100 Years

By Adrienne M. Roehrich, Chemistry Editor

Photo of the author with her 100 year old grandmother 10-1-2012

100 is such a nice round number. 

Should I start with a disclaimer? I’m a chemist, not a biologist. Perhaps I should leave a post on centenarians to the biologists, but I have a vested interest in the topic. On October 1 of this year, my grandmother turned 100, so I’ve been a little obsessed with living until 100. In the United States, an estimated 1 in 4400 people reach the age of 100 and the highest number worldwide. The next highest number of centenarians reside in Japan, with a rate of 1 in 3500 people. 

The question is, why do these people live so long? This is a highly studied question. When one delves into the literature, as with most questions, there is no simple answer and often studies conflict with each other. There are different modes of study: some scientists study those who have become centenarians to try to determine what they have done to reach this rare milestone while other scientists work in theories, then animal models to study what pathways lead to longevity.

Studies have found that healthy centenarians in some areas have high levels of vitamin A and vitamin E1 and higher red blood cell glutathione reductase and catalase activities.2,3 But the presence of higher levels of these vitamins and glutathione reductase is not present in all centenarians, and the mere presence of these high levels does not necessarily indicate longevity.

 

Molecules that may or may not help longevity

You may have heard exclamations about antioxidants or calorie restriction. While antioxidants (the aforementioned vitamin A and vitamin E) are known to protect the body from the harmful effects of free-radicals, which occur in the normal processes of the body, evidence does not support that simply adding more antioxidants to the diet will slow aging. There are studies also showing that calorie restriction may have beneficial effects in terms of markers of aging in some animals, but many animals that are commonly used as human models do not extend longevity under calorie restriction, and such a course of action may have deleterious effects. The safety and benefits of long-term calorie restriction is currently unknown. Scientists are working towards answering these questions. 

Genetics plays an important role. The best predictor of a person reaching 100 is having a sibling live past 100. Variations in genes abound, but other than children of long-lived parents living longer, specifics are elusive. Oddly, being born in the Fall (September through November) is linked with a higher likelihood of becoming a centenarian.4 And functional independence for a longer period of time (past the age of 90) was found to be strongly correlated to centenarians. 90% of the participants in the New England Centenarian study were found to have been so.

Hormones are integral to our body function and have been studied for their potential pathways in longevity. Testosterone has been focused on, and lately a study of Korean eunuchs gave a higher rate of centenarians, 3 in 81 individuals. Due to the wide variability of the amount of testosterone produced by individuals, whether more or less testosterone exposure is beneficial or deleterious is unknown. 

What causes aging? This question is so important the National Institutes of Health (NIH) has devoted National Institute on Aging, the leading research institute on aging. A summary in more detail than I have gone into here is given on the NIH NIA’s site about preventing aging

If we look at the cellular level, scientists discovered that complete copying of DNA is dictated by telomeres and the enzyme telomerase, which earned 3 scientists the Nobel Prize in Physiology and Medicine in 2009. The unique DNA sequence in the telomeres protects chromosomes from degradation. When telomeres are shortened, cells age. Eventually, the telomeres will shorten, and cells will age and die. Unfortunately, extending telomeres or increasing the activity of telomerase enzyme does not help anti-aging, it contributes towards the growth of cancerous cells. 

A conversation with Dr. Mark D Johnson on twitter gave me these neat facts: Complete natural Homo sapiens LifeSpan = 120 years! All mammals except humans, bonobos, and chimpanzees, live six times their growth cycle. We grow within 20 years. That means natural mammal lifespan of 120. 

Overall, the contributing factors towards ageing and longevity are deemed to be complicated and there is no short-order anti-aging remedy.

