Unit 3 Bio Notes PDF

4.1 Studying Cells Key Concepts: Definition of a Cell: Fundamental unit of life; all living organisms are made of cells. Types of Cells: Prokaryotic (bacteria, archaea) and eukaryotic (plants, animals, fungi, protists). Microscopy: 1. Light Microscopes:...

4.1 Studying Cells Key Concepts: Definition of a Cell: Fundamental unit of life; all living organisms are made of cells. Types of Cells: Prokaryotic (bacteria, archaea) and eukaryotic (plants, animals, fungi, protists). Microscopy: 1. Light Microscopes: Use visible light; up to 400x magnification; suitable for live specimens with limited resolution. 2. Electron Microscopes: Transmission Electron Microscope (TEM): Internal structures at high magnification. Scanning Electron Microscope (SEM): Surface details; provides 3D imagery. 3. Magnification vs. Resolving Power: Magnification enlarges images; resolving power distinguishes between two adjacent structures. Cell Theory: Proposed by Schleiden, Schwann, and Virchow: 1. All living things are made of cells. 2. The cell is the basic unit of life. 3. New cells arise from pre-existing cells. 4.4 The Endomembrane System and Proteins Overview of the Endomembrane System: Components: ○ Plasma membrane, nuclear envelope, lysosomes, vesicles, endoplasmic reticulum (ER), Golgi apparatus.  ○ Does not include mitochondria or chloroplast membranes. Functions: Modifies, packages, and transports proteins/lipids. Key Organelles: 1. Endoplasmic Reticulum (ER): ○ Rough ER (RER): Ribosomes attached. Synthesizes and modifies proteins (e.g., folding, adding side chains). Produces phospholipids for membranes. Abundant in protein-secreting cells (e.g., liver). ○ Smooth ER (SER): Lacks ribosomes. Synthesizes lipids, carbohydrates, and steroid hormones. Detoxifies drugs and poisons. Stores calcium ions (e.g., in sarcoplasmic reticulum for muscle contractions). 2. Golgi Apparatus: ○ Processes and tags proteins/lipids for specific destinations. ○ Structure: Flattened membrane sacs (cisternae). Cis face: Receiving side for vesicles. Trans face: Shipping side. ○ Adds sugar molecules to proteins/lipids (glycosylation). 3. Lysosomes: ○ Digestive enzymes break down macromolecules, recycle organelles, and destroy pathogens. ○ Function in immune responses (e.g., phagocytosis by macrophages). 4. Transport Vesicles: ○ Shuttle proteins/lipids between ER, Golgi, plasma membrane, and other organelles. 4.5 Cytoskeleton Structure and Functions: Microfilaments (Actin Filaments): ○ Thinnest (7 nm diameter); made of actin. ○ Functions: Cellular movement, shape maintenance, division (e.g., cleavage furrow), and intracellular transport. ○ Powered by ATP and work with myosin for muscle contractions. Intermediate Filaments: ○ Diameter: 8–10 nm; purely structural. ○ Functions: Maintain cell shape, anchor nucleus and organelles. ○ Examples: Keratin (in hair, nails, skin). Microtubules: ○ Largest (25 nm diameter); hollow tubes of α-tubulin and β-tubulin dimers. ○ Functions: Resist compression, vesicle transport, chromosome segregation during cell division. ○ Structural components of flagella and cilia (9+2 arrangement). Special Structures: Centrosomes and Centrioles: ○ Microtubule organizing centers in animal cells. ○ Play a role in spindle formation during cell division. Flagella and Cilia: ○ Flagella: Few, long structures for movement (e.g., sperm). ○ Cilia: Numerous, short structures for movement or substance transport (e.g., respiratory tract). 4.6 Connections between Cells and Cellular Activities Extracellular Matrix (ECM) in Animal Cells: Composition: Collagen, proteoglycans, and integrins. Functions: ○ Provides structural support. ○ Facilitates cell communication (e.g., blood clotting mechanisms). Intercellular Junctions: 1. Plasmodesmata (Plant Cells): ○ Channels connecting adjacent plant cells; allow nutrient and water transport. 2. Tight Junctions (Animal Cells): ○ Watertight seals between epithelial cells (e.g., bladder lining). 3. Desmosomes (Animal Cells): ○ Spot-weld-like connections; resist stretching (e.g., skin, cardiac tissue). 