A crash course in organic chemistry Jakob Magolan
I’d like you to ask yourself,
what do you feel when you hear
the words “organic chemistry?”
What comes to mind?
There is a course offered
at nearly every university,
and it’s called Organic Chemistry,
and it is a grueling, heavy
introduction to the subject,
a flood of content
that overwhelms students,
and you have to ace it if you want
to become a doctor or a dentist
or a veterinarian.
And that is why so many students
perceive this science like this …
as an obstacle in their path,
and they fear it and they hate it
and they call it a weed-out course.
What a cruel thing for a subject
to do to young people,
weed them out.
And this perception spread
beyond college campuses long ago.
There is a universal anxiety
about these two words.
I happen to love this science,
and I think this position
in which we have placed it
is inexcusable.
It’s not good for science,
and it’s not good for society,
and I don’t think it has to be this way.
And I don’t mean that this class
should be easier. It shouldn’t.
But your perception of these two words
should not be defined
by the experiences of premed students
who frankly are going through
a very anxious time of their lives.
So I’m here today because I believe
that a basic knowledge
of organic chemistry is valuable,
and I think that it can be made
accessible to everybody,
and I’d like to prove that to you today.
Would you let me try?
Audience: Yeah!
Jakob Magolan: All right, let’s go for it.
(Laughter)
Here I have one of these
overpriced EpiPens.
Inside it is a drug called epinephrine.
Epinephrine can restart
the beat of my heart,
or it could stop a life-threatening
allergic reaction.
An injection of this
right here will do it.
It would be like turning
the ignition switch
in my body’s fight-or-flight machinery.
My heart rate, my blood pressure would
go up so blood could rush to my muscles.
My pupils would dilate.
I would feel a wave of strength.
Epinephrine has been the difference
between life and death for many people.
This is like a little miracle
that you can hold in your fingers.
Here is the chemical structure
of epinephrine.
This is what organic chemistry looks like.
It looks like lines and letters …
No meaning to most people.
I’d like to show you what I see
when I look at that picture.
I see a physical object
that has depth and rotating parts,
and it’s moving.
We call this a compound or a molecule,
and it is 26 atoms that are stitched
together by atomic bonds.
The unique arrangement of these atoms
gives epinephrine its identity,
but nobody has ever
actually seen one of these,
because they’re very small,
so we’re going to call this
an artistic impression,
and I want to explain to you
how small this is.
In here, I have less than
half a milligram of it dissolved in water.
It’s the mass of a grain of sand.
The number of epinephrine
molecules in here is one quintillion.
That’s 18 zeroes.
That number is hard to visualize.
Seven billion of us on this planet?
Maybe 400 billion stars in our galaxy?
You’re not even close.
If you wanted to get
into the right ballpark,
you’d have to imagine every grain of sand
on every beach,
under all the oceans and lakes,
and then shrink them all
so they fit in here.
Epinephrine is so small
we will never see it,
not through any microscope ever,
but we know what it looks like,
because it shows itself
through some sophisticated machines
with fancy names
like “nuclear magnetic
resonance spectrometers.”
So visible or not, we know
this molecule very well.
We know it is made
of four different types of atoms,
hydrogen, carbon, oxygen and nitrogen.
These are the colors
we typically use for them.
Everything in our universe
is made of little spheres
that we call atoms.
There’s about a hundred
of these basic ingredients,
and they’re all made
from three smaller particles:
protons, neutrons, electrons.
We arrange these atoms
into this familiar table.
We give them each a name and a number.
But life as we know it
doesn’t need all of these,
just a smaller subset, just these.
And there are four atoms in particular
that stand apart from the rest
as the main building blocks of life,
and they are the same ones
that are found in epinephrine:
hydrogen, carbon, nitrogen and oxygen.
Now what I tell you next
is the most important part.
When these atoms
connect to form molecules,
they follow a set of rules.
Hydrogen makes one bond,
oxygen always makes two,
nitrogen makes three
and carbon makes four.
That’s it.
HONC – one, two, three, four.
If you can count to four,
and you can misspell the word “honk,”
you’re going to remember this
for the rest of your lives.
(Laughter)
Now here I have four bowls
with these ingredients.
We can use these to build molecules.
Let’s start with epinephrine.
