with arrow on the graph and the samples of each peak of the graph are
kept.
PRACTICAL 4 : POLYACRYLAMIDE GEL ELEKTROPHORESIS

METHODS:
A) Resolving Gel 14% Preparation

Solution Volume
1.5M Tris HCl pH 8.8 2.5mL
28% acrylamide – 0.74% Bis Acrylamide 5.0mL
Temed 25µL
1% Ammonium Persulfat 250µL
H2O 2.5mL
Table 1
Table 1 shows the solution that needs to use to prepare separating gel 14%

1. The mixed solution of separating gel is transferred to gel cassette by using Pasteur
pipette.

2. A layer of water was laid over the gel to produce a flat and smooth surface also to
reduce the entry of oxygen into cassette that can disturb the polymerization process.

3. After that, the gel was polymerized for 30 minutes and the layer of water was sucked
out from the top layer of the separating gel

B) Stacking Gel 4% Preparation

Solution Volume
0.5M Tris HCl pH 6.8 0.5mL
10% acrylamide – 2.5% Bis Acrylamide 1.0mL
Sucrose 40% 2.0mL
Temed 10µL
1% Ammonium Persulfat Riboflavin 100µL
 Table 2

Table 2 shows the solution needs to prepare stacking gel 4%

1. The solution of the stacking gel is placed on the surface of the separating gel until it is
close to the surface of the gel cassette

2. The comb is inserted to form wells on the gel and the gel is polymerized for 30 minutes
under pendaflour light (if riboflavin is used)

3. The comb was removed and the wells on the gel were rinsed with distilled water.

C) Electrophoresis

Solution Volume
Bromophenol blue 0.2% 200µL
Sucrose 40% 800µL

Table 3

1. Firstly, sample buffer solution was prepared.

2. Then, 10µL of the sample buffer is added to 20µL of supernatant that has been diluted,
whey, P1, P2 and P3 (peak of the chromatography) samples
3. After that, each of the samples were inserted into the wells accordingly.

4. Electrophoresis is run at 30mA until Bromophenol blue reached the end of the gel. The
gel is run for two and half hours.

Well Sample Volume (µL)

Sample Buffer Total
2 Supernatant 50 10 60
3 Whey 20 10 30
4 Standard α-lactalbumin 20 10 30
5 FD 20 10 30
6 Peak 1 20 10 30
7 Peak 2 20 10 30
8 Peak 3 20 10 30
Table 4

D) Staining

1. Firstly, the electrophoresis is switched off and the plate is removed from the gel
cassette.

2. The plate and the gel were separated by using a thin spatula and the gel was transferred
to a container that containing staining solution for about half An hour or one hour.

3. Next, the gel is the decolorized by placing it in decolorizing solution for a night. The
decolorizing solution is changed a few times until the background color became clear.

4. At least, the length of the gel is measured and the length of the Bromophenol blue on
the gel and the bands of the protein formed at every well is measured too. The Rf value of
every protein can be determined.
E) UV absorbance spectrum for α-lactalbumin

1.Absorbances for every sample from the peaks are read using spectrophotometer at
wavelength 260nm by using 3mL quartz cuvette and Tris buffer was used as blank.
Dilution is done when the absorbance value exceeds 1.0

2. The same method was repeated by using 280nm and 290nm wavelength. Absorbance at
240nm to 340nm was read to get UV spectrum every peak.

3. The graph of the UV spectrum is plotted for α-lactalbumin sample and is compared to
the UV spectrum of the standard α-lactalbumin.
DATA AND CALCULATION

Practical 3 : Gel Filtration Chromatography

1.

Tube Number Volume (ml) Absorbance (A600)

1 1 0.000
2 2 0.000
3 3 0.000
4 4 0.000
5 5 0.000
6 6 0.000
7 7 0.009
8 8 0.010
9 9 0.011
10 10 0.011
11 11 0.012
12 12 0.019
13 13 0.272
14 14 0.535
15 15 0.293
16 16 0.120
17 17 0.046
18 18 0.032
19 19 0.026
20 20 0.014
21 21 0.009
22 22 0.000
23 23 0.000
24 24 0.000
25 25 0.000
26 26 0.000
27 27 0.000
28 28 0.000
 29 29 0.000
30 30 0.000

Table 5

Table 5 shows the absorbance value at 600nm for fraction from column Sephadex G-75.
This is for determination of Void volume (Vo).

2. Graph 1 for absorbance value at 600nm versus the number of tube from the tube 1 to
tube 19 is plotted.

3.

