Cell Structure and Function

Peroxisome

There are many ways that peroxisomes are similar to lysosomes. They are small vesicles found around the cell. They have a single membrane that contains digestive enzymes for breaking down toxic materials in the cell. They differ from lysosomes in the type of enzyme they hold. It houses enzymes involved in oxidation reactions, which produce hydrogen peroxide as a by-product. The enzymes break down fatty acids and amino acids, and they also detoxify some substances that enter the body. For example, alcohol is detoxified by peroxisomes found in liver cells. Importantly, peroxisomes—unlike lysosomes—are not part of the endomembrane system. That means they don't receive vesicles from the Golgi apparatus.

Cell Surface Area to Volume Ratio

A cell prefers a large SA:V ratio because they rely on a large SA for diffusion to get substances into and out of the cell. But how does a cell achieve this large ratio? If we assume a cell is a cube, the ratio would be 6s²/s³ = 6/s. So, as we increase the length of one side, the ratio decreases. This isn't what we want, so cells need to be small to in order to minimize the ratio. If we the cell is a sphere, then the ratio is 4πr²/(4/3)πr³ = 3/r. Similarly, the cell needs to be small in order to minimize the ratio. When a cell grows, there is comparatively less membrane for the substances to diffuse through, resulting in the center of the cell not receiving the substances that it needs. Diffusion is less efficient, cell processes slow down and the cell stops growing. The cell then needs to divide into two smaller cells, which each have a larger SA:V volume and can diffuse materials more efficiently again. Cells have other ways of increasing this ratio, including folding their memranes--we see this in the mitochondria.

Diffusion

is a type of passive transport. During diffusion, substances move from an area of high concentration to an area of low concentration, until the concentration becomes equal throughout a space. This is also true for some substances moving into and out of cells. Because the cell membrane is semipermeable, only small, uncharged substances like carbon dioxide and oxygen can easily diffuse across it. Charged ions or large molecules require different kinds of transport.

Calculating Solute Potential

Ψs = -iCRT i = ionization constant (how many ions are in the solute? If the molecule doesn't dissolve, this is 1.) C = Molar concentration (mol/L) R = Pressure constant, which is also the universal gas constant (0.0831 liters x bars/mol x K) T = Temperature in Kelvin The unit for water potential is in bars.

Flagellum

A long, hairlike structure that grows out of a cell and enables the cell to move. They are found in bacteria, archaea, and eukaryotes, though they are most commonly found in bacteria. They are typically used to propel a cell through liquid (i.e. bacteria and sperm). However, flagella have many other specialized functions. Some eukaryotic cells use flagellum to increase reproduction rates. Other eukaryotic and bacterial flagella are used to sense changes in the environment, such as temperature or pH disturbances. The flagellum is made up of microtubules composed from a protein called tubulin. Nine microtubule pairs surround another two pairs of microtubules in the center to form the core of the flagellum; this is known as the nine-plus-two arrangement, just like the one found in cilia. These bundled microtubules use ATP to bend back and forth in a whip-like motion together. Although few multicellular eukaryotes have true flagellum, almost half the human population produces cells with them in the form of sperm. In order to move through the vaginal tract to meet the egg, sperm must be able to swim, or move, very long distances (in comparison of cell to body size). On the other hand, bacterial flagella are structured and function completely differently than the eukaryotic counterparts. These flagella are made of a protein called flagellin. ATP isn't needed because bacterial flagellum can use the energy of the proton-motive force. This means the energy is derived from ion gradients - usually hydrogen or sodium - which lie across cell membranes. These flagella are helix shaped and rotate quickly like a windmill to move the organism instead of whipping back and forth. A cell can have multiple flagellum that could be attached an one end, both ends, or all over the organism.

Prokaryotes and Structures

A unicellular organism that lacks a nucleus and membrane bound organelles. The majority of prokaryotic is found in a central region of the cell called the nucleoid, and it typically consists of a single large loop called a circular chromosome. Bacteria are very diverse in form, so not every type of bacterium will have all of the same features. Most bacteria are, however, surrounded by a rigid cell wall made out of peptidoglycan, a polymer composed of linked carbohydrates and small proteins. The cell wall provides an extra layer of protection, helps the cell maintain its shape, and prevents dehydration. Many bacteria also have an outermost layer of carbohydrates called the capsule. The capsule is sticky and helps the cell attach to surfaces in its environment. Some bacteria also have specialized structures found on the cell surface, which may help them move, stick to surfaces, or even exchange genetic material with other bacteria. For instance, flagella are whip-like structures that act as rotary motors to help bacteria move. Fimbriae are numerous, hair-like structures that are used for attachment to host cells and other surfaces. Bacteria may also have rod-like structures known as pili, which come in different varieties. For instance, some types of pili allow a bacterium to transfer DNA molecules to other bacteria, while others are involved in bacterial locomotion—helping the bacterium move. Archea (a group of unicellular prokaryotic organisms distinct from bacteria) may also have most of these cell surface features, but their versions of a particular feature are typically different from those of bacteria. For instance, although archaea also have a cell wall, it's not made out of peptidoglycan—although it does contain carbohydrates and proteins. Despite these differences between prokaryotes and eukaryotes, all cells have these four parts in common: a plasma membrane, cytoplasm, ribosomes, and DNA. Plasma membrane - also known as cell membrane.

