The crazy-complicated structure of the ribosome, solved by x-ray crystallography (Source)
Drug development used to be accomplished by the chemical equivalent of what you might call the spaghetti method: Throw a bunch of molecules against the wall and see what sticks. More recently, pharmaceutical companies have applied a more rational approach, using the molecular structures of drug targets to design molecules that “fit” them like a lock to a key.
The technique most often used to solve those molecular structures is x-ray crystallography. With this approach, which turned 100 years old in November, a high-powered beam of x-rays is shot at a crystal of protein molecules. The x-rays collide with the crystal’s atoms, scattering at specific angles. Working backwards from that information, researchers can figure out the original structure.
… a method of determining the shape and structure of things that we can’t see with our own eyes. Imagine that you have captured Wonder Woman’s invisible airplane. You can’t see it. But you know it’s there because when you throw a rubber ball at the space, the ball bounces back to you. If you could throw enough rubber balls, from all different sides, and measure their trajectory and speed as they bounced back, you could probably get a pretty good idea of the shape of the plane.
Anyhoo, as the name of the technique implies, the key to crystallography is, well, crystals. But not all proteins crystallize, and even with those that do, it can be hard to grow crystals large enough for the technique to work.
Recently, though, a pair of technology developments have made it possible (in some cases) to work around these problems.
The first development was the commissioning in the past few years of ultra-bright x-ray sources in California (the Linac Coherent Light Source at Stanford) and Japan. These so-called “x-ray free electron lasers” (X-FELs) shoot incredibly bright, incredibly short x-ray pulses, pulses that are so intense that they destroy a sample in a fraction of a second, but not before the x-rays (which travel at the speed of light, natch) have bounced off of it.
The reason crystals are required in crystallography is that any one diffraction event is hard to see. The regularly spaced molecules inside a crystal amplify that relatively weak signal, simplifying detection and structure determination. As it turns out, the brighter an x-ray source, the smaller the crystal required to obtain such data has to be, and with X-FELs, the crystals can be very small indeed – on the order of millionths of a meter (micrometers) in size, and perhaps even smaller.
Which brings me to the second development. In the March issue of the journal Nature Methods, a team of researchers led by Michael Duszenko in Germany showed that some proteins that cannot crystallize in a test tube will crystallize inside insect cells. Protein chemists often use cells as molecular factories to obtain large quantities of protein. But the goal is to extract the protein from the cells, not have them crystalize inside of them. Generally speaking, protein crystallization inside cells is a bad thing, the kind of thing researchers really don’t want to see; Duszenko and his team are the first to capitalize on this so-called “in vivo crystallization” phenomenon.
The crystals Duszenko’s team collected are quite small, of course –- they fit inside cells, after all — and in that initial study, they were on the order of 1 micrometer wide and 15 micrometers long. But as it turns out, they are big enough for the X-FEL. In the March paper, the team showed that these crystals will diffract x-rays in the X-FEL, but they didn’t solve the resulting structure.
The team sprayed a stream of tiny enzyme crystals (each about 1 x 1 x 11 micrometers) into the path of the X-FEL, which fired discrete pulses of x-ray, each just 40 femtoseconds, or 0.000000000000040 seconds long, 120 times per second. Every so often, one of those pulses would collide with a crystal, and a nearby camera would capture the event.
The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.
The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.
Big Molecules with Small Building Blocks
The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.
We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.
When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.
Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.
The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.
Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.
On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.
The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!
If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.
The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?
If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.
In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.
Sugar and Fuel
A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.
Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.
Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.
Polysaccharides: Fuel and Form
Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.
Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.
Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.
Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.
The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.
Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.
The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.
That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.
These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.
Lipids: The Fatty Trifecta
Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.
Fats: the Good, the Bad, the Neutral
Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?
Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.
Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.
Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.
Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.
The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.
You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.
In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.
A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.
Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.
Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.
Phospholipids: An Abundant Fat
You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.
Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.
There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.
Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.
The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.
Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.
Steroids: Here to Pump You Up?
Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.
But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.
Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.
Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.
As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.
Levels of Structure
Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.
For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.
This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.
Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.
The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.
In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.
A Plethora of Purposes
What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.
As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.
How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.
Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.
DNA vs. RNA: A Matter of Structure
DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.
So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.
RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.
DNA vs. RNA: Function Wars
An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.
These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.
RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.
