Podcast
Questions and Answers
What is the primary function of SDS in SDS-PAGE?
What is the primary function of SDS in SDS-PAGE?
- To separate proteins based on their isoelectric point
- To enhance the color intensity of protein bands during staining
- To denature proteins and provide a uniform negative charge (correct)
- To increase the solubility of proteins in the gel matrix
Why is the amount of SDS bound to a protein proportional to the size of the protein?
Why is the amount of SDS bound to a protein proportional to the size of the protein?
- Larger proteins have more hydrophobic regions that bind SDS.
- The binding capacity of SDS is proportional to the surface area of the protein. (correct)
- SDS binds to specific amino acids, and larger proteins have more of these amino acids.
- Smaller proteins are more easily denatured by SDS, leading to greater binding.
Which of the following is NOT a benefit of using SDS in SDS-PAGE?
Which of the following is NOT a benefit of using SDS in SDS-PAGE?
- Increased resolution of protein bands
- Improved protein staining efficiency
- Prevention of protein degradation during electrophoresis
- Enhanced visualization of the protein's tertiary structure (correct)
What is the purpose of using reducing agents like beta-mercaptoethanol or DTT in SDS-PAGE?
What is the purpose of using reducing agents like beta-mercaptoethanol or DTT in SDS-PAGE?
Which of the following is NOT a typical application of SDS-PAGE?
Which of the following is NOT a typical application of SDS-PAGE?
What is the main purpose of using FBS (Fetal Bovine Serum) in cell cultures?
What is the main purpose of using FBS (Fetal Bovine Serum) in cell cultures?
Why is FBS obtained from fetal calves?
Why is FBS obtained from fetal calves?
What is the specific reason for sterilizing, filtering, and conducting quality control on FBS before using it in cell cultures?
What is the specific reason for sterilizing, filtering, and conducting quality control on FBS before using it in cell cultures?
What is the primary purpose of using polyacrylamide gel in protein electrophoresis?
What is the primary purpose of using polyacrylamide gel in protein electrophoresis?
Which of the following characteristics of polyacrylamide gels contributes to their suitability for protein separation?
Which of the following characteristics of polyacrylamide gels contributes to their suitability for protein separation?
What property of proteins allows them to be separated by electrophoresis?
What property of proteins allows them to be separated by electrophoresis?
Which of the following best describes the term 'amphoteric' in the context of proteins?
Which of the following best describes the term 'amphoteric' in the context of proteins?
What determines the net electric charge of a protein molecule?
What determines the net electric charge of a protein molecule?
What does the isoelectric point (pI) of a protein represent?
What does the isoelectric point (pI) of a protein represent?
Why can't acrylamide be handled carelessly during the preparation of the gel?
Why can't acrylamide be handled carelessly during the preparation of the gel?
Besides proteins, what other types of molecules can be effectively separated using polyacrylamide gel electrophoresis?
Besides proteins, what other types of molecules can be effectively separated using polyacrylamide gel electrophoresis?
What is the primary purpose of adding beta-mercaptoethanol to the Laemmli buffer in SDS-PAGE?
What is the primary purpose of adding beta-mercaptoethanol to the Laemmli buffer in SDS-PAGE?
What is the purpose of the SDS in the running buffer for SDS-PAGE?
What is the purpose of the SDS in the running buffer for SDS-PAGE?
What is the correct ratio of 10x electrophoresis buffer to double-distilled water, stated in these instructions?
What is the correct ratio of 10x electrophoresis buffer to double-distilled water, stated in these instructions?
According to this protocol, which of the following samples requires the most amount of protein solution for preparation?
According to this protocol, which of the following samples requires the most amount of protein solution for preparation?
What temperature and duration are used to thermally denature the prepared protein samples?
What temperature and duration are used to thermally denature the prepared protein samples?
Based on the information provided, which of the following components is NOT present in the running buffer?
Based on the information provided, which of the following components is NOT present in the running buffer?
If a protein has a molecular weight of 60 kDa, where would a band of this protein likely be found relative to the provided new protein marker?
