Xplainer: How do you date a pregnancy?



Pregnancy
By Catherine Anderson, DXS contributor
[This post first appeared Musings of Genegeek.]

In the first case-based class of medical school, students are asked to answer a virtual patient’s question about the development of the fetus. These students are smart and they know all about betaHcG and are anxious to showcase their knowledge of the menstrual cycle with fluctuating levels of various hormones (FSH, progesterone, etc.). Yet one question brings confusion, “How pregnant is this woman?” The related question, “When does pregnancy start?” leaves the students flummoxed. Is it at conception? But how do you know when that happens? Or does implantation make more sense? It’s a great example of how detailed facts need the larger context.
The usual dating is gestational age, based on the first day of your last menstrual period. However, you can also date a pregnancy with embryological age, starting at conception.
How you date a pregnancy can depend on your perspective. My very general guideline:
  • Pregnant woman is the focus = gestational age (e.g., obstetricians) 1
  • Focus on embryological/fetal development = embryological age (e.g., developmental biologist) 2
But why are there two types of dates? We might need a bit of a primer on the menstrual cycle and how it relates to pregnancy.

Implantation happens between days 20 and 22. Pregnancy is often detected after the first missed period.
This graphic is intentionally simple, removing all the hormones and other fun stuff (Ed: which you can find here). You’ll note that it says approximately day 14 and day 28. In textbooks, we often see that women have 28-day cycles and everything has a nice schedule. However, women are not textbooks and sometimes have shorter or longer cycles and/or have ovulation at slightly different times. Therefore, knowing when fertilization and conception happen can be a bit tricky. An obvious marker is the first day of the last menstrual period (LMP). Why the last day? Well, another variable is the length of menses but everyone has a first day so to be consistent, that is the marker used.
We generally use gestational age when discussing pregnancy. So when someone says that they are 8 weeks pregnant, they mean it has been 8 weeks since the first day of the LMP (last menstrual period).
But that means that the first two weeks of pregnancy has nothing happening. If you are concerned about development, you don’t start counting at week 3 but start at the time of fertilization, two weeks later. Therefore, the embryological age is generally two weeks later.
But remember, we have essentially picked gestational age as the convention for discussing pregnancy dates. If  there are markers in development to suggest that the embryological age is different (for example, the fetus is 12 weeks, not 13 weeks), the gestational age is often reported to the mother. In our example, the dating would be changed to 14 weeks.
Due to the difference in these dates, we see confusion beyond medical students thinking about this for the first time. It was recently reported that Arizona had changed its abortion law to be the most restrictive – but it hadn’t. It had just joined other states in making the limit 20 weeks gestational age. Remember, this is the accepted convention for pregnancy dating – but many articles picked up on that initial two weeks of nothingness in gestational age and confused it with embryological age. Was this an example of details without understanding of the greater context?
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  1. Synonyms include obstetrical and menstrual age. 
  2. Synonyms include developmental, conception, and fetal age. 

Opinions expressed in this piece are those of the author and do not necessarily reflect or conflict with the opinions of DXS editors or contributors.
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Dr. Catherine Anderson is a Clinical Instructor for the Faculties of Medicine and Dentistry for UBC in Vancouver, Canada. She also leads the Future Science Leaders program, helping teens excel in science and technology. She received her PhD in Medical Genetics and has spent the last 10 years helping people understand the biological sciences: the information and the impact on our lives. You can follow her on Twitter @genegeek.

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

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

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

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

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

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

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

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

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

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

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

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

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



Colon cancer is associated with some risk factors. These include

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

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

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

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

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

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

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

Miscarriage: When a beginning is not a beginning

The “Pregnant Woman” statue
at Ireland Park, Toronto, by Rowan Gillespie

Photo credit: Benson Kua.
[Editor's note: We are pleased to be able to run this post by Dr. Kate Clancy that first appeared at Clancy's Scientific American blog, the wonderful Context and Variation. Clancy is an Assistant Professor of Anthropology at the University of Illinois. She studies the evolutionary medicine of women’s reproductive physiology, and blogs about her field, the evolution of human behavior and issues for women in science. You can follow her on Twitter--which we strongly recommend, particularly if you're interested in human behavior, evolutionary medicine, and ladybusiness--@KateClancy.]
Over the course of my training to become a biological anthropologist with a specialty in women’s reproductive ecology and life history theory, or ladybusiness expert, I have learned a lot about miscarriage. Only it wasn’t miscarriage, it was spontaneous abortion. Except that some didn’t like the term spontaneous abortion and used intrauterine mortality (Wood, 1994). Or fetal loss. Fetal loss is probably the most common.
There is also pregnancy loss (Holman and Wood, 2001). You can use that term, too. Oh, or a Continue reading

As Seen on TV! Age Your Wine in 10 Seconds!!!!

Old, old wine. (Source)

Anyone who watches TV, reads magazines, or flips through catalogs has seen some interesting products. Maybe they seem plausible to you, maybe they don’t. However, a little investigation shows they are based less on science and well…actually working, and more on wishful thinking. At worst they’re actual con-jobs, designed to separate you from your money as efficiently as possible (which I guess is a certain standard of success).


