Why Are Snowflakes Always Six-Sided?

(Today’s offering is a guest post by engineer Linda Gaines.)

It’s a well-known fact that all snowflakes have six sides. Or at least I thought it was. Why Google is unable to Google that fact and has on at least two occasions created a Doodle with an eight-sided snowflake is a mystery. What’s less mysterious is how scientists can be so sure that all snowflakes have six sides. Have we examined all snowflakes? No, of course not, but the explanation lies in two words: hydrogen bonding. Thanks to the intermolecular force of hydrogen bonding, all snowflakes have six sides, and hydrogen bonding also makes life as we know it possible. Now that’s an important bond.

You can’t really understand hydrogen bonding, though, without understanding why water molecules are arranged like they are. Water seems like a simple enough molecule. It consists of one oxygen atom with two hydrogen atoms bonded to it. The hydrogen atoms bond to the oxygen atom at a distance of exactly 104.5 degrees from each other (1). Why that particular angle?

An oxygen atom has a total of eight electrons. Two of them take up all the available spots in the shell closest to the atom’s nucleus. The remaining six electrons are relegated to the atom’s outermost (or valence) electronic shell. But this shell can actually hold eight electrons, so two spots are open. A hydrogen atom has one electron on its only electronic shell, and since that shell holds two electrons, it’s got room for one more.

Because oxygen has two available spaces and hydrogen has one, oxygen can share that space with two hydrogen atoms. Both hydrogen atoms share their single electron with the oxygen, and the oxygen shares an electrons with each of the hydrogen atoms. The remaining four of the oxygen’s electrons aren’t a part of this sharing arrangement, though. Electrons kick around in pairs, so these four non-sharing electrons form two pairs.

With these two pairs sitting alone and the other two electrons each sharing with a hydrogen, a water molecule has a tetrahedron (or three-sided pyramid) shape with four attachments emerging from the oxygen nucleus. Two of those attachments are electron clouds containing two electrons each (the pairs), and the other two attachments are hydrogen atoms with two electrons moving between the oxygen and hydrogen orbits. In a true tetrahedron, the attachments would all be 109.5 degrees from each other. With the water molecule, though, the hydrogen atoms are 104.5 degrees from each other because the two paired-electron clouds are grabby with space and force the electrons shared with the hydrogen atoms a little closer together.

So we’ve learned that the hydrogen and oxygen form a covalent bond, which means they share their electrons. What I haven’t told you is that the oxygen is very grabby with that electron, so the sharing isn’t exactly equal. The oxygen has a stronger hold on the electron and is pulling that negative charge closer to it and away from the hydrogens. What results is a slightly negative oxygen and slightly positive hydrogens. The oxygen actually has two areas of negativity, right across from where it’s bonded with each hydrogen. Water molecules can use these areas of slight charge to form a fairly strong bond with other molecules, a bond called a hydrogen bond. While not every molecule containing hydrogen can form this kind of bond with other molecules, molecules in which hydrogen is in this unequal sharing situation will be able to.

In the case of water molecules bonding to other water molecules, the two slightly negative areas of the oxygen can each bond with a slightly positive hydrogen from another water molecule. When all four slightly charged areas have each bonded with another water molecule via hydrogen bonding, the result is a tetrahedral (four-sided pyramid) shape.

These bonds make water an unusual substance. When the temperature drops and water starts to solidify, the hydrogen bonding becomes very important. The hydrogen bonding dictates the shape of the ice crystals. You’ve learned that each water molecule is linked to four other water molecules in a tetrahedral arrangement. 

As the water freezes, these tetrahedrons come closer together and crystallize into a six-ring or hexagonal structure. Look at the image to see how this happens. Each point on the hexagon is an oxygen atom, and each side is a hydrogen bonded to one oxygen. As the water approaches freezing temperature, the water molecules continue to crystallize in this tetrahedral arrangement.

But water does something unlike most substances. As it nears freezing, instead of continuing to contract, it expands slightly from about 4 degrees to 0 degrees Celsius as the motion of the molecules slows with the cold, and the hydrogen bonds extend the molecules to their fullest distance from each other. It’s like a ring of people holding hands, elbows bent, and then gradually straightening their arms to the fullest extension so that they’re at the greatest distance from each other. When water molecules do this, the hexagonal structure expands into a larger and larger hexagonal structure.

The snowflake, with its six sides, is what results from this process: It is a large, gorgeous ice crystal. Ice crystals are like mineral rock crystals. The macroscopic (large) shape you see is dictated by the microscopic, molecular crystalline structure. Ice has a hexagonal crystalline structure, so a snowflake has a hexagonal structure. Sodium chloride, aka table salt, has a cubic molecular structure, so the salt crystals you shake on your food have a cubic shape.

It’s interesting that hydrogen bonding causes snowflakes to be six sided (are you listening, Google?), but it carries far greater consequences than beautiful snowflakes. Breaking those hydrogen bonds apart so that water can transform from liquid to gas takes a lot of heat, so the boiling point of water is much higher than it is for other, similar molecules. Based on similar molecules, water’s boiling point should be about -80 degrees Celsius (-176 degrees Fahrenheit) (!) instead of the 100 degrees Celsius (212 degrees Fahrenheit) it really is (1).

And then there’s the fact that ice floats, which means that the solid form of water is less dense than the liquid form. It is highly unusual for the solid form of a substance to be less dense than its liquid. But because those hydrogen bonds force water into a pretty open, hexagonal crystalline structure as the temperature nears 0 degrees Celsius, molecules are not packed as closely together as they are at warmer temperatures.


