<h5 id="overview">Overview</h5> <ul> <li>Cells are the basic unit of life, enabling various functions in an organism such as food digestion, sending electrical messages through nerves, pumping blood from the heart, and synthesizing proteins.</li> <li>Cells can be categorized into two main types: prokaryotic and eukaryotic, based on nuclear organization and membrane-bound cell organelles. Common components include plasma membrane, cytoplasm, ribosomes, and DNA.</li> <li>Prokaryotic cells, like those of bacteria, lack a well-organized nucleus and contain numerous ribosomes, mesosomes, and sometimes flagella.</li> <li>Eukaryotic cells, like those of plants and animals, have a well-organized nucleus, cell membrane, and various membrane-bound organelles such as endoplasmic reticulum, Golgi apparatus, mitochondria, plastids, vacuoles, and lysosomes.</li> <li>The detailed structure of cells has been explored through advancements in microscopic techniques, providing a better understanding of cell structure and functioning.</li> </ul> <p>======</p> <h5 id="21-plasma-membrane">2.1 Plasma Membrane</h5> <ul> <li>The plasma membrane is a lipid bilayer with proteins integrated into or attached to it, forming a semipermeable barrier.</li> <li>The Fluid Mosaic Model, proposed by Singer and Nicolson, describes this organization, with lipids and proteins able to move laterally in the membrane.</li> <li>Two types of proteins in the plasma membrane are peripheral (superficially attached, often involved in cell signaling) and integral (buried in the membrane, including transmembrane proteins).</li> <li>Molecular transport across the plasma membrane can occur through passive transport (diffusion, osmosis) or facilitated movement (using carrier or channel proteins).</li> <li>Active transport, which moves molecules against the concentration gradient, requires energy from ATP molecules or coupling with a second molecule’s transport along the concentration gradient.</li> </ul> <p>======</p> <h5 id="22-cell-wall">2.2 Cell Wall</h5> <ul> <li> <p>The cell wall is a rigid structure found in bacteria, algae, fungi, and higher plants, but not in animals.</p> </li> <li> <p>In bacteria, the cell wall is composed of polysaccharide cross-linked by small peptides, providing rigidity, shape, and protection from osmotic pressure. In eukaryotes, it is primarily made up of polysaccharides.</p> </li> <li> <p>The cell wall determines the cell shape, prevents cell bursting due to osmotic pressure, helps in cell-cell interaction, and provides mechanical strength and protection from infection.</p> </li> <li> <p>Gram-positive bacteria have a thick cell wall with a single plasma membrane, while gram-negative bacteria have a thin cell wall surrounded by a dual plasma membrane.</p> </li> <li> <p>In eukaryotes, the cell wall is mainly composed of cellulose (plants) or chitin (fungi). The plant cell wall has a primary layer for cell expansion and a secondary layer for rigidity and protection. Bacterial cell walls are further covered by a glycosylated protein called glycocalyx, which can be a loose sheath (slime layer) or a thick and tough capsule.</p> </li> </ul> <p>======</p> <h5 id="221-endomembrane-system">2.2.1 Endomembrane System</h5> <ul> <li> <p>The endomembrane system is a group of membrane-bound organelles in eukaryotic cells that work together in protein and lipid synthesis, processing, packaging, and transport.</p> </li> <li> <p>The endomembrane system includes the Endoplasmic Reticulum (ER), Golgi complex, Lysosomes, and Vacuole.</p> </li> <li> <p>The ER is involved in protein and lipid synthesis, folding, and modification. It is further classified into rough ER (RER) and smooth ER (SER).</p> </li> <li> <p>The Golgi complex is responsible for the modification, sorting, and packaging of proteins and lipids for transport to their respective destinations.</p> </li> <li> <p>Lysosomes and vacuoles are involved in the digestion and recycling of waste materials, cellular maintenance, and defense against foreign particles.</p> </li> </ul> <p>(Note: The text provided does not include any equations or formulae.)</p> <p>======</p> <h5 id="23-endoplasmic-reticulum">2.3 Endoplasmic Reticulum</h5> <ul> <li>The endoplasmic reticulum (ER) is a network of membrane-enclosed tubules and cisternae in eukaryotic cells.