What is mRNA? Although the news may make it seem like it’s this new-fangled thing, mRNA (short for messenger RNA) is actually something that our cells use naturally all the time. Here’s a brief overview of mRNA (natural and synthetic) from a biochemist’s perspective.

Basically, our genes are like original copies of protein recipes and mRNAs are like Xeroxed copies of those recipes that get handed out to the protein-making chefs (complexes called ribosomes). Depending on what our cells need when, different mRNAs get made, leading to different proteins to get made. This lets our cells do things like make nerve-cell-y stuff in some cells and heart-cell-y stuff in other cells and only make machinery for replication when it’s time for cells to copy their contents and divide in two. The genetic code is universal, meaning that the ribosomes can read and make protein from any mRNA. They’re only limited by what they have recipe copies for. Our cells don’t normally have the recipe for making viral proteins, but, if we introduce copies of the recipe, such as through vaccination with mRNA vaccines, our ribosomes can make them, and then our immune system can learn to recognize those proteins as foreign and attack the virus if it shows up with them. The details of the immunology part are beyond my expertise but I will provide some links to more from experts 

The vaccines are only introducing recipe copies, not “originals” so our cells can’t make more of them. They’re limited to what gets put in, and the recipes that get put in are temporary, subject to decay just like our cells’ own recipe copies. The “only” difference between synthetic mRNA, like that in vaccines, and our cell’s own mRNAs is their sequence, how they’re made, and how they get to the ribosomes. 

In our cells, all the original recipes for making all the proteins and functional RNAs we will ever need are written in the form of DNA as genes. Those genes are present in the form of really long, really coiled-up pieces of DNA called chromosomes, which you can think of like cookbooks. And the full complement of cookbooks, referred to as the genome, is stored in a membrane-bound compartment of the cell called the nucleus. This protects them from damage, which is important because we don’t want to mess up those original copies! But, it also separates them from the chefs (protein/RNA complexes that use the instructions to make the corresponding proteins), which are located in the cytoplasm (general cellular interior). Therefore, in order to make a protein, cells first make a messenger RNA (mRNA) copy of the gene in a process called transcription. 

The pre-mRNA that’s first made gets processed a little to remove regulatory regions called introns (in a process called mRNA splicing) and it gets a cap and a tail to protect its ends, and then that mature mRNA gets exported into the cytoplasm to meet the chefs. In addition to protecting the original recipes, this set-up allows for signal amplification because you can make lots of copies of the original and each copy can be used lots of time. It also allows multiple different versions of a protein to be made by processing the recipe copies differently during maturation (e.g. through alternative splicing). https://bit.ly/altsplicing 

So, to summarize the “us” part – we have original protein recipes written in DNA as genes -> mRNA copies get made in a process called transcription in the nucleus -> those mRNA copies get exported into the cytoplasm to be used by ribosomes to make proteins. 

Now, what about viruses? Here the terminology can get a bit tricky because there are different types of viruses and the RNA viruses, including SARS-CoV-2 (“the coronavirus”) have original copies of genes written in RNA, but they still make more mRNA copies from the original to get your cells to make more of their proteins. 

so, original protein recipes written in RNA as genes -> mRNA copies get made in the cytoplasm in a process called transcription -> those mRNA copies, already in the cytoplasm, get used by ribosomes to make proteins. 

note: These viruses are non-integrating. They never get into your nucleus, and don’t go near your DNA. (note: adenoviruses are DNA based and do go into the nucleus but they do NOT get into your DNA because they don’t have the integration equipment that is needed to do so). So, SARS-CoV-2 itself can’t get into your DNA. And this is even “more true” for mRNA from vaccines. Our cells “know” what mRNA is, they “know” that it belongs in the cytoplasm, and they “know” to make protein from it. 

