DoubleXplainer: What is a vagina?

Development of the female (right) and male (left)
sex anatomy (now unreversed; thanks Peter Edmonds!). (Source)

By Emily Willingham, DXS managing editor

What is a vagina?

First, let’s just practice saying the word. Vagina. Vuh-ji-nuh. VAGINA!

OK. Why are we practicing this? So that we can avoid suffering from the fluttery sensibilities of one Rep. Mike Callton of Michigan who, upon hearing colleague Rep. Lisa Brown use the word vagina during a speech on the Michigan House floor, commented:

What she said was offensive. It was so offensive, I don’t even want to say it in front of women. I would not say that in mixed company.

So here we have a fellow who is so squeamish about female anatomy that he won’t even use the appropriate terminology for that anatomy in front of the people who have the body part. So beflustered are his tender feelings about the word vagina that he and the Republican leadership of the Michigan house of representatives refused to allow Rep. Brown speak again when discussing a bill about retirement of school employees. I assume they were concerned that somehow, she’d drag in the dreaded V-word again while talking about pensions.

All for the transgression of saying the word “vagina.” Vagina.

You know what? It’s not a mellifluous word. It has that giraffey g in it, an ugly “vuh” sound. It would probably be more palatable in general if we had decided to term this particular part of female anatomy something else, perhaps “hibiscus.” Unfortunately, as with so much in anatomy, we had to rely on Latin instead of flowers, and in Latin, vagina means “sheath” or “scabbard.” In other words, a place to put a sword… or a penis. Or, as I like to call them, “sperm delivery systems.”

The offensive body part is indicated. (Source)
People tend to have a misunderstanding about the vagina. They think that what they’re seeing on the outside of the woman is the vagina. Unless their viewpoint is very up close and personal, it isn’t. Those are the labia majora and labia minora, sometimes referred to crassly as “the lips,” and making up part of the vulva (actual vulva pic, fair warning). There’s a big pair (the majora) and a little pair (the minora). In men, the two sides of the big pair zip early in development to encase the testes (see top image). The little pair forms the shaft of the penis. In women, both pairs stay apart. No zipping (ETA: see good interactive explanation here). But that’s not the vagina. 
Behold the clitoris. (Source

 

For those who are unfamiliar, you can usually find the entrance to the vagina if you peek between the labia minora. If you’ve never poked around knowledgeably in the female anatomy, let’s orient ourselves a little. Up at the very top, tucked away under the labia majora, is the clitoral hood. Look under the hood–this is highly recommended on specific occasions–and you’ll find the clitoris. This fabulous body part has far more to it than first appearances might suggest. What you see there under the hood is a small fraction of what a woman gets (recommended reading!), and we have this clitoris to thank for a woman’s superior orgasmic capacities. Yes, I said “superior.” The male echo of the clitoris is the glans penis (actual penis pic, fair warning), and the two anatomical features share some commonalities, including the ability to become erect. Of course, if you have a clitoris, no one notices if you become aroused in algebra class. Clitoris FTW!

Just below all of those interesting bits is the urethral opening. Men have this opening at the tip of the penis, where it serves a double duty, releasing semen and urine, preferably not simultaneously. In women, this opening is dedicated to elimination only. Follow that sucker up a few inches, and you hit the bladder. Don’t go in there. That’s an “exit only” kind of orifice, like your nostrils.

Move down just a tad more and… that’s it! There between the labia minora, that’s the vaginal opening. That’s where the actual vagina is. The part of the female anatomy that got a female legislator blocked from speaking just for saying it.

