The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.
The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.
Big Molecules with Small Building Blocks
The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.
We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.
When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.
Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.
The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.
Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.
On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.
The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!
If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.
The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?
If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.
In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.
Sugar and Fuel
A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.
Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.
Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.
Polysaccharides: Fuel and Form
Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.
Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.
Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.
Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.
The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.
Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.
The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.
That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.
These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.
Lipids: The Fatty Trifecta
Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.
Fats: the Good, the Bad, the Neutral
Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?
Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows. Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.
Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.
Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.
Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.
The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.
You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.
In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.
A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.
Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.
Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.
Phospholipids: An Abundant Fat
You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.
Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.
There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.
Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.
The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.
Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.
Steroids: Here to Pump You Up?
Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.
But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.
Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.
Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.
As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.
Levels of Structure
Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.
For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.
This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.
Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.
The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.
In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.
A Plethora of Purposes
What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.
As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.
How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.
Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.
DNA vs. RNA: A Matter of Structure
DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.
So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.
RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.
DNA vs. RNA: Function Wars
An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.
These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.
RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.
The Cell Motion BioBus, ready to be boarded by all interested parties. And I do mean parties
About two years ago, I received one of those university-wide mass emails aimed to solicit scientist volunteers to help teach science at an underprivileged school in Manhattan. Given my interest in science education and communication, I read on. The request was on behalf of something called the Cell Motion BioBus, which is a 1974 San Francisco transit bus that has been converted into a high-tech mobile microscopy lab, and for that particular day, the duties of the scientist volunteer involved teaching 3rd graders about the tiny crustacean,Daphnia.
A few weeks later, I found myself inside The BioBus, hanging out and talking science with a bunch of very excited 8-year-olds. We spoke about the habitat whereDaphnia lives, the food it eats, and how it reproduces. We examinedDaphnia anatomy using diagrams on the computer, being sure to locate the heart. After this lesson, the kids went on to mount realDaphnia samples onto microscope slides so that they can look at these tiny “water fleas” at high magnification. The kids did not hold back with their enthusiasm, laughing and giggling while pointing outDaphnia legs, antennae, and the beating heart. It was such a wonderful experience that I wrote about it.
Watching their faces light up with wonder and amazement over something so simple was incredibly gratifying for me, and I immediately came to understand why Dr. Ben, a Columbia University-bred PhD physicist, turned down several coveted offers to become an academic lab head. He, along with Sarah Weisberg, is currently fulfilling the dream of bringing science education to often-overlooked communities. However, as with many a good initiative, funding is limited.
To help keep The BioBus afloat, we at Double X Science are profiling this organization in our new series Good Deeds, Good Science. The timing couldn’t be more perfect because The BioBus is currently looking for help to get home after spreading some sciencey goodness to schools in Illinois, Kansas, Colorado, New Mexico, and Texas. Here is a letter from Sarah:
Dear Science Fan:
I am writing to tell you about a great non-profit organization I’ve been volunteering with, called the Cell Motion BioBus. The BioBus brings practicing scientists (graduate level and above) to teach K-12 students aboard their mobile lab — a converted 1974 transit bus that now houses a research-level microscope lab. I myself have seen how students of all ages and backgrounds respond to the BioBus, and it’s usually along the lines of, “That was AWESOME!”
The BioBus is also an amazing story of grassroots fundraising and charitable giving: the lab was built using donated equipment and labor and right now, the BioBus is at the end of a cross-country tour, during which it was able to bring research-level science to schools in places like rural Kansas, funded by small donations from its supporters.
Now, the BioBus needs help finishing its fundraising campaign so it can return to NYC and continue teaching in 2012. Please help by visiting www.fundly.com/biobus and giving what you can — this is grassroots work, and any amount helps!
Thanks so much, and Happy New Year!
Below is are a few videos of The BioBus trip thus far, which you can find on The BioBus YouTube Channel. If you are willing and able,please donate to this cause. Putting a science-induced smile on a kids face will be well worth it!