Cell Theory

A widely accepted explanation of the relationship between cells and living things: 1. All living things are composed of one or more cells. 2. The cell is the basic unit of life. 3. New cells arise from pre-existing cells.

Facilitated Diffusion

Although gases can diffuse easily between the phospholipids of the cell membrane, many polar or charged substances (like chloride) need help from membrane proteins. Membrane proteins can be either channel proteins or carrier proteins. Even though a concentration gradient may exist for these substances, their charge or polarity prevents them from crossing the hydrophobic center of the cell membrane. Substances transported through facilitated diffusion still move with the concentration gradient, but the transport proteins protect them from the hydrophobic region as they pass through. Because facilitated diffusion occurs when there is a concentration gradient, they do not require ATP.

Why do Mitochondria and Chloroplasts have their own DNA and Ribosomes?

Both mitochondria and chloroplasts contain their own DNA and ribosomes. Why would these organelles need DNA and ribosomes, when there is DNA in the nucleus and ribosomes in the cytosol? Strong evidence points to endosymbiosis as the answer to the puzzle. Symbiosis is a relationship in which organisms from two separate species live in a close, dependent relationship. Endosymbiosis (endo- = "within") is a specific type of symbiosis where one organism lives inside the other. Bacteria, mitochondria, and chloroplasts are similar in size. Bacteria also have DNA and ribosomes similar to those of mitochondria and chloroplasts. Based on this and other evidence, scientists think host cells and bacteria formed endosymbiotic relationships long ago, when individual host cells took in aerobic (oxygen-using) and photosynthetic bacteria but did not destroy them. Through millions of years of evolution, the aerobic bacteria became mitochondria and the photosynthetic bacteria became chloroplasts.

Plasma Membrane

Both prokaryotic and eukaryotic cells have a plasma membrane, a double layer of lipids that separates the cell interior from the outside environment. This double layer consists largely of specialized lipids called phospholipids. A phospholipid is made up of a hydrophilic, water-loving, phosphate head, along with two hydrophobic, water-fearing, fatty acid tails. Phospholipids spontaneously arrange themselves in a double-layered structure with their hydrophobic tails pointing inward and their hydrophilic heads facing outward. This energetically favorable two-layer structure, called a phospholipid bilayer, is found in many biological membranes. Proteins are also an important component of the plasma membrane. Some of them pass all the way through the membrane, serving as channels or signal receptors, while others are just attached at the edge. Different types of lipids, such as cholesterol, may also be found in the cell membrane and affect its fluidity. The plasma membrane is the border between the interior and exterior of a cell. As such, it controls passage of various molecules—including sugars, amino acids, ions, and water—into and out of the cell. How easily these molecules can cross the membrane depends on their size and polarity. Some small, nonpolar molecules, such as oxygen, can pass directly through the phospholipid portion of the membrane. Larger and more polar, hydrophilic, molecules, such as amino acids, must instead cross the membrane by way of protein channels, a process that is often regulated by the cell. The surface area of the plasma membrane limits the exchange of materials between a cell and its environment. Some cells are specialized in the exchange of wastes or nutrients and have modifications to increase the area of the plasma membrane. For instance, the membranes of some nutrient-absorbing cells are folded into fingerlike projections called microvilli, singular, microvillus. Cells with microvilli cover the inside surface of the small intestine, the organ that absorbs nutrients from digested food. The microvilli help intestinal cells maximize their absorption of nutrients from food by increasing plasma membrane surface area.

Exocytosis

Cells must take in certain molecules, such as nutrients, but they also need to release other molecules, such as signaling proteins and waste products, to the outside environment. Exocytosis (exo = external, cytosis = transport mechanism) is a form of bulk transport in which materials are transported from the inside to the outside of the cell in membrane-bound vesicles that fuse with the plasma membrane. Some of these vesicles come from the Golgi apparatus and contain proteins made specifically by the cell for release outside, such as signaling molecules. Other vesicles contain wastes that the cell needs to dispose of, such as the leftovers that remain after a phagocytosed particle has been digested. These vesicles are transported to the edge of the cell, where they can fuse with the plasma membrane and release their contents into the extracellular space. Some vesicles fuse completely with the membrane and are incorporated into it, while others follow the "kiss-and-run" model, fusing just enough to release their contents ("kissing" the membrane) before pinching off again and returning to the cell interior.

