The Science of Everything Podcast - Episode 117: Intracellular Protein Sorting

Episode Date: April 30, 2021

A discussion of the transportation and sorting of proteins within the eukaryotic cell, including an overview of the endomembrane system, the mechanisms of nuclear transport, transmembrane transport, and vesicular transport. I also consider the structure and functions of the endoplasmic reticulum, the Golgi apparatus, and lysosomes, and how they are joined together in a complex network of protein transportation and vesicular traffic. Recommended pre-listening is Episode 116: The Cell Membrane. If you enjoyed the podcast please consider supporting the show by making a PayPal donation or becoming a Patreon supporter. https://www.patreon.com/jamesfodor https://www.paypal.me/ScienceofEverything

you're listening to The Science of Everything podcast, episode 117, Intracellular Protein Sorting. I'm your host, James Fodor. So this episode continues on from the previous episode, 116, the cell membrane. And here we're talking about the cell membrane in the intracellular context. So specifically, that means we're going to be looking at the endermembrane system, the system of membranes inside the cell. And particularly, we're going to be looking at how proteins are sorted and sent to different parts of the enderm membrane system,

and different organelles within the cell and also sent outside of the cell. So we're going to be talking about nuclear transport, transport to mitochondria and chloroplasts, as well as organelles such as the endoplasmic reticulum, the gall gaparitis, and how transports vesicles work, moving proteins around different parts of the cell. Recommended pre-listening is, unsurprisingly, the previous episode, 116 on the cell membrane. And without further due then, let's get started and start talking about the endo membrane system. So the endomebrane system is composed of different membranes that are suspended in the cytoplasm within a eukaryotic cell. So remember that we've got a double lipid membrane surrounding the entire outside of the cell, and that's called the plasma membrane.

But the plasma membrane is not just sort of outside the cell. It's also inside the cell. Basically, the plasma membrane has bits that are dispersed throughout the interior of the cell, and that's called the endome membrane system. I mean, it's separate from the plasma membrane, but it's topologically continuous with it. explain what that means in a moment. So it's sort of the same but different, if you see what I mean. Now, these internal membrane, or this internal membrane system gives rise to a number of organelles within the eukaryotic cell. And we've talked about these in a previous episode, but just to go through them again, so there's the nucleus where the DNA is, and that's where, you know,

genes are transcribed and so forth. There's the endoplasmic reticulum, which surrounds the nucleus. The Golgi apparatus, which is sort of a stack of membrane. It's kind of like a stack of pancakes on the side, if you like, which are functionally related to the endoplasmic reticulum, but also distinct. Then there are lysosomes, vesicles, and endosomes, which are basically like little spheres or oblong membrane shapes that have different digestive and storage roles. And then, of course, there's a plasma membrane itself. In addition to that, there's also the mitochondria, which are the energy factories, and the chloroplasts, which are the photosynthesizing organelles in plants, certain other organisms as well. Now, what the endometrain system has in common is,

a, what I mentioned before, a topological relationship with the outside of the cell. So the way it works is that there are these membrane structures that are enclosed in different parts of the cell, and this includes the rough endoplasmic reticulum, the smooth endoplasmic reticulum, the gallicirac, lysos, and vesicles. And all of these enclosed areas are, in a sense, outside the cell. Or, as the saying goes, it's topologically equivalent to being outside the cell. So basically, the cell has these sort of enclosed areas that are, outside the cell. And the sense in which they're outside is that basically in order to go

from being, say, in a lysosome or being in the Gorgaparatus to being outside the cell, you don't have to actually cross any cell membrane. All you have to do is butt off in a vesicle, which is just like an enclosed sort of spherical region of membrane, and then the vesicle moves across the cytoplasm, and then it fuses with the external plasma membrane, and then the internal proteins that are resigned in that vesicle, then just sort of diffuse out into the extracellular fluid. there's no crossing of any plasma membrane that occurs there. And so in a sense, well, in a very real sense, the inside of these organelles is just outside the cell. It's just sort of an outside inside, if you like. It's kind of similar to the way in which the gastrointestinal tract right from the stomach through the anus, right from the mouth through to the anus, is basically outside of the body. I mean, it's located inside the body and that it's surrounded by the body, but you haven't actually crossed any membrane. if, say, the food is just swallowed and goes into the stomach, it hasn't actually really

entered the body yet, it's just contained within the body, and it needs to then, you know, cross the epithelium and be absorbed into the bloodstream or in the small intestine, or wherever that happens. That has to happen before the food or other material actually enters into the body proper. So it's similar like that with a cell. It's sort of got the outside, inside. And that's very useful for a lot of purposes, as we'll see in a moment. And it also means that these different membrane-enclosed organelles, which again includes the nuclear envelope, which is the membrane that surrounds the nucleus, the endoplasmic reticulum, the galloporitis,

as well as lysosomes, endosomes, and other vesicles. All of these are equivalent to each other in the sense that you don't need to cross a plasma membrane to get from one to the other. All you have to do is butt off from a vesicle, and then the vesicle moves along in the cytoplasm and then fuses with another membrane, and then, you know, the protein consonants

are dumped out into the inside of that structure. There are a number of structures that are not part of the end of membrane system. In particular, mitochondria, and chloroplasts are outside of that system. And the reason for that is because mitochondria and chloroplasts are actually surrounded by two sets of double membrane layers. So each membrane layer consists of a lipid bilayer, so two layers of lipids. But that's a single membrane, right? The mitochondria, as well as the chloroplasts, have two of those double layers that surround them. And the reason for

that is thought to be because of their evolutionary origins. It's thought that originally mitochondria and chloroplasts were free-living organisms, which then became endosymbiotic, so they started living inside of larger cells, and the over-evolutionary history, they became sort of dependent on those larger cells, and now, you know, we only find them inside eukaryotic cells. But originally they were free living, and so there was sort of their original outside membrane, and then there was the membrane of the host cell, if you like, that surrounded them. And so that's why they have now two membrane layers around them. And because of that, they are a separate system from the endomebrane system.

because the end of membrane, all other components, that there's only one lipid layer surrounding them, whereas the mitochondria and the chloropolisera 2. So they are not part of the same conveyor belt system as you like, where you can move things around between all those compartments with just a single vesicle budding off and then fusing with somewhere else. Also, it's important to understand that the nucleus is actually topologically contiguous with the cytosol,

so just the sort of the main fluid that forms the main part of the cell. It's a little bit confusing because the nucleus is an or, Morganel, and you do actually have to pass through particular pores, which we're talking about in a moment, to get from the cytosol into the nucleus. However, the nucleus is not a membrane-bound structure in the same way that, say, the endoplasmic particulum or the Golgapararotus, because you don't have to cross a membrane to get in there. Actually, what happens is essentially the proteins and RNA and other things that move in there, and out from the nucleus, have to squeeze between gaps in the surrounding double membrane structure in order to get into the

nucleus. So there's an envelope that surrounds nucleus, and that is the nuclear envelope, and that's a sort of a double-layered structure, and then the proteins and other things squeeze between gaps in that structure, which is where the nuclear pores are. So proteins and RNA and other substances that need to traffic into and out of the nucleus. They don't cross a membrane into the nucleus and then cross another one or anything. What happens is they just squeeze between gaps in the nuclear envelope. And so that means that the interior of the nucleus is actually equivalent to the cytosol. And that's important, because it means the inside of the nucleus is also not part of the endomebrane system.

