The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.
The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.
Big Molecules with Small Building Blocks
The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.
We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.
When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.
Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.
The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.
Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.
On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.
The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!
If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.
The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?
If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.
In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.
Sugar and Fuel
A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.
Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.
Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.
Polysaccharides: Fuel and Form
Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.
Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.
Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.
Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.
The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.
Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.
The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.
That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.
These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.
Lipids: The Fatty Trifecta
Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.
Fats: the Good, the Bad, the Neutral
Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?
Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.
Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.
Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.
Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.
The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.
You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.
In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.
A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.
Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.
Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.
Phospholipids: An Abundant Fat
You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.
Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.
There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.
Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.
The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.
Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.
Steroids: Here to Pump You Up?
Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.
But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.
Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.
Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.
As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.
Levels of Structure
Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.
For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.
This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.
Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.
The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.
In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.
A Plethora of Purposes
What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.
As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.
How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.
Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.
DNA vs. RNA: A Matter of Structure
DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.
So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.
RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.
DNA vs. RNA: Function Wars
An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.
These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.
RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.
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.
Nope. This island does not represent your genes. (Source)
When you read news stories about what affects a developing human in the womb or how cancer or obesity arises, you probably also see references to genes and environment. Some articles may focus on genes versus environment, or mention that something is “mostly” genetic or that the “environment” contributes to a disorder or trait in some way. What some people may not realize is that “environment” to a scientist talking about genetics may be something very different from “environment” to a non-scientist reading a news article. While a scientist may be vividly imagining a bustling microenvironment of native molecules in the way only scientists seem to do, the general reader may simply be thinking about “toxins” or “chemicals.” That’s why Double X Science is here to help with a primer on what those scientist types may mean when they talk about genes and environment. See how useful we are? Tell your friends! (Speaking of environmental influences… ). Where does environment begin and end? Let’s begin at the end No gene is an island. Your genes consist in part of a special codethat is really an instruction manual. Your cellsrely on internal translators to decode these instructions and use them as a guide to make various proteins, the molecules that give your cells, tissues, organs, organ systems, and you much of their structure and function. Proteins do thousands of jobs, from breaking down food to building and replacing tissues (news release) to governing cell division. Most of your cells are engaged in making proteins, a complex, exquisitely regulated and multi-step process. But they don’t do it in a vacuum. That code the cell uses to build the protein? That instruction manual is susceptible to all kinds of interference. Pages get torn out or folded over or stuck together. The words of the code can be changed, sometimes subtly, sometimes unmistakably, and all kinds of factors can jumble up those words so that cell ends up making a protein that isn’t quite what was intended. It’s even possible to use the cellular version of Liquid Paper(TM) to mask the code so that the cell doesn’t recognize its existence. Sometimes, these changes have no observable effect. Sometimes, they have big bad effects, such as disease, or helpful outcomes, such as disease resistance. That code sits in a cell in a body (you) made of trillions of cells doing hundreds of different jobs, taking in things from the environment, playing host to millions of other organisms (themselves an environment), altering and shifting with every passing second as the whole system works to keep you together and functioning within certain acceptable limits for human life. All of these processes can influence the code, leading the cell to use it, change it, use only certain parts of it, Liquid Paper over it, tweak what results from its instructions, or just ignore it. It’s impossible for any code in that situation to function in the total absence of influence from its environment, in part because the code itself is just the beginning. Much of the environment’s influence is reflected in what the cell does with the instructions, not just what the instructions say. This multitude of environmental influences is one reason that even people with identical genetic codes can have differences in diseases we think of as being largely genetic. No gene–no code–is an island. You are not your genes. You are your genes and your environment. No nucleus is an island. Most of our genes are packaged neatly with the rest of our DNA around molecular spools inside a cellular vault called the nucleus. This vault is a choosy sentry, letting in only certain molecules carrying proper ID. Yet inside the nucleus, there is an environment. This environment is not “toxins” or “chemicals,” the things that many people probably think of when someone says “environment” and talks about genes. But it is a busy place with its own milieu. Some parts of the code are in use, some sit quiet, and many molecules bustle and hustle to maintain, copy, process, or protect these important instructions. Every little bit of this hustle and bustle can influence some aspect of what happens to a code in the nucleus, interfering with or enhancing its use or resulting in accidental changes that may have big effects further down the line. The nucleus is the final stop in the chain of environmental influence, wherever that influence may originate. No cell is an island. Outside of that vault is the big, wide world of the cell. The cell is the molecular version of a busy metropolis (see beautiful video, The Inner Life of the Cell, below), a complex system of cellular highways that the cell uses to deliver packages internally, take in deliveries from the outside world, and transfer the millions of molecules it’s using and making to the right places at the right time. There’s a generator, a recycling center, guards at the gate, and a protein production facility and processing plant, complete with a post office. And that cell sits in an environment, usually, of many many other cells, also busy with their duties. What happens outside of that cell affects the inside of the cell, altering traffic flows, protein production and packaging, signaling and delivery along the routes, and, ultimately, processes inside the vault called the nucleus, the final destination in the chain of environmental effects. From outside the cell, through the cell, and to the nucleus, every step along the way is one that environment can affect, all the way down to what the cell does with its genes–the codes–for the proteins it makes.
