cytology.pdf

Mooc 5 Module 18 Eukaryotic Cell Structure and Their Variations Academic Script Single membrane bound and membrane-less organelles INTRODUCTION: Organelles are components within a cell that performs specific functions for a cell. A simple real life analogy would be organelles are to a cell as org...

Mooc 5 Module 18 Eukaryotic Cell Structure and Their Variations Academic Script Single membrane bound and membrane-less organelles INTRODUCTION: Organelles are components within a cell that performs specific functions for a cell. A simple real life analogy would be organelles are to a cell as organs are to a human. In biology organs are defined as confined functional units within an organism. The analogy of bodily organs to microscopic cellular substructures is obvious, as from even early works, authors of respective textbooks rarely elaborate on the distinction between the two. History:  In biology organs are defined as confined functional units within an organism. Credited as the first to use a diminutive of organ (i.e. little organ) for cellular structures was German zoologist Karl August Möbius (1884), who used the term "organula". From the context, it is clear that he referred to reproduction related structures of protists, he justified his suggestion to call organs of unicellular organisms "organella" since they are only differently formed parts of one cell, in contrast to multicellular organs of multicellular organisms. Thus, the original definition was limited to structures of unicellular organisms.  Books around 1900 from Valentin Häcker,Edmund Wilson and Oscar Hertwig still referred to cellular organs.  Later, both terms came to be used side by side: Bengt Lidforsswrote 1915 (in German) about "Organs or Organells".  Around 1920, the term organelle was used to describe propulsion structures ("motor organelle complex", i.e., flagella and their anchoring) and other protist structures, such as ciliates. Alfred Kühn wrote about centrioles as division organelles.  In his 1953 textbook, Max Hartmann used the term for extracellular (pellicula, shells, cell walls) and intracellular skeletons of protists.  In 1978, Albert Frey-Wyssling suggested that the term organelle should refer only to structures that convert energy, such as centrosomes, ribosomes, and nucleoli. Common features among prokaryotic and eukaryotic cell: 1. DNA, the genetic material contained in one or more chromosomes and located in a non-membrane bound nucleoid region in prokaryotes and a membrane-bound nucleus in eukaryotes. 2. Plasma membrane, a phospholipid bilayer with proteins that separates the cell from the surrounding environment and functions as a selective barrier for the import and export of materials. 3. Cytoplasm, the rest of the material of the cell within the plasma membrane, excluding the nucleoid region or nucleus, that consists of a fluid portion called the cytosol and the organelles and other particulates suspended in it. 4. Ribosomes, the organelles on which protein synthesis takes place. Some of the organelles are double membrane (maintaining model of double leaflet membrane model) bound, single membrane bound or membrane less. Single membrane organelles Single membrane organelles: 1. Endoplasmic Reticulum 2. Golgi body 3. Lysosome 4. Microbody 5. Vacuole ENDOPLASMIC RETICULUM The endoplasmic reticulum (ER) is an organelle of cells in eukaryotic organisms that forms an interconnected network of tubules, vesicles, and cisternae. Rough endoplasmic reticula are involved in the synthesis of proteins and are also a membrane factory for the cell, while smooth endoplasmic reticula are involved in the synthesis of lipids, including oils, phospholipids and steroids, metabolism of carbohydrates, regulation of calcium concentration and detoxification of drugs and poisons. Sarcoplasmic reticula solely regulate calcium levels. History: The lacey membranes of the endoplasmic reticulum were first seen by Keith R. Porter,Albert Claude, and Ernest F. Fullam in the year 1945. Structure: The general structure of an endoplasmic reticulum is a membranous network of cisternae(sac-like structures) held together by the cytoskeleton. The phospholipid membrane encloses a space, the cisternal space (or lumen), which is continuous with the perinuclear space but separate from the cytosol. The functions of the endoplasmic reticulum vary greatly depending on its cell type, cell function, and cell needs. The ER can even modify to change over time in response to cell needs.. Fig 1. Rough and smooth endoplasmic reticulum Types of endoplasmic reticulum: The three most common varieties are called rough endoplasmic reticulum, smooth endoplasmic reticulum, and sarcoplasmic reticulum  Rough endoplasmic reticulum: The surface of the rough endoplasmic reticulum (RER) is studded with protein-manufacturing ribosomes giving it a "rough" appearance (hence its name). The binding site of the Ribosome on RER is a Glycoprotein receptor called Ribophorin. However, the ribosomes bound to the RER at any one time are not a stable part of this organelle's structure as ribosomes are constantly being bound and released from the membrane. A ribosome binds to the ER only when it begins to synthesize a protein destined for the secretory pathway. Here, a ribosome in the cytosol begins synthesizing a protein until a signal recognition particle recognizes the pre-piece of 5- 15 hydrophobic amino acids preceded by a positively charged amino acid. This signal sequence allows the recognition particle to bind to the ribosome, causing the ribosome to bind to the RER and pass the new protein through the ER membrane. The pre-piece is then cleaved off within the lumen of the ER and the ribosome released back into the cytosol. The membrane of the RER is continuous with the outer layer of the nuclear envelope. Although there is no continuous membrane between the RER and the Golgi apparatus, membrane-bound vesicles shuttle proteins between these two compartments. Vesicles are surrounded by coating proteins called COPI and COPII. COPII targets vesicles to the golgi and COPI marks them to be brought back to the RER. The RER works in concert with the Golgi complex to target new proteins to their proper destinations. A second method of transport out of the ER is areas called membrane contact sites, where the membranes of the ER and other organelles are held closely together, allowing the transfer of lipids and other small molecules. The RER is key in multiple functions:  Lysosomal enzymes with a mannose-6-phosphate marker added in the cis-Golgi network.  