cell form and function.pptx

 In protein folding the polypeptide -Denaturation is a process by which a protein loses its native conformation, chain undergoes na...

 In protein folding the polypeptide -Denaturation is a process by which a protein loses its native conformation, chain undergoes native three- resulting in the loss of its biological function due to factors such as elevated dimensional conformational temperatures which increase the kinetic energy of the protein and therefore changes dictated by the primary disrupt the hydrogen bonds and pH extremes which can alter the ionization state of amino acid chains. Moreover, organic solvents such as ethanol can amino acid sequence- a interfere with hydrophobic interactions. Protein unfolding leads to aggregation Molecular chaperones maintain cellular proteostasis, phenomenon called Anfinsen’s and precipitation because its hydrophobic core is exposed to the aqueous an equilibrium ensuring proteins retain their three- dogma. environment. dimensional structures and functional states. They assist in assembly and disassembling protein -Renaturation occurs when a denatured protein folds into its native, complexes, translocating proteins across cellular membranes, folding polypeptides, and refilling functional formation. It initiates through the removal of denaturing conditions misfolded proteins, which are crucial in stress by processes such as dilution or dialysis and with the help of a series of conditions. An example of this would be the Hsp70 intermediate states such as molten globules, which lack a fully developed chaperone system. tertiary structure and have some secondary structure. The folding pathway is guided by intramolecular forces that drive the protein to its lowest energy Step 1- Initial binding: As the newly synthesized state. This can be interpreted as an energy landscape where the unfolded polypeptide emerges from the ribosome, it remains in states reside at the top of the funnel and the native state at the bottom. an uncoiled configuration with its nonpolar residues Kinetic energy is a barrier the protein must overcome to avoid local energy exposed and liable to coalesce. The heat shock minima (incorrectly folded states) to reach the global energy minimum (native protein Hsp70, assisted by its co-chaperone Hsp40, state). loosely engages with the peptide in an ATP-fueled reaction. Hsp40 stimulates Hsp70's ATPase activity, amplifying its affinity for the nascent polypeptide substrate. This attachment occurs as Hsp70 occupies its ATP-bound conformational state, sanctioning a reversible liaison with the emerging peptide. Step 2- Atp hydrolysis and Tight binding occur as inorganic phosphate is generated, facilitated by the stimulatory effect of Hsp40 and the ATPase activity of Influenced by the following Hsp70. These reactions induce a conformational shift intramolecular forces: in Hsp70, transitioning it to a state that strongly -van der Waals interactions retains the polypeptide. In this ADP-bound formation, Hsp70 exhibits a high affinity for the polypeptide, -electrostatic forces stabilizing it in an intermediate folding phase. This -hydrophobic effects firm attachment prevents premature folding and -covalent disulfide bonds between sulfur aggregation, thereby holding the polypeptide in a condition fit for subsequent folding steps. The specific atoms of two cysteine residues where system includes a structural transition in the oxidation of cysteines occurs and chaperone Hsp70, where the substrate-binding contributes to overall stability domain firmly clamps around the polypeptide, guaranteeing a secure grip.  Membrane proteins exhibit asymmetric orientation concerning the lipid bilayer. Once in place, they cannot move across the membrane from one surface to the other. The three types include; integral peripheral and lipid Glycoprotein with anchored. Integral proteins hydrocarbon chains facilitate molecular transport Lipids are hydrophobic molecules, meaning that Sphingolipids- based on the amine sphingosine which has a across the membrane and act they are readily soluble in non-polar solvents in covalently linked to the long hydrocarbon chain with a single site of unsaturation as gateways and anchoring which the storage of energy reserves, formation amino acid side chain. near the polar end. They are synthesised in the endoplasmic points for cellular components. of cellular barriers, and transmission of signals all Phospholipids- Form bilayers reticulum and further modified in the Golgi apparatus and Glycolipids: Contain carbohydrate groups(hydrophilic portion) located on Peripheral proteins, attached to rely on lipids’ heterogeneous mixes. Some are in aqueous environments play a role in the formation of lipid rafts, which are the outer monolayer of the plasma membrane ranging from a the lipid bilayer via non- amphipathic, containing both polar and nonpolar which create the monosaccharide to oligosaccharides and a lipid tail with either a glycerol- covalent interactions, play a regions, essential for their role in membrane specialised microdomains within cell membranes that are forming glycoglycerolipids or sphingosine forming glycosphingolipids. The role in the regulation of fundamental structure for involved in signal transduction and membrane trafficking. structure. The hydrophobic effect self-assembles cell membranes. They are carbohydrate groups of glycolipids act as specific markers recognised by membrane-bound enzyme lipids into bilayers, micelles, or vesicles, forming They regulate apoptosis, inflammation, cell growth, and other cells, proteins, or pathogens which is crucial for immune responses activities, cellular signaling, and synthesised through the the structural basis of cellular membranes. differentiation, and participate in exocytosis, endocytosis, and host-pathogen interactions. They can bind to specific receptors cytoskeletal attachment, acylation of glycerol-3- and vesicular transport. This ensures the delivery of proteins triggering intracellular signaling cascades that regulate cellular processes. thereby responding to phosphate to form and lipids to their target destinations. Certain glycolipids such as glycocalyx, form a protective layer on the cell environmental changes. Lipid- phosphatidic acid, filled by surface that shields the cell from physical and chemical damage. anchored proteins which are the addition of polar head Glycosylation, which occurs in the ER and Golgi apartments, involves the covalently