Human ovum (egg). The zona pellucida is a thick clear girdle surrounded by the cells of the corona radiata (radiant crown). Via Wikimedia Commons.
It was September of 2006. Due to certain events taking place on a certain evening after a certain bottle (or two) of wine, my body was transformed into a human incubator. While I will not describe the events leading up to that very moment, I will dissect the way in which we propagate our species through a magnificent process called fertilization.
During the fertilization play, there are two stars: the sperm cell and the egg cell. The sperm cell hails from a male and is the end product of a series of developmental stages occurring in the testes. The egg cell (or ovum), which is produced by a female, is the largest cell in the human body and becomes a fertilizable entity as a result of the ovulatory process. But to truly understand what is happening at the moment of fertilization, it is important to know more about the cells from which all human life is derived.
Act I: Of sperm and eggs
A sperm cell is described as having a “head” section and a “tail” section. The head, which is shaped like a flattened oval, contains most of the cellular components, including DNA. The head also contains an important structure called an acrosome, which is basically a sac containing enzymes that will help the sperm fuse with an egg (more about the acrosome below). The role of the tail portion of sperm is to act as a propeller, allowing these cells to “swim.” At the top of the tail, near where it meets the head, are a ton of tiny structures called mitochondria. These kidney-shaped components are the powerhouses of all cells, and they generate the energy required for the sperm tail to move the sperm toward its target: the egg.
The egg is a spherical cell containing the usual components, including DNA and mitochondria. However, it differs from other human cells thanks to the presence of a protective shell called the zona pellucida. The egg cell also contains millions of tiny sacs, termed cortical granules, that serve a similar function to the acrosome in sperm cells (more on the granules below).
Act II: A sperm cell’s journey to the center of the universefemale reproductive system
Given the cyclical nature of the female menstrual cycle, the window for fertilization during each cycle is finite. However, the precise number of days per month a women is fertile remains unclear. On the low end, the window of opportunity lasts for an estimated two days, based on the survival time of the sperm and egg. On the high end, the World Health Organization estimates a fertility window of 10 days. Somewhere in the middle lies a study published in the New England Journal of Medicine, which suggests that six is the magic number of days.
Assuming the fertility window is open, getting pregnant depends on a sperm cell making it to where the egg is located. Achieving that goal is not an easy feat. To help overcome the odds, we have evolved a number of biological tactics. For instance, the volume of a typical male human ejaculate is about a half-teaspoon or more and is estimated to contain about 300 million sperm cells. To become fully active, sperm cells require modification. The acidic environment of the vagina helps with that modification, allowing sperm to gain what is called hyperactive motility, in which its whip-like tail motors it along toward the egg.
Once active, sperm cells begin their long journey through the female reproductive system. To help guide the way, the cells around the female egg emit a chemical substance that attracts sperm cells. The orientation toward these chemicals is called chemotaxis and helps the sperm cells swim in the right direction (after all, they don’t have eyes). Furthermore, sperm get a little extra boost by the contraction of the muscles lining the female reproductive tract, which aid in pushing the little guys along. But, despite all of these efforts, sperm cell death rates are quite high, and only about 200 sperm cells actually make it to the oviduct (also called the fallopian tube), where the egg awaits.
Act III: Egg marks the spot
With the target in sight, the sperm cells make a beeline for the egg. However, for successful fertilization, only a single sperm cell can fuse with the egg. If an egg fuses with more than one sperm, the outcome can be anything from a failure of fertilization to the development of an embryo and fetus, known as a partial hydatidiform mole, that has a complete extra set of chromosomes and will not survive. Luckily, the egg has ways to help ensure only one sperm fuses with it.
When it reaches the egg, the sperm cell attaches to the surface of the zona pellucida, a protective shell for the egg. For the sperm to fuse with the egg, it must first break through this shell. Enter the sperm cell’s acrosome, which acts as an enzymatic drill. This “drilling,” in combination with the propeller movement of the sperm’s tail, helps to create a hole so that the sperm cell can access the juicy bits of the egg.
