Could the oil energy needed to light up this drill come directly from soil bacteria instead of the soil? Image credit: Obakeneko; via Wikimedia Commons
By Jeffrey Perkel, DXS tech editor It’s no secret that America’s petroleum addiction is a problem in need of a solution. “Drill, baby, drill” notwithstanding, this country eventually will have to find a way to survive without low-cost oil – or at least, find another way to make it.
A recent MIT press release suggests one route to energy independence: soil bacteria. The release, “Teaching a microbe to make fuel,” details a recent study from MIT graduate student Jingnan Lu, research scientist Christopher Brigham, and their lab director, Anthony Sinskey.
What Brigham, Lu, and their colleagues did was convince a soil bacterium called Ralstonia eutropha to turn carbon into gasoline –- specifically, the four-carbon molecules iso-butanol and 3-methyl-1-butanol.
Ralstonia eutropha bacteria in culture
How’d they do that? It was a simple matter of microbial engineering. As detailed in MIT’s description:
… in the microbe’s natural state, when its source of essential nutrients such as nitrate or phosphate is restricted, “it will go into carbon-storage mode,” [Brigham says,] essentially storing away food for later use when it senses that resources are limited.
“What it does is take whatever carbon is available, and stores it in the form of a polymer, which is similar in its properties to a lot of petroleum-based plastics,” Brigham says. By knocking out a few genes, inserting a gene from another organism and tinkering with the expression of other genes, Brigham and his colleagues were able to redirect the microbe to make fuel instead of plastic.
That last sentence makes the process sound easier than it was. It took a full year of work to effect that transformation, Brigham tells me, and no wonder: Bacteria don’t normally make gasoline. But they do make amino acids, the protein building blocks that all living things need to survive. The team realized that Ralstonia bacteria create one particular group of amino acids (the so-called branched-chain amino acids) using chemical intermediates that they could coopt to turn sugar into fuel.
To realize that potential, Brigham and his colleagues first had to get Ralstonia to refocus its energies, literally. When stressed, the bacteria store carbon in a polymer–a chain of molecules–called PHB. The bacterium executes this particular biochemical program extremely effectively, cranking out enough polymer to account for more than 80% of the cell’s mass. Brigham and Lu had to redirect that enzymatic zeal towards gasoline instead. So, they knocked out the genes involved in building PHB.
Next, they added some missing chemical pieces. I said earlier that the branched-chain amino acid pathway includes an intermediate that could be used to make gasoline. To do that, the cells need a missing bit of hardware — specifically, an enzyme to convert that chemical intermediate into something the gasoline-making enzymes can use. That enzyme is called KIVD, and Ralstonia does not make it. But another bacterium, Lactococcus lactis, does make it. Brigham and Lu borrowed the related bit of genetic material from Lactococcus lactis, expressed it in Ralstonia, and –- not much happened.
As University of California, Berkeley, biochemical engineer Jay Keasling explained to me, the cell in such situations is literally a chemical factory. For the factory to run smoothly, all the factory workers –- the enzymes -– need to be fully engaged at the right time. That won’t happen if one enzyme is cranking out lots of its product but others are not. Intermediate products will start piling up, reducing efficiency and potentially poisoning the cell.
In this case, with KIVD, the cells had all the necessary pieces to make gasoline. But they weren’t producing them at the same levels. In other words, the factory had more workers at one part of the assembly line than at others. As a result, productivity was relatively low (about 10 mg isobutanol per liter of culture). To boost that output, the researchers dialed up expression levels of several proteins to get them all in sync. They also shut down a handful of other chemical assembly lines, too, “carbon sinks” that could siphon off intermediates.
When all was said and done, the cells could produce about 310 mg of gasoline per liter of culture. That gas conveniently drifts into the culture medium surrounding the cells, from which it is easily extracted. Now, says Brigham, the trick is optimizing the process.
In the meantime, others are working towards the same goal. Researchers have considerable experience getting bacteria and yeast to produce compounds they don’t normally make — the antimalarial drug artemisinin, for instance -– and microbial biofuel development is a research target at the Joint BioEnergy Institute (headed by Keasling), Synthetic Genomics, and LS9, among other places.
Often, those biofuel strategies rely on plants to produce their starting materials. And that’s the really cool part about Sinskey’s work: Ralstonia can eat almost anything, Brigham says, from carbon dioxide and organic acids to fatty acids and sugar. Brigham envisions coupling these organisms to waste streams, such that they can suck out the nutrients and turn them into fuel, no plants required.
