Mommy, Where Does Blood Come From?

With the recent rise of the vampire star in popular culture, this scientist thinks we’ve all been seeing a little more blood in everything from movies, to television, to magazine ads. While it might not be immediately apparent from these corn-syrup-and-food-colouring imitations, our blood is pretty complex stuff. Like so much of our bodies, what seems like a simple (if slightly goopy) liquid is really a mixture of different types of cells and substances. Also like much of the rest of us, the makeup of this serological soup needs to be closely regulated to keep us alive. When it comes to controlling the composition of our bodies, enzymes have the gene-wrangling power that places them squarely in the drivers seat.

            If CSI: Miami has taught me anything, it’s that sunglasses are required to investigate crimes, and each person has unique DNA. In fact, each cell in your body carries the exact same DNA sequence, the same genetic code. So how do some cells end up as heart muscle, and some as fingernail, and some as bone marrow? If all of the DNA is the same, how can it hold information for making so many different kinds of cells? What makes different kinds of cells different isn’t their DNA, but the proteins that exist in that cell. Proteins are made by decoding specific parts of the DNA, so the body controls what cells are what by regulating what pieces of the DNA get decoded to make protein. It’s kind of like having a whole recipe book with many recipes that could make up many meals. If you want a pancake and poached egg breakfast, you use those specific recipes to come up with the desired end product.

            To control what proteins get made in each cell, we control which recipes are available to the chef. Our DNA isn’t just crammed willy-nilly into our cells, but has a defined structure in which it is wound up very tightly. There are proteins called histones that the DNA folds around to help condense it into a smaller space. The DNA itself, as well as the histones, can be modified by attaching specific chemical groups. In this way, the DNA can be effectively labeled with respect to which proteins should and shouldn’t be made in that cell. This labeling doesn’t happen on it’s own, however. There are specific enzymes that attach and detach these groups from our genetic material, thus controlling which genes get made into protein (expressed) or are wound up too tightly to be accessed (repressed).

            One of the chemical groups enzymes attach to DNA is the methyl group: one carbon atom attached to three hydrogen atoms. A team of researchers in Texas recentlyinvestigated what would happen if an enzyme responsible for methyl-labeling was removed from stem cells in the bone marrow. Normally, these cells are responsible for morphing into all the different types of cells that make up our blood and bone marrow, in addition to making more stem cells. When this DNA-labeling enzyme was absent, the cell made the wrong proteins at the wrong times and could not make functional blood cells. Their experiment showed that DNA labeling by this enzyme is a key part of how the body produces the blood cells we need to live.

None of us could survive if we only made one type of cell. It’s our bodies’ ability to pick and choose the right recipes for the right occasion that results in our different body parts and organs. With enzymes playing such a key role, maybe the vampires are just missing an enzyme they need to make their own blood. Human blood, a vampire’s complete breakfast.

Playing Evolution: Making Enzymes from Scratch

Photo credit www.jacehallshow.com

In researching almost any topic in biology I am consistently amazed at how natural selection produces things so well suited for their specific roles. From an animal perfectly filling an ecological niche, to an organ efficiently performing a biological task, to a molecule precisely providing the ideal chemistry for its function. It is truly astounding how a process that moves along through random mutation events can result in perfectly coordinated systems at every level. Although natural evolution results in sublimely well-tuned components for every biological system, it also takes a stupendously long time to go about its business. Enter the twenty-first century scientist. While scientists in nanorobotics and materials science are making game-changing leaps and bounds in our ability to manipulate ourselves and our environment, enzyme engineers are starting to give them a run for their money. Have a tough chemical job to do? One that has never been done before? Why not engineer a brand-spanking-new custom enzyme to catalyze your worries away?

            Many of the enzymes that exist naturally are made of protein. The protein itself is a long chain made of different amino acids linked together. You can think of it kind of like a long charm bracelet: the links of the chain form the structure of the chain, while different charms on each of the links make each part of it unique. With proteins, there are 20 types of amino acids or “charms” to choose from that can be strung together in different combinations.

           

            Much like how a ball of wool doesn’t do you a heck of a lot of good on a cold day, a enzyme doesn’t do much at all as one long strand. Mittens or a scarf, however, can be very functional, and so can an enzyme when it is tangled up into a very specific shape. In fact, it is the three dimensional shape that gives a folded enzyme its ability to perform chemistry. So how do enzymes stay folded in the right shape? Going back to the charm bracelet example, some charms (amino acids) can interact specifically with each other to reinforce specific shapes. The “chain” itself also has a tendency to form certain structures: telephone chord-like coils (alpha-helices) and flat sheets formed by the chain doubling back over itself repeatedly (beta-sheets). Additionally, over one third of all proteins contain atoms of iron, zinc, copper, or other metals. By interacting strongly with specific groups of amino acids, these metals can lock part of an enzyme structure in place, helping the rest of the enzyme to also hold its active shape.

            If the interactions that keep an enzyme folded properly and functional seem complex, that’s because they are. A single enzyme has hundreds of individual interactions between individual amino acids and metal groups, some of which can be removed or replaced, and some of which are vitally important either to keep the enzyme in the right shape, or to perform specific chemical functions. Scientists have been trying to tease this apart for years by deleting or swapping out specific amino acids in natural enzymes and observing the effects of these changes. Much like tinkering with an engine vs. building one from scratch, however, you can only learn so much about how something works without creating one of your own. This is exactly what a group of scientists from the University of Michigan reported recently in Nature Chemistry. These intrepid researchers designed an enzyme from scratch: designing a structural “scaffold” (complete with a structure-stabilizing metal) into which they incorporated a small area capable of performing similar chemistry to one of our body’s own enzymes. By testing which enzyme design concepts make the chemistry faster or slower, these researchers are testing and applying the basic principals we currently think govern how all enzymes work.