Think of those people holding hands, stiff-arming each other as far apart as possible. If they all started slam dancing, their handholds would break, and they could get closer to one another. Water molecules are a bit like that when the temperature goes above 4 degrees Celsius. When ice melts, some of the hydrogen bonds break, and the water molecules can be closer together. The far-apart water molecules in ice form a less-dense substance than the close-together molecules of liquid water, so ice floats in liquid water.

This property of water is integral to life on Earth. When a freshwater lake starts to freeze, the ice floats on the top, insulating the water below and preventing it from freezing. The fish, plants, and other life in the lake remain alive beneath the protective and insulating icy layer. If ice sank instead, over periods of deep freeze during its 4.5 billion year existence, this blue planet would have developed an icy, inhospitable core. Instead, the fact that ice floats meant that Earth was a perfect incubator for life in its oceans. All because oxygen is just a little bit grabby with electrons.

(1) Petrucci, Ralph H. (1989) General Chemistry (Fifth Edition). New York: MacMillan.

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • 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.
Carbohydrates

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.

Proteins

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.

Nucleic Acids

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.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology

Freezing Point: Science never tasted so good!

Learning about freezing point can lead to a tasty reward!

When trying to devise cool activities for my kids, I generally stick with either a culinary or a scientific theme.  This is mostly because cooking and science are what I know best.  But when the opportunity arises to combine the two in a fun-filled, hands-on, and awesomely secret educational activity, I do my best to keep from micturating in my undergarments. 

In my experience, the best example of culinary science fusion involves a lesson on the concept of freezing point, mainly because the end product of this stealth lesson can be topped with whipped cream and a cherry.  That’s right, I’m talking about teaching science while making ice cream.

To fully appreciate the culinary chemistry behind this frozen delight, it’s important to understand the concept of freezing point and melting point.  Simply put, the freezing point is the temperature at which a liquid freezes and the melting point is the temperature at which a solid melts.  For most substances, the melting point and the freezing point are the same. 

Let’s use water as an example.  If water is cooled below 0°C (32°F), it will transform into ice.  Therefore, the freezing point of water is 0°C.  However, if the temperature of ice is raised above 0°C, it will melt.  Therefore, the melting point of water is also 0°C. 

HOWEVER, these points can be manipulated.  For anyone who lives in an area where winter happens, you’ve probably seen the massive seasonal salt inventory at The Home Depot.  The idea is that by putting salt on walkways, usually in the form of either rock salt (NaCl) or calcium chloride (CaCl2), you will prevent the build up of ice and snow and thus prevent any nasty slips.  This is because salt will lower the freezing point of water, thereby helping to keep it from turning into an icy mess, even when temperatures are below freezing.  But, it will only work if the walkway is warmer than -9°C (or 15°F). 

How does this relate back to ice cream?  Well, we can use the same idea of lowering the freezing point of water and apply it to making cream freeze.  The set-up involves two resealable plastic bags (one quart-sized and one gallon-sized), ice, lots of salt, cream, milk, sugar, vanilla, and your flavoring of choice. 

Into the quart-sized resealable plastic bag, combine the cream, milk, sugar, vanilla, and flavoring (follow the recipe below and ensure that the bag is fully sealed).  Fill the second resealable plastic bag about halfway with crushed ice and all of the salt.  Place the cream-filled bag into the ice-filled bag and seal.  Then…shake! 

When salt is added to the ice water, the temperature of the mixture drops.  Because the temperature of the ice-salt mixture is lower than the cream mixture, a temperature gradient is created and the cream mixture easily freezes.  After about five to ten minutes of shaking, you will have yourself some fresh-churned sciencey deliciousness!  Enjoy!


Science Experiment Ice Cream:

½ Cup Heavy Cream

½ Cup Milk

¼ Cup Sugar

¼ Tsp. Real Vanilla Extract

Crushed or Shaved Ice

1 Cup of Table Salt or Sea Salt

1 Quart-Sized Ziploc Bag

1 Gallon-Sized Ziploc Bag

Here is a video of my and a few of my pals doing this experiment with my daughter.  We did this last year and my daughter STILL talks about it!  



The set-up:

Shakin’ it up:

The big reveal: 


For more information check these out:

General Chemistry Online Why does salt melt ice?


Jeanne Garbarino, Double X Science Editor

What does ‘safe’ mean when we’re talking about chemicals?

It’s not easy being green. First, you have decide which green to be. (Source)

[We at Double X Science had been considering a "toxins" post but then found the following post by Jennifer Mo, a happily childfree vegetarian who lives in California with a cat named Brie but variously nicknamed Walnut "for her brain capacity" or Toxokitty for her history of toxoplasmosis--which, as it turns out, turns up in Jennifer's guest post, below. This post first appeared at Jennifer's blog, It's Not Easy to Be Green, where she writes about environmental issues as a "rationalist and a pragmatist." You can also follow Jennifer on Twitter @noteasy2begreen. We appreciated the pragmatics of this particular post quite a bit and thank Jennifer for allowing us to host it at Double X Science. We are particularly taken with the fact that she asks if we'd ever wanted to call our own brain a troglodyte.]