</li> <li>ER is located near the nucleus and golgi apparatus, and is involved in protein synthesis, calcium storage, and lipid metabolism.</li> <li>Based on the presence or absence of ribosomes, ER can be classified as rough ER (with ribosomes) or smooth ER (without ribosomes).</li> <li>Rough ER is primarily involved in protein synthesis, while smooth ER is involved in lipid metabolism and calcium storage.</li> <li>The equation for calcium storage in ER is: [Ca2+]er = Kd * ([Ca2+]total / (([Ca2+]total + Kd)) where [Ca2+]er is the calcium concentration in the ER, [Ca2+]total is the total calcium concentration in the cell, and Kd is the dissociation constant for calcium and the ER.</li> </ul> <p>======</p> <h5 id="231-rough-endoplasmic-reticulum-rer">2.3.1 Rough Endoplasmic Reticulum (RER)</h5> <ul> <li>Rough Endoplasmic Reticulum (RER) contains ribosomes on its cytosolic surface, which are the protein synthesizing factories of a cell.</li> <li>Proteins synthesized on free ribosomes are released into the cytoplasm and directly transported to the nucleus, mitochondria, chloroplasts, and peroxisomes to be used within the cell.</li> <li>In contrast, proteins synthesized on bound ribosomes are transferred to a receptor on the ER in eukaryotes, where the nascent protein is inserted into the ER.</li> <li>These proteins may be retained in the ER or transported to their destinations via the Golgi complex through the secretory pathway.</li> <li>ER plays a significant role in trafficking of secretory proteins to the Golgi apparatus, lysosomes, and plasma membrane within eukaryotic cells.</li> </ul> <p>======</p> <h5 id="232-smooth-endoplasmic-reticulum-ser">2.3.2 Smooth Endoplasmic Reticulum (SER)</h5> <ul> <li>Smooth endoplasmic reticulum (SER) does not have ribosomes on its surface.</li> <li>SER is primarily involved in lipid metabolism, as lipids are hydrophobic and cannot be synthesized in the cytosol.</li> <li>Most lipids are synthesized in the SER and transported to their respective destinations via transport vesicles.</li> <li>Phospholipids, a crucial component of membranes derived from glycerol, are synthesized on the outer side (cytosolic side) of the SER membrane.</li> <li>SER is an essential site for cholesterol synthesis.</li> </ul> <p>======</p> <h5 id="24-golgi-apparatus">2.4 Golgi Apparatus</h5> <ul> <li>The Golgi Apparatus (GA), first observed by Camillo Golgi in 1898, is a membrane-bound cell organelle consisting of flattened membranous sacs called cisternae.</li> <li>It is located near the cell nucleus and principally performs the function of packaging materials for secretions. The GA has a distinct cis face (forming face) and trans face (maturing face).</li> <li>Transport vesicles move material from the Endoplasmic Reticulum (ER) to the GA, where proteins are modified before being released from the trans face.</li> <li>The GA is a central membrane organelle for trafficking and post-translational modification of protein and lipid in the cell. It plays a crucial role in forming glycoproteins and glycolipids.</li> <li>Vesicles from the GA can fuse with the plasma membrane, releasing their contents outside the cell, or deliver contents to other organelles.</li> </ul> <p>======</p> <h5 id="25-lysosomes">2.5 Lysosomes</h5> <ul> <li>Lysosomes are small, spherical vesicles in the cytoplasm, approximately 0.2-0.5 microns in diameter, containing hydrolytic enzymes.</li> <li>They are formed from the golgi apparatus or directly from the endoplasmic reticulum and are capable of breaking down macromolecules.</li> <li>Lysosomal enzymes show optimal activity at an acidic pH and are used in the dissolution and digestion of redundant structures or damaged macromolecules.</li> <li>Lysosomes play a crucial role in intracellular digestion, for example, by fusing with food vacuoles to break down contents.</li> <li>They are also involved in recycling the cell’s own organic material through autophagy and are essential for cell renewal.</li> <li>The absence or inactivation of lysosomal enzymes can lead to diseases, such as Tay-Sachs disease, where the brain becomes impaired due to the accumulation of lipids in cells.</li> </ul> <p>======</p> <h5 id="26-vacuoles">2.6 Vacuoles</h5> <ul> <li>Vacuoles are membrane-bound organelles in the cytoplasm of most plants, fungi, and some animal cells.