Tertiary Structure of Protein: Videos & Practice Problems

The tertiary structure of proteins represents their overall three-dimensional shape, which is crucial for their function. Unlike secondary structures, such as alpha helices and beta sheets, which are stabilized by backbone interactions, tertiary structures are primarily stabilized by interactions between the side chains, or R groups, of amino acids. This means that R groups can interact even if they are not adjacent in the sequence; they can be far apart along the polypeptide chain. The folding of the protein allows these distant R groups to come into proximity, facilitating various interactions that contribute to the stability and functionality of the protein.

In a typical protein structure, you can observe various secondary structures: beta strands and beta sheets are often depicted in red, while alpha helices are shown in green. Additionally, long loops that change the direction of the backbone and beta turns, which are abrupt changes in direction, play significant roles in connecting these secondary structures. Together, these elements contribute to the formation of the tertiary structure, illustrating how secondary structures come together to create a complex, functional protein.

Understanding the specific interactions between R groups is essential for grasping the nuances of tertiary structure. These interactions can include hydrogen bonds, ionic bonds, hydrophobic interactions, and disulfide bridges, all of which are vital for maintaining the protein's shape and stability. As you delve deeper into the study of protein structures, practicing these concepts will enhance your comprehension of how proteins achieve their functional forms.

The tertiary structure of proteins is primarily stabilized by interactions between the R groups of amino acids rather than by the backbone interactions. These R group interactions are predominantly non-covalent, and there are four key types to understand: ionic bonds (or salt bridges), the hydrophobic effect, hydrogen bonds, and van der Waals interactions. While most of these interactions are non-covalent, covalent interactions, specifically disulfide bonds formed between cysteine residues, also play a significant role in stabilizing the tertiary structure.

Ionic bonds occur between ionizable R groups, which can be remembered using the mnemonic "yucky crazy dragons eat knights riding horses," representing the seven amino acids with ionizable side chains. For example, lysine (K) and aspartic acid (D) can form an ionic bond due to their charged R groups.

The hydrophobic effect is observed when non-polar amino acids, such as valine, cluster together to minimize their exposure to water, thereby stabilizing the protein structure. Hydrogen bonds typically form between polar amino acids, such as serine and asparagine, allowing for additional stabilization through interactions between their R groups.

Van der Waals interactions, while not specifically numbered, occur between all atoms in the polypeptide chain and contribute significantly to the overall stability of the tertiary structure by keeping different parts of the protein in close proximity.

Finally, disulfide bridges, a type of covalent interaction, form between two cysteine residues when they are in close proximity, creating a strong bond that further stabilizes the protein's three-dimensional shape. This bond is represented by the connection between the sulfur atoms of the cysteine side chains.

In summary, the interplay of these five types of R group interactions—ionic bonds, the hydrophobic effect, hydrogen bonds, van der Waals interactions, and disulfide bridges—collectively contribute to the complex and functional tertiary structure of proteins, which is essential for their biological activity.