bonded to lipid groups. addition of a carbohydrate side chain to a glycoprotein. The role of molecules, serve a function in glycoproteins is cell-to-cell recognition and the transport of white blood cell localization and protein cells throughout the body when a foreign cell is recognized. interactions, thereby providing There are distinct lipid and protein a mechanism for the spatial organisation and modulation of compositions in the inner and outer cellular activities. leaflets that exhibit asymmetry, The N terminus which harbors which is essential for membrane signal peptides, plays a role in trafficking and transduction. Lipids co-translating targeting and can move through lateral diffusion, insertion process into the ER. within the same leaflet or transverse This mechanism ensures that Fatty acids- long, amphipathic unbranched diffusion(flip flop) in which the terminus is correctly Cholesterol(sterol)- interacts with hydrocarbon chains with a carboxylic group on phospholipid translocators facilitate oriented towards the cytosol or phospholipids and sphingolipids, reducing translocated into the ER lumen, the end, consisting of an even number of these. Flippases move from outer to maintaining the initial membrane fluidity at high temperatures, carbons due to biosynthetic pathways involving inner leaflet and floppases move from asymmetry. The C terminus Phosphoglycerides- Consist of a glycerol backbone while preventing crystallisation at low acetyl-CoA. Saturated fatty acids have a higher inner to outer leaflet. esterified to two fatty acids and a phosphate group. temperatures and stabilising the membrane contains retention signals and melting point and are tightly packed due to the post-translational modification Membrane fluidity, function and permeability is by fitting between fatty acid chains. They absence of double bonds while unsaturated fatty sites that direct the protein to influenced by the structural diversity of the polar head also serve as precursors for bioactive Functions of lipid rafts: transport acids have one or more double bonds and its location. These modifications group attached and the presence of one saturated molecules including steroid hormones and nutrients and ions across therefore a lower melting point and are not as ensure the protein maintains its and one unsaturated fatty acid. bile acids. membranes, bind activated immune correct orientation, reinforcing densely packed. Mitochondria- Its primary function is to produce Electron transport and Mitochondrial matrix: ATP through oxidative phosphorylation which is a process linked to the electron transport coenzyme oxidation Encodes a small number of mitochondrial fighting embedded in the inner membrane. Electron transport polypeptides along with polypeptides They often form elongated, tubular networks encoded by genes residing within the involves the highly that can extend throughout the cytoplasm and nucleus. The matrix also contains ribosomes have roles in cellular signaling, calcium storage, exergonic oxidation of and molecules of circular DNA to manufacture apoptosis, and even heat generation. NADH and FADH2 with their RNAs and protein and a mixture of O2 as the terminal enzymes, substrates, and cofactors that are Intermembrane space electron acceptor and so involved with processes inflicting amino acid, accounts for the lipid, energy, and iron metabolism. The region between outer and inner mitochondrial membrane where the free formation of water. The Outer membrane diffusion of ions and small molecules occurs downhill gradient of the It is a barrier between the cytosol and due to the presence of porins. Cytochrome c ETC signifies that the is present here which plays a role in the intermembrane space and contains electron transport chain and apoptosis. An The F0 complex is a hydrophobic assembly of proteins within the mitochondrial membrane. It overall process of enzymes involved in lipid metabolism, electrochemical gradient is created here functions as a rotor and proton channel due to protons flowing down their electrochemical exergonic and occurs adrenaline oxidation, and fatty acid which is an accumulation of protons, driven gradient from the intermembrane space to the matrix and therefore driving the rotation of spontaneously. elongation such as monoamine by the electron transport chain the c-ring. F1 is a hydrophilic, knob-like structure that is the catalytic site of ATP synthase. As oxidase. It is permeable due to the subunit driven by proton flow through the F0 complex rotates, it induces changes in the a porins( voltage-dependent anion and B subunits these changes lead to the binding of ADP AND Pi in the site, their condensation into ATP, and therefore its release. channels) and has a smooth structure Mitochondrial fission involves the division of a single mitochondrion into since it’s missing the folds found in the two smaller mitochondria. It ensures an even distribution of mitochondria Cristae inner membrane. Inner membrane between the daughter cells during mitosis, segregates damaged or Are folds of the inner mitochondrial It has a unique lipid composition that is rich dysfunctional mitochondria, and allows the cell to adapt to metabolic membrane that house the machinery in cardiolipin, making the membrane highly changes and stress by generating smaller mitochondria. Fusion involves required for aerobic respiration and increase impermeable to ions and most small the elongation of an organelle by which two mitochondria merge to form its surface area, providing more space to molecules in which this impermeability is it. This process allows compensation for defects in individual mitochondria ETC complexes and ATP synthases, crucial for maintaining the proton gradient as the mixing of mitochondrial contexts such as proteins and lipids occurs. maximizing the capacity for ATP production. essential for ATP production. The ETC is They also provide localized regions, and present here which is a series of protein Fusion helps to maintain the integrity and distribution of the mitochondrial intercostal spaces, where protons can complexes and electron carriers that conduct genome by enabling the exchange of mitochondrial DNA and can mitigate accumulate during electron transport. oxidative phosphorylation( conveying the effects of cellular stress by distributing and diluting damaged Cristae junctions are narrow tubular electrons from reduced coenzymes or components. The balance between fission and fusion is