No losers here – just LEUCINE! Lighten up! But stay lucid!  today I’m elucidating the amino acid Leucine (Leu, L) and the difference between glucogenic & ketogenic – what does it mean?

blog form (refreshed from last December):

It’s Day 4 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 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, as we’ll go into more below, 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, let’s!

In a lot of ways, the amino acid Leucine (Leu, L) is a lot like yesterday’s valine (Val, V) starting with the composition of their side chains (R groups). As you might remember, Val’s side chain is a a V-shaped thing made up of hydrocarbon groups (the V is highly convenient for remembering!) Leucine is more of a Y than a V. It’s basically valine with a “linker” CH₂ between the central C (Cα) & the branched end, making it an “isobutyl” group (butyl meaning 4 because it has 4C) instead of an “isopropyl” group (propyl meaning 3) like valine has.

Y does that matter?

Proteins are made up of long “polypeptide chains” of amino acids linked backbone-wise through peptide bonds. These chains fold up into functional proteins whose structure complements the tasks they carry out. They have several layers of structure that come from

  1. the the order of amino acids linked up in the chain (primary structure
  2. how the backbones of those amino acids interact through hydrogen bonds to give common motifs like α-helices and β-strands (secondary structure). 
  3. How the side chains interact to give you structure on top of that structure (tertiary structure) and then 
  4. how different chains sometimes interact to give you quaternary structure (not all proteins have multiple chains and only those that do have quaternary structure

You can get structure and not just “protein spaghetti” because the movement of peptide backbones is restricted by the nature of the peptide bond. Atoms (like individual carbons (C’s), hydrogens (H’s), oxygens (O’s), and nitrogens (N’s) are really small, but they’re made up of even smaller things – subatomic particles. These include protons, which are positively-charged, neutrons, which are non-charged, and electrons, which are negatively-charged. Atoms join together to form molecules by sharing pairs of electrons to form strong covalent bonds – 1 pair for a single bond, 2 for a double (which is stronger), and 3 for a triple. 

Peptide bonds are a type of “amide bond” – they involve a carbonyl (-(C=O)-) attached to a nitrogen. And they’re special because the nitrogen, oxygen, and Cα (the carbon hookup up to the side chain) have to be aligned in the same plane in order for them to share electrons through resonance (electron delocalization), a phenomenon whereby atoms “donate” their extra electrons to a sort of shared pool. They “want” to participate in that because it helps stabilize them (you can think of it kinda like a play group where parents can help watch each other’s kids so there’s less burden on any one). So it’s “worth it” to stay stuck in a plane. 

Therefore, when amino acids link up through peptide bonds, you end up with a sort of “chain of planes” where you can only have rotation at certain spots. And that rotation is further restricted by the nature of the side chain because of “steric hindrance,” which is basically a fancy way of saying, “dude – that’s my personal space!” Atoms (even though they’re super tiny) do take up space and space can only be taken up by one thing at a time – so the peptide can only twist a certain way if there’s room for its side chain to get situated without hitting anything. And bigger, bulkier things require more space. 

So we saw glycine (with just an H as a side chain) was super flexible, alanine (CH₃) a little less so, but not too bad, then valine was “stiffer.” What about leucine? It has that “extra” methylene compare to valine. You might think that this added bulk makes leucine less flexible, but actually it’s the opposite. The real bulky part is the “v” and the “extra” methylene group serves to distance that bulkiness from the backbone, which allows the backbone to be more flexible. So Leu can form helices more easily than V can.

Like valine, leucine is ESSENTIAL, meaning our body can’t make it so we need to get it “pre-made” through food) as opposed to “non-essential” amino acids like glycine & alanine that we definitely need, but we can make ourselves.

Also like valine, Leucine is NONPOLAR, meaning its charge (coming from the negatively-charged electrons and positively-charged protons its atoms contain) is evenly distributed. This makes it HYDROPHOBIC – the water that surrounds it down’t want to hang out with it because the water is highly polar (it has partly positive and partly negative parts so it wants to hang out with oppositely-charged things and leucine doesn’t fit the bill. As a result, the water molecules around proteins form networks that exclude leucine and other nonpolar amino acids, leading them to seek refuge in the core of proteins, hidden from the water. This “hydrophobic effect” is the driving force for protein binding.

