Unit 2 study guide

BIO 362 C/D – Fall 2025 Unit 2 Study Guide

Cytoskeleton - Actin

Concepts to Understand

  • Cytoskeleton is dynamic: Actively reorganizes and changes in response to various cellular conditions and signaling.

  • Cytoskeleton determines cell polarity: Orientation and organization of the cytoskeleton play a crucial role in cell shape and function.

  • g-actin vs f-actin

    • g-actin (globular actin): Monomeric form of actin that polymerizes to form filaments.

    • f-actin (filamentous actin): Polymers of g-actin that form helical structures.

  • Actin polarity: F-actin has a plus (barbed) end and a minus (pointed) end, essential for the direction of growth and functionality.

  • Treadmilling: A dynamic process where there is an addition of g-actin at the plus end while ATP-actin is lost from the negative end, maintaining a constant length while undergoing turnover.

  • Actin treadmilling/polymerization can generate force: Actin dynamics create mechanical forces important for processes such as cell motility.

  • Actin-associated proteins regulate dynamics and organization: These proteins modulate polymerization, depolymerization, and filament organization.

  • Different actin organizations can be in the same cell: Cells can have various configurations of actin filaments, each serving different functions simultaneously.

  • How myosin works: Myosin motors interact with actin filaments to convert chemical energy into mechanical work.

  • Organization of actin in muscles (sarcomeres): Actin and myosin filaments are arranged in a highly organized structure to facilitate muscle contraction.

Details to Memorize

  • Profilin: Promotes the exchange of ADP for ATP on g-actin, facilitating polymerization.

  • Thymosin: Sequesters g-actin and prevents polymerization.

  • Cofilin: Binds to ADP-actin filaments, promoting disassembly.

  • Arp2/3 complex: Initiates new filament growth, forming branched actin networks.

  • Formin: Nucleates the formation of long, unbranched actin filaments.

  • Capping protein: Binds to the barbed end of actin filaments to prevent further polymerization.

  • Fimbrin: Bundles actin filaments tightly together in parallel arrangements.

  • Alpha-actinin: Organizes actin filaments into loose arrays, important in striated muscle tissues.

  • Filamin: Cross-links actin filaments into a three-dimensional network.

  • Where you find each of the above in a migrating cell: These proteins are distributed in various cytoplasmic regions involved in cell movement, influencing actin dynamics and organization.

  • Myosin structure: Composed of heavy chains, light chains, and includes a motor domain that interacts with actin.

  • Myosin/ATP hydrolysis cycle: Demonstrates how myosin interacts with actin and utilizes ATP for movement and contraction.

  • Myosin light chain kinase (MLCK): Phosphorylates myosin light chains, regulating myosin activity and muscle contraction.

Sarcomere Structure

  • Alpha-actinin: Anchors actin filaments at the Z disc in sarcomeres.

  • Titin: Provides elasticity and stability along the myosin filaments in sarcomeres.

  • Thick filament/myosin bundle (Myosin II): Myosin II molecules dimerize and form thick filaments, crucial for contraction.

  • Myosin V: Involved in transporting cargo within cells along actin filaments.

Cytoskeleton - Microtubules

Concepts to Understand

  • Microtubule subunits are dimers: Composed of alpha and beta-tubulin that polymerize to form tubules.

  • Dynamic instability: The rapid switching between polymerization and depolymerization in microtubules characterized by two states:

    • Catastrophe: Rapid disassembly occurs at the plus end.

    • Rescue: Polymerization resumes after a period of disassembly.

  • GTP-cap: A protective structure at the plus end of growing microtubules essential for stability.

  • Microtubule organizing centers (MTOCs): Structures such as centrosomes that organize microtubules in cells.

  • Minus end stability: Microtubules must be anchored to MTOCs, providing stability unless otherwise capped.

  • Gamma-tubulin rings: Serve as nucleation sites for microtubule formation.

  • Microtubule-associated proteins (MAPs): Regulate microtubule dynamics and stabilization.

  • +TIP proteins: Bind to the growing ends of microtubules to promote stability and prevent depolymerization.

  • Why there are both minus and plus end proteins: Different proteins regulate growth and shrinkage at either end, providing functional versatility.

  • Intracellular transport and attachment to organelles: Microtubules serve as tracks for motor proteins (kinesin and dynein) to transport cellular cargo.

  • Cilia and Flagella: Microtubule-based structures that enable cellular movement and fluid movement across surfaces.

  • Basal bodies: Organizing centers for cilia and flagella, structurally similar to centrioles.

  • Ciliopathies: Disorders arising from dysfunctions in cilia leading to various health issues.

  • Ciliary vs cytoplasmic dynein: Ciliary dynein is specialized for ciliary movement, while cytoplasmic dynein is involved in transport within the cytoplasm.

  • Regulation of ciliary dynein: Controlled by signaling pathways that influence ciliary beating.

  • Interflagellar transport: A transport system involving the movement of proteins between the basal body and the tip of cilia.

Details to Memorize

  • Centrosome structure/centriole structure: Composed of microtubule triplets organized in a cylindrical shape.

  • Gamma-tubulin: Key component of microtubule nucleation and anchoring.

  • Gamma-tubulin ring structure: Forms a cap that aids in nucleation of new microtubules.

  • Stathmin: Sequesters tubulin dimers and prevents their incorporation into microtubules.

  • Kinesin-13: A motor protein that promotes disassembly of microtubules.

  • Xmap215: Stabilizes the plus end of microtubules, promoting polymerization.

