For Dad: A guide on strokes, including a glossary of terms

A scanning electron micrograph of a blood clot.  Image credit: Steve Gschmeissner/Science Photo Library (http://www.sciencephoto.com/media/203271/enlarge#) 


On Monday January 1st, I overheard my dad telling my mom how his left arm was numb and that he had no strength in his left hand.  I immediately ran into the medicine cabinet, grabbed two aspirin, practically shoved them down my dad’s throat, and told him to get his coat.  He was going to the ER. 

As it turns out, my dad was having a stroke, which is basically the cessation of blood flow to an area in the brain.  Luckily, my dad only suffered a very mild stroke, and after several days of monitoring and a battery of tests, he was released from the hospital. 

While we are all relieved that he dodged what could have been a fatal bullet, I came to realize that there was only a superficial understanding of what was actually happening.  So, to help demystify the process for my dad (and anyone else in this situation), I’ve decided to write a mini-guide on strokes.  Below you will find some handy information about strokes, including what they are, as well as a glossary of relevant terms.   

Why we need blood flow in the brain

Before I get into what happens to the brain when a stroke occurs, it is important to first understand why unrestricted blood flow in blood vessels in the brain is important.  The brain is a type of tissue, and like all tissues in our body, it needs a constant access to nutrients and oxygen.  Furthermore, tissues produce waste, and this waste needs to be removed.

The human cardiovascular system. Image Credit: Wikipedia.
Evolution’s solution to this problem is the development of a vast network of blood vessels existing within our tissues.  For instance, take a good look at your very own eyeballs.  Especially when we are tired, we can see tiny blood vessels called capillaries, which help to deliver key nutrients and oxygen, keeping our organs of sight healthy and happy.  Now consider that this type of blood vessel network exists in all tissues in our bodies (because it does).  Depending on the needs of the tissue, these vessels vary in size and number.  Sometimes the blood vessels are large, like the aorta, and sometimes they are super tiny, like the capillaries in our eyes.  However, all serve the same function: to make sure that cells can breath, eat, and get rid of waste.

When blood is prevented from traveling to a specific area within a tissue, the cells in that area will not get enough fuel and oxygen and will begin to die.  For instance, the restriction of blood flow to the heart leads to the death of heart tissue, causing a heart attack.  Similarly, the interruption of normal blood flow within the brain causes the affected cells in the brain to essentially starve, suffocate, and die, resulting in a stroke.  The medical term for a lack of oxygen delivery to tissues due to a restriction in blood flow is ischemia.  In general, the heart, brain, and the kidneys are the most sensitive to ischemic events, which, when occurring in these organs, can be fatal.      

So, what exactly is a stroke?

Some strokes can be categorized as being ischemic.  As mentioned above, an ischemic stroke occurs when blood flow (and the associated oxygen supply) is restricted in an area within the brain, leading to tissue death.  A major cause of ischemic strokes is a progressive disease called atherosclerosis, which can be translated to mean “the hardening of the arteries.” 

Severe atherosclerosis of the aorta.
Image Credit: Wikipedia.
Affecting the entire cardiovascular system, atherosclerosis is the result of cholesterol build-up inside of our blood vessels, causing their openings to become narrower.  These cholesterol plaques can eventually burst, leading to the formation of a blood clot.  Ischemic strokes occur as a result of a blood clot, medically known as a thrombus, that blocks the flow of blood to the brain, a phenomenon often related to complications from atherosclerosis.  A ruptured cholesterol plaque and resulting blood clot can occur in the brain, or it can occur elsewhere in the body, such as in the carotid arteries, and then travel to the brain.  Either way, the blood clot will block blood flow and oxygen delivery to sensitive brain tissue and cause a stroke.           

Strokes that result from the bursting of a blood vessel in the brain can be categorized as being hemorrhagic.  In this situation, there may be a pre-existing condition rendering the blood vessels in the brain defective, causing them to become weak and more susceptible to bursting.  More often than not, a hemorrhagic stroke is the result of high blood pressure, which puts an awful lot of stress on the blood vessels.  Hemorrhagic strokes are less common than ischemic strokes, but still just as serious. 

How do you know if you’ve had a stroke?

The symptoms of a stroke can vary depending on which part of the brain is affected and can develop quite suddenly.  It is common to experience a moderate to severe headache, especially if you are hemorrhaging (bleeding) in the brain.  Other symptoms can include dizziness, a change in senses (hearing, seeing, tasting), muscle tingling and/or weakness, trouble communicating, and/or memory loss.  If you are experiencing any of these warning signs, it is important to get to the hospital right away.  This is especially important if the stroke is being caused by a blood clot since clot-busting medicationsare only effective within the first few hours hours of clot formation. 

