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

The Bright Crystal

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.
Over at Boing Boing, Maggie Koerth-Baker recently came up with a really fantastic analogy to explain this idea. X-ray crystallography, she wrote, is

… 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.

(Source)
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.

Now, in a paper published Nov. 29 in Science, they have. They did it by combining X-FEL and in vivo crystallization to solve the structure of a trypsanosomal enzyme called cathepsin-B, a potential drug target for African sleeping sickness.

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.

Serial femtosecond crystallography (Source Continue reading

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.

From alchemist to chemist: What kind of chemistry is that?


Figure 1: The Alchemist Discovering Phosphorus

What does the word chemistry  mean to you? For many, it was a class in high school or college to get through. In these introductory courses, called general chemistry, one gets a mix of all the flavors of chemistry – but the flavors are very different. To those who hear the calling of chemistry, it isn’t just any chemistry that will do. Some courses are more interesting to them than others. 

Many instructors start their general chemistry course with a history, introducing alchemy. Alchemy is considered to be the process by which to turn [name item of your choice] into gold. Alchemists were chemists by accident in that they performed many chemical reactions in their quests, discovering a number of elements in the process - embodied by Hennig Brandt’s discovery of phosphorus from the refinement of urine.
Alchemy relates to all the fields of chemistry. In perhaps the most famous of alchemy pictures, that by Joseph Wright of Derby entitled “The Alchemist Discovering Phosphorus,” the alchemist is kneeling by a very large round bottom flask. For many in modern chemistry, the round bottom flask signifies hours in the organic chemistrylaboratory mixing chemicals together to create something new.


Organic chemistry is the “branch of chemistry that deals with the structure, properties, and reactions of compounds that contain carbon” according to the American Chemical Association (ACS). Organic chemistry is the largest of chemistry fields in terms of number of people working in it. Organic chemists strive to make new compounds, usually to improve upon an existing one for a purpose and the field is often thought of in terms of synthesis applications.


The actual process of converting urine to phosphorus generally falls along the lines of inorganic chemical reactions. The form of phosphorus in urine is in the chemical sodium phosphate (Na3PO43-). Heating phosphates along with the organic products also in urine will form carbon monoxide (CO) and elemental phosphorus (P). The sodium phosphate, carbon monoxide, and elemental phosphate are all inorganic chemicals, falling under the field of inorganic chemistry.


Inorganic chemistry is “concerned with the properties and reactivity of all chemical elements,” according to UC-Davis chemwiki. While organic chemistry requires the presence of carbon in a specific type of bond, inorganic chemistry involves all the elements present in the periodic table. Inorganic chemistry delves into theories surrounding the bonding of metals to molecules and the shapes of molecules themselves.


Figure 2: Components of Urine
While the process of collecting phosphorus from urine requires organic and inorganic chemical reactions, the process of making the products in urine is biochemistry. Note in figure 2 that the primary product in urine is urea.


For students of biochemistry, images of the urea cycle (aka the Krebs cycle) are well known. According to the ACS, biochemistry is “the study of the structure, composition, and chemical reactions of substances in living systems.” Besides the chemical cycles to produce and use up necessary chemicals in biology, biochemistry encompasses protein structure and function (including enzymes), nucleic acids such as DNA, and biosynthesis.


As the alchemist turned urine to phosphorus, he added heat. The addition of heat to a reaction involves thermodynamics, a subsection of physical chemistry. If heat hadn’t been added, the reaction products would have been kinetic, which is another subsection of physical chemistry.


In a suite of physical chemistry courses, a student would also take quantum mechanics, rounding out the aim of physical chemists, which is to “develop a fundamental understanding at the molecular and atomic level of how materials behave and how chemical reactions occur,” according to the ACS. Physical chemists work by applying physics and math to the problems that chemists, biologists, and engineers study.


The alchemists who took exact measurements of their reactants and products, using quantitative methods, employed analytical chemistry. Presumably, the alchemists did this because every ounce of gold was precious, and they wanted to know how much substance they started with to produce the coveted metal.


Analytical chemistry focuses on obtaining and processing information about the composition and structure of matter. There are so-called wet lab ways to determine these quantities that often been employed. However, most analytical labs consist of the precision instrumentation that you may have seen on forensic crime shows, such as a mass spec, short for mass spectrometer, a frequent player on CSI.