It’s a common demand from the public to scientists: prove to us something is safe before unleashing your monster on the world. And on one hand, it’s a totally fair, reasonable request to not be treated as lab rats. I get that. I hate the idea of having big chemical corporations profiting off their creations that create long term problems for ordinary people and the environment. On the other, whether you’re talking about GMOs or synthetic chemicals, it’s a problematic request for a couple of key reasons:
  • It assumes a binary between safe and unsafe without regard to exposure level or other circumstances. Just about everything can be harmful under the right (or perhaps I should say wrong?) conditions. Take water, for example.Tons Continue reading

Why blueberries won’t turn you blue and other blueberry facts

Blueberries. Credit.


by Adrienne Roehrich, Chemistry Editor

Blueberries in the Northwestern semisphere are the fruit of several shrubs in the genus Vaccinium L.  They grow in all provinces in Canada and all but two of the United States (Nebraska and North Dakota). In the Northwestern semisphere, one can find 43 species of blueberries, depending on the region. Blueberries are found and produced in all hemispheres of the world. However, the species can vary by region.

Taxonomy:
Kingdom: Plantae (Plants)
Subkingdom: Tracheobionta (Vascular plants)
Subdivision: Spermatophyta (Seed plants)
Division: Magnoliophyta (Flowering plants)
Class: Magnoliopsida (Dictyledons)
Subclass: Dilleniidae
Order: Ericales
Family: Ericaceae
Genus: Vaccinium

There are 43 species and 46 accepted taxa overall. Some of the species include fruits we do not necessarily recognize as blueberry, including farkleberry, bilberry, ohelo, cranberry, huckleberry, whortleberry, deer berry, and lingonberry.  (Source

Blueberries are a very popular fruit in the U.S., and is consumed in fresh, frozen, and canned forms. While blueberries are a great fruit to eat to meet your suggested fruit intake, it also is one of the foods that are purported to have properties that it just does not have. This undeserved reputation results from the high levels of anti-oxidants, leading those predisposed to looking for “super foods” to classify blueberries into the anti-oxidant super food category. While eating more healthy foods is always a good idea, no food has curative effects all on its own.

Other aspects of blueberry nutrition includes it as a source of sugar. One cup (148 g) of blueberries contains about 15 g of sugar and 4 g of fiber, a single gram of protein, and half a gram of fat. If you are counting carbs, this cup has 21 g of them. That one cup of blueberries averages about 85 calories, which is approximately the same as a medium apple or orange. While almost all the vitamins and minerals nutrition gurus like to report on are present to some amount, for the 2000-calorie diet, that one cup of blueberries will provide the recommended daily value of 24% of Vitamin C, 36% of Vitamin K, and 25% of manganese. The remaining values range from 0-4%. (Values obtained from Nutrition.com and verified through multiple sources.)

The Wikipedia entry is quite good and well researched (as of August 18, 2012). 

The photo above shows all of the life stages of a blueberry. Berries go from the little red nub at the end of the branch to round and juicy blueberries through fertilization of the ovary, which swells rapidly for about a month, then its growth ceases. The green berry develops with no change in size. The chemicals responsible for the blue color, anthocyanins, begin to turn the berry from green to blue as it develops over about 6 days. The volume of the berry increases during the change in color phase.

Will blueberries turn you blue? In short, no. You can achieve blue skin through the ill-advised practice of drinking silver or you can achieve orangish-yellow skin by eating a large number of carrots. This is because the chemicals causing the skin color are fat soluble and are present in a large quantity in the fat just under the skin, giving the skin those colors. Anthocyanin, the primary chemical causing the blue color in blueberries, is not fat soluble and will not reside in the fat under your skin.

Anthocyanins is a class of over 30 compounds. The chemical structure is generally as shown below. They are polyphenolic, which indicates the 3 ring structures. The “R” indicates different functional groups that change depending on which anthocyanin the structure represents. 


Interestingly, anthocyanins are also pH indicators because their color ranges from yellow to red to blue depending on the local pH. The blue color indicates a neutral pH. The wikipedia page on anthocyanins is also informative (as of August 18, 2012). 

As mentioned before, blueberries are a popular fruit. Recipes abound, but here is one from my own Recipe Codex for Surprise Muffins with blueberries:

Ingredients
  • 6 Tbsp. butter
  • 3/4 cup sugar
  • 2 eggs
  • 1/2 cup milk
  • 1/2 – 1 pint blueberries, fresh or frozen (defrosted)
  • Food coloring, optional
  • 2 cups all-purpose flour
  • 1/4 tsp. salt
  • 1 Tbsp. baking powder
  • Your favorite mini-treat (Hershey’s Kisses, Hugs, Reese’s Mini Cups, strawberry jam, etc.)
Directions
  1. Preheat the oven to 350º. In a large bowl, cream the butter and sugar. You can use a wooden spoon, a potato masher or handheld electric mixer. Mix in the eggs, one at a time, and add the milk.
  2. Rinse the strawberries and cut off the green stem. Mash the berries with a potato masher or puree in a blender. Then stir the berries into the butter and milk mixture. TIP: For muffins with a more blue color, add a few drops of blue food coloring.
  3. In a separate bowl, sift the flour, salt and baking powder. Stir well. Add the flour mixture to the berry mixture. Use a wooden spoon to stir until all the white disappears.
  4. Line the muffin tin with paper liners. Drop the batter from a tablespoon to fill the cups halfway.
  5. Add a surprise: an unwrapped mini treat or 1/2 teaspoon of jam. Then spoon more batter to fill almost to the top.
  6. Bake until the muffins begin to brown and a toothpick inserted near the center (but not in the mini-treat) comes out clean, about 20-25 minutes.
  7. Remove the muffins from the tin and cool.
Or perhaps you are in less of a cooking scientist mood and more in a home lab mood. Try this at-home lab with blueberries about dyes. Adapted from the Journal of Chemical Education.

