Amino Acids

Professor Dave here, let's talk about amino acids. Your body is full of large molecules called biomolecules, and the first thing we have to do to understand biochemistry is to learn about the different kinds of biomolecules. There are a few different classes, like proteins, carbohydrates, lipids, and nucleic acids, and most of them are polymers that are comprised of repeating units called monomers. Mono means one, poly means many, so a polymer is formed when many monomers link together. Each polymer has its own type of monomer, so we need to know about these different kinds of monomeric units, and the ways they combine to form the large molecules that do all the complex things in your body. The first type of monomer we will learn about is the amino acid. Amino acids look like this. They all have an amino group on one end and a carboxyl group on the other end. The carbon in between those functional groups, which we call the alpha carbon, will bear a side chain, sometimes referred to as an R group. This is a group that varies depending on which amino acid we are looking at. If the R group is just a hydrogen atom, we call this amino acid glycine. If it's a methyl group, we call this alanine. There are about 20 of them, and they have a wide variety of R groups that can be put into different categories. Some of them will be hydrophobic, like leucine. These are the ones with R groups that are alkyl substituents. Some of them have R groups that are aromatic, like phenylalanine. Some have R groups that are basic, like lysine, because of the lone pair of electrons on the nitrogen atom. Some have R groups that are acidic, like aspartic acid, because of the carboxyl group. Some have R groups that can act as nucleophiles, like serine, because of the hydroxyl group. Every amino acid has its own unique structure and reactivity, and it's the variation in these R groups that determines the characteristics of the molecule that forms when a bunch of these amino acids join together. Some of these amino acids humans can't make on their own, so we have to eat them in our diet. They are called essential amino acids. Others we are able to make inside our bodies, so those are called non-essential amino acids, meaning it's not essential that we eat them. So amino acids are monomers, and monomers are the units that join together to form a polymer. How exactly then do amino acids polymerize? Before we learn about that, let's first understand that inside the body, instead of the one structure we've been looking at, there are actually equilibria between different forms of the amino acid. The amino group can be protonated, since it is slightly basic, and the carboxyl group can be deprotonated, since it is slightly acidic, and there are equilibria between the cationic form, the zwitterionic form, and the anionic form. We know what cations and anions are, they're positively charged and negatively charged species, and a zwitterion is a molecule that has both a positive and negative charge. The form that an amino acid will take depends on the pH of its environment. A more acidic solution will favor the cationic form, since basic groups will pick up protons from the hydronium in solution, and a more basic solution will favor the anionic form, since acidic groups will readily deprotonate in the presence of hydroxide. Inside the body, the pH is regulated very precisely, and in most areas it's fairly close to neutral pH, so the zwitterionic form is typically dominant. The side chains can also have different states of protonation or deprotonation depending on the pH, such as lysine, where the R group can have NH2 or NH3+. For now, let's just look at something simple, like alanine. At physiological pH, it will take this form. What sort of chemistry can this do? It might not be obvious just looking at it, but with the help of other molecules in the body, these can polymerize to form proteins. So let's move ahead and learn all about proteins.