Lesson: Molecular Machines in Nature

The array of super-tiny atomic-scale molecular machines in the world is truly mind-boggling!

In this Lesson: Molecular Machines in Nature we will be discussing how nature uses all six of the simple machines and some really cool molecules to do work right within the cell! This happens in plants, insects, animals, and even in bacteria and in viruses. All it takes is to reframe the idea of what you call a machine or motor.

Chlorophyl: The Original Green Solar Panel

Did you know that around 3.5-3.8 billion years ago chlorophyll evolved in ancient organisms called Archaeans (ancient bacteria). It was the beginning of the great period of oxygenation on our planet. Chlorophyll played a big part of that.

Cyanobacteria and later plants, have oxygen as the waste product of photosynthesis. Thus slowly Earth became oxygenized. This Great Oxygenation Event wiped out most of the anaerobic organisms including the purple bacteria. So plants are green because chlorophyll is more suited for a star that shines in blue or a red light (UV and Infrared).

How exactly is it that chlorophyll is a molecular machine? I’m glad you asked! It has to do with that ring at the top of the molecule (see below).

Chlorophyll Molecular Motor

There are five atoms in that central ring. Magnesium (element 12) and Nitrogen (element 7). The magnesium is ionized and just two of the Nitrogens are ionized.

As the magnesium reacts, it spins being attracted and repulsed by the positive and negative Nitrogens. This transforms photons into electrons and those electrons travel down that long tail creating O2, Sugars, and water.

It’s remarkable to think every day we eat tiny little green electric motors and solar panels and that is how we get our power. When animals eat plants, and we eat animals or insects, we still get that power. We are living batteries and power plants powered by plants!

DNA: Take It Apart and Reassemble It – FAST!

Most people know what DNA (DeoxyriboNucleic Acid) is. But two things that you might NOT know is that:

  1. DNA and its family – Genes, Nucleotides, Chromosomes, and Messenger RNA (RiboNucleic Acid) only code for proteins.
  2. DNA must be built, unbuilt and a new copy made in every cell in every living thing on this planet and that is done by a series of machines that physically manipulate the DNA polymer molecule.

To accomplish this amazing feat of bioengineering DNA uses DNA transcription machines to unzip the double helix DNA, then create two versions of the same DNA and then put it all back together again. Transcription motors do this so fast they are almost as fast as jet engines! The spin and unlock the DNA and then they have to ACCURATELY put that DNA back together again every time.

This screenshot is used courtesy of Veritaseum.

Question: What do you think would happen if the DNA got put together again and even one base pair nucleotide was wrong?

The tiny spinning and reassembling molecular machines are incredibly efficient. In fact, they RARELY get the reassembly process wrong. That’s because the way DNA works is very much like a form of LEGOS. The nucleotides will only click with a certain nucleotide and none others.

Here’s an interesting question: Is DNA a sugar, a plastic, or an acid?

  • DNA does have a sugar backbone in its double helix
  • DNA technically is a polymer (a long chain of carbon-bonded molecules) just like plastic
  • DNA has an acidic Ph as the nucleotides (ladder rungs) are made of amino acids

Sugars are everywhere. Just like carbon, we need the molecular shape of sugars to support and sustain life, and carbon is an excellent building tool. So yes, DNA does have a sugar aspect to it.

DNA is a polymer, so it is plastic. But is DNA a plastic are are all plastic polymers — but not all polymers are plastic. Remember a polymer is simply a long chain of carbon atoms.

Why do you think DNA is acidic? Is there something about ions and energy that might be built into DNA? Why does DNA only code for proteins and not more specific traits?

When we reframe this idea as a LEGO block issue, it becomes much easier to understand how and why the transcription molecular motor works so very well. It doesn’t change the fact that that it is extraordinarily complex, but it does make it easier, right?

Dynein Motor: We’re Walking, We’re Talking

Would you believe that in your body right now, in every cell of every living organism there is an army of walking machines called Dynein Motors? They are tiny machines that carry proteins around inside the cell on highways called microtubules. They are the most amazing molecular motors in my opinion.

Watch DNA Transcription and Dynein Motors in Action!

Of course, these amazing motors are not “alive” in the real sense of that word. They are molecular machines that react to the microtubule highways in the cell and they place one “foot” in front of the other and move around the cell.

If we were to look at a Dynein Motor could we determine which of the six simple machines it uses to move? Let’s have a look.

How many simple machines do you see?

Notes for an Educator:

The goal of this lesson is to introduce biotech, bioengineering, and biochemistry students to the idea that nature uses engineering principles, biological truths and physics and chemistry to bring atoms and molecules to life. It is an important idea that seemingly miraculous and complicated things can be understood by breaking them down into pieces and then reframing the whole.

It would be an interesting activity to do this with an animal and a simple molecule model. Even proteins can make more sense when they are viewed as machines. This is also useful for building team cohesion.

If we can see the smaller parts of a group, we can better understand how we can all come together on common ground. Intolerance or arguments become pieces of data. We need to name them and then reframe them in a positive light.

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