Question

What type of interaction would you expect between the \(\mathrm{R}\) groups of the following amino acids in a quaternary structure? a. phenylalanine and isoleucine b. aspartic acid and histidine c. asparagine and tyrosine d. alanine and proline

Short answer

Phenylalanine and isoleucine: hydrophobic. Aspartic acid and histidine: ionic. Asparagine and tyrosine: hydrogen bonding. Alanine and proline: hydrophobic.

Step-by-step solution

- Identify the Nature of \(\text{R}\) Groups

First, determine the nature (polar, non-polar, acidic, basic) of the \(\mathrm{R}\) groups for each amino acid. - Phenylalanine and isoleucine have non-polar \(\mathrm{R}\) groups. - Aspartic acid has an acidic \(\mathrm{R}\) group, while histidine has a basic \(\mathrm{R}\) group. - Asparagine has a polar \(\mathrm{R}\) group, and tyrosine has a polar \(\mathrm{R}\) group with an aromatic ring. - Alanine and proline both have non-polar \(\mathrm{R}\) groups.

- Determine Type of Interaction

Next, determine the type of interaction expected between these \(\mathrm{R}\) groups in the context of a protein's quaternary structure.

- Analyze Non-Polar Interactions

For non-polar \(\mathrm{R}\) groups like phenylalanine and isoleucine, as well as alanine and proline, hydrophobic interactions are expected. These \(\mathrm{R}\) groups will likely cluster together away from water.

- Analyze Acid-Base Interactions

For acidic and basic \(\mathrm{R}\) groups such as aspartic acid and histidine, ionic interactions or salt bridges are expected. These occur due to the attraction between the negatively charged carboxyl group of aspartic acid and the positively charged amino group of histidine.

- Analyze Polar Interactions

For polar \(\mathrm{R}\) groups like asparagine and tyrosine, hydrogen bonding is likely. The \(\mathrm{R}\) groups can form hydrogen bonds with each other or with water molecules.

Conclusion

Summarize each pair's interaction type: - Phenylalanine and isoleucine: Hydrophobic interactions - Aspartic acid and histidine: Ionic interactions - Asparagine and tyrosine: Hydrogen bonding - Alanine and proline: Hydrophobic interactions

Key concepts

Non-Polar Amino Acids

Non-polar amino acids like phenylalanine, isoleucine, alanine, and proline have \(\text{R}\) groups that do not interact with water molecules. These \(\text{R}\) groups are hydrophobic, meaning they avoid water and tend to group together to minimize surface area exposure to water. This tendency to cluster plays a critical role in the folding and stabilization of protein structures. In a quaternary structure where multiple protein subunits come together, these non-polar \(\text{R}\) groups will typically align to form hydrophobic cores.

Acidic and Basic Amino Acids

Acidic and basic amino acids have \(\text{R}\) groups that are either positively or negatively charged at physiological pH. Aspartic acid, for instance, has a negatively charged carboxyl group, making it acidic, while histidine has a positively charged amino group, making it basic. When these opposite charges come into proximity, they can form ionic bonds or salt bridges. These interactions help stabilize the protein's structure by providing electrostatic attractions between the positively and negatively charged \(\text{R}\) groups.

Polar Amino Acids

Polar amino acids like asparagine and tyrosine contain \(\text{R}\) groups that can form hydrogen bonds. Hydrogen bonds occur due to the attraction between a partially positive hydrogen atom and a partially negative atom like oxygen or nitrogen. These interactions not only help to stabilize protein structures but also enable polar \(\text{R}\) groups to interact with water molecules, making these regions of the protein hydrophilic or water-attracting.

Hydrophobic Interactions

Hydrophobic interactions occur when non-polar \(\text{R}\) groups, such as those in phenylalanine, isoleucine, alanine, and proline, cluster together. This clustering reduces their exposure to the surrounding aqueous environment. These interactions are particularly crucial in the interior of proteins where water exclusion helps to maintain structural integrity. Hydrophobic interactions stabilize the protein's overall shape by driving the folding process.

Ionic Interactions

Ionic interactions, often referred to as salt bridges, occur between positively and negatively charged \(\text{R}\) groups, such as those in aspartic acid and histidine. These interactions result from electrostatic attraction. Ionic interactions are particularly strong in the aqueous environment of the cell and help to stabilize the protein’s tertiary and quaternary structures by holding the protein's different parts together.

Hydrogen Bonding

Hydrogen bonding is another key interaction in protein structures, especially involving polar amino acids like asparagine and tyrosine. A hydrogen bond forms when a hydrogen atom covalently bonded to an electronegative atom like oxygen or nitrogen is attracted to another electronegative atom. In proteins, hydrogen bonds can occur between \(\text{R}\) groups or between \(\text{R}\) groups and the backbone, contributing significantly to the protein’s stability and specificity.

Quaternary Structure

The quaternary structure of a protein involves the arrangement and interactions of multiple polypeptide chains or subunits. These subunits can interact through various bonds and forces including hydrogen bonds, ionic interactions, and hydrophobic interactions. In the context of quaternary structure, the nature of the \(\text{R}\) groups involved dictates how the different subunits will interact, guiding the overall architecture and function of the multi-subunit protein complex.