BIOS 420 Cell Biology Final Exam Summary PDF

BIOS 420: Cell Biology Concept Summary for Final Exam ORGANIZATION OF CYTOPLASM AND CYTOSKELETON PROTEINS Organization of the Cell and Compartmentalization by Membranes Cell Compartmentalization: Cells are compartmentalized by systems of membranes, creating distinct environments for...

BIOS 420: Cell Biology Concept Summary for Final Exam ORGANIZATION OF CYTOPLASM AND CYTOSKELETON PROTEINS Organization of the Cell and Compartmentalization by Membranes Cell Compartmentalization: Cells are compartmentalized by systems of membranes, creating distinct environments for various cellular processes. Non-membrane components can also be highly organized within the cell. Cytosol and Micro-Organization: The cytosol (intracellular fluid) may contain regions with specialized micro-organization, contributing to cellular function. Role of the Cytoskeleton: The cytoskeleton maintains cell shape, provides a surface track for organelles and vesicles, anchors organelles in place, and facilitates their movement. Types of Cytoskeletons: Three major cytoskeletal components: 1. Microtubules: Composed of tubulin proteins, involved in maintaining cell shape, organizing internal structures, and facilitating transport. 2. Intermediate Filaments: Provide structural support and mechanical strength. 3. Actin Filaments: Composed of ATP-actin monomers, involved in cell movement, shape changes, and muscle contraction. Cytoskeleton as Polymers: All cytoskeletal components are polymers—long chains of monomeric units that assemble into complex structures. Cytoskeleton Structure and Function Electron Microscopy (EM) Studies: EM studies revealed the cytoskeleton consists of three key components: microtubules, microfilaments (actin filaments), and intermediate filaments. Functions of the Cytoskeleton: 1. Maintains cell shape. 2. Provides surface tracks for organelle and vesicle movement. 3. Anchors organelles in place. 4. Facilitates organelle and vesicle transport. Examples of Cytoskeletal Roles Red Blood Cells (RBCs): The cytoskeleton in RBCs maintains shape and flexibility, crucial for their deformation as they pass through capillaries. o Key Components: 1. Microtubules: Stabilize RBC shape. 2. Spectrin: Forms a flexible lattice beneath the plasma membrane, allowing RBC deformation. 3. Ankyrin: Anchors the spectrin-actin network to the plasma membrane. 4. Actin Filaments: Form a meshwork, maintaining shape and enabling flexibility. o Other Proteins: Actin-associated proteins (e.g., tropomyosin, protein 4.1) regulate interactions between actin and other cytoskeletal components, contributing to RBC stability. 1 BIOS 420: Cell Biology Concept Summary for Final Exam Polarized Epithelial Cells: In polarized epithelial cells, the cytoskeleton maintains structure, polarity, and function, especially in microvilli. o Actin Filaments: Form a network stabilizing microvilli and increasing surface area for absorption. o Microtubules: Have polarity that directs intracellular transport and positioning of organelles. o Intermediate Filaments: Keratins are associated with desmosomes and hemidesmosomes, providing mechanical strength and anchoring cells. Microtubules as Highways for Protein and Organelle Transport Microtubules: Act as intracellular highways for protein and organelle transport, supported by motor proteins that move cargo along the microtubule tracks. Motor Proteins: 1. Kinesin: Moves cargo toward the positive (+) end (typically toward the plasma membrane and ER). 2. Dynein: Moves cargo toward the negative (-) end (typically toward the Golgi complex or nucleus). Microtubule Polarity and Transport: Microtubules have intrinsic polarity: o The positive (+) end directs outward transport. o The negative (-) end directs inward transport. Organelles and vesicles rely on this network for positioning and movement. Motor Proteins: Myosin, Kinesin, and Dynein Myosin (Actin filaments): Moves toward the plus (+) end of actin filaments. Involved in muscle contraction, vesicle transport, cell division, and migration. Kinesin (Microtubules): Moves toward the plus (+) end of microtubules (cell periphery). Involved in anterograde transport and organelle positioning. Dynein (Microtubules): Moves toward the negative (-) end of microtubules (cell center). Involved in retrograde transport, cilia/flagella movement, and endocytosis. Duchenne Muscular Dystrophy (DMD) Inheritance: X-linked recessive disorder affecting primarily males; females are carriers. Phenotype: o Progressive muscle degeneration starting from age 1–6, leading to loss of mobility by age 12 and death by age 20. Etiology: Caused by defects in the DMD gene, leading to absence of dystrophin, a cytoskeletal protein that links the plasma membrane to actin filaments. Pathophysiology: Muscle cell damage and loss, replaced by fat and connective tissue, resulting in muscle weakness and eventual muscle cell death. Cytoskeletal Components and Cell Junctions Actin-Linked Junctions: o Junction Type: Adherens Junctions o Cytoskeleton: Actin filaments o Function: Maintain cell-cell adhesion and shape, important for tissue integrity and movement. 2 BIOS 420: Cell Biology Concept Summary for Final Exam Desmosomes: o Junction Type: Desmosomes o Cytoskeleton: Intermediate filaments (keratins) o Function: Provide mechanical strength to tissues under stress. Hemidesmosomes: o Junction Type: Hemidesmosomes o Cytoskeleton: Intermediate filaments (keratins) o Function: Anchor cells to the basement membrane. Cell-Matrix Junctions: o Junction Type: Focal Adhesions (actin-based) and Hemidesmosomes (intermediate filament-based) o Function: Connect cells to the extracellular matrix (ECM), enabling cell signaling and migration. Microtubules and Tubulin Characteristics Microtubule Composition: Composed of tubulin monomers (alpha and beta), forming hollow structures. Tubulin Subunits: o Alpha and beta tubulin bind GTP. o Alpha tubulin binds GTP tightly but does not hydrolyze it. o Beta tubulin binds and hydrolyzes GTP, regulating microtubule dynamics. Tubulin Dimer: The basic building block of microtubules, formed by the combination of alpha and beta tubulin dimers. Role of Microtubules in the Cytoskeleton Vesicular Trafficking: Microtubules serve as tracks for cargo transport, with kinesin and dynein moving vesicles along them. Spindle Apparatus in Cell Division: Microtubules form the spindle during mitosis, aiding in chromosome segregation. Motility: Microtubules form the core of cilia and flagella, which generate movement for cells or fluid. Microtubule-Specific Drugs: Mechanisms of Action Inhibition of Polymerization: o Colchicine: Prevents tubulin polymerization, blocking mitosis. o Vinblastine/Vincristine: Inhibit microtubule assembly, arresting the cell cycle. Stabilization of Microtubules: o Taxol (Paclitaxel): Stabilizes microtubules, preventing disassembly and arresting cell division. Microtubules: Cilia and Flagella Microtubules are integral components found inside ciliated cells and flagella. Axoneme: The central microtubule structure in cilia and flagella, providing the core support. Outer Microtubule Doublets: Surround the axoneme, forming the structural framework. 3 BIOS 420: Cell Biology Concept Summary for Final Exam Dynein Arms: Protein complexes that are attached to the microtubules, aiding in movement. Examples of Ciliated Cells in the Human Body Respiratory System: o Located on the epithelium from terminal bronchioles to the larynx. o Cilia clear harmful materials from the airways. Fallopian Tubes: o Ciliated epithelial cells help move the egg and sperm through the tubes. o Assist in the movement of the ovum from the ovary. Undulipodium Structure (Cilia & Flagella) Undulipodium refers to motile filamentous projections in eukaryotic cells. The microtubule arrangement in undulipodium is 9(2) + 2, where: o 9 outer microtubule doublets surround 2 central microtubules. Axoneme: The core microtubule structure that forms the backbone of cilia and flagella. Kinetosome and Centrosome Kinetosome (also called the basal body): o Base of the undulipodium. o Contains 9 triplet microtubules with no central microtubules (9(3) + 0). Centrosome: Contains centrioles from which spindle fibers develop during cell division. Ciliary Motion Dynein (motor proteins) are key to ciliary movement: o Inner and outer dynein arms help generate force. o ATPase activity of dynein powers the bending motion of the cilia. o Cilia beat in a coordinated, rapid, rotational motion. Cilia vs. Flagella Cilia: Hair-like projections that beat in coordinated fashion. Flagella: Whip-like projections that beat independently of each other. o Prokaryotes: Flagella perform rotary movement. o Eukaryotes: Flagella undergo bending movement. NUCLEUS Nucleus Structure: o Nuclear Envelope: Double membrane structure. Chromatin Types: o Euchromatin: ▪ Uncondensed, lightly staining. ▪ Genetically active, gene-expressing, gene-rich (higher GC content). o Heterochromatin: ▪ Highly condensed, darkly staining. ▪ Genetically inactive, silenced genes (methylated), gene-poor (high AT content). ▪ Contains long stretches of repeat sequences (satellite DNA). ▪ Constitutive Heterochromatin: Found at centromeres and telomeres. ▪ Facultative Heterochromatin: Can be activated or silenced, varies by cell type. Nucleolus: o Condensed region of chromatin. o Site of ribosome synthesis. 