Vaccination attitudes are contagious

The power of social ties may be stronger than you think.

by Tara Haelle Continue reading

Vaccine fears: What can you do?

An infant girl suffering from pertussis, a vaccine-preventable disease,
struggles to breathe. Those indentations in her ribs are
one of the signs of her extreme difficulty drawing breath. Via CDC. 

What’s not to fear directly about vaccines? There’s a needle that someone pokes into your child. Your child screams. You tense up. What’s in there? you wonder. Viral or bacterial bits that, in ways that are mysterious to a non-immunologist, will keep your child well when intuition seems to say they ought to make your child sick.
Needles, screaming, microbial bits…these naturally would make any parent blanch. The number of vaccines has added to the fear for at least a decade, leading to non–evidence-based calls to “spread out” the schedule or reduce the number of vaccinations.
In fact, the evidence supports the schedule as it’s recommended.
The fear of vaccination is not new. Since Edward Jenner and his cowpox inoculation at the turn of the 19th century, people have latched onto the fear of the known—those needles!—and unknown—what’s in those things?
What might be considered the first anti-vaccine cartoon appeared in response to Jenner’s proposed inoculation of cowpox to combat smallpox.
The vision of cows growing out of arms is comical, but the reality of possible side effects from today’s vaccines can lead some parents to keep their children away from the doctor’s office. Indeed, this anxiety has done so since the days of the 19th century anti-vaccination leagues, aligned against the widespread use of Jenner’s smallpox vaccine.
The vaccine wars in those days were just as bitter and divisive as they are today, including an 1885 march in England in which anti-vaccination forces carried a child’s coffin and an effigy of Jenner himself. Today’s most fanatical crusaders against vaccines may not carry coffins or effigies, but death threats against those who promote vaccines for public health are not unknown.
The fact that the vast majority of parents overcame those fears and had their children vaccinated has led to some of the greatest public health successes of the 20th century. Thanks to the willingness of people to participate in vaccination programs, smallpox disappeared and polio became a thing of the past in much of the world. Indeed, people in those eras knew, often from personal experience, what these diseases could do—maim and kill—and the fear of those very real outcomes outweighed fears of the vaccinations.
But today, we’re different. In the United States, most of us under a certain age have never witnessed a death from diphtheria or tetanus or smallpox or measles. We haven’t seen a child drained of life as a rotavirus rapidly depletes the molecules she needs to live. Many of us have not witnessed the sounds of pertussis, the vomiting, the exploding lungs in an agony of infant death. Why? Because of vaccines.
This very success has, ironically, led to the resurgence of fear and misgiving about vaccines. No longer weighed against anxiety of death or disability from disease, the fear of vaccines now aligns against the bright picture of a nation of children largely free of life-threatening illness.
Without the collective memory of days when children played on the playground one day and died the next of vaccine-preventable disease, the calculus of parental fear pits only the side effects of vaccines against the healthy child. Vaccination requires intentional agency—parental agreement—to impose on that healthy child the very small risk that vaccines carry. Some parents simply are not comfortable either with that intentionality or that risk.
Feeding this reluctance is the explosion of Internet sites that warn against vaccines or disseminate incorrect information about them. The Centers for Disease Control and Prevention (CDC) has provided abundant information about vaccines, including a page devoted to countering erroneous information with facts.
This information will not move the fiercest anti-vaccine groups that lump the CDC in with pharmaceutical companies and others in an alleged conspiracy to harm millions via a money-making vaccine industry. However, it certainly helps concerned parents who simply seek to calm fears, weigh evidence, and make an informed decision about choosing vaccines over the life-threatening illness and compromised public health that result when people don’t vaccinate.
Indeed, these threats to public health have grown considerably with recent large outbreaks of measles and pertussis, including a growing measles outbreak in Europe involving more than 26,000 cases of measles, more than 7000 hospitalizations, and nine deaths as of this writing. The growing threat has led to calls for more stringent requirements for childhood vaccines, including dropping exemptions and requiring that all children be vaccinated over parental objections. This tactic likely would increase vaccination rates among children attending school.
But instead of strong-arming parents into having their children vaccinated, what we really need is a two-fold approach to education. First, we need sober, non-sensationalist reporting from the news media about vaccine-related stories, including stories about side effects, research, and court cases. These articles—and their sensational headlines—are in all likelihood among the prime drivers of the rumor mill against vaccines.
Second, when parents read these stories and turn to a medical professional for input, that input must come as part of a two-way communication between the health professional and the parent, not in lecture format or as patronizing. A little, “I understand your concerns because I’ve had them, too, but here’s what I know that gives me confidence in vaccines,” is considerably better than, “Your child has to be vaccinated, or you can get out of my office.” The onus is on parents to ask with open minds and an understanding that the medical professional in front of them has likely devoted considerable time to gaining the education and expertise necessary to address their questions. Health care isn’t a competition about who knows more. It’s about evidence-based health practices.
As centuries of history attest, no efforts will completely eradicate vaccine fears. Motivations fueling anti-vaccine sentiment that go beyond information gaps range from personal economic benefit to a desire to out-expert the experts to the inertia of fear.
But a careful and persistent information campaign and outreach efforts from medical professionals in the trenches may help keep vaccination rates sufficiently high. Parental investment in gaining information from trained professionals and making decisions based on facts rather than fear is also an indispensable component. To ensure adequate rates requires either these efforts or a resurgence of the deadly diseases that have graphically demonstrated the real balance of the threats at issue here.
Which one would we rather have? 


