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The Bumbling Biochemist

The Bumbling Biochemist

on a mission to make biochemistry fun and accessible to all

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thebumblingbiochemist

#Biochemistry/#structuralbiology PhD student on a mission to make biochemistry fun and accessible sometimes through my #scicomm superhero alter ego
Today's task was tackling the "I solved some cryst Today's task was tackling the "I solved some crystal structures but they didn't tell me much of anything so I moved on" section of my thesis. And, as I think I’ve said before, crystallography isn’t like riding a bike… So as I worked on this, I thought I’d repost this post on X-ray crystallography from November. ⠀ blog form: http://bit.ly/xraycrystallography2 ⠀ ⠀ We’ve been “looking” a lot at proteins, the main workhorses of our cells, which do everything from provide structural support to help mediate and speed up (catalyze) complex reactions.  We’ve “looked” a lot at the amino acid “letters” that proteins are made up of - and at the smaller parts called atoms those letters themselves are made of (individual hydrogens, carbons, oxygens, etc.). But how do we actually *look* at proteins and their parts? One way is with a technique called X-ray crystallography. ⠀ ⠀ All those pretty protein models you see in figures might make it seem like you’re looking at proteins directly. But, we’re doing all this “seeing” of proteins without actually seeing them - the reason we can see things is that when light hits a solid object, like the two things we’re trying to tell apart, some light waves get reflected at us and it’s the cornea & lenses’ job to take those light waves and bend them to focus them onto our eyes’ retinas. And photoreceptors in the retina send signals to the brain to interpret. ⠀ ⠀ But the light waves we use for X-ray crystallography are way too energetic for such focusing - they don’t get slowed down enough when they travel through glass so they wouldn’t get “bent” by a lens like visible light does - and they’d basically fry any conventional lens we tried to use to focus them (they’d even fry our detector so we have a “beam stop” in the direct path of the beam to absorb any of the concentrated rays that go through undeflected). Therefore, we have to work with evidence from the waves that scatter from the protein in the crystal.⠀PART 2 👇
Don’t let your proteins suffer - brew them a nic Don’t let your proteins suffer - brew them a nice buffer! Buffers are pH-stabilizing salt waters - basically it’s just the liquid you put molecules like proteins in when you want to study them in the lab and keep them happy & working outside of their natural intracellular home. So making them isn’t the “fun” part of experiments. But it’s really important - and something I do a lot. So I thought I’d give Henderson and Hasselbalch some thought… ⠀ blog form (refreshed from last February & has more figs): http://bit.ly/phbuffers ⠀ ⠀ A lot of the buffers I make are made to serve as nice soothing baths for the proteins I’m working with - and just like you wouldn’t want to take a bath in lye (super basic (high pH)) or vinegar (super acidic (low pH)), you shouldn’t ask the proteins and other molecules you’re working with to do so! And you certainly shouldn’t expect them to act the same in those different conditions. Instead, you usually make up baths for them that resemble their native homes (like the inside of cells) but with minimum molecular “clutter.” While it’s easy to focus on the protein we put in the buffer and forget everything else, the buffer itself matters too! A lot! And it’s precisely because of its buffer-ness that we’re able to “ignore it.”⠀ ⠀ Since I do a lot of protein purifications, I need to make a lot of buffers - and it’s not just for protein purifying that buffer-making is required. Basically (no pun intended (this time) - honestly!) every time you want to see how molecules act and interact, you have to make sure that they’re in an okay environment, and you want to make sure that environment stays consistent - especially if you’re trying to compare things.⠀PART 2 👇
Caps off (and on) to messenger RNA (mRNA) - a topi Caps off (and on) to messenger RNA (mRNA) - a topic about which there is much to say! So let’s look at its lifetime - birth, maturation, and decay! DNA tends to get the most attention because it’s what our cells use to store our genetic blueprint (genome). But, even though humans and all organisms that we know of (yeah, viruses technically aren’t “living” even though they are quite ingenious), RNA plays a crucial role in every cell in every living thing. It can serve different roles, but one of the main roles is in the form of messenger RNA (mRNA), which acts as an intermediary between proteins and their DNA “recipes” (genes). ⠀ ⠀ blog form (refreshed from last January): https://bit.ly/mrnalife ⠀ ⠀ How it works is that the genome is kinda like a set of cookbook volumes (chromosomes), where the recipes are genes, many of which contain instructions for making proteins. These “original copies” of the recipes are really important to protect because they’re permanent & get passed onto all the cells made from that cell. So, when a cell wants to make a protein, it makes RNA copies of the DNA genes, edits them to cut out regulatory regions (introns) and add a cap and a tail, and passes these copies off to the protein-making complexes (ribosomes). Not only does this protect the original DNA, but it also allows you to make lots of copies of the encoded protein at once. And, when you’ve made enough, you can degrade the recipe copies - and RNA is less stable than DNA, so this is easier. ⠀ ⠀ Yesterday, I told you about how we can deliver mRNA directly to cells to get them to make proteins, which is the strategy being taken with mRNA vaccines - introduce mRNA for viral proteins, get the cells to make those proteins -> immune system learns to recognize them without person ever getting sick. http://bit.ly/mRNAbiochemistry PART 2 👇
What is mRNA? Although the news may make it seem l 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.    blog form (has more figures): http://bit.ly/mRNAbiochemistry     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.  PART 2 👇
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