Halloween and poisoned treat rumors: What are the facts?

1920s Halloween postcard.
Via Wikimedia Commons. Public domain in USA.
Many of us probably heard the stories as kids: the razor in the apple, the poison in the Pixy Stix, the mean elderly lady who inexplicably wouldn’t let children run through her flowerbeds and thus was clearly planning some dire Halloween revenge on those who did. As adults, some with children, we see these rumors in a new way, one that perhaps has us trailing our children at a respectful distance, making sure they heed our warnings to go only to the houses of people they know. (OK, I don’t do that, but some parents do).

But how frequent are these acts of Halloween malevolence? Which of the most infamous rumors are, in fact, facts?

Who better to answer those questions that the queen of poison writers–that’s a good thing–Deborah Blum, author of (natch) The Poisoner’s Handbook: Murder and the Birth of Forensic Medicine in Jazz Age New York, one of the most lyrical, fascinating, and macabre interweavings of history, forensics, and chemistry you’ll ever encounter. So, for more of that narrative craft and to sift the facts from the rumors, get thee over to Blum’s blog site at Wired, where she’s got the post that answers your childhood–and adult–questions about the real-life ghouls of Halloween night, including one terrible story about a father who killed his son. 

Blum writes:

This was the 1960s and even then, people told stories, warned their children, about the psychopaths out there who might drop poisoned candy into one’s hands. In the long history of the holiday, truthfully, this has almost never happened. But the very nature of Halloween – the witch at the door, the monster in the closet – lends itself to such ideas. Wasn’t there a crazy woman on Long Island in 1964, after all, who handed out arsenic to trick-or-treaters she thought too old for the candy hunt? 

It hardly mattered that as Snopes points out, she didn’t kill anyone. And her deliberate poisoning attempt seems to be an odd exception to the general goodwill of the holiday. The psychopath at the door is an urban myth.  

How chili powder can kill



Source. Credit.

How can chili powder kill a child? Dr. Rubidium explains.
by Dr. Rubidium, Ph.D., DXS contributor

On the evening of Sunday, January 6th, 2-year-old Joileen G. was pronounced dead at a San Bernardino hospital. A few hours into Monday, Joileen’s caregiver for that Sunday — Amanda Sorensen — was arrested. On Wednesday, Ms. Sorensen, who is also the girlfriend of Joileen’s father, was charged with “…malice aforethought murder…” and “…assault… by means of force that to a reasonable person would be likely to produce bodily injury, resulting in the child’s death.” The alleged “means of force” wasn’t a belt or a fist, but chili powder.

Though it will likely take weeks before the exact cause and manner of death are known from an autopsy and toxicology tests, various media outlets are reporting that Joileen died of “chili powder poisoning.”

Millions to billions of people enjoy chili peppers world-wide each day, from eating handfuls of whole chili peppers to a few shakes of hot sauce on their eggs. Chili peppers and their products aren’t considered a poison, but that’s because most of us have far too narrow a view of poisons. The field of poisons is actually very broad, as are its definitions. 

For example, for toxicologists, a poison is any substance that is harmful when administered to a living organism. But quantity (dose) and species (you versus, say, a turtle) and route (mouth? skin?) and what it’s combined with count, too. Other factors influencing whether or not something will poison you include age, sex, health, and genetics

In other words, almost anything can be a poison at the right (or wrong Continue reading

Friday Roundup: Jane Austen’s arsenic poisoning, breastfeeding and bones, dog bites that trigger pregnancy, and a cranky crab

Jane Austen. Engraving via Wikimedia Commons, in the U.S. public domain.

Curious about how climate has changed over the long term–the very, very long term? This video from the National Oceanic and Atmospheric Administration puts it all into perspective:


  • Jane Austen poisoned by arsenicA mystery author claims that all signs point to arsenic poisoning as the cause of Jane Austen’s death. The rationales that treatments with arsenic may have been fatal are plausible, but how about the idea that it was…murder?
  • Peanut butter recalled for Salmonella concerns, but no illnesses reported.
  • In other recall news, Kotex tampons also have been recalled for bacterial contamination. Please read.
  • You may have heard that when women spend a lot of time together, their cycles synchronize. You may have heard wrong, and Kate Clancy tells us why.
  • Birth control: Not just about sex. According to a report, many, many women use birth control for reasons having nothing to do with…birth control.
  • This just in: Girls can be engineers, too.
  • Chilling trauma patients to save them. Trauma surgeons may be turning to deep chilling their patients to stop their bleeding to death before livesaving surgery can be completed. 

If you found the climate change video depressing, how about some astronauts falling down on the moon? Watching smart courageous people fall over is always entertaining, right?

