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Bio Sci 93 Shaffer Week 2

by: Dana Roach

Bio Sci 93 Shaffer Week 2 Bio Sci 93

Dana Roach

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Here are the reading guide notes with additional lecture notes for clarification from Week 2 of Bio Sci 93 with Shaffer.
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This 13 page Class Notes was uploaded by Dana Roach on Thursday October 8, 2015. The Class Notes belongs to Bio Sci 93 at University of California - Irvine taught by SHAFFER, J. in Fall 2015. Since its upload, it has received 28 views. For similar materials see DNA TO ORGANISMS in Biology at University of California - Irvine.


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Date Created: 10/08/15
What are the major functions of the plasma membrane What does it mean that the plasma membrane is selectivelv permeable The plasma membrane is the boundary that separates a cell from its surrounding and regulates what enters and exits the cell This is called selective permeability meaning it allows some substances to cross the membrane more easily than other a fundamental characteristic to life The plasma membrane controls the passage of substances What kinds of biomolecules are found in plasma membranes Lipids carbohydrates and proteins are key parts of a plasma membrane Phospholipids are the most abundant lipid in plasma membranes What does it mean that phospholipids are amphipathic How does property affect their orientation in the membrane Phospholipids are amphipathic molecule meaning it has both hydrophilic and hydrophobic regions and are the most abundant lipids in a cell membrane Having these two characteristics leads to the formation of a bilayer with the hydrophilic heads on the outside and the hydrophobic tails on the inside Mbst membrane proteins are also amphipathic making it so that they reside in the phospholipid bilayer with their hydrophilic parts facing outward What does it mean that this is a fluid mosaic model How many different types of molecules can you find in this drawing Fluid mosaic model model of a cut away of an animal cell showing not only the outside of the cell but also the components and structure of the phospholipid bilayer cholesterol integral proteins phospholipids glycolipids the fibers of extra cellular matrix ECM outside the cell microfilaments of cytoskeleton inside the cell carbohydrates on the extracellular side of the membrane attached to embedded glycoproteins and peripheral proteins on the cytoplasmic side of the membrane What evidence do we have that plasma membranes are fluid and not static structures One example of this evidence is the knowledge that a membrane is held together by hydrophobic interaction which are much weaker than covalent bonds leading to rapid horizontal movement Neighboring phospholipids exchange places about 10 7 times per second Proteins move more slowly but can still shift within the membrane if not attached to cytoskeleton or extracellular matrix You couldn t just assume that the proteins don t move because there could be other explanations for the lack of39movement such as the non compatibility of the two animal cells perhaps they need to be the same species or belong to the same biological family or it has to be at a certain temperature Explain how each of the following factors affect membrane fluidity aTenuxNa ueMembranes remain fluid so long as the temperature decreases until the phospholipids settle and become tightly packed ex bacon grease This temperature limit is dependent on type of lipid b saturation level of fatty acidSZMembranes remain fluid at lower temps If it has lots of unsaturated hydrocarbon phospholipid tails since they can t be packed tightly together C cholesterol Cholesterol in the membranes affects it at different temperatures At body temperature is makes the membrane less fluid by restrainingmovement of the phospholipids but in limiting ability to pack tails together is lower the temperature required for a membrane to solidify In this way cholesterol acts as a fluidity buffer for the membrane lf phospholipids are the main determinant of a membrane s fluidity what kinds of biomolecules affect a membrane s function 2 The membrane lipid composition of the warmer native grass would probably be more liquid and have more movement of phospholipids and proteins where as the cooler native grass would most likely have less movement and more cases of membrane solidification Unless the cool native grass had more cholesterol embedded in the phospholipid bilayer or unsaturated phospholipid tails in which case there would still be reduced movement but less membrane solidification On the other hand the hot grass might need specialty lipids that prevent extreme liquidity of the membrane Compare and contrast the structures and functions of inteqral proteins and peripheral proteins Phospholipids are the main fabric of the membrane but proteins determine the membrane s functions Integral proteins penetrate the hydrophobic interior of the lipid bilayer the majority of which are transmembrane proteins spanning the entire membrane The hydrophobic portions of these proteins contain one or more stretches of nonpolar amino acids which are usually curled into alpha helices The hydrophilic parts are exposed to water but some even have hydrophilic channels through the membrane that let substances through Peripheral proteins are not embedded in the phospholipid bilayer but rather lay directly under it that are loosely bonded to the surface of the membrane and are often exposed to the surfaces of the integral proteins Proteins are sometimes held in place by the cytoskeleton or the ECM integrins for example attach to give the cell a stronger framework What is a transmembrane protein Transmembrane proteins proteins that span the entirety of the membrane and connect to both the outside and the inside What are the six major functions of membrane proteins Figure 77 provides a summary Transport Enzymatic activity Signal transduction cellcell recognition intercellular joining attachment to the cytoskeleton and ECM What are the major functions of membrane carbohydrates such as glycolipids and glycoproteins Some carbohydrates are bonded to lipids forming either glycolipids but most are bonded to proteins forming glycoproteins They function as markers that distinguish one cell from another What types of molecules can cross the lipid bilayer without extra help Why can they do this There is a constant movement of small molecules and ions moving