The nuclear envelope is, which is sort of the membrane structure that surrounds the nucleus, but not the actual inside of the nucleus itself. Now, so far, we've mostly been talking about the endomebrane system, which is this system of, again, topologically equivalent membrane-bound structures inside the cytosol, so it's your endoplasmic, particiulum, Golgi apparatus, endosomes, lysosomes, and also out to the cell surface. And all of these organelles can connect with each other via viscars. secular transport because they're equivalent topologically, and so you don't have to cross the plasma

membrane to move from one to the other. You just vesicles butt off and then they move across the cytosol and then they fuse with the target membrane and then they dump out the content. So that's how that works for the endom membrane system. But I have mentioned that there are parts of the cell that are outside of the ender membrane system, specifically the nucleus, as well as the mitochondria and the chloroplasts. There are also small organelles called peroxosomes, which are outside the ender membrane system, although I'm not really going to talk about them very much, but they're involved in oxidative, you know, digestion of certain toxic chemicals and so forth. So how do proteins and other traffic get to these other organelles or other parts of the cell

that aren't accessible via the end of membrane system? Also, how do proteins get from the cytosol into the end of membrane system in the first place? Well, there are two other mechanisms, again, aside from vesicular transport that are used here. The first is called gaited transport, which is used to get access to the nucleus. And the second is called transmembrane transport, which is used to gain access to the mitochondria and chloroplasts, as well as into the endoplasmic reticulum in the first place. So what we're going to do for pretty much the entire rest of the episode here is we're going to look at each of these three mechanisms in more detail.

So again, we've been talking about the different organelles or parts of the cell and how they're related to each other topologically. We've established that there's an endomebrane system, which is sort of most of the organelles, and that uses vesicular transport, but you have to get into the enderm membrane system initially, and that uses a different mechanism called transmembrane trance. transport. That is also used to get to the mitochondria and chloroplast because they're outside the end

membrane system because they've got double membranes around them. Finally, you've got to get to the nucleus, which is its own can and worms because to get in there, you basically have to squeeze between gaps in the nuclear envelope. And that uses a different system, again, called gated transport. So there's three different types of mechanisms here associated with the different sort of regions of the cell. And we're going to go through those one at a time. In doing so, I'm going to be talking about some of the different mechanisms that are used and also some of the functions of these particular organelles. so why they exist basically. And there's a lot more detail here that I'm kind of going to skip over a bit because this is sort of an introduction or an overview, but hopefully you'll sort of get the broad ideas

that we're wanting to cover. So first let's talk about nuclear transport. How do proteins get into the nucleus? And also how does RNA get out of the nucleus? Because remember, genes are transcribed, converted from DNA to RNA in the nucleus. And that RNA then has to get out of the nucleus to be translated in the cytoplasm. That's when the RNA is converted from B, RNA to protein. That happens, that's done by ribosomes, which exist in the cytosol, in the cytoplasm. So basically, the RNA's got to get out of the nucleus to be translated into the cytosol. But proteins also have to get back into the nucleus, right? Because the nucleus needs proteins, it needs proteins in order to transcribe the DNA for a start,

and there's lots of other functions that have to be performed in the nucleus. Cell division, for example, requires that the chromatids be pulled apart, and there's proteins that are needed to keep the DNA bundled up correctly. There's lots of proteins that need to access the nucleus, do their stuff there. So they have to find a way of getting back from the cytosol, which is where they're translated, back into the nucleus. So the point is, there's a lot of traffic. A lot of stuff needs to get out of the nucleus, a lot of stuff needs to get into the nucleus, and this has to be happening regularly. So how does this happen when the nucleus is surrounded by this membrane system,

the nuclear envelope? Well, it happens by transport through what are called nuclear pores. A nuclear pore is a large complex of proteins, which is called a pore complex, that spans the envelope. And it kind of, they kind of exist between gaps within the membrane, double membrane system, if you like. So it's not quite the same as like an ion channel across the plasma membrane. It's sort of larger, but also it's structured quite differently. And there are about 1,000 of these nuclear pore complexes in the nuclear envelope of vertebrate cell. So, I mean, that's a lot, but it's actually not that many if you think of compared to, say, ion channels where there might be, well, a much, much larger number than that. So they're fairly large, and each needs to sort of allow for quite a lot of traffic

through it. Now, these pore complexes that consist of eight protein subunits arranged in kind of a circle, so it's like a symmetric relationship with the octahedral symmetry. And the basic mechanism here is that the proteins and also RNA, which needs to go out. So basically you've got RNA going out and proteins going in. And the basic mechanism is that the cell allows things to pass through the pores, but it does so in a controlled way. So it wants to make sure, they need to be mechanisms to ensure that only proteins and other things that need to come into the nucleus are imported, and then only the RNA and other things that need to be exported are allowed out. You don't want to just have any old thing coming in and going out,

because then you don't have control of what needs to go where. So how is that selectivity managed? Well, let's start by talking about proteins that need to be imported into the nucleus, and that takes place by way of what are called nuclear localization signals. And one of these signals is basically just a sequence in a proteins. So like a sequence of amino acids. Often it could be at the start of the protein, but it doesn't have to be. And these are fairly short sequences, you know, a few dozen nucleotide, a few dozen amino acids,

which basically say, hey, I, like this protein here, I need to go into the nucleus. So once that protein has been translated, so it's been, you know, converted from the RNA transcript, this nuclear localization sequence will, you know, float around essentially in the cytosol. And eventually it will find a molecule to buy. to that, the nuclear localization signal. And these molecules are called importans. So they're just, proteins essentially, bind to nuclear localization simple. So you've got your signal, which is attached to the cargo protein that used to go into the nucleus, and there's the important, which is like, oh, you know, I bind to that, and it binds to the signal, it binds to the nuclear

localization signal. This is effectively a way of tagging that protein for import into the nucleus. Similarly, there are export signals that tag proteins that need to be removed from the nucleus. So the basic idea here is that the cell has molecular mechanisms for tagging proteins that need to go into the nucleus and proteins that need to be exported from the nucleus. Now, what happens next is a little bit complicated and a bit hard to explain without a diagram. So I'm going to simplify it a little bit just to give you the basic idea. And the basic idea is this. There is another type of special molecule which is called RAN GTP. So the GTP just stands for, you know, guanine triphosphate.

So that's just basically an energy-rich molecule. And the RAN just is, that's just a particular protein. we don't need to worry about it too much. But the basic idea is what happens is that you've got your cargo protein with its nuclear localization symbol and it binds from importing, right? And together, that complex is able to move through the nuclear port and enter the nucleus, all well and good. Then what happens is when it arrives in the nucleus, the importin dissociates.