Emily Willingham, Double X Science Editor
Twitter,
@ejwillingham
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A version of this post originally appeared on the blog of PKIDs, Parents of Kids with Infectious Diseases. The mission of PKIDs includes educating the public about infectious diseases and methods of prevention and transmission. Follow PKIDs on Twitter @PKIDs.

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

Pertussis: Get the vax or at least listen to why you should

by Tara Haelle, DXS contributor

The past few weeks have seen big news for vaccines. A bill related to vaccine exemptions was signed into law, a court ruled against a parent’s refusal to vaccinate and a recent study points out the value of vaccinating a household — especially mom — to protect a young infant from pertussis (whooping cough).


The latest news is that Governor Jerry Brown in California signed a bill last Sunday that had been sitting on his desk since September 6 and was the target of a number of rallies by parents who didn’t want to see it pass. Among those fighting the bill was Dr. Bob Sears, who says he walks a middle ground with vaccine policy but in reality tends to flirt with those who fear vaccines and rely on misinformation. Although some parents claimed the bill took away their right to choose whether their children get vaccinated, it actually just ensures they get good medical information before they make that choice.

Photo by Dave Gostisha at sxc.hu.
The bill-now-law, AB 2109, proposed by a pediatrician, requires parents to get a statement signed by a health care practitioner that the parents/guardians have received accurate, evidence-based information about the risks and benefits of vaccines before they can use a personal belief exemption to prevent their children from being vaccinated. This law is a tremendous triumph both for informed consent in medical decisions and for the public health of children in California, which saw a considerable outbreak of pertussis (whooping cough) in 2010. Washington state passed a similar law last year and saw 25 percent drop in exemptions filed. Other states are considering similar laws in a nationwide overall shift toward strengthening exemption requirements.


Why are these laws so important? In short, they kill two birds with one stone: They make it more difficult for parents to casually opt out of vaccines on philosophical grounds (as opposed to religious or medical reasons), and they require parents who want to opt out to at least hear out a pediatrician on accurate information about the actual risks (which do exist) and benefits (there are so many) of immunizations. Parents who are determined not to vaccinate their children can still refuse, but many parents who might have signed those forms out of convenience — it can be easier to sign than to get to the doctor’s office for the shot — will now at least hear the impact a decision not to vaccinate can have on the community. (Hopefully, they go to a health care practitioner other than Dr. Sears, whose stances have gradually been moving further and further toward unscientific and misinformation of those who oppose vaccines.) 