Items You Need
  • 4 microwavable/stove top staff glasses, pots, or containers at least 1/2 cup in volume
  • tablespoons or 1/4 cup measuring cup
  • water
  • spatula
  • alum (available in the grocery store spice aisle)
  • cream of tartar (available in the grocery store spice aisle)
  • hot pads and tongs
  • at least four small (1-2 in.) squares of white cotton cloth
  • yellow onion skins
  • blueberries
  • spoon
  • paper towels
  • vinegar
  • baking soda
  • a dropper
  • notebook for experimental observations
Procedure
In each step, you will want to record your observations, paying special attention to colors.
  1. Pour 4 tablespoons (1/4 cup) into container 1. Add a pea-sized scoop of alum and about half that amount of cream of tartar and stir. Bring the solution to a boil on the stove top or by microwaving for about 60 seconds. (Your microwave may vary.) Add two small squares of white cotton cloth and boil for two minutes. Set the container aside. The squares will be used in steps 4 and 6.
  2. Tear the outer, papery skin from a yellow onion into pieces no more than 1 inch square. Place enough pieces in a second container to cover its bottom with  2 or 3 layers of onion skin. Add about 4 tablespoons of water to the container. Bring the solution to a boil on the stove top, continuing to boil for 5  minutes.
  3. Wet a new square of cloth with water. Place it in container 2 so it is completely submerged and boil for 1 minute. Using tongs, remove the cloth and rinse it with water. Place the cloth square in the appropriate area on a labeled paper towel.
  4. Use tongs to remove one of the cloth squares from beaker 1. Repeat step 3 using this square. Compare to the dyed cloth square from step 3.
  5. Pour 4 tablespoons of water in a third container. Add 4-5 blueberries to the container and mash them with a spoon. Bring the solution to a boil on the stove, and continue to boil for 5 minutes.
  6. Repeat steps 3 and 4 substituting the blueberry mixture in container 3 for the onion skin mixture in container 2.
  7. Mix a small scoop of baking soda with a tsp of water in a clean container. With a dropper, place 1-2 drops of the baking soda solution in one corner of each cloth square. What happens? Rinse the dropper thoroughly, then place 1-2 drops of vinegar on the opposite corner of each square. What happens? Rinse the fabric squares under cool running water. Is there a change? Allow the squares to dry overnight. Is there any change of the cloth dries?
Optional: Try variations in the procedure such as changing the amount of dye source, the length of time the cloth spends in the dye solution, and the temperature of the dye solution.

Questions to consider
The solution in step 1 is called a mordant. Based on your observations, what is the purpose of a mordant?
Is the dye produced by blueberries really blue? Why might some people not want to wear clothes dyed with blueberries?

———————-
All in all, enjoy your blueberries. As a shrub, it is quite pretty. As a fruit, it is quite yummy. And as the tool in an experiment, it is quite fun.

These views are the opinion of the author and do not necessarily reflect or disagree with those of the DXS editorial team.

Book Review: Science Myths Unmasked: Exposing the misconceptions and counterfeits forged by bad science books


 

By DXS Biology Editor Jeanne Garbarino

Do you remember that old candle experiment involving a lit candle in a jar? You know, the one where you place a lit candle in a bowl of water, then place a jar over the candle, and rather quickly, the candle extinguishes? If you were like me, you probably learned that the candle goes out because all of the oxygen gets used up (oxygen is a requirement for combustion).  However, according to David Isaac Rudel in his multi-volume series Science Myths Unmasked, this is one of the many science demonstrations that are wholly misinterpreted.

Unfortunately, the science textbooks used by thousands of schools across the US are chock-full of what Rudel calls “pseudo-explanations” for many complicated scientific phenomena. Instead of presenting clear explanations, including the establishment of a basic scientific foundation, many science textbooks present certain concepts using shortcuts, with the assumption that these so-called shortcuts make it easier for kids to understand science. 

Rudel argues that these shortcuts, which are often associated with an “abuse of [scientific] language,” only confuse students. In fact, included on the back cover of Science Myths Unmasked, Volume 2: Physical Sciences is a quote from Richard Feynman regarding science textbooks: “They said things that were useless, mixed-up, ambiguous, confusing, and partially incorrect. How anybody can learn science from these books, I do not know, because it’s not science.”

My husband, a public high school chemistry and biology teacher, is wholeheartedly aligned with this particular opinion of Feynman and Rudel and for many years, has not used a textbook to teach science. When I asked why, he simply stated, “They just confuse the kids.” 

As an example to what is wrong with science textbooks, let’s get back to the candle-in-a-jar experiment. In Science Myths Unmasked Volume 2: Physical Science, this very common scientific demonstration is thoroughly dissected, explaining why “the candle goes out when the oxygen content of the air is no longer high enough to support combustion” is an incorrect conclusion found in many textbooks, especially since it overlooks how the products of combustion affect the candle flame. After elaborating on the precise conditions point by point, and providing an outline for easy demonstrations to “expose the myth,” the following is stated:

Candles in closed containers do not go out because they use up all the oxygen.  Rather, the hot carbon dioxide (and to a lesser extent water vapor) given off in combustion accumulates at the top, pushing down other gases (most importantly, oxygen), and eventually stifles the flame. 

If the jar’s rim is submerged in water, the liquid rises not because water is replacing the oxygen used up in combustion.  Rather, the air inside the jar cools as the flame dies down and hot gases offload heat to the glass container.  As the air cools, it applies less pressure to the water than it did when the jar was first put over the candle.  The water rises as a result of the decreasing pressure from the air against it.           