So it sort of, it basically lets off its cargo and the cargo protein goes into the nucleus and all as well. But then it picks up a cargo of ran GT. That then leads to the important molecule going back out of the nucleus again and going back into the cytoplasm, which then allows it to pick up another cargo of a protein to bring back in again. Now, this whole process requires energy. That's why there's RAND-GTP there. That's, as part of this process, is hydrolyzed to GDP, which is the two-phosphate version that has less energy, so it needs to have a continual input of energy for this to keep going. So that's not surprising in moving things around. selectively that's going to require energy. And again, I've simplified the process a bit here, but the basic point is that the way I think about it is you've got this kind of cargo ship, which is the important, that is constantly moving into and then back out of the nucleus and bringing the protein cargoes with it. But only ones, of course, that have the right signal saying, hey,

I'm going into the nucleus. But as it does so, it also moves back out cargoes of the RAN GTP, which kind of power it moving, the important moving back outside of the nucleus again. Now, I've talked about things moving into the nucleus, but there's basically the same process happens in reverse as well. There's a protein called Exportin, which does basically the same thing, except it starts from the nucleus. It picks up its cargo with nuclear export signals and then moves outside of the nucleus and drops it off, and then comes back in again. So there's this continual system of importance bringing in their cargo with the right signals to bring them into the nucleus, and then export in with their cargoes, taking them outside the nucleus. And this is all powered by the RAN-GTP protein with the triphosphates as an energy source. So that's the basic mechanism that is used to both transport proteins into the nucleus

and also transport mostly messenger RNA and other types of RNA outside into the cytoplasm where, of course, they're needed. And this has to be quite a regular, a large amount of traffic, because obviously there's different genes being transcribed and needing to have the RNA in the cell and then proteins that need to come from the outside inside and messengers and all sorts of things moving around. So this is a fairly regular traffic. So note that this involves proteins moving across a double membrane system because the endomebrane system surrounding the nucleus has as two membranes. It's sort of like a membrane sort of wound back on itself. But it doesn't cross the membrane

structure directly. They pass through, the proteins pass through basically pause that are stuck in gaps between the membrane system. So that's what makes it distinct from what we're going to talk about next, which is transmembrane transport. So gated transport is not transmembrane transport because it doesn't directly pass across the membrane. It basically sneaks through gaps between it. What I'm now going to talk about, moving from nuclear transport to transport to mitochondria and chloroplast, is transmembrane transport. So remember I mentioned that mitochondria and chloroplasts, as well as peroxosomes,

but I won't say anything more about those, both of these organelles are outside the enderm membrane system because they're surrounded by two membranes instead of just the one, which is the rest of the organelles in the enderm membrane system, and that comes about because they have endosimbiosis, there's basically the original membrane of the ancestor prokaryot-like organisms, and then the membrane surrounding that from the ancestor eukaryotic cell that gobble them up, so to speak. So vesicular traffic's not going to work here because vesicular traffic only works

if you've got two topologically equivalent compartments, so you can butt off a vesicle from one and then infuse to another. It doesn't work here because there's two membrane systems, so you wouldn't be able to get into the inside membrane, because you'd infuse with the other one, but then you're sort of stuck in between the two membrane, so it doesn't work. Also, nuclear transport is not going to work because these aren't the nucleus, and they don't have the same nuclear pores that exist for the nucleus. So there needs to be a different mechanism here.

And that mechanism, as I've said, is called trans membrane transport. So basically the proteins sneak directly across the membrane instead of passing through gaps between it. So how does this work? Well, first to understand why are things going to the mitochondria in the first place. And I'll just talk about mitochondria just for simplicity, but similar mechanisms operate in the chloroplast. So the mitochondria originally, it's thought, had all of the genocondria. genes necessary for its function, when it was a free-living sort of pro-carriot-type organism. But over a long time of evolution, it's lost most of the genetic material, and it only makes

about 13 proteins that are necessary for its function. The rest of the proteins that it needs are coded for by genes that have moved back to the nucleus with all of the other genes for the cell. That means that these proteins that are encoded by genes in the nucleus have to find some way of getting from the cytosol, which is where they're translated, just like other proteins, into the mitochondria. So how do that? that happened? Well, just like proteins that need to go into the nucleus, proteins that need to go into the mitochondria are tagged. So this is called a signal sequence. It's basically the same in concept as the nuclear localization signals, but these are just signals that direct the proteins to go,

say, to the mitochondria, or again, the chloroplast or wherever else. And again, often these can be at the in terminal, which means basically the very start of the protein, but they're not always located there. So again, what we have is a situation where the ribosomes are transatlomes are translating along and they're sort of starting out and then the protein starts to be extruded from the ribosome and then you know the signal sequence wherever it's located becomes exposed to the cytosol and what happens is that there are special proteins in the cytosol that are called chaperone proteins and these bind to the protein that's coming out of the ribosome and prevent it from folding up and this is important we'll see why in it in a moment so these chaperone proteins prevent the

protein from folding as it normally would as it comes out from the ribosome and also helped to deliver it to special receptors on the mitochondrial out of membrane surface. So so far, we've got the protein with the signal sequence. It's bound by special chaperone protein, specifically a main one is cytosolic heat shop protein, HSP 70, but don't worry about that. It's just special proteins that help it to stay unfolded, and the signal sequence then binds to special receptors on the surface of the outer layer of the mitochondria. and then what happens is that these receptors on the cell on the outer surface of the mitochondria

become associated with what's called a tom complex so the sort of key acronyms to remember here are tom and tim so you can remember this because tom stands for translocase of the outer membrane and tim stands for translocase of the inner membrane so there's a few different tims and they're just different protein complexes right but i'm just going to speak as if there's just one just for simplicity so the tom is on the outside membrane and the timers on the inside membrane, remembering that there's a double membrane system around the mitochondria. So you've got your protein with the signal sequence that associates with the receptor, and then that receptor in turn associates with the tom complex, and the protein then enters into the tom complex and begins to move into the intermembrane space,

the space between the outer and inner mitochondrial membranes. As that occurs, the imported protein then becomes associated with the Tim complex, which is in the membrane of the inner mitochondrial membrane, and the protein then begins to move into the matrix, which is inside the innermost space of the mitochondria inside the inner membrane. And as it emerges there, the signal sequence is generally the first to emerge, because that's usually at the end terminus, so the sort of head of the protein. That's snipped off, because the strobs done now. The protein's sort of entered where it needs to go. And then what happens is that special chaperone proteins, the mitochondrial Remember we talked about the cytosolic heat shock protein 70 that helped the protein to be targeted towards the mitochondria and helped to keep it unfolded in the cytosol. Well, there's the versions of those in the mitochondrial matrix, mitochondrial heat shock protein 70s. And these bind to the protein as it's coming through the Tim Complex and basically pull it along. So this is powered by ATP, which is hydrolycerase to ADP, so that acts as a source of energy. So more and more of these chaperone proteins are binding to the protein as it's coming in and pulling it in until,

it's all the way through the Tom complex, all the way through the Tim Complex, and then it's pulled all the way through, and then finally, it's entered into the mitochondrial matrix, where the Chaparone proteins can dissociate, and then the protein can fold up and achieve its sort of mature functional confirmation. So, hopefully you see why it's necessary to have these chaperone proteins in the cytosol and then in the mitochondria to keep the protein unfolded. The reason is because it has to sneak through, first, the Tom Complex, and then between the two membranes and the intermembrane space, and then through the Tim Complex. And these are fairly small channels that it has to pass through.