4. Gap Junctions (Animal Cells): ○ Protein-lined pores for ion/nutrient transport; important in cardiac muscle contraction. Chapter Summary Table: Components of Prokaryotic vs. Eukaryotic Cells Component Function Prokaryo Animal Plant tes Cells Cells Plasma Selective barrier; controls Yes Yes Yes Membrane transport Cytoplasm Site of metabolic reactions Yes Yes Yes Nucleus Contains DNA; controls No Yes Yes cell activities Ribosomes Protein synthesis Yes Yes Yes Mitochondria ATP production No Yes Yes Chloroplasts Photosynthesis No No Yes Lysosomes Digestion and recycling No Yes No Cell Wall Structural support Yes No Yes Overview: Structure and Function Definition: The plasma membrane is the cell’s outermost layer, defining its boundaries and regulating interactions with the environment. Functions: 1. Selective Barrier: Controls entry/exit of substances (selectively permeable). 2. Cell Communication: Contains markers for self-recognition and intercellular signaling. 3. Flexibility: Allows shape changes (e.g., red and white blood cells navigating capillaries). 4. Signal Transmission: Integral proteins (receptors) detect extracellular signals and initiate intracellular responses. Key Components of the Plasma Membrane 1. Phospholipids: ○ Form the bilayer, the core structure of the membrane. ○ Amphiphilic properties:  Hydrophilic heads face aqueous environments (interior and exterior). Hydrophobic tails face inward, creating a water-repelling core. ○ Arrange to form micelles, liposomes, or bilayers in aqueous solutions. ○ Role: Separates internal cell environment from the external environment. 2. Proteins: ○ Integral Proteins: Embedded in the bilayer. Functions: Transport molecules across membranes. Act as receptors for signal transduction. Structure includes hydrophobic and hydrophilic regions aligning with the phospholipid bilayer. ○ Peripheral Proteins: Loosely attached to the inner/outer surface of the membrane. Functions: Enzymatic activity. Cytoskeletal attachment. Cell recognition. 3. Cholesterol: ○ Found between phospholipids in the bilayer. ○ Functions: Maintains membrane fluidity across temperature variations. Prevents membranes from becoming too rigid or too fluid. 4. Carbohydrates: ○ Found on the exterior surface, attached to proteins (glycoproteins) or lipids (glycolipids). ○ Functions:  Cell recognition and signaling. Forms the glycocalyx, which attracts water and aids in cell-cell attachment. Fluid Mosaic Model Description: Plasma membrane consists of a fluid-like bilayer of lipids interspersed with proteins and carbohydrates, forming a dynamic structure. Features: ○ Proteins and lipids move laterally within the layer, contributing to flexibility. ○ The membrane can self-seal small punctures. Membrane Permeability Selective Permeability: Allows only specific molecules to pass based on: ○ Size. ○ Charge (non-polar molecules pass easily; polar molecules need transport proteins). ○ Transport mechanisms (e.g., facilitated diffusion, active transport). Membrane Fluidity Influenced by: 1. Fatty Acid Composition: Saturated fatty acids: Make the membrane more rigid. Unsaturated fatty acids: Create "kinks," increasing fluidity. 2. Cholesterol:  Acts as a temperature buffer. Prevents membrane freezing in cold temperatures or over-fluidity in heat. Specialized Roles of Membrane Components 1. Integral Proteins: ○ Form channels for ions and molecules (e.g., glucose, sodium). ○ Bind extracellular signaling molecules (hormones, neurotransmitters) to initiate cellular responses. ○ Sometimes exploited by viruses (e.g., HIV binds to CD4 receptors on T-cells). 2. Carbohydrates (Glycocalyx): ○ Facilitate immune recognition (self vs. non-self). ○ Enable embryonic development and tissue formation. Application in Biology Immune System and Membranes: ○ Glycoproteins/glycolipids distinguish self from non-self. ○ Mismatched glycoproteins during organ transplants trigger immune rejection. Virus Interaction: ○ Viruses (e.g., HIV) use specific cell receptors to invade. ○ Rapid mutation of viral surface markers makes vaccines difficult to develop. Key Concepts for AP Biology: 1. Big Idea 2:  ○ Membrane structure supports dynamic homeostasis. ○ Selective permeability regulates molecular exchange. 