It’s also particularly notable that California and Washington are the most recent states to tighten opt-out procedures for parents because they are home to some of the more recent pertussis outbreaks. More on that in a moment.

First, a bit of background on vaccine exemptions: Only 20 states have personal belief exemptions, and until last year, eight of these simply require nothing more than a parent signature. Now that number is down to six. (Other types of requirements for philosophical exemptions include writing out your reasons for exemption, requiring the forms to be notarized, requiring education on the risks/benefits, direct involvement from the state or local health department or renewals.)


All states have medical exemptions for patients who have auto-immune disorders, have proof that their bodies do not respond to immunization, have documented allergic reactions or have other circumstances which make it too risky for them to be immunized. In fact, these are the very people that the rest of the population protects through herd immunity when vaccination rates are up where they should be. All but two states have religious exemptions (Mississippi and West Virginia are the exceptions).


And that brings us to some less covered but still significant news about one state’s ruling on a particular case involving religious exemption. Last week, the U.S. district court in Ohio ruled that one woman’s claim of religious objection was insufficient for her children to be exempted from being vaccinated. Read the whole story here. To be fair, this is a complex case involving far more than vaccines; the mother is clearly neglectful and the overall situation is pretty crappy. However, the fact that the court found “the mere assertion of a religious belief … does not automatically trigger First Amendment protections,” and that “it has long been recognized that local authorities may constitutionally mandate vaccinations” is significant in a state that offers both religious and personal belief exemptions.


Because of the danger to public health when clusters of kids are not vaccinated, my personal opinion on this issue is that “personal belief” exemptions should not be offered in any state, and religious exemptions should be extremely difficult to get, if they are offered at all (which may be the best overall route). Some cite the Amish, Mennonite and Christian Scientists, though actually the majority of Amish children, at least, are vaccinated, and it doesn’t appear that any Amish objections to vaccines are for religious reasons. Christian Scientists have successfully been convicted of neglect in other incidents where their children died from inadequate medical care, though their religion is the only one I’m aware of that vaccination actually, explicitly violates. 

The constitutionality of religious exemptions is dubious as well. At the very least, however, anyone seeking any exemption should certainly to see a doctor first to be sure they have accurate information and not simply what they have seen online or heard at the playground. Those who absolutely will not vaccinate in states without exemptions may also opt to home school or send their children to private schools that don’t have requirements. But considering the increasing rates of measles and the increasing epidemics of pertussis, the need for high vaccination coverage in communities is more important than ever.

It is true that the pertussis vaccine is not as effective as the old one used to be, something I wrote about a few weeks ago.  It’s also true that pertussis peaks every five years or so, but even taking into account the peaks, the overall rate of cases has been steadily on the move upward. Dr. Offit, the chief of the Division of Infectious Disease at Children’s Hospital of Philadelphia and a very vocal advocate of vaccines, said he believes that parents’ refusals to vaccinate are playing their own small part in the increase.


“The major contributor is waning immunity. The minor contributor is the choice not vaccinate,” he said. He noted that there are researchers working on the problem, as this Nature article notes (paywall), including attempts to make a better vaccine with more adjuvants, the additives that enhance the body’s immune response to a vaccine. While vaccinated children and adults have been high among the numbers of those getting whooping cough, getting the vaccine remains among the best ways to reduce your risk of contracting it — or of having less rough of a time with it if you do get it. Dr. Offit also pointed out that pregnant women in particular should be sure they get their booster.


Which brings us to the study published last week that relates to the most important reason to get vaccinated, at least from the perspective of preventing deaths — to protect the babies who are too young for the vaccine but most likely to contract it and die from it.

The study, published in the journal Epidemiology last week, looked at how frequently pertussis was transmitted to others within the same household and how effective “cocooning” is. Cocooning is vaccinating all the household members who can get the vaccine for the purpose of protecting young babies who can’t yet be vaccinated for the disease.