In the Science Myths Unmasked series, a great number scientific factoids and processes that are often misrepresented in the classroom are correctly explained, and in great detail.  In addition to the candle experiment described above, Rudel tackles simple machines, circuits, phase change, and waves, just to name a few. However, this book is not for those without at least some background in science, as it does get technical. I would, though, recommend that these books find a way onto the shelves of science educators, as it seems they would benefit the most from the lessons and demonstrations covered. It is also good for people who, like me, have a scientific background and wish to properly explain scientific concepts to their kids, as I am sure those questions are bound to come up.  

For more on the Science Myths Unmasked series, go here.    

Explosions, Just a Bit More Than Fireworks

Image by Nux. (Source)

By Adrienne M Roehrich, Chemistry Editor


It’s that time of the year in the U.S. – when we blow up pretty bombs in celebration of the approval of the Declaration of Independence, declaring the independence from the Kingdom of Great Britain. Around this time of year, there is no dearth of articles about the chemistry of fireworks, but the chemistry editor here could not let her secret love of this topic pass by.


What is an explosive? An explosive is a combination of materials that when reacted produce an abundance of light, sound, heat, and pressure. A firework encompasses all 4 of those: we are familiar with the light – the whole reason we view fireworks, we are familiar with the sound – the boom that follows especially large displays, we are familiar with the pressure if we are close enough – that’s the force that pushes into you and the “shock wave” pictured in movies after large explosions; and we are familiar with the heat – ever held a sparkler?


There are three main types of explosives: chemical, nuclear, and mechanical. The bulk of this post will focus on chemical explosives with a short bit about nuclear and mechanical.


If we start at the beginning – well, we’ll skip to the “accepted” first explosive – black powder. Black powder, also called gun powder and the precursor to fireworks, is coined a chemical explosive. Chemical explosions generally fall into a specific classification of chemical reactions called oxidation.


The earliest definition of oxidation was the addition of the element oxygen to a compound, also called combustion. Due to limits of this definition, it was later changed to be the loss of electrons from an element (within a compound.) The original definition can easily be shown in terms of explosives. The simple mixing of hydrogen and oxygen with the addition of just a bit of heat, will form water in an explosive display:


2H2 + O2 –> 2H2O



The little flame used to catalyze the reaction in the video is actually much more energy than is necessary to cause this reaction to occur, but it’s difficult to get an even littler source of heat and safely demonstrate this reaction. You might also note a lot more energy comes out of that reaction once started in terms of light and heat and sound. I’ve been the one lighting that reaction in a demo without both ears plugged and I couldn’t hear out of one ear for the rest of the lecture.


If we focus on the loss of electrons version of oxidation, we get specific colors. This is what the flame video by The Fabulab focused on in their entry for Alan Alda’s Flame Challenge. I direct your attention to 1:08 and the discussion of electrons.


Metals are the simplest example (and most used) example of oxidation as the loss of electrons and the color change associated. Because some electrons are lost, we now have a different set of electrons changing energy and a different color appears.



From here, it is easy to see how fireworks fall into this category of explosives. Fireworks are always being further refined to produce a specific set of light and sound. For a bit more information, this video gets fairly specific.

The vast majority of explosives in use today are considered chemical explosives. This covers a range of materials, including the aforementioned black powder and fireworks, nitroglycerin, dynamite, plastic explosives (C4 for Mythbusters and sci-fi television show fans), and the ones with water now restricting the amount of water one is allowed to bring onto an airplane in the U.S.


Another type of explosive is a nuclear explosive. The energy in these explosives come from a nuclear reaction. Wikipedia differentiates types of nuclear explosions into stellar and man-made. Another way to differentiate nuclear reactions is by fission and fusion. The explosions at the heart of stars fall under nuclear fusion and are called stellar nucleosynthesis.


Nuclear fusion is the process of forcing 2 atoms into 1 new, larger atom.  The CNO cycle, diagrammed here, is one of the nuclear fusion reactions occurring in stellar nucleosynthesis.


Source

Nuclear fission is the process involved in nuclear weapons. 


Nuclear fission is the process of dividing an atom into 2 or more smaller atoms. In both nuclear fusion and nuclear fission processes, specific types of radiation are emitted because the new atoms produced do not have the same energy as the starting material. The radiation emitted in these reactions is not just from a change of electrons but from a change from the nucleus of the atom. This emission of radiation is part of the light and heat from the sun and the light and heat of a nuclear bomb.


The third and last type of explosive I will cover is a mechanical explosive. These explosions occur as a purely physical process, but can then incite a chemical explosion. Mechanical explosions occur due to a sudden release of a build up of pressure. A specific kind of these explosions are under conditions where a liquid is pressurized in a vessel and a rupture brings it above its boiling point, called a boiling liquid expanding vapor explosion, BLEVE. Steam powered trains were sometimes damaged by these type of explosions. An explosion of a water heater falls into this category. Mechanical explosions are the rarest and perhaps least covered types of explosives.


Water heater explosion by the Mythbusters. 



These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team.

#DispatchesDNLee: Handling lady-business in the field

An African-American woman and scientist in Tanzania

by Danielle Lee, Ph.D.

Actual field diary entry, Tuesday, August 7, 2012, ~8:30 am

I cried this morning. In the shower. I was trying (poorly) to suppress screams of pain as I let the water run on my leg. I knew it was going to be bad when I saw blood on my pants as I pulled my field cover pants off. 

