This blog has been created partly as a companion to Chemistry for the Biosciences, the textbook that I co-author with Tony Bradshaw, and to act as an archive of posts I write for other sites (particularly the OUPblog). Like the book itself, it explores how life on the scale of atoms and molecules has an impact on biology - at the scale of cells, tissues, and organisms - and seeks to demystify a range of biological and chemical concepts.

The blog's name takes as its inspiration the cover of the first edition of Chemistry for the Biosciences, which depicts a gecko seemingly clinging to its surface. To find out what links geckos to chemistry, read this.

Thursday, 15 March 2012

Why do we eat food?

You may well be thinking that the question posed in the title of this blog has an all-too-obvious answer. We all know that we eat food to keep ourselves alive. But why do we find ourselves slaves to our appetites and rumbling stomachs? What is actually happening inside each of us that couldn’t happen without another slice of toast, or piece of fruit, or that most vaunted of mid-afternoon pick-me-ups, the sneakily-consumed bar of chocolate?

We’re all familiar with the concept of something needing fuel to keep it going. Just as a power station requires gas or coal to power its turbines and generate energy, so we need fuel – in the form of food – to power our continued existence.

The foods we eat provide us with a range of nutrients: vitamins, minerals, water, fat, carbohydrates, fibre, and protein. These nutrients are put to different uses – as building materials to construct the tissues and organs from which our bodies are made; as the components of the molecular machinery that keeps our cells running as they should. All of these uses are unified by a common theme: a requirement for energy to make them happen. And this is where one particular type of nutrient comes into its own. Step forward the carbohydrates.

Carbohydrates are better known to us as sugars – but in fact the sweet crystals we know as sugar are only part of this group. Carbohydrates come in very different shapes and sizes. One of the smallest is glucose, which acts as a chemical building block: multiple copies of glucose can join together to form a range of much larger molecules. For example, starch – found in potatoes and flour – is a carbohydrate formed from many individual molecules of glucose joined together in long chains. (Based on taste alone, you wouldn’t think that starch was made of glucose: even though individual molecules of glucose taste sweet to us, once they are linked together to form starch the sweetness is lost.)

To understand how the sugar in our food can power the processes occurring in our cells every minute of every day, let’s follow some starch on its journey through the body. Many of the foods we consume aren’t in a form our bodies can do anything useful with. Instead, they need to be digested. And so it is with carbohydrates such as starch. This process of digestion starts as soon as the food enters our mouth: our saliva contains special substances (called enzymes) that start attacking the long chains of starch, breaking it into smaller fragments.

Digestion continues as our food is swallowed and slides down into our stomach, where an arsenal of other chemical weapons set to work on the mouthful we’ve just consumed. Before long, what were initially mouth-watering morsels are reduced to something rather less appetising and leave the stomach to enter the long, snaking tunnel of our intestines. By now, the long chains of starch have been broken down into glucose, which is small enough to pass through the lining of our intestine and into our bloodstream. Our bloodstream acts as a short- and long-distance transport network, carrying the newly-arrived sugar molecules to cells all over the body.

When glucose arrives at its destination and first enters the cell, it undergoes a chemical make-over to transform it into a new substance called pyruvate. And this is where the real fun begins.

At this point, let me introduce you to a special inhabitant of our cells, the capsule-shaped mitochondrion (or mitochondria, if you’re referring to more than one). In essence, mitochondria provide each cell with its own power supply. The more active a cell is – and so the more energy it needs – the more mitochondria it contains. Muscle cells, which require a lot of energy to power their movement during muscle contraction, may contains thousands of mitochondria; by contrast, skin cells, which only require a modest energy supply, may contain only a few hundred.

But how do mitochondria actually power a cell? Well, mitochondria act as factories for a special chemical called ATP. ATP is like a portable mini-battery: it stores energy, and can be shuttled off to wherever in the cell that energy is needed (at which point the stored energy can be released).

So what has the production of ATP by mitochondria got to do with us eating carbohydrates? I mentioned earlier how glucose is converted into pyruvate when it enters the cell. This pyruvate is then shipped into the mitochondrion. Once inside the mitochondrion, pyruvate enters a chemical production line, a series of linked chemical reactions and molecular processes that use the pyruvate ultimately to produce ATP. (I won’t go into details, despite the fact that, to a biochemist like me, the process is ingenious. Just take my word for it if you will.)

This process of mini-battery production relies on more than just glucose to keep it going: it also needs a constant supply of oxygen. Indeed, this reliance upon oxygen is the whole reason why we need to breathe every minute of our lives. If we stop breathing, we stop supplying oxygen to the mitochondria in our cells – and they can no longer produce ATP. Without ATP, there is no energy to power the processes needed to keep a cell alive. Without energy, cells die.

