I’ve been working hard this year to understand the secret world of amino acids. But amino acids are kind of useless all by themselves. It’s the way they join together that makes them so vitally important for life, or at least for life on Earth.

We’ve already looked at the anatomy of an amino acid. For today’s post, the crucial components are the amino group of one amino acid and the carboxyl group of another.

First, we remove one oxygen atom (the red ones) from the carboxyl group and two hydrogens (the white ones) from the amino group. One oxygen plus two hydrogens equals a water molecule: H₂O.

Next, the carbon (in grey) in the carboxyl group reaches out for the nitrogen (in blue) in the amino group. When the two come together, they form what’s called a peptide bond.

This can happen over and over and over. One amino acids links up with another, which in turn links up with a third, which links with a forth and a fifth and a sixth….

I said at the beginning of this post that amino acids are kind of useless by themselves. That’s not quite fair. They can do plenty of fun, interesting chemistry on their own; but it’s this ability of theirs to form long peptide chains that makes them so useful (especially in a structural sense) for living organisms.

It’s entirely possible, in this big, wide universe of ours, that life exists without amino acids. But life without peptide bonds or something similar? Life without some easy way to string molecules together? Why, that would be pure science fiction!

P.S.: Or pure science fantasy, depending on how you define those terms.

An acid is a chemical that can give up a proton to another chemical. Two out of three textbook definitions agree on this (we can worry about the Lewis definition some other time). But why are there so many chemicals out there giving away free protons?

The story begins with a hydrogen atom (one proton, one electron).

A second electron would complete hydrogen’s valence shell, which is something all atoms want to do. So hydrogen will try to bond with another atom, in the hope that by sharing electrons through chemical bonds, it can get the extra electron it so desperately needs.

Sadly, this arrangement doesn’t always work out in hydrogen’s favor. Rather than getting to borrow some other atom’s electron, sometimes hydrogen gets cheated out of the one electron it already had. This can happen for several reasons, such as:

• Greedy Atoms: Some atoms, especially oxygen, chlorine, and fluorine, tend to hog electrons from other atoms. I described this electron-hogging tendency in a previous post on electro-negativity.
• Electrons Gone Wild: Some molecular structures allow electrons to run around inside the molecule. This is called electron delocalization, or sometimes electron resonance.

Whether due to electron delocalization, electro-negativity, or electro-something else, the single proton of a hydrogen atom can end up feeling neglected and lonely. And the more neglected and lonely that proton feels, the more likely it is that this will happen:

And the more likely it is that this will happen, the more acidic the chemical in question is said to be.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

I have repeatedly complained about how much I hate chemistry. But that’s changing. The more I learn about atoms and molecules, the more I learn about how they interact with each other, the more they blow my mind. It’s hard to hate a subject that is so consistently mind-blowing.

Recently, my mind was blown by something called electron delocalization (or electron resonance, if you prefer old school chemistry lingo). Basically, this is a fancy term for what happens inside a molecule when electrons go wild.

So within a molecule, there are certain positions that each atom is supposed to take, and they’re supposed to stay put (more or less). But electrons… electrons like to run around and play. Depending on molecular structure and the types of chemical bonds (pi bonds vs. sigma bonds), some molecules turn into awesome electron jungle gyms.

For example, here’s a benzene molecule.

The ring shape of benzene is like a racetrack for electrons. Electrons can just run round and round to their subatomic hearts’ content. As a result benzene molecules—and other, more complicated molecules that incorporate benzene rings—are very stable. Extremely stable. This might seem counterintuitive, but the more “electron delocalization” occurs in a molecule, the more stable a molecule tends to become.

If you have even a passing familiarity with quantum physics, you might guess what’s really happening here. Electrons don’t merely run around inside a molecule; electrons exist simultaneously in multiple locations inside that molecule. And the more spread out electrons are allowed to be, the more they can help tie the molecule together.

But while electron delocalization is great fun for electrons, and while it helps stabilize a molecule overall, certain parts of a molecule can feel a little left out. Certain protons (hydrogen ions) in particular will feel neglected and lonely. In the next edition of Molecular Mondays, we’ll find out what happens to them.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

Molecules are supposed to be nice and stable, with all the bonding sites on each of their atoms used up… no more and no less. At least, that’s how I was taught to picture them in school, and that’s how I’ve been drawing them on my blog. But in the case of amino acids, it turns out this is wrong (sort of).