I had been running into the same bush on line 3 between traps C and D every day. It has scraped me good, but this time it really hurt. I fell down and screamed in pain. Shabani* was breaking across the field to come to see about me. It really was of no use. He couldn’t help me. I just needed a minute or two to recover. I soon walked it off.

But in that moment standing in the shower, I let out a yelp. I tried to hold my scraped leg under the hot water to clean the wound. But it stung like the devil.

Lee_Legs_2057I cried, much like I did as little girl. I looked down at my scarred legs and immediately recollected the summer of 1981. I was such a tomboy, playing in the yard and in the streets with my boy cousins, and clumsy, so clumsy. My legs and arms were covered in bandages like tattoos. This obviously frustrated my bio-dad to no end. I vividly remember him threatening to spank me if I got another scratch on my legs. He scolded that I was a girl and I had no business being scarred up like that. I was shook. I tried to play more girl-like and carefully, but it was of no use. I liked climbing trees and tussling too much to stop. So I resorted to hiding my scars from him.

But as I looked at my abused legs, I couldn’t help but think how ‘unlady-like’ my stems were. What boy is going like me with my legs looking like that or with feet badly needing a pedicure?

And it makes me wonder, Do male researchers ever have conversations like these with themselves or with each other? Unlike our male counterparts, female researchers or long-term travelers and hikers have a few extra hygiene and grooming regimes to consider.

What about that time of the month?

How do I keep a happy lady garden in the middle of the bush?

Do I or don’t I shave my legs?

First, the monthly menses

Dealing with the logistics of menses is always an inconvenience to me. My previous field research experiences taught me that tampons are the most wonderful invention, ever! They are especially handy if you have a heavier flow or will be busy for long periods of time in the field. Wear a pad for backup so as not to soil and permanently stain your good field pants. However, the last time I was in a developing nation doing field ecology, I said if I could halt my period for the time I was there, then I would certainly do it. I was able to do just that: I had a hysterectomy 3 years ago(yay for me), but am sorry I can’t offer more first-hand advice for managing menses to younger researchers. [Ed. note: Some birth control pill formulations promise to limit bleeding to four times a year.]

I did make note that you can get feminine products in Tanzania, primarily sanitary napkins. They come in small-quantity packages, and there are not many varieties. It’s like the options that were available in 1980. If you have a preference for certain products, e.g., dry-weave, wings, long/short, light/super-absorbent variety pack, then I recommend bringing your own.

Second, maintaining your lady-garden

Since said hysterectomy, I have become more sensitive to microflora imbalance. It didn’t occur to me to be prepared for yeast infections. I eventually asked one of the other U.S female researchers if she had suffered from yeast infections since living in Tanzania. She told me that she had but that she was prepared. Her doctor pre-prescribed vaginal antifungals to take with her on her trip. I was not warned, but it occurred to me that if I was drinking bottled water because of the risks of local water disrupting my GI tract, then maybe my private parts would be sensitive as well. I began washing my sensitive areas with bottled water and noticed an immediate improvement. I also began taking acidophilus pills to get my system on track.

But let’s not underestimate the importance of your clothes and underwear-cleaning regime. You may discover you are allergic to the washing powder sold and used there. If that is the case, then I recommend hand-washing your unmentionables with bar soap and hanging them up to air dry in a dust-free location.

No matter what may be the root of your sensitivity (including old-fashioned stress), I highly recommend all female researchers to include vaginitis treatment ointments/creams and/or pills in your sundry first-aid and medicines kits. It is as important as packing anti-itch creams and anti-diarrheal pills in my book.

Finally, to shave or not to shave?

I have vanity issues, I admit. I (unnecessarily) obsess over grooming. Should I continue to shave my legs and underarms? Hirsute woman problems. The truth is, this grooming obsession didn’t matter. There was no need to obsessively attend to whiskers above my lip or on my chin or get a pedicure or even (welp) wear deodorant. Taking cues from local women, I noticed no one shaved their legs or under their arms – at least not as obsessively as we do in the West. And everyone had dusty feet! LOL, seriously red dust was everywhere and people wore sandals or flip flops or went barefoot for many occasions and traveled long distances, too!

A week before my departure, I ran out of my solid, invisible unscented deodorant. I thought that I would just go to the drug store and buy more. Nope! I visited 4 stores and could only find was liquid roll-on anti-perspirant that was flowery smelling. It did nothing for me, but it didn’t really matter. It wasn’t uncommon to smell a ‘day’s worth of work’ on people throughout the day, but I felt uncomfortable.

These were my obsessions. However, doing these are things made me feel human, like a woman even. But it was a relief to relax my obsessive pre-occupation with my body for a while.

The take-home message is if there are some things that help you make it through the day or season, then bring them, e.g., tweezers, hand mirror, a pumice stone, or certain brand of hygiene product. Yes, most basic products are available at the local dukas or apothecaries, and prices are fair. However, the varieties are limited. There is no better way to be reminded of how first-world you are than when you ask for a single-use, fancy-pants, non-essential comfort-only products in a developing nation.

*Shabani – Shabani Lutea was my field research assistant. He works for Sokoine University of Agriculture and is experienced trapping and handling wild African Pouched rats (without gloves!) He is the most awesome field research assistant there ever was, forever branded as the Rat Whisperer, because he really is that good.

About the author

DNLee is a post-doctoral researcher at Oklahoma State University. She is currently studying African-Pouched Rats, Cricetomys gambianus, an interesting yet largely mysterious animal that uses its keen sense of smell to detect landmines. She spent summer 2012 in Morogoro, Tanzania, studying the animals in the wild and in captivity. This is DNLee’s second installment in her series for Double X Science about her field experiences in Tanzania.

