Peroxisomes and Cell Cycle Regulation, Apoptosis, and Cancer PDF

water (H₂O), helping to detoxify the cell by neutralizing harmful hydrogen peroxide PEROXISOMES (effectively cleaning up its own waste). Oxidases:...

water (H₂O), helping to detoxify the cell by neutralizing harmful hydrogen peroxide PEROXISOMES (effectively cleaning up its own waste). Oxidases: Create hydrogen peroxide (H₂O₂), which can be toxic to the body. Peroxisomes manage this by converting the H₂O₂ into safer byproducts. Functions of Peroxisomes 1. Detoxification: ○ Peroxisomes detoxify reactive oxygen species (ROS) such as hydrogen peroxide (H₂O₂) and superoxide (O₂*), which are harmful to cells. Peroxisomes: ○ Peroxidase enzymes in peroxisomes break down Peroxisomes are membrane-bound hydrogen peroxide (H₂O₂) organelles found in the cytoplasm into water (H₂O) and oxygen of eukaryotic cells. (O₂). This detoxifies the cell They are involved in various by reducing harmful ROS. metabolic processes, particularly ○ Reaction: those related to oxidation reactions *H₂O₂ + e⁻ + H⁺ → and the detoxification of harmful H₂O + OH (hydroxy substances. radical)**: Here, They are not part of the endoplasmic hydrogen peroxide is reticulum (ER) system, but there are reduced by electrons indications that some of the and protons, proteins that make up generating water and peroxisomes are synthesized by a hydroxyl radical, ribosomes associated with the which is then further ER. neutralized. Prominent in cells of the kidney, ○ Other ROS: Peroxisomes liver, photosynthetic cells, and also handle other reactive germinating seedlings that store fats molecules such as organic in their seeds. peroxides, which can damage cell membranes and Key enzymes in peroxisomes: proteins. 2. Oxidation: Catalase: Breaks down hydrogen ○ Peroxisomes catalyze the peroxide (H₂O₂) into oxygen (O₂) and oxidation of substrates  (molecules) using hydrogen transported into the peroxide (H₂O₂) as an peroxisomes for breakdown. oxidizing agent. These fatty acids accumulate ○ Oxidizing agent: In this in body fluids and destroy the case, hydrogen peroxide myelin sheath in nervous (H₂O₂) acts as the oxidizing tissue, leading to agent, and it facilitates the neurological damage. breakdown of toxic 5. Metabolism of compounds by catalyzing Nitrogen-Containing Compounds: oxidation reactions. ○ Peroxisomes also participate ○ The end result is the in the metabolism of detoxification of harmful nitrogen-containing substances through oxidation compounds, which are reactions. involved in various 3. Beta-Oxidation of Fatty Acids: biochemical pathways in ○ Fatty acid metabolism is cells. another important function of peroxisomes. They are involved in beta-oxidation, a process where fatty acids are How Are Peroxisomes Made? broken down into smaller units. There are two primary ways that ○ In animal cells, peroxisomes peroxisomes are made in cells: break down long-chain fatty 1. Binary Fission (Increase in Size acids (16-22 carbons), very and Division): long-chain fatty acids (26+ ○ Peroxisomes can replicate by carbons), and binary fission, similar to branched-chain fatty acids. bacteria. They grow larger in This process is essential for size and then divide into two energy production and fat smaller peroxisomes. metabolism. 2. De novo Synthesis (From 4. Genetic Disease: X-linked Scratch): Adrenoleukodystrophy: ○ Peroxisomes can also be ○ A defect in an integral synthesized de novo (from membrane protein scratch). This process responsible for transporting typically begins with the very long-chain fatty acids endoplasmic reticulum into the peroxisome can lead (ER) contributing proteins to a condition known as and lipids, which then form X-linked the peroxisomal membrane adrenoleukodystrophy and enzymes. (ALD). ○ In ALD, the very long-chain fatty acids cannot be Summary The cell cycle involve the meiosis process can have some variations in Peroxisomes are crucial for detoxification, the sense that meiosis involves two fatty acid metabolism, and the breakdown of cell divisions reactive oxygen species. They contain After the M phase, you now have the enzymes such as peroxidase for G1 phase and this phase can vary in detoxifying hydrogen peroxide, and they are length involved in beta-oxidation of fatty acids. ○ In some cells it can be very Peroxisomal dysfunction, such as in long, in some it can be very X-linked adrenoleukodystrophy, can lead short to serious health problems, including nerve ○ In G1, cells grow in size, damage. They are produced by binary metabolize various fission or de novo synthesis involving the molecules, and synthesize ER. macromolecules and organelles, preparing to enter the next round of cell division. Cell Cycle Regulation, Apoptosis, and ○ The cell divides if it will Cancer proceed to the next stage of S where the DNA synthesis stage so some cells might opt to enter the G0 stage and from the G0 stage some cells might go back to the cell cycle. They might be induced to