Structure & Organisation of Cell

1. Structure & Organisation of Cell

2. Cell nucleus: • A cell's information center, the cell nucleus is the most conspicuous organelle found in a eukaryotic cell. It houses the cell's chromosomes and is the place where almost all DNA replication and RNA synthesis (transcription) occur. The nucleus is spherical and separated from the cytoplasm by a double membrane called the nuclear envelope. The nuclear envelope isolates and protects a cell's DNA from various molecules that could accidentally damage its structure or interfere with its processing. During processing, DNA is transcribed, or copied into a special RNA, called messenger RNA (mRNA). This mRNA is then transported out of the nucleus, where it is translated into a specific protein molecule. • The nucleolus is a specialized region within the nucleus where ribosome subunits are assembled. In prokaryotes, DNA processing takes place in the cytoplasm

3. Mitochondria • generate energy for the cell. The mitochondrion (plural mitochondria) is a double-membrane=-bound organelle found in most eukaryotic organisms. Some cells in some multicellularorganisms may, however, lack them (for example, mature mammalian red blood cells). • Mitochondria are self-replicating organelles that occur in various numbers, shapes, and sizes in the cytoplasm of all eukaryotic cells. Respiration occurs in the cell mitochondria, which generate the cell's energy by oxidative phosphorylation, using oxygen to release energy stored in cellular nutrients • Mitochondria multiply by binary fission, like prokaryotes. The organelle is composed of compartments that carry out specialized functions. These compartments or regions include the outer membrane, the intermembrane space, the inner membrane, and the cristae and matrix

4. Chloroplasts • also generate energy for the cell and can only be found in plants and algae, and they conduct photosynthesis, where the photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in plant and algalcells. They then use the ATP and NADPH to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, much amino acid synthesis, and the immune response in plants.

5. Endoplasmic reticulum: • The endoplasmic reticulum (ER) is a transport network for molecules targeted for certain modifications and specific destinations, as compared to molecules that float freely in the cytoplasm. The ER has two forms: the rough ER, which has ribosomes on its surface that secrete proteins into the ER, and the smooth ER, which lacks ribosomes. The smooth ER plays a role in calcium sequestration and release.

6. Golgi apparatus: • The primary function of the Golgi apparatus is to process and package the macromolecules such as proteins and lipids that are synthesized by the cell.

7. Lysosomes and Peroxisomes: • Lysosomes contain digestive enzymes (acid hydrolases). They digest excess or worn-out organelles, food particles, and engulfed viruses or bacteria. • Peroxisomes have enzymes that rid the cell of toxic peroxides. They are involved in catabolism of very long chain fatty acids, branched chain fatty acids, D-amino acids, and polyamines, reduction of reactive oxygen species – specifically hydrogen peroxide – 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. 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.

8. Centrosome: • the cytoskeleton organiser: The centrosome produces the microtubules of a cell – a key component of the cytoskeleton. It directs the transport through the ER and the Golgi apparatus. Centrosomes are composed of two centrioles, which separate during cell division and help in the formation of the mitotic spindle. A single centrosome is present in the animal cells. They are also found in some fungi and algae cells • .

9. Vacuoles: • Vacuoles sequester waste products and in plant cells store water. They are often described as liquid filled space and are surrounded by a membrane. Some cells, most notably Amoeba, have contractile vacuoles, which can pump water out of the cell if there is too much water. The vacuoles of plant cells and fungal cells are usually larger than those of animal cells

10. Cell wall • is a structural layer surrounding some types of cells, just outside the cell membrane. It can be tough, flexible, and sometimes rigid. • It provides the cell with both structural support and protection, and also acts as a filtering mechanism. They further permit the creation of stable osmotic environments by preventing osmotic lysis and helping to retain water. • Cell walls are present in most prokaryotes (except mycoplasma bacteria), in algae, plants and fungi but rarely in other eukaryotes including animals. • A major function is to act as pressure vessels, preventing over-expansion of the cell when water enters. • Cell walls in some plant tissues also function as storage deposits for carbohydrates that can be broken down and resorbed to supply the metabolic and growth needs of the plant. For example, endosperm cell walls in the seeds of cereal grasses, nasturtiumand other species, are rich in glucans and other polysaccharides that are readily digested by enzymes during seed germination to form simple sugars that nourish the growing embryo.