Now, these bonds between atoms,
they’re made of electrons.
Atoms use electrons like arms
to reach out and hold their neighbors.
Two electrons in each bond,
like a handshake,
and like a handshake,
they are not permanent.
They can let go of one atom
and grab another.
That’s what we call a chemical reaction,
when atoms exchange partners
and make new molecules.
The backbone of epinephrine
is made mostly of carbon atoms,
and that’s common.
Carbon is life’s favorite
structural building material,
because it makes
a good number of handshakes
with just the right grip strength.
That’s why we define organic chemistry
as the study of carbon molecules.
Now, if we build the smallest molecules
we can think of that follow our rules,
they highlight our rules,
and they have familiar names:
water, ammonia and methane,
H20 and NH3 and CH4.
The words “hydrogen,”
“oxygen” and “nitrogen” –
we use the same words
to name these three molecules
that have two atoms each.
They still follow the rules,
because they have one, two
and three bonds between them.
That’s why oxygen gets called O2.
I can show you combustion.
Here’s carbon dioxide, CO2.
Above it, let’s place water and oxygen,
and beside it, some flammable fuels.
These fuels are made
of just hydrogen and carbon.
That’s why we call them hydrocarbons.
We’re very creative.
(Laughter)
So when these crash
into molecules of oxygen,
as they do in your engine
or in your barbecues,
they release energy and they reassemble,
and every carbon atom
ends up at the center of a CO2 molecule,
holding on to two oxygens,
and all the hydrogens end up
as parts of waters,
and everybody follows the rules.
They are not optional,
and they’re not optional
for bigger molecules either,
like these three.
This is our favorite vitamin
sitting next to our favorite drug,
(Laughter)
and morphine is one of the most
important stories in medical history.
It marks medicine’s first
real triumph over physical pain,
and every molecule has a story,
and they are all published.
They’re written by scientists,
and they’re read by other scientists,
so we have handy representations
to do this quickly on paper,
and I need to teach you how to do that.
So we lay epinephrine flat on a page,
and then we replace all the spheres
with simple letters,
and then the bonds
that lie in the plane of the page,
they just become regular lines,
and the bonds that point
forwards and backwards,
they become little triangles,
either solid or dashed to indicate depth.
We don’t actually draw these carbons.
We save time by just hiding them.
They’re represented
by corners between the bonds,
and we also hide every hydrogen
that’s bonded to a carbon.
We know they’re there
whenever a carbon is showing us
any fewer than four bonds.
The last thing that’s done
is the bonds between OH and NH.
We just get rid of those
to make it cleaner,
and that’s all there is to it.
This is the professional way
to draw molecules.
This is what you see on Wikipedia pages.
It takes a little bit of practice,
but I think everyone here could do it,
but for today, this is epinephrine.
This is also called adrenaline.
They’re one and the same.
It’s made by your adrenal glands.
You have this molecule swimming
through your body right now.
It’s a natural molecule.
This EpiPen would just give you
a quick quintillion more of them.
(Laughter)
We can extract epinephrine
from the adrenal glands
of sheep or cattle,
but that’s not
where this stuff comes from.
We make this epinephrine in a factory
by stitching together smaller molecules
that come mostly from petroleum.
And this is 100 percent synthetic.
And that word, “synthetic,”
makes some of us uncomfortable.
It’s not like the word “natural,”
which makes us feel safe.
But these two molecules,
they cannot be distinguished.
We’re not talking about two cars
that are coming off an assembly line here.
A car can have a scratch on it,
and you can’t scratch an atom.
These two are identical in a surreal,
almost mathematical sense.
At this atomic scale,
math practically touches reality.
And a molecule of epinephrine …
it has no memory of its origin.
It just is what it is,
and once you have it,
the words “natural” and “synthetic,”
they don’t matter,
and nature synthesizes
this molecule just like we do,
except nature is much better
at this than we are.
Before there was life on earth,
all the molecules were small, simple:
carbon dioxide, water, nitrogen,
just simple things.
The emergence of life changed that.
Life brought biosynthetic factories
that are powered by sunlight,
and inside these factories,
small molecules crash into each other
and become large ones:
carbohydrates, proteins, nucleic acids,
multitudes of spectacular creations.
Nature is the original organic chemist,
and her construction also fills our sky
with the oxygen gas we breathe,
this high-energy oxygen.