Secreted proteins, either secreted constitutively with no tag or secreted in a regulatory manner involving clathrin and paired basic amino acids in the signal peptide.  Integral membrane proteins that stay embedded in the membrane as vesicles exit and bind to new membranes. Rab proteins are key in targeting the membrane; SNAP andSNARE proteins are key in the fusion event.  Initial glycosylation as assembly continues. This is N-linked (O- linking occurs in the Golgi).  N-linked glycosylation: If the protein is properly folded, glycosyltransferase recognizes the AA sequence NXS or NXT (with the S/T residue phosphorylated) and adds a 14-sugar backbone (2-N-acetylglucosamine, 9-branching mannose, and 3-glucose at the end) to the side-chain nitrogen of Asn.  Proper protein folding happens here with the presence of chaperonins.  Smooth endoplasmic reticulum: The smooth endoplasmic reticulum (SER) has functions in several metabolic processes, including synthesis of lipids and steroids, metabolism of carbohydrates, regulation of calcium concentration, drug detoxification, attachment of receptors on cell membrane proteins, and steroid metabolism. It is connected to the nuclear envelope. Smooth endoplasmic reticulum is found in a variety of cell types (both animal and plant), and it serves different functions in each. The Smooth ER also contains the enzyme glucose-6- phosphatase, which converts glucose-6-phosphate to glucose, a step in gluconeogenesis. The SER consists of tubules and vesicles that branch forming a network. In some cells, there are dilated areas like the sacs of RER. The network of SER allows increased surface area for the action or storage of key enzymes and the products of these enzymes. Fig 2: Rough and smooth endoplasmic reticulum membrane is continuous with nuclear envelope. Sercoplasmic reticulum: The sarcoplasmic reticulum (SR), is smooth ER found in smooth and striated muscle. The only structural difference between this organelle and the ER is the medley of proteins they have, both bound to their membranes and drifting within the confines of their lumens. This fundamental difference is indicative of their functions: The ER synthesizes molecules, while the SR stores and pumps calcium ions. The SR contains large stores of calcium, which it sequesters and then releases when the muscle cell is stimulated. The SR's release of calcium upon electrical stimulation of the cell plays a major role in excitation-contraction coupling. Functions: 1. The endoplasmic reticulum serves many general functions, including the facilitation of protein folding and the transport of synthesized proteins in sacs called cisternae. 2. Transport of proteins--Secretory proteins, mostly glycoproteins, are moved across the endoplasmic reticulum membrane. Proteins that are transported by the endoplasmic reticulum and from there throughout the cell are marked with an address tag called a signal sequence. The N-terminus (one end) of a polypeptide chain (i.e., a protein) contains a few amino acids that work as an address tag, which are removed when the polypeptide reaches its destination. Proteins that are destined for places outside the endoplasmic reticulum are packed into transport vesicles and moved along the cytoskeleton toward their destination. 3. The endoplasmic reticulum is also part of a protein sorting pathway. It is, in essence, the transportation system of the eukaryotic cell. The majority of endoplasmic reticulum resident proteins are retained in the endoplasmic reticulum through a retention motif. This motif is composed of four amino acids at the end of the protein sequence. The most common retention sequence is KDEL (lys-asp-glu- leu).Insertion of proteins into the endoplasmic reticulum membrane: Integral membrane proteins are inserted into the endoplasmic reticulum membrane as they are being synthesized (co- translational translocation). Insertion into the endoplasmic reticulum membrane requires the correct topogenic signal sequences in the protein.  Post-translational modification of proteins are done here by Glycosylation: Glycosylation involves the attachment of oligosaccharides. Disulfide bond formation and rearrangement: Disulfide bonds stabilize the tertiary and quaternary structure of many proteins.  Drug metabolism: The smooth ER is the site at which some drugs are modified by microsomal enzymes, which include the cytochrome P450 enzymes.  Having Glucose 6 Phosphatase enzyme SER helps in gluconeogenesis.  Sarcoplasmic reticulum is big reservoir of calcium needed for muscular excitation and contraction. Fig 3. Secretory protein transport by Endoplasmic reticulum GOLGI APPARATUS The Golgi apparatus, also known as the Golgi complex or Golgi body, is an organelle found in most eukaryotic cells. It was identified in 1897 by the Italian physician Camillo Golgi and named after him in 1898. Part of the cellular endomembrane system, the Golgi apparatus packages proteins inside the cell before they are sent to their destination; it is particularly important in the processing of proteins for secretion. History: Due to its fairly large size, the Golgi apparatus was one of the first organelles to be discovered and observed in detail. The apparatus was discovered in 1897 by Italian physician Camillo Golgi during an investigation of the nervous system. Structure: Found within the cytoplasm of both plant and animal cells, the Golgi is composed of stacks of membrane-bound structures known as cisternae. An individual stack is sometimes called a dictyosome. A mammalian cell typically contains 40 to 100 stacks. Between four and eight cisternae are usually present in a stack; however, in some protists as many as sixty have been observed. Each cisterna comprises a flat, membrane enclosed disc that includes special Golgi enzymes which modify or help to modify cargo proteins that travel through it. The cisternae stack has four functional regions: the cis-Golgi network, medial-Golgi, endo-Golgi, and trans-Golgi network. Vesicles from the endoplasmic reticulum (via the vesicular-tubular clusters) fuse with the network and subsequently progress through the stack to the trans Golgi network, where they are packaged and sent to their destination. Each region contains different enzymes which selectively modify the contents depending on where they reside. The cisternae also carry structural proteins important for their maintenance as flattened membranes which stack upon each other. Fig 4: The Golgi body Function: Cells synthesise