Nature's Incredible ROTATING MOTOR (It’s Electric!) - Smarter Every Day 300

Flagellar motor: A molecular motor found in bacteria and some other single-celled organisms, responsible for their locomotion. It's a complex structure that rotates, propelling the organism through its environment. Flagellum: The whip-like appendage of a bacterium or other single-celled organism that enables movement. It's driven by the flagellar motor. Proton: A positively charged subatomic particle found in the nucleus of an atom. In this context, a proton refers to a hydrogen ion (H+), which plays a crucial role in the flagellar motor's energy generation. Hydrogen ion: A positively charged hydrogen atom (H+), essentially a proton. The movement of hydrogen ions across a membrane provides the energy for the flagellar motor. Chemotaxis: The movement of an organism in response to a chemical stimulus. Bacteria use chemotaxis to move towards nutrients or away from harmful substances. Electrochemical gradient: A difference in electrical potential and chemical concentration across a membrane. This gradient provides the energy for many cellular processes, including the rotation of the flagellar motor. CHeY: A protein involved in bacterial chemotaxis. It acts as a signal transducer, triggering changes in the direction of flagellar rotation. MOT-AB: A protein complex within the bacterial flagellar motor that acts as an ion pump, facilitating the flow of protons and driving the motor's rotation. Cryo-electron microscopy: A microscopy technique used to visualize biological macromolecules at high resolution. Samples are flash-frozen in vitreous ice, and images are obtained using an electron beam. Angstrom: A unit of length equal to 0.1 nanometers (10⁻¹⁰ meters), often used to describe atomic-scale dimensions. Amino acid: The building blocks of proteins. The specific sequence of amino acids determines a protein's three-dimensional structure and function. Alpha helix: A common secondary structure in proteins, characterized by a coiled structure. Transformation (in genetics): The process by which genetic material (DNA) is transferred from one organism to another, often resulting in the recipient organism acquiring new traits. In this context, the instructions for building the flagellar motor are transferred into E. coli bacteria. Expression (in genetics): The process by which genetic information encoded in DNA is used to synthesize a functional protein. Purification: The process of separating and isolating a specific molecule (e.g., the flagellar motor) from a complex mixture. Pulse-width modulation: A control technique used to regulate the speed or position of a motor by varying the duration of power pulses. Type 3 secretion system: A protein complex found in some bacteria that acts like a molecular syringe, injecting proteins into other cells. It shares some structural similarities with the flagellar motor. Principal Investigator (PI): The lead scientist on a research project. 2D classification: A computational method used in cryo-electron microscopy to group similar images together, aiding in the reconstruction of a 3D model. 3D modeling: The process of creating a three-dimensional representation of a molecule or structure based on experimental data (e.g., cryo-EM images). Electron density: A measure of the electron distribution in a molecule, which provides information about its structure. This is used in cryo-EM to build 3D models. This segment provides a detailed analogy comparing the bacterial flagellar motor to a submarine's propeller, clarifying its location within the bacterial cell's double membrane and its function in locomotion. The discussion establishes the context for understanding the motor's mechanism and its role in bacterial movement. what we see here, the two membranes that are here, and there's proton filled in here. [D] did you say proton? [P] yeah, it's filled with protons, hydrogen ions in here. [D] oh, hydrogen ions. okay. [P] the hydrogen ions in here filled, and on the inside here, there's very little hydrogen ion. there's a it's a gradient. [D] forgive me. we have to go slow for me. when you say proton, you're meaning an atom that is lacking an electron? [P] yes, just a proton. it's a hydrogen ion. this is high concentration of protons in this region and low concentration of proton in the inside of the bacteria. now, protons, every time there's a gradient, for example, there's a dam, water is up there, and there's a lower, there's less water, there's a gradient, energy can be generated, or it could be used, that potential energy could be used to kinetic energy. [D] there's a potential difference of electrochemical force of some sort? [P] yes. that's the gradient that this motor uses to turn itself. what happens is, if you see here, this flagella, which is a propeller, is connected to a motor system. [d] how does it know when to turn the motor on? [P] there are sensors on the outside of the bacteria. once it knows that there's a threat or there's more energy near me, it senses that it gets a chemical signal, and there's a cascade of signals that go through. one of the protein well known for this is called chey, c-h-e and Y, capital Y, Qy. the moment it senses that I need to run away from this location or I want to go to a different location, that protein comes and binds to it, and it encourages the motor to turn in clockwise direction. [d] okay, so we need to talk about what you just said because you just created a coordinate system inside the bacteria. you put sensors on the outside of the bacteria. well, it already exists. okay, there are sensors on the outside of the bacteria. somehow the bacteria knows where a sensor is triggered and it knows how to trigger what motor on what side of the bacteria. [P] yes, and how to turn it. [d] and which direction to turn it? [P] which direction. so that particular protein it will make it go in clockwise. this is clockwise direction. when it is not attached to it, it will go in counterclockwise. the default motion is counterclockwise. when the motor turns counterclockwise-[D] you say counterclockwise from which direction? [P] from this direction. [d] from the outside. [P] from the outside, yeah. [d] the outside, okay. [P] yeah. so counterclockwise would be this. and when the motor is running in counterclockwise, the bacteria will