They found that transmission rates within the home are high, especially for mothers passing the illness on to their children. Therefore, making sure all pregnant women are vaccinated before their baby arrives would, according to their calculations, cut the risk in half that a baby would contract pertussis. The evidence for sibling vaccination, though weaker, still points to the value of overall cocooning: “Vaccination of siblings is less effective in preventing transmission within the household, but may be as effective overall because siblings more often introduce an infection in the household.”


Indeed, this year, siblings’ bringing home the disease appears more likely than ever in the states experiencing big outbreaks this year. Just how bad are the numbers? Well, 2010 was the last five-year peak, which totaled 27,550 cases. It’s currently September of 2012, and the numbers last reported to the CDC were at 29,834, and that doesn’t even include over 3,700 cases in Minnesota that haven’t been officially reported to the CDC yet. These numbers, which include 14 deaths (primarily of babies under 3 months), may very well end up doubling the 2011 total of 18,719 if they continue at the current rate through the end of the year. It’s the biggest pertussis outbreak since 1959.


Not surprisingly, the majority of the states leading in pertussis cases are also among those that offer personal belief exemptions. Washington, despite their new law, is sitting at 4,190 cases, quadrupling their 2011 count of 965. This is the state where 7.6 percent of parents opted for exemptions (among all grade levels, not just kindergarten) in 2008-09, more than four times the national rate of about 1.5 percent. Minnesota and Wisconsin have similarly high rates and both have personal belief exemptions. The most recent numbers out of Minnesota are 3,748 — they had just 661 cases last year. Wisconsin is leading the nation with 4,640 cases, up from 1,192 in 2011, at last report in the Sept. 28 Morbidity and Mortality Weekly Report (pdf) at the CDC.


But the increases are being seen across the nation, as this CDC map shows. Texas (1,287 cases to date this year), Pennsylvania (1,428 cases) and Colorado (897 cases, though they averaged 158 over the past four years) are among other states with personal belief exemptions (though the Texas one has significant restrictions and hoops to jump through). But it’s clear the decreased effectiveness of the vaccine is playing the biggest role, especially in places like Iowa (1,168 cases) and New York (2,107), neither of which offer personal belief exemptions.


Again, though, a less effective vaccine does not mean a worthless vaccine. It still offers 85 percent protection when you get the shot or the booster, and even as it loses some effectiveness as the years go by, you’re far less likely to have a severe case if you do get the disease. And you’re protecting those around you, including the babies who have only been here a few months and are the most susceptible to catching and dying from the disease.


Bottom line — it’s worth it to get the shot, and to make sure your kids do too.


Opinions expressed in this article do not either necessarily reflect or conflict with those of the DXS editorial team or contributors.
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[Tara Haelle (www.tarahaelle.com) is a health and science writer and a photojournalist based in Peoria, IL after years as a Texan, where she earned her undergraduate degrees and MA in journalism at UT-Austin. She’s the mental health editor for dailyRx.com in addition to reporting on pediatrics, vaccines, sleep, parenting, prenatal care and obesity. Her blog, Red Wine & Apple Sauce, focuses on health and science news for moms, and you can follow her on Twitter at @health_reporter and @tarasue. She’s also swum with 9 different species of sharks, climbed Kilimanjaro and backpacked in over 40 countries, but that was in the years of B.C. (Before Children). She finds that two-year-olds are tougher to tussle with than tiger sharks.]

Why don’t more girls get the HPV vaccine??

Double X Science is pleased to be able to repost, with permission, this important piece courtesy of author Kate Prengaman and her Xylem blog, focused on spreading science and new ideas.