This breach of the zona pellucida and fusion of the sperm and egg sets off a rapid cascade of events to block other sperm cells from penetrating the egg’s protective shell. The first response is a shift in the charge of the egg’s cell membrane from negative to positive. This change in charge creates a sort of electrical force field, repelling other sperm cells.
Though this response is lightning fast, it is a temporary measure. A more permanent solution involves the cortical granuleswithin the egg. These tiny sacs release their contents, causing the zona pellucida to harden like the setting of concrete. In effect, the egg–sperm fusion induces the egg to construct a virtually impenetrable wall. Left outside in the cold, the other, unsuccessful sperm cells die within 48 hours.
Now that the sperm–egg fusion has gone down, the egg start the maturation required for embryo-fetal development. The fertilized egg, now called a zygote, begins its journey into the womb and immediately begins round after round of cell division, over a few weeks resulting in a multicellular organism with a heart, lungs, brain, blood, bones, muscles, and hair. It’s an amazing phenomenon that I’m honored to have experienced (although I didn’t know I was until several weeks later).
The Afterword: A note on genetics
A normal human cell that is not a sperm or an egg will contain 23 pairs of chromosomes, for a total of 46 chromosomes. Any deviation from this number of chromosomes will lead to developmental misfires that in most cases results in a non-viable embryo. However, in some instances, a deviation from 46 chromosomes allows for fetal development and birth. The most well-known example is Trisomy 21(having three copies of the 21st chromosome per cell instead of two), also called Down’s Syndrome.
The egg and sperm cells are unlike any other cell in our body. They’re special enough to have a special name, gametes, and they each contain one set of chromosomes, or 23 chromosomes. Because they have half the typical number per cell, when the egg and sperm cell fuse, the resulting zygote contains the typical chromosome number of 46. Now you know how we get half of our genes from our father (who made the sperm cell) and half from our mother (who made the egg cell). Did I just put in your head an image of your parents having sex? It’s the birds and the bees, folks—it applies to everyone!
All text and art except as otherwise noted: Jeanne Garbarino, Double X Science Editor
World Health Organization. “A prospective multicentre trial of the ovulation method of natural family planning. III. Characteristics of the menstrual cycle and of the fertile phase,” Fertil Steril(1983);40:773-778
Allen J. Wilcox, et al. “Timing of Sexual Intercourse in Relation to Ovulation — Effects on the Probability of Conception, Survival of the Pregnancy, and Sex of the Baby,” New England Journal of Medicine, (1995); 333:1517-1521
Poland ML, Moghisse KS, Giblin PT, Ager JW,Olson JM. “Variation of semen measures within normal men,” Fertil Steril (1985);44:396-400
Alberts B, Johnson A, Lewis J, et al. “Fertilization,” Molecular Biology of the Cell. 4th edition. New York: Garland Science; 2002.