Turning more towards my own field of expertise, the Maillard Reaction, a chemical reaction that makes cooked food tasty, also turns 100. Obviously, the actual chemical reaction goes back longer than 100 years – to when amino acids began to react with sugars at elevated temperatures. However, the French chemist Louis-Camille Maillard first reported the nature of these reactions in 1912.5 Maillard chemistry not only describes the molecules in baked bread, grilled veggies, and brewing of beer, but also other molecules as products, so many that chemists did not study Maillard chemistry in detail until World War II. Nearly 60 years ago, African American chemist John E. Hodge reported a mechanism for the Maillard reaction6

Hodge’s Flowchart of the Maillard Reaction
Products of the Maillard reaction range from molecules that are both welcome and abhorrent. The usually enjoyed flavor and aroma of roasted coffee is a product of the Maillard reaction, as is the char on the surface of grilled food which is considered to be carcinogenic. 

Roasted Coffee Beans, photo by Adrienne Roehrich
Grilled Yams, photo by Adrienne Roehrich

Do you know someone or something that has reached the anniversary of 100 years on this earth? 


References:
(1) Mecocci, P.; Polidori, M. C.; Troiano, L.; Cherubini, A.; Cecchetti, R.; Pini, G.; Straatman, M.; Monti, D.; Stahl, W.; Sies, H.; Franceschi, C.; Senin, U. Free Radical Biology and Medicine 2000, 28, 1243.
(2) Klapcinska, B.; Derejczyk, J.; Wieczorowska-Tobis, K.; Sobczak, A.; Sadowska-Krepa, E.; Danch, A. Acta Biochimica Ponoica 2000, 47, 281.
(3) Andersen, H. R.; Jeune, B.; Nybo, H.; Neilsen, J. B.; Andersen-Randberg, K.; Grandjean, P. Age and Ageing 1998, 27, 643.
(4) Journal of Aging Research 2011, 2011.
(5) Maillard, L.-C. Comp. Rend. 1912, 66.
(6) Hodge, J. E. Journal of Agricultural and Food Chemistry 1953, 1, 928.

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

Pregnancy 101: The science behind the wand of destiny


You hold a stick in your hands, one that you’ve just peed on. It foretells a future of sorts, for you. But the magic behind that stick is really all about a biochemical sandwich and a scientific test named ELISA.

By Jeanne Garbarino, DXS Editor

OH MY GOD OH MY GOD OH MY GOD OH MY GOD OH MY GOD OH MY GOD

Over and over again, that was all I could say.  At the same time, I heard my husband on the other side of the bathroom door, in a very panicked voice asking, “Why are you saying oh my god? WHAY ARE YOU SAYING OH MY GOD?!?!” 

Though, he really knew why.

The events immediately preceding our synchronous freak out session involved unwrapping a small plastic wand, removing its lilac cap, and subsequently inserting its absorbent tip into my stream of pee. Yes, folks, we are talking about the wand of destiny that is the pregnancy test.

Shortly after that lucky sperm cell unites with the prized product of the ovulatory process, theegg, a woman will immediately begin to experience changes required for growing another human inside of her body. One of the first detectable signs of pregnancy is a surge in a hormone called human chorionic gonadotropin or hCG. 

Once the fertilized egg finds a cozy resting place in the wall of the uterus (a process termed implantation), the production of hCG is significantly ramped up. On average, implantation usually takes about 8-10 days for normal, healthy pregnancies[1]. It is around this point on the baby growing timeline that home pregnancy tests can begin to detect the increased presence of hCG.

Chronologically speaking, we have sex, a sperm cell fertilizes an egg cell, said fertilized egg implants into uterus, our bodies up the production of hCG, and we pee on a stick to find out if all of these things really happened. But, exactly how do these little wands of destiny work?

The technology harnessed within the pregnancy test involves a biochemical assay called a “Sandwich ELISA” (ELISA = enzyme-linked immunoabsorbant assay, more on the “sandwich” part in a bit).  The general function of an ELISA is to detect (and sometimes quantify) the presence of a substance in a liquid. In the case of a home pregnancy test, the substance is hCG and the liquid part is our urine. 
Once pee is applied to the pregnancy test, it travels along the absorbent fibers, reaching defined areas that are coated with molecules, called “capture” antibodies, specifically designed to capture hCG. To help you visualize antibody science, picture a lacrosse stick, except the mesh pocket can only fit one specific type of ball:

Now, back to the sandwich part. On a home pregnancy test, there are three separate zones containing capture antibodies. Using their sharp wit and radical humor, scientists came up with “sandwich” to describe this sort of ELISA as they felt it was analogous to two slices of bread surrounding some delicious filling. Hilarious, right?