It wouldn't be able to move through as if it was all folded up as a protein does in its functional form. It would be too big and too clunky. It has to snake through basically these small pores, and so it has to stay unwound in order to do that. This isn't the case for the nuclear pores, because the nuclear pores are really big. They're fat, and so they can take proteins that are wound up, that are folded up. But when you're directly crossing a membrane in this way, it's necessary for the protein to be unfolded because it needs to snake through these sort of small channels through the membrane. So for that reason, the mechanism is very different and the imported proteins need to be kept

unfolded until they're finally in the inner matrix space. So just to recap that, basically, there are signal regions that tell the cell, hey, these proteins need to be imported into the mitochondria. So as soon as the proteins begin to emerge from the ribosome in the cytosol, special chaperone proteins bind to it. There's a receptor that binds to the signal sequence, which then in turn associates with receptors and the outer membrane of the mitochondria. The protein to be important into the mitochondria then passes through first a tom complex, which is basically a channel that allows the imported protein to pass into the intermembrane space in the mitochondria. Then the protein passes through the Tim Complex, which is the sort of channel to the internal space. So it's the channel

through the inner mitochondria membrane, and then it's pulled through both the Tim and ultimately the Tom Complex by the Chaparone proteins inside the matrix. It's pulled all the way through, signal, sequence is cleaved, and then it finally is out to fold up. So you basically sort of snake it through, and it's pulled through two different complex. You're Tom and the Tim through the outer, and then through the inner membrane. This is all I've been talking about in the context of mitochondria, but it's pretty similar in the case of chloroplasts, although there is an additional complication there because chloroplasts actually have a third level. It just keeps going, right? There's a, there's the outer, the inner membrane, and then finally there is, there are the phylocord membrane,

which is another internal stack of membranes, which is where the photosynthesis takes place. So there's another signal that needs to tell that, hey, I've gone through the outer membrane, I've gone through the inner membrane, and now finally, I actually need to move into the phylocoid, and so it has to move through there again. So there's a whole other sequence that has to get it in there, but I'm not going to go through the details of that now. So the point there is that hopefully I've illustrated the basic process there. It's quite different to the nuclear pore case because, as I've said, the protein can't just move through in a folded up form. It needs to snake its way through, not across one, but actually across two different membranes using the Tom and the Tim Complex

and the Chaparine proteins to help it. So that's how proteins get into mitochondria and into chloroplasts. Now let's finally turn to the endomebrane system, which I started off talking about, but we haven't come back to it so far. So I've talked about how proteins get into the nucleus. They pass between gaps in the nuclear envelope, which are controlled by nuclear pores. We've talked about how proteins get into the mitochondria and in chloroplasts because they are able to snake through these channels that cross the double membrane system. Now I'm going to talk about how proteins first get into the endomebrane system, which is sort of everything else in the cell, and then how they move through the endometriac system, because it's like a conveyor belt. There's many different phases

of it and the different organelles do different things as you go from the endoplasmic particulum to the galliciratis, endosomes and lysos and so forth. So how do proteins get into the endomebrane system in the first place. You might think, well, aren't they sort of made there? Well, they sort of are, but the important thing to understand is to take everything back to the beginning. Proteins are translated by ribosomes from MRNA templates that are exported from the nucleus into the cytosol and which where the ribosomes are, and the ribosomes then translate them. And so the proteins are made in the cytosol. That's why they then have to be exported into the nucleus or into the mitochondria or in this case into the endoplasmic reticulum, which is where the

sort of endo membrane structure sort of begins, if you like. However, there's a little catch here because the endoplasmic reticulum is divided into sort of two bits, if you like, the rough endoplasmic reticulum and the smooth endoplasmic reticulum. And there's an important difference between them. The rough endoplasmic reticulum is called rough because it kind of looks sort of bumpy or spiky if you look at it through the microscope. But the reason it looks like that is because it has ribosomes studded all across its surface, very large numbers of them. So what's the deal here? Aren't the ribosomes sort of hanging around in the cytosol, just merrily translating proteins wherever they are.

Well, yes, there are lots of ribosomal ribosomes that just are translating wherever in the cytosol. But it turns out that certain classes of proteins, they begin translation in the cytosol, just like any other protein, but they contain signals. Remember, we keep talking about these signal peptides? Well, they're coming back again. Some proteins contain signal peptides, not to take them to the mitochondria, but actually to say, hey, I need to go into the endoplasmic reticulum. them. When that happens, again, often these signal sequences are at the end terminus, so the very

start of the protein, but not always. They can be in the middle. They can be in different places, but let's say that they're at start just to simplify things. If these signal sequences are at the very start of the protein, what happens is the ribosome starts translating them, and then once that signal sequence has been translated and pokes out into the cytosol, special recognition particles called signal recognition particles, then bind to the signal sequences, and in turn, these signal recognition particles, bound to the growing protein, then bind to signal recognition particle receptors on the ER membrane. So it's very similar in the overall logic of it to how proteins are imported into nucleus, where you have the nuclear localization signals, which then bind to the

import in, which then takes the protein across the nuclear port into the membrane, and then the special signal sequence is cleaved off. It's pretty much the same thing here. You've got the ER signal sequence, which binds to the signal recognition particles, which then move to the surface of the endoplasmic reticulum, the rough endoplasmic reticulum, and then bind to a receptor for the signal recognition particle on the ER surface. That in turn leads to the growing polypeptide chain being inserted into special channels inside the ER-Lumin. So, well, these channels, I should say, they cross from the cytosol into the E.R. Lumen. That's just the inside of the end of plasma reticulum.

And the growing polypeptide then begins to be extruded into the inside of the E.R. So basically what happens is it starts being translated in the cytosol, but then once the signal sequence, the E.R. signal sequence emerges, it's like, oh, hang on, this needs to go into the endoplasoparticulum. So the signal recognition particle notices that, brings it over to the ER, and once that's recognized, the growing polypeptide chains inserted into the channels, which allow it to be then extruded into the ER loomint. And as typically happens, as that's occurring, the signal sequence is chopped off, because again, its job is finished and it doesn't need to be there anymore. So that's the basic idea. There's a signal, a single sequence that's recognized by proteins, which then carries it over, and the protein is then extruded.

and it's finished being translated so that it's extruded and released into the ER lumen. So it starts in the cytosol, but ends up in the ER. So unlike in the mitochondria, where it's translated fully and then it moves into, and crosses the membranes into the mitochondrial matrix here, the protein is only begins to be translated in cytosol, and then it finishes being translated into the ER limit, even though the ribosome itself stays in the cytosol. So that's why these ribosomes associate with the outer surface of the ER, because they're translating proteins that need to end up in the ER-Lumen. So that's why you have the rough ER, whereas the endoplasm

reticulum with all of these bound ribosomes associated with it. Once the protein's been translated, those ribosomes drops are done, and so typically they dissociate back into the cytosol. They don't stick around. So they're not permanently affixed there, for the most part, they're transiently located there when they're actually translating a protein. Now, there is a smooth endoplasmate reticulum that lacks these ribosomes. Its main function is in lipid synthesis, so it makes lipids that are necessary for the plasma membrane and also for the ender membrane and other systems that require lipids inside the cell. It also makes steroid hormones, which obviously are related because they're lipids as well, and it involved in some sort of detoxification process. So hepatocytes, which are liver cells,

have very large, smooth endoplasmic reticular because that's where the enzymes reside that are necessary for detoxifying the blood, for example. So although we're talking mostly here about the rough endoplasmate reticulum, the smooth endoplasmium is also quite important. Now, what I've described so far is the process of bringing proteins from outside in the cytosol into the endoplasm reticulum. And this process is called co-translational translocation because it occurs while the proteins are being translated, not they're translated and then they're moved in like in the mitochondria. So it's quite different there. But it's more complicated than that because there also needs to be a way of getting transmembane proteins into the end of placenticulum. And basically what this means is that, remember, we talk.

