M.Ed., Stanford University
Winner of multiple teaching awards
Patrick has been teaching AP Biology for 14 years and is the winner of multiple teaching awards.
A lot of times, when I start trying to teach about cell organelles, I can just hear kids start saying why do I have to study this? Or even worse, why do I have to study this again? Because a lot of you have studied this before in Junior High, even Elementary school. Maybe even built yourself a little poster cell diagram. For kids, it’s about as interesting as trying to study a map of 1980s USSR, who cares?
Well, let me give you a quick example of why I think it’s pretty interesting and intriguing to learn about the cellular organelles and their functions. Take a quick moment to go onto Google. Type in the terms mitochondria and ageing and just scheme a couple of the articles you find. Go on, I’ll wait. Did you do it? See what I mean? Scientists are starting to think a lot of the problems that people suffer as they age, is actually due to the deterioration and malfunctioning of that cellular organelle called the mitochondria.
Now I don’t know about you, but I think it’s pretty cool and what’s even better, is that scientists are starting to think that they may be able to fix some of these problem. And hey, if you can figure out ways to make me not get old, that’s intriguing to me.
Now problem we AP Biology teachers face, is that when we start teaching about cellular organelles, we turn it essentially into a Geography lesson. Here is the diagram, learn the names, here is the list of organelles learn their functions. So I’m not going to spend the time doing that, because I figured you can do that easily enough. You probably already have. What I will do though, is that I’ll help you start to see how the cell organelles work together. So I’m going to begin by discussing of the structure of the membrane, because most eukaryotic cellular organelles are made in large part out of membrane. So if you understand its structure, that helps.
Next, I’ll discuss the Endosymbiotic theory, which is the explanation of how these organelles came to be. The last thing I’ll do, is I’ll talk about protein synthesis. Now ribosome do protein synthesis, but there’s a lot of organelles that actually are helping the ribosomes do that job. So that’s a good model for trying to figure out, I know all these functions let’s take a look at how protein synthesis is actually carried out by the entire cell, with all those organelles helping supporting the ribosomes in their job. That’s the kind of question that you’re going to see on the AP Bio exam.
Let’s start this whole thing off with a structure of the cell membrane. Now, cell membrane is made out of a chemical called a Phospholipid, which is a member of the large category called a lipid. So what’s the difference between a phospholipid and a regular triglyceride fat? Well, the standard triglyceride fat, look like this. It has a glycerol molecule with three fatty acid tails. Well, what about a phospholipid, what’s the difference? It’s that phospho- part. It’s got a phosphate head.
Now these fatty acid tails here, they’re all covalently bonded. Nicely set up so that all of their electronegativities roughly are the same. This phosphate head here on the other hand is a charged or polar molecule. Now so, what to do? Well, polar molecules can do a process called hydrogen bonding. They will do that with water molecules. Now you may be thinking hydrogen bonding what’s that? Well, hopefully you did know that, but hydrogen bonds are the weak attractions between the slightly positive hydrogen ions, say of a water molecule, and slightly negative oxygen atoms, also of a water molecule.
So when you have a polar molecule like a phosphate, then you’ll start seeing a bunch of water molecules starting to cluster around it and shoving their slightly positive hydrogen into the region of the strong and negative ion.
Now the stereotype, you can kind of see that the fatty acid tails here, are like the docky kids who are into Pokémon. While the polar head here, is like you’re the cool kid who everybody wants to hang out with. The water molecules are the cool ones. They’re all into other things like sports etcetera. They think it’s just goofy that anybody ever play imaginary games where they put your imaginary people against others. I mean they’re into much cooler things like fantasy football which, never mind let’s move on.