Chloroplasts

Chloroplasts are found only in plants and photosynthetic algae. (Humans and other animals do not have chloroplasts.) The chloroplast's job is to carry out a process called photosynthesis. In photosynthesis, light energy is collected and used to build sugars from carbon dioxide. The sugars produced in photosynthesis may be used by the plant cell, or may be consumed by animals that eat the plant, such as humans. The energy contained in these sugars is harvested through a process called cellular respiration, which happens in the mitochondria of both plant and animal cells. Two membranes contain and protect the inner parts of the chloroplast. They are appropriately named the outer and inner membranes. In between the inner and outer membranes is the intermembrane space. The inner membrane surrounds the stroma (the fluid present within the inner membrane of chlorplast) and the grana (stacks of thylakoids), regulating passage of materials in and out of the chloroplast. The thylakoid system is suspended in the stroma. The thylakoid system is a collection of membranous sacs called thylakoids. The chlorophyll is found in the thylakoids (floating in the stroma) and is the sight for the process of light reactions of photosynthesis to happen. The thylakoids are arranged in stacks known as grana. Each granum contains around 10-20 thylakoids. As energy rich molecules are created by the light-dependent reactions, they move to the stroma where carbon (C) can be fixed and sugars are synthesized. This is where light-independent, or the Calvin Cycle, takes place. Chloroplast DNA (which has its own genome) and ribosomes are found floating around the stroma.

Microtubules

Despite the "micro" in their name, microtubules are the largest of the three types of cytoskeletal fibers, with a diameter of about 25 nm. A microtubule is made up of tubulin proteins arranged to form a hollow, straw-like tube, and each tubulin protein consists of two subunits, α-tubulin and β-tubulin. Microtubules, like actin filaments, are dynamic structures: they can grow and shrink quickly by the addition or removal of tubulin proteins. Also similar to actin filaments, microtubules have directionality, meaning that they have two ends that are structurally different from one another. In a cell, microtubules play an important structural role, helping the cell resist compression forces. In addition to providing structural support, microtubules play a variety of more specialized roles in a cell. For instance, they provide tracks for motor proteins called kinesins and dyneins, which transport vesicles and other cargoes around the interior of the cell. During cell division, microtubules assemble into a structure called the spindle, which pulls the chromosomes apart.

Osmosis

Diffusion of water through a selectively permeable membrane where the water moves from areas of more solutes to areas of less solutes. Why does this occur? In diffusion, air molecules would naturally move from a high concentrated area to a low concentrated area. In the case of osmosis, you can once again think of molecules—this time, water molecules—in two compartments separated by a membrane. If neither compartment contains any solute, the water molecules will be equally likely to move in either direction between the compartments. But if we add solute to one compartment, it will affect the likelihood of water molecules moving out of that compartment and into the other—specifically, it will reduce this likelihood. Why should that be? There are some different explanations out there. The one that seems to have the best scientific support involves the solute molecules actually bouncing off the membrane and physically knocking the water molecules backwards and away from it, making them less likely to cross. Regardless of the exact mechanisms involved, the key point is that the more solute water contains, the less apt it will be to move across a membrane into an adjacent compartment. This results in the net flow of water from regions of lower solute concentration to regions of higher solute concentration.

Centrioles

Every animal-like cell has two small organelles called centrioles. They are there to help the cell when it comes time to divide. They are put to work in both the process of mitosis and the process of meiosis. You will usually find them near the nucleus but they cannot be seen when the cell is not dividing. And what are centrioles made of? Microtubules. A centriole is a small set of microtubules arranged in a specific way. There are nine groups of microtubules. When two centrioles are found next to each other, they are usually at right angles. The centrioles are found in pairs and move towards the poles (opposite ends) of the nucleus when it is time for cell division. You will not see well-defined centrioles when the cell is not dividing. You will see a condensed and darker area of the cytoplasm near the nucleus called the centrosome.

Cilia

Found in eukaryotic cells, cilia are hairlike projections that extend from the plasma membrane and are used for locomotion. They are also involved in mechanoreception, the ability to detect and respond to certain kinds of stimuli. A cilium is made up of microtubules coated in plasma membrane. The microtubules are small hollow rods made of the protein tubulin. Each cilium contains nine pairs of microtubules forming the outside of a ring, and two central microtubules. This structure is known as an axoneme, and the arrangement as '9+2', an arrangement ubiquitous in motile (capable of motion) cilia. The motor proteins (dynein) are large flexible molecules that allow the cilia to be motile. The proteins hydrolyze ATP for energy. As the proteins are activated, they undergo conformational changes which allow for complex movements.Besides movement of the cell itself, cilia can help to remove contaminants from organs or tissue by helping to move fluids over the cell.

Gap Junctions

Functionally, gap junctions in animal cells are a lot like plasmodesmata in plant cells: they are channels between neighboring cells that allow for the transport of ions, water, and other substances. tructurally, however, gap junctions and plasmodesmata are quite different. In vertebrates, gap junctions develop when a set of six membrane proteins called connexins form an elongated, donut-like structure called a connexon. When the pores, or "doughnut holes," of connexons in adjacent animal cells align, a channel forms between the cells. (Invertebrates also form gap junctions in a similar way, but use a different set of proteins called innexins.) Gap junctions are particularly important in cardiac muscle: the electrical signal to contract spreads rapidly between heart muscle cells as ions pass through gap junctions, allowing the cells to contract in tandem. Not all junctions between cells produce cytoplasmic connections. Instead, tight junctions create a watertight seal between two adjacent animal cells. The purpose of tight junctions is to keep liquid from escaping between cells, allowing a layer of cells (for instance, those lining an organ) to act as an impermeable barrier.