in the previous episode about transmembrane proteins that span the membrane of the plasma membrane, you know, the outside of the cell. There's lots of proteins that extend on either side of that membrane, and they have to get there somehow. You might think, well, aren't they just produced in the cytosol and then sort of stuck in there? For the most part, no. For the most part, actually, the way it works is that these proteins, they begin to be translated, as all proteins begin to be translated in the cytosol, but then because they have their, again, their ER signal sequences, those are recognized by the appropriate proteins, which then move them across to the ER, the surface of the enderplacer reticulum, and then they're inserted into the translocation channel

and so forth. So that all happens normally. But then what happens is that there's actually an additional signal sequence that's a stop sequence. So the way it works is that the signal sequence says, hey, stick me into the ER Lumen and start basically funneling me into the ER Lumen, kind of like poking spaghetti through a hole, if you like, except the spaghetti's being formed as you're poking it through because the protein's being translated. However, unlike in the previous case where the whole protein is just pushed all the way through the hole, and then the signal sequence is clipped, and then it is released and enters the Ileum. In this case, there's a stop sequence.

So at some point of poking the spaghetti through the hole, there's a sequence that when it enters, or when it sort of reaches the channel, says, oh, time to stop. And so what happens is then the protein disassociates from the translation channel. And this stop sequence will have to be hydrophobic because it needs to exist inside the, the plasma membrane, so obviously there has to be a way to hold it there. It won't be stable if it's hydrophilic. So this always needs to be a hydrophobic region to be stable within the membrane. Now, at this point, the fact that there's a stop signal, it doesn't mean that the protein's done. It will continue to be translated. So the noodle keeps growing, if you like,

but it just keeps growing in the cytosol. It doesn't keep being pushed into the E.Lumin, because it's being fixed in place at the location of the stop sequence. So depending on the location of the initial start, you know, signal transfer sequence as well as the final sort of stop transfer sequence, you can have any combination of how much of the protein is in the cytosol and how much in the ER. You can have most of it in the ER, most of it in the cytosol, or some combination of those. You can have transmembrane protein sort of wherever you like. Indeed, you can actually through having more than one start and stop sequence, have multiple transmembrane regions that cross the membrane multiple times. So all you have to do to have that is,

multiple start and stop regions. So it's sort of threaded, the protein is threaded across the membrane multiple times. And there are many important proteins that have this form. So G-protein couple of receptors, for example, are a very common type of protein that have, I believe it's seven transmembrane helix regions. And we'll talk more about those in a future episode when we do cell signaling. But the point is that there are lots and lots of proteins that have this multiple transmembrane region, and that just comes about through these multiple start and stop regions where it basically like threads it through, and then tells it to stop, and then tells it to throw it through again, tells it to stop, so that the protein can sort of loop in and out across the membrane.

And so there'll be bits that are inside the E.Lumet and bits that are outside in the cytosol. Now, many of these need to end up on the outside of the cell, but the beauty of this system is that the proteins can be produced and sort of organized and fixed up entirely within the cell. You've got part of the er lumen, part of it in the cytosol, but that's all still in the cell. And then, through vesicle budding and fusion, which we'll talk about in a moment, because the end of membrane system is all topologically equivalent, you can just move that whole unit to the outside of the cell and basically put the proteins on the outside surface of the cell without having to move them through another or across another membrane. As you might imagine, that's going to be a bit of a nightmare when the whole thing is studded inside a membrane. How do you move like a bit of the membrane through a membrane? doesn't really make sense. No, instead, you just move the whole membrane and fuse it with the outer surface of the cell.

So this is a really elegant system that the cell has for basically sticking the proteins in the membrane and then just moving the membrane through in little pieces called vesicles, right, through the different interior organelles and eventually out to the outer surface of the cell, where it just sits and does, and the proteins then go and do their work. Okay, but apart from the fact that, okay, sure, there are some proteins that need to be stuck into the membrane, which then eventually move to the outside of the cell on the outer cell membrane, what other functions does the endoplasm reticulum form, specifically the rough endoplasmic reticulum that has all of these ribosomes studded on it?

I mean, what does it do? Why does some proteins need to be put in there, apart from the self-service ones? Well, many of the proteins that need to eventually go to organelles endomebrane system, including the endoplasm itself, as well as the Golgi apparatus and lysosomes, and any proteins that need to be excreted from the cell. eventually, most of those proteins are directed into the endoplasm of reticulum, because again, it's just an easy way to get them to those locations. Otherwise, they would have to cross a membrane directly, just like the proteins do

that are directed to the mitochondria, and that's quite difficult to do. So instead of doing it that way, the cell just sticks everything that needs to go there into the endoplasm particular particular particular reticulum, basically on the conveyor belt, and then they'll just naturally be moved through vesicle budding and fusion, which we'll get to in a moment. So it's this very convenient system where you just sort of stick everything in the ER and then give them signal sequences obviously that tells the ER where it needs to go, and then they'll eventually find their way to where they need to go

in a sort of straightforward way that doesn't require lots of additional receptors. So that's why they're all put in there. But the ER isn't just a place where you put proteins that that sorts proteins out where they need to go. I mean, it does do that, but it also has a more active role. It is also involved in assisting protein folding. Protein folding is a very complicated process that involves the protein going from its initial sort of straight linear configuration,

which is how it is originally translated into a very complicated folded up form, which is then going to be active and allows it to do its functions. This typically doesn't happen spontaneously for a lot of proteins in eukaryotes. In fact, it requires help from other proteins that are called chaperone proteins. We already mentioned those when we talked about the proteins that are imported into the mitochondria. In fact, those proteins actually stopped it from folding up because it needs to be, you know, kept in the spaghetti form in order to enter, you know, remember through the Tom and the Tim channels in order to get in the matrix.

But in this case, proteins, once they're inside the rough endoplasic reticulum, do need to fold up. And so there is a huge variety of families of chaperone proteins that help with this. I won't talk through them all here. It won't really mean much anyway. But there's lots and lots of proteins that help with folding up of the proteins as they're produced and dumped out inside the endoplasum particulum. Only properly folded up proteins are transported from the ruffeer to the Golkia apparatus, which is sort of next in line along the conveyor belt. Unfolded proteins cause an unfolded protein response as a strong.

stress response in the endoplasm reticulum. So basically, if there's a buildup of unfolded proteins, this triggers a signal which is sent back to the nucleus and tells that, hey, we need help here. And basically what happens is that more of the chaperone proteins are produced to help clear out the backlog of unfolded proteins. So there's an elaborate mechanism here of dealing with proteins that don't fold up properly. Another very important thing that the endoplasum reticulum does is it engages in protein glycosylation. Glycosolation is a process in which a carbohydrate is covalently attached to, in this case, a protein, although it can also be lipids. Most proteins in the end inplacet in particular are glycosylated by adding fairly large

oligocaccharide chains to asparagine side chain. So there's a particular amino acid asparagine. Remember there's 20 different ones, so this one isparagine. The side chains of these asparogens, I don't know really why it's asparogens, but those are the amino acid side chains where the oligosaccharides, so the big sugar chains essentially are added to. They're not added to every one, and it differs a bit between different proteins, but most proteins will have some sort of glycostallation occurring. This modification serves a number of functions.