2. Fluid Mosaic Model: Highlights the dynamic and complex composition of membranes. 3. Key Mechanisms: ○ Role of amphiphilic phospholipids in bilayer formation. ○ Importance of proteins in transport, signaling, and structure. ○ Cholesterol's role in maintaining membrane integrity. 5.2 Passive Transport Key Concepts: Passive transport allows the movement of substances across membranes without cellular energy. Substances move from high to low concentration down a concentration gradient. Includes diffusion, facilitated diffusion, and osmosis. Selective Permeability of Membranes: Plasma membranes are selectively permeable, allowing only certain molecules (e.g., lipid-soluble molecules) to pass freely. Polar molecules, ions, and larger molecules require transport proteins. Diffusion: The net movement of molecules from an area of high concentration to low concentration. Factors affecting diffusion rate: ○ Concentration gradient : Greater differences increase rate. ○ Temperature : Higher temperatures increase kinetic energy.  ○ Molecular mass : Smaller molecules diffuse faster. ○ Solvent density : Less dense solvents allow quicker diffusion. Facilitated Diffusion: Uses channel and carrier proteins for substances that cannot diffuse directly. Channel proteins : Provide a hydrophilic passage for ions or molecules. Carrier proteins : Bind to molecules, change shape, and transport them across. Osmosis: Movement of water across a semipermeable membrane from high water potential (low solute) to low water potential (high solute). Key terms: ○ Isotonic solution : No net water movement; solute concentrations are equal. ○ Hypertonic solution : Higher solute concentration outside cell; water exits the cell, causing shrinkage (crenation). ○ Hypotonic solution : Lower solute concentration outside cell; water enters the cell, causing swelling (lysis in animal cells). Tonicity in Living Systems: Osmoregulation maintains balance in hypotonic or hypertonic environments. Plant cells develop turgor pressure in hypotonic solutions, preventing lysis. Plasmolysis occurs when plant cells lose water in hypertonic solutions. 5.3 Active Transport Key Concepts: Active transport moves substances against their concentration or electrochemical gradients, requiring energy (ATP). Maintains ion gradients essential for processes like nerve signaling. Types of Active Transport: 1. Primary Active Transport : ○ Direct use of ATP to pump substances. ○ Example: Sodium-potassium pump (Na+/K+ ATPase): Pumps 3 Na⁺ out and 2 K⁺ in, maintaining an electrochemical gradient. Generates a net negative charge inside the cell. 2. Secondary Active Transport (Co-transport) : ○ Uses energy stored in an electrochemical gradient created by primary active transport. ○ Example: Sodium-glucose symporter moves glucose into the cell with Na⁺. Carrier Proteins in Active Transport: Uniporters : Transport one molecule in one direction. Symporters : Transport two molecules in the same direction. Antiporters : Transport two molecules in opposite directions. 5.4 Bulk Transport Endocytosis: Moves large particles into the cell using vesicles. 1. Phagocytosis :  ○ "Cell eating"; engulfs large particles or microorganisms. ○ Example: Neutrophils engulf bacteria. 2. Pinocytosis : ○ "Cell drinking"; engulfs extracellular fluid and small molecules. 3. Receptor-mediated Endocytosis : ○ Specific molecules bind to cell surface receptors. ○ Example: Uptake of LDL cholesterol. Exocytosis: Exports materials out of the cell via vesicles. Example: Release of neurotransmitters at synapses. Key Comparisons: Transport Method Energy Material Transported Use Diffusion Passive Small, nonpolar molecules Osmosis Passive Water Facilitated Diffusion Passive Ions, glucose Primary Active Active Na⁺, K⁺, Ca²⁺ Transport Secondary Active Active Glucose, amino acids Transport Phagocytosis Active Large macromolecules, bacteria Pinocytosis Active Extracellular fluid Receptor-mediated Active Specific macromolecules Endocytosis Study Notes: Eukaryotic and Prokaryotic Cells Eukaryotic vs. Prokaryotic Cells Feature Eukaryotic Cells Prokaryotic Cells Nucleus Present, surrounded by a double Absent; DNA located in