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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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Learn about the site and the bumbling biochemist.
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Current topics include RNAi, protein biochemistry, and women in science.
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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
If you’re tired after Thanksgiving, don’t blam If you’re tired after Thanksgiving, don’t blame the turkey! Time to pardon the turkey from the “turkey makes you tired” myth. starting with a bad pun about amino acids (protein letters)…What’s Tweety bird’s fave amino acid? tWiptophan! Tryptophan (Trp) is abbreviated W & you can remember this by saying it like Tweety! You might have heard of it in the context of different bird - yup, Tryptophan’s the source of the “turkey makes you tired” MYTH because Trp is a precursor to the chemical signaling molecules serotonin & melatonin that help regulate mood and sleepiness and stuff. But it’s not that simple!⠀ ⠀ blog form: ⠀https://bit.ly/turkeytiredmyth ⠀ Let’s start by taking a look at the main player, behind the myth, tryptophan. As I mentioned, tryptophan is an amino acid - and it’s one of the amino acids which, in addition to serving as a protein letter, can serve as a precursor to other things. There are 20 (common) amino acids, each with a generic backbone to allow for linking up through peptide bonds to form chains (polypeptides) that fold up into functional proteins, as well as unique side chains (aka “R groups” that stick off like charms from a charm bracelet). http://bit.ly/aminoacidalphabet ⠀ ⠀ If you look at tryptophan, you’ll see it has a couple of ring things. These ring things will come into play later because they help make Trp “hydrophobic” - basically if something’s hydrophobic, water doesn’t want to hang out with it. And your blood’s mostly water… So in order to travel through the blood it piggybacks on protein called albumin which doesn’t mind hanging out with it. This affects the transport of Trp throughout the body and where/when it can be taken up by cells. So those rings are important - but what *are* they?⠀PART 2 👇
Spent much of this morning trying to work out some Spent much of this morning trying to work out some "how much of this enzyme to add" calculations, so, while I try to figure this all out, I thought I might need to repost my "what is an enzyme activity unit" and when it is/isn't it helpful rant...⠀ ⠀ blog form: http://bit.ly/enzymeactivity⠀ ⠀ One of my favorite activities is talking about enzyme activities. But one of my least favorite activities is tracking down what people are using to define their enzyme’s specific activity. So, biochemists - I call upon you to unite against undefined units! I hope “U” will permit a little rant about a pet peeve of mine that’s peeving me that has to do with ENZYME ACTIVITY. Say you want to tile a floor - so you buy a bunch of tiles but you need help laying them down. So you want to hire some tilers. But how many to hire? Depends on how many tiles you need to lay, how quickly you want the job done, & how quickly the tilers tile.⠀ ⠀ So you check out the ads. One company says that their tilers can tile a 100 sq. ft room in 1 hour. Another tiler claims he can lay down 100 tiles in 1 hour. And another company says they’ll send you 3 workers for the price of 1. What’s the better deal? We need more info!!!!!! Even if they are all telling the truth, there are still a lot of unanswered questions. Here are some questions I’d like to ask them…⠀ ⠀ Company 1: How big are those tiles you used? The tiler could have laid down 1 giant tile - 10 ft by 10ft - and have filled the whole room. But what if you have smaller tiles? If he can only lay 1 tile an hour it’s gonna take a long time to tile the same size room.⠀ ⠀ In that case, the second tile company’s looking a lot better! But how many tilers will they send? The more tilers there are working, the faster the job can get done - assuming that all the workers are working at that same rate…⠀ ⠀ How about that 3 for 1 deal? Are all 3 tilers of equal tile-laying-skillness? What if they send you 1 tiler and 2 dog-walkers? Even if that tiler’s pretty good, those dog-walkers aren’t gonna be much help. ⠀PART 2 👇
Don’t let your proteins suffer - brew them a buf Don’t let your proteins suffer - brew them a 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: 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, & you want to make sure that environment stays consistent - especially if you’re trying to compare things.⠀ ⠀ Just like (unless you’re looking for effects of temperature) you wouldn’t want to compare a reaction performed in a cold room to 1 performed at “room temp,” you don’t want to compare reaction performed at different pHs (unless that’s the only variable you’ve changed because you’re looking for effects of pH). Bottom line - don’t change anything you aren’t interested in - this is what we refer to as “controlling variables.” A variable we commonly control is pH, & we keep it in a narrow range using chemicals called “buffering agents.”⠀PART 2 👇
If you’re one of the many people getting a “co If you’re one of the many people getting a “coronavirus test,” you might be wondering how they work and what the heck is going to be done to that swab they just stuck up your nose… There are some new-fangled coronavirus tests out there, but the mainstay of testing continues to be done with a tried, true, and tremendously sensitive technique called “RT-PCR.” So today I thought I’d repost the very first post I ever made on SARS-CoV-2, the “novel coronavirus” which causes the disease COVID-19. That was back in March, but this post is, unfortunately, perhaps even more relevant now - including the plea to help flatten the curve! ⠀ blog form: http://bit.ly/coronavirustesting ⠀ ⠀ Most of the tests, including the US’s official CDC tests, utilize what is called Reverse-Transcriptase Polymerase Chain Reaction (RT-PCR), to detect SARS-CoV-2’s genetic information. SARS-CoV-2 is an RNA virus - instead of storing its genetic blueprint (genome) in DNA like we do, it keeps it in RNA. And as single strands. ⠀ ⠀ Within this RNA are instructions for making proteins that the virus needs. A virus really only “cares” about one thing - making more copies of itself and infecting more cells, and so the genes you find in its RNA reflect what it needs to do this. A few examples:⠀ * It has to make copies of its RNA, so it needs an RNA-dependent RNA polymerase (RdRP) that can travel along the RNA strand and use it as a template for making a complementary RNA strand - which can then be used to make a copy of the original template strand which can then be used to make a copy of the complementary strand which… you get the point - thanks to the complementary base-pair-ing nature of RNA & DNA (the letter A binds to U (or T in DNA) and G to C) it’s “copyable” And, since the virus encodes for an RNA-dependent RNA polymerase, it’s able to copy its genome. ⠀ * Then it has to coat those RNA copies in a protein “shell” called a nucleocapsid for protection on its journey, so it needs a gene for the nucleocapsid protein (this is called the N gene and it is what the CDC tests look for).⠀PART 2 👇
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