Ribosome Rant

I realize this is a departure from the content I normally post here, but I just started writing a rant on a different site and I think it really belongs here. The Nobel Prizes are being announced this week. The prize in chemistry went to Venkatraman Ramakrishnan, Thomas A. Steitz, and Ada Yonath for their work on the the structure of ribosomes. There's a sentiment that I've been seeing somewhat and it got me annoyed enough to actually write this. Here are some examples of the sentiment I am talking about...

I don’t care. For some reason, this year I’m not getting into Wednesday Madness nearly as much as I have in previous years. I’ll be happy if they give it to, uh, a chemist.

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Oh well. Here’s an idea. In lieu of giving out Nobel Prizes in Chemistry to achievements in chemistry (since they only seem to give it to actual chemists every other year anyway, it won’t be much of a stretch), let’s start handing them out to the authors with the best paper titles ever.

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As already announced biologists walked away with this year’s Nobel prize in chemistry once again, this time for work in determining the structure of Ribosomes.

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As chemists we would like to see the Nobel chemistry prize go to a chemist. Our Nobel hopefuls may be a measurable magnitude more chemically interesting, as measured by ChemFeeds, but there is more work for them to do until these topics become world renowned (which seems to be the dominant prerequisite these days).

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And again the Nobel for Chemistry goes to "bio-chemists"....
Congratulations...but as a strictly synthetic organic chemist...I am a bit ticked off.
With all the biology and the nanoscience development in recent years, it'll be eons before an organic chemist wins the prize again.

Alright guys, the applicant to get into school to work on an undergraduate degree (I do already have my A.S. at least) has some news for you: biochemistry is chemistry. I find this reaction deplorable. Chemistry is all about atoms and the bonds between them, what things are made of and how they interact with each other. That is exactly what this prize was awarded for. Perhaps word has not yet reached the innermost confines of your biology-free ivory towers, but ribosomes are made out of atoms and ribosomes have bonds—lots of them. Ribosomes participate in chemical reactions. This really should go without saying.

I could be way off here, but I don't think I would see this in other branches of science. If an annual physics prize went to scientists who did work in astrophysics, would physicists complain that the astronomers are taking physics prizes? I think not, but maybe some of them would. Maybe some of them sequester themselves in ivory towers devoid of any science that is not their own particular specialization, just as apparently some chemists do. My impression is that many, if not most, physicists have a passion for the universe and its fascinating nature. They want to see the physics in everything. I want to see the chemistry in everything. And I'd like to think I'm in good company, but the reactions I've seen to this Nobel Prize have cast some doubts on that.

How arrogant must one be to think, "Only research in the area of chemistry that I focus on should win prizes"? Some might protest that this is an unfair characterization, but if one is willing to dismiss the entirety of biochemistry, I am more than willing to err on the side of assuming that one would go on to dismiss other purportedly unworthy subjects in a similar manner. This exclusive approach is the exact opposite of what I want to stand for. I want chemistry to be inclusive. If we excise some of it because it deals with biological molecules and can therefore be considered biology, we might as well excise the parts that deal with minerals and make that geology and so on until we have divided everything up and there are no more chemists, just former chemists working in other fields of science.

The ribosome people did not win because the biologists are taking over and they did not win because ribosomes are famous and other work was too obscure. They won because they did good chemistry that is of abundant benefit to humanity.

Aspirin

It's been a while and I need to get a feel for this. I'm also not done with the chapter on acids and bases. So I thought it would be cool to show you aspirin. My book does it, although there's some other stuff before it that I sort of went over, kind of, more or less, already. This will also be an opportunity for me to try to use a program other than MS Paint to render something. We'll see how it works...

Well, that seems to work. I had to make it on this ChemSketch program and then copy the thing into MS Paint in order to upload it here, but whatever. Much easier than drawing everything from scratch.

