Cellular Organization and Function Overview

Anatomy and Physiology 1, Chapter 3, The Cellular Level of Organization. So Chapter 3 is all about cells, and we are currently building our way through the hierarchy or levels of life. So in Chapter 2, we talked about atoms. And then we talked about molecules and when we group molecules together we can make larger structures called organelles Which fill the cell so we're going to talk about organelles and review cells today And this will give us a good general biology Review to lead us into the new chapters for anatomy cell theory So cells are the building blocks of all organisms. There is no living thing on the planet that is not made up of cells or at least one cell. All cells come from the division of pre-existing cells. So cells have to come from other cells. They can't just appear from thin air. And cells are the smallest units that perform all vital physiological functions. So at the cellular level, the individual cell is maintaining its own physiology and its own homeostasis. So if all the cells maintain homeostasis, then the whole being will be at homeostasis. Cytology is a branch of cell biology, and it is the study of cells. And cells can be grouped into two big categories. We have sex cells, also known as germ or reproductive, and these are going to include either the male sperm or the female oocyte, which is an immature female egg. And then we've got somatic cells, which are all other body cells except for the egg and sperm. So we're going to be talking about some of the main structures of a cell and we're going to be referring to some pictures. So we'll kind of flip back and forth from picture to definition as we go so we can get a visual to go along with the verbal. So let's start first with the plasma or cell membrane. The plasma or cell membrane would be this pink area here that is around the cell. So if we go forward a little bit, we'll see an explanation of the plasma membrane. So the plasma or cell membrane is going to separate the cytoplasm from the extracellular fluid of the cell. So what is extracellular fluid? Extracellular fluid is the fluid that surrounds the cell or bathes the cell. So the plasma membrane is going to separate the... cytoplasm inside the cell from the extracellular fluid that's found on the outside of the cell. So going back to our first picture here is our plasma or cell membrane in peak and then outside this white space could represent extracellular fluid, the fluid that bathes the cell. And then on the inside of the cell we find the cytoplasm. And we'll talk a little bit more about what that means. And we're going to do that right after we continue on with the plasma membrane. So functions of the plasma membrane. The reason we have these plasma membranes are to isolate the cell from other cells and its environment. That provides a barrier. And it's also going to help the cell to control what comes into it and what goes out of it, which is important. We're going to allow things like ions and nutrients to come into the cell. And we're going to allow things like waste to go out of the cell, along with maybe products that are made inside the cell that we want to send out to other locations in the body. So we'll have good control over that. The cell membrane also makes the cell sensitive to its environment. The cell can respond to chemical signals because it will have receptors on it or in the membrane. And these receptors will allow the cell to respond to molecules in its environment. And finally, structural support. So the cell membrane is going to offer the cell structural support by again keeping what's out out and what's in in. And it will also help to anchor the cells together. So cells are going to be connected to each other to make tissues. And in order to do that, those membranes in some tissue instances, we'll talk about that more later when we get to chapter four. But it's going to allow tissues to stick together because there will be junctions or connections between the individual cells in their membranes. The plasma membrane is made up of a phospholipid bilayer. So it is largely made up of lipids, specifically phospholipids. It's kind of a reminder from the last chapter, but the phospholipids are made up of a hydrophilic head, which hydrophilic means water loving. These heads are going to face outward on both sides of the membrane towards watery environments. Hydrophobic fatty acid tails are going to face the inside of the double membrane. And this phospholipid bilayer will create a barrier to ions and water soluble compounds. Cytoplasm is defined as all the materials inside the cell, outside of the nucleus, and includes the cytosol, which is the fluid inside the cell, and that fluid is going to contain dissolved materials, things like nutrients, proteins, ions, and waste products, high protein and potassium levels, and low carbohydrate, lipid, amino acid, and sodium levels. In that cytosol are also, or in the cytoplasm, are also organelles, and these are structures with specific functions that we're going to be talking about and that we have already talked about a little bit. So organelles can be divided into two categories. We have the non-membranous type and Just like the name suggests, these guys are not going to have a membrane, so they are in direct contact with that fluid called the cytosol. This is going to include the cytoskeleton, centrioles, ribosomes, proteasomes, microvilli, cilia, and flagella. So we will talk about each of those. And then we've got the membranous organelles which are going to have a membrane. So these are isolated from that fluid by a plasma membrane, which is the lipid bilayer that we previously talked about. This will include the endoplasmic reticulum, the Golgi apparatus, lysosomes, peroxisomes, and mitochondria. So the cytoskeleton first. The cytoskeleton is a bit what it sounds like. It is sort of like our skeleton is for us, giving us shape, support, and structure. And the difference is that it of course is not made out of bone, it's made out of protein, and it's going to give the cell shape and structure. Some of the proteins included in making up the cytoskeleton are the microfilaments, intermediate filaments, and microtubules. So again these are protein tube-like structures that are going to give the cell shape and structure. And we can see this in this picture here. This is the edge of a cell and you can see all these little look like little threads or tubes that are running every which way. These are the cytoskeleton and they are giving the cell the shape and structure that it needs. Here is a microscopic view of an actual cell and again you can see a very complex web of these microfilaments that are creating this skeleton. Here is a view under a light microscope of some cells and you can see the fluorescent dye or labeling here allows you to easily see that cytoskeleton which is giving that cell the shape and structure Microvilli are little finger-like projections on the surface of a cell that increase its surface area. This is going to allow for more space for nutrients to absorb across the cell. We're going to see a lot of microvilli in the digestive tract, specifically the small intestine, where we're attempting to absorb 90% of our dietary nutrients. Centrioles are going to form the spindle apparatus during cell division. So if you remember back to general biology when we talk about mitosis, you'll remember that during mitosis there are some fibers called spindle fibers that help to pull apart the chromosomes when we have cell division. Centrosome is the cytoplasm near the nucleus that surrounds. those centrioles. Again the centrioles are what creates the spindle fibers. So we're going to look at a picture of microvilli and we're also going to see a picture of some centrioles. So we're going to have to go back to look at the microvilli to our original cell picture. And here is an example of some microvilli. These are short little finger like projections. that are going to increase the surface area of the cell so that we are able to better absorb nutrients. Going back to the centriole, this is a picture of centrioles. So a centriole is again the thing that's going to split up the chromosomes during cell division. And they're located pretty near the nucleus. You can see in this picture, which is a little bit small, but there's a kind of an orb of cytoplasm around those centrioles. That is what we defined as the centrosome. Cilia are also finger-like projections, but they're a bit longer. They're slender extensions of the plasma membrane and their job is to move fluid across the cell. So we're not absorbing with cilia we're trying to sweep fluid across the cell surface. A flagellum is a whip-like extension of the cell membrane so these are like long tails like you would see on a sperm cell. So here is a cilium and you can see that it is whipping in what is called a power stroke. And that whipping motion is again what will help it to sweep fluids across the cell surface. Okay, next on the list are ribosomes. And ribosomes are super important because they make protein. And protein is one of the most important molecules for living things. It's... They're typically these ribosomes are made up of two parts, a small and a large subunit, and ribosomes even have their own RNA, which is a thing that we talked about from chapter two. Ribosomes can be found in two ways. We can either find them freely floating around in the cytoplasm. Those are called free ribosomes. And these guys make protein that enters the cytosol directly. So as soon as they crank out a new protein, that protein goes right into the cytosol. Fixed ribosomes, on the other hand, are actually stuck to the endoplasmic reticulum, specifically the rough endoplasmic reticulum. We call it the rough ER because it has a sandpapery-like appearance and the sandpapery appearance is due to those bumpy ribosomes that are stuck to the surface. the ER. So these ribosomes are going to make proteins that will then be inside of the ER and they will be put in little packages that will be sent out to the cell. So we're going to talk about that a little bit more in just a few minutes. Proteasomes are organelles that contain enzymes and the enzymes specifically are known as proteases. Now we can see the end of this word, ASE, A-S-E, and typically that is going to designate a type of enzyme. So this type of enzyme will break down protein. Okay. So this is the bottom half of our original cell and you can see just to orient you this is the nucleus and Then surrounding the nucleus we have the endoplasmic reticulum This area here is the rough because you can see that the ER in this Area that I'm pointing is covered with these little ribosomes that give the ER a studded appearance That's the rough ER Then here we have some free ribosomes that are just freely found in the cytosol. So here's a close-up view of our centriole with centrosome cytoplasm around. Okay. So heading back to where we were, we were just about to go into the endoplasmic reticulum. So there are five types of membranous organelles, the endoplasmic reticulum, which we've mentioned a little, the Golgi apparatus, lysosomes, paroxysomes, and mitochondria. So the endoplasmic reticulum, we now know there is a smooth and