There it is, the vagina, bridging the outside
and inside worlds and freaking out Michigan
legislators since time began. (Source)

 

The vagina is an amazing structure. Nothing else in human anatomy has the flexibility of this thing. It starts there at the opening and extends several inches into the body, leading to the cervix. Cervix means “neck” (think of cervical collars), and it is indeed the neck of the uterus. If you’ve given birth vaginally, you know that the baby exits the uterus through this neck, travels very quickly through the vagina, and enters the world through the vaginal opening. If you’ve seen the cervical or the vaginal opening, you will be astonished that an entire baby can fit through either. But the uterus, the most powerful muscle in the body, handles the cervical part, contracting and pulling and contracting and pulling until the cervix is juuuuuust wide enough for an infant human head to fit through… sort of. The vagina deals with the rest.

And once that infant–someone like you, Mike Callton–leaves the cervix, it is in the vagina. If you didn’t arrive here via C-section, you got here by making your first extended trip–through a vagina. The vagina is so accommodating and flexible that it can stretch to many times its usual diameter to allow an entire human infant to exit a woman’s body and enter the world. If you’ve never put a finger in a vagina, try it if you can find a willing partner or if you have a vagina of your own. Then imagine that cozy-feeling vagina stretching fairly effortlessly to accommodate an entire infant.

That flexibility isn’t relevant only to childbirth. When a woman becomes aroused during sex, the vagina elongates to facilitate the process of sperm delivery and penis accommodation. It also self lubricates and has a ton of nerves near the opening, all part of making sex that super fun thing that people with vaginas or penises tend to think it is. But it wouldn’t be so fun–or pragmatically useful–without the vagina. There. I said it. Thirty times in this single blog post. And you should, too.

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

See also our Pregnancy 101 series, by Jeanne Garbarino, biology editor

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

Robotic hysterectomy more expensive: but better?

In a word, no (unless you have cancer).

by Jennifer Gunter, MD, FRCS(C), FACOG, DABPM

So, let’s take cancer out of the picture and discuss hysterectomy for non-cancerous (benign) reasons.

First of all. A hysterectomy (removing the uterus) can be done via one of these four methods:

  1. Vaginal, a small incision at the top of the vagina and the uterus is removed entirely through the vagina without any incision on the abdomen.
  2. Laparoscopic surgery, where incisions are made in the belly and an operating telescope is inserted. The uterus is then removed either through a small incision in the belly wall or through the vagina.
  3. A robotic surgery, which is laparoscopic surgery (see #2) performed with specialized equipment. The surgeon actually sits at a consult and operates the equipment remotely. An assistant is scrubbed in during the case to help with the equipment.
  4. An abdominal hysterectomy. This requires an incision in the belly and has much longer recovery times than the other 3 options. This is what most people visualize when they think of surgery.

The American Congress of OB/GYN (ACOG) recommends vaginal hysterectomy as the least invasive method (least invasive is almost always the best option) with the best outcomes. Sometimes a vaginal hysterectomy isn’t feasible for technical reasons and then a laparoscopic approach is favored. There is no study that suggests a robotic hysterectomy offers any medical advantage over a vaginal or a laparoscopic hysterectomy when cancer isn’t the reason for the surgery.

So if there is no advantage to robotic hysterectomies, why are gynecologists pushing them? And make no mistake, they are pushing them as 3 years ago 0.5% of hysterectomies were robotic and now that number has soared exponentially to 10% (JAMA, 2013)

Why this exponential increase? I can think of four reasons:

  1. They need the practice. The gynecologists want to learn the new technique (see the marketing angle below), but it takes quite a few cases to get good.
  2. A marketing tool. Hey, robots are cool, they’re new, they must be better! People will want robots.
  3. Hospitals are pushing GYNs to use the surgical robot, the robot that cost about $1.7 million to buy in addition to $125,000 in annual maintenance. Hospitals need to keep the robot in use to cover these expenses. That money can only come from your insurance company, your tax dollars (Medicaid and Medicare), or directly from you.
  4. They don’t know the literature and believe the hype from the reps who sell the robots.