“Normally,” viral genomes get introduced when a virus latches onto a cell, merges its membrane with that of the cell, and releases its contents into the cytoplasm. When this happens, *all* of the viral recipes are introduced, so the cells make more copies of the whole, active virus. This gives the immune system plenty to learn to recognize, but it also can make you sick. The idea with mRNA vaccines is to just provide a single protein recipe – enough for cells to learn to recognize and attack, but not enough to make an actual, harmful, virus. http://bit.ly/covidvaccinebiochemistry 

What recipe to choose? In the case of SARS-CoV-2, mRNA vaccines use the Spike protein (S), which is that protein that juts out crown-like from the surface of the virus. Why Spike? For one thing, it’s basically the first part of the virus that your body sees. For another thing, there’s a lot of it per virus. And for another, really important, thing, it’s the virus’ “ticket in” – it is able to bind to a cellular receptor called ACE-2, which lets it latch on and ultimately come on in. https://bit.ly/coronavirusspike 

If the immune system is introduced to the S protein ahead of time, it can learn to make little proteins called antibodies which bind specifically to the Spike protein in a way that blocks them from docking to ACE-2, thus “neutralizing” the virus before it can infect you. https://bit.ly/neutralizationtests 

note: I say “learn” but really it’s a massive trial-and-error approach whereby immune cells randomly mix and match antibody parts and then if one binds to the foreign protein but not the body’s own proteins, the cell that made that winner starts proliferating (lots more copies of it are made), etc. There are also immune cells called T-cells which do a kinda similar sort of thing, but they recognize short chopped up protein pieces that cells display from surface receptors. I’m not an immunologist, so I’m not gonna try to go into details, sorry, but I’ll give a bit more and some links later. 

When a person is infected with SARS-CoV-2, the Spike recipe gets in with the rest of the viral genome through the viral’s natural infection process. But how do you just get the Spike recipe in by itself? Adenoviral-vectored vaccines stick that recipe into another, harmless, virus to use that virus’ normal machinery to sneak in the recipe. http://bit.ly/viralvectorvaccines 

But the only genetic info that the mRNA vaccines stick in are recipe copies of the Spike gene. In order to get them in without the help of viral machinery, scientists mask them in lipids (oily molecules), salts, sugar, and positively charged particles (cations) that counteract the natural negative charge of the RNA and of the outside of cellular membranes. Our membranes are made up of a bilayer “sandwich” of molecules called phospholipids which have lipid-y tails that glob together in the center of the sandwich and water-loving heads facing out that are often negatively-charged. The cations in the LNP help neutralize the RNA’s negative charge so that everything doesn’t just repel each other because of the whole “opposite charges attract, like charges repel thing.” And the lipids help it be membrane-like, which will help it disrupt the membrane and sneak in. 

note: here’s an ingredient list if you’re interested: https://bit.ly/3heYl90 

These “lipid nanoparticles” (LNPs) get swallowed by cells in a process called endocytosis, which kinda traps them in intracellular membrane-bound bubbles called endosomes. The LNP formula is such that, as the endosome matures and becomes more acidic, some of the once-neutral molecules in it (ionizable cartionic lipids) become positively-charged and this helps them disrupt the endosomal membrane and spill out into the cell. 

Our cells don’t have polymerases (DNA/RNA copiers) in the cytoplasm, only in the nucleus. So, normally, the virus uses a viral polymerase to make more mRNA copies from its original. But, with the vaccines, you aren’t giving the polymerase, so cells are stuck with the copies you give them initially. Therefore, you give them lots of copies, each of which can be used over and over. But then, they get degraded. The go bye-bye. That’s it. Our cells are well-equipped to destroy RNA (which is one of the reasons we store our original recipes in DNA!) RNA-chewers called RNAses are always on the lookout for naked RNA and de-capping and de-tailing complexes remove the protective ends from mRNAs after a while. more on this here: https://bit.ly/3bOWMrZ 

The exact half-life of mRNAs (a measure of how long, on average, an mRNA lasts before it gets degraded) varies, but no mRNAs last forever. The average half-life of mRNA is ~7 hours. https://bit.ly/3ewcT2t The mRNA vaccines have a longer half-life due to some stabilizing features, as explained in this nice (but somewhat technical) article: https://bit.ly/3nZnPIW but they’re still degraded. 

