Question

In organic chemistry, how does small molecule synthesis and reaction compare to biological functions and actions by various biochemistries? Is there a relationship that we should be aware of? How do small molecule affect biological process and how do biological process and molecules effect small molecule reactions?

Answer 1

Each molecule has a characteristic size and shape that determines its function in the living cell. The shapes of molecules are determined by the positions of the atoms’ orbitals. When an atom forms covalent bonds, the orbitals in its valence shell are rearranged. For instance, atoms with s and p orbitals will often have a structure in which one s orbital is hybridized with 3 p orbitals to form a pyramidal shape called a tetrahedron. Molecular shape is crucial in biology because of the way it determines how most molecules recognize and respond to each other. One nerve cell in the brain signals another by releasing molecules of a specific shape to go find matching receptor molecules on the surface of the receiving cell. The signal molecules pass across a tiny gap (otherwise known as the synapse) between the two nerve cells and attach to the receptors by forming weak bonds which then stimulate the receiving cell. This process is very much like the way a key fits into a lock, where the matching puzzle-piece shapes help in the forming of weak bonds. Molecules that have shapes similar to the brain’s signal molecules can affect mood and pain perception. For example, morphine, heroine, and other opiate drugs mimic endorphins (natural signal molecules of the brain). The drugs artificially give pain relief and exhilaration by binding endorphin receptors in the brain.

Another aspect of this lock-and-key relationship between structure and function is the structure and function of enzymes. The active site is the part of the enzyme where substrates bind and undergo a chemical reaction. The lock-and-key fit in enzyme language is the induced fit where the active site will encourage the enzyme to locate the correct substrate. In essence, the active site modifies the reaction in order to change the activation energy of that reaction.