4 BIOS 420: Cell Biology Concept Summary for Final Exam o Makes up about 25% of the nucleus. o Contains protein and RNA, combines with proteins to form rRNA. Fibrous Lamina: o Meshwork of filaments near the inner nuclear membrane and peripheral chromatin. o Composed of lamins (class V intermediate filaments) and membrane-associated proteins. o Provides mechanical support, regulates DNA replication and cell division. Nucleoplasm: o Gel-like substance in the nucleus that stores chromatin (DNA plus proteins). Nuclear Envelope Breakdown/Reformation during Mitosis: o Prophase: Lamins are phosphorylated, causing breakdown of the nuclear lamina. o Early Telophase: Lamins are dephosphorylated, leading to fusion of nuclear fragments. Defective Lamin - Hutchinson-Gilford Progeria Syndrome (HGPS): o Autosomal recessive disorder. o Phenotype: ▪ Rapid aging, resembling individuals aged 70-80 in children aged 7-8. o Incidence: 1 in 6,000,000. o Etiology: Mutation in lamin A gene (1q21), causing nuclear disruptions and chromosomal alterations. o Treatment: None. o Prognosis: Lethal in the mid to late teens, typically from heart attack or congestive heart failure. Nuclear Pore Complex (NPC) Overview: Mechanical Support: o Cytoskeleton (intermediate filaments) provides mechanical support to the NPC. o The nuclear pore complex looks like a basket with tangled structures, formed by nucleoporins. Diagram of Nuclear Pore, Nuclear Envelope, Lamina, & Cytoskeleton Interactions: Nuclear Pore: o Composed of nucleoporins, proteins forming the pores in the nuclear envelope. Nuclear Importation: Nuclear Location Signals (NLS): o NLS is a specific signal sequence (e.g., SV-40 large T antigen N-terminal: pro-lys- lys-lys-arg-lys-val). o Nucleoplasmin: Contains a C-terminal lys-arg-10 AA-lys-lys-lys-lys sequence for importation. o Histones: Have basic amino acids at the N-terminal and are imported into the nucleus. Highly Controlled Process: o Movement of essential macromolecules such as DNA polymerase and RNA polymerase is strictly regulated. o Nuclear Import Receptors (Importins) play a key role in mediating the import process. Steps of Nuclear Importation: 1. Recognition: The NLS is recognized by importin (nuclear import receptor). 5 BIOS 420: Cell Biology Concept Summary for Final Exam 2. Binding: The cargo protein binds to importin. 3. Shuttling: The cargo protein + importin complex shuttles across the nuclear pore into the nucleus. 4. Ran-GTP Activation: ▪ Inside the nucleus, Ran-GTP (active form) is generated by Ran-GEF (Guanine nucleotide Exchange Factor), which exchanges GDP for GTP on Ran. ▪ NTF2 assists in the transport of Ran-GDP from the cytosol to the nucleus. 5. Cargo Release: Ran-GTP binds to importin, causing it to release the cargo protein inside the nucleus. 6. Export of Importin: ▪ Ran-GTP-importin complex exits the nucleus to the cytosol. 7. GTP Hydrolysis: ▪ In the cytosol, Ran-GAP (GTPase Activating Protein) catalyzes the hydrolysis of Ran-GTP to Ran-GDP. ▪ Ran-GDP dissociates from importin, making it ready for another import cycle. Ran: o Part of the Ras superfamily in the nucleus. o Ran-GAP is in the cytosol, and Ran-GEF is in the nucleus. Nuclear Exportation: Exportins (Nuclear Export Receptors): o Steps of Exportation: 1. Ran-GTP binds to exportin. 2. Cargo with nuclear export signal binds to exportin-Ran-GTP complex. 3. The exportin + Ran-GTP + cargo is transported to the cytosol. 4. GTP Hydrolysis: Ran-GTP is converted to Ran-GDP, with the help of Ran- GAP. 5. Release: Ran-GDP detaches from exportin, causing the cargo protein to stay in the cytosol. 6. Recycling: Exportin returns to the nucleus, ready for another round of export. Key Proteins: o Ribosomes (composed of RNA and proteins) are assembled in the nucleus but need to be exported. Cellular Processes in the Nucleus Related to DNA 1. DNA Storage: o The nucleus is responsible for storing the cell's genetic material, which is in the form of DNA (deoxyribonucleic acid), a double-stranded molecule consisting of chains of nucleotides. 2. DNA Replication: o DNA replication is the process of creating an identical copy of the DNA. o Complementary Strands: DNA serves as a template for its own replication. o Watson-Crick Model of DNA Replication: Based on the semi-conservative model, where each new DNA molecule contains one original (parental) strand and one newly synthesized strand. 6 BIOS 420: Cell Biology Concept Summary for Final Exam o Meselson and Stahl Experiment: Demonstrated that DNA replication is semi- conservative. Key Players in DNA Replication: o DNA polymerase: Synthesizes the new DNA strand by adding nucleotides. o DNA helicase: Unwinds or "unzips" the double-stranded DNA. o DNA primase: Synthesizes a short RNA primer to provide a starting point for DNA polymerase. o Single-strand binding proteins: Keep the DNA strands separated. o Leading strand: The strand synthesized continuously in the 5’ to 3’ direction. o Lagging strand: Synthesized in pieces called Okazaki fragments due to the antiparallel nature of DNA strands. o DNA ligase: Seals the Okazaki fragments to form a continuous strand. 3. DNA Transcription: o Gene: A DNA sequence that encodes a protein. o Transcription: The process where a gene is transcribed into an mRNA (messenger RNA) molecule, which is the copy of the gene. o RNA polymerase: The enzyme responsible for synthesizing RNA. o RNA polymerase II: Specifically synthesizes mRNA in eukaryotes. o Transcription occurs in the 5’ to 3’ direction. Key Steps in Transcription: o Regulation: Transcription factors, mediators, and chromatin remodeling complexes ensure the DNA is accessible for RNA polymerase to copy. o Gene Expression: The gene is expressed as an mRNA molecule. 4. Processing of Eukaryotic mRNA: o Exons and Introns: ▪ Exons: The coding portions of the gene that will be expressed. ▪ Introns: Non-coding, intervening sequences. ▪ Eukaryotic genes often contain both exons and introns, requiring splicing of mRNA to remove introns and join exons together. o Splicing: A process that occurs in the nucleus to remove non-coding introns and join the coding exons. o Alternative Splicing: The same gene can be spliced in different ways in different cell types to produce different mRNA isoforms. mRNA Modifications: o 5' Capping: Addition of a protective 5’ cap to the mRNA which: ▪ Enhances mRNA stability. ▪ Helps in the recognition and export of the mRNA. ▪ Facilitates later translation initiation. o Polyadenylation: Addition of a poly-A tail to the 3’ end of mRNA, which: ▪ Protects mRNA from degradation. ▪ Increases mRNA stability. ▪ Aids in mRNA export and translation initiation. 5. mRNA Export from the Nucleus: o Nuclear Export: mRNA must be "protected" by proteins (e.g., hnRNP, EJC, CBC on the 5' cap, and poly-A-binding proteins at the 3’ end) to be exported through the nuclear pore complex. o Nuclear Export Receptor: Recognizes the mRNA-protein complex and facilitates its passage through the nuclear pore. 7 BIOS 420: Cell Biology Concept Summary for Final Exam o Once in the cytosol, the mRNA undergoes further processing, including: ▪ Removal of CBC and replacement by initiation factors (IF) to prepare for translation. ▪ Translation initiation: mRNA is translated into protein by ribosomes. 6. Translation: o After the mRNA is exported to the cytoplasm and processed, it is translated into protein with the help of ribosomes. CHROMOSOME STRUCTURE 1. DNA Nucleotide Structure: o A nucleotide is the building block of DNA and consists of three components: ▪ Phosphate group ▪ Deoxyribose sugar (a 5-carbon sugar) ▪ Nitrogenous base (either purine or pyrimidine) 2. Base Pairing (Watson-Crick Model): o Base Pairing: Nucleotides on opposite strands of DNA form hydrogen bonds between their nitrogenous bases, following the Watson-Crick base pairing rules: ▪ Thymine (T) pairs with Adenine (A). ▪ Cytosine (C) pairs with Guanine (G). o Antiparallel Strands: The two DNA strands run in opposite directions (one runs 5’ to 3’, the other 3’ to 5’). o The purines (A, G) form hydrogen bonds with pyrimidines (T, C), creating complementary base pairs. 3. 3D Structure of DNA: o Double Helix: The DNA structure is a right-handed double helix. o The helix is made up of two polynucleotide strands coiled around each other, held together by base pairing and the sugar-phosphate backbone. o Grooves: The helix creates major and minor grooves, which are important for: ▪ Base pair recognition: Specific patterns of bases are exposed in the grooves, enabling proteins to bind and interact with the DNA. ▪ Binding sites for proteins: These grooves serve as recognition sites for proteins involved in processes such as transcription, replication, and repair. 4. Base Pair Recognition: o The grooves in the DNA double helix play a crucial role in allowing proteins to recognize and bind to specific base pairs within the DNA sequence. 5. B-Form DNA: o The most common form of DNA in cells is B-form, which is: ▪ Right-handed: The helix twists in a clockwise direction. ▪ It contains approximately 10-10.5 base pairs per turn. DNA Packaging in Chromosomes 1. Chromosome Structure: o Chromosomes are thread-like structures located inside the nucleus of cells. o DNA is packaged in chromosomes to fit within the limited space of the nucleus while still being able to be accessed for processes like replication and gene regulation. 2. Chromatin: o Chromatin is a complex of DNA and proteins, primarily histones. 8 BIOS 420: Cell Biology Concept Summary for Final Exam o A chromosome is approximately 1/3 DNA and 2/3 protein by mass. o Chromatin exists in two forms: ▪ Euchromatin: Loosely packed, actively transcribed. ▪ Heterochromatin: Tightly packed, transcriptionally inactive. 3. Can Chromosomes Be Seen? o Chromosomes are not visible in a non-dividing cell; they exist as chromatin (thread-like). o Chromosomes become visible during cell division when chromatin condenses to form distinct structures. Assembly of Nucleosome (Basic Unit of Chromatin) 1. Nucleosome Structure: o A nucleosome consists of a histone octamer (8 histone proteins) around which DNA is wrapped. o The nucleosome is often described as "a bead on a string" structure. o N-terminal histone tails (the "tails" of histones) are highly mobile and can change conformation based on other bound proteins. 2. Histone Proteins: o Histones are positively charged proteins, which interact with the negatively charged DNA (due to the phosphate groups). o The positive charge on histones, especially lysine and arginine, helps in the tight binding of DNA to the histone proteins. 3. Histone Modifications: o Histones are subject to various covalent modifications on their N-terminal tails: ▪ Acetylation: Reduces the positive charge of lysine residues. ▪ Methylation: Occurs on lysine and arginine residues. ▪ Phosphorylation: Adds a negative charge to serine residues. o Modifications are cell cycle-dependent and play a crucial role in regulating gene expression. Histone Modifications and Gene Regulation 1. Activation vs. Silencing of Genes: o Acetylation of histones generally activates gene expression by making DNA more accessible to transcription machinery (like RNA polymerase). o Methylation of histones, especially DNA methylation, can silence genes. o Deacetylation (removal of acetyl groups) and methylation of histones contribute to gene repression. 