across the plasma membrane Other molecules though include nonpolar molecules such as hydrocarbons C02 and 02 are hydrophobic and therefore can dissolve the lipid bilayer easily andmove across without help What types of molecules cannot cross the lipid bilayer on their own Why can t they How do transport proteins help these molecules through Specific ions and many polar molecules can t cross it on their own They can t cross it because they are hydrophilic and therefore can t pass through These molecules get through with the help of transport proteins also referred to as channel proteins that provide a hydrophilic channel for certain molecules and atomic ions use to travel through the membrane Each transport protein is specific to the substance it transports A specific example is an aquaporin which specifically helps water travel into the cell A carrier protein is another example which holds onto their passengers and change shape in a way that shuttles them across the membrane Answer concept check 72 question 2 in the space below 2 Because water is especially guarded against a cell since too much or too little of it severely affects cell functionality and so the only way it can access into the membrane quickly is through these transport proteins otherwise it would just slowly seep through the membrane and the cell could die in the mean time Describe the structure and the function of the following molecules found in the extracellular matrix Collagen glycoprotein in the EMC ofmost animal cells that is the most abundant and whose function is to dorm strong fibers outside the cells and which is embedded in a network woven out of proteoglycans Makes up 40 of total protein in the human body Proteoglycans molecule consists of a small core protein with many carbohydrate chains covalently attached so that it may be up to 95 carbohydrate Fibronectin bind to integrins that attach cells to each other by connecting ECM to ECM Integrins cellsurface receptor proteins that are built into the plasma membrane What is diffusion How does a solute s concentration oradient affect the direction that a solute diffuses Diffusion the result of thermal energy of molecules the movement of particles of any substance so that they spread out into the available space Individual molecules move randomly but a population of molecules may be directional Concentration gradient the region along which the density of a chemical substance increases or decreases Each substance diffuses down its own concentration gradient unaffected by other substances gradients However a solute s concentration gradient can affect the direction the solute diffuses because more concentrated likes to go to less concentrated to become equal and reach equilibrium Why is diffusion considered to be passive transport Passive Transport diffusion of a substance across a biological membrane transport that does not require expending any energy Diffusion is considered passive transport because it occurs spontaneously with no additional energy required The concentration gradient itself represents potential energy and drives diffusion What is osmosis How is it similar to yet different from diffusion Osmosis the diffusion of free water across a selectively permeable membrane whether artificial or cellular It is similar to diffusion in the fact that it has its own concentration gradient of sorts water diffuses across the membrane from region of higher free water lower solute to that of lower free water concentration higher solute The only difference is that osmosis only occurs across a membrane and it is the solvent water moving across rather than the solute Examine Figure 711 and answer the what if question in the space below If the orange dye was able to cross the membrane the solution would end up moving to the side with more solute thus creating a higher 0 overall solution on that side However if the two sides were already equal then it would equally mix on both sides slightly raising both Define the following terms with related to tonicity and give an example of each Tonicitz the ability of surrounding solution to cause a cell to gain or lose water that is dependent on solute concentration which cannot cross the membrane relative to the concentration inside the cell Hypotonic having less solute than what s inside the cell leading to the flooding of the cell resulting in lyseing bursting of the cell WATER BALLOON Isotonic same concentration both inside and outside the cell resulting in no net movement across the membrane HVpertonic having more solute than what s inside the cell and so the water in the cell will move to the outside leading to the cell shriveling and dying SALT WATER AND FRESH WATER FISH Osmoregulation the control of solute concentrations and water balance Complete the table below to summarize the effects of tonicity on animal and plant cells For each empty box explain what will happen to a cell placed in that environment and why it happens Hypotonic solution Isotonic solution Hypertonic solution Lysed Shriveled Ammal Ge water floods in Normal Water flows out Turgid normal Turgor pressure Plant cell pressure that Flaccid Plasmolyzed opposes further water uptake What is facilitated diffusion How is it similar to yet different than passive transport Eacilitaged diffusion the transport of polar molecules and ions across the plasma membrane through the help of transport proteins It is similar to passive transport in the sense that it helps these molecules cross the plasma membrane in a regulate way but it requires the help of specific protein This is still considered passive transport because the solutes are moving down their concentration gradients What are channel proteins ion channels gated channels and carrier proteins How are their structures and functions similar yet different Channel Proteins proteins with hydrophilic corridors that provide corridors for specific molecules or ions across the plasma membrane Ion Channels channel proteins that transport ions Gated Channels corridors into the cell that open or close in response to a stimulus Some are electrical and others only function when the substance it carries binds to the channel Carrier Proteins Proteins that carry substances from one side of the membrane to the other They work through passive transport What is active transoort How is it similar yet different to passive transport and facilitated diffusion What is required for active transport to work Active Transport pumping a solute across a membrane against the direction of the concentration gradient