swim forward. so it's just the board goes straight. [d] and that has to do with the shape of… if I were to design this, I would say that would have to do with the shape of the impeller. so the tail? [p] yes. the way the flagella is made, it's like a whip. so when it starts rotating, it thrusts, the force goes backwards and it moves it forward. now, you would think that it would also do the same thing when it's going in the opposite direction, right? [d] yeah. [P] now, what happens is when it's going in the counterclockwise, there are multiple flagellas on the bacteria body. all of them start forming a bundle, and multiple propellers form into one big propeller and pushes this straight and it goes boom, straight. now, when it has to sense it like there's a danger, I need to stop, I need to reanalyze my situation gradient, I need to test, I need my sensors on and test it again, it turns clockwise. when it does that, the bundle opens up. when they open up, it just pauses the whole bacteria and the bacteria starts stumbling all around. [D] starts floating, yeah. it no longer has a certain… there's got to be a word Latin in here, taxis. [P] yeah, chemotaxis. chemotaxis, yeah. exactly. we call this whole process of bacteria's mobility like chemotaxis. it's a chemical signal that allows the bacteria to taxis or move from one place to another. everything happens in milliseconds. there are some videos that show bacteria moving from one place to another, and it's just like crashing. it's a biased, random walk. researchers have This segment focuses on the high-resolution structure of the flagellar motor, revealing details previously unseen. The discussion of the MotAB component, its interaction with the FliG protein, and the mechanism for reversing direction provides a comprehensive understanding of the motor's engineering marvel. The personal connection of the researcher to his work adds a human element. got this motor that for the first time we can see an image down to the protein level. the question is, how do we get that image? how is prash able to see this motor and understand its component parts in a way we haven't been able to understand previously? to answer this question, Prash took me over to the imaging lab where they use a series of cryo-electron microscopes to look at the structures to understand how they work. he introduced me to Miriam and Scott, who were kind enough to show me around. so now we're with Scott and Miriam, and these are the imaging experts. am I saying that correctly? [s] sure. [M] yeah. [d] okay. yeah. does that work? [s] absolutely. so all of our sample goes onto a grid that's right here. it's a mesh work on there. [d] what's it made out of? [M] copper. [s] copper. so they can make it made out of a copper, gold. there's some other materials that we use for other various niche purposes. most of them are copper. [M] you have whatever sample you have that's in a buffer. it will get plunge frozen. you literally just drop it in, drop your sample into liquid ethane and just gets flash frozen. so your sample is in vitreous ice. [s] we're just making a network that can hold little tiny sheets of ice with protein trapped in it. [M] so that's what you start off with. and then after plunging, then we load it into that little... cartridge. [s] our middle room here is our glacius microscope. so we'll walk in and look at it. so this is the glacius. this is our screening microscope. [d] so this is like a quick look. [s] it's a quick look. we have a source at the top that transmits an electron beam all the way through the column, and we put our sample in the middle and a detector at the bottom. [d] so you're shooting through it? [s] we're shooting transmission. we are going all the way through that sample. [d] the process that the scientists use to get these images is incredible, and I'm going to take a crack at explaining it with a super sophisticated animation style. so behold, markers and paper. all right, so there's two types of bacteria at work here. you've got salmonella and e. coli. now, salmonella, that's where the flagellum motor is located. that's these little yellow things back here. so that's the flagellum, and that's the little motor. ecoli, a different bacteria, has a little factory in it that can make things if you tell it what to do. so so this process is called transformation. so basically, I just took that motor off, and I'm not going to put the motor itself into the factory in ecoli. I'm going to put the instructions of how to make the motor into ecoli. ecoli is not the only type of cell that has a little factory like this, but this is the one that the scientists chose to 3d print this particular motor. this is called transformation. this little factory goes to work, right? it makes a bunch of these little motors, and then you have a bacterial cell that has all these little protein structures in it. the act of creating this is called expression. we are now going to take all of these motors and do this process called purification. we're going to pop this and we're going to use this grid and we're going to basically dump all of the stuff that's been purified onto this grid array. we're going to flash freeze it. and then after that, we're going to use this really fancy 200 KVA microscope and we're going to go through and we're going to look at the grid. now, when we look at the grid, we're going to screen these. so this is like a course view of what we're doing. we're going to go through and we're going to say, hey, look, there's one right there. that's important. over here. oh, that's important. and then you're going to go all the way through this whole grid, look in and see which one has motors in it. how many motors does it have? it might be a lot. you're then going to move it over to the big microscope, the 300 KVA microscope. and that's where we're really going to take our close up images. so what they do is they zoom in, and then they're going to take 50 frames of each individual little motor. the reason they have to do that is because at this level, you're down at the Angstrom type level, like the atomic level. things shake a little bit down at that level. so you have to take 50 images in order to compile that together, you have to make sure you take out that dithering. so at that point, you then have an image of a structure. now, that