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

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

How chili powder can kill



Source. Credit.

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

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

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

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

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

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

Colon Cancer Awareness Month: Get your ass screened. We mean it.

Don’t want this growing in your colon?
Get screened. Via Wikimedia Commons.

It started a few months after I had my second son. A pain. Sharp, unrelenting, abdominal. Occasional blood from a place where blood isn’t supposed to appear: the rectum. There. Got the R-word out of the way.

After I had laparoscopy for presumed endometrial scarring as the cause of the pain, the pain nevertheless persisted. So, I was referred to a gastrointestinal (GI) specialist, or gastroenterologist. The GI doc I saw first was a man who, I later, discovered, was the GI doctor for my uncle and my father. They loved him. There probably was a sort of “hail fellow well met” male camaraderie between doctor and patient there that made them sympatico. Me, not so much. He looked at me, looked at my age (36), and decided that all I needed was to take some ibuprofen. He literally sent me home with instructions to take some ibuprofen a few times a day and call him, not in the morning, but maybe in a couple of weeks.

Two years later, after more episodes of blood in the toilet, continued pain, and, pardon me, but I think this information is important, a whole lot of mucus coming out of there, I went to another GI doctor. For whatever reason–even though my symptoms weren’t necessarily a match for colon cancer, even though I didn’t, to my knowledge, have any risk factors for colon cancer, even though I was still quite young to have colon cancer–he decided to do a colonoscopy.

As I emerged from the anesthesia after the procedure, I saw my GI doctor talking with my husband. “How did it go?” I asked, groggy. He sort of smiled at me and said, “You’re not going to remember any of this, but those symptoms you had saved your life.” Unbeknownst to him, amnesia meds don’t work on me–I’ve had ample subsequent opportunities to test that hypothesis–and I did remember it.

How did it save my life? 
What they found in my colon, near where it meets my lower small intestine, was a large, flat growth, about two inches (5 cm) by one inch (2.5 cm). In GI parlance, it was a large, flat (sessile) polyp, which is not a good kind of polyp. Closer analysis of the thing after my GI doctor deftly removed it during a second procedure revealed it to be a tubulovillous adenoma with cancerous tendencies. In fact, my medical records from that doctor now say the word “cancer” on them. 

Adenomas, the type of tumor this was, are “of greatest concern” in the colon. They come in three types: tubular, tubulovillous, and villous. The larger the size, the greater the cancer risk. Mine was large and on its way to becoming cancer. According to my GI doctor, I’d've been dead in another 5 years had I not had that colonoscopy and appropriate intervention. 

In other words, if I’d waited until the recommended age for a first colon cancer screening–age 50–I’d have already been dead for seven years. In fact, I would have died this year from colon cancer.

My mind was saying, “This would have been It. This would have been the thing, in a different time, that would have killed me. My potential death was growing inside of me, and I managed to put a stop to it.” 

It’s true: Colon cancer can be prevented
Finding and removing polyps in the colon can prevent colon cancer from developing. But first, you have to have the screening. Because more than 90% of cases of colorectal cancer happen in people ages 50 or older, the starting age for screening is currently set at age 50. 

If you have symptoms like the following, though, don’t delay. If a GI doctor dismisses you as my first one did–that polyp of mine was probably growing in there for a few years–get a second opinion.

  • Blood in or on the stool (as I had)
  • Stomach pain or aches that do not go away (as I had)
  • Unexplained weight loss
  • A change in bowel habits (diarrhea, constipation, frequency)
  • A feeling of incomplete emptying



Colon cancer is associated with some risk factors. These include

  • Age 
  • Having previously had colon polyps or colorectal cancer yourself
  • A family history of polyps or colorectal cancer
  • A history of having inflammatory bowel disease (Crohn’s or ulcerative colitis; not to be confused with irritable bowel syndrome or IBS)
  • A family history of inherited disorders related to polyps of the colon

Of these factors, I thought going into my GI doctors that I had none. Only later did I learn that my father also had had some polyps found and removed, although of the more typical and less-threatening variety and at a later age (in his 50s). In addition, in the past year, my octogenarian maternal grandmother had a large colorectal cancer removed that had likely begun its evolution from a polyp years ago, but she had never undergone screening. I cannot stress enough how important it is for a family to share health history so that these risks can be known and for anyone to have appropriate screening either at the recommended age or in the presence of symptoms.

Speaking of family, there is my own. My having been diagnosed with a precancerous growth at age 38 means that my first-degree relatives–siblings, parents, children–should have screening at least by that age and preferably years before.