a rough section. Well, we've talked about the rough. The endoplasmic reticulum contains storage chambers known as cisternae. And the main function of the endoplasmic reticulum in general is to make proteins, carbs, and lipids. It will store these molecules or materials and then eventually transport them within the ER and then out of the ER. The ER can also help with detoxing drugs and toxins. So the smooth endoplasmic reticulum, we call it smooth because it does not have any ribosomes stuck to it, so it has a nice smooth appearance. Its job is to make phospholipids and also cholesterol, which is used in cell membranes. In addition, it can help make steroid hormones for the reproductive system. The rough endoplasmic reticulum is the one we've already looked at that's covered with ribosomes, and that's going to give it, again, that studded appearance. Its job is to make protein, and it's going to, well, ribosomes technically make the protein but it's going to be involved in protein synthesis and it's going to enclose these products in what are called transport vesicles and those transport vesicles will be used for delivery of those materials to the golgi So in this picture we have a view of the rough endoplasmic reticulum, which is the area with all the studded ribosomes on it. And then we've also got the smooth endoplasmic reticulum, which you can see does not have any ribosomes on it. The Golgi apparatus we're going to talk about next and once we've covered the Golgi apparatus then we're going to be ready for a drawing that is going to help us to see the relationship between the rough ER. and also the Golgi. So the Golgi apparatus is going to assist the rough endoplasmic reticulum or the endoplasmic reticulum in general. Vesicles are going to enter So these vesicles I'm referring to are the vesicles produced by the endoplasmic reticulum. They're going to enter what's called the forming face of the Golgi apparatus, and then they will exit the other side of the Golgi, which is called the maturing face. The functions of the Golgi are to modify and package secretions, such as hormones or enzymes, to be released out of the cell. It can help to renew or modify the plasma membrane. And it can also create another type of organelle, which is called the lysosome. And the lysosome is going to be a little sack of enzymes that are going to help with breakdown of different things. And so we'll talk about those too. So this is a picture of the Golgi and it does look like sort of like a stack of membranes. On one side, you can see the transport vesicles from the endoplasmic reticulum are coming near the Golgi, and what they'll eventually do is fuse with it. And then once the products inside these transport vesicles are modified, they will then leave the maturing face, which is the other side of the Golgi, in new vesicles, which are called secretory. vesicles. So again we're going to make a drawing of this to sort of help hopefully make it a little bit more solid in your mind. So lysosomes are the last thing we need to look at before we go into our drawing. So lysosomes contain powerful enzymes that are produced by the Golgi apparatus. So powerful enzyme containing vesicles that are made by the Golgi. And their job is to destroy bacteria that could possibly sneak into the cell. They can also help to break down molecules that we want to break down and recycle. And they can recycle damaged organelles. So if we have an organelle that is not functioning properly, these lysosomes can actually fuse with that damaged organelle. These enzymes inside the lysosome can then break down the organelle. and at that point reabsorb nutrients and products back into the cell. So it's almost like our waste disposal system of the cell. If you could imagine the cell was like a city and every part had a job or a function to do. The lysosomes are our waste disposal system. So let's take a look at a drawing to better help us understand the function of the endoplasmic reticulum and the Golgi. as well as the lysosomes. Okay, so we're going to look at how the rough ER works with the Golgi apparatus to package products to send them out to the rest of the body or out of the cell. So we start with the nucleus and we'll put some DNA inside the nucleus so that we know that it is a nucleus and then around That nucleus we have the rough and the smooth endoplasmic reticulum. Now the rough is going to be notable because of the ribosomes that are on the surface of the endoplasmic reticulum. the smooth does not have ribosomes on it so we'll abbreviate that as ser and we'll abbreviate this one as RER okay so the rough Endoplasmic reticulum is responsible for modifying and packaging proteins. So if you remember protein can come in different shapes and in chapter 2 we talked about how one of the shapes an alpha helix so we're going to use that as our example. This alpha helical protein is produced and then it is budded off of the rough endoplasmic reticulum in what's called a transport vesicle because as you might have guessed it transports things. So now we've got this brand new protein inside of a transport vesicle which is going to transport that protein to the next stop. And that next stop is our Golgi apparatus or Golgi body. And as we talked about before the Golgi has a face that accepts transport vesicles so that transport vesicle will come to the Golgi and fuse with it. allowing that protein to move into the Golgi. Now the Golgi will modify that protein and repackage it on the maturing phase into what's called a secretory vesicle. So now the protein is in a secretory vesicle. So now the protein... So now the protein is in a secretory vesicle, which is destined for the cell membrane. So this is going to be our cell membrane, and that secretory vesicle is going to head straight to the cell membrane, fuse with it, and eject the product out of the cell. This is called exocytosis. Exocytosis. Or to eject something from the cytoplasm. Exit cytoplasm. Now sometimes secretory vesicles that are made of phospholipids will head straight to the cell membrane and they are used to patch up the membrane or add to the membrane because the membrane is made of phospholipids. Finally, the Golgi can also produce a separate organelle called a lysosome, which we talked about before. And lysosomes are filled with digestive enzymes, and their job is to recycle or dissolve products that may enter the cell or even a bacterium that might enter the cell or if there's a broken down organelle it could possibly recycle and digest that broken down organelle. So the flow is again as follows. Rough endoplasmic reticulum with the help of the ribosomes, proteins are produced and the rough ER packages the proteins and modifies them into a transport vesicle. Transport vesicle is going to transport that new protein to the Golgi. The transport vesicle fuses with the Golgi, allowing the protein to enter the Golgi where the Golgi is. Golgi will modify and repackage that protein for its final destination. Then we put that into a secretory vesicle which looks a lot like a transport vesicle but it is destined to fuse with the cell membrane where we will eject the protein out of the cell which is called exocytosis. We can also send phospholipids in the form of secretory vesicle which is made of phospholipids to the membrane to incorporate within the membrane and again or lastly the Golgi produces lysosomes which are filled with digestive enzymes to help break down damaged organelles or things that enter the cell like bacteria that should not be there. So this is a figure from the text that shows the Golgi producing secretory vesicles to be ejected from the cell. So here is a secretory vesicle with a protein being pinched off. fusing with the cell membrane and ejecting the product out of the cell. This again is called exocytosis or ejection from the cell. We also can bud off a portion of the Golgi that can be incorporated into the membrane which is called membrane renewal and that would be made of phospholipids and in addition the Golgi also produces the lysosome which is the enzyme containing vesicle we talked about that can dissolve invaders or broken down damaged organelles So reiterating in the notes, lysosomes contain a powerful enzyme and can break down bacteria, molecules, and recycle damaged organelles. In addition, they can also self-destruct a damaged or inactive cell. So if the lysosome membrane breaks down and all of those enzymes are released inside the cell, this will destroy the cell and the materials will be recycled. So if the cell is damaged or inactive, rather than causing problems for neighboring cells, it will literally self-destruct. That's called autolysis. Paroxysomes are also small vesicles that contain enzymes produced by the division of existing paroxysomes, and they can break down organic compounds like fatty acids. The mitochondria are little, a lot of times in our book they look like little kidney bean shaped organelles and they have a very smooth outside but on the inside their inner membrane has lots of folds and those are called the cristae and the fluid surrounding the cristae is known as the matrix. They are able to take energy from food or glucose to produce the molecule ATP which is the energy currency of the cell. So here is what the mitochondria look like. Here's one up close, kidney being shaped. If we slice it right down the middle you can see the enfolded membrane or cristae and you can also see the space where the matrix would be found. So the nucleus is the largest organelle and this we refer to as the cell's control center. It has its own membrane called the nuclear envelope which is a double membrane like the cell membrane. It's a bilayer and in between the two layers of the nuclear envelope we call that the perinuclear space. But in the membrane, because the nucleus needs to be able to communicate with the rest of the cell, there are going to be little pores called nuclear pores, which are communication passages in the envelope. So this picture here shows the nucleus and here is its membrane, which is the nuclear envelope. And in that envelope are multiple nuclear pores. This allows the nucleus to communicate with the rest of the cell. You can kind of think of it as the director of the cell so it needs to be able to talk to the other organelles. This is the nuclear membrane up close and you can see that it is in fact a double membrane with a space in between called the perinuclear space. The nuclear pore is a large, well it's not large, but it's an opening that allows the nucleus to communicate. So the nucleus has in it a matrix and in that matrix are filaments that help support the nucleus. So that would be the inner filling and then the nucleoli are nuclear organelles that are going to make RNA and assemble ribosomal subunits. The nucleosome is DNA coiled around histones. If it's We see it loosely coiled into what's called chromatin in cells that are not dividing or tightly coiled in chromosomes that form before division. So let's take a look at the difference between those two. So here's our DNA which we talked about back in chapter 2 and DNA it looks like a ladder that's been twisted. It's a double helix. The DNA is then wrapped tightly around these little blue looking spheres which are called