In which I am elsewhere

Today I am featured on the ace Any Other Woman, writing about the pill and how it works. Clare, Aisling and Anna have built a truly wonderful community of intelligent, smart, funny and brilliant women on their blog, and I'm honoured, and a teensy bit bouncy-over-excited, that they've given me space to get my geek on over there. 

So come over, say hello, bring cake. 

K x

Feeling Nervous: Action Potentials & Comic Strips

I went to visit my sister at University recently, and found pinned to her notice-board a picture that I drew and posted to her when she first moved in. The picture is a comic strip describing an action potential. An action potential is the series of events that occur in your nerves to transmit messages along them. Clearly I know EXACTLY what the cool kids want on their walls at university. 


I've spoken before about how much I love action potentials, and how one of the proteins involved was my first molecular love affair. That protein, the voltage-gated sodium channel, will be appearing the in Really Awesome Protein series soon, because it's a phenomenally impressive molecular machine. For today though, I thought I'd share the comic strip I produced for my sister. And use it to explain how your nerves transmit messages (I should note that I drew the picture, however Emma went out and bought pens so she could colour it in, so all credit for the colour goes to her). 


Now I meant it when I said I love action potentials. Learning about them was one of the first things in science that really made me sit up and take notice. The complexity of it, and the speed. When you get your head around it, the speed just Blows. Your. Mind. Truly, stick with me, it will.
To understand how nerves transmit messages, one of the first things you need to know is that your nerves exist in a state of relative negativity. The inside of the nerve cells is negative compared to the outside. The difference between the two, known as the resting potential, is -70 millivolts (mV). This resting potential is maintained by a sodium potassium pump (called, er.. Joe), which actively pumps two positively charged sodium ions (Na+) out of the nerve, each time it lets a potassium ion (K+) in. It does this all the time.

 

"Once there were three proteins living in a membrane

"Joe used to spend all his time trying to keep the resting potential at -70 mV"

The voltage-gated sodium channel (or Bob, as he is known to his molecular buddies) can sense this negative charge. In general, when the charge is -70 mV, it doesn't do much. Chats to neighbouring proteins, about Glee apparently. However, if it senses that the voltage is changing slightly, it starts to get excited. If it senses the voltage change to the threshold level, which is -55 mV, it gets REALLY excited. What it does at this point is open its gate, and through this gate rushes sodium. Sodium is a positively charged ion (Na+) and so the moment it has access to a negatively charged region, it's heading STRAIGHT THERE. Sodium (and other positive ions) can't bear to see negativity, they need to rush in and get things positive. 

  

"But sometimes Bob and Patrick get a bit... excited"

"Bob sense some action in the neighbourhood and lets sodium rush through him"

The sodium channel has a second gate, one that isn't affected by voltage. Instead, it is operated by time. Nanoseconds after the voltage gate opens, the second gate slams shut, so that the positivity can't get TOO carried away. In the short time it had though, the sodium managed to generate an impressive amount of positivity, rocketing the voltage from -55 mV up to +40 mV. This change in voltage is known as the depolarisation of the membrane. 

Following depolarisation, another nearby protein, Patrick the potassium channel, opens. Potassium then rushes out of the cell, forcing the inside of the cell to become negative again.

"Patrick wants to join in so he opens himself to potassium"

In fact, Patrick is a bit over-zealous and lets the membrane potential get too low. This undershoot is known as the refractory period, and during this phase, whilst Joe is restoring normality, no other action potentials can start in this region of the membrane. 

"Joe tries desperately to restore normality while their neighbours Bert and Paul joined in..."

However, the sudden sharp depolarisation at Bob, Joe and Patrick's house causes the voltage in a neighbouring region of membrane to increase to the threshold level. This increase causes another sodium channel (Bert, now) to open, and the whole cycle begins again. And again. And again. A wave of depolarisation passes along the nerve. It only ever moves in one direction because the refractory period of each cycle prevents the depolarisation from going backwards. Bob can't get excited by the activity at Bert's place, because his region of the membrane is currently just TOO negative. 