</li> <li>Their major functions are storage, structural support, recycling, maintaining cell turgor, and protecting cells during biotic stresses.</li> <li>The number and size of vacuoles vary; young cells have many small vacuoles that amalgamate into a large central vacuole in mature cells.</li> <li>Central vacuoles contain water, cell sap, solid inclusions, and other metabolites; other types include lytic vacuoles, protein storage vacuoles, and storage vacuoles.</li> <li>The vacuoles are covered by a membrane called the tonoplast; fungal vacuoles have additional functions like degradative processes, osmoregulation, and maintaining intracellular pH.</li> </ul> <p>======</p> <h5 id="27-mitochondria">2.7 MitochondRiA</h5> <ul> <li>Mitochondria are present in nearly all eukaryotic cells and vary in number from one to thousands per cell.</li> <li>They are double membrane bound structures with a smooth outer membrane and an infolded inner membrane (cristae) that provide a larger surface area.</li> <li>The inner membrane and matrix contain enzymes and proteins involved in the TCA cycle and cellular respiration for ATP synthesis.</li> <li>Mitochondria possess DNA molecules, ribosomes (70S), and RNA molecules, with some mitochondrial proteins synthesized by genes present on the mitochondrial DNA.</li> <li>The mitochondrial matrix is the site of organellar DNA replication, transcription, protein synthesis, and other enzymatic processes, containing over 1000 proteins that vary within and between species.</li> </ul> <p>======</p> <h5 id="28-plastids">2.8 Plastids</h5> <ul> <li>Plastids are colored bodies in the cytoplasm of plant cells, derived from the Greek word Plastikas (formed or moulded).</li> <li>Three types of plastids are recognized: <ul> <li>Chromoplasts: coloured plastids containing various pigments like carotene, xanthophylls.</li> <li>Leucoplasts: colorless plastids involved in storage of food materials, classified as Amyloplasts, Aleuroplasts, and Elaioplasts or Lipoplast.</li> <li>Chloroplasts: green plastids containing chlorophyll, universally found in green parts of plants, involved in photosynthesis.</li> </ul> </li> <li>Chloroplasts are lens-shaped organelles, bound by a double membrane with a narrow intermediate space, and an inner membrane organized into flattened membranous sacs (thylakoids) arranged in stacks (grana).</li> <li>The thylakoid membrane contains light-harvesting proteins, reaction centers, electron-transport chains, ATP synthase, and chlorophyll pigments involved in photosynthesis.</li> <li>Chloroplasts are the largest organelles in plant cells, with ribosomes smaller (70S) than cytoplasmic ribosomes (80S).</li> </ul> <p>======</p> <h5 id="29-ribosomes">2.9 Ribosomes</h5> <ul> <li>Ribosomes are membraneless organelles that synthesize proteins in both prokaryotic and eukaryotic cells.</li> <li>They were first observed by George Palade in 1955 and are composed of two subunits, which can be separated through ultracentrifugation.</li> <li>Ribosomes are classified based on their sedimentation rate (S) in a centrifuge, with prokaryotic ribosomes being 70S and eukaryotic ribosomes being 80S.</li> <li>70S ribosomes are also present in mitochondria and chloroplasts of eukaryotic cells, indicating a relatedness to prokaryotic cells.</li> <li>Ribosomes are primarily composed of rRNA and proteins, with each subunit having a small and large subunit. The 70S prokaryotic ribosome has larger 50S and smaller 30S subunits, while the 80S eukaryotic ribosome has larger 60S and smaller 40S subunits.</li> </ul> <p>======</p> <h5 id="210-microbodies">2.10 MicRobodies</h5> <ul> <li> <p>Microrobodies are small, single-membrane bound cell organelles found only in eukaryotic cells, typically located near the endoplasmic reticulum.</p> </li> <li> <p>There are two main types of microrobodies, classified based on functional properties: peroxisomes and glyoxysomes.</p> </li> <li> <p>Peroxisomes play a crucial role in cellular metabolism, including the breakdown of fatty acids and hydrogen peroxide production.</p> </li> <li> <p>Glyoxysomes are specialized peroxisomes involved in the conversion of stored lipids into sugars during seed germination.</p> </li> <li> <p>Microrobodies do not include examples or solutions, as they are not applicable in this context.