histones and where the DNA wraps around a collection of histones and forms this little globule that's called a nucleosome. This loose coil it's very loose and relaxed that's called chromatin and that's what the the DNA looks like in a non-dividing cell. So a cell that is not going through mitosis would be very loosely coiled. But when that DNA becomes very tightly coiled and forms a chromosome, that is what we see in a cell that's preparing for division or mitosis. So if you recall in chapter 2 we talked about how the nucleus stores information in the form of a genetic code. This is the chemical language of DNA instructions, which has the bases A, T, C, and G. We call those the nitrogenous bases, and they are organized into groups of three, which are called triplets. Gene is the DNA instructions for one protein, and that we refer to as a unit of heredity or something that's hereditary. So we're going to talk now about protein synthesis which is when we make functional polypeptides or proteins in the cytoplasm. And we're going to need to do that by activating the genes and begin with transcription. So let's look at a drawing for how transcription and translation work simply, and then we'll come back to our notes. Okay, so we're going to start with transcription. Transcription is step one in the formation of protein, and it is going to happen in... It is going to happen in the nucleus and we are going to use an enzyme called RNA polymerase. to produce a strand of messenger RNA. So we're going to simplify this down and just kind of be breezy about it, and then we will go through the notes to kind of tie it all together. But we're going to begin in the nucleus, and there's our DNA. And remember that the nucleus has a double membrane, which is its nuclear envelope. We've also got nuclear pores and these pores are what is going to allow the nucleus to communicate with the rest of the cytoplasm or cell. So what's going to happen is RNA polymerase is going to I like to think of it as dock itself. It's going to dock itself on the DNA and through a series of steps it's going to travel along the DNA reading it if you will and then it's going to copy down a strand copy down on a strand of messenger RNA the instructions for how to make a protein okay so again the RNA polymerase is going to read the DNA and copy down or transcribe which is where we get the transcription word from we're going to transcribe or copy down the instructions for how to make a protein on a strand messenger RNA. So that's very simply what transcription is. This messenger RNA strand is a single strand so it's able to slip right through the nuclear pore out into the cytoplasm. So once these instructions make it out into the cytoplasm we now need to actually follow the instructions to create a protein and we're going to do that by moving on to step two which is called translation. So here's our messenger RNA strand and on it you can see that there are these nitrogenous bases which is the genetic language and these are our instructions for how to make a protein. Now translation is the next step. So we've got our instructions that we took from the nucleus in the form of messenger RNA, but we need to imagine that these instructions are in a language we can't understand. so we need to translate them, which is why this phase is called translation. We are going to take the information we have here and try to create a protein or polypeptide. Translation will happen in the cytoplasm. And we are going to use messenger RNA, transfer RNA, and a ribosome to help us with the process. And the ribosome should make sense because if you recall, they make protein. So it makes sense to have that guy involved. Now you'll notice that the nitrogenous bases are grouped into threes. These are called triplet. triplets or codons. So this triplet or codon. And you can see that there are multiple triplets or codons going down the line. And each one of these triplets or codons will code for a specific amino acid. Now if we're trying to make a protein, that makes a lot of sense because we make protein from amino acid. Amino acids joined by peptide bonds is how we create that polypeptide or protein. Okay, so we're ready to reset to translation and reminder that translation is happening in the cytoplasm and we've got our messenger RNA strand here. We've drawn in our ribosome, which is here and we've also got up at the top. I've now added transfer RNAs or tRNAs. tRNAs what they sound like. They're going to transfer amino acids to the process. Now remember that we're trying to make protein or polypeptide and in order to make protein we do need amino acids because that's what proteins are made of which is something we talked about back in chapter 2. So this represents a transfer RNA and different books give them different shapes but my book gives them a shape. similar to this. So the parts of a transfer RNA are this is our amino acid, the whole thing is the transfer RNA, and then down at the bottom we have the anticodon which is the sort of the matching puzzle piece to the codons which we labeled down here or the groups of three. Remember that Something else we talked about in chapter 3 that the nitrogenous base A or adenine will bind with U or uracil. C or cytosine will bind with G or guanine. So we're going to keep that there to remind ourselves as we look through translation so that we don't forget. So we'll keep referring to that. So step 1, the ribosome will... dock itself on the messenger RNA strand as we see here and I like to personify everything so I tend to think of the ribosome as having a personality even though we know that is not the case but the ribosome is going to read the first codon A U G and he is going to call out to the cytoplasm not literally but in our everyday explanation and he's going to ask are there any anticodons that match with this first codon? Well, if we take a look and remember the rule A goes with U and C goes with G then we should have a transfer RNA that has an anticodon of UAC. So if we look up here, we do in fact see that transfer RNA number one matches with this first slot. So that transfer RNA is going to come down and bring with it its amino acid. Okay, so we don't have a protein yet because we've only got one amino acid, but we're going to read the second codon, CCA. So that means our anticodon should be GG. U and what do you know here is GGU number two so we bring that transfer RNA down to the second slot and It brings with it its amino acid So at this point the ribosome is full and the next step will be that the first amino acid Will move over and attach itself to the new transfer RNA. Okay, so now we've moved that over and we formed in between the two amino acids a peptide bond, which is exactly how we make a protein. Okay, so now the ribosome has moved down a step and We have a new codon exposed AAA which will bind with U U and U and here we have a tRNA that's anti-codon matches so we will bring down that tRNA and it will bring with it its amino acid. So as you can guess these two guys will move over to the new amino acid forming a longer chain and at that point this tRNA's job is done so it can head back to the cytoplasm and we will again move down another step. Okay, and now we're ready to move on to the next step. The ribosome is still moving forward and this codon is going to match with the anti-codon AAU, which is this one. So again, it will come down bringing with it its amino acid. The old guy is going to pass his amino acids over to the new one. So now we have an even longer chain. The old guy will be able to go back to the cytoplasm and wait to be used again. Now the ribosome will click down one more step. Alright, so now we have a codon AAU that will match with the anticodon UUA, which we see here with tRNA number 5. It will move down, bringing with it, again, its amino acid. So the old guy will pass his amino acids to the new guy. So again our chain continues to grow and the old guy will head back to the cytoplasm. Ribosome will click down a step. Okay, so now we are at the last codon, which is known as the stop codon, and this will be the end of translation once we make it to the stop codon. So the codon here is UAA, which will correspond with A. U U and we can see that we've got one remaining tRNA which will come down once again bringing with it its amino acid so the old tRNA will once again pass on the amino acids to the new tRNA and this tRNA, the old guy, will go back to the cytoplasm and now we are left at the end at the stop codon. Everything will disassemble and we will be left with what we wanted to make all along which is a brand new shiny polypeptide made from your genetic code. Okay, so to review what we just drew in your actual notes, we had first the process of transcription, where we began with RNA polymerase, which is an enzyme, binding. It begins at the start signal on the DNA and reads the DNA code to form messenger RNA, which was grouped into three base sequences known as codons or triplets. At the end of this transcription, the mRNA detaches and then will actually move through the nuclear pores as we showed in our drawing. So once the messenger RNA is edited, it will officially again leave the nucleus through the nuclear pores. So here's your book's version of how the messenger RNA is formed. So we have our DNA and here's our RNA polymerase splitting the double helix and moving down the DNA strand, creating a messenger RNA strand as it moves. The messenger RNA is the result and once again it's going to leave the nucleus once it's edited through the nuclear pores. Which brings us to translation, the second part. This is when we actually make protein or polypeptides. So once the mRNA leaves it will bind to the ribosome and each codon will translate to amino acid which is brought by the transfer RNA as we showed in our drawing. The anticodon is what binds to the codon on the messenger RNA strand and we join those amino acids together by peptide bonds. So in this figure you can see the messenger RNA coming out through the pore into the cytoplasm. and our ribosome assembles to look like this. So our ribosome is sitting on the messenger RNA strand and we begin bringing in transfer RNAs with corresponding anticodons. Remember each one is carrying an amino acid as it sits down on its codon. We bring in an additional transfer RNA to dock itself down as well and we will pass the first amino acid over to bind with the new amino acid. And we are starting a chain. The first tRNA will then leave and go back to the cytoplasm and the ribosome will move down. As we can see here, so this one is leaving to go back to the cytoplasm. We bring in a new tRNA and it's got its amino acid. So what will happen next as we expect? The old tRNA will pass his amino acids over to the new tRNA's amino acid, which will form a longer chain of three. The old guy will also leave, and then we will move down the ribosome until we reach the stop codon. When we reach the stop codon, the whole thing will disassemble, and we will be left with a completed polypeptide, which is what we aimed to make in the beginning. So next is diffusion and osmosis. The cell membrane is a barrier but it has to be what's called semi-permeable or selectively permeable, which means we do need nutrients to get in