No tissue or organ is an island. A lot of cells working together to do the same thing in your body make up a tissue. Tissues combined together to perform a function are an organ. Let’s take the organ named after living, the liver. It keeps you alive by filtering your blood and reconstructing substances that might harm your cells into less-harmful compounds. Just about everything you ingest gets passed through here. When the liver takes up something like ethanol, the alcohol we ingest at wine o’ clock, and gets to work making it less awful for your body, guess what does that work? The cells that make up the liver. The liver’s environment is their environment is each individual cell’s environment, and eventually, the influence will pass to the nucleus, the final destination in the chain of environmental influence, where the code lies. You are not an island. And whatever you encounter in this world may well influence you right down to the level of your genes. But while many people might think of “toxins” or “chemicals” when they think of environmental influences on genes, your chemical exposures–and chemicals include oxygen, water, body fluids, nutrients and not-so-nutrients in your foods, medications you may take–are among many, many examples of environmental factors that may reach via a chain reaction all the way to your genes. Some of these factors affect your genes by way of your sensory system: A hug, an angry encounter, a sick child, a laugh with a friend–you respond to each of these environmental influences, often by way of hormones that have a chat with your cells. Your cells respond by adjusting how they use the code in the nucleus so that in the face of anger or love or worry, your body still functions within the essential parameters of life. Below, we list with tongue slightly in cheek a sampling of other factors that constitute an “environment” that could influence your genes and how your cell uses them and the proteins they encode. Whether you know it or not, you’re encountering a million factors every day, big and small, that may trigger some effect way down there in the nuclear vaults of your cells, one that reverberates body wide. Some examples of “environment” that might influence genes Environmental influence on genes and how your cells use their instructions and the resulting proteins can come from almost anywhere, any factor, from outside of you and within you. It’s not just about exposures to “bad” chemicals or “toxins.” While the list of potential environmental factors influencing genes and how the cell uses them is practically infinite, we give you just a few examples for thought below:
Your parents, siblings, friends, extended family, co-workers, soccer team–you know, other people
Jeanne, would you like some…peeeaaasss? License information here.
I was seven weeks deep when it hit me. Suddenly, I was in a chronic state of queasiness. Under most circumstances, I had it under control. Sure, I would gag every time I brushed my teeth, but (mostly) I could keep it all down. Then I went to my aunt Diane’s house for dinner.
Aunt Diane rolls with a crowd of self-made Italian chefs and, as a result, most of her cooking falls under the “rustic Italian” umbrella. It is not uncommon to see sitting in her cupboard a massive inventory of jarred plum tomatoes or for an entire section of her freezer to be dedicated to homemade vodka sauce, always frozen in those takeaway containers that originally brought us egg drop soup. Under normal circumstances, I’d be psyched to eat over.
I don’t recall the entire menu, but there is one side dish that has been forever burned into memory, and not in a good way. I remember starring at my plate, specifically at the heaping pile of sautéed peas. I kept rearranging the peas on my plate, sometimes spreading them out, sometimes piling them up. Then Diane looked at me and excitedly asked, “Jeanne, did you try my peas? I made them just for you!” I don’t know what compelled her to make these peas for me. Perhaps it was because I am a vegetarian and the rest of the meal involved meat? But, there they were, staring me down, and there Diane was, watching with anticipation, waiting for my approval.