a large number of different macromolecules. The Golgi apparatus is integral in modifying, sorting, and packaging these macromolecules for cell secretion (exocytosis) or use within the cell. It primarily modifies proteins delivered from the rough endoplasmic reticulum but is also involved in the transport of lipids around the cell, and the creation of lysosomes. In this respect it can be thought of as similar to a post office; it packages and labels items which it then sends to different parts of the cell. Fig 5: Protein trafficking by Golgi body Post translational protein modification: Enzymes within the cisternae are able to modify the proteins by addition of carbohydrates (glycosylation) and phosphates (phosphorylation). In order to do so, the Golgi imports substances such as nucleotide sugars from the cytosol. These modifications may also form a signal sequence which determines the final destination of the protein. For example, the Golgi apparatus adds a mannose-6- phosphate label to proteins destined for lysosomes. The Golgi plays an important role in the synthesis of proteoglycans, which are molecules present in the extracellular matrix of animals. It is also a major site of carbohydrate synthesis. This includes the production of glycosaminoglycans (GAGs), long unbranched polysaccharides which the Golgi then attaches to a protein synthesised in the endoplasmic reticulum to form proteoglycans. Enzymes in the Golgi polymerize several of these GAGs via a xylose link onto the core protein. Another task of the Golgi involves the sulfation of certain molecules passing through its lumen via sulfotranferases that gain their sulfur molecule from a donor called PAPs. This process occurs on the GAGs of proteoglycans as well as on the core protein. The level of sulfation is very important to the proteoglycans' signalling abilities as well as giving the proteoglycan its overall negative charge. The phosphorylation of molecules requires that ATP is imported into the lumen of the Golgi. Transport: The vesicles that leave the rough endoplasmic reticulum are transported to the cis face of the Golgi apparatus, where they fuse with the Golgi membrane and empty their contents into the lumen. Once inside the lumen, the molecules are modified, then sorted for transport to their next destinations. The Golgi apparatus tends to be larger and more numerous in cells that synthesise and secrete large amounts of substances; for example, the plasma B cells and the antibody-secreting cells of the immune system have prominent Golgi complexes. Those proteins destined for areas of the cell other than either the endoplasmic reticulum or Golgi apparatus are moved towards the trans face, to a complex network of membranes and associated vesicles known as the trans-Golgi network (TGN). This area of the Golgi is the point at which proteins are sorted and shipped to their intended destinations by their placement into one of at least three different types of vesicles, depending upon the molecular marker they carry. Transport mechanism: The transport mechanism which proteins use to progress through the Golgi apparatus is not yet clear; however a number of hypotheses currently exist. Until recently, the vesicular transport mechanism was favoured but now more evidence is coming to light to support cisternal maturation. The two proposed models may actually work in conjunction with each other, rather than being mutually exclusive. This is sometimes referred to as the combined model.  Cisternal maturation model: the cisternae of the Golgi apparatus move by being built at the cis face and destroyed at the trans face. Vesicles from the endoplasmic reticulum fuse with each other to form a cisterna at the cis face, consequently this cisterna would appear to move through the Golgi stack when a new cisterna is formed at the cis face. This model is supported by the fact that structures larger than the transport vesicles, such as collagen rods, were observed microscopically to progress through the Golgi apparatus. This was initially a popular hypothesis, but lost favour in the 1980s.  Vesicular transport model: Vesicular transport views the Golgi as a very stable organelle, divided into compartments in the cis to trans direction. Membrane bound carriers transport material between the endoplasmic reticulum and the different compartments of the Golgi. Experimental evidence includes the abundance of small vesicles (known technically as shuttle vesicles) in proximity to the Golgi apparatus. Fig 6: Different transport model by Golgi body. Vesicles: A vesicle is a small bubble within a cell, and are thus a type of organelle. Enclosed by lipid bilayer, vesicles can form naturally, for example, during endocytosis (protein absorption). Alternatively, they may be prepared artificially, when they are called liposomes. If there is only one phospholipid bilayer, they are called unilamellar vesicles; otherwise they are called multilamellar. The membrane enclosing the vesicle is similar to that of the plasma membrane, and vesicles can fuse with the plasma membrane to release their contents outside of the cell. Vesicles can also fuse with other organelles within the cell. There are three types of vesicle coats: clathrin, COPI and COPII. Clathrin coats are found on vesicles trafficking between the Golgi and plasma membrane, the Golgi and endosomes, and the plasma membrane and endosomes. COPI coated vesicles are responsible for retrograde transport from the Golgi to the ER, while COPII coated vesicles are responsible for anterograde transport from the ER to the Golgi. Vesicles may be transport vesicles (towards lysoymes )or secretory vesicles. Vesicular fusion happens with the help of surface markers called SNAREs identify the vesicle's cargo, and complementary SNAREs on the target membrane act to cause fusion of the vesicle and target membrane. Such v-SNARES are hypothesised to exist on the vesicle membrane, while the complementary ones on the target membrane are known as t-SNAREs. Some times lysosome and endosomes, vacuoles are also thought as vesicles. LYSOSOME Lysosomes are cellular organelles that contain acid hydrolase enzymes that break down waste materials and cellular debris. These are non- specific. They can be described as the stomach of the cell. They are found in animal cells, while their existence in yeasts and plants are disputed. Some biologists say the same roles are performed by lytic vacuoles, while others suggest there is strong evidence that lysosomes are indeed in some plant