Ok, now that you’ve calmed down from laughing so hard, let us get back to the science. The first “slice of bread” is called the reaction zone, the “sandwich filling” is called the test zone, and the “last slice of bread” is called the control zone (see figure 2). Each of these zones is coated with capture antibodies, but differ from each other in how they work. 

The antibodies on the reaction zone will capture only hCG and will detach from the strip upon exposure to urine. The test zone also contains capture antibodies that can only bind hCG, except they are securely attached to the absorbent strip, plus, there is an added dye. The control zone contains a general antibody (a lacrosse stick that will fit any ball) plus a dye, and serves to let the frantic user know that the test is functional. 

Not pregnant

Pregnant
As urine travels up the absorbent strip, it takes with it the reaction zone antibodies. If the urine is obtained from a pregnant woman, the reaction zone antibodies will be bound to hCG molecules found in the pee. When the pee solution reaches the test zone, there are two possible outcomes. If you are pregnant, the hCG/reaction zone antibody complexes will stick to the test zone antibodies and cause the dye to release (sometimes in a little “+” formation). If you are not pregnant, the reaction zone antibodies will just pass on through without saying hello.

The test culminates at the control zone, which is lined with general capture antibodies. Going back to picturing antibodies as lacrosse sticks, you will see that only the shape and size of the mesh pocket varies; the stick part is always the same. The general capture antibodies on the control zone will recognize and bind to the “stick” part of the reaction zone antibodies, and release a dye while doing so. This is how we know that the test worked correctly. 

Biochemically speaking, the home pregnancy test is nothing but a soggy antibody sandwich that smells of urine. From a family planning standpoint, however, this technology can impact us in ways beyond belief. But, aside from the potential for the “are you pregnant” window to induce one into a hyperventilated state, the process happening within that handheld chemistry lab is actually quite impressive. In a matter of minutes, we can know if it is ok to go out and party with friends, or if it would be a better choice to stay in and begin to nest – all from the comfort of our own bathrooms. Three cheers for science!
For a cool animation showing how a pregnancy test works, go here. Visit WomensHealth.gov for more information about pregnancy tests.  Planned Parenthood offers scientifically accurate information about women’s reproductive health. For blogs, check out this list on Babble, and this list on BlogHer.      


[1]Wilcox AJ, Baird DD, Weinberg CR. Time of implantation of the conceptus and loss of pregnancy. N Engl J Med. (1999) Jun 10;340(23):1796-9.


Explosions, Just a Bit More Than Fireworks

Image by Nux. (Source)

By Adrienne M Roehrich, Chemistry Editor


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


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


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


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


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


2H2 + O2 –> 2H2O



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


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


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



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

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


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


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


Source

Nuclear fission is the process involved in nuclear weapons. 


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


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


Water heater explosion by the Mythbusters. 



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

Friday Roundup: Land-walking octopus, he’s having a baby, defining veggies, & lots for the ladies

Post-Thanksgiving links: All about food…or sorta food

  • You made it through Thanksgiving even though you ran out of vanilla extract? Let science help you out the next time you fall short of that one important ingredient. Scientists have compiled a list of suitable substitutes for cooks everywhere. 
  • Did you wake up this morning with fingers twice their normal size? Find out where the salt was in that Thanksgiving meal. 
  • Is pepper spray a vegetable? Oh, for the days when pizza sauce and ketchup were the only faux veggies. Here’s more on pepper spray from this week’s Double X Science blog of the week author, Deborah Blum. 