Photo credit: All photos, courtesy of Danielle Lee, Ph.D. Continue reading

Dinosaur Aunts, Bacterial Stowaways, & Insect Milk

Today’s guest post (originally posted here) is from Katie Hinde, an Assistant Professor in Human Evolutionary Biology at Harvard University.  Katie studies how variation in mother’s milk influences infant development in rhesus monkeys.  You can learn more about Katie and mammalian lactation by visiting her blog, Mammals Suck… Milk!.  Follow Katie on Twitter @Mammals_Suck.




Dinosaur Aunts, Bacterial Stowaways, & Insect Milk


Milk is everywhere. From the dairy aisle at the grocery store to the explosive cover of the Mother’s Day issue of Time magazine, the ubiquity of milk makes it easy to take for granted. But surprisingly, milk synthesis is evolutionarily older than mammals. Milk is even older than dinosaurs. Moreover, milk contains constituents that infants don’t digest, namely oligosaccharides, which are the preferred diet of the neonate’s intestinal bacteria (nom nom nom!)  And milk doesn’t just feed the infant, and the infant’s microbiome; the symbiotic bacteria are IN mother’s milk. 

Evolutionary Origins of Lactation
The fossil record, unfortunately, leaves little direct evidence of the soft-tissue structures that first secreted milk. Despite this, paleontologists can scrutinize morphological features of fossils, such as the presence or absence of milk teeth (diphyodonty), to infer clues about the emergence of “milk.” Genome-wide surveys of the expression and function of mammary genes across divergent taxa, and experimental evo-devo manipulations of particular genes also yield critical insights. As scientists begin to integrate information from complementary approaches, a clearer understanding of the evolution of lactation emerges.
 

In his recent paper, leading lactation theorist Dr. Olav Oftedal discusses the ancient origins of milk secretion (2012). He contends the first milk secretions originated ~310 million years ago (MYA) in synapsids, a lineage ancestral to mammals and contemporaries with sauropsids, the ancestors of reptiles, birds, and dinosaurs. Synapsids and sauropsids produced eggs with multiple membrane layers, known as amniote eggs. Such eggs could be laid on land. However, synapsid eggs had permeable, parchment-like shells and were vulnerable to water loss. Burying these eggs in damp soil or sand near water resources- like sea turtles do- wasn’t an option, posits Oftedal. The buried temperatures would have likely been too cold for the higher metabolism of synapsids. But incubating eggs in a nest would have evaporated water from the egg. The synapsid egg was proverbially between a rock and a hard place: too warm to bury, too permeable to incubate. 

Ophiacodon by Dmitri Bogdanov

Luckily for us, a mutation gave rise to secretions from glandular skin on the belly of the synapsid parent. This mechanism replenished water lost during incubation, allowing synapsids to lay eggs in a variety of terrestrial environments. As other mutations randomly arose and were favored by selection, milk composition became increasingly complex, incorporating nutritive, protective, and hormonal factors (Oftedal 2012). Some of these milk constituents are shunted into milk from maternal blood, some- although also present in the maternal blood stream- are regulated locally in the mammary gland, and some very special constituents are unique to milk. Lactose and oligosaccharides (a sugar with lactose at the reducing end) are two constituents unique to mammalian milk, but are interestingly divergent among mammals living today. 

Illustration by Carl Buell
Mammalian and Primate Divergences:  Milk Composition
         
Among all mammals studied to date, lactose and oligosaccharides are the primary sugars in milk. Lactose is synthesized in mammary glands only. Urashima and colleagues explain that lactose synthesis is contingent on the mammalian-specific protein alpha-lactalbumin (2012). Alpha-lactalbumin is very similar in amino-acid structure to C-type lysozyme, a more ancient protein found throughout vertebrates and insects. C-type lysozyme acts as an anti-bacterial agent. Oligosaccharides are predominant in the milks of marsupials and egg-laying monotremes (i.e. the platypus), but lactose is the most prevalent sugar in the milk of most placental (aka eutherian) mammals. Interestingly, the oligosaccharides in the milk of placental mammals are most similar to the oligosaccharides in the milk of monotremes. Unique oligosaccharides in marsupial milk emerged after the divergence of placental mammals. 

Marsupial and monotreme young seemingly digest oligosaccharides. Among placental mammals, however, young do not have the requisite enzymes in their stomach and small intestine to utilize oligosaccharides themselves. Why do eutherian mothers synthesize oligosaccharides in milk, if infants don’t digest them?

In May, Anna Petherick’s post “Multi-tasking Milk Oligosaccharides” revealed that oligosaccharides serve a number of critical roles for supporting the healthy colonization and maintenance of the infant’s intestinal microbiome. Beneficial bacterial symbionts contribute to the digestion of nutrients from our food. Just as importantly, they are an essential component of the immune system, defending their host against many ingested pathogens. The structures of milk oligosaccharides have been described for a number of primates, including humans, and data are now available from all major primate clades; strepsirrhines (i.e. lemurs), New World monkey (i.e. capuchin), Old World monkey (i.e. rhesus), and apes (i.e. chimpanzee). 

        
Among all non-human primates studied to date, Type II oligosaccharides are most prevalent (Type II oligosaccharides contain lacto-N-biose I). Type I oligosaccharides (containing N-acetyllactosamine) are absent, or in much lower concentrations than Type II(Taufik et al. 2012). 

