Question

What type of interaction would you expect between the \(\mathrm{R}\) groups of the following amino acids in a tertiary structure? a. cysteine and cysteine b. aspartic acid and lysine c. serine and aspartic acid d. leucine and leucine

Short answer

a. Disulfide bond; b. Ionic bond; c. Hydrogen bond; d. Hydrophobic interactions.

Step-by-step solution

Understand the question

The question asks for the type of interactions that occur between specific \(\text{R}\) groups (side chains) of amino acids in a protein's tertiary structure. Familiarize with the properties of these amino acids' \(\text{R}\) groups.

Analyze cysteine and cysteine

Cysteine has a thiol group (\(\text{-SH}\)). When two cysteine residues are near each other, they can form a covalent bond known as a disulfide bond (\(\text{-S-S-}\)).

Analyze aspartic acid and lysine

Aspartic acid has a negatively charged carboxylate group (\(\text{COO}^-\)) and lysine has a positively charged amino group (\(\text{NH}_3^+\)). Therefore, they will attract each other and form an ionic bond.

Analyze serine and aspartic acid

Serine contains a hydroxyl group (\(\text{OH}\)), which can form hydrogen bonds. Aspartic acid has carboxyl groups that can donate or accept hydrogen bonds. Therefore, serine and aspartic acid will interact through hydrogen bonding.

Analyze leucine and leucine

Leucine has a nonpolar aliphatic side chain. When two leucine residues are near each other, they will tend to avoid water and form hydrophobic interactions.

Key concepts

Disulfide Bonds

Disulfide bonds are a special type of covalent bond that play a crucial role in the stability of tertiary structures in proteins. They occur between the sulfur atoms of cysteine residues. Each cysteine amino acid contains a thiol group \( -SH \). When two cysteine residues come close to each other, the thiol groups can react to form a disulfide bond \( -S-S- \).

Disulfide bonds are strong and help maintain the protein’s shape. This interaction is particularly important in proteins that need to be stable in harsh environments, like those outside of cells.

They help stabilize the folded structure of the protein, ensuring it remains intact and functional.
For instance, in the exercise given, the interaction between cysteine and cysteine exemplifies the formation of a disulfide bond.

Ionic Bonds

Ionic bonds form between oppositely charged \( R \) groups (side chains) of amino acids. These bonds occur due to the electrostatic attraction between a positively charged group and a negatively charged group.

In proteins, this usually involves interactions between side chains of amino acids like aspartic acid and lysine. Aspartic acid has a carboxylate group \( \text{COO}^- \), which is negatively charged, while lysine has an amino group that is positively charged \( \text{NH}_3^+ \).

When these two types of \( R \) groups come close to each other, they attract, forming an ionic bond.

Ionic bonds are relatively strong and contribute significantly to a protein’s tertiary structure by pulling different regions of the protein together.

Hydrogen Bonds

Hydrogen bonds are weak interactions that occur when a hydrogen atom is shared between two electronegative atoms like nitrogen or oxygen. These bonds play a significant role in stabilizing the tertiary structure of proteins.

For example, in the given exercise, serine and aspartic acid can form a hydrogen bond due to their side chains. Serine has a hydroxyl group \( \text{OH} \) and aspartic acid has carboxyl groups that can both donate and accept hydrogen atoms to form hydrogen bonds.

These interactions are crucial for the proper folding and flexibility of proteins, and while they are relatively weaker than covalent bonds, their cumulative effect greatly influences protein stability.

Hydrophobic Interactions

Hydrophobic interactions occur between nonpolar \( R \) groups of amino acids. These interactions play a pivotal role in the folding of proteins by driving nonpolar side chains to the interior of the protein structure to avoid the aqueous environment.

Amino acids like leucine, which have nonpolar aliphatic side chains, are perfect examples. When two leucine residues come close to each other, they tend to cluster together away from water, creating a hydrophobic interaction.

These interactions help to stabilize the protein’s structure by collapsing nonpolar residues inwards, thus promoting the compact, functional form of the protein. Although weaker than some other types of bonds, hydrophobic interactions are essential for the three-dimensional shape of the protein.