I’m going to forego Reagent Friday today to talk about something important. Some days you might feel like you can’t escape organic chemistry. You leave the lecture hall and have to study but you wonder if this subject will ever go away. It is driving you insane and you need to make your true feelings known to the world.
This is so true Kayla.
Organic Chemistry Really Is Shit
A few years ago I remember having a discussion about the color of poo. If you were to eat items that were completely clear and colorless – or let’s say, white, would your poo be white as well?
A sage participant in the conversation told us that it wasn’t possible, because a large portion of the color of poo is due to the breakdown products of red blood cells. The average red blood cell lasts about 3-4 months in the body and then gets broken down and recycled. The deep red color of blood is due to the pigment heme, which is the main component of the protein hemoglobin. Here’s what it looks like.
Note the abundance of double bonds, which are responsible for its deep red color. Generally, the more adjacent double bonds one has in a molecule, the longer will be the wavelength of the light absorbed (i.e. less energy) (note 1) That’s a good part of the reason why bleach (sodium hypochlorite) is so good at removing stains from clothes, since the electron-rich double bonds will be munched up by the electropositive chlorine of hypochlorite producing (colorless) chlorohydrins. But I digress.
When the spleen breaks down hemoglobin, the iron is recycled and the heme is degraded to a new compound – biliverdin – which has a green color. If you’ve ever had a green bruise, biliverdin is responsible for that. Also, at least one answer to the age old question of “Why is my poop green?” can be the result of biliverdin from the bile being excreted before it can get further broken down into other metabolites.
However the next stop for biliverdin in the body is generally that it is converted into a red pigment called bilirubin through the action of the enzyme biliverdin reductase (note 2)
Bilirubin has a unique and dubious chemical distinction: breakdown of bilirubin in the body leads to the pigments of both poo and pee. Urobilin and stercobilin respectively. How would you like to be known for that?
So that covers the colors. But what about the most odious feature of poo, its loathsome smell? This time heme is not to blame!!! The guilty party is actually a molecule called skatole, which is a metabolite of the amino acid tryptophan. I have handled skatole (in the lab) and can confirm from personal experience that it does, in fact, smell like poo.
So yes, organic chemistry is shit. It’s a lot of other nasty things too. While we’re at it, we should not neglect to mention that organic chemistry is also death and decay. These names should require no explanation.
We can keep going down this road and find organic chemistry behind every loathsome phenomenon you care to name - vomit, bad breath, stinky feet – the list goes on. Behind every unpleasant shock your senses have ever bestowed on you, organic chemistry is to blame.
Organic Chemistry Is A Lot of Other Things Too
But this is only one side of the story. It would be unjust not to end by stating the opposite case. If there is organic chemistry in death, there is organic chemistry in life too. Just before you were born, your mother had the hormone oxytocin coursing through her body, which is responsible for inducing labor. Furthermore, while organic chemistry is shit, piss, death, and decay, it is also pleasure, excitement, and yes – ecstasy.
Organic chemistry is the smell of poo, vomit, and stinky feet, but also the scent of freshly cut grass, roses, and damp earth on a rainy spring day.
Did you know that masculinity and femininity have their roots in organic chemistry (and they’re not that different, chemically)?
In short, organic chemistry is a part of so many things that surround you, so many things that your body already recognizes, that when you come to understand organic chemistry, you are gaining a greater appreciation not only of our world, but also yourself. And just like the world around you, you can find in organic chemistry anything you look for – pleasure and pain, beauty and ugliness, and yes – shit.
- In more technical terms, the greater the number of double bonds in the π system, the smaller will be the gap in energy between the highest-occupied-molecular orbital (HOMO) and the lowest-unoccupied molecular orbital (LUMO). Yet another way of putting it is that the molecule will absorb at longer wavelengths. Compare butadiene (2 double bonds) which is colorless, and Vitamin A (retinol, 5 double bonds) which is yellow
- If you look closely, you’ll note that we’ve achieved the net loss of a C–N π bond and the formation of two new bonds to hydrogen (a reduction)