While the alchemists were only trying to produce a substance to enrich pockets, they ultimately led to a rich science with several subfields, each with a trail leading from the practice of alchemy.

Adrienne M Roehrich, Double X Science Chemistry Editor
References:

(1734-1797), Joseph Wright of Derby. “English: The Alchemist Discovering Phosphorus or the Alchemist in Search of the Philosophers Stone.” Derby Museum and Art Gallery, Derby, U.K., 1771.

Lawton, Graham. “Pee-Cycling.” New Scientist, 20 December 2006 2006.

Weeks, Mary Elvira. “The Discovery of the Elements. Xxi. Supplementary Note on the Discovery of Phosphorus.” Journal of Chemical Education 10, no. 5 (1933/05/01 1933): 302.

Double Xpression: Meghan Groome

Meghan Groome, PhD, Director of K12 Education and Science & the City, New York Academy of Sciences
[Ed. note: Double X Science has started a new series: Double Xpression: Profiles of Women into Science. The focus of these profiles is how women in science express themselves in ways that aren’t necessarily scientific, how their ways of expression inform their scientific activities and vice-versa, and the reactions they encounter.]
Today’s profile is an interview with Meghan Groome, PhD, New York Academy of SciencesDirector of K12 Education and Science & The City, who answered our questions via email with DXS Biology Editor Jeanne Garbarino.

DXS: First, can you give me a quick overview of what your scientific background is and your current connection to science?

MG: I was a bio major since age two. Growing up (and still today) I had a deep love of all things gross, icky, creepy, and crawly and a deep dislike of anything math related. My parents didn’t really know what to do with me, so a theme to my scientific background is that although I was a straight-A student in my bio classes, no one had any idea that I should be doing enrichment programs or making an effort to learn math. I figured that by being a great bio major, I would become a great scientist. So I was an excellent consumer of scientific knowledge but only realized late in life that I needed to be a producer to actually become a scientist.

Being a straight-A student doesn’t actually get you a job when you graduate from a small liberal arts college with a degree in biology and theater, and out of desperation, I took a job teaching. While I wasn’t a good scientist, I turned out to be an excellent teacher and loved the creativity, energy, and never-ending questions that go along with being a science teacher. If you teach from the perspective that science is an endless quest for knowledge, you’ll never get bored taking kids on that journey.

While my background is in biology, my graduate degree is in science education, and I study gender dynamics and student questioning the middle-school classrooms. I currently work for the New York Academy of Sciences as the Director of K12 Education and public programs and spend most of my day convincing scientists that education outreach is not only part of their jobs but a lot of fun.

DXS: What ways do you express yourself creatively that may not have a single thing to do with science?

MG: I’m also a photographer and spend a lot of time wandering around neighborhoods in Brooklyn with a special love of decaying buildings and empty lots. I love how nature conquers things that we humans consider to be permanent – like how we have to constantly beat back the invading hordes of plants and animals even in one of the most man-made environments in the world.

I was also a theater major, so (I) have a strong background in costume design and stage directing. I hate acting but love dance. If I had any talent I would have become a musical theater star but unfortunately enthusiasm and determination can only get you so far.

DXS: Do you find that your scientific background informs your creativity, even though what you do may not specifically be scientific?

MG: I find great joy in seeing how nature conquers human engineering. When I learned about Lynn Margulis’ Gaia hypothesis, I began seeing it everywhere and I think I love photography because I’m documenting the Earth fighting back.

Most of my creative energy comes from working with kids and listening to the wonderful way in which they think about the natural world. Adults can be so rigid in their thinking and are often afraid to say ideas that are out of the mainstream thinking. The older a kid gets, the more we expect them to conform to the adult way of thinking. Middle-school kids are old enough to express their wacky ideas, and young enough to not recognize that their ideas are considered “wrong.”

DXS: Have you encountered situations in which your expression of yourself outside the bounds of science has led to people viewing you differently–either more positively or more negatively?

MG: People tell me all the time “You’re not what we expected” and I’m not really sure how to respond.

In the science education world, my research is informed by my experiences teaching in a very poor district and from a social justice perspective. It’s a rather controversial theoretical framework because it says, “I have an agenda to use my research to bring about equity in an unequal world.” From a research perspective, it means you need to be explicit in your point of view and your biases and have much greater validity and reliability to show that your research is solid. My work is very passion driven so I’ve had to learn when it’s appropriate to pull out my soap box and go full-out social justice to them.