Take our new friend glycine, the simplest amino acid. I’ve been drawing glycine like this:

This is a perfectly acceptable depiction of a glycine molecule. Glycine does sometimes look like this, but not usually in biological processes. In biological processes, it tends to look more like this:

One proton (a.k.a. one hydrogen ion) was shed from glycine’s carboxyl group. The two oxygen atoms (portrayed in red) kept that hydrogen’s electron. The dashed lines indicate that the oxygen atoms and the nearby carbon atom now share this electron, and the minus sign shows that there’s now a negative electrical charge in that region of the molecule.

So where did that rogue proton go? Through an intramolecular acid-base reaction, it moved to the nitrogen atom (portrayed in blue) of the amino group. Nitrogen is now bonded to four other atoms, despite the fact that it’s only supposed to have three bonding sites. Also, the area around the nitrogen now has a positive electrical charge, indicated by the plus sign.

A molecule like this with localized regions of differing electrical charge is called a zwitterion (which is such a cool term—it comes from the German word zwitter, meaning hybrid). It’s not hard for me to imagine that zwitterions like glycine are a lot more versatile in chemical reactions than “normal” molecules with all their bonding sites properly accounted for.

Going forward, I’m going to draw amino acids in their zwitterionic forms, not just because I love the word but because I think they’re more relevant to the biochemical stuff I’m currently researching.

P.S.: Spell check is weird. While writing today’s post, I was stunned to find that spell check had no issue with the word zwitterions (the plural) but it flags zwitterion (the singular) as a mistake.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

How many amino acids are there? As I continue my mission to understand the amino acids, this has become an incredibly frustrating question. Everywhere I go, I get a different answer, in part because many sources fail to specify which category of amino acids they’re talking about.

There are 9 amino acids

I got this from a nutrition website. In terms of your diet, there are nine essential amino acids. What’s essential about them? It’s essential that you, as a human being, get them in your diet because the human body cannot make them on its own.

There are 20 amino acids

This seems to be the most common answer. There are twenty standard amino acids. Why are they standard? Because your DNA (and the DNA of all organisms on Earth) directly codes for these specific amino acids, and so these twenty amino acids are incorporated into all the proteins found in your body (and the bodies of every other living thing on Earth).

There are 21 amino acids

The amino acid selenocysteine is also found in some of the proteins in our bodies. It’s just not directly coded by our DNA, so it’s considered non-standard.

There are 23 amino acids

There are two more non-standard amino acids that are only found in prokaryotic organisms (bacteria and archaea). So in total, across all life forms on Earth, there are 23 proteinogenic amino acids, meaning there are 23 amino acids incorporated into proteins.

There are hundreds of amino acids

As important as the 23 proteinogenic amino acids are, there are literally hundreds—maybe thousands—more. The rest are sometimes called non-coding because they’re not coded for by DNA. They’re also called non-proteinogenic because they’re not incorporated into proteins (at least not here on Earth). Sometimes they’re called unnatural, which seems rather unfair. Many of these “unnatural” amino acids serve vital biochemical purposes. Life is made of more than proteins, you know!

Anyway, next Molecular Monday (two weeks from today) we’re finally going to meet an actual amino acid.

Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

I’m getting closer to the point where amino acids make sense to me. Right now, I can look at chemical formulas and pick out which chemicals I think are amino acids and which ones are definitely not. That’s progress.

But I still have a ways to go. So far here on the blog, I’ve introduced you to amino groups and carboxyl groups. By definition, amino acids must include at least one of each of these functional groups. So let’s stick a carboxyl group to an amino group and see what happens.

Oh, come on, guys! You each have one available bonding site. What’s the problem?

This is a chemical called carbamic acid. The “carb” part of the name comes from “carboxyl,” and the “am” part is for “amino.” Although this is not considered an amino acid, it has a pair of functional groups that should still be useful for biological processes. They should be, except…

So apparently carbamic acid has a tendency to reshuffle its constituent atoms, trying to find a more comfortable and stable arrangement. In the process, the molecule just falls apart, leaving us with ammonia and carbon dioxide.