There is some understandable reluctance to have a colonoscopy. Outside of the obvious ignominy of having someone shove a tube up your rectum while you lie anesthetized (I woke up during my second–yep, there’s a tube in there), there is the preparation for it. I’ve done just about every prep known to modern medicine, having now had five colonoscopies–all my follow-ups have been clear, and I don’t need another for four years now (!). Yes, they’re unpleasant, and they take quite a bit of willpower. You have to drink what they tell you, take the pills that they tell you, not eat when they tell you, and consume only what they say is OK. You’ll never want to see Jell-O or Gatorade again, and I can’t stare down a bowl of clear bouillon any more without feeling a tad nauseated. 

But the goal of a prep is a completely clean colon. The cleaner you get it, the more accurate your findings will be and the less likely you’ll have to do it again simply because you conducted–pardon me–a  crappy prep. 

March is Colon Cancer Awareness month. Be aware and embrace the reality that polyps happen and that so far, finding them requires this daylong unpleasantness. But also embrace the fact that the prep won’t kill you. Instead, it will help you prevent a cancer that does, in fact, kill 50,000 people a year in the United States alone. 

This year, five years after that first colonoscopy would have been the year I’d've been one of those people. Thanks to that procedure, I am instead alive and well enough to tell you about it, and my three young sons still have their mother. I’d starve for a week and drink Gatorade until I puked to make sure of that outcome.
————————————————————–
By Emily Willingham, DXS Managing Editor

Pregnancy 101: My placenta looked like meatloaf, but I wasn’t about to eat it.

By Jeanne Garbarino, Biology Editor
An historic view interpretation of the placenta (source). 

She gave me a few minutes to meet my daughter before she reeled me back into a state that was my new reality.  “You’re not finished Jeanne.  You still need to birth your placenta.”  What?!?! More pushing? But I was lucky and the efforts required to bring my placenta ex vivo were minimal. 

This is the second placenta my body helped make.  OK,
so it doesn’t EXACTLY look like meatloaf…  

The idea of a placenta, which is the only human organ to completely and temporarily develop after birth, was fascinating.  That thing sitting in a rectangular periwinkle bucket was what allowed me to grow another human.. inside of my body!  There was no way I was not going to check it out, as well as create a permanent record of its relatively short-lived existence. 

My first impression was that it looked like “meatloaf.”  Not necessarily a well made meatloaf, but perhaps one that is made by my mother (sorry mom).  But, alas, chaos reigned and I wasn’t able to really take a good look.  However, for my second birth and hence second placenta, my midwife indulged me with a more detailed look and a mini-lesson.   

Baby’s eye view:
Where geekling deux spent 39 weeks and 4 days. 

Her gloved hands, still wet with my blood and amniotic fluid, slid into the opening that was artificially created with a tool resembling a crocheting needle.  She opened the amniotic sac wide so I could get a baby’s eye view of the crimson organ that served as a nutritional trading post between me and my new bundle of joy. 

She explained that the word “placenta” comes from from the Greek word plakoeis, which translates to “flat cake” (however, I’m sure if my mom’s meatloaf was more common in ancient Greece, the placenta would be named differently).   “It’s one of the defining features of being a mammal,” she explained as I was working on another mammalian trait – getting my baby to nurse for the first time.

That was about all I could mentally digest at the time, but still, more than three years later, the placenta continues to fascinate me, mostly due to the fact that it is responsible for growing new life.  It’s a natural topic for this long overdue Pregnancy101post, so let’s dive in!
Development of the placenta
It all starts when a fertilized egg implants itself into the wall of the uterus.  But, in order to fully understand how it works, we should start with an overview of the newly formed embryo. 

The very early stages of us (and many other things that are alive).
The trophoblast invades the uterus,
leading to implantation of the blastocyst.

As soon as a male sperm cell fuses with a female egg cell, fertilization occurs and the cells begin to multiply.  But, they remain contained within a tiny sphere.  As the cells continue to divide, they are given precise instructions depending on their location within that sphere, and begin to transform into specific cell types.  This process, which is called cellular differentiation, actually seals the fate every cell in our body, sort of like how we all have different jobs – some of us are transport things, some of us are involved in policing the neighborhoods, some of us build structures, some of us communicate information, some of us deal with food, some of us get rid of waste, etc.  Every cell gets a job (it’s the only example of 100% employment rates!).

Now back to the cells in the fertilized egg.  As they start to learn what their specific job will be, the cells within the sphere will start to organize themselves.  After about 5 days after fertilization, the sphere of cells becomes something called a blastocyst, which readies itself for implantationinto the wall of the uterus. 

