Ologies with Alie Ward - Smologies #37: PROTEINS + DNA with Raven “The Science Maven” Baxter

Episode Date: February 3, 2024

This one’s got it all: teeny tiny cellular factories, mitochondrial relevancy, what big smelly vats of poop have to do with curing cancer, how many trips to the sun your unravelled DNA could make, and mysteries of the brain. Dr. Raven The Science Maven has a background in molecular biology and a Ph.D in Science Communication, which she puts to work while Alie generally does her best to suppress high pitched noises of excitement. Learn to appreciate your proteins and pick up some noodle analogies while you’re here. That’s so Maven!Follow Raven on Instagram and TwitterVisit Raven's website and YouTube channelA donation went to Project for AwesomeFull-length (*not* G-rated) Molecular Biology episode + tons of science linksMore kid-friendly Smologies episodes!Become a patron of Ologies for as little as a buck a monthOlogiesMerch.com has hats, shirts, hoodies, totes!Follow @Ologies on Twitter and InstagramFollow @AlieWard on Twitter and InstagramSound editing by Steven Ray Morris, Jarrett Sleeper of MindJam Media and Mercedes Maitland of Maitland Audio ProductionsMade possible by work from Noel Dilworth, Susan Hale, Kelly R. Dwyer & Erin TalbertSmologies theme song by Harold Malcolm

Oh, hey, it's the half a cookie you forgot you saved from lunch. Alley Ward, and we're here with a Smologies episode. If you don't know what Smologies is, Smologies are shorter kid-friendly episodes that we have cut together and put out per parental requests for some cleaner versions that they can listen to with the whole fam. So these are for Smologites, for the small people in your life, or if you've just got to listen to something shorter with a wide audience who doesn't want to hear me swearing. Okay, this episode is great. I loved it. Let's get right into it. Molecular biology. So molecule comes from the Latin for mass or moles or extremely minute

particle. And biology, of course, is the study of life. So molecular biology is the study of the little itty bitty squiggly intricate structures that keep us alive and breathing and finding off illnesses and falling in love and digesting a pizza. So molecular biology is how molecules interact with each other to form life processes and how proteins do a lot of our dirty work. Thisologist has been an assistant professor of biology and a STEM college coordinator for high school students, has worked in a private lab researching cancer cures and has done a TEDx talk and been recognized by Fortunes 40 under 40. Now I have been a fan of hers

for quite a while, so we hopped on a call to talk about what a molecular biologist does, the grossest parts of her lab work, protein folding, DNA strands, and more. With science communicator and molecular biologist, Dr. Raven the Science only Raven Baxter that people may have heard of. Such a good name. You know, I loved having it until the Disney Channel came in and just decided they were going to do do their own thing. I think a lot of people think of you as Raven the Science Maven. Like a lot of times I don't even think about you having a last name. I just think of you as Raven the Science Maiden.

Have you always been kind of science minded? Absolutely. Quite often, I would find that I just get drawn to the natural environment and looking at the clouds or digging in the dirt. Things that kids do, you know, but I was very, I feel like I engaged in scientific inquiry from a very young age. When I went to college, I tried different majors out. And as I transitioned in my academic journey, found genetics, and was so thrilled to learn that our

bodies are so cool that they speak their own language, which is the genetic code. And I'm sitting in this class like, oh my gosh, you know, none of my friends are in this class. They have to, they have to learn about this. This is so cool. Our bodies are speaking a language and, and like, we're the only ones that are taking a class on it. Right. So like, not only did I think it was super cool, but I wanted to share that with everyone that I knew. But I just went down that rabbit hole genetics and molecular biology and I never came out.

So the language is our DNA, the genetic code, and it is a sequence of nucleotides that contain instructions for proteins, yes. And those proteins are doing the work inside of ourselves to generate our life processes. So the way that I like to see it is just a scaled down version of how cities work, where you have the mayor, you know, he's at City Hall and that's that's often like the central point of his city, and the mayor has like his staff that he talks to and you know, he tells so-and-so to do this

and then they go do that. So it tells another person to do another thing and they go do that job. And everything that happens out from city hall affects the entire city. And that's how I think about molecular biology. It's a super simplified version of it. And where your DNA is the mayor and the mayor's staff are like proteins

that are carrying out different functions. Oh, that's amazing. They look from what I've seen kind of like gift wrap, right? Are there a lot of spirals happening? What are these proteins shaped like? That's hilarious. So proteins are really interesting. They have different shapes and sizes.