divide by certain factors or you might have some cells that may opt to stay in G0 to undertake terminal differentiation The S phase is so named because DNA synthesis occurs during this stage. ○ Additionally, numerous proteins are synthesized, and genes are transcribed and translated to produce various The shortest period is labeled as the proteins essential for different M phase and this is when the cell stages of the cell cycle. undergoes cell division. ○ It is only in this phase that It can be mitosis in the somatic cells DNA replication, DNA and also in the young germ cells synthesis takes place. It can also be meiosis in the germ DNA Replication: cells as they undergo maturation The main event of the  S phase is the - mature muscle tissues duplication of the - mature red blood cells cell's DNA. Each chromosome is 3) Divide when induced replicated to - liver cells in mature liver produce two sister The liver has a unique ability to chromatids, ensuring regenerate, allowing it to regrow up that each daughter to 70% of its mass after partial cell will receive an removal, such as in living-donor liver identical set of transplantation or injury. This genetic information process involves mature during cell division. hepatocytes re-entering the cell Protein Synthesis: cycle to divide and increase their In addition to DNA numbers, supported by other liver replication, the S cells and growth factors like phase is also a period hepatocyte growth factor (HGF). of intense protein Regeneration is rapid, with synthesis. Proteins significant recovery occurring within involved in DNA 1–2 weeks, although full restoration replication, repair, may take longer. However, this and other cellular ability depends on the remaining functions are liver tissue being healthy, as chronic produced to support conditions like cirrhosis can impair the cell's preparation regeneration. This exceptional for division. property makes the liver vital for S phase is followed by G2 procedures like transplantation. ○ A phase where now the cell -lymphocytes prepares to undergo cell WBCs such as lymphocytes (T division cells and B cells) retain the ability to divide and proliferate, especially Variations in the occurrence of Cell when responding to infections or Cycle immune challenges. 1. Cells that undergo continuous cell Summary division to replace cells that die: Continuous Division Needed? Only stem - epithelial cells of mucosal layer of cells in the bone marrow undergo stomach, intestines, body cavities continuous cell division to produce RBCs, - epithelial cells of stratum germinativum of WBCs, and platelets. skin Mature RBCs and platelets do not divide, - hematopoetic stem cells while some WBCs can divide under specific - spermatogonia conditions (e.g., lymphocyte activation). 2) Do not divide after maturation - mature nerve tissues Normal length of cell cycle in adult tissues of Xenopus laevis: 20 hours Cell cycle in cleaving embryos: < 30 mins - S phase- less than 3 mins (adult tissue at least 5 hours) - no G1, short G2: large fertilized egg, large cytoplasm Cleavage of a fertilized egg into progressively smaller cells Second picture (first pic with red dot) is the zygote. It is a large egg. It undergoes cell division. After fertilization, the first stage of development is called cleavage, where the fertilized egg (zygote) begins to divide into smaller cells through a process called mitosis. Because the egg cell is large, the two daughter cells created from the first division don't need to grow in size. Instead, they continue dividing, producing even smaller cells. As the cell divisions continue, the group of cells forms a solid ball known as a morula. After this, the morula transforms into a structure called the blastula, which has a hollow center. These stages are part of early development, leading toward the formation of more complex structures in the embryo.  protein synthesis during G1, preparing the cell for DNA replication in S phase. When rapamycin inhibits mTORC1, the cell's growth is slowed, and the transition to S phase is blocked. This results in cell cycle arrest in the G1 phase, preventing cells from dividing. Rapamycin’s ability to inhibit mTORC1 makes it useful in immunosuppression, cancer treatment, and aging research by controlling excessive cell proliferation and promoting autophagy. Note: mTOR (Mechanistic Target of Rapamycin): mTOR is a protein that acts as a master regulator of cell growth, metabolism, and survival. It forms part of two distinct protein complexes: mTORC1 and mTORC2. mTORC1 (mTOR Complex 1): This is one of the complexes that mTOR forms, and it primarily regulates cell growth, protein Rapamycin is a drug that targets a synthesis, and metabolism in protein complex called mTOR response to nutrients, energy, and (mechanistic target of rapamycin), growth signals. which is a key regulator of cell mTORC1 is sensitive to rapamycin, growth, metabolism, and protein meaning rapamycin can inhibit it