In particular, some proteins won't fold properly unless they're glycosylated. Also, other proteins are not stable unless they contain those oligocorides. So the oligosacrides seem to help with protein folding instability, and they're added on to all of the proteins or most of the proteins that find their way into the endoplasin particulate. As I mentioned, these sugar chains that are added help the endoplasted reticulum to recognize misfolded proteins. And basically the way this works, although it's quite complicated, but just to give you the idea, is that these oligosaccharides, these big sugar units are added to the protein in particular places. And if the protein, if chaperone proteins within the endoplasted particulum don't find these sugar units where they're expecting them to, then they know that the protein hasn't folded up properly, and therefore the sugar units haven't been added. and then it's like, well, okay, we've got to unfold it or we've got to try it again. We've got to unfold this bit and then add the sugar back on.

So it basically allows the shrapron proteins within the end of the placer reticulum to know whether the protein in question has folded up correctly or not. So it seems that the sugars that add play a critical role there. If, however, despite the cell's best efforts, the misfolded proteins can't be corrected, they can't get them to fold correctly. What happens is that they're tagged, exported from, the endoplasted particulum, and then degraded by a special system called the proteosome system, which is a big complicated end.

It's basically like a tube that just kind of, I think it's like a grinder. The misfolder protein goes in and it gets churned up and broken down into its pieces, which are then recycled. So that's back in the cytosol. So anything that doesn't make the cut after, you know, it's like, I guess, students at university, like they get a few tries and they try to help, give it a remedial plan. Then if it doesn't work, they're expelled because, well, insufficient academic performance or whatever. however you want to call it, they're exported through special channels and then broken up in the size of like, I guess their university metaphor doesn't really work there because we don't want to

grade our students. But anyway, so the point is that there are complex mechanisms involving adding protein chains and many chaperone proteins within the ER that help proteins to fold up correctly and give them a few sort of goes. But if it doesn't work, then they're eventually exported and degraded. For those proteins that do correctly fold with the chaperones and all the the oligrosaccharides that have been added and so forth. And again, this also includes proteins that are just floating around within the lumen and also those that are studded in the membrane. So talking about sort of both cases there, trans membrane proteins and proteins just within

the lumen. As long as they're folded up correctly, then they'll be moved along to the Golgi apparatus, which is the next in the sort of conveyor belt of the end of membrane system. But it's at this point that we need to talk about transport vesicles, which I mentioned a number of times, but haven't really explained in detail. And the reason that we need to talk about them here is because so far, the mechanisms of transport that we've discussed have not involved vesicles. But at this point, moving from the rough ear into the gold gear apparatus, this is where vesicles

first appear. And as I mentioned, vesicular transport is the main mechanism of transport from different regions of the end of membrane system. So this is the first place where we're seeing that. You need to have special mechanisms to get the proteins into the EI in the first place, which are the signal recognition sequences and the translocation channels and all that that we talked about. But that's to get in the first place. Now to move along, you know, different passing the conveyor belt, that's when we're going to use the vesicular trafficking. So a vesicle is a structure inside or sometimes outside the cell that consists of a lipid bilayer that surrounds some sort of internal space. So often there'll be proteins or some other

substances that are, they're sort of sitting around inside the bubble there. So I think of a vesicle as a bubble, basically, a bubble surrounded by a bilipid membrane and then containing stuff. In this case, it's generally going to be proteins. It could be ions or, I mean, it could be all sorts of things, but here it's generally going to be protein, you know, protein goods effectively that need to be moved around. Now, many vesicles are surrounded by coats, which is a collection of proteins that help to give it shape to basically curve the membrane. Membranes will spontaneously curve, but often they need sort of help to bud off, and the coat of the vesicle are special types of proteins that surround it and sort of bend it and prepare it for budding. Budding is the process where

basically a bit of the membrane is pinched off to form a little sort of spherical unit, that is a vesicle, which then can float through the cytosol and fuse with another membrane. That's how vesicular trafficking works. Now, this budding off process requires these special coat proteins, which again help the budding occur, because they're not just going to butt off spontaneously, they'll need, they need to be pinched, and the proteins do the pinching. So there are three different types of vesicle coats called Clathrin, Cop 1, and Cop 2. I don't know why they're called that.

There's probably something you can look up, but for our purposes, it doesn't really matter very much. And I'm not really going to talk that much about them. I just mention them because you'll see them if you sort of look into materials here. And they're relevant because they're used in different places. So COP2 or COP2 are the special proteins that, again, pinch out the vesicles from the end of plastic plastic particulum to the Golgi apparatus. COP1 or COP1 protein, vesicular coat proteins are those. that are used to move vesicles back the other way from the Golgi apparatus back to the endoplasmium. And finally, Clathrin is used to move between other components of the endermbrane system,

so including the plasma membrane endosomes, Golgi to secretary vesicles and so forth. So they're used in different parts of the end of membrane system. But hitherto, I'm not really going to worry too much about the distinction between them. You know, they're different proteins and they have their own specific functions. But the basic idea is that they just form a little cage surrounding the membrane that will form the vesicle, which helps to pinch it off and then pull it into a distinct unit. There's also another protein which is called dynamin. So you can think of the clathrid coat as kind of like forming a cage, which buds the membrane together. And then dynamin is like a noose that

pulls around the little neck that's left and pinches it off so that the vesicle is detached from the source membrane. And then it floats through the cytosol and eventually reaches its target membrane where it fuses with it. So that's the basic idea of how vesicular transport works. Now, I mentioned that these vesicles are sort of just floating around the cytosol, but they're not actually just sort of floating through it typically. They're actually guided by the cytoskeleton. So they're actually pulled along by special proteins that sort of walk along the cytoskeleton, which is a network of tubes that connect different parts of the cell and give it structure. And I'll talk about that. The cytoskeleton is a whole interesting other

topic for another episode. So I'm not going to go into details of that here. But they're actually These vesicles actually pulled along by special proteins that kind of literally walk along the cytoskeleton and pull its cargo of vesicles with it until it reaches the required spot. So it's more complicated than this, but I'm just going to talk about it as if they float through the cytosol, just again for a bit of simplicity here. So I've talked a bit about how vesicles barred off. It's basically these clathrin and similar coding proteins that surround it, pinch it forward, and then diamond sort of ties the noose off, and then it pinches off, the coding dissociates,

and then the vesicle floats through and goes to where it needs to. but how does the vesicle dock on the other end? How does it deliver its cargo to where it needs to? Well, the whole process kind of happens in reverse. Basically, there's special proteins called RAB proteins, which associate with what are called tethering proteins. So again, as usual, there's kind of a signal and a receptor for that signal. So the tethering proteins are found on the target membrane.