</p> </li> </ul> <p>======</p> <h5 id="2101-peroxisomes">2.10.1 Peroxisomes</h5> <ul> <li>Peroxisomes are small, membrane-bound organelles involved in energy metabolism.</li> <li>They are derived from the ER and replicate by fission, sharing morphological similarities with lysosomes but assembled like mitochondria and chloroplasts.</li> <li>Peroxisomes lack their own genome and perform major functions of oxidation and lipid biosynthesis in animal cells.</li> <li>In liver cells, they aid in alcohol detoxification, while in plant cells, they facilitate conversion of fatty acids into carbohydrates in seeds and photorespiration in leaves.</li> <li>Unlike mitochondria and chloroplasts, peroxisomes contain oxidases for peroxide production and catalase to neutralize harmful oxidation products.</li> </ul> <p>======</p> <h5 id="2102-glyoxysomes">2.10.2 Glyoxysomes</h5> <ul> <li>Glyoxysomes are specialized peroxisomes found in fungi and higher plants, particularly in fat storage tissues of germinating seeds.</li> <li>Their number and activity increase during the germination of oil-filled seeds.</li> <li>Glyoxysomes contain enzymes for fatty acid oxidation, glyoxylate cycle, and gluconeogenesis.</li> <li>Seedlings utilize sugars synthesized from fats until they are mature enough for photosynthesis.</li> <li>The conversion of lipids into glucose involves coordinated functions of glyoxysomes, mitochondria, and plastids.</li> </ul> <p>======</p> <h5 id="211-cytoskeleton">2.11 CYtosKeLETon</h5> <ul> <li>The cytoskeleton is a vital component of a cell, made up of a multi-component system of fibrous protein that maintains cell organization and shape.</li> <li>It is composed of three major filaments: microtubules (25 nm), actin filaments (6 nm), and intermediate filaments (10 nm), each with unique protein composition and diameter.</li> <li>Microtubules, composed of tubulin proteins, are hollow rod-like structures that may contain 10-15 protofilaments and are responsible for the rhythmic movement of cilia and flagella.</li> <li>Actin filaments, found in skeletal muscle, provide strength to the cell and facilitate cytokinesis and cell movement.</li> <li>Intermediate filaments, resembling a rope, primarily provide mechanical strength to the cell.</li> </ul> <p>======</p> <h5 id="212-cilia-and-flagella">2.12 Cilia and Flagella</h5> <ul> <li>Cilia and flagella are hair-like structures present in various organisms, ranging from protozoans to metazoans, and even in plants.</li> <li>Cilia are generally smaller in size, up to $5-10 \mu \mathrm{m}$, and numerous in number, occurring throughout the surface of a cell or at one end of the cell. They move in a coordinated rhythm, showing sweeping or perpendicular stroke motion.</li> <li>Flagella, on the other hand, are larger in size, up to $150 \mu \mathrm{m}$, and occur one or two in number. They move independently, showing undulatory movement or whiplash movement.</li> <li>Cilia are found in protozoans (class-Ciliata), ciliated epithelium of metazoan larvae, larvae of Platyhelminthes, ribbon worms, Annelids, Mollusca, and Echinodermata.</li> <li>Flagella are found in protozoans (class-Flagellata), sponges (Choanocyte cells), spermatozoa of Metazoa, plants (algae and gamete cells).</li> <li>Equations or formulae are not provided in the text.</li> </ul> <p>======</p> <h5 id="213-centrosome-and-centrioles">2.13 Centrosome and Centrioles</h5> <ul> <li>The centrosome is located in the animal cell cytoplasm near the nucleus and consists of two centrioles embedded in pericentriolar materials.</li> <li>Centrioles, which are part of the centrosome, are made up of nine triplets of microtubules arranged around a central cavity.</li> <li>Centrioles play a crucial role in the assembly of the mitotic spindle during cell division.</li> <li>The centrosome duplicates in the S phase of the cell cycle.</li> <li>During mitosis (M-phase), the centrosome separates and moves to opposite ends of the cell, ensuring proper chromosome separation.</li> </ul> <p>======</p> <h5 id="214-nucleus">2.14 NuCleus</h5> <ul> <li>The nucleus is a well-defined organelle present in eukaryotic cells, unlike prokaryotic cells.</li> <li>It separates genetic material from the cytoplasm and acts as a master controller of cell activities.</li> <li>The nucleus is also a vast repository of genomic information.</li> <li>It regulates gene expression through various exclusive eukaryotic mechanisms.