2. Ubiquitination: o Polyubiquitination: Marks proteins for degradation through the proteasome. o Monoubiquitination: Acts as a regulatory signal that can be reversed by deubiquitinating enzymes. o Histone Ubiquitination: Can regulate transcriptional activation or silencing depending on the context. 3. DNA Methylation: o DNA methylation (adding a methyl group to DNA, particularly at CpG sites) typically silences genes. o MeCP2 protein binds to methylated DNA, leading to gene silencing by recruiting histone deacetylases and methylases, which contribute to chromatin remodeling. o Methylation changes play a key role in development and cell differentiation. 4. Biological Methylation: 9 BIOS 420: Cell Biology Concept Summary for Final Exam o The methyl group is provided by S-Adenosylmethionine (SAM), which is the methyl donor. o Methylation is a common epigenetic modification that regulates gene expression and can be heritable. Epigenetics: Inheritance Beyond DNA Sequence 1. Definition of Epigenetics: o Epigenetics refers to inheritance of gene expression patterns that do not involve changes to the DNA sequence itself. o Epigenetic modifications influence gene expression and can lead to changes in an organism's phenotype. o These changes can be temporary or stable, and they can be passed on to offspring. 2. Types of Epigenetic Modifications: o DNA Methylation: Addition of a methyl group (typically to the 5’ CpG site) can silence gene expression. o Histone Modifications: Post-translational modifications such as acetylation, methylation, and phosphorylation affect chromatin structure and gene expression. o RNA Interference (RNAi): Small RNA molecules regulate gene expression by interfering with RNA molecules. 3. Resetting of Epigenetic Marks: o Epigenetic marks may be reset during meiosis or within an organism’s lifetime, influencing gene expression in a reversible manner. 4. Inheritance of Epigenetic Modifications: o Epigenetic changes can be inherited both maternally and paternally, influencing traits and gene expression patterns in offspring without altering the underlying DNA sequence. Genomic Imprinting: 1. Definition: o Genomic imprinting refers to parent-of-origin-specific expression of genes, meaning that the expression of certain genes depends on whether they are inherited from the mother or father. o Imprinting is often regulated by DNA methylation that silences one allele depending on the parent. 2. Imprinted Genes: o Imprinted genes are genes where the methylation pattern (which turns off or silences the gene) is inherited from either the mother or father, leading to differential expression based on the parental origin. 3. Imprinting Disorders: o Prader-Willi Syndrome (PWS): Caused by a deleted paternal chromosome or inactive maternal chromosome on chromosome 15. Symptoms include mental retardation, obesity, delayed puberty, and constant hunger. o Angelman Syndrome: Caused by a deleted maternal chromosome on chromosome 15. Symptoms include mental retardation and motor dysfunction. 10 BIOS 420: Cell Biology Concept Summary for Final Exam o Both conditions result from gene silencing and a genetic deletion on one chromosome, but the symptoms are dependent on whether the deleted gene is from the maternal or paternal chromosome. Chromatin Packing and DNA Packaging: 1. Levels of DNA Packaging: o DNA is first wrapped around histone proteins, forming the nucleosome (the basic structural unit of chromatin). o Each nucleosome consists of an octamer of histones around which about 146 base pairs of DNA are wrapped. 2. Formation of Chromatin: o Multiple nucleosomes form a chromatin fiber. o Chromatin fibers fold into loops, and when further condensed, they form visible chromosomes during cell division. 3. Chromatin Structure: o The structure of nucleosomes and chromatin fibers plays a crucial role in regulating gene expression. o The packing of chromatin determines how accessible the DNA is for processes like transcription, replication, and repair. Chromosome Maintenance during Metaphase Structural Maintenance of Chromosomes (SMC) Proteins: SMC proteins are critical for maintaining chromosome structure during metaphase, especially in holding chromatids together and ensuring correct chromosome condensation. 1. Cohesins: o Function: Cohesins are responsible for linking sister chromatids after DNA replication, ensuring they remain connected during the condensation process. o Role: They act as inter-cross-linkers, holding chromatids together to prevent premature separation until proper alignment during metaphase. 2. Condensins: o Function: Condensins facilitate the supercoiling of chromosomes, enabling them to condense properly for mitosis. o Role: They act as intra-cross-linkers, assisting in tightly coiling the DNA into compact structures during chromosome condensation. Centromere vs. Kinetochore: Centromere: Definition: The centromere is the region of the chromosome where the sister chromatids are most tightly bound. It plays a key role in attaching the chromosome to the spindle fibers through the kinetochore. Function: The centromere is essential for proper chromosome segregation during mitosis, serving as the anchor for microtubules during cell division. Kinetochore: Definition: The kinetochore is a disc-shaped protein complex that assembles on the centromere during cell division. It is essential for connecting the chromosome to the spindle microtubules and facilitating proper chromosome movement. Function: The kinetochore coordinates chromosome alignment and separation during mitosis. 11 BIOS 420: Cell Biology Concept Summary for Final Exam Proteins Associated with Centromeres and Kinetochores: 1. CENP Proteins: o CENP-A: A histone H3 variant found in centromere chromatin, it plays a crucial role in the formation of the kinetochore. Its incorporation in chromatin helps specify the location of the centromere on the chromosome. o CENP-B: Found in centromere chromatin, CENP-B binds to specific DNA sequences within the centromere region, playing a role in centromere structure and function. o CENP-C: A protein located at the kinetochore. It is a GTP-binding protein involved in stabilizing the kinetochore and facilitating the attachment of microtubules for chromosome segregation. o CENP-D: Present at the kinetochore, CENP-D is kinesin-like, and plays a role in the spindle microtubule attachment to the kinetochore. Composition and Function of Telomeres Telomeres: Definition: Telomeres are specialized regions at the ends of linear chromosomes. They are composed of repetitive nucleotide sequences that protect the chromosome from degradation or fusion with other chromosomes. Associated Proteins: Telomeres are bound by specific proteins that help in the protection and maintenance of these repetitive sequences. Function of Telomeres: Chromosome Protection: Telomeres play a critical role in preventing the chromosome ends from being mistaken as sites of DNA damage. They help protect chromosome ends from fusion with neighboring chromosomes. Preserving Genome Integrity: By shielding the ends of chromosomes, telomeres help preserve the genome and maintain chromosome stability. Aging: Shortening of telomeres over time is associated with aging and cellular senescence. As cells divide, telomeres progressively shorten, eventually leading to the loss of their protective function. Telomere Synthesis: Telomerase: o Function: Telomerase is an enzyme responsible for maintaining the length of telomeres by adding repetitive nucleotide sequences onto the ends of chromosomes. o Mechanism: Telomerase uses an RNA sequence within its structure as a template to synthesize the repeating DNA sequence at the telomere. o Polymerase Activity: Telomerase also possesses polymerase activity, enabling it to extend the telomere by adding more repeating units to the chromosome ends. THE CELL CYCLE AND MITOSIS Cell Cycle Phases: G1 Phase: o First substage of interphase. 12 BIOS 420: Cell Biology Concept Summary for Final Exam o The cell synthesizes RNA and proteins needed for cell growth and DNA replication. S Phase (Synthesis Phase): o DNA replication occurs to double the genetic material. G2 Phase: o Last substage of interphase. o The cell synthesizes proteins needed for spindle formation and mitosis. Variation in the Length of the Cell Cycle: The length of the cell cycle can vary depending on the cell type and external factors, but generally follows the phases mentioned above. Mitosis Overview Mitotic Phases: 1. Prophase: o Chromosomes become visible and condense. o The nuclear envelope starts to break down. o Lamins (proteins of the nuclear envelope) are phosphorylated, leading to the disintegration of the envelope by the end of prophase. o Formation of the spindle apparatus begins. 2. Prometaphase: o Microtubules attach to chromosomes at the kinetochore (protein complex at the centromere of the chromosomes). o Kinesins contribute to establishing spindle bipolarity, positioning chromosomes between the spindle poles, and focusing the spindle poles. o Dynein contributes to spindle positioning, regulating spindle length, and maintaining pole focusing. 3. Metaphase: o Chromosomes align at the metaphase plate, which is equidistant from the two spindle poles. o The mitotic spindle is fully organized and interacts with chromosomes via kinetochore microtubules. Spindle Apparatus and Microtubules: Spindle Apparatus: o A cytoskeletal structure made of microtubules that facilitates the separation of sister chromatids during mitosis. o Centrosome: The main microtubule organizing center (MTOC) that contains centrioles and organizes the spindle fibers. o Three types of microtubules involved: ▪ Astral Microtubules: Radiate outward, helping to position the spindle in the cell and anchor it to the cell cortex. ▪ Kinetochore Microtubules: Attach to the centromere of chromosomes at the kinetochore. ▪ Interpolar Microtubules: Extend between the two poles and overlap to help maintain spindle structure. Motor Proteins: o Kinesins: Responsible for maintaining spindle bipolarity, positioning chromosomes, and focusing the spindle poles. 