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I'll focus on a side question, that I'm more prepared to answer.
At the end of the day, proteins are biiiiig arse molecules. Mostly composed of carbon, hydrogen, oxygen, and nitrogen. For example, here's a protein called "myoglobin", that carries oxygen within your blood:
Blue = nitrogen, red = oxygen, grey = carbon, white = hydrogen, salmon = iron, yellow = sulphur. Disregard the mix of sticks and balls in the model, they're both representing atoms.
If you pay close attention to the model, you'll notice a repetitive pattern: 1) nitrogen, 2) carbon connected to some large junk, 3) carbon connected to a "dangling" oxygen. That is not just in the myoglobin, but in all proteins.
If you flattened that pattern and removed the hydrogens (to simplify it), you'd get something like this:
That happens because the bodies of living beings don't build those huge molecules out of nowhere; they do it with smaller molecules called "aminoacids". That pattern there is the amide group, you could see it as the "solder" between aminoacids.
Here's the representation of a few "free" aminoacids:
The fun part is that R, the "side chain". I called it "junk" but it's actually a big deal - because it's what gives each protein a different shape and property. For example, it's thanks to that junk that the myoglobin has a specific shape, that forms a "ring" of nitrogens, just at the right size to host an iron cation, but still leaves one of the sides of the iron cation free - so it could connect to something else. (Hopefully diatomic oxygen. As in, it's how myoglobin transports that oxygen within your body. But if you get poisoned with carbon monoxide or cyanide, it gets stuck there, and it's hard to take it off so the protein stops transporting oxygen.)
The R side chains are not referred to as radicals. R- is common in organic chemistry and refers to a part of a molecule not shown for some reason. Generally because it's not the focus in the specific figure. Generally you'll have a R = (whatever combination of atoms) defined below.
Radicals are a specific atom with an unpaired valence electron. Sometimes also called "free radicals".
Edit, here's an example of a non-amino acid use of R:
Fixed - thanks for pointing this out. My brain farted the word out of nowhere, the correct term in this context would be "side chain".
I'm aware of the usage of R in org chem.
Sorry, I hope I didn't come off as condescending or anything. Getting thoughts into words is difficult sometimes haha. But I just take any chance I can (there's not too many) to talk about chemistry.
Your original post explained everything very well, thanks for contributing.
Don't worry, you didn't sound condescending - you went straight for the issue, and then added further info.
Completely off-topic: I'm curious on your example. Most benzopyrazine synthesis routes that I've seen use IBX instead of SSA. Is this a recent development?
Myoglobin is in the muscles. Hemogoblin is in the blood and is essentially 4 myoglobin molecules that can combine into one hemoglobin. IIRC, the combination of the 4 makes it easier to switch between accepting and donating oxygen, where myoglobin is better just at the taking oxygen.