synthesis. directly. ○ Rapamycin is a drug that inhibits the protein complex mTORC1, which plays a central role in regulating cell Key transition points in the cell cycle growth, metabolism, and the cell cycle. By blocking mTORC1, rapamycin affects the transition from the G1 phase to the S phase of the cell cycle. mTORC1 promotes cell growth and  S Phase: During this phase, the cell replicates its DNA, ensuring that it has two complete sets of chromosomes—one for each daughter cell after mitosis. Once DNA replication is completed in S phase, the cell moves into G2 phase. G2 Phase: This phase occurs after DNA replication (S phase) and before mitosis (M phase). The G2 to M transition is influenced by several factors, including the cell's size, the integrity of its DNA, and the completion of DNA replication. The cell must reach an adequate size, ensure that DNA replication is fully completed, and verify that there is no DNA damage before proceeding to mitosis. If DNA damage is detected, the cell will delay the transition to M phase until the issue is resolved. Metaphase-Anaphase Transition Influenced by: ○ Chromosome attachments to At the restriction point (G1), the cell must spindle be checked to ensure that sufficient growth factors are present in the medium for continued progression through the cell cycle. Transition Between Cell Cycle The cells should have the Phases and Soluble Factors appropriate nutrients The cells should have attained the The transition between different phases of correct cell size the cell cycle is regulated by soluble factors If there is DNA damage, it must be that facilitate progression from one phase to repaired before the cell is allowed to the next. These factors are particularly proceed to the S phase. important in the G2-M phase transition. Cell Fusion Experiments G2 M transition To investigate these factors, cell fusion Influenced by cell size experiments were performed, and the DNA damage following results were observed: DNA replication 1. Fusion of S Phase and G1 Phase: phase. This indicated that ○ When cells in G1 phase the progression through were fused with cells in S these phases is also linked phase, the G1 cells were by specific factors that induced to enter the S regulate cell division. phase, even though they were not yet prepared for it. Soluble Factors: Maturation ○ This transition was triggered Promoting Factor (MPF) by soluble factors present in the S phase, such as Maturation Promoting Factor pulverized chromosome (MPF) is a soluble factor complex fragments from DNA that plays a crucial role in regulating condensation. As a result, the transition from G2 phase to M both cells in the fusion phase (mitosis) in the cell cycle. underwent S phase. 2. Fusion of M Phase and G1 Phase: Composition of MPF: ○ When cells in G1 phase were fused with cells in M MPF is made up of two key phase, the G1 cells were molecules: induced to undergo mitosis, 1. Cyclin-Dependent Kinase even though they had not (Cdk): This enzyme is gone through the necessary present throughout the cell preparations from earlier cycle, but it is inactive unless phases (such as G1, S, and bound to the appropriate G2). cyclin. ○ This transition was driven by 2. Mitotic Cyclin (Cyclin B): soluble factors found in the M This protein binds to Cdk and phase, which caused the G1 activates it. Without Cyclin B, cells to begin the process of Cdk cannot perform its chromosome function. condensation, a key feature of prophase in mitosis. This Function of MPF: demonstrated that soluble The MPF complex (Cdk + Cyclin B) factors from the M phase can induces mitosis by activating push cells into mitosis various proteins that trigger the prematurely. events necessary for the cell to 3. Fusion of S Phase and M Phase: progress into mitosis. ○ The fusion of S phase and Cyclins are specific proteins whose M phase cells showed that levels fluctuate throughout the cell pulverized chromosome cycle. Different types of cyclins are fragments, a feature of present during various phases: condensed chromosomes ○ Cyclin D is prominent in the in mitosis, were induced by G1 phase. soluble factors from the M  ○ Cyclin E regulates the the activity of MPF is dependent on the transition from G1 to S concentration of Cyclin B. phase. When Cyclin B levels are high, MPF is ○ Cyclin A is active during S active, and the cell can enter mitosis. phase and G2 phase. When Cyclin B levels drop, MPF activity ○ Cyclin B binds to Cdk to form decreases, and the cell exits mitosis. MPF, promoting the transition from G2 to M phase. Cdk Concentration: Cdk (the Cyclin-Dependent Kinase part of MPF) remains constant throughout the cell cycle. *The key point is that Cdk itself is always present, but its activity depends on the presence of Cyclin B. Without Cyclin B, Cdk cannot activate the processes needed for mitosis. Key Concept: Cyclin B and MPF activity increase Mitotic Cyclin and MPF Activity as the cell enters mitosis, and then drop after