Question

Which of the following amino acids are more likely to be found on the exterior of a globular protein, and which on the interior? Explain. (a) Valine (b) Aspartic acid (c) Phenylalanine (d) Lysine

Short answer

Valine and phenylalanine are likely inside; aspartic acid and lysine are likely outside.

Step-by-step solution

Understand Properties of Amino Acids

Amino acids can be classified as either hydrophobic (water-repelling) or hydrophilic (water-attracting) based on the nature of their side chains. Hydrophobic amino acids likely reside in the interior of proteins, while hydrophilic amino acids are likely on the exterior, interacting with the aqueous environment.

Analyze Characteristics of Valine

Valine is an amino acid with a nonpolar, hydrophobic side chain. Because of its hydrophobic nature, valine is more likely to be found in the interior of a globular protein.

Analyze Characteristics of Aspartic Acid

Aspartic acid contains a polar, acidic side chain that is hydrophilic. This characteristic makes it more likely to be found on the exterior of a globular protein, where it can interact with water molecules.

Analyze Characteristics of Phenylalanine

Phenylalanine has a nonpolar, aromatic side chain, making it hydrophobic. It is more commonly found in the interior of globular proteins to avoid water interaction.

Analyze Characteristics of Lysine

Lysine features a long, polar, and positively charged side chain, making it strongly hydrophilic. This propensity for interacting with water means it is more likely to be found on the exterior of globular proteins.

Key concepts

Hydrophobic and Hydrophilic Interactions

Proteins, the workhorses of the cell, are composed of amino acids that can either attract or repel water, defining their roles as hydrophilic or hydrophobic. These interactions are crucial in determining where amino acids position themselves within a protein structure.

• Hydrophobic Interactions: Amino acids with nonpolar side chains, such as valine and phenylalanine, tend to be hydrophobic. This means they repel water molecules and prefer to cluster together within the interior of proteins. This grouping creates a stable core, protected from external water molecules, which is energetically favorable.
• Hydrophilic Interactions: In contrast, amino acids like aspartic acid and lysine contain polar or charged side chains. These features attract water, making them hydrophilic. They thrive on the protein's surface, interacting pleasantly with the aqueous environment which stabilizes the protein through favorable interactions with water molecules.

These interactions are fundamental in determining the three-dimensional shape of proteins, influencing their functional roles in biological processes.

Globular Proteins

Globular proteins, unlike fibrous proteins, exhibit a compact, spherical shape crucial for their function. This shape is the result of intricate folding, heavily influenced by hydrophobic and hydrophilic interactions. Within globular proteins, amino acids must properly align to ensure the protein maintains its structure and function.

• Interior Composition: The core typically consists of hydrophobic amino acids like valine and phenylalanine that avoid interaction with water. This makes the protein's core more stable, ensuring it remains intact and functional in the cell's aqueous environment.
• Exterior Composition: The surface is more frequently populated with hydrophilic amino acids such as aspartic acid and lysine. This allows these proteins to interact with the environment, including transport of substances or other proteins.

Such structural arrangements in globular proteins not only stabilize their form but also facilitate dynamic functions necessary for life, such as enzyme catalysis, transport, and signal transduction.

Protein Structure

The structure of proteins is critical to their function and can be divided into several levels of organization. Understanding these levels helps us to better appreciate how proteins shape their roles in the cell.

• Primary Structure: This is the linear sequence of amino acids in a protein, determined by peptide bonds. It is like a string of beads, where each bead is an amino acid. The order of amino acids dictates how the protein will fold.
• Secondary Structure: Proteins form local structures such as alpha-helices and beta-sheets, stabilized by hydrogen bonds. These shapes give a protein its initial folds.
• Tertiary Structure: Here, the protein achieves its three-dimensional shape due to interactions among side chains, like hydrophobic and hydrophilic interactions, disulfide bridges, and ionic bonds. This level of structure is critical in defining the protein's function.
• Quaternary Structure: Some proteins consist of multiple polypeptide chains and their arrangement in a multi-subunit complex is the quaternary structure. Not all proteins have this level of structure, but those that do rely on it for combined functionality.

By understanding protein structures, scientists can better comprehend how proteins work and how mutations or alterations in their sequence might lead to dysfunction or disease.