Nope. This island does not represent your genes. (Source)
When you read news stories about what affects a developing human in the womb or how cancer or obesity arises, you probably also see references to genes and environment. Some articles may focus on genes versus environment, or mention that something is “mostly” genetic or that the “environment” contributes to a disorder or trait in some way. What some people may not realize is that “environment” to a scientist talking about genetics may be something very different from “environment” to a non-scientist reading a news article. While a scientist may be vividly imagining a bustling microenvironment of native molecules in the way only scientists seem to do, the general reader may simply be thinking about “toxins” or “chemicals.” That’s why Double X Science is here to help with a primer on what those scientist types may mean when they talk about genes and environment. See how useful we are? Tell your friends! (Speaking of environmental influences… ). Where does environment begin and end? Let’s begin at the end No gene is an island. Your genes consist in part of a special codethat is really an instruction manual. Your cellsrely on internal translators to decode these instructions and use them as a guide to make various proteins, the molecules that give your cells, tissues, organs, organ systems, and you much of their structure and function. Proteins do thousands of jobs, from breaking down food to building and replacing tissues (news release) to governing cell division. Most of your cells are engaged in making proteins, a complex, exquisitely regulated and multi-step process. But they don’t do it in a vacuum. That code the cell uses to build the protein? That instruction manual is susceptible to all kinds of interference. Pages get torn out or folded over or stuck together. The words of the code can be changed, sometimes subtly, sometimes unmistakably, and all kinds of factors can jumble up those words so that cell ends up making a protein that isn’t quite what was intended. It’s even possible to use the cellular version of Liquid Paper(TM) to mask the code so that the cell doesn’t recognize its existence. Sometimes, these changes have no observable effect. Sometimes, they have big bad effects, such as disease, or helpful outcomes, such as disease resistance. That code sits in a cell in a body (you) made of trillions of cells doing hundreds of different jobs, taking in things from the environment, playing host to millions of other organisms (themselves an environment), altering and shifting with every passing second as the whole system works to keep you together and functioning within certain acceptable limits for human life. All of these processes can influence the code, leading the cell to use it, change it, use only certain parts of it, Liquid Paper over it, tweak what results from its instructions, or just ignore it. It’s impossible for any code in that situation to function in the total absence of influence from its environment, in part because the code itself is just the beginning. Much of the environment’s influence is reflected in what the cell does with the instructions, not just what the instructions say. This multitude of environmental influences is one reason that even people with identical genetic codes can have differences in diseases we think of as being largely genetic. No gene–no code–is an island. You are not your genes. You are your genes and your environment. No nucleus is an island. Most of our genes are packaged neatly with the rest of our DNA around molecular spools inside a cellular vault called the nucleus. This vault is a choosy sentry, letting in only certain molecules carrying proper ID. Yet inside the nucleus, there is an environment. This environment is not “toxins” or “chemicals,” the things that many people probably think of when someone says “environment” and talks about genes. But it is a busy place with its own milieu. Some parts of the code are in use, some sit quiet, and many molecules bustle and hustle to maintain, copy, process, or protect these important instructions. Every little bit of this hustle and bustle can influence some aspect of what happens to a code in the nucleus, interfering with or enhancing its use or resulting in accidental changes that may have big effects further down the line. The nucleus is the final stop in the chain of environmental influence, wherever that influence may originate. No cell is an island. Outside of that vault is the big, wide world of the cell. The cell is the molecular version of a busy metropolis (see beautiful video, The Inner Life of the Cell, below), a complex system of cellular highways that the cell uses to deliver packages internally, take in deliveries from the outside world, and transfer the millions of molecules it’s using and making to the right places at the right time. There’s a generator, a recycling center, guards at the gate, and a protein production facility and processing plant, complete with a post office. And that cell sits in an environment, usually, of many many other cells, also busy with their duties. What happens outside of that cell affects the inside of the cell, altering traffic flows, protein production and packaging, signaling and delivery along the routes, and, ultimately, processes inside the vault called the nucleus, the final destination in the chain of environmental effects. From outside the cell, through the cell, and to the nucleus, every step along the way is one that environment can affect, all the way down to what the cell does with its genes–the codes–for the proteins it makes.