essential for connections between the cristae and the oxygen). The protein gradient, which drives cellular homeostasis and a disruption could lead to neurodegenerative inner boundary membrane that regulate the ATP synthesis from ADP and inorganic disorders. Excessive fusion can result in hyper-fused mitochondria that are flow of ions and metabolites between phosphate, is generated by ETC in ATP resistant to mitophagy (degradation of defective mitochondria) and different compartments. The inner boundary synthase(Complex V). accumulate damage while excessive fission can result in fragmented membrane lies parallel to the outer mitochondria and impaired bioenergetics. membrane, acting as a barrier to  Copper-containing cytochromes, particularly Cytochromes perform their roles in the latter phases cytochrome c oxidase, are indispensable for Flavoproteins utilise either flavin adenine of the electron transport chain through their heme the terminal step of the electron transport dinucleotide or flavin mononucleotide as a The complexes cofactor, which is an iron ion enclosed within a chain. This multicomponent protein contains prosthetic group. They assist in electron Complex I received 2 electrons from NADH and porphyrin ring. The iron ion can exchange between an array of redox-active groups, including transport through reversible redox reactions passes them to CoQ via FMN and a Fe-a protein. ferrous and ferric redox states, enabling the transfer Iron-sulfur clusters facilitate the relay of electrons paired heme molecules and dual copper where flavin mononucleotide undergoes a two- During this process, 4 H+ are pumped out of the of electrons. Cytochromes are arranged into both within and between proteins involved in sites named CuA and CuB. Electrons from electron reduction, switching among its oxidised matrix by complex I distinctive types contingent on differences in their cellular respiration. These electron carriers cytochrome c are accepted at the binuclear quinone form, semiquinone intermediate state, heme architecture and the nature of their axial consist of coordinated iron and inorganic sulfur CuA center and transferred in succession to and fully reduced hydroquinone structure. Complex II-catalyzing the oxidation of succinate ligands. atoms, often positioned alongside cysteine the adjacent heme a, then the distal CuB- Within Complex I (NADH oxidoreductase), flavin to fumarate in the mitochondrial Krebs cycle protein residues. Within Complex I, the iron-sulfur heme a3 site, where molecular oxygen mononucleotide acts as the preliminary electron and transferring electrons from succinate to The Q-cycle underway in Complex III facilitates the clusters serve as intermediaries, transporting binding and reduction take place. acceptor from NADH, helping in the transfer of ubiquinone in the passing of electrons from ubiquinol to soluble electrons from flavin mononucleotide to electrons to a cluster of iron-sulfur clusters. This cytochrome c via cytochrome b and cytochrome c1. ubiquinone after redox cycling between oxidation Cytochrome c oxidase catalyzes the procedure is coupled with the translocation of Complex III passes electrons from CoQH2 to Cytochrome c then conveys the electrons to states. Complex II also employs iron-sulfur conversion of dioxygen to water, protons over the internal mitochondrial cytochrome c via cytochromes b and c1 and a Fe-S cytochrome oxidase, otherwise known as Complex IV, centers to transfer electrons from flavin adenine accomplishing the ultimate phase in the membrane, adding to the creation of the proton protein. CoQH2 carriers 2 H+ across the inner which contains both cytochrome a and cytochrome dinucleotide to ubiquinone, directly linking the electron transport chain. This sequential motive compel. Complex II, then again, employs membrane and 2 more H+ are pumped out of the a3. These cytochromes in Complex IV mediate the tricarboxylic acid cycle to the electron transport reaction involves cytochrome c delivering flavin adenine dinucleotide as a prosthetic matrix. final reduction of molecular oxygen into water through chain. The cytochrome bc1 complex contains electrons initially to the CuA center, next to group to oxidise succinate to fumarate in the a mechanism connected to the transference of iron-sulfur clusters as well, such as the Rieske heme a, and finally to the remote CuB-heme TCA cycle, conversely reducing flavin adenine Complex IV receives electrons from cytochrome c protons across the inner mitochondrial membrane. iron-sulfur protein which conveys electrons from a3 center. Coupling the diminution of oxygen dinucleotide to its FADH2 structure. The and passes them via cytochrome a and a3 to This gradient of protons formed across the membrane ubiquinol to cytochrome c1. The precise to hydrogen oxide aids the translocation of electrons from the reduced FADH2 are then molecular oxygen, which is reduced to water as 2 generates the electrochemical potential necessary for arrangements and redox potentials of these protons over the inner mitochondrial passed onto iron-sulfur groups and at last to more H+ are pumped from the matrix by complex IV. ATP synthesis by means of oxidative phosphorylation clusters ensure electrons are efficiently membrane, augmenting the electrochemical ubiquinone (coenzyme Q). Complex II doesn't in the latter phases of the electron transport chain. In communicated while minimizing the production of potential requisite for adenosine triphosphate pump protons but directly moves electrons to ATP synthase uses the energy from the proton Complex IV, the varied cytochromes collaborate in the damaging reactive oxygen species, directing synthesis. Precise coordination of these ubiquinone, incorporating TCA cycle movement gradient generated during electron transport to ultimate conversion of oxygen to water, coupling this respiration and coordination. redox centers ensures efficient electron with the electron transportation chain. synthesise ATP from ADP and Pi. reaction to the export of hydrogen ions over the inner conveyance and curtails the formation of membrane, a process imperative for subsequent ATP reactive oxygen species, which can impair generation. cellular constituents. Coenzyme Q, also called ubiquinone, acts as a lipid-soluble electron shuttle Ordering of Electron Carriers within the inner mitochondrial membrane responsible for transporting The position of each carrier is determined by its standard reduction electrons throughout the