11. PLASMA MEMBRANE • The cell membrane (also known as the plasma membrane (PM) or cytoplasmic membrane, and historically referred to as the plasmalemma) is a biological membrane that separates the interior of all cells from the outside environment (the extracellular space) which protects the cell from its environmentconsisting of a lipid bilayer with embedded proteins. T • he cell membrane controls the movement of substances in and out of cells and organelles. In this way, it is selectively permeable to ions and organic molecules. • In addition, cell membranes are involved in a variety of cellular processes such as cell adhesion, ion conductivity and cell signalling and serve as the attachment surface for several extracellular structures, including the cell wall, the carbohydrate layer called the glycocalyx, and the intracellular network of protein fibers called the cytoskeleton.

12. Passive osmosis and diffusion Some substances (small molecules, ions) such as carbon dioxide (CO2) and oxygen (O2), can move across the plasma membrane by diffusion, which is a passive transport process. Because the membrane acts as a barrier for certain molecules and ions, they can occur in different concentrations on the two sides of the membrane. Diffusion occurs when small molecules and ions move freely from high concentration to low concentration in order to equilibrate the membrane. It is considered a passive transport process because it does not require energy and is propelled by the concentration gradient created by each side of the membrane. Such a concentration gradient across a semipermeable membrane sets up an osmotic flow for the water. Osmosis, in biological systems involves a solvent, moving through a semipermeable membrane similarly to passive diffusion as the solvent still moves with the concentration gradient and requires no energy. While water is the most common solvent in cell, it can also be other liquids as well as supercritical liquids and gases.

13. Transmembrane protein channels and transporters: • Transmembrane proteins extend through the lipid bilayer of the membranes; they function on both sides of the membrane to transport molecules across it.Nutrients, such as sugars or amino acids, must enter the cell, and certain products of metabolism must leave the cell. Such molecules can diffuse passively through protein channels such as aquaporins in facilitated diffusion or are pumped across the membrane by transmembrane transporters. Protein channel proteins, also called permeases, are usually quite specific, and they only recognize and transport a limited variety of chemical substances, often limited to a single substance. Another example of a transmembrane protein is a cell-surface receptor, which allow cell signaling molecules to communicate between cells.

14. Endocytosis: • Endocytosis is the process in which cells absorb molecules by engulfing them. The plasma membrane creates a small deformation inward, called an invagination, in which the substance to be transported is captured. Endocytosis is a pathway for internalizing solid particles ("cell eating" or phagocytosis, small molecules and ions ("cell drinking" or pinocytosis), and macromolecules. Endocytosis requires energy and is thus a form of active transport.

15. Exocytosis: • Just as material can be brought into the cell by invagination and formation of a vesicle, the membrane of a vesicle can be fused with the plasma membrane, extruding its contents to the surrounding medium. This is the process of exocytosis. • Exocytosis occurs in various cells to remove undigested residues of substances brought in by endocytosis, to secrete substances such as hormones and enzymes, and to transport a substance completely across a cellular barrier. In the process of exocytosis, the undigested waste-containing food vacuole or the secretory vesicle budded from Golgi apparatus, is first moved by cytoskeleton from the interior of the cell to the surface. The vesicle membrane comes in contact with the plasma membrane. The lipid molecules of the two bilayers rearrange themselves and the two membranes are, thus, fused. A passage is formed in the fused membrane and the vesicles discharges its contents outside the cell

16. Extracellular matrix (ECM) • is a three-dimensional network of extracellular macromolecules, such as collagen, enzymes, and glycoproteins, that provide structural and biochemical support of surrounding cells. • Cell adhesion, cell-to-cell communication and differentiation are common functions of the ECM. • The animal extracellular matrix includes the interstitial matrix and the basement membrane . • Interstitial matrix is present between various animal cells (i.e., in the intercellular spaces). Gels of polysaccharides and fibrous proteins fill the interstitial space and act as a compression buffer against the stress placed on the ECM. • Basement membranes are sheet-like depositions of ECM on which various epithelial cells rest.