The importance of ATP to our very existence is also highlighted in surprising ways: Agatha Christie’s Sparkling Cyanide was first published in 1945, and features two characters whose meals at a restaurant prove to be their last: they are both poisoned with cyanide. Cyanide has its lethal effect by blocking the chemical production line taking place in our mitochondria. If cells can’t produce ATP, they lose their energy source and quickly die (just like in the absence of oxygen). And if this happens in cells throughout the body simultaneously, it’s not long before the body as a whole can no longer function, as Agatha Christie’s characters had the misfortune to discover.

Wednesday, 1 February 2012

Why are plants green?

After the greyness of winter, the arrival of spring is heralded by a splash of colour as plants emerge from the soil, and trees seemingly erupt with leaves. Soon, much of the countryside has moved from being something of a grey, barren wasteland to a sea of verdant green. But why is it that so much vegetation is green? Why not a sea of red, or blue? To answer this question let me take you on a colourful journey from the sun to within the cells of plant leaves.

As humans, our waking hours are punctuated by mealtimes: we must consume food on a regular basis if our bodies are to be able to generate the energy we need to survive. Plants, however, fuel their survival in an altogether different way. Plants don’t need to ‘eat’ as such; instead, they generate their own food supply. This manufacturing of food is powered by energy that plants capture from sunlight.

It might seem odd to say that sunlight contains energy, but our everyday experience shows this to be so: if we sit outside on a sunny day, our skin quickly becomes warm. This warmth is the result of our skin cells absorbing the energy contained in the rays of sunlight.

Sunlight is made up of millions of individual rays containing a huge range of different energies. Imagine standing on a beach, watching the waves rolling in. These waves aren’t identical in size: there will be some small waves that contain little energy, which fall gently on the sand, and other much larger ones that come crashing down; these contain a lot more energy. And so it is with the rays of sunlight: some rays have a small amount of energy; other rays have much more.

This leads us on to another, perhaps surprising, phenomenon: we see rays of light of different energies as different colours, as beautifully illustrated by rainbows, which we’ll all have seen from time to time (most often on a typical British summer afternoon, as bright sunshine is suddenly replaced by a downpour of rain). When sunlight – a mix of rays of different energies – hits drops of rain, the individual rays are separated according to their energy. Suddenly, a mix of rays that, to us, have no obvious colour become transformed into the characteristic colours of the rainbow: red, orange, yellow, green, blue, indigo, violet. We call this range of colours the visible spectrum.

Sunlight also contains rays that fall outside of the visible spectrum, none of which are visible to us, but which are visible to other creatures. For example, many insects can view ultra-violet light, which has greater energy than the violet light at the one extreme of our visible spectrum. In fact, some flowers look much more visually interesting to insects than they do to us: insects can see extra marks and patterning that show up in ultra-violet light, but which are simply invisible to us. (You can see a couple of examples here and here.)

But what has this to do with the colour of plants? Why do we see plants as green? The cells of a plant leaf contain compartments called chloroplasts, which house some special machinery that enables the plant cells to capture the energy in sunlight and to use it to power the formation of food. Chloroplasts contain a substance called chlorophyll, which is an example of a pigment – a substance with an obvious colour. This pigment isn’t there just to make the plant look pretty to the human eye: it is the component of the chloroplast that actively absorbs energy from sunlight. However, it can only absorb rays of light that have particular energies – those corresponding (in broad terms) to red and blue light. By contrast, the rays of light that fall in between red and blue light in the visible spectrum cannot be absorbed. Instead, they bounce off the surface of the leaf and into our eyes (if we’re looking at them). And what colour lies between red and blue in our spectrum? You’ve guessed it: green. The reason we see plants as green is because green is the colour of the rays of light that get bounced back by the chlorophyll in the plant cell.

In fact, this concept holds true for any colour that we see. The reason that tomatoes appear red is that they don’t absorb red light: it is bounced back from the surface of the tomato to be detected by our eyes. Tomatoes exhibit their red colour thanks to the pigment lycopene, which absorbs blue and green light, but bounces back red.

Let’s end this journey with a brief flit across the Atlantic to see why plant leaves don’t always appear green. Parts of the Eastern seaboard, in the US and Canada, are famed for the fiery displays of colour by trees in the autumn. This dramatic change in colour is a consequence of chlorophyll being degraded as air temperatures drop with the change in season, leaving behind other pigments that had previously been masked by the chlorophyll. As chlorophyll is degraded, the greenness fades, to be replaced with vivid reds and oranges. It’s now the turn of other light rays to be bounced back – giving us something truly to feast our eyes on.

Sunday, 11 December 2011

Why are we told always to finish a course of antibiotics?