electron transport chain. Its redox-active quinone potential. This means that electron transfer from NADH or FADH 2 at the portion and lengthy isoprenyl tail enable ubiquinone to play a key role. top to O2 at the bottom is spontaneous and exergonic. Existing in three varying redox forms—fully oxidized ubiquinone, partially Pairs of oxidized/reduced forms of the same molecule are arranged with The electron transport chain complexes, within the intricate folds of reduced semiquinone, and completely reduced ubiquinol—ubiquinone the most negative reduction potential on the top and the rest in order of the inner mitochondrial membrane, form a superstructure known as undergoes redox cycling to transfer electrons between protein complexes, reduction potential the respirasome. Woven into this network is the mobile electron thereby displaying its redox activity and transporting electrons throughout the Under standard conditions, the reduced form of any redox pair will shuttles coenzyme Q and cytochrome c, ferrying particles between chain. Alongside shorter cycles, it undergoes lengthy reductions and spontaneously reduce the oxidized form of any redox pair below it on the oxidative partners. Through their distance and diffusion time within oxidations while facilitating complex electron transfers within the mitochondria table the respirasome, Complexes I, III, and IV establish a supremely through its versatile forms. efficient relay system that rapidly propels electrons down the ETC. Reduction potential This process accelerates oxidative phosphorylation and maximises If a redox pair has a positive E ʹ0, the most oxidized form has a high ATP generation to fuel the cell's activities. By assembling the Within Complex I, the acceptor ubiquinone obtains electrons from the reduced affinity for electrons and is a good electron acceptor complexes, the respirasome also reserves the likelihood of errant carrier NADH via the flavin mononucleotide and iron-sulphur constituents, electrons causing harm, guarding against the production of changing into the reduced ubiquinol. In Complex II, the reduced ubiquinol Alternatively, a highly negative E ʹ0 is a measure of how good a donor dangerous reactive oxygen species and preserving the smooth gets electrons from the FMN through iron-sulphur groups when in its reduced the reduced form of the pair is functioning of the cellular machinery. Moreover, the dynamic state. The consequently formed ubiquinol then permeates the inward A highly negative Eʹ0 means that the oxidized form is a poor acceptor character of respirasome formation and dissociation grants membrane, donating its electrons to the varied cytochrome bc1 complex (think about the energy needed to convert NAD+ to NADH) mitochondria the flexibility to remodel their operational framework within Complex III. This sharing of electrons simultaneously moves positively in response to fluctuating demands and stresses, ever maintaining charged hydrogen ions out of the mitochondrial matrix and into the the cell's vital equilibrium and functional prowess through intermembrane space, adding to the development of a proton gradient that environmental change. impels the synthesis of ATP through oxidative phosphorylation. Jahnavi Mohan 20481793 Cell Form and Function Lecture 4 The Endomembrane system: Part I Compartments of the endomembrane Structure and function of the rough and Orientation of Lipids and Proteins in Membranes system and how their functions are smooth ER During Vesicular Transport: inter-related to support the Shared Functions: coordinated -The creation and modification of substances essential ER (endoplasmicfunction reticulum) of the system. ER to Golgi Device: for cellular processes, like proteins and lipids, is carried 1)During translation, newly synthesized proteins are -Rough ER: Involved in protein synthesis, ribosome- out by both smooth and rough ER. rich. Proteins that have just been synthesized enter translocated into the rough endoplasmic reticulum (RER) -Because of their interconnected membrane networks, lumen. the ER lumen to undergo appropriate folding and chemicals can interchange, and cellular activity can be modification. 2)During translation, transmembrane proteins meant to coordinated. be found in the ER membrane are introduced into the -The smooth ER, which is important in calcium Distinct Functions: lipid bilayer, where their hydrophobic regions interact storage, detoxification, and lipid synthesis, lacks -While smooth ER is more focused on lipid synthesis, with the hydrophobic membrane core. ribosomes. detoxification, and calcium storage, rough ER is mainly Golgi apparatus: 3)The ER membrane incorporates phospholipids and involved in protein synthesis and modification. cholesterol, among other lipids produced there. -receives lipids and proteins from the ER for -Ribosomes adhered to the surface of rough ER give it a additional sorting, packing, and processing. 4)Peripheral proteins are linked to the vesicle surface, rough appearance; smooth ER is ribosome-free. while transmembrane proteins are lodged in the vesicle -delivers changed molecules to their intended -The rough ER can synthesize more proteins than the membrane. As vesicles branch off from the ER, they locations by sorting and packing them into vesicles. smooth ER since it has ribosomes on it. carry proteins and lipids in their original orientation. Lysosomes: -Repair and recycle damaged molecules and organelles to preserve cellular equilibrium. Lysosomes or the plasma membrane via the Golgi Vacuoles: Interrelation and Coordination: Structure and Origins of Membranes: apparatus: -present in various protist, fungal, and plant cells. 4)Delivering their cargo, vesicles originating from the -Organelles used as storage for waste materials, Protein trafficking: After being synthesized in the rough -Phospholipid Bilayer: A phospholipid bilayer is the ER merge with the Golgi apparatus's cis face. ions, water, and nutrients. ER, proteins are sorted and altered in the Golgi apparatus. fundamental building block of biological membranes. 