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Dangerous Experiments

Dangerous Experiments is the LabSpaces spot for guest bloggers. The purpose of the blog is to give new and old bloggers a space to experiment with blogging. If you'd like to contribute to this experiment, send us an e-mail or contact us on twitter at either @LSBlogs or @LabSpaces.

My posts are presented as opinion and commentary and do not represent the views of LabSpaces Productions, LLC, my employer, or my educational institution.

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Monday, April 11, 2011

This week's guest blogger is Katie Fleming.  She loves science, with an overwhelming Border collie-style bouncing enthusiasm. This crazy geeky love has gotten her a first class degree in biochemistry, a job as a freelance scientific production editor, and some serious aspirations to be a real-life science writer. She spends her spare time eating too much cake, gazing lovingly at molecular structures and blogging about biochemistry and the awesome science of everyday life at She would love to see you there.  Katie can also be found on Twitter.


When I was first asked to feature here as a guest blogger I was a little nervous, my usual writing style is a bit like a scientific tea party, lots of excitable biochemical discussion and cake, so I wondered what subject I should pick. Then I remembered an article I read last year by Thomas Mayer and Andreas Marx about their five ‘desert island molecules’. These were the molecules that they felt stood out due to “their chemical or biological property, their impact on science, or the ingenuity and/or serendipity behind their discovery”. It was a brilliant article, and the idea of it really appeals to me. I love molecules, and I do wonder why aren’t the general public more excited by them? Admittedly I wouldn’t expect to meet many other people who have alerts on their phone for when the protein data bank updates their molecule of the month feature, but compared to the wonderful amount of popular interest in astronomy and the wider universe, there is a disappointing lack of excitement amongst the general public about molecular science.

Millions of people (quite rightly) tuned in to watch Wonders of the Universe, and yet there are no comparable programmes about molecular biology. Similarly, do you know how long I had to walk around the otherwise glorious Science Museum in London recently to find a display of a molecular structure other than DNA? A very very long time. And in the end I didn’t even find one. I was gutted, I had to eat some cheesecake to recover.

This is something I just don’t understand; the molecules in your body are exciting, mind-blowing, awe-inspiring, amazing, and numerous other adjectives I can’t think of right now. So today, as a celebration of some of the most stunningly beautiful molecules in your body, and to try and convince more people to embrace the wonders of biochemistry I present my top three ‘desert island molecules’, chosen not for their usefulness, or their scientific value, but just to represent why I really love my subject, and why I write about it.

The voltage-gated Na+ channel

Diagram of a voltage-sensitive sodium channel α-subunit. G - glycosylation, P - phosphorylation, S - ion selectivity, I - inactivation, positive (+) charges in S4 are important for transmembrane voltage sensing. Credit: Cthuljew/CC3.0/Wikipedia

While this is a slightly geeky thing to admit, I fell in love with the voltage-gated Na+ channel when I was 17, it was my first molecular love affair and to be honest, I’ve never looked back. Now I’m such a self-confessed nerd that I have a periodic table shower curtain and I blog in my spare time about the awesomeness of biochemistry and the science of everyday life. But that sodium channel, nestling into the membrane of a nerve cell really did start it all off. It is involved in creating action potentials; the process of passing an impulse along a nerve cell. It is therefore ultimately responsible for sending messages around the body via the nervous system. To fully describe how it works would take a whole new post, but in brief, an action potential is the depolarisation of a small section of nerve cell. Nerve cells are usually negatively charged on the inside, but when the Na+ channel senses a positive charge, it opens its gates and allows positively charged sodium to rush headlong into the cell, desperate to get to the negative inside and start a positivity party. Microseconds later, another gate in the channel slams shut, to stop the positivity getting too carried away. A different channel then opens, letting positive potassium leak out and getting the cell back to its usual negative state; potassium channel are effectively molecular party poopers. Meanwhile though, the brief positive charge has stimulated another nearby sodium channel to open, causing a depolarisation in the neighbouring membrane space, the party continues next door, before it too is shut down. This pattern continues until the wave of the action potential has passed down the entire nerve to the synapse. What is truly astonishing about this is the speed, think of how quickly your nerves transmit messages, how long it takes you to move your arm once you decide to do so... no time at all, it feels almost instantaneous, and yet for every message that passes along a nerve, there are millions of action potentials transmitting it. That’s millions of Na+ channels opening and closing, millions of tiny molecular conformational changes taking place, millions of tiny positive ion parties. Just try and get your head around how fast they must be happening and you’ll understand... simply mind blowing.