No tissue or organ is an island. A lot of cells working together to do the same thing in your body make up a tissue. Tissues combined together to perform a function are an organ. Let’s take the organ named after living, the liver. It keeps you alive by filtering your blood and reconstructing substances that might harm your cells into less-harmful compounds. Just about everything you ingest gets passed through here. When the liver takes up something like ethanol, the alcohol we ingest at wine o’ clock, and gets to work making it less awful for your body, guess what does that work? The cells that make up the liver. The liver’s environment is their environment is each individual cell’s environment, and eventually, the influence will pass to the nucleus, the final destination in the chain of environmental influence, where the code lies. You are not an island. And whatever you encounter in this world may well influence you right down to the level of your genes. But while many people might think of “toxins” or “chemicals” when they think of environmental influences on genes, your chemical exposures–and chemicals include oxygen, water, body fluids, nutrients and not-so-nutrients in your foods, medications you may take–are among many, many examples of environmental factors that may reach via a chain reaction all the way to your genes. Some of these factors affect your genes by way of your sensory system: A hug, an angry encounter, a sick child, a laugh with a friend–you respond to each of these environmental influences, often by way of hormones that have a chat with your cells. Your cells respond by adjusting how they use the code in the nucleus so that in the face of anger or love or worry, your body still functions within the essential parameters of life. Below, we list with tongue slightly in cheek a sampling of other factors that constitute an “environment” that could influence your genes and how your cell uses them and the proteins they encode. Whether you know it or not, you’re encountering a million factors every day, big and small, that may trigger some effect way down there in the nuclear vaults of your cells, one that reverberates body wide. Some examples of “environment” that might influence genes Environmental influence on genes and how your cells use their instructions and the resulting proteins can come from almost anywhere, any factor, from outside of you and within you. It’s not just about exposures to “bad” chemicals or “toxins.” While the list of potential environmental factors influencing genes and how the cell uses them is practically infinite, we give you just a few examples for thought below:
Your parents, siblings, friends, extended family, co-workers, soccer team–you know, other people
You may have had the experience: A medication you and a friend both take causes terrible side effects in you, but your friend experiences none. (The running joke in our house is, if a drug has a side-effect, we’ve had it.) How does that happen, and why would a drug that’s meant to, say, stabilize insulin levels, produce terrible gastrointestinal side effects, too? A combination of techy-tech scientific approaches might help answer those questions for you — and lead to some solutions.
It’s no secret I love lab technology. I’m a technophile. A geek. I call my web site “Biotechnically Speaking.” So when I saw this paper in the September issue of Nature Biotechnology, well, I just had to write about it.
The paper is entitled, “Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators.” If you read that and your eyes glazed over, don’t worry –- the article is way more interesting than its title.
Those trees on the right are called SPADE trees. They map cellular responses to different stimuli in a collection of human blood cells. Credit: (c) 2012 Nature America [Nat Biotechnol, 30:858--67, 2012]
Here’s the basic idea: The current methods drug developers use to screen potential drug compounds –- typically a blend of high-throughput imaging and biochemical assays – aren’t perfect. If they were, drugs wouldn’t fail late in development. Stanford immunologist Garry Nolan and his team, led by postdoc Bernd Bodenmiller (who now runs his own lab in Zurich), figured part of that problem stems from the fact that most early drug testing is done on immortalized cell lines, rather than “normal” human cells. Furthermore, the tests that are run on those cells aren’t as comprehensive as they could be, meaning potential collateral effects of the compounds might be missed. Nolan wanted to show that flow cytometry, a cell-analysis technique frequently used in immunology labs, can help reduce that failure rate by measuring drug impacts more holistically.
Nolan is a flow cytometry master. As he told me in 2010, he’s been using the technique for more than three decades, and even used a machine now housed in the Smithsonian.
In flow cytometry, researchers treat cells with reagents called antibodies, which are immune system proteins that recognize and bind to specific proteins on cell surfaces. Each type of cell has a unique collection of these proteins, and by studying those collections, it is possible to differentiate and count the different populations.
Suppose researchers wanted to know how many T cells of a specific type were present in a patient’s blood. They might treat those cells with antibodies that recognize a protein known as CD3 to pick those out. By adding additional antibodies, they can then select different T-cell subpopulations, such as CD4-positive helper T cells and CD8-positive cytotoxic T cells, both of which help you mount immune responses.