The act of implantation is largely due to the cells found on the perimeter of the blastocyst sphere.  These cells, collectively known as the trophoblast, release a very important hormone – human chorionic gonadotropin (hCG) – that tells the uterus to prepare for it’s new tenant.  (If you recall, hCG is the hormone picked up by pregnancy tests.)  Around day 7, the trophoblast cells start to invade the lining of the uterus, and begin to form the placenta.  It is at this point that pregnancy officially begins.  (Here is a cool video, created by the UNSW Embryology Department, showing the process of implantation.)

Structure of the placenta

Eventually the trophoblast becomes the recognizable organ that is the placenta.  Consider the “flat cake” analogy, with the top of the cake being the fetal side (the side that is in contact with the baby), and the bottom of the cake being the maternal side (the side that is in contact with the mother).     

Cross section of the placenta: Blood vessels originating from the fetus sit in a pool
of maternal blood, which is constantly replenished my maternal arteries and veins.
The red represents oxygenated blood, and the blue represents de-oxygenated blood.

Projecting from the center of the fetal side of the placenta are two arteries and one vein, coiled together in a long, rubbery rope, often bluish-grey in color.   This umbilical cord serves as the tunnel through which nutrients and waste are shuttled, and essentially serves to plug the baby into the mother’s metabolic processes.  At the umbilical cord-placenta nexus, the umbilical cord arteries and vein branch out into a network of blood vessels, which further divide into a tree-like mass of vessels within the placenta. 

These tree-like masses originating from the umbilical cord (and thus fetus) sit in a cavity called the intervillous space, and are bathed in nutrient-rich maternal blood.  This maternal blood, which provides the fetus with a means for both nutrient delivery and waste elimination, is continually replenished via a network of maternal arteries and veins that feed into the intervillous space.  Furthermore, these arteries and veins help to anchor the placenta into the uterine wall.  One of the most interesting aspects about the mother-feus relationship is that the blood vessel connection is indirect.  This helps to prevent a detrimental immune response, which could lead to immunological rejection of the fetus (sort of like how a transplanted organ can become rejected by the recipient).  
Functions of the placenta

Just like a plant needs sunlight, oxygen, and water to grow, a baby needs all sorts of nutrients to develop.  And since a baby also produces waste, by nature of it being alive and all, there is an absolute requirement for waste removal.  However, because we can’t just give a developing fetus food or a bottle, nor are we able to change diapers in utero, the onus lies completely on the biological mother. 

This is where the placenta comes in. Because the fetus is plugged into the circulatory system of the mother via the umbilical cord and placenta, the fetus is provided with necessary nutrients and a mechanism to get rid of all the byproducts of metabolism.  Essentially, the placenta acts as a waitress of sorts – providing the food, and cleaning it all up when the fetus is done eating. 

But it’s not just about nutrition and waste.  The placenta also serves as a hormone factory, making and secreting biological chemicals to help sustain the pregnancy.  I mentioned above that the placenta produces hCG, which pretty much serves as a master regulator for pregnancy in that it helps control the production of maternally produced hormones, estrogen and progesterone.  It also helps to suppress the mother’s immunological response to the placenta (along with other factors), which cloaks the growing baby, thereby hiding it from being viewed as a “foreign” invader (like a virus or bacteria). 

Another hormone produced by the placenta is human placental lactogen (hPL), which tells the mother to increase her mammary tissue.  This helps mom prepare for nursing her baby once it’s born, and is the primary reason why our boobs tend to get bigger when we are pregnant.  (Yay for big boobies, but my question is, what the hell transforms our rear ends into giant double cheeseburgers, and what biological purpose does that serve??  But I digress…)

Despite the fact that the mother’s circulatory system remains separate from the baby’s circulatory system, there are a clear mixing of metabolic products (nutrients, waste, hormones, etc).  In essence, if it is in mom’s blood stream, it will very likely pass into baby’s blood stream.  This is the very reason that pregnant mothers are strongly advised to stay away from cigarettes, drugs, alcohol, and other toxic chemicals, all of which can easily pass through the placental barrier lying between mother and fetus.  When moms do not heed this warning, the consequences can be devastating to the developing fetus, potentially leading to birth defects or even miscarriage.        

There are also situations that could compromise the functions of the placenta – restriction of blood supply, loss of placental tissue, muted placental growth, just to name a few – reducing the chances of getting and/or staying pregnant.  This placental insufficiency is generally accompanied by slow growth of the uterus, low rate of weight gain, and most importantly, reduced fetal growth.     

