Mol Bio Lecture 5 Pt 2 PDF

3.Explain how a cell undergoes apoptosis with an emphasis on intrinsic versus extrinsic induction, key mediators of each process including Bcl-2 and p53, the signaling steps, and the timing and stages of the process ◦Identify the role of the caspase cascade in apoptosis ◦Identify the role of mitocho...

3.Explain how a cell undergoes apoptosis with an emphasis on intrinsic versus extrinsic induction, key mediators of each process including Bcl-2 and p53, the signaling steps, and the timing and stages of the process ◦Identify the role of the caspase cascade in apoptosis ◦Identify the role of mitochondria in apoptosis ◦Explain the consequence for DNA as part of the process and why this consequence helps differentiate the process from necrosis Intrinsic Pathway (Mitochondrial-Mediated Apoptosis) The intrinsic pathway is triggered by internal signals such as DNA damage, oxidative stress, or cellular damage. The mitochondria play a central role in this pathway, and key proteins from the Bcl-2 family regulate the release of pro-apoptotic factors from mitochondria. Key Steps of the Intrinsic Pathway: 1. Cellular Stress Sensing: ○ Internal stresses like DNA damage, hypoxia, or ER stress activate p53, a tumor suppressor protein. ○ p53 upregulates the expression of pro-apoptotic proteins such as Bax and Bak, which are part of the Bcl-2 family. 2. Mitochondrial Outer Membrane Permeabilization (MOMP): ○ Bax and Bak oligomerize and form pores in the outer mitochondrial membrane. ○ This permeabilization leads to the release of cytochrome c and other pro-apoptotic factors like Smac/DIABLO from the mitochondria into the cytoplasm. 3. Apoptosome Formation: ○ Cytochrome c binds to Apaf-1 (apoptotic protease-activating factor 1) and forms a large complex called the apoptosome. ○ The apoptosome recruits and activates procaspase-9, converting it into active caspase-9. 4. Caspase Cascade Activation: ○ Caspase-9 cleaves and activates procaspase-3, initiating the executioner phase of apoptosis, where caspase-3 cleaves essential cellular proteins, leading to cell dismantling. Role of Bcl-2 in the Intrinsic Pathway:  is an anti-apoptotic member of the Bcl-2 family that inhibits Bax Bcl-2 and Bak, preventing mitochondrial permeabilization. When Bcl-2 is upregulated, it blocks apoptosis by inhibiting the release of cytochrome c. Downregulation of Bcl-2, or overexpression of pro-apoptotic Bcl-2 family members (like Bax), favors apoptosis by promoting cytochrome c release. Extrinsic Pathway (Death Receptor-Mediated Apoptosis) The extrinsic pathway is triggered by external signals through death receptors located on the cell membrane. These receptors belong to the tumor necrosis factor (TNF) receptor family, including Fas (CD95) and TNF receptor-1. Key Steps of the Extrinsic Pathway: 1. Ligand Binding to Death Receptors: ○ FasL (Fas ligand) binds to Fas receptor, or TNF-α binds to TNF receptor-1 on the cell surface. ○ This binding leads to the recruitment of adaptor proteins like FADD (Fas-associated death domain) to the intracellular death domain of the receptor. 2. Formation of the Death-Inducing Signaling Complex (DISC): ○ The death domain of the receptor binds to adaptor proteins like FADD, which then recruits procaspase-8. 3. Activation of Caspase-8: ○ Procaspase-8 is cleaved into its active form, caspase-8. ○ Caspase-8 directly activates caspase-3 and other downstream caspases, initiating the execution phase of apoptosis. 4. Cross-Talk with the Intrinsic Pathway: ○ In some cells, caspase-8 can also activate Bid, a pro-apoptotic Bcl-2 family member. Bid promotes mitochondrial permeabilization, linking the extrinsic and intrinsic pathways. The Role of the Caspase Cascade in Apoptosis Caspases are a family of cysteine proteases that cleave specific proteins to dismantle the cell. There are two main types of caspases in apoptosis:  Initiator caspases (caspase-8, caspase-9): Responsible for starting the apoptotic signal. Executioner caspases (caspase-3, caspase-7): Cleave structural proteins and enzymes, leading to the disassembly of the cell. Caspase Cascade: (like caspase-8 in the extrinsic pathway and Initiator caspases caspase-9 in the intrinsic pathway) are activated first and cleave executioner caspases like caspase-3. Executioner caspases degrade key proteins, such as nuclear lamins, cytoskeletal proteins, and enzymes involved in DNA repair, leading to cell shrinkage, chromatin condensation, and DNA fragmentation. The Role of Mitochondria in Apoptosis Mitochondria are central to the intrinsic pathway of apoptosis. The release of cytochrome c from the mitochondria into the cytoplasm is a critical step in initiating apoptosis. Key Roles of Mitochondria in Apoptosis: 1. This is triggered by mitochondrial outer Cytochrome c Release: membrane permeabilization (MOMP) caused by pro-apoptotic Bcl-2 family proteins such as Bax and Bak. 2. Formation of the Apoptosome: Once cytochrome c is released, it binds to Apaf-1 in the cytosol, forming the apoptosome and activating caspase-9. 3. Other Pro-Apoptotic Factors: Mitochondria also release other factors like Smac/DIABLO, which neutralize inhibitors of apoptosis proteins (IAPs), further promoting the caspase cascade. DNA Fragmentation and Its Consequence in Apoptosis One of the key features of apoptosis is the fragmentation of DNA: 1. Activation of Endonucleases: Caspase-activated DNase (CAD) is activated by caspase-3. CAD cleaves DNA at internucleosomal  regions, resulting in the characteristic ladder pattern of fragmented DNA during apoptosis. 2. Chromatin Condensation: Apoptotic cells undergo chromatin condensation and DNA cleavage into nucleosomal fragments. 