Garbage in, fuel out: Now that’s a microbial trick I can get behind.
(If you’re interested, you can read Brigham and Lu’s work here.)
Image: Christopher Brigham / http://web.mit.edu/newsoffice/2012/genetically-modified-organism-can-turn-carbon-dioxide-into-fuel-0821.html
It is no mystery that there are few women who work in the construction industry. For years the sector has been overwhelmingly male dominated, with women making only 9.6% of the construction industry workforce. The industry, while remaining male dominated, has been increasingly facing a crisis due to the lack of available qualified workers. As the demand for labor surpasses the supply, construction companies expand their recruitment efforts, including a formerly untapped labor source, women. Construction jobs allow for upward mobility directly linked to years of experience and ability to do the work well, making it a desirable career choice for many. However, while sex discrimination is illegal, many construction sites have anti-women attitudes, making construction jobs less desirable and/or torturous for women.
The United States Department of Labor Advisory Committee on Construction Safety and Health reported in 1999 that 88% of women construction workers surveyed had experienced sexual harassment at work. I searched high and low for more current data, but no extensive study has been done since then. Most recent information I found would just claim that things are “getting better” for women in construction, and while I don’t deny that there are more women in construction fields, I am not convinced that sexual harassment and bullying is a thing of the past. Progress is great, but a hostile environment affects a person’s ability to do their job correctly. I know first hand because it happened to me.
I studied Civil Engineering, and most Engineering students know that in order to improve one’s chances of getting hired when you graduate you should have at least one internship or apprenticeship during your undergraduate studies. Internships give you some real life experiences that are just impossible to get from a classroom. During my sophomore year of Engineering school I applied and was hired for an internship as a Construction Manager Assistant for a major construction management company in New York City. My work consisted of being in a construction site and maintaining the project schedule by monitoring project progress, coordinating activities among the different trades, and resolving problems. The finished product was to be a high-rise residential building overlooking Central Park. To this day I am grateful for all that I learned while in a construction site. That experience has helped me along in my professional career in more ways than I can imagine, from dealing with a team, to learning how to schedule major projects. However, being one female out of a total of about 10 women in a site with hundreds of men, was quite alienating and frustrating, at times.
The first day of my internship I arrived with three other interns, two young men and one other female. After being briefed on job site safety we were asked to visit the project’s head foreman, who called in two of his construction managers who would become our mentors. The first manager that arrived looked at all of us and immediately stated “I’ll take the two boys” and feeling a need to apologize, looked at me and the other female intern and said “sorry ladies, I don’t deal with women on this job.” Shortly after another manager arrived, upon seeing us two waiting he said “arethese the interns? I was expecting a couple of guys.” Since we were all that was left he had no choice. He led us to a Field Engineer, a recent college graduate and the only other woman on site that day, and told her to “take care of us.” Apparently, he could not be bothered with being our mentor.
Throughout the summer the two male interns were given jobs overseeing major tasks relating to mechanical equipment, electrical work, and concrete pouring, while the other female intern and I were asked to check if the finished apartments were painted, the marble was installed in the bathrooms, and the light fixtures were properly centered. It was easy to see that as females, we were given the tasks that required the least amount of effort and intelligence. After all, who goes to Engineering school to learn how to watch paint dry? It was aggravating to be doing such boring work; we wanted to be involved in actual construction tasks so as to truly learn engineering techniques applied in the field. After a few weeks of unsuccessfully trying to ask our mentor to give us more interesting work, we decide to seek help from the only female construction manager on site. She was a 50 year old Puerto Rican woman named Milly, who used to be a secretary for the company and fell in love with construction. She paid her way through night school and earned a degree in Mechanical Engineering. After finishing her degree she was hired as a Construction Manager overseeing all the mechanical trades.