mitosis. Mitotic Cyclin Activity: Cdk concentration remains steady, but it only becomes active when Mitotic Cyclin (Cyclin B) concentration starts bound to Cyclin B. to rise as the cell progresses through G2 phase (just before mitosis). The activity of Cyclin B reaches its peak as the cell enters the G2-M transition (where the cell prepares for mitosis). After mitosis (M phase), the concentration of Cyclin B drops quickly, causing the cell to exit mitosis. MPF Activity: MPF (Maturation Promoting Factor) activity follows the same pattern as Cyclin B. Activation of Mitotic Cdk-Cyclin B Since MPF is made up of Cdk Complex (Cyclin-Dependent Kinase) and Cyclin B, Initial Inactivity:  This is the cell's way of making sure mitosis When Cyclin B binds to Cdk doesn't happen if the DNA is not properly (Cyclin-Dependent Kinase), they form a prepared. complex called MPF (Maturation Promoting Factor). Key Points: However, this complex is initially inactive. Cdk-Cyclin B complex is initially inactive This is because two inhibitory due to inhibitory phosphates. phosphates (added by inhibiting Activating kinase and phosphatase work kinases) prevent the complex from together to remove the inhibitory functioning. phosphates and fully activate the complex. DNA damage or incomplete replication Activating Kinase: prevents phosphatase from activating the complex, ensuring the cell doesn't enter The complex remains inactive until an mitosis prematurely. activating kinase adds a single phosphate to the complex, which partially activates it. Phosphatase: Once the activating kinase adds the phosphate, an enzyme called phosphatase removes the inhibitory phosphates from the complex. This leaves behind the activated phosphate, fully activating the MPF complex. Positive Feedback: The activated MPF complex further stimulates phosphatase, which activates more of the inactive complexes. This creates a positive feedback loop, ensuring the cell is ready for mitosis. DNA Damage and Incomplete Replication: If there is DNA damage or if DNA replication is incomplete during the G2 phase, the activity of phosphatase is inhibited. As a result, the inhibitory phosphates Activities of MPF After Activation remain attached to the complex, preventing the cell from entering the M phase (mitosis). 1. Constant Cdk Concentration:  3. Mitotic Spindle Formation: The concentration of Mitotic Cdk (Cyclin-Dependent Kinase) remains Why: The mitotic spindle is necessary for constant throughout the cell cycle. chromosome alignment and separation. However, Mitotic Cyclin B is absent in some Role of MPF: phases and gradually increases towards the MPF activates Microtubule Associated end of the G2 phase. It peaks before mitosis Proteins (MAPs) by phosphorylating them, (M phase). which helps to assemble tubulin into microtubules. 2. Cyclin B Degradation: These microtubules then form the mitotic spindle fibers and asters in the polar regions At the end of mitosis, Cyclin B is of the cell, facilitating chromosome degraded, which is necessary to exit movement. mitosis and return to the interphase. 4. Targeted Protein Degradation: Key Functions Activated by MPF (Through Phosphorylation) Why: The cell needs to degrade certain proteins at the end of mitosis to exit from 1. Breakdown of the Nuclear Envelope: the process. Why: The nuclear envelope must break Role of MPF: down so that spindle fibers can attach to the Cyclin B is degraded at the end of mitosis, chromosomes during mitosis. which allows the nuclear envelope to Role of MPF: reassemble, chromosomes to decondense, MPF activates phosphorylation of the Lamin and the mitotic spindle fibers to degrade. proteins in the nuclear lamina (the inner Securin, a protein that inhibits anaphase, membrane of the nuclear envelope). is also degraded via the Phosphorylation inactivates the lamins, Anaphase-Promoting Complex (APC). causing the nuclear envelope to This allows the separation of sister disassemble and allowing spindle fibers to chromatids during anaphase. attach to the chromosomes. Summary of MPF's Role in Mitosis: 2. Chromosome Condensation: MPF activation leads to critical events like nuclear envelope breakdown, chromosome Why: Chromosomes need to condense so condensation, mitotic spindle formation, and they can be separated during mitosis. protein degradation. Role of MPF: It regulates these events by phosphorylation MPF activates condensin (a protein that of target proteins, ensuring the cell helps in chromosome condensation) by proceeds correctly through mitosis. phosphorylating it. This causes the At the end of mitosis, the Cyclin B is chromosomes to become more tightly degraded, and the cell exits mitosis, packed (condensed), which is necessary for resetting for the next cycle. proper segregation.  