Salty Water (Chemistry)

EDIT: I've now written a post about buffers, as well!  LINK

                 A few days ago, I was scrounging around my closet looking for a very comfortable, black, V-neck cotton shirt.  Very standard, very normal, very lab friendly.

                “Have you seen it?” I asked my fiancé frantically.  He seemed dumbfounded by my eagerness.

                After searching for a bit longer, I finally remembered that I had to throw out the silly shirt last winter.  The area just above the belt of my jeans had been riddled with tiny holes.  In fact, many of my shirts had met the same fate and the zipper of my favorite fleece vest had finally detached from the fabric last week and ceased to be useful.

Labs destroy clothes.  More exactly: the acids in my lab destroy my clothes.  (Yes, I’m fully aware that this is why lab coats were invented, but I’m too … lazy? … to ever put one on.  Why not just go buy new clothes?)

The most common acid we use in lab is hydrochloric acid (HCl), which is pretty nasty.  It’s what chemists call a “strong acid.”  Figure 3.1 shows a molecule of hydrochloric acid: one hydrogen atom bound to one chlorine atom.  A hydrogen atom carries one electron, while a single chlorine atom has seventeen.  The hydrogen kindly shares its one electron with chlorine and chlorine begrudgingly shares one electron with hydrogen, thus creating a bond between them.  This “sharing” is wildly unequal, however; the electrons play at chlorine’s house far more than hydrogen’s. (I’ll discuss bonding, electrons, and everyone’s general happiness in a different post.  For now, trust me – that chlorine really wants hydrogen’s electron.)  The chlorine is actually so delighted with the hydrogen’s electron that, for all it cares, the hydrogen can leave its electron and fall off the molecule.  Often, hydrogen does.  A hydrogen atom that has lost its electron is now an ion and known as H⁺.  

Three sets of definitions exist for acids*.  Arrhenius claims that acids are molecules that increase the concentration of H⁺ in water.  HCl certainly does this.  Johannes Bronsted and Thomas Lowry say an acid is a molecule that can donate H⁺ to bases.  HCl certainly does this as well.

So what are bases?  Arrhenius says bases are molecules that increase the concentration of hydroxide ions (OH^-) in water.  The strong base, sodium hydroxide (NaOH) fits this definition quite well.  (Incidentally, NaOH is also highly available in my lab and is used quite regularly.)  Much like the chlorine atom, the hydroxide ion only wants one of sodium’s electrons and not much else (Figure 3.2).  Very often, the sodium leaves one electron and falls off the molecule, creating Na⁺ and OH^-.

Let’s pause for a moment and recap (Figure 3.3): HCl will fall apart into H⁺ and Cl^-.  NaOH will fall apart into Na⁺ and OH^-.  If we have these four things hanging out together, will anything else happen?

It turns out, H⁺ and OH^- will readily come together to form H₂O = water!  Water is great stuff.  It’s not acidic (like HCl), it’s not basic (like NaOH); it’s neutral and perfectly safe compared with NaOH and HCl.

If you add one HCl molecule to one NaOH molecule, they will create one H₂O molecule, one Na⁺ ion and one Cl^- ion** (Figure 3.4).  This is why acids (low pH) and bases (high pH) are said to neutralize each other – mix a high pH (NaOH) with a low pH (HCl) and get a neutral pH (water).  

Common table salt (NaCl) is actually an organized array of Na⁺ ions and Cl^- ions.  Everyone knows that if you drop salt into water, it will dissolve.  The “dissolving” is actually the complete breakdown of the organized array into individual Na⁺ and Cl^- ions in water (Figure 3.5).

Look at the right sides of Figures 3.4 and 3.5.  Both show water with Na⁺ and Cl^- floating around.  This means that if you mix equal amounts of the nasty acid HCl with the strong base of NaOH, you get nothing more harmful than if you had dissolved common table salt into water.

 

Unfortunately, without the base around to neutralize the acid spilled on our benches, this chemical will continue to eat holes in my shirts.  I should really wear a lab coat.

