Structure of Dipeptide Unit in Protein | UPSC Mains ZOOLOGY-PAPER-II 2025

Write on the following in about 150 words each: 5.(d) Structure of dipeptide unit of a protein

How to Approach

The question asks for the structure of a dipeptide unit of a protein. The approach should involve defining a dipeptide, explaining its formation through a peptide bond, and detailing the key structural features of the peptide bond and the overall dipeptide molecule. It is crucial to highlight the N-terminal and C-terminal ends and the role of R-groups. A diagrammatic representation would be highly beneficial, though not explicitly asked for in a written answer, conceptual clarity should be presented.

Model Answer

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Introduction

Proteins, the fundamental macromolecules performing a vast array of functions in living organisms, are polymers of amino acids. These amino acid monomers are linked together by peptide bonds to form polypeptide chains. A dipeptide represents the simplest form of such a chain, comprising exactly two amino acid units joined by a single peptide bond. Understanding the structure of a dipeptide is therefore essential for comprehending the more complex architecture and functional diversity of larger proteins. It serves as a foundational building block, exhibiting characteristic features crucial to protein stability and reactivity.

Structure of Dipeptide Unit of a Protein

A dipeptide is an organic compound formed by the covalent linkage of two amino acids. This union occurs through a specific chemical bond known as a peptide bond, which is an amide linkage.

Formation of the Peptide Bond

The formation of a dipeptide involves a condensation reaction (also known as dehydration synthesis) between the carboxyl group (-COOH) of one amino acid and the amino group (-NH₂) of another amino acid. During this reaction:

A hydroxyl group (-OH) is removed from the carboxyl group of the first amino acid.
A hydrogen atom (-H) is removed from the amino group of the second amino acid.
These removed atoms combine to form a molecule of water (H₂O), which is released.
The remaining carbon atom from the carboxyl group forms a covalent bond with the nitrogen atom from the amino group, creating the peptide bond (-CO-NH-).

The chemical representation of a dipeptide can generally be shown as:
H₂N-CHR₁-CO-NH-CHR₂-COOH
where R₁ and R₂ represent the distinctive side chains (R groups) of the two amino acids involved.

Key Structural Features of a Dipeptide

Amino Acid Residues: A dipeptide consists of two amino acid residues. Each residue retains its central alpha-carbon, which is attached to its unique R-group.
Peptide Bond: This is the defining feature, a rigid and planar amide bond (-CO-NH-). Due to partial double-bond character from resonance, there is restricted rotation around the C-N peptide bond. This rigidity is crucial for dictating protein conformation.
N-terminus and C-terminus: A dipeptide has a free amino group (-NH₂) at one end, known as the N-terminal end, and a free carboxyl group (-COOH) at the other end, known as the C-terminal end. These terminal groups are ionizable and contribute to the dipeptide's overall charge and solubility.
Side Chains (R-groups): The chemical properties and biological functions of a dipeptide are largely determined by the specific R-groups of its constituent amino acids. These R-groups project away from the main polypeptide backbone.

For example, if Glycine (Gly) and Alanine (Ala) combine, two different dipeptides can be formed: Gly-Ala or Ala-Gly, depending on which amino acid contributes its carboxyl group and which contributes its amino group, highlighting the directionality of the peptide bond and the resulting N- and C- termini.

Conclusion

In essence, a dipeptide unit is the simplest polymeric structure of a protein, formed by two amino acids linked via a single peptide bond. This amide linkage, characterized by its planarity and partial double-bond nature, is a cornerstone of protein architecture. The presence of distinct N-terminal and C-terminal ends, along with the unique side chains of the constituent amino acids, dictates the dipeptide's specific chemical properties and its potential physiological roles. Understanding this basic unit is fundamental to appreciating the intricate folding and diverse functions of complex proteins.

Answer Length

This is a comprehensive model answer for learning purposes and may exceed the word limit. In the exam, always adhere to the prescribed word count.

Additional Resources

Key Definitions

Dipeptide

An organic compound composed of two amino acids covalently linked together by a single peptide bond, formed through a condensation reaction.

Peptide Bond

An amide type of covalent chemical bond linking the carboxyl group of one amino acid to the amino group of another amino acid, with the elimination of a water molecule.

Key Statistics

From the 20 common proteinogenic amino acids, approximately 400 different dipeptides can be formed by connecting them, and most have been detected in nature. (Source: Bachem, 2017)

Source: Bachem

The trans form of the peptide bond is overwhelmingly preferred over the cis form in most peptide bonds, with roughly a 1000:1 ratio in trans:cis populations in folded proteins. (Source: Wikipedia - Peptide bond)

Source: Wikipedia

Examples

Aspartame - An Artificial Sweetener

Aspartame (L-aspartyl-L-phenylalanine methyl ester) is a well-known synthetic dipeptide approved as a low-calorie artificial sweetener. It is approximately 200 times sweeter than sucrose and is widely used in foods and beverages, demonstrating the commercial significance and distinct properties of certain dipeptides. It is derived from aspartic acid and phenylalanine.

Carnosine - Antioxidant Dipeptide

Carnosine (β-alanyl-L-histidine) is a naturally occurring dipeptide found in high concentrations in skeletal muscle, brain, and gastrointestinal tissues. It acts as a potent antioxidant, scavenging reactive oxygen species and carbonyl compounds, and is being studied for its potential roles in mitigating metabolic syndrome and protecting against oxidative stress.

Frequently Asked Questions

▶What is the primary difference between a dipeptide and a protein?

A dipeptide consists of only two amino acids linked by one peptide bond, making it the smallest peptide unit. A protein, on the other hand, is a much larger macromolecule typically composed of 50 or more amino acids linked together to form one or more long polypeptide chains, often folded into complex three-dimensional structures to perform specific biological functions.

▶Why is the peptide bond considered rigid and planar?

The peptide bond has a partial double-bond character due to resonance between the carbonyl carbon, oxygen, and the amide nitrogen. This partial double-bond prevents free rotation around the C-N bond, making the peptide group rigid and planar. This structural constraint is crucial for limiting the conformational flexibility of the polypeptide chain and influencing protein folding.