Nucleolus

If you look at a microscope image of the nucleus, you may notice - depending on the type of stain used to visualize the cell - that there's a dark spot inside it. This darkly staining region is called the nucleolus, and it's the site in the nucleus where new ribosomes are assembled. How do you make a ribosome? Some chromosomes have sections of DNA that encode ribosomal RNA, a type of structural RNA that combines with proteins to make the ribosome. In the nucleolus, new ribosomal RNA (rRNA) combines with proteins to form the subunits of the ribosome. The newly made subunits are transported out through the nuclear pores to the cytoplasm, where they can do their job. Some cell types have more than one nucleolus inside the nucleus. For instance, some mouse cells have up to 6 nucleoli. Prokaryotes, which do not have a nucleus, don't have nucleoli and build their ribosomes in the cytosol.

Chromatin and Histones

In both their loose and compact forms, the DNA strands of chromosomes are bound to structural proteins, including a family of proteins called histones. These DNA-associated proteins organize the DNA and help it fit into the nucleus, and they also play a role in determining which genes are active or inactive. The complex formed by DNA and its supporting structural proteins is known as chromatin.

Intermediate Filaments

Intermediate filaments are a type of cytoskeletal element made of multiple strands of fibrous proteins wound together. As their name suggests, intermediate filaments have an average diameter of 8 to 10 nm, in between that of microfilaments and microtubules. Intermediate filaments come in a number of different varieties, each one made up of a different type of protein. One protein that forms intermediate filaments is keratin, a fibrous protein found in hair, nails, and skin. Unlike actin filaments, which can grow and disassemble quickly, intermediate filaments are more permanent and play an essentially structural role in the cell. They are specialized to bear tension, and their jobs include maintaining the shape of the cell and anchoring the nucleus and other organelles in place.

Mitochondria

Mitochondria (singular, mitochondrion) are often called the powerhouses or energy factories of the cell. Their job is to make a steady supply of adenosine triphosphate (ATP), the cell's main energy-carrying molecule. The process of making ATP using chemical energy from fuels such as sugars is called cellular respiration, and many of its steps happen inside the mitochondria. They are usually oval-shaped and have a double membrne structure: an outer one, surrounding the whole organelle, and an inner one, with many inward protrusions called cristae that increase surface area. These cristae are important because the increase in SA holds the proteins involved in the electron transport chain. The space between the membranes is called the intermembrane space, and the compartment enclosed by the inner membrane is called the matrix. The matrix is a liquid area that contains the soluble enzymes of the Krebs cycle which completely oxidize the acetyl-CoA to produce CO2, H2O and hydrogen ions. Although mitochondria are found in most human cell types (as well as most cell types in other animals and plants), their numbers vary depending on the role of the cell and its energy needs. For instance, muscle cells typically have high energy needs and large numbers of mitochondria, while red blood cells, which are highly specialized for oxygen transport, have no mitochondria at all.

Extracellular Matrix

Most animal cells release materials into the extracellular space, creating a complex meshwork of proteins and carbohydrates called the extracellular matrix (ECM). A major component of the extracellular matrix is the protein collagen. Collagen proteins are modified with carbohydrates, and once they're released from the cell, they assemble into long fibers called collagen fibrils. Collagen plays a key role in giving tissues strength and structural integrity. In the extracellular matrix, collagen fibers are interwoven with a class of carbohydrate-bearing proteoglycans, which may be attached to a long polysaccharide backbone. The extracellular matrix also contains many other types of proteins and carbohydrates. The extracellular matrix is directly connected to the cells it surrounds. Some of the key connectors are proteins called integrins, which are embedded in the plasma membrane. Proteins in the extracellular matrix, like the fibronectin molecules, can act as bridges between integrins and other extracellular matrix proteins such as collagen. On the inner side of the membrane, the integrins are linked to the cytoskeleton. Integrins anchor the cell to the extracellular matrix. In addition, they help it sense its environment. They can detect both chemical and mechanical cues from the extracellular matrix and trigger signaling pathways in response.

Microfilaments

Of the three types of protein fibers in the cytoskeleton, microfilaments are the narrowest. They have a diameter of about 7 nm and are made up of many linked monomers of a protein called actin, combined in a structure that resembles a double helix. Because they are made of actin monomers, microfilaments are also known as actin filaments. Actin filaments have directionality, meaning that they have two structurally different ends. Actin filaments have a number of important roles in the cell. For one, they serve as tracks for the movement of a motor protein called myosin, which can also form filaments. Because of its relationship to myosin, actin is involved in many cellular events requiring motion. Actin filaments may also serve as highways inside the cell for the transport of cargoes, including protein-containing vesicles and even organelles. These cargoes are carried by individual myosin motors, which "walk" along actin filament bundles. Actin filaments can assemble and disassemble quickly, and this property allows them to play an important role in cell motility (movement), such as the crawling of a white blood cell in your immune system. Finally, actin filaments play key structural roles in the cell. In most animal cells, a network of actin filaments is found in the region of cytoplasm at the very edge of the cell. This network, which is linked to the plasma membrane by special connector proteins, gives the cell shape and structure.