This mexican wave of positivity parties along a nerve membrane is the transmission of a nervous impulse. Now, of course my comic strip is an over-simplification (not to mention a demonstration of a stunning lack of artistic talent). There are MANY more sodium channels than just dear old Bob. In fact each depolarisation is the result of multiple channels opening. The  basic principle, however, is the same. And the main thing you need to take away from this isn't necessarily the details of the molecular behaviour but how fast they do what they do. To demonstrate, just do me a favour, right now... wave at me. To make that action you had to send hundreds of thousands of nervous impulses. That's millions of tiny depolarisations occurring to shoot the message along each nerve. And how long did it take you to wave? It felt almost instantaneous. If the thought of that intricate and beautiful molecular orchestration of depolarisation happening at such insane speed doesn't blow your mind, then I think there's probably something wrong with you. It is absolutely awe-inspiring. And that is why ALL the cool kids want a picture of it on their walls at Uni. 

Really Awesome Proteins: The Major Histocompatibility Complex

Part two in the RAP series is the major histocompatibility complex (MHC). This little protein really is brilliant. It’s a crucial part of your body’s defence against illness. If you think of your body like a battleground, and viruses or bacteria as bad-ass invaders, your immune system is your army. Complete with a full range of artillery and a stunning intelligence network. The MHC is part of that intelligence network.  

Almost all proteins have an expiry date, a time when they are ravaged by the stresses of cellular life and are frankly past their best. Since proteins are so crucial to life, it doesn’t do to have old shoddy proteins wobbling around performing their tasks in a half-arsed manner, like it’s permanently a Monday morning in your cells. Instead, the cell has a recycling system, where it breaks down proteins that are past their use-by date into fragments known as peptides. These peptides are attached to the MHC, and taken to the surface of the cell where they are displayed for all to see. Or, more relevantly, for receptors on the surface of T-cells to see. 

This is the MHC. The peptide is displayed in the handy little groove between those two stylish pink helices up there.

Most of the time, T-cell receptors recognise these peptides as being ‘self’ molecules, peptides that came from proteins of the body. However, if for example a virus hijacks the cell, there are viral protein floating around. And if these viral proteins need to be broken down, viral peptides will be displayed by the MHC on the cell surface. And T-cell receptors will spot them. At this point I like to imagine frantic flashing lights and alarms sounding CODE RED as the immune system springs into action to destroy the foreign invaders. You: 1, Virus: 0. Boom. 

So that’s one reason the MHC is really awesome, but there’s more. The MHC has extraordinary allelic polymorphic. This means that if you look around you in a crowded room, on a tube, at a concert, at anyone who isn’t your identical twin, you will see yourself surrounded by people who have different MHC genes to you. And to each other. This is actually really uncommon, most genes only have relatively few variations. There are three MHC genes though, HLA-A, HLA-B and HLA-DRB1 and there are around 1000, 1600 and 800 variations of these, respectively. That’s. A. Lot. Every person has in their genome just two variations of each of the three genes, which clearly means that the chances of any two people having the same final six are fairly slim. The result, a near unique MHC profile, unless you have an identical twin. 

This unique profile is the reason for tissue rejection in transplant operations. When the T-cell receptors recognise peptides, they’re not just seeing the peptide but the combination of MHC and peptide. They view them together, as a pair. If the cell is originally from a donor, the MHC will be slightly different, and the T-cell receptor will spot this too, and set off those alarm klaxons for destruction. Your body is pretty anti-anything that isn’t itself. The best way to avoid this tissue rejection is the get donor tissue from someone who is closely related to you, because you inherit your MHC gene variants, your siblings are the most likely to have a similar profile to you. I suppose being responsible for tissue rejection isn’t entirely really awesome, but the staggering variation in gene alleles is pretty damn mind-blowing. And it leads us to a question. 

