Before he could be “SAM I am” he was METHIONINE. Have you Met yet? You can find him in green eggs & ham…The protein letter (amino acid) methionine (Met, M) is really cool. It can serve as a methyl (-CH₃) donor that can build new molecules and modify existing ones. Additionally, it is your ticket to the peptide wedding we call translation, which links individual amino acids together into chains called polypeptides that fold up into beautiful functional proteins!
refreshed & video added 12/13/21
It’s Day 13 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 Methionine (Met, M)
Methionine is classified as a “nonpolar” amino acid. We’ve seen a lot of these, but Met’s a bit different. Let me step back a step & explain – Atoms link up through strong covalent bonds by sharing electrons (which are tiny, negatively-charged, subatomic particles that whizz around an atomic nucleus containing positively-charged protons and neutral neutrons). When there’s an imbalance between protons & electrons, you get charged regions – this can happen when there’s an uneven # (in which case you get a “formally charged” molecule called an ion) or if the electrons are just unevenly distributed – which can happen if one of the sharing partners hogs the electrons – we call such electron hogs electronegative and by skewing the charge distribution they make the molecule POLAR.
Oxygen’s very electronegative, so it pulls electrons away from the Hs in H₂O, making water highly polar, with the O partly negative and the H’s partly positive. Opposite charges attract so water can form networks of Os hanging with Hs. If they let other molecules into their network we say those things have been “dissolved” – and it can only happen if water’s happy to hang out with them, so those things need to have charge (full like you get with ions or partial like you get with polar bonds). If they do, we call them hydrophilic (water-loving). If they don’t, water excludes them and we call them hydrophobic.
We’ve seen a lot of nonpolar amino acids – alanine, valine, leucine, isoleucine, phenylalanine – all of those had side chains that were pure hydrocarbons (only contain hydrogen (H) & carbon (C)). Those are nonpolar because carbon and hydrogen share their shared electrons pretty fairly, so you don’t have that charge imbalance.
Unlike those guys, Met is NOT a pure hydrocarbon. Instead its side chain is “interrupted” by a sulfur (S) atom (I know – how rude, right?!) But it’s still nonpolar because C & S have similar electronegativities (they want e⁻ about the same amount). This nonpolar-ness makes it HYDROPHOBIC, so water excludes it and it tends to seek refuge with other nonpolar parts of proteins in their core, providing structural support.
In chem speak, Met’s side chain is an “S-methyl thioether.” “thio” refers to sulfur (hence meTHIOnine) & “ether” tells you that the S is attached to C on each side (C-S-C). An “ether” (without the “thio”) is an oxygen single-bonded to C on each side (C-O-C), and a thioether is just the sulfur-swapped version (similarly to how a thiol (-SH) is the sulfur version of an alcohol (-OH)).
We saw a thiol when we looked at the amino aid cysteine (Cys, C) which has a side chain of -CH₂-SH (and is the only other amino acid to have sulfur). In that case, the sulfur was at the end and able to do some different things… It could give and take H⁺ (act as an acid/base) and thus serve important roles in protein enzymes (reaction speeder-uppers that mediate chemical reactions by doing things like holding molecules together in the right orientation and optimal environment). It could also give and take electrons, switching between reduced forms and oxidized forms where cys side chains can form -S-S- crosslinks called disulfide bonds that help clamp things together for extra sturdiness and serve as antioxidants to protect cells from protein & DNA damaging reactive oxygen species (ROS).
Unlike that S in cysteine, the S in methionine is NOT very reactive. BUT it *is* reactive enough to play a key role in metabolism (buildup & breakdown of biological molecules). Turns out it’s easier to move a methyl (-CH₃) group from sulfur to something else than from carbon to something else, so methionine can serve as a methyl group donor. It’s easier, but not easy! So methionine needs some energetic help, which it gets from ATP (adenosine triphosphate).
