Question

A question of competition. Would a homopolymer of alanine be more likely to form an \(\alpha\) helix in water or in a hydrophobic medium? Explain.

Short answer

It is more likely to form an \(\alpha\) helix in a hydrophobic medium.

Step-by-step solution

Understanding Alanine and Homopolymer

Alanine is an amino acid with a small, hydrophobic side chain (a methyl group). A homopolymer of alanine means a polymer consisting entirely of alanine residues. The nature of alanine contributes to the overall properties of the homopolymer.

Structure of an α Helix

An \(\alpha\) helix is a common secondary structure in proteins, characterized by a right-handed coil where the backbone is held together by hydrogen bonds between every fourth amino acid. This formation is stabilized by these hydrogen bonds and influenced by the surrounding environment.

Environmental Influence on α Helix Formation

In a water environment (aqueous), the hydrophilic property of water can disrupt the formation of an \(\alpha\) helix by interacting with the backbone and side chains of the homopolymer. Conversely, in a hydrophobic medium, there is less competition for hydrogen bonding, allowing the helix to maintain more stable interactions internally due to the reduced interference.

Impact of Hydrophobicity

Alanine's hydrophobic side chain favors interactions that exclude water, which supports the stability of the \(\alpha\) helix in non-polar, hydrophobic environments. The lack of polar interference in a hydrophobic medium helps maintain the structure of the \(\alpha\) helix more effectively.

Conclusion - Medium Preference

Given the properties of both the alanine side chains and the nature of hydrogen bonding in different environments, a homopolymer of alanine is more likely to form an \(\alpha\) helix in a hydrophobic medium rather than in water.

Key concepts

Alpha Helix

An \(\alpha\) helix is an important structural motif commonly found in proteins. It is characterized by a right-handed helix where the amino acids coil around each other. This coiling creates a stable structure by using hydrogen bonds. Each carbonyl (C=O) group of the backbone forms a hydrogen bond with the amino hydrogen (N-H) of the fourth amino acid along the chain.

The environment around the \(\alpha\) helix plays a crucial role in its stability. In aqueous environments, water can interfere with the hydrogen bonds by forming its own interactions with the protein's backbone. In contrast, in a hydrophobic environment, there is less of this interference. This allows the intramolecular hydrogen bonds to hold the \(\alpha\) helix structure more stably.

• The \(\alpha\) helix is essential for the protein's structural integrity and function.
• Its stability is highly influenced by environmental conditions.

Hydrophobic Interaction

Hydrophobic interactions are critical in determining how proteins fold and maintain their shapes. These interactions involve molecules with non-polar side chains, such as alanine, which do not mix with water. When placed in a hydrophobic environment, these non-polar molecules tend to aggregate, minimizing their exposure to aqueous surroundings.

Such interactions are less competitive in hydrophobic environments due to the absence of polar entities like water. This results in less disturbance in structures such as the \(\alpha\) helix, allowing for more stable hydrogen bonding within the molecule itself.

• Hydrophobic interactions help stabilize protein structures in varied environments.
• They play a significant role in biological processes and cellular functions.

Amino Acids

Amino acids are the building blocks of proteins, each containing an amino group (\(-NH_2\)), a carboxyl group (\(-COOH\)), a hydrogen atom, and a unique side chain attached to a central carbon atom. The side chain, or R group, determines the characteristics and chemical reactivity of the amino acid.

Alanine is a simple amino acid with a small, hydrophobic side chain (a methyl group). This small non-polar side chain makes alanine less reactive with water, influencing its behavior in forming secondary structures like the \(\alpha\) helix. In particular, alanine's properties favor helix formation in hydrophobic environments where its side chain can interact favorably without interference from polar molecules like water.

• Amino acids like alanine are crucial for forming protein structures.
• Their side chains significantly influence protein folding and stability.