They fold into these different shapes that determine their functions. But they don't start folded. Okay, let's back up a little. We can just start from the beginning, right? Yeah. We have our DNA, which is inside of our nucleus, and it's very neatly packaged in the nucleus, and it gets read by other proteins, right,

inside of your nucleus, into a different code called RNA, which is almost the same as DNA, but it uses a slightly different code called RNA, which is almost the same as DNA, but it uses a slightly different code. And then that RNA is read by proteins called polymerases. And the polymerases then translate the information from your RNA to create a protein. As the protein's being made, it's basically like a spaghetti noodle

as it comes out of this polymerase. And then as it's coming out, it folds into these different shapes. But the two basic shapes are beta sheets, which kind of look like a brick of ramen noodles. Or alpha helices, which are those curly pieces that look like, I don't know, rigatoni. I actually don't know. Is rigatoni even the curly one? Oh, no, it's few silly, few silly. Okay, you're right. Okay, so then they're in those two different

beta or alpha helix shapes. And then what do they do from there? From there, all of these shapes and structures are determined by the protein's amino acid composition. And so depending on the composition of the protein itself, it'll fold and shape into different levels of protein folding. So there's primary structure, secondary structure, tertiary structure, and quaternary structure. And those different proteins, the complicated ones or the simpler ones, are they bouncing

around in our bloodstream to send messages or are they packaged to form different organelles and different organs? Like what happens to those curly folded, very specific proteins? I mean they do so many different things. Where do we even start? They get packaged in the Golgi apparatus and shipped out to different parts of the cells. One place where they can go is they can get packaged out in a vesicle, which is basically just a little, you can call it maybe like a little fat bubble, you know?

The proteins can get packaged into vesicles and sent to the cell membrane, where they can release proteins out into the extracellular environment or present the proteins onto the cell surface. Okay, so right now, no matter what you're doing, there are tiny proteins cruising around your cytosol, which is the ooze that makes up the cytoplasm in your cells. And a Golgi apparatus is sorting some of them and just popping them into fat envelopes. And you just have no idea how hard they're working in trillions of tiny factories,

just attaching labels to things and passing chemical notes back and forth like two teenage lovers in an afterschool detention. So cells use molecules to communicate. For example, there are certain cell pathways that cause cancer, or there's certain cell pathways that we can study to understand like cellular responses to immunity, things like that. cellular responses to immunity, things like that. And now you have worked in cancer research, you've worked around big vats of E. Coli,

you have done some really awesome work. What was it like getting your masters and then studying this on a corporate level? What types of things were you looking at? How does a molecular biologist do their work? Do you need the most gargantuan microscopes to look at these curly Q proteins? How do you do it?

Yes, you do. Really? OK. The kind of work that I was doing looked a lot different, almost on a weekly basis or monthly basis. I was doing cell transfections, which is a fancy word for running experiments to insert DNA into cells. Or I was doing CRISPR projects. Or I was trying to generate a new cell line that expresses a particular protein that we're interested in.

Or isolating DNA from bacteria by the gallant, which is why I had to make, you know, basically gallants of poop, like you just said. Because I was using E. coli as an expression host for the DNA and had to get the DNA out of them. And it was really interesting. I was working with different types of cell lines, breast cancer cell lines, skin cancer cell lines, and even neuronal cell lines, which is really cool. I did some work on trying to understand

or find the best drugs to treat Parkinson's disease or brain diseases like Alzheimer's as well. and find the best drugs to treat Parkinson's disease or brain diseases like Alzheimer's as well. And that involves some really interesting and fun work using neuronal cells. Neuronal cells, side note, are types of neurons in the brain. And now when we think of a neuron, you might picture like a kind of hand

at the end of a long arm that has a bulbous other end. Or maybe it looks like a tree, hence the word dendrite from its root tree. But some research estimates there may be up to a thousand different types of the cells in our nervous system, depending on their structure and function or location. So okay, my point is our brains don't know everything about our brains. And studying our brains with our brains requires machines devised by our brains to study themselves, which is creepy and also not cheap. The equipment that we use is often very expensive.

I had the pleasure of working with a super cool machine called the Perkin-Elmer Opera, I think it's called. Introducing the Opera Phoenix High Content Screening System from Perkin-Elmer for the speed and sensitivity you need. No compromise. It was super cool because it's a high content screening system. So we were able to test hundreds and thousands of drug compounds on different cell lines to find out what drugs work the best

against a certain type of cancer. And then we would formulate the drug. And so you're just like low key curing cancer when you go into work. That's how it gets done, right? Yeah, that's the very beginning part of it. Like, when you talk about clinical trials, that's where it starts with the molecular biologists, trying to find what drugs you should even be looking at in the first place. I have so many questions from patrons. Can I just lob some at you?