Milly became our mentor and made sure that we were always learning something from the tasks we were assigned. She also encouraged us to work separately because, as she would say “you’ll probably be the only woman on any site, better get used to it.” As expected, the work that we were given required us to constantly be around the tradesmen working, as opposed to before when we were mainly in empty finished apartments. I can only speak for myself, because I never asked the other female female intern how she felt or what kind of treatment she received, but it was at this point that I became the target of a lot of sexist, rude, and inappropriate remarks from some of the men. Many times as I walked on by, working men who would stop their work to stare and wolf whistle. Several times a day I had to say “no thank you” to men asking for my number or requesting to take me out on a date. On a few occasions I got called a bitch for refusing to reply to inappropriate remarks. Some men felt the need to give me “get fit” advice and make comments about my body, often pointing at my lack of physical strength as a sign of why I did not belong on a construction site: never mind that technological advances and strict safety codes has made the use of physical strength obsolete in most jobs. Once, I found myself in the middle of a storage room with one construction worker (whom I had never seen before that day) blocking the doorway and refusing to let me leave unless I accepted his request for a date.
I worked on the site for a year, after which I decided the stress of a workplace where I constantly felt harassed, belittled, and intimidated was not worth the effort. The constant fear that someone would make me feel uncomfortable or make a rude remark was making me lose my concentration, and on an active construction site, that is an actual safety hazard. I requested to work with the Project Managers who dealt with the Engineering consultants from the main office and only went on site for field meetings. Today, I am better equipped to deal with everyday sexism, but at 18 years old I was not. I never did report any of the many incidents of sexism and harassment that I endured. I was reluctant to do so for fear of being tagged as a complainer who could not handle the job.
Writing this was one of the hardest things I’ve had to do. I still love the construction industry and promote it as a great career choice for men and women who enjoy being active on their jobs. For every man that demeaned me, there were dozens who uplifted me. For every man that made a sexist comment, there were scores who respected me and valued my work. For every man that harassed me, there were hundreds more who protected me as their coworker. The issue is not that all men refuse to work with women, the issue is that a few men who do not, make the working environment hostile and dangerous for women. Those few that harassed me had the power to ruin my day, alter my mind, and destroy my self confidence. We need to increase the number of women in the construction industry so that we are not a rarity. We must also encourage labor unions and construction employers to include sexual harassment training as part of their health and safety plans. Women deserve to have access to skilled trades, and they deserve to be respected as a fellow colleague.
[Patricia Valoy is a Civil Engineer and an Assistant Project Manager at STV, an architectural, engineering, planning, environmental and construction management firm based in New York City. She is a graduate of the Columbia University School of Engineering in Applied Science, where she majored in Civil Engineering with a concentration in Construction Management. Patricia also is a co-host of a weekly radio show called, “Let Your Voice Be Heard.” The show’s mission is to spread awareness of social and political issues. In addition, she writes a blog about feminist issues and mentors high school and college students interested in pursuing careers in STEM fields. You can follow Patricia on Twitter at @besito86 and read her blog at www.patriciavaloy.blogspot.com.]
When I take a look around my office I see a lot of men, mostly older White men. There are also women, mostly administrative assistants, accountants, and marketing personnel, but few like me. I am an engineer, and I am young, female, Ivy League educated, and Hispanic. I took the same science and mathematics classes all my male peers took. I was given the same tests, the same homework assignments, and the same projects. Yet, every day I have to battle stereotypes of what some think women should be.
Courtesy of Indiana University.
Engineering, and most science fields, have long been male-dominated professions. Yet, in spite of traditional gender roles pigeonholing women to domestic duties, women haven’t necessarily settled into domesticity without first making many great advances in the science fields. We cannot forget Merit-Ptah, an ancient Egyptian physician, and also the first woman to be known by name in the history of the field of Medicine. Or the ancient Greek philosopher Hypatia, also the first historically noted woman in Mathematics. These women were not given positions in Science to fill a status quo, they earned it, just like women today.
Stereotypes are part of my daily life. In high school I was discouraged by a school teacher to apply to Engineering school, because she claimed it was “harder than I was imagining it to be.” She told me that I wanted to pursue a degree in Engineering because of the money I would earn, but it was clear to her that I did not have a passion for it. Never mind that I outperformed all my classmates, including all my male peers, and that I was about to graduate at the top of my class. As a professional adult, I still face these misconceptions about women in science fields. I get my bosses’ mail delivered to me every day because the delivery man, after four years, still thinks that I am a secretary. I politely remind him every day that I am in fact, also an engineer, like my boss, but it seems to fall on deaf ears. So I find myself not only doing my work, but also delivering mail. A week ago I was asked by a new employee which department I belonged in, and the conversation went like this:
Me: “Hi, are you new to our office?”
