By The Numbers

                 If I wasn’t a scientist, I would be a baker.  I love making cookies, cupcakes, muffins, bread… I made soft pretzels from scratch once!  Today, I’ll be baking up some strawberry muffins and last night I finished a loaf of white bread while watching the Super Bowl.  Yes, I like to bake.

                According to Alton Brown, cooking and baking are just science, which is the absolute truth.  In many ways, the two disciplines parallel each other.  There’s a fair amount of ingenuity, flying by the seat of your pants, and creativity born of necessity.  Both subscribe to thinking through odd little problems every day, in addition to knowing where “the box” is we’re all supposed to think outside of and breaking it into pieces.  It’s fun!

                Everyone is familiar with the concept of a dozen.  “I want a dozen cookies!” means you’ll be getting twelve.  A baker’s dozen will throw you one extra.  The word is just a shorthand way of saying a number.  Much like score (20), gross (144), and pair (2), dozen means you have twelve of a certain something.  Let’s hope it is cookies and not, say, mice in your apartment.

                Scientists also have a word to mean a particular number of things: mole.  

                Let’s be real – it’s a weird word.  Moles are animals that live in the ground or are sometimes found on the prototypical green-faced witches (with a hair – always a hair!).  However, the word is actually Latin and means “heap” or “pile.”  This makes enormous sense when I tell you that a mole doesn’t stand for a big number – it stands for a HUGE number.  A mole doesn’t mean 1,000 things or even 1 million things.  No, no… it is far larger than that.  

A mole stands for: 602,000,000,000,000,000,000,000 things.

You can’t even quite wrap your mind around how big the number is.  If you had that many cookies, you’d drown in them.

Typically, the number is shorthanded to 6.02 x 10²³.  Meaning, you need to move the decimal 23 places to the right and then you’ll have the number written correctly with all the zeros and commas.  The nerdier of my bunch will refer to October 23^rd as “Mole Day,” but celebrating officially occurs between 6:02 am and 6:02 pm only.  No judgment.

I could go into how this number came to be set (it even involves my favorite Amedeo Avogadro!), but I’m going to leave that to science books.  Instead, I’m going to discuss why it’s so important to think in terms of moles when you’re a scientist.

Think about a situation where you have two proteins that you know bind to each other.  Let’s call them Molecule A and Molecule B.   Molecule A is much larger and heavier compared with Molecule B.  I’ve tried to visually show this in Figure 84.1.

For most experiments, you’d like to add the same number of Molecule A and Molecule B to a tube.  Molecules are too small to see so it’s not like we can count them out like muffins.  But, we can accurately measure mass in a laboratory.  Unlike a cookie that might have more or less batter in it, the mass of one Molecule A or one Molecule B does not change.  Ever. 

Let’s say one molecule of Molecule A weighs 1 g (molecules are obviously much much lighter than 1 g, but this is just an example) and one molecule of Molecule B weighs 0.1 g.  

What happens if we weight out 1 g of each (Figure 84.2)?  How many molecules of Molecule A and Molecule B will we have?  Well, one molecule of Molecule A weighs 1 g so we’ll only have one molecule.  One molecule of Molecule B weighs 0.1 g so we’ll have ten molecules.  Whoops.  That didn’t work out!  We probably should have gone for 10 g of Molecule A (10 molecules) and 1 g of Molecule B (10 molecules).

So what do scientists do?  Do they figure out the mass of one molecule, multiply by how many molecules they want and then weigh that out??

Sort of.  

Atoms and molecules are insanely small so their masses are insanely small.  My examples above are very unrealistic (but I wanted to demonstrate the concept without using super small numbers that would be confusing for you and me).  Weighing out three molecules of something isn’t exactly possible.  But!  Remember how big a mole is?  It’s really freaking big.  Instead of worrying about the mass of one molecule, we worry about the mass of a mole of molecules.  Remember, the mass of one molecule never changes so the mass of 10 molecules will never change and so the mass of 6.02 x 10²³ molecules will never change.

Let’s give some real life examples.

NaCl – table salt.  It’s just chilling in your kitchen right now.  The mass of one NaCl molecule is 9.7 x 10^-23 g (0.00000000000000000000097 g), but a mole of NaCl is 58.44 g.  Which is easier to weigh out?