cells. Lysosomes digest excess or worn-out organelles, food particles, and engulf viruses orbacteria. The membrane around a lysosome allows the digestive enzymes to work at the 4.5 pH they require. Lysosomes fuse with vacuoles and dispense their enzymes into the vacuoles, digesting their contents. They are created by the addition of hydrolytic enzymes to earlyendosomes from the Golgi apparatus. They are frequently nicknamed "suicide-bags" or "suicide-sacs" by cell biologists due to their autolysis. Fig 7: The lysosome History: Lysosomes were discovered by the Belgian cytologist Christian de Duve in the 1960s. Structure: The size of a lysosome varies from 0.1–1.2 μm. At pH 4.8, the interior of the lysosomes is acidic compared to the slightly alkaline cytosol (pH 7.2). The lysosome maintains this pH differential by pumping protons (H ions) + from the cytosol across the membrane via proton pumps and chloride ion channels. The lysosomal membrane protects the cytosol, and therefore the rest of the cell, from the degradative enzymes within the lysosome. The cell is additionally protected from any lysosomal acid hydrolases that drain into the cytosol, as these enzymes are pH-sensitive and do not function well or at all in the alkaline environment of the cytosol. This ensures that cytosolic molecules and organelles are not lysed in case there is leakage of the hydrolytic enzymes from the lysosome. Function: Lysosomes are the cell's waste disposal system and can digest some compounds. They are used for the digestion of macromolecules from phagocytosis (ingestion of other dying cells or larger extracellular material, like foreign invading microbes), endocytosis (where receptor proteins are recycled from the cell surface), and autophagy (where in old or unneeded organelles or proteins, or microbes that have invaded the cytoplasm are delivered to the lysosome). Autophagy may also lead to autophagic cell death, a form of programmed self-destruction, or autolysis, of the cell, which means that the cell is digesting itself. Lysosomes (common in animal cells but rare in plant cells) contain hydrolytic enzymes necessary for intracellular digestion. In white blood cells that eat bacteria, lysosome contents are carefully released into the vacuole around the bacteria and serve to kill and digest those bacteria. Uncontrolled release of lysosome contents into the cytoplasm is also a component of necrotic cell death. Fig 8: Function of lysosome Endosome: An endosome is a membrane-bound compartment inside eukaryotic cells. It is a compartment of the endocytic membrane transport pathway from the plasma membrane to the lysosome. Molecules internalized from the plasma membrane can follow this pathway all the way to lysosomes for degradation, or they can be recycled back to the plasma membrane. Molecules are also transported to endosomes from the Golgi and either continue to lysosomes or recycle back to the Golgi. Furthermore, molecules can be directed into vesicles that bud from the perimeter membrane into the endosome lumen. Therefore, endosomes represent a major sorting compartment of the endomembrane system in cells. Endosomes are approximately 500 nm in diameter when fully mature. Endosomes comprise three different compartments: early endosomes, late endosomes, andrecycling endosomes. Fig 9: Endosome MICROBODY: A microbody is a cytoplasmic organelle of a more or less globular shape that comprises degradative enzymes bound within a single membrane. Microbodies are specialized as containers for metabolic activity. Types include peroxisomes, glyoxysomes, glycosomes and Woronin bodies. There are three components of microbody— 1. Peroxisome 2. Glyoxisome 3. Glycosome 4. Woronin bodies PEROXISOME Peroxisomes (also called microbodies) are organelles found in virtually all eukaryotic cells. They are involved in the catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, polyamines, and biosynthesis of plasmalogens, i.e.ether phospholipids critical for the normal function of mammalian brains and lungs. They also contain approximately 10% of the total activity of two enzymes in the pentose phosphate pathway, which is important for energy metabolism. It is vigorously debated if peroxisomes are involved in isoprenoid and cholesterol synthesis in animals. Other known peroxisomal functions include the glyoxylate cycle in germinating seeds ("glyoxysomes"), photorespiration in leaves, glycolysis in trypanosomes ("glycosomes"), and methanol and/or amine oxidation and assimilation in some yeasts. History: Peroxisomes were identified as organelles by the Belgian cytologist Christian de Duve in 1967 after they had been first described by a Swedish doctoral student, J. Rhodin in 1954. Structure: A peroxisome is only about 1 micrometer in diameter. It is bounded by a typical cellular membrane, consisting of a phospholipid bilayer with embedded proteins. Fig 10.Peroxisome Functions: 1. Peroxisomes contain enzymes of β-oxidation (break down fats and produce Acetyl-CoA), as well as enzymes of many other important pathways like amino acid and bile acid metabolism, oxidation/detoxification of various harmful compounds in the liver (ex. alcohol).A major function of the peroxisome is the breakdown of very long chain fatty acids through beta-oxidation. In animal cells, the very long fatty acids are converted to medium chain fatty acids, which are subsequently shuttled to mitochondria where they are eventually broken down to carbon dioxide and water. In yeast and plant cells, this process is exclusive for the peroxisomes. 2. The first reactions in the formation of plasmalogen in animal cells also occur in peroxisomes. Plasmalogen is the most abundant phospholipid in myelin. Deficiency of plasmalogens causes profound abnormalities in the myelination of nerve cells, which is one reason why many peroxisomal disorders affect the nervous system. However the last enzyme is absent in humans, explaining the disease known as gout, caused by the accumulation of uric acid. 3. By the presence of urate oxidase uric acid is metabolized otherwise gout may happen. 4. Curing oxidative stress--Certain enzymes within the peroxisome, by using molecular oxygen, remove hydrogen atoms from specific organic substrates (labeled as R), in an oxidative reaction, producing hydrogen peroxide (H2O2, itself toxic): Then, peroxidase, another peroxisomal enzyme, uses this H2O2 to oxidize other substrates, including phenols, formic acid, formaldehyde, and alcohol, by means of the peroxidation reaction: , thus eliminating the poisonous hydrogen peroxide in the process. This reaction is important in liver and kidney cells, where the peroxisomes detoxify various toxic substances that enter the blood. About 25% of the ethanol humans drink is oxidized toacetaldehyde in this way.