How do hydrophobic amino acids and hydrophilic amino acids cause proteins to have a specific shape?
1 Answer
It is called the Hydrophobic Effect - and it is the main driver of protein folding (thermodynamically).
Explanation:
Amino acid chains have numerous amino acids in them. Some of them form alpha helicies, some for beta sheets - and these are examples of secondary structure.
However, amino acids can basically be broken up into two groups - those that love water and those that hate water. If you take a drop of cooking oil and put it in water, and then mix it up, you'll have all these fine tiny dots of oil....and after a few moments, they'll condense back into the same drop of oil. This is because in a larger drop, they have less surface area with which to interact with water. Amino acids do the same thing.
The hydrophobic amino acids (like the tiny drops of oil above) want to get out of water, so they all condense to the middle. This called the Hydrophobic Effect. Once this is done, the hydrogen bonding and polar groups interact to stabilize the overall 3D structure on the inside and outside of the protein. But it is the internal condensation of all those hydrophobic amino acids that drives the process.