            Designing enzymes from scratch to perform tasks that natural enzymes already perform is almost the definition of reinventing the wheel. It is, however, incredibly valuable in at least two respects: it demonstrates that we understand how enzymes work well enough to design them from the bottom up, and it opens the door to engineering brand new enzymes that catalyze chemistry not found in nature. Imagine creating an enzyme that quickly breaks down Styrofoam or other long-lasting pollutants. Enzymes are the most powerful chemists in nature, and if we can design their abilities, rather than simply co-opting them, they can be our most powerful industrial and biotechnological tools as well.

Making Mutants, the Safe Way

The practice of medicine has come a long way from the days of the four humours. Instead of being filled with a delicate balance blood, snot, and various forms of “bile,” we now understand that our bodies are made of millions of cells, each with a specific job to do. We are now able to pinpoint the exact type of cell not doing its job in many diseases, and to figure out just what job it’s not doing. This knowledge can help us change or replace parts in our cells in order to treat some diseases. In the future, making our own engineered human mutants may help us accomplish medical feats not possible with traditional drugs.

            Each cell in our body is specialized to perform a specific function. Our nerve cells conduct electricity to pass messages around the body, our red blood cells carry oxygen, and cells on the inside of our stomachs secrete acids to help with digestion. In order to carry out these jobs, our different types of cells produce specific enzymes and other proteins. Without these specialized components, the cells don’t function like they should. For some diseases there may be only a single protein that is not being produced, and this deficiency results in a whole host of symptoms. For example, type I diabetes is an entire disease caused by the body being unable to make a single protein: insulin. All proteins are made by decoding DNA sequences, and researchers are looking at treating diseases like diabetes by adding back the specific DNA needed to make the proteins that are missing or damaged. By inserting these specific DNA sequences into the genetic material already in our cells, we hope to engineer helpful cellular mutants that can produce missing proteins and reverse disease.

            Sticking helpful genes into human cells can be a great way to fill the gap of a missing protein, but there are many dangers inherent in introducing new DNA. If a new piece of DNA is inserted into one of your chromosomes, it can land in any number of places, including in the middle of another gene. This can potentially result in mutation of a different protein, in which case you might cure the first disease but could actually cause another. A more common and potentially more dangerous scenario is if the new piece of DNA disrupts an oncogene (see DNA Repair just doesn’t give me the same Buzz). In this case adding the extra DNA can cause cancer.

            While humans have only been sticking extra bits of DNA into cells for a few years, viruses have been accomplishing this task for millennia. For many viruses, part of their life cycle involves taking part of their DNA and inserting it into a chromosome of the cell they’re invading. In order to do this efficiently, viruses use a specific DNA-insertion tool: an enzyme called an integrase. This enzyme recognizes specific sequences on the DNA to be inserted and on the host cell DNA and stitches in the inserted piece at specific sites on the host chromosome.

            Nature doesn’t always do what we want it to (sometimes disease happens), but it also produces some pretty useful tools that we can borrow. In the case of gene-based therapies, the danger is not knowing where an introduced piece of DNA will insert into our own DNA, and whether or not that might cause even more problems. By borrowing the ability of viral integrases to insert DNA pieces into specific places in the genome, we drastically cut down this risk. Scientists are now working on giving patients the specific DNA segments needed to replace proteins missing in certain diseases and including viral integrase enzymes to make sure that DNA is inserted in safe spots in our genome.

            To most people messing with their DNA, the prospect of cancer, and viral enzymes are all pretty scary concepts. By understanding how each component works, however, we are able to use these concepts to treat diseases in innovative ways. Knowing more about almost anything can help it to be less worrisome and more useful.

Animals on Steroids – Steroids on Oxygen?

In today’s society, the word “steroid” conjures up images of hulking body-builders and sheepish forfeitures of Olympic medals. What most people don’t realize is that steroids actually play a role in all of our lives. In fact, right now there are a whole host of steroids performing the very important role of keeping you alive. Whether we’re pumping up or vegging out, we’re all chock full of steroids. What might be even more amazing is that in addition to keeping animals, plants, and fungi functioning like they should, steroids may also be able to tell us a bit about how and when such multi-celled beings came to be.

            As I alluded to above, steroids aren’t just for greased-up gym junkies. On the contrary, they are enormously prevalent substances produced by all kinds of plants, animals, and fungi. Steroids are molecules made of four rings of carbon fused together in a bent line. This basic structure contains 17 atoms of carbon, and modifying this welded-ring core with additional carbon or oxygen atoms makes hundreds of different steroids. The central steroid in human biology is cholesterol, and it is a vital component of every cell in your body. We also use it to make other steroids like the dreaded hormones that complicate adolescence and control much of our development and body maintenance. While fruit bats, magnolias, and button mushrooms don’t have the same type of awkwardness during puberty, they also produce a preponderance of different steroids nonetheless critical for their own lifestyles.

Cholesterol

            While cholesterol is indeed present in your hamburger, your body also makes it from the simpler molecules you get from digesting all kinds of food. There are three major atomic ingredients in the cholesterol recipe: carbon, hydrogen, and oxygen. The first two come from the food-begotten hydrocarbon building blocks. The necessary oxygen comes from the O₂ in the air we breathe. Like so many things our body makes, the real construction workers are our enzymes. There are many enzymes involved in making steroids, some of which are dedicated to incorporating oxygen from O₂ into the steroid being produced. These enzymes are aptly named “oxygenases”. The job of an oxygenase is not an easy one, and the reaction between O₂ and the hydrocarbons is incredibly slow if no oxygenase is around to speed it along. Many oxygenases use tools like metals and vitamins to manipulate the oxygen into reacting with the carbon in order to come up with the final steroid product.

