Amino acids and protein folding

Definitions & Key takeaways

Amino acids are the building blocks of protein. Protein folding is the process by which a single polypeptide chain, or peptide, assumes its unique 3-dimensional conformation or "fold." This folded conformation is necessary for the protein to carry out its biological function.

Some proteins fold spontaneously, while others require the help of other proteins, known as chaperones, to fold correctly. In some cases, misfolded proteins can form aggregates that can be harmful to a cell. This is thought to play a role in a variety of human diseases, including Alzheimer's disease and Huntington's disease.

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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.
So, amino acids are, essentially, a carboxylic -COOH group, an amine -NH2 group, a side chain, and a hydrogen bound to an alpha carbon.
Now, an interesting geometric property called chirality - means that the same amino acid can exist in two forms, that look like mirror images of each other.
These two forms are called enantiomers of one another. We have the left, or levo-oriented amino acids, as well as the right, or dextro-oriented amino acids.
While similar, they are definitely not the same. Think of shoes.
While made out of the same materials, and generally looking alike, the left and the right shoe are not interchangeable, at least not without a lot of pain involved.
As it turns out, proteins are made out of only L-amino acids. Now, protein production itself happens in cellular structures called ribosomes, which use the messenger RNA which is essentially a blueprint that tells the ribosome exactly the order of amino acids that are needed.
At this point, the protein is just a growing string of amino acids - as it grows, it’s either being injected into another organelle, called the endoplasmic reticulum, which will help the protein take shape or it’s being translated directly into the cytosol.
Now, the proteins have multiple levels of structure to them - primary, secondary, tertiary, and quaternary structure, creating a hierarchy.
As an analogy, think of the alphabet. It can be used to create words, which can make simple sentences, which can further be made into complex sentences.
As an example, the letters themselves would be considered the primary structure “I N E X A M I S T H E H O U R S T W O”.
Then simple words like “EXAM” and “HOURS” would represent secondary structures. Tertiary structure would be when the entire chain folds together, perhaps making a simple sentence like “THE EXAM IS IN TWO HOURS!” And the quaternary structure might actually be a few peptide chains coming together to form a more complex protein, making a complex sentence that says “THE EXAM IS IN TWO HOURS AND I HAVEN’T SLEPT AT ALL”.
When it comes to proteins, the primary structure is simple enough - it’s just a linear sequence of amino acids connected through peptide bonds - like a string of pearls.
Now, the peptide bonds between the amino acids are very rigid, but by comparison the single bonds connecting the amide functional group of the peptide bond to the the alpha carbon are flexible.
That allows significant freedom of rotation, and through that rotation, the protein can fold into one of two types of secondary structure - α-helix or β-pleated sheets.
The α-helix resembles a spring. The helical structure brings the C=O of the first amino acid near the N-H of the fifth amino acid, the second C=O gets near the sixth N-H, and so on.
In other words: each of these instances is separated by 4 amino acids. Having the O and H get close to one another allows for a strong hydrogen bond to form, and that makes the α-helical structure really stable!
β-pleated sheets also rely on hydrogen bonding - but slightly differently. Imagine a neatly folded piece of paper.
In β-pleated sheets, hydrogen bonds form between the N-H on one flap of paper and the C=O on another flap of paper, and these bonds almost hold or “glue” the sheets together.
That makes beta-sheets really stable as well. Now, tertiary structure is the overall shape of the polypeptide chain, and it includes the secondary structures as well as other features.
For example, two sulfur containing cysteines, can bind to form a disulfide bridge. Also, hydrophobic amino acids form bonds with one another and orient themselves towards the inside of the protein, so that they’re able to avoid contact with water.
It’s as if the hydrophobic amino acids are being a bit shy. Basically, the way a polypeptide chain twist and turns to form its tertiary structure is a bit like the way headphones get tangled up in your pocket.
Quaternary structure is the final level, and it’s the level at which multiple polypeptide chains come together to form a larger protein structure.
A classic example involves the 4 polypeptide subunits that have to come together to form a single hemoglobin protein, which is, roughly, a tetrahedral arrangement.
Alright, as a quick recap. There are 20 amino acids - 5 dispensable, 6 conditionally essential, and 9 essential.
The primary structure of a protein is the linear sequence of amino acids. The secondary structure includes both α-helix or β-pleated sheets, both of which rely on hydrogen bonds.
The tertiary structure binds the secondary structures through various other bond interactions like disulfide bridges or hydrophobic reactions, and, the quaternary structure creates the final shape of a protein by connecting multiple polypeptides in the form of tertiary structures.