Because I adore my aunt Diane and I wanted to make her happy (after all, she did just cook an entire meal for my small family), I scooped up a moderate amount of peas with my fork and deposited them in my mouth. I had to use every fiber of my being to chew them, and even more effort to actually swallow. My body was not cooperating and I had to implement a state of near meditation to keep them from coming back up. Luckily, I kept my cool and was able coerce my face into showing a smile while simultaneously telling my aunt and friend that her peas were delicious.
Credit: Jeanne Garbarino.
My husband picked up on my soaring level of discomfort and without missing a beat, ate all my peas when Diane wasn’t looking. We ended the evening with my stomach contents intact, but barely.
The next morning, as I was preparing my 18 month-old daughter’s daycare lunch, I remembered that we were provided with a parting gift of sautéed peas. I took them out of the fridge and proceeded to aliquot them into containers more suitable for a toddler. As I removed the lid, the onion-tinged aroma of Diane’s sautéed spring peas smacked me across my face. My body was clearly angry about what I had done to it the night before and, as if it were in a state of protest, I found myself sprinting to the bathroom where I began to puke.
From that day forth, I could not eat peas, let alone see or smell them, without eliciting extreme nausea. It didn’t matter what time of day, the mere presence of peas, although not necessary, was sufficient to make me toss my, well, peas.
It has long been known that nausea and vomiting are common symptoms of pregnancy. In fact, documentation of this phenomenon goes as far back as 2000 BC. However, the term “morning sickness” is a complete misnomer. For one, pregnancy-related nausea and vomiting is not just a morning thing. It can happen at any time of day. Second, the term “sickness” suggests a state of unhealthiness. We know that perfectly healthy pregnant women who deliver perfectly healthy babies experience morning sickness, and this type of nausea and vomiting is not an indicator of maternal and/or fetal health.
But, that doesn’t change the fact that it sucks.
Morning sickness, more appropriately known as nausea and vomiting in pregnancy (NVP), affects approximately two-thirds of women in their first trimester of pregnancy. In many cases, morning sickness subsides at the end of the first trimester. In other cases, the symptoms of morning sickness can last for the entire pregnancy. For both my pregnancies, I experienced morning sickness for the first 5 months.
I feel so lucky.
No one really knows the exact mechanisms responsible for the onset morning sickness. We do know that the drastic hormonal changes that occur during early pregnancy certainly play a role; however, these effects are likely indirect. For instance, estrogen levels do not differ between pregnant women with morning sickness and those who do not experience symptoms. Furthermore, there is no causal relationship between human chorionic gonadotropin (hCG), the early pregnancy hormone detected by pregnancy tests, and morning sickness, despite the fact that peak hCG levels and peak severity of pregnancy-related nausea and vomiting occur at approximately the same time.
Based on these observations, scientists suggest that the hormonal fluctuations in pregnant women can elicit different responses in an individual, rendering some extremely susceptible and others remarkably resistant to the same stimulus (with regard to nausea and vomiting). This begs the question: Is there a genetic predisposition to morning sickness?
While a “morning sickness” gene has not been identified, a few lines of evidence point toward a potential for inheriting the tendency. For instance, identical twins, are fairly likely to share a tendency to morning sickness. Also, you are more likely to experience morning sickness if your mom experienced it, too. Even though genetics may be involved, the onset of morning sickness is probably what scientists call “multifactorial,” a result of a very complex interaction between genetics and environment, making it difficult to find a treatment that is effective and safe for everyone.
Until more is known, we are stuck eating saltines and sour candy. At least it’s something, right?
Food aversions and morning sickness
Make them if you dare. Credit: Jeanne Garbarino.
For my first pregnancy, it was smoked salmon, which I probably shouldn’t have been eating in the first place. For my second pregnancy, it was peas. (Interestingly, my aunt Diane initially provided both foods, which, after that initial consumption, was immediately followed by the onset of morning sickness.) The mere sight of either peas or smoked salmon elicited an uncomfortable queasiness that often culminated with a sprint to the porcelain throne. Apparently, this type of experience is pretty normal.
Developing an aversion to a specific tastes and smells during pregnancy is an extremely common phenomenon. In fact, between 50–90% of pregnant women worldwide experience some level of food aversion, with the most common aversions being meat, fish, poultry, and eggs. Furthermore, research suggests that food aversions developed during pregnancy are actually novel as opposed to an exaggeration of a pre-existing dislike for a certain food.