            Steroids, produced with the help of oxygenases, are one of the major things separating multi-cellular plants, animals, and fungi from life forms made of a single,simple cell, like bacteria. While all “higher” life forms produce steroids, as a rule, bacteria don’t. In fact, steroids are so important to the membranes of more complicated organisms that evolution of everything from venus flytraps to the mailman may not have been possible if our common ancestors couldn’t make steroids. When it comes to steroid production, we need a lot of oxygenases and a lot of oxygen. Way back in the history of life on earth, however, there wasn’t much oxygen floating around in the air like there is today. When there was no oxygen, there were also no steroid-producing oxygenases. As oxygen levels rose, these enzymes evolved, steroids were produced, and in a few hundred million years you were born, went through puberty, and learned all about it. Because of this necessary sequence of events, scientists are able to look at the emergence of steroid production and make connections with changes in the earth’s atmosphere and the evolution of the earliest common relative we share with the coconut.

Studying modern biology can not only help us understand how we are now, but give us insight into where we came from. As for me, the next time someone questions whether an athlete is on the ‘roids, I’ll turn to them and ask, “Isn’t everyone?”

Every Bug for Themselves! How Changing Enzymes Create Resistant Infections

Sooner or later pretty much everyone is going to have to take a course of antibiotics. Whether it’s a bacterial chest infection, strep throat, or a cut finger that gets out of hand, a bottle of “twice a day, with food, until finished” meds will eventually find its way onto our kitchen counters. Like most of the medicines we take, many of us don’t worry about how they let us reclaim our own bodies, as long as our symptoms get better and stay that way. Unlike many of the medications we take,  antibiotics target processes that aren’t controlled by our own bodies, but rather by the chemistry of another life form. Unfortunately for us, these little buggers multiply faster than we do, adapt faster than we do, and have big population numbers on their side. Lets take a look at how antibiotics effect bacterial enzymes, and what the bugs do to bite back.

In humans, enzymes are vital catalysts for much of the chemistry we need to sustain life. This includes breaking down our food, building up new body parts, and keeping everything repaired, supplied with nutrients, and responsive to our environment. The same is true for bacteria. Fortunately for modern medicine, many of the mechanisms and enzymes bacteria use are very different from those in humans. Additionally, there are many things that bacterial cells do, such as building cell walls, that human cells don’t. Many antibiotics work by targeting the enzymes that are different between the bacteria and people. As an example, bacteria need their cell walls to live, so a drug that shuts down an enzyme needed to make the cell wall will kill the bacterium but will not affect human cells that don’t have the same cellular machinery. By picking on enzymes bacteria need that humans don't have, antibiotic drugs are able to kill bacteria, and fight bacterial infections, without causing damage to the human patient.

If antibiotics kill bacteria by shutting down enzymes needed for important chemistry, how can misuse of antibiotics result in resistant strains of bacteria? To understand the answer to this question, we have to understand that bacteria reproduce much, much faster than people do. In fact, some bacteria produce more than one new generation per hour. To reproduce they have to copy their DNA, and sometimes mistakes are made resulting in changes to the DNA sequence. These changes can result in changes in the sequences of proteins within the cell, some of which will be in the enzymes targeted by the drugs. Some of the changes might result in enzymes that don't work and a new bacterium that will die, but the odd bacterium will coincidentally have an enzyme that still works, but is no longer affected by the drug. This can happen if the place the drug binds to the enzyme is disrupted, the enzyme interacts differently with something else in the cell, or even if the enzyme itself is not changed but something else interacts with the drug, stopping it from effecting its original target. Changes can also occur in other enzymes so that they pick up the catalytic slack and the original enzyme isn’t necessary anymore. 

Individual DNA mutation events are pretty infrequent and random, so a very very small percentage of the bacterial population will experience a mutation leading to a change in the target of a specific drug. These lucky few, however, will survive when the drug kills all of the bacteria without a lucky mutation. So in a typical infection with many drug-susceptible bacteria and a tiny percentage of drug-resistant bugs, the drug will kill the bacteria that it can, and those resistant to the drug will survive, eventually making up the whole bacterial population in that patient. This means that using antibiotics selectively encourages the growth of resistant bacteria, and every time a single antibiotic is used, resistant strains have an opportunity to become more common.

Antibiotics can help us to get rid of infections by killing off most of the bacteria and giving our immune system a chance to fight off the resistant few. Also, these drugs are often used in combination for tricky infections so that bugs resistant to one drug will probably be killed off by the other. The fact remains, however, that all of the antibiotics currently available are getting less and less effective as more and more resistant strains emerge. In the face of this problem, we all need to be careful about the way that these drugs are used, effectively conserving the resource of antibiotic effectiveness. So the next time you have the option to buy a product with an antibiotic added, consider the old-fashioned version. 


Sometimes all you need is soap.

Moonlighting Enzymes: Supporting Keg Parties Everywhere

Our lab is situated in close proximity to a high concentration of fraternity houses, and as the fall term commences the warm autumn atmosphere reeks of fresh loose-leaf, cheap beer, and hang-over bacon. Any truly savvy and overindulgent undergrad should be writing a little thank-you note to one of the crucial factors that enables this year-opening bash: the enzyme alcohol dehydrogenase (ADH). This little microbrew miracle has been helping humans indulge in handcrafted libations for around nine thousand years and is perfectly suited to this function. Or is it? A recent study questions the evolutionary history of ADH and suggests that it might have more important things to do than aid in our enjoyment of an evening martini.

            Given that enzymes are integral components of so much of our body chemistry, it can be hard to remember that they haven’t always been there. Just like everything else, they had to come, to evolve, from somewhere. ADH is no exception. These days, it’s studied as the first enzyme in the metabolic pathway helping us to break down ingested alcohol (ethanol). Without it, we couldn’t efficiently clear alcohol from our systems and it could accumulate to lethal levels over the course of a lively cocktail party. In fact, one form of the enzyme acts in our stomachs, starting to break down the intoxicating molecule before it ever reaches our bloodstream. But where and how did ADH evolve? Were the molecules in our prehistoric ancestors preparing for a time when our species would start breaking out the booze?