13 BIOS 420: Cell Biology Concept Summary for Final Exam o Dynein: Involved in spindle positioning, the metaphase checkpoint, and regulating spindle length. o These motor proteins create a balance of forces on the microtubules, contributing to the self-organization of the spindle and the separation of chromatids during mitosis. Kinetochore and Centromere: The kinetochore is a complex of proteins that assembles at the centromere of chromosomes and links the chromosome to the spindle microtubules. The kinetochore is crucial for the segregation of sister chromatids to opposite poles during anaphase by harnessing the pulling force from the attached microtubules. Chromosome Segregation and Cytokinesis Cohesin and Chromatid Separation: Cohesin: o Cohesin is a protein complex that holds sister chromatids together after DNA replication. It is crucial for maintaining the cohesion between chromatids until the appropriate time for separation. o Tension at centromeres is generated through the bipolar attachment of kinetochores to the mitotic spindle during metaphase. o During anaphase, separase is activated, which cleaves the Scc1 subunit of cohesin, leading to the removal of cohesin complexes and allowing the sister chromatids to separate. Separation of Sister Chromatids: o Cohesin dissolution is necessary for sister chromatids to be separated during anaphase. The cleavage of cohesin by separase at the centromere triggers this separation. Condensin and Chromosome Condensation: Condensin is another protein complex that helps in the folding and condensation of chromosomes during mitosis. It works alongside cohesin to ensure the proper structural organization of chromosomes for segregation. Kinetochore and Chromosome Movement: Kinetochore: o The kinetochore is a protein structure that assembles at the centromere of each chromosome and serves as the attachment point for microtubules of the mitotic spindle. o The biorientation of sister chromatids, where each chromatid's kinetochore is attached to microtubules from opposite poles, is crucial for accurate chromosome alignment and segregation. Motor Proteins: o Motor proteins, such as kinesins and dyneins, generate forces that move chromosomes during mitosis. They help in the positioning of chromosomes along the spindle and the segregation of sister chromatids during anaphase. Anaphase Chromosome Movement: During anaphase, the loss of cohesin and the pulling forces from the microtubules cause the sister chromatids to move toward opposite poles. 14 BIOS 420: Cell Biology Concept Summary for Final Exam The spindle checkpoint ensures that chromosome segregation only occurs when all chromosomes are correctly aligned and attached to the spindle, ensuring accuracy in chromosome division. Telophase and Cytokinesis: Telophase: o The final stage of mitosis where the chromosomes begin to de-condense, and the nuclear envelope starts to reform around the separated chromosome sets. Cytokinesis: o Cytokinesis is the process of cytoplasmic division, which follows mitosis. o During cytokinesis, myosin II accumulates in the cleavage furrow and assembles with F-actin to form a contractile ring. o The contractile ring generates the force necessary for the cleavage furrow to constrict, eventually pinching the cell in two, leading to the formation of two daughter cells. Myosin II and Actin: o The interaction between myosin II (a motor protein) and actin filaments is critical for cytokinesis. The sliding of actin filaments by myosin II causes the contraction of the contractile ring, ultimately dividing the cytoplasm and ensuring that each daughter cell gets an appropriate share of organelles and resources. Nuclear Lamina and Nuclear Envelope Reformation: During telophase, the nuclear lamina (protein structure that supports the nuclear envelope) reforms around the chromosomes. This process involves the reassembly of the nuclear envelope around the separated sets of chromosomes, ensuring that each daughter cell has its own distinct nucleus. Meiosis I: Reduction Division (Reduction in Chromosome Number) Meiosis I is the first division in meiosis, where the chromosome number is halved, going from diploid (2n) to haploid (n). 1. Prophase I: o Chromosome Condensation: Chromosomes become visible as sister chromatids. o Homologous Chromosomes Pairing: Homologous chromosomes (chromosomes with the same genes but possibly different alleles) come together and form pairs, a process called synapsis. o Crossing Over: Homologous chromosomes exchange genetic material at points called chiasmata. This increases genetic diversity. o Spindle Formation: Spindle fibers form, and the nuclear envelope starts to break down. 2. Metaphase I: o Homologous Chromosomes Align: Homologous chromosome pairs (tetrads) align at the metaphase plate. o Independent Assortment: The orientation of homologous chromosome pairs is random, contributing to genetic variation. 3. Anaphase I: o Separation of Homologous Chromosomes: The homologous chromosomes are pulled toward opposite poles. Unlike mitosis, sister chromatids remain attached at this point. 4. Telophase I: 15 BIOS 420: Cell Biology Concept Summary for Final Exam o Chromosomes at Opposite Poles: The separated chromosomes reach the poles of the cell. o Cytokinesis: The cytoplasm divides, resulting in two daughter cells, each with half the original chromosome number (haploid, n). Meiosis II: Equational Division (Similar to Mitosis) Meiosis II is similar to mitosis but involves the division of haploid cells. The goal is to separate the sister chromatids. 1. Prophase II: o Chromosome Condensation: Chromosomes condense again. o Spindle Formation: Spindle fibers form in each of the two haploid cells. o Nuclear Envelope Breakdown: The nuclear envelope dissolves in both haploid cells. 2. Metaphase II: o Chromosomes Align at Metaphase Plate: Chromosomes line up at the metaphase plate in each haploid cell. o Attachment of Spindle Fibers: Each sister chromatid is attached to spindle fibers from opposite poles. 3. Anaphase II: o Separation of Sister Chromatids: The sister chromatids are pulled apart toward opposite poles. 4. Telophase II: o Chromosomes at Opposite Poles: The chromatids reach the poles of each cell. o Nuclear Envelope Reforming: A new nuclear envelope forms around each set of chromosomes. o Cytokinesis: The cytoplasm divides, resulting in four non-identical haploid daughter cells. Sub-Stages of Prophase I in Meiosis 1. Leptotene: o Chromosomes condense into long, thin threads and begin to prepare for pairing. 2. Zygotene: o Homologous chromosomes pair up (synapsis) and form the synaptonemal complex. 3. Pachytene: o Crossing over occurs between homologous chromosomes, exchanging genetic material. 4. Diplotene: o The synaptonemal complex breaks down, and chromosomes begin to separate, but remain connected at chiasmata (points of crossover). 5. Diakinesis: o Chromosomes reach maximum condensation, the nuclear membrane breaks down, and chiasmata move to the chromosome ends. These stages are essential for genetic recombination and preparing chromosomes for separation during meiosis. Synaptonemal Complex: Key Points Definition: A protein structure formed during prophase I of meiosis that aligns homologous chromosomes for crossing over. Structure: 16 BIOS 420: Cell Biology Concept Summary for Final Exam o Central element: Protein structure between homologs. o Lateral elements: Protein filaments that connect to each homolog and help in alignment. Function: o Aligns homologous chromosomes for accurate pairing. o Facilitates crossing over by bringing chromosomes close together at chiasmata. o Stabilizes chromosomes during recombination. Holiday Model of Recombination: Key Points Holiday Junctions: Key intermediates in genetic recombination, formed during crossing over between homologous chromosomes. Structure: A symmetrical four-arm junction where base pairing is maintained. Process: The arms slide in a specific pattern to exchange genetic material between chromosomes. Function: Facilitates genetic diversity by swapping DNA between chromosomes at the crossover points. Errors of Meiosis in Humans Non-disjunction: Failure of chromosomes or chromatids to separate properly during meiosis. o Meiosis I: Failure of homologous chromosomes to separate. o Meiosis II: Failure of sister chromatids to separate. Effects of Non-disjunction Aneuploidy: Abnormal number of chromosomes. o Monosomy (2n - 1): Missing one chromosome. ▪ Example: Turner syndrome (45, X0) – Females with only one X chromosome. o Trisomy (2n + 1): Extra chromosome. ▪ Example: Down syndrome (47, +21) – Extra chromosome 21. Polyploidy (3n): Three sets of chromosomes, often leading to stillbirth. REGULATION OF CELL DIVISION Key Transition Points in the Cell Cycle The cell cycle is tightly regulated by checkpoints to ensure proper progression and fidelity of division. Main Checkpoints in the Cell Cycle: 1. G1/S Checkpoint (Restriction Point): o Occurs at the transition from G1 to S phase. o Purpose: Ensures no DNA damage before DNA replication begins. If DNA is damaged, the cell cycle is halted to prevent the replication of damaged DNA. 2. G2/M Checkpoint: o Occurs at the transition from G2 phase to M phase. o Purpose: Ensures all DNA has been replicated properly before entering mitosis, preventing the loss or mutation of genetic information in daughter cells. 3. Metaphase/Anaphase Checkpoint (Spindle Checkpoint): o Occurs during metaphase before moving to anaphase. o Purpose: Ensures that all chromosomes are attached to the spindle fibers properly. This ensures accurate chromosome segregation during anaphase. Additional Considerations for Checkpoints: 17 BIOS 420: Cell Biology Concept Summary for Final Exam Growth and Resources: The checkpoints also assess whether the cell has enough resources (e.g., nutrients, energy) to proceed with division. DNA Integrity: If there are mutations or errors during replication, the checkpoints will halt the cycle to allow for repair or trigger cell death mechanisms (e.g., apoptosis). Regulation of Checkpoints in the Cell Cycle Each checkpoint in the cell cycle is tightly controlled by a network of chemical signals, primarily driven by cyclins, cyclin-dependent kinases (Cdks), and other regulatory proteins that help ensure that conditions are favorable for the cell to proceed with division. How Each Checkpoint Is Maintained 1. G1/S Checkpoint (Restriction Point): o Signals: The G1/S checkpoint is mainly regulated by the retinoblastoma protein (Rb) and cyclin D/Cdk4/6 complex. o Mechanism: ▪ Cyclin D binds to Cdk4/6, activating them to phosphorylate the Rb protein, which in turn releases E2F transcription factors. ▪ E2F activates the transcription of genes necessary for DNA replication. ▪ If there is DNA damage, p53 levels increase and activate p21, which inhibits Cdk2/Cyclin E complexes, preventing progression into S phase. o Checkpoint Function: Ensures that cells only proceed to DNA replication if DNA is undamaged and favorable conditions are met. 2. G2/M Checkpoint: o Signals: The main proteins here are Cdk1 (Cyclin B/Cdk1 complex) and the ATM/ATR kinases. o Mechanism: ▪ Cdk1 activation, controlled by Cyclin B, drives the cell into mitosis (M phase). ▪ If DNA is damaged or incompletely replicated, ATM (ataxia-telangiectasia mutated) or ATR (ATM and Rad3-related) kinases are activated. ▪ These kinases activate Chk1/Chk2 pathways, leading to the inhibition of Cdk1 through Wee1 kinase phosphorylation, preventing the cell from entering mitosis until issues are resolved. o Checkpoint Function: Ensures that the cell does not enter mitosis until all DNA has been accurately replicated and is undamaged. 