Let’s take a quick look at this next slide which shows us several different ways to draw a phospholipid. Where this is what it would actually look like. Here is a much simpler diagram. If you’ve ever had to draw one, you’ll know why we draw it like this. So again, you’re the cool kid. All the cool kids want to interact with you. Well, let’s imagine you had to go to a party, and your parents shackle your younger brothers behind you and they’re into Pokémon. That’s when you wind up being a phospholipid. The docky brothers are the ones that you had behind you. If you have a number of other friends, who also have their shackled docky brother behind them, you can actually form this ring called a micelle, where you’re shoving the fatty acid, hydrophobic, not water-interacting tails behind you. Whereas your hydrophilic, water-loving, cool phosphate polar heads, are arranged outside.
Now you add in enough of these phospholipids and they can actually form a double layer which is called a bilayer. Here we see the phosphate hydrophilic, water-loving, portions are exposed to the water, while there’s this hydrophobic region here just a fatty acid tails.
Now imagine you had the quarterback of the team. He represents a chlorine ion, another highly alluring ion. As it’s floating around in here, it’s going to interact with all the cool kids at the party. They can interact with you, but as it starts to give into this region of pokemonity, all the water molecules here are saying come back quarter back, come back.
The pokemonity of the other hand has absolutely no attraction for that Chlorine ion. So it gets pulled back. And this is why polar molecules like Chlorine ions or Potassium ions can’t cross the membrane. That’s one of the basic principles of the semi-permeability of a membrane is that, the polar or large molecules can’t simply pass through by phospholipids bilayer.
Let’s take a better look at how the overall structure of the membrane is. Here we see that phospholipids by there. What other molecules are in the membrane? Well, here we see a bunch of proteins. It’s the proteins that give the special qualities of a particular membrane. Whether it’s the cell membrane, the outer plasma membrane, the membrane of the particular region of the Golgi apparatus or the Endoplasmic Reticulum.
Some of these proteins could function as say receptors for communication between different cells. Some of them are specialized enzymes. Others act as docking stations for other molecules to come and interact with that membrane. As you can see there are other molecules. These are cholesterols that help stiffen the membrane while these hexagons these branched hexagon chains those are polysaccharides. Now root with that being sugar as in a polysaccharide is glycol. So if you hook up one of these polysaccharide chains to a protein, now you have yourself something called a glycoprotein whereas, if it’s attached to one of the lipids or fats that make up part of the membrane, then you have yourself a glycolipid. Again the two biggies however, are the proteins and the phospholipids.
Let’s take a quick video that will quickly review some of this tuff. Go on. We’ll make our way YouTube. Now let’s go ahead and make the video larger. Let’s go ahead and start it, here we can see the outer layer of the cell. As we get closer and closer, we start to see the individual phospholipids.
Here are the phosphate head. Now do you notice how they’re floating and moving? This is called the Fluid Mosaic model. If we take a giant eyedropper and hit it, they can just shift and flow. That’s the fluid part of it, and because it’s made of lots of little pieces, it’s a mosaic. These phosphate heads are going up, why? Because the water molecules, those cool kids, are yanking up saying come back! Come back! Stay away from Pokemonity.
Here’s our glycolipids attached here and here. These blue guys represent the cholesterol. If we back up a little bit, we can start to see things like these channels here that can allow different substitutes to go in or out of the cell. There’s an enzyme interacting. Here is an ATP protein that’s pumping materials in and out of the cell. Now you may recall that earlier I mentioned how the difference between the hydrophilic heads and the hydrophobic tails made that membrane semi-permeable. A living cell membrane is actually selectively permeable. Remember all those proteins; it’s those proteins that form the different channels and pumps etcetera that give it that selective capability; the ability to change its mind moment to moment, second by second.
While most cell organelles have a single membrane, they’re some that actually have two membranes or even three. For the longest time scientists were puzzled, how could this process have evolved? They came up with all sorts of complex ideas that involved weird enfolding of the outer membrane. Doctor Lynn Margulis however, took a completely different route and figured it out. This is called the Endosymbiotic theory.
If we take a look at the word endosymbiosis it actually again tells you what is this idea. Endo you hopefully know is a root where that mean inside. Sym means together like in the word symphony, bio means life and if you see s at the end of a word, it probably means some kind of process.
