Ch 4 · Amino acids · AS & A Level Chemistry 9701
Topic 4 of 4 in Nitrogen compounds — AS & A Level Chemistry 9701 — 46 lessons.
Introduction
An amino acid carries both a basic -NH_2 group and an acidic -COOH group on the same molecule. Their combination gives amino acids acid-base behaviour unlike a simple amine or carboxylic acid, allows them to link together into peptides, and lets a mixture of them be separated by electrophoresis according to how their net charge changes with pH.
Key ideas — Zwitterions and the isoelectric point
In the solid state and in aqueous solution, an amino acid exists predominantly as a zwitterion: the basic -NH_2 group accepts a proton from the acidic -COOH group of the same molecule, giving -NH_3^+ and -COO^- groups on one molecule with no overall net charge.
🧑🏫 Teacher's explanation
Imagine a molecule that is a 'social butterfly' but also carries its own internal balance. An amino acid has two parts that want to react: an acidic part (the carboxyl group, -COOH) and a basic part (the amino group, -NH_2). In water, they don't just sit there; they play a game of 'pass the proton'. The basic part grabs a hydrogen ion (H^+) from the acidic part.
📖 Definitions
🔍 Worked example — Easy
An amino acid has a carboxyl group with pK_a = 2.3 and an amino group with pK_b = 9.7. Calculate the theoretical isoelectric point (pI) using the formula pI = pK_a + pK_b/2 (assuming the pK_a provided is for the conjugate acid of the amino group).
🔍 Worked example — Standard
A solution contains a mixture of two amino acids. Amino Acid A has a pI of 5.5. Amino Acid B has a pI of 8.2. If the solution is adjusted to pH 7.0, which amino acid will migrate towards the cathode (negative electrode) during electrophoresis?
🔍 Worked example — Exam-style
Calculate the net charge of an amino acid at pH 10.0 if its pK_a (carboxyl) is 2.0 and its pK_a (amino) is 9.0.
⚠️ Common errors
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🎯 Exam question
Key ideas — Formation of peptide bonds
The -COOH group of one amino acid condenses with the -NH_2 group of another, releasing a molecule of water and forming an amide linkage called a peptide bond, -CONH-. Two amino acid molecules joined this way form a dipeptide: H_2NCH_2COOH + H_2NCH_2COOH arrow H_2NCH_2CONHCH_2COOH + H_2O A third amino acid condensing with either end of the dipeptide, releasing a further water molecule, gives a tripeptide.
🧑🏫 Teacher's explanation
Think of amino acids like Lego bricks that have two different types of connectors: a 'plug' (the amino group, -NH_2) and a 'socket' (the carboxyl group, -COOH). To build a chain, you must plug the socket of one brick into the plug of another.
📖 Definitions
🔍 Worked example — Standard
Write the balanced equation for the formation of the dipeptide Glycyl-Glycine from two Glycine molecules, including state symbols.
⚠️ Common errors
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🎯 Exam question
Key ideas — Electrophoresis of amino acids and dipeptides
In electrophoresis, a sample is spotted onto paper soaked in a buffer of fixed pH, and an electric field is applied across it. At a pH below its isoelectric point, an amino acid is predominantly protonated and carries an overall positive charge, so it migrates towards the negative electrode (cathode). At a pH above its isoelectric point, it is predominantly deprotonated and carries an overall negative charge, migrating towards the positive electrode (anode). At its isoelectric point, an amino acid carries no net charge and does not migrate at all. Amino acids or dipeptides with different isoelectric points, or different numbers of acidic/basic side groups, migrate different distances in the same buffer, allowing a mixture to be separated and identified.
🧑🏫 Teacher's explanation
Imagine a crowd of people walking through a hallway. If everyone is wearing heavy backpacks (extra protons), they might move slowly or be pushed by a wind blowing towards one side. If everyone is carrying empty bags (losing protons), they move differently. Electrophoresis is like using an electric 'wind' to sort these people based on whether they are carrying a positive or negative charge.
📖 Definitions
🔍 Worked example — Easy
An amino acid has an isoelectric point (pI) of 6.0. Predict the net charge and the direction of migration in a buffer solution at pH 4.0.
🔍 Worked example — Standard
A mixture contains two amino acids, A and B. Amino acid A has a pI of 5.5. Amino acid B has a pI of 8.2. If electrophoresis is performed in a buffer at pH 7.0, which amino acid will migrate towards the anode (positive electrode)?
🔍 Worked example — Exam-style
A dipeptide is formed from two amino acids. If the first amino acid has a side chain that is acidic (pKa ≈ 4.0) and the second has a side chain that is basic (pKa ≈ 10.0), describe the net charge of the dipeptide at pH 7.0.
⚠️ Common errors
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🎯 Exam question
(a) What can be concluded about the isoelectric point (pI) of this amino acid relative to pH 6.0? (b) Explain your answer to part (a). [2] [2 marks]
Key ideas — Relating isoelectric point to net charge in solution
Comparing the buffer pH with an amino acid's isoelectric point predicts its net charge directly: if the solution pH is less than pI, there is a higher concentration of H^+ than at the isoelectric point, so the carboxylate group is more likely to be protonated back to -COOH while -NH_3^+ remains protonated, leaving the molecule with an overall positive charge. If the solution pH is greater than pI, the amine group is more likely to lose its proton to -NH_2 while -COO^- remains deprotonated, leaving an overall negative charge. Only when the solution pH exactly equals pI does the neutral zwitterion predominate, giving zero net charge and no migration in an electric field.
🧑🏫 Teacher's explanation
Think of an amino acid like a person carrying two magnets: one positive and one negative. In a neutral state, these magnets balance out perfectly, so the person doesn't move if you try to pull them with a giant magnet. This balanced state is called the zwitterion.
📖 Definitions
🔍 Worked example — Easy
An amino acid has a pI of 6.0. Predict the net charge of the amino acid in a solution with pH = 4.0.
🔍 Worked example — Standard
An amino acid has a pI of 5.5. Predict the net charge of the amino acid in a solution with pH = 8.0.
🔍 Worked example — Exam-style
In an electrophoresis experiment, an amino acid with pI = 7.2 is placed in an electrophoresis chamber with a buffer at pH = 7.2. In which direction will the amino acid migrate towards the electrodes?
⚠️ Common errors
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🎯 Exam question
Worked example
Question. Glycine has an isoelectric point of pH\ 6.0. A mixture of glycine and lysine (isoelectric point pH\ 9.7) is spotted onto electrophoresis paper soaked in a buffer of pH\ 7.0, and a voltage is applied. (a) State and explain the direction in which glycine migrates. [2] (b) State and explain the direction in which lysine migrates. [2] (c) State what would be observed if the buffer pH were changed to 6.0. [1]
🔍 Worked example — Easy
Calculate the net charge of an amino acid at pH 4.0 if its pI is 6.0.
🔍 Worked example — Standard
An amino acid has a pI of 5.5. In a buffer of pH 8.0, what is its net charge and direction of migration toward a positive electrode?
🔍 Worked example — Exam-style
A mixture contains amino acid A (pI = 4.0) and amino acid B (pI = 10.0). Predict the migration direction for both in a buffer of pH 7.0 toward the anode (+).
⚠️ Common errors
Common mistakes
Practice
Answers