ATP is the RNA letter A and it’s a molecule made up of the sugar adenosine attached to 3 phosphate groups. Phosphate is a phosphorus atom surrounded by 4 oxygen atoms. Depending on what those oxygens are attached to, phosphate can have a charge of -1, -2, or -3. But it always has that negative charge. And opposite charges repel. So if you stick phosphates next to each other, it’s like trying to clamp a spring – it takes a lot of energy to hold them together, so we call phosphate-phosphate bonds “high energy” – if you break them, it’s like releasing the clamp on the spring – energy is released and it can be “captured” and used – similar to how you might use a spring to move the ballpoint of your pen back into the casing, or launch a PEZ out of a PEZ dispenser.
Cells usually use the energy for things like breaking molecules up and stitching together pieces to make new molecules – we call this making and breaking “metabolism” – anabolism refers to the building up and catabolism is a term used for the breaking down. Some steps of breakdown require energy-spending, but ultimately you get energy out of them and this energy is stored in the form of ATP, which can be “cashed in” like arcade tokens.
When Met decides to cash one in, its S goes on the attack. This sulfur is able to do this because, in addition to the pairs of electrons it shares with the carbons on either side of it, it has 2 “lone pairs” of electrons (pairs of electrons it isn’t sharing). It would like some help taking care of these energetic electrons, so it seeks out something with some positivity. And it looks around and sees ATP, where, although the phosphates are negative overall, the carbon next to them is partly positive and electrophilic because its shared electrons are being pulled away by the phosphates. So that carbon is “electrophilic” (want electrons) and Met’s S is nucleophilic (wants to share electrons). Win-win! Or not…
One of S’s free pairs of e⁻ attacks ATP at the carbon one closest to the adenosine. This pushes off the phosphate groups to form S-adenosyl methionine (SAM, aka AdoMet). But it’s not quite a win-win… S now says “I do not like this, SAM I am…” The S is now sharing more e⁻ than it wants to, making it positively-charged, which an electronegative atom like sulfur really doesn’t like. So it pulls electron density away from the methyl carbon, making that carbon a good electrophile. It can get out of this awkward situation by “kicking off” that methyl group. But the methyl on its own would be an awful leaving group so it won’t just “pop off” – instead, it needs to get snatched off by a nucleophile. A nucleophile can attack it and steal it in an SN2 reaction. Basically you have a concerted breaking of the methyl-sulfur bond and making of the new methyl-nucleophile bond. The sulfur keep the electrons from the bond so it’s no longer positively-charged, so it’s much happier. Big picture – you’ve transferred a methyl (-CH₃) group to another molecule . This may seem like no big deal – but it is a big deal – a huge one! C & H’s “blah-ness” make them great scaffolds, but they’re hard to join up/break up because they share so fairly. Therefore, being able to add a methyl group is a big deal. There are also SAM-dependent methyltransferases that use a different mechanism, a radical mechanism, which can extend hydrocarbon chains. Which is is a major accomplishment! We see SAM a lot in anabolic (molecule-building) reactions.
SAM-making is accomplished with the help of Methionine AdenosylTransferase (MAT) (aka S-adenosylmethionine synthetase). The reaction goes:
methionine + ATP -> SAM + PPi + Pi (and then that PPi gets further broken to get a bigger energetic boost and leaving you with 3 Pi)
And then SAM can go transfer that methyl group to something else.
note: the little “i” in Pi and PPi refers to “inorganic” and it indicates that these phosphate groups are “free-floating” and not attached to any hydrocarbon-y (aka organic) thing
One place we saw SAM was in the conversion of the brain-signaling molecule norepinephrine to epinephrine, but it shows up all over the place. more here: http://bit.ly/tyrosinehormones
Met is ESSENTIAL in the dietary sense – you need to get it from food because you can’t make it. But thanks to Met, its sulfur sister Cysteine is non-essential – methionine can be used to make cysteine. When SAM gives up the methyl it becomes SAH-d 🙁 Without its methyl it’s S-adenosylhomocysteine (SAH). Chop off the adenosine with the help of adenosylhomocysteinase (aka S-adenosylhomocysteine hydrolase) and you get homoscysteine, which has -CH₂-CH₂-SH as a side chain. Then, with the help of a couple more enzymes, you swap that serine’s O for that S to give you cysteine and a-ketobutyrate. Alternatively, you can use methionine transferase to make a new methionine from it. Wait, what? Didn’t I say it was essential?! It is – you can “recycle” it but you can’t make it from scratch. You can also break it down into things that can enter the glucose (blood sugar)-making pathway (glucogenesis), so we say it’s GLUCOGENIC.