Interactions between protein molecules are often quite specific, involving certain chemical groups reacting with others, in a specific environment. This is to prevent proteins from wandering around binding to everything they see, like teeny molecular floozies. Usually, in protein interactions, the side chains of the amino acids are the chemical groups that do the binding. These side chains are the groups that vary between the 20 different amino acids. 

However, the MHC can bind a nearly limitless variety of peptides that could include any combination of these side chains. How is it possible that six types of MHC molecule can bind and display so many different things? 

This is where the MHC really does get really awesome. It doesn’t bind the side chains; instead it interacts with the parts of the amino acid that are the same. Each end of the peptide is buried into a handy groove on the surface of the MHC molecule, and it is held there by interactions with its backbone, the constant chemical groups of the amino acids. The middle region of the peptide, which can be between 5 and 9 amino acids long, bulges outwards, waiting to be spotted by a scouting T-cell receptor. 

Close-up of the binding site, you can see the ends of the peptides are snuggled in tight while the rest bulges comfortably out.

I don’t know about you, but I think that’s downright amazing. This one protein molecule can bind and display thousands upon thousands of peptides to your immune system, screening them for invading baddies like a highly efficient airport security system.  It has developed a way to be able to bind the maximum possible variety of different peptides, to be maximally efficient. Airport security could probably learn a lot from this bad boy. A genuinely Really Awesome Protein. 

Molecular Biology: Not So Sexy Science

A couple of things recently have got me thinking. Following the success of BBC Stargazing Live, @xtaldave on Twitter jokingly suggested the BBC should commission Molecular Biology Live. There followed an amusing round of tweets about what that would include. Mostly a lot of pipetting, and waiting around. With the occasional cup of tea. TheLeadingEdge also posted his second lab frustration post, in which he detailed things that bench scientists find frustrating in the lab. 

The point of this is really that while what molecular and structural biologists study is fascinating, exciting and important, the general public are not that engaged with it, because day-to-day it is often frustrating and often repetitive and slightly dull. It's a shame, though. And it got me thinking what our problem is. 

First, I think we're stuck in the middle, size-wise. The things we're studying aren't big enough to see, so they can't be gazed upon with ease and their beauty marvelled at, like the night sky can. Equally, they're not small enough to need really cool sounding experiments requiring half of Switzerland to study, like quantum physics. You can study them in a lab, but much of the time you rely on experiments that will indicate the presence of things you can't see, unless you're a structural biologist, you often won't see exactly what you're working with. And even as a structural biologist, you may spend years or even decades trying to 'see' it.

They can be TERRIBLY pretty when you do see them, though.

Take me for example, in my MRes project I'm trying to find the structure of a protein that inhibits the cell death pathway. It's interesting because the cell death pathway often doesn't work properly in cancer, and understanding why will slowly inch us closer to understanding what's going on in cancer cells. When I tell people this, they get excited. And it is exciting, but it's very long-term exciting. Despite what the media says, there will likely never be one big discovery that will rid the world of cancer, it's brilliant to be involved in trying to understand it, but there can be no illusions that this work will save the world. It's simply one more piece of a hugely complicated puzzle. 

On the other hand, I think it would be immediately and hugely exciting to uncover the structure of a molecule that no-one has 'seen' before. The reason I'm persisting in trying to get my protein to settle down and behave so that I can shoot X-rays at it and get a computer to do some complicated maths for me is that I think it would be amazing to be one of the first people to really see what this molecule looks like. Not because it might save the world, but because it is an unknown, to be the first to 'know' it would be cool. To a certain extent it is discovery for its own sake (the driving force behind much of science!) 

This is not how I look in the lab. For a start she looks like she knows what she's doing. 

What I'm getting at is that what I'm doing is kind of awesome, but it's hard to show people WHY that's so. If you followed me in the lab day-to-day, you would be bored senseless (apart from that Friday night when everyone else had gone home and I was dancing to Bloodhound Gang around the centrifuge, you might have enjoyed that). So what I wanted to ask, this very cold Friday afternoon, is this... to the non-scientists, are you interested in molecular biology? If not, why not? What might GET you interested? And to the scientists, especially my molecular massive, how do you think we can get people more interested in molecular biology? Or do you think that we simply can't? 