So the word means living together inside. So endosymbiosis is the idea that some organelles like chloroplast or mitochondria, came about when one larger cell ate another one. Then didn’t kill it and left the smaller cell inside the larger cell.
You might be thinking what do you mean, ate, but didn’t kill it? Well, let’s go through the basic process of how a cell eats. You have heard of how white blood cells can work. Where they work by finding some smaller cells say a bacteria. Now if my white blood cell is this bag, I’m going to use this as a smaller cell. So here I have my bacteria, here is my white blood cell. What it does is it does a process known as endocytosis and that means into the cell process. What it does is it takes in the cell and now pinches it off inside of a sac made of the white blood cells membrane. Who controls that membrane? The white blood cell. Who doesn’t? The bacteria. So now the bacteria is stuck inside. Next up another small sac called a lysosome which is filled with digestive enzymes comes, merges with the smaller digestive sac that the cell phone is stuck in or the bacteria. Those digestive enzymes destroy the bacteria killing it and the white blood cell just burps it out. It seems pretty simple.
Well, the idea that with mitochondrion chloroplast something interfered with this normal process. So let’s take a look at how that can happen. Let’s suppose millions, actually probably close to billion years ago, there were some bacteria. Now this bacteria here is anaerobic bacteria which means it cannot do aerobic respiration. Here is a smaller aerobic bacteria.
So now let’s suppose this anaerobic bacteria is about to eat the aerobic bacteria. So just like I just demonstrated, it does endocytosis.
It wraps it in a membrane sac. But something interferes with this process that sends that digestive enzyme-filled lysosome, to merge with the sac, that the aerobic bacteria is stuck in. Does anything kill the bacteria? No. So this little aerobe is now stuck inside. It’s actually not that bad for the aerobe, because just think, will it ever got eaten again? No, it just got eaten by the largest part on the planet. In fact, because this is an anaerobic bacteria, it’s rather inefficient in how it can break down food. So in fact it’s taking in tons of food and breaking in half during glycolysis. So this little aerobe is getting showered with the excess food that the inefficient anaerobic bacteria is having to consume. It’s pretty digested food; protection and free food, good deal.
What about the anaerobic bacteria? Well, this aerobe is getting so much Pyruvate, the break down part of glycolysis, then it starts leaking out excess of the amounts of ATP. So the anaerobic bacteria starts to get some of the benefits of aerobic bacteria. Wait, there’s more anaerobic bacteria can’t survive being around large concentrations of oxygen gas. Well, it turns out aerobic bacteria can convert oxygen gas into water when they do their aerobic respiratory process. So the larger outer cell gets some of the benefits, the energy benefits of aerobic respiration and the protection from oxygen benefits, the aerobic respiration. So both of them together have an advantage over any of the others around them who don’t have this combination. That means natural selection favors them, and so as time goes on, the inner guys start to specialize towards doing just aerobic respiration, while the larger guy out there tends to keep focusing on delivering the Pyruvic acid to what is now a primitive mitochondria.
Now some of you maybe thinking yeah right. But if you start to look at some of the evidence, you may start to go yeah right. If we look at organelles like the chloroplast or the mitochondria, we see that they have a double membrane which is very simply explained by this process, not so simply explained by the enfolding.
Well, if you look even closer, that animal’s membrane shares a lot of qualities to the membrane of a bacteria, not so much to the membrane of a eukaryote cell. Bacteria, they have circular molecules of DNA and they don’t wrap their DNA molecules around histone, guess what? Mitochondria and chloroplast have circular molecules of DNA and again it’s not wrapped in histone proteins, even though out in the nucleus in the rest of the eukaryotic cell, it’s got linear DNA wrapped around those histone proteins.
