Question

Alpha amino acids are organic acid molecules that also happen to contain an amino group \(\left(-\mathrm{NH}_{2}\right)\) on the second carbon atom of the acid's chain. Proteins are condensation polymers of such alpha amino acids. The reaction by which the long chain of the protein forms is very similar to the reaction by which nylon forms, resulting in the formation of the linkage which is called an "amide" (or "peptide") linkage. Show how the following two amino acids could react with each other to produce an amide linkage, resulting in the formation of a dimer (a "dipeptide"). How could this dipeptide then go on to react with additional amino acids to form a polypeptide?

Short answer

Two alpha amino acids, AA1 with side chain R1 and AA2 with side chain R2, can react with each other through a condensation reaction, forming an amide (peptide) linkage, and resulting in a dipeptide: AA1-AA2: H₂N-CH[CO]-R1-[NH-CH[COOH]-R2 This dipeptide can react with another amino acid, AA3 with side chain R3, through a similar condensation reaction: AA1-AA2-AA3: H₂N-CH[CO]-R1-[NH-CH[CO]-R2-[NH-CH[COOH]-R3 This process can continue with more amino acids to form a polypeptide chain.

Step-by-step solution

The general structure of alpha amino acids

Start by recalling the general structure of alpha amino acids, which consist of an amino group (-NH2), a carboxyl group (-COOH), and a side chain (R) attached to a central carbon atom (alpha carbon). The general structure can be written as: H₂N-CH[COOH]-R Let's call the first amino acid AA1, with side chain R1, and the second amino acid AA2, with side chain R2: AA1: H₂N-CH[COOH]-R1 AA2: H₂N-CH[COOH]-R2

Formation of the amide (peptide) linkage

Next, visualize the condensation reaction between AA1 and AA2, which happens when the amino group (-NH2) of AA2 reacts with the carboxyl group (-COOH) of AA1. In this reaction, a molecule of water (H₂O) is eliminated. The amide (peptide) linkage formed in this process is written as -C(O)NH-. After the reaction, we get the dipeptide structure: AA1-AA2: H₂N-CH[CO]-R1-[NH-CH[COOH]-R2

Reaction of the dipeptide with another amino acid

Now, let's consider an additional amino acid, AA3, with side chain R3: AA3: H₂N-CH[COOH]-R3 The dipeptide can react with this new amino acid through another condensation reaction, between the free amino group (-NH2) on AA3 and the free carboxyl group (-COOH) on AA2. This will result in water elimination and formation of a peptide linkage between AA2 and AA3.

Formation of the polypeptide

The resulting polypeptide would have the following structure: AA1-AA2-AA3: H₂N-CH[CO]-R1-[NH-CH[CO]-R2-[NH-CH[COOH]-R3 This process can continue with more amino acids, resulting in the formation of a long chain called a polypeptide. In summary, the condensation reaction between amino acids forms an amide (peptide) linkage, resulting in a dipeptide. This dipeptide can further react with additional amino acids through the same condensation process to form a polypeptide.

Key concepts

Alpha Amino Acids

Alpha amino acids are the building blocks of proteins. They are called "alpha" because the amino group \((-\mathrm{NH}_2)\) is attached to the alpha carbon, which is the carbon next to the carboxyl group \((-\mathrm{COOH})\). Each alpha amino acid has the following components:

• An amino group (\(-\mathrm{NH}_2)\).
• A carboxyl group (\(-\mathrm{COOH})\).
• A hydrogen atom.
• A unique side chain (denoted as \(R\)).

These components are all connected to the alpha carbon.
The side chain (R) varies among different amino acids and gives each amino acid its unique properties.

Condensation Reaction

A condensation reaction is a process where two molecules combine, resulting in the loss of a small molecule, often water \(H_2O\). In the case of peptide linkage formation, the amino group of one amino acid reacts with the carboxyl group of another.

• The hydrogen from the amino group and the hydroxyl part from the carboxyl group are eliminated as water.
• This results in the formation of an amide (or peptide) linkage, represented as \(-C(O)NH-\).

Such reactions are fundamental in forming dipeptides, where two amino acids link together, and can continue forming longer chains, eventually leading to a polypeptide.

Polypeptide Synthesis

Polypeptide synthesis refers to the process of creating long chains of amino acids, called polypeptides, through repeated condensation reactions. A polypeptide begins as a simple dipeptide and can grow into a sizeable molecule:

• Starting with a dipeptide, more amino acids can attach via additional condensation reactions.
• The free amino group of the growing chain reacts with the carboxyl group of a new amino acid.
• This chain can extend indefinitely, eventually folding and taking specific shapes to become functional proteins.

The endless variety of polypeptides arises due to different sequences and combinations of amino acids, enabled by the unique side chains present in the alpha amino acids.