If a protein has a molecular weight of 60 kDa, where would a band of this protein likely be found relative to the provided new protein marker?
How much of the prepared sample should be loaded into each gel well?
How much of the prepared sample should be loaded into each gel well?
What is Bovine Serum Albumin (BSA) primarily used for in biochemical applications?
What is Bovine Serum Albumin (BSA) primarily used for in biochemical applications?
Which of the following statements about BSA is true?
Which of the following statements about BSA is true?
What is the primary protein found in milk?
What is the primary protein found in milk?
Which group of compounds is NOT a major component of milk?
Which group of compounds is NOT a major component of milk?
How does BSA stabilize enzyme functions?
How does BSA stabilize enzyme functions?
Which of the following is a use of BSA in molecular biology?
Which of the following is a use of BSA in molecular biology?
What role do immunoglobulins play in milk?
What role do immunoglobulins play in milk?
What is the typical mass range of casein found in milk?
What is the typical mass range of casein found in milk?
What is the relationship between the intensity of the electric field and the voltage applied during protein electrophoresis?
What is the relationship between the intensity of the electric field and the voltage applied during protein electrophoresis?
Which agent is commonly used as a cross-linker in the preparation of polyacrylamide gels?
Which agent is commonly used as a cross-linker in the preparation of polyacrylamide gels?
What is the effect of using gels with lower densities during protein electrophoresis?
What is the effect of using gels with lower densities during protein electrophoresis?
How does SDS influence protein molecules during electrophoresis?
How does SDS influence protein molecules during electrophoresis?
Which of the following factors does NOT significantly influence the migration rate of proteins in electrophoresis?
Which of the following factors does NOT significantly influence the migration rate of proteins in electrophoresis?
What is the role of ammonium persulfate in the polymerization of acrylamide gels?
What is the role of ammonium persulfate in the polymerization of acrylamide gels?
Why are denaturing conditions important in protein electrophoresis?
Why are denaturing conditions important in protein electrophoresis?
Which statement regarding protein migration through polyacrylamide gel is accurate?
Which statement regarding protein migration through polyacrylamide gel is accurate?
If a protein has a pI of 7.0, at what pH would it migrate the least during electrophoresis?
If a protein has a pI of 7.0, at what pH would it migrate the least during electrophoresis?
Which factor would directly increase the pore size in a polyacrylamide gel?
Which factor would directly increase the pore size in a polyacrylamide gel?
Which of the following is a direct consequence of using excessively high concentrations of both acrylamide and bis-acrylamide in gel preparation?
Which of the following is a direct consequence of using excessively high concentrations of both acrylamide and bis-acrylamide in gel preparation?
Why is the concentration of both acrylamide and bis-acrylamide crucial when creating a polyacrylamide gel for electrophoresis?
Why is the concentration of both acrylamide and bis-acrylamide crucial when creating a polyacrylamide gel for electrophoresis?
A protein is found to migrate towards the anode during electrophoresis at pH 8.0. Which statement is most likely to be correct?
A protein is found to migrate towards the anode during electrophoresis at pH 8.0. Which statement is most likely to be correct?
What is the most accurate description of how the chemical property of a protein affects its behavior during electrophoresis?
What is the most accurate description of how the chemical property of a protein affects its behavior during electrophoresis?
If a protein migrates very slowly or not at all during electrophoresis, assuming the electrical field is properly applied, this indicates that:
If a protein migrates very slowly or not at all during electrophoresis, assuming the electrical field is properly applied, this indicates that:
Which of the following best describes the role of bis-acrylamide in polyacrylamide gel electrophoresis?
Which of the following best describes the role of bis-acrylamide in polyacrylamide gel electrophoresis?
If a protein migrates slower during polyacrylamide gel electrophoresis, which of the following is the MOST likely reason?
If a protein migrates slower during polyacrylamide gel electrophoresis, which of the following is the MOST likely reason?
Which of the following best explains why native proteins cannot be separated solely by mass using electrophoresis?
Which of the following best explains why native proteins cannot be separated solely by mass using electrophoresis?