Once in the hospital, the caregiver will likely give anyone suspected of having a stroke a CT scan.  From this test, doctors will be able to determine if you had a stroke, what type of stroke you had (ischemic versus hemorrhagic), or if there is some other issue.  However, as was the case with my dad, a CT scan may not show evidence for a stroke.  This issue can arise as a result of timing (test performed before brain injury set in) or size of affected area (too small to see).  When not in an emergency situation, doctors may also or instead choose to prescribe an MRItest to look for evidence of a stroke.    

If a stroke has been confirmed, the next steps will be to try and figure out the underlying cause.  For ischemic strokes, it is important to find out if there is a blood clot and where it originated.  Because my dad had an ischemic stroke, he had to undergo a series of tests that searched for a blood clot in his carotid arteries though ultrasound, as well as in the heart, using both an electrocardiogram(EKG) and an echocardiogram(ultrasound of the heart).  The patient might also be asked to wear a Holter Monitor, which is a device worn for at least 24 hours and can detect potential heart abnormalities that may not be obvious from short-term observations, like those obtained via an EKG.  If a stroke is due to a hemorrhagic event, an angiogramwould be performed to try an pinpoint the compromised blood vessel.  

A stroke you did have.  Now what?

Once a stroke has been confirmed and categorized, the patient will most likely be transferred to the stroke unit of the hospital for both treatment and further observation.  If a clot has been detected, a patient will receive clot-busting medications (assuming this detection occurs within several hours of clot formation).  Alternatively, a clot can be mechanically removed with surgery (animation of clot removal, also known as a thrombectomy).  Patients might also be given blood-thinning medications to either ensure that clots do not increase in size or to prevent new clots from forming.   As for secondary prevention, meaning preventing another stroke from happening, patients might be given blood pressure and cholesterol lowering medications. 

If a disability arises due to stroke, a patient might need to undergo rehabilitation.  The type and duration of stroke rehabilitation is dependent on the area of brain that was affected, as well as the severity of the injury.  

Major risk factors and predictors of stroke

There are many situations that could predispose one to having a stroke, and many of these conditions are treatable.  The absolute greatest predictor of a stroke is blood pressure.  High blood pressure, also known as hypertension, will significantly raise your risk of having a stroke.   Other modifiable stroke risk factors include blood cholesterol levels, smoking, type 2 diabetes, diet, alcohol/drug use, and a sedentary life style.  However, there are also risk factors that you cannot change including family history of stroke, age, race, and gender.  But that shouldn’t stop one from practicing a healthy lifestyle!

In conclusion, strokes are no joke.  I am glad that my dad is still here (yes, dad, if you are reading this, we are in fact friends) and that he escaped with relatively no real consequences.  Let’s just not do this again, ok?  

Stroke Glossary

Anti-coagulants:These are medications that help to reduce the incidence of blood clotting.  The repertoire includes aspirin, Plavix, Warfarin, and Coumadin.  Also called blood thinners.
Atherosclerosis:Literally translated as “hardening of the arteries,” this condition is hallmarked by the build-up of cholesterol inside of blood vessels.  Atherosclerosis can lead to many complications including heart disease and stroke.

Atherosclerotic Plaque: The build of fatty materials, cholesterol, various cell types, and calcium.

Cardiovascular System: The network of blood vessels and heart that works to distribute blood throughout the body. 

Carotid Arteries: Arteries that carry blood away from the heart toward the head, neck, and brain.

CT Scan: Cross sectional pictures of the brain using X-rays.

Echocardiogram:An ultrasound of the heart.  In stroke vicitms, electrocardiography is used to detect the presence of a blood clot in the heart.

Electrocardiogram (EKG or ECG): The measurement of the electrical activity of the heart.  It is performed by attaching electrodes to a patient at numerous locations on the body, which function to measure electrical output of the heart.

Embolic Stroke: A type of ischemic stroke, an embolic stroke occurs when a blood clot forms (usually in the heart) and then travels to the brain, blocking blood flow and oxygen delivery to brain tissue.

Hemorrhagic Stroke: A type of stroke that results form the bursting of a blood vessel in the brain.

Hypertension: High blood pressure, defined as having 140/90 mmHg or above.

Ischemic Stroke: The restriction of blood flow to an area within the brain.

Magnetic Resonance Imaging (MRI): An imaging technique employing a magnetic field that can contrast different soft tissues in the body.

Thrombolytic Medications: Medications that are approved to dissolve blood clots.  Also called “clot-busting” medications.

Thrombus:Blood clot.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Structure of the placenta

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

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

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

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

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

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

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

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

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

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

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

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

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

Cultural norms and the placenta

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

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

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

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

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


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

Source


XX Tech Report: Rapid detection and treatment for deadly blood infections

Methicillin-resistant Staphylococcus aureus (green), a frequent agent
in blood infections, under attack from a white blood cell.
Photo: Wikimedia Commons, public domain.