  • Katanin: Severing protein that cleaves microtubules, aiding in turnover.

  • Tau: MAP that stabilizes microtubules, preventing disassembly.

  • MAP2: Involved in maintaining microtubule spacing and organization.

  • Kinesin-1: A motor protein transporting vesicles along microtubules toward the plus end.

  • Kinesin ATP cycle: Describes the ATP hydrolysis cycle that powers kinesin movement.

  • Dynein structure (general): Multi-chain protein complex that acts as a motor moving toward the minus end.

  • Cilia/flagella structure: Comprised of microtubule doublets arranged in a 9+2 pattern surrounded by an membrane.

  • Basal body: Anchors cilia and flagella, structurally similar to centrioles.

  • Nexin: Connects adjacent microtubule doublets in cilia and flagella, maintaining structure.

  • Radial spoke: Structural element providing support and mechanical flexibility in cilia and flagella.

  • Central pair: Two central microtubules within the ciliary structure aiding in movement.

  • Dynein arms (inner/outer): Motor domains that provide the force for ciliary movement through ATP hydrolysis.

  • Non-motile cilia structure: Specialized structures involved in sensing rather than movement.

Cytoskeleton – Intermediate Filaments and Other

Concepts to Understand

  • Differences between intermediate filaments and other cytoskeletons: Intermediate filaments provide structural support, are more stable than actin and microtubules, and do not exhibit dynamic instability.

  • Cortical cytoskeleton: Layer of cytoskeleton beneath the plasma membrane that supports cell shape and organization.

  • Role of sun/kash domain proteins: Involved in linking the cytoskeleton to the nuclear envelope, particularly during cell signaling and movement.

  • Structure of nuclear envelope: Comprised of inner and outer membranes with nuclear pores and associated proteins.

  • Role of spectrin family proteins: Provide mechanical support and maintain the integrity of the plasma membrane.

Details to Memorize

  • Intermediate filament organization: Non-polar filaments that provide tensile strength to cells.

  • Keratin: A type of intermediate filament found in epithelial cells.

  • Neurofilaments: Intermediate filaments found in neurons providing structural support.

  • Plectin: Cross-linking protein that anchors intermediate filaments to other cytoskeletal components.

  • Septin: GTP-binding proteins involved in cytoskeletal organization, particularly during cytokinesis.

  • Spectrin: Forms networks beneath the plasma membrane, contributing to cell shape and resilience.

  • Ankyrin: Adapter protein that links spectrin to membrane proteins, maintaining cell integrity.

  • Sun-domain protein: Links the nucleus to the cytoskeleton, particularly involved in nuclear positioning.

  • Kash-domain protein: Plays a role in linking the nuclear envelope to actin filaments.

  • Lamin: Key component of the nuclear lamina providing structural support to the nucleus.

Extracellular Matrix (ECM)

Concepts to Understand

  • Cells produce and secrete the ECM: ECM is synthesized and secreted by cells, playing a critical role in tissue structure.

  • ECM can be modified in response to environment: Changes in mechanical or biochemical stimuli lead to modifications in ECM structure and composition.

  • ECM protein categories: Includes proteoglycans, fibrous proteins, and glycoproteins, each contributing to different ECM functions.

Details to Memorize

  • Functions of ECM: Listed as five primary functions which may include:

    • Providing structural support to tissues

    • Facilitating cell attachment and migration

    • Acting as a reservoir for signaling molecules

    • Regulating cellular activities through biochemical signals

    • Influencing tissue development and repair.

  • Proteoglycans: Composed of a core protein and glycosaminoglycan (GAG) side chains; examples include:

    • Hyaluronan: A major component providing viscosity and hydration.

    • Aggrecan: A proteoglycan crucial for cartilage structure; contains repeating disaccharide units like Chondroitin/keratan sulfate.

  • Fibrous proteins: Major types include:

    • Collagen Type I: Provides tensile strength, prevalent in skin and bone.

    • Collagen Type IX: Associated with cartilage, providing elasticity.

    • Elastin: Provides stretchability to tissues such as lungs and blood vessels.

  • Glycoproteins: Include:

    • Fibronectin: Mediates cell attachment to ECM and guides cell movement.

  • Basal lamina components: Critical for tissue support and filtration; includes:

    • Laminin: Binds cells to the ECM.

    • Type IV collagen: Forms the base of the basement membrane.

    • Perlecan: Involved in regulating ECM structure and signaling.

    • Nidogen: Links laminin and collagen IV, stabilizing the basal lamina.

  • ECM regulation/modification: Mediated by enzymes such as:

    • Matrix Metalloproteases (MMPs): Degrade various components of the ECM, facilitating remodeling and repair.

  • Cell junctions: Structures that anchor cells together and allow for communication between cells.

Concepts to Understand about Cell Junctions

  • Epithelial vs connective tissue: Epithelial tissue covers body surfaces and organs, while connective tissue provides support and structure.

  • Organization of an epithelial cell: Structured in layers with distinct apical and basal surfaces, facilitating selective absorption and secretion.

  • Mechano-transduction: The process by which cells convert mechanical stimuli into biochemical signals.

  • Cadherin cell sorting: Cadherins are calcium-dependent adhesion proteins that mediate cell-cell junctions and affect tissue morphology.

  • Adhesion belt and tissue shape changes: Cell adhesion belts formed by cadherins regulate tissue integrity and shape during development.

  • Connecting cytoskeleton and cytoplasm of neighboring cells in a tissue: Junctions provide continuity and communication