New Employee: “Yes, I work in the Marketing department. Do you work with Corporate?”
Me: “No, I work in the Transportation and Infrastructure department.”
New Employee: “Are you an administrative assistant?”
Me: “No, an Engineer.”
New Employee: “Oh, you’re an Accountant.”
Me: “Noooo, an Engineer, a Civil Engineer!”
New Employee: “Oh, wow! I would have never guessed…you don’t look like one.”
While I admit to becoming irritated, it was more disconcerting that this co-worker was also a young woman like myself. She reacted in a way that was natural and all too common, because there really aren’t enough women being positively represented in the fields of Science, Technology, Engineering, and Mathematics (STEM). I quite enjoy shaking up perceived ideas of what society assumes I should be, as a woman, a woman of color, and a woman in a male-dominated field, but when will all this shock and awe over women in science fields end? Nonetheless, I love the work I do and the feeling of accomplishment I get when I finish a project. And contrary to 18th century views of the female brain, we have shown that when given the same curriculum as men, we can equally excel.
According to a research study done by the University of Washington, the main culprit for girls not becoming enthusiastic about careers in mathematics and science is gender-stereotyping. The study speaks of the widespread cultural belief in the “girls don’t do math” stereotype. In the study, 247 school-age children (126 girls and 121 boys) were asked to sort four kinds of words: boy names, girl names, math words and reading words, into categories, with the use of an adapted keyboard on a laptop. The lead author of the study, Dario Cvencek, concluded that: “Not only do girls identify the stereotype that math is for boys, but they apply that to themselves. That’s the concerning part. Girls are translating that to mean, ‘Math is not for me.’”
While the study found that both genders equate mathematics with boys, it is unclear why this stereotype is so pronounced at such a young age, though there seems to be a connection with the way in which we speak to young children about mathematics. Dario Cvencek explains: “When a girl does poorly on a math test, often she’s told, ‘That’s fine. You did your best.’ When a boy does poorly, he is more likely to be told, ‘You can do better. Try harder next time.’”
Stereotypes are hurtful, and I believe that stereotype threat, the notion that we experience anxiety in a situation where we have the potential to confirm a negative stereotype, is all too real. We cannot expect young girls to be interested in pursuing careers in science, technology, engineering, and mathematics, if we continue to associate them with one gender. Stereotyping career choices is not in our best interest as we cannot achieve success if we believe that half of our population is not capable of contributing to the betterment of our society. I challenge every educator and parent to reevaluate the way they educate their children. Think about the toys we give them. Building blocks and other shape-sorting toys are equally entertaining for girls as they are for boys, and they help develop cognitive skills, something Barbie and Easy-Bake Ovens will never achieve. Teaching is powerful, and encouraging children to challenge themselves should not depend on the child’s gender.
I am passionate about increasing the number of women represented in STEM fields, not merely because I believe we should be equally represented in all career fields, but because I know we can positively contribute to the advancement of our society. Having both sexes equally represented opens the door for a more diverse range of ideas, which in turn can result in a more robust range of services and products. Additionally, having more women in STEM fields ensures that women’s health and well-being become common practice, and not women’s issues.
Careers in STEM fields require high-level skills and earn higher wages, they are also always in high demand, and experts predicts an even stronger demand for professionals in STEM fields in the future. Our economy is in crisis and 60% of women are the breadwinners or co-breadwinners in their families. If we continue to believe that these high paying careers are only for men, we are not cashing in on the earning power of women. Ultimately, it is not about filling a status quo, it is about using our population, men and women, to the best of their abilities.
Patricia Valoy is a Civil Engineer and an Assistant Project Manager at STV, an architectural, engineering, planning, environmental and construction management firm based in New York City. She is a graduate of the Columbia University School of Engineering in Applied Science, where she majored in Civil Engineering with a concentration in Construction Management. Patricia also is a co-host of a weekly radio show called, “Let Your Voice Be Heard.” The show’s mission is to spread awareness of social and political issues. In addition, she writes a blog about feminist issues and mentors high school and college students interested in pursuing careers in STEM fields. You can follow Patricia on Twitter at @besito86 and read her blog at www.patriciavaloy.blogspot.com.
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.