By Jeffrey Perkel, Ph.D., DXS technology editor


[Ed. note: Introducing our new technology editor, Jeffrey Perkel

Jeffrey, a recovering scientist, has always had a passion for the technology and the gadgetry of science. He has been a scientific writer and editor since 2000, when he left academia to join the staff of The Scientist magazine as a Senior Editor for Technology. Before that, he studied transcription factor biology at the University of Pennsylvania and Harvard Medical School -- training that, surprisingly, has little application in the real world. In 2006, he and his family headed west to Pocatello, Idaho, and has been a freelance writer ever since. You can see why Double X Science is thrilled to have him on the team! You can find Jeffrey at his Website or on Twitter at @j_perkel. Welcome, Jeff!]

A story published earlier this week on NBCNews.com both alarmed me and piqued my interest.

It alarmed me because, well, I don’t like microbes much (despite, or perhaps because of my background in microbiology), and this article is about people getting very, very sick from sepsis (aka septicemia or bacteremia, an infection of the blood), which presents itself as a whole-body inflammatory response and a significantly increased risk of organ failure. It is an important area of microbiology because sepsis results from a bacterial infection, and the article says that 20% to 50% of infected patients die from sepsis.

My interest was piqued, however, because the piece goes on to talk about how a new genetic testing device that the US Food and Drug Administration approved in June could possibly help rein in the disease. That’s because it can reduce the time for diagnosing sepsis from days to hours. And when it comes to sepsis, time is critical.

Sepsis is confirmed by testing for the presence of specific types of bacteria in blood samples from patients and identifying what bacteria, if any, are in the circulation. If they are present, the researchers need to find out if the bugs are resistant to any antibiotic. Unfortunately, all that takes time – time the patient often doesn’t have. As the news story notes,

A 2010 study in the journal Critical Care Medicine found that for every hour of delay in administering antibiotics, mortality rose by 7.6 percent.

The new testing system is called the Verigene Gram-positive Blood Culture Test, marketed by Nanosphere Inc., a nanotechnology company in Northbrook, Ill. NBCNews.com describes the system:

About the size of a small microwave oven, the Verigene Gram-positive Blood Culture Nucleic Acid Test is the first system approved by the FDA to identify quickly certain bacteria responsible for bloodstream infections — and whether some are resistant to the top drugs used against them.

 

Instead of the three days required for a traditional blood culture panel, results from the Verigene test come back within three hours, identifying up to a dozen specific bacteria known to cause sepsis, including strains of Staphylococcus, Streptococcus, Enterococcus and Listeria.

Of particular importance, the system can catch some particularly nasty bugs, methicillin-resistant Staphylococcus aureus (MRSA; see Maryn McKenna’s excellent Superbug if you really want to terrify yourself on this subject) and vancomycin-resistant Enterococci.

In its press release announcing the Verigene test’s approval, the FDA said that, compared to standard microbiology methods, the Verigene test results “were consistent with traditional blood culture methods in 93 percent to 100 percent of the comparisons.”

The test is remarkably simple, and even automated, requiring a dedicated sample processing instrument and a reader from Nanosphere.

The patient sample is added to a glass slide covered with capture signals that recognize DNA from sepsis-causing bacteria. The capture signals are placed on the glass slide in a defined order, each programmed to recognize only one strain of bacteria. This uniform order helps scientists identify which strain of bacteria, if any, is responsible for the infection. If the patient blood sample contains bacteria, the signals on the glass slide will capture its DNA, and the special scanner and software can detect this capture.   

What sets the Verigene test apart from the previously available tests for sepsis is precisely how they do the detecting. The test adds sub-microscopic gold balls, called gold nanoparticles, to the glass slide. These gold nanoparticles are studded with more capture signals. When bacteria match up with the same specific capture signals, the nanoparticles will attach to that area. This ball gives scientists the ability to more rapidly detect which type of bacteria, if any, is present, and thus select the right course of antibiotic treatment.

The reaction is developed by coating the gold nanoparticles with silver, a process called signal amplification, which increases sensitivity up to 100,000 times, and then hitting it with light. Those spots containing the nanoparticles scatter light; those without it, do not. The effect is so strong, the original paper detected it using a “conventional flatbed scanner,” like something you’d have in your home office.

According to Nanosphere’s website, the whole thing requires less than five minutes’ worth of hands-on time, plus 2.5 hours to get the result. That falls within the necessary time frame to diagnose sepsis and begin life-saving antibiotic therapy.

Hopefully, this is a technology that neither your family nor mine will ever need. But it’s nice to know it’s there. And now, you know how it works.

(If you’re interested in the research paper that led to this test, from company cofounders Robert Letsinger and Chad Mirkin, both of Northwestern University, you can read it here.)

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