Complementing the development of food aversions is the report that dietary changes in pregnant woman are often related to changes in olfaction, or sense of smell. More specifically, some pregnant women experience increased sensitivity to certain odors, and usually in an unpleasant way. This heightened sensitivity is thought to be protective against foods that could pose a problem for mother and baby, such as those that have become rancid.
When I was pregnant, the self-perceived powerfully pungent scent of peas could have probably knocked me over if it was translated into some other physical force. I wish I had a gas mask.
Is there some benefit to morning sickness?
In general, nausea and vomiting are a defense mechanism, acting to protect us from the accidental ingestion of toxins. While morning sickness is likely a very complicated condition that needs further study, a popular explanation suggests that morning sickness is beneficial to both mother and fetus.
Several lines of observations support this idea, formally called the “maternal and embryo protection hypothesis”: (a) peak sensitivity to morning sickness occurs at approximately the same time that embryo development is most susceptible to toxins and chemical agents; and (b) women who experience morning sickness during their pregnancy are less likely to miscarry compared to women who do not experience morning sickness.
In essence, the maternal and embryo protection hypothesis suggests that morning sickness is an adaptive process, contributing to evolutionary success (measured in terms of how many of your genes are present in later generations). However, morning sickness is not found in all societies. One possible explanation for this is that those societies that do not widely experience morning sickness are significantly more likely to have plant-based diets (meats spoil much faster than plants). Another argument against evolutionary adaptation is that morning sickness has been documented only in three other species: domestic dogs, captive rhesus macaques, and captive chimpanzees.
It makes sense that the pregnancy-related nausea and vomiting widely known as morning sickness is a means to help protect mom and baby. It makes sense that women have a mechanism to detect and/or expel toxins and potentially harmful microorganisms if ingested. But the idea that morning sickness is actually a product of evolution is still under debate.
And even as a biologist, if I ever have to go through morning sickness again, the idea that it could be protective won’t really bring me comfort as I am puking up my guts. But, biology is biology and sometimes we just have to deal with it.
Andrews, P. and Whitehead, S. Pregnancy Sickness. American Physiological Society. 1990 February;5: 5-10.
Flaxman, S.M. and Sherman, P.W. Morning Sickness: A mechanism for protecting mother and baby. The Quarterly Review of Biology. 2000 June; 75(2):
Goodwin, TM. Nausea and vomiting of pregnancy: an obstetric syndrome. American Journal Obstetrics and Gynecology. 2002; 185(5): 184-189.
Kich, K.L. Gastrointestinal factors in nausea and vomiting of pregnancy. American Journal Obstetrics and Gynecology. 2002; 185(5): 198-203.
Nordin, S., Broman, D.A., Olofsson, J.K., Wulff, M. A Longitudinal Descriptive Study of Self-reported Abnormal Smell and Taste Perception in Pregnant Women. Chemical Senses. 2004; 29 (5): 391-402
Have you seen the headlines? Skip them You’ve probably seen a lot of headlines lately about autism and various behaviors, ways of being, or “toxins” that, the headlines tell you, are “linked” to it. Maybe you’re considering having a child and are mentally tallying up the various risk factors you have as a parent. Perhaps you have a child with autism and are now looking back, loaded with guilt that you ate high-fructose corn syrup or were overweight or too old or too near a freeway or not something enough that led to your child’s autism. Maybe you’re an autistic adult who’s getting a little tired of reading in these stories about how you don’t exist or how using these “risk factors” might help the world reduce the number of people who are like you. Here’s the bottom line: No one knows precisely what causes the extremely diverse developmental difference we call autism. Research from around the world suggests a strong genetic component[PDF]. What headlines in the United States call an “epidemic” is, in all likelihood, largely attributable to expanded diagnostic inclusion, better identification, and, ironically, greater awareness of autism. In countries that have been able to assess overall population prevalence, such as the UK, rates seem to have held steady at about 1% for decades, which is about the current levels now identified among 8-year-olds in the United States. What anyone needs when it comes to headlines honking about a “link” to a specific condition is a mental checklist of what the article–and whatever research underlies it–is really saying. Previously, we brought you Real vs Fake Science: How to tell them apart. Now we bring you our Double X Double-Take checklist. Use it when you read any story about scientific research and human health, medicine, biology, or genetics. The Double X Double-Take: What to do when reading science in the news 1. Skip the headline. Headlines are often misleading, at best, and can be wildly inaccurate. Forget about the headline. Pretend you never even saw the headline. 