            The rules of enzyme evolution parallel those of organism evolution: an ecological (or functional) niche has to exist before the process of natural selection can result in something filling that niche. In the case of ADH this means the availability of ingestible alcohol. If there is no dietary alcohol to break down, there should be no enzyme evolution specifically to break it down. By far, the greatest source of alcohol available for animal consumption is fermentation of fruit sugars, so the appearance of fruit in the prehistoric world should predate that of ADH. This is assuming that ADH really did evolve to break down alcohol. It is this assumption that is being questioned by a group of Mexican scientists.

            In a sobering study examining the functional capacities and evolutionary histories of a range of ADH enzymes, the real purpose of human ADH was called into question. In actuality, humans have several forms of ADH from three very different classes of enzyme using very different means to achieve ethanol transformation. Only one class of ADH is considered to be important for human alcohol breakdown. As it turns out, this class of ADH evolved before the appearance of fruit-bearing plants. That is to say that the type of enzyme we use today to reduce both inhibitions and alcohol toxicity showed up before there was any alcohol to indulge in.

If ADH’s only job was to enable aperitifs, it would not have evolved to do so before the functional niche existed. Instead, it is more likely that ADH has a somewhat serendipitous ability to metabolize the alcohol we drink, and we exploit that ability. In fact, all of the human ADHs are better at catalyzing transformation of different (non-liquor-related) compounds in our bodies, such as bile acids and serotonin. It seems that the party-pleasing activity human ADH is best known for is a handy trick this enzyme would file under “other abilities.”

How'd he DO that? Real Chemical Magicians

Enzymes 101: Peaking into the black box

            The term “enzyme” has a pretty specific meaning to people who define themselves by such terms as “enzymologists” (go figure). To most people, however, it’s a less well-understood term. For many of the folks I know, the term “enzyme” can be virtually interchangeable with “protein,” or perhaps only recognized in the context of specific and dubious dietary supplements. For the purposes of this and further discussions, I’d like to talk about enzymes as proteins or nucleic acid that act as a catalyst to speed along chemical reactions. That’s what enzymes are and what they do, but how on earth do they do it? In this post we’ll use broad strokes to discuss some of the general strategies enzymes use to put eons of biochemical evolution to work.

            It can be a bit hard to really appreciate, and I mean fully appreciate, what enzymes do for us, and how difficult this task is chemically. When I think of the power of enzyme chemistry it always brings me back to early organic chemistry classes. As a bright-eyed, eager young undergrad I dutifully learned the rules of traditional organic chemistry: what bonds can be broken by what chemicals under what impossibly harsh boiling acidic conditions. We learned that by the natural laws of energy, matter, and all that is chemically holy there are just certain reactions that wouldn’t happen at room temperature during the length of an average PhD. How then, I would ask, could these types of reactions be magically popping up in textbooks looking perfectly and innocently plausible? The professor’s answer? Enzymes.

            Upon receiving such a disyllabic and seemingly self-evident answer I’m sure that I nodded my head knowingly, pretending that I fully understood how the biochemical black box could perform chemical black magic. Since then I’ve made a few strides toward actually understanding the mechanisms behind these baffling enzymatic chemoacrobatics, and continue to be amazed by the underlying simplicity and elegance in complicated enzyme systems. As an introduction to the broad concepts of enzyme mechanisms I’ll talk about the very basic catalytic strategies they use, and leave more detailed mechanisms for a later date. So let’s talk about shape, strain, orientation sequestration, and transformation. Lets talk about enzymes.

            One of the ways that enzymes are able to shift chemical reaction rates into high gear is simply by bringing the necessary components, or substrates, together. Understandably, this seems trivial on the surface but practically it is both very important and very effective. Being macromolecules (proteins or nucleic acid), enzymes have lots of different chemical groups: hydroxyl groups, aromatic groups, amine groups, etc. These have been positioned during evolution of specific enzymes to be in just the right places to interact very specifically with their substrate molecules. The “lock and key” analogy is used a lot in explaining these interactions, and is as apt an analogy as any. Basically the enzyme is able to bind very specific compounds, while completely ignoring others. By doing this for more than one substrate, they are able to bring two or more reacting molecules into very close proximity and hold them there, allowing them to interact much more efficiently. Additionally, enzymes don’t bind their substrates in just any old way, but in a precise orientation, effectively lining up slot A with tab B. This very simple enzyme function is kind of like a good match maker, taking the chance out of two compatible things coming together and setting the mood just right for the chemistry to happen.

            Another power that enzymes have is a consequence of their size; enzymes are huge compared to the small molecules involved in many of the reactions they catalyze. This means that they can completely surround these small molecules, and in so doing can control the immediate environment in which the reaction is taking place. Practically this can mean separating the substrates from interfering water molecules or creating pockets of positive or negative charge in specific places. This gives the substrate molecule(s) a custom-built productivity space where all of the elements are designed to help the chemistry along and exclude interfering substances.

            The general mechanisms we’ve talked about so far involve concepts that I like to think of in terms of “tweaking the chemical circumstances,” but enzymes can play a much more “active” role in chemical reactions as well. One way that enzymes can shove a reaction in the right direction is an offshoot of the “lock and key” tight interaction concept mentioned above. Some enzymes bind their substrates in such a way that they actually bend, twist, or otherwise strain their shape. This changes the energy state of the molecule and helps to push the chemical reaction to its conclusion. Alternatively, the enzymes themselves can actually react chemically with their substrates, forming a covalent bond between enzyme and substrate. This bond is broken by the end of the reaction cycle to release the product and regenerate the enzyme. This latter mechanism is often referred to as providing an alternate path for the chemical reaction to go through, effectively using the substrate-enzyme reaction as a handy detour to avoid more difficult chemistry.