Acetic acid,HCOOH – vinegar!  It’s catching up with your salt right now.  The mass of one acetic acid molecule is 7.6 x 10^-23 g (0.00000000000000000000076 g), but a mole is 46 g!

                You get the picture.  The mass of a mole of molecules (or atoms) is referred to as its molar mass.

                So, let’s look at our Molecule A and Molecule B example again, but with realistic numbers.

                Pretend the molar mass of Molecule A is 10 g and the molar mass of Molecule B is 2 g.  If you want to weigh out an equal number of molecules for A and B, then weigh out 10 g of Molecule A and 2 g of Molecule B.  How many molecules of each do you have?  6.02 x 10²³.  Instead of saying 6.02 x 10²³ molecules, however, we say “One mole of each.”   Ta-da!  So simple!  Check out Figure 84.3!

                Knowing the molar mass allows us to know exactly how much of a substance to weigh out and tells us exactly how many molecules/atoms/pigeons we are weighing out.  It’s a fabulous little number.

                One last, extra credit problem.  We’ll use the same numbers from Figure 84.3.

                I want an equal number of Molecule A and Molecule B.  I weigh out 25 g of Molecule A.  How many molecules of Molecule A do I have?  How much should I weigh out of Molecule B?  How many moles of each do I have?

                Answer in Figure 84.4!

REFERENCES

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

Restricted!

           My husband and I are hopelessly addicted to the TV show Fringe.  We’re consistently a season behind because we choose to watch once the episodes are out on DVD.  While I can hardly sit still to watch a two hour movie, I’ll happily stay up late watching more and more episodes of a good TV show (this also includes - but is not limited to - Game of Thrones, Rome, Mad Men, Prison Break, Lost, Big Love, Nip/Tuck, and The Tudors.  We’re looking forward to Boardwalk Empire, Downton Abbey, and Breaking Bad, as well).  

Most recently, the Fringe shape-shifters were attacking humans in our universe.  A shape-shifter is a specialized being who can take on the look of someone else; the same idea is found in Harry Potter’s Polyjuice Potion or X-Men’s Rebecca Romijn.  However, these Fringe suckers are extra cool because not only can they look like someone else, but their cells will actually have the DNA of the person.  Unfortunately for the shape-shifters, the transformations aren’t happening correctly.  In an effort to figure out their problems so their pursuit of world-domination can continue, a rather meek looking shape-shifter named Nadine captured a biochemist under the guise of asking for help to cure her shape-shifter-ness.  Once this biochemist catches on to the fact that Nadine is up to no good, he tries to add restriction enzymes to a serum he intends to give her.  She grabs his hand saying “I know a thing about biochemistry and enzymology!  Those restriction enzymes will destroy my DNA and, thus, me.”

                I raised my eyebrows at this statement, then chuckled, then furrowed my brow trying to decide if this far-fetched idea would indeed kill the mythical shape-shifter (because, yes, ALL of this can happen, folks).

                But, let’s back it up here.  What in the world is a restriction enzyme in the first place?

                I’ve talked about enzymes before – they are specialized proteins designed to perform one specific reaction.  In the Fun with Radioactivity post, I discussed how one class of enzymes called kinases will move a phosphate group from one protein to another.  Restriction enzymes are a different class of enzymes and they cut DNA at very specific places. 

 

                One of the first restriction enzymes discovered came from the bacteria Haemophilus influenzae.  Scientists originally believed this was the cause of influenza, hence its name.  In 1968, several biochemists at Johns Hopkins University isolated an enzyme from H. influenzae and named it HindIII.  

                HindIII = Haemophilus influenza, strain d, third enzyme isolated

                This enzyme will cleave DNA whenever it comes across this exact sequence: A A G C T T.  Wherever it sees this EXACT string of DNA bases, HindIII will bind to that area and cut the DNA in half.  Disrupting a DNA molecule in this way will destroy its usefulness.  Think about burning a hole in the middle of a recipe card, then another hole somewhere else, and so on... – you’re slowly destroying the card and all the information written on it (Central Dogma post).  Genomes (entire DNA molecules) are very large!  You can imagine that the enzyme will run into A A G C T T quite often simply by the rules of chance.  HindIII never misses an opportunity – it will find it and it will cut the DNA.