According to ACOG:

Robotic surgery is not the only or the best minimally invasive approach for hysterectomy. Nor is it the most cost-efficient. It is important to separate the marketing hype from the reality when considering the best surgical approach for hysterectomies

And

…there is no good data proving that robotic hysterectomy is even as good as—let alone better—than existing, and far less costly, minimally invasive alternatives.

 A robot adds $2000 to a hysterectomy. If every non-cancer (benign) hysterectomy in the United States were performed with a robot, ACOG estimates that $960 million to $1.9 billion will be added to the health care system each year.

If your GYN is recommending robotic surgery over a vaginal or a traditional laparoscopic hysterectomy and you don’t have cancer, you need to ask, “Why?” (and take a look to see if robotic surgery is featured prominently on the web page and the practice’s marketing).

New technology isn’t always better. While a robot can lead to improved outcomes for complex cancer cases (they allow the surgeon to do the case with a laparoscopically rather than with a big incision), using a robot for a benign hysterectomy is like driving a Ferrari with the speedometer set so the car can’t exceed 15 miles an hour. It might look cooler, but it’s going to cost you a lot more up front and in maintenance and it’s not going to get you around the city any faster or safer than a Honda.

We are all stewards of the health care system. Wasting $2000 per patient on the costs to run a robot for a benign hysterectomy is simply funding the salaries of the people who sell surgical robots and increasing the cost of health care for everyone else, because we all pay when care becomes more expensive with higher premiums and co-payments.

Dr. Jennifer Gunter is an OB/GYN and a pain medicine physician who has authored the book, The Preemie Primera guide for parents of premature babies. In addition to her academic publications, her writing has appeared inUSA Today, the A Cup of Comfort seriesKevinMD.comEmpowHer.com, Exceptional Parent, Parents Press, Sacramento Parent, and the Marin Independent Journal.

Image source: Wikimedia Commons and Wikimedia Commons

From the editors: What does it look like when a robot does a hysterectomy? This (yes, apparently promotional) video, produced by a hospital in California, gives us a look:

Pregnancy 101: On the cervical mucus plug and why I’ve never been more happy to hold something so disgusting in my hand

Like the eye of Sauron drawn to the One Ring, one cannot resist looking at the mucus plug.
June 3rd, 2007 fell on a Sunday. I awoke that morning feeling disappointed that I was still pregnant. My due date had come and gone and, honestly, I was sick of being a human incubator. I had enough of the heartburn, involuntary peeing, and the overall beached-whale feeling. The baby in utero was resting comfortably on my sciatic nerve, and I could barely walk. And perhaps even more important was the fact that I just wanted to finally meet the child I had grown from just a few cells!

Feeling like it would never come to be, I slowly waddled into the bathroom and somehow negotiated the tall edge of the bathtub in order to take a shower. As I stood allowing the hot water to pour down my back, I looked down at the giant watermelon growing from my abdomen and literally began to beg. “Little baby, please please PLEASE make your way out today!” Right at that moment, and I kid you not, my cervix released my mucus plug and deposited it into the palm of my hand.

Video of a mucus plug being poked and prodded with tweezers. Watch at your own risk.
Suddenly, I saw the light at the end of the pregnancy tunnel. I excitedly called for my husband. “Jim! You have to come see this!!” He came running in as he was already on edge, given the circumstances. “My mucus plug came out! Do you want to see it?” As much as he tried to resist looking at something that was potentially grotesque (and it was), instinct overrode logic. His actions did not match the words coming out of his mouth, which were along the lines of “hell no!” and, like Sauron responding to the wearing of the ring, his eyes were slowly drawn down to what was gently wobbling in the palm of my hand.   

The human eye is poised for setting its gaze upon things that are aesthetically pleasing and the mere mention of the word “mucus” could potentially elicit a queasy feeling in one’s gut. However, mucus plays a significant biological role in our bodies. In general, the mucus serves as a physical barrier against microbial invaders (bacteria, fungi, viruses) and small particulate matter (dust, pollen, allergens of all kinds). Protective mucus membranes line a multitude of surfaces in our bodies, including the digestive tract, the respiratory pathway, and, of course, the female reproductive cavity.