3. Metaphase/Anaphase Checkpoint (Spindle Checkpoint): o Signals: This checkpoint is controlled by the anaphase-promoting complex (APC/C) and Mad2/BubR1 complexes. o Mechanism: ▪ Spindle assembly checkpoint (SAC) ensures that all chromosomes are properly aligned and attached to spindle fibers before anaphase begins. ▪ If kinetochores are not properly attached to microtubules, Mad2 and BubR1 proteins inhibit the APC/C, preventing the degradation of securin (an inhibitor of separase). ▪ If all chromosomes are attached and properly aligned, APC/C is activated, leading to the degradation of securin, activation of separase, and the separation of sister chromatids. 18 BIOS 420: Cell Biology Concept Summary for Final Exam o Checkpoint Function: Prevents chromosome missegregation by ensuring all chromosomes are properly attached to the spindle before proceeding with anaphase. Evidence for Chemical Signals in Cell Cycle Regulation Experiment with Cell Fusion: o Observation: In an experiment where cells in different phases of the cell cycle (e.g., G1 and S or M phases) were fused, the G1 cell received signals from the other cell that forced it to enter the same phase as the other cell. o Conclusion: This experiment suggests that chemical signals exist that can diffuse freely between the nucleus and cytoplasm, triggering the cell to move to the next phase of the cycle. For example: ▪ Fusing G1 cell with S-phase cell: The G1 cell enters S phase after receiving signals from the S-phase cell, indicating that S-phase entry is regulated by diffusible chemical signals (such as cyclins). ▪ Fusing G1 cell with M-phase cell: The G1 cell is pushed into mitosis, suggesting the presence of mitotic cyclins or other cell cycle regulators that can initiate mitosis in the G1 cell. This evidence supports the idea that chemical signals (mainly cyclins and Cdks) are crucial for the regulation of the cell cycle, allowing cells to progress from one phase to another only when conditions are favorable. Chemical Signals Controlling Cell Cycle Progression The chemical signals that regulate the cell cycle, particularly in the transition between cell cycle phases, are mainly cyclins and cyclin-dependent kinases (Cdks). These proteins control and drive the progression of the cell cycle by activating or inactivating key target proteins at each phase. Key Players in Cell Cycle Regulation 1. Cyclins: o Cyclins are regulatory proteins whose levels fluctuate during the cell cycle. Their levels rise and fall at specific points, ensuring that cell cycle progression occurs at the correct time. o Cyclins bind to Cdks (cyclin-dependent kinases), activating their kinase activity and allowing them to phosphorylate target proteins, which drive the cell through different stages of the cell cycle. o There are different types of cyclins that are active during different stages of the cell cycle: ▪ Cyclin D: Works in the G1 phase to promote progression from G1 to S phase. ▪ Cyclin E: Functions in late G1 and early S phase, helping to initiate DNA replication. ▪ Cyclin A: Active during S phase and also helps with DNA replication. ▪ Cyclin B: Critical for progression from G2 to M phase (promoting mitosis). 2. Cyclin-Dependent Kinases (Cdks): o Cdks are enzymes that require binding to cyclins to become active. Once activated, they phosphorylate specific target proteins to control the progression of the cell cycle. o Each Cdk-cyclin complex drives progression through specific checkpoints in the cell cycle. 19 BIOS 420: Cell Biology Concept Summary for Final Exam ▪Cdk4/6 + Cyclin D: Promotes entry into S phase. ▪Cdk2 + Cyclin E: Promotes DNA replication and the G1/S transition. ▪Cdk2 + Cyclin A: Controls DNA replication during S phase. ▪Cdk1 + Cyclin B: Drives entry into mitosis by triggering the G2/M checkpoint. 3. Maturation-Promoting Factor (MPF): o MPF is the Cdk1/cyclin B complex that regulates the G2/M transition. MPF activity peaks right before mitosis, helping the cell enter the mitotic phase. o MPF (Maturation-Promoting Factor) has kinase activity and is a dimer of cyclin B and Cdk1 (a specific cyclin-dependent kinase). o It phosphorylates key proteins that trigger the breakdown of the nuclear envelope, chromosome condensation, and the formation of the mitotic spindle. o MPF activity is regulated by the accumulation of cyclin B during G2 and the subsequent activation of Cdk1. Regulation of MPF and the Role of Cyclins and Cdks Cyclin B accumulates during S and G2 phases, leading to the formation of the cyclin B/Cdk1 complex (MPF). MPF activity is tightly controlled: o Before mitosis, cyclin B binds to Cdk1, activating it and allowing the cell to progress through G2 and into mitosis. o The activity of MPF is regulated by the inhibitory phosphorylation of Cdk1 by Wee1 kinase and the activating phosphorylation by Cdc25 phosphatase. o At the end of mitosis, cyclin B is degraded by the anaphase-promoting complex (APC/C), which leads to the inactivation of MPF and exit from mitosis. Fluctuations in Cyclins and Cell Cycle Regulation Cyclins exhibit periodic fluctuations in their levels throughout the cell cycle: o Cyclin D rises in early G1 and activates Cdk4/6 to push the cell through the G1/S checkpoint. o Cyclin E rises as G1 progresses into S phase, and binds to Cdk2, helping the cell enter S phase and initiate DNA replication. o Cyclin A appears after the S phase begins, binds to Cdk2, and ensures proper DNA replication. o Cyclin B accumulates during G2 phase, forming the Cdk1/cyclin B complex (MPF), which drives the transition to M phase. These fluctuations, driven by the synthesis and degradation of cyclins, act as chemical signals to ensure proper cell cycle progression. Regulation of Cyclin-Dependent Kinases (Cdks) Cyclin-dependent kinases (Cdks) are essential regulators of the cell cycle, but their activity is tightly controlled by various mechanisms to ensure proper timing of cell cycle transitions, especially during mitosis. Here's a summary of how Cdks are regulated: Activation of Cdk-Cyclin Complexes 1. Cyclin Binding: o Cyclins bind to Cdks to partially activate them. The binding of cyclins to Cdks is necessary but not sufficient for full activation. 20 BIOS 420: Cell Biology Concept Summary for Final Exam 2. Cdk-Activating Kinase (CAK): o To fully activate the Cdk-cyclin complex, an additional kinase called Cdk-activating kinase (CAK) adds a phosphate group to the Cdk at a specific activating site. o This phosphorylation is required for the Cdk-cyclin complex to be fully active and capable of phosphorylating target substrates involved in cell cycle progression. Inhibition of Cdk-Cyclin Complexes Several mechanisms prevent Cdk-cyclin complexes from prematurely initiating cell cycle events, such as mitosis. These mechanisms include inhibitory phosphorylation and the binding of Cdk inhibitors. 1. Inhibitory Phosphorylation by Wee1 Kinase: o The Wee1 kinase adds an inhibitory phosphate to the Cdk-cyclin complex, which inactivates it and prevents progression to the next phase of the cell cycle. o This phosphorylation prevents premature activation of the complex, ensuring that cell cycle events do not occur until the appropriate conditions are met. 2. Activation by Cdc25 Phosphatase: o Cdc25 is a phosphatase that removes the inhibitory phosphate added by Wee1, thus activating the Cdk-cyclin complex. o The dephosphorylation of Cdk is a critical step in triggering mitosis and other cell cycle transitions. Cdc25 is often referred to as the "mitotic trigger" because it directly enables progression into mitosis by activating MPF (Maturation-Promoting Factor). Cdk Inhibitors (CKIs) In addition to the phosphorylation mechanisms, Cdk inhibitors (CKIs) can also regulate Cdk-cyclin complexes by binding to them and inactivating their kinase activity. Cdk inhibitors can bind to and block the active site of the Cdk-cyclin complex, preventing its activity, even if the activating phosphate is present. CKIs are especially important for maintaining the G1/S checkpoint and regulating progression through other phases of the cell cycle. o Examples of CKIs: ▪ p21 and p27 are important CKIs that regulate the cell cycle by inhibiting the activity of cyclin-dependent kinases. ▪ When the cell is under stress or DNA damage, CKIs prevent progression until the damage is repaired. Families of Cyclins and Cyclin-Dependent Kinases (CDKs) There are various cyclins and cyclin-dependent kinases (Cdks) involved in regulating different phases of the cell cycle. These complexes are named based on the specific phases they control, and they work together to ensure that cell division proceeds in an orderly manner. Here's a breakdown of the key families: Cyclin Families and Their Associated Cdks B-Cyclins (e.g., Clb1, 2, 3, 4) – Regulate the transition into and progression through mitosis. G1 Cyclins (e.g., Cln) – Control the transition from G1 phase to S-phase. D Cyclins (e.g., D1, D2, D3) – Regulate early G1 phase progression. E Cyclins – Act at the G1/S transition, helping to initiate DNA replication. 21 BIOS 420: Cell Biology Concept Summary for Final Exam Cyclin-Cdk Complexes and Their Functions 1. G1/S-Cyclin: Controls the transition from G1 to S-phase, ensuring that the cell is ready to replicate DNA and that no DNA damage is present. 2. S-Cyclin (S-Cdk): Active during S-phase to promote DNA replication. 