and we also need products and waste to be able to get out. So permeability is going to determine what can move in and out of a cell or a membrane. So a membrane that lets nothing in and out would be considered impermeable. If a membrane let anything in or let anything out, that would be freely permeable. Movement that is restricted is called selective permeability and that is what we will find that our cells are. They're very picky about what comes in and goes out. The plasma membrane is selectively permeable, which again will allow some materials to move freely, but others will be restricted. This again is a good safeguard for our cell. So diffusion is the movement of a substance from an area of high concentration to an area of low concentration. In a substance, ions and molecules are always moving around. So again, the rule of diffusion... where things move from a high to a low concentration as demonstrated in this picture from the textbook. So we have a beaker of water here and a colored sugar cube is placed into the water and there is a large amount of color right around that sugar cube so that would be where the high concentration is and out here in the water there is a very low concentration of color. So remembering the rule, we move from high to low concentration, the color will begin to spread from the high concentrated area towards the low concentrated area, which means the color will spread out until eventually we have equal coloration in the beaker of water. So diffusion will continue. until the concentration gradient is eliminated and there is an equal distribution throughout the entire solution. Osmosis is the diffusion of water from a high to a low concentration. So again the same exact rule of high to low, but when we hear the word osmosis we should think of water not a substance other than water. So same rule. diffusion but we're focusing on the water so this is movement of water from a high to a low concentration so we can take a look at that using these two figures so we have a u-shaped tube here and in the very middle we have a semi permeable membrane or selectively permeable membrane kind of like the cell membrane And in the solution we have water molecules which are the small blue dots and then the pink solution or the pink dots represent something else like possibly sodium for example. So if we look at the concentration of each on either side of the membrane you'll notice that on the left side There's a lot of blue dots which represent water and less pink dots which could represent possibly sodium. On the right, there's more sodium and less blue dots or less water. So according to the rule of diffusion, water will move from a high to a low concentration. Right now, there's more water on the left than there is on the right. So that should mean that water is going to move. from the left side where it is greater toward the right side where it is less. And we do see that so the water moved to the right but you can now see that the volume on the right side has increased and this balance or this fluctuation will continue until we have an equal amount of water on the left as we do on the right. So osmolality or osmotic concentration is the total solute concentration in a solution. Tonicity describes how a solution affects a cell, which is particularly important in cell physiology. An isotonic solution is a solution where there is no movement of water into or out of the cell that is severe. There's not much movement at all. So the cell is quite happy. In this solution, this is a nice balanced solution. Hypotonic solution is when there is a lower solute concentration than in the cell. Now what that means is that water will actually move into the cell until the cell becomes very swollen and it can actually cause the cell to pop open. And one way I always remember this hypotonic is going to cause the cell to swell is there's a nice round O here in the word hypotonic and that nice round O reminds me of a swollen cell. Hypotonic solution is when there's a higher solute concentration around the cell than in the cell so what that's going to do is actually cause water to move out of the cell towards the solute and that's going to cause the cell to shrivel. So we'll look at this in a couple of pictures. So a cell in an isotonic solution will stay the same size and shape. A cell in a hypotonic solution will gain water. That's when we talked about the nice swollen cell. It can rupture which is called hemolysis when we're talking about a blood cell. A cell in a hypertonic solution can lose water and shrink which is known as Crenation. So here's a red blood cell in an isotonic solution where the water molecules and the solute molecules are even on the inside and outside of the cell. So this is going to create very little extreme flow. This is going to be a nice balanced flow making the cell quite happy. This is a very good cell solution. So in this solution the water flows into the cell and that can cause the cell to swell and possibly rupture which we call lysis. In a hypertonic solution water moves out of the cell. The red blood cell can shrivel which is called Crenation. Endocytosis comes in two major forms that we'll talk about now. We have penocytosis, which is when the cell drinks extracellular fluid or brings in endosomes or pockets of extracellular fluid. Phagocytosis is when we take in solids. So the cell can reach out with cytoplasmic extensions, which are called pseudopodia. and grab extracellular structures or even a bacterium, for example, and pull it in and later digest it. So cellular eating, bringing in solids. Exocytosis, which we already discussed, is when we release objects from the cytoplasm or exit objects from the cytoplasm. Membrane potential. is defined as when a positive and negative charge is separated This creates a potential difference and we see this in cells. So there is a slight excess of positivity on the exterior of the membrane of a cell which is due to sodium mainly. The positive and negatives across the membrane are attracted to each other but the membrane keeps them apart, which we call membrane potential. The measurement is in millivolts or a thousandth of a volt and the plasma membrane will act as a dam basically keeping the positive and negative charge apart across the membrane. They cannot rush together to attract. So that unequal charge across the plasma membrane is known as the membrane potential. The resting membrane potential of a cell can range from negative 10 millivolts to negative 100 millivolts depending on the cell type. So our last large topic would be mitosis. So cell division is a form of cell reproduction. A single cell can produce two daughter cells when it divides. At the end of the cell's life it can undergo genetically controlled death. apoptosis. So in the cell life cycle we have what's called interphase. This is when the cell is not actively dividing but spending, this is where cells spend the majority of their lives, and during this phase they can begin to prepare for mitosis or division. Somatic cells recall our general body cells and in humans somatic cells are going to contain 46 chromosomes so this would not include the egg and the sperm. The egg and the sperm undergo meiosis. So in mitosis we're going to see a few phases which we will review. So duplication of chromosomes in the nucleus and then separation into two identical sets will happen during mitosis. and it's going to consist of four main phases. Prophase, metaphase, anaphase, and finally telophase. Cytokinesis is the division of the cytoplasm. This is what happens at the very end, and that will produce two daughter cells, brand new cells. So here is a great slide that shows a review of the main parts of mitosis. So we'll begin here in prophase. So prophase is step one of mitosis. Remember interphase is where we were before this, just kind of hanging out, getting ready for mitosis to begin. And right before mitosis begins, we're going to double the chromosomes in the cell to prepare for division. So prophase, during that time, the DNA or the chromatin, will actually condense and chromosomes become visible during this phase. So the chromosomes condense and then spindle fibers, which are these guys, will appear and they'll be very clear inside the cell. When we move to metaphase, in metaphase the chromosomes or chromatids will move to a central zone of the cell called the metaphase plate. and the metaphase plate is kind of an imaginary line that the cells line up on. The spindle fibers attach to those chromatids and in anaphase the center point of the chromatid pair called the centromere will split and the chromatids will separate. The daughter chromosomes are pulled to opposite ends of the cell. And then in telophase, the new cells get ready to return to interphase, the nuclear membranes reform, and the chromosomes gradually uncoil. And this will be followed by the actual splitting of the two cells, which is called cytokinesis, where the two cells split apart and we are completely done with mitosis. So mitotic rate is the rate of cell division. Slower mitosis means a longer cell life. Cell division does require energy in the form of ATP, which we talked about previously as well. Okay, so a tumor or neoplasm is defined as a mass of abnormal cell growth. When cells grow out of control and grow when they are not instructed to grow, they can form these masses. Tumors can be benign, which means contained. not life-threatening unless they're large and these are not likely to spread. A malignant tumor will spread into surrounding tissue which is known as an invasion. Cancer results from abnormal proliferation of cells, so when cells grow out of control, which can be caused by mutations in genes. These genes are involved with cell growth. Modified genes are called oncogenes and mutagens are agents that can cause mutations. Carcinogens, including mutagens, are cancer-causing agents. And metastasis is the spread of cancer to other areas, which begins with the invasion of tissue surrounding that particular tumor. So here's an example of how metastasis can actually happen. Here we can see in the tissue an abnormal cell and this abnormal cell begins to grow into a mass, which we call a tumor. And if these cells continue to spread, they can enter circulation. And that's bad news because circulation provides a highway for these bad cells to spread, escape, and form. new masses. So all cells contain the same number of chromosomes and genes. We're talking about a human in particular. Now again we talked about how somatic cells are going to have 46 in humans and if we talk about sex cells then of course we're going to have half the complement which would be 23 in eggs and 23 in sperm. But each one of your cells contains copies of your genetic makeup. Cells undergo differentiation, which means they become specialized by turning off genes not needed by that cell. And when cells become specialized, they become really good at specific jobs. So this will allow cells to form different types of cells like liver cells, fat cells, and even neurons, which we will talk about all of those eventually. This concludes chapter 3, the last of the chapters of general biology review, as we head now into chapter 4, which would be a study of the tissues or histology.

