Bio 1Q PDF

# §1. Cell Structure ## Biosphere - ecosystem -> communities -> population -> organisms. ## Ecosystem - A relatively self-contained, interacting community of organisms, and the environment in which they live and with which they interact. - Consists of biotic and abiotic factors. ## Community - Ar...

# §1. Cell Structure ## Biosphere - ecosystem -> communities -> population -> organisms. ## Ecosystem - A relatively self-contained, interacting community of organisms, and the environment in which they live and with which they interact. - Consists of biotic and abiotic factors. ## Community - Array of organisms inhabiting a particular ecosystem. ## Species - A group of organisms with similar morphological and physiological features, which can interbreed to produce fertile offspring and are reproductively isolated from other species. ## Population - All individuals of a species living within a bounds of a specified area. ## Organism - Any living thing. ## Niche - The role of an organism in an ecosystem (how organism fits into ecosystem). | | Organisms | Features | Molecules | Atoms | |:-------------------|:-------------|:----------------------------------------|:-------------|:---------------------------------------------:| | **Fukaryotic cells** | Prokaryotic cells | Diameter (Size) | DNA | Circular, naked, lies free in cytoplasm | | | | 10-100 um | Ribosones | Only 70s | | | | Linear associated with histones | Cell wall | Peptidoglycan, murein (polysaccharide with Aa) | | | | Forming a chromosome, enclosed in nucleus | Cell division | Binary fission | | | | ~ both 80s and 70s | | Transcription & translation simultaneously as | | | | | | nucleus is absent | | Cellulose/Lignin/Chitin | | | | | | (Contour polysaccharide) | | | | | | **Mitosis and cytokinesis** | | | | | | **Consequently** | | | | | ## Nucleus - 10µm, largest organelle, surrounded by a double membrane nuclear envelope. - Is continuous with RER. - Nuclear envelope consists of a thin lipid bilayer. - **Nuclear pore:** gaps in nuclear envelope that allow exchange between nuclear and cytoplasm. - **Leaving substance** - mRNA and ribosomes for protein synthesis. - **Centering substance** - proteins, nucleotides, ATP, hormones... - DNA is organised into discrete units called chromosomes. Each chromosome condenses from a single DNA molecule associated with proteins. DNA and proteins together are called chromatin. Chromatin condenses to form discrete chromosomes as a cell prepares to divide. - **Nucleolus** is located within the nucleus and is the site of rRNA synthesis. - Used to make ribosomes. - **Nuclear lamina:** meshwork of nuclear intermediate filaments, lines the interior of the nuclear envelope, maintains the shape of nucleus, composed of protein. ## Ribosomes - Particles made of ribosomal RNA and protein. Carry out protein synthesis in two locations: in cytosol (free ribosomes), RER, or nuclear envelope (bound ribosomes). - Consists of large and small subunits. ## Endomembrane System - Regulation of protein traffic and metabolic functions. **Components of Endomembrane System:** - Nuclear envelope - Endoplasmic reticulum - Golgi body - Lysosome and vacuoles - Plasma membrane **These components are either continuous or connected via transport vesicles.** ## Endoplasmic Reticulum (ER) - Biosynthetic factory that accounts for more than half of the total membrane in many eukaryotic cells. - Continuous with nuclear envelope. - An extensive membrane system with 80s ribosomes. - Provides pathway for the transport of materials through the cells. - Forms complex 3D system of sheet-like membranes and tubes enclosing fluid-filled sacs (cavity). - Proteins made by ribosomes on RER enter sacs and move through them. - Transport vesicles bud off the RER and join to form the Golgi body. ## Golgi Body - Ribosomes on RER secrete glycoproteins. - Distributes transport vesicles, proteins surrounded by membranes. - Is a membrane factory for the cell. ## Smooth ER (SER) - Meshwork of tubular membranes with fluid-filled sacs. - Synthesizes lipids, steroids, cholesterol, reproductive hormones. Has enzymes attached. Included in metabolic processes. - Metabolizes carbohydrates. - Detoxifies drugs and poisons. - Stores calcium ions. - No ribosomes attached. ## Golgi Body - A stack of flattened membranes enclosing hollow sacs (cisternae) formed by transport vesicles. - Modifies products of ER. - Manufactures certain macromolecules. - Sorts and packages material into transport vesicles. - Golgi body has two sides: "cis" and "trans". "Cis" face is close to ER, place where vesicles from ER are added to Golgi body. "Trans" face gives rise to vesicles that pinch off the Golgi body. 1. Vesicles move from ER to Golgi. 2. Vesicles fuse to form new cis-Golgi cisternae (cis-receiving) 3. Cisternal maturation: Golgi cisternae move in a cis-trans direction. 4. Vesicles form and leave trans-Golgi, carrying specific products to other locations or to the plasma membrane for secretion. 5. Vesicles transport some proteins backward to less mature Golgi body cisternae, where they function. 