Another thing these letters have in common -leucine and valine (and isoleucine which we’ll look at in another post) are aliphatic, branched-chain amino acids. Aliphatic is a term we use to describe hydrocarbons (carbon-backbone-based things) with the Cs linked in chains as opposed to rings (ring-y ones are called aromatic). But chains can be linear (all C’s in a row) or branching. Branching can occur at different points along a chain. In the case of leucine, the branch point is at the end. 

Breakdown of all 3 of these BCAAs follows the same pathway and uses the same enzymes in the first few steps. But depending on which you start with, you’ll get different products out that can join up with different pathways at different steps. note: enzymes are reaction speeder-uppers, usually proteins, that help make reactions happen by holding reactants together and in the optimal position, etc.

Metabolism refers to the making (anabolism) and breaking-down (catabolism) of biochemicals in your body. These reactions are multi-step and etabolic pathways are interconnected like a giant subway system. But just like you can’t transfer to the line you want at some stations, not all metabolic pathways connect up (at least not efficiently) – and this is the case with glucogenic vs ketogenic amino acids.

Glucogenic amino acids can be converted into glucose (blood sugar) through gluconeogenesis (new sugar making), whereas ketogenic amino acids are converted into ketone bodies. “Ketone bodies” include acetoacetate, beta-hydroxybutyrate, & acetone. They’re better known as products of fat breakdown (and in the reverse process they can be used to make fats). But they can also come about from the breakdown of amino acids – but not all of them! 

Some amino acids are one or the other, some are both – it all depends on the original structure of the amino acids (our starting material) and what enzymes our bodies have for processing them. 

ketogenic only: leucine, lysine

glucogenic only: alanine, cysteine, glycine, threonine, serine, asparagine, aspartate, methionine, valine, glutamate, glutamine, proline, histidine, arginine

both: tryptophan, isoleucine, phenylalanine, tyrosine

Leucine is one of 2 amino acids (the other being lysine) that is strictly ketogenic (it can only make ketone bodies, not glucose). To understand why, let’s look at how leucine gets broken down. 

The 1st step to breaking down an amino acid is removing the nitrogen – if you look at the structure of sugars and fats, you won’t see nitrogen there. So if you want to make those things from it (get on board on of those subway trains) you’ll have to ditch the N. And, for the BCAAs, this is accomplished by Branched-Chain AminoTransferase (BCAT). You don’t just want to chop off the amine group to make ammonia (NH₄⁺) because that’s toxic to your cells. Instead, if you want to get rid of that nitrogen you’ll have to pass it off carefully from molecule to molecule until you can ditch it in your pee as urea.

The first pass-off comes from BCAT transferring the amine from a BCAA like leucine to α-ketoglutarate. α-ketoglutarate is one of the products of the citric acid cycle (TCA) which is part of the sugar-breaking-down process (which will come into play later). It’s basically the amino acid glutamate but with a carbonyl (C=O) instead of an amino group. So if you swap those out you get glutamate. The BCAA provides the amine for the swap and BCAT helps with the transfer. The glutamate can then go off and get rid of the nitrogen through the urea cycle (or it can be used as glutamate). 

And the leftovers, the deaminated BCAA, having lost its amino is now no longer an amino acid – instead it’s a branched-chain α-keto acid (BCKA). In the case of leucine, you get α-ketoisocaproate (α-KIC) The “keto” refers to “ketone” which is a carbonyl (C=O) hooked up to carbons on either side (so -C-(C=O)-C-). It gets to keep the “acid” part of its name because you haven’t touched the carboxylic acid group. 

These α-keto acids can then go through further processing with the help of the Branched-Chain α-keto acid dehydrogenase (BCKDH) complex. α-KIC gets converted into isovaleryl-CoA. And after some more processing steps you get acetyl-CoA. 