How does the cross-linking density of a polyacrylamide gel influence the outcome of protein electrophoresis?
How does the cross-linking density of a polyacrylamide gel influence the outcome of protein electrophoresis?
If the concentration of bis-acrylamide is increased during the preparation of a polyacrylamide gel, what is the MOST likely result?
If the concentration of bis-acrylamide is increased during the preparation of a polyacrylamide gel, what is the MOST likely result?
Why is it essential to use denaturing conditions for protein separation by SDS-PAGE?
Why is it essential to use denaturing conditions for protein separation by SDS-PAGE?
What is the primary role of TEMED in the polymerization of polyacrylamide gels?
What is the primary role of TEMED in the polymerization of polyacrylamide gels?
How does the interaction between the electric field and protein molecules during electrophoresis primarily arise?
How does the interaction between the electric field and protein molecules during electrophoresis primarily arise?
Why is acrylamide, even after polymerization, considered a health hazard in protein electrophoresis?
Why is acrylamide, even after polymerization, considered a health hazard in protein electrophoresis?
Which of the following best describes the role of BSA in blocking unoccupied binding sites in a western blot?
Which of the following best describes the role of BSA in blocking unoccupied binding sites in a western blot?
Why is BSA preferred over other proteins for saturating reaction vessel surfaces in molecular biology?
Why is BSA preferred over other proteins for saturating reaction vessel surfaces in molecular biology?
Which of the following is a unique function performed by BSA in laboratory settings that is not related to its blocking ability?
Which of the following is a unique function performed by BSA in laboratory settings that is not related to its blocking ability?
What is the primary difference in protein composition between bovine serum and milk as detailed in the text?
What is the primary difference in protein composition between bovine serum and milk as detailed in the text?
In addition to casein, what other types of proteins are mentioned as being present in milk?
In addition to casein, what other types of proteins are mentioned as being present in milk?
Which of the following statements best describes the structural differences between casein and serum albumin as highlighted in the provided text?
Which of the following statements best describes the structural differences between casein and serum albumin as highlighted in the provided text?
How does the composition of milk vary?
How does the composition of milk vary?
Which characteristic of BSA contributes to its utility in stabilizing enzymes?
Which characteristic of BSA contributes to its utility in stabilizing enzymes?
If a protein has multiple disulfide bridges, what would be observed in an SDS-PAGE if a reducing agent was intentionally omitted?
If a protein has multiple disulfide bridges, what would be observed in an SDS-PAGE if a reducing agent was intentionally omitted?
Which of the following experimental adjustments would least impact the effectiveness of SDS-PAGE?
Which of the following experimental adjustments would least impact the effectiveness of SDS-PAGE?
How does SDS contribute to the resolution of protein bands in SDS-PAGE?
How does SDS contribute to the resolution of protein bands in SDS-PAGE?
A researcher performing SDS-PAGE observes vertical streaking in their gel. This would be least likely caused by:
A researcher performing SDS-PAGE observes vertical streaking in their gel. This would be least likely caused by:
If a sample of FBS had undergone complete denaturation via SDS-PAGE but still appeared to show some bands at the top of the gel, this would most likely be because:
If a sample of FBS had undergone complete denaturation via SDS-PAGE but still appeared to show some bands at the top of the gel, this would most likely be because:
Given that 1g of protein binds 1.4g of SDS, which of the following is a correct interpretation about the migration of two proteins of 20kDa and 60kDa?
Given that 1g of protein binds 1.4g of SDS, which of the following is a correct interpretation about the migration of two proteins of 20kDa and 60kDa?
When preparing an SDS-PAGE, what is the key reason for ensuring that the samples are completely devoid of any particulates or undissolved matter?
When preparing an SDS-PAGE, what is the key reason for ensuring that the samples are completely devoid of any particulates or undissolved matter?
In SDS-PAGE, what would be the first indication of a buffer solution being prepared incorrectly with a much lower concentration of SDS than required?
In SDS-PAGE, what would be the first indication of a buffer solution being prepared incorrectly with a much lower concentration of SDS than required?