2. What is the basis of the article? Science news originates from several places. Often it’s a scientific paper. These papers come in several varieties. The ones that report a real study–lots of people or mice or flies, lots of data, lots of analysis, a hypothesis tested, statistics done–is considered “original research.” Those papers are the only ones that are genuinely original scientific studies. Words to watch for–terms that suggest no original research at all–are “review,” “editorial,” “perspective,” “commentary,” “case study” (these typically involve one or only a handful of cases, so no statistical analysis), and “meta-analysis.” None of these represents original findings from a scientific study. All but the last two are opinion. Also watch for “scientific meeting” and “conference.” That means that this information was presented without peer review at a scientific meeting. It hasn’t been vetted in any way. 3. Look at the words in the article. If what you’re reading contains words like “link,” “association,” “correlation,” or “risk,” then what the article is describing is a mathematical association between one thing (e.g., autism) and another (e.g., eating ice cream). It is likely not describing a biological connection between the two. In fact, popular articles seem to very rarely even cover scientific research that homes in on the biological connections. Why? Because these findings usually come in little bits and pieces that over time–often quite a bit of time–build into a larger picture showing a biological pathway by which Variable 1 leads to Outcome A. That’s not generally a process that’s particularly newsworthy, and the pathways can be both too specific and extremely confusing. 4. Look at the original source of the information. Google is your friend. Is the original source a scientific journal? At the very least, especially for original research, the abstract will be freely available. A news story based on a journal paper should provide a link to that abstract, but many, many news outlets do not do this–a huge disservice to the interested, engaged reader. At any rate, the article probably includes the name of a paper author and the journal of publication, and a quick Google search on both terms along with the subject (e.g., autism) will often find you the paper. If all you find is a news release about the paper–at outlets like ScienceDaily or PhysOrg–you are reading marketing materials. Period. And if there is no mention of publication in a journal, be very, very cautious in your interpretation of what’s being reported. 5. Remember that every single person involved in what you’re reading has a dog in the hunt. The news outlet wants clicks. For that reason, the reporter needs clicks. The researchers probably want attention to their research. The institutions where the researchers do their research want attention, prestige, and money. A Website may be trying to scare you into buying what they’re selling. Some people are not above using “sexy” science topics to achieve all of the above. Caveat lector. 6. Ask a scientist. Twitter abounds with scientists and sciencey types who may be able to evaluate an article for you. I receive daily requests via email, Facebook, and Twitter for exactly that assistance, and I’m glad to provide it. Seriously, ask a scientist. You’ll find it hard to get us to shut up. We do science because we really, really like it. It sure ain’t for the money. [Edited to add: But see also an important caveat and an important suggestion from Maggie Koerth-Baker over at Boing Boing and, as David Bradley has noted over at ScienceBase, always remember #5 on this list when applying #6.] —————————————————————————– Case Study Lately, everyone seems to be using “autism” as a way to draw eyeballs to their work. Below, I’m giving my own case study of exactly that phenomenon as an example of how to apply this checklist. 1. Headline: “Ten chemicals most likely to cause autism and learning disabilities” and “Could autism be caused by one of these 10 chemicals?” Double X Double-Take 1: Skip the headline. Check. Especially advisable as there is not one iota of information about “cause” involved here. 2. What is the basis of the article? Editorial. Conference. In other words, those 10 chemicals aren’t something researchers identified in careful studies as having a link to autism but instead are a list of suspects the editorial writers derived, a list that they’d developed two years ago at the mentioned conference. 