Cells of the immune system Source: http://stemcells.nih.gov/info/scireport/chapter6.asp
In a basic flow cytometry experiment, each antibody is labeled with a unique fluorescent dye –- the antibody targeting CD3 might be red, say, and the CD4 antibody, green. The cells stream past a laser, one by one. The laser (or lasers –- there can be as many as seven) excites the dye molecules decorating the cell surface, causing them to fluoresce. Detectors capture that light and give a count of how many total cells were measured and the types of cells. The result is a kind of catalog of the cell population. For immune cells, for example, that could be the number of T cells, B cells (which, among other things, help you “remember” previous invaders), and macrophages (the big cells that chomp up invaders and infected cells). By comparing the cellular catalogs that result under different conditions, researchers gain insight into development, disease, and the impact of drugs, among other things.
But here’s the problem: Fluorescent dyes aren’t lasers, producing light of exactly one particular color. They absorb and emit light over a range of colors, called a spectrum. And those spectra can overlap, such that when a researcher thinks she’s counting CD4 T cells, she may actually be counting some macrophages. That overlap leads to all sorts of experimental optimization issues. An exceptionally talented flow cytometrist can assemble panels of perhaps 12 or so dyes, but it might take months to get everything just right.
That’s where the mass cytometry comes in. Commercialized by DVS Sciences, mass cytometry is essentially the love-chid of flow cytometry and mass spectrometry, combining the one-cell-at-a-time analysis of the former with the atomic precision of the latter. Mass spectrometry identifies molecules based on the ratio of their mass to their charge. In DVS’ CyTOF mass cytometer, a flowing stream of cells is analyzed not by shining a laser on them, but by nuking them in superhot plasma. The nuking reduces the cell to its atomic components, which the CyTOF then measures.
Specifically, the CyTOF looks for heavy atoms called lanthanides, elements found in the first of the two bottom rows of the periodic table, like gadolinium, neodymium, and europium. These elements never naturally occur in biological systems and so make useful cellular labels. More to the point, the mass spectrometer is specific enough that these signals basically don’t overlap. The instrument will never confuse gadolinium for neodymium, for instance. Researchers simply tag their antibodies with lanthanides rather than fluorophores, and voila! Instant antibody panel, no (or little) optimization required.
Periodic Table of Cupcakes, with lanthanides in hot pink frosting. Source: http://www.buzzfeed.com/jpmoore/the-periodic-table-of-cupcakes
Now back to the paper. Nolan (who sits on DVS Sciences’ Scientific Advisory Board) and Bodenmiller wanted to see if mass cytometry could provide the sort of high-density, high-throughput cellular profiling that is required for drug development. The team took blood cells from eight donors, treated them with more than two dozen different drugs over a range of concentrations, added a dozen stimuli to which blood cells can be exposed in the body, and essentially asked, for each of the pathways we want to study, in each kind of cell in these patients’ blood, what did the drug do?
To figure that out, they used a panel of 31 lanthanides –- 10 to sort out the cell types they were looking at in each sample, 14 to monitor cellular signaling pathways, and 7 to identify each sample.
I love that last part, about identifying the samples. The numbers in this experiment are kind of staggering: 12 stimuli x 8 doses x 14 cell types x 14 intracellular markers per drug, times 27 drugs, is more than half-a-million pieces of data. To make life easier on themselves, the researchers pooled samples 96 at a time in individual tubes, adding a “barcode” to uniquely identify each one. That barcode (called a “mass-tag cellular barcode,” or MCB) is essentially a 7-bit binary number made of lanthanides rather than ones and zeroes: one sample would have none of the 7 reserved markers (0000000); one sample would have one marker (0000001); another would have another (0000010); and so on. Seven lanthanides produce 128 possible combinations, so it’s no sweat to pool 96. They simply mix those samples in a single tube and let the computer sort everything out later.