How Drugs Work: Cold and Flu Medications

Oh, it’s that time of year again. My morning commute is full of people coughing an astonishing array of germs in my general direction. Usually while also stealing my seat. Those people sensible enough not to be on the trains are curled up under duvets, inhaling menthol-scented steam and gazing at daytime TV wondering why Jeremy Kyle exists. That's right. It's cold & flu season.

I definitely always look this good when I'm ill. Yup. 

Now, I'm the kind of person nerd who doesn't like to take any medication unless I know what it does and how it works. I think more people should be like this, actually, not just because it's often super-amazing and cool, but also because it's good to know what you're taking, and why. As a general rule in life, it is always better to be informed about what you’re putting into your body (unless it relates to the number of calories in white chocolate cookies, it is definitely better NOT to know that. Ever.)

So, you’re ill. You reach for the cold & flu tablets/drink/sachet. And now you want to know what's in there? How does it make you feel better? The thing with these remedies is that they mainly treat symptoms. None of them actually attack or destroy the virus that's making you feel ucky. Instead they alleviate the symptoms, while you lie still and allow your immune system to kick some serious viral butt. All your body really needs, most of the time, is for you to rest while it works. I actually really like this excuse for doing nothing... "Yes, I can see how it looks to YOU like I've been watching BBC's Pride and Prejudice for 5 hours straight but as it happens, I've been waging constant battle against pathogenic viruses so I’m very tired and that's why you should bring me tea now". 

Entirely gratuitous picture of Colin Firth? On this blog?
Never. He's um... got a cold. He's here to learn how his Lemsip works.  

Getting in the way of your lovely peaceful rest however is the fact that you ache all over, you can’t breathe through your nose and your throat is lined with razor blades.  Even with the distraction of Colin Firth in a wet white shirt, that’s not conducive to comfort. That’s why you take the medicine. And this is what the medicine does…

Wild berry and hot orange. We only do fancy flavoured cold remedies around here. 

Active ingredient one: paracetamol

Paracetamol is in nearly all cold and flu remedies, billed as a painkiller and a fever reducer. It’s an incredibly interesting drug, actually, it’s one of those where we thought we knew how it worked, and then it turned out we weren’t entirely right. Initially it was considered to be a non-steroidal anti-inflammatory drug (NSAID), which I’ve chatted about before. NSAIDs are supposed to act against pain by inhibiting an enzyme, COX-2, which is involved in producing chemicals that cause an inflammatory response (pain, redness, swelling). The same chemicals are also present in the hypothalamus, the internal thermostat of the brain, and are involved in raising body temperature. It seems obvious to assume that paracetamol blocks COX-2 from producing these chemicals and therefore neatly lowers your temperature. And indeed that might well be the case, although no-one is sure.

Last year an article in Nature Communications suggested another way in which paracetamol might kill pain. Once it’s in the body, paracetamol is broken down into smaller chemicals. David Andersson and his colleagues showed that two of these smaller metabolites of paracetamol can block a receptor in the spinal cord. Their theory is that blocking this receptor stops messages of pain being sent from your body, up the spinal cord, to the brain. Of course this doesn’t answer the question of reducing body temperature, but it’s entirely possible that paracetamol acts in more than one way, like a multi-tasking super drug. Either way, it’s certainly a good painkiller, either by reducing inflammation, blocking the transmission of ouchy-messages, or a bit of both.