5)Proteins and lipids go through additional processing The plasma membrane : These changed proteins are then packed into vesicles and Hydrophilic (attracting water) heads and hydrophobic in the Golgi apparatus, such as glycosylation and -controls the movement of molecules into and out transported to different locations, including the plasma (repelling water) tails are characteristics of sorting into distinct vesicles for transportation to their of the cell and establishes the cell's perimeter. membrane, lysosomes, and vacuoles. phospholipids. Phospholipids self-assemble form a final locations. Lipid Metabolism: Before being integrated into cellular bilayer in an aqueous medium, with the hydrophilic 6)Vesicle membranes may integrate peripheral membranes or contained in vesicles for secretion, lipids heads pointing outward towards the water and the membrane proteins linked to the cytoplasmic face of synthesized in the smooth ER may undergo modifications hydrophobic tails pointing inside, away from it. the Golgi apparatus, or the peripheral membrane in the Golgi apparatus. -Integral Proteins: The lipid bilayer encases integral proteins may stay linked to the vesicle surface. Waste Management: Endocytosis, phagocytosis, or membrane proteins. Transmembrane proteins can fully autophagy provide materials to lysosomes for breakdown. or partially enter the membrane. Phospholipids' After breakdown, the byproducts are exported for hydrophobic tails engage with the hydrophobic sections excretion or recycled. of these proteins to bind the phospholipids inside the Cellular Communication: The cell's reactions are membrane. coordinated by the plasma membrane, which also -Proteins on the Membrane Peripheral: These proteins interacts with external signals. Cellular processes can be are attached to the membrane's surface and interact regulated by signaling molecules found in vesicles with phospholipid polar head groups or integral originating from the Golgi system. proteins. Generation of Lipid Species in the Basic Structure of Various Vesicles: Golgi Function in Modifying Endomembrane System: Coated Vesicles: Cargo: Biosynthesis Routes: The endoplasmic reticulum (ER) is the site of de novo lipid synthesis. Many lipid -A protein coat that covers their cytoplasmic surface helps in Protein Sorting and Localization: By moving species, such as phospholipids (phosphatidylcholine, the generation and cargo selection of coated vesicles. proteins to their intended compartments, phosphatidylethanolamine, and phosphatidylserine), Secretory Vesicles: vesicular trafficking makes ensuring that sphingolipids, and cholesterol, are synthesized by -The secretion of chemicals from the cell is facilitated by proteins are properly localized within the different enzymes. secretory vesicles. endomembrane system. This makes it easier Enzymatic Modifications: Different lipid species with -Usually, they include proteins or other compounds, including for organelles like lysosomes and the Golgi distinct characteristics and roles are produced by hormones or enzymes, that are meant for export. apparatus to sort and process proteins. enzymatic modifications of lipid species, such as -After developing a bud from the Golgi apparatus, secretory phosphorylation, acylation, and glycosylation. vesicles release their contents into the extracellular Membrane Dynamics and Homeostasis: By Selective Transport: Lipids are moved by vesicular environment by controlled exocytosis. controlling the transfer of lipids and transport, lipid transfer proteins, and lipid transport membrane proteins among various complexes between various organelles and organelles, vesicular trafficking preserves endomembrane system compartments. These membrane integrity and homeostasis. This processes of selective transport play a part in the mechanism enables the inclusion of freshly unique lipid composition of every membrane. synthesized proteins and lipids and the dynamic remodeling of membranes. How vesicular trafficking contributes to functioning of the endomembrane system Cellular Communication and Signaling: Asymmetrical Distribution of Lipids and Protein Sorting and Localization: By moving proteins to their Secretory vesicles play a crucial role in Proteins: intended compartments, vesicular trafficking makes ensuring that cellular communication and signaling Lipid Asymmetry: A membrane's two leaflets, or proteins are properly localized within the endomembrane system. through the release of hormones, monolayers, may have very different lipid This makes it easier for organelles like lysosomes and the Golgi neurotransmitters, and signaling chemicals compositions. Certain lipid transporters, flippases, and apparatus to sort and process proteins. into the extracellular environment. By scramblases that transfer lipids selectively between the internalizing ligands and receptors from the inner and outer leaflets of the membrane are Membrane Dynamics and Homeostasis: By controlling the transfer plasma membrane, endocytic vesicles responsible for maintaining lipid asymmetry. of lipids and membrane proteins among various organelles, control cell signaling by adjusting the density vesicular trafficking preserves membrane integrity and of cell surface receptors and their activity. homeostasis. This mechanism enables the inclusion of freshly synthesized proteins and lipids and the dynamic remodeling of Protein Asymmetry: Certain proteins can be localized membranes. to either the cytoplasmic or exoplasmic face of the membrane, exhibiting asymmetric distribution of Cellular Communication and Signaling: membrane proteins. Protein sorting signals and Secretory vesicles play a crucial role in cellular communication interactions with other membrane components and signaling through the release of hormones, determine this imbalance. Transmembrane proteins, for neurotransmitters, and signaling chemicals into the extracellular example, can be oriented within the membrane by environment. By internalizing ligands and receptors from the cytoplasmic or luminal targeting sequences. plasma membrane, endocytic vesicles control cell signaling by adjusting the density of cell surface receptors and their activity. Models of Golgi Formation/Function: Role of Quality Control in the ER/Endosomal Cisternal Maturation Model: System: Chaperone-Mediated Folding: To maintain correct shape, newly synthesised proteins are folded with the help of The Golgi cisternae are dynamic structures that develop molecular chaperones in the extracellular matrix (ER), with time, in accordance with this paradigm. Via vesicular such as binding immunoglobulin protein (BiP). transport, freshly synthesized proteins and lipids pass Chaperones aid in the proper folding of unfolded proteins through the Golgi stack and enter the cis-Golgi network by preventing their aggregation. (CGN). Misfolded or unfolded proteins are the target of ER- Cargo molecules