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Glycine biochemistry

I’m kicking off the 2021 bumbling biochemist’s version of an advent calendar - #20DaysOfAminoAcids - with the “opening up” of GLYCINE! full text & figures: http://bit.ly/glycineproteinhistory The peptide bond in all proteins has restricted movement because the C, N, & O share electrons between the 3 of them (usually you just have electron-sharing between 2 atoms). This communal sharing is called electron delocalization or “resonance stabilization.” As the “stabilization” part suggests, this electronic orgy of sorts makes the atoms happy. So they “want” to share like this, but they can only do so if the 3 of them are all on the same plane. So movement along the peptide bond is restricted to twisting between planes in a chain. You can learn a lot more about them here: http://bit.ly/peacepeptide But even that twisting is restricted, depending on the nature of the side chain because of “steric hindrance” - that’s basically a fancy way of saying 2 things can’t be in the same place at once (even if they’re super super small). Bulky things need more space, leaving them with fewer available ways to move without hitting something - like the atoms of the peptide backbone. So bulkier side chain - more steric hindrance The thing about glycine is that its side chain is just an H - which is pretty damn small - movement-wise it’s like there’s barely anything there at all! As a result glycine has very low steric hindrance, so glycine residues are very flexible (remember residue’s just what we call an amino when it’s in a peptide chain so has lost that water-equivalent (I don’t mean to harp on about this I was just confused about it for a really long time but embarrassed to ask!)) So glycine’s smallness lets its backbone take on awkward angles that would be major no-nos for other amino acids. To see what I mean, take a look at a Ramachandran plot, which shows the angles taken by atoms in a molecule - usually colored heat-map style to show you the most common and least common angles. When we’re solving a crystal structure we often check that the angles are geometrically solid & one of the things you’ll see in the “report card” for a structure is “Ramachandran outliers.” And usually it’ll be reported as “non-glycine” Ramachandran outliers - basically glycine can “break the normal rules” so it’s ok to find it at weird angles. Here’s the link for the paper in the figure: https://doi.org/10.1002/prot.10286  Glycine’s “loosey-goosey-ness” makes it good for flexible regions of proteins BUT bad for places you need strong structure. So it’s often found in sharp turns leading into or out of more orderly structures like helices & sheets. It’s typically only found in small amounts in protein, though it is the most abundant in the weird triple-helices of the protein collagen that helps make our skin stretchy but sturdy. But it’s found a lot of other places too. In its free form it acts as a neurotransmitter - a chemical messenger relaying news throughout the brain. And it is a member of the antioxidant tripeptide glutathione, which helps control oxidation status in our bodies. More on that here: http://bit.ly/dttreducingagents It’s also useful outside the body. Our lab has a lot of it because it can be used as a buffer (pH-stabilizer). glycine’s useful for keeping pH steady around 6ish. Which makes it good for using as a buffer in Trie-Glycine SDS-PAGE gels (used to separate proteins by size) & it’s used in many cosmetics & toiletries. But where does it come from when our cells use it? Glycine is characterized as a “nonessential” amino acid - this doesn’t mean we don’t need it - we certainly do! - it just means that we don’t need to get it “pre-made” in our food because our bodies have other ways of making it. It can be biosynthesized from another amino acid we’ll get to later this month, serine (which itself can be made from 3-phosphoglycerate which is formed when sugar is broken down). more on that here: http://bit.ly/metabolismglycolysis  Where does it go? The main pathway for glycine breakdown (catabolism) is the “glycine cleavage system” (GCC). Glycine decarboxylase cuts off ammonia (NH₄⁺) & carbon dioxide (CO₂) and transfers the leftover CH₂ to THF (that same cofactor we saw earlier when we were making glycine from serine (anabolism) Instead of just breaking it down, you can build from it - glycine serves as a precursor to other molecules including DNA (it provides the central C2N subunit of the purines (adenine & guanine)) & porphyrins (things like heme - the iron & oxygen holding helper that lets the red blood cell protein hemoglobin transport oxygen throughout your body). But its main function is “proteinogenic” meaning it gets used for protein-making. Coincidentally, glycine is spelled by all the codons starting with the RNA letterS GG (guanine) - so GGU, GGC, GGA, & GGG How does it measure up? chemical formula: C₂H₅NO₂ molar mass: 75.067 g/mol systematic IUPAC name: 2-aminoethanoic acid