3. Distinct Feature from Necrosis: In necrosis, the cell swells and bursts, releasing its contents, including DNA, in a disorganized manner. This causes inflammation. In contrast, apoptosis results in controlled DNA fragmentation without releasing harmful cellular components, preventing inflammation. Timing and Stages of Apoptosis The entire process of apoptosis can occur within a few hours and consists of distinct stages: 1. Initiation Phase: ○ Intrinsic or extrinsic signals activate initiator caspases (caspase-8 or caspase-9). 2. Execution Phase: ○ Executioner caspases (caspase-3, caspase-7) are activated, leading to cleavage of cellular proteins. ○ The cell begins to shrink, and chromatin condenses. 3. DNA Fragmentation and Cell Dismantling: ○ DNA is fragmented by endonucleases. ○ The cell membrane forms apoptotic bodies, which are small, membrane-bound vesicles that contain cell fragments. 4. Phagocytosis: ○ Apoptotic bodies are quickly engulfed by surrounding phagocytic cells (like macrophages), preventing the release of intracellular contents and inflammation. Summary of Differences from Necrosis Apoptosis is a controlled, energy-dependent process that prevents inflammation by containing cell contents within apoptotic bodies. Necrosis, on the other hand, is uncontrolled and leads to cell lysis, which causes the release of cellular contents into the extracellular space, triggering an inflammatory response. Thus, apoptosis is a clean and non-inflammatory way for the organism to remove unwanted cells, while necrosis often leads to collateral damage in surrounding tissues. 4.Explain the role of both apoptosis and autophagy in cellular or organismal development or function Both apoptosis and autophagy play critical roles in maintaining cellular homeostasis, facilitating organismal development, and ensuring proper function at the cellular and tissue levels. These processes are tightly regulated to ensure the removal of damaged or unnecessary cells and the recycling of cellular components. Below is a breakdown of their respective roles in development and function: Apoptosis in Development and Function Apoptosis, or programmed cell death, is crucial for shaping tissues, eliminating unnecessary or harmful cells, and maintaining balance in the body. Some key roles include: 1. Embryonic Development Tissue and Organ Sculpting: During development, apoptosis eliminates excess or improperly positioned cells. For example, the separation of fingers and toes in the embryo is driven by apoptosis of the cells in the webbing between them. Neuronal Development: In the developing nervous system, more neurons are produced than needed. Apoptosis removes excess neurons to ensure proper neural connections and prevent overcrowding. Elimination of Redundant Structures: Apoptosis removes temporary structures (like the tail in a human embryo) during development as they are no longer required for the mature organism. 2. Immune System Regulation Elimination of Self-Reactive Cells: In the thymus, apoptosis removes T-cells that are reactive to self-antigens, preventing autoimmune diseases. Control of Immune Response: After an immune response, apoptosis eliminates excess immune cells (e.g., T-cells) to restore homeostasis and prevent excessive inflammation. 3. Tissue Homeostasis Cell Turnover: Apoptosis maintains tissue homeostasis in adult organisms by balancing cell proliferation and death, particularly in tissues with high turnover rates like the skin and intestines.  Removal of Damaged Cells: Cells with irreparable DNA damage or cellular stress undergo apoptosis to prevent the propagation of mutations or defective cells that could lead to cancer or tissue malfunction. Autophagy in Development and Function Autophagy, the process of "self-eating," allows cells to degrade and recycle their components. It serves as a survival mechanism in times of nutrient deprivation or stress, but also has essential roles in development and normal cellular function. 1. Nutrient Recycling and Survival Response to Starvation: During times of nutrient scarcity (such as during embryogenesis or in adult tissues during fasting), autophagy breaks down non-essential proteins and organelles to release nutrients and provide energy for essential cellular functions. Cellular Quality Control: Autophagy selectively degrades damaged organelles (such as mitochondria through mitophagy) and misfolded proteins, preventing the accumulation of defective components that could disrupt cellular function. 2. Embryonic Development Cell Differentiation: Autophagy plays a role in the differentiation of specific cell types during embryogenesis, including the degradation of unnecessary cellular components to facilitate the transition to specialized cell types. Metamorphosis in Insects: In organisms like Drosophila, autophagy is involved in remodeling tissues during metamorphosis, breaking down larval tissues to generate adult structures. 3. Immune Function Host Defense: Autophagy is involved in eliminating intracellular pathogens like bacteria and viruses through a process known as xenophagy, contributing to innate immune defense. Antigen Presentation: Autophagy helps present antigens to immune cells, assisting in the activation of adaptive immunity and the development of a precise immune response. 4. Aging and Longevity Proteostasis and Cellular Longevity: By maintaining cellular quality control, autophagy prevents the accumulation of damaged proteins and organelles, a process linked to aging and age-related diseases. Enhanced autophagy is associated with increased cellular and organismal lifespan in various models.