And then we talked about molecules and when we group molecules together we can make larger structures called organelles Which fill the cell so we're going to talk about organelles and review cells today And this will give us a good general biology Review to lead us into the new chapters for anatomy cell theory So cells are the building blocks of all organisms. There is no living thing on the planet that is not made up of cells or at least one cell. All cells come from the division of pre-existing cells.

So cells have to come from other cells. They can't just appear from thin air. And cells are the smallest units that perform all vital physiological functions. So at the cellular level, the individual cell is maintaining its own physiology and its own homeostasis. So if all the cells maintain homeostasis, then the whole being will be at homeostasis.

Cytology is a branch of cell biology, and it is the study of cells. And cells can be grouped into two big categories. We have sex cells, also known as germ or reproductive, and these are going to include either the male sperm or the female oocyte, which is an immature female egg. And then we've got somatic cells, which are all other body cells except for the egg and sperm. So we're going to be talking about some of the main structures of a cell and we're going to be referring to some pictures.

So we'll kind of flip back and forth from picture to definition as we go so we can get a visual to go along with the verbal. So let's start first with the plasma or cell membrane. The plasma or cell membrane would be this pink area here that is around the cell.

So if we go forward a little bit, we'll see an explanation of the plasma membrane. So the plasma or cell membrane is going to separate the cytoplasm from the extracellular fluid of the cell. So what is extracellular fluid?

Extracellular fluid is the fluid that surrounds the cell or bathes the cell. So the plasma membrane is going to separate the... cytoplasm inside the cell from the extracellular fluid that's found on the outside of the cell. So going back to our first picture here is our plasma or cell membrane in peak and then outside this white space could represent extracellular fluid, the fluid that bathes the cell.

And then on the inside of the cell we find the cytoplasm. And we'll talk a little bit more about what that means. And we're going to do that right after we continue on with the plasma membrane. So functions of the plasma membrane.

The reason we have these plasma membranes are to isolate the cell from other cells and its environment. That provides a barrier. And it's also going to help the cell to control what comes into it and what goes out of it, which is important.

We're going to allow things like ions and nutrients to come into the cell. And we're going to allow things like waste to go out of the cell, along with maybe products that are made inside the cell that we want to send out to other locations in the body. So we'll have good control over that. The cell membrane also makes the cell sensitive to its environment.

The cell can respond to chemical signals because it will have receptors on it or in the membrane. And these receptors will allow the cell to respond to molecules in its environment. And finally, structural support. So the cell membrane is going to offer the cell structural support by again keeping what's out out and what's in in.

And it will also help to anchor the cells together. So cells are going to be connected to each other to make tissues. And in order to do that, those membranes in some tissue instances, we'll talk about that more later when we get to chapter four. But it's going to allow tissues to stick together because there will be junctions or connections between the individual cells in their membranes. The plasma membrane is made up of a phospholipid bilayer.

So it is largely made up of lipids, specifically phospholipids. It's kind of a reminder from the last chapter, but the phospholipids are made up of a hydrophilic head, which hydrophilic means water loving. These heads are going to face outward on both sides of the membrane towards watery environments. Hydrophobic fatty acid tails are going to face the inside of the double membrane. And this phospholipid bilayer will create a barrier to ions and water soluble compounds.

Cytoplasm is defined as all the materials inside the cell, outside of the nucleus, and includes the cytosol, which is the fluid inside the cell, and that fluid is going to contain dissolved materials, things like nutrients, proteins, ions, and waste products, high protein and potassium levels, and low carbohydrate, lipid, amino acid, and sodium levels. In that cytosol are also, or in the cytoplasm, are also organelles, and these are structures with specific functions that we're going to be talking about and that we have already talked about a little bit. So organelles can be divided into two categories. We have the non-membranous type and Just like the name suggests, these guys are not going to have a membrane, so they are in direct contact with that fluid called the cytosol. This is going to include the cytoskeleton, centrioles, ribosomes, proteasomes, microvilli, cilia, and flagella.

So we will talk about each of those. And then we've got the membranous organelles which are going to have a membrane. So these are isolated from that fluid by a plasma membrane, which is the lipid bilayer that we previously talked about. This will include the endoplasmic reticulum, the Golgi apparatus, lysosomes, peroxisomes, and mitochondria.

So the cytoskeleton first. The cytoskeleton is a bit what it sounds like. It is sort of like our skeleton is for us, giving us shape, support, and structure. And the difference is that it of course is not made out of bone, it's made out of protein, and it's going to give the cell shape and structure.

Some of the proteins included in making up the cytoskeleton are the microfilaments, intermediate filaments, and microtubules. So again these are protein tube-like structures that are going to give the cell shape and structure. And we can see this in this picture here.

This is the edge of a cell and you can see all these little look like little threads or tubes that are running every which way. These are the cytoskeleton and they are giving the cell the shape and structure that it needs. Here is a microscopic view of an actual cell and again you can see a very complex web of these microfilaments that are creating this skeleton. Here is a view under a light microscope of some cells and you can see the fluorescent dye or labeling here allows you to easily see that cytoskeleton which is giving that cell the shape and structure Microvilli are little finger-like projections on the surface of a cell that increase its surface area. This is going to allow for more space for nutrients to absorb across the cell.

We're going to see a lot of microvilli in the digestive tract, specifically the small intestine, where we're attempting to absorb 90% of our dietary nutrients. Centrioles are going to form the spindle apparatus during cell division. So if you remember back to general biology when we talk about mitosis, you'll remember that during mitosis there are some fibers called spindle fibers that help to pull apart the chromosomes when we have cell division.

Centrosome is the cytoplasm near the nucleus that surrounds. those centrioles. Again the centrioles are what creates the spindle fibers. So we're going to look at a picture of microvilli and we're also going to see a picture of some centrioles. So we're going to have to go back to look at the microvilli to our original cell picture.

And here is an example of some microvilli. These are short little finger like projections. that are going to increase the surface area of the cell so that we are able to better absorb nutrients. Going back to the centriole, this is a picture of centrioles.

So a centriole is again the thing that's going to split up the chromosomes during cell division. And they're located pretty near the nucleus. You can see in this picture, which is a little bit small, but there's a kind of an orb of cytoplasm around those centrioles. That is what we defined as the centrosome.

Cilia are also finger-like projections, but they're a bit longer. They're slender extensions of the plasma membrane and their job is to move fluid across the cell. So we're not absorbing with cilia we're trying to sweep fluid across the cell surface.

A flagellum is a whip-like extension of the cell membrane so these are like long tails like you would see on a sperm cell. So here is a cilium and you can see that it is whipping in what is called a power stroke. And that whipping motion is again what will help it to sweep fluids across the cell surface. Okay, next on the list are ribosomes.

And ribosomes are super important because they make protein. And protein is one of the most important molecules for living things. It's... They're typically these ribosomes are made up of two parts, a small and a large subunit, and ribosomes even have their own RNA, which is a thing that we talked about from chapter two. Ribosomes can be found in two ways.

We can either find them freely floating around in the cytoplasm. Those are called free ribosomes. And these guys make protein that enters the cytosol directly. So as soon as they crank out a new protein, that protein goes right into the cytosol. Fixed ribosomes, on the other hand, are actually stuck to the endoplasmic reticulum, specifically the rough endoplasmic reticulum.

We call it the rough ER because it has a sandpapery-like appearance and the sandpapery appearance is due to those bumpy ribosomes that are stuck to the surface. the ER. So these ribosomes are going to make proteins that will then be inside of the ER and they will be put in little packages that will be sent out to the cell. So we're going to talk about that a little bit more in just a few minutes.

Proteasomes are organelles that contain enzymes and the enzymes specifically are known as proteases. Now we can see the end of this word, ASE, A-S-E, and typically that is going to designate a type of enzyme. So this type of enzyme will break down protein.

Okay. So this is the bottom half of our original cell and you can see just to orient you this is the nucleus and Then surrounding the nucleus we have the endoplasmic reticulum This area here is the rough because you can see that the ER in this Area that I'm pointing is covered with these little ribosomes that give the ER a studded appearance That's the rough ER Then here we have some free ribosomes that are just freely found in the cytosol. So here's a close-up view of our centriole with centrosome cytoplasm around. Okay. So heading back to where we were, we were just about to go into the endoplasmic reticulum.

So there are five types of membranous organelles, the endoplasmic reticulum, which we've mentioned a little, the Golgi apparatus, lysosomes, paroxysomes, and mitochondria. So the endoplasmic reticulum, we now know there is a smooth and a rough section. Well, we've talked about the rough.

The endoplasmic reticulum contains storage chambers known as cisternae. And the main function of the endoplasmic reticulum in general is to make proteins, carbs, and lipids. It will store these molecules or materials and then eventually transport them within the ER and then out of the ER.