Additionally, if you take a look at the ribosomes of mitochondria and chloroplast, they share a lot of the qualities that prokaryotic ribosomes have, not sharing the qualities of the larger outer eukaryotic cell. Guess what? When you want to make more mitochondria, who does it? Well, the mitochondria makes more mitochondria. It undergoes a process that looks a whole heck of a lot like bacterial binary fission not at all like the mitosis process that the rest of the cell uses to do cell division. That’s endosymbiosis.
Now there are some suggestions that there are some other organelles like the flagella that may have come about through endosymbiosis, but I wouldn’t be too concerned about that. Just as a little side, additional evidence for this there’s been some researchers who’ve seen in the modern day, they have seen protista, little single cell creatures eating green algae, again not killing them. So there you have endosymbiosis happening in the modern day. If we flash forward ten million or so, we may see these protista developing into own internal chloroplast.
With endosymbiosis covered, now you’ve got a good idea how to address one of the big major questions that they could ask about cells, in the essay portion of the AP exam. The other big category that they can get into is proteins, because proteins are a really big thing in Biology.
Now you’ve often seen some of those multi-part questions in the essays, where they may say describe protein synthesis. And then describe how a protein after it’s been synthesized by the ribosomes, how does that protein get ready for export from the cell. So let’s go through that and it will really help tie in all the different organelles of the cell.
Let’s take a quick look at this really nice video from YouTube. Here we see it. Let’s go ahead and make it bigger. Now before I get this started and start playing it, I want to just quickly point some stuff out. Here we see the Endoplasmic Reticulum, here is the nucleus, down here we see the multiple membranes of the chloroplast. Here we see the multiple membranes of the mitochondria. Trust that to this little vesicle over there single membrane, single membrane here. So again the doubled membrane organelles like the chloroplast and the mitochondria, very strong evidence that they are from this Endosymbiotic origin.
Let’s hit play and take a look at how this happens. Now you know that ribosomes build proteins following the instructions of messenger RNA coming from the nucleus. Now the ribosomes are made out of a pair of parts called sub-units. Now here in this wonderful video with a stop motion animation, you can see a messenger RNA came out the nucleus. And here it combines with a couple of ribosomes. It starts to read off the ribosome.
Let’s pause it for a moment, because I want to show you something. If you take a look here is the protein, the chain of amino acids that’s being built.
This purple thing right here used to be part of that chain. How did the ribosome know to start copying and send it into the Rough Endoplasmic Reticulum? It knows, because the first several amino acids in the chain, act as a targeting sequence to indicate, to the cell put those in the rough ER. Once it’s in there however, that is no longer needed. That’s what that little magento there. That’s the clipped off beginning targeting sequence.
Later on, you’ll see this protein here, this chain of amino acids you’ll see it getting forward of that and sent to other places. Again, how does it know? Because at every step some of the beginning portions can act as targeting sequences. A good analogy for this is if you’ve ever gotten a package from UPS, a lot of times if you pay close attention, they have the original address labeling may have been this long. but as it goes through the various sub-stations of UPS, they rip off each tag as it goes through each station. By the time it gets to you, all that’s left is your address as opposed to the addresses of the various stations in between you and say Amazon.
Let’s go ahead and get it started again. Here we see our amino acid chain and it starts to float through the endoplasmic reticulum folding up perhaps helped by some enzymes, it folds up into it’s tertiary structure until it docks with the correct proteins embedded within the membrane of the endoplasmic reticulum. Those proteins help pinch this off. Now we have a small sac called a vesicle. So let’s pause it again.
We saw the small sac or vesicle merge with one of the sacs that make up the Golgi complex. You know that the Golgi complex is involved in processing proteins for export from the cell. That’s what we see here. Here is our initial protein. The cis-Golgi is just the name of the sac that’s closest to the rough ER. The medial-Golgi is the one in the middle, trans means across, so it’s across from where the Rough Endoplasmic Reticulum is. So we’re going to have these proteins here involved in identifying this is cis-Golgi, medial-Golgi or trans-Golgi.
Others of them are the various enzymes that are going to do any minor modifications that need to be done to the protein. Let’s go ahead and start it up again.
