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Tertiary Structure of Proteins
The tertiary structure of the protein refers to the spatial arrangement of amino acids that are found far away from one another on the polypeptide chain. Simply put, it is the three-dimensional structure that the single polypeptide takes in its local environment. Since the majority of proteins fold in an aqueous environment, the hydrophobic effect plays the most important role in helping the polypeptide take on its tertiary form. Recall that the hydrophobic effect is the process by which non-polar molecules will aggregate in an aqueous solution to form larger, non-polar systems. This occurs because the larger, non-polar system is thermodynamically more stable within the water environment. Therefore, when the protein folds into its tertiary structure, the amino acids carrying the non-polar side chains will end up on the inside of the protein, as far away from water as possible. On the other hand, the amino acids with the polar, hydrophilic side chains will end up being on the surface, where they then interact with the polar water molecules via hydrogen bonds. These hydrogen bonds will stabilize the structure of the protein. Since the core of the protein consists of a compact region of non-polar amino acids, these amino acids will interact with one another via van der Waals forces (London-dispersion forces). In certain proteins, especially those that are destined to be extracellular, cross-links can also form within the polypeptide. These cross-links are most commonly disulfide bonds between two cysteine amino acids. These cystine units help conform the protein into its tertiary structure. Ionic bonds can also form between those amino acids that have opposite charges, such as lysine and aspartate amino acids. Overall, although the hydrophobic effect is the driving force in helping form the tertiary structure of the protein, other interactions such as van der Waals forces, disulfide bonds, hydrogen bonds and ionic interactions also play a role in stabilizing the tertiary structure.
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