And it’s not just the growth of the placenta that is important – where the placenta attaches to the uterus is also very important.  When the placenta grows on top of the opening of the birth canal, the chances for a normal, vaginal birth are obliterated.  This condition, known as placenta previa, is actually quite dangerous and can cuase severe bleeding in the third trimester.  0.5% of all women experience this, and it is one of the true medical conditions that absolutely requires a C-section. 

Then, there is the issue of attachment.  If the placenta doesn’t attach well to the uterus, it could end up peeling away from the uterine wall, which can cause vaginal bleeding, as well as deprive the baby from nutrient delivery and waste disposal.  This abruption of the placenta  is complicated by the use of drugs, smoking, blood clotting disorders, high blood pressure, or if the mother has diabetes or a history of placental abruption. 

Conversely, there are times when the blood vessels originating from the placenta implant too deeply into the uterus, which can lead to a placenta accreta.  If this occurs, the mother generally delivers via C-section, followed by a complete hysterectomy. 

Cultural norms and the placenta

There are many instances where the placenta plays a huge role in the culture of a society.  For instance, both the Maori people of New Zealand and the Navajopeople of Southwestern US will bury the placenta.  There is also some folklore associated with the placenta, and several societies believe that it is alive, pehaps serving as a friend for the baby.   But the tradition that seems to be making it’s way into the granola culture of the US is one that can be traced back to traditional Chinese practices: eating the placenta. 

Placentophagy, or eating one’s own placenta, is very common among a variety of mammalian species.  Biologically speaking, it is thought that animals that eat their own placenta do so to hide fresh births from predators, thereby increasing the chances of their babies’ survival.  Others have suggested that eating the nutrient-rich placenta helps mothers to recover after giving birth.

However, these days, a growing number of new mothers are opting to ingest that which left their own body (likely) through their own vaginas.  And they are doing so though a very expensive process involving dehydrating and encapsulating placental tissue.  

Why would one go through this process?  The claims are that placentophagy will help ward of post partum depression, increase the supply of milk in a lactating mother, and even slow down the ageing process.  But, alas, these are some pretty bold claims that are substantiated only by anecdata, and not actual science (see this).

So, even though my placentas looked like meatloaf, there was no way I was eating them.  If you are considering this, I’d approach the issue with great skepticism.  There are many a people who will take advantage of maternal vulnerabilities in the name of cold hard cash.  And, always remember, if the claims sound to good to be true, they probably are!   


Thanks for tuning into this issue of Pregnancy101, and enjoy this hat, and a video!

Source


You – Yes, You – Are an Astronomer

On January 7, 1610 (402 years ago today!), Galileo first identified three moons of Jupiter, the first satellites ever observed orbiting another planet. He later found a fourth, and today those moons — Io, Europa, Ganymede, and Callisto — are known as the Galilean moons in his honor. Galileo was able to do this because he used a telescope to observe: every new way to see reveals something new to be seen.

You can buy a telescope that’s more or less equivalent to Galileo’s ‘scope here for a very low price. (It’s actually much better, in my opinion, since the housing is made of plastic instead of cardboard! Also, you don’t have to grind your own lenses.) I don’t endorse most products, but I’ll happily plug this one: it’s a non-profit group whose aim is to get people looking at the skies, and I’ve used these ‘scopes in my astronomy classes. What was a specialist’s tool in 1610 is something available for everyone today; you can even see the four Galilean moons of Jupiter with a decent pair of binoculars.

I spent the holidays with my family in Iowa: my parents live in a very very very small town, without much light pollution. It was clear at night several days, and so we went out in the backyard to see what we could see. With my parents’ binoculars, we managed to see all four Galilean moons, and over three nights of viewing, saw how their positions changed as they orbit Jupiter. We were doing astronomy in the backyard: no specialized equipment, no special training, no observatory needed. Even in a city, you can still see the brighter planets (Jupiter is the third-brightest object in the night sky, after the Moon and Venus), and if your city is like mine, amateur astronomy groups are around that set up public nights to show you the sights.

You don’t need to be a trained professional to be an astronomer. You don’t need a huge telescope. You just need to look up. You can learn to read the night sky, identify planets, look for interesting nebulae and stars. If the sky is clear tonight, you can go outside and see Jupiter after sundown, and if you have binoculars or a small telescope, all four Galilean moons will even be visible. Jupiter is high above the horizon, and the brightest object other than the Moon tonight. Go look, and when you’re done, call yourself an astronomer. I’ll back you up.

(This post originally appeared at Galileo’s Pendulum.)