Rab are found on the vesicle. So rab associates with the tethering proteins. That's basically saying, oh, you know, this is where we need to go, this is where we need to be. we found our target. Then in order to sort of bring the vesicle very close to the target membrane, because they have to be very close to each other in order to fuse, you've got to expel whatever water exists between them. So that requires basically special mechanisms to kind of pull them very close. And there are special proteins called snare proteins. And you can think of them as kind of like, you know, those, I'm not exactly how to just, those like metal twisting things that you have on bread or

whatever, you twist them around and they sort of form a tight, tight seal. So you can, you know, you can use them for tying bread or, like, combining wires together or something like that. I don't quite know what they're called. But anyway, it's kind of like that. These proteins, the sneer proteins are basically, they kind of twist around each other. So there's one of the sneer proteins on the vesicle and then one on the target membrane. And when they get close enough to each other, they twist around each other to form a kind of a tight seal between the membranes of the vesicle and the target membrane, wherever it is, and thereby allowing the membranes to come into contact, and then when they do, they'll fuse together, because remember the previous episode,

we talked about the lipid biolayer, the lipid molecules all sort of move freely between, sort of laterally across the membrane, and so once the lipids are in direct contact with each other, they'll fuse together naturally, so you just have to bring them really close to each other, and that's what the snare proteins are for. And then the proteins will fuse, and now there's no barrier between the inside of the vesicle and the wherever the target membrane is. So the cargo protein would just naturally diffuse into wherever it's going. So again, basically, it's the signal proteins called rab on the outside surface of the vesicle, which find their way and bind to a tethering protein.

That then pulls in the vesicle, allowing the snare proteins, one on the vesicle and one on the target membrane, to sort of wind up with each other, pulling the vesicle very close together and forming a tight seal which then allows it to join up and fuse with the target membrane and dump out its cargo. So that's how the delivery mechanism works for vesicle, vesicular transport. I should say there are some other mechanisms of vesicular delivery that don't require full fusion, so there's a mechanism called kiss and run, where the vesicle basically just comes close enough to sort of just touch the target membrane, dumps out its cargo and then sort of runs off again without a full fusion, where it sort of joins into and becomes part of the target membrane.

But I'm not going to focus on that too much here. I think that's less well understood than the full fusion mechanism. And we only need to get a general idea of how this fusion transport works. So I've talked about some of the mechanisms of fusion transport, but just sort of coming back to how it relates the endoplasent reticulum to the gallge apparatus, which is the next end of membrane system. Well, the basic idea is that what you've got is you've got these vesicles that are constantly budding off from the ER and traveling to the Golgi apparatus

and delivering folded up and kind of almost ready to go proteins into the Golgaardis. There's also reverse traffic, so there's stuff that's going from the Gorgia apparatus back to the interplacetulum. Let's now then talk about the Gorgi apparatus. The Gogi apparatus is a series of compartments that are kind of like, as I said, a layer of pancakes stacked against each other. That's a bit different from the interplacent reticulum. And an important difference is that the Gorgi apparatus is highly structured.

So unlike the interplacet reticulum, where there's not a particular, like, forward and backwards part of it. It just, it's kind of one thing. The Golgi, the stack of Golgi compartments are separated from each other so that you can't just move straight from one stack to another one. The only way to get there is by budding off in a vesicle and then the vesicle moves to the next one and then it fuses with it. That's different from the end of the plasma particulum, which is all interconnected. Also, the Golgi apparatus is highly structured. So there's a cis Golgi network, which is the closest, basically, stack to the endoplasmic reticulum and a trans-Golgi network, which is the furthest away. And then there's various intermediate, medial stages in between. And each of these

kind of layers, if you like, in the Golgapritis, has its own distinct function. So they have a unique set of enzymes that are used for carrying out particular purposes. And the membrane structure is different. So they're structurally and functionally distinct from each other, unlike the different parts of the rough end of pipes in particular, which are all kind of similar to each other, just in a different place. Not so with the Golguaparitis. It's all highly structured in a kind of a linear way,

the cis, the medial, and the trans parts to it, and there's multiple layers. And each of them connects to each other via these, not directly, but indirectly, via these vesicles that butt off and then fuse with the next bit. But I've talked about it as if it's a conveyor belt, but it's actually multiple conveyor belts, because the vesicles are going both forwards and backwards.

The vesicles are carrying proteins forward from cis to trans and eventually onto secretary granules and other vesicles that will fuse with the outer cell membrane. That's in the forward direction. But there are also vesicles carrying proteins in the backward direction, which is from trans to the cisgoge and ultimately back to the rough endoplasm reticulum. So there's traffic in both directions occurring through this vesicular budding and transportation. Now I mentioned that each of these stacks has its own set of enzymes, its own structure, its own functions. They're all carrying out different specified reactions, but you might ask, well,

what are they doing? I mean, the endoplasm particulum's already been busy sorting out proteins and modifying them through glycosylation and other stuff like that, helping them fold up. What is the Goli-Ci apparatus doing that the endoplasiculum hasn't already done? Well, in a sense, it's more of the same. So the Gull-K apparatus doesn't help with protein folding. That's already sorted out in the endoplasiculum. Remember, unfolded or improperly folded proteins don't leave the endoplasiculum. They're sorted out there. However, the Golgi apparatus is very important with glycosylation. Remember, that's adding of the oligosaccharise, the sort of sugar molecules on the surface or the outside of the proteins.

So the Golgapiritis is highly involved in that as well, editing what the endoplasted reticulum is done and then adding more oligocerides on. So there's a lot more sugar processing that happens there. Again, we don't fully understand the purpose of all of these oligosacrides that are added, although it appears that they do perform particularly important functions, especially on the outside of the cell for transmembrane proteins, these oligocachyzed seem to play an important role in basically just sort of protecting the outside of the cell. I think I mentioned this in the previous episode, just sort of keeping things at a distance.

So they also limit the degree to which proteins are chomped down or digested by proteolytic enzymes inside the cell. So those are two purposes that they said, but there's probably others as well. So a lot of what's happening in the different compartments, the different layers in the cell, stack of the Golgi apparatus is just different enzymes performing different glycosylation functions. I won't go through all those because they're kind of complicated,

but just think that there's sort of different things happening in each of the stacks, and they have their own set of enzymes and associated lipid structure for that. Now, one other thing I want to say about the Golgi apparatus is that I've been talking as if the only way to get from one layer in the stack, transmedial, and sis and so forth, to the next one is via vesicle budding off and transportation. And that absolutely does occur. However, it's also thought that the entire gold gapiritis is dynamic. So it's not just static and each of the layers sits there. What actually is thought to happen is that you start off with the cyst layer,

and that whole stack eventually matures and moves up and becomes the medial layer. And then that whole stack eventually matures and moves on to becomes the trans layer and so forth, and it keeps going to the very end. So it's kind of like, you know, cohorts of people. They gradually get older and they get promoted and they move up the organization. It's not like that there's a set of people that are like always, you know, new, entry, always in middle management or whatever. It's different cohorts that mature and move along.

