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Chapter 6-7 (The Fundamental Units of Life: ~ All organisms are made of…

- - - - Light Microscope (LM):
        ~ visible light passes through the specimen and then through a glass lense.
        ~ Lense refract the light, magnified, then projected to the viewing eye.
      - Importance of Microscopy
        
        ~ Magnification: Enlargement, Amplification.
        ~ Resolution: Clarity, a clear image.
        ~ Contrast: difference of lighting and stains on the image.
      - Electron Microscope (EM) - (1950s):
        focuses on beams of electrons or onto its surface.
        
        Disadvantages of an EM:
        ~ the methods to prepare the specimens, kill the cells.
      - Scanning Electron Microscope (SEM):
        ~ Useful to study topography of a specimen.
        ~ Scans the surface of the specimen, usually coated with a thin film of gold.
        ~ Result: a 3D image.
      - Transmission Electron Microscope (TEM):
        ~ used to view thin specimens through which electrons can pass generating a projection image.
        ~The TEM is analogous in many ways to the conventional (compound) light microscope.
    - - It enables researchers to prepare specific cell components in bulk and identity and functions, a task not unusually possible with intact cells.
  - - - Eukaryotic: "true-nulceus"
        ~ DNA located in the nucleus.
        ~ Membrane-bound organelle
        ~ Larger than prokaryotes.
      - Prokaryotic: "before nucleus"
        ~ DNA located in the nucleoid.
        ~ No membrane-bound organelle
        ~ Smaller than eukaryotes.
      - Plasma Membrane: to protect the cell from its surroundings.
        ~ Composed of a phospholipid bi-layer with embedded proteins, selectively permeable to ions and organic molecules and regulates the movement of substances in and out of cells.
      - Surface Area of Cells:
        ~ each square micrometer of membrane, only a limited amount of a particular substance can cross per second, so ratio surface of volume is critical.
        
        The need for a surface area large enough to accommodate the volume helps explain the microscopic size of most cells and the narrow, elongated shapes of others, such as nerve cells.
  - - - ~ Nuclear Matrix: a framework of protein fibers extending throughout the nuclear interior.
    - - ~ tRNA transfer RNA: type of RNA that carries amino acids to the ribosome
        ~ mRNA messenger RNA: type of RNA that carries instructions from DNA in the nucleus to the ribosome
        ~ ribosomal RNA: type of RNA molecule READS THE DNA SEQUENCE that plays a structural role in ribosomes
    - - ~ Free Ribosomes: suspended in the cytosol.
        ~ Bound Ribosomes: are attached to the outer endoplasmic reticulum or nuclear envelope.
  - - - Involves:
        ~ E.R, Golgi Apparatus, Secretory Vesicles, Lysosomes, and Nuclear Membrane.
    - - Function: Production, Processing, and transport of proteins and lipids.
      - ~ Consists a network of membranous tubules and sacs called cisternae (reservoir of liquid.)
        ~ The E.R membrane seperates the internal compartment called the ER Lumen (cavity) from the cytosol.
      - ~ Rough endoplasmic reticulum has ribosomes attached to the cytoplasmic side of the membrane and the smooth endoplasmic reticulum lacks attached ribosomes.
        ~ The smooth one is a tubule network and the rough one is a series of flattened sacs.
        
        Functions of Smooth E.R: lipids are synthesized, calcium levels are regulated, and toxic substances are broken down.
        Structure: has no ribosomes therefore it is smooth.
        In both animal and plant cells
        
        Functions of Rough E.R:transport of substances such as proteins within the cytoplasm.
        Located next to the nucleus, ribosomes on the surface.
        Found in both plant and animal cells.
    - - Can use hydrolytic enzymes to recycle the cell;s own organic material, called autophagy.
  - - - Mitochondria: organelles that convert the chemical energy stored in food into compounds that are more convenient for the cell to use.
        ~ Cellular Respiration
        ~ Extract ATP from sugars, fats, and other fuels.
      - Chloroplast: organelle in plants that transforms light energy into sugars (plants only).
        ~ chlorophyll traps sun's energy.
    - - ~ Variations of the numbers of mitochondrias correlates with in the cell's level of metabolic activity.
    - - Specialied peroxisomes called glyoxysomes are found in fat-storing tissues of plant seeds.
  - - - ~ Centrosomes: a structure present in the cytoplasm of animal cells that functions as a microtubule-organizing center and is important during cell division; has 2 centrioles.
        ~ Centrioles: a structure in the centrosome of an animal cell composed of a cylinder of microtubule triplets arranged in a 9+0 pattern.
      - ~ Cilia: a short appendage containing microtubules in eukaryotic cells.
        
