If you liked it then you shoulda put benzene on it! Add a methylene linker and you get the phenomenal PHENYLALANINE. My idea of romantic is AROMATIC! A picture says 1000 words, but sometimes a single snapshot can’t suffice. This is the case w/RESONANCE structures, as we’ll see with today’s amino acid, PHENYLALANINE (Phe, F). yeah, P was taken by proline so Phe gets F… I know, what the F, right?  

video added 12/7/21

It’s Day 7 of #20DaysOfAminoAcids –   the bumbling biochemist’s version of an advent calendar. Amino acids are the building blocks of proteins. There are 20 (common) genetically-specified ones, each with a generic backbone with to allow for linking up through peptide bonds to form chains (polypeptides) that fold up into functional proteins, as well as unique side chains (aka “R groups” that stick off like charms from a charm bracelet). Each day I’m going to bring you the story of one of these “charms” – what we know about it and how we know about it, where it comes from, where it goes, and outstanding questions nobody knows. ⠀

More on amino acids in general here http://bit.ly/aminoacidstoproteins but the basic overview is:⠀

amino acids have generic “amino” (NH₃⁺/NH₂) & “carboxyl” (COOH/COO⁻) groups that let them link up together through peptide bonds (N links to C, H₂O lost, and the remaining “residual” parts are called residues). The reason for the “2 options” in parentheses is that these groups’ protonation state (how many protons (H⁺ ) they have) depends on the pH (which is a measure of how many free H⁺ are around to take).⠀

Those generic parts are attached to a central “alpha carbon” (Ca), which is also attached to one of 20 unique side chains (“R groups”) which have different properties (big, small, hydrophilic (water-loving), hydrophobic (water-avoided), etc.) & proteins have different combos of them, so the proteins have different properties. And we can get a better appreciation and understanding of proteins if we look at those letters. So, today let’s look at phenylalanine⠀

We’ll get into the details more, so don’t worry if the terms sound jargon-y at this point, but here’s an overview of what we’re dealing with… Phenylalanine is AROMATIC. The term “aromatic” initially referred to the odors of these types of compound, but that’s not what makes aromatic molecules (aka arenes) special. What really makes them special is that they have a ring (actually a polygon) structure in which the ring’s carbons all share electrons (e⁻) through “charge delocalization” leading to “resonance stabilization” – basically, atoms bond through sharing electrons. And the ring’s corner C’s have extra so they donate their “extra” to a communal stock that they share. That makes them happy. And helps them interact with other things. But it requires them to live in a plane. So you end up with a flat circular molecule with electrons spread out like a donut above and below it. 

Phe’s aromatic part is based off of a BENZENE ring, which is the simplest aromatic hydrocarbon, consisting of 6C & 6H (thus having the formula C₆H₆). Legend has it that the idea of benzene’s structure came to German chemist August Kekule in a dream about a snake biting its own tail. But there are multiple versions of this tale and some scientists say that Kekule wasn’t first to think of it, but I’m staying out of all that…

Anyways, in less-disputed history, benzene gets its name from gum benzoin, which has been used in medicines. cosmetics, and fragrances since apothecary times. Benzoin comes from Arabic for “incense of Java.” When benzene is attached to something else (i.e. serving as a “functional group”) we call it a “phenyl” (from the French for the Greek for “shining” cuz it was found in byproducts of refining gases for lighting) & Phe without benzene would be the amino acid alanine (the R group of Ala’s just a methyl) so we get the name phenylalanine. Sorry there’s no cool story here, but sometimes it’s a relief when names are descriptive! Although somewhat confusingly, “benzyl” refers to whole thing (methyl+benzene) not just benzene (which is “phenyl”). 

Ready to dive in?

Amino acids, like all matter for that matter, are made up of atoms, which are the basic “units” of elements (carbon (C), hydrogen (H), nitrogen (N), oxygen (O), etc.). Atoms are themselves made up of even smaller stuff – subatomic particles, which include positively-charged protons held together (with the help of neutral neutrons) in a dense central atomic nucleus and tiny little negatively-charged electrons whizzing around. Unlike the protons which are held super tight and are key to an atom’s identity (e.g. hydrogen ALWAYS has 1 and carbon ALWAYS has 6), electrons are more free to explore as long as they stay within the protons’ “sight.”