3. M-Cyclin (M-Cdk): Active during mitosis, particularly to control the transition from metaphase to anaphase and separation of sister chromatids. Regulation of Cdk-Cyclin Complexes 1. S-Cdk in DNA Replication: S-Cdk is active just before S-phase, helping to form the pre-replicative complex and recruit initiator proteins needed for DNA replication. It ensures that the DNA is ready for replication by activating DNA polymerase and replication machinery. 2. Activation of M-Cdk for Mitosis: The M-Cdk complex (Cdk1 and M-cyclin) is inactive until it receives two key regulatory signals: o Cdk-activating kinase (CAK) adds an activating phosphate to M-Cdk. o Wee1 kinase adds an inhibitory phosphate, keeping the complex inactive until conditions are favorable. To fully activate M-Cdk, Cdc25 phosphatase removes the inhibitory phosphate (via positive feedback), which activates the M-Cdk complex and promotes mitotic progression. Roles of M-Cdk During Mitosis Phosphorylation Targets: o Histone H1 (chromatin condensation) o Nuclear lamins (breakdown of the nuclear envelope) o Other targets involved in condensin and cohesin regulation for chromosome structure and movement. Microtubule Formation: M-Cdk also regulates microtubule dynamics to aid spindle formation during mitosis. Collaboration with Other Kinases: M-Cdk works in conjunction with other kinases like Polo-like and Aurora kinases to ensure proper chromosome segregation. Anaphase Promoting Complex (APC) and Mitosis APC (Anaphase-Promoting Complex): o Ensures that mitosis progresses by triggering the transition from metaphase to anaphase. o APC is activated by Cdc20, and it recruits ubiquitin ligases to tag proteins for degradation. M-Cyclin Degradation: o The APC/C complex ubiquitinates M-cyclin, marking it for degradation by the proteasome. o The degradation of M-cyclin is essential to move past mitosis into the next phase of the cell cycle (exit from mitosis). Ubiquitin Ligases and Degradation of Cell Cycle Proteins SCF Complex: 22 BIOS 420: Cell Biology Concept Summary for Final Exam o A multiprotein ubiquitin ligase complex that regulates Cdk inhibitors (CKIs) by adding polyubiquitin chains, marking them for degradation in the proteasome. o The SCF complex targets phosphorylated CKI proteins to ensure that Cdk inhibition is removed when no longer needed during cell cycle progression. Proteasomal Degradation: o Once proteins are polyubiquitinated, they are transported to the 26S proteasome, where they are unfolded, cleaved, and degraded into smaller peptides. Regulation of the Cell Cycle in Response to Signals The regulation of the cell cycle is tightly controlled by various signals that ensure proper progression through the phases. These signals can either promote or inhibit the action of cyclin- dependent kinases (Cdks), depending on the internal and external conditions of the cell. Key Signals Affecting the Cell Cycle: 1. Environmental Favorability: o Cells will check if the environment (nutrient availability, cell size, etc.) is favorable for cell division. If not, the cell will halt progression at key checkpoints. 2. DNA Damage: o DNA damage can activate mechanisms that halt the cell cycle to prevent the replication of damaged DNA. This occurs primarily at the G1/S checkpoint (before DNA replication) and the G2/M checkpoint (before mitosis). 3. Unreplicated DNA: o If DNA is not fully replicated (especially in the S-phase), this can trigger the inhibition of M-Cdk (which would normally drive the cell into mitosis). M-Cdk activity is also regulated to prevent re-replication of DNA. 4. Chromosome Attachment to Spindle: o If chromosomes are not properly attached to the mitotic spindle (during metaphase), the APC/C (Anaphase Promoting Complex) is inhibited, and the cell will not proceed to anaphase. DNA Damage Checkpoints: There are DNA damage checkpoints at both G1/S and G2/M transitions, which are critical for preventing cells from proceeding through the cell cycle with damaged or unreplicated DNA. G1/S DNA Damage Checkpoint: ATM/ATR Kinases: These are activated in response to DNA damage. o ATM (Ataxia-telangiectasia mutated) and ATR (ATM and Rad3-related) are sensor kinases that detect DNA damage and initiate checkpoint signaling. p53 Activation: o When DNA damage is detected, ATM/ATR kinases activate Chk1/Chk2 kinases, which in turn phosphorylate and activate p53. o Under normal conditions, Mdm2 binds to p53, marking it for degradation. However, when p53 is phosphorylated, Mdm2 is released, stabilizing p53. P53 Function: o Active p53 acts as a transcription factor, binding to the p21 gene's regulatory region. o This leads to the transcription of p21, a Cdk inhibitor. o p21 inhibits G1/S-Cdk and S-Cdk complexes, halting progression from G1 to S- phase and allowing the cell time to repair its DNA. 23 BIOS 420: Cell Biology Concept Summary for Final Exam Result: If DNA damage is detected in G1, the cell is arrested in G1 to repair the DNA before proceeding to S-phase. G2/M DNA Damage Checkpoint: The G2/M checkpoint ensures that the DNA has been fully replicated and that there is no DNA damage before mitosis begins. ATM/ATR Kinases: These kinases are also involved in the G2/M checkpoint, where they activate downstream proteins (e.g., Chk1, Chk2) that halt the cell cycle if DNA damage is detected during G2. p53 in G2: Similar to the G1 checkpoint, p53 can be activated in G2 if DNA damage is detected. The cell will arrest in G2 to allow time for DNA repair. Inhibition of Cdk Activity by p21: P21 is a Cdk inhibitor that plays a crucial role in halting the cell cycle in response to DNA damage. It binds to and inhibits the activity of G1/S-Cdk and S-Cdk complexes, preventing the cell from moving past G1 into S-phase (or from G2 into M-phase) while DNA repair is in progress. APOPTOSIS Definition: Apoptosis is a form of programmed cell death that occurs in a controlled, orderly manner. o Physiologic Apoptosis: Normal, regulated process in development, tissue turnover, and response to external signals. o Aberrant Apoptosis: Pathological cell death, often due to injury or disease, such as necrosis or in response to external damage. Roles of Apoptosis: o Embryogenesis: Eliminates unwanted cells during development (e.g., sculpting of tissue, like the shaping of fingers and toes). o Metamorphosis: Involved in the transition from larval to adult forms (e.g., in amphibians). o Tissue Turnover: Removes old or damaged cells, maintaining homeostasis in tissues. o Response to Pathology: Plays a role in disease processes by removing damaged or infected cells. Implications of Dysregulated Apoptosis: o Autoimmune Disorders: Failure to eliminate self-reactive immune cells can lead to autoimmunity. o Neurodegenerative Diseases: Excessive apoptosis contributes to diseases like Alzheimer's and Parkinson’s. o Cancer: Defective apoptosis allows cancerous cells to survive and proliferate. o AIDS: Apoptosis of immune cells, especially T-cells, leads to immune system dysfunction. Failure of Apoptosis Regulation: o Dysregulated apoptosis can lead to pathological conditions, either through excessive cell death (e.g., neurodegeneration) or failure to eliminate harmful cells (e.g., cancer or autoimmune disease). 24 BIOS 420: Cell Biology Concept Summary for Final Exam Signals Inducing Apoptosis External Signals: Various factors can trigger apoptosis, including: o UV and Gamma Radiation: DNA damage induced by radiation can activate apoptotic pathways. o Chemotherapeutic Drugs: Drugs used in cancer treatment often trigger apoptosis in rapidly dividing tumor cells. o Growth Factor Withdrawal: Lack of growth factors (e.g., insulin, epidermal growth factor) can lead to apoptosis, especially in cells that are dependent on these signals for survival. o Cytokines: Signaling molecules such as TNF-α (Tumor Necrosis Factor-alpha) and TGF-β (Transforming Growth Factor-beta) can activate apoptosis by binding to specific receptors. Regulation of Apoptosis: o Apoptosis is tightly regulated by both positive and negative signals. o Positive regulation: Signals that promote apoptosis (e.g., damage or stress signals). o Negative regulation: Survival signals (e.g., growth factors, anti-apoptotic proteins like Bcl-2) that inhibit the apoptotic process. Caspases in Apoptosis Caspases: A family of cysteine proteases central to the execution of apoptosis. o Activation: Caspases are typically produced as inactive precursors (procaspases) and are activated in response to apoptotic signals. o Function: Once activated, caspases cleave key cellular substrates, such as structural proteins and enzymes, leading to: ▪ Breakdown of the nuclear envelope ▪ Fragmentation of DNA ▪ Degradation of cellular components required for normal function. Major Steps in Apoptosis 1. Initiation of Apoptosis o Triggered by external (e.g., TNF-α) or internal signals (e.g., DNA damage). o Activation of caspases (proteases) that initiate the cell death process. 2. Membrane Blebbing o Breakdown of the cytoskeleton causes the cell membrane to form blebs (bubble- like protrusions). o Membrane integrity is maintained, preventing leakage of contents. 3. DNA Fragmentation (DNA Laddering) o Caspases activate DNases, leading to DNA cleavage at nucleosomal sites. o Results in DNA laddering (fragmented DNA visible as a ladder pattern on gels). 4. Chromatin Condensation and Cell Shrinkage o Chromatin condenses at the nuclear membrane, and the cell shrinks in size. o Formation of apoptotic bodies (membrane-bound fragments). 5. Phagocytosis o Apoptotic bodies display "eat-me" signals (e.g., phosphatidylserine) that attract phagocytes. 25 BIOS 420: Cell Biology Concept Summary for Final Exam o Macrophages engulf and digest the apoptotic bodies, clearing the dead cell without inflammation. Caspase Activation in Apoptosis 1. Caspase Activation and Targets o Caspases are proteases that cleave key cellular substrates, triggering apoptosis. o Key targets include: ▪ Cytoskeletal proteins (e.g., actin, intermediate filaments) ▪ Nuclear proteins (e.g., lamins, histones) ▪ DNA repair enzymes 2. Initiator Caspases o Initiator caspases (e.g., Caspase-8, Caspase-9) are activated upon dimerization triggered by apoptotic signals. o Adaptor proteins (e.g., FADD, Apaf-1) bind to the initiator caspase, facilitating its activation. 3. Executioner Caspases o Activated initiator caspases cleave and activate executioner caspases (e.g., Caspase-3, Caspase-7). o Executioner caspases then cleave a variety of substrates, leading to cell death. Key Effects of Apoptosis: 1. Loss of Membrane Asymmetry o Phosphatidylserine (normally on the inner leaflet) flips to the outer membrane, marking the cell for phagocytosis. 