[citation needed] In addition, when excess H2O2 accumulates in the cell, catalase converts it to H2O through this reaction: In higher plants, peroxisomes contain also a complex battery of antioxidative enzymes such as superoxide dismutase, the components of the ascorbate-glutathione cycle, and the NADP-dehydrogenases of the pentose-phosphate pathway. It has been demonstrated the generation of superoxide (O2 -) and nitric oxide ( NO) radicals. Fig 11: Function of peroxisome Glyoxysome: Glyoxysomes are found in germinating seeds of plants as well as in filamentous fungi. Glyoxysomes are peroxisomes with additional function - glyoxylate cycle. The glyoxylate cycle, a variation of the tricarboxylic acid cycle, is an anabolicmetabolic pathway occurring in plants, bacteria, protists, fungi. Glycosome: Glycosomes, besides peroxisomal enzymes, also possess glycolysis enzymes and are found in kinetoplastida like Trypanosomes. Woronin bodies: Woronin bodies are special organelles found only in filamentous fungi. One established function of Woronin bodies is the plugging of the septal pores after hyphal wounding, which restricts the loss of cytoplasm to the sites of injury. VACUOLES A vacuole is a membrane-bound organelle which is present in all plant and fungal cells and some protist, animal cells. Vacuoles are essentially enclosed compartments which are filled with water containing inorganic and organic molecules including enzymes in solution, though in certain cases they may contain solids which have been engulfed. Vacuoles are formed by the fusion of multiple membrane vesicles and are effectively just larger forms of these. The organelle has no basic shape or size; its structure varies according to the needs of the cell. History: Vacuoles were found by Antony Van Leuenhook. Structure: A vacuole is any membrane-bound organelle with little or no internal structure. It takes nothing from the cell, and produces nothing for the cell. It does, however, store things for the cell. In a sense, it is a "vacuum". Though common in many cells, they are most prominent in plant cells, taking up most of the central space. Though the contents of the vacuole vary from organism to organism, as a rule, they contain:  atmospheric gases  inorganic salts  Organic acids  Sugars  Pigments It is the pigments in the vacuoles that give flowers, such as this rose, their colors. Function: In general, the functions of the vacuole include:  Isolating materials that might be harmful or a threat to the cell  Containing waste products  Containing water in plant cells  Maintaining internal hydrostatic pressure or turgor within the cell  Maintaining an acidic internal pH  Containing small molecules  Exporting unwanted substances from the cell  Allows plants to support structures such as leaves and flowers due to the pressure of the central vacuole  In seeds, stored proteins needed for germination are kept in 'protein bodies', which are modified vacuoles. Vacuoles also play a major role in autophagy, maintaining a balance between biogenesis(production) and degradation (or turnover), of many substances and cell structures in certain organisms. They also aid in the lysis and recycling of misfolded proteins that have begun to build up within the cell. Plant cell vacuole: Most mature plant cells have one large central vacuole that typically occupies more than 30% of the cell's volume, and that can occupy as much as 80% of the volume for certain cell types and conditions. A vacuole is surrounded by a membrane called the tonoplast. Also called the vacuolar membrane, the tonoplast is the cytoplasmic membrane surrounding a vacuole, separating the vacuolar contents from the cell's cytoplasm. As a membrane, it is mainly involved in regulating the movements of ions around the cell, and isolating materials that might be harmful or a threat to the cell. The central vacuole in plant cells is enclosed by a membrane termed the tonoplast, an important and highly integrated component of the plant internal membrane network (endomembrane) system. This large vacuole slowly develops as the cell matures by fusion of smaller vacuoles derived from the endoplasmic reticulum and Golgi apparatus. Because the central vacuole is highly selective in transporting materials through its membrane, the chemical palette of the vacuole solution (termed the cell sap) differs markedly from that of the surrounding cytoplasm. For instance, some vacuoles contain pigments that give certain flowers their characteristic colors. The central vacuole also contains plant wastes that taste bitter to insects and animals, while developing seed cells use the central vacuole as a repository for protein storage. Function in plant cell: Among its roles in plant cell function, the central vacuole stores salts, minerals, nutrients, proteins, pigments, helps in plant growth, and plays an important structural role for the plant. Under optimal conditions, the vacuoles are filled with water to the point that they exert a significant pressure against the cell wall. This helps maintain the structural integrity of the plant, along with the support from the cell wall, and enables the plant cell to grow much larger without having to synthesize new cytoplasm. In most cases, the plant cytoplasm is confined to a thin layer positioned between the plasma membrane and the tonoplast, yielding a large ratio of membrane surface to cytoplasm. The structural importance of the plant vacuole is related to its ability to control turgor pressure. Turgor pressure dictates the rigidity of the cell and is associated with the difference between the osmotic pressure inside and outside of the cell. Osmotic pressure is the pressure required to prevent fluid diffusing through a semipermeable membrane separating two solutions containing different concentrations of solute molecules. The response of plant cells to water is a prime example of the significance of turgor pressure. When a plant receives adequate amounts of water, the central vacuoles of its cells swell as the liquid collects within them, creating a high level of turgor pressure, which helps maintain the structural integrity of the plant, along with the support from the cell wall. In the absence of enough water, however, central vacuoles shrink and turgor pressure is