        A motile cillium is specialized for locomotion or moving fluid past the cell; formed from a core of 9 outer doublet microtubules and 2 inner single microtubules (the "9+2" arrangement) ensheathed in an extension of the plasma membrane.
        
        Primary cillium usually nonmotile and plays sensory and signaling role; lack 2 inner microtubules (the "9+0" structure).
        
        ~ Flagella: a long cellular appendage apecialized for locomotion.
        
        Like motile cilia, eukaryotic flagella have a core with 9 outer doublet microtubules and 2 inner single mictrotubules (the "9+2" arrangement) ensheathed in an extension of the plasma membrane.
        
        ~ Basal Body: a eukaryotic cell structure consisting of a "9+0" arrangement of microtubule triplets. The basal body may organize the microtubule assembly of a cilium or flagellum and is structurally very similar to a centriole.
        ~ Dyneins: in cilia and flagella, a large motor protein extending from 1 microtubule doublet to the adjacent doublet. ATP hydrolysis drives changes in its shape that lead to bending of cilia and flagella.
        
        ~ Cortex: outer region of cytoplasm in a eukaryotic cell, lying just under the plasma membrane, that has a more gel-like consistency that the inner regions due to the presence of multiple microfilaments; in plants, ground tissue that is between the vascular tissue and the dermal tissue in a root or eudicot stem.
  - - - ~ Primary Cell Wall: The wall laid down during cell growth, not a barrier
        
        limit size and shape of cell, prevents rupture due to uptake of water, provides support.
        
        Polysaccharides: pectin, cellulose, hemicellulose. Primary wall is hydrophilic.
        
        ~ Middle Lamella: Pectin rich region between two adjacent cell walls that "glues" them together.
        ~ Secondary Cell Wall: laid down to the inside of the primary wall, consists of three layers, tends to be very thick.
        
        almost entirely cellulose, lignin present, pectin absent.
        
        Wall laid down after a cell has ceased growth and elongation.
    - - Plasmodesmata in Plant Cells
        ~ Plasmodesmata: channels through cell walls that connect the cytoplasms of adjacent cells.
      - Other Junctions in the Animal Cell:
        
        ~ Gap Junctions: proteins - connexins, connect insides of cells together, bottom layer.
        
        ~ Desmosomes: N/A for protein, use int. filaments for adhesion, 2nd top later
        
        ~ Tight Junctions: protein - claudins, prevent fluid leaks, top most layer.
    - - ~ Fibronectin: assembled into the extracellular matrix, an insoluble network that separates and supports the organs and tissues of an organism.
        
        plays a crucial role in wound healing.
      - ~ Integrins: the principal receptors used by animal cells to bind to the extracellular matrix.
        
        They are heterodimers and function as transmembrane linkers between the extracellular matrix and the actin cytoskeleton.
- - - - Passive transport is diffusion of a substance across a membrane with no energy investment
        ~ Diffusion: Movement of molecules from an area of higher concentration to an area of lower concentration.
        ~ Concentration Gradient: difference from one concentration substance from one location to another.
        
        Each substance diffuses down its own concentration gradient, unaffected by the other concentration gradients of other substances.
        
        ~ Passive Transport: cell doesn't need energy,
        high to low concentration.
        
        In the case of water, presence of aquaporin = rapid movement of certain cells.
      - Water Balance of Cells Without Cell Walls
        ~ Tonicity: A description of the relative solute concentration in a solution as compared to another solution.
        
        If there is a higher concentration of non-penetrating solutes in the surrounding solution, water will tend to leave the cell, vice versa.
        
        ~ Isotonic: Two solutions that have an equal concentration of solutes.
        ~ Hypertonic: A solution that has a higher concentration of solutes than another.
        ~ Hypotonic: A solution that has a lower concentration of solutes than another.
        
        ~ Osmoregulation: the processes by which animals control solute concentrations in the interstitial fluid and balance water gain and loss.
      - Facilitated Diffusion: Passive Transport Aided by Proteins
        ~ Facilitated Diffusion: the movement of specific molecules across cell membranes through protein channels.
        ~ Ion: Channel proteins that transport ions.
        ~ Gated Channels: a protein channel in a cell membrane that opens or closes in response to a particular stimulus.
      - Effects of Osmosis on Water Balance
        ~ Osmosis: no energy. high to low concentration of water molecules.
        
