A portion of a polypeptide chain contains the following sequence of amino acids:
—Leu—Val—Cys—Asp— 
a. Which amino acids are likely to be found on the inside of the protein structure? Why?

Verified step by step guidance

1. Step 1: Understand the context of the problem. Proteins are made up of amino acids, and their structure is influenced by the chemical properties of these amino acids. Hydrophobic (nonpolar) amino acids tend to be found on the inside of the protein structure, away from water, while hydrophilic (polar or charged) amino acids are often on the outside, interacting with the aqueous environment.
2. Step 2: Identify the amino acids in the given sequence: Leu (Leucine), Val (Valine), Cys (Cysteine), and Asp (Aspartic acid). Each of these amino acids has distinct chemical properties that determine their likely location in the protein structure.
3. Step 3: Classify the amino acids based on their polarity and hydrophobicity: Leu and Val are nonpolar and hydrophobic, meaning they are likely to be found on the inside of the protein structure. Cys is polar but can form disulfide bonds, which may stabilize the protein interior. Asp is polar and negatively charged, making it hydrophilic and more likely to be found on the outside of the protein.
4. Step 4: Explain why hydrophobic amino acids are found on the inside. In aqueous environments, proteins fold in a way that minimizes the exposure of hydrophobic amino acids to water. This is driven by the hydrophobic effect, which stabilizes the protein structure by burying nonpolar residues in the core.
5. Step 5: Conclude that Leu and Val are most likely to be found on the inside of the protein structure due to their hydrophobic nature, while Asp is likely to be on the outside. Cys may be found on the inside if it forms disulfide bonds, but its location can vary depending on the specific protein structure.

Key Concepts

Hydrophobic and Hydrophilic Amino Acids

Amino acids can be classified as hydrophobic (water-repelling) or hydrophilic (water-attracting) based on their side chains. Hydrophobic amino acids, such as Leucine (Leu) and Valine (Val), tend to be found in the interior of proteins, away from the aqueous environment, while hydrophilic amino acids, like Aspartic acid (Asp), are more likely to be on the surface, interacting with water.

Protein Folding and Structure

Proteins fold into specific three-dimensional shapes that are crucial for their function. This folding is driven by the interactions between amino acids, including hydrophobic interactions, hydrogen bonds, and ionic bonds. The sequence of amino acids determines how the protein will fold, influencing which residues are buried inside and which are exposed.

Amino Acid Properties

Each amino acid has unique properties based on its side chain, which affects its behavior in a protein. For example, Cysteine (Cys) can form disulfide bonds, contributing to protein stability, while Aspartic acid (Asp) carries a negative charge at physiological pH, making it more likely to be found on the protein's surface. Understanding these properties helps predict the location of amino acids within the protein structure.