Now how do these things happen? Well, we saw a pinch off of the trans-Golgi. And here comes more Secretory vesicles and they start to reform to cis-Golgi. What happens is that, the identifiers say I’m cis-Golgi or medial-Golgi, they go backwards as each protein gets modified. Here is our original protein. We’re going to see it get pinched off and sent off towards the trans-Golgi. Let's pause it for a moment.
Here are some of the proteins that ere in the trans-Golgi. They get pinched off and now this small sac or vesicle which is about to merge with the outer plasma membrane, this is called a Secretory vesicle. It’s involved in secreting. You’ll see it merge with the membrane and dump its contents out. So let’s go ahead and start that up again.
Now simultaneously with this, the plasma membrane could be taking in a protein. Maybe some food particle or something. So it pinches it off, that’s endocytosis. Let’s pause this for a moment. Remember our lysosome guy, filled with digestive enzymes, here comes some food particle. Remember this, vesicles we wrapped our little cell in, we send it to a lysosome, and then the digestive enzymes are going to chop off that guy. The digestive enzymes I often think of like serial killers. So here is our jail cell. We don’t allow those enzymes out, the digestive enzymes or serial killer stay inside there. So here comes our unsuspecting little protein food molecule. Comes in and we go ahead and start it up again. Here we see it combining in and it starts to enter the lysosome and it gets destroyed. Here comes another enzyme to replace any enzymes that happen to get damaged in this whole process, being sent from the Golgi apparatus. That’s basically how it works.
You just solve a bunch of different organelles of the cell being involved in making the proteins. Whether it’s for excretion from the cell or making proteins to be used in other organelles, such as the lysosome. Other organelles that we didn’t see in this that are involved, obviously the mitochondria is providing the energy for this entire process. How the vesicle is being moved around the cell in order to get to it then you need to go.
A organelle that a lot of times everybody ignores called the cytoskeleton is the framework of proteins. Some proteins like myosin other ones like actin. They form rails and little movement heads that can grab a hold of these organelles, and move them around and deliver them to where they need to go. There you can see a simple process like protein synthesis, made much more complex. But using basic understanding of how each of the individual organelles function, we can see how protein synthesis can be a fairly complex concept.
I’ve touched on in this lecture three of the big things that are likely to appear, not only in the multiple choice section, but things that are going to appear in the essay portions of the AP exam. So if you see something on the structure of the membrane, make sure you toss out words like phospholipid by there. You got yourself a point. Toss out things like, there are proteins that act as channels or receptors, or enzymes, and enzymes embedded within and on the surface of the membrane, you’ve got yourself another point.
It’s likely they may even say, give your point for mentioning the term a Fluid Mosaic model. The idea that it can move in shifts, it’s dynamic. If you remember the video we saw where it touched it and made it bounce around, another point. You can get more points by talking about its selective permeability. You can control what goes in and out, because the polar and non polar regions of the phospholipid bilayer. There goes another point. As you can you can get a lot of points without having to vomit up too much information.
Again, average score in essay is between 2 to 4 points, so I just went through about five and that means I’m getting myself towards getting a 4 or 5 on the actual exam.
With the whole Endosymbiotic theory, if you see something on that, mention the organelles involved; the chloroplast, the mitochondria. One maybe even two points. Talk about the ribosomes as evidence. Talk about the circular DNA if it’s naked, that just means it doesn’t have the histone proteins, you’re getting more points. Again this stuff is not hard.
The last thing is the protein synthesis. If they ask about that process, mention the rough endoplasmic reticulum is where those ribosomes are landing. They’re sending that information off to the Golgi apparatus and then the cellular membrane the outer plasma membrane is where the secretory vesicles, pinched off from the Golgi apparatus merge to dump their stuff out. You could even possibly get an elaboration point if you start mentioning mitochondria and cytoskeleton some of other things I mentioned right at the end. So there you go. You’re good to go.