Tube Number Volume (mL) Absorbance (A280)

1 2 0.000
2 4 0.000
3 6 0.000
4 8 0.000
5 10 0.000
6 12 0.000
7 14 0.034
8 16 0.102
9 18 0.053
10 20 0.053
11 22 0.063
12 24 0.084
13 26 0.123
14 28 0.174
15 30 0.199
16 32 0.173
17 34 0.126
18 36 0.067
19 38 0.050
20 40 0.178
21 42 0.841
22 44 1.817
23 46 1.927
24 48 1.526
25 50 0.601
26 52 0.178
27 54 0.042
28 56 0.008
29 58 0.001
30 60 0.000
 Table 6

Table 6 shows the absorbance value at 280nm for the protein sample to determine the
peak for α-Lactalbumin

4. Graph 2 shows the absorbance value at 280nm versus the tube of the sample eluting
from column Sephadex G-75.

5. Volume of column = π r2h

= 22/7 x 0.752 x 27.6
= 47.8 cm3

Numbers of test tube needed = 47.8 cm3

2ml
= 23.9
~ 24

Practical 4 : Polyacrylamide Gel Electrophoresis

1.

λnm Absorbance value

Standard α-lactalbumin Peak 1 Peak 2 Peak 3
(x4)
240 0.886 0.387 0.386 3.308
250 0.475 0.306 0.259 2.836
260 0.518 0.238 0.232 2.884
270 0.663 0.191 0.234 3.180
280 0.725 0.153 0.216 3.068
290 0.525 0.108 0.131 2.320
300 0.083 0.075 0.031 1.216
310 0.000 0.059 0.007 0.328
320 0.000 0.047 0.001 0.112
330 0.000 0.037 0.000 0.068
340 0.000 0.034 0.000 0.052
Table 8

Table 8 shows the absorbance value at 240nm to 340nm for standard α-lactalbumin,
peak 1, peak 2 and peak 3.
2. Graph 3 for absorbance value for 240nm to 340nm versus λnm is plotted

Test Tubes P1 P2 P3
Absorbance 0.013 0.161 0.006
ug protein ( from calibration 1.5 26.7 0.5
curve )
Volume of sample (ml) 0.5 0.5 0.5
Protein concentration (mg/ml) 0.003 0.053 0.001
Initial volume (ml) 2 6 2
Total protein 0.006 0.320 0.002
Protein concentration in 2ml 0.006 0.160 0.002
(mg/ml)

Calculation :

1.) The concentration of protein is determined by the formula :

Table 9
Table 9 shows the concentration of protein determined from Bradford Assay.

Protein Concentration of standard α-lactalbumin (mg/mL)

= 1.55 (A280) – 0.76 (A260) mg/mL
=1.55 (0.725) – 0.76 (0.518)
=0.730mg/ml
DISCUSSION :
Method of gel filtration chromatography separates molecules according to size and shape.
It has two phase, the mobile phase and stationary phase. A mixture of substances to be
fraction is dissolved in the mobile phase. The stationary phase consist of gel matrix which
is has narrow size range. The larger molecules can pass through the pores column rapidly
than the small molecules because the column containing such molecular sieves, so, the
molecules that are too large excluded from the solvent volume inside the column. We
used Tris buffer during the experiment that had to be added always to make sure that the
column does not dry. The buffer also needed so that the big protein can move faster than
the small protein. The sample that had been added into the column must be freeze dry
first so that we can get enough amount of protein for the experiment. The sample must be
added carefully into the column to ensure that gel are not destroyed. We need to collect
2ml for each fraction with speed 20-30 ml/hour and take the reading of absorbance at
280nm for each fraction we get. A graph of reading of absorbance vs the volume of elute
had to be plot to get the V ๐. There are two graphs that we had been plotted. The first
graph is the void volume graph. From this graph, we can determine the void volume
value. The highest peak which is has the higher point is the void volume value. Void
volume is the volumes that consist of bigger molecules compared to the other tubes. That
is why it has the highest point; it may contain big amount of protein than other tubes. The
second graph is the graph that show absorbance readings at A280 of 2ml fraction of elute.
Each tube that yields all the peaks will keep for the next experiment.

CONCLUSION :
1) There are solid stationary phase and a liquid mobile phase in gel filtration
chromatography. It also separate protein components of whey milk according to size;
larger molecule eluted out first followed by the smaller size one
2) α-lactalbumin exists in peak 2 according to electrophoresis.