Given the provided sample preparation table, if a researcher needs to prepare a 60 µl sample of almond milk, maintaining the same proportions of water and Laemmli buffer, how much almond milk is necessary?
Given the provided sample preparation table, if a researcher needs to prepare a 60 µl sample of almond milk, maintaining the same proportions of water and Laemmli buffer, how much almond milk is necessary?
If a sample was prepared using the protocol, but the thermal denaturation step at 99°C for 10 minutes was accidentally skipped, how would this affect the protein banding pattern on the gel?
If a sample was prepared using the protocol, but the thermal denaturation step at 99°C for 10 minutes was accidentally skipped, how would this affect the protein banding pattern on the gel?
During the preparation of the samples, a researcher misread the table and mixed the protein power drink with 20µl of water instead of the instructed 27µl. How would this error impact the migration of the bands of the proteins within the power drink sample?
During the preparation of the samples, a researcher misread the table and mixed the protein power drink with 20µl of water instead of the instructed 27µl. How would this error impact the migration of the bands of the proteins within the power drink sample?
A researcher accidentally used a 5x concentrated Laemmli buffer instead of the 4x concentrated buffer stated in the protocol. How would this affect the resulting protein separation during SDS-PAGE?
A researcher accidentally used a 5x concentrated Laemmli buffer instead of the 4x concentrated buffer stated in the protocol. How would this affect the resulting protein separation during SDS-PAGE?
If the gel running process was interrupted after the protein samples had traveled halfway through the gel, and the gel is later restarted with fresh buffer, what would likely happen to the protein band pattern?
If the gel running process was interrupted after the protein samples had traveled halfway through the gel, and the gel is later restarted with fresh buffer, what would likely happen to the protein band pattern?
A researcher notices the 'old' protein marker has faint bands compared to a 'new' protein marker. Which of the provided factors is the most likely cause of the alteration in the appearance of the marker?
A researcher notices the 'old' protein marker has faint bands compared to a 'new' protein marker. Which of the provided factors is the most likely cause of the alteration in the appearance of the marker?
If a researcher incorrectly uses the 10x concentrated electrophoresis buffer directly without dilution with double-distilled water, what impact would this have on the migration of proteins during electrophoresis?
If a researcher incorrectly uses the 10x concentrated electrophoresis buffer directly without dilution with double-distilled water, what impact would this have on the migration of proteins during electrophoresis?
Based on the sample preparation instructions, samples loaded into wells 2, 4, 6, and 7 contain equal volumes of protein solution. Which of the following statements correctly compares the total mass of the protein loaded into well 2 vs well 4 and well 7?
Based on the sample preparation instructions, samples loaded into wells 2, 4, 6, and 7 contain equal volumes of protein solution. Which of the following statements correctly compares the total mass of the protein loaded into well 2 vs well 4 and well 7?
Flashcards
Electrophoresis
Electrophoresis
A method that separates molecules based on their size and charge by applying an electric field.
Polyacrylamide Gel Electrophoresis (PAGE)
Polyacrylamide Gel Electrophoresis (PAGE)
A type of electrophoresis using polyacrylamide gel as the medium, commonly used for separating proteins and nucleic acids.
Polyacrylamide
Polyacrylamide
The substance that forms the gel matrix in PAGE, allowing separation of molecules based on their size and charge.
N,N'-methylenebisacrylamide (bis-acrylamide)
N,N'-methylenebisacrylamide (bis-acrylamide)
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Amphoteric
Amphoteric
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Isoelectric Point (pI)
Isoelectric Point (pI)
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SDS-PAGE
SDS-PAGE
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Electric Field Strength in Electrophoresis
Electric Field Strength in Electrophoresis
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Polyacrylamide Gel in Electrophoresis
Polyacrylamide Gel in Electrophoresis
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Acrylamide and Bis-acrylamide in Gels
Acrylamide and Bis-acrylamide in Gels
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Gel Polymerization
Gel Polymerization
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Gel Density and Protein Migration
Gel Density and Protein Migration
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Denaturing Conditions in Electrophoresis
Denaturing Conditions in Electrophoresis
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Protein Migration Rate
Protein Migration Rate
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SDS-PAGE Electrophoresis
SDS-PAGE Electrophoresis
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What is Bovine Serum Albumin (BSA)?