This is hardly the only way to Acetyl-CoA. Acetyl-CoA can come from carbs, fats, or proteins. Regardless of the source, it can enter the citric acid cycle (aka tricarbocylic acid (TCA) or Krebs cycle) which, thanks to acteyl-CoA’s many sources, acts as a kind of central hub of the metabolism subway system.

The TCA oxidizes Acetyl-CoA into ATP  & CO₂. Oxidation refers to the loss of electrons (with the gaining partners said to be reduced). Acetyl-CoA loses electrons that get captured by the electron carriers NADH & FADH₂, which enter oxidative phosphorylation to cash in those electrons for the big ATP payoff. More on that here: 

For each “turn of the TCA cycle” you get one ATP (or GTP), 3 NADH, 1 FADH₂, & 2 CO₂. And you wind up with a molecule of oxaloacetate (OAA). OAA can join up with another acetyl-CoA to do it all again, or it can get shuttled off to make glucose (blood sugar) via gluconeogenesis. So you might think – oh cool, you get acetyl-CoA from leucine, so you you can use leucine to make acetyl-CoA to make oxaloacetate (OAA) and shuttle that OAA off to make glucose through gluconeogenesis. 

BUT the thing is – in order to enter the TCA, acetyl-CoA has to hook up with oxaloacetate. So the oxaloacetate you make basically just pays you back for the one you spent to get Acetyl-CoA in the cycle to begin with. So leucine is NOT considered glucogenic. In order to be considered “glucogenic” an amino acid has to be able to be broken down into something that is “already in” the TCA without having to spend something from the TCA to get in. 

So why enter at all? ENERGY! In addition to that initial ATP payout those electrons can get cashed in for major energy money. After oxidative phosphorylation you can get up to 22 ATP per acetyl-CoA

But entering the TCA isn’t the only fate for acetyl-CoA. It can instead be shuttled off to make fatty acids. Or it can go the ketone body way….

Acetoacetate is basically 2 acetyl-CoA molecules ditching their Co-As & shacking up. Beta-hydroxybutyrate is a reduced form of that where one of the ketone’s is converted to a hydroxyl )-OH) group. And acetone is a spontaneous product from the breakdown of those – it’s the decarboxylated form of acetoacetate & unlike those other two, it can’t easily be converted back into acetyl-CoA. The liver can do that – but indirectly – it first turns it into lactic acid, then that gets oxidized into pyretic acid and then you can turn that pyruvic acid into acetyl-CoA. 

Ketone bodies are a normal way to get energy from lipids (not water-soluble) through your blood. Ketone bodies are soluble so they can travel from the liver where they’re made throughout your body. The problem is just when you can’t keep up. during times of starvation or heavy prolonged exercise, the liver starts running out of OAA because you’re not feeding the pathway from sugar. And without OAA you can’t get acetyl-CoA into the pathway, so it instead takes the alternate ketone route. The ketones released can be taken in by cells throughout your body (even in your brain) and there’s enough OAA there (at least initially) to use it. 

When ketone bodies are produced faster than they can be consumed you get ketosis – which is ketone overload – in your blood (ketonemia) & pee (ketonuria). And having all those carboxylic acid groups messes up the pH of these fluids. Diabetics are at risk for diabetic ketoacidosis when their insulin levels are too low – basically their cells aren’t taking in and using sugar, and insulin’s “opposite” hormone-wise, glucagon, goes unchecked, “yelling” at cells to burn fat. So they do –  they turn to breaking down fat and protein leading to high levels of ketones being made. 

Other cool things: leucine can stimulate muscle production by activating a regulator of protein synthesis called mTOR. It was first isolated (in an unsure state) by Proust (I’m guessing not the Marcel one…) who was trying to study why different types of cheese taste different. Then in 1820 Henri Braconnot (the same Braconnot of glycine fame) isolated it from acid hydrolysis of muscle fiber and wool. And he called it leucine because it was a white crystalline substance (“leuk” means white)  ⠀

how does it measure up?

coded for by: UUA, UUG, CUU, CUC, CUA, and CUG.
empirical formula: C₆H₁₃NO₂ 
molecular weight: 131.175 g·mol−1

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉

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