Yes. Okay. But before we pepper her with curiosities, we will of course donate to a cause of the ologist choosing. And Raven said she didn't have a preference, she just liked the money to go to whomever needs it. And as it happened, our mutual buddy Hank Green's Project for Awesome happened to be at the final couple of seconds as they reached the $2 million mark. So we made a donation in Raven's name.

Project for Awesome is a project of the foundation to decrease world suck. And you can learn more about them at projectforawesome.com. And that donation was made possible by sponsors of the show, whom I shall now yammer about very briefly. Okay, you had questions for Raven. A lot of folks had questions, including Brandon Butler and Ashley Immanuel. Is the mitochondria actually the powerhouse of the cell? What is the mitochondria of eukaryotic cells, meaning not bacteria,

basically. And what mitochondria do is they break down sugars and turn them into energy. It's almost like something that breaks down gasoline in our car. Honestly, yeah. That's pretty much. Okay, I look this up and wouldn't you know it, molecular biology happens to be a little bit more complicated than a Honda Civic engine. But still, mitochondria do sort of burn our food fuel and produce a source of energy. This whole process

is called oxidative phosphorylation, and it does require oxygen, just like a combustion engine. Also, there can be a bunch of mitochondria shoved into one cell. Your hard-working heart muscles right now are really jam-packed with mitochondria. So yes, mitochondria is the powerhouse of the cell. It is useful information to know if you're into breathing and being alive and stuff. Now, as long as we are gossiping about spiral structures, let's get into the heroic helix, shall we? Kiana Spinelli asks, I was told several times when I was younger that there were six plus feet of a DNA strand in just one cell.

Is this true or is that flimflam? Oh my gosh. So I don't know the exact answer to this, but I would not be surprised because DNA is supercoiled inside of your nucleus. I mean, it's, it doesn't just hang out in there like spaghetti. It's wrapped around itself. It's wrapped around things called histones and it's very tightly and neatly packaged inside of your nucleus. So I wouldn't be surprised if you stretched it all out that it did end up being six feet or six and a half feet. Okay. I was so curious. I had to double check this. And geneticist Dr. Barry Starr does confirm that it's about six feet or two meters of DNA strands inside each cell. And then he calculated that each human being has around 10 billion miles of DNA

in them, meaning that your DNA, your DNA right now, just as you're sitting here eating Pirates Booty or whatever, your DNA could stretch to the sun and back. 61 times. What? You beautiful freak. You just living, pooping work of magic. All of us. A few people asked about motor proteins. Penny wants to know, can you tell us about motor proteins? How the heck do they work? They carry cargo, basically, the cargo that are containing molecules, proteins, whatever. It could be anything. It could be carrying organelles.

They can carry different structures within the cell. They can move chromosomes. They're just, they're working hard, okay? They're working hard. And they move in particular ways. Think of this as a highway and one end of the highway is a negative side and the other side is positive. Dining walks towards the negative end

and they're carrying their cargo from the peripheral side of the cell to the center of the cell. And then Kinesin is like Dymine's sister. And they are walking in the opposite direction. So they, they're walking towards the positive side and they carry their cargo from the center of the cell to the periphery of the cell. So in order to move their little feet, they use ATP, which is the energy currency of the cell, which comes from the mitochondria. So now we've come full circle back to the mitochondria.

They're going so fast. John Sanson has a question about where did DNA even come from? Like how did random bits of atoms and molecules know to build themselves into proteins and then assemble into DNA strands, which now tell other things to build other DNA strands? This is something that I think about too much. And it freaks me out. My brain is melting.

That's a great... that's a question about the origin of life. Because all living organisms on Earth use DNA to generate their life process. And we don't necessarily know exactly how this all started. And this will be a question that we're, we are likely trying to answer for many, many years to come. But I love thinking about it because of all the possibilities. So for years, the hypothesis has been that DNA started with the simpler single strand RNA. But in the past decade or so, other scientists are just begging to differ and say that DNA, which kind of

has a trickier sugar molecule as well as that double helix shape, could have arisen at the same time. It's even possible that a hybrid RNA DNA molecule first arose and then split off into two forms. Who's to know? If you have a time machine, let us know. Now one thing we are sure about is that these replicated codes have been encased in cellular goo and structures for billions of years, billions with a B. Okay, a few people. Katrina Nugent, Adele, Mieson, Ville, Verve, en français, Davis Born, asked epigenetics, what's going on? How does it change DNA expression and pass it on to the next generation? Katrina asked, will my children have my same weird quirks and habits?