As a result, we at Double X Science are starting a new series: “As Seen on TV!” In these features, we’ll look at some of the products shilled on talk shows and infomercials, items lurking between the articles you read in magazines, or things you might find on the shelves of the stores where you shop.

Our first entry is one I spotted in SkyMall, the catalog you (if you’re like me) read if you forget to bring a book on an airplane. Where else can you find dog water bowls shaped like toilets or sports chairs built deliberately too large for anyone, so you look tiny sitting in them? While the catalog is full of impractical items (to put it mildly), some of them go beyond that into the realm of…imagination. Yeah, I’ll call it that. It avoids potential lawsuits.

It’s the Aging Accelerator! With Magnets!

Here’s the idea: depending on which device you buy, you insert either a glass or a bottle of wine, and within 10 seconds! it ages the wine, with the unspoken assumption that this is desirable. (It also evidently works for whiskey, but I’ll skip that discussion in the current article.) Now, anything that promises to drastically alter something within 10 seconds! is probably suspicious to begin with, but that’s the part I’m going to leave alone. After all, magnets do work quickly, so if the device does what it claims to do, it’s quite possible that 10 seconds will be enough time for the magic to happen.

Well, it seems like magic to me. I went to a winery last weekend, and spoke to one of the vintners there (yup, that’s the name for ‘em). She told me that not all wines should be aged, and the reason has to do both with the way wine is made and how it is stored.

First, not all wine should be aged! All wines actually go bad over time, including many of the usual types you may see in the store. That time may be pretty long, but you don’t want to just buy any bottle, stick it in your basement, and wait 20 years to drink it – most of them won’t taste good. According to my source, the days are gone where you might buy bottles of wine and put them in a cellar for your children. (Who has a wine cellar now anyway? I live in a second-floor apartment!) Basically, my source tells me to ask an expert if you have any doubts, but basically all wine is sold today in a drinkable state – no aging is necessary or even wanted. (I can’t endorse it, but Wikipedia has a list of wines that can be aged, and possible ranges.) Earth’s magnetic field has nothing to do with the aging process, whatever the ad says.

Second, the reason some wines age better than others has to do with their chemistry: how much sugar is in the grapes and how much tannin content they have. Red wines typically are higher in tannins because the skins are thrown in with the flesh of the fruit – and tannins act as a preservative. Sugar also acts as a preservative, but it’s not as effective, so white wines (lower in tannins, higher in sugar) don’t keep as well.

The point I’m trying to make is that wine aging isn’t mysterious, either why it happens or how. I don’t have the “Aging Accelerator” package in front of me, so I can’t tell you if they give advice on which wines to put in it and which ones to avoid, but the picture shows both reds and whites. So let’s turn to the way the device is supposed to work: magnetism.

They certainly have one thing right: neodymium magnets are very strong! (Neodymium is one of the “rare earth” elements, found near the bottom of the periodic table, so sometimes you’ll see them referred to as “rare earth magnets”.) When I’ve used neodymium magnets for various experiments, two of them attracting each other pinched my fingers hard enough to create blood blisters.

Admittedly magnets can seem mysterious: understanding exactly how they work requires looking at electrons and atoms, which might seem a little out of the ordinary. However, challenging isn’t the same thing as magical, but some people seem to think that magnets are capable of all sorts of feats, from curing arthritis to – yes – aging wine.

How magnets actually work could be the topic of an “Everyday Science” post, but in brief: the way a material responds to a magnet is called its magnetic susceptibility. Some materials, like neodymium, are very susceptible, but most things aren’t, including the human body. (Some organisms such as pigeons use Earth’s magnetic field to navigate, but exactly how they do it is still not known.) I couldn’t find any particular data on the magnetic susceptibility of tannins or other molecules in wine, but my feeling is it’s not large. Tannins are big biological molecules – think DNA or proteins – and those don’t tend to be magnetic.

But here’s the deal: suppose tannins are magnetic. Why then would exposing them to a magnetic field age the wine? Simply putting a strong magnet near your wine would merely rearrange the molecules inside the liquid – it’s like stirring it, in other words. Obviously stirring something can change the way it tastes, since it can mix sediments in, but that’s not the same thing as aging.

So, let’s wrap up: why should we be suspicious of paying $60 or $100 for an “Aging Accelerator”?
  • The concept misuses a well-understood physical principle – magnetism. Just because someone doesn’t understand how it works doesn’t mean it can perform miracles.
  • The aging process is chemical, and we understand how that works – it involves tannins, sugars, and other molecules. There are no secrets, in other words, and nothing simple to make your wine taste better.
  • Basically, if it sounds like a magic trick, it probably is – but its main result will be to magic money out of your pocket.
We’ll see these kinds of rules repeated throughout the series!

Stay tuned for further installments of “As Seen on TV!”


