Extraction of native protein from Yeast,

Chicken, Plant, Fish and quantification

using Bradford Protein Assay
Brandon Lam, Wasi Hossian. M15604

Introduction
Proteins are critical components for each and every of our daily bodily function. Furthermore, proteins are
universal biomolecules, which means they play an equally critical role in every other organism from
harnessing sunlight for food production to the emission of fluorescence light. Amino acids are the basic
building blocks of proteins, they give proteins their immensely diverse capabilities through the endless
possibilities in folding and sequence. The extraction of protein is a fundamental technique in proteomics, in
which humans attempt to study the sequence and function of proteins. The aim of practical 1 and 2 was to
isolate proteins from 4 general organisms (Yeast, Plant, Fish and Chicken), purify them, and then to quantify
the extracted proteins using Bradford Reagent Assay.

Extraction
The process of extracting proteins is dependent on many factors which include, the type of cells the protein
is extracted from, the location of the protein in the sample (intracellular/extracellular), the localization of the
protein within the cell and the downstream application of the extracted protein.
Extraction of protein is heavily dependent on cellular disruption methods and the preservation of the native
proteins structure. The various techniques used to disrupt cells include physical, chemical or mechanical
means. The different criteria that each cell type have, will determine the cellular disruption method used. For
instance, some bacteria have peptidoglycan in their cell walls, thus they need to undergo enzyme digestion
before being lysed with an osmotic gradient. Often, the method of cellular disruption will cause protein
degradation, hence the method of disruption used should also consider the susceptibility of the target protein
to degradation. Additives are also used to preserve the structure of the isolated protein. Through the
maintenance of pH, low temperature, and inhibition of proteases, additives can effectively preserve the form
of proteins.
Another important factor in choosing the method of extraction is the localization of the protein within the
cell. Not all every protein exist in the cytosol of cells, in a eukaryotic cell, membrane-bound organelles exist
within the cell, and some of these organelles contain the protein of interest. Consequently, it is important to
note the location of the protein of interest in order to correctly lyse the organelle containing the protein.
Lastly, the most important aspect to consider, is applications of the extracted protein. Do we want to study
its function and structure? Or are we only interested in its size and composition? As some disruption
methods damages the conformation of the target protein, hindering the study of its form and function, these
questions, when carefully considered, can help us plan the cellular disruption method we use to successfully
achieve the aim of our experiment.
In this study, various methods of protein extraction were utilised for each tissue type. A mild lysis detergent
procedure was used for protein extraction from yeast cells, when Y-PER (yeast protein extraction reagent)
was added to the yeast pellet. The reagent is effective because it eliminates the need for any mechanical
equipment such as glass beads. Moreover, the low yield associated with mechanical isolation is removed[1].
Y-PER also contains specific inhibitors to inhibit the proteases found in yeast in order to prevent the

degradation of the isolated proteins. After 20 minutes of agitation, the cell lysate was centrifuged at 14,000g
for 10 minutes to pellet the cell debris. The supernatant was stored on ice for future studies.
Mechanical grinding in the presence of a detergent was used for extraction from plant cells from leaves. The
mechanical isolation was done by massaging the tissue sample in a P-PER solution in a polypropylene mesh
bag. Mechanical isolation is required because of the tough cellulose walls in the plant cells, which are not
present in the yeast or mammalian cells. The P-PER aids in chemical isolation by digesting the cell wall
through the enzymatic action of cellulase and pectin. P-PER is also compatible with gel electrophoresis
during SDS-PAGE, while its protein extracts are compatible with being quantified by Bradford Protein
Assay[2]. The resultant liquid from mechanical isolation was collected and put through zonal centrifugation
with organic and aqueous layers. As proteins are zwitterionic in solution, they would be more soluble on the
aqueous side of the partition and hence this aqueous layer is collected and stored on ice for 2 weeks for
future studies.
A detergent, T-PER was used for fish and chicken meats as well without any mechanical isolation. Like PPER, it is compatible with the protein assay. It is designed for use on all mammalian tissues, unlike
mechanical isolation methods, which need to be specialized for different tissues, such as milder extraction
methods for softer tissues like spleen and liver. It increases solubility of proteins without compromising
function, and buffered at a neutral pH of 7.6, it preserves the hydrogen bonds in proteins. It contains a
cocktail of protease inhibitors to prevent breakdown of proteins by native proteases. Moreover, it is effective
in that it can extract the target protein from various cellular components [3]. The homogenous lysate was
centrifuged at 10,000g for 5 minutes to pellet tissue debris. The supernatant was collected and stored on ice
for 2 weeks for future studies.