reduced, compromising the plant's rigidity so that wilting takes place. Plant vacuoles are also important for their role in molecular degradation and storage. Sometimes these functions are carried out by different vacuoles in the same cell, one serving as a compartment for breaking down materials (similar to the lysosomes found in animal cells), and another storing nutrients, waste products, or other substances. Several of the materials commonly stored in plant vacuoles have been found to be useful for humans, such as opium, rubber, and garlic flavoring, and are frequently harvested. Vacuoles also often store the pigments that give certain flowers their colors, which aid them in the attraction of bees and other pollinators, but also can release molecules that are poisonous, odoriferous, or unpalatable to various insects and animals, thus discouraging them from consuming the plant. Fig 12:Vacuole in plant cell Spitzenkörper: The Spitzenkörper is a structure found in fungal hyphae which is the organizing center for hyphal growth and morphogenesis. It consists of many small vesicles and is present in growing hyphal tips, during spore germination and where branch formation occurs. Its position in the hyphal tip correlates with the direction of hyphal growth. The spitzenkörper is a part of the endomembrane system system in fungi. The vesicles are organized around a central area that contains a dense meshwork of microfilaments. Polysomes are often found closely to the posterior boundary of the Spitzenkörper core, microtubules extend into and often through the Spitzenkörper and Woronin bodies are found in the apical region near the Spitzenkörper. Fig 13. Spitzenkorper Non-membrane bound organelles Under the more restricted definition of membrane-bound structures, some parts of the cell do not qualify as organelles. Nevertheless, the use of organelle to refer to non-membrane bound structures such as ribosome is common. This has led some texts to delineate between membrane-bound and non-membrane bound organelles. These structures are large assemblies of macromolecules that carry out particular and specialized functions, but they lack membrane boundaries. Such cell structures include:  Ribosome  Cytoskeleton  Centrosome---Centriole and microtubule-organizing center (MTOC)  Proteasome RIBOSOME The ribosome is a large complex of RNA and protein which catalyzes protein translation, the formation of proteins from individual amino acids using messenger RNA as a template. This process is known as translation. Ribosomes are found in all living cells. The sequence of DNA encoding for a protein may be copied many times into messenger RNA (mRNA) chains of a similar sequence. Ribosomes can bind to an mRNA chain and use it as a template for determining the correct sequence of amino acids in a particular protein. Amino acids are selected, collected and carried to the ribosome by transfer RNA (tRNA molecules), which enter one part of the ribosome and bind to the messenger RNA chain. The attached amino acids are then linked together by another part of the ribosome. Once the protein is produced, it can then 'fold' to produce a specific functional three-dimensional structure. A ribosome is made from complexes of RNAs and proteins and is therefore a ribonucleoprotein. Each ribosome is divided into two subunits. The smaller subunit binds to the mRNA pattern, while the larger subunit binds to the tRNA and the amino acids. When a ribosome finishes reading an mRNA molecule, these two subunits split apart. Ribosomes are ribozymes, because the catalytic peptidyl transferase activity that links amino acids together is performed by the ribosomal RNA. Fig 14: Eukaryotic ribosome History:  Together with Albert Claude and Christian de Duve, George Emil Palade was awarded the Nobel Prize in Physiology or Medicine, in 1974, for the discovery of the ribosomes.  The Nobel Prize in Chemistry 2009 was awarded to Venkatraman Ramakrishnan, Thomas A. Steitzand Ada E. Yonath for determining the detailed structure and mechanism of the ribosome. Structure of ribosome: Eukaryotes have 80S ribosomes, each consisting of a small (40S) and large (60S) subunit. Their 40S subunit has an 18S RNA (1900 nucleotides) and 33 proteins. The large subunit is composed of a 5S RNA (120 nucleotides),28S RNA (4700 nucleotides), a 5.8S RNA (160 nucleotides) subunits and ~49 proteins. Several proteins, including L32/33, L36, L21, L23, L28/29 and L13 were implicated as being at or near the peptidyl transferase center. Types of ribosomes: Free ribosomes Free ribosomes can move about anywhere in the cytosol, but are excluded from the cell nucleus and other organelles. Proteins that are formed from free ribosomes are released into the cytosol and used within the cell. Since the cytosol contains high concentrations of glutathione and is, therefore, a reducing environment, proteins containing disulfide bonds, which are formed from oxidized cysteine residues, cannot be produced in this compartment. Membrane-bound ribosomes When a ribosome begins to synthesize proteins that are needed in some organelles, the ribosome making this protein can become "membrane-bound". In eukaryotic cells this happens in a region of the endoplasmic reticulum (ER) called the "rough ER". The newly produced polypeptide chains are inserted directly into the ER by the ribosome undertaking vectorial synthesis and are then transported to their destinations, through the secretory pathway. Bound ribosomes usually produce proteins that are used within the plasma membrane or are expelled from the cell via exocytosis. The ribosomes found in chloroplasts and mitochondria of eukaryotes also consist of large and small subunits bound together with proteins into one 70S particle. These organelles are believed to be descendants of bacteria and as such their ribosomes are similar to those of bacteria. Fig 15: Free and bound ribosome Function: Ribosomes are the workhorses of protein biosynthesis, the process of translating mRNA into protein. The mRNA comprises a series of codons that dictate to the ribosome the sequence of the amino acids needed to make the protein. Using the mRNA as a template, the ribosome traverses each codon (3 nucleotides) of the mRNA, pairing it with the appropriate amino acid provided by an aminoacyl-tRNA. aminoacyl-tRNA contains a complementary anticodon on one end and the appropriate amino acid on the other. The small ribosomal subunit, typically bound to a aminoacyl-tRNA containing the amino acid methionine, binds to an AUG codon