This graphic summarizes a boatload of data on cell signaling pathways impacted by different drugs. Credit: (c) 2012 Nature America [Nat Biotechnol, 30:858--67, 2012]
When all was said and done, the team was able to draw some conclusions about drug specificity, person-to-person variation, cell signaling, and more. Basically, and not surprisingly, some of the drugs they looked at are less specific than originally thought -– that is, they affect their intended targets, but other pathways as well. That goes a long way towards explaining side effects. But more to the point, they proved that their approach may be used to drive drug-screening experiments.
But today, I’m writing about those of us who have at least two X chromosomes. You may know that usually, carrying around a complete extra chromosome can lead to developmental differences, health problems, or even fetal or infant death. How is it that women can walk around with two X chromosomes in each body cell–and the X is a huge chromosome–yet men get by just fine with only one? What are we dealing with here: a half a dose of X (for men) or a double dose of X (for women)?
The answer? Women are typically the ones engaging in what’s known as “dosage compensation.” To manage our double dose of X, each of our cells shuts down one of the two X chromosomes it carries. The result is that we express the genes on only one of our X chromosomes in a given cell. This random expression of one X chromosome in each cell makes each woman a lovely mosaic of genetic expression (although not true genetic mosaicism), varying from cell to cell in whether we use genes from X chromosome 1 or from X chromosome 2.
Because these gene forms can differ between the two X chromosomes, we are simply less uniform in what our X chromosome genes do than are men. An exception is men who are XXY, who also shut down one of those X chromosomes in each body cell; women who are XXXshut down two X chromosomes in each cell. The body is deadly serious about this dosage compensation thing and will tolerate no Xtra dissent.
If we kept the entire X chromosome active, that would be a lot of Xtra gene dosage. The X chromosome contains about 1100 genes, and in humans, about 300 diseases and disorders are linked to genes on this chromosome, including hemophilia and Duchenne muscular dystrophy. Because males get only one chromosome, these X-linked diseases are more frequent among males–if the X chromosome they get has a gene form that confers disease, males have no backup X chromosome to make up for the deficit. Women do and far more rarely have X-linked diseases like hemophilia or X-linked differences like color blindness, although they may be subtly symptomatic depending on how frequently a “bad” version of the gene is silenced relative to the “good” version.
The most common example of the results of the random-ish gene silencing XX mammals do is the calico or tortoiseshell cat. You may have heard that if a cat’s calico, it’s female. That’s because the cat owes its splotchy coloring to having two X chromosome genes for coat color, which come in a couple of versions. One version of the gene results in brown coloring while the other produces orange. If a cat carries both forms, one on each X, wherever the cells shut down the brown X, the cat is orange. Wherever cells shut down the orange X, the cat is brown. The result? The cat can haz calico.
Cells “shut down” the X by slathering it with a kind of chemical tag that makes its gene sequences inaccessible. This version of genetic Liquid Paper means that the cellular machinery responsible for using the gene sequences can’t detect them. The inactivated chromosome even has a special name: It’s called a Barr body. The XXer who developed a hypothesis to explain how XX/XY mammals compensate for gene dosage is Mary Lyon, and the process of silencing an X by condensing it is fittingly called lyonization. Her hypothesis, based on observations of coat color in mice, became a law–the Lyon Law–in 2011.
Yet the silencing of that single chromosome in each XX cell isn’t total. As it turns out, women don’t shut down the second X chromosome entirely. The molecular Liquid Paper leaves clusters of sequences available, as many as 300 genes in some women. That means that women are walking around with full double doses of some X chromosome genes. In addition, no two women silence or express precisely the same sequences on the “silenced” X chromosome.
What’s equally fascinating is that many of the genes that go unsilenced on a Barr body are very like some genes on the Y chromosome, and the X and Y chromosomes share a common chromosomal ancestor. Thus, the availability of these genes on an otherwise silenced X chromosome may ensure that men and women have the same Y chromosome-related gene dosage, with men getting theirs from an X and a Y and women from having two X chromosomes with Y-like genes.