  • Bones and breastfeeding fads. Would you consider giving your baby pap, “a mixture of flour or bread crumbs cooked in milk or water, or a bread broth called panada, or milk flavoured with spices, sugar, or eggs? These bones tell the story of breastfeeding practices before our time.
  • Ever wondered why smells–like baking cookies or a pinewood fire in the grate–are so evocative and memory stirring? Here’s why.
  • Perhaps you’ve heard about fecal transplants–they are exactly what they sound like–and thought, “Ewwww.” The thing is, they seem to work, but as Maryn McKenna writes, they are not easy to come by.
  • Rick Perry’s debate brain freeze: Parents, you know this happens to you, too, just not on national television. In a presidential debate.
  • In the downer category, orangutans in Indonesia killed by the hundreds every year.
  • Remember when ketchup became a vegetable in the Reagan years? Now Congress wants to add pizza sauce to that category. Someone should tell Congress that there are no do-overs on a healthy childhood.
  • For your “Weirdest News of the Day” reading: People in this village genuinely believe that a dog bite can trigger pregnancy–in men or women–with puppies. It is mass hysteria.
  • Have you been reading confusing and conflicting information about the HPV vaccineHere’s a piece that clears all of that up. 

And finally, we give you this crab because it made us laugh. And laugh. Feel free to suggest captions.

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

Drill, baby, drill — microbial-style

Could the oil energy needed to light up this drill
come directly from soil bacteria instead of the soil?
Image credit: Obakeneko; via Wikimedia Commons

By Jeffrey Perkel, DXS tech editor

It’s no secret that America’s petroleum addiction is a problem in need of a solution. “Drill, baby, drill” notwithstanding, this country eventually will have to find a way to survive without low-cost oil – or at least, find another way to make it.


A recent MIT press release suggests one route to energy independence: soil bacteria. The release, Teaching a microbe to make fuel,” details a recent study from MIT graduate student Jingnan Lu, research scientist Christopher Brigham, and their lab director, Anthony Sinskey.

What Brigham, Lu, and their colleagues did was convince a soil bacterium called Ralstonia eutropha to turn carbon into gasoline –- specifically, the four-carbon molecules iso-butanol and 3-methyl-1-butanol.


Ralstonia eutropha bacteria in culture
How’d they do that? It was a simple matter of microbial engineering. As detailed in MIT’s description:
… in the microbe’s natural state, when its source of essential nutrients such as nitrate or phosphate is restricted, “it will go into carbon-storage mode,” [Brigham says,] essentially storing away food for later use when it senses that resources are limited. 
 “What it does is take whatever carbon is available, and stores it in the form of a polymer, which is similar in its properties to a lot of petroleum-based plastics,” Brigham says. By knocking out a few genes, inserting a gene from another organism and tinkering with the expression of other genes, Brigham and his colleagues were able to redirect the microbe to make fuel instead of plastic.

That last sentence makes the process sound easier than it was. It took a full year of work to effect that transformation, Brigham tells me, and no wonder: Bacteria don’t normally make gasoline. But they do make amino acids, the protein building blocks that all living things need to survive. The team realized that Ralstonia bacteria create one particular group of amino acids (the so-called branched-chain amino acids) using chemical intermediates that they could coopt to turn sugar into fuel.


To realize that potential, Brigham and his colleagues first had to get Ralstonia to refocus its energies, literally. When stressed, the bacteria store carbon in a polymer–a chain of molecules–called PHB. The bacterium executes this particular biochemical program extremely effectively, cranking out enough polymer to account for more than 80% of the cell’s mass. Brigham and Lu had to redirect that enzymatic zeal towards gasoline instead. So, they knocked out the genes involved in building PHB.


Next, they added some missing chemical pieces. I said earlier that the branched-chain amino acid pathway includes an intermediate that could be used to make gasoline. To do that, the cells need a missing bit of hardware — specifically, an enzyme to convert that chemical intermediate into something the gasoline-making enzymes can use. That enzyme is called KIVD, and Ralstonia does not make it. But another bacterium, Lactococcus lactis, does make it. Brigham and Lu borrowed the related bit of genetic material from Lactococcus lactis, expressed it in Ralstonia, and –- not much happened.

As University of California, Berkeley, biochemical engineer Jay Keasling explained to me, the cell in such situations is literally a chemical factory. For the factory to run smoothly, all the factory workers –- the enzymes -– need to be fully engaged at the right time. That won’t happen if one enzyme is cranking out lots of its product but others are not. Intermediate products will start piling up, reducing efficiency and potentially poisoning the cell.


In this case, with KIVD, the cells had all the necessary pieces to make gasoline. But they weren’t producing them at the same levels. In other words, the factory had more workers at one part of the assembly line than at others. As a result, productivity was relatively low (about 10 mg isobutanol per liter of culture). To boost that output, the researchers dialed up expression levels of several proteins to get them all in sync. They also shut down a handful of other chemical assembly lines, too, “carbon sinks” that could siphon off intermediates.