Mitotic Cyclin-Cdk (MPF) adds a phosphate group (PO4) to CDC20, an activator of the Anaphase-Promoting Complex (APC). **2. Role of APC: APC is a ubiquitin ligase, meaning it attaches ubiquitin molecules to its target proteins. Ubiquitination marks these proteins for degradation by the Proteasome (the cellular "waste disposal" system). MPF activity in terms of targeted protein degradation, particularly during Anaphase in Ubiquitination is a process where a small mitosis (and Anaphase II in meiosis): protein called ubiquitin is attached to another protein in a cell. Think of ubiquitin Targeted Protein Degradation During as a "tag" that marks proteins for specific Mitosis jobs. Here's how it works in simple terms: **1. Separase and Securin: 3. Ubiquitination of Key Proteins: Separase (also called Separin) is an enzyme that catalyzes the degradation of Securin: By tagging Securin with ubiquitin, cohesin, the protein holding sister APC marks it for degradation. This removal chromatids together. of Securin activates Separase, allowing it to degrade cohesin and separate the sister The degradation of cohesin allows the sister chromatids. chromatids to be pulled to opposite poles of Mitotic Cyclin: Mitotic Cyclin is also the cell during anaphase (the stage of ubiquitinated by APC and degraded to mitosis). ensure the cell exits mitosis properly. Summary of the Process: **2. Role of Securin: Mitotic Cdk-Cyclin adds phosphate groups to CDC20, which activates APC. Securin inhibits Separase by binding to it, APC is a ubiquitin ligase that adds ubiquitin preventing premature activation. to Securin and Mitotic Cyclin, marking them Active MPF (Mitotic Cyclin-Cdk complex) for degradation. plays a key role in triggering the The degradation of Securin allows degradation of Securin. Separase to activate and degrade cohesin, allowing chromosome separation during Mechanism of Protein Degradation via anaphase. MPF Activity Mitotic Cyclin degradation also helps the cell exit mitosis and reset for the next cycle. **1. MPF Activation of APC:  the proteasome, a large complex responsible for protein degradation. Activation of Proteasome via The proteasome recognizes the Ubiquitination polyubiquitin tag, removes the ubiquitin chain, and unfolds the target protein for **1. Ubiquitin-Activating Enzyme (E1): degradation inside its catalytic core. The target protein is then broken down into E1 is the first enzyme in the smaller peptides, which can be recycled or ubiquitination process. further degraded. It activates ubiquitin by attaching it to itself using energy from ATP, making it ready for Summary of Key Steps: conjugation. Ubiquitin is activated by the E1 **2. Ubiquitin Conjugating Enzyme (E2): enzyme. The activated ubiquitin is transferred After E1 activates ubiquitin, E2 (the ubiquitin to E2. conjugating enzyme) carries the activated E3 (ubiquitin ligase) attaches ubiquitin. ubiquitin to the target protein (like E2 is responsible for transferring the Securin or Mitotic Cyclin). ubiquitin molecule to the target protein. A polyubiquitin chain is formed on the target protein, marking it for **3. Ubiquitin Ligase (E3): degradation. The tagged protein is directed to the E3 is the ubiquitin ligase, which mediates proteasome, which removes the the transfer of ubiquitin from E2 to the target ubiquitin and degrades the protein. protein. ○ The proteasome breaks In this case, the target proteins being down proteins tagged with tagged for degradation include Securin and ubiquitin (a marker for Mitotic Cyclin. destruction). ○ It converts these proteins into **4. Ubiquitin Chain Formation: smaller peptides or amino acids, which can be recycled Multiple ubiquitin molecules are attached to to build new proteins or used the target protein, forming a polyubiquitin for energy. chain. Key Roles in Cell Cycle Regulation: This chain serves as a signal for Ubiquitination is crucial for degradation. controlling the cell cycle, as it regulates the degradation of key **5. Recognition and Degradation by proteins such as Securin and Mitotic Proteasome: Cyclin. The degradation of these proteins The polyubiquitin chain directs the target allows the cell to progress through protein (e.g., Securin or Mitotic Cyclin) to mitosis and ensures that the cycle is properly regulated.  This process is part of the cell's 3. Cell Size: quality control mechanism, ensuring ○ The cell must reach a that damaged or unneeded proteins sufficient size to ensure are efficiently removed. proper division and distribution of cellular components to daughter cells. 