Not all genes expressed on the (mostly) silenced X are Y chromosome cross-dressers, however. The fact is, women are more complex than men, genomically speaking. Every individual woman may express a suite of X-related genes that differs from that of the woman next to her and that differs even more from that of the man across the room. Just one more thing to add to that sense of mystery and complexity that makes us so very, very double X-ey.
[ETA: Some phrases in this post may have appeared previously in similar form in Biology Digest, but copyright for all material belongs to EJW.]
(Today’s guest post comes to us from Carrie Fitzgerald, a professor of astronomy at Montgomery College in Maryland. She directs the Montgomery College Observatory; this piece originally ran on her blog.)
Driving past the woodsy grounds of the US Naval Observatory on Massachusetts Avenue, you can’t help but notice the prominent “USNO Master Clock” displaying the time in bright red digits. That is part of their mission, after all, to “determine the positions and motions of celestial bodies, motions of the Earth, and precise time.”
How exactly do they do what they do? And who are these modern day keepers of time and celestial motion?
In the physics and engineering department at MC, we are particularly lucky to have Amy Fredericks as an adjunct astronomy professor, teaching the evening section of our Astronomy 101 course. Not only is Amy a dedicated and enthusiastic instructor, she is also a real live astronomer at the US Naval Observatory!
For students who have wondered how I set the times of the Observatory Open House nights (I base it on when civil twilight ends), or how I know how much of the Moon’s visible disk is illuminated (81% last open house), well, I owe it all to Amy and the USNO Data Services. If I were a leprechaun, the data services portion of the USNO website would be the pot of gold at the end of the rainbow. It’s even better though, because the data services page is super easy to find.
Have you ever wanted to know more about what goes on inside the USNO and what goes into maintaining something as complex as the data services? Amy was generous enough to satisfy our curiosity about what she does during the daylight hours.
Q. I know you as our brilliant and intrepid evening astronomy instructor at Montgomery College, but you have a whole other life at the US Naval Observatory. How long have you been there, and what do you do? A. I have worked at USNO for 6 years, in the Astronomical Applications Department. You could say I’m both an astronomer and a computer programmer. My department, working in concert with Her Majesty’s Nautical Almanac Office in the UK, produces the Astronomical, Nautical, and Air Almanacs. I work in the AA Department’s Software Products Division, which produces software and web applications related to the almanacs and also astrometry and celestial navigation.
I maintain the web applications and assist in the testing and maintenance of all our software products. Our website is http://aa.usno.navy.mil/.
Q. Is there a typical day for you at work? If so, what is it like? A. A typical day may include making updates to our website or our data services, attending status meetings on the latest upgrade to one of products, or helping to get that upgrade ready by testing it.
Q. The USNO in Washington, DC has telescopes. What kind of telescopes do you have and what are they used for? A. The biggest telescope we have in DC is the 26-inch refractor. It is the telescope that Asaph Hall used in 1877 at our old Foggy Bottom location to discover the moons of Mars. It is still used today (despite DC’s light pollution!) to study double stars and the moons of the outer planets. We have a few smaller telescopes that are also used for research. Our “dark sky” site is USNO’s Flagstaff Station in Arizona. That’s where we have some big reflecting telescopes that are used for viewing fainter objects than we can see from DC. One of them was used to discover Charon, the biggest moon of Pluto, in the 1970s.
Q. What is your favorite thing about being at the USNO? A. Our products are used by the military, the scientific community, and the public. I love being able to support all of our users. And, of course, I love the people I work with at the Observatory.
Q. Are you ever able to bring what you do at the USNO into the classroom? A. Sometimes I make passing references to it but not too much. I’m always trying to think of ways! I know friends at other colleges have assigned their students to use our website in their homework.
Q. The USNO is also the official residence of the vice president, so I have to ask…in all the time you’ve been at the USNO, any vice president sightings? A. Sadly, no! Just his helicopter and motorcade on occasion. He does use our library for news interviews, so the librarians probably see him the most.