P.S. - The topic of acids and bases can be endless!  So many more topics are here to discuss, such as the Henderson-Hasselbach equation, what in the world a buffer is and why it resists a change in pH, what is pH and how is it measured, what do you mean by “strong” acid, are there “weak” acids? (yes) and does H⁺ even exist? Things to cover at another point…  EDIT: I have added a post on this!  LINK

* The complete definitions of acids and bases.

(Svante) Arrhenius: Acids increase the concentration of H⁺ in water.  Bases increase the concentration of OH^- in water.

Bronsted-Lowry: Acids are H⁺ donors.  Bases are H⁺ acceptors.

(Gilbert) Lewis:  Acids are molecules capable of accepting an electron pair (empty orbital).  Bases are able to donate an electron pair (unpaired electrons).

 ** I chose to use H⁺ in this post instead of the more correct H₃O⁺ for clarity reasons.

References

Zumdahl, Steven S. “Chemical Principles, 4^th Edition” (2002) Houghton Mifflin Company, Boston, MA.

Black shirt – Old Navy, circa 2006.  J

Spanish Influenza, Part 1 (Biochemistry)

I        In March 2004, Science Magazine published a trio of papers concerning the influenza virus from the 1918 pandemic known as the Spanish Influenza.  Typical at-risk populations for influenza are the very young and quite old, making a histogram of fatalities versus age appear U-shaped (Figure 2.1).  The influenza of 1918 was peculiar because its graph was W shaped (Figure 2.1).  There was a spike in the middle representing a large amount of deaths for those aged 15 – 45.  Not only that, but this wave of influenza infected nearly one third of all Americans and killed roughly 30 million people worldwide.  These numbers are in stark contrast to the Center for Disease Control reported 5 – 20% infection rate of the US population during a “typical” flu year.  Researchers would like to understand why this virus was so virulent and hope to apply their findings to future pandemic outbreaks.

                Influenza A infects all kinds of animals - from humans to whales!  Scientists tend to focus on bird (avian), pig (swine), and human influenzas because relationships between the three are very interesting.  

The reservoir of influenza A viruses lies within the gastrointestinal tracts of birds.  These viruses can cause birds to suffer mild symptoms, but may also be asymptomatic or lethal.  A pig can become infected by an avian virus and develop a runny nose or fever.  (Can you imagine a pig with a runny nose?  Poor thing!)  A human, however, most likely is not able to be infected by an avian virus.  Why?

                In order to become “infected” by a virus, our cells must allow a virus inside them.  Think of your body as a neighborhood, your cells as homes within the neighborhood and viruses as burglars.  Obviously the burglars (viruses) want to break inside the homes (cells) and steal valuables (replication machinery), but neighborhoods have police and neighborhood watches (immune system) to ensure this does not happen.  Houses (cells) also have locks, which need keys!

Now, if a burglar breaks violently into a house, it is more likely that someone will notice something amiss and check it out.  It is to the benefit of the burglar to have a key, gain entrance quietly, and do damage once safely inside.  A virus works by carrying a key to our cells’ locks, softly entering without harm, then stealing our cells’ machinery and nutrients to replicate itself over and over until our cells can hold no more virus particles, at which point, the cell bursts open and spills all the newly made viruses into the neighborhood to infect more nearby cells.  Viruses are gross. 

A certain protein, known has hemagglutinin (key), on the influenza viral surface can recognize a specific molecule (lock) found on the outside of host cell.  As long as hemagglutinin can properly bind the molecule (a sialic acid bound to a galactose, which is bound to some cellular protein), then the virus can enter the cell.  The sialic acid can be linked to the galactose one of two ways: α2,3 or α2,6.  The gastrointestinal tract of birds is coated with cells bearing α2,3-linked sialic acid.  The respiratory tract of pigs has both.  The human respiratory tract only has α2,6-bound molecules.  The hemagglutinin of an infectious avian virus is not a proper key for human cells and thus cannot infect them.  Most researchers agree that for an influenza virus to jump from birds to humans, the hemagglutinin molecule must gain the ability to bind α2,6 linked sialic acid.

