Proteins: the mind-blowing molecular machines that are you

Nanotechnology.

Sci-fi writers have long dreamt of a future where microscopic robots help us achieve all kinds of neat sci-fi stuff - from repairing our bodies, to assembling any imaginable object with atomic precision.

...sorry science fiction, you were a bit too late:

Nature has been playing around with molecular robotics for eons, we just use a different word for its nanotech miracles -

Proteins.

Proteins are everywhere! If Ballmer had been the CEO of a biotech company instead of Microsoft, he'd be chanting "proteins! proteins! PROTEINS!" in that historic speech.

Alright, so what exactly do they do? Oh, nothing too special, just... everything

Act I: The Machine

When something important is going on in your body, you can be sure proteins are involved:

• Proteins allow you to move?? of course - actins and myosins make your muscles contract and relax;
• They make vision?? possible - opsins are the light- and color-sensitive proteins inside you eyes;
• They digest?? your food - specialized proteins (enzymes) break down that burger into nutrients for your body...
• ...and enable you to think??! Receptors that allow neurons in your brain to exchange signals are - you guessed it - proteins.

And while we're at it, let's also mention RuBisCO. No, it's not an 80s groove band (although, how cool would that be), rather a protein that enables CO2 fixation in the process of photosynthesis -

- in other words, allowing all plants ?? on Earth to exist, no biggie...

Still think I'm exaggerating the "molecular robots" part though? Just scroll back to the top and check out the visualization of a dynein - a protein that quite literally walks around inside our cells, carrying various important cargo.

Let's take a closer look at how these insane machines are made in the first place (spoiler - it's with the help of other proteins) -

Act II: The Translator

As you might have suspected, the blueprints for building proteins are stored in the DNA.

Here's a head-scratcher though: in the previous essay we mentioned that DNA records information using 4 chemicals (nucleobases). Proteins are long molecular chains made up of 20 varieties of unrelated chemicals (amino acids).

So how does one become another?

This looks like a job for... a translator! In fact, this is exactly how this process is called.

After the DNA is uncoiled and carefully copied by a special protein (RNA-polymerase) into a mobile data-molecule called RNA, this happens:

Looks quite mechanical, doesn't it? Like a magnetic tape... being fed into a 3D-printer!

Some more (skippable) details if you're curious -

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The newly minted RNA leisurely swims into a ribosome - a molecular factory (made out of proteins) that does four things:

1. Takes in the RNA like a data tape,
2. Positions its molecular "reading head" onto a group of 3 RNA bases, known as a codon,
3. Matches the codon to a special pre-fabricated molecule with an attached amino acid,
4. Sticks the new amino acid at the end of the emerging protein.

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But wait,

how does this amino string, "pooped" out by the ribosome, become all those amazing and complex things like muscle fibers, receptors, and enzymes...

- didn't we say earlier it's just 20 building blocks to choose from?!

Act III: The Fold

Imagine you were tasked with building a car from scratch. And a mobile phone. And while you're at it - a small space station.

...and you had only 20 different types of components at your disposal ??

How does mother nature solve this challenge?

~ By doing origami! ~

And no, it's not a romantic metaphor, what happens millions of times per second in each of your body's cells is literally lots and lots of extremely elaborate folding.

Here's the key idea: let's give a particular charge to each of those 20 components, so that they can attract and repel each other.

Now, if you let go of a string of those charged components, it will spontaneously fold in on itself, forming all kinds of kinks and shapes -

And biology wouldn't be biology if that process didn't go in layers, forming progressively more complex structures with each round of folding!

So, each specific string of amino acids folds into a very specific 3D shape,

- and even with a moderate-length protein of 100 aminos, we can encode 201?? possible shapes in that sequence...

That's much, much more than the total number of atoms in the entire universe

How do we even begin to handle this amount of complexity, let alone try to usefully engineer it?!

This is where the merging of biotechnology with computation becomes fundamental.

In the next (and final) essay of this chapter, we will look at the tools and methods that are enabling us to tackle the immense complexity of living systems -

- making biotechnology go exponential ??