All of these molecules are infused
with the energy of the sun.
They store it like batteries.
So nature is made of chemicals.
Maybe you guys can help me
to reclaim this word, “chemical,”
because it has been stolen from us.
It doesn’t mean toxic,
and it doesn’t mean harmful,
and it doesn’t mean man-made or unnatural.
It just means “stuff,” OK?
(Laughter)
You can’t have
chemical-free lump charcoal.
That is ridiculous.
(Laughter)
And I’d like to do one more word.
The word “natural” doesn’t mean “safe,”
and you all know that.
Plenty of nature’s
chemicals are quite toxic,
and others are delicious,
and some are both …
(Laughter)
toxic and delicious.
The only way to tell
whether something is harmful
is to test it,
and I don’t mean you guys.
Professional toxicologists:
we have these people.
They’re well-trained,
and you should trust them like I do.
So nature’s molecules are everywhere,
including the ones that have decomposed
into these black mixtures
that we call petroleum.
We refine these molecules.
There’s nothing unnatural about them.
We purify them.
Now, our dependence on them for energy –
that means that every one of those carbons
gets converted into a molecule of CO2.
That’s a greenhouse gas
that is messing up our climate.
Maybe knowing this chemistry
will make that reality easier to accept
for some people, I don’t know,
but these molecules
are not just fossil fuels.
They’re also the cheapest
available raw materials
for doing something
that we call synthesis.
We’re using them like pieces of LEGO.
We have learned how to connect them
or break them apart with great control.
I have done a lot of this myself,
and I still think it’s amazing
it’s even possible.
What we do is kind of like assembling LEGO
by dumping boxes of it
into washing machines,
but it works.
We can make molecules that are
exact copies of nature, like epinephrine,
or we can make creations of our own
from scratch, like these two.
One of these eases the symptoms
of multiple sclerosis;
the other one cures a type of blood cancer
that we call T-cell lymphoma.
A molecule with the right size and shape,
it’s like a key in a lock,
and when it fits, it interferes
with the chemistry of a disease.
That’s how drugs work.
Natural or synthetic,
they’re all just molecules that happen
to fit snugly somewhere important.
But nature is much better
at making them than we are,
so hers look more impressive than ours,
like this one.
This is called vancomycin.
She gave this majestic beast
two chlorine atoms
to wear like a pair of earrings.
We found vancomycin in a puddle of mud
in a jungle in Borneo in 1953.
It’s made by a bacteria.
We can’t synthesize this
cost-efficiently in a lab.
It’s too complicated for us, but we
can harvest it from its natural source,
and we do, because this is
one of our most powerful antibiotics.
And new molecules are reported
in our literature every day.
We make them or we find them
in every corner of this planet.
And that’s where drugs come from,
and that’s why your doctors
have amazing powers …
(Laughter)
to cure deadly infections
and everything else.
Being a physician today
is like being a knight in shining armor.
They fight battles
with courage and composure,
but also with good equipment.
So let’s not forget the role
of the blacksmith in this picture,
because without the blacksmith,
things would look a little different …
(Laughter)
But this science is bigger than medicine.
It is oils and solvents and flavors,
fabrics, all plastics,
the cushions that
you’re sitting on right now –
they’re all manufactured,
and they’re mostly carbon,
so that makes all of it organic chemistry.
This is a rich science.
I left out a lot today:
phosphorus and sulfur and the other atoms,
and why they all bond the way they do,
and symmetry
and non-bonding electrons,
and atoms that are charged,
and reactions and their mechanisms,
and it goes on and on and on,
and synthesis takes a long time to learn.
But I didn’t come here to teach
you guys organic chemistry –
I just wanted to show it to you,
and I had a lot of help with that today
from a young man named Weston Durland,
and you’ve already seen him.
He’s an undergraduate
student in chemistry,
and he also happens to be
pretty good with computer graphics.
(Laughter)
So Weston designed
all the moving molecules
that you saw today.
He and I wanted to demonstrate
through the use of graphics like these
to help someone talk
about this intricate science.
But our main goal was just to show you
that organic chemistry
is not something to be afraid of.
It is, at its core, a window
through which the beauty
of the natural world looks richer.
Thank you.
(Applause)