By DXS Physics Editor Matthew Francis 




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Breast cancer screening and treatment, especially in younger women

[Editor's note: I was on Twitter, as usual, a couple of days ago, and started seeing tweets with the hashtag #SSCAbc. They contained information that I, an avid consumer of science and medical information, don't normally see addressed in breast cancer stories, including for young women with breast cancer and how to talk to children about having breast cancer. I've aggregated some of those tweets below, but you can read more at the hashtag here, which represents the Seattle Cancer Care Alliance, whose representatives were conducting the Twitter session.]

[View the story "Seattle Cancer Care Alliance: Talking about breast cancer" on Storify]

Seattle Cancer Care Alliance: Talking about breast cancer

http://www.sccablog.org/2012/10/tweeting-for-breast-cancer-awareness-month/ Twitter handles @SeattleCCA, @UWMedicineNews, and @HutchinsonCtr; also @jrgralow and @SeattleMamaDoc

Storified by Emily Willingham · Mon, Oct 15 2012 13:00:07

“@stales: MT @SeattleMamaDoc: Exercise lowers hormone levels, consequently lowers risk of breast cancer.#SCCAbc #SCCAbc”MESFER AL SHAHRANI
#SCCAbc Topic 3: If your mother or sister had breast cancer, especially < age 40, you may be at increased risk.Julie Gralow
RT @jrgralow: Breast cancer in multiple family members, especially at young age, increases risk. Great info: http://ow.ly/euFq8 #SCCAbcWendySueSwanson MD
THIS IS A TRIPLE WHAMMY: Breast feeding is good for mom, great for baby, & lowers breast cancer risk (less estrogen while nursing) #SCCAbcWendySueSwanson MD
RT @SeattleCCA: Recap T2: earlier age at first #pregnancy, more pregnancies & #breastfeeding can decrease #breastcancer risk #SCCAbcAlicia C. Staley
Tough for many of us—and not necessary–but earlier pregnancies (esp under age 20) dec risk of breast cancer #SCCAbcWendySueSwanson MD
RT @SeattleMamaDoc: Tell your teens. Scream it from the rooftop RT @jrgralow: #SCCAbc Oral contraceptives do NOT increase breast cancer riskDominique B.
TOPIC 4 Q1: What is the recommended age for a #mammogram, and why? #SCCAbcSeattle Cancer Care
RT @jrgralow: We recommend starting age 40 for most women. If you have higher or lower risk than average this will vary. #SCCAbcUW Medicine News
Mammograms can decrease rate of death from breast cancer, especially true in those women over age 50 #SCCAbc http://1.usa.gov/puQ0NcWendySueSwanson MD
RT @seattlecca: T4 Q2: What else can a woman do other than a #mammogram to screen for #breastcancer? #SCCAbcUW Medicine News
RT @jrgralow: #SCCAbc Topic 4: Younger women have denser breasts, making mammos less reliable. Here’s some info: http://ow.ly/euH6tUW Medicine News
RT @jrgralow:Topic 4: Ultrasound is great in young, dense breast when abnormality is noted. So far, not a good screening tool yet. #SCCAbcUW Medicine News
#SCCAbc Topic 4: Breast MRI more sensitive than mammo in young women. For women with strong family history we recommend breast MRI .Julie Gralow
BRCA1 & BRCA2 are genes that can be passed in families & inc your risk of breast cancer. There’s blood tests 4 BRCA1&2 gene changes. #SCCAbcWendySueSwanson MD
#SCCAbc Topic 3: We can test for BRCA1/2, also sometimes PTEN or p53 or other tests may be applicable.Julie Gralow
RT @SeattleMamaDoc If concerned abt costs of genetic test, call ur insurance prior to tests. I also rec genetic counseling visits. #SCCAbcAlicia C. Staley
RT @SeattleMamaDoc Mammos, like most things, arent perfect. Esp in the young. If high risk 2 fam history/genes, ask abt breast MRI #SCCAbcAlicia C. Staley
RT @uwmedicinenews: Topic 5 Q1: how would you recommend speaking with young children about a loved one’s breast cancer? #SCCAbcHutchinson Center
More than anything, take ur time in explaining breast ca diagnosis with children. There isn’t urgent rush for all details at once #SCCAbcWendySueSwanson MD
@jrgralow Children learn fear of cancer from us. Be open/provide info, take them to chemo if they want, helps normalize #gr8 advice #SCCAbcUW Medicine News
RT @jrgralow: SCCAbc Topic 5: I love this book (by one of my patients) on talking about chemo with kids. http://ow.ly/euInm #SCCAbcSeattle Cancer Care
RT @jrgralow: Young Survival Coalition offers great support for young women w breast cancer http://www.youngsurvival.org/ #SCCAbcWendySueSwanson MD
RT @SeattleMamaDoc: Tip: Let people help you on YOUR terms when navigating cancer diagnosis &raising children. #SCCAbcUW Medicine News
#SCCAbc Topic 5: 2 great sets of info on coping and relationships and cancer. http://ow.ly/euITz http://ow.ly/euIUHJulie Gralow
Consider freezing eggs before chemo RT @jrgralow #SCCAbc T2: Chemo can put young women into early menopause, decrease future ferility.Ruth Ann Crystal, MD
RT @jrgralow: #SCCAbc Topic 1: Presidents Cancer Panel report on healthly lifestyles and cancer: http://ow.ly/er0pE #SCCAbcAlicia C. Staley
T4Q1: Thanks to @Safeway for supporting SCCA’s #MammoVan, will be in Safeway parking lots throughout Oct: http://ow.ly/euGjx #SCCAbcSeattle Cancer Care
RT @SeattleMamaDoc: PS– Breast feeding after breast cancer is okay: http://ti.me/coREKR #SCCAbc cc @brochmanSara