But when it comes to matters of ladybusiness, the function of mucus goes beyond that of a microbial defense system. Produced by specialized cells lining the cervix, which is the neck of the uterus and where the uterus and vagina meet, mucus also plays a role in either facilitating or preventing sperm from traveling beyond the vagina and into the upper reproductive tract.

For instance, cervical mucus becomes thinner around the time of ovulation, providing a more suitable conduit for sperm movement and swimming (presumably toward the egg). Furthermore, some components from this so-called “fertile” cervical mucus actually help prolong the life of sperm cells. Conversely, after the ovulation phase, normal hormonal fluctuations cause cervical mucus to become thicker and more gel-like, acting as a barrier to sperm. This response helps to prepare the uterus for pregnancy if  fertilization happens.

During pregnancy, a sustained elevation of a hormone called progesterone causes the mucus-secreting cells in the cervix to produce a much more viscous and elastic mucus, known as the cervical mucus plug. In non-scientific terms, the mucus plug is like the cork that keeps all of the bubbly baby goodness safe from harmful bacteria. It is quite large, often weighing in around 10 g (0.35 oz) and consists mostly of water (>90%) that contains several hundred types of proteins. These proteins do many jobs, including immunological gatekeepers, structural maintenance, regulation of fluid balance, and even cholesterol metabolism (cholesterol is an ever important component of healthy fetal development).
As a woman nears the end of a pregnancy, the cervix releases the mucus plug as it thins out in preparation for birth. Often, the thinning of the cervix can release some blood into the mucus plug, which is why some describe the loss of the mucus plug as a “bloody show.” However, losing the mucus plug is not necessarily an indication that labor is starting. Activities like sex or an internal cervical examination can cause the mucus plug to dislodge. It can fall out hours, days, or even weeks before labor begins. In my case, the loss of my mucus plug was associated with the onset of labor, which is why I have never been so happy to hold something so disgusting in my hand. 


Last week, I told the story of my two births, including the loss of my mucus plug, at an event called The Story Collider. I described the mucus plug as “a big hot gelatinous mess.” I pushed it a bit further by providing the following graphic imagery: “Picture a Jell-O jiggler, but instead of brightly colored sugar, it’s made up of bloody snot.” I was pleased with the audience response, which mostly consisted of animated face smooshing accompanied by grossed-out groans and sighs. For the rest of the evening, I heard people call to me from all over the bar by screaming “MUCUS PLUG!!!” Given the importance of the mucus plug during pregnancy (and mucus in general) combined with its comedic potential, its no wonder that it was a hit. Go mucus!


Jeanne Garbarino, Double X Science biology editor

References

Kamran Moghissi, Otto W. Neuhaus, and Charles S. Stevenson. Composition and properties of human cervical mucus. I. Electrophoretic separation and identification of proteins.. J Clin Invest. 1960 September; 39(9): 1358–1363.

Lee DC, Hassan SS, Romero R, Tarca AL, Bhatti G, Gervasi MT, Caruso JA, Stemmer PM, Kim CJ, Hansen LK, Becher N, Uldbjerg N. Protein profiling underscores immunological functions of uterine cervical mucus plug in human pregnancy. J Proteomics. 2011 May 16;74(6):817-28. Epub 2011 Mar 23.

Ilene K. Gipso. Mucins of the human endocervix. Frontiers in Bioscience 2001 October; 6, d1245-1255.