Active ingredient two: phenylephrine

Phenylephrine is your decongestant, and this time we do know how it works. It binds to a receptor, the alpha-adrenergic receptor, and this causes blood vessels in your nose to contract and get narrower. Obviously this means there is less blood supply to the area, and this helps you feel less bunged up in two ways, first, constricted blood vessels in the mucus producing layer of the nasal passages means less mucus. Second, part of the bunged up feeling comes from swelling in your sinuses, contracting the blood vessels reduces this swelling, so your nasal passages open again, and you can smell your Heinz Tomato Soup (I’m assuming everyone eats Heinz Tomato Soup when they’re ill, no?).

Whilst we know how phenylephrine works, for a while there has been on-going debate about how effective it really is, some studies say that there isn’t enough evidence to prove that it does anything useful, whereas others say there is. In any case, that’s how phenylephrine would work, if indeed it does work.

Active ingredient three: guaifenesin

The third and final ingredient in some cold and flu medicines is guaifenesin. It’s listed in your cold and flu medication as an expectorant, a drug that loosens chesty coughs. However, yet again, the way in which guaifenesin works is… well, basically it’s not at all understood. The general idea is that it reduces the viscosity of the mucus in your airways, making it less gloopy and therefore easier to cough up. However, no-one appears to really know how it does this. On top of this, there are other theories, that it somehow blocks your natural ‘cough reflex’, or that it increases the action of cilia, helping to clear mucus out of the airway faster.  Again, no-one knows how it would do either of those things. Guaifenesin then is something of an international drug of mystery. It’ll help you cough up mucus… but if it told you how, it’d have to kill you.

So, there you have it, the main active ingredients in cold and flu medicines. A complicated and reticent lot, that either work mysteriously or can’t decide whether or not they’re going to work. These are your companions in the fight against viral doom. Or, the things that’ll make you feel vaguely human while your immune system does its thing.  It depends how overdramatic you’re feeling, or whether you’ve got man-flu. 

Really Awesome Proteins: Rhodopsin

I have been an absent blogger. I’m very sorry. I got busy working, and the starting my Masters. But I’m back now, and to celebrate I’m launching a new regular feature of the blog, the Really Awesome Protein or RAP series. This does not mean I’m going to attempt to spread the protein love via ghetto-speak, gangster rhymes and poor beat boxing, although I am totally up for trying that. Actually it just means that once a month or so I am going to try and convince you that the molecules in your body are as exciting, mind-blowing, awe-inspiring, and amazing as anything out there in the cosmos. This series is to be a celebration of some of the most stunningly beautiful and phenomenally clever molecules in nature.


-------------------------------------------------------

My first RAP is one of my favourites, it’s also the favourite protein of one of my university housemates (in this case by favourite protein, I mean the only protein he knows the name of). Without further ado, I give you… rhodopsin…

Rhodopsin is a protein in your eye. Without it you could not see. There are many molecules that make up the cells of the human eye and all of them are intricate and beautiful in their mechanism. Rhodopsin though, is my favourite, not for any discernible reason, it just is.

The change in retinal when it gets hit by light... on the left L-shape
and on the right, lovely and straight. This change is HOW YOU SEE!

Rhodopsin is the actual light-sensing molecule, so it’s pretty key to the business of seeing. It lives in the membrane of light-detecting cells (photoreceptors) in the eye. It’s actually made up of two parts, a big bunch of protein that stretches across the membrane called opsin, and a teeny little molecule called retinal. Retinal is a chromophore, which means that it changes shape when it absorbs a particle of light.

In fact, just one bond of retinal changes position when it absorbs light, turning it from a slightly L-shaped molecule into a straight molecule. That’s it. One tiny little change, in the way one single chemical bond is arranged. And this is the key to sight.

You see, proteins are quite tightly packed molecules within themselves, so when retinal changes from an L-shape to a straight line, the opsin protein has to shift itself around slightly to accommodate this change in shape. It’s as if you’re standing on a really packed tube train, nestled into someone’s armpit with no room to move, and someone suddenly sticks their leg out into the space where your leg was… and your leg has to move. On a train, very bad etiquette and probably deserving of a highly meaningful tut, if not a muttered “honestly!”, but in a protein it’s fairly standard practise. A nearby ‘leg’, or in this case amino acid, shuffles out of the way of the retinal, possibly tutting slightly, and this change in conformation can be recognised by another protein, transducin.

