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.