membrane (nuclear envelope) nucleoid region Size Larger (10–100 μm) Smaller (0.1–5 μm) Chromosom Linear, multiple chromosomes Single, circular es chromosome Organelles Membrane-bound organelles No membrane-bound (e.g., mitochondria, ER, Golgi) organelles Cell Wall Present in plants (cellulose) and Peptidoglycan (bacteria), fungi (chitin) other types (archaea) Ribosomes Larger (80S) Smaller (70S) Division Mitosis and meiosis Binary fission Eukaryotic Cell Components and Functions Plasma Membrane Structure: Phospholipid bilayer with embedded proteins. Function: Controls the passage of substances (e.g., nutrients, oxygen) in and out of the cell; maintains homeostasis. Special Adaptation: Microvilli increase surface area for absorption in specialized cells (e.g., intestinal lining). Cytoplasm Contents: Cytosol (gel-like fluid), organelles, and cytoskeleton. Function: Site for metabolic reactions; provides structural support. Organelles: List and Functions Organelle Function Nucleus Stores DNA; site of RNA synthesis; controls cell activities. Nucleolus Produces ribosomal RNA (rRNA) and assembles ribosomes. Ribosomes Protein synthesis; found free in cytoplasm or bound to rough ER. Rough ER Protein synthesis and modification; studded with ribosomes. Smooth ER Lipid synthesis, detoxification, calcium storage. Golgi Apparatus Modifies, sorts, and packages proteins and lipids for transport. Mitochondria ATP production via cellular respiration; contains its own DNA. Chloroplasts Photosynthesis; converts light energy to chemical (plants) energy (glucose). Lysosomes Digestive enzymes for breakdown of macromolecules (animals) and organelles. Peroxisomes Oxidation of fatty acids and amino acids; detoxifies hydrogen peroxide. Vesicles/Vacuoles Storage and transport; central vacuole in plants regulates water. Cytoskeleton Structural support, intracellular transport, cell division. Centrosomes Microtubule-organizing center; role in cell division. (animals) Cell Wall (plants) Provides structural support and protection; composed of cellulose. Key Concepts for AP Biology Framework Big Idea 1: Evolution Drives Unity and Diversity Evidence of Endosymbiosis: Mitochondria and chloroplasts evolved from prokaryotic cells. Learning Objective 1.15: Shared conserved processes (e.g., ribosomes, DNA) indicate common ancestry. Big Idea 2: Utilization of Free Energy Compartmentalization: Internal membranes (e.g., ER, Golgi) enhance efficiency by localizing reactions. Learning Objective 2.13: Internal organelles contribute to maintaining homeostasis and energy use. Big Idea 4: Biological Interactions Organelle Interactions: Golgi modifies proteins from the rough ER; mitochondria provide ATP for cellular work. Learning Objective 4.5: Subcellular structures interact to perform essential functions. Specialized Structures in Eukaryotic Cells Animal Cells Unique Features: ○ Lysosomes: Contain hydrolytic enzymes for digestion. ○ Centrosomes: Involved in microtubule formation during cell division. Plant Cells Unique Features: ○ Chloroplasts: Photosynthesis to produce glucose. ○ Central Vacuole: Maintains water balance; stores nutrients and waste. ○ Cell Wall: Protects and provides structural integrity. Prokaryotic Cell Components and Functions Structure Function Capsule Protection; adherence to surfaces. Cell Wall Maintains shape; prevents dehydration. Nucleoid Contains the genetic material (DNA). Pili/Fimbri Attachment to surfaces or conjugation ae (genetic exchange). Flagella Movement. Evolutionary Insight: Endosymbiotic Theory Mitochondria and Chloroplasts: ○ Similar in size to bacteria. ○ Contain circular DNA and 70S ribosomes. ○ Suggest an origin from engulfed prokaryotes. Size and Efficiency Small Size: Increases surface area-to-volume ratio, facilitating efficient nutrient/waste exchange. Adaptations in Eukaryotes: ○ Development of organelles. ○ Folding of membranes (e.g., cristae in mitochondria). Applications and Connections Celiac Disease: Damaged microvilli reduce nutrient absorption. Bioremediation: Microbiologists utilize microbes to clean pollutants. Surface Area-to-Volume Ratio: Predicts cell efficiency in diffusion processes.