The ER can also help with detoxing drugs and toxins. So the smooth endoplasmic reticulum, we call it smooth because it does not have any ribosomes stuck to it, so it has a nice smooth appearance. Its job is to make phospholipids and also cholesterol, which is used in cell membranes. In addition, it can help make steroid hormones for the reproductive system. The rough endoplasmic reticulum is the one we've already looked at that's covered with ribosomes, and that's going to give it, again, that studded appearance.

Its job is to make protein, and it's going to, well, ribosomes technically make the protein but it's going to be involved in protein synthesis and it's going to enclose these products in what are called transport vesicles and those transport vesicles will be used for delivery of those materials to the golgi So in this picture we have a view of the rough endoplasmic reticulum, which is the area with all the studded ribosomes on it. And then we've also got the smooth endoplasmic reticulum, which you can see does not have any ribosomes on it. The Golgi apparatus we're going to talk about next and once we've covered the Golgi apparatus then we're going to be ready for a drawing that is going to help us to see the relationship between the rough ER. and also the Golgi.

So the Golgi apparatus is going to assist the rough endoplasmic reticulum or the endoplasmic reticulum in general. Vesicles are going to enter So these vesicles I'm referring to are the vesicles produced by the endoplasmic reticulum. They're going to enter what's called the forming face of the Golgi apparatus, and then they will exit the other side of the Golgi, which is called the maturing face. The functions of the Golgi are to modify and package secretions, such as hormones or enzymes, to be released out of the cell. It can help to renew or modify the plasma membrane.

And it can also create another type of organelle, which is called the lysosome. And the lysosome is going to be a little sack of enzymes that are going to help with breakdown of different things. And so we'll talk about those too.

So this is a picture of the Golgi and it does look like sort of like a stack of membranes. On one side, you can see the transport vesicles from the endoplasmic reticulum are coming near the Golgi, and what they'll eventually do is fuse with it. And then once the products inside these transport vesicles are modified, they will then leave the maturing face, which is the other side of the Golgi, in new vesicles, which are called secretory. vesicles. So again we're going to make a drawing of this to sort of help hopefully make it a little bit more solid in your mind.

So lysosomes are the last thing we need to look at before we go into our drawing. So lysosomes contain powerful enzymes that are produced by the Golgi apparatus. So powerful enzyme containing vesicles that are made by the Golgi.

And their job is to destroy bacteria that could possibly sneak into the cell. They can also help to break down molecules that we want to break down and recycle. And they can recycle damaged organelles.

So if we have an organelle that is not functioning properly, these lysosomes can actually fuse with that damaged organelle. These enzymes inside the lysosome can then break down the organelle. and at that point reabsorb nutrients and products back into the cell. So it's almost like our waste disposal system of the cell. If you could imagine the cell was like a city and every part had a job or a function to do.

The lysosomes are our waste disposal system. So let's take a look at a drawing to better help us understand the function of the endoplasmic reticulum and the Golgi. as well as the lysosomes.

Okay, so we're going to look at how the rough ER works with the Golgi apparatus to package products to send them out to the rest of the body or out of the cell. So we start with the nucleus and we'll put some DNA inside the nucleus so that we know that it is a nucleus and then around That nucleus we have the rough and the smooth endoplasmic reticulum. Now the rough is going to be notable because of the ribosomes that are on the surface of the endoplasmic reticulum.

the smooth does not have ribosomes on it so we'll abbreviate that as ser and we'll abbreviate this one as RER okay so the rough Endoplasmic reticulum is responsible for modifying and packaging proteins. So if you remember protein can come in different shapes and in chapter 2 we talked about how one of the shapes an alpha helix so we're going to use that as our example. This alpha helical protein is produced and then it is budded off of the rough endoplasmic reticulum in what's called a transport vesicle because as you might have guessed it transports things. So now we've got this brand new protein inside of a transport vesicle which is going to transport that protein to the next stop. And that next stop is our Golgi apparatus or Golgi body.

And as we talked about before the Golgi has a face that accepts transport vesicles so that transport vesicle will come to the Golgi and fuse with it. allowing that protein to move into the Golgi. Now the Golgi will modify that protein and repackage it on the maturing phase into what's called a secretory vesicle.

So now the protein is in a secretory vesicle. So now the protein... So now the protein is in a secretory vesicle, which is destined for the cell membrane.

So this is going to be our cell membrane, and that secretory vesicle is going to head straight to the cell membrane, fuse with it, and eject the product out of the cell. This is called exocytosis. Exocytosis.

Or to eject something from the cytoplasm. Exit cytoplasm. Now sometimes secretory vesicles that are made of phospholipids will head straight to the cell membrane and they are used to patch up the membrane or add to the membrane because the membrane is made of phospholipids. Finally, the Golgi can also produce a separate organelle called a lysosome, which we talked about before.

And lysosomes are filled with digestive enzymes, and their job is to recycle or dissolve products that may enter the cell or even a bacterium that might enter the cell or if there's a broken down organelle it could possibly recycle and digest that broken down organelle. So the flow is again as follows. Rough endoplasmic reticulum with the help of the ribosomes, proteins are produced and the rough ER packages the proteins and modifies them into a transport vesicle. Transport vesicle is going to transport that new protein to the Golgi. The transport vesicle fuses with the Golgi, allowing the protein to enter the Golgi where the Golgi is.

Golgi will modify and repackage that protein for its final destination. Then we put that into a secretory vesicle which looks a lot like a transport vesicle but it is destined to fuse with the cell membrane where we will eject the protein out of the cell which is called exocytosis. We can also send phospholipids in the form of secretory vesicle which is made of phospholipids to the membrane to incorporate within the membrane and again or lastly the Golgi produces lysosomes which are filled with digestive enzymes to help break down damaged organelles or things that enter the cell like bacteria that should not be there.

So this is a figure from the text that shows the Golgi producing secretory vesicles to be ejected from the cell. So here is a secretory vesicle with a protein being pinched off. fusing with the cell membrane and ejecting the product out of the cell.

This again is called exocytosis or ejection from the cell. We also can bud off a portion of the Golgi that can be incorporated into the membrane which is called membrane renewal and that would be made of phospholipids and in addition the Golgi also produces the lysosome which is the enzyme containing vesicle we talked about that can dissolve invaders or broken down damaged organelles So reiterating in the notes, lysosomes contain a powerful enzyme and can break down bacteria, molecules, and recycle damaged organelles. In addition, they can also self-destruct a damaged or inactive cell.

So if the lysosome membrane breaks down and all of those enzymes are released inside the cell, this will destroy the cell and the materials will be recycled. So if the cell is damaged or inactive, rather than causing problems for neighboring cells, it will literally self-destruct. That's called autolysis.

Paroxysomes are also small vesicles that contain enzymes produced by the division of existing paroxysomes, and they can break down organic compounds like fatty acids. The mitochondria are little, a lot of times in our book they look like little kidney bean shaped organelles and they have a very smooth outside but on the inside their inner membrane has lots of folds and those are called the cristae and the fluid surrounding the cristae is known as the matrix. They are able to take energy from food or glucose to produce the molecule ATP which is the energy currency of the cell.

So here is what the mitochondria look like. Here's one up close, kidney being shaped. If we slice it right down the middle you can see the enfolded membrane or cristae and you can also see the space where the matrix would be found. So the nucleus is the largest organelle and this we refer to as the cell's control center.

It has its own membrane called the nuclear envelope which is a double membrane like the cell membrane. It's a bilayer and in between the two layers of the nuclear envelope we call that the perinuclear space. But in the membrane, because the nucleus needs to be able to communicate with the rest of the cell, there are going to be little pores called nuclear pores, which are communication passages in the envelope. So this picture here shows the nucleus and here is its membrane, which is the nuclear envelope. And in that envelope are multiple nuclear pores.

This allows the nucleus to communicate with the rest of the cell. You can kind of think of it as the director of the cell so it needs to be able to talk to the other organelles. This is the nuclear membrane up close and you can see that it is in fact a double membrane with a space in between called the perinuclear space. The nuclear pore is a large, well it's not large, but it's an opening that allows the nucleus to communicate.

So the nucleus has in it a matrix and in that matrix are filaments that help support the nucleus. So that would be the inner filling and then the nucleoli are nuclear organelles that are going to make RNA and assemble ribosomal subunits. The nucleosome is DNA coiled around histones. If it's We see it loosely coiled into what's called chromatin in cells that are not dividing or tightly coiled in chromosomes that form before division. So let's take a look at the difference between those two.

So here's our DNA which we talked about back in chapter 2 and DNA it looks like a ladder that's been twisted. It's a double helix. The DNA is then wrapped tightly around these little blue looking spheres which are called histones and where the DNA wraps around a collection of histones and forms this little globule that's called a nucleosome.

