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CIE A-Level Chemistry Study Notes

34.4.3 Amino Acid Electrophoresis

Amino acid electrophoresis is a vital analytical technique in biochemistry and molecular biology. It enables the separation and characterization of amino acids and peptides based on their electrical charge and molecular size, providing essential data for understanding their structure and function.

Introduction to Electrophoresis

Electrophoresis is a laboratory method used to separate mixtures of charged molecules, such as amino acids and peptides, within an electric field. In this process:

  • Electric Field: Amino acids or peptides are placed in a gel matrix and exposed to an electric field.
  • Charged Molecules: These molecules are inherently charged and will migrate towards the electrode with the opposite charge.
  • Size and Charge Relation: The rate of migration depends on the size and charge of the molecule. Smaller and more highly charged molecules move faster.
Electrophoresis set up in a laboratory

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Role of pH in Electrophoresis

The pH of the medium is a critical factor in electrophoresis:

  • Isoelectric Point (pI): This is the pH at which an amino acid or peptide has no net electrical charge. At this point, the molecule does not move in an electric field.
  • Above the pI: At a pH higher than the isoelectric point, the amino acid or peptide will be negatively charged and migrate towards the positively charged electrode.
  • Below the pI: Conversely, at a pH lower than the isoelectric point, it will be positively charged and move towards the negatively charged electrode.

Detailed Electrophoresis Process

The electrophoresis of amino acids and peptides involves several key steps:

1. Sample Preparation: This involves dissolving the amino acids or peptides in a buffer solution that maintains the desired pH.

2. Loading the Gel: The samples are carefully placed into wells in the gel.

3. Applying Electric Current: When the electric field is applied, the charged molecules start migrating.

4. Staining and Visualisation: After the run, the gel is stained to make the bands of separated molecules visible.

Illustration of gel electrophoresis

Image courtesy of MedSchoolCoach

Amino Acid and Peptide Separation

The separation in electrophoresis is based on:

  • Molecular Weight and Size: Smaller molecules migrate faster through the gel matrix than larger ones.
  • Charge: Molecules with a higher charge density move more rapidly.

Interpreting Electrophoresis Results

The interpretation of electrophoresis results involves:

  • Band Observation: The position and intensity of bands on the gel provide information about the molecular weight and quantity.
  • Standard Comparison: Known molecular weight standards are run alongside the samples for accurate interpretation.
  • Effect of pH: The pH of the buffer can significantly affect the migration pattern and must be carefully selected.

Applications in Amino Acid Analysis

Electrophoresis is employed in various applications, including:

  • Amino Acid Identification: Differentiating and identifying amino acids based on their migration patterns.
  • Peptide Analysis: Studying the composition and structure of peptides.
  • Protein Digest Analysis: Breaking down proteins into smaller peptides and amino acids for detailed analysis.

Overcoming Challenges

Several challenges must be addressed in amino acid electrophoresis:

  • Sample Preparation: Accurate sample preparation is crucial for reliable results.
  • Choosing the Right Gel: The type of gel (e.g., polyacrylamide, agarose) depends on the size of the molecules being analyzed.
  • Buffer Selection: The pH of the buffer plays a significant role in the separation process and must be chosen based on the isoelectric points of the molecules under study.

Electrophoresis in Biochemical Research

This technique is crucial for:

  • Protein Characterisation: Electrophoresis helps in identifying and characterising proteins based on their amino acid composition.
  • Clinical Diagnosis: It is used in diagnosing diseases by identifying abnormal patterns of amino acids or peptides in biological samples.
  • Biotechnological Applications: In the biotechnology field, it's used for analyzing and synthesizing peptides and proteins.

In summary, amino acid electrophoresis is an indispensable tool in the field of biochemistry and molecular biology. It provides a detailed and nuanced understanding of amino acids and peptides, essential for both academic research and practical applications. By mastering this technique, students can gain deeper insights into the molecular mechanisms of life and contribute significantly to scientific advancements in various fields.

FAQ

The strength of the electric field in electrophoresis significantly affects the separation of amino acids. A higher electric field strength results in a faster migration of charged amino acids through the gel. However, if the field is too strong, it can cause excessive heat generation, which might lead to the distortion of bands or even melting of the gel. On the other hand, a weaker electric field results in slower migration, which could improve the resolution and separation of closely related amino acids but also significantly increases the run time. Therefore, the electric field strength must be optimally balanced to ensure efficient separation without compromising the integrity of the gel or the quality of the separation. This balance is particularly crucial when dealing with a mixture of amino acids with similar sizes and charges, as precise separation is needed to distinguish between them. Additionally, the voltage should be consistent throughout the process to ensure uniform migration and accurate interpretation of results.