Leah Gerber is an Associate Professor of ecology at Arizona State University. Her research is motivated by a desire to connect academic pursuits in conservation science to decision tools and effective conservation solutions. This approach includes a solid grounding in natural history and primary data collection, quantitative methods and an appreciation for the interactions between humans and the environment. She is keenly aware of the need for the communication of scientific results to the public and to government and non-governmental agencies. This communication is essential for the translation of scientific results into tenable conservation solutions.
DXS: First, can you give me a quick overview of what your scientific background is and your current connection to science?
LG: I learned about ecology and environmental conservation as an undergraduate and quickly became motivated to do science that impacted the real world of conservation. Learning about the impacts of humans on nature was a wake-up call for me, and inspired me to channel my feeling of concern for the demise of nature in a positive way.
From there, I have walked the tightrope between science and policy. After getting my undergraduate degree in environmental biology, I wanted to do more than just the science. So I enrolled in a masters program at the University of Washington – an interdisciplinary program called Marine Affairs. It was a great experience, but I wanted to have more substance to my science background – I wanted to know how to do the science in addition to how to apply the science.
This compelled me to enter a PhD at the University of Washington, which was largely funded by NOAA. My thesis involved trying to figure out how to make decisions about endangered species – how to determine which were endangered and which were threatened. This was a perfect project given my interest in developing tools to solve problems. After finishing my PhD, I did a postdoc at the National Center for Ecological Analysis and Synthesis (NCEAS) and developed approaches for marine reserve design and endangered species recovery. I was at NCEAS for three years before starting on the tenure track at Arizona State University. I’ve been at ASU for about 10 years now.
A major theme in my work has remained constant – that is, how to use the information we are generating in the natural and social sciences to better manage our natural world. Pre-tenure I focused a lot more on doing the science, publishing in good journals, and hoping that it made its way into good policy. Now that I am midcareer, meaning that I have a good amount of papers and tenure, I am enjoying the opportunity to work with practitioners outside of academia. For instance, I just got off the phone with someone from National Geographic regarding my recent publicationon seafood health and sustainability. In that study, we performed an analysis regarding seafood in the context of health and sustainability, to answer simple questions like, what to order when out to sushi? How do we educate about health benefits and risks? We will be organizing a workshop to help restaurant chains, grocery stores, as well as environmental NGOs identify a path forward in informing consumers about healthy and sustainable seafood choices. As a tenured professor, I feel fortunate to have the opportunity to work at the science-policy interface and to give society some science that is truly applicable.
DXS: It is too bad that you have to wait until you are more established and have tenure to go out and engage with the public, because this type of thing is just so important!
LG: Yes, I agree. There isn’t a clear path in academia when it comes to public engagement. But in recent years I have felt optimistic – the landscape within academia is starting to change, and at ASU this change is noticeable. We have a fabulous president, Michael Crow, who has really transformed ASU from just another state institution to a leader in sustainability. Part of this is the establishment of the Global Institute for Sustainability, and one of Michael Crow’s mantras is “community embeddedness.” He is really on board with this type of thing and I have seen evidence of his commitment trickle down throughout the University. For instance, when I first arrived, I had to justify and explain why I was serving on these federal recovery teams for endangered species. Now I feel that there is no justification needed. Developing solutions is not only so important for society, but should also be a key aspect of what we do at Universities.
DXS: We were introduced by another fantastic science communicator, Liz Neeley, who you met at a communications workshop. Why is it important to take part in this type of training?
LG: I met the Fantastic and Fashionable Liz through the Leopold Leadership Program, offered through the Woods Institute for the Environment at Stanford University. The Leopold Leadership training was the best professional development experience of my career, and has made me a better translator and communicator of science to policy. Pre-Leopold, I had little training in communications, and there I was, in a teaching position where I taught hundreds students. I thought to myself, well, how do I do this? The Leopold experience has solidified my commitment to teaching students about communication and engaging in policy.
One development emerging from this training is a science communication symposium at the AAAS meeting. Elena Bennett and I are giving a talk on overcoming institutional barriers for community engagement, and we will address the issues head on. We put out a survey asking others if they faced institutional barriers, and how they might work to engage more.
DXS: What ways do you express yourself creatively that may not have a single thing to do with science?
LG: I have 2 young kids, a 3yo and a 7yo. Being a mom helps me keep it real - I love that I get to enjoy the awe of discovering the world with my girls. We just got a puppy this weekend and we are having fun dressing her up and painting her nails (only partly joking). Other things that I do that are creative – truthfully, I am uninteresting – I don’t bake bread or go to the opera. I just work and take care of my kids. I practice yoga for my own sanity and also love to work in the garden. Doing these things gives me a reason to pause and step off the treadmill of keeping up with everything.