Speaking of pepper spray, science answers your burning questions

  • Plants flirt, play hard to get, embrace. Yes, that said “plants.” 
  • He’s having a baby! Carin Bondar tells us all about the world of seahorse paternal birth.
  • Chilean desert coughs up fossil whale family, puzzles scientists. Tiny scientist, huge whale fossil at link
  • Oh, those mysterious cows. Why do they come home? More important, why do they (maybe) line up along the Earth’s magnetic field, and why do scientists argue about it?
  • Asking, “Are you improbable or inevitable?”, Robert Krulwich tells us that the math determines that we are improbable. But we’re here, so aren’t we…inevitable?
  • Have you read about “the gene” for ADHD or the “drinking gene”? Stop reading that bad writing! There’s a difference between a trait that a gene confers and the many, many ways someone can manifest that trait. Read more from David Dobbs over at Neuron Culture in “Enough with the ‘slut gene’ already: Behaviors ain’t traits.” 
  • Science: It’s not all glamour and heels. Here’s a day in the life of a scientist in Australia for those who are wondering what a scientist might do all day.
  • Speaking of how scientists might spend their days, how about spending them watching 400 YouTube videos of dogs chasing their tails? Via DiscoBlog at Discover Science.
Geek o’rama
  • Use this app to follow live cameras trained on the wild places animals live in Sri Lanka, Kenya, the UK, and other places. When you spot an animal, identify it for science. Via GeekDad at Wired, Citizen science from Instant Wild! The featured Webcam as we posted these links had captured a porcupine in action. 
  • Maybe you’ve never been in a lab in your life and wouldn’t know PCR from a VCR. That doesn’t matter when you watch this video of stop-motion animation using thousands and thousands of the tiny tubes scientists use when they conduct PCR (polymerase chain reaction). The video is actually a promotional video from vendors of equipment for this kind of lab test.

  • Conditions in Antarctica are almost unimaginable inhospitable for humans, yet scientists visit there yearly to conduct valuable research. Valuable, dangerous research, but the scenery? Stunning. Via BoingBoing. 


Hey, ladies!

  • The brain is encased in a skull for protection, with a nice fluid surrounding it for extra cushioning. But the human brain was never meant to endure years of the Newtonian physical pounding that comes with playing football. Now, researchers are beginning a brain study to test the brains of 100 former National Football League players to see what harm has been done and how to identify it early. Watch the video below. Imagine the brains inside those skulls. Recall that for every action, there is an equal and opposite reaction. Yikes.

  • Most parents find letting go difficult, whether it’s when their child leaves for a week-long school trip or takes off for college. Add an autism spectrum condition to the mix, and what you get is a heartbreaking but heartfelt connection between mother and son that they both find difficult to stretch. 
  • Have you banked cord blood? Here’s why cord blood banking may not have the payoff you expect
  • You’ve done it. We’ve done it. You walk from one room to another on a mission and when you get into the other room…you forget why you’re there. Now, instead of blaming age, you can blame the door
  • Look around: Do you a see a lot of stuff you just can’t bring yourself to throw away? Read this.
  • When it comes to sex–studies of it, studies of how it develops–males get a lot of the attention, and the female sex has even (gasp) been referred to as the “default” sex, as in, if there aren’t signals to become male, then females develop by default. That ain’t true, and as it turns out, females have a pathway dedicated to developing and maintaining them just as males do. So there, scientists. 
  • Is it hard for women to self promote? This one is about academe, but it applies across many work places.
  • Speaking of workplaces, apparently the women of Generation Y are still facing discrimination there [PDF]. 
  • People (in UK, at least) still think antibiotics work against colds. They don’t. 
  • You may have read about this person’s efforts to perform a butt injection on a woman using “Fix a Flat.” It’s probably best to just love your butt for what it is, which isn’t Fix a Flat.
  • In smarter news, NASA is rolling out Aspire 2 Inspire, targeting girls interested in science. Know a girl who’s interested in science? You can start with the Aspire 2 Inspire video below about women in science:

“Yet more must be done to address the projected shortfall of 280,000 math and science teachers that our nation will face by 2015. We need public and private investments in math and science education and we need a commitment to making a difference on a national scale.”

She couldn’t be more right. 

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


Figure 1: The Alchemist Discovering Phosphorus

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

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


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


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


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


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


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


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


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


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


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


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

Adrienne M Roehrich, Double X Science Chemistry Editor
References:

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

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

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

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25 myths about the flu vaccine debunked

Setting the record straight on the flu vaccine

by Tara Haelle
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