When all was said and done, the cells could produce about 310 mg of gasoline per liter of culture. That gas conveniently drifts into the culture medium surrounding the cells, from which it is easily extracted. Now, says Brigham, the trick is optimizing the process.


In the meantime, others are working towards the same goal. Researchers have considerable experience getting bacteria and yeast to produce compounds they don’t normally make — the antimalarial drug artemisinin, for instance -– and microbial biofuel development is a research target at the Joint BioEnergy Institute (headed by Keasling), Synthetic Genomics, and LS9, among other places.


Often, those biofuel strategies rely on plants to produce their starting materials. And that’s the really cool part about Sinskey’s work: Ralstonia can eat almost anything, Brigham says, from carbon dioxide and organic acids to fatty acids and sugar. Brigham envisions coupling these organisms to waste streams, such that they can suck out the nutrients and turn them into fuel, no plants required.


Garbage in, fuel out: Now that’s a microbial trick I can get behind. 


(If you’re interested, you can read Brigham and Lu’s work here.)


Image: Christopher Brigham / http://web.mit.edu/newsoffice/2012/genetically-modified-organism-can-turn-carbon-dioxide-into-fuel-0821.html

Historical Chemists Part II

If you have been watching tweets from @DoubleXSci since early December, you’ll have noticed tweets about Notable Historical and Modern Women in Science. Nearly 100 women were presented over twitter. Those women will be presented in a series here on the blog with the original tweeted links and information as well as with some additional information not able to be presented in 140 characters. We hope you look up more on these women. 


Leonora Neuffer Bilger was the 1953 Garvan Medal winner and a big influence at the University of Hawaii
(1893-1975) Dr. Bilger received her PhD in chemistry from the University of Cinncinnati in 1916. She graduated and went straight into a position as head of the chemistry department at Sweet Briar College. A brief stint at the University of Cinncinnati gave her skills that she later used in her position as Chair of the Department of Chemistry at the University of Hawaii to design a new chemistry laboratory facility. Her post as University of Hawaii Department Head began in 1943 and lasted 11 years. Her research was on asymmetric nitrogen compounds, for which she won the Garvan Medal. 

Nutritional Chemist Mary Letitia Caldwell was a role model and mentor over 6 decades
(1890-1972) Born in Bogota, Columbia of missionaries, she arrived in the U.S. to attend high school.  Dr. Caldwell was supported by her family in her pursuit of education and science. Due to gender restrictions, Caldwell attended a women’s college and stayed on there for teaching initially. This gave her the start on what she is known for: being a role model and mentor for other women for six decades. She received her A.B in 1913 from Western College for Women, her master’s degree in 1919 from Columbia, and her PhD in 1921 from Columbia, where she stayed on to teach. She entered the relatively new at the time field of nutritional chemistry, laying the groundwork for those after her. While Caldwell was well-known for the quality of research and diligence in her work, she also maintained a work-life balance, as an avid hiker, doting aunt, and gardener. 

Emma Perry Carr
Photo from Wikimedia Commons

Emma Perry Carr was a pioneer in UV spectroscopy and a beloved teacher

(1880-1972) Emma Perry Carr first attended Mr. Holyoke College then transferred to and received her B.S. from the University of Chicago in 1905. After a short duration as an instructor at Mt. Holyoke, Dr. Carr returned to the University of Chicago to receive her PhD in 1910. She returned to Mt. Holyoke to become a full professor and head of the department by the age of 33, a post she held for 33 years. Dr. Carr was also a devoted aunt,a fashionable dresser, and a talented storyteller. She had a relationship with Mary Sherrill, another professor at Mt. Holyoke, whom she shared a residence with for 26 years. Emma Perry Carr was the first recipient of the Garvan Medal.

Marie Sklodowska Curie
Photo from Wikimedia Commons

Physicist & Chemist Marie Sklodowska Curie was the first twice Nobel Prize laureate.  

(1867-1934) Much has been written about Marie Curie. She is, perhaps, the first historical figure to come to mind when a person says “Notable Woman in Science.” She is the first person to have been a twice Nobel Laureate. Marya Sklodowska was born in Poland, and lived through the loss of her eldest sister and mother by age 11. After graduating first her in class from high school, she attended a secret university because Polish universities could not admit women. She wished to go to Paris to study, so she worked and saved her money to do so. She was the first women to receive her Licence es Sciences Physiques from the Sorbonne in 1893, graduating first in her class again. She received her Licence es Sciences Mathematiques in 1894 from the same institution. In 1903, she attained her PhD from the University of Parish, the same year she was awarded the Nobel Prize in Physics. Difficulties continued in her personal life, such as the death of her husband in 1906, her own ill health due to radiation poisoning, and her constant fight for her place in her work. She broke so many barriers, being the first woman in so many circumstances. 