They’re reigned in by the positive pull of the nucleus, so they can’t just wander off (at least not unless you give them a ton of energy and/or offer a great new home). But they can roam a bit –  especially the ones that are furthest away (the valence electrons). And they can interact with the roaming electrons from other atoms. You can never know exactly where an electron will be, but there are certain places you’re most likely to find them, and we call these electronic “orbitals” You can think of them kinda like clouds that electrons spend most of their time in. 

Atoms can join together by merging their atomic orbitals to form molecular orbitals, which we’ll get into more later. But for now just go with it… These electron shares are called COVALENT BONDS, and they’re strong (unlike non-covalent bonds which are just “attractions”). Covalent bond are what holds all the atoms of the amino acid together to make an amino acid and they’re also responsible for linking amino acids into chains. And then non-covalent bonds are the attractions between different parts of the chain with each other and/or with other molecules that help the protein fold up. So you can “unfold” proteins without “unchaining” them (a fact we take advantage of in SDS-PAGE where we use heat and the detergent SDS to unfold proteins into linear chains so that when we run them through a gel to separate them based on size, their “shape” doesn’t get in the way and make a tiny protein look huge or a huge one tiny) http://bit.ly/sdspageruler 

A lot of times in biochemistry and organic chemistry, the atoms that are sharing electrons in covalent bonds are carbon & hydrogen, and we call molecules with carbon/hydrogen skeletons HYDROCARBONS. Hydrocarbons make great skeletons because carbon can hook up to up to 4 things so you have lots of options & directions to branch out on. And the H? Hydrogen can come and go more easily than other atoms so you can “swap it out” & it’s really small (smaller than all the other atomic alternatives) so if it does stick around it doesn’t get in the way too much. 

“Pure” hydrocarbons (just H’s & C’s) are pretty “boring” (and you know that’s saying something if it’s coming from me…). Their real potential comes from what you swap in and where. We call the swapped-in parts “functional groups” and they can be everything from the amino & carboxylic acid groups of the generic part of amino acids to a plethora of options you can find in the side chains. Depending on what you swap it with, you can alter the properties. 

For instance, H & C share their shared electrons pretty fairly, so there’s an even charge distribution in pure hydrocarbons. We call such molecules “nonpolar” and we’ve already seen several of these (valine, leucine, & isoleucine). But, we also saw that when we swapped one of valine’s methyl (-CH₃) groups for a hydroxyl (-OH) group we went from nonpolar, to polar since O is a major electron hog, so it steals electrons from the H making it partly negative and leaving the H partly positive.

This polar/nonpolar thing matters because water is super polar – it has an O pulling electrons from 2 H’s. So you have a partly negative O and 2 partly positive H’s. And they can get attracted to other partly- or fully-charged things and surround them – we call such water-loving things “hydrophilic”. But nonpolar things don’t offer charged regions. So the water excludes them, and nonpolar amino acids end up seeking refuge in the center of proteins. And since the amino acids are linked up, the protein has to figure out how to let the nonpolar ones chill in the core while the polar ones hang at the surface. And this “hydrophobic effect” is the driving force behind protein folding.  http://bit.ly/hydrophobesarenotafraid 

So that’s one way we can categorize amino acids: polar (and thus hydrophilic) vs. nonpolar (and thus hydrophobic) (though it’s really more of a spectrum). In the case of phenylalanine, it’s a pure hydrocarbon – C’s & H’s all around, so we can say it’s nonpolar and hydrophobic. But there are other ways to classify amino acid side chains.

Even the wacky ones are based off of a hydrocarbon scaffold (except glycine which just has an H…).  And we see hydrocarbons so much in biochemistry and o-chem that we further characterize them and give different kinds different names. They can be classified as AROMATIC (aka “aryl”) or ALIPHATIC (everything else – chains or non-aromatic rings). So far, all the amino acids we’ve talked about were aliphatic, some of them were branched, but none of them were “ring-y” (let alone special ring-y). BUT Phe’s side chain (a “benzyl” group) *is* aromatic, meaning it contains a “resonance-stabilized” ring. Aromatic vs aliphatic is not as simple as ring vs no ring. It has to be a special kind of ring where electrons are shared evenly between the atoms of each “point” of the ring (usually C, sometimes N or O), something we call ELECTRON DELOCALIZATION. 

