Amino acids and protein folding

Proteins are vital for the normal function of a cell.

Essentially, a protein is, at its simplest, a very long chain of individual units, called amino acids, bound to each other by peptide bonds to form an amino acid chain.

They sorta resemble a string of beads, and they get twisted and folded into a final protein shape.

To make a protein, we need to get to know two things - the “ingredients”, which are the amino acids, and the “recipe” - or how the finished amino acid chain folds into the protein.

Humans use 20 amino acids in our day-to-day protein making.

Let’s get to know them a bit better. So, we have: alanine (Ala), arginine (Arg), asparagine (Asn), aspartic acid (Asp), cysteine (Cys), glutamic acid (Glu), glutamine (Gln), glycine (Gly), histidine (His), isoleucine (Ile), leucine (Leu), lysine (Lys), methionine (Met), phenylalanine (Phe), proline (Pro), serine (Ser), threonine (Thr), tryptophan (Trp), tyrosine (Tyr), valine (Val). Phew, that’s 20.

One way to divide them, is into the ones that we make ourselves, and the ones that we cannot.

There are 5 amino acids that are dispensable - alanine, aspartic acid, asparagine, glutamic acid, and serine - because we can make them de novo ourselves at any time, and in good quantity.

Then, there’s 6 of them that we call conditionally essential because we can make them most of the time, but not always - arginine, cysteine, glutamine, glycine, proline, and tyrosine.

Finally, there are 9 of them that we cannot make ourselves - His, Ile, Leu, Lys, Met, Phe, Thr, Trp, and Val, and as a result we have to obtain them from our diet. We call these the essential amino acids.

Okay, so, the amino acid. Just from the name, you can tell they’ve got an amine group, or “NH2”, and also an acid, in this case a carboxylic acid group “COOH”.

The amine and carboxylic acid groups are both bound to the same carbon, called the alpha carbon.

Now, at a physiologic pH of 7.4, the amine group has a positive electrical charge, and the carboxyl group has a negative charge.

Having both a positive and a negative charge makes amino acids a type of zwitterion - which is German for “hybrid”, or “double ion”.

Now, the alpha carbon also has a side chain, sometimes marked as “R”.

And this side chain gives the amino acid certain properties, which can play an important role in the overall protein structure.

First the side chain can be hydrophilic or hydrophobic - so water loving or water hating. Hydrophobic amino acids have nonpolar side chains.

This might be in the form of an alkyl side group, which is a saturated hydrocarbon, seen in valine, glycine, alanine, leucine, isoleucine, methionine, and proline.

Alternatively, it might be in the form of an aromatic side group - which involves a 6-carbon ring, like in phenylalanine, tyrosine, and tryptophan.

Now, hydrophilic amino acids have polar side chains.

These polar side chains might be acidic - like when their side chains contain additional carboxyl -COOH groups, like aspartic acid and glutamic acid.

Other hydrophilic amino acids have polar side chains that are basic, like lysine, histidine, and arginine.

At physiological pH the acidic groups lose a hydrogen and the basic groups gain a hydrogen.

Finally, some polar side chains are neutral, for example they can contain hydroxyl groups, -OH, like serine, threonine, or tyrosine, or sulfhydryl groups -SH, like cysteine, or carboxamide groups (R-C=0-NH2) like asparagine or glutamine.

Now, keep in mind that the charge on an amino acid really depends on its side chain as well as the pH.

For example, at a very low pH, the amine group is positive, while the carboxyl group is neutral.

And at a very high pH, the amine group is neutral, while the carboxyl group has a negative charge.

And at a pH that’s somewhere in between, both groups are electrically charged and they cancel each other out, resulting in no net charge for the amino acid.

The “just right” pH, also known as the pI, or isoelectric point, is different for every amino acid, and it depends on the specific side chains.

For amino acids to link up in a chain, the carboxylic -COOH group of one amino acid has to bind to the amine -NH2 group on another amino acid, creating a single peptide bond.

This is a condensation reaction - meaning that two amino acids are basically smushed together, and the OH from the carboxyl group, along with one of the hydrogens from the amine group, get released as a water molecule in the formation of an amide bond.

While technically being a single bond, it actually has the properties of a structurally stronger double bond, thanks to the property of resonance.

Now, resonance is a property of a molecule where electrons get shared across the molecule, while keeping the arrangement of atoms the same.

Basically, the electrons from neighboring functional groups in the amino acid are “borrowed”, and that makes peptide bond stronger and more stable.