(1909-1997) Mary Feiser was encouraged by her parents to excel academically. She attended Bryn Mawr and received her B.S. in chemistry in 1930. She then attended Radcliffe college and worked on her master’s thesis in the lab of Louis F. Feiser at Harvard. She received her A.M. in 1931 and married in 1932. She opted to continue to work in her husband’s lab instead of pursue a PhD because of the funding and Harvard facilities. With her help, 15 papers and 17 books were published by Feiser. However, Harvard never granted her a salary nor official title for 29 years. Even at 85 years of age, Mary Feiser continued to write and publish organic chemistry books, which were well received.

(1876-1950) Dorothy Hahn received her B.A. in chemistry from Bryn Mawr and went to work at Mt. Holyoke College under the auspices of Emma Perry Carr. Together, the two women were a force producing many women chemists. While Dr. Carr ran the chemistry department, it is said Dr. Hahn ran the organic chemistry department. Dr. Hahn pursued and recieved her Ph.D. from Yale University in 1916 due to a fellowship from the AAUW (American Association of University Women). Hahn also preceeded well-known scientists Gilbert Lewis and Irving Langmuir on a theory of valence electrons. Professor Hahn was a huge influence on organic chemistry, teaching, and women in chemistry. 

Allene Rosalind Jeanes was a pioneering researcher with several patents.
(1906-1995) Allene Rosaland Jeanes was born and raised in Texas. She received her A.B with highest honors from Baylor University in 1928. She graduated with her M.A. from the University of California – Berkeley in 1929. She taught for awhile in a few different colleges, then decided to return to graduate school. She attained her PhD from the University of Illinois in 1938. While she wanted to go into pharmaceutical research, opportunities were limited. She took a position at the National Institute of Health. Her research took her through several government positions and had applications in the food industry. She was honored with many awards, including the Garvan Medal and Federal Women’s Award from the U.S. Civil Service Commission.

Nuclear Chemist Ellen Gleditsch was virtually unknown despite her accomplishments.
(1879-1968) The story of Ellen Gleditsch is not well known in her native Norway nor abroad, and signifies how difficult it was for women to be recognized for their work. She received her degree in pharmacology in 1902. She worked with Marie Curie for 5 years, and received her Licencee es Sciences from the Sorbonne in 1912. She went to work at Yale University despite the animosity toward her from the men at the U.S. institutions of Yale and Harvard and received her D.Sc. form Smith College in 1914. In 1929, Oslo University became embroiled in controversy over the decision to advance Ellen Gleditsch to the position of professional chair, and it took a letter from Marie Curie to help quell the public outrage. During her time in Oslo, she also provided a home for scientists fleeing Nazi Germany. She continued to be an advocate and mentor for women in the sciences until her death at age 88.

(1912-1998) Born in Missouri, Anna Jane Harrison was raised on a farm and her childhood science education tended to be “go out and find caterpillars.” She learned about Caterpillar tractors from her father for that assignment. Her high school science teachers inspired her interest in science, so she went to the University of Missouri to earn a B.A. in chemistry in 1933, a B.S. in education in 1935, a M.A. in chemistry in 1937, and a Ph.D. in physical chemistry in 1940. She was the first woman to earn a PhD at the institution. After meeting Lucy Picket and Emma Carr at a meeting of the American Chemical Society (ACS), she went on to work at Mt. Holyoke College, carrying on the traditions established there by Emma Carr and Dorothy Hahn. She also has several more “firsts” including being the first woman to chair the Division of Chemical Education of the ACS and the first woman elected president of the ACS in the 102 year history of the organization up to then. She was honored with the honorary degree of D.Sc. from ten instutitions. She enjoyed traveling and once stated, “What I really like is to go places one isn’t supposed to go.”

Mentioned Awards
The Garvan Medal is an award from the American Chemical Society to recognize distinguished service to chemistry by women chemists.
Nobel Prize: From the site: 
Every year since 1901 the Nobel Prize has been awarded for achievements in physics, chemistry, physiology or medicine, literature and for peace. The Nobel Prize is an international award administered by the Nobel Foundation in Stockholm, Sweden. In 1968, Sveriges Riksbank established The Sveriges Riksbank Prize in Economic Sciences in Memory of Alfred Nobel, founder of the Nobel Prize. Each prize consists of a medal, personal diploma, and a cash award.

Federal Women’s Award from the U.S. Civil Service Commission was awarded to a woman for a high level of scientific achievement.