structure at that point, it could be like this, it could be like this, it could be at any number of different aspects. and Prash is get the 3d model, it looks something like this. we can see all sides. now what we see is a low-resolution model. we try to collect all the good signals and remove all the bad signals and try to come up with a high-resolution structure. what you see here is an 8 Angstrom. from here, 8 Angstrom to 4 Angstrom, it took us about two weeks to get there, 2-3 weeks. [d] you're removing bad data to get to the high resolution. [P] get to the high resolution. [d] then once you get to the high resolution, then you actually start drawing and mapping the proteins. [p] yes, exactly. to get this map, we're trying to put the pieces in, the puzzle pieces in, and try to find what protein, what amino acid goes in which place. so since we know the sequence of the protein, we have the pieces. we just have to fit it in this electron density. [d] so we have these 2d images that we wrapped together using software into a 3d model. and at this point, we know it's made up of proteins, which are made up of amino acids. and so the question I had is, how do you know what chemical is where? and it's my understanding that biochemists are just smart, and they know that certain amino acids are shaped in certain ways, like physical shapes. so it's like a puzzle piece, and they just know what they look like. so they're like, oh, here's blobafil, or here's quadraline. I don't know these words, but they can physically put the puzzle pieces in on the computer, and they can figure out what the structure looks like, which is incredible. [p] so if you see this curve, there's a curve here. [d] the coil. [p] the coil, and that's alpha helix. this coil, now we know alpha helix, only certain amino acids make in a certain orientation or sequence would make that coil. so this prior information helps us trace this puzzle. so if you see now, we can fill these gaps with these proteins. [d] this is a shape a biochemist person would not be intimidated by this shape. [P] no, that's very common. it's commonly found in almost every protein. not every protein, but like 90%-[d] it's intimidating to me, hah looks like a bunch of squiggles. yeah, but this is normal. [P] this is normal. [d] this is easily interpretable data. [P] yes, it is. [d] did you map these by hand and then just turn the image on? is that what just happened? or did you tell the computer to find the shape? [p] no, we mapped this. our previous researchers have mapped this in the past. we use the information as like, oh, they have done part of this. let's use that and see if that fits in here. if it does, it's good. if not, we go in and do it by hand. [d] wow. [P] yeah, it can be doing one at a time. it can take weeks to months sometimes, depending on how big your protein is. [d] but you like it? [P] oh, yes. this is the best part. this is where we exists, and it's amazing. it's complex, and it reminds me of an electric motor, and I love it. I love this thing, and I think it's incredible. there are implications for the fact that something so complex exists and is so integral to the creation of human life. I mean, this is fascinating stuff. so it also opens up a huge debate. people say, well, how can something this complex come to be out of nothing? the logic goes like this.. if this motor system is composed of complex individual parts,, and all these parts work together to perform the overall function of rotating, then how did the individual parts come to be?? did it all have to happen at the same time?? or is there some evolutionary advantage to the cell for every intermediate stage of development? is 15% of this motor advantageous to the cell?? what function would 50% of the structure perform?? what were the steps these components took to assemble into such a complex molecular machine in the first place?? scientists are trying to figure this out, and I encourage you to read their papers. many seem to be focusing on the type 3 secretion system, which works like a hypodermic needle that a cell can use to inject other things.. this device looks similar, but it's quite different in its protein structure. the complexity and origin of the bacterial flagellar motor is a really interesting conundrum. as I was a younger man, and I would read things on the I would find people saying, hey, you got to believe all this over here. people say, hey, you got to believe all this over here. there's a big war going on. it's between science and faith. you're either in one camp or the other. get your flag and figure out where you're going to put your flag. and the more I have matured and started to not really care about defending where my flag is, the more I've been able to learn from people no matter where they are. I'm still working on this. there's a really interesting book that I'm reading. I can't speak for everything in the book. I'm not done with it. it's called where the conflict really lies. it talks about this interplay between science, religion, naturalism. it's very interesting. it goes more into the areas of philosophy, and I love it because it challenges me, and it's fantastic. so this is what I would encourage you. if you have your flag in a camp somewhere, I would encourage you to not defend a flag. I would encourage you to look at a flagellar motor and just think about it and think about how it is and what it be. it's a fantastic thing to think about. how did this get here? you have intelligence and you get to make up your mind. and I love that about consciousness. I love that about life. and so for me, the flagellar motor makes me happy. I feel joy. you know how when you go outside at night and you look up at the stars and you see all these stars and you feel small and you feel wonder, that's what this makes me feel like, even though it is small. I feel awe and reverence toward this thing. and as a Christian, this makes me want to thank God that it exists. I feel compelled with gratitude that this thing is so awesome. so that's just where I'm at. but what I would encourage you to do is just think critically. you have a brain. don't defend a flag. just think about how things are. and I hope you are very happy and experience the same joy I feel about this, no matter what you think about it. so anyway, enough about that.