DXS: Do you find that your scientific background informs the creativity you have with your kids or your yoga practice, even though what you do may not specifically be scientific?
LG: I think there is synergy with my science and my kids and my yoga practice in helping me to accept things and be mindful – but not in any conscious way. For instance, when doing my science, the type A person that I am, I have an inclination to keep pushing, pushing, pushing. My kids and my yoga help me to shift gears and accept that things are going to happen when they happen. I try to let the kids be kids, including the associated chaos, and accept that this is a snapshot in time that they will be little. Now I find joy in that chaos. Having kids and yoga gives me a little more perspective, and the knowledge that things aren’t lined up and neatly placed in a box. It rounds me out.
DXS: Are your kids are major influencers in your career?
LG: My first child, Gabriella, was born just after I submitted my application for tenure – so it was good timing. And I was able to slow down. I quickly realized that I wasn’t able to work a 60+hour week. Before kids, I lived to work. Now, I work to live. I absolutely love my job and I feel so lucky that I have a career that I believe in and that I am actually paid to do it – it’s not just a hobby. But having kids made me chill out a little. If I get a paper rejected, I can let it go instead of lamenting about it for weeks. It has made me healthier. I don’t necessarily know if it has had positive impact on my career – time will tell. While my publication rate may be slightly smaller, I think my work now has different dimensions, and greater depth.
I am still pretty passionate about my work, and my kids know what I do and are proud of it. They share it with their classmates, and take every opportunity to wax poetic about how their mom saves animals in the ocean. They also have a built in conservation effort – my 7YO gets irritated when she can’t find a compost bin, and her new thing is to only fill her cup half way because she will only drink a little bit of water.
DXS: When you decided to have children, did your colleagues view you differently? Did they consider that you were sending your career down the tubes or was it a supportive environment?
LG: I honestly had a really positive experience. I can’t think of any negative sentiments from my colleagues, and they were actually really supportive. For instance, when I was pregnant with my first daughter, ASU did not have a maternity leave policy. Before that, you would have to take sick leave. So my colleague worked within the parameters of the unit to give me maternity leave. And then with my second daughter, our new president had established a maternity policy.
The support of my colleagues at ASU has made me feel loyal to my institution. Normally, I am loyal to people and not institutions, but overall, the support has been fabulous. Of course, with having the kids in each case, I did decline a lot of invitations – some pretty significant ones – but I did not have a desire to drag a newborn to give a talk, especially when I was nursing. And it was hard for me to do this at times, especially given my career driven nature, and I had to learn to accept that there would be other opportunities.
I had to shift it down a notch and realize that the world wasn’t going to freeze over, and that I could shift it back to high gear later. With “mommy brain”, I knew I wasn’t going to be at the top of my game at that point in my life. But I have incredible role models. Most notable is Jane Lubchenco, currently the Director of the National Oceanic and Atmospheric Administration. During the first part of her career, she shared a position with her husband – each did 50% – and they did that on purpose so they’d be able to enjoy having children and effectively take care of them. Now, she is in the National Academy, is having major scientific impacts, and she did it all despite having kids. If she can do it, why cant the rest of us?
DXS: Given your experiences as a researcher, as a mother, and now as a major science communicator, do you feel that your ability to talk to people has evolved?
LG: Absolutely. I think that the Leopold Training Program, which selects 20 academics from North America to participate in retreats to learn how to be better communicate and lead, has re-inspired all who attended. It has recharged our batteries and allowed us to make realizations that doing good science and putting it out there via scientific publication is just not enough. We also have to push it out there and make it available to a broader, more diverse population. As part of the training, we also learned about different thinking styles – super analytical or super emotional – and after I returned, I had my lab group participate in this type of exercise. And now I feel like I can better assess a persons thinking style and adjust the way I communicate accordingly.
DXS: Did you always have the ability to talk to the general public or does having kids help you to better understand some of the nuances associated with science communication?
LG: I think so. In fact, I am thinking back to when I had a paper in Sciencecome out around the time that I had my first child. It got a lot of news coverage and was featured in Time magazine. I thought it was so cool at the time, but looking back on it I realized that have come a long way. I said something to a journalist, who then asked me to translate it into “plain English.” It was a little bit of a jab.
Now, with kids, I can tell you a lot more about my research and can better see the broader impact. Talking to them helps me to do that. Here is a conversation about my research with my daughter:
L: Mama is working on figuring out how to help the whales that people like to eat. It’s a big problem because some people like to eat whales and some like to see them swimming in the ocean.
