Eukaryote tumbles

Synophalos xynos, a shrimp-like arthropod from the Early Cambrian of China (~515 mya). Thought to be closely related to stem-crustaceans like Waptia, it was about 2cm long (0.75″) and had a bivalved carapace with a segmented body ending in a forked tail.

Unlike any other known arthropods, however, it formed long “conga line” chains of up to twenty individuals, with the tail of each animal locking securely into the shell of the next. The function of the these chains is unknown, although suggestions include some sort of mating behavior, migration, or defense against predators.

Instead of sticking to a glucose-based system, which is dependent on oxygen, when a naked mole rat is deprived of oxygen, it switches its metabolism so that its brain cells start burning fructose for energy instead of glucose.  

Fructose can be turned into energy anaerobically - which means it doesn’t require the presence of oxygen to be broken down into cellular energy.

CLASSIFIED INFORMATION COMPROMISED

CLASSIFIED INFORMATION COMPROMISED

For a long time (~40 years), we thought humans only had 20 proteinogenic amino acids (i.e. amino acids that get directly incorporated into proteins by RNA). At this point this is just Biological Dogma: if you look up a list of amino acids you are pretty much guaranteed to see a list of 20. If you ask a biologist how many amino acids there are in humans they are very likely to say 20.

The 20 amino acids are all encoded by specific triples for RNA bases (for instance a cysteine is encoded by UGU and UGC triples), which are all encoded by specific DNA bases. It was accepted dogma (by which I mean this thing is literally called the Central Dogma of Molecular Biology) that DNA -> RNA, and that RNA codons -> amino acid chains (i.e. proteins). This is basically the Newton’s Laws of biology.

Then in 2000 some jackass scientist* came along and complicated things for everyone made a discovery. Turns out there is a 21st proteinogenic amino acid: selenocysteine.

The reason no one had noticed this before is that biology is fucking bullshit. You see, there is one RNA triple (UGA) which is a stop codon: it tells the molecular machinery to stop reading the RNA, the protein is done, move along. However under particular (read: bullshit) circumstances, the stop codon can be read as a normal codon, and it produces selenocysteine. Specifically if the RNA adopts a particular loop structure (a SECIS element), then the stop codon will be interpreted as a selenocysteine. God knows *how* this particular loopy thing causes this effect. On second thought God probably took one look at this thing and said “fuck it, I’m gonna be a clockmaker”.

If at this point you’re thinking “gosh biology sure is BULLSHIT”: congratulations, you have taken the first step on the road to enlightenment.

* Thressa Stadtman

PS: The original paper is here, although it’s behind a paywall so I would like to take this opportunity to remind all of you that sci-hub exists.

My bacteriology professor discussed this–apparently the bacterial SECIS element (a palindromic sequence, that forms a section of double-stranded RNA) makes the ribosome pause–it physically blocks the ribosome and prevents release factors from binding, even though the A site has reached a stop codon. SelB, a selenocysteine-specific elongation factor, interacts with the stem and loop to recruit a selenocysteine-tRNA. Termination doesn’t occur, and elongation continues after selenocysteine is attached to the nascent polypeptide.

Eukaryotes and archaea have a totally different process, too.

(Certain bacteria and archaea have a 22nd rare proteinogenic amino acid, pyrrolysine. Its translation seems to work similarly.)

And selenoproteins are old. They’re present in all three domains of life, and as we currently understand it, all three domains’ selenocysteine-incorporating machinery is homologous–i.e. all descend from one ancestral protein, before Archaea/Eukarya existed. That’s at least a few billion years…