Plasmodesmata

Plant cells, surrounded as they are by cell walls, don't contact one another through wide stretches of plasma membrane the way animal cells can. However, they do have specialized junctions called plasmodesmata (singular, plasmodesma), places where a hole is punched in the cell wall to allow direct cytoplasmic exchange between two cells. Plasmodesmata are lined with plasma membrane that is continuous with the membranes of the two cells. Each plasmodesma has a thread of cytoplasm extending through it, containing an even thinner thread of endoplasmic reticulum. Molecules below a certain size (the size exclusion limit) move freely through the plasmodesmal channel by passive diffusion. The size exclusion limit varies among plants, and even among cell types within a plant. Plasmodesmata may selectively dilate (expand) to allow the passage of certain large molecules, such as proteins, although this process is poorly understood.

Primary Active Transport

Primary active transport utilizes chemical energy from ATP to drive protein pumps that are embedded in the cell membrane. With energy from ATP, the pumps transport ions against their electrochemical gradients—a direction they would not normally travel by diffusion. One important transporter responsible for maintaining the electrochemical gradient in cells is the sodium-potassium pump. The primary active transport activity of the pump occurs when it is oriented such that it spans the membrane with its extracellular side closed, and its intracellular region open and associated with a molecule of ATP. In this conformation, the transporter has a high affinity for sodium ions normally present in the cell in low concentrations, and three of these ions enter into and attach to the pump. Such binding allows ATP to transfer one of its phosphate groups to the transporter, providing the energy needed to close the pump's intracellular side and open the extracellular region. The change in conformation decreases the pump's affinity for sodium ions—which are released into the extracellular space—but increases its affinity for potassium, allowing it to bind two potassium ions present in low concentration in the extracellular environment. The extracellular side of the pump then closes, and the ATP-derived phosphate group on the transporter detaches. This enables a new ATP molecule to associate with the pump's intracellular side, which opens and allows the potassium ions to exit into the cell—returning the transporter to its initial shape beginning the cycle again (3 Na+ outside and 2 K+ inside). Due to the pump's primary active transport activity, there ends up being an imbalance in the distribution of ions across the membrane. There are more potassium ions inside the cell and more sodium ions outside the cell. Therefore, the inside of the cells ends up being more negative than the outside. An electrochemical gradient is generated as a result of the ion imbalance.

Plasma Membrane Proteins and Carbohydrates

Proteins are a major component of plasma membranes. There are two main categories of membrane proteins: integral and peripheral. Integral membrane proteins are, as their name suggests, integrated into the membrane: they have at least one hydrophobic region that anchors them to the hydrophobic core of the phospholipid bilayer. Some stick only partway into the membrane, while others stretch from one side of the membrane to the other and are exposed on either side. Proteins that extend all the way across the membrane are called transmembrane proteins. Some integral membrane proteins form a channel that allows ions or other small molecules to pass, and these are called channel proteins. These channel proteins work towards the concentration gradient and therefore don't need ATP to function. Another important integral protein is the carrier protein which allows larger molecules to enter by acting as a glove and protecting it until the molecule enters the cell. As opposed to channel proteins, these can act against concentration gradients which require ATP. However, carrier proteins also support passive transport. Peripheral membrane proteins are found on the outside and inside surfaces of membranes, attached either to integral proteins or to phospholipids. Unlike integral membrane proteins, peripheral membrane proteins do not stick into the hydrophobic core of the membrane, and they tend to be more loosely attached. An example would be hormones that tell the cell to do something and then leave. Carbohydrates are the other major component of plasma membranes. In general, they are found on the outside surface of cells and are bound either to proteins (forming glycoproteins) or to lipids (forming glycolipids). These carbohydrate chains may consist of 2-60 monosaccharide units and can be either straight or branched. Along with membrane proteins, these carbohydrates form distinctive cellular markers, sort of like molecular ID badges, that allow cells to recognize each other. These markers are very important in the immune system, allowing immune cells to differentiate between body cells, which they shouldn't attack, and foreign cells or tissues, which they should.

Receptor-mediated endocytosis

Receptor-mediated endocytosis is a form of endocytosis in which receptor proteins on the cell surface are used to capture a specific target molecule. The receptors, which are transmembrane proteins, cluster in regions of the plasma membrane known as coated pits. This name comes from a layer of proteins, called coat proteins, that are found on the cytoplasmic side of the pit. When the receptors bind to their specific target molecule, endocytosis is triggered, and the receptors and their attached molecules are taken into the cell in a vesicle. The coat proteins participate in this process by giving the vesicle its rounded shape and helping it bud off from the membrane. Receptor-mediated endocytosis allows cells to take up large amounts of molecules that are relatively rare (present in low concentrations) in the extracellular fluid. Although receptor-mediated endocytosis is intended to bring useful substances into the cell, other, less friendly particles may gain entry by the same route. Flu viruses, diphtheria, and cholera toxin all use receptor-mediated endocytosis pathways to gain entry into cells.