17. Each type of connective tissue in animals has a type of ECM: collagen fibers and bone mineral comprise the ECM of bone tissue; reticular fibers and ground substance comprise the ECM of loose connective tissue; and blood plasma is the ECM of blood. • The plant ECM includes cell wall components, like cellulose, in addition to more complex signaling molecules. Some single-celled organisms adopt multicellularbiofilms in which the cells are embedded in an ECM composed primarily of extracellular polymeric substances (EPS).

18. FUNCTION • Due to its diverse nature and composition, the ECM can serve many functions, such as providing support, segregating tissues from one another, and regulating intercellular communication. The extracellular matrix regulates a cell's dynamic behavior.. • Formation of the extracellular matrix is essential for processes like growth, wound healing, and fibrosis. An understanding of ECM structure and composition also helps in comprehending the complex dynamics of tumor invasion and metastasis in cancer biology as metastasis often involves the destruction of extracellular matrix . • The stiffness and elasticity of the ECM has important implications in cell migration, gene expression, and differentiation.

19. ECM is composed of an interlocking mesh of fibrous proteins and glycosaminoglycans which are :. Proteins • Collagens are the most abundant protein in the ECM. In fact, collagen is the most abundant protein in the human body and accounts for 90% of bone matrix protein content. Collagens are present in the ECM as fibrillar proteins and give structural support to resident cells. Collagen consists of amino acids wound together to form triple-helices of elongated fibrils. • Elastins, in contrast to collagens, give elasticity to tissues, allowing them to stretch when needed and then return to their original state. This is useful in blood vessels the lungs in skin, and the ligamentumnuchae, and these tissues contain high amounts of elastins. Elastins are synthesized by fibroblasts and smooth muscle cells.

20. Proteoglycans • Glycosaminoglycans are carbohydrate polymers and mostly attached to extracellular matrix proteins to form proteoglycans. Proteoglycans have a net negative charge that attracts positively charged sodium ions (Na+), which attracts water molecules via osmosis, keeping the ECM and resident cells hydrated. Proteoglycans may also help to trap and store growth factors within the ECM.

21. different types of proteoglycan found within the extracellular matrix. • Heparan sulfate (HS) is a linear polysaccharide found in all animal tissues. It occurs as a proteoglycan (PG) in which two or three HS chains are attached in close proximity to cell surface or ECM proteins.[t is in this form that HS binds to a variety of protein ligands and regulates a wide variety of biological activities, including developmental processes, angiogenesis, blood coagulation, and tumour metastasis. • Chondroitin sulfates contribute to the tensile strength of cartilage, tendons ligaments and walls of the aorta. They have also been known to affect neuroplasticity • Keratan sulfates have a variable sulfate content and, unlike many other GAGs, do not contain uronic acid, They are present in the cornea, cartilage, bones, and the horns of animals.

22. Non-proteoglycan polysaccharide • Hyaluronic acid (or "hyaluronan") is a polysaccharide consisting of alternating residues of D-glucuronic acid and N-acetylglucosamine, and unlike other GAGs, is not found as a proteoglycan. Hyaluronic acid is found on the inner surface of the cell membrane and is translocated out of the cell during biosynthesis. Hyaluronic acid acts as an environmental cue that regulates cell behavior during embryonic development, healing processes, inflammation, and tumor development. It interacts with a specific transmembrane receptor, CD44.

23. Glycoproteins • Fibronectins are glycoproteins that connect cells with collagen fibers in the ECM, allowing cells to move through the ECM. Fibronectins bind collagen and cell-surface integrins, causing a reorganization of the cell's cytoskeleton to facilitate cell movement. Fibronectins are secreted by cells in an unfolded, inactive form. Binding to integrins unfolds fibronectin molecules, allowing them to form dimers so that they can function properly. Fibronectins also help at the site of tissue injury by binding to platelets during blood clotting and facilitating cell movement to the affected area during wound healing.