Biology Explainer: The big 4 building blocks of life–carbohydrates, fats, proteins, and nucleic acids

The short version
  • The four basic categories of molecules for building life are carbohydrates, lipids, proteins, and nucleic acids.
  • Carbohydrates serve many purposes, from energy to structure to chemical communication, as monomers or polymers.
  • Lipids, which are hydrophobic, also have different purposes, including energy storage, structure, and signaling.
  • Proteins, made of amino acids in up to four structural levels, are involved in just about every process of life.                                                                                                      
  • The nucleic acids DNA and RNA consist of four nucleotide building blocks, and each has different purposes.
The longer version
Life is so diverse and unwieldy, it may surprise you to learn that we can break it down into four basic categories of molecules. Possibly even more implausible is the fact that two of these categories of large molecules themselves break down into a surprisingly small number of building blocks. The proteins that make up all of the living things on this planet and ensure their appropriate structure and smooth function consist of only 20 different kinds of building blocks. Nucleic acids, specifically DNA, are even more basic: only four different kinds of molecules provide the materials to build the countless different genetic codes that translate into all the different walking, swimming, crawling, oozing, and/or photosynthesizing organisms that populate the third rock from the Sun.

                                                  

Big Molecules with Small Building Blocks

The functional groups, assembled into building blocks on backbones of carbon atoms, can be bonded together to yield large molecules that we classify into four basic categories. These molecules, in many different permutations, are the basis for the diversity that we see among living things. They can consist of thousands of atoms, but only a handful of different kinds of atoms form them. It’s like building apartment buildings using a small selection of different materials: bricks, mortar, iron, glass, and wood. Arranged in different ways, these few materials can yield a huge variety of structures.

We encountered functional groups and the SPHONC in Chapter 3. These components form the four categories of molecules of life. These Big Four biological molecules are carbohydrates, lipids, proteins, and nucleic acids. They can have many roles, from giving an organism structure to being involved in one of the millions of processes of living. Let’s meet each category individually and discover the basic roles of each in the structure and function of life.
Carbohydrates

You have met carbohydrates before, whether you know it or not. We refer to them casually as “sugars,” molecules made of carbon, hydrogen, and oxygen. A sugar molecule has a carbon backbone, usually five or six carbons in the ones we’ll discuss here, but it can be as few as three. Sugar molecules can link together in pairs or in chains or branching “trees,” either for structure or energy storage.

When you look on a nutrition label, you’ll see reference to “sugars.” That term includes carbohydrates that provide energy, which we get from breaking the chemical bonds in a sugar called glucose. The “sugars” on a nutrition label also include those that give structure to a plant, which we call fiber. Both are important nutrients for people.

Sugars serve many purposes. They give crunch to the cell walls of a plant or the exoskeleton of a beetle and chemical energy to the marathon runner. When attached to other molecules, like proteins or fats, they aid in communication between cells. But before we get any further into their uses, let’s talk structure.

The sugars we encounter most in basic biology have their five or six carbons linked together in a ring. There’s no need to dive deep into organic chemistry, but there are a couple of essential things to know to interpret the standard representations of these molecules.

Check out the sugars depicted in the figure. The top-left molecule, glucose, has six carbons, which have been numbered. The sugar to its right is the same glucose, with all but one “C” removed. The other five carbons are still there but are inferred using the conventions of organic chemistry: Anywhere there is a corner, there’s a carbon unless otherwise indicated. It might be a good exercise for you to add in a “C” over each corner so that you gain a good understanding of this convention. You should end up adding in five carbon symbols; the sixth is already given because that is conventionally included when it occurs outside of the ring.

On the left is a glucose with all of its carbons indicated. They’re also numbered, which is important to understand now for information that comes later. On the right is the same molecule, glucose, without the carbons indicated (except for the sixth one). Wherever there is a corner, there is a carbon, unless otherwise indicated (as with the oxygen). On the bottom left is ribose, the sugar found in RNA. The sugar on the bottom right is deoxyribose. Note that at carbon 2 (*), the ribose and deoxyribose differ by a single oxygen.

The lower left sugar in the figure is a ribose. In this depiction, the carbons, except the one outside of the ring, have not been drawn in, and they are not numbered. This is the standard way sugars are presented in texts. Can you tell how many carbons there are in this sugar? Count the corners and don’t forget the one that’s already indicated!

If you said “five,” you are right. Ribose is a pentose (pent = five) and happens to be the sugar present in ribonucleic acid, or RNA. Think to yourself what the sugar might be in deoxyribonucleic acid, or DNA. If you thought, deoxyribose, you’d be right.