Now let's make sense of this. There are a few functional groups here, and we'll learn all about functional groups some day. Won't that be exciting? The one we're interested in now is the carboxylic acid group. One of the carbons is attached to an oxygen by a double bond and a second oxygen by a single bond, with that second oxygen itself being attached to hydrogen. This arrangement of atoms makes it easy for a certain reaction to occur. That reaction is a Brønsted-Lowry acid-base reaction. Here's a mechanism...
Okay, those arrows look terrible. I'll have to work on that next time. Anyway, that's the same as the mechanism for the Brønsted-Lowry acid-base reaction I covered in my last post. This reaction can happen in the human body, assuming aspirin gets into the body in the first place. Aspirin is not found in nature. I've sometimes heard it said that aspirin was found in willow bark, but that's incorrect. Willow bark contains salicylic acid. Aspirin is acetylsalicylic acid. The stuff in willow bark would look just like aspirin, but the group attached to that oxygen on top would be replaced with a hydrogen. Aspirin became the analgesic of choice, as opposed to salicylic acid or another derivative of it, because it lacked the irritating side effects of those drugs.

So the reaction can and does occur in the human body. When this happens, the conjugate base, or acetylsalicylate, is formed. The conjugate base is ionic (with a negative charge on the oxygen that gave up hydrogen) and cannot cross cell membranes. Fortunately, this isn't a huge problem because, like other Brønsted-Lowry acid-base reactions, the reaction that turns aspirin into its conjugate base is reversible. My textbook notes that it's the acid that is present in the stomach, and the base that is present in the intestines. This should be pretty intuitive. When conditions are highly acidic, aspirin, which is only a weak acid, even when it does protonate something, will get protonated right away by the acid around it. In basic conditions, there's not much acid around to do the reverse reaction and what is there might be even weaker than aspirin as an acid anyway.

So yeah, aspirin.

Acid-Base Definitions

Do you know what acids and bases are? Seriously? I know I used to think I did and I totally didn't. I mean, I knew some examples of acids and bases, but the chemistry behind them was completely unknown to me even after I took chemistry in high school and even when I started taking it in college. But finally, in one class I was introduced to three acid-base definitions. I knew there were more, but I had no idea how many. This post will introduce some of them. Really, I've only ever used two of them and those two, which happen to coincide with each other a lot, are the only two that will be important here, but I think the historical definitions are interesting and this is my blog or whatever and so I get to make a post including them.

Lavoisier definition
In case you didn't know who Lavoisier was, he was one of the founders of chemistry and you are not worthy. Through a series of experiments, he determined that oxygen combining with other elements could lead to "acidic" (the word comes from the Greek word for "sharp") properties. He extrapolated from this that oxygen was the element that contributed the acidity. This is where oxygen got its name, which means "acid-generating." There was a small problem with this: Lavoisier was wrong. Considering that he basically invented chemistry, I think he's allowed to be wrong every once in a while.

Liebig definition
You know who Liebig was too, right? Because he was another great chemist. Anyway, this was sort of the first real definition. A Liebig acid is a molecule that contains at least one hydrogen atom that can be replaced by a metal. This was only a definition for acids. Back then, bases were loosely defined as the opposites of acids. Known acids were generally liquids, so a base was whatever compound would react with an acid to neutralize it into a solid salt. Such reactions are known as acid-base reactions and we'll deal with them other posts pretty soon.

Arrhenius definition
This was one of the three definitions I originally learned and it was the main definition everyone used for a long time. But that was in the past. The distant past. Like before I was born, even. Probably before you were born too. Arrhenius acids are molecules that, in water, lose hydrogen atoms, generating hydrogen ions in the solution. Well, we now know that they're actually hydronium ions. Oh, hydronium is important. You should know what it looks like. Here, I'll paint one for you.
If you weren't stupid, you'd remember what a water molecule looks like. Man, I'm not posting water again here just for you. Go back and find the post where I did show it or something. Anyway, this is like water, but with another hydrogen. Oxygen normally only forms two bonds. I guess I never talked about formal charges or whatever, but the oxygen is positively charged now. Really. We'll talk about it later if you want. Hydronium is properly written as H₃O⁺. But you should be aware that a common shorthand is just to just write H⁺.

So those are Arrhenius acids, but there are also Arrhenius bases. They are molecules that, in water, generate hydroxide ions. You want a hydroxide ion? Here you go.
Note that when it has oxygen has one too many bonds, it is positively charged, but when it has one too few bonds, it is negatively charged. Unlike H⁺, hydroxide ions actually can and do exist in water. The shorthand for hydroxide is ⁻OH. That's how I would notate it if I were writing stuff down by hand, but superscripts and subscripts, although necessary for chemical notation, can be annoying to do on Blogger, so I'll probably stick to just typing "hydroxide" most of the time.