This is changing, but for a long time I kept my personality under wraps in a professional setting. It’s only now — with 10 years professional experience, great organizations on my resume, and a PhD — that I can be clever, confront those I disagree with, and even smile. Anyone who’s ever had a beer with me knows that I’m a goofball and will do just about anything to make someone laugh. I’m a science person, a theater person, a teacher, researcher, policy maker, consultant, and have seen a lot of exquisitely bad and good stuff in my life and so I am frequently the voice of an outsider even though I look and sound like a total insider. That can really freak people out especially if they’ve only read my bio or seen me in my most professional mode.
DXS: Have you found that your non-science expression of creativity/activity/etc. has in any way informed your understanding of science or how you may talk about it or present it to others?

MG: I approach teaching science from a fairly theatrical perspective. In my class we dance, sing, laugh, talk about the real world. I’ve never used the textbook, and I’m very insistent that everything be in the first person when writing or speaking about science. I much prefer teaching regular classes — not honors or AP — and can’t stand kids who remind me of myself in high school.

I approach scientists in the same way and try to make them comfortable admitting that their more than a brain on a stick. I’ve found one of the biggest fears of young scientists is that their PI will find out that they’re interested in something more than life in the lab so I always try to work within the existing power structure and make sure the PIs and Deans indicate to them that working with the (New York) Academy (of Sciences) is okay.

DXS: How comfortable are you expressing your femininity and in what ways? How does this expression influence people’s perception of you in, say, a scientifically oriented context?

MG: This question confounds the heck out of me. I am still such a tomboy and have always chosen to present myself as a somewhat genderless individual. I’ve always considered myself “smart not pretty” because I can control how smart I am but not how pretty. A few years ago, my sisters pulled me aside and told me I needed to stop dressing like such a slob. They started buying me pretty, fashionable clothes and insisting that I wear skirts above the knee and get a real hair cut.

Since I started working at the Academy, I have a very public facing role and have grown to accept that I should look nice. This goes along with slowly feeling comfortable letting my personality out in professional settings but I still consider myself a tomboy and consider my outward appearance to be a costume designed to do a job.

So I guess the answer is, femininity, what femininity?

DXS: Do you think that the combination of your non-science creativity and scientific-related activity shifts people’s perspectives or ideas about what a scientist or science communicator is? If you’re aware of such an influence, in what way, if any, do you use it to (for example) reach a different corner of your audience or present science in a different sort of way?

MG: I think very few people are brains on a stick but that being a scientist often requires us to pretend we have no life outside the lab. I’ve now worked with hundreds of young scientists who spend time working with kids and I’m so pleased to see how quickly they shift from lab geek to real person when talking with a 4th grader. I want scientists to be evangelicals for science, and I want that to include the fact that scientists are real, fallible, wacky, wonderful people too.

DXS: If you had something you could say to the younger you about the role of expression and creativity in your chosen career path, what would you say?

MG: I was always encouraged to be an individual and be myself. I credit my parents with allowing me to pursue my passion and not try to box me in to one identity. It’s never been easy to forge my own path, and I dedicate a lot of myself to my work.

My advice to my younger self would be to slow down a bit, know that you don’t have to get 100% on everything, and know that the problems of the world don’t have to be solved right now.

And perhaps to learn how to be a bit more like a girl. It’s incredibly powerful to see yourself as smart and pretty.


———————————————————————
Meghan Groome is the Director of K12 Education and Science & the City at the New York Academy of Sciences, an organization with the mission to advance scientific research and knowledge, support scientific literacy, and promote the resolution of society’s global challenges through science-based solutions. After graduating from Colorado College in Biology and Theatre, she desperately needed a job and took one as a substitute teacher at a middle school in Ridgewood, NJ. She discovered that she had a knack for making science interesting and enjoyable, mostly through bringing in gross things, lighting things on fire (but always in a safe manner), and having a large library of the world’s best science writing and science fiction. After teaching in both Ridgewood and Paterson, NJ, she completed her PhD at Teachers College (TC) Columbia University with a focus on student question-asking in the classroom. While at TC, she was a founding member of an international education consulting firm and worked on projects from Kenya to Jordan with a focus on designing new schools and school systems in the developing world. 