The fourth sugar given in the figure is a deoxyribose. In organic chemistry, it’s not enough to know that corners indicate carbons. Each carbon also has a specific number, which becomes important in discussions of nucleic acids. Luckily, we get to keep our carbon counting pretty simple in basic biology. To count carbons, you start with the carbon to the right of the non-carbon corner of the molecule. The deoxyribose or ribose always looks to me like a little cupcake with a cherry on top. The “cherry” is an oxygen. To the right of that oxygen, we start counting carbons, so that corner to the right of the “cherry” is the first carbon. Now, keep counting. Here’s a little test: What is hanging down from carbon 2 of the deoxyribose?

If you said a hydrogen (H), you are right! Now, compare the deoxyribose to the ribose. Do you see the difference in what hangs off of the carbon 2 of each sugar? You’ll see that the carbon 2 of ribose has an –OH, rather than an H. The reason the deoxyribose is called that is because the O on the second carbon of the ribose has been removed, leaving a “deoxyed” ribose. This tiny distinction between the sugars used in DNA and RNA is significant enough in biology that we use it to distinguish the two nucleic acids.

In fact, these subtle differences in sugars mean big differences for many biological molecules. Below, you’ll find a couple of ways that apparently small changes in a sugar molecule can mean big changes in what it does. These little changes make the difference between a delicious sugar cookie and the crunchy exoskeleton of a dung beetle.

Sugar and Fuel

A marathon runner keeps fuel on hand in the form of “carbs,” or sugars. These fuels provide the marathoner’s straining body with the energy it needs to keep the muscles pumping. When we take in sugar like this, it often comes in the form of glucose molecules attached together in a polymer called starch. We are especially equipped to start breaking off individual glucose molecules the minute we start chewing on a starch.

Double X Extra: A monomer is a building block (mono = one) and a polymer is a chain of monomers. With a few dozen monomers or building blocks, we get millions of different polymers. That may sound nutty until you think of the infinity of values that can be built using only the numbers 0 through 9 as building blocks or the intricate programming that is done using only a binary code of zeros and ones in different combinations.

Our bodies then can rapidly take the single molecules, or monomers, into cells and crack open the chemical bonds to transform the energy for use. The bonds of a sugar are packed with chemical energy that we capture to build a different kind of energy-containing molecule that our muscles access easily. Most species rely on this process of capturing energy from sugars and transforming it for specific purposes.

Polysaccharides: Fuel and Form

Plants use the Sun’s energy to make their own glucose, and starch is actually a plant’s way of storing up that sugar. Potatoes, for example, are quite good at packing away tons of glucose molecules and are known to dieticians as a “starchy” vegetable. The glucose molecules in starch are packed fairly closely together. A string of sugar molecules bonded together through dehydration synthesis, as they are in starch, is a polymer called a polysaccharide (poly = many; saccharide = sugar). When the monomers of the polysaccharide are released, as when our bodies break them up, the reaction that releases them is called hydrolysis.

Double X Extra: The specific reaction that hooks one monomer to another in a covalent bond is called dehydration synthesis because in making the bond–synthesizing the larger molecule–a molecule of water is removed (dehydration). The reverse is hydrolysis (hydro = water; lysis = breaking), which breaks the covalent bond by the addition of a molecule of water.

Although plants make their own glucose and animals acquire it by eating the plants, animals can also package away the glucose they eat for later use. Animals, including humans, store glucose in a polysaccharide called glycogen, which is more branched than starch. In us, we build this energy reserve primarily in the liver and access it when our glucose levels drop.

Whether starch or glycogen, the glucose molecules that are stored are bonded together so that all of the molecules are oriented the same way. If you view the sixth carbon of the glucose to be a “carbon flag,” you’ll see in the figure that all of the glucose molecules in starch are oriented with their carbon flags on the upper left.

The orientation of monomers of glucose in polysaccharides can make a big difference in the use of the polymer. The glucoses in the molecule on the top are all oriented “up” and form starch. The glucoses in the molecule on the bottom alternate orientation to form cellulose, which is quite different in its function from starch.

Storing up sugars for fuel and using them as fuel isn’t the end of the uses of sugar. In fact, sugars serve as structural molecules in a huge variety of organisms, including fungi, bacteria, plants, and insects.

The primary structural role of a sugar is as a component of the cell wall, giving the organism support against gravity. In plants, the familiar old glucose molecule serves as one building block of the plant cell wall, but with a catch: The molecules are oriented in an alternating up-down fashion. The resulting structural sugar is called cellulose.

That simple difference in orientation means the difference between a polysaccharide as fuel for us and a polysaccharide as structure. Insects take it step further with the polysaccharide that makes up their exoskeleton, or outer shell. Once again, the building block is glucose, arranged as it is in cellulose, in an alternating conformation. But in insects, each glucose has a little extra added on, a chemical group called an N-acetyl group. This addition of a single functional group alters the use of cellulose and turns it into a structural molecule that gives bugs that special crunchy sound when you accidentally…ahem…step on them.