6. Certain proteins are transported back to ER. ## Lysosome - Membranous sac of hydrolytic enzymes that can digest macromolecules (proteins), fats, old organelles, etc. - **Autophagy**: cellular recycling process, digestion of old organelles. ## Peroxisome - Single membrane bound organelle that removes H+ transferring it to O2 and producing H2O as by product. - Has enzyme called catalase, which converts H2O2 to H2O. - Oxidizes substrates such as fatty acids by removing H+. - Function in fatty acid metabolism and detoxification. ## Cytoskeleton - Network of fibers extending throughout the cytoplasm. - Organizes the cell's structures and activities, anchoring many organelles. - Interacts with motor proteins to produce motility. Inside the cell, vesicles travel along "monorails" provided by cytoskeleton. ## Microtubules - Hollow rods made of globular proteins (tubulin). - Each tubulin protein is a dimer consisting of α and β tubulin. - **Maintenance of cell shape** (compression-resisting "girders") - **Cell motility** (as in cilia or flagella) - **Chromosomes movement in cell division** - **Organelle movements** - **Globular microtubules guide vesicles** ## Microfilaments (Actin filaments) - Two intertwined stands of actin, each a polymer of globular subunits (7nm in diameter). - **Maintenance of cell shape** (tension-bearing elements) - **Changes in cell shape** (form 3D network (cortex) to support cell shape) - **Muscle contraction** (make up the core of microvilli of intestinal cells) - **Cytoplasmic streaming** (in plant cells only) - **Cell motility** (in pseudopodia) - **Cell division** (cleavage furrow formation) ## Cytoplasmic Streaming: - In plant cells only. Circular flow of cytoplasm within cells, spreads movement of organelles and distribution of materials within the cell. ## Fibrous Intermediate Filaments - Fibrous protein supercoiled into thicker cables. - Consists of one of several different proteins e.g. keratins, depending on cell type. - **Maintenance of cell shape** (tension-bearing elements) - **Anchorage of nucleus** and certain other organelles. - **Formation of nuclear lamina** ## Centrosomes and Centrioles: - Only in animal cells - **MTOC.** - Each centrosome comprised of a pair of centrioles, each composed of nine sets of triplet microtubules arranged in a ring. - Microtubules grow out from a centrosome near the nucleus. ## Cilia / Flagella - Cellular extensions containing microtubules. - **Flagellum:** undulating motion. - **Cilia:** alternating power and recovery strokes. ## Microfilaments - That function in cellular motility contain myosin in addition to actin. - In muscle cells actin filaments are arranged parallel to one another. - Thicker filaments composed of myosin interdigitate with thinner actin fibers. ## Extracellular Structures: ### Cell Walls of Plants ### Intercellular Junctions ### ECM of animal plants - Support, adhesion, movement, regulation. - ECM is made up of glycoproteins e.g. collagen, proteoglycans, fibronectin. - ECM proteins bind to receptor proteins in the plasma membrane called Integrins. - Collagen fibers are embedded in a network of proteoglycans. - **Proteoglycans:** consist of small protein with many carbohydrate chains. - **Fibronectin:** binds to membrane spanning receptor proteins, called integrins, also binds to the ECM proteins such as collagen, fibrin etc. ## Integrin - Cell surface receptor proteins built into the plasma membrane. - Function as signal transmitter between ECM and cytoskeleton, thus integrate changes occurring outside and inside the cell. Their communication regulates cell's behavior. ## ECM - Can influence activity of genes in nucleus, through mechanical and chemical signaling pathways - Mechanical includes fibronectin, integrins, and microfilaments of the cytoskeleton. ## Cell Junctions - Plasma membranes of adjacent cells are tightly pressed against each other, bound by specific proteins. Formation of continuous seal around cells allows the establishment of a barrier that prevents leakage of ECF across a layer of cells. ## Tight Junctions - Water tight seal. Do not allow cell signaling. ## Desmosomes (anchoring junctions) - Fasten cells together into strong sheets. Intercellular junctions that anchor cell cytoskeletal intermediate filaments made of sturdy keratin proteins. Found particularly in tissue that undergoes mechanical stress. - **Does not allow cell signaling.** ## Gap junctions (communicating junctions) - Provide cytoplasmic channels between adjacent cells. - Consists of membrane proteins extending from the membranes of two cells, these proteins create pores, through which ions, sugars, ATP, and other small molecules can pass. - **Necessary for communication between cells.