Merete Hein MD, Erika V. Valore MS, Rikke Bek Helmig MD, PhD, Niels Uldbjerg MD, PhD, Tomas Ganz PhD, MD. Antimicrobial factors in the cervical mucus plug. American Journal of Obstetrics and Gynecology 2002 July Volume 187, Issue 1, 137-144

Naja Becher, Kristina Adams Waldorf, Merete Hein & Niels Uldbjerg. The cervical mucus plug: Structured review of the literature. Acta Obstetricia et Gynecologica. 2009; 88: 502_513

The sperm don’t care how they got there, Rep. Akin

17 c. rendition of human inside sperm.
Public domain in US.
[Trigger warning: frank language about sexual assault]
By Emily Willingham
By now, you’ve probably heard the phrase: legitimate rape. As oxymoronic and moronic as it seems, a Missouri congressman and member of the House Science, Space, and Technology committee used this term to argue that women who experience “legitimate rape” likely can’t become pregnant because their bodies “shut that whole thing down.”
If his words and ideas sound archaic, it’s because they are. Welcome to the 13th century, Congressman Todd Akin. It’s possible that this idea that a woman couldn’t become pregnant because of rape arose around that time, at least as part of the UK legal code. People once thought that a woman couldn’t conceive unless she enjoyed herself during the conception–i.e., had an orgasm–so if a rape resulted in pregnancy, the woman must somehow have been having a good time. Ergo, ’twas not a rape. This Guardian piece expands on that history but doesn’t get into why such a concept lingers into the 21st century. A lot of that lingering has to do with a strong desire on the part of some in US political circles to make a rape-related pregnancy the woman’s fault so that she must suffer the consequences. Those consequences, of course, are to be denied abortion access, to carry a pregnancy to term, and to bring a child of rape into the world.
This idea that pregnancy could determine whether or not a rape occurred was still alive and kicking in 20th century US politics, so Akin’s comments, as remarkably magic-based and unscientific as they are, are still not that shocking to some groups. In 1995, another Republican member of the House, Henry Aldridge, made a very similar observation, saying that women can’t get pregnant from rape because “the juices don’t flow, the body functions don’t work.” A year after Aldridge made those comments, a paper published in a US gynecology journal reported that pregnancies from rape occur “with significant frequency.” That frequency at the time was an estimated 32,101 pregnancies resulting from rape in a single year. In other words, the “body functions” did work, and “that whole thing” did not shut down in 32,000 cases in one year alone.
Consider that current estimates are that 1 out of every 6 women in the United States will be a victim of completed or attempted rape in her lifetime and that by the close of the 20th century, almost 18 million women were walking around having experienced either an attempted or a completed rape. The standard expectation for pregnancy rates, whether from an act of violence (rape) or mutually agreed, unprotected intercourse, is about 5%.
In his comments, Akin used the phrase “legitimate rape.” He joins with his colleague of 17 years ago in ignorance about human reproduction. But he also joins legions of people with a history stretching back hundreds of years, people who blamed women for everything having to do with sex and human reproduction. In the medieval world, if a woman bore a daughter and not a son, that was her fault. If she made a man so hot blooded that he forced himself on her, that was her fault for being so attractive, not his for being a rapist. In Akin’s world, in Aldridge’s world, a woman doesn’t need abortion access or a morning after pill to prevent a pregnancy following rape because the determinant of whether or not the rape was “legitimate” is whether or not she becomes pregnant. And the woman, you see, in the Akin/Aldridge cosmos, can “shut that whole thing down” and keep “bodily functions” from working if the rape was, you know, a real, legit-type rape.
In addition to quick primer on human reproduction, I’m offering here a couple of quick points about rape.
Rape is usually an act of violence or power. It is not just an act of sex. It uses sex as a weapon, as though it were a gun or a billy club. It is an act of violence or power against another person without that person’s consent. Nine out of ten rape victims are female. There is not a category of “not legitimate” rape. Sexual violence inflicted without consent is rape. Period.