Most of us have at one time or another been prescribed a course of antibiotics by our GP. But how many of us heed the instruction to complete the course – to continue taking the tablets or capsules until none remain? Very often, our strict adherence to the prescription fades in line with our symptoms: the prescription may last for, say, seven days, but we’re often feeling much better after just two or three. So why bother continuing to take the antibiotic? After all, if we’re feeling better, the antibiotic has done its job, right? Well, you may think so. But, in fact, stopping a course of antibiotics early can have potentially lethal consequences. How can that be?

To answer this question, we must travel inside our body to mingle with the bacteria the antibiotics have been prescribed to kill. At face value, all the bacteria in a given population might seem identical. But look a little deeper, and you’ll see subtle differences. And one difference is the way in which they respond to a given antibiotic.

I described in a previous post how antibiotics are designed selectively to attack bacteria rather than causing harm to our own cells, which must necessarily get exposed to the antibiotic as it travels through our body in search for the alien intruder within. But different bacteria, even from within the same population, may respond differently to a particular dose of antibiotic. The ‘weak’ ones may be susceptible to a relatively low dose – they may be killed after just a few days of exposure to the antibiotic; by contrast, others may be much more resilient, and will still be alive after a few days of treatment.

The important point here is that the population as a whole is made up of bacteria exhibiting a range of tolerances – at one end of spectrum, a few real weaklings; at the other, a few really resilient ones. And, in between, we find many average, run-of-the-mill individuals, who can hold out against the antibiotic for so long – but not for very long. (I saw the same kind of distribution within a population when we grew some tomato plants this summer: some were noticeably short, some were unusually tall, but a majority hovered somewhere in between.)

But what’s causing this difference in tolerance? I mentioned in a previous post that each time a genome is copied there’s a chance a mutation (an error) will creep in to one of the genes making up that genome. Well, every time a bacterium reproduces it has to make a copy of its genome to pass on to its offspring – and, every time, there’s a chance an error will creep in. The chances are that the variation in tolerance to antibiotics that we witness in this population of bacteria is due to slight variations in their genomes; it could be that our resilient individuals show this resilience because they picked up mutations not present in their weak or average cousins.

Now, let’s return to our bacterial infection and imagine that we’ve started to take a course of antibiotics. It takes just a day or two to kill the real weaklings. And, in three or four days, even the Mr Averages will start to feel the proverbial heat. At this point, the population as a whole will have gone into noticeable decline, and we may start to feel much better as the number of alien invaders reduces.

But what has actually happened by the three or four day stage? The population as a whole may have shrunk in size – we’ll have rid ourselves of the few real weaklings and the larger number of Mr Averages – but we’ll be left with the few hangers-on at the other end of the spectrum, the real bruisers.

Before we started taking the antibiotics, the antibiotic-resilient bacteria (our ‘bruisers’) were fighting for a share of the available food with all the other members of the population. (It’s important to note that, when I talk of ‘weak’ or ‘resilient’ individuals I’m only referring to their tolerance level to antibiotics, not their ability to scavenge for food, and other aspects of survival in an antibiotic-free world.) In essence, the bruisers were being kept in check by everyone else – they remained in the minority because the whole population, including the weaklings and the Mr Averages, was growing at about the same rate. Now, three or four days in, the bruisers suddenly find themselves with much less competition for food. Imagine going to the buffet table at a wedding with 200 guests, all of whom are vying for a slice of the pie (quite literally), versus going to the same-sized buffet table with the same amount of food at a wedding attended by just 20 guests. At which wedding are you most likely to be able to fill your proverbial boots?

Now let’s consider what happens after day three or four, once the supply of antibiotic has stopped. At this point, remember, there are just a relatively small number of antibiotic-resilient bacteria left, but no weak or average ones. When the resilient bacteria suddenly find themselves the guests at an unexpected banquet – with competition for food gone – they do what bacteria do best: they reproduce. And without the previous competition for food, they can do so rapidly. So, we’ve suddenly gone from a mixed population in which the majority didn’t take kindly to antibiotics and only a few were the bruisers, to one in which virtually everyone is unusually tolerant to antibiotics. And this is where the real danger can lurk.

I mentioned above that the resilient bacteria may exhibit their resilience because they have accumulated more errors in their genomes than their weak or average cousins as successive generations have reproduced. As this resilient population now continues to thrive, it risks accumulating even more errors. And one of those errors could be what it takes to tip the balance from the bacterium being highly-tolerant of the antibiotic to it being completely resistant. You don’t need to be a medical expert to realise that complete resistance to an antibiotic is a really bad thing. If a bacterium has overwhelmed our immune system, and we don’t have an antibiotic to act as a back-up defence system, we have no weapons left to fight with.

If we carry on taking our antibiotics as prescribed, the story ends quite differently: even the resilient bacteria lose the will to live in the end. But we have to keep up the pressure by finishing the course of antibiotics. That way, any resilient individuals don’t get to dominate, and we reduce the risk of one of them picking up a mutation that makes them virtually invincible – but which is potentially lethal for us. In future, you know what you need to do…