[Today we have a wonderful guest post from Marie-Claire Shanahan, continuing the conversation about what makes someone a good role model in science. This post first appeared at Shanahan's science education blog, Boundary Vision, and she has graciously agreed to let us share it here, too. Shanahan is an Associate Professor of Science Education and Science Communication at the University of Alberta where she researches social aspects of science such as how and why students decide to pursue science degrees. She teaches courses in science teaching methods, scientific language and sociology of science. Marie-Claire is also a former middle and high school science and math teacher and was thrilled last week when one of her past sixth grade students emailed to ask for advice on becoming a science teacher. She blogs regularly about science education at Boundary Visionand about her love of science and music at The Finch & Pea.] What does it mean to be a good role model? Am I a good role model? Playing around with kids at home or in the middle of a science classroom, adults often ask themselves these questions, especially when it come to girls and science. But despite having asked them many times myself, I don’t think they’re the right questions. Studying how role models influence students shows a process that is much more complicated than it first seems. In some studies, when female students interact with more female professors and peers in science, their own self-concepts in science can be improved . Others studies show that the number of female science teachers at their school seems to have no effect . Finding just the right type of role model is even more challenging. Do role models have to be female? Do they have to be of the same race as the students? There is often an assumption that even images and stories can change students’ minds about who can do science. If so, does it help to show very feminine women with interests in science like thescience cheerleaders? The answer in most of these studies is, almost predictably, yes and no. Diana Betz and Denise Sekaquaptewa’s recent study “My Fair Physicist: Feminine Math and Science role models demotivate young girls” seems to muddy the waters even further, suggesting that overly feminine role models might actually have a negative effect on students.  The study caught my eye when PhD studentSara Callori wrote about it and shared that it made her worry about her own efforts to be a good role model. Betz and Sekaquaptewa worked with two groups of middle school girls. With the first group (144 girls, mostly 11 and 12 years old) they first asked the girls for their three favourite school subjects and categorized any who said science or math as STEM-identified (STEM: Science, Technology, Engineering and Math). All of the girls then read articles about three role models. Some were science/math role models and some were general role models (i.e., described as generally successful students). The researchers mixed things even further so that some of the role models were purposefully feminine (e.g., shown wearing pink and saying they were interested in fashion magazines) and others were supposedly neutral (e.g., shown wearing dark colours and glasses and enjoying reading).* There were feminine and neutral examples for both STEM and non-STEM role models. After the girls read the three articles, the researchers asked them about their future plans to study math and their current perceptions of their abilities and interest in math.** For the most part, the results were as expected. The STEM-identified girls showed more interest in studying math in the future (not really a surprise since they’d already said math and science were their favourite subjects) and the role models didn’t seem to have any effect. Their minds were, for the most part, already made up. What about the non-STEM identified girls, did the role models help them? It’s hard to tell exactly because the researchers didn’t measure the girls’ desire to study math before reading about the role models. It seems though that reading about feminine science role models took away from their desire to study math both in the present and the future. Those who were non-STEM identified and read about feminine STEM role models rated their interest significantly lower than other non-STEM identified girls who read about neutral STEM role models and about non-STEM role models. A little bit surprising was the additional finding that the feminine role models also seemed to lower STEM-identified girls current interest in math (though not their future interest). The authors argue that the issue is unattainability. Other studies have shown that role models can sometimes be intimidating. They can actually turn students off if they seem too successful, such that their career or life paths seem out of reach, or if students can write them off as being much more talented or lucky than themselves. Betz and Sekaquaptewa suggest that the femininity of the role models made them seem doubly successful and therefore even more out of the students’ reach.
The second part of the study was designed to answer this question but is much weaker in design so it’s difficult to say what it adds to the discussion. They used a similar design but with only the STEM role models, feminine and non-feminine (and only 42 students, 20% of whom didn’t receive part of the questionnaire due to an error). The only difference was instead of asking about students interest in studying math they tried to look at the combination of femininity and math success by asking two questions:
“How likely do you think it is that you could be both as successful in math/science AND as feminine or girly as these students by the end of high school?” (p. 5)
“Do being good at math and being girly go together?” (p. 5)
Honestly, it’s at this point that the study loses me. The first question has serious validity issues (and nowhere in the study is the validity of the outcome measures established). First, there are different ways to interpret the question and for students to decide on a rating. A low rating could mean a student doesn’t think they’ll succeed in science even if they really want to. A low rating could also mean that a student has no interest in femininity and rejects the very idea of being successful at both. These are very different things and make the results almost impossible to interpret.