Fifteen different hemagglutinin proteins have been identified.  Each time one of these proteins has gained the ability to infect human cells, it has resulted in a pandemic.  A 1957 pandemic was due to H2, the 1968 pandemic was due to H3 and the 1918 pandemic was due to H1.

However, the gain of hemagglutinin binding α2,6 linked sialic acid can only be part of the answer to the question of virulence.  The 1957 and 1968 pandemics were far less severe than 1918.  

Several theories do exist as to why the Spanish flu was so deadly.  Due to World War I, many young men were living in close quarters at army camps, so the disease was able to spread quickly.  A lack of medicine due to the war also meant that secondary infections (such as pneumonia) were more likely to lead to death.   However, researchers believe that the virus itself could answer a multitude of questions if we could simply study it.  Unfortunately, no intact virus has survived.  Much like Jurassic Park, we’ve had to find the “Dino DNA” (or viral DNA, as it were).  Believe it not, scientists were able to find it! 

Stay tuned…

References

Histogram: The x axis represents age and the y axis represents how many people died of influenza at that age.

Seasonal influenza information: http://www.cdc.gov/flu/about/qa/disease.htm

Stevens, J. et al. “Stucture of the Uncleaved Human H1 Hemagglutinin from the Extinct 1918 Influenza Virus.” Science (2004) 303, pgs 1866 – 1869.

Gamblin, S. J. et al. “The Structure and Receptor Binding Properties of the 1918 Influenza Hemagglutinin.” Science (2004) 303, pgs 1838 – 1842

Holmes, Edward C. “1918 and All That.” Science (2004) 303, pgs 1787 – 1788.

Absolute Zero (Chemistry)

           Near the end of the summer, my fiancé was tearing through a book about an American surgeon in Paris.  Every so often, he’d make an incredulous comment towards the pages.  Finally, I asked him to explain the plot since he was clearly enjoying it.

                “It’s about a surgeon who’s chasing his father’s murderer,” he said.

                “That sounds interesting,” I answered dismissively.  

                “No, no!  That’s just the background.  The real story involves severed heads.”

                “Severed heads?”

                “Yup.  And other people’s bodies.  Wait until you read the ending.”

                Well, okay then.  Turns out, the crazies in the book are reattaching heads on other people’s bodies at the extremely low temperature of absolute zero.  (Oh, and there’s a twenty year old murder mystery plus an all encompassing love story in there, as well.  There’s a lot going on.  Throw some Nazis in, too.)  

Why absolute zero?  The theory of cryopreservation is that you are hitting a “pause” button on a person’s life.  All the biological processes that are currently occurring in our bodies will abruptly stop if we are dipped into a super-cold environment.  In theory, we could stay that way indefinitely.  Our food would sit in our stomach waiting to be digested, our last thought would be held in our mind, our heart would remain mid-beat.  Once warmed, those processes could continue as if they were never interrupted.  It would be as if waking from a long sleep.  (But, unlike Austin Powers’ experience, we wouldn’t need to pee for five minutes.)

Biological processes occur within cells and are driven by proteins (and metabolites, nucleic acids, etc).  These components are all comprised of atoms.  More specifically, they rely on an atom’s ability to move.  Within any molecule, bound by their bonds and environment, atoms writhe around in space.  As the temperature is cooled, an atom will move less and less.  Eventually, you will reach a temperature where all atomic movements are as slow as they can be.  This number goes by many names: -273°C, 0 K, -459.7 °F, or absolute zero.  

In the early 19^th century, several scientists were heavily studying gases, particularly the relationships between volume, pressure, mass, and temperature.  Much of this work lead to the creation of the Ideal Gas Law, but we are going to focus on one particular relationship known as Charles’ Law.  Named for Jacques Charles, the work was published by Joseph Louis Gay-Lussac.  He carefully measured the volume of a particular amount (mass) of gas at different temperatures and found that as the temperature increased, so did the volume of the gas.  