The thing is, sperm don’t care how they get inside a vagina. They may arrive by turkey baster, catheter, penile delivery, or other creative mechanisms. Any rancher involved in livestock reproduction can tell you that violating a mammal with an object that delivers sperm is no obstacle to impregnating said mammal, no matter how stressed or unwilling the mammal may be.
Akin and Aldridge aren’t the first politicians to manifest a sad lack of understanding of the female body and of human reproduction. Mitt Romney himself has provoked a few howls thanks to his ignorance about birth control, leading Rachel Maddow to offer up a primer on female anatomy for the fellas out there. 
Here’s my own quick primer. About the female: The human female takes some time producing a ready egg for fertilization. That time is often quoted as 28 days, but it varies quite a bit. When the egg is ready, it leaves the ovary and begins a journey down the fallopian tube (also called the oviduct) to the uterus. During its brief sojourn in the fallopian tube, if the egg encounters sperm, fertilization likely will take place. If the egg shows up in the fallopian tube and sperm are already there, hanging out, fertilization is also a strong possibility. In other words, if the egg is around at the same time as the sperm, regardless of how the sperm got there, fertilization can–and often will–happen. The fertilized egg will then continue the journey to the uterus, where implantation into the wall of the uterus happens. Again, if a fertilized egg shows up, the uterine wall doesn’t care how it got fertilized in the first place.
Now to the human male. With ejaculation, a man releases between 40 and 150 million sperm. If ejaculated into the vagina, these sperm immediately begin their short lifetime journey toward the fallopian tube. Some can arrive there in as little as 30 minutes. A woman who has been raped could well already be carrying a fertilized egg by the time authorities begin taking her report. Sperm can live up to three days, at least, possibly as long as five days, hanging out around the fallopian tube. So if an egg isn’t there at the time a rape occurs, if the woman releases one in the days following, she can still become pregnant. Again, the fallopian tubes and ovaries do not care how the sperm got there, legitimately or otherwise.
Although Akin talks about “legitimate rape,” what he and Aldridge and so many other men truly are seeking to do is a twofold burdening of women for having the temerity to experience and report rape. If a woman becomes pregnant because of a rape, you see, then it was not rape. Point one. Point two, because of point one, a woman who reports a rape but becomes pregnant was really engaged in a willing sexual act and therefore must bear–literally–the consequences and, yes, punishment of engaging in that act. She must carry a pregnancy to term. She cannot have access to morning after pills or abortion to prevent or end a rape-related pregnancy because if she’s pregnant, it wasn’t rape, and if she’s pregnant, well, that’s totally her fault for not having her body “stop juices” and “shut that whole thing down.” Got that?
Get this: If you’re a woman who has just been raped, among the many other considerations you deserve, you deserve a morning after pill as part of your rape treatment, if you so desire. Because the hormones in the pills can prevent the impending release of an egg, among other things, create an inhospitable uterine environment for pregnancy, this series of pills can block the implantation of a fertilized egg in the uterine wall** they can save you the added pain, burden, and anguish of a pregnancy resulting from a rape. That, Srs. Akin and Aldridge, is the only established way to “shut that whole thing down,” and it’s a right that every single woman should have.

**A commenter has alerted us (thank you!) to information that came out in June regarding FDA claims about implantation prevention with the morning after pill, which may not be accurate. More on that here and here (NYT). Planned Parenthood cites the IUD as a form of emergency contraception that presumably would prevent implantation. 
These views are the opinion of the author and do not necessarily reflect or disagree with those of the DXS editorial team.

Related links worth reading (updated 8/21/12)

  • io9 breaks down more of the data about rapes and pregnancies, including information about why mammals don’t tend to engage in sperm selection
  • David Kroll notes the problem with having Akin on the House sci and tech committee
  • At the New Statesman, what people really mean when they talk about “legitimate rape”
  • Jezebel’s guide to “legitimate rape”
  • Kate Clancy puts rape stats in context and discusses why pre-eclampsia is not a mechanism for “shutting that whole thing down”
  • Melanie Tannenbaum lays it out and talks about the “Just-world fallacy” that drives thinking like Akin’s