            The concepts of catalytic mechanism explored above are incredibly general, and the specifics that happen in each individual system can be complex enough to fill the contents of a research career (or several). With all of the complicated and truly challenging chemistry that’s going on in our bodies every day, however, I think it’s inspiring that such simple and intuitive concepts are at the root of such complex mechanisms. It’s amazing what we can understand about our own chemistry if we choose to start looking inside the black box.

DNA Repair just doesn’t give me the same Buzz

Ask any graduate student and they might tell you caffeine is a lifeline. Ask a health enthusiast and they might tell you it’s a poison. Ask a physician and between sips they might advise you that it’s fine in moderation. If you decide to ask the researchers behind a recent paper in the Proceedings of the National Academy of Sciences, however, they’ll let you know that caffeine can help prevent skin cancer. As a bonus, they’ll even tell you why. In my post last week I started what I intend to be an ongoing discussion on enzymes: what they are, what they do, and how they affect every facet of life. The last post was a (very) general introduction. Some posts will dig into the nuts and bolts of the chemical reactions enzymes help along and how the heck they do it. Some posts, like this one, will discuss the broader roles of enzymes in biology. So grab your coffee cup and sunscreen (just in case) as we talk about some counterintuitive caffeine consequences.

            Before we can talk about what role enzymes play in cancer, we need a very brief description of how cancer works. Cancer occurs in pretty much all life forms that exist, like us, as groups of cells. This is in contrast to single-celled organisms like bacteria and yeasts. Cancer is basically uncontrolled growth of specific cells. All the cells in our body usually divide to form new cells, thus growing the tissue, at specific rates and under specific circumstances. Cancer happens when the cells divide very rapidly without obeying the rules, so to speak, of when they are supposed to replicate. One of the reasons that normal cell division is so regulated is to make sure that the new cells coming out of cell division are healthy and have accurate copies of the parent-cell DNA. When replication is happening too quickly, there is no time for the cell “quality control” mechanisms to check that everything is honky dory, and the result can be new cells with mistakes in the genetic code. These aberrant cells not only have functional problems due to the mutations, but will also go on to divide rapidly, causing a cascade of rapidly dividing, unhealthy cells that form the tumors associated with cancer.  So what is the trigger for this cascade? What causes that initial cell to start dividing too fast? As I mentioned, normal cell division is closely regulated, and if something causes a problem in one of the tools the cell uses to regulate division, the regulation system can go out the window. The genes coding for these regulatory tools are often called oncogenes (basically “cancer genes”) as mutations in these genes are likely to cause cancer.

            There are many things coming at us every day that can cause DNA damage. These range from UV-rays to charbroiled steak to chemicals we make inside our own cells or mistakes by our cellular DNA-manipulation machinery. In fact, lots of DNA damage is done every day inside each one of us, so why are we still up and walking around? Enter the enzyme. Not one enzyme, in fact, but an arsenal of enzymes, each with a specific job to do in DNA-maintenance. In thinking of enzymes in your body, you can think of each one having a very specific skill, like trades-people working to build a house. The plumber doesn’t put in the electrical work and only the floor guy puts in the tile. With enzymes it goes even further, so that in laying floor tiles you’d have one guy to lay the grout, one guy to pick up the tile, another to position it, another to press it down, another to wipe it clean, etc.  In talking of DNA, there is a set of enzymes for making the DNA, specific sets of enzymes to repair specific types of DNA damage, and specific sets of enzymes to detect specific types of damage at specific times and signal to the DNA-repair enzymes to get to work.

            Before we get too jittery, lets talk about how caffeine affects this process. We all have an enzyme called ATR that is involved in a couple things we’ve talked about. This enzyme is a kinase, meaning that it catalyzes transfer of a phosphate group from one molecule onto another. This might seem a bit inconsequential in the context of something as huge as cancer. This one transfer reaction, however, is a recognizable signal in the cell and is passed along and amplified. Eventually it triggers the action of enzymes tasked with repairing certain types of DNA damage, including that caused by UV-rays. The enzyme ATR also happens to be part of the division regulation “tools” that we talked about. It’s a kinase that performs its role as part of a cell division checkpoint, a time when activities in the cell determine if it will go on to divide, or kill itself in a process called apoptosis.

Caffeine binds to ATR and stops it from doing its job. This means that when some kinds of DNA-damage is detected, ATR does nothing (instead of transferring that all-important phosphate), the DNA is not repaired, and instead of replicating, the cell dies. Wait a second, this sounds like a bad thing; how does this prevent cancer? The problem with DNA repair enzymes is that for certain types of DNA damage, there is no way for them to ensure that the DNA is put back together exactly like it was before the damage. Sometimes these enzymes can only physically fix the break and hope that the sequence is repaired by luck, or that it was in a spot that didn’t matter much anyway. If this type of repair happens in an unlucky spot, like an oncogene, the repair makes DNA that looks physically okay, but the resultant mutation can have cancerous consequences. In these cases, NOT repairing the DNA effectively causes cellular suicide before the very first cancer cell can form.

Enzymes have a role in everything our bodies do, from detecting signals and passing messages, to constructing and repairing cellular components. Everything is controlled in a delicate balance, and often this control is itself achieved by enzymes. As this example illustrates, turning an enzyme “off” is an important component of cellular control mechanisms. Although our bodies have many built-in off switches, outside chemicals can also interact with our enzymes with ultimate results that can be difficult to predict. So next time you’re chowing down you can look at your food and ask, “Hey, what enzyme are you hooking up with?”

It’s a Molecule, it’s a Chemist, it’s Super Enzyme!