on the mRNA and recruits the large ribosomal subunit. The ribosome then contains three RNA binding sites, designated A, P and E. The A site binds an aminoacyl- tRNA; the P site binds a peptidyl-tRNA (a tRNA bound to the peptide being synthesized); and the E site binds a free tRNA before it exits the ribosome. Protein synthesis begins at a start codon AUG near the 5' end of the mRNA. mRNA binds to the P site of the ribosome first. The ribosome is able to identify the start codon by use of the Shine- Dalgarno sequence of the mRNA in prokaryotes and Kozak box in eukaryotes. Fig 16: Protein translation by ribosome CENTROSOME: In cell biology, the centrosome is an organelle that serves as the mainmicrotubule organizing center(MTOC) of the animal cell as well as a regulator of cell-cycle progression. Fungi and plants use other MTOC structures to organize their microtubules. Although the centrosome has a key role in efficient mitosis in animal cells, it is not essential. Histrory: It was discovered by Edouard Van Beneden in 1883 and was described and named in 1888 by Theodor Boveri. In the theory of evolution the centrosome is thought to have evolved only in the metazoan lineage of eukaryotic cells. Structure: Centrosomes are composed of two orthogonally arranged centrioles surrounded by an amorphous mass of protein termed the pericentriolar material (PCM). The PCM contains proteins responsible for microtubule nucleation and anchoring including γ-tubulin, pericentrin and ninein. In general, each centriole of the centrosome is based on a nine triplet microtubule assembled in a cartwheel structure, and contains centrin, cenexin and tektin. Function: Centrosomes are associated with the nuclear membrane during prophase of the cell cycle. In mitosis the nuclear membrane breaks down and the centrosome nucleated microtubules (parts of the cytoskeleton) can interact with the chromosomes to build the mitotic spindle. The mother centriole, the one that was inherited from the mother cell, also has a central role in making cilia and flagella. Fig 17: The centrosome CENTRIOLE Centrioles are cylindrical structures that are composed of groupings of microtubules arranged in a 9 + 3 pattern. The pattern is so named because a ring of nine microtubule "triplets" are arranged at right angles to one another. Centrioles are found in animal cells and help to organize the assembly of microtubules during cell division. Centrioles replicate during the interphase stage of mitosis and meiosis. Centrioles called basal bodies form cilia and flagella. Centrioles are cylindrical structures, usually in pairs oriented at right angles to one another. The wall of each centriole cylinder is made of nine interconnected triplet microtubules, arranged as a pinwheel. The interior of each centriole appears empty, except for a "cartwheel" structure at one end. Electron micrographs show appendages that protrude from the outer surface at one end of a mature centriole, and fibrous structures connecting the two centriole cylinders.  Centriolar microtubules are relatively stable. The a,b tubulin heterodimers present in centriolar triplet microtubules are modified by polyglutamylation. Additional tubulins, designated d, e, z & h, as well as other proteins, are either present in centrioles or required for their formation. There is some variability in composition among different organisms.  Basal bodies of cilia and flagella are also centriole. History: Edouard van Beneden and Theodor Boveri made the first observation and identification of centrioles in 1883 and 1888 respectively, while the pattern of centriole replication was first worked out independently by Etienne de Harven and Joseph G. Gall circa 1950. Structure: A centriole is a cylindrically-shaped cell structure found in most eukaryotic cells, though it is absent in higher plants and most fungi. The walls of each centriole are usually composed of nine triplets of microtubules (protein of the cytoskeleton). Function: Centrioles are involved in the organization of the mitotic spindle and in the completion of cytokinesis. Centrioles were previously thought to be required for the formation of a mitotic spindle in animal cells. Centrioles are a very important part of centrosomes, which are involved in organizing microtubules in the cytoplasm. The position of the centriole determines the position of the nucleus and plays a crucial role in the spatial arrangement of the cell. Buehler has suggested that the centriole may form a primitive directional "eye", sensitive to certain wavelengths in the Infra red spectrum. An aster is a cellular structure shaped like a star, formed around each centrosomeduring mitosis in an animal cell. Astral rays, composed of microtubules. Fig 18: The centriole In organisms with flagella and cilia, the position of these organelles is determined by the mother centriole, which becomes the basal body. An inability of cells to use centrioles to make functional cilia and flagella has been linked to a number of genetic and developmental diseases. The last common ancestor of all eukaryotes was a ciliated cell with centrioles. Some lineages of eukaryotes do not have centrioles anymore, for example land plants. Microtubule-organizing center (MTOC): The microtubule-organizing center (MTOC) is a structure found in eukaryotic cells from which microtubules emerge. MTOCs have two main functions: the organization of eukaryotic flagella and ciliaand the organization of the mitotic and meiotic spindle apparatus, which separate the chromosomes during cell division. The MTOC is a major site of microtubule nucleation and can be visualized in cells by immunohistochemical detection of γ-tubulin. The morphological characteristics of MTOCs vary between the different phylas and kingdoms. In animals, the two most important types of MTOCs are the basal bodies associated with cilia and the centrosome associated with spindle formation. Movements of the microtubules are based on the actions of the centrosome. Each daughter cell after the cessation of mitosis contains one primary MTOC Before cell division begins, the interphase MTOC replicates to form two distinct MTOCs (now typically referred to as centrosomes). Pericentriolar material: Proteins present in the pericentriolar material or on the surface of centrioles include centrin, pericentrin, ninein, cenexin. During cell division, these centrosomes move to opposite ends of the cell and nucleate microtubules to help form the mitotic/meiotic spindle. If the MTOC does not replicate, the spindle