Second these “successes” are likely different in kind. Succeeding in academics is time dependent and it makes sense to ask young students if they aspire to be successful in science. Feminine identity is less future oriented and more likely to be seen as a trait rather a skill that is developed. It probably doesn’t make sense to ask students if they aspire to be more feminine, especially when femininity has been defined as liking fashion magazines and wearing pink.
Question: Dear student, do you aspire to grow up to wear more pink?
Answer (regardless of femininity): Um, that’s a weird question.
With these questions, they found that non-STEM identified girls rated themselves as unlikely to match the dual success of the feminine STEM role models. Because of the problems with the items though, it’s difficult to say what that means. The authors do raise an interesting question about unattainability, though, and I hope they’ll continue to look for ways to explore it further.
So, should graduate students like Sara Callori be worried? Like lots of researchers who care deeply about science, Sara expressed a commendable and strong desire to make a contribution to inspiring young women in physics (a field that continues to have a serious gender imbalance). She writes about her desire to encourage young students and be a good role model:
When I made the decision to go into graduate school for physics, however, my outlook changed. I wanted to be someone who bucked the stereotype: a fashionable, fun, young woman who also is a successful physicist. I thought that if I didn’t look like the stereotypical physicist, I could be someone that was a role model to younger students by demonstrating an alternative to the stereotype of who can be a scientist. …This study also unsettled me on a personal level. I’ve long desired to be a role model to younger students. I enjoy sharing the excitement of physics, especially with those who might be turned away from the subject because of stereotypes or negative perceptions. I always thought that by being outgoing, fun, and yes, feminine would enable me to reach students who see physics as the domain of old white men. These results have me questioning myself, which can only hurt my outreach efforts by making me more self conscious about them. They make me wonder if I have to be disingenuous about who I am in order to avoid being seen as “too feminine” for physics.
To everyone who has felt this way, my strong answer is: NO, please don’t let this dissuade you from outreach efforts. Despite results like this, when studies look at the impact of role models in comparison to other influences, relationships always win over symbols. The role models that make a difference are not the people that kids read about in magazines or that visit their classes for a short period of time. The role models, really mentors, that matter are people in students’ lives: teachers, parents, peers, neighbours, camp leaders, and class volunteers. And for the most part it doesn’t depend on their gender or even their educational success. What matters is how they interact with and support the students. Good role models are there for students, they believe in their abilities and help them explore their own interests.
My advice? Don’t worry about how feminine or masculine you are or if you have the right characteristics to be a role model, just get out there and get to know the kids you want to encourage. Think about what you can do to build their self-confidence in science or to help them find a topic they are passionate about. When it comes to making the most of the interactions you have with science students, there are a few tips for success (and none of them hinge on wearing or not wearing pink):
§ Be supportive and encouraging of students’ interest in science. Take their ideas and aspirations seriously and let them know that you believe in them. This turns out to be by far one of the most powerfulinfluences in people pursuing science. If you do one thing in your interactions with students, make it this.
§Share with students why you love doing science. What are the benefits of being a scientist such as contributing to improving people’s lives or in solving difficult problems? Students often desire careers that meet these characteristics of personal satisfaction but don’t always realize that being a scientist can be like that.
§Don’t hide the fact that there are gender differences in participation in some areas of science (especially physics and engineering). Talk honestly with students about it, being sure to emphasize that differences in ability are NOT the reason for the discrepancies. Talk, for example, about evidence that girls are not given as many opportunities to explore and play with mechanical objects and ask them for their ideas about why some people choose these sciences and others don’t. There are so many ways to encourage and support students in science, don’t waste time worrying about being the perfect role model. If you’re genuinely interested in taking time to connect with students, you are already the right type.
* There are of course immediate questions about how well supported these are as feminine characteristics but I’m willing to allow the researchers that they could probably only choose a few characteristics and had to try to find things that would seem immediately feminine to 11-12 year olds. I still think it’s a shallow treatment of femininity, one that disregards differences in cultural and class definitions of femininity. (And I may or may not still be trying to sort out my feelings about being their gender neutral stereotype, says she wearing grey with large frame glasses and a stack of books beside her).
**The researchers unfortunately did not distinguish between science and math, using them interchangeably despite large differences in gender representation and connections to femininity between biological sciences, physical sciences, math and various branches of engineering.
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