Bradford Protein Assay

The Bradford Protein Assay is a dye-binding assay, in which a differential colour change occurs in response
to varying protein concentrations. Under acidic conditions where there is an abundance of H+ ions, the dye,
Coomassie Brilliant Blue G-250, appears red as it is doubly protonated. However, when the dye binds to a
protein, it is converted to an unprotonated blue form. It is this blue protein-dye form that is detected at 595
nm in the assay using a spectrophotometer. This can be used to create a standard protein concentration
curve[4].With each binding of blue protein-dye complex, the absorbance reading at 595nm increases linearly
within a specific range of absorbance. Using the spectrophotometer and the generated curve, we can
determine the concentration of protein present in the sample by the absorbance reading, thus characterization
of the protein of the protein can be carried out. When the concentration of the protein is known, the volume
of sample needed for loading in SDS-PAGE gel can be calculated, as done during Practical 3.
The Braford Protein Assay is known for its efficiency, inexpensiveness and the very wide range of proteins it
can detect. However, it is inhibited by detergents, such as the ones added to the various samples. It is also
important to note that the Coomassie dye disrupt the native state of the protein and this hinders further
analysis of the protein such as studying its function. Also, it is only linear over a short range (from 02000g/mL), thus dilution of the samples were necessary before measuring the absorbance.

Results
ConcBSA
(g/l)

0.0

0.25

0.5

0.75

1.4

VBSA (l)

0.0

18.8

38.0

56.3

105.0

VWater (l)

150

131.2

113.0

93.7

45.0

Absorbanc
0
0.287
0.648
0.848
1.190
e
Table 1: Absorbance reading at 595nm with zero calibration at null concentration.

Standard curve of Concentration of BSA (g/l) against UV Absorbance

1.4

f(x) = 0.84x + 0.1

1.2 R = 0.94
1
0.8

Absorbance (A)

0.6
0.4
0.2
0

0.2

0.4

0.6

0.8

1.2

1.4

1.6

Concentration of BSA (g/l)

Figure 1: A linear regression of UV absorbance against various BSA protein concentration

Absorbance

Organisms
Dilutio
n
5x

YEAST

PLANT

FISH

0.152

CHICKE
N
1.169

0.310

10x

0.224

0.938

0.886

25x

0.115

-0.034

0.532

0.610

0.995

Table 2: Table of recorded Absorbance reading of diluted protein samples

(g/l) Concentration

Organisms
Dilutio
n
5x

YEAST

PLANT

FISH

0.0563

CHICKE
N
1.211

0.243

10x

0.141

0.966

0.926

25x

0.0122

0.514

0.599

1.112

Table 3: Table of concentration of diluted protein samples calculated from the standard curve
Organisms
YEAS
T

PLANT

CHICKE
N

FISH

Concentration (g/l)
Volume of sample
containing 20g of
protein (l)
Mass of protein in
12.5l of sample (g)

1.215

0.257

5.605

5.561

16.46

17.82

3.568

3.596

15.188

3.21

Mixing proportions
12.5 + 0 12.5 + 0 + 3.55 + 8.95 3.60 + 8.90
(Sample + dH2O +
+ 12.5
12.5
+ 12.5
+ 12.5
buffer) (l)
Table 4: Sample preparation for SDS-PAGE. Table of calculated values for undiluted protein sample.

Discussion
Standard Curve for Bradford Protein Assay
The standard curve was plotted using the UV absorbance reading at 595nm from protein standards of Bovine
Serum Albumin of concentrations varying from 0 1.4 g/L. As explained earlier, though many proteins
display a curve relationship of absorbance reading to concentration, BSA, at concentrations ranging from 0
2.0 g/L, will display a linear relationship instead. In our experiment, the concentration of BSA used is
within the threshold of maintaining a linear relationship. Hence, a linear regression is the best model to use
for the standardization curve. Furthermore, an r-squared value of 0.9449 was obtain for the linear regression
plot, signifying a very significant statistical fitting of data to the fitted regression line.

Absorbance Readings from Various Dilutions

Various dilution were done on each protein sample (5x, 10x and 25x). The reason behind this, was to keep
the absorbance of the samples within the range of the standard curve so that the calculated concentration
falls within the concentration range and will be relatively more accurate as compared to when the
absorbance of the samples is out of range. This way, the actual concentration can be calculated by
multiplying by the dilution factor.
Table 3 shows our results from protein extraction. The amount of protein extracted from each organism
seems to vary largely. Sample from the chicken have a slightly larger concentration than fish. The
concentration of the yeast protein sample is relatively low, about 5 times lower than that of the chicken
protein sample. Contrastingly, the plant protein sample have close to zero concentration of protein. However,
it is too early to make any conclusions right now. Only after analysing the sources of errors and consulting
our own knowledge of protein expression in these organisms, can we make a valid conclusion.

