Is the side chain of lysine polar or nonpolar? How would lysine interact with phenylalanine (side chain? Explain why.
http://webhost.bridgew.edu/fgorga/proteins/polar.htm
To determine whether the side chain of lysine is polar or nonpolar, we need to examine the chemical properties of its side chain. Lysine is an amino acid with a basic amino group (-NH2) as its side chain.
The amino group (-NH2) in lysine is polar due to the presence of a nitrogen atom with a lone pair of electrons. Nitrogen is more electronegative than hydrogen, so it attracts the electron density towards itself, creating a partial positive charge on the hydrogen atom and a partial negative charge on the nitrogen atom. This charge distribution in the amino group makes the side chain of lysine polar.
Now, let's discuss how lysine would interact with phenylalanine, specifically their side chains.
The side chain of phenylalanine consists of a phenyl group (-C6H5) which is nonpolar. The phenyl group is composed of a benzene ring, which contains only carbon and hydrogen atoms with symmetrical electron distribution. As a result, the phenylalanine side chain is nonpolar.
When lysine interacts with phenylalanine, the polar amino group of lysine can form hydrogen bonds with the nonpolar benzene ring of phenylalanine. Hydrogen bonding occurs when a hydrogen atom that is covalently bonded to an electronegative atom (in this case, nitrogen) is attracted to another electronegative atom (in this case, carbon). Although nitrogen is not as electronegative as oxygen or fluorine, it can still form weak hydrogen bonds.
The hydrogen bonding between the amino group of lysine and the benzene ring of phenylalanine can stabilize the interaction between the two amino acids. This interaction can play a role in protein folding, protein-protein interactions, and other biochemical processes where amino acids come into contact.
In summary, the side chain of lysine is polar due to the presence of an amino group. When interacting with phenylalanine, the polar amino group of lysine can form weak hydrogen bonds with the nonpolar benzene ring of phenylalanine, facilitating their interaction.