2. Nuclear Changes o Reduction in nuclear size and chromatin condensation. o Internucleosomal DNA cleavage, resulting in DNA laddering. 3. Cell Shrinkage and Membrane Blebbing o The cell shrinks, and membrane blebbing occurs due to cytoskeletal breakdown. 4. Final Breakdown o The cell undergoes fragmentation into apoptotic bodies, which are then cleared by phagocytes. Apoptosis: Programmed Cell Death Apoptosis is initiated through two major pathways: Extrinsic (Receptor-mediated) and Intrinsic (Mitochondrial). Both pathways activate caspases, which drive the cell to undergo controlled death. 1. Extrinsic (Receptor-Mediated) Pathway Trigger: External signals, such as TNF-α, TGF-β, and Fas ligand, bind to cell surface death receptors (e.g., Fas receptor). Signal Cascade: Binding of these ligands leads to recruitment of adaptor proteins (e.g., FADD), which activate initiator caspases (mainly Caspase-8). Caspase Activation: Caspase-8 activates executioner caspases (e.g., Caspase-3), which initiate the downstream apoptotic process. 2. Intrinsic (Mitochondrial) Pathway Trigger: This pathway is activated by internal stress signals like DNA damage, growth factor withdrawal, or mitochondrial dysfunction. 26 BIOS 420: Cell Biology Concept Summary for Final Exam Mitochondrial Involvement: The Bcl-2 family of proteins (pro-apoptotic proteins like Bax, Bak, and anti-apoptotic proteins like Bcl-2) regulate mitochondrial outer membrane permeabilization (MOMP). Cytochrome C Release: MOMP causes the release of cytochrome c from mitochondria into the cytoplasm. Apoptosome Formation: Cytochrome c binds to Apaf-1, forming the apoptosome, which activates initiator caspase-9. Caspase Activation: Caspase-9 activates executioner caspases (e.g., Caspase-3), leading to the execution phase of apoptosis. CANCER AND STEM CELL Origin of Cancer Environmental Factors: Responsible for ~80% of cancer cases (e.g., tobacco use, diet, radiation, pollution). Viral Etiology: Contributes to ~20% of cancer cases (e.g., HPV, Hepatitis B, Epstein-Barr virus). Cancer Nomenclature Neoplasia: Another term for cancer, referring to abnormal cell growth. Transformed Cells: Cells that have become cancerous through genetic mutations. Oncogenic: Refers to factors or genes that cause cancer. Oncology: The study of cancer, including its development, diagnosis, and treatment. Carcinogenesis: A Multi-Stage Process Initiation: Begins with the accidental production of a mutant cell (e.g., due to environmental factors or genetic mutations). Progression: As cells proliferate, additional mutations accumulate, leading to loss of normal structure and function (cells pile up instead of forming organized layers). Transformation: Cells lose contact inhibition, continue to divide uncontrollably, and form foci of transformed (cancerous) cells. Key Contributions to Tumorigenesis Increased Cell Division & Decreased Apoptosis: Tumor cells often have disrupted balance between cell division and apoptosis, contributing to uncontrolled growth. o Increased Division with Normal Apoptosis o Normal Division with Decreased Apoptosis Warburg Effect: Altered glucose metabolism in tumor cells: o Normal Cells: Prefer oxidative phosphorylation and differentiation. o Tumor Cells: Shift to aerobic glycolysis, producing lactate from glucose to fuel cell division and supply energy, building blocks, and NADPH. Steps in Metastasis Invasion: Cancer cells invade surrounding tissues, breaking through the basement membrane to enter the bloodstream. Transport: Cancer cells travel through the bloodstream to distant sites. Adhesion: Some cells adhere to the blood vessel walls in distant organs. Extravasation: Cells escape from the blood vessels and establish micrometastases (small secondary tumors). Colonization: These cells proliferate and form full-blown metastases, often in distant organs like the liver. 27 BIOS 420: Cell Biology Concept Summary for Final Exam Origin of Cancer: Key Points Environmental Factors: 80% of cancer cases are influenced by environmental factors such as chemicals, radiation, and lifestyle choices. o Carcinogens: Substances like benzo(a)pyrene, a component of cigarette smoke, are known to mutate p53, a tumor suppressor gene, leading to cancer. Viral Etiology: 20% of cancers are linked to viral infections. o Human Papillomavirus (HPV): Involved in 90% of cervical cancers. o Rous Sarcoma Virus (RSV): Identified as a cancer-causing virus, with the Src gene being the oncogene responsible for transformation. o Viral Oncogenes: ▪ Proto-oncogenes are normal genes that regulate cell growth; when mutated, they become oncogenes, contributing to cancer. ▪ Many viral oncogenes arise from cellular proto-oncogenes. For example, the Src oncogene in RSV is a mutated version of a normal cellular gene involved in cell growth and division. Mechanisms of Oncogene Activation Proto-oncogenes to Oncogenes: o Proto-oncogenes are normal genes that help regulate cell growth and differentiation. Mutations in these genes can lead to their conversion into oncogenes, which promote uncontrolled cell division and cancer. o Mutations that cause this transformation can arise from environmental factors (e.g., chemicals, radiation) or viral infections. o Viral Oncogenes: Many viral oncogenes, such as Src in RSV, originate from cellular proto-oncogenes. When these genes are altered or overexpressed, they drive cell proliferation, leading to cancer. Oncogenes & Tumor Suppressor Genes Oncogenes: Genes that, when mutated or overexpressed, drive cancer development by promoting cell proliferation and survival. o Key Oncogenes: ▪ Src (Rous Sarcoma Virus) ▪ Ras ▪ Myc ▪ HER2/Neu Tumor Suppressor Genes (Anti-Oncogenes): Genes that prevent cancer by regulating cell division, DNA repair, and apoptosis. When these genes are mutated, cancer is more likely to occur. o p53: Known as the "guardian of the genome," mutated in about 50% of human cancers. It regulates the transcription of genes that control the cell cycle and apoptosis. ▪ Mutations in p53 can be caused by environmental carcinogens like benzo(a)pyrene from cigarette smoke. ▪ p53 Protein Function: p53 is a DNA-binding protein that regulates the transcription of other proteins involved in cell division regulation. ▪ Activation of p53: p53 becomes active in response to signals such as: ▪ Hyperproliferative signals (uncontrolled growth) ▪ DNA damage ▪ Telomere shortening 28 BIOS 420: Cell Biology Concept Summary for Final Exam ▪ Hypoxia (lack of oxygen) ▪ Stable Active p53: Once activated, p53 can induce pathways for: ▪ Cell cycle arrest: Halting the cell cycle to repair damage. ▪ Senescence: Inducing irreversible growth arrest. ▪ Apoptosis: Promoting programmed cell death to prevent damaged cells from dividing. o Other key tumor suppressor genes include: ▪ RB (Retinoblastoma protein) ▪ NF1 (Neurofibromatosis type 1) ▪ APC (Adenomatous polyposis coli) ▪ DCC (Deleted in colorectal cancer) ▪ WT-1 (Wilms' tumor 1) Signaling Pathways Involved in Tumorigenesis Tumorigenesis is driven by alterations in cellular signaling pathways that affect processes like proliferation, apoptosis, and senescence. Key pathways often impacted include: o Cell Cycle Pathways: Mutations in oncogenes (e.g., Ras, Myc) or tumor suppressor genes (e.g., p53) can lead to dysregulation of the cell cycle, allowing uncontrolled cell proliferation. o Apoptosis Regulation: p53 plays a central role in regulating apoptosis. In response to DNA damage, p53 can induce: ▪ Cell cycle arrest (to allow DNA repair), ▪ Senescence (irreversible cell cycle arrest), ▪ Apoptosis (programmed cell death) if the damage is too severe to repair. o Senescence Pathways: p53 activation can also lead to cellular senescence, a state of permanent cell cycle arrest that acts as a tumor suppressive mechanism by preventing the proliferation of damaged cells. Oncogene and Tumor Suppressor Gene Targets Oncogenes: Mutated or overexpressed normal genes (proto-oncogenes) that promote tumorigenesis. o Examples include Ras, Myc, HER2, and BCR-ABL. Tumor Suppressor Genes (Anti-Oncogenes): Genes that regulate cell division, DNA repair, and apoptosis to prevent cancer. Mutations or deletions of these genes lead to uncontrolled cell growth. o p53 is the most commonly mutated tumor suppressor gene in cancer, involved in regulating the cell cycle, DNA repair, and apoptosis. Other examples include RB, NF1, and APC. Chromosomal Changes in Cancer Chronic Myelogenous Leukemia (CML): A classic example of a cancer driven by chromosomal changes, specifically a reciprocal translocation between chromosomes 9 and 22. o BCR-ABL Fusion Protein: The translocation results in the formation of a hybrid BCR-ABL gene on chromosome 22. This gene produces a fusion protein that has increased tyrosine kinase activity, leading to excessive phosphorylation of cellular substrates and uncontrolled cell division in lymphoid cells. o CML Reciprocal Translocation: ▪ BCR gene (chromosome 22) is fused with the ABL gene (chromosome 9), creating the BCR-ABL fusion gene. 29 BIOS 420: Cell Biology Concept Summary for Final Exam ▪This fusion protein activates kinases and promotes uncontrolled cell proliferation in hematopoietic cells. How Gleevec Blocks BCR-ABL Activity in CML Gleevec (Imatinib): A targeted therapy drug that inhibits the abnormal BCR-ABL kinase activity. o Mechanism of Action: ▪ Gleevec binds directly to the BCR-ABL fusion protein, preventing it from interacting with its substrates. ▪ This blocks kinase activity, which is essential for the growth and survival of the CML cells. ▪ By inhibiting this pathway, Gleevec can significantly reduce the proliferation of CML cells and is a highly effective treatment for chronic myelogenous leukemia. Categorization of Cancer 1. Sarcoma: Cancer of connective tissues (e.g., bone, cartilage, muscle). 2. Carcinoma: Cancer of epithelial tissues (e.g., skin, lung, breast, colon). 3. Blastoma: Cancer originating from embryonic (immature) tissues (e.g., neuroblastoma, retinoblastoma). 4. Leukemia: Cancer of white blood cells (e.g., acute lymphocytic leukemia, chronic myelogenous leukemia). 5. Melanoma: Cancer of melanocytes (pigment-producing cells) in the skin. Treatment of Cancer 1. Surgery: Removal of tumors or affected tissues. 