Endoplasmic Reticulum

Structurally, the endoplasmic reticulum is a network of membranes found throughout the cell and connected to the nucleus. The membranes are slightly different from cell to cell and a cell's function determines the size and structure of the ER. For example, some cells, such as prokaryotes or red blood cells, do not have an ER of any kind. Cells that synthesize and release a lot of proteins would need a large amount of ER. You might look at a cell from the pancreas or liver for good examples of cells with large ER structures. There are two basic types of ER. Both rough ER and smooth ER have the same types of membranes but they have different shapes. Rough ER looks like sheets or disks of bumpy membranes while smooth ER looks more like tubes. Rough ER is called rough because it has ribosomes attached to its surface. Smooth ER (SER) acts as a storage organelle. It is important in the creation and storage of lipids and steroids. This is where lipids are made in the cell. Steroids are a type of ringed organic molecule used for many purposes in an organism. Rough ER is very important in the synthesis and packaging of proteins. Ribosomes are attached to the membrane of the ER, making it "rough." The RER is also attached to the nuclear envelope that surrounds the nucleus. Inside the ER, the proteins made from the ribosomes fold and undergo modifications, such as the addition of carbohydrate side chains. These modified proteins will be incorporated into cellular membranes—the membrane of the ER or those of other organelles—or secreted from the cell. If the modified proteins are not destined to stay in the ER, they will be packaged into vesicles, or small spheres of membrane that are used for transport, and shipped to the Golgi apparatus. The rough ER also makes phospholipids for other cellular membranes, which are transported when the vesicle forms.

Tonicity

The ability of an extracellular solution to make water move into or out of a cell by osmosis is know as its tonicity. A solution's tonicity is related to its osmolarity, which is the total concentration of all solutes in the solution. A solution with low osmolarity has fewer solute particles per liter of solution, while a solution with high osmolarity has more solute particles per liter of solution. When solutions of different osmolarities are separated by a membrane permeable to water, but not to solute, water will move from the side with lower osmolarity to the side with higher osmolarity. If the extracellular fluid has lower osmolarity than the fluid inside the cell, it's said to be hypotonic—hypo means less than—to the cell, and the net flow of water will be into the cell. In the reverse case, if the extracellular fluid has a higher osmolarity than the cell's cytoplasm, it's said to be hypertonic—hyper means greater than—to the cell, and water will move out of the cell to the region of higher solute concentration. In an isotonic solution—iso means the same—the extracellular fluid has the same osmolarity as the cell, and there will be no net movement of water into or out of the cell. Hypotonic, hypertonic, and isotonic are relative terms. That is, they describe how one solution compares to another in terms of osmolarity. For instance, if the fluid inside a cell has a higher osmolarity, concentration of solute, than the surrounding fluid, the cell interior is hypertonic to the surrounding fluid, and the surrounding fluid is hypotonic to the cell interior.

Structure of the Plasma Membrane

The currently accepted model for the structure of the plasma membrane, called the fluid mosaic model. According to the fluid mosaic model, the plasma membrane is a mosaic of components—primarily, phospholipids, cholesterol, and proteins—that move freely and fluidly in the plane of the membrane. Interestingly enough, this fluidity means that if you insert a very fine needle into a cell, the membrane will simply part to flow around the needle; once the needle is removed, the membrane will flow back together seamlessly. The plasma membrane is semipermeable, meaning that it only allows certain substances to pass through. The principal components of the plasma membrane are lipids (phospholipids and cholesterol), proteins, and carbohydrate groups that are attached to some of the lipids and proteins. A phospholipid is a lipid made of glycerol, two fatty acid tails, and a phosphate-linked head group. Biological membranes usually involve two layers of phospholipids with their tails pointing inward, an arrangement called a phospholipid bilayer. The fatty acid chains are hydrophobic while the phosphate groups are hydrophillic. Cholesterol, another type of lipid that is embedded among the phospholipids of the membrane, helps to minimize the effects of temperature on fluidity. Membrane proteins may extend partway into the plasma membrane, cross the membrane entirely, or be loosely attached to its inside or outside face. Carbohydrate groups are present only on the outer surface of the plasma membrane and are attached to proteins, forming glycoproteins, or lipids, forming glycolipids.