Imagine if there was a vaccine that could prevent cancer. Everyone would want it, right?
Surprisingly, no. There IS a vaccine to prevent cervical cancer, which, according to the CDC, affects about 12,000 women every year. Unlike most cancers, cervical cancer is caused by a sexually transmitted virus, Human Papillomavirus, also known as HPV. The virus can cause abnormal cell growth in the cervix, which can turn cancerous. The vaccine, approved in 2006, works against many common strains of HPV.
The vaccine is recommended for girls ages 11-12, and also provided to women up through their early twenties.  The goal is to protect girls long before they are ever sexually active, so that they never contract HPV in the first place. As of 2011, the vaccine is also recommended for adolescent boys.
Contracting HPV is so common that more than half of all sexually active men and women in the United States will become infected with HPV at some point in their lives. According to a CDC factsheet on the HPV vaccine, “about 20 million Americans are currently affected, and 6 million more are infected every year.” In most people, HPV infections never lead to symptoms but the virus can cause development of cervical cancer and, more rarely, cancers of the vagina and anus, as well as genital warts. Furthermore, men can develop cancer from HPV. The virus is transmitted through skin to skin contact, which reduces the efficacy of condoms at preventing the spread of this disease.

Yet, despite the dangers associated with HPV, only 33.9% of American girls, ages 13-17, reported to the CDC in 2010 that they had been fully vaccinated (3 doses) against HPV.  When I mapped the state by state rates of vaccination, I found a dramatic distribution, from only 19% of girls in Idaho to nearly 60% in South Dakota and Rhode Island.

Map created by Kate Prengaman
Much of the resistance to vaccinating adolescent girls against cancer-causing HPV comes from  many people who are uncomfortable with or resistant to the fact that adolescent girls will grow up and have sex. I expected to see a strong correlation between states with Abstinence-only sex education and low vaccination rates, but the pattern in the map is weaker than I had anticipated. I also considered that the cost of the vaccines might play a role, although if they are not covered by a family’s health insurance, there are federal programs in place to subsidize the cost. There’s also some correlation there, but again, not as strong as you see, for example, when mapping teenage birthrates.
Map created by Kate Prengaman
Clearly, the pink map, lovely as it is, does not provide an answer for why more adolescent girls are not receiving the HPV vaccine. There is an unfortunate anti-vaccination movement in this country, with people choosing not to protect their kids from dangerous diseases because of unfounded fears that vaccines can cause autism, among other things. Last fall, Michelle Bachmann even used a presidential debate to stir up more fears that the HPV vaccines could cause mental disabilities, a enormous error that the medical community quickly tried to correct.
The truth is that these vaccines are safe. The truth is that HPV is really common, and it can cause cancer, and if you ever have sex, you have a good chance of getting it. Why aren’t more parents of adolescents taking the lead on protecting their kids’ future health?  If you have any ideas for other factors that might explain the patterns of vaccination, let me know in the comments and I  will try adding to my map.  Thanks!

About the guest author:

Kate Prengaman is a science writer and outdoor enthusiast currently based in Madison, WI. Formerly a botanist, Kate is pursuing her masters in science journalism at UW, reading and writing as much as possible.  She loves talking to people, telling stories, finding adventures,  geeking out over wildflowers, and eating delicious things. She blogs at Xylem

Bad flu season in full swing, but flu shot still helpful

Bad flu season in full swing, but flu shot still helpful

Source: Wikimedia Commons; credit: CDC.

The flu season that is unfolding is a killer, with influenza having already taken dozens of lives across the United States. Deaths from flu during the flu seasons are actually the norm, ranging from 3000 to 50,000 annually, but this year’s outbreak arrived early and features a strain that is infamous for its virulence. Forty-four states now have met the cutoff for “widespread” flu activity as of this writing, and in hotspots like Boston, MA, cases are 10 times the number from the same time last year. In many areas, hospitals have taken to setting up temporary tent shelters outside the buildings to manage the flood of cases and prevent spread inside the facility. ETA: This USA Today article gives an overview of how clinicians are experiencing this outbreak on the ground. [Update: As of 1/18/13, a total of 48 states are now at widespread status, and 29 children have died. Forty percent of hospitalized children have had no known underlying medical conditions.]