In human milk, there is a much greater diversity and higher abundance of milk oligosaccharides than found in the milk of other primates. Most primate taxa have between 5-30 milk oligosaccharides; humans have ~200. Even more astonishingly, humans predominantly produce Type I oligosaccharides, the preferred food of the most prevalent bacterium in the healthy human infant gut- Bifidobacteria (Urashima et al 2012, Taufik et al. 2012).

         
Human infants have bigger brains and an earlier age at weaning than do our closest ape relatives. Many anthropologists have hypothesized that constituents in mother’s milk, such as higher fat concentrations or unique fatty acids, underlie these differences in human development. But only oligosaccharides, a constituent that the human infant does not itself utilize, are demonstrably derived from our primate relatives (Hinde and Milligan 2011). At some point in human evolution there must have been strong selective pressure to optimize the symbiotic relationship between the infant microbiome and the milk mothers synthesize to support it. The human and Bifidobacteria genomes show signatures of co-evolution, but the selective pressures and their timing remain to be understood.

Vertical Transmission of Bacteria via Milk
In the womb, the infant is largely protected from maternal bacteria due to the placental barrier. But upon birth, the infant is confronted by a teeming microbial milieu that is both a challenge and an opportunity. The first inoculation of commensal bacteria occurs during delivery as the infant passes through the birth canal and is exposed to a broad array of maternal microbes. Infants born via C-section are instead, and unfortunately, colonized by the microbes “running around” the hospital. But exposure to the mother’s microbiome continues long after birth. Evidence for vertical transmission of maternal bacteria via milk has been shown in rodents, monkeys(Jin et al. 2011), humans(Martin et al. 2012), and… insects. 

Yes, INSECTS!

A number of insects have evolved the ability to rely on nutritionally incomplete food sources. They are able to do so because bacteria that live inside their cells provide what the food does not. These bacteria are known as endosymbionts and the specialized cells the host provides for them to live in are called bacteriocytes. For example, the tsetse fly has a bacterium, Wigglesworthia glossinidia,* that provides B vitamins not available from blood meals. Um, if you are squeamish, don’t read the previous sentence.     
 *I submit the tsetse fly and its bacterial symbiont (Wigglesworthia glossinidia
for consideration as the number one mutualism in which the common name of the host 
and the Latin name of the bacteria are awesome to say out loud! 
Bring on your challenger teams.
Hosokawa and colleagues recently revealed the Russian nesting dolls that are bats (Miniopterus fuliginosus), bat flies (Nycteribiidae), and endosymbiotic bacteria (proposed name Aschnera chenzii)(2012). Bat flies are the obligate ectoparasites of bats (Peterson et al. 2007). They feed on the blood of their bat hosts, and for nearly their entire lifespan, bat flies live in the fur of their bat hosts. Females briefly leave their host to deposit pupae on stationary surfaces within the bat roost. 

Bat flies are even more crazy amazing because they have a uterus and provide MILK internally through the uterus to larva! Male and female bat flies have endosymbiotic bacteria living in bacteriocytes along the sides of their abdominal segments (revealed by 16S rRNA). Additionally, females host bacteria inside the milk gland tubules, “indicating the presence of endosymbiont cells in milk gland secretion”. 

The authors are not yet certain of the specific nutritional role that these bacterial endosymbionts play in the bat fly host. The bacteria may provide B vitamins, as other bacterial symbionts of blood-consuming insects are known to do. My main question is what is the exact role of the bacteria in the milk gland tubules? Are they there to add nutritional value to the milk for the larva, to stowaway in milk for vertical transmission to larva, or both?  

Conclusions
The studies described above represent new frontiers in lactation research. The capacity to secrete “milk” has been evolving since before the age of dinosaurs, but we still know relatively little about the diversity of milks produced by mammals today. Even less understood are the consequences and functions of various milk constituents in the developing neonate. Despite the many unknowns, it is increasingly evident that mother’s milk cultivates the infant’s gut bacterial communities in fascinating ways. A microbiome milk-ultivation, if you will, that has far reaching implications for human development, nutrition, and health.  Integrating an evolutionary perspective into these newly discovered complexities of milk dynamics allows us to reimagine the world of “dairy” science.

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Hinde & Milligan. 2011. Primate milk synthesis: Proximate mechanisms and ultimate perspectives. Evol Anthropol 20:9-23.
Hosokawa et al. 2012. Reductive genome evolution, host-symbiont co-speciation, and uterine transmission of endosymbiotic bacteria in bat flies. ISME Journal. 6: 577-587
Jin et al. 2011. Species diversity and abundance of lactic acid bacteria in the milk of rhesus monkeys (Macaca mulatta). J Med Primatol. 40: 52-58
Martin et al. 2012. Sharing of Bacterial Strains Between Breast Milk and Infant Feces. J Hum Lact. 28: 36-44
Oftedal 2012. The evolution of milk secretion and its ancient origins. Animal. 6: 355-368.
Peterson et al. 2007. The phylogeny and evolution of host choice in the Hippoboscoidea(Diptera) as reconstructed using four molecular markers. Mol Phylogenet Evol. 45 :111-22
Taufik et al. 2012. Structural characterization of neutral and acidic oligosaccharides in the milks of strepsirrhine primates: greater galago, aye-aye, Coquerel’s sifaka, and mongoose lemur. Glycoconj J. 29: 119-134.
Urashima, Fukuda, & Messer. 2012. Evolution of milk oligosaccharides and lactose: a hypothesis. Animal. 6: 369-374.