Fa L-Ala L-Ala L-Ala L-Ala! There’s a lot to love about ALANINE! It’s the smallest CHIRAL amino acid ever seen (mostly in the L-form!). Alanine is kinda the “generic” amino acid.  It’s not the smallest (glycine beats it) but its methyl (CH₃) comes in 2nd. It isn’t very reactive, and is isn’t “essential” in the sense that we need to get it directly from our food but it IS very important. Just ask your muscles – which rely on the glucose-alanine cycle to remove nitrogen “waste” and get fresh sugar. 

video added 12/2/21

It’s Day 2 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 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 today’s the spotlight’s on Alanine (abbreviated Ala, A), which is “coded for” by the RNA codon “words” starting with GC – so GCU, GCC, GCA, & GCG. 

note: when we say “coded for” it basically just means spelled out the protein’s genetic instructions. The “original copy” of a protein’s instructions are written in DNA in the form of genes (stretches of chromosomes). messenger RNA (mRNA) copies of these protein “recipes” are made and handed off to protein-making complexes called ribosomes who read its code and stitch together the corresponding amino acids (which are brought by transfer RNAs (tRNAs) that have a complementary 3-letter “anticodon”).  

Alanine is one of 2 protein amino acids that was made from scratch (via synthesis) before it was actually shown to be a protein letter. It was first made in cells a really really really long time ago. But it was first made & purified in the lab 1850 by Adolph Strecker. He named it alanin (German), using the first syllable of the word aldehyde to denote its origin – he made it from aldehyde-ammonia, finding it by chance when he was trying to find a way to make lactic acid https://doi.org/10.1021/cr60033a001 ⠀ 

As for bragging rights for isolating it from protein (and proving it), that’s a bit complicated…. In 1875 Schützenberger and Bourgeois isolated it from base hydrolysis of silk – or so they say… They didn’t do any rigorous analyzing of it but they said it seemed to be that Alanine thing Strecker had made. A few years later Schützenberger did some more thorough analysis – that original silk mix they’d found had a mix of stuff & Schützenberger further separated the stuff by fractional crystallization (different chemicals will crystallize under different conditions so if you change the conditions over and over in the right ways you can get a mixture to separate itself). Once he’d done that, he measured how much carbon, nitrogen & hydrogen the fractions had. One was consistent with alanine, but he didn’t do any other tests on it so he didn’t have proof that those atoms were hooked up the alanine way. Then in 1888, Theodor Weyl purified it from hydrolysis of silk (silk happens to be really rich in alanine). And he characterized it further and claims credit.

I’m not one to care about credit – science is a team effort and every contribution helps. What I care about is what is find out. So that’s what I want to now tell you about.

Alanine (Ala, A) has a methyl group (-CH₃) for its R. Atoms bond together by sharing electrons (negatively-charged subatomic particles that whizz around the atoms’ dense central nuclei where the positively-charged protons & neutral neutrons hang out). If they share fair, and there’s an equal number of protons & neutrons, the charges cancel out and the molecule is evenly charged everywhere. But if they don’t share fairly, the more electronegative (electron-hogging) atoms will pull electron density away from the less electronegative atoms, shifting the electron cloud and disrupting the even charge balance leading to a charge imbalance we call POLARITY.

But C & H share pretty fairly and, as a result, CH₃ is considered “non polar.” Alanine may be non polar, but water definitely isn’t. It’s super polar (with O being the hog) and this is part of what makes it so great at dissolving things – opposite charges attract, so the partly negative O’s can hang out with partly or fully positive parts of other molecules, and the partly positive H’s can chill with partly or fully negative parts of other molecules. But methyl doesn’t offer these partial charge opportunities. So water wants to exclude it. This exclusion makes non polar things like methyl seem water-avoiding, so we call them HYDROPHOBIC. 

Water excluding such things leads those things to gather in the center of the protein, away from water, and this “hydrophobic effect” is the main driver for protein folding. 