In the data from Pfizer when then they used a different mRNA, one with the recipe for a luciferase protein which can be used to give off light that can be measured so they could see if the protein was getting made, and put it into mice intramuscularly, they saw lucisferase near the injection site at 6 hours and the protein was gone by day 9. Since protein can stick around longer than the mRNA, the mRNA was gone before then, I just don’t know the exact data on that. https://bit.ly/3vPwal8  

But not before they’ve been used to make lots of Spike! A lot of people have asked me about what happens to the proteins that get made, and that’s way beyond my expertise, but from what I’ve gathered, a few scenarios can happen

  • the protein gets made and then chopped up by the proteasome, and then pieces of the protein (peptides) get displayed from the surface of the cell where immune cells can learn to recognize them (note: this is something that happens even to normal proteins as a sort of way the immune system keeps an eye on what’s going on – if it recognizes the proteins as self, “nothing happens” but if it doesn’t recognize it, then the adaptive immune response kicks in to find T-cell receptors that will specifically bind it, giving you “cell-mediated immunity”)
  • the protein gets secreted, or is present in dead cell debris, and is swallowed by an immune cell – the cell then does a similar chop up and display thing, followed by generation of a specific immune response. If I understand correctly, this time the peptides are displayed on a different protein (MHC class II instead of MHC class I) and that leads to the generation of antibodies, including the superstar “neutralizing antibodies” which bind in such a way that they prevent the virus from getting into cells
  • the protein gets displayed from the surface of the cell like it does from the viral membrane, and antibodies get made against it that way

here is a good article: https://www.cas.org/blog/covid-mrna-vaccine 

and an FAQ: https://bit.ly/3eujpGQ  

The injected mRNA can either be taken up locally by the muscle cells it was injected into, or it can drain to the lymph nodes, where a bunch of immune cells hang out. Yes, a few cells will get killed in the process, but only the ones that took in the mRNA – the mRNA itself is temporary and it can’t get passed on from cells. So only the cells that take it in will be affected. And it’s not enough to actually cause any harm. Furthermore, I heard on a podcast episode (an episode of This Week in Virology (TWiV) but I don’t remember which one) that most of the uptake takes place in those lymph nodes, so you will only be causing negligible muscle damage (and the little there is helps stimulate the immune system to come to the area (accompanied by a little soreness)).

Another concern some people have is that mRNA vaccines have never been FDA-approved for human use before. But, in their defense, although mRNA has been around “forever,” the technology to make them outside of cells and deliver them into cells hasn’t been around that long. The mRNA is made in a process called in vitro transcription. You might remember me saying that the process of making RNA copies of DNA is called transcription. In our cells it occurs in our nuclei, but here it occurs outside of cells, “in vitro” using a DNA polymerase called T7. More on that here: http://bit.ly/t7rnap 

That technology has been around for a while, but scientists had a lot of trouble with figuring out how to get the mRNA safely into cells without it getting degraded first or triggering generic inflammatory responses. A scientist called Katalin Karikó, who is currently senior VP at BioNTech figured out how to get it to work, which involved introducing naturally-occurring modifications to make the mRNA more “human-like.” http://bit.ly/katalinkariko 

I got the Pfizer vaccine and am incredibly grateful – being able to get vaccinated is an immense privilege many people unfortunately still do not have. I strongly encourage everyone to get vaccinated (with any vaccine) when they get the opportunity. Not only will you protect yourself, but you will also protect people who are unable to be vaccinated and people who are immunocompromised and might not respond strongly to the vaccines. They’re counting on us. And I hope that they can count on you. 

the New York times published a cool interactive & video-ed article behind-the-scenes at how Pfizer makes their Covid-19 vaccine: https://nyti.ms/3vONLtq  

If you want a more detailed post on mRNA vaccines, check out http://bit.ly/covidvaccinebiochemistry 

more Covid-19 resources: https://bit.ly/covid19bbresources ⠀ 

more on topics mentioned (& others) #365DaysOfScience All (with topics listed) 👉 http://bit.ly/2OllAB0

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