Pattern, Plan, and Chance Events

Here’s the planned pattern for TeachDNA Blog: 3 Fridays in a row one month, then next month silence; repeat. But sometimes, perchance, an interval of silence is going to be interrupted by a surprise essay. Because biology has occasional exceptions to almost every rule! And TeachDNA likes to be biomimetic.

So, following up the re-introduction to the Genetic Code and the cute peptide word game, I wanted to address the question of why anyone would be fascinated by that pattern-plan system. Therefore I headed over to the Protein Data Bank (PDB) , to point y’all to their huge collection of amazingly beautiful 3D protein structures, the system’s natural products.

But arriving at the RCSB-PDB front page, I was stunned by January’s Molecule of the Month: not just one molecule but a recently discovered menagerie of many very “ornate” - and astonishingly symmetrical - All-RNA Quaternary Structures. You read right, all RNA, no protein. Look at them!! What do these things do? why do they exist in nature? Nobody knows yet. Surprise!!

But back to protein structure, as determined first by X-ray crystallography and now by cryo-electron tomography: not just single protein molecules (impressively intricate things themselves) but also complexes of two or three or more protein molecules (of the same kind or different kinds), self-assembling to form incredibly intricate machines with surprising abilities.

Here’s a few especially awesome structures to gaze at and play with. They’re all 100% natural protein complexes, with machinelike arrays of moving parts. (Some people say that they must have been intelligently designed.) Take a look: in descending order of complexity…

part of a bacterial propeller: https://www.rcsb.org/3d-view/8Z5X/1

ATP synthase: https://www.rcsb.org/3d-view/1QO1/1

Photosystem II: https://www.rcsb.org/3d-view/1IZL/1

Calcium channel: https://www.rcsb.org/3d-view/6WHG/1

Potassium channel: https://www.rcsb.org/3d-view/2WLL/1

Insulin and receptor: https://www.rcsb.org/3d-view/8GUY/1

Just insulin: https://www.rcsb.org/3d-view/4E7V/1

And here’s a beautifully symmetrical single protein molecule whose only job is to catch a particle of light (blue light), get excited, and then relax by giving off a particle of (lower-energy, green) light. It’s called GFP, the Green Fluorescent Protein. Jellyfish make it.

https://www.rcsb.org/3d-view/1EMA/1

If high school Genetics class had shown things like this, I probably wouldn’t have slept through it and earned a failing grade!

But if you are teaching high school level biology, then showing stuff like this to your students is tricky, maybe scary. You, the teacher, can’t explain how any of the parts work, so… how does the lesson go? What are the learning objectives? How do you deal with the impossibility of anyone in the room comprehending any details at all? Discuss. Indeed it is debatable whether this information SHOULD be shared with novices, with the general public, or whether the truth is better kept hidden at the top of a long staircase. We don’t want it in picture books for young children, do we? Send a message if you want to talk about anything.

RCSB does offer a lot of learning/teaching resources on PDB-101, including videos explaining how researchers determine the detailed shapes of these things that are ten million times smaller than a cell. Enjoy, explore and share!