** ## Motor protein - Cell motility requires interaction between cytoskeleton and motor proteins. - Convert chemical energy into mechanical motion. ## Dynein & Kinesin - Tubulin polymerizes as a polar protein polymer with + and - side. - Kinesin mostly moves towards positive, dynein moves towards negative. - Kinesin transports cargo from interior to periphery, dynein transports from periphery to interior. - Motor proteins are also enzymes that hydrolyse ATP - ADP + Pi. - Kinesin works on microtubules. - Dynein is involved in bending of flagellum and cilia, has two feet. One maintains contact with microtubule; another attaches and reattaches one step further along the microtubule. ## Membrane Structure: - **Amphipatic:** molecules that contain both hydrophilic and hydrophobic regions. - **Fluid mosaic model:** proteins are scattered and move freely. - **Plasma membrane:** selective barrier that allows sufficient passage of oxygen, nutrients, and waste to service the volume of every cell. - **Made of phospholipid bilayer.** **Factors affecting membrane fluidity:** more fluid = more permeable - Length of tails of phospholipids: shorter = more fluid. - Number of double bonds: less = more fluid. - Temperature: higher = less fluid (cholesterol increases fluidity at low T, decreases fluidity at high T.) Cholesterol keeps the bilayer together and prevents phospholipids from overpacking. - **Integral proteins:** penetrate hydrophobic interior of the lipid bilayer. - **Transmembrane proteins:** integral proteins that span the membrane. - **Peripheral proteins:** loosely bound to the surface of the membrane. - **Non-polar molecules pass lipid bilayer faster.** ## Tonicity: - Ability of extracellular solution to make H2O move into or out of cell via osmosis. - **Isotonic environment:** no net movement of water, cell is flaccid. - **Hypertonic:** H2O moves out of cell = cell shrink/plasmolysed. - **Hypotonic:** H2O moves into the cell = cell bursts/becomes turgid. ## Turgor pressure: - Force that pushes plasma membrane against cell wall. ## Membrane potential - Electrical potential difference across the plasma membrane when the cell is in a non-excited state - in/ex. ## Electrochemical gradient - Determines the direction that ions will flow through an open ion channel. ## Electrogenic pump: - Transport protein that generates voltage across a membrane. ## Phagocytosis - Cell engulfs particles by extending pseudopodia. ## Pinocytosis - Endocytosis of droplets of ECF into tiny vesicles. ## Receptor-mediated endocytosis - Specialized type of pinocytosis; intake of specific substances. ## Functions of membrane proteins: - Transport - Enzymatic activity - Signal transduction - Cell recognition - Intercellular joining - Attachment to the cytoskeleton and ECM ## Cell recognize each other: - By binding to surface molecules, often containing carbohydrates, on the extracellular surface of plasma membrane. - Membrane carbohydrates may be covalently bounded to lipids or proteins (forming glycolipids or glycoproteins). - Carbohydrates act as cellular tag. ## Permeability of plasma membrane: - **Non-polar molecules can dissolve in lipid bilayer and pass rapidly.** - **Transport membrane proteins allow passage of hydrophilic substances. ** - **Channel proteins have a hydrophilic channel that certain molecules and ions can use as tunnel.** - **Channel proteins called aquaporins, facilitate passage of water.** - **Carrier proteins**, bind to molecules and change shape to shuttle them across the membrane. - **Transport protein is specific for the substance it moves.** ## Diffusion: - Net movement of molecules or ions from a region of high concentration to a region of low concentration (down concentration gradient). - **Passive process** as molecules have natural kinetic energy. - As a result of diffusion molecules reach equilibrium. **Factors influencing diffusion:** - **Steeper concentration gradient:** higher temperature, increased surface area = all increase rate of diffusion. - **Non-polar molecules** can pass directly through membrane. (steroids, hormones). - **Gases and water molecules** can diffuse directly through membrane. - **It is the tendency of a molecule to spread out evenly into the available space.** ## Facilitated diffusion - Movement of molecules from a region of high conc. to a region of low conc. down a concentration gradient (passive) - **Molecules go through channel proteins (aquaporins, ion channels (gated channels))** - **Carrier proteins undergo subtle changes in shape (induced fit hypothesis). ** ## Osmosis - Diffusion of water down water potential gradient. - **Ψ is the tendency of water to move out of solution.** - **Pure water has Ψ = 0.** - **Negative Ψ means solution has more solute than solvent. ** ## Active Transport - Movement of substances from a low concentration to a region of high concentration against concentration gradient. - **Occurs via specific carrier proteins for specific ions that use energy from ATP.** - **Allows to maintain concentration gradients that differ from their surroundings.** - **e.g. Na+/K+ pump:** 3 Na out, 2 K in. ## Cotransport: - Coupled transport by membrane proteins. (plants) ## Proton pump: - Driven by ATP, pumps H+ out of companion cells cytoplasm into cell wall, creating high conc. of H+(pH low) in cell wall. ## H+ ion-sucrose cotransporter - Drives movement of H+ ion from a region of high conc. to low conc. down H+ conc. gradient via facilitated diffusion, along with sucrose, against its conc. gradient via secondary active transport (co-transport).