These variations on the simple theme of a basic carbon-ring-as-building-block occur again and again in biological systems. In addition to serving roles in structure and as fuel, sugars also play a role in function. The attachment of subtly different sugar molecules to a protein or a lipid is one way cells communicate chemically with one another in refined, regulated interactions. It’s as though the cells talk with each other using a specialized, sugar-based vocabulary. Typically, cells display these sugary messages to the outside world, making them available to other cells that can recognize the molecular language.

Lipids: The Fatty Trifecta

Starch makes for good, accessible fuel, something that we immediately attack chemically and break up for quick energy. But fats are energy that we are supposed to bank away for a good long time and break out in times of deprivation. Like sugars, fats serve several purposes, including as a dense source of energy and as a universal structural component of cell membranes everywhere.

Fats: the Good, the Bad, the Neutral

Turn again to a nutrition label, and you’ll see a few references to fats, also known as lipids. (Fats are slightly less confusing that sugars in that they have only two names.) The label may break down fats into categories, including trans fats, saturated fats, unsaturated fats, and cholesterol. You may have learned that trans fats are “bad” and that there is good cholesterol and bad cholesterol, but what does it all mean?

Let’s start with what we mean when we say saturated fat. The question is, saturated with what? There is a specific kind of dietary fat call the triglyceride. As its name implies, it has a structural motif in which something is repeated three times. That something is a chain of carbons and hydrogens, hanging off in triplicate from a head made of glycerol, as the figure shows.  Those three carbon-hydrogen chains, or fatty acids, are the “tri” in a triglyceride. Chains like this can be many carbons long.

Double X Extra: We call a fatty acid a fatty acid because it’s got a carboxylic acid attached to a fatty tail. A triglyceride consists of three of these fatty acids attached to a molecule called glycerol. Our dietary fat primarily consists of these triglycerides.

Triglycerides come in several forms. You may recall that carbon can form several different kinds of bonds, including single bonds, as with hydrogen, and double bonds, as with itself. A chain of carbon and hydrogens can have every single available carbon bond taken by a hydrogen in single covalent bond. This scenario of hydrogen saturation yields a saturated fat. The fat is saturated to its fullest with every covalent bond taken by hydrogens single bonded to the carbons.

Saturated fats have predictable characteristics. They lie flat easily and stick to each other, meaning that at room temperature, they form a dense solid. You will realize this if you find a little bit of fat on you to pinch. Does it feel pretty solid? That’s because animal fat is saturated fat. The fat on a steak is also solid at room temperature, and in fact, it takes a pretty high heat to loosen it up enough to become liquid. Animals are not the only organisms that produce saturated fat–avocados and coconuts also are known for their saturated fat content.

The top graphic above depicts a triglyceride with the glycerol, acid, and three hydrocarbon tails. The tails of this saturated fat, with every possible hydrogen space occupied, lie comparatively flat on one another, and this kind of fat is solid at room temperature. The fat on the bottom, however, is unsaturated, with bends or kinks wherever two carbons have double bonded, booting a couple of hydrogens and making this fat unsaturated, or lacking some hydrogens. Because of the space between the bumps, this fat is probably not solid at room temperature, but liquid.

You can probably now guess what an unsaturated fat is–one that has one or more hydrogens missing. Instead of single bonding with hydrogens at every available space, two or more carbons in an unsaturated fat chain will form a double bond with carbon, leaving no space for a hydrogen. Because some carbons in the chain share two pairs of electrons, they physically draw closer to one another than they do in a single bond. This tighter bonding result in a “kink” in the fatty acid chain.

In a fat with these kinks, the three fatty acids don’t lie as densely packed with each other as they do in a saturated fat. The kinks leave spaces between them. Thus, unsaturated fats are less dense than saturated fats and often will be liquid at room temperature. A good example of a liquid unsaturated fat at room temperature is canola oil.

A few decades ago, food scientists discovered that unsaturated fats could be resaturated or hydrogenated to behave more like saturated fats and have a longer shelf life. The process of hydrogenation–adding in hydrogens–yields trans fat. This kind of processed fat is now frowned upon and is being removed from many foods because of its associations with adverse health effects. If you check a food label and it lists among the ingredients “partially hydrogenated” oils, that can mean that the food contains trans fat.

Double X Extra: A triglyceride can have up to three different fatty acids attached to it. Canola oil, for example, consists primarily of oleic acid, linoleic acid, and linolenic acid, all of which are unsaturated fatty acids with 18 carbons in their chains.

Why do we take in fat anyway? Fat is a necessary nutrient for everything from our nervous systems to our circulatory health. It also, under appropriate conditions, is an excellent way to store up densely packaged energy for the times when stores are running low. We really can’t live very well without it.

Phospholipids: An Abundant Fat

You may have heard that oil and water don’t mix, and indeed, it is something you can observe for yourself. Drop a pat of butter–pure saturated fat–into a bowl of water and watch it just sit there. Even if you try mixing it with a spoon, it will just sit there. Now, drop a spoon of salt into the water and stir it a bit. The salt seems to vanish. You’ve just illustrated the difference between a water-fearing (hydrophobic) and a water-loving (hydrophilic) substance.