Going back to what we discussed above, atoms bond covalently by sharing pairs of electrons. In a single bond, 2 atoms share 1 pair of e⁻ & in a double bond they share 2 pairs. Double bonds are stronger & hold atoms closer together. Carbon has 4 valence electrons (it has 6 *total* electrons in its neutral form, but the inner 2 are held tight and aren’t going anywhere). When it’s in an aromatic ring, it “spends” 1 electron each on shacking up with the carbons on either side of it, and then 1 on the hydrogen, but that still leaves it with 1 “extra” that it can donate to the “communal stock” (kinda like the electronic version of a  give a penny, take a penny, jar) and these electrons can be shared jointly among those participating in the “co-op” (which, as we’ll see requires living in a plane).

There aren’t enough e⁻ for each to have a full double bond, so you get something in between; the atoms are closer together than they’d be with single bonds, BUT not as close as double bonds. For instance, a usual C-C single bond length is 154 pm, & a C=C double bond is 135 pm. The C-C bonds in Phe’s ring are in between these, at 139pm. Here, pm doesn’t refer to time of day – instead it stands for picometer, which is 1 trillionth of a meter. So we’re talking really really short even for the “long” ones. 

How to represent this? If we’re restricted to draw single bonds (1 line) & double bonds (2 lines) we can show “in-between-ness” using RESONANCE STRUCTURES. We draw two EQUIVALENT versions w/alternating single & double bonds, each with an “average” bond length. And we can indicate resonance by drawing a double-headed arrow ↔︎ between them & [ ] around them.

It’s really important to realize that this DOES NOT MEAN e⁻ ARE SWAPPING BACK & FORTH BETWEEN THESE STRUCTURES! NEITHER of these conformations really exists, it’s simply way to show the real thing’s somewhere in between. Sometimes, in order to avoid this confusion, resonance is represented by an inner circle (sometimes dashed) instead of alternating lines, but the alternating line representation can be helpful for figuring out things like how many other groups can be attached.

Charge delocalization makes molecules really STABLE (kinda like an electronic playgroup, the “parent” atoms help each other share their energetic electrons!) & PLANAR (flat) because, as we’ll see, they have to line up to share nicely. This need to line up in a plane is the same reason why peptide bonds are planar, which is the main reason protein backbones are so restricted in their contortions. In the case of the peptide bond, you don’t have a ring but you still have resonance. In fact, you can have resonance anywhere you see alternating single & double bonds. And sometimes even when you don’t… Lone pairs of electrons (such as on N or O) can “take the place” of double bonds because these lone pairs can occupy p orbitals…

While the full details are outside the scope of this post, SOOOO much of chemistry can be understood if you remember the key facts that: 

  1. nuclei are positive (thanks, protons!)
  2. the electrons surrounding them are negative, but shiftable. 
  3. opposite charges attract
  4. like charges repel
  5. this is true even at the subatomic level

So, the nuclei of 2 atoms repel each other (electrostatic repulsion) due to their charge same sign-ness, but attract the other’s electrons thanks to their charge opposite-sign-ness. So in order to bond, the attraction has to outweigh the repulsion, and this can only happen if they’re lined up right, so bonds have characteristic distances and angles. 

“Normal” bonds (single bonds) are sigma bonds (σ bonds) – they’re formed when atoms overlap their atomic s orbitals end-to-end, so that the electrons they share are in between the 2 of them (if you were to draw a straight line from the nucleus of 1 to the nucleus of another, you’d be most likely to find their shared electrons hanging out somewhere around that path). 

But there’s only so much room there – kind like how housing situations are tight in cities so people start moving to the suburbs. Therefore, if you want to share more electrons you’ll have to do it a little further out. 2 atoms can only form 1 sigma bond with each other. But sigma bonds are the “best” strength-wise, so in a double bond, atoms will still form 1 sigma but then they’ll switch to something called a Pi bond (π bond) for the second. So, in Phe’s ring, each carbon forms a sigma bond with a hydrogen and sigma bonds with the carbons on either side of it. And then that last electron, the one that gets “donated” to the commune is shared in a π bond.