Met can also be used to “modify” existing molecules – like how we saw yesterday that lysines (another protein letter) in the tails of the histone proteins DNA wraps up around can be methylated to serve as an “epigenetic” flag that can alter gene expression, by modifying what genes are accessible.
There’s something else special about Methionine – something that might have made it a logical place to start this whole #20DaysOfAminoAcids… It’s each protein-to-be’s ticket to the peptide wedding chapel!
TRANSLATION is the process of making proteins by linking amino acids together through peptide bond formation in the order specified by the protein’s messenger RNA (mRNA) (a temporary RNA copy of the permanent DNA gene). It’s kinda like a peptide wedding with some major polygamy going on. Each “marriage” involves a 1-to-1 bond, but in most cases, one of the partners is “free” while the other’s already married to a whole chain of other amino acids. The marriage process is PEPTIDE BOND FORMATION – Amino acids have an “N side” – an amino group – and a “C side” – a carboxyl group. Proteins are synthesized N to C -> peptide bond forms between the carboxyl end of the growing chain and the free amino group of the incoming amino acid. And it all takes place in a biological “chapel” – a big RNA/protein complex called the RIBOSOME, which is made up of lots of protein and ribosomal RNA (rRNA) molecules that hold the players together & help facilitate the peptide bonding (it acts as both the chapel and the priest).
The ribosome travels along the mRNA (or the mRNA travels through it) and joins together amino acids based on the sequence of RNA letters it encounters. It reads in non-overlapping words of 3 RNA letters called codons, and it knows what to add because transfer RNAs (tRNAs) with a complementary 3-letter anticodon on one part and the corresponding amino acid hooked onto another part come pass it off to the growing chain while the ribosome holds it in place and facilitates the transfer.
Each protein has at least 1 codon that spells it (there’s some redundancy) but a single codon will only spell one thing (there’s no degeneracy). For example, yesterday we saw how AAA & AAG both spell lysine. But AAA and AAG will always only ever spell lysine. more on this here: http://bit.ly/nirenbergcodecracking
These codon words are non-overlapping, so where you start determines your “reading frame” and can have big consequences. more here: http://bit.ly/learngeneticcode
THI SIS NOT THE SAM EAS THA T
T HIS ISN OTT HES AME AST HAT
TH ISI SNO TTH ESA MEA STH AT
So how does it know where to start?!! A START CODON serves as an assemble-and-go point. And this start codon is the same as the Met codon. Met only has a single codon – AUG – and that codon will only ever spell methionine, but it can also “moonlight” as a START CODON. – So Met can serve as an INITIATOR tRNA. Note: when bacteria use it in this initiator role, they first add a formyl group (-(C=O)-H) to it to make formylmethionine (fMet).
Once the ribosome gets going, if it encounters another AUG, it treats it like any other codon – adding a methionine and going on its way. So you can find Met throughout protein sequences – but you’ll *always* find it as the very first letter unless it gets removed after the fact which sometimes happens. You can learn more about translational initiation here: http://bit.ly/2KNe00D
Met was 1st isolated in 1921 by John Howard Mueller, and I love how its naming is described by Barger and Coyne: “Since the amino acid has a good title to be regarded as a constituent of protein, a shorter name than γ-methylthiol-a-amino butyric acid seems desirable, and, after consultation with Dr. Mueller, we suggest for it the name methionine, in allusion to the characteristic grouping” https://doi.org/10.1021/cr60033a001
How does it measure up?
systematic name: 2-amino-4-(methylthio)butanoic acid
coded for by: AUG
chemical formula: C5H11NO2S
molar mass: 149.21 g·mol−1
that paper: Lin H. S-Adenosylmethionine-dependent alkylation reactions: when are radical reactions used?. Bioorg Chem. 2011;39(5-6):161-170. doi:10.1016/j.bioorg.2011.06.001 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3188380/
another helpful resource: Application: Useful SN2 Reactions. (2019, June 5). University of Illinois Springfield. https://chem.libretexts.org/@go/page/28176