Question

Many plasma proteins found in an aqueous environment are globular in shape. Which amino acid side chains would you expect to find on the surface of a globular protein and in contact with the aqueous environment? Which would you expect to find inside, shielded from the aqueous environment? Explain. (a) Leu (b) Arg (c) Ser (d) Lys (e) Phe

Short answer

Answer: Amino acids with hydrophilic side chains, such as Arg, Ser, and Lys, are more likely to be found on the surface of a globular protein and in contact with the aqueous environment. Amino acids with hydrophobic side chains, like Leu and Phe, are expected to be inside the protein, shielded from the water.

Step-by-step solution

Understand the properties of hydrophobic and hydrophilic amino acids

Hydrophobic amino acids have non-polar side chains, which means they do not interact well with water. They tend to be found in the interior of globular proteins to minimize their contact with water. Hydrophilic amino acids have polar or charged side chains, allowing them to form favorable interactions (like hydrogen bonds) with water. These amino acids usually reside on the surface of globular proteins, exposed to the aqueous environment.

Categorize the amino acids as hydrophobic or hydrophilic

Based on the given amino acids, we can classify them as follows: (a) Leu (Leucine) - Hydrophobic, non-polar aliphatic side chain (b) Arg (Arginine) - Hydrophilic, positively charged side chain (c) Ser (Serine) - Hydrophilic, polar side chain with a hydroxyl group (d) Lys (Lysine) - Hydrophilic, positively charged side chain (e) Phe (Phenylalanine) - Hydrophobic, aromatic side chain

Determine the location of amino acids in a globular protein

Based on the properties of each amino acid, we can now determine their location in a globular protein. (a) Leu: Inside the protein, shielded from the aqueous environment (hydrophobic) (b) Arg: On the surface of the protein, in contact with the aqueous environment (hydrophilic) (c) Ser: On the surface of the protein, in contact with the aqueous environment (hydrophilic) (d) Lys: On the surface of the protein, in contact with the aqueous environment (hydrophilic) (e) Phe: Inside the protein, shielded from the aqueous environment (hydrophobic) So, we can expect amino acids with hydrophilic side chains (Arg, Ser, and Lys) to be on the surface of a globular protein and in contact with water, while amino acids with hydrophobic side chains (Leu and Phe) will be found inside the protein, shielded from the aqueous environment.

Key concepts

Amino Acid Polarity

Amino acids are the building blocks of proteins, each with a unique side chain that determines its polarity and thus its chemical behavior. Polarity in amino acids refers to the distribution of electric charge across the molecule.
Amino acids can be classified as either polar or non-polar based on the nature of their side chains.

• Polar Amino Acids: These have side chains containing groups that can form hydrogen bonds with water, such as hydroxyl, carboxyl, or amine groups. This makes them hydrophilic ("water-loving") and usually positions them on the surface of proteins where they can interact with the aqueous environment.
• Non-Polar Amino Acids: These have side chains made up of hydrocarbons, making them hydrophobic ("water-fearing"). They tend to cluster in the interior of proteins, away from water.

Recognizing whether an amino acid is polar or non-polar helps predict its role and position within a protein, especially in complex structures like globular proteins.

Hydrophobic vs Hydrophilic Interactions

The interaction of amino acid side chains with water or other molecules is crucial for understanding how proteins fold and function. This interaction is primarily governed by whether the side chains are hydrophobic or hydrophilic.

• Hydrophobic Interactions: Hydrophobic amino acids prefer to avoid water and tend to aggregate with each other to minimize exposure to the aqueous environment. This promotes the folding of proteins into compact structures, with hydrophobic residues often tucked inside the protein core.
• Hydrophilic Interactions: Contrarily, hydrophilic amino acids readily engage with water, enabling them to form hydrogen bonds or ionic interactions. This often places them on the surface of proteins, allowing the protein to remain soluble in water.

These interactions are fundamental to the stable configuration and dynamic properties of proteins, influencing how they interact with other biological molecules and perform their functions.

Protein Structure and Function

Proteins have various structures, ranging from simple sequences of amino acids to complex three-dimensional formations that determine their function. Understanding protein structure begins with knowing these structural levels:

• Primary Structure: This is the linear sequence of amino acids in a protein chain. It dictates all higher-level structures and ultimately, the protein's function.
• Secondary Structure: This involves local folding patterns, like α-helices and β-sheets, stabilized by hydrogen bonds between backbone atoms.
• Tertiary Structure: The overall three-dimensional shape of a single protein molecule, determined by interactions between side chains, including hydrophobic and hydrophilic interactions.
• Quaternary Structure: Some proteins form complexes with other protein molecules, producing quaternary structures.

Globular proteins, commonly found in biological processes, have a tertiary structure where hydrophilic residues face outward to interact with the environment, while hydrophobic residues are internally oriented, driving unique biological activities beyond structural roles.