undergo changes and sorting as they go Associated Degradation (ERAD), a quality control through the Golgi apparatus. Older cisternae at the trans- mechanism. Misfolded proteins are identified by ubiquitin Golgi network side of the stack are recycled back to the ligases, which then ubiquitinate them to signal them for cis-Golgi when the cisternae themselves grow. proteasomal breakdown. This process eliminates abnormal proteins, preserving the quality of ER proteins. According to this hypothesis, Golgi cisternae are dynamic structures that are constantly assembling, developing, Calnexin/Calreticulin Cycle: These two ER chaperones and disassembling rather than static entities. interact with glycoproteins that have N-linked glycans that have been monoglucosylated. They help Role of Unfolded Protein Response (UPR) in the ER: glycoproteins fold and stop them from leaving the ER too When misfolded or unfolded proteins build up in the extracellular soon. Glycoproteins are either targeted for destruction or reticulum (ER), a cellular stress response pathway known as the reglucosylated by UDP-glucose glucosyltransferase Unfolded Protein Response (UPR) is triggered. In order to guarantee Vesicular Transport Model: (UGGT) in an attempt to fold them back into their original proper ER functioning and maintain ER homeostasis, the UPR does shape. the following: According to this paradigm, cargo molecules pass through -Upregulating Chaperone Expression: In order to promote protein the Golgi stack by vesicular transport, and Golgi cisternae folding and lessen ER stress, the UPR increases the expression of ER are seen as stable structures. chaperones such BiP. COPII-coated vesicles carry newly synthesized proteins and lipids from the ER to the Golgi. Cargo molecules are -Inhibiting Protein Synthesis: In order to lessen the amount of freshly sorted and packed into clathrin-coated vesicles for synthesised proteins that enter the ER and relieve ER stress, the transport to the plasma membrane or later UPR attenuates global protein synthesis. compartments, or into COPI-coated vesicles for retrograde transport to earlier compartments within the -Increasing ERAD Activity: The UPR increases the breakdown of Golgi stack. misfolded proteins and facilitates the removal of abnormal proteins from the ER by upregulating ERAD components. This model highlights how crucial vesicular transport is to be preserving the Golgi apparatus's structural integrity -If ER stress is severe, inducing apoptosis: The UPR can initiate and functionality. apoptotic pathways to eradicate injured cells and stop additional Jahnavi Mohan 20481793​ Cell Form and Function Lecture 5 (any overflow Lecture 6) The Endomembrane system: Part II  Role of the early and late endosomes in Key mechanisms involving sequence tags trafficking of cargo within the endosomal and modifications. system Early Endosomes: After internalizing from the plasma membrane, endocytic vesicles first come into Signal Peptides/Signal Sequences: During translation, contact with early endosomes, which are the primary proteins are directed to the endoplasmic reticulum sorting compartments. Their main duties consist of: (ER) by short amino acid sequences found at their N- terminus. Certain signal peptides found in proteins Sorting: Via clathrin-mediated endocytosis and other headed for the endosomal pathway generally point endocytic mechanisms, early endosomes take up them towards the ER, where they are then transferred cargo from the plasma membrane. Cargo is sorted to endosomes. into early endosomes according to a number of criteria, such as post-translational modifications, pH Sorting Signals: The amino acid sequences of proteins sensitivity, and receptor-ligand interactions. that are meant to be placed in particular endosomal Recycling: Inside early endosomes, some cargo compartments contain sorting signals. Sorting molecules like transporters and receptors are sorted machinery inside the cell can identify these signals into recycling tubules and then brought back to the and send the protein to the right place. Sorting signals plasma membrane. This mechanism, called recycling, that are recognized by early endosomal sorting controls cellular signaling and homeostasis while complexes, for instance, may be present in proteins guaranteeing a steady supply of membrane proteins that are targeted to early endosomes. Proteins containing short amino acid sequences or structural Key types of vesicles involved in endosomal on the cell surface. motifs known as retrieval tags indicate when a protein needs trafficking Post-translational modifications: Within endosomal to be retrieved from one compartment and placed in another. Late Endosomes: Compared to early endosomes, compartments, post-translational alterations can affect To speed up the retrieval process, these tags frequently Clathrin-Coated Vesicles: Transport of cargo from the late endosomes, often referred to as multivesicular the location and function of proteins. Examples of interact with certain sorting equipment or coat proteins. This trans-Golgi network (TGN) to early endosomes and bodies, have different traits and purposes. these modifications include phosphorylation, is how it operates: between endosomal compartments is facilitated by clathrin-coated vesicles. On the cytoplasmic side of Cargo Sorting: Molecules bound for recycling, ubiquitination, and glycosylation. breakdown, or secretion are further sorted by late ER Retrieval Signals: Retrieval signals can point proteins that the vesicle membrane, clathrin, a protein coat, forms endosomes. Through inward budding of the break free from the ER and make their way to the Golgi a lattice structure that helps with vesicle production endosomal membrane, cargo intended for apparatus back to the ER. The C-terminus of ER-resident and cargo selection. Cargo receptors on these vesicles destruction is sequestered into intraluminal vesicles , proteins contains the well-known retrieval signal known as the are frequently able to identify particular sorting creating MVBs. This procedure aids in the cargo's KDEL sequence (lysine-aspartate-glutamate-leucine). Proteins signals on cargo proteins. separation from the cytoplasm and gets it ready for with this pattern are recognized by Golgi apparatus KDEL lysosomal breakdown. receptors, which then cause COPI-coated vesicles to retrieve Caveolae: Packed with sphingolipids and cholesterol, the protein and transport it to the ER. caveolae are flask-shaped