This loose coil it's very loose and relaxed that's called chromatin and that's what the the DNA looks like in a non-dividing cell. So a cell that is not going through mitosis would be very loosely coiled. But when that DNA becomes very tightly coiled and forms a chromosome, that is what we see in a cell that's preparing for division or mitosis.

So if you recall in chapter 2 we talked about how the nucleus stores information in the form of a genetic code. This is the chemical language of DNA instructions, which has the bases A, T, C, and G. We call those the nitrogenous bases, and they are organized into groups of three, which are called triplets. Gene is the DNA instructions for one protein, and that we refer to as a unit of heredity or something that's hereditary. So we're going to talk now about protein synthesis which is when we make functional polypeptides or proteins in the cytoplasm.

And we're going to need to do that by activating the genes and begin with transcription. So let's look at a drawing for how transcription and translation work simply, and then we'll come back to our notes. Okay, so we're going to start with transcription.

Transcription is step one in the formation of protein, and it is going to happen in... It is going to happen in the nucleus and we are going to use an enzyme called RNA polymerase. to produce a strand of messenger RNA.

So we're going to simplify this down and just kind of be breezy about it, and then we will go through the notes to kind of tie it all together. But we're going to begin in the nucleus, and there's our DNA. And remember that the nucleus has a double membrane, which is its nuclear envelope. We've also got nuclear pores and these pores are what is going to allow the nucleus to communicate with the rest of the cytoplasm or cell.

So what's going to happen is RNA polymerase is going to I like to think of it as dock itself. It's going to dock itself on the DNA and through a series of steps it's going to travel along the DNA reading it if you will and then it's going to copy down a strand copy down on a strand of messenger RNA the instructions for how to make a protein okay so again the RNA polymerase is going to read the DNA and copy down or transcribe which is where we get the transcription word from we're going to transcribe or copy down the instructions for how to make a protein on a strand messenger RNA. So that's very simply what transcription is.

This messenger RNA strand is a single strand so it's able to slip right through the nuclear pore out into the cytoplasm. So once these instructions make it out into the cytoplasm we now need to actually follow the instructions to create a protein and we're going to do that by moving on to step two which is called translation. So here's our messenger RNA strand and on it you can see that there are these nitrogenous bases which is the genetic language and these are our instructions for how to make a protein.

Now translation is the next step. So we've got our instructions that we took from the nucleus in the form of messenger RNA, but we need to imagine that these instructions are in a language we can't understand. so we need to translate them, which is why this phase is called translation.

We are going to take the information we have here and try to create a protein or polypeptide. Translation will happen in the cytoplasm. And we are going to use messenger RNA, transfer RNA, and a ribosome to help us with the process. And the ribosome should make sense because if you recall, they make protein.

So it makes sense to have that guy involved. Now you'll notice that the nitrogenous bases are grouped into threes. These are called triplet.

triplets or codons. So this triplet or codon. And you can see that there are multiple triplets or codons going down the line. And each one of these triplets or codons will code for a specific amino acid.

Now if we're trying to make a protein, that makes a lot of sense because we make protein from amino acid. Amino acids joined by peptide bonds is how we create that polypeptide or protein. Okay, so we're ready to reset to translation and reminder that translation is happening in the cytoplasm and we've got our messenger RNA strand here.

We've drawn in our ribosome, which is here and we've also got up at the top. I've now added transfer RNAs or tRNAs. tRNAs what they sound like.

They're going to transfer amino acids to the process. Now remember that we're trying to make protein or polypeptide and in order to make protein we do need amino acids because that's what proteins are made of which is something we talked about back in chapter 2. So this represents a transfer RNA and different books give them different shapes but my book gives them a shape. similar to this.

So the parts of a transfer RNA are this is our amino acid, the whole thing is the transfer RNA, and then down at the bottom we have the anticodon which is the sort of the matching puzzle piece to the codons which we labeled down here or the groups of three. Remember that Something else we talked about in chapter 3 that the nitrogenous base A or adenine will bind with U or uracil. C or cytosine will bind with G or guanine.

So we're going to keep that there to remind ourselves as we look through translation so that we don't forget. So we'll keep referring to that. So step 1, the ribosome will... dock itself on the messenger RNA strand as we see here and I like to personify everything so I tend to think of the ribosome as having a personality even though we know that is not the case but the ribosome is going to read the first codon A U G and he is going to call out to the cytoplasm not literally but in our everyday explanation and he's going to ask are there any anticodons that match with this first codon? Well, if we take a look and remember the rule A goes with U and C goes with G then we should have a transfer RNA that has an anticodon of UAC.

So if we look up here, we do in fact see that transfer RNA number one matches with this first slot. So that transfer RNA is going to come down and bring with it its amino acid. Okay, so we don't have a protein yet because we've only got one amino acid, but we're going to read the second codon, CCA.

So that means our anticodon should be GG. U and what do you know here is GGU number two so we bring that transfer RNA down to the second slot and It brings with it its amino acid So at this point the ribosome is full and the next step will be that the first amino acid Will move over and attach itself to the new transfer RNA. Okay, so now we've moved that over and we formed in between the two amino acids a peptide bond, which is exactly how we make a protein. Okay, so now the ribosome has moved down a step and We have a new codon exposed AAA which will bind with U U and U and here we have a tRNA that's anti-codon matches so we will bring down that tRNA and it will bring with it its amino acid. So as you can guess these two guys will move over to the new amino acid forming a longer chain and at that point this tRNA's job is done so it can head back to the cytoplasm and we will again move down another step.

Okay, and now we're ready to move on to the next step. The ribosome is still moving forward and this codon is going to match with the anti-codon AAU, which is this one. So again, it will come down bringing with it its amino acid.

The old guy is going to pass his amino acids over to the new one. So now we have an even longer chain. The old guy will be able to go back to the cytoplasm and wait to be used again.

Now the ribosome will click down one more step. Alright, so now we have a codon AAU that will match with the anticodon UUA, which we see here with tRNA number 5. It will move down, bringing with it, again, its amino acid. So the old guy will pass his amino acids to the new guy. So again our chain continues to grow and the old guy will head back to the cytoplasm. Ribosome will click down a step.

Okay, so now we are at the last codon, which is known as the stop codon, and this will be the end of translation once we make it to the stop codon. So the codon here is UAA, which will correspond with A. U U and we can see that we've got one remaining tRNA which will come down once again bringing with it its amino acid so the old tRNA will once again pass on the amino acids to the new tRNA and this tRNA, the old guy, will go back to the cytoplasm and now we are left at the end at the stop codon.

Everything will disassemble and we will be left with what we wanted to make all along which is a brand new shiny polypeptide made from your genetic code. Okay, so to review what we just drew in your actual notes, we had first the process of transcription, where we began with RNA polymerase, which is an enzyme, binding. It begins at the start signal on the DNA and reads the DNA code to form messenger RNA, which was grouped into three base sequences known as codons or triplets.

At the end of this transcription, the mRNA detaches and then will actually move through the nuclear pores as we showed in our drawing. So once the messenger RNA is edited, it will officially again leave the nucleus through the nuclear pores. So here's your book's version of how the messenger RNA is formed.

So we have our DNA and here's our RNA polymerase splitting the double helix and moving down the DNA strand, creating a messenger RNA strand as it moves. The messenger RNA is the result and once again it's going to leave the nucleus once it's edited through the nuclear pores. Which brings us to translation, the second part. This is when we actually make protein or polypeptides.

So once the mRNA leaves it will bind to the ribosome and each codon will translate to amino acid which is brought by the transfer RNA as we showed in our drawing. The anticodon is what binds to the codon on the messenger RNA strand and we join those amino acids together by peptide bonds. So in this figure you can see the messenger RNA coming out through the pore into the cytoplasm. and our ribosome assembles to look like this.

So our ribosome is sitting on the messenger RNA strand and we begin bringing in transfer RNAs with corresponding anticodons. Remember each one is carrying an amino acid as it sits down on its codon. We bring in an additional transfer RNA to dock itself down as well and we will pass the first amino acid over to bind with the new amino acid. And we are starting a chain.

The first tRNA will then leave and go back to the cytoplasm and the ribosome will move down. As we can see here, so this one is leaving to go back to the cytoplasm. We bring in a new tRNA and it's got its amino acid. So what will happen next as we expect?

The old tRNA will pass his amino acids over to the new tRNA's amino acid, which will form a longer chain of three. The old guy will also leave, and then we will move down the ribosome until we reach the stop codon. When we reach the stop codon, the whole thing will disassemble, and we will be left with a completed polypeptide, which is what we aimed to make in the beginning.