After graduating, Dr. Groome became a Senior Policy Analyst at the National Governors Association on Governor Janet Napolitano’s Innovation America Initiative. Prior to her work at the Academy, Dr. Groome worked at the American Museum of Natural History and authored the policy roadmap for the Empire State STEM Education Network and taught urban biodiversity in the Education Department. At the Academy, she is responsible for the Afterschool STEM Mentoring program, which places graduate students and postdocs in the City’s afterschool programs, and the Science Teacher program, where she designs field trips and content talks to the City’s STEM teachers. Connect with her on Twitter, and read her NYAS blog!

Sesame Street helps unlock the secrets to the brain during children’s learning

By Tara Haelle, Health Editor
[This post appeared previously at Red Wine and Apple Sauce.]

Looking to let go of a little “mommy guilt” for using the television now and then to give yourself a breather? There may be plenty of evidence that leaving children to watch too much television is a bad idea, but there is something to the idea that educational TV is, well, educational. We have the brain scans to prove it!

A study published in PLOS Biology used functional MRI scans to check out the brains of 26 children and 20 adults while they watched 20 minutes of Sesame Street. The actual purpose of the study wasn’t to find out if Sesame Street was educational per se. Rather, it was to observe the neural processes in the brain while a child is learning “naturalistically” and then see whether what they saw could predict how well the children would perform on standardized IQ tests.

Often, participants in studies receive fMRI scans while they are doing some sort of task that is supposed to simulate learning and/or stimulate certain neural processes. For example, a study subject might be asked to put together a three-dimensional puzzle on a computer (so their head remains still enough for the scan) to see how the brain interprets spatial relations.

However, these sorts of oversimplified “lab” tasks are not always representative of real-world activities, so it’s not clear whether what the researchers see on the brain images during these tasks is necessarily indicative of what REAL-life spatial relations thinking looks like. Are the neural processes seen in an fMRI scan while putting together blocks on a computer screen the same as what’s seen in the brain while a person builds a treehouse?

In this study, the researchers found a partial answer to exactly that kind of question, and the answer is no.

The children in study, ranging in age from 4 to 11 and all typically developing, watched the same 20-minute montage of short clips with Big Bird, Cookie Monster, the Count, Oscar and the rest of the gang teaching numbers and letters, shapes and colors, planets and countries, and so on. Meanwhile, the fMRI was taking a snapshot of their brain every two seconds.

The fMRI (which uses a giant magnet, not radiation, to peek into the brain) works by dividing the brain into a 3-D grid so that it can measure the intensity of the brain signals in each little section (about 40,000 of them, called voxels). The researchers collected a total of 609 images of each participant’s brain, which they could then use to map out the neural processes of the participants while they were watching.

They also had the children (23 of them), in a separate fMRI scanning period, perform a one of those lab-only fMRI tasks. In this case, the kids matched isolated pairs of faces, numbers, words and shapes on the computer (they pressed a button if the two images shown matched) while the fMRI images of their brains were created.

Finally, the children (19 of them) took IQ tests that primarily tested their math and verbal skills. Then the researchers analyzed the maps of neural processes in the children and their comparisons with the adults.

They found a couple of interesting things. First, the kids whose neural “maps” were most similar to the adults also performed the best on the IQ tests. This means kids’ brain structure matures in a predictable way, which the researchers called “neural maturity.”

“Broadly speaking, the children showed group-level similarity to adults in cortical regions associated with vision (occipital cortex), auditory processing (lateral temporal cortex), language (frontal and temporal cortex), visuo-spatial processing and calculation (intraparietal cortex), and several other functions,” the authors wrote.

The fMRI scan on the left represents correlations in neural activity between children and adults, in the middle between children and other children, and on the right between adults and other adults. Such neural maps, says University of Rochester cognitive scientist Jessica Cantlon, reveal how the brain’€™s neural structure develops along predictable pathways as we mature.

Second, the brain maps created during the Sesame Street viewing accurately predicted how the children performed on the IQ tests. Kids who did better on the verbal tasks showed more mature neural patterns in a part of the brain that handles speech and language, called the Broca area. Meanwhile, the kids whose math scores were highest had more neural maturity in a part of the brain that processes numbers, called intraparietal sulcus.