Cartoon representation of a complex between DNA and the protein p53 Credit: Thomas Splettstoesser/CC

p53 has the coolest description ever; it is usually referred to as the “guardian of the genome”. There’s nothing about that nickname that isn’t entirely cool, although it does mean that I invariably picture p53 as a little molecule with a cape. p53 is actually an incredible little multi-tasking wonder protein, it helps to prevent the development of tumours in a number of ways, but the most important are activating the mechanisms that repair DNA when it gets damaged and initiating the process of programmed cell death, this means that if a cell threatens to become a tumour cell, p53 shuts it down. p53 is hugely important in preventing the development of tumours, and in that role is it is a wonderful example of the beautiful, complex and intricate mechanisms our body has in place to avoid diseases such as cancer. And then of course there is the fact that cancer still exists, which says even more about molecular biology, because you have to be pretty damn awesome to get past the guardian of the genome. In fact numerous cancers are partly mediated by mutations in the p53 gene, leading to a flawed protein that cannot do its job properly. Sort of like introducing kryptonite to Superman. p53 though, is just one example of hundreds of proteins in the body that work to maintain the status quo, working together in different ways to prevent damage to cells, organs and ultimately the whole body.


Sensory rhodopsin II (rainbow colored) embedded in a lipid bilayer (heads red and tails blue) with Transducin below it. Gtα is colored red, Gtβ blue, and Gtγ yellow. There is a bound GDP molecule in the Gtα-subunit and a bound retinal (black) in the rhodopsin. The N-terminus terminus of rhodopsin is red and the C-terminus blue. Presumed anchoring of transducin to the membrane has been drawn in black. Credit: Wikipedia

I’ve chosen rhodopsin to represent the human eye, frankly there are many molecules that make up the cells of the human eye and all of them are just phenomenally intricate and beautiful in their mechanism. Rhodopsin though, is my favourite, not for any discernible reason, it just is. Plus it is the actual light-sensing molecule. It lives in the membrane of light-detecting cells (photoreceptors) in the eye; and when light reaches it, the light is absorbed by the molecule, causing a change in the conformation of the molecule. In fact, just one bond changes orientation. This tiny minute change in the position of one chemical bond then triggers a cascade of events that produce a message that is sent along the optic nerve to the brain. To me, that is beyond amazing. That such a small change can be so crucial to something as complex and wonderful as sight entirely captures the reason that I think molecular biology is so stunning. I genuinely don’t have the words to express how incredible it is, I’d need to type a string of adjectives several pages long, and you’d all have nodded off and I still wouldn’t have really expressed myself. For this reason, rhodopsin is my number one molecule. It demonstrates everything that I love about biochemistry.

So those are my top three molecules, and with them some of the reasons why I think biochemistry and molecular biology should be the next big thing in popular science. Bring on the biochemical tea party!

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Blog Comments

Brian Krueger, PhD
Columbia University Medical Center
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You're a big fan of G-proteins!  Two of your three picks are from the same class ;)


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I know, I have a bit of a thing for G-proteins. They're just so incredibly clever!

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I really enjoyed reading your post. Your enthusiasm is great. I was also very interested in tumor suppressor genes- I think that is a fascinating subject. I worked on the cannabinoid receptor- another g-protein coupled 7-transmembrane domain protein. The myriad of effects from activation of that receptor are amazing!! :-)

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Glad you enjoyed it :-D

That's the thing about G-protein coupled receptors, once they're activated they can trigger a ridiculous number of events, it's incredible how such complex signalling pathways with such varying results can all start with just one little receptor!

Brian Krueger, PhD
Columbia University Medical Center
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Katie, if you were to build a museum exhibit to make biological molecules more interesting, what would it look like?  I think you're right on the money when you say that it's sad that the only thing people know about molecular biology is that DNA is twisted :P  How can we better engage the public and show them that tiny things in their body are just as cool as the stars in the sky?

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Good question! Well, what I would LOVE to see is someone using 3D to explore molecules of the body. I wrote a blog post last year about a company using 3D technology with PyMol to look at protein structures in much better detail, which is completely awesome! The Science Museum in London has an iMax theatre, so if it were me I would try to create some kind of 3D exploration of some of the key molecules involved in specific processes. There are hundreds of possiblities but for example you could look at the influenza virus, show the key proteins that are important for viral infection and the proteins that are targeted by antiviral drugs, exploring the drug binding sites.

Actually now 3D TV is becoming bigger, that could even work as a television programme!

Aside from the whole 3D thing, one of the museum exibits I would like to create or see would be the molecular basis of disease, looking at how mutations change protein structure, for example, and then why that leads to disease. You could look at cancer, diabetes, the common cold, influenza, HIV, bacterial infections... all things that many people are aware of in everyday life. I think relating it back to something more 'real-life' is helpful when you're trying to maintain interest. I certainly remember that being the case for me when I was studying!


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Several years ago, a group developed a planaterium show called The Molecularium to teach about molecular interactions

It would be cool if something like this could be expanded and be used to teach about disease, etc.


Guest Comment

Great post! I couldn't agree more that we've become obsessed with looking up in our scientific programmes and I for one would love to see a guided tour of the subcellular world. I love how people become attached to their favourite molecule, i'm a self confessed adhesion protein addict!

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