Here is the full transcript of organic chemistry professor Jakob Magolan’s interesting talk: A Crash Course in Organic Chemistry @ TEDxUIdaho May 2017 conference.
Listen to the MP3 Audio: A crash course in organic chemistry – Jakob Magolan
Jakob Magolan – Associate Professor of Organic Chemistry, University of Idaho
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?
All right, let’s go for it.
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.
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, these things 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 that 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.
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, 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. 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% 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?
You can’t have chemical-free lump charcoal. That is ridiculous. 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 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 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. 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. 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.