                As time went on, more and more of these types of enzymes were isolated from different bacteria.  I believe the current number is somewhere in the hundreds (a list of restriction enzymes and the sequences they cut can be found here: LINK).  Each one of the restriction enzymes listed recognizes a very specific stretch of DNA bases and will cut the DNA when it finds with that sequence.  Every time.  Without fail.

                At this point, you might be scratching your head.  If bacteria have so many of these enzymes that are responsible for cutting and destroying DNA, then how are the bacteria alive?  Wouldn’t these enzymes chew up the bacteria’s own DNA and kill it?

                Ah.  That’s where the word “restriction” comes into play!

                Scientists believe that bacteria developed these enzymes as a defense mechanism.  I’ve talked about how cells can be invaded (Influenza, HPV, amoebas, infections of the kidney!) and bacteria are no different.  They can also be invaded.  Viruses that specifically infect bacteria are called phage.  Unsurprisingly, phage carry their own genomes and are ready to hijack the bacteria to do its bidding.  But!  The bacteria have these restriction enzymes to restrict what can come inside.  These enzymes will chew up the phage’s DNA and not theirs as long as the enzymes can tell the difference.  Typically, bacteria will decorate their own DNA with a chemical group called a methyl group.  Restriction enzymes are unable to bind to methylated DNA.  Unfortunately for phage, their DNA isn’t methylated and thus vulnerable to the restriction enzymes.  

                Rather smart, aren’t the bacteria?  Bacteria are actually fascinatingly interesting.  They are far simpler than a human being but sophisticated in so many ways.  Scientists have learned an immeasurable amout of knowledge concerning life and its mysteries by studying bacteria.

                So, now we know what a restriction enzyme is and what it does, but we haven’t answered the most burning question of all: can they kill a shape-shifter?

                Well – probably not. 

 The biochemist on Fringe put a mixture of restriction enzymes into a serum he planned to inject into Nadine.  

Let’s say he was successful at injecting the serum.  Now, the enzymes are floating around in her bloodstream.  Their nearest available cells are going to be red blood cells, which carry no genome and would be unaffected by restriction enzymes, and white blood cells.  In order to destroy the white blood cells (or ANY cell), the restriction enzymes must be able to get across the cell membrane.  That’s easy if you are small, like water, but much much MUCH more difficult if you are a large protein.  It’s like trying to fit an elephant through your white picket fence.  You need a door or a hole, which aren’t readily available.  

Let’s say they could get in, though.  Genomes are precious and therefore protected in the nucleus, which is another fence to force their way through.  

But okay, let’s say they get across the plasma membrane and the nuclear membrane, now what does it face?  Our genomes are very packaged (unlike phage and bacterial genomes).  All the individual bases aren’t readily accessible so the enzymes might be able to cut here and there, but certainly they wouldn’t destroy the whole molecule.  It’s far too protected.

Our bodies also have another defense in their midst – immune response.  Like restriction enzymes, our bodies know what belongs inside us and what does not.  Most certainly a strange new enzyme would be detected by our immune system and attacked.  The immune response isn’t always perfect - we do get sick, of course - but our bodies “fight off infection” in a reasonable time period.

100% of Fringe is far-fetched, but c’mon!  They’re so creative with the available scientific knowledge.  I appreciate it!

Phage: Also called “bacteriophage,” these are viruses that infect bacteria

Methyl group: One carbon atom bound to three hydrogen atoms. These groups are placed on DNA as a way to mark it.

NOTE: The scientists credited with the discovery of restriction enzymes, Werner Arber, Daniel Nathans, and Hamilton O. Smith, were awarded the 1978 Nobel Prize in Physiology or Medicine.  Restriction enzymes are used every single day in labs all over the world to cut DNA.  I could list off about fifty different enzymes I've used in my entire ten years working in the lab.  They are essential to Step 1 of purifying a protein, as discussed in From DNA to Protein, Step 1. 

REFERENCES

History of Restriction Enzymes: http://www.nature.com/scitable/topicpage/restriction-enzymes-545

Alberts et al. "Molecular Biology of the Cell, 4th Edition." Garland Science, New York, New York (2002).

Smith and Wilcox. "A restriction enzyme from Hemophilus influenzae. I. Purification and general properties." (1970) J Mol. Biol. 51(2) pgs 379 - 391 

Nobel Prize Winners of 1978: http://www.nobelprize.org/nobel_prizes/medicine/laureates/1978/