Now might be a good time to mention that in aqueous systems (systems with water as the solvent—I'm not going to elaborate on this for now), hydronium and hydroxide act as a sort of currency of acidity and bacisity. When a reaction takes place, the actual atoms from the acid/base aren't the ones that are participating. I'll illustrate this with a classic acid-base reaction...

HCl + NaOH → NaCl + H₂O.

So, hydrochloric acid and sodium hydroxide yield sodium chloride and water. Sodium chloride is the salt in this case. In other reactions, other salts would be formed. A salt and water are the products of Arrhenius acid-base reactions. But keep in mind that water is the solvent in which this whole thing is taking place. HCl is a gas and NaOH is a solid. When we do this reaction in a lab, we're likely to just mix samples of water that have the compounds dissolved in them. The bond between the chlorine and the hydrogen breaks and the hydrogen reacts with a water molecule to form hydronium while the chlorine atom becomes a chloride ion and sits there dissolved in the water. The bond between sodium and oxygen likewise breaks and we're left with hydroxide and a sodium ion, which also sits there dissolved in the water.

The hydronium ion produced by dissolving the acid in water can and will react with another water molecule. But the product of that reaction leaves the original hydronium ion turned into an ordinary water molecule and the water molecule attacked by hydronium as the new hydronium ion. This process occurs repeatedly, but without really changing anything because the number of hydronium ions remains constant. The same is true with the base. If hydroxide reacts with a water molecule, the hydroxide gains a proton and is now a water molecule while the water molecule it reacted with lost a proton and is now a hydroxide ion. The charges are rapidly transferred from one water molecule to the next, but they remain there. This tranfer would continue for a long time, but when we mix the two solutions, in addition to reacting with water, the hydroniums and hydroxides can react with each other. Whenever this reaction takes place, the two ions neutralize each other and we're left with only water (H₃O⁺ + ⁻OH → 2H₂O). This reaction also produces heat, so if you do it at home for some reason, keep that in mind so that you don't die or whatever. If you were wondering, the sodium and chloride ions stay dissolved. You have seen what happens when you add sodium chloride to water, right? Seriously, you'd better have. If not, go do it right now.

So that's the Arrhenius definition. There are several other definitions, some of them relevant to certain fields, but two definitions are by far the most popular and important, so I'll introduce them now.

Brønsted-Lowry definition
This is the definition that seems to be used the most in my textbook and introductory chemistry courses. It is more inclusive than the Arrhenius definition. A Brønsted-Lowry acid is a proton donor. A Brønsted-Lowry base is a proton acceptor. One big difference between this and the older Arrhenius definition is that water is not necessarily present as a solvent. It can be and often is, but it's not necessary. The most important difference to keep in mind might be that not every Brønsted-Lowry base will lose hydroxide. Every Brønsted-Lowry acid must have a hydrogen atom that can be lost in order to give off a proton, but the bases need not look anything like Arrhenius bases. What a Brønsted-Lowry base does need is the ability to form a bond to a proton. That means it needs free valence electrons that can be recruited to form the bond. Lone pairs of electrons work best, but electron pairs in π-bonds also have basic potential.

My next few posts will be dealing with Brønsted-Lowry acids and reactions with them, so this is the definition to pay the most attention to. Hopefully, you'll get a feel for what chemicals act as good acids and bases and how acid-base reactions work. For now, definitely remember that an acid is a proton donor and a base is a proton acceptor.

You might have deduced that once an acid has donated a proton, what's left is capable, under the right circumstances, of accepting a proton and recreating the original acid. Likewise, a base that accepts a proton now has a proton that could be donated to something else, recreating the original base. These are conjugate acid/bases. That is, whenever an acid-base reaction occurs, the acid becomes its conjugate base and the base becomes its conjugate acid. The reaction could potentially reverse. Here's one reaction...

H—A (acid) + :B (base) → :A⁻ (conjugate base) + H—B⁺ (conjugate acid)

Now we'll reverse the reaction...