Photo credit whatsthesmatter@blogspot.com

Enzymes 101: The Introduction    

       

It’s amazing how many things our bodies can accomplish without us ever realizing that it’s happening. This is especially amazing when we consider that many of these tasks are absolutely vital to keeping us alive and conscious enough to appreciate it. How many times a day do you notice that you’re blinking? How often do you register your heart beating? For many, the answer is probably rarely (although probably now that you’re thinking about it). There are thousand of actions going on in your body, however, that you will never notice directly, no matter how hard you concentrate on them. These are the chemical reactions that make the difference between semi-organized piles of organic mush, and the living, breathing, navel-gazing individuals we all are. So if you’re happy and you know it, thank your chemistry; without it I can guarantee neither condition would be true.

Some of the chemistry that occurs in our bodies is as simple and spontaneous as the old vinegar and baking soda volcano trick. Any reaction that explodes into reality in a fourth-grade classroom is hardly an energetic challenge. Other reactions, however, are a lot tougher to coax along. Even when some important reactions do occur spontaneously (that is, without other factors interfering in the process) the speed of these chemical reactions, or reaction rate, might be so slow that it wouldn’t be likely to happen over the course of one’s lifetime, much less the multiple times a second required for it to be biologically useful. With all of this difficult chemistry so necessary to stay alive, how do we accomplish these constant chemical feats? Enter the enzyme.

Before discussing the amazing power of enzymes as tools or, as I like to think of them, master chemists, we need to go over a few defining concepts. Enzymes are catalysts. What this means is that although they help to chemically transform something into something else, they emerge from that reaction just the same as when they went in. This is like a baker: without him there is a very VERY small chance that all of the ingredients would jump into the oven together and become a cake, but while they come out transformed into a different and delicious form, he stays the same and is ready to bake another cake. What this means for your body is that unlike sugars, oxygen, and numberless other chemicals that your body has to constantly take in to supply the “ingredients” for your life-chemistry, a single enzyme can contribute over and over to the same chemical reaction without having to be replaced.

Now we have a bit of an idea of what an enzyme’s role in a chemical reaction is, but what is the enzyme itself? Enzymes are macromolecules made up of protein or nucleic acid (or both). A macromolecule is basically what it sounds like: a big molecule. Proteins and nucleic acids are big molecules made up of chains of smaller units. These chains then fold up into a shape that gives the enzyme its function. We’ll talk more about the specific forms and families of enzymes in future articles.

The more you learn about nature, the more you learn what a spectacular problem solving force evolution can be. When it comes to chemistry, the problem-solving power of enzymes is more astounding than the most outrageous magic any fiction writer could ever come up with. So stayed tuned for future posts when I’ll explore the magic mechanisms, resplendent reactions, and elegant evolution of nature’s best chemists!

Is that a Fruitloop in your Backpack?

As any six-year-old can tell you, toucans are named Sam, speak English, and push mini fruit doughnuts like they’re going out of style. As any ornithologist can tell you, toucans are jungle birds playing a vital role in helping spread the seeds in their favourite fruits far from the parent plant. As any geocacher can tell you a good GPS unit can save you a lot of crawling on your belly through the underbrush. Recently a group of scientists combined the latter two nuggets of wisdom to develop tools for studying avian roles in forest dynamics. Turns out you can learn a lot more from Toucans than what passes as part of a complete breakfast.

            Like all other forms of life, plants employ a wide variety of strategies to ensure the success of the next generation and the propagation of their own genes. Whereas human parents tend to perform two am feedings and invest in high quality car seats, members of the plant community are more limited in their ability to nurture their descendants. Indeed, the extent of plant “parenting” is often limited to giving their seeds the best possible chance of settling on a great growing location. Unlike human infants, the best place for young plants tends not to be under the watchful leaf of their parent plant but much further afield. There are several reasons that a little more separation is often the right answer for a seedling plant. Firstly, competition for resources like light, water, and soil nutrients is often higher around the base of their parent plant. There are also plant parasites like insects and fungi that tend to congregate around the older plants.

            In order to give young plants the autonomy so desperately desired by myriad human teenagers, plants produce seeds with built-in travel mechanisms. Some seeds have sails or propellers for dispersal by wind, some float for water dispersal, and still more have hooks to catch on the fur of animals or the socks of hikers and be carried away. By far the most delicious solution, however, is encasing seeds within fruits. In this case animals are able to eat the fruit and unwittingly scatter the tougher seeds as they travel, often with a batch of home-made fertilizer. This is the strategy used by the tropical Virola nobilis tree, the fruits of which are frequent breakfast choices for toucans.

            While seed dispersal is an important key to understanding forest ecosystems, studying how animals and birds disperse seeds by tracing either party can be difficult or even impossible. To get around the technical limitations inherent in clumsy, flightless humans trying to follow swift, winged toucans, a group of scientists employed some pretty slick technology. This group attached mini-backpacks equipped with GPS and 3D accelerometer units to wild toucans to study the feeding habits and movements of the toucans. The clumsy humans, instead of swinging through the trees, used the accelerometer readings to determine when the birds were eating, used the GPS readings to determine when and where they were traveling, and used zoo-dwelling toucans snacking on the same food to determine how long after eating they generally regurgitated the seeds. Using these methods, researchers can study how bird populations contribute to the overall makeup of the forest.

            Ecosystems, like forests, are truly a community effort. Every plant, animal, bacterium, fungus, and forgotten grad student plays a specific role in the maintenance of that ecosystem and the survival of all the other species. It’s no breakfast cereal cash cow, but through seed dispersal, real toucans are a vital piece of the forest ecosystem puzzle.

Dude looks like a Lady

If anyone can tell us how far we’ve come from Victorian views of sexuality, it’s the makers of women’s undergarments. As we’ve shed our voluminous petticoats and embraced the “man bag,” we’ve also started to accept that human sexuality has a few more shades of gray than may have been acknowledged in days of yore. While it’s not much of a stretch to use clothing to blur gender boundaries, you might be surprised to learn just how delicate your physical gender can be. When it comes to gonads, it really can be the cut of your genes that matters.