3. Look at the words in the articles. Suspected. Suggesting a link. In other words, what you’re reading below those headlines does not involve studies linking anything to autism. Instead, it’s based on an editorial listing 10 compounds [PDF] that the editorial authors suspect might have something to do with autism (NB: Both linked stories completely gloss over the fact that most experts attribute the rise in autism diagnoses to changing and expanded diagnostic criteria, a shift in diagnosis from other categories to autism, and greater recognition and awareness–i.e., not to genetic changes or environmental factors. The editorial does the same). The authors do not provide citations for studies that link each chemical cited to autism itself, and the editorial itself is not focused on autism, per se, but on “neurodevelopmental” derailments in general. 4. Look at the original source of information. The source of the articles is an editorial, as noted. But one of these articles also provides a link to an actual research paper. The paper doesn’t even address any of the “top 10” chemicals listed but instead is about cigarette smoking. News stories about this study describe it as linking smoking during pregnancy and autism. Yet the study abstract states that they did not identify a link, saying “We found a null association between maternal smoking and pregnancy in ASDs and the possibility of an association with a higher-functioning ASD subgroup was suggested.” In other words: No link between smoking and autism. But the headlines and how the articles are written would lead you to believe otherwise. 5. Remember that every single person involved has a dog in this hunt. Read with a critical eye. Ask yourself, what are people saying vs what real support exists for their assertions? Who stands to gain and in what way from having this information publicized? Think about the current culture–does the article or the research drag in “hot” topics (autism, obesity, fats, high-fructose corn syrup, “toxins,” Kim Kardashian) without any real basis for doing so? 6. Ask a scientist. Why, yes, I am a scientist, so I’ll respond. My field of research for 10 years happens to have been endocrine-disrupting compounds. I’ve seen literally one drop of a compound dissolved in a trillion drops of solvent shift development of a turtle from male to female. I’ve seen the negative embryonic effects of pesticides and an over-the-counter antihistamine on penile development in mice. I know well the literature that runs to the thousands of pages indicating that we’ve got a lot of chemicals around us and in us that can have profound influences during sensitive periods of development, depending on timing, dose, species, and what other compounds may be involved. Endocrine disruptors or “toxins” are a complex group with complex interactions and effects and can’t be treated as a monolith any more than autism should be. What I also know is that synthetic endocrine-disruptors have been around for more than a century and that natural ones for far, far longer. Do I think that the “top 10” chemicals require closer investigation and regulation? Yes. But not because I think they’re causative in some autism “epidemic.” We’ve got sufficiently compelling evidence of their harm already without trying to use “autism” as a marketing tool to draw attention to them. Just as a couple of examples: If coal-burning pollution (i.e., mercury) were causative in autism, I’d expect some evidence of high rates in, say, Victorian London, where the average household burned 11 tons of coal a year. If modern lead exposures were causative, I’d be expecting records from notoriously lead-burdened ancient Rome containing descriptions of the autism epidemic that surely took it over. Bottom line: We’ve got plenty of reasons for concern about the developmental effects of the compounds on this list. But we’ve got very limited reasons to make autism a focal point for testing them. Using the Double X Double-Take checklist helps demonstrate that. By Emily Willingham, DXS managing editor
It’s that time of the year in the U.S. – when we blow up pretty bombs in celebration of the approval of the Declaration of Independence, declaring the independence from the Kingdom of Great Britain. Around this time of year, there is no dearth of articles about the chemistry of fireworks, but the chemistry editor here could not let her secret love of this topic pass by.
What is an explosive? An explosive is a combination of materials that when reacted produce an abundance of light, sound, heat, and pressure. A firework encompasses all 4 of those: we are familiar with the light – the whole reason we view fireworks, we are familiar with the sound – the boom that follows especially large displays, we are familiar with the pressure if we are close enough – that’s the force that pushes into you and the “shock wave” pictured in movies after large explosions; and we are familiar with the heat – ever held a sparkler?
There are three main types of explosives: chemical, nuclear, and mechanical. The bulk of this post will focus on chemical explosives with a short bit about nuclear and mechanical.
If we start at the beginning – well, we’ll skip to the “accepted” first explosive – black powder. Black powder, also called gun powder and the precursor to fireworks, is coined a chemical explosive. Chemical explosions generally fall into a specific classification of chemical reactions called oxidation.
