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.