Secondary Active Transport

The electrochemical gradients set up by primary active transport store energy, which can be released as the ions move back down their gradients. Secondary active transport uses the energy stored in these gradients to move other substances against their own gradients. As an example, let's suppose we have a high concentration of sodium ions in the extracellular space (thanks to the primary active transport from the sodium-potassium pump). If a route such as a channel or carrier protein is open, sodium ions will move down their concentration gradient and return to the interior of the cell. In secondary active transport, the movement of the sodium ions down their gradient is coupled to the uphill transport of other substances by a shared carrier protein (a cotransporter). For instance, a carrier protein lets sodium ions move down their gradient, but simultaneously brings a glucose molecule up its gradient and into the cell. The carrier protein uses the energy of the sodium gradient to drive the transport of glucose molecules. In secondary active transport, the two molecules being transported may move either in the same direction (i.e., both into the cell), or in opposite directions (i.e., one into and one out of the cell). When they move in the same direction, the protein that transports them is called a symporter, while if they move in opposite directions, the protein is called an antiporter.

Endomembrane System

The endomembrane system (endo = "within") is a group of membranes and organelles in eukaryotic cells that works together to modify, package, and transport lipids and proteins. It includes the nuclear envelope, lysosomes, vesicles, and the endoplasmic reticulum and Golgi apparatus. Although not technically within the cell, the plasma membrane is included in the endomembrane system because it interacts with the other endomembranous organelles. The endomembrane system does not include the membranes of either mitochondria or chloroplasts.

Lysosome

The lysosome is an organelle that contains digestive enzymes and acts as the organelle-recycling facility of an animal cell. It breaks down old and unnecessary structures so their molecules can be reused. Lysosomes are part of the endomembrane system, and some vesicles that leave the Golgi are bound for the lysosome. Lysosomes can also digest foreign particles that are brought into the cell from outside.

Cytosol

The part of the cell referred to as cytoplasm is slightly different in eukaryotes and prokaryotes. In eukaryotic cells, which have a nucleus, the cytoplasm is everything between the plasma membrane and the nuclear envelope. In prokaryotes, which lack a nucleus, cytoplasm simply means everything found inside the plasma membrane. One major component of the cytoplasm in both prokaryotes and eukaryotes is the gel-like cytosol, a water-based solution that contains ions, small molecules, and macromolecules. In eukaryotes, the cytoplasm also includes membrane-bound organelles, which are suspended in the cytosol. The cytoskeleton, a network of fibers that supports the cell and gives it shape, is also part of the cytoplasm and helps to organize cellular components. Even though the cytosol is mostly water, it has a semi-solid, Jello-like consistency because of the many proteins suspended in it. The cytosol contains a rich broth of macromolecules and smaller organic molecules, including glucose and other simple sugars, polysaccharides, amino acids, nucleic acids, and fatty acids. Ions of sodium, potassium, calcium, and other elements are also found in the cytosol. Many metabolic reactions, including protein synthesis, take place in this part of the cell.

Cell Wall

Though plants don't make collagen, they have their own type of supportive extracellular structure: the cell wall. The cell wall is a rigid covering that surrounds the cell, protecting it and giving it support and shape. Fungi also have cell walls, as do some protists (a group of mostly unicellular eukaryotes) and most prokaryotes. Like the animal extracellular matrix, the plant cell wall is made up of molecules secreted by the cell. The major organic molecule of the plant cell wall is cellulose, a polysaccharide composed of glucose units. Cellulose assembles into fibers called microfibrils. In bacteria, cell walls are composed of peptidoglycans. Fungi have cell walls formed of chitin, a large, structural polysaccharide made from chains of modified glucose.

Eukaryotes

Unlike prokaryotic cells, eukaryotic cells have: 1. A membrane-bound nucleus, a central cavity surrounded by membrane that houses the cell's genetic material. 2. A number of membrane-bound organelles, compartments with specialized functions that float in the cytosol. 3. Multiple linear chromosomes, as opposed to the single circular chromosome of a prokaryote. Despite these differences between prokaryotes and eukaryotes, all cells have these four parts in common: a plasma membrane, cytoplasm, ribosomes, and DNA. Plasma membrane - also known as cell membrane.

Vacuole

Vacuoles are storage bubbles found in cells. They are found in both animal and plant cells but are much larger in plant cells which is the large central vacuole. The large central vacuole stores water and wastes, isolates hazardous materials, and has enzymes that can break down macromolecules and cellular components, like those of a lysosome. Vacuoles might store food or any variety of nutrients a cell might need to survive. They can even store waste products so the rest of the cell is protected from contamination. Eventually, those waste products would be sent out of the cell.