        Water diffuses across the membrane region of higher free water concentration to that of lower free water concentration until solute concentrations on both sides of the membrane.
      - Water Balance of Cells with Cell Walls
        ~ Turgid: when water diffuses into a plant causing the plant cell to swell. the cell wall will prevent bursting.
        ~ Flaccid: Limp. A walled cell is flaccid in surroundings where there is no tendency for water to enter.
        ~ Plasmolysis: when water diffuses out of the plant cell causing the cell to shrivel.
    - - The Need for Energy in Active Transport
        ~ Active Transport: the movement of ions or molecules across a cell membrane into a region of higher concentration, assisted by enzymes and requiring energy.
        
        Enables a cell to maintain internal concentrations of small solutes transporting them against the gradients.
        
        ~ Sodium-Potassium Pump: It is a vital transmembrane ATPase found in animal cells. It moves sodium ions out of cells & potassium ions into cells against steep conc. gradients.
      - How Ions Pumps Maintain Membrane Potential
        ~ Membrane Potential: Gradient of electrical potential energy across a cell membrane.
        
        It's like a battery.
        
        ~ Electrochemical Gradient: since ions are acted upon by two different forces, we must know the strngths and directions of both forces. to determin the electrochemical gradient.
        
        Ions will diffuse down their electrochemical gradients.
        
        ~ Electrogenic Pump: Create membrane potential which are a source of potential energy.
        
        ~ Proton Pump: Active transport of H+ ions (protons) out of the cell by a carrier protein, which creates membrane potential.
        
        During transport back into the cytoplasm, the movement of H+ ions down the electrochemical gradient provides the potential energy necessary to move sucrose from low to high concentration. This is considered to be active transport as a result.
        
        Cells in the leaves of land plants use this type of transport to move sucrose produced in photosynthesis into the plant's veins for transport to other locations within the plant.
      - Cotransport: Coupled Transport by a Membrane Protein
        ~ Co-Transport: Steps...
        
        Hydrogen is pumped out of the cell, against its concentration gradient.
        
        Hydrogen begins to move down the concentration gradient.
        
        when hydrogen re-enters the cell, it opens a "door" for the sucrose to enter the cell.
    - - The Permeability of the Lipid Bilayer
        ~ Non-Polar Molecules:
        
        Hydrocarbons: CO2 and O2; hydrophobic, as the lipids; they can dissolve in the lipid bilayer of the membrane and cross it easily.
        -- impedes direct passage through membrane ions and polar molecules (hydrophyllic).
        
        ~ Polar Molecules: C6H12O6 and other sugars; pass slowly , even in water, do not cross rapidly relative to non-polar molecules.
      - Transport Proteins
        ~ Specific ions and a variety of polar molecules can't move through the cell membranes on their own.
        
        ~ Transport Proteins (Channel Proteins): Function by having a hydrophyllic channel that certain molecules or atomic ions use as a tunnel through the membrane.
        
        Aquaporins: channel proteins in plasma membrane specialized for passage of water.
        -- cells an increase rate of osmosis by installing more aquaporins and decrease rate by removing them.
        -- significant amounts of water diffuse even through the hydrophobic, phospholipids of the plasma membrane.
        
        ---> Without? Only tiny fraction of these water molecules would pass through the same area of the cell membrane in a second, so the channel protein brings about a tremendous increase in rate.
    - - Bulk transport across the plasma membrane occurs by exocytosis and endocytosis
        ~ Large molecules; proteins and polysaccharides, occurs across the membrane in packaged vesicles.
        
        ~ Exocytosis: a process in which material inside a cell is packaged into vesicles and excreted into the extracellular medium.
        
        A vesicle loaded with cargo is formed as a protein coat wraps around it.
        
        The vesicle is released from the Golgi, carrying cargo molecules. The protein coat is shed.
        
        The vesicle fused with the plasma membrane and releases the cargo to the outside
        
        ~ Endocytosis: a process in which the plasma membrane invaginates or fold inward, to form a vesicle that brings substances into the cell.
        
        ~ Pinocytosis: a form of endocytosis that involves the formation of membrane vesicles from the plasma membrane as a way for cells to internalize the extracellular fluid.
        
        important in cells that are actively involved in nutrient absorption such as cell that line the intestine in animals.
        
        ~ Receptor-Mediated Endocytosis: a common form of endocytosis in which a receptor is specific for a given cargo.
        
        Cargo binds to receptor and receptors aggregate. The receptors cause coat proteins to bind to the surrounding membrane.
        
        The plasma membrane invaginates as coat proteins cause a vesicle to form. The vesicle is released in the cell. The protein coat is shed. The vesicle fuses with an internal organelle such as a lysosome. Cargo is released into the cytosol.
        
        ~ Phagocytosis: a form of endocytosis that involves the formation of a membrane vesicle which engulfs a particle such as a bacterium.
    - - Lipids and proteins are the staple ingredients of membranes, although carbohydrates are also important.
        
