BY AFSHAN NABI (MBG/III)
afshan.nabi@ug.bilkent.edu.tr
“What senses do we lack that we cannot see or hear another world all around us?”
– Frank Herbert, “Dune”
Proteins are machines.
Over the course of your life, your body has encountered, at the very least, 19,000–20,000 different types of proteins. People are trying to find the exact figure; but that is still an astounding number of machines to carry around.
These proteins are made up of linear chains of amino acids. Amino acid chains then fold up into a variety of shapes. Think of this as nature playing string games, only instead of fingers, chemical bonds hold these strings of amino acids together to form remarkable shapes. And since nature does everything on a grander and more functional scale, these string shapes are extremely complicated and do all kinds of useful stuff.
They are tiny, of course, but extremely efficient and vital for our survival. Without them, you would not be able to think, taste food, move around, fight infections, etc.
If you are curious, you may ask: How do they do all this? Very simply put, they bind to other things and subtly change their shapes. That, unfortunately, does not explain anything.
(Imagine you are eating pizza with an alien friend. This friend from outer space says, “Mm, this is delicious. How do humans make pizza?” You, busy enjoying the pizza, answer: “Using machines.” This is true, but it is an incomplete picture. You leave out a bunch of details: crops and vegetables sown, grown and harvested, meat grown and processed, transport of all these ingredients to Sun Brothers, mixing and the final preparation in the oven.)
Nevertheless, we can zoom in on a particular protein and see how it spends its time.
Consider a protein called the proteasome. This is a machine where proteins suffer “death by a thousand cuts.” It is barrel shaped, with both ends covered. The lid of the barrel recognizes the proteins marked for death, uses energy to unfold them and passes them into the barrel. Inside the barrel, the death-marked protein is broken down into small chains of amino acids. These small chains are released from the barrel and used for, among other things, the creation of new proteins.
In this way, old, dysfunctional, unwanted and dangerous proteins are destroyed, and their remains recycled to ensure that new proteins can be created as the need arises.
And life goes on…
The above proteasome example shows how proteins are able to interact with other proteins to perform a specialized function – in this case, protein recycling.
Now consider human beings – fascinating creatures that build cities, write poetry, run for office and take too many selfies. In some ways, they are similar to proteins: they have relationships with other humans; they perform all kinds of different tasks; they die, but upon death are buried or burnt, and their nutrients ultimately reach the earth and are recycled to create new life. When one of them dies, someone else takes on his role, and the show goes on.
Now, imagine that you become a protein as well, but with your special vision of the human world, you want to let proteins know that they perpetuate humanity. You start by telling them that their presence and cooperation in great numbers somehow form life. Life consists of billions and billions of animals, plants, bacteria and fungi. Among the animals is a special species – the humans. They have self-awareness. They are doing great things, like trying to understand protein structure, and working to become a spacefaring civilization.
They might listen to you with great wonder. Or they might just throw you out of their protein bar for being a heretic and defying the revelations of the holy Central Dogma. But, in all probability, they will not understand you and will ignore you to continue their binding to other stuff and shape-changing.
Seeing how we are somewhat similar to proteins, what if we are perpetuating something much greater than ourselves?