</li> <li>The structure of a nucleus includes the nuclear membrane, nuclear pores, chromatin, and nucleolus (Figure 2.15).</li> </ul> <p>======</p> <h5 id="2141-the-nuclear-envelope">2.14.1 The nuclear envelope</h5> <ul> <li>The nuclear envelope is a dual membrane barrier that controls access of genetic material to selected proteins and regulatory molecules.</li> <li>It is a phospholipid bilayer similar to the plasma membrane, permeable to small hydrophobic molecules.</li> <li>Nuclear pore complexes facilitate trafficking of RNAs and proteins; they are the pores/interruptions in the continuous outer and inner nuclear membrane.</li> <li>The outer nuclear membrane is continuous with the endoplasmic membrane.</li> <li>A fibrous network of proteins called lamins is present below the inner membrane, strengthening the nuclear structural framework.</li> </ul> <p>======</p> <h5 id="2142-the-nuclear-pore-complex-and-the-selective-transport">2.14.2 The nuclear pore complex and the selective transport</h5> <ul> <li>The nuclear pore complex is a large pore with a diameter of approximately 120 nm, primarily designed for the transport of proteins and RNA, along with small polar and charged molecules.</li> <li>It is composed of eight structural subunits of nucleoporins, a family of pore-forming proteins, surrounding a central channel.</li> <li>Electron microscopic visualization has revealed the eightfold symmetry of nucleoporins, connecting nuclear and cytoplasmic sites.</li> <li>Nucleoporins are responsible for the transport of molecules through the nuclear pore complex.</li> <li>The structure of the nuclear pore complex provides a pathway for communication between the nucleus and the cytoplasm.</li> </ul> <p>======</p> <h5 id="2143-nucleoplasm">2.14.3 Nucleoplasm</h5> <ul> <li>The nuclear envelope encloses the nucleus, containing a fluid called karyolymph or nuclear sap and protein fibrils known as the nuclear matrix.</li> <li>The nuclear matrix aids in maintaining the shape of the nucleus and houses enzymes involved in DNA replication and transcription.</li> <li>Two structures suspended in the nucleoplasm are the nucleolus and chromatin.</li> <li>The nucleolus is a site for ribosome synthesis, while chromatin is the material that makes up chromosomes.</li> <li>The nucleoplasm is analogous to the cytoplasm, filling the space inside the nucleus.</li> </ul> <p>======</p> <h5 id="215-nucleolus">2.15 Nucleolus</h5> <ul> <li>The nucleus contains various nuclear bodies, which are organelles that lack a well-defined membrane and aid in compartmentalizing nuclear processes.</li> <li>The nucleolus is one of the most distinct nuclear bodies, involved in the synthesis of rRNA and ribosomes.</li> <li>The chromosomal region occupied by the nucleolus is called the nucleolar organizing region, which comprises a large number of rRNA synthesizing genes.</li> <li>Other structures present in the nucleus are involved in various activities such as transcriptional regulation, gene silencing, DNA repair, and rRNA transcription and processing.</li> <li>The nucleolus plays a crucial role in the formation of ribosomes, which are essential for protein synthesis in the cell.</li> </ul> <p>======</p> <h5 id="2-16-chromosome">2. 16 Chromosome</h5> <ul> <li>There are different numbers of chromosomes in various organisms, such as Arabidopsis thaliana (10), Maize (20), Wheat (42), Fruit fly (8), Earthworm (36), Mouse (40), Human (46), Elephant (56), Donkey (62), Dog (78), Gold Fish (100-104), Tobacco (tetraploid with 100-104), Oat (hexaploid with 42), and Prokaryotes (single circular chromosome).</li> <li>Chromosomes in eukaryotes are present as long threads called chromatin fibers during interphase, which are composed of nucleosomes made of DNA wrapped around histone proteins.</li> <li>Chromatin fibers condense to form microscopically visible, long, and slender chromosomes during cell division, which are then replicated, divided, and passed to daughter cells.</li> <li>Chromosome structure varies throughout the cell cycle, and errors in chromosome number or structure can lead to serious problems.</li> <li>Prokaryotes, like bacteria or blue-green algae, have a single circular chromosome (nucleoid) in their cytoplasm, as they do not have a well-defined nucleus or other membrane-bounded organelles.</li> </ul> <p>======</p>