Generally speaking, compounds that have an unequal sharing of electrons (like ions or anything with a covalent bond between oxygen and hydrogen or nitrogen and hydrogen) will be hydrophilic. The reason is that a charge or an unequal electron sharing gives the molecule polarity that allows it to interact with water through hydrogen bonds. A fat, however, consists largely of hydrogen and carbon in those long chains. Carbon and hydrogen have roughly equivalent electronegativities, and their electron-sharing relationship is relatively nonpolar. Fat, lacking in polarity, doesn’t interact with water. As the butter demonstrated, it just sits there.

There is one exception to that little maxim about fat and water, and that exception is the phospholipid. This lipid has a special structure that makes it just right for the job it does: forming the membranes of cells. A phospholipid consists of a polar phosphate head–P and O don’t share equally–and a couple of nonpolar hydrocarbon tails, as the figure shows. If you look at the figure, you’ll see that one of the two tails has a little kick in it, thanks to a double bond between the two carbons there.

Phospholipids form a double layer and are the major structural components of cell membranes. Their bend, or kick, in one of the hydrocarbon tails helps ensure fluidity of the cell membrane. The molecules are bipolar, with hydrophilic heads for interacting with the internal and external watery environments of the cell and hydrophobic tails that help cell membranes behave as general security guards.

The kick and the bipolar (hydrophobic and hydrophilic) nature of the phospholipid make it the perfect molecule for building a cell membrane. A cell needs a watery outside to survive. It also needs a watery inside to survive. Thus, it must face the inside and outside worlds with something that interacts well with water. But it also must protect itself against unwanted intruders, providing a barrier that keeps unwanted things out and keeps necessary molecules in.

Phospholipids achieve it all. They assemble into a double layer around a cell but orient to allow interaction with the watery external and internal environments. On the layer facing the inside of the cell, the phospholipids orient their polar, hydrophilic heads to the watery inner environment and their tails away from it. On the layer to the outside of the cell, they do the same.
As the figure shows, the result is a double layer of phospholipids with each layer facing a polar, hydrophilic head to the watery environments. The tails of each layer face one another. They form a hydrophobic, fatty moat around a cell that serves as a general gatekeeper, much in the way that your skin does for you. Charged particles cannot simply slip across this fatty moat because they can’t interact with it. And to keep the fat fluid, one tail of each phospholipid has that little kick, giving the cell membrane a fluid, liquidy flow and keeping it from being solid and unforgiving at temperatures in which cells thrive.

Steroids: Here to Pump You Up?

Our final molecule in the lipid fatty trifecta is cholesterol. As you may have heard, there are a few different kinds of cholesterol, some of which we consider to be “good” and some of which is “bad.” The good cholesterol, high-density lipoprotein, or HDL, in part helps us out because it removes the bad cholesterol, low-density lipoprotein or LDL, from our blood. The presence of LDL is associated with inflammation of the lining of the blood vessels, which can lead to a variety of health problems.

But cholesterol has some other reasons for existing. One of its roles is in the maintenance of cell membrane fluidity. Cholesterol is inserted throughout the lipid bilayer and serves as a block to the fatty tails that might otherwise stick together and become a bit too solid.

Cholesterol’s other starring role as a lipid is as the starting molecule for a class of hormones we called steroids or steroid hormones. With a few snips here and additions there, cholesterol can be changed into the steroid hormones progesterone, testosterone, or estrogen. These molecules look quite similar, but they play very different roles in organisms. Testosterone, for example, generally masculinizes vertebrates (animals with backbones), while progesterone and estrogen play a role in regulating the ovulatory cycle.

Double X Extra: A hormone is a blood-borne signaling molecule. It can be lipid based, like testosterone, or short protein, like insulin.

Proteins

As you progress through learning biology, one thing will become more and more clear: Most cells function primarily as protein factories. It may surprise you to learn that proteins, which we often talk about in terms of food intake, are the fundamental molecule of many of life’s processes. Enzymes, for example, form a single broad category of proteins, but there are millions of them, each one governing a small step in the molecular pathways that are required for living.

Levels of Structure

Amino acids are the building blocks of proteins. A few amino acids strung together is called a peptide, while many many peptides linked together form a polypeptide. When many amino acids strung together interact with each other to form a properly folded molecule, we call that molecule a protein.

For a string of amino acids to ultimately fold up into an active protein, they must first be assembled in the correct order. The code for their assembly lies in the DNA, but once that code has been read and the amino acid chain built, we call that simple, unfolded chain the primary structure of the protein.

This chain can consist of hundreds of amino acids that interact all along the sequence. Some amino acids are hydrophobic and some are hydrophilic. In this context, like interacts best with like, so the hydrophobic amino acids will interact with one another, and the hydrophilic amino acids will interact together. As these contacts occur along the string of molecules, different conformations will arise in different parts of the chain. We call these different conformations along the amino acid chain the protein’s secondary structure.