invaginations of the plasma Fusion with Lysosomes: To create endolysosomes, membrane. They have a role in cargo trafficking late endosomes merge with lysosomes, which are Retromer Complex: The trans-Golgi network (TGN) or the between the plasma membrane and endosomes, as acidic organelles that contain hydrolytic enzymes. well as the internalization of certain membrane This fusion sends late endosome contents to plasma membrane are the sites where endosomes release lysosomes for enzymatic processing and breakdown, their proteins. Retrieval signals found in cargo proteins, such proteins and lipids. Particularly crucial for the including ILVs and cargo intended for degradation. as the sorting motifs NPxY or YxxΦ (Φ stands for a bulky internalization of signaling molecules and lipid hydrophobic residue), are recognized by the retromer. metabolism is caveolae-mediated endocytosis. Processes of exocytosis and endocytosis Vesicles are precisely guided to their locations within the cell and attach at the right target Exocytosis: The process by which cells discharge membranes thanks to a number of mechanisms. chemicals from internal vesicles into the extracellular Molecular motors, cytoskeletal components, area is known as exocytosis. There are several types of tethering factors, and SNARE proteins all work exocytosis shown below: together in these processes. An outline of these mechanisms is provided here: Vesicle Formation: Cytoskeletal components including microtubules and actin filaments carry intracellular Support for the Cytoskeletal System: vesicles carrying cargo molecules to the plasma membrane. The cytoskeleton, in particular microtubules and actin filaments, provides molecular motors with Fusion and Docking: A fusion pore is created when the tracks to travel along during vesicle transit vesicle membrane and plasma membrane combine. throughout the cell. This permits the vesicle's contents to be discharged into the extracellular area. Vesicles are transported along these tracks by molecular motors, such as myosins for actin Release of Cargo: The cargo molecules are discharged filaments and kinesins and dyneins for into the extracellular environment, where they can microtubules. engage in intercellular communication or carry out their physiological actions. The orientation of actin filaments and the polarity of microtubules—which have positive ends facing Endocytosis: The process by which cells take up the cell centre and negative ends facing the molecules from the extracellular milieu and incorporate periphery—determine the directionality of vesicle them into intracellular vesicles is known as endocytosis. transport. Multiple forms of endocytosis exist as shown below: Mechanisms of Targeting: Phagocytosis: The process by which cells take up big particles, including bacteria, dead cells, or cellular The final location of vesicles inside the cell is detritus, is known as phagocytosis. determined by certain targeting signals, such as Phagocytosis is carried out by specialized cells known Rab GTPases or vesicle coat proteins. as phagocytes, which include neutrophils and macrophages. Transport vesicles are coated with vesicle coat proteins, such as clathrin or COPI/COPII Pinocytosis: Fluid-phase endocytosis, another name for complexes, which then connect with particular pinocytosis, is the non-specific uptake of solutes and targeting machinery at the membranes of their extracellular fluid into tiny vesicles. destination. It is present constitutively in the majority of cells and aids in the uptake of nutrients and extracellular fluid  Peroxisome Functions and how peroxisomes are Overview of the makeup of lysosomes and formed: their roles in cellular processes: Fatty Acid Oxidation: Enzymes like acyl-CoA oxidase and Autophagy peroxisomal β-oxidation enzymes work with peroxisomes to Lysosomes play a role in the process of catalyze the oxidation of fatty acids, especially very long- chain fatty acids (VLCFAs). Acetyl-CoA is produced by this autophagy, which involves the engulfment of process and can be used for the biosynthesis of other damaged organelles and protein aggregates by molecules or the creation of energy. double-membrane vesicles known as autophagosomes. After then, autophagosomes Detoxification: Through the activity of catalase and other and lysosomes combine to form autolysosomes, peroxisomal antioxidant enzymes, peroxisomes play a which are where the material that has been critical role in the detoxification of hazardous chemicals, engulfed is broken down and recycled. including hydrogen peroxide (H2O2) and other reactive oxygen species (ROS). By converting H2O2 into oxygen and water, catalase lowers oxidative stress in cells. Endocytosis and Phagocytosis Role of autophagy Lysosomes are involved in the breakdown of Plasmalogen Biosynthesis: Plasmalogens are a form of extracellular material that is internalized through Cellular Quality Control: By specifically destroying damaged phospholipid that is widely distributed in cell membranes, the processes of endocytosis and phagocytosis. organelles (such mitochondria) and protein aggregates, especially in the heart and brain. Peroxisomes play a role in Lysosomal enzymes break down the material autophagy acts as a cellular quality control system. This keeps this process. The function of plasmalogens in membrane harmful or dysfunctional cellular components from building up structure, cell signaling, and lipid metabolism. that has been ingested when phagosomes and and aids in maintaining cellular homeostasis. endocytic vesicles carrying extracellular cargo combine with lysosomes. Nutrient Recycling: In times of nutrient shortage or metabolic stress, autophagy offers cells a backup supply of nutrients. Digestion of Cellular Structures: Lysosomes play Autophagy produces fatty acids, amino acids, and other a role in the cellular structures' turnover and metabolites that are useful for biosynthesis and energy remodeling, including membranes, organelles, production by recycling cytoplasmic material. and cytoskeletal elements. Cells can adjust to Development and Differentiation: Autophagy is crucial for a shifting environmental conditions and maintain number of cellular functions, such as tissue remodeling, cellular homeostasis thanks to this process. differentiation, and development. It aids in the removal of Jahnavi Mohan 20481793​ Lecture 6 Peroxisomes, Protein Targeting & Sorting. Plus: protein folding, quality control and ER stress response