            And now for the basic biology version of the hated “birds and the bees” discussion: Mom provides the egg (one set of genes), and Dad provides sperm (a second set of genes). When the two meet up, under circumstances best described by parents the world over, they fuse and the two sets of genes form the necessary DNA to make a whole little person. The genes in question are in bundles called chromosomes (23 pairs in human cells), and the sex of the bouncing baby is determined by whether they carry the X or Y flavour of the sex chromosome. As all women have two X chromosomes and men have one X and one Y, the sex of the baby is dependant on whether the lucky egg-meeting sperm is of the X or Y persuasion. So the gender of the baby is determined, forever and always, by the sperm that wins the race, right? Normally, yes, but biology also has some tricks up its sleeve.

            The reason that the X and Y chromosomes are so all-important in gender decisions, beyond their nifty alphabetical designations, is the genes they carry. Some of these encode for proteins that produce sex hormones. Hormones are small molecules in your body, and the ones from the ovaries and testes are responsible for all the differences between male and female bodies. Incredibly, every function, feature, and fashion sense that defines our genders boils down to the initial decision for a single cell type to become either Sertoli cells (which are part of the testicle) or ovarian granulosa cells. These cells later play a key role in production of gender-appropriate hormones, resulting in development of everything from genitalia in the womb to scruffy adolescent mustaches.

            If the difference between developing Sertoli cells and granulosa cells is the rather important one of gender, surely this process occurs early and is promply cast in stone, right? Actually, like so many things in our body, the cellular decision to develop into one cell type or the other is controlled by a balance of inputs from two opposing “male” and “female” signaling pathways. Even more surprisingly, regardless of the identity of that initial sperm, if key components of one pathway are disrupted, the opposite gender will win out. That is to say that even if someone is genetically male (XY), if there is something wrong with this signaling pathway from the Y chromosome, they will develop like a female, and vise versa. If that gender jack-in-the-box doesn’t knock your unisex socks off, consider that new research indicates this can happen at any point in life. A recent paper describes how disrupting the “male” pathway in adult mouse testes resulted in these organs actually turning into ovaries.

            These experiments don’t offer practical applications, nor is this at all likely to happen spontaneously (don’t worry guys, you can stop clutching your pants in terror). They do, however, give us fascinating insight into what our genders really are and where they come from. Boy meets Girl, and Sperm meets Egg, but the new life emerging from those unions always looks just like its real Dad: biochemistry.

Glowing Green Mushrooms Seem Pretty Magical to Me…

            If you ask me (or any mycologist) the term “magic mushrooms” isn’t nearly specific enough to describe the psychedelic variety usually implied. The truth of the matter is that lots of mushrooms are pretty darn magical. Aside from providing a tasty side dish, these fabulous fungi produce an astounding array of chemical compounds with powerful effects. From delectable truffles, to potent poisons, many mushrooms have a profound ability to spice up an otherwise bland afternoon. One of the most amazing fungal feats, however, is best appreciated not by eating, but by looking. That green glow isn’t in your head, it’s the forest night-light: fungal bioluminescence!

            Before delving into their Lite-Bright-like capabilities, we should answer the question: what exactly is a mushroom? When it comes to the world of fungi, our umbrella-shaped friends are literally just the tip of the iceberg. The mushrooms we see growing above ground (and appearing on our dinner plates) are only one part of a larger fungal organism. The Fungi are a very diverse group of organisms and have many shapes and forms. Most fungi, however, grow in an inter-connected mesh of microscopic tubes called mycelium. The cells that make up the mycelium are called hyphae. Somewhat similar to slime-mold plasmodium, hyphae are cells with multiple nuclei; and somewhat similar to filamentous algae, they grow in long strands about 20 times finer than human hair. They grow progressively longer at their tips, and branches form on existing hyphae to form complicated networks. Some mycelium networks can only be described as huge. In fact, a single fungus has been identified that is estimated to cover 900 ha and be about 9000 years old.

            Although fond of edible fungi, I can’t say I’ve ever ordered a Monterey jack and mycelium burger, so where do mushrooms come into this hyphae-delic picture? As I mentioned, mushrooms are a part of the larger fungal organism, specifically the spore-spreading part. Mushrooms are called fruiting bodies and grow above the ground to spread the spores of the underground mycelium. You can think of the fungus as a specialized structure or “organ” of the fungus that has a specific job to do: spread the genetic material of the fungus to a wider area than the mycelium is likely to grow.

Because they grow above ground, mushrooms are also “the face” that the fungus presents to the world. Like any good spokesperson, some mushrooms have an enlightening way of advertising: they glow. The neon green glow, reminiscent of glow-in-the-dark rubber toys, is a result of some very interesting biochemistry called bioluminescence. Bioluminescence literally means light from life, and it is produced by all kinds of life forms, including plants, animals, bacteria, and fungi. The two main players are luciferin (the general name for the group of pigments that are used in bioluminescence), and luciferase (the enzyme helping the reaction along). Like many things that seem pretty magical in biology, bioluminescence is all about chemistry: the luciferase combines luciferin and oxygen to make a high-energy molecule. Like Calvin after one too many bowls of Chocolate Frosted Sugar Bombs, this high-energy molecule is not very stable. It undergoes a second chemical reaction to form a lower-energy molecule, releasing the excess energy as light.

Although not the tastiest of mushrooms (and frequently rather poisonous) bioluminescent fungi have fascinated night-time forest-wanderers for centuries. Their light has been used to mark a luminous path in the woods, and even to illuminate the cabin of the early Turtle submarine. A campfire may make a good s’more, but with Nature’s amazing chemistry there is more than one way to light up the night.

Did Dinosaurs use Celsius or Fahrenheit?

Photo Credit en.wikinoticia.com

As humans there are three ways we’re used to having our temperature taken: under the tongue, in our ears, and the “other” way. Regardless of our personal preferences, we can probably all agree that it is pretty darn difficult to apply any of these techniques to a dinosaur. So barring time machine development, how do we measure the body temperature of our pre-historic pals? Surprisingly, the trick is in the teeth. From molars to metabolism scientists are using some pretty “cool” chemistry to dig up answers.