This is rhodopsin. Now, how is that not BEAUTIFUL? The little cyan molecule in the middle is retinal, still in its L-shape form. As soon as it changes, transducin will KNOW about it. 

Transducin’s job is effectively to sit very close by and watch rhodopsin until it moves. This might sound like watching paint dry, except rhodopsin moves every time it absorbs a photo of light, which is very very often when your eyes are open. Transducin probably gets a bit more bored at night… actually that raises an interesting question, when you ‘see’ in your dreams, are your eyes involved? Or are all your transducin molecules just sitting there sighing at the unmoving rhodopsin and hoping you wake up soon?

But I digress, transducin is a G-protein, which will feature as a RAP in its own right at a later date. As soon as transducin recognises the shape-change in rhodopsin, it becomes activated, and scurries off to contact another protein. This protein triggers some changes in the cell that cause a message to be sent to the next cell. This message is passed along to a nerve cell, which shoots it off to the brain to let it know that you’ve seen light. Lots of and lots of these messages make up the overall picture that we get when we see images.

Rhodopsin lets us see beautiful things LIKE THIS. Thanks, Rhodopsin.

So that’s it… one tiny minute change in the position of one chemical bond can trigger 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 actually my number one molecule, and the first RAP in this series. It demonstrates everything that I love about biochemistry.

Structural biology laughs in the face of doom

#SciDoom FoS is having its first ever theme week, asking the question “are we doomed?”... as a new member of the FoS community I thought I’d toss my two pennies-worth of scattered thoughts in, as a quick introduction to me, if nothing else. 

----------------------------------

So, are we doomed? By the way, I hope everyone else reading this is also saying doomed in a really deep and threatening voice in their head. 

There are a lot of different ways to look at this question, and over the past few weeks I’ve been considering them all. Ultimately, as individuals we are all doomed to die, so in one way, we are certainly all doomed. But what about as a species? We could be doomed by our treatment of the planet, by our eternal battle with microbes, the bacteria and viruses that we cannot outsmart, by cancers created by genetic mutations within ourselves, or by a great big asteroid bumping into us in space. 

There are so many factors that I couldn’t decide which imminent doom to analyse, so instead I decided to think about it as a structural biologist, which is what I’m going to be when I grow up. As a structural biologist, my personal instinct is that we’re not doomed. This is because every time I look at a molecular structure I’m struck by how incredible life is. People say that looking out into the universe can make you feel small and insignificant, well if that’s true then looking inwards to your microscopic molecular make-up can make you feel big, complex, impressive, and really flipping awesome. 

An example:  Move your finger. 

Right, I can’t even list all the protein molecules that just enabled you to do that, there are thousands of them. They’re involved in transmitting the message from your brain to your hand, in contracting the muscles, in providing the energy to do all those things, and in generally keeping you running well enough to be able to move your finger in the first place. And all of them are built from just 20 different amino acids, according to specifications written in just 4 bases in your DNA. That. Is. Phenomenal. And that’s just the beginning. 

The best part is not only how mind-blowingly awesome (and beautiful) molecular structures are, but the fact that we know what they look like. We’ve figured out how to look at them, which is in itself something of a challenge. We’ve found ways to investigate and start to understand how they work. And then we’ve studied what happens when they stop working, and how we can try to use drugs to fix those problems. We haven’t solved everything, not by a very long way, but we know so much, and everything we know just reinforces how incredible our bodies are.  

The reason I write is to share my wonder and excitement at the molecular world, and to invite as many people as possible to join in it. Ultimately, and perhaps I am just a shameless optimist, I can’t bring myself to believe that a species as wonderful as we are can be doomed.... although do watch out for asteroids, and of course the eventual death of the sun. When that happens, we are indeed doomed. But you won’t be around to see it, so the blind optimism stands for now.