At the same time, you've got vesicles moving back and forward between each of these different layers. So it's a very dynamic process where you have the whole stacks that are maturing and moving on, as well as vesicles budding and moving off backwards and forwards between them, as well as, of course, vesicles moving backwards and forwards between the end of placement reticulum and the Gog apparatus itself. Now, there is a directionality to this. The directionality is basically overall, the directionality is forwards from the endoplasm

reticulum towards the cis, medial trans, and then out towards the further, more peripheral parts of the endosome system, more peripheral parts of the endosome system, which are lysosomes, endosomes, and eventually the salt surface, which I'll talk about in a moment. So there is a directionality to it, but there's a lot of movement forwards and back. backwards in both directions. Having discussed the end of the particiolum and having discussed the gallge apparatus now, I'm going to conclude by talking a bit about lysosomes and vacuoles. So once the proteins have moved from the enderplasia reticulum all the way through the gallge apparatus, they're then transported to the next stage in the end of membrane system.

And that differs depending on the final destination of the proteins, but in some cases it's going to be to lysosomes. Lysosomes are membrane-bound organelles contained in many animal cells, and they're basically spherical, so they kind of look like vesicles, but unlike vesicles, they're not just sort of temporary structures that are used to move things. They have a very important function in breaking down many types of biomolecules. So they contain hydrolytic enzymes. And lysosomes enzymes are designed to function in fairly low pH, so four and a half to five pH is optimal for these enzymes.

So it's kind of like the stomach and that is an acidic for the enzymes to function properly. And there are many different types of lysosomes, and they all have different compositions specialized for different enzymes for metabolizing different compounds. And so lysosomes are very important for metabolizing different things. So this would include things that have been netinocytosed, perhaps toxins or pathogens, or parts of the cell like mitochondria that aren't needed anymore that need to be broken down. So many of those things can be transported into lysosomes and then broken down. Of course, you need enzymes there to do that. And so many of the enzymes that are produced in the endoplasm reticulum and then moved through the gallagoprides, eventually need to be put into lysosomes so that those lysos are ready to break down whatever they need to, to basically metabolize those bonds and break down the biomolecules into the smaller components. So that's one example of a sort of a final destination, if you like, of proteins through the endem membrane system.

There are others, other proteins that go to secretary vesicles. So they're exported out to the cell surface and then dumped into the extracellular space. So an example of this would be neurotransmitters and neurons, which are involved in the signaling process between two different neurons. Or hormones for any cell that produces hormones. So these are examples of cases where proteins that need to be actually exported into the extracellular space between the cells. Additionally, there are transmembrane cells that need to be exported to the cell surface, but that stay attached. because they're transmembrane proteins on the surface of the cell membrane, so they're not exported so much as they sit on the surface. So that's another destination of proteins.

So there's quite a few final destinations here, including the lysosomes, secretary of vesicles, the sole surface, as well as other structures called endosomes, which I'm not really going to talk about here. Some types of plant and fungus cells also have vacuels, which are basically big storage compartments. They're particularly used for storing, you know, like energy sources, starch and so forth for, you know, use later. That is another endpoint for some types of proteins that need to be involved in that, but not so much found in animal cells. So that brings me to the conclusion of the discussion of this intracellular protein sorting. And before we finish out the episode, let me go for a brief review of some of the things we've talked about, because we have gone through a lot here.

So the starting point here was talking about the different sets of organelles and structures that are found inside a eukaryotic cell, and the topological relationships between them. So remember, we've got one big system called the endomebrane system. system, which relates most of the structures inside a cell, including the plasma membrane, so the very atom membrane, endosomes, lysosomes, vacuels, the Golgiaeparatus, endoplasic particulum, and the nuclear envelope. All of these are equivalent to each other in that you can get from one to the other just

by vesicle budding off and then fusing. And we talked about the mechanisms of that. However, there are also regions of the cell that are inaccessible to this end of membrane system. There's the nucleus, which is contiguous with the cytosol, except set up to the cell. except it's split off from it because it's surrounded by the nuclear envelope. So there has to be a different way to get into that. And also there's the mitochondria and the chloroplasts, which are surrounded by two layers of membranes,

not just the one, as in the case of the end of membrane system, and so there has to be yet another method for getting proteins into those. And so we talked about each of those three methods. We talked about the gated transport, which moves proteins through the nuclear pore complexes into the nucleus. We talked about transmembrane transport, which moves proteins in an unfolded. the state across both of the double membrane systems surrounding mitochondria and also chloroplasts.

And we talked about vesicular transport, which allows vesicles with containing proteins and other materials to butt off and move from one compartment to another and then fuse and dump out their cargo. And each of those different mechanisms of protein transport has their own associated, you know, proteins and complexes and machinery associated with it. The very basic idea of how it all works, though, is that each protein, when it's produced in the cytosol, well, all of those that need to move out of the cytosol, have associated signal sequence that tells the cell where it needs to go, be it into the nucleus, into the mitochondria, or into the endoplasm reticulum. And these signal sequences are recognized by appropriate

proteins, which then essentially carry or help the protein move to where it needs to go, again, nucleus ER, mitochondria, whatever, and then binds with receptors in that location, which help it to move inside, again, be it through the nuclear pore complex, or the Tom and the Tim complexes, which help it to move into the mitochondria, or the translocation channels which help it to move into the E.Lumon. There are also special mechanisms that allow the proteins that are being translocated into the EL Lumen to wedge and sort of just stay stuck inside the, stuck within the plasma membrane so that they can then be permanent transmembrane proteins.

We talked about how that works through a sort of a sequence of start and stop signals that allow it to sort of start moving through, but then become wedged in there and not move any further through it. And we also talked about some of the mechanisms of vesicular budding involving, you know, clathrin and COP 102 and the other coat proteins, which help it to pinch off, and then the dynamine protein, which kind of is the noose that tightens it up, and then there's the rab and the tethering and the snare proteins,

which help to bring the vesicle into its target, and then bind it up and fuse it together. And so there's all of these complex mechanisms that help to ensure that proteins are recognized and transported and moved into and get to where they need to go. And eventually most of these signal sequences are cleaved off once their job is done, although sometimes they're not, as in the case of some of those that end up embedded in the membranes, for example, for the transmembrane proteins. So, hopefully that's sort of fairly clear, although the details are quite complicated.

The basic mechanisms are sort of comparable or sort of similar in many different cases. And so this has been a fairly brief summary of the endomebrane system and the different organelles and the protein transport and sorting mechanisms within the cell. There's obviously a lot more to say here. And in a future episode, we'll look a bit more about how proteins move. In a future episode, we'll look a bit more about how cells endocytose, so they take up material from the external environment and bring them into the cell, which we didn't really talk about here,

and also talk more about cell signaling, so how cells talk to each other and send signals from one cell to another. So look out for those. Those will be coming soonish, hopefully. If you have enjoyed this episode, consider making a donation to the podcast. You can make a one-off PayPal donation or become a Patreon supporter

by going to the Patreon, the Science of Everything podcast. If you'd like to send me an email, you can do so at my email address, which is FOD12 at gmail.com. That's FODES12 at gmail.com. Please also consider leaving a favorable review on iTunes or the other aggregator of your choice.

That helps to send the word out about the podcast. Finally, you can also give the podcast page a like on Facebook if you'd like to again support the show and also get information about new episodes and other updates which I post periodically. So thanks once again for listening and I'll talk to you next time.