Careful control of the buffer's pH in amino acid electrophoresis is crucial because it directly influences the charge of the amino acids and, consequently, their migration through the gel. Each amino acid has a specific isoelectric point (pI) — the pH at which it carries no net electrical charge. At a pH equal to the amino acid's pI, it will not migrate in the electric field. If the pH is above the pI, the amino acid will carry a negative charge and move towards the positive electrode. Conversely, if the pH is below the pI, it will be positively charged and move towards the negative electrode. Thus, the pH of the buffer must be chosen carefully to ensure the amino acids have the desired charge for effective separation. Incorrect pH can lead to poor resolution, overlapping bands, or even no migration, resulting in inaccurate results. This precise control of pH is particularly important when separating a complex mixture of amino acids, as the goal is often to achieve maximum separation based on their varying isoelectric points.


Electrophoresis, despite being a powerful tool for amino acid separation, has several limitations. One key limitation is its sensitivity to sample impurities. Contaminants in the sample can affect the migration of amino acids, leading to distorted or smeared bands. This issue can be mitigated by ensuring rigorous sample purification before electrophoresis. Another limitation is the quantification accuracy; electrophoresis is excellent for qualitative analysis but less precise for quantifying amino acid concentrations. To address this, other quantitative techniques like mass spectrometry can be used in conjunction with electrophoresis. Additionally, the resolution of electrophoresis may not be sufficient to separate amino acids with very similar sizes and charges. Using gels with different pore sizes or gradient gels can help improve resolution. Also, the process can be time-consuming, particularly with complex mixtures. Automated electrophoresis systems can speed up the process while maintaining accuracy. Lastly, the interpretation of results requires expertise, as the patterns on the gel can be complex. Training and experience, alongside the use of molecular markers and standards, can assist in accurate interpretation of the electrophoresis results.

Electrophoresis results can be instrumental in determining the purity of an amino acid sample. When an amino acid sample is subjected to electrophoresis, each amino acid or peptide, assuming they differ in size or charge, will migrate differently, forming distinct bands on the gel. The purity of the sample can be assessed by the number and intensity of these bands. In a pure amino acid sample, ideally, there should be a single, well-defined band. Multiple bands or smeared bands indicate the presence of impurities or a mixture of different amino acids. The intensity of the band also correlates with the concentration of the amino acid; a very faint band might suggest a low concentration or impurities that did not bind well with the staining agent. Additionally, comparing the sample's band pattern with that of known pure standards can provide further insight into the sample's purity. This method is particularly useful for checking the purity of synthesized or isolated amino acids in research and industrial applications.


In amino acid electrophoresis, the choice of gel is influenced by factors such as the size and charge of the amino acids or peptides, and the resolution required. Polyacrylamide gels are commonly used due to their fine pore size, which offers high resolution and is suitable for separating small molecules like amino acids and short peptides. The concentration of acrylamide can be varied; a higher concentration creates a denser gel, ideal for separating smaller molecules. In contrast, lower concentrations are better for larger molecules. Another factor is the buffer system, which should be compatible with the gel type to maintain pH and ion strength during electrophoresis. Additionally, the physical properties of the gel, such as its strength and flexibility, are also considered to ensure it can withstand the electrophoresis conditions without breaking or distorting. The choice of gel is thus a critical decision that affects the efficiency and accuracy of the separation process.


Practice Questions

Describe how the principle of electrophoresis can be used to separate amino acids, and explain how the pH of the buffer solution affects their migration in the gel.

Electrophoresis separates amino acids based on their size and charge. In this process, amino acids are placed in a gel and subjected to an electric field. They migrate towards the electrode with an opposite charge, and their speed of migration depends on their size and charge. The pH of the buffer solution is critical because it determines the charge of amino acids. At a pH equal to an amino acid's isoelectric point, it has no net charge and does not migrate. Above its isoelectric point, an amino acid becomes negatively charged and moves towards the positive electrode, whereas below this point, it's positively charged and moves towards the negative electrode. Thus, pH can be adjusted to affect the migration and separation of different amino acids.

In an electrophoresis experiment to separate a mixture of amino acids, a student observed that some amino acids migrated towards the positive electrode while others towards the negative electrode. Explain why this happens and how it helps in separating the amino acids.

This observation is due to the different charges amino acids carry at a given pH. Amino acids have different isoelectric points, the pH at which they have no net charge. In an electrophoresis experiment, if the pH of the buffer is set between the isoelectric points of the amino acids in the mixture, some amino acids will have a net positive charge and others a net negative charge. Those with a net positive charge will migrate towards the negative electrode, while those with a net negative charge will move towards the positive electrode. This charge-based migration under an electric field allows for the effective separation of amino acids, as they will move at different rates and to different extents depending on their charge at the used pH.

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