So next is diffusion and osmosis. The cell membrane is a barrier but it has to be what's called semi-permeable or selectively permeable, which means we do need nutrients to get in and we also need products and waste to be able to get out. So permeability is going to determine what can move in and out of a cell or a membrane.

So a membrane that lets nothing in and out would be considered impermeable. If a membrane let anything in or let anything out, that would be freely permeable. Movement that is restricted is called selective permeability and that is what we will find that our cells are.

They're very picky about what comes in and goes out. The plasma membrane is selectively permeable, which again will allow some materials to move freely, but others will be restricted. This again is a good safeguard for our cell.

So diffusion is the movement of a substance from an area of high concentration to an area of low concentration. In a substance, ions and molecules are always moving around. So again, the rule of diffusion...

where things move from a high to a low concentration as demonstrated in this picture from the textbook. So we have a beaker of water here and a colored sugar cube is placed into the water and there is a large amount of color right around that sugar cube so that would be where the high concentration is and out here in the water there is a very low concentration of color. So remembering the rule, we move from high to low concentration, the color will begin to spread from the high concentrated area towards the low concentrated area, which means the color will spread out until eventually we have equal coloration in the beaker of water. So diffusion will continue. until the concentration gradient is eliminated and there is an equal distribution throughout the entire solution.

Osmosis is the diffusion of water from a high to a low concentration. So again the same exact rule of high to low, but when we hear the word osmosis we should think of water not a substance other than water. So same rule.

diffusion but we're focusing on the water so this is movement of water from a high to a low concentration so we can take a look at that using these two figures so we have a u-shaped tube here and in the very middle we have a semi permeable membrane or selectively permeable membrane kind of like the cell membrane And in the solution we have water molecules which are the small blue dots and then the pink solution or the pink dots represent something else like possibly sodium for example. So if we look at the concentration of each on either side of the membrane you'll notice that on the left side There's a lot of blue dots which represent water and less pink dots which could represent possibly sodium. On the right, there's more sodium and less blue dots or less water.

So according to the rule of diffusion, water will move from a high to a low concentration. Right now, there's more water on the left than there is on the right. So that should mean that water is going to move.

from the left side where it is greater toward the right side where it is less. And we do see that so the water moved to the right but you can now see that the volume on the right side has increased and this balance or this fluctuation will continue until we have an equal amount of water on the left as we do on the right. So osmolality or osmotic concentration is the total solute concentration in a solution.

Tonicity describes how a solution affects a cell, which is particularly important in cell physiology. An isotonic solution is a solution where there is no movement of water into or out of the cell that is severe. There's not much movement at all. So the cell is quite happy. In this solution, this is a nice balanced solution.

Hypotonic solution is when there is a lower solute concentration than in the cell. Now what that means is that water will actually move into the cell until the cell becomes very swollen and it can actually cause the cell to pop open. And one way I always remember this hypotonic is going to cause the cell to swell is there's a nice round O here in the word hypotonic and that nice round O reminds me of a swollen cell. Hypotonic solution is when there's a higher solute concentration around the cell than in the cell so what that's going to do is actually cause water to move out of the cell towards the solute and that's going to cause the cell to shrivel.

So we'll look at this in a couple of pictures. So a cell in an isotonic solution will stay the same size and shape. A cell in a hypotonic solution will gain water. That's when we talked about the nice swollen cell. It can rupture which is called hemolysis when we're talking about a blood cell.

A cell in a hypertonic solution can lose water and shrink which is known as Crenation. So here's a red blood cell in an isotonic solution where the water molecules and the solute molecules are even on the inside and outside of the cell. So this is going to create very little extreme flow. This is going to be a nice balanced flow making the cell quite happy.

This is a very good cell solution. So in this solution the water flows into the cell and that can cause the cell to swell and possibly rupture which we call lysis. In a hypertonic solution water moves out of the cell. The red blood cell can shrivel which is called Crenation. Endocytosis comes in two major forms that we'll talk about now.

We have penocytosis, which is when the cell drinks extracellular fluid or brings in endosomes or pockets of extracellular fluid. Phagocytosis is when we take in solids. So the cell can reach out with cytoplasmic extensions, which are called pseudopodia. and grab extracellular structures or even a bacterium, for example, and pull it in and later digest it.

So cellular eating, bringing in solids. Exocytosis, which we already discussed, is when we release objects from the cytoplasm or exit objects from the cytoplasm. Membrane potential. is defined as when a positive and negative charge is separated This creates a potential difference and we see this in cells.

So there is a slight excess of positivity on the exterior of the membrane of a cell which is due to sodium mainly. The positive and negatives across the membrane are attracted to each other but the membrane keeps them apart, which we call membrane potential. The measurement is in millivolts or a thousandth of a volt and the plasma membrane will act as a dam basically keeping the positive and negative charge apart across the membrane. They cannot rush together to attract.

So that unequal charge across the plasma membrane is known as the membrane potential. The resting membrane potential of a cell can range from negative 10 millivolts to negative 100 millivolts depending on the cell type. So our last large topic would be mitosis. So cell division is a form of cell reproduction. A single cell can produce two daughter cells when it divides.

At the end of the cell's life it can undergo genetically controlled death. apoptosis. So in the cell life cycle we have what's called interphase.

This is when the cell is not actively dividing but spending, this is where cells spend the majority of their lives, and during this phase they can begin to prepare for mitosis or division. Somatic cells recall our general body cells and in humans somatic cells are going to contain 46 chromosomes so this would not include the egg and the sperm. The egg and the sperm undergo meiosis. So in mitosis we're going to see a few phases which we will review. So duplication of chromosomes in the nucleus and then separation into two identical sets will happen during mitosis.

and it's going to consist of four main phases. Prophase, metaphase, anaphase, and finally telophase. Cytokinesis is the division of the cytoplasm. This is what happens at the very end, and that will produce two daughter cells, brand new cells. So here is a great slide that shows a review of the main parts of mitosis.

So we'll begin here in prophase. So prophase is step one of mitosis. Remember interphase is where we were before this, just kind of hanging out, getting ready for mitosis to begin. And right before mitosis begins, we're going to double the chromosomes in the cell to prepare for division.

So prophase, during that time, the DNA or the chromatin, will actually condense and chromosomes become visible during this phase. So the chromosomes condense and then spindle fibers, which are these guys, will appear and they'll be very clear inside the cell. When we move to metaphase, in metaphase the chromosomes or chromatids will move to a central zone of the cell called the metaphase plate.

and the metaphase plate is kind of an imaginary line that the cells line up on. The spindle fibers attach to those chromatids and in anaphase the center point of the chromatid pair called the centromere will split and the chromatids will separate. The daughter chromosomes are pulled to opposite ends of the cell. And then in telophase, the new cells get ready to return to interphase, the nuclear membranes reform, and the chromosomes gradually uncoil. And this will be followed by the actual splitting of the two cells, which is called cytokinesis, where the two cells split apart and we are completely done with mitosis.

So mitotic rate is the rate of cell division. Slower mitosis means a longer cell life. Cell division does require energy in the form of ATP, which we talked about previously as well. Okay, so a tumor or neoplasm is defined as a mass of abnormal cell growth. When cells grow out of control and grow when they are not instructed to grow, they can form these masses.

Tumors can be benign, which means contained. not life-threatening unless they're large and these are not likely to spread. A malignant tumor will spread into surrounding tissue which is known as an invasion.

Cancer results from abnormal proliferation of cells, so when cells grow out of control, which can be caused by mutations in genes. These genes are involved with cell growth. Modified genes are called oncogenes and mutagens are agents that can cause mutations.

Carcinogens, including mutagens, are cancer-causing agents. And metastasis is the spread of cancer to other areas, which begins with the invasion of tissue surrounding that particular tumor. So here's an example of how metastasis can actually happen.

Here we can see in the tissue an abnormal cell and this abnormal cell begins to grow into a mass, which we call a tumor. And if these cells continue to spread, they can enter circulation. And that's bad news because circulation provides a highway for these bad cells to spread, escape, and form.

new masses. So all cells contain the same number of chromosomes and genes. We're talking about a human in particular.

Now again we talked about how somatic cells are going to have 46 in humans and if we talk about sex cells then of course we're going to have half the complement which would be 23 in eggs and 23 in sperm. But each one of your cells contains copies of your genetic makeup. Cells undergo differentiation, which means they become specialized by turning off genes not needed by that cell. And when cells become specialized, they become really good at specific jobs.

So this will allow cells to form different types of cells like liver cells, fat cells, and even neurons, which we will talk about all of those eventually. This concludes chapter 3, the last of the chapters of general biology review, as we head now into chapter 4, which would be a study of the tissues or histology.

Transcript for:Cellular Organization and Function Overview

Transcript for:
Cellular Organization and Function Overview