G: What we have to do is let the people eat the whales in the ocean, and buy some whales from the pet store to put back in the ocean. How much do whales cost?
L: Good idea. But you can’t buy whales at the store. They are too big. And if we take them all out of the ocean there will be none left.
G: Well instead we should ask the people to eat bad things like sharks.
L: Another good idea. But if we take sharks out there will be no predators to eat the big fish. And the whole ecosystem would collapse.=
G: Well then the people should eat other things like fish instead of whales. They should buy a fishing pole and catch a fish and eat those instead of whales.
L: What about chicken, shouldn’t people just eat chicken?
G: Mama, we can’t kill chickens. Chickens are nicer than fish, so that’s why we have to eat fish.
L: What about just eating vegetables?
G: Oh mama, some people are meat-eaters. And there are no more dinosaurs. They all got extinct. They should have saved some of the dinosaur meat in the freezer for the meat-eaters. When the dinosaurs come back, there will be enough meat to eat and people won’t want to eat whales.
The simplicity of taking myself out of my research bubble and engaging with a creative (and nonlinear?) 7YO has taught me how to be a better communicator – with the media, with my students, and with the general population.
DXS: Do you think these efforts in science communication are helping to shift other peoples perspectives about who a scientist actually is? For instance, are we changing the old crazy haired white guy stereotype?
LG: Well, I hope so. A couple of examples – again, as a mom, one of my daughters a Girl Scout and I get to help with the troop. One of the themes was to teach about environmental and conservations awareness. We did this Crayola molding experiment where we put our fingers into cold water. We then did the same thing except we put modeling clay over our fingers before putting them into the cold water and to learn about adaptations to extreme environments. Also, we play games where they simulate fishing – what if there is plastic? What happens to you if you eat that? My hope is that this shows these young girls that science is both interesting and fun.
Another thing that just happened today is that I was contacted by Martha Stewart’s office, and it seems that some of my research results will be featured in the October issue of Martha Stewart Living. The message here is that I happen to care about the ocean, but I also love sushi. I also I care about health. I am not just a nerd in a lab coat. I am a mom, I do yoga, I have wonderful friends, and here is the kind of science that I do. It seems to me that it is better to connect with others when I can give them something that is relevant to their lives instead of a more abstract ecological theory.
DXS: If you had something you could say to the younger you about getting on your chosen career path, what would you say?
LG: I feel like I have been very effective at figuring out how to get from point A to point B, but less successful at savoring the process. I think that I’d tell myself to make time to celebrate the small victories. I have also learned to identify what kind of research is most exciting, and I would tell myself to say “no” to everything that is only moderately interesting. I tell my grad students that if you don’t dive in head first, you won’t ever know. So why just not give it a try! And if it doesn’t work, move on. Also, if something isn’t making you happy, change! Academia isn’t for everyone, and there is a lot more to life than science.
Mary Anning and a small, non-fossilized dog. (Source)
[Today, we're featuring a post by Mike Rendell, author and keeper of Georgian Gentleman, a blog chronicling aspects of 18th century life. Mike spent 30 years as a lawyer--poor fellow--before he retired to time travel in his mind back to the 18th century, where he has set up mental shop permanently. By what he calls a "curious stroke of luck," he has all of the 18th century papers of his great-great-great-great (that's four) grandfather, including diaries, accounts, letters, and even shopping lists. In 2011, he published the story of this ancestor's life as a social history, "The Life of a Georgian Gentleman,' and thus, a blog was also born. We thank Mike for having graciously given us permission to publish his post here because we are huge fans of Mary Anning, who, as was typical, did not receive recognition from or entree into male scientific society of her day. We have added in a few explanatory links, too.]
Today the spotlight is turned not on a well-educated man, or a wealthy daughter with aristocratic connections, but on a girl who was amongst the poorest of the poor; who in many ways led a miserably hard and short life; who could barely read and write, and yet was someone who amazed the scientific world in the first half of the nineteenth century.
Her name was Mary Anning, born in Lyme Regis in Dorset on 21st May 1799. She cannot be said to have had an auspicious start in life. She was one of ten children – but eight died in childhood. An elder sister had already been called Mary but she had perished in a fire when her clothes were ignited from some burning wood shavings. Our heroine was born five months after this tragic death, and was named Mary in memory of her dead sibling.