4. DNA Damage: ○ If DNA damage is detected, the cell halts progression to repair the damage before replication begins. Key Molecules Involved: 1. G1 Cdk-Cyclin: Restriction Point: G1 to S-Phase Regulates progression through the restriction point. The restriction point in the G1 phase is a Function: Phosphorylates proteins critical checkpoint that determines whether required for S-phase entry, including the cell is ready to enter the S-phase (DNA the Retinoblastoma (Rb) protein. synthesis phase). This checkpoint ensures that the cell has met all the necessary 2. Retinoblastoma (Rb) Protein: conditions for DNA replication to proceed safely and efficiently. Role: Acts as a gatekeeper, preventing the cell from entering the S-phase prematurely. Inhibits the activity of E2F, a Influencing Factors: transcription factor necessary for the expression of genes involved 1. Growth Factors: in DNA replication. ○ External signals (like Mechanism: hormones) stimulate cell ○ When the cell is not ready for proliferation by promoting S-phase, Rb binds to E2F, synthesis of molecules keeping it inactive. needed for the S-phase. ○ If conditions are favorable, 2. Nutrients: G1 Cdk-Cyclin ○ Adequate nutrient availability phosphorylates Rb, causing ensures the cell has the it to release E2F. resources to synthesize DNA and other cellular 3. E2F Transcription Factor: components.  Function: Upregulates genes RAS Pathway and Cell Cycle encoding proteins essential for Progression S-phase, such as those involved in DNA replication and nucleotide The RAS pathway promotes cell synthesis. proliferation by producing proteins essential Once Rb is phosphorylated and for cell cycle progression, particularly for the E2F is released, the cell is G1 to S-phase transition. committed to DNA synthesis. 1. Activation: Growth factors bind receptors, activating the RAS protein, which switches from Consequences of Rb Mutation: GDP-bound (inactive) to GTP-bound (active). Mutations in the Rb protein disrupt 2. Signaling Cascade: its ability to inhibit E2F, leading to ○ Active RAS triggers the unregulated cell cycle progression. RAF-MEK-ERK pathway, This unchecked division can result in leading to phosphorylation cancer, such as retinoblastoma, a and activation of transcription type of eye cancer commonly factors. linked to Rb mutations. ○ These factors stimulate genes for E2F and G1 Cdk-Cyclin production. 3. G1 to S-Phase Transition: Summary of Restriction Point ○ G1 Cdk-Cyclin Control: phosphorylates Rb, releasing E2F to activate genes for Healthy Cells: DNA replication. ○ Growth factors, nutrients, and appropriate cell size Clinical Relevance: Mutated RAS causes activate G1 Cdk-Cyclin, uncontrolled cell proliferation, contributing to leading to Rb cancers like pancreatic and lung cancer. phosphorylation. ○ Rb releases E2F, allowing Cell Cycle Checkpoints and DNA transcription of S-phase Damage Response genes. Cells Not Ready: G1-S DNA Damage Checkpoint ○ If DNA damage or insufficient conditions exist, Rb remains 1. Mechanism: bound to E2F, blocking ○ DNA damage activates S-phase entry. ATM/ATR kinases. ○ These phosphorylate This checkpoint is a key safeguard to checkpoint kinases (e.g., maintain genomic stability and prevent Chk1, Chk2), which inhibit uncontrolled cell proliferation. Mdm2, stabilizing p53.  2. Outcomes: 2. Steps: ○ p21 Upregulation: Inhibits ○ Pre-Replication Complex G1 Cdk, preventing Formation: Origin phosphorylation of Rb. Recognition Complex (ORC), Without phosphorylated Rb, MCM helicase, and helicase E2F remains inactive, halting loaders bind to replication the transition to S-phase, origins, licensing DNA for allowing DNA repair. replication. ○ Puma Activation: A ○ Deactivation: pro-apoptotic protein that Cdk: Inhibits ORC inhibits Bcl-2 (an apoptosis and helicase loaders inhibitor), leading to during the S-phase, programmed cell death if the blocking relicensing damage is irreparable. while activating DNA 3. Associated Disease: synthesis. ○ Ataxia Telangiectasia: A Geminin: Binds MCM disease caused by defective to prevent its ATM kinase, resulting in reactivation. impaired DNA damage response. Symptoms include unsteady posture and dilated blood vessels Spindle Assembly Checkpoint in the eyes and face. (Metaphase-Anaphase Transition) 1. Function: Ensures proper chromosome alignment and spindle G2-M DNA Damage Checkpoint fiber attachment before anaphase. 2. Mechanism: 1. Mechanism: ○ Unattached kinetochores ○ DNA damage or incomplete recruit Mad and Bub replication inhibits proteins, generating a "wait phosphatase activity, signal" that blocks Cdc20. preventing activation of i. If a chromosome isn’t mitotic Cdk-cyclin, arresting attached to the the cell in G2 phase. spindle fibers, special ○ This ensures no damaged proteins called Mad DNA progresses to mitosis. and Bub gather at the problem spot (the kinetochore). ii. These proteins send DNA Replication Licensing (G1-S a "wait signal" to the Transition) cell, telling it not to proceed yet. 1. Purpose: Ensures DNA is replicated only once per cycle.  ○ Without Cdc20, the Oncogenes Anaphase-Promoting Complex (APC) remains 1. Definition: Genes that, when inactive, preventing the mutated or overexpressed, can degradation of securin and drive the development of cancer. ensuring cohesion between ○ Oncogenes originate from sister chromatids is proto-oncogenes, normal maintained. cellular genes that regulate growth and survival. ○ Can be acquired from: Viruses that infect Key Diseases Linked to Checkpoints humans or animals. Mutations in normal 1. Ataxia Telangiectasia: Defective proto-oncogenes. ATM kinase leads to poor DNA 2. Role of Oncogenes: damage response, unsteady ○ Encode proteins that posture, and blood vessel dilation. promote excessive cell 2. Retinoblastoma: Mutations in the proliferation. Rb protein result in uncontrolled ○ Inhibit apoptosis, allowing E2F activation, promoting abnormal cells to survive and unregulated cell cycle progression divide. and cancer. Apoptosis is a process of By coordinating these checkpoints, the cell programmed cell cycle ensures accurate DNA replication, death, where cells chromosome alignment, and prevents the deliberately destroy propagation of damaged DNA, maintaining themselves in a genomic stability. controlled and organized way. It’s Cancer and Apoptosis: Role of like the cell's version Cell Cycle Dysregulation of "self-destruct" for the good of the Cancer: Result of Defects in Cell Cycle organism. Regulation Cancer arises when normal controls over cell growth, division, and Examples of Oncogene Dysregulation apoptosis are disrupted. Defects in cell cycle checkpoints and 1. Bcl-2: apoptotic pathways can lead to the ○ Normally inhibits apoptosis to survival and proliferation of regulate cell survival. abnormal cells. ○ Oncogenic Role: Mutation leads to overactivation of Bcl-2, excessively blocking apoptosis.  ○ Result: Abnormal cells evade programmed cell death, accumulating to form tumors. 2. Mdm2: ○ Normally a ubiquitin ligase that degrades p53, a tumor suppressor protein involved in DNA repair and apoptosis. ○ Oncogenic Role: Mutation in Mdm2 causes p53 overproduction. Paradoxically, in this context, excessive p53 fails to induce apoptosis or cell cycle arrest. Allows unchecked proliferation of cells RB Gene: Hereditary vs. with damaged DNA, Non-Hereditary Retinoblastoma leading to cancer. Hereditary Retinoblastoma Cause: Inherited mutation in one Summary: copy of the RB gene. Genetic Mechanism: Individuals Oncogenes disrupt the balance between inherit a single mutated allele (from cell proliferation and apoptosis, allowing one parent), and the second allele damaged or abnormal cells to evade death can undergo a mutation later in life, and proliferate uncontrollably. Dysregulation leading to cancer. of proteins like Bcl-2 and Mdm2 exemplifies Manifestation: Typically occurs at how these mechanisms can contribute to an early age, primarily affecting the cancer development. retina (eye cancer in children). The mutation is present in all cells of the body, making it more widespread. Non-Hereditary Retinoblastoma Cause: Occurs due to two spontaneous mutations in the RB gene, one in each allele. Genetic Mechanism: Unlike hereditary, the mutations are not inherited, and they occur in the same individual later in life.  Manifestation: Typically occurs later which regulates cell in childhood or adulthood and may proliferation. only affect the retina or other tissues ○ APC normally forms a where mutations arise. destruction complex that inhibits the Wnt pathway, thus preventing excessive cell proliferation. p53 Tumor Suppressor Gene – ○ Mutation of APC: Leads to TP53 in Humans continuous activation of the Wnt pathway, causing Li-Fraumeni Syndrome unchecked cell division, which can result in colon Cause: Mutations in the TP53 gene cancer. can lead to various cancers, such as breast, brain, lung, skin, adrenal, and bone cancers. Hereditary and Non-Hereditary: Apoptosis: Normal Occurrence The mutations can either be and Mechanism inherited or occur spontaneously. Mechanism: ○ TP53 regulates apoptosis, preventing damaged cells from proliferating. ○ Mutations in p53 prevent apoptosis, allowing defective cells to survive and proliferate. ○ Viral Interaction: The E6 protein from the human papillomavirus (HPV) targets p53, leading to its degradation and inhibiting apoptosis, contributing to cancer development. Necrosis vs. Apoptosis Necrosis: ○ Definition: A form of APC Tumor Suppressor Gene uncontrolled cell death that affects neighboring cells. Associated with: Familial ○ Characteristics: Adenomatous Polyposis (FAP) Extensive and non-inherited colon cancer. vacuolation, Mechanism: mitochondrial ○ APC is a key component of swelling, rupture of the Wnt signaling pathway,  the plasma Tadpole tail removal membrane. during Leads to inflammation metamorphosis. and damage to Tissue sculpting surrounding tissue. between fetal fingers ○ Common Causes: Ischemia, and toes. trauma, stroke, Endometrial shedding neurodegenerative diseases during menstruation. (e.g., Alzheimer's, Removal of excess or Parkinson's). damaged cells during Apoptosis (Programmed Cell neural development. Death): ○ Definition: A controlled Key Players in Apoptosis process that removes defective or unnecessary Caspases: cells without damaging ○ Types: neighboring cells. Initiator Caspases ○ Key Features: (e.g., Caspase-2, -8, The cell shrinks, the -9, -10) activate nuclear envelope downstream disassembles, and executioner DNA is fragmented caspases. into small pieces. Executioner The cell is engulfed