:A⁻ (conjugate base) + H—B⁺ (conjugate acid) → H—A (acid) + :B (base)

The system can bounce back and forth between these two. So where does that leave us? The rule I learned in general chemistry and used all the time in my organic chemistry classes was that the equilibrium favors the side with the weaker acid. Unhelpful if you don't know which acid is weaker, but we have ways of figuring that out.

Under the Brønsted-Lowry definition, acidity and basicity are relative to what something is reacting with. Water, for example, is an acid when it's reacting with hydroxide (it donates a proton) and a base when reacting with hydronium (it accepts a proton). Also, you might have deduced that the conjugate acid of water is hydronium and the conjugate base of water is hydroxide. If you deduced that, good job. You get a gold star.

Lewis definition
This definition was formulated by Gilbert N. Lewis. You do know who he was, right? A Lewis acid is an electron pair acceptor. A Lewis base is an electron pair donor. This definition is more inclusive than the Brønsted-Lowry definition. A base still needs free valence electrons to donate, but the acid in the reaction no longer needs to provide hydrogen. So while all Lewis bases are also potential Brønsted-Lowry bases, not all Lewis acids are Brønsted-Lowry acids.

I'll say more about Lewis acids later. This material is in the last section of the acids and bases chapter in my textbook and it's time to move on to some specific Brønsted-Lowry acid-base reactions.

Vitalism and the Origins of Organic Chemistry

Time flies. I can't believe how long it's been since my last post here. I am slacking a little, but part of the reason that posts here have been infrequent is that I've been spending more time with friends, which is something I had a goal of doing. So I'm not too upset. And I am here, right now, updating this blog. So here we go...

In order to appreciate the distinction between organic chemistry and the rest of chemistry, it take some appreciation for the history of the science. Organic chemistry is frequently defined as being the chemistry of carbon or the chemistry of compounds containing carbon.

My textbook puts it rather simply:

Organic chemistry is the chemistry of compounds that contain the element carbon.

Wikipedia is a bit more specific:

Organic chemistry is a discipline within chemistry which involves the scientific study of the structure, properties, composition, reactions, and preparation (by synthesis or by other means) of chemical compounds that contain carbon.

What neither of these simple definitions tell us is that not all compounds containing carbon are considered organic. My textbook doesn't seem to mention it, but looking up "organic compounds" on Wikipedia reveals this:

For historical reasons discussed below, a few types of compounds such as carbonates, simple oxides of carbon and cyanides, as well as the allotropes of carbon, are considered inorganic.

This is because of the now defunct concept of vitalism. People believed that organic matter and inorganic matter were fundamentally different (as an aside, some attribute this to Aristotle, but I haven't looked into it). Carbonates, oxides of carbon, and cyanides (and carbides, another class of inorganic carbon-containing compounds) are all found naturally outside living systems (in minerals, for example). Other carbon-containing compounds were only known to be associated with life. Then this whole view of things got wrecked in 1828 by Friedrich Wöhler doing this reaction:
Pretty cool, huh? Wöhler combined ammonia with a solution of cyanic acid ammonium chloride (dissolved in water) with silver cyanate and got, as a product, urea, which was previously only known to be produced by the kidneys of animals (mammals and some other animals produce urea as a waste product). Although this didn't immediately strike the deathblow for vitalism (which has, in some form or another, survived to this day, although thankfully not among chemists), it laid the foundation for organic chemistry as a field (these compounds were now something that could potentially be synthesized in laboratories and there wasn't necessarily any essential "life force" that was generating them).

The distinction between organic chemistry and inorganic chemistry is important today because organic compounds have some specific properties of their own that can be studied in detail and because organic chemistry is so important in biological systems. Being biological systems ourselves, we have an interest in organic chemistry as it relates to our health. Pharmacy is one branch of applied organic chemistry.

Addendum:

I forgot to mention this, but before taking organic chemistry, I was under the impression, from general chemistry, that organic compounds had both carbon and hydrogen. My organic chemistry professor pointed out early on that technically, not all organic compounds have hydrogen. For example, carbon tetrachloride (CCl₄) is considered an organic compound, but has no hydrogen. However, most organic compounds do contain hydrogen.