Functions of Peroxisomes: Biogenesis of Peroxisomes: ROS Production and Defense Mechanisms: Since peroxisomes are results of metabolic processes Translocation to the mitochondria and endoplasm: Fatty Acid Oxidation: Using peroxisomal β-oxidation Formation from the Endoplasmic Reticulum (ER): Through a including fatty acid oxidation, they are a major source of enzymes, peroxisomes catalyze the oxidation of process known as growth and division, peroxisomes can reactive oxygen species (ROS), especially hydrogen Newly produced proteins are translocated into the long-chain, very-long-chain, and branched-chain form from scratch in the ER. On ribosomes connected to the peroxide (H2O2). ER and mitochondria, where they undergo fatty acids. Acetyl-CoA is produced by this ER membrane, proteins intended for peroxisomes are Peroxisomes include enzymes like glutathione additional folding and processing, with the help of mechanism and can be utilized in biosynthetic produced before being injected into the membrane. peroxidases, peroxiredoxins, and catalase that detoxify molecular chaperones. pathways or further metabolized for the production H2O2 by turning it into oxygen and water, thereby of energy. Budding and Fission: Pre-peroxisomal vesicles are produced counteracting the damaging effects of ROS. In instance, Chaperones like calnexin/calreticulin and through the processes of budding and fission, wherein the catalase is essential for breaking down H2O2 quickly into immunoglobulin-binding protein (BiP) help move Detoxification of ROS: Peroxisomes play a role in ER membrane forms specialised areas known as oxygen and water. proteins into the ER lumen and fold them correctly. the metabolism of reactive oxygen species (ROS), peroxisomal membrane domains (PMDs). These vesicles BiP binds to developing polypeptides to stop them including hydrogen peroxide (H2O2), a result of develop into full, functional peroxisomes after branching off Peroxisomes are adaptable organelles that play a key role from folding and aggregating too soon, and several metabolic processes, including the from the ER. in several metabolic processes necessary for maintaining calnexin/calreticulin interacts with N-linked glycans oxidation of fatty acids. Enzymes like catalase, homeostasis and proper cellular function. To maintain to help fold glycoproteins. which are found in peroxisomes, reduce oxidative Matrix Protein Import: Post-translationally, peroxisomal appropriate cellular function and protection against stress in cells by converting H2O2 into water and matrix proteins are synthesised in the cytoplasm and oxidative stress, their biogenesis, protein targeting oxygen. imported into peroxisomes. Peroxisomal targeting signals mechanisms, ROS generation, and defense mechanisms (PTS1 and PTS2), which are found at the C- or N-termini of against ROSof The Folding are closely regulated. Proteins: Biosynthesis of Plasmalogens: The brain and heart matrix proteins, respectively, mediate this import process. have a large amount of plasmalogens, a form of The process of developing polypeptides folding into their phospholipid, which is present in cellular proper three-dimensional structures is aided by molecular membranes. Peroxisomes play a crucial role in the chaperones. manufacture of plasmalogens, which are essential for lipid metabolism, cell signaling, and membrane Protein intermediates that are partially folded or unfolded structure. can be stabilised by chaperones, which also keep the protein Targeting of Proteins to Peroxisomes: from misfolding or aggregating. Peroxisomal targeting signals (PTS) are unique targeting By creating an environment that is favourable for proper signals found in peroxisomal matrix proteins that guide folding, protecting hydrophobic areas, and promoting them towards peroxisomes. The most prevalent PTS is protein-protein interactions, chaperones encourage fruitful the PTS1 motif, a tripeptide sequence found at the C- folding pathways. terminus of matrix proteins that is typically Ser-Lys-Leu or a variant. The PTS2 motif, which is often found at the Heat shock proteins (HSPs), such as Hsp70, Hsp90, and N-terminus of matrix proteins, is less frequent. Hsp60, as well as chaperonins like GroEL/GroES in bacteria and CCT/TRiC in eukaryotes, are examples of molecular chaperones involved in protein folding.  Co-translational Translocation: Targeting Signals: Organelle-Specific Sorting and Localization: Additional sorting mechanisms within the organelles guarantee During their production on ribosomes, many proteins Signal Peptides (ER Targeting): Usually found near the the appropriate localization and function of proteins once they that are meant for the ER are translocated across polypeptide chain's N-terminus, signal peptides are present in have been targeted to certain organelles. These mechanisms the ER membrane. We call this procedure co- proteins that are intended for the ER. The ribosome-nascent could include vesicular transport channels, membrane fusion translational translocation. chain complex is directed to the ER membrane for co- events, and protein-protein interactions. translational translocation upon identification of signal When a signal peptide emerges from the ribosome peptides by the signal recognition particle (SRP) during Molecular chaperones and protein complexes are examples of and is recognised by the signal recognition particle translation. organelle-specific machinery that helps with protein folding, (SRP), co-translational translocation starts. assembly, and function in organelles. Mitochondrial Targeting Sequences: Proteins destined for the Hydrophobic amino acids make up the signal mitochondria have sequences known as mitochondrial peptide, which is normally found at the N-terminus of targeting sequences, which can be found either inside the the developing polypeptide chain. protein (internal targeting signals) or at the N-terminus (presequences). Protein import into mitochondria is facilitated The ribosome-nascent chain complex (RNC) is bound by these sequences, which are recognised by translocases and by the SRP upon recognition of the signal peptide, mitochondrial import receptors. momentarily stopping translation. Nuclear Localisation Signals (NLS): These signals are found in proteins that are specifically aimed towards the nucleus and they facilitate the movement of these proteins through nuclear Post-translational Translocation: pore complexes. Short amino acid sequences, such as lysine