REFERENCES :
1. Boyer Rodney, 2002. Biochemistry Laboratory: Modern Theory and Techniques.
Benjamin Cummings. Pg 124-201
INTRODUCTION

Objective : Practical 3 : To separate the protein components of whey through gel

filtration chromatography
Practical 4 : 1) To purify α-lactalbumin through electrophoresis
2) To determine the concentration of α-lactalbumin by UV
absorbance spectrum.

Theory :

The most important technique isolating and purifying the proteins is

chromatography. Liquid chromatography has been a powerful tool for isolating proteins,
peptides, and other molecules from complex mixtures. Through our broad
chromatography offerings in affinity chromatography, gel filtration chromatography, ion
exchange chromatography, and high performance liquid chromatography (HPLC), we are
proud to offer our customers a wide range of chromatography products to meet all their
liquid chromatography needs. But, for this practical 3, we use gel filtration
chromatography. There are two phases in the gel filtration chromatography; the mobile
phase and the stationary phase. In column chromatography, the stationary phase, a solid
adsorbent, is placed in a vertical glass (usually) column and the mobile phase, a liquid, is
added to the top and flows down through the column (by either gravity or external
pressure). Column chromatography is generally used as a purification technique: it
isolates desired compounds from a mixture. The mixture to be analyzed by column
chromatography is applied to the top of the column. The liquid solvent (the eluent) is
passed through the column by gravity or by the application of air pressure. An
equilibrium is established between the solute adsorbed on the adsorbent and the eluting
solvent flowing down through the column. Because the different components in the
mixture have different interactions with the stationary and mobile phases, they will be
carried along with the mobile phase to varying degrees and a separation will be achieved.
The individual components, or elutants, are collected as the solvent drips from the bottom
of the column. Gel filtration chromatography separates proteins, peptides, and
oligonucleotides on the basis of size. Molecules move through a bed of porous beads,
diffusing into the beads to greater or lesser degrees. Smaller molecules diffuse further
into the pores of the beads and therefore move through the bed more slowly, while larger
molecules enter less or not at all and thus move through the bed more quickly. Both
molecular weight and three dimensional shape contribute to the degree of retention. Gel
Filtration Chromatography may be used for analysis of molecular size, for separations of
components in a mixture, or for salt removal or buffer exchange from a preparation of
marcromolecules. For the practical 4, we do the electrophoresis using gel polycrylamide.
The major difference among the various methods is the type of the support medium.
Cellulose and cellulose acetate are used as a support medium for low molecular weight
biochemicals while polyacrylamide and agarose gel are widely used as support medium
for larger molecules. From polyacrylamide electrophoresis, characteristics of protein α-
lactalbumin can be determined. Electrophoresis through polyacrylamide gels leads to
enhanced resolution of sample components because the separation is based on both
molecular sieving and electrophoretic mobility. Samples are put inside the well
accordingly. Molecules with charges will move towards the positive charge or negative
charge according to their charges. Protein can have either a net positive or negative
charge so protein with cation moves to cathode whether anion will move to anode. But
there is isoelectric point for the protein. Isoelectric point is the pH at which a particular
molecule or surface carries no net electrical charge. The pI value can also affect the
solubility of a molecule at a given pH. Such molecules have minimum solubility in water
or salt solutions at the pH which corresponds to their pI and often precipitate out of
solution. Biological amphoteric molecules such as proteins contain both acidic and basic
functional groups. Amino acids which make up proteins may be positive, negative,
neutral or polar in nature, and together give a protein its overall charge. At a pH below
their pI, proteins carry a net positive charge; above their pI they carry a net negative
charge. Proteins can thus be separated according to their isoelectric point (overall charge)
on a polyacrylamide gel using a technique called isoelectric focusing, which utilizes a pH
gradient to separate proteins. Calculation for isoelecric point for protein:

For the staining of the gel, we use the methanol for reduce the size of pores in the gel and
to eliminate SDS from protein. It also decolorizes gel after treatment process with the gel.
Its clears the background color of the gel so that the bands can be observed. Lastly, about
the UV absorbance spectrum that can determine the characteristics of the protein α-
lactalbumin. Actually, absorption spectra in the UV (200-400nm) and visible region of
spectrum (400-700) are due to energy transition of both bonding and non-bonding outer
electrons of the molecule. The major advantages of difference spectrophotometry is that it
enables the detection of relatively small absorption changer in the system which has a
large absorption.