Unlike the end-to-end hookup of clouds in sigma bonds, π bonds are formed by overlaps of orbitals “side-to-side” and the overlapping atomic orbitals are “p orbitals”, which look a bit like hourglasses that are perpendicular to the plane of the ring. So if you want to overlap them you have to line them up in a plane. 

All double bonds have π bonds, but not all double bonds have delocalization – you can only get that if you have a series of interconnected π bonds so that you can have a mega-merging of orbitals that electrons can roam around in. For aromatic compounds, these mega-merged molecular orbital looks a bit like a donut, with electron density concentrated above and below the plane and electrons floating around through it. 

But it’s more of a “lazy river” than a water slide – it’s gotta be flat (though speed-wise they’re moving super fast, no laziness there!) A consequence of this flatness with it’s charge spread out “predictably” above & below is that you can get something called “π stacking” which is basically where they can stack pancake-like, with the aromatic rings syncing up (but not combining) their electron clouds with one another to provide stabilizing interactions. You see this with aromatic amino acids and with nucleotides – the “bases” of DNA & RNA  (the unique parts of the letters) are aromatic rings and they can stack with one another helping keep DNA zipped up and allowing proteins to interact with it through aromatic amino acids like Phe. As IUBMB president Alexandra Newton puts it, “Phe is cuddly” 

And it’s also “essential” – Yesterday, we looked at how William C. Rose did studies to figure out which amino acids are essential in the dietary sense, meaning that your body can’t make them from other things so you have to eat them “pre-made.” http://bit.ly/threoninetale 

Phenylalanine was one of the ones he found to be essential. But just because you can’t make it doesn’t mean you can’t make things from it!  Similarly to isoleucine, it is both GLUCOGENIC (can be used to make glucose (blood sugar) (entering the pathway as fumarate) and KETOGENIC (can be used to make fats & ketone bodies) (entering the pathway as acetoacetate)  http://bit.ly/luckyleucine 

But about half of it is actually used to make another amino acid, Tyrosine. An enzyme called PHENYLALANINE HYDROXYLASE (PAH)adds a hydroxyl (-OH) group to Phe at the 4th position in the ring (We call this “para” position (where things sticking out from ring are straight across from each other. If the things are right next to each other (adjacent) we call it ortho, and one apart gives you meta). This changes the R group to 4-hydroxylbenzyl. In other words, congrats, you’ve just made Tyr!

Assuming that enzyme is functional…A defect in PAH causes a disease called PHENYLKETONURIA (PKU). People with PKU can’t convert Phe to Try, so Phe (and its other pathway products) builds up. This causes a variety of problems. In addition to not being able to make tryptophan (which your body needs to make catecholamines like adrenaline), it  prevents other amino acids from getting into the brain, leading to neurological problems.

Once scientists figured out about PKU, they started screening for at birth as one of those heel-prick blood tests, because if you catch it early it can be controlled with a super strict diet that severely restricts Phe intake and supplements Tyr. And governments started mandating food-makers to put those warnings on food labels, “phenylketonurics: contains phenylalanine” when it’s found in places you’d might not expect it to be. Like WTF does F have to do with an artificial sugar? The sweetener aspartame is a dipeptide dipeptide of aspartic acid and phenylalanine. Breaking it down produces Phe (but since this sweetener’s way sweeter than sugar you barely need any so it’s almost “calorie-free”). So the warning gives people with PKU a heads-up. much more here: http://bit.ly/pkustoryandscience 

As you might have guessed based on the fact that Tyr is just Phe with a hydroxyl added on, Tyr is also aromatic. And there’s one other Aromatic Amino Acid (AAA) – tryptophan (Trp, W). Phe is the most hydrophobic of the 3 of them, and, while all 3 absorb UV light – tryptophan is responsible for most UV light absorption (at 280 nm). We can use this absorption to determine protein concentration: http://bit.ly/bradforduv

Phe was first described in 1879 by Schulze & Barbieri who found it in yellow lupine seedlings and it was first synthesized by Erlenmeyer and Lipp in 1882. https://doi.org/10.1021/cr60033a001 

How does it measure up? 

coded for by: UUU, UUC (thanks to the triple U, phenylalanine’s UUU codon was the first part of the genetic code to be “cracked” by Nirenberg & Matthaei (in 1961)
chemical formula: C9H11NO2
molar mass: 165.192 g·mol−1

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0

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