Once those interactions have occurred, the protein can fold into its final, or tertiary structure and be ready to serve as an active participant in cellular processes. To achieve the tertiary structure, the amino acid chain’s secondary interactions must usually be ongoing, and the pH, temperature, and salt balance must be just right to facilitate the folding. This tertiary folding takes place through interactions of the secondary structures along the different parts of the amino acid chain.

The final product is a properly folded protein. If we could see it with the naked eye, it might look a lot like a wadded up string of pearls, but that “wadded up” look is misleading. Protein folding is a carefully regulated process that is determined at its core by the amino acids in the chain: their hydrophobicity and hydrophilicity and how they interact together.

In many instances, however, a complete protein consists of more than one amino acid chain, and the complete protein has two or more interacting strings of amino acids. A good example is hemoglobin in red blood cells. Its job is to grab oxygen and deliver it to the body’s tissues. A complete hemoglobin protein consists of four separate amino acid chains all properly folded into their tertiary structures and interacting as a single unit. In cases like this involving two or more interacting amino acid chains, we say that the final protein has a quaternary structure. Some proteins can consist of as many as a dozen interacting chains, behaving as a single protein unit.

A Plethora of Purposes

What does a protein do? Let us count the ways. Really, that’s almost impossible because proteins do just about everything. Some of them tag things. Some of them destroy things. Some of them protect. Some mark cells as “self.” Some serve as structural materials, while others are highways or motors. They aid in communication, they operate as signaling molecules, they transfer molecules and cut them up, they interact with each other in complex, interrelated pathways to build things up and break things down. They regulate genes and package DNA, and they regulate and package each other.

As described above, proteins are the final folded arrangement of a string of amino acids. One way we obtain these building blocks for the millions of proteins our bodies make is through our diet. You may hear about foods that are high in protein or people eating high-protein diets to build muscle. When we take in those proteins, we can break them apart and use the amino acids that make them up to build proteins of our own.

Nucleic Acids

How does a cell know which proteins to make? It has a code for building them, one that is especially guarded in a cellular vault in our cells called the nucleus. This code is deoxyribonucleic acid, or DNA. The cell makes a copy of this code and send it out to specialized structures that read it and build proteins based on what they read. As with any code, a typo–a mutation–can result in a message that doesn’t make as much sense. When the code gets changed, sometimes, the protein that the cell builds using that code will be changed, too.

Biohazard!The names associated with nucleic acids can be confusing because they all start with nucle-. It may seem obvious or easy now, but a brain freeze on a test could mix you up. You need to fix in your mind that the shorter term (10 letters, four syllables), nucleotide, refers to the smaller molecule, the three-part building block. The longer term (12 characters, including the space, and five syllables), nucleic acid, which is inherent in the names DNA and RNA, designates the big, long molecule.

DNA vs. RNA: A Matter of Structure

DNA and its nucleic acid cousin, ribonucleic acid, or RNA, are both made of the same kinds of building blocks. These building blocks are called nucleotides. Each nucleotide consists of three parts: a sugar (ribose for RNA and deoxyribose for DNA), a phosphate, and a nitrogenous base. In DNA, every nucleotide has identical sugars and phosphates, and in RNA, the sugar and phosphate are also the same for every nucleotide.

So what’s different? The nitrogenous bases. DNA has a set of four to use as its coding alphabet. These are the purines, adenine and guanine, and the pyrimidines, thymine and cytosine. The nucleotides are abbreviated by their initial letters as A, G, T, and C. From variations in the arrangement and number of these four molecules, all of the diversity of life arises. Just four different types of the nucleotide building blocks, and we have you, bacteria, wombats, and blue whales.

RNA is also basic at its core, consisting of only four different nucleotides. In fact, it uses three of the same nitrogenous bases as DNA–A, G, and C–but it substitutes a base called uracil (U) where DNA uses thymine. Uracil is a pyrimidine.

DNA vs. RNA: Function Wars

An interesting thing about the nitrogenous bases of the nucleotides is that they pair with each other, using hydrogen bonds, in a predictable way. An adenine will almost always bond with a thymine in DNA or a uracil in RNA, and cytosine and guanine will almost always bond with each other. This pairing capacity allows the cell to use a sequence of DNA and build either a new DNA sequence, using the old one as a template, or build an RNA sequence to make a copy of the DNA.

These two different uses of A-T/U and C-G base pairing serve two different purposes. DNA is copied into DNA usually when a cell is preparing to divide and needs two complete sets of DNA for the new cells. DNA is copied into RNA when the cell needs to send the code out of the vault so proteins can be built. The DNA stays safely where it belongs.

RNA is really a nucleic acid jack-of-all-trades. It not only serves as the copy of the DNA but also is the main component of the two types of cellular workers that read that copy and build proteins from it. At one point in this process, the three types of RNA come together in protein assembly to make sure the job is done right.


 By Emily Willingham, DXS managing editor 
This material originally appeared in similar form in Emily Willingham’s Complete Idiot’s Guide to College Biology