        ~ Amphipathic: a molecule with both a hydrophilic region and a hydrophobic region, such as a phospholipid.
        
        ~ Fluid Mosaic Model: a model in which the membrane is a fluid structure with a "mosaic" of various proteins embedded in or attached to a double layer (bilayer) of phospholipids.
      - The Fluidity of Membranes
        ~ three major factors that
        affect membrane fluidity:
        
        Ratios of different types of lipids.
        
        Saturated vs. Unsaturated phospholipids.
        
        Amount of cholesterol.
        
        ~ Cholesterol have the ability to both increase and decrease membrane fluidity.
        
        It inserts itself in between the fatty acid tails of the bilayer.
        
        At high concentrations, cholesterol blocks phospholipids from moving laterally (decreases fluidity).
        
        At low concentrations, prevents phospholipid tails from packing in tightly (increases fluidity).
      - Evolution of Differences in Membrane Lipid Composition
        ~ Variations on the cell membrane lipid compositions of many species appear to be evolutionary adaptations that maintain the appropriate membrane fluidity under specific environmental conditions.
        
        The ability to change the lipid composition of cell membrane in response to changing temperatures has evolved in organisms that live where temperatures vary.
        
        Winter Wheat: tolerate extreme cold.
        
        Certain archaea and bacteria: can change proportion of unsaturated phospholipids in their cell membrane.
      - Membrane Proteins and Their Functions
        ~ Different types of cells contain different sets of membrane proteins, and the various membranes within a cell each have a unique collection of proteins.
        
        ~ Integral Proteins: Often extend through the membrane (trans-membrane), with two hydrophilic ends.
        
        The hydrophobic midsection usually consists of one or more alpha helical stretches of hydrophobic amino acids.
        
        ~ Peripheral Proteins: Attached to the surface of the membrane, often to integral proteins.
        
        Attachments of membrane proteins to the cytoskeleton on the cytoplasmic side and fibers of the extracellular matrix on the exterior provide a supportive framework for the plasma membrane.
        
        A single cell may have cell-surface membrane proteins that carry out several different functions, such as transport through the cell membrane, enzymatic activity, or attaching a cell to either a neighboring cell or the extracellular matrix.
        
        Signal Transduction: a membrane protein may have a binding site with a specific shape that fits the shape of the chemical messenger.
        
        external messenger may cause the protein to alter its shape.
        
        Cell-Cell Recognition: Some glyco-proteins serve as I.D tags that are specifically recognized my membrane proteins of other cells.
        
        Short-lived.
        
        Enzymatic Activity: A protein that is built into the membrane may be an active site.
        
        Inter-cellular Joining:
        ~ Membrane proteins of adjacent cells may hook together in various kinds of junctions, such as gap junctions or tight junctions.
        
        long-lasting.
        
        Transport:
        ~ Left: A protein with a membrane may provide a hydrophyllic channel across the membrane.
        ~ Right:Transport proteins shuttle a substance from one side to other by changing shape.
        
        some hydrolyze ATP as energy to actively pump.
        
        Attachment to the cytoskelton and extracellular matirix (ECM)
        ~ Micro-filaments may be non-covalently bound to membrane proteins.
        
        Proteins that bind to ECM can coordinate extracellular and intra-celluar changes.
        
        HIV Resistance:
        a) Left; HIV can infect a cell with CCR5 on its surface, as in most people.
        b) Right; HIV cannot infect a cell lacking CCR5 on its surface, as in resistant individuals.
      - The Role of Membrane Carbohydrates in Cell-Cell Recognition
        ~ two cells in an animal may communicate by interaction between molecules protruding from their surfaces.
        
        cells recognize other cells by binding to molecules,often containing carbohydrates, on the extracellular surface of the plasma membrane.
        
        ~ Glycolipids: They are lipids with attached carbohydrate (sugar chains).
        
        These molecules are called cell markers or antigens and can be recognized by the cells of the immune systems as self (of the organism) or non-self (of cells belonging to other organisms).
        
        ~ Glycoproteins: Intrinsic proteins, They are embedded in the cell-surface membrane with attached carbohydrate (sugar) chains of varying lengths and shapes.
        
        Glycoproteins play a role in cell adhesion and as receptors for chemical signals.
      - Synthesis and Sidedness of Membranes
        ~ The 2 lipid layers may differ in lipid composition, and each protein has directional orientation in the membrane.
        
        How the membrane sidedness arises?
        -- asymmetrical arrangement of proteins
        -- lipids
        -- associated carbohydrates in the plasma membrane is determined as the membrane is being built by the ER and Golgi Apparatus.