But the researchers’ other finding was that those areas of neural maturity seen during Sesame Street viewing — the ones that matched up with the children’s scores on the IQ test — were not seen during the fMRI task of matching faces, numbers, words and shapes. Basically, the “let’s try to simulate what learning looks like in the brain” task designed specifically for fMRI scans didn’t help much. But the more naturalistic, organic learning that takes places while watching Sesame Street did work.

Researchers now know they can use activities like viewing educational TV to scan children’s brains and learn more about how they learn — and it’s more accurate and helpful than invented computer tasks. It’s possible this technology and research could be applied to understanding better what’s going on with certain learning disabilities.

But a nice additional finding is that, hey, Sesame Street really IS educational! Of course, my son’s favorite show is a different PBS production — Dinosaur Train (which I admit I enjoy too) — so I also feel a better that little D spends a half hour or two, several days a week, learning from Buddy the Tyrannosaurus Rex, Tiny the Pteranodon, Mr. Conductor and Dr. Scott the Paleontologist about dinosaurs, carnivores, herbivores and how to test a hypothesis. All aboard!

Pregnancy 101: Fertilization is another way to come together during sex

Human ovum (egg). The zona pellucida is a thick clear girdle surrounded by
the cells of the corona radiata (radiant crown). Via Wikimedia Commons.
It was September of 2006. Due to certain events taking place on a certain evening after a certain bottle (or two) of wine, my body was transformed into a human incubator. While I will not describe the events leading up to that very moment, I will dissect the way in which we propagate our species through a magnificent process called fertilization.
During the fertilization play, there are two stars: the sperm cell and the egg cell. The sperm cell hails from a male and is the end product of a series of developmental stages occurring in the testes. The egg cell (or ovum), which is produced by a female, is the largest cell in the human body and becomes a fertilizable entity as a result of the ovulatory process. But to truly understand what is happening at the moment of fertilization, it is important to know more about the cells from which all human life is derived.
Act I: Of sperm and eggs

A sperm cell is described as having a “head” section and a “tail” section. The head, which is shaped like a flattened oval, contains most of the cellular components, including DNA. The head also contains an important structure called an acrosome, which is basically a sac containing enzymes that will help the sperm fuse with an egg (more about the acrosome below). The role of the tail portion of sperm is to act as a propeller, allowing these cells to “swim.” At the top of the tail, near where it meets the head, are a ton of tiny structures called mitochondria. These kidney-shaped components are the powerhouses of all cells, and they generate the energy required for the sperm tail to move the sperm toward its target: the egg.
The egg is a spherical cell containing the usual components, including DNA and mitochondria. However, it differs from other human cells thanks to the presence of a protective shell called the zona pellucida. The egg cell also contains millions of tiny sacs, termed cortical granules, that serve a similar function to the acrosome in sperm cells (more on the granules below).  


Act II: A sperm cell’s journey to the center of the universefemale reproductive system
Given the cyclical nature of the female menstrual cycle, the window for fertilization during each cycle is finite. However, the precise number of days per month a women is fertile remains unclear. On the low end, the window of opportunity lasts for an estimated two days, based on the survival time of the sperm and egg. On the high end, the World Health Organization estimates a fertility window of 10 days. Somewhere in the middle lies a study published in the New England Journal of Medicine, which suggests that six is the magic number of days.

Assuming the fertility window is open, getting pregnant depends on a sperm cell making it to where the egg is located. Achieving that goal is not an easy feat. To help overcome the odds, we have evolved a number of biological tactics. For instance, the volume of a typical male human ejaculate is about a half-teaspoon or more and is estimated to contain about 300 million sperm cells. To become fully active, sperm cells require modification. The acidic environment of the vagina helps with that modification, allowing sperm to gain what is called hyperactive motility, in which its whip-like tail motors it along toward the egg.

Once active, sperm cells begin their long journey through the female reproductive system. To help guide the way, the cells around the female egg emit a chemical substance that attracts sperm cells. The orientation toward these chemicals is called chemotaxis and helps the sperm cells swim in the right direction (after all, they don’t have eyes). Furthermore, sperm get a little extra boost by the contraction of the muscles lining the female reproductive tract, which aid in pushing the little guys along. But, despite all of these efforts, sperm cell death rates are quite high, and only about 200 sperm cells actually make it to the oviduct (also called the fallopian tube), where the egg awaits.