Let’s pretend you are Charles; what did you actually do?  First, you would have procured a specific mass of a specific gas (let’s say 1 gram of Gas A).  You then measured the volume of 1 gram of Gas A at 32°F, 70°F and 100°F.  Then, you graphed your data (temperature on the x axis and volume on the y axis) and would have been happy to see that your points made a straight line. Mathematically, this means that the temperature of Gas A and volume of Gas A have a direct relationship.

       Now, you’d repeat your experiment with 1 gram of Gas B or 1 gram of Gas C (Figure 1.1).  You would be showing over and over that, no matter the gas, this direct relationship is always seen.  All the gases would expand and contract at their own pace (the lines don’t all slope the same, some are steeper than others), but the points for each gas always fell on a straight line.

What does this have to do with absolute zero?  Ah, we’re getting there!

Since you are smart, you decide to put all this data into one mega-graph and draw lines through the points (Figure 1.2).  Look carefully at the lines.  What do you see…?

Each line, no matter what gas we’re talking about, all hit the x axis in the same place.  

As a gas gets cooler, a gas gets smaller.  If the gas becomes very very cold, its volume must become very very small.  In terms of Charles’ Law, this point where our lines cross the x axis is telling us what temperature the gas is when its volume is zero*.  Each gas will hit a volume of zero at the exact same temperature.  In other words, you can’t seem to get any gas colder than -459.7°F.    

This is quite extraordinary!  All gases have the same, inherent, lowest possible temperature!  Neat.  

On the Celsius scale of temperature, -459.7°F is -273°C.  The Kelvin scale shifts all Celsius temperatures up 273 degrees so that 0 K is representing the coldest temperature anything can be.

-273°C = 0 K; -272°C = 1 K; 100°C = 373 K

Far more intelligent people than me in the field of physics and mathematics proved and defined absolute zero using thermodynamics.  The explanations of them go far beyond what this chemist knows, but should you like to read more about it, I suggest looking up the works of the ever impressive William Thomson (aka Lord Kelvin) and the slightly crazy, but definitely genius Ludwig Boltzmann.  

Meanwhile, our Frankenstein surgeons are performing their operations at absolute zero because it’s the coldest, slowest, and most paused atoms (and, in turn, proteins, cells and biological processes) can get.  Of course, the book doesn’t describe how their machines can still work at such cold temperatures given that the atoms within them are governed by the same natural rules…

* A gas can never have a volume of zero because the atoms that comprise the gas have size.  The idea of a gas being at volume zero is purely theoretical.  I’ll discuss this more in another topic on gases!

References

Zumdahl, Steven S. “Chemical Principles, 4^th Edition” (2002) Houghton Mifflin Company, Boston, MA.

Folsom, Allan. “The Day After Tomorrow.” (1995) Hachette Book Group, New York, New York.

Hello!

                In July 2010, I defended my thesis to a room of approximately 30 people.  I had spent the past six years pursuing my doctorate in biological chemistry at an Ivy League school and my research, which I so proudly presented, dealt with proteins on the molecular level.  

The audience was varied, but consisted of the predictable people: my awesome advisor, who knew and had guided my research for the past five years; my thesis committee, who met with me once a year to discuss my progress; and the twenty or so labmates and friends who came out of obligation (probably) or excitement (probably not).  For any that came out of excitement, I thank you heartily.  All the aforementioned people would, if not completely understand my research, know the basics.  I also would wager that if they sipped a bit more coffee or let their brain wander a few minutes less, they could easily have understood my work.  It was the final four audience members (my family) that I know politely listened to my title, understood not one bit of how those ten words fit together (or what some of them even meant) and quietly slipped away from listening for the entire hour.  I believe I caught my sister playing animatedly with her cell phone around the thirty minute mark.  Afterwards, these same four people snapped happy, champagne-streaked photographs and declared:

                “I had no idea what you were talking about, but you definitely sounded smart!”

                This left me feeling a little deflated.   