24. Laminins are proteins found in the basal laminae of virtually all animals. Rather than forming collagen-like fibers, laminins form networks of web-like structures that resist tensile forces in the basal lamina. They also assist in cell adhesion. Laminins bind other ECM components such as collagens and nidogens. • Fibroblasts are the most common cell type in connective tissue ECM, in which they synthesize, maintain, and provide a structural framework; fibroblasts secrete the precursor components of the ECM, including the ground substance. Chondrocytes are found in cartilage and produce the cartilaginous matrix. Osteoblasts are responsible for bone formation.

25. CELL-CELL INTERACTIONS /CELL-MATRIX INTERACTIONS • A cell communicates and interacts with other cells (cell-cell interactions) and with its extracellular matrix (ECM) (cell-matrix interactions)

26. CELL MATRIX INTERACTION • The extracellular matrix is a fibrillar meshwork comprised mainly of collagen that shapes and reinforces tissues and provides a scaffold for cell adhesion. Moreover, physical properties of the matrix such as its stiffness, viscoelasticity, and architecture provide cells with cues that direct important cell functions such as differentiation and motility. The interplay between cells and the surrounding extracellular matrix is essential to guide physiological processes such as tissue morphogenesis and wound healing. Abnormalities in matrix mechanics can promote pathological situations such as cancer metastasis and fibrosis.

27. Many cells bind to components of the extracellular matrix. Cell adhesion can occur in two ways; by focal adhesions, connecting the ECM to actin filaments of the cell, and hemidesmosomes, connecting the ECM to intermediate filaments such as keratin. This cell-to-ECM adhesion is regulated by specific cell-surface cellular adhesion molecules (CAM) known as integrins.Integrins are cell-surface proteins that bind cells to ECM structures, such as fibronectin and laminin, and also to integrin proteins on the surface of other cells.

28. Fibronectins • bind to ECM macromolecules and facilitate their binding to transmembraneintegrins. The attachment of fibronectin to the extracellular domain initiates intracellular signalling pathways as well as association with the cellular cytoskeleton via a set of adaptor molecules such as actin.

29. CELL–CELL INTERACTION • Cell–cell interaction refers to the direct interactions between cell surfaces that play a crucial role in the development and function of multicellular organisms. These interactions allow cells to communicate with each other in response to changes in their microenvironment. This ability to send and receive signals is essential for the survival of the cell. Interactions between cells can be stable such as those made through cell junctions, which are multiprotein complexes that provide contact between neighboring cells. • These junctions are involved in the communication and organization of cells within a particular tissue. Others are transient or temporary such as those between cells of the immune system or the interactions involved in tissue inflammation. These types of intercellular interactions are distinguished from other types such as those between cells and the extracellular matrix. The loss of communication between cells can result in uncontrollable cell growth and cancer.

30. Tight junctions • are multi-protein complexes that hold cells of a same tissue together and prevent movement of water and water-soluble molecules between cells. These are areas where the membranes of two adjacent cells join together to form a barrier. The cell membranes are connected by strands of transmembrane proteins such as claudins , occludin and junctional adhesion molecules (JAMs) and tricellulins.. Tight junctions bind cells together, prevent molecules from passing in between the cells, and also help to maintain the polarity of cells. They are only found in vertebrates, animals with a backbone and skeleton; invertebrates have septate junctions instead.

31. Gap junctions • Gap junctions are the main site of cell-cell signaling or communication that allow small molecules to diffuse between adjacent cells. In vertebrates, gap junctions are composed of transmembrane proteins called connexins. They form hexagonal pores or channels through which ions, sugars, and other small molecules can pass. The permeability of these junctions is regulated by many factors including pH and Ca2+ concentration.

32. PLASMODESMATA • Gap junctions are present in both vertebrates and invertebrates from mesozoa to mammals, whereas higher plants use structures called “plasmodesmata” for direct intercellular communication. • Plasmodesmata are narrow channels that act as intercellular cytoplasmic bridges to facilitate communication and transport of materials between plant cells and algal cells. The plasmodesmata serve to connect the symplastic space in the plant and are extremely specialized channels that allow for intercellular movement of water, various nutrients, and other molecules (including signalling molecules). Plasmodesmata are located in narrow areas of cell walls called primary pit fields, and they are so dense in these areas (up to one million per square millimeter) that they make up one percent of the entire area of the cell wall. They can also be termed as "bridges" between two plant cells.