The earliest definition of oxidation was the addition of the element oxygen to a compound, also called combustion. Due to limits of this definition, it was later changed to be the loss of electrons from an element (within a compound.) The original definition can easily be shown in terms of explosives. The simple mixing of hydrogen and oxygen with the addition of just a bit of heat, will form water in an explosive display:
2H2 + O2 –> 2H2O
The little flame used to catalyze the reaction in the video is actually much more energy than is necessary to cause this reaction to occur, but it’s difficult to get an even littler source of heat and safely demonstrate this reaction. You might also note a lot more energy comes out of that reaction once started in terms of light and heat and sound. I’ve been the one lighting that reaction in a demo without both ears plugged and I couldn’t hear out of one ear for the rest of the lecture.
If we focus on the loss of electrons version of oxidation, we get specific colors. This is what the flame video by The Fabulab focused on in their entry for Alan Alda’s Flame Challenge. I direct your attention to 1:08 and the discussion of electrons.
Metals are the simplest example (and most used) example of oxidation as the loss of electrons and the color change associated. Because some electrons are lost, we now have a different set of electrons changing energy and a different color appears.
From here, it is easy to see how fireworks fall into this category of explosives. Fireworks are always being further refined to produce a specific set of light and sound. For a bit more information, this video gets fairly specific.
The vast majority of explosives in use today are considered chemical explosives. This covers a range of materials, including the aforementioned black powder and fireworks, nitroglycerin, dynamite, plastic explosives (C4 for Mythbusters and sci-fi television show fans), and the ones with water now restricting the amount of water one is allowed to bring onto an airplane in the U.S.
Another type of explosive is a nuclearexplosive. The energy in these explosives come from a nuclear reaction. Wikipedia differentiates types of nuclear explosions into stellar and man-made. Another way to differentiate nuclear reactions is by fission and fusion. The explosions at the heart of stars fall under nuclear fusion and are called stellar nucleosynthesis.
Nuclear fusion is the process of forcing 2 atoms into 1 new, larger atom. The CNO cycle, diagrammed here, is one of the nuclear fusion reactions occurring in stellar nucleosynthesis.
Nuclear fission is the process involved in nuclear weapons.
Nuclear fission is the process of dividing an atom into 2 or more smaller atoms. In both nuclear fusion and nuclear fission processes, specific types of radiation are emitted because the new atoms produced do not have the same energy as the starting material. The radiation emitted in these reactions is not just from a change of electrons but from a change from the nucleus of the atom. This emission of radiation is part of the light and heat from the sun and the light and heat of a nuclear bomb.
The third and last type of explosive I will cover is a mechanicalexplosive. These explosions occur as a purely physical process, but can then incite a chemical explosion. Mechanical explosions occur due to a sudden release of a build up of pressure. A specific kind of these explosions are under conditions where a liquid is pressurized in a vessel and a rupture brings it above its boiling point, called a boiling liquid expanding vapor explosion, BLEVE. Steam powered trains were sometimes damaged by these type of explosions. An explosion of a water heater falls into this category. Mechanical explosions are the rarest and perhaps least covered types of explosives.
Water heater explosion by the Mythbusters.
These views are the opinion of the author and do not necessarily either reflect or disagree with those of the DXS editorial team.
It’s not easy being green. First, you have decide which green to be. (Source)
[We at Double X Science had been considering a “toxins” post but then found the following post by Jennifer Mo, a happily childfree vegetarian who lives in California with a cat named Brie but variously nicknamed Walnut “for her brain capacity” or Toxokitty for her history of toxoplasmosis–which, as it turns out, turns up in Jennifer’s guest post, below. This post first appeared at Jennifer’s blog, It’s Not Easy to Be Green, where she writes about environmental issues as a “rationalist and a pragmatist.” You can also follow Jennifer on Twitter @noteasy2begreen. We appreciated the pragmatics of this particular post quite a bit and thank Jennifer for allowing us to host it at Double X Science. We are particularly taken with the fact that she asks if we’d ever wanted to call our own brain a troglodyte.]
It’s a common demand from the public to scientists: prove to us something is safe before unleashing your monster on the world. And on one hand, it’s a totally fair, reasonable request to not be treated as lab rats. I get that. I hate the idea of having big chemical corporations profiting off their creations that create long term problems for ordinary people and the environment. On the other, whether you’re talking about GMOs or synthetic chemicals, it’s a problematic request for a couple of key reasons:
It assumes a binary between safe and unsafe without regard to exposure level or other circumstances. Just about everything can be harmful under the right (or perhaps I should say wrong?) conditions. Take water, for example.TonsContinue reading →
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
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