After I graduated with my Ph.D., left my thesis lab (in tears) and began my post-doc, I felt like I knew how to do just about nothing.  (I’m learning that the end of grad school/beginning of post doc-ing is a dark time).  People ask my fiancé (lawyer) all the time about law matters or my brother in law (chef!) about cooking, but, oddly, no one asks me about the intricacies of pouring an agarose gel.  (C’mon, people!  I pour excellent agarose gels!!)  I felt like if there was some major catastrophe, then my brother in law could feed us all, my fiancé could help build a new government or mediate disputes and I could … correctly describe the proper set of procedures to perform mutagenesis?  How freaking useful of me.

 One night, I was out with many people who would never wear jeans and last night’s pajama t-shirt to work (clearly, this encompasses nearly everyone else in the world) and I was asked about what I do.  I usually try to deflect these questions (because I don’t like the glazed-over looks – it makes me think I’m talking to waxed figures) but this person was persistent.  Suddenly, the whole table was staring at me with a bit of wonder (but mostly confusion, if I’m being honest).  I was surprised.  People really did want to understand what I worked on.  

“Okay,” I said.  “Hand me a napkin.”

I proceeded to draw some shapes and arrows and explained my drug discovery research.  I actually got excited because they were nodding and asking me questions.  One of my friends even asked why I chose to pursue one compound over another and the benefits of using oral drugs over vaccines.  In this format, almost everyone at the table was engaged and understood.

                Then I realized that I do have a talent.  It’s minor and not catastrophe worthy, but could be useful to many people.  I can read scientific literature and spit it back out with clarity to those who didn’t choose science as a profession (I sometimes think those people are brilliant) or don’t have the time to read articles.  (And they take time - holy dense reading.)  I can explain it to both scientists (a highly technical, jargon-filled way – I did pass my defense, after all) and non-scientists.  

                I think I’ve also been heavily influenced by the podcast “Stuff you missed in history class” by Howstuffworks.com.   Their podcasts are short, clear blurbs about different historical topics.  They give adequate background to set up why the historical event was remembered, then discuss everything they know about the topic.  I love it!  Would people like that for different scientific topics?  I’d be interested to read about how aspirin works, who Dmitri Mendeleev was, or how the Spanish influenza virus adapted from birds to humans.  Science is full of such good stories but when they are presented in a dry, dense paper, what non-scientist wants to read it?  Hell, I don’t even want to read it.  But, when broken down in the right way and explained with the proper references, it’s actually really cool!  (I swear!!)  And I’m not talking about writing the watered down version of science that is usually presented in TV segments; I mean real scientific advances or topics explained thoroughly, accurately, and in a way that non-scientists can relate. 

My interests lie in chemistry, biological chemistry and disease.  This means that I like understanding things at an atomic level.  I’m not so interested in “your liver is failing” so much as I want to understand what liver proteins are not functioning properly and why.  How does that dysfunction lead to patient symptoms?  I want to understand deeper than the organ and deeper than the cell – tell me about the workers inside the cell.    I also really enjoy basic chemistry (I should - I tutored it for five years.)  How can you tell a hydrogen atom from a boron atom by just shining light on it? What does table salt and water have to do with hydrochloric acid and sodium hydroxide? Who in the world is Amedeo, anyway?

   I’m going to start with some topics on the Spanish Influenza (biological chemistry) and absolute zero (chemistry) – both are timely given that it’s January (oops February!).  As I go along, I’ll pull from the major scientific journals (something I should be reading anyway given my career) and I’ll mix in some historical and little known details about some scientists.  I also have spent entirely too much time working in or near cancer institutes, so I’ll cover different cancer topics, as well.  I have a lot of ideas.

I’ve spent the past eight years giving presentations about varied scientific topics and tutoring/teaching introductory chemistry.  It’s all interesting when explained properly and in a way that invites non-scientists to discuss and question.  I hope you’ll stick around.

Oh, P.S. – I do plan to keep my posts short and add colorful pictures.  No one likes a scientist who wants to hear herself drone on and on.  …and on.