What is Bovine Serum Albumin (BSA)?
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What is the purpose of 'saturating' reaction vessels with BSA?
What is the purpose of 'saturating' reaction vessels with BSA?
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What is casein?
What is casein?
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What are the albumins present in milk?
What are the albumins present in milk?
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What is electrophoresis?
What is electrophoresis?
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What is polyacrylamide gel electrophoresis (PAGE)?
What is polyacrylamide gel electrophoresis (PAGE)?
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What is SDS-PAGE?
What is SDS-PAGE?
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What is the isoelectric point (pI)?
What is the isoelectric point (pI)?
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Running buffer
Running buffer
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Laemmli denaturing buffer
Laemmli denaturing buffer
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Protein molecular weight marker
Protein molecular weight marker
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Loading the gel
Loading the gel
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Thermal denaturation
Thermal denaturation
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Separation of proteins via SDS-PAGE
Separation of proteins via SDS-PAGE
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What is Sodium Dodecyl Sulfate (SDS)?
What is Sodium Dodecyl Sulfate (SDS)?
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How does SDS binding relate to protein size?
How does SDS binding relate to protein size?
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What is the effect of SDS on protein structure?
What is the effect of SDS on protein structure?
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What is the role of reducing agents in SDS-PAGE?
What is the role of reducing agents in SDS-PAGE?
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What are the applications of SDS-PAGE?
What are the applications of SDS-PAGE?
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What is FBS?
What is FBS?
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What are the crucial steps in preparing FBS for cell cultures?
What are the crucial steps in preparing FBS for cell cultures?
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Acrylamide
Acrylamide
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Sodium Dodecyl Sulfate (SDS)
Sodium Dodecyl Sulfate (SDS)
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Electric Field Strength and Voltage
Electric Field Strength and Voltage
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Gel Composition
Gel Composition
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Gel Density and Pore Size
Gel Density and Pore Size
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Role of SDS in Electrophoresis
Role of SDS in Electrophoresis
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Safety in Electrophoresis
Safety in Electrophoresis
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How does SDS binding relate to size?
How does SDS binding relate to size?
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What's SDS's effect on protein structure?
What's SDS's effect on protein structure?
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Why are reducing agents used in SDS-PAGE?
Why are reducing agents used in SDS-PAGE?
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What is acrylamide?
What is acrylamide?
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What does SDS-PAGE stand for?
What does SDS-PAGE stand for?
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Bovine Serum Albumin (BSA)
Bovine Serum Albumin (BSA)
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Casein
Casein
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Albumins in Milk
Albumins in Milk
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What is the Significance of Milk?
What is the Significance of Milk?
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What is the purpose of running buffer?
What is the purpose of running buffer?
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What is the role of Laemmli denaturing buffer?
What is the role of Laemmli denaturing buffer?
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What is a protein molecular weight marker?
What is a protein molecular weight marker?
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What is thermal denaturation in SDS-PAGE?
What is thermal denaturation in SDS-PAGE?
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What does SDS do in SDS-PAGE?
What does SDS do in SDS-PAGE?
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What are disulfide bonds and why are they important in SDS-PAGE?
What are disulfide bonds and why are they important in SDS-PAGE?
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Study Notes
Protein Electrophoresis via SDS-PAGE
- Electrophoresis separates molecules based on uneven electric charge.
- Polyacrylamide gel electrophoresis (PAGE) is used for protein separation.
- PAGE separates protein molecules from 5 kDa to 300 kDa.
- PAGE separates polynucleotides from 5 to 2,000 base pairs.
- Silver staining visualizes DNA fractions.
- PAGE is cost-effective.
- Acrylamide monomers and cross-linking agents form polyacrylamide gels.
- N,N-methylenebisacrylamide is a common cross-linking agent.
- Polymerization is a free radical reaction.