Yesterday we looked at glycine, which is the simplest amino acid – its side chain is just an H. Now with alanine we’re dealing with a methyl group, CH₃. The addition of just 1 carbon and a couple hydrogens may seem small BUT has BIG effects. One of the main effects is that it makes Ala CHIRAL. By chiral I mean that Alanine (and all of the amino acids except for gylcine) has nonsuperimposable mirror images – like how the mirror image of your left hand looks like your right hand but they can’t fit into the same glove. 

This newfound chirality comes about because the central carbon carbon (Cα) is now bound to 4 DIFFERENT groups (the amino group, the carboxyl group, a hydrogen, and this methyl). And those groups can attach in 2 different ways (STEREOISOMERS). Stereoisomers are molecules that have the same “ingredients” & same atomic connectivity (the same atoms are bonded to the same atoms ( i.e. X-Y-Z & X-Y-Z NOT X-Y-Z & X-Z-Y) BUT their bonds are arranged differently in space

Why does alanine have ‘em but glycine doesn’t? Not all molecules have STEREOISOMERS, only those w/CHIRAL CENTERS (aka STEREOGENIC CENTERS), which are often carbons (Cs) connected to 4 different things. Every carbon (C) has 4 electrons (e⁻) to “spend” in bond formation –  it can form up to 4 single bonds & when it bonds to different things it can do so in different ways…

Imagine (or actually do it) taking 4 DIFFERENT rings, arranging 4 fingers in a “circle” like you’re grabbing something, & choosing which ring to put on which finger. If you imagine your fingers are all the same (they’re just “placeholders” & it’s relative positions of rings that matter), you have 2 different options. Each CHIRAL CENTER is like a hand w/4 different rings

A molecule can have an infinite # of “hands” & each hand gives you 2 stereoisomers, so you end up with 2^n possible stereoisomers, where n is # of chiral centers,

A special type of stereoisomer are ENANTIOMERS. These are “mirror-image” stereoisomers – like your left & right hand. They look like you could just flip 1 over & overlay them, BUT when you do so you have 1 hand palm-side-up & 1 hand palm-side-down, so they’re NOT superimposable. You get pairs of ENANTIOMERS when ALL the chiral centers are “swapped.” if they’re NOT all swapped, they’re DIASTEREOMERS.

DIASTEREOMERS have DIFFERENT physical & chemical properties but ENANTIOMERS have the same physical & chemical properties (except for the direction they rotate light, which we can indicate with +/- signs) BUT enantiomers can have different “biochemical” properties because our bodies respond differently to them since they fit (or don’t fit) differently into the molecules in our cells which they interact with (like only having left-handed gloves).

When we make a compound  in a test tube, we get a mix of stereoisomers, BUT when organisms make things naturally, they usually make a single stereoisomer because, just like our receptors are “handed”, so are the proteins (enzymes) that help the cells make the compounds. So we can get by with having receptors that only recognize that single stereoisomer

A Latin term for left is levaoratotory – and dextrorotatory means right – and this leads to the L/D nomenclature (naming system) – it originally referred to direction of light rotating but now refers to being configured like something that rotated light a certain way… When it comes to amino acids, the L/D notation is based off of comparing it’s configuration L-glyceraldehyde (the simplest sugar). And for glyceraldehyde the L indicated levarotatory as in it rotates light left. But even though they’re all “hooked up” like glyceraldehyde, not all L amino acids are levorotatory.

For example, L-alanine is dextrorotatory whereas L-serine is levorotatory – to avoid confusion we can write L(+)-alanine and L(-)-serine. This makes clear that the L is meant to indicate configuration, whereas the +/- indicates optical activity

All the amino acids  in proteins are in the L form. But the D form does have some uses. In fact, bacteria build cell walls out of peptidoglycan, which ends in D-Ala-D-Ala. The antibiotic ampicillin mimics this D-Ala-D-Ala, tricking the wall builder (transpeptidase) into trying to add it instead and getting stuck, leading to the cells being unable to build strong walls, so they burst & die. 

Yesterday we looked at how glycine has very flexible backbone because its R’s so small, BUT CH₃, while still small, is bigger than H. So its backbone rotation’s limited by STERIC HINDRANCE (you can’t have neighboring atoms clash). This makes Ala more like other amino acids than glycine. 