There’s something that always sort of bugged me about chemistry. With over 90 different naturally occurring elements and so many different kinds of chemical bonds that can form between them, there should be a virtually infinite number of molecules. The larger and more complicated molecules are, the more varieties should be possible.

So how come certain molecules, molecules which seem to make sense on paper, are so rare in nature or don’t seem to exist at all? Perhaps the example of carbamic acid provides a clue.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

Amino acids: they’re still too complicated for me. So instead, I present to you a carbonyl group.

A carbonyl group is composed of a single carbon atom double bonded to a single oxygen atom. The carbon still has two free bonding sites, so the carbonyl group can bond to at least one—maybe two—other chemicals.

Up next, we have a hydroxyl group.

It’s a single oxygen atom bonded to a single hydrogen atom. The oxygen still has one available bonding site.

Now, let’s put the two together.

Let’s call this a carbonylhydroxyl group. Actually, no. Let’s not do that. Let’s cut out the middle of that word and just call it a carboxyl group, because that’s less of a mouthful. Notice, by the way, that the carbon still has one bonding site left.

Like the amines we met last Molecular Monday, carboxyl groups are free to bond with other stuff, forming larger molecules known as carboxylic acids.

Examples of carboxylic acids include acetic acid (found in vinegar), fatty acids (which I probably get too much of in my diet), and—wait for it!—amino acids!

Okay, so now that we know about carboxyl groups and amines (a.k.a. amino groups), we’re ready to start building amino acids. Right, guys?

Dang it. Back to my research.

P.S.: In the process of researching today’s post, I stumbled upon a new word: zwitterion. I have no idea what a zwitterion is, but it’s now my #1 favorite word.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

So I wanted to start talking about amino acids today. But let’s face facts: amino acids are complicated. They’re also hard to draw. So instead, let’s talk about ammonia. Here’s a drawing of an ammonia molecule:

It’s just one nitrogen atom with three hydrogen atoms attached. Nice. Friendly. Easy to draw.

Let’s make it even easier! Let’s take away one of those hydrogen atoms.

This is no longer an ammonia molecule. Instead, chemists call this an amine. With that hydrogen out of the way, this amine is free to bond with something else. Perhaps something more interesting than an ordinary hydrogen atom.

How about we take away another hydrogen atom?

This is called a secondary amine (the amine from before was a primary amine). It can bond with two other chemicals, allowing for the construction of some sort of weird, complicated super molecule.

Okay, let’s take away the third hydrogen…

… and now we have a tertiary amine (also known as a nitrogen atom). I bet we could build some really wacky (and useful) large molecules out of this.

By now, you can probably guess why I’m writing about these amines for my first post on amino acids. It’s because amines give amino acids their name (or at least the first part of their name). Primary, secondary, and tertiary amines are key structural components in all amino acids.

In the next edition of Molecular Mondays, we’ll talk about the other key structural component of amino acids: the acid part.

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Today’s post is part of a special series here on Planet Pailly called Molecular Mondays. Every other Monday, I struggle valiantly to understand and explain some concept in the field of chemistry. Please note: I suck at chemistry, but I’m trying to learn. If I made a mistake, please, please, please let me know so I can get better.

I have a confession: I really hate Molecular Mondays. Chemistry was my worst subject in school, and it’s still not exactly fun for me today.

Last year, I started writing this Molecular Mondays series as a way to force myself to do a little chemistry research. I agonized my way through a long chain of posts on oxidation/reduction and an even longer chain on the assorted properties of water. I also studied sulfuric acid on Venus, hydrogen peroxide on Mars, and platinum group metals in the asteroid belt.

I’m still trying to figure out my writing plans for 2016. I was secretly hoping I could quietly cancel Molecular Mondays and never have to do chemistry research again! But as much as I hate this series, I cannot deny that I’ve learned something from it.

Having at least a basic understanding of chemistry makes many other aspects of science easier to follow. A lot of things that used to go right over my head now make sense to me. When I read scientific papers, I get a whole lot more out of them.

So I have decided (grudgingly) to keep Molecular Mondays going. And thanks to a few papers I recently tried to read (and failed to understand) concerning life on Titan, I think I know what my next research focus needs to be.

So get ready. Two weeks from today, we’re going to start meeting the amino acids.

P.S.: And at some point in the more distant future, once I know what the heck I’m talking about regarding amino acids, I promise to revisit Titan and see if anyone’s home.