Error Analysis
The lowest protein yield was from the plant tissue, which had a concentration of 0.0563mg/ml at 5 times
dilution, followed by the yeast cell which was 0.243mg/ml, while the proteins from both chicken and fish
tissue had a high concentration of 1.211mg/ml and 1.112mg/ml.
The concentration of proteins extracted from yeast was relatively low because yeast cells have many
endogenous yeast proteases and thick proteinaceous cell envelope. Moreover, while the remaining samples
were from whole tissues and the yeast sample was from a small pellet, thus the amount of yeast proteins to
be extracted might have been much lower from the start. Furthermore, yeast cells are shown to have low
protein extraction levels, thus these might have contributed to the low yeast protein concentration. A
possible way to tackle this problem may be to do multiple extractions using Y-PER so that more yeast
protein can be extracted. If not, a more effective protein extraction method can used than Y-PER, such as
using the Alkaline extraction procedure. These ways, the amount of yeast protein extracted can be higher

and the protein concentration level will increase. As mentioned above, the Bradford Assay can be degraded
by detergents such as Y-PER. Thus, there may be possible errors in the quantitation of the protein extracted.
To rectify this, BCA (bicinchoninic acid) assay can be used instead since it is less sensitive to degradation by
detergents. If not, the detergents can be attempted to be removed by dialysis to reduce degradation of the
Bradford Assay.
The plant cells too face the same problem, since the lysis was done by P-PER, which is a mild lysis
detergent too, so it may have resulted in errors in the quantitation using Bradford Assay. The plant cells have
an extracellular cell wall, so mechanical grinding was required through gentle grinding in a mesh bag.
However, the grinding may not have been vigorous enough, so the plant cell walls may still have been
mostly intact, so the plant proteins may not have been released and the plant protein concentration would
appear low. A way to rectify this error would be to use a more vigorous mechanical extraction method such
as the french press machine so that more proteins can be extracted, instead of hand massaging. Moreover,
there may have been possible human error contributing to the errors in value of protein concentration. Since
both layers looked similar, the wrong layer may have been pipetted out and mistaken as the protein layer,
leading to an abnormally low protein concentration. There was also no standardization or quantification of
the initial amount of tissue or cell samples. Thus, we may have taken too little leaves, so very little plant
proteins could be extracted, leading to the low plant protein concentration. One way to rectify this is to
standardize the initial amount of tissue samples used by mass. Therefore, these may be the reasons why the
plant and yeast protein concentrations were much lower than the chicken and fish protein concentrations.

Conclusion
In conclusion, we have been successful in fulfilling the aim of the experiment. Moderately high
concentrations were extracted from each of the samples with the exception of plants and yeast to a lesser
extent, and the protein quantitation was successful too. However, the purity of the extracted protein will be
tested in future studies.

References
[1] THERMOFISHER.COM,. Y-PER YEAST PROTEIN EXTRACTION REAGENT - THERMO FISHER SCIENTIFIC
HTTPS://WWW.THERMOFISHER.COM/ORDER/CATALOG/PRODUCT/78990 (ACCESSED AUG 13, 2015).
[2] THERMOFISHER.COM,. P-PER PLANT PROTEIN EXTRACTION REAGENT - THERMO FISHER SCIENTIFIC
HTTPS://WWW.THERMOFISHER.COM/ORDER/CATALOG/PRODUCT/89803 (ACCESSED AUG 13, 2015).
[3] THERMOFISHER.COM,. T-PER TISSUE PROTEIN EXTRACTION REAGENT - THERMO FISHER SCIENTIFIC
HTTPS://WWW.THERMOFISHER.COM/ORDER/CATALOG/PRODUCT/78510 (ACCESSED AUG 13, 2015).
[4] BIO-RAD PROTEIN ASSAY HTTP://WWW.BIO-RAD.COM/LIFESCIENCE/PDF/BULLETIN_9004.PDF (ACCESSED AUG 13,
2015).
[5] THERMOFISHER.COM,. PIERCE COOMASSIE (BRADFORD) PROTEIN ASSAY KIT - THERMO FISHER SCIENTIFIC
HTTPS://WWW.THERMOFISHER.COM/ORDER/CATALOG/PRODUCT/23200 (ACCESSED AUG 13, 2015).