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UPSC MainsZOOLOGY-PAPER-II201610 Marks
Q16.

Give the structural formula of an amino acid and show how a peptide bond formation occurs. Also explain how amino acids differ from each other.

How to Approach

This question requires a detailed understanding of biochemistry, specifically protein structure. The approach should involve first drawing the general structural formula of an amino acid, then explaining the peptide bond formation mechanism with a diagram. Finally, a clear explanation of how amino acids differ from each other based on their side chains is crucial. The answer should be concise, accurate, and demonstrate a strong grasp of fundamental biochemical principles. Focus on clarity and precision in explaining the chemical processes involved.

Model Answer

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Introduction

Amino acids are the building blocks of proteins, essential for all life forms. These organic molecules contain both an amino and a carboxyl functional group, along with a side chain specific to each amino acid. The sequence and arrangement of these amino acids determine the protein's structure and function. The linkage between amino acids is achieved through a peptide bond, a covalent chemical bond formed through dehydration synthesis. Understanding the structure of amino acids and the mechanism of peptide bond formation is fundamental to comprehending protein biochemistry and its role in biological processes.

Structural Formula of an Amino Acid

A typical amino acid has a central carbon atom (α-carbon) bonded to four different groups:

  • An amino group (-NH2)
  • A carboxyl group (-COOH)
  • A hydrogen atom (-H)
  • A side chain (R-group)

The R-group varies in structure and properties for each amino acid, determining its unique characteristics. The general formula can be represented as:

H2N – CH(R) – COOH

Peptide Bond Formation

Peptide bond formation is a dehydration reaction, meaning a molecule of water is removed. It occurs between the carboxyl group of one amino acid and the amino group of another. The process involves:

  1. The carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another.
  2. A water molecule (H2O) is eliminated.
  3. A covalent bond, the peptide bond (-CO-NH-), is formed between the carbon atom of the carboxyl group and the nitrogen atom of the amino group.

Peptide Bond Formation
(Image depicting peptide bond formation - source: Wikimedia Commons)

This process continues, adding amino acids one by one to form a polypeptide chain. The polypeptide chain has a free amino group at one end (N-terminus) and a free carboxyl group at the other end (C-terminus).

Differences Among Amino Acids

Amino acids differ from each other primarily due to their R-groups. These R-groups vary in size, shape, charge, hydrogen-bonding capacity, and chemical reactivity. Based on the properties of their R-groups, amino acids can be categorized into several classes:

  • Nonpolar, Aliphatic R groups: These R-groups are hydrophobic and tend to cluster together in the interior of proteins (e.g., Glycine, Alanine, Valine, Leucine, Isoleucine).
  • Aromatic R groups: These R-groups contain aromatic rings and are relatively nonpolar (e.g., Phenylalanine, Tyrosine, Tryptophan).
  • Polar, Uncharged R groups: These R-groups are hydrophilic and can form hydrogen bonds with water (e.g., Serine, Threonine, Cysteine, Asparagine, Glutamine).
  • Positively Charged (Basic) R groups: These R-groups are positively charged at physiological pH (e.g., Lysine, Arginine, Histidine).
  • Negatively Charged (Acidic) R groups: These R-groups are negatively charged at physiological pH (e.g., Aspartic acid, Glutamic acid).

These differences in R-group properties influence the three-dimensional structure of proteins, their interactions with other molecules, and their overall function. For example, hydrophobic amino acids are often found in the core of proteins, away from water, while hydrophilic amino acids are often found on the surface, interacting with the aqueous environment.

Protein Primary Structure: The specific sequence of amino acids in a polypeptide chain is known as the primary structure. This sequence is genetically determined and dictates the higher levels of protein structure.

Conclusion

In conclusion, amino acids are the fundamental units of proteins, linked together by peptide bonds formed through dehydration synthesis. The diversity of amino acids arises from their unique R-groups, which dictate their chemical properties and influence protein structure and function. Understanding these principles is crucial for comprehending the complexities of biological systems and the role of proteins in maintaining life. Further research into protein folding and dynamics continues to reveal the intricate relationship between amino acid sequence and biological activity.

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.

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Additional Resources

Key Definitions

Polypeptide
A linear polymer of amino acids linked by peptide bonds. Polypeptides are the primary structural component of proteins.
Dehydration Synthesis
A chemical reaction in which monomers are joined together by removing a water molecule. Peptide bond formation is an example of dehydration synthesis.

Key Statistics

There are 20 standard amino acids commonly found in proteins.

Source: Lehninger Principles of Biochemistry (2017)

Proteins constitute approximately 50% of the dry weight of a cell.

Source: Molecular Biology of the Cell (2014)

Examples

Sickle Cell Anemia

A single amino acid substitution (glutamic acid to valine) in the beta-globin chain of hemoglobin causes sickle cell anemia, demonstrating the critical importance of amino acid sequence in protein function.

Frequently Asked Questions

▶What is the role of ribosomes in peptide bond formation?

Ribosomes are cellular organelles responsible for protein synthesis. They catalyze the formation of peptide bonds between amino acids during translation, using mRNA as a template.

Topics Covered

BiologyBiochemistryAmino AcidsProteinsPeptide Bonds
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