Mary had luck, of a sort, on her side. When she was eighteen months old she was being held in the arms of a neighbour called Elizabeth Haskings who was in a group of women watching a travelling show. A storm sprang up and the group took shelter beneath an elm tree, but a bolt of lightning struck the tree, killing three of the women including Elizabeth. Yet Mary was apparently unscathed. Fate had something quite remarkable in store for the young girl…
Mary’s parents were Dissenters, meaning that education opportunities were limited and the family were subject to legal discrimination. A member of the Congregationalist Church, she attended Sunday School and here learned the rudiments of reading and writing. The Congregational Church, unlike the Anglican Church, attached great importance to education, particularly for young girls, and she was encouraged in her development by the pastor Revd James Wheaton. Her prized possession was apparently a copy of theDissenters’ Theological Magazine and ReviewContinue reading →
A few days ago, I received an email from my friend HelenJonsen about a fundraising effort that is very near and dear to her heart. Helen and her family are volunteering for the 3rdAnnual Hope & Heroes Walk to show their support for the clinic that helped her own daughter, in her journey with cancer. Taking place on April 29th, 2012 in Manhattan’s Clinton Cove Park, this fundraiser is to help ensure that the unique clinical care programs and cutting edge research funded by Hope & Heroes will continue.
Specifically associated with Columbia University’s Herbert Irving Child & Adolescent Oncology Center, Hope & Heroes boasts the ultimate NY start. In 1997, Beth, a teenage Hodgkin’s Disease patient, decided to write the then NY Yankees first baseman, Tino Martinez. Tino responded to Beth’s letter and invited her watch the Yankees during their spring training. Tino and Beth “hit” it off, and their friendship inspired Tino to become more proactive in the lives of other young cancer patients by pledging a donation for every RBI he made. The NY sports scene quickly caught wind of this, and a local sportswriter, Mike Lupica, dubbed this effort “Hope and Heroes.”
While the cancer center had been accepting donations for the purpose of supporting the innovative programs started by its director, Dr. Michael Weiner, the effort had finally been given a name. But, it wasn’t until 2002 when Hope & Heroes filed for a 501(c)(3), giving this charity an official stamp.
According to Jeremy Shatan, the acting Executive Director of Hope & Heroes, the clinic sees about 100-150 new patients each year and about 5,000 – 7,000 total patient visits. This number includes patients who are currently receiving treatment as well as those who have recovered but are still being monitored.
The money donated to Hope & Heroes Children’s Cancer Fund is used, in part, to finance many special programsthat would otherwise be impossible. Benefitting both the young patients and their families, these programs include the use of complementary medicine folded in to an often harsh regimen of surgery, chemotherapy, and/or radiation. In addition, Hope & Heroes also helps to provide emotional counseling to those in need, as well as allow these young cancer patients to participate in translational research studies, which opens the possibility for novel treatments.
The Hope & Heroes Children’s Cancer Fund has forged a permanent place in the hearts of many, including Helen and her family. We at Double X Science find this effort to beyond a “good deed.” Please show support for this organization by donating. Because you never know when a kid will need it.
To donate to the 3rd Annual Hope & Heroes Walk, go here.
This is a time-lapse video of images captured from the International Space Station from August to October 2011. You’ll see the auroras (borealis for the north, australis for the south) and, well, the entire island Earth. Bora Zivkovic, blog editor at Scientific American posted this last month. According to Bora, we owe thanks to Ron Garan, the photographer and astronaut who took the pictures and to Michael Königfor editing them into this lovely visual voyage. Enjoy!
The twitter feed from @DoubleXSci since early December has featured Notable Historical and Modern Women in Science. Nearly 100 women were presented. Those women will be presented in a series here on the blog with the original tweeted links and information as well as with some additional information not able to be presented in 140 characters. Each woman could have multiple pages written on her; however, I have limited each to a paragraph. I hope you look up more on these women.
The International Year of Chemistry 2011 recently wrapped up, so I’d like to share a little more about some historical women in chemistry.
The first historical woman in chemistry is perhaps Miriam the Alchemist, who lived in the 1st or 2nd century C.E. Her writings survived centuries. She has several aliases: Mary, Maria, and Miriam the Prophetess or Jewess. Even though she was an alchemist, which was mostly a mystical field during her time, her inventions and contributions yielded long-lived practical laboratory equipment. Miriam the Alchemist contributed major inventions and improvements to existing technology, as well as the water bath. The water bath is still in use today for many chemical experiments, as was dubbed “bain-marie” in the 14th century.