- Acrylamide is a potent neurotoxin.
- Protein electrophoresis can be performed using polyacrylamide gels.
- These gels are prepared from a solution of acrylamide monomers and cross-linking agents.
- Acrylamide in its monomeric form is a potent neurotoxin, even after polymerization (with remnants of free monomers).
- N,N-methylenebisacrylamide (bis-acrylamide) is the most commonly used cross-linking agent.
- Polymerization can be chemically initiated by using ammonium persulfate and N,N,N,N-tetramethylethylenediamine (TEMED).
- The cross-linking density and pore sizes can be adjusted by selecting the concentrations of acrylamide and bis-acrylamide.
- Higher molecular weight proteins migrate slower; gels with lower density used for higher MW proteins, and vice versa.
Protein Properties
- Amino acids, peptides, and proteins are amphoteric (amphiprotic/amphoteric).
- They can act as both bases and acids.
- Their net charge depends on environmental conditions.
- Amino acid residues can be both basic and acidic.
- Ionization of carboxyl and amino groups affect protein charge (COOH ↔ COO⁻ + H⁺; NH₂ + H⁺ ↔ NH₃⁺).
- The isoelectric point (pI) is where the net charge is zero.
- Each protein has a specific pI.
SDS-PAGE
- SDS-PAGE uses sodium dodecyl sulfate (SDS).
- SDS forms complexes with proteins, fixing their charge-to-mass ratio.
- SDS gives proteins a negative charge, making them migrate towards the positive anode.
- SDS denatures proteins (unfolds polypeptide chains).
- 1g protein binds 1.4g of SDS.
- Staining SDS-protein complexes is more efficient than staining proteins alone.
- SDS prevents enzymatic protein degradation.
- Reducing agents (1% beta-mercaptoethanol or DTT) break disulfide bonds.
- Gel density & pore size affect protein migration rate, required voltage, and buffer heating.
- Higher molecular weight proteins migrate slower, while those with lower molecular weights migrate faster.
Protein Samples Examined
- FBS (Fetal Bovine Serum): a by-product of meat/dairy industry; serum obtained from fetal hearts.
- BSA (Bovine Serum Albumin): a common, neutral, and non-reactive protein used in biochemistry and molecular biology. It doesn't typically disrupt reactions.
- Animal-origin milk: milk contains proteins (casein, alpha-lactoalbumin, beta-lactoglobulin, and immunoglobulins).
SDS-PAGE Procedure
- Dilute 10x electrophoresis buffer with double-distilled water (e.g., 80 ml of concentrated buffer diluted to 800 ml ddH2O).
- Dilute FBS, BSA, milk, and protein power drink with ddH2O, according to a table, and mix with Laemmli buffer containing beta-mercaptoethanol.
- Prepare 40 µl samples by mixing the appropriate amounts of protein, water, Laemmli buffer, and sample.
- Sample thermal denaturation at 99°C for 10 minutes in a thermal block.
- Prepare gel (remove comb and protective tape, etc.)
- Apply samples and marker.
- Electrophoresis at 200 V for approximately 40 minutes.
- Capture gel images using GelDoc system with Bio-Rad's StainFree technology.
Reagent List
- Running buffer (Tris, glycine, 0.1%SDS).
- Protein electrophoresis gels (pre-cast or prepared).
- Laemmli denaturing buffer for proteins (including 0.1 ml beta-mercaptoethanol per 0.9 mL Laemmli buffer).
- Beta-mercaptoethanol
- Bovine Serum Albumin (BSA)
- Fetal bovine serum (FBS)
- Milk samples (animal-origin, non-animal origin).
- Protein power drink.
- Molecular weight marker with specific sizes (e.g., 250, 150, 100, 75, 50, 37, 25, 15, and 10 kDa).
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Description
Explore the principles and techniques of protein electrophoresis using SDS-PAGE. This quiz covers the separation of proteins based on size, the properties of amino acids, and the mechanisms behind polyacrylamide gel electrophoresis. Test your knowledge on visualization techniques and the effects of environmental conditions on protein charge.