Caspases (e.g., by neighboring cells Caspase-3, -6, -7) (phagocytosis) for carry out the death removal. program. ○ Mechanism: Normal Occurrence of Apoptosis Caspases are initially produced as inactive precursors (pro-caspases) and are activated during apoptosis. Targets of Caspases: ○ Protein Kinases (e.g., FAK, PKB, PKC, Raf1) involved in cell adhesion, signaling, and survival. ○ Lamins: Structural proteins Essential for development and in the nuclear envelope that maintenance of organismal integrity. undergo cleavage during ○ Examples: apoptosis. ○ Cytoskeleton Proteins: Caspases cleave actin,  tubulin, and other proteins, activates Caspase-3 to disrupting the cell's shape. initiate apoptosis. ○ Endonuclease CAD: Activated by caspases to cleave DNA, causing fragmentation. Summary of Key Concepts: Tumor Suppressor Genes (e.g., RB, p53, APC) regulate cell growth Apoptotic Pathways and prevent cancer by controlling the cell cycle, promoting apoptosis, Extrinsic Pathway (Receptor-Mediated) and inhibiting uncontrolled proliferation. Mechanism: RB Gene: Mutations can be ○ Death receptors on the cell hereditary or spontaneous, with surface (e.g., CD95/FAS) hereditary mutations causing bind to corresponding ligands early-onset cancer and affecting all (e.g., from cytotoxic T-cells). body cells. ○ Binding leads to receptor p53: Plays a critical role in trimerization, activating preventing cancer by initiating adaptor proteins and apoptosis in response to DNA recruiting Procaspase-8, damage; mutations lead to various which is converted to cancers and prevent cell death. Caspase-8. APC: Involved in the Wnt pathway; ○ Caspase-8 activates mutations result in uncontrolled Caspase-3 (executioner cell proliferation, leading to colon caspase), leading to cancer. apoptosis. Apoptosis: A process of programmed cell death that is Intrinsic Pathway essential for development, homeostasis, and removing Trigger: DNA damage, oxidative damaged cells. It occurs via extrinsic stress, or lack of growth factors. or intrinsic pathways involving Mechanism: caspases. ○ Activation of Death Promoting Proteins (e.g., Bax, Bak) counteracts Bcl-2 Absence of Growth Factors in (a pro-survival protein). Apoptosis ○ Cytochrome c is released from the mitochondria, The absence of growth factors is forming the Apoptosome considered by some as a third mechanism with Apaf-1 and for apoptosis, though it is often grouped Procaspase-9. under the intrinsic pathway. The core idea ○ The Apoptosome activates is that growth factors are critical for cell Caspase-9, which further survival and proliferation. When growth factors are absent, cells can trigger apoptosis as part of their natural response to stress or unfavorable conditions. Mechanism: Growth factors normally activate signaling pathways (e.g., PI3K-Akt pathway), which promote cell survival by inhibiting pro-apoptotic proteins and activating anti-apoptotic proteins (e.g., Bcl-2). When growth factors are absent, these survival signals are lost, and pro-apoptotic proteins (e.g., Bad, Bax, Bak) are activated, which leads to mitochondrial dysfunction. This activation causes mitochondrial outer membrane permeabilization (MOMP), which allows the release of cytochrome c into the cytosol. The released cytochrome c Additional info: participates in the formation of the Apoptosome, a complex that activates Caspase-9, which in turn Soluble Factors: activates Caspase-3 and leads to apoptosis. What they do: Soluble factors are signals or molecules (like proteins) In this context, the absence of growth that guide the cell through the factors may not be considered a completely cycle. They tell the cell when it’s separate pathway but rather a condition that time to move forward to the next triggers the intrinsic apoptotic pathway. phase, such as from G1 to S, or G2 Some references might treat it as an to M. independent mechanism, but fundamentally, How they work: These factors it shares the same end-result of activate enzymes (like CDKs) that mitochondrial-mediated cell death through push the cell past checkpoints caspase activation. and help it progress through the cell Thus, the absence of growth factors can cycle. serve as a signal to initiate the intrinsic pathway and lead to programmed cell death in a way similar to DNA damage, oxidative stress, or other intracellular Restriction Points: signals.  What they do: Restriction points are checkpoints in the cell cycle where the cell decides whether it is ready to continue or if it should stop and fix something (like DNA damage). How they work: They check if the cell has the necessary conditions (like enough nutrients, DNA integrity, and proper growth signals). If the conditions aren’t right, the cell won’t move forward and might pause or stop dividing. So, in simple terms: Soluble factors are the "go" signals that tell the cell when to move forward. Restriction points are the "stop or check" signals that make sure everything is okay before the cell continues.