Agnes Fay Morgan (1884-1968) was a pioneer in vitamin research. She earned her B.S., M.S., and Ph.D. from the University of Chicago. She also established Iota Sigma Pi, an honor society for women chemists. Morgan received the Garvan Medal and the Borden Award and was the only one of her family to attend college. Her efforts brought both nutrition and home economics to scientific disciplines. Besides her teaching position and doing research in academia, she also was an accomplished administrator and worked with the government on many occasions. She had many firsts in her research and an enormous number of publications.
Colloid Chemist Marjorie Jean Young Vold (1913-1991) was a prolific and distinguished scientist. She earned her B.S. and Ph.D. from University of California, Berkeley. Vold balanced academic and industrial chemist careers spanning over five decades. At the age of 45, she was diagnosed with multiple sclerosis but continued her dual chemistry careers despite being confined to a wheelchair. She was the LA Times Woman of the Year and received the Garvan Medal. One month before her death, Vold submitted her final paper, which was published posthumously.
Lucy Weston Pickett (1904-1997) chose a career in chemistry over marriage. She earned her B.A. and M.A. from Mt. Holyoke College and her Ph.D. from the University of Illinois and advanced through her academic career to become department chair. She received the Garvan Medal and two honorary D.Sc. degrees. She was so influential in her career that a fund was established in her name upon her retirement, which she requested be used to bring female speakers to the department.
Mary Lura Sherrill (1888-1968) was known for synthesis of antimalarial drugs. She earned her B.A. and M.A. from Randolph-Macon College and her Ph.D. from the University of Chicago. Her academic career included becoming the chair of her department. She also received the Garvan Medal.
Chemist, Ecologist, and Home Economist Ellen Swallow Richards (1842-1911) was one of Vassar College’s first graduates, with an A.B. She earned her B.S. from MIT as its first woman graduate and her M.A. from Vassar College the same year. She had many firsts, including improving the standard of living by applying chemistry to sanitation, opening up science for women, and developing the home economics movement. Richards was also the first woman member of the American Institute of Mining and Metallurgical Engineers and first woman teacher at the MIT department of sanitary chemistry. She was awarded an honorary doctorate from Smith College.
Grace Medes (1886-1967) was a pioneer in metabolism research. She earned her B.A. and M.A. from the University of Kansas and her Ph.D. from Bryn Mawr. Her academic career progressed until she became a department head and chairman. She earned the Garvan Medal and several Distinguished Service Citations. Dr. Medes was at the forefront of cancer research and named a rare disease, tyrosinosis [PDF].
Bacteriologist and Chemist Mary Engle Pennington (1872-1952) was a food preservation pioneer. Despite completing the requirements for a B.S. degree at the University of Pennsylvania, she was granted only a Certificate of Proficiency. She earned her Ph.D. from the University of Pennsylvania. Dr. Pennington worked with the government although she hid her gender to receive her credentials. Called “ice woman” due to her advances in food preservation and refrigeration, she was known for a warm personality. Pennington was awarded numerous fellowships and was a member of many other professional organizations and honoraries, and received the Notable Service Medal and the Garvan Medal.
Pauline Beery Mack (1891-1974) was an instructor and publisher and loved chemistry. She earned her B.A. from Missouri State University, M.A. from Columbia University, Ph.D. from Pennsylvania State College, and a D.Sc. from Moravian College for Women, Western College for Women. She began the publication the Chemistry Leaflet which eventually became published by the American Chemical Society. She received the Distinguished Daughters of Pennsylvania Medal, the Garvan Medal, and the Astronauts Silver Snoopy Award. Dr. Mack also maintained a busy life outside of science, including basketball and music. She taught more than 12,000 undergraduates over her 30 years at Penn State. She was adept at securing funding for her research, no small feat for a woman in the 1930s. Mack continued into an administrative career and worked full time until she was 79.
The Garvan Medal is an award from the American Chemical Society to recognize distinguished service to chemistry by women chemists.
The Borden Award is given in recognition of distinctive research by investigators in the United States and Canada which has emphasized the nutritive significance of milk or any of its components.
LA Times Woman of the Year began as annual awards ceremony to honor women for individual achievement and was awarded from 1950 to 1976.
Lavoisier Prize (Lavoisier Medal) is awarded by the SCF to an individual or institution to distinguish the work or activities involving the chemistry honor.
Astronauts Silver Snoopy Award candidates will have made contributions toward enhancing the probability of mission success, or made improvements in design, administrative/technical/production techniques, business systems, flight and/or systems safety or identification and correction or preventive action for errors.