Created: May 14, 2021
Modified: May 14, 2021
Modified: May 14, 2021
amino acid
This page is from my personal notes, and has not been specifically reviewed for public consumption. It might be incomplete, wrong, outdated, or stupid. Caveat lector.- Structure: NH2 - C - COOH (amine - C - acid/carboxyl), usually with a side chain hanging from the central (alpha) carbon.
- Roughly speaking, the amine side is a base (wants to gain a proton) and the carbonyl side is of course an acid. They bond by giving off a water molecule, resulting in NH2 - C - (C=O) - NH - C - (C=O) - NH - C - … chain. The (C=O) - N bond is called a peptide bond.
- What actually happens during the bond? Peptide bond formation (video) | Proteins | Khan Academy
- The nitrogen has a lone pair, which attacks the carbon atom in the carboxyl group. The carbon atom is a bit positively-charged, because it's attached to electronegative oxygen atoms which suck away some negative charge. So it attracts the lone pair. An electron from the lone pair jumps to the carbon, so another electron has to jump away---and this goes to the OH oxygen, dissolving the bond. This hydroxyl ion now has three lone pairs and a negative charge; it wants another proton so that it can become a water molecule. Meanwhile, the nitrogen has a positive charge, so it wants to get rid of a proton. Through the wonder of acid-base chemistry, this exchange happens.
- In reality, the molecules on both sides of the bond may be zwitterions, where the carboxyl group is negatively charged and the amine group is positively charged. Then maybe this reaction could happen differently, where the OH directly gives an electron to the N, which now has an extra lone pair and attacks the carbon.