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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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  • biochemistry (hopefully) made accessible (and fun!)

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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
My thumbs got weary just seeing the experiments I My thumbs got weary just seeing the experiments I planned out for today - lots of serial dilution-ing - thank goodness for master mixes and multichannel pipets! Oh - and my eyes would like me to please thank sharpies, cluster tubes, and color coding! Today - time- and thumb-saving tips from the bumbling biochemist! (especially for when you have serial dilutions and/or a lot of reactions to do that are mostly the same) blog form: http://bit.ly/mastermixesmultichannels Let’s start with the Master Mix. In my first lab rotation (where you try out different labs before choosing) the postdoc I was working with used this term and I’d never heard it but then I learned that it’s actually really common. So what is it? Often the lab you have to set up a bunch of reactions that are almost the same - they just differ in 1 or 2 things - like you want to radiolabel different RNAs and all the things you need for the labeling (water, buffer, kinase, ATP) are the same, but the RNAs are different. Since all the reactions are the same except for that thing, you can prepare a “master mix” of all the “same stuff” - so you only have to add 1 thing per different thing instead of 4 It’s kinda like if a company has a form they need all their employees to sign. If the company had to type up the form individually for each person, that would take a really long time - and each time introduces the chance for the company to make a typo - and it can be pretty easy to get exhausted and or boredly mind-wandery, etc. after typing the same thing out over and over. The lab version of this is what I call “pipetting apathy” So, the company instead makes 1 form and just leaves room for the employee to sign. If there are a couple of things that can vary (e.g. maybe they need to print their name and sign, and/or write down the date) they can leave space for those too. Then they only have to type it up once, can distribute this single document to all their employees, and don’t have to worry that they accidentally gave 1 employee a form where they left out the “not” before “liable” - getting their employee to sign that the company *is* liable for damages… PART 2 👇
The art and science of reading science articles! T The art and science of reading science articles! The main way in which scientists communicate their findings with people around the world is through journal articles, but they’re not always the easiest things to read. I spent most of my morning reading lots of science articles, studying up on some really cool stuff. Also this morning I was responding to someone who asked for advice on reading journal articles. I don’t know how helpful my advice was, but I figured other people might hopefully maybe benefit from it, so thought I’d share. ⠀ ⠀ blog form: http://bit.ly/readingsciencearticles ⠀ ⠀ warning: I’m super exhausted so this post is going to be poorly formatted - but science papers hopefully are not! Speaking of format, these papers tend to have (variations on) a specific format so let’s briefly review what the general layout is before I get to the tips I have on what I find works best for me. This is probably one of the most important things to stress - each person will have their own style that works best for them and the best way to get more comfortable reading papers is to read a lot of them. So, what should you expect when you do?⠀ ⠀ There are several key components of a scientific paper and here’s a brief overview. The actual layouts of papers and section names differ from journal to journal. But they usually contain these core components…⠀ ⠀ Abstract - this is like a book’s “blurb” but with major spoilers. It tells the potential reader what the paper’s about - what’s the question they were looking at & why; what did they do to answer it; and what were their key takeaways. Some papers do “graphical abstracts” which, as I’m guessing you could guess - I love! Graphics make me giddy - go figure!⠀ ⠀ Background - What was known about the topic beforehand? What was missing? Why should we care?⠀ ⠀ The organization of the rest of it can vary - some put methods here, others put them at the end - and if they’re really detailed, sometimes there are extended methods in the “supplementary information”⠀PART 2 👇
Solving the structure of the peptide hormone insul Solving the structure of the peptide hormone insulin (figuring out the 3D arrangement of its atoms) was the crowning achievement for the pioneering crystallographer Dorothy Crowfoot Hodgkin - it took her 34 years, but she did it - and lives of countless diabetics have been saved because of it, as the structure has enabled pharma companies to develop optimized versions for treating diabetes. But where do peptides and proteins’s structure come from and why does it matter?⠀ ⠀ blog form (originally posted in November but I’ve been busy with really exciting stuff): http://bit.ly/insulindiabetes ⠀ ⠀ Insulin is a hormone (chemical messenger) your body uses to help control blood sugar levels. When blood sugar (glucose) levels are high, insulin is released by the pancreas and travels throughout the body where it binds to insulin receptor proteins embedded in the membranes surrounding cells and passes along the message to let glucose in. This lowers the blood glucose levels and lets the cells put that glucose to use making ATP for energy storage (through glycolysis and cellular respiration) and/or breaking glucose down partway for pieces that it can restitch together to make different molecules (like other sugars, proteins, or fats). ⠀ ⠀ I’m grateful that I don’t have diabetes, but, for people who do, their body has a hard time making and/or “hearing” insulin’s call to “let glucose in!” As a result, they have trouble controlling blood sugar levels, so they often use devices called glucometers to measure blood glucose levels & then, if the levels are too low, they can take insulin. More on those here: http://bit.ly/glucometers ⠀PART 2 👇
Dorothy Crowfoot Hodgkin (May 12, 1910 – July 29 Dorothy Crowfoot Hodgkin (May 12, 1910 – July 29, 1994) was a true pioneer in x-ray crystallography – She wanted to get a look at biologically-important molecules. But the technology didn’t exist to do it – so she developed it. And used it to harness x-rays to solve the structure of increasingly complex molecules including the antibiotic penicillin in 1945, the most complex vitamin (vitamin B12) in 1955, and – her lifelong goal – the protein hormone insulin in 1969. She won the Nobel Prize in Chemistry in 1964 – the 3rd woman to do so – you might know that – but did you know that she also won the Soviet Union’s version of the Nobel Peace Prize? In addition to an incredible scientist, Hodgkin was active in opposing nuclear weapons and, in addition to advocating for women in science everywhere, she directly mentored several female scientists who went on to become influential crystallographers in their own right. ⠀ ⠀ blog form (originally posted in Jan 2020): http://bit.ly/dorothycrowfoothodgkin ⠀ ⠀ X-ray crystallography is a technique used to study the structure of molecules that are way too small to see with the naked eye, too small to even see with a light microscope. Instead of visible light (whose wavelengths are too long), it uses a much more energetic form of light – x-rays, which have much shorter wavelengths, better-suited for probing the small distances between a molecule’s linked atoms (individual carbons, hydrogens, oxygens, etc.). But that energy comes at a cost – x-rays can’t be focused with lenses like visible light can, so scientists have to work backwards from the “jumbled” x-rays that scatter when they hit a molecular crystal – and Dorothy Crowfoot Hodgkin largely made this possible! ⠀PART 2 👇
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