2. Radiotherapy: Use of high-energy radiation to kill cancer cells or shrink tumors. 3. Chemotherapy: Use of cytotoxic drugs to kill or inhibit the growth of cancer cells. Properties of Chemotherapy Drugs Cytotoxic: Drugs that prevent cell division, targeting rapidly dividing cancer cells. Nutrient Deprivation: Target the cancer cells' food sources, starving them of essential nutrients. Induction of Apoptosis: Trigger programmed cell death in cancer cells. Anti-Angiogenesis: Stop the growth of new blood vessels (angiogenesis), starving tumors of oxygen and nutrients. Anti-Cancer Drugs Targeting the Ras-MAP Kinase Pathway Ras-MAP Kinase Pathway: This signaling pathway transmits signals from receptors on the cell surface to the DNA in the nucleus. It involves a series of kinases, including MAPKs (mitogen-activated protein kinases) and ERK (extracellular signal-regulated kinases), that regulate cell growth, differentiation, and survival. Targeting the Ras-MAP Pathway: In cancer, mutations in Ras or components of the MAPK pathway lead to uncontrolled cell proliferation. Kinase inhibitors, designed to block specific steps in this pathway, can help treat cancers driven by such mutations. Other Molecular Cancer Treatments 1. Immunotherapy: o Principle: Boosts the body’s immune system to recognize and attack cancer cells. o Examples: Checkpoint inhibitors (e.g., PD-1/PD-L1 inhibitors), CAR-T cell therapy, monoclonal antibodies. 2. Anti-Angiogenesis: 30 BIOS 420: Cell Biology Concept Summary for Final Exam oPrinciple: Inhibits the formation of new blood vessels (angiogenesis) that supply tumors with oxygen and nutrients. o Examples: Bevacizumab (Avastin) blocks VEGF (vascular endothelial growth factor). 3. Gene Therapy: o Principle: Replaces defective or mutated genes in cancer cells with normal, healthy genes. o Goal: Restore normal cell function or sensitize cancer cells to treatment. 4. Designer Molecular Drugs: o Principle: Drugs are designed to selectively target cancer cells while minimizing harm to normal, healthy cells. o Approach: Targeting cancer-specific mutations, overexpressed proteins, or tumor microenvironment characteristics. STEM CELLS Stem Cells: Key Characteristics and Functions 1. Self-Renewal and Differentiation: o Self-Renewal: Stem cells can replenish themselves through division, maintaining a constant stem cell pool throughout the organism’s life. o Differentiation: Stem cells also produce differentiated cells, which are specialized for specific functions in the body. 2. Types of Stem Cells: o Adult Stem Cells: Found in various tissues with high cell turnover (e.g., skin, gut). These stem cells generate cells specific to their tissue type and are crucial for tissue maintenance and repair. o Tissue-Specific Stem Cells: Each tissue has its own distinct stem cell population that generates cells unique to that tissue. These stem cells have distinct developmental histories and molecular signatures. 3. Stem Cell Division: o Symmetric Division: Can produce two identical stem cells, maintaining the stem cell pool. o Asymmetric Division: Produces one stem cell and one progenitor cell. Progenitor cells can differentiate into specialized cells after limited divisions. 4. Progenitor Cells: o Definition: Intermediate cells that are committed to differentiation but still proliferate before differentiating into terminally differentiated cells. o Transit-Amplifying Cells: A subset of progenitor cells that undergo several divisions to amplify the number of differentiated cells before committing to their final differentiated state. 5. Unipotent vs. Multipotent: o Unipotent Stem Cells: Can produce only one type of differentiated cell. o Multipotent Stem Cells: Can produce multiple types of differentiated cells, often within a specific tissue type (e.g., blood stem cells can produce red blood cells, white blood cells, and platelets). 6. Tissue Homeostasis: o Stem cells maintain tissue equilibrium (homeostasis) by constantly producing new cells (via division) and replacing lost cells (due to differentiation or apoptosis). 31 BIOS 420: Cell Biology Concept Summary for Final Exam o This process is likened to the flow of water in a river, where new cells are produced "upstream" and old, differentiated cells are removed "downstream." 7. Stem Cell Markers: o Lgr5: A specific marker for stem cells, particularly in tissues like the intestine, where stem cells are critical for tissue turnover. 8. Aging and Declining Stem Cell Function: o Over time, the ability of stem cells to self-renew and produce terminally differentiated cells declines, contributing to tissue aging and loss of regenerative capacity. 9. Cancer and Stem Cells: o Uncontrolled proliferation of stem cells, or failure to properly regulate stem cell division, can lead to cancer. This is a hallmark of tumorigenesis, where mutations may disrupt normal stem cell behavior. Renewal of the Gut Epithelial Lining The epithelial lining of the small intestine undergoes constant turnover, with stem cells and progenitor cells playing key roles in this regenerative process. Here's a breakdown of how this process works: 1. Stem Cells in the Crypt Base: o Location: Stem cells are located at the base of the crypts in the intestinal epithelium. o Function: These stem cells are responsible for generating all the cell types in the epithelial lining. They divide and give rise to progenitor cells that move upward towards the villi. 2. Cell Movement and Differentiation: o Progenitor Cells: The progeny of stem cells move upward, primarily from the crypts to the villi. These progenitor cells divide several times before they cease dividing and begin differentiating. o Paneth Cells: These cells, which support stem cells, are non-dividing differentiated cells. They migrate downward towards the base of the crypts, where they survive for extended periods (weeks) while continuing to secrete protective factors. 3. Types of Differentiated Cells: o Absorptive (Brush-Border) Cells: ▪ These cells are the most numerous (outnumbering other cell types 10:1 or more). ▪ They have microvilli on their apical surface, increasing the surface area for nutrient absorption. ▪ The microvilli also anchor enzymes that break down small peptides and disaccharides into monomers for absorption. o Goblet Cells: ▪ These cells secrete mucus, playing a protective role by lubricating and shielding the gut lining. o Paneth Cells: ▪ Located near the crypt base, they secrete cryptdins (defensin proteins) and growth factors to regulate microbial populations and maintain crypt integrity. o Enteroendocrine Cells: 32 BIOS 420: Cell Biology Concept Summary for Final Exam ▪ These cells secrete serotonin and peptide hormones into the bloodstream. ▪ Example: Cholecystokinin (CCK) is secreted in response to nutrients in the gut. CCK signals the release of digestive enzymes from the pancreas and bile from the gallbladder, and also signals the brain to reduce hunger after eating. 4. Tissue Dynamics: o Self-Renewal: The balance of stem cell self-renewal and differentiation ensures continuous replacement of cells that line the gut. o Turnover Rate: The entire epithelial lining is renewed about every 4–5 days, with cells from the crypts being displaced upward, differentiating, and eventually being sloughed off into the gut lumen. Other Systems with Maintenance of Stem Cells Epidermis (Skin) Structure: o The epidermis is the outer covering of the body, providing a protective barrier. o Beneath the epidermis lies a thick layer of connective tissue. Cell Types: o Keratinocytes: The primary cells of the epidermis responsible for synthesizing keratin, a tough protein that strengthens the skin. o Basal Layer: Contains basal cells (a small number of stem cells) and transit- amplifying progenitor cells that proliferate and differentiate into more specialized cells. o Prickle Cells: Above the basal cells, these cells are larger and play a role in cell adhesion. o Granular Cell Layer: Contains waterproofing keratin proteins, forming a barrier between the metabolically active cells and the outermost dead cells. o Squames: The outermost cells, filled with keratin, eventually shed from the skin. Cell Turnover: The time it takes for a cell to exit the basal layer and shed as a squame is about 1-2 weeks. Hematopoietic System (Blood Cells) Hematopoietic Stem Cells: Located in the bone marrow, these multipotent stem cells give rise to all blood cells (red and white blood cells). o They divide slowly and generate multipotent progenitor cells that are capable of producing many different types of blood cells. Progenitor Cells: These are rapidly dividing cells that further differentiate into unipotent cells (specialized for a single lineage, such as red blood cells or specific types of white blood cells). Skeletal Muscle Repair (Satellite Cells) Satellite Cells: These are quiescent stem cells located on the surface of muscle fibers. They remain inactive under normal conditions but become activated during muscle injury or growth. Repair Process: o Upon injury, satellite cells proliferate, and some fuse with muscle fibers to repair or regenerate damaged muscle tissue. 33 BIOS 420: Cell Biology Concept Summary for Final Exam o Satellite cells are essential for muscle fiber repair and growth after injury. Other Tissues with Stem Cells Skeletal Muscle: Unlike many tissues, skeletal muscle stem cells (satellite cells) are quiescent and only divide in response to injury or growth signals. Pancreas and Liver: These organs can regenerate to some extent without relying on stem cells. Differentiated cells in these tissues can divide to replace lost cells and maintain tissue homeostasis. Sensory Epithelia: o In some tissues, such as the adult mammalian ear and eye, sensory cells are not renewable. Once these sensory cells are lost (e.g., through injury), they cannot be replaced, highlighting a limitation in some tissues' regenerative capabilities. Key Concepts in Tissue Renewal and Repair 1. Stem Cells: Can self-renew (maintain stem cell population) and produce differentiated cells. 2. Progenitor Cells: Transit-amplifying cells that divide a limited number of times before differentiating. 3. Quiescent Stem Cells: Some stem cells, like satellite cells in muscle, remain inactive unless needed for repair or growth. 4. Differentiated Cells: In some tissues, like the pancreas and liver,