So the next chapter of my life is the chapter of proteins. They're what is expressed out of the nucleic acids that have genetic information in them. I'm going to talk about amino acids only a LITTLE bit because I have an older post here where I talked about amino acids and how to know their structures and three letters codes and blah blah blah. But I'll still cover amino acids a little tonight, and if I make mistakes in the structures it's cause I'm tired and sad.
All amino acids have this basic structure...an "alpha carbon" with an attached N-end, COO-end and an "R" group...which can be one of many (technically 22 if you include the two naughty ones) side chains.
These are the aliphatic amino acids, meaning, they've got non-aromatic characteristics. Glycine is the only one without a "real" side chain, it only has a Hydrogen (technically, 2) on the alpha carbon which will make it REALLY important ...soon. There's also alanine, valine, leucine, and isoleucine.
There's also this cat tail, interrupting everything I do.
Then we've got a few amino acids that have either Sulfur or -OH groups on them. Serine, cysteine (which is important in disulfide bonds, a huge huge important topic for SOON), threonine, and methionine.
Then we've got some aromatic stuff up in here, with phenylalanine, tyrosine (which ALSO has an OH group) and tryptophan, which I suck at drawing.
Proline, another important one..it's cyclic and the only one where the side chain actually wraps back around to the alpha-Nitrogen. This shit is mad important in proteins...they introduce turns in chains and do all sorts of crazy stuff that we'll discuss in future times.
Histidine, lysine, arginine are our basic amino acids...
And then we have the acidic amino acids, aspartic and glutamic acids, and their amides, glutamine and asparagine .
Typically, pkas of the NH3 and COOH will be pretty consistently 9-10 and 1.8-2ish, respectively. But sometimes, that's not the case.
Some amino acids have special pka's, either for side chains, for NH3/COOH groups, or in all three cases.
Cysteine and threonine are two cases, where the SH group on the Cys gets a pka of about 9, giving the NH3 a much higher pka (almost 11). For threonine, the NH3's pka is 10.4 and the COOH's is 2.6
Proline has a high pka on the NH3 as well.
Then we have tyrosine, with the side chain pka of 10, and histidine, one of the basic amino acids, with an unusually low pka of 6, which deals with resonance stabilization of the imidazole group that's H's side chain.
Naturally, the other two basic ones, K & R will have high pkas...note that for R, since the guanidino group has remarkable resonance, the positive charge can move all around, giving it stability and the super high pka.
Then the acidic amino acids and their amides. D's side chain has a pka of 3.9 (one carbon away from alpha carbon, donating to the COOH) and G's side chain has a pka of 4.2 (two carbons away from the alpha carbon, donating to the COOH).
Sorry, I got lazy. this is just stuff that makes SENSE but should be repeated regardless. The side chains of basic amino acids have positive overall charges when protonated, which they'll have at physiological pH. They'll be positively charged when they're fully protonated.
Meanwhile, the acidic amino acids will be neutral when they're fully protonated.
I fucking knew the book was wrong but listened to it anyway. Selenocysteine only has one carbon between the alpha carbon and the Selenium. Sec and Pyl are the two "special ones". In prokaryotes, proteins with Sec's are used in catabolic stuff and in eukaryotes, there's about 25 sec-proteins and they're typically used in anabolic processes. Pyrrolysine is found in enzymes of archeal species, and are involved in catabolism.
I really briefly want to talk about making peptide bonds between amino acids, since that's kind of important, and we'll talk about other important stuff later, too.
So firstly, you're going to need to activate the amino acid to make sure formation of peptide bonds is favorable...cause remember, things like to fall apart, not come together, unless something is favoring that. You need to protect all the side chains that could be reactive cause if they're the ones reacting instead of the N/C terminals, you're not going to do this right. Also, every time you add a new amino acid, which has a protective group on it, once the amino acid is added to the chain, you're going to need to remove that group. Two PG's used in this case are the BOC and fMOC groups.
This is the full stepwise route to making a polypeptide chain but the mechanisms are shitty
and you can't really make out the type...so I'll very briefly summarize what's what.
In 1, firstly, you attach the C-terminal of either the amino acid or peptide sequence that you're gonna keep adding shit to onto a resin (SPSS) and you leave the N-terminal (alpha-NH3) exposed. You need to deprotonate the NH3 to an NH2 to make it a better nucleophile.
Meanwhile, in 2, you're taking the next amino acid that you're going to add to your chain. It has a free COOH (c-terminal) and in this case, a BOC-protected alpha-NH3 (N-terminal). You take this new amino acid and you activate it with carbodiimide, converting it to a carbonyl ester to make it more reactive.
Then, the NH2 you got when you deprotonated the crap that you attached on the resin is going to attack the BOC-protected, C-terminal activated THING you made in step 2, to give you a covalent addition of an amino acid to your chain.
So now you just need to deprotect the new N-terminal, and you can use Fluoroacetic acid to do this. That gives you a brand new NH3+ group that you can now deprotonate and initiate in a new reaction.
Once you're done adding amino acids onto the chain, you can deprotect the side chains and the resin with HF.
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