To start out, let’s talk about metabolism, baby. Our metabolic rate is how fast we break down food, build up body mass, and generate heat. In general, a high metabolic rate means a higher general activity level and higher body temperature. Animals considered to be “warm blooded” have a high metabolic rate and generate their own heat internally, while “cold blooded” animals have a low metabolic rate and get much of their heat from the environment (picture a lizard sunning itself on a rock). This doesn’t mean, however, that “cold blooded” animals always have a lower body temperature, but that their temperatures fluctuate with their environment. In fact, their peak temperatures can be even higher than their “warm blooded” cousins. For this reason, these terms have been replaced by “endotherms” that generate temperature internally, and “ectotherms” that have their body temperature highly dependent on factors outside the body.

Our understanding of dinosaur body temperature has undergone a pretty major makeover over the last two decades. The image of dinosaurs as cold-blooded overgrown lumbering lizards has morphed into a portrait of a much more active and agile group of animals. This increased athletic prowess implies an increased metabolic rate, and sparked the idea that dinosaurs may have been endothermic. Being the investigative creatures that they are, scientists set out to study dinosaur metabolism and body temperature by measuring bone growth patterns, modeling behavior, and studying clues about athletic performance found in footprints. Although many of these studies pointed to an endothermic lifestyle, no real agreement on body temperature was reached.

That was until a group of researchers used the chemistry of dino tooth enamel as a trans-millennial thermometer to accurately measure the average body temperatures of some pre-historic behemoths. Wait just a second, temperature from tooth enamel? How can that work? The answer lies in the power of isotope chemistry. To understand this we have to go down the level of individual atoms of the elements carbon and oxygen. While most atoms of carbon have 12 particles in their nuclei and most oxygen atoms have 16, a very small percentage have extra neutrons and make carbon atoms with 13 particles and oxygen atoms with 18 particles. At high temperatures these “heavy atoms” act pretty much the same as all the other atoms, but at low temperatures they are more likely to bond to each other than one of the lighter atoms. You can think of this like a bad cocktail party: if everyone is really low energy you’re more likely to stick with your friends, but if the party really gets going you're going to meet and mingle with more people. In a technique called “clumped isotope thermometry” scientists measure the proportion of heavy carbon and oxygen that bonded together during tooth formation, effectively measuring the energy level of the tooth-growing party, or dinosaur body temperature.

From analyzing several teeth from large Jurassic Sauropods (“long-necks” to those who remember “The Land Before Time”) researchers calculated their body temperature to be between 36 and 38 ^oC. This is around the same range as most modern mammals. It’s not as simple as whipping out the thermometer from the medicine cabinet, but an inspiring example of how our basic scientific understanding of the world around us can enable scientists to solve seemingly impossible problems. Today dinosaur temperatures, tomorrow, conversations with Neanderthals? Don’t be too quick to rule it out…

I've Got a Lovely Bunch of Coconut (Genetics)

If the venerable gentlemen of Monty Python have taught me anything, it’s that there is a lot you can do with coconuts. While making horse-clomping sounds and ad-hock bikinis spring to mind, researchers are using these psuedo-nuts for a more academic pursuit: studying early human movements in the southern seas. More than just delicious tropical beverage containers, coconuts can tell us a lot about travel and colonialism thousands of years ago. From DNA to ancient trade routes, scientists are shining a light on ancient history with modern biology.

photo credit: www.hotbeautyhealth.com

We might worry about long weekend traffic when setting out for a summer getaway, but we rarely stay home for fear of inadequate food and drinking water. A concept that is often overlooked in our grocery store culture is how much the availability of food has shaped our societies. Case in point: human exploration and societal expansion in the tropics was directly influenced by the coconut. Not only did this fruit-bearing palm provide a convenient source for a key piña colada ingredient, it also represented a portable source of water, oil, fuel, and building materials. By virtue of these life-sustaining qualities, this single plant played an enormous role in the ability of would-be navigators in the southern Pacific and Indian oceans to exercise their sea legs thousands of years ago.

            As Sir Isaac Newton so eloquently phrased his own musings on coconuts: “every action has an equal and opposite reaction.” While coconuts were enabling early globetrotters to set sail, these same expeditions were helping to spread the coconut plant throughout the tropics. Furthermore, people were cultivating coconuts to have specific human-friendly traits. Shorter, self-pollinating plants bearing rounder, juicier fruit allowed people to spend less time climbing and growing palm trees, and more time chowing down on sweet coconuts. From this point of view, our societies are built on what we eat, but we also have a formative influence on our dinner. Ah the tangled food webs we weave.

            Now that we know just how tied up our early exploratory urges were with coconuts, how can these fibrous historians give us insight on human history? The answer lies, like so many things in this genomic age, in their DNA. Researchers compared genetic markers from 1322 coconuts from all over the world and used this information to trace the development of modern coconuts from various geographic locations. They found that coconut cultivation was started independently in two locations: the outskirts of the southern Indian coast, and the south Asian seas between the Malay Peninsula and New Guinea. What's more, they could trace ancient nautical trade routes connecting Madagascar and southeast Asia by observing where the genetic signatures of the two lineages mixed. Coconuts growing on these ancient trade routes still have blended genetics, while those growing in environmentally similar conditions but off the main drag clearly belong to one group or the other. This data, and associated historical records, also shows the Philippine origin of Panama coconuts planted 2250 years ago, that the Spanish brought coconuts from the Pacific to Mexico, and how Caribbean coconuts brought by Europeans were originally picked up in India.

The ever-present human urge to modify and exploit our surroundings usually results in a fascinating tangle of anthropology and biology. No man (or society) is an island, but without each other, both us and the coconuts might have been stuck there.