cannot form, and mitosis ceases prematurely.y-tubulin is a protein located at the centrosome that nucleates the microtubules by interacting with the tubulin monomer subunit in the microtubule at the minus end Organization of the microtubules at the MTOC, or centrosome in this case, is determined by the polarity of the microtubules defined by y-tubulin CYTOSKELETON The cytoskeleton (also CSK) is a cellular "scaffolding" or "skeleton" contained within a cell's cytoplasm and is made out of protein. The cytoskeleton is present in all cells; it was once thought to be unique to eukaryotes. History: Kritikou et al,1942 discovered actomyosin. Fig 19: The cytoskeleton Structure: The cytoskeleton is made up of three kinds of protein filaments:  Actin filaments (also called microfilaments)  Intermediate filaments and  Microtubules  Actin Filaments Monomers of the protein actin polymerize to form long, thin fibers. These are about 8 nm in diameter and, being the thinnest of the cytoskeletal filaments, are also called microfilaments. (In skeletal muscle fibers they are called "thin" filaments.) Some functions of actin filaments:  form a band just beneath the plasma membrane that o provides mechanical strength to the cell o links transmembrane proteins (e.g., cell surface receptors) to cytoplasmic proteins o pinches dividing animal cells apart during cytokinesis  generate cytoplasmic streaming in some cells  generate locomotion in cells such as white blood cells and the amoeba  interact with myosin ("thick") filaments in skeletal muscle fibers to provide the force of muscular contraction.  Intermediate Filaments These cytoplasmic fibers average 10 nm in diameter (and thus are "intermediate" in size between actin filaments (8 nm) and microtubules (25 nm)(as well as of the thick filaments of skeletal muscle fibers). There are several types of intermediate filament, each constructed from one or more proteins characteristic of it.  keratins are found in epithelial cells and also form hair and nails;  nuclear lamins form a meshwork that stabilizes the inner membrane of the nuclear envelope;  neurofilaments strengthen the long axons of neurons;  vimentins provide mechanical strength to muscle (and other) cells.  Microtubules  are straight, hollow cylinders whose wall is made up of a ring of 13 "protofilaments";  have a diameter of about 25 nm;  are variable in length but can grow 1000 times as long as they are wide;  are built by the assembly of dimers of alpha tubulin and beta tubulin;  are found in both animal and plant cells. In plant cells, microtubules are created at many sites scattered through the cell. In animal cells, the microtubules originate at the centrosome.  The attached end is called the minus end; the other end is the plus end.  grow at the plus end by the polymerization of tubulin dimers (powered by the hydrolysis of GTP), and  shrink by the release of tubulin dimers (depolymerization) at the same end. Microtubules participate in a wide variety of cell activities. Most involve motion. The motion is provided by protein "motors" that use the energy of ATP to move along the microtubule. Microtubule motors There are two major groups of microtubule motors:  kinesins (most of these move toward the plus end of the microtubules) and  dyneins (which move toward the minus end). Cilia and flagella are built from arrays of microtubules. Function: Cells contain elaborate arrays of protein fibers that serve such functions as:  establishing cell shape  providing mechanical strength  locomotion  chromosome separation in mitosis and meiosis  intracellular transport of organelles Fig 20: Components of cytoskeleton PROTEASOME Proteasomes are protein complexes inside all eukaryotes and archaea, and in some bacteria. In eukaryotes, they are located in the nucleus and the cytoplasm. The main function of the proteasome is to degrade unneeded or damaged proteins by proteolysis, a chemical reaction that breaks peptide bonds. Enzymes that carry out such reactions are called proteases. Proteasomes are part of a major mechanism by which cells regulate the concentration of particular proteins and degrade misfolded proteins. The degradation process yields peptides of about seven to eight amino acids long, which can then be further degraded into amino acids and used in synthesizing new proteins. Proteins are tagged for degradation with a small protein called ubiquitin. The tagging reaction is catalyzed by enzymes called ubiquitin ligases. Once a protein is tagged with a single ubiquitin molecule, this is a signal to other ligases to attach additional ubiquitin molecules. The result is a polyubiquitin chain that is bound by the proteasome, allowing it to degrade the tagged protein. History: The importance of proteolytic degradation inside cells and the role of ubiquitin in proteolytic pathways was acknowledged in the award of the 2004 Nobel Prize in Chemistry to Aaron Ciechanover, Avram Hershko and Irwin Rose. Structure: In structure, the proteasome is a cylindrical complex containing a "core" of four stacked rings around a central pore. Each ring is composed of seven individual proteins. The inner two rings are made of seven β subunits that contain three to seven protease active sites. These sites are located on the interior surface of the rings, so that the target protein must enter the central pore before it is degraded. The outer two rings each contain seven α subunits whose function is to maintain a "gate" through which proteins enter the barrel. These α subunits are controlled by binding to "cap" structures or regulatory particles that recognize polyubiquitin tags attached to protein substrates and initiate the degradation process. The overall system of ubiquitination and proteasomal degradation is known as the ubiquitin- proteasome system. Fig 21: Proteasome mediated protein degradation. Function: The proteasomal degradation pathway is essential for many cellular processes, including the cell cycle, the regulation of gene expression, and responses to oxidative stress. The protein degradation: 1. Ubiquitylation and targeting Proteins are targeted for degradation by the proteasome by covalent modification of a lysine residue that requires the coordinated reactions of three enzymes. 2. Unfolding and translocation After a protein has been ubiquitinated, it is recognized by the 19S regulatory particle in an ATP-dependent binding step. 3. Proteolysis The mechanism of proteolysis by the β subunits of the 20S core particle is through a threonine-dependent nucleophilic attack.