This is really interesting and something that I wish I spent more time on when I was on my genetics kick. But epigenetics, it's a part of molecular bio that's looking at heredity, but not heredity that's caused by actual alterations in DNA itself, right? The DNA has a code and that set of code, again, codes for proteins and protein products. But epigenetics, it's like they are changes on the DNA, like literally on it. But it's really cool. It's a different way of looking at heredity. So for a very, very quick primer on epigenetics, your DNA is a big old long code, kind of like a recipe or an ingredients list.

And that double helix is like a big old long scroll, just meters of it, right? In each cell. So how does a cell with all the instructions for all the other cells know to be a heart cell or a gromy one bristly mustache hair or line my guts? So certain genes are turned on or off by signals or gromy one bristly mustache hair or line my guts. So certain genes are turned on or off by signals

or even proteins according to the function of the cell. But the proteins can also turn on and off other expressions of the cell in response to environmental factors and then replicate from there. And that is called your epigenome. Now, speaking of hearts, many patrons wanted to know

what was closest to Ravens, and Katie, Matt Zaccato, Earl of Gremelkin, Kathleen Sacks, Ira Gray, and Ashley Emanuel all had favorite questions, essentially favorite type of cell or protein or organelle or nitrogenous base, just normal questions you'd ask really any celeb. George Powell wants to know, what's your favorite protein? You know what?

That's a really good question. I personally am fascinated by how people name proteins. There is a protein called the Pokemon protein. What? Yeah, there's a protein called Sonic hedgehog, which is actually a critical gene involved in human development. And there's a Nemo one, there's a Ken and Barbie protein. There's scramblease, which is an enzyme that scrambles phospholipids between the inside and the outside of the cell membrane.

There's picaturin protein. There's Spock 1 that's in zebrafish, and it causes the fish to develop pointy ears like Spock. No. Yeah. I mean, Earl of Grammlekin asked, do you have a favorite protein or protein name? And I had no idea why they asked about the name. Who gets to name these?

The scientists that discover them get to name them. Oh my gosh. A lot of animation fans, apparently. Yeah. Yeah. I mean, these are, they're really funny. And what about the thing you love the most about what you do? I truly love building community.

And I think that because I am who I am, I tend to build communities that are very diverse because I show a lot of different sides of myself that I feel like people from different walks of life and different backgrounds can relate to. And I try to be very transparent about who I am and what I'm interested in and what I'm passionate about so that people who even aren't in science can latch on to something about a scientist that they see and maybe be more willing to listen and learn about science because they do relate. And I also love bringing these communities together and conversations about important things and watching people in my community learn from each other and teach each other.

That's probably the best thing that I enjoy about what I do. So ask Smart Maven's very simple, shameless questions because you only live once and maybe your molecules may get rebuilt and refolded into proteins and become a frog. But why not learn while you're a person? So to follow or see Raven's videos or Ted Talk, you can head to her website, Simevan.com or find her on Instagram at Raven the Science Maven or on Twitter at Raven Simevan. Those links plus links to her YouTube and her videos will be up also at alleyward.com slash oligies slash molecular biology. You can follow me if you like on Instagram and Twitter.

I'm at alleyward with one L on both. We're also at ol like, on Instagram and Twitter. I'm at Alli Ward with 1L on both. We're also at Allergies on Twitter and Instagram. Also linked is alleyward.com slash smallergies, which has dozens more kids safe and shorter episodes that you can blaze through. And thank you Mercedes-Maitland of Maitland Audio and Jared Sleeper of Mind Jam Media for editing those, as well as Zeke Rodriguez-Thomas.

And since we like to keep things small around here, the rest of the credits are in the show notes. And at the end of the episode, I give you a piece of advice. And this piece of advice is if you're not sure what to read, ask your friends or ask your parents or elders what books they liked reading. There are books that I never would have picked up unless I had asked, hey, you guys like any books lately? And then I got really great recommendations for books that I ended up loving.

So sometimes you'll get out of your comfort zone a little bit and you'll read something and learn something that you never knew that you liked. So yeah, ask for opinions from other people. You don't have to take all of the opinions, but sometimes it's nice to jump into someone else's head and see what they like reading. Okay, until next time, Smologites, bye bye.