This structural “genericness” makes Ala a structural biologist’s friend. (note: “structural biology” is a field that investigates the link between the “shape” (form) and function of biochemical molecules. Think fork vs. spoon vs. knife but for proteins). It’s so “friend”-ly because you can stick in A as “placeholder” when you can’t see a protein region clearly in x-ray crystallography “pictures”. And its reactivity genericness makes it a protein biochemist’s friend because we can use it to test the importance of specific residues for a protein’s function – mutate that residue to Ala & look for an effect. Sometimes you know what specific residues you want to test, but other times you don’t know what will be important, so scientists sometimes do “alanine mutagenesis scans” where they basically try ‘em all out. 

Ala may be “boring,” but it wins “Most likely to form α-helix!.” The α- helix is a common “secondary (2°) structure” (a motif within a protein’s overall “3° structure” that comes from backbone-backbone interactions)

In addition to usefulness in the lab, alanine is super useful in our bodies through the GLUCOSE-ALANINE CYCLE: Alanine plays an important role in transferring extra nitrogen from peripheral tissues like muscles to your body’s main “detox” center, the liver. The nitrogen “piggy-backs” on the sugar breakdown product pyruvate which, once in the liver and freed of the nitrogen (which gets excreted as urea) it can be recycled into more sugar to be sent back to the muscles. 

When your muscles are breaking down sugars and proteins for energy, they’re doing it for the energy, waste be damned! They keep breaking stuff down, but waste products start piling up & slowing things down. Thankfully, your body has waste removal processes including the GLUCOSE-ALANINE cycle which takes “waste” from muscle cells, converts it to the amino acid alanine, then ships it out to the liver which can “recycle” it to make new sugar to ship back to the muscles. This also provides a way to get rid of the extra nitrogen that comes when your muscles break down proteins for energy – alanine acts as a nitrogen carrier that passes extra nitrogen off to the urea cycle in the liver, which releases it as urea. 

Pyruvate is formed as the end process of glycolysis –  the process of breaking down the sugar glucose (which itself is often a breakdown product of bigger carbs like starch). If there’s time and enough oxygen, pyruvate can be broken down further via oxidative phosphorylation to give you more energy. But when your muscles are being worked really hard, there isn’t time/enough oxygen, so pyruvate can start piling up & slowing things down – it’s kinda like the sanitation workers have gone on vacation so your recycling bins aren’t being emptied.

It’s not that pyruvate’s bad – it’s just not being used. So you want to ship it to facilities that can use it. Pyruvate is basically alanine with a carbonyl (C=O) instead of an amino group. So if you swap that carbonyl for an amino group you’ll get alanine. And this is what happens. Amino groups from all sorts of amino acids can be transferred to α-ketoglutarate which is a product of the citric acid cycle (aka Krebs cycle). In this way, sugar & protein breakdown can “team up” in just one example of the extensive crosstalk between the various metabolic processes going on all the time in your cells. 

It’s important to be able to interconvert molecules so that you don’t have to have tons and tons of versions of enzymes that basically do the same thing but for different molecules. Instead of needing enzymes to take all the amino acids to the liver and work with them, if you can specialize with just working with one of them, your cells’ life is a lot easier. So some of the amino acids can pass off their amine groups to these sugar parts to give you the amino acid glutamate. Then, through transamination, the amino group from the amino acid glutamate is transferred to pyruvate to form alanine. This transfer of an amino group is called transamination so, fittingly, the enzyme that helps it happen is called alanine transaminase (ALT). 

glutamate + pyruvate + ALT -> alanine + α-ketoglutarate

the α-ketoglutarate can then stay in the muscle and shuttle another amine group to make another Ala, while the alanine you just made can be exported out and shipped to the liver. Once in the liver, ALT can deaminate it – remove the amino group to give you pyruvate again. And the amino group can be released from the glutamate as ammonia and then the less toxic and more excretable urea

how does it measure up?
chemical formula: C3H7NO2
molar mass: 89.094 g·mol−1
systematic name: 2-aminopropanoic acid

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

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