                                                

Act III: Egg marks the spot

With the target in sight, the sperm cells make a beeline for the egg. However, for successful fertilization, only a single sperm cell can fuse with the egg. If an egg fuses with more than one sperm, the outcome can be anything from a failure of fertilization to the development of an embryo and fetus, known as a partial hydatidiform mole, that has a complete extra set of chromosomes and will not survive. Luckily, the egg has ways to help ensure only one sperm fuses with it.

When it reaches the egg, the sperm cell attaches to the surface of the zona pellucida, a protective shell for the egg. For the sperm to fuse with the egg, it must first break through this shell. Enter the sperm cell’s acrosome, which acts as an enzymatic drill. This “drilling,” in combination with the propeller movement of the sperm’s tail, helps to create a hole so that the sperm cell can access the juicy bits of the egg.

This breach of the zona pellucida and fusion of the sperm and egg sets off a rapid cascade of events to block other sperm cells from penetrating the egg’s protective shell. The first response is a shift in the charge of the egg’s cell membrane from negative to positive. This change in charge creates a sort of electrical force field, repelling other sperm cells.



Though this response is lightning fast, it is a temporary measure. A more permanent solution involves the cortical granuleswithin the egg. These tiny sacs release their contents, causing the zona pellucida to harden like the setting of concrete. In effect, the egg–sperm fusion induces the egg to construct a virtually impenetrable wall. Left outside in the cold, the other, unsuccessful sperm cells die within 48 hours.  

Now that the sperm–egg fusion has gone down, the egg start the maturation required for embryo-fetal development. The fertilized egg, now called a zygote, begins its journey into the womb and immediately begins round after round of cell division, over a few weeks resulting in a multicellular organism with a heart, lungs, brain, blood, bones, muscles, and hair. It’s an amazing phenomenon that I’m honored to have experienced (although I didn’t know I was until several weeks later).

The Afterword: A note on genetics

 

A normal human cell that is not a sperm or an egg will contain 23 pairs of chromosomes, for a total of 46 chromosomes. Any deviation from this number of chromosomes will lead to developmental misfires that in most cases results in a non-viable embryo. However, in some instances, a deviation from 46 chromosomes allows for fetal development and birth. The most well-known example is Trisomy 21(having three copies of the 21st chromosome per cell instead of two), also called Down’s Syndrome.

The egg and sperm cells are unlike any other cell in our body. They’re special enough to have a special name, gametes, and they each contain one set of chromosomes, or 23 chromosomes. Because they have half the typical number per cell, when the egg and sperm cell fuse, the resulting zygote contains the typical chromosome number of 46. Now you know how we get half of our genes from our father (who made the sperm cell) and half from our mother (who made the egg cell). Did I just put in your head an image of your parents having sex? It’s the birds and the bees, folks—it applies to everyone!


All text and art except as otherwise noted: 
Jeanne Garbarino, Double X Science Editor
Twitter @JeanneGarb
Animations

I love this video, merely for the fact that it is of B-quality and has a sound track clearly inspired from a porn flick, not to mention that it helps to put things in a more visual context:

This one is great as it has more of a sci-fi Death Star appeal:




References and further reading:
  • Potter RG Jr. “Length of the Fertile Period,” Milbank Q (1961);39:132-162
  • World Health Organization. “A prospective multicentre trial of the ovulation method of natural family planning. III. Characteristics of the menstrual cycle and of the fertile phase,” Fertil Steril (1983);40:773-778
  • Allen J. Wilcox, et al. “Timing of Sexual Intercourse in Relation to Ovulation — Effects on the Probability of Conception, Survival of the Pregnancy, and Sex of the Baby,” New England Journal of Medicine, (1995); 333:1517-1521
  • Poland ML, Moghisse KS, Giblin PT, Ager JW,Olson JM. “Variation of semen measures within normal men,” Fertil Steril (1985);44:396-400
  • Alberts B, Johnson A, Lewis J, et al.Fertilization,” Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002.
  • How Human Reproduction Works” (contains a video of sperm fusing with egg)
  • Colorado State University’s “Structure of the gametes before fertilization” and “Fertilization.”