Public health officials from the US Food and Drug Administration and the Centers for Disease Control and Prevention(CDC) are urging people who have not gotten their flu shots to do so, saying that there is still time for the vaccination to work for you against the flu. The most vulnerable population is children, and 18 children have already died in the United States during this year’s season. According to reports, far less than half of the eligible population in the US has gotten a flu vaccination.

People express reluctance to get the flu vaccine for several reasons. Among them are fears that the vaccine contains mercury as part of a preservative, thimerosal, that has been used for years in various immunizations, although it’s been removed from many. For the flu, only vaccines from multidose vials contain this preservative, which is needed to protect the contents from contamination when the vials are opened for repeated use. Single-dose shots and the inhaled Flu Mist do not contain this preservative, which an abundance of studies have shown does not cause harm despite diligent efforts from anti-vaccine organizations to argue otherwise. For more information about this preservative in multidose vials of flu vaccines, the CDC offers a Q&A.

Another source of reluctance is the fact that the flu vaccine, like several other vaccines–or indeed, having the infection itself–is not 100% protective against the illness. In fact, it appears to be about 60% effective in preventing illness, although those who have been vaccinated and do fall ill with the strain included in the vaccine might experience less intense symptoms. The CDC also offers a Q&A addressing why some people who have been vaccinated still catch the flu. My personal feeling is that I’d rather give my children that 60% chance in a rampant flu season with a virulent strain that’s hospitalized tens of thousands than give them no protection at all. Any number of interventions don’t carry a 100% guarantee of effectiveness, but they certainly enhance the favorable odds. My children and I all received the Flu Mist vaccine back in October. ETA: A recent report found that different forms of the vaccine have different levels of effectiveness in different age groups and that the vaccines and vaccine program require improvement. For more information about the report, which concluded as we’ve written here that flu vaccines offer moderate protection and have a good safety profile, please see this post by an epidemiologist.

People also forgo a shot because they think that only people in poor health or with pre-existing conditions are susceptible to the most dreaded outcomes with flu: hospitalization and death. That’s not actually the case. “Influenza” is the name we give to the highly variable viruses that play games of genetic mix-and-match in different species, with results that are unpredictable and rapidly changing. No one’s previous experience with flu will necessarily be predictive of later experiences with the virus. Some flu strains do hit certain populations with specific existing health problems, but other strains kill the young and healthy preferentially. And whether or not you yourself are in perfect health, if you get the flu, you risk passing it along to someone who is not. ETA: For a personal look at who some of those people are, please see the Faces of Influenza site. Some people cannot get a flu shot for medical reasons, and anyone who has had a reaction to a vaccine should obviously consult with their medical professional about vaccines.

A final source of reluctance is that the flu vaccine each year is developed based on educated guesses. No one can predict with certainty which strains will gain the upper hand. As it happens, one strain in circulation this year falls outside of the vaccine target, but medical authorities report that so far, 91% of strains identified in circulation are targets of the vaccine. Because we are talking about influenza and several circulating strains, if you do not get a vaccination, it’s entirely possible for influenza viruses to hit you or your family hard more than once this flu season.

Bottom line? Without a vaccination, you’re 100% exposed no matter what your age, health, diet, exercise routine, or supplement intake. And if you get sick, you’ll endanger everyone you’ve been around and contaminate every place you’ve been. Flu carries innumerable potential and unpredictable outcomes, from complete recovery to death, and hospitalizations this year are extremely high. People with a genuine case of influenza end up floored for days, in body-wide pain, with high fevers and wracking coughs and a risk for pneumonia, hospitalization, and death, sometimes with unpredictable rapid progression. Even for those who don’t end up in the hospital, complete recovery from these deadly and unpredictable viruses typically takes weeks, meaning lost school, lost productivity, lost work, lost wages. Meanwhile, the vaccine cost ranges from free to about 20-40 bucks at various pharmacies.

Here is a basic video explaining some of the complexities of the flu vaccine and its success rate:

The opinions expressed in this article do not necessarily reflect or conflict with those of the DXS editorial team or contributors.