The following statements describe the propensity and role of amino acids in the secondary structure of proteins

A. Alanine has a high frequency of occurrence in α- helices
B. Proline has a high frequency of occurrence in α- helices
C. The 𝛘 does not affect the helix propensity of serine, threonine and valine
D. Peptide bonds involving ‘N’ of proline may display cis-trans isomerism
Choose the correct combination.

(1) A and D
(2) B and C
(3) B and C
(4) C and D

Amino Acid Propensity in Protein Secondary Structure

Proteins adopt specific secondary structures such as alpha-helices, beta-sheets, and turns, primarily governed by the intrinsic properties of amino acids. Understanding these propensities is crucial for students preparing for CSIR NET Life Science and related competitive exams. Let’s explore the correct combination of statements regarding amino acid roles in secondary structures and their implications.

Correct Answer:

The correct combination is (1) A and D.

Explanation:

A. Alanine has a high frequency of occurrence in α-helices ✅

Alanine is a small, nonpolar amino acid with a strong propensity for forming alpha-helices due to its ability to fit well within the helical structure without causing steric hindrance.

B. Proline has a high frequency of occurrence in α-helices ❌

Proline is known as a helix breaker due to its rigid cyclic structure. It introduces kinks in the helical structure, making it unfavorable for alpha-helix formation.

C. The χ (chi) angle does not affect the helix propensity of serine, threonine, and valine ❌

The chi (𝛘) angle, which represents the side-chain torsional angle, significantly affects helix formation. Serine, threonine, and valine are known to disrupt helices due to steric hindrance and hydrogen bonding competition.

D. Peptide bonds involving ‘N’ of proline may display cis-trans isomerism ✅

Unlike most amino acids, which predominantly adopt the trans configuration in peptide bonds, proline can exist in both cis and trans forms. This property plays a critical role in protein folding and structure.

Nearby Topics for Better Understanding

1. Factors Affecting Secondary Structure Formation

Several factors influence whether an amino acid prefers an alpha-helix, beta-sheet, or turn:

• Hydrogen Bonding: Stabilizes helices and sheets.
• Steric Hindrance: Bulky side chains may disrupt helix formation.
• Electrostatic Interactions: Charged amino acids can stabilize or destabilize secondary structures.

2. Amino Acids with High Helix Propensity

• Alanine – Strong alpha-helix former
• Leucine, Methionine, Glutamate – Favor alpha-helices
• Glycine, Proline – Helix breakers

3. Beta-Sheet Forming Amino Acids

• Valine, Isoleucine, Phenylalanine – Favor beta-sheets due to their bulky side chains and ability to engage in hydrogen bonding

4. Role of Proline in Protein Folding

Proline is often found in turns and loops rather than helices. It plays an essential role in protein folding due to its unique ability to exist in both cis and trans configurations, influencing protein stability and function.

Conclusion

Understanding amino acid propensities in secondary structures is essential for mastering protein biochemistry. Alanine strongly favors alpha-helices, whereas proline disrupts them and contributes to structural bends due to its cis-trans isomerism. This knowledge is valuable for CSIR NET Life Science aspirants, aiding in conceptual clarity and application-based learning.

By grasping these fundamental concepts, students can effectively tackle questions on protein structure and function, ensuring better performance in competitive exams.