Water Potential

Water potential is a measure of how likely water is to move from one location (say outside the cell) to another (inside the cell). For example, let's say a plant cell placed in a hypotonic solution. Due to osmosis, water has a higher potential (tendency) to move INTO the cell than it does to move OUT of it. Therefore, water potential is GREATER outside the cell than inside the cell because the water outside the cell has the GREATER POTENTIAL TO MOVE. Just like any solute will diffuse DOWN its concentration gradient—from high to low concentration, water will always move from an area of greater water potential to an area of lesser water potential. Water potential is made up of 2 parts--solute/osmotic potential and pressure potential. Add both together to get the total water potential. First, the solute or osmotic potential, Ψs, is inversely proportional to solute concentration. This is because if you increase solute concentration, your potential to move out of the cell becomes more negative beause of osmosis. This is also true according to the equation--if C gets bigger, water potential becomes more negative. If water potential becomes more negative, so does water potential. Pressure potential, Ψp, is directly proportional to physical pressure. If you have a syringe filled with water and you press down on the plunger (increasing pressure), water will leave the syringe through the needle (the only opening, which increases potential). Plant cells work the same way, if water pressure increases inside the cell, that pressure will drive water back out. The cell wall will not break, but it is a little bit elastic and will bulge outward. This is called turgot. The water pressure that causes turgor is called turgor pressure. If no physical pressure is applied to a solution, then according to the equation, the solute potential is equal to the water potential.

Cytoskeleton

We often think about cells as soft, unstructured blobs. But in reality, they are highly structured in much the same way as our own bodies. They have a network of filaments known as the cytoskeleton (literally, "cell skeleton"), which not only supports the plasma membrane and gives the cell an overall shape, but also aids in the correct positioning of organelles, provides tracks for the transport of vesicles, and (in many cell types) allows the cell to move. In eukaryotes, there are three types of protein fibers in the cytoskeleton: microfilaments, intermediate filaments, and microtubules.

Golgi apparatus

When vesicles bud off from the ER, where do they go? Before reaching their final destination, the lipids and proteins in the transport vesicles need to be sorted, packaged, and tagged so that they wind up in the right place. This sorting, tagging, packaging, and distribution takes place in the Golgi apparatus (Golgi body), an organelle made up of flattened discs of membrane. The receiving side of the Golgi apparatus is called the cis face and the opposite side is called the trans face. Transport vesicles from the ER travel to the cis face, fuse with it, and empty their contents into the lumen of the Golgi apparatus. As proteins and lipids travel through the Golgi, they undergo further modifications. Short chains of sugar molecules might be added or removed, or phosphate groups attached as tags. Finally, the modified proteins are sorted (based on markers such as amino acid sequences and chemical tags) and packaged into vesicles that bud from the trans face of the Golgi. Some of these vesicles deliver their contents to other parts of the cell where they will be used, such as the lysosome or vacuole. Others fuse with the plasma membrane, delivering membrane-anchored proteins that function there and releasing secreted proteins outside the cell. Cells that secrete many proteins—such as salivary gland cells that secrete digestive enzymes, or cells of the immune system that secrete antibodies—have many Golgi stacks. In plant cells, the Golgi apparatus also makes polysaccharides (long-chain carbohydrates), some of which are incorporated into the cell wall.

Phagocytosis and Pinocytosis

are two forms of endocytosis, which is a term for the various types of active transport that moves particles into a cell by enclosing them in a vesicle made out of plasma membrane. In phagocytosis, large particles such as cells or cellular debris are transported into the cell. An example of this would be a macrophage engulfing a pathogen. Once a cell has successfully engulfed a target particle, the pocket containing the particle will pinch off from the membrane, forming a membrane-bound compartment called a food vacuole. The food vacuole will later fuse with an organelle called a lysosome, the "recycling center" of the cell. Lysosomes have enzymes that break the engulfed particle down into its basic components (such as amino acids and sugars), which can then be used by the cell. Pinocytosis (literally, "cell drinking") is a form of endocytosis in which a cell takes in small amounts of extracellular fluid. Pinocytosis occurs in many cell types and takes place continuously, with the cell sampling and re-sampling the surrounding fluid to get whatever nutrients and other molecules happen to be present. Pinocytosed material is held in small vesicles, much smaller than the large food vacuole produced by phagocytosis.

Electrochemical Gradient

is the combination of both the electrical and chemical gradient. The chemical gradient refers to the concentration gradient of a molecule which is what we're used to. For instance, if theres 50 K+ molecules inside the cell and 0 on the outside, then the chemical gradient is to move out of the cell. Now let's say theres 50 K+ and 50 Cl- molecules on the inside and 0 of both on the outside and the transport proteins only allow K+ to go through. Since theres 50 K+ on the inside and none on the outside, the chemical gradient is to move out of the cell. However, if this occurs, there will be a build up of positive charge on the outside and a relative negative charge on the inside, since positive charges are leaving and negative charges are staying (Cl-). The K+ charges are also attracted to Cl- negative charges. This is called the electrical gradient which is driven by electrical forces, and in this case the gradient is moving towards the bottom. It is counteracting the chemical gradient (which dictates that K+ move out of cell, whereas electrical gradient dictates that K+ stay in cell), and the combination of both is what makes up the electrochemical gradient.

Nuclear Envelope

layer of two membranes that surrounds the nucleus of a cell. Each of these membranes contains two layers of phospholipids, arranged with their tails pointing inward (forming a phospholipid bilayer). Nuclear pores, small channels that span the nuclear envelope, let substances enter and exit the nucleus. Each pore is lined by a set of proteins, called the nuclear pore complex, that control what molecules can go in or out.