requiring cells to expend energy Active transport allows a cell to maintain internal regulation of solutes that is different than the outside concentrations Facilitated diffusion passively uses proteins to move solutes across the membrane while passive transport is done independently Examine details of the sodiumpotassium pump a specific type of active transport Summarize the function of the sodiumpotassium pump in your own words SodiumPotassium pump A protein exists in the membrane and Na binds to it causing phosphorylation by ATP thus changing the shape to be less inclined to Na and more inclined to K but this process is then reversed when K is then released into the cell Review the differnces of passive and active transport Answer the question associated with the figure in the space below Na is moving out of the cell and K is moving in the cell both against the gradient What is the membrane potential and how does it form How does the membrane potential result in an electrochemical gradient Membrane potential the voltage across a membrane ranging from 50 to 200 millivolts Membrane potential favors the passive transport of cations into the cells and anions out of the cells therefore both drive diffusion of ions one chemical and one electrical Electrochemical gradient the combination of39both the chemical and electrical drive on an ion to move across the plasma membrane Why is it not totally correct to say that an ion diffuses down its concentration gradient Why is it more appropriate to say that an ion diffuses down its electrochemical gradient Because as in the example of39Na the positively charged ion is attracted to the negatively charged inside of the cell and driven by the concentration of39Na What is an electrogenic pump What is a proton pump Electroaenic pump a transport protein that generate voltage across a membrane Proton pump the main electronegative pump of plants fungi and bacteria that actively transports protons out of the cell transferring the positive charge to the extracellular solution How does cotransport move molecules across a membrane How do proton pumps contribute to cotransport Cotransport mechanism in which a transport proteincotransporter can couple the downhill diffusion of the solute to the uphill transport of a second substance against its own concentration gradient How do large molecules such as proteins and polysaccharides move across cell membranes They are moved across the cell membranes in vesicles which requires energy Compare and contrast exocytosis and endocytosis in terms of the way they move molecules across cell membranes Give an example of each Exocztosis secretion of certain molecules by the fusion of vesicles with the plasma membrane The vesicle buds from the Golgi apparatus moves along microtubules to the plasma membrane where the specific protein rearrange the lipid molecules of the two bilayers so the two membranes fuse and then the contents of the vesicle spill out The vesicle membrane becomes a part of the cell membrane 7Insulin production in the pancreas Endocztosis The cell takes in molecules and particulate matter by forming ne vesicles from the plasma membrane Different proteins than exocytosis but the process is just the reverse of it Three types phagocytosis cellular eating pinocytosis cellular drinking and receptor mediated endocytosis a form of pinocytosis ZCholesterol in the form of lowdensity lipoproteins which act as ligands any molecule that binds specifically to a receptor site on another molecule Define the three subtypes of endocytosis and give an example of each Phagocytosis cellular eating by extending pseudopodia around it and packaging it within a membranous sac called a food vacuole bacterium and amoeba Pinocytosis cellular drinking in which a cell continually gulps drops lets of extracellular fluid into tiny vesicles Nonspecific to what it transports Pinocytotic vesicles and ECF Receptoremediated endocytosis specialized type of pinocytosis that enable the cell to acquire bulk quantities of specific substances even though they may not be very concentrated in the extracellular fluid ZCholesterol in the form of lowdensity lipoproteins which act as ligands any molecule that binds specifically to a receptor site on another molecule Complete the following table to summarize transport mechanisms across plasma membranes Direction that Membrane solute moves Energy molecules up down required Examples involved concentration yes no gradient Diffusion No Down No water nonpOIar molecules Faculitated Yes channel Down NO Water diffu5on proteins Active transport Yes trapSport Up Yes Na K proteins Cotransport Cotransporters Up Yes sucrose H cotransporter Exocytosis veS39CleS GOIg39 Either Yes Insulin app Endocytosis Vesncles plasma Either Yes Extracellular membrane FIUId Describe how the following parameters are important to microscopy Magnification The ratio of an object s image size and it s real size Light microscopes can magnify up to 1000 times the actual size of the specimen Resolution Measure of clarity of the image it is the minimum distance two points can be separated and still be distinguished as separate points Light microscopes have resolution up to 02micrometer or 200 nanometers Contrast Difference in brightness between the light and dark areas of an image Staining and labelling cell components helps with this Approximately how big is a frog egg What is the range of sizes for most bacteria How many times smaller is an atom compared to a mitochondrion 13mm Frog egg 110 micrometers most bacteria 10 4 times smaller What is the major difference between a light microscope and an electron microscope Light Microscope a microscope where visible light passes through th specimen and then through the glass lenses The lenses refract the light in a way that magnifies the image of the specimen as it is projected into the eyecamera Can see a cell but not some details of a cell such as organelles Electron Microscope microscope that focuses a beam of electrons through the specimen or onto its surface Resolution is inversely related to the wavelength of the light or electrons Resolution on modern electron microscopes is about 0002nm Complete the following table to help you organize information about types of microscopy Use Figure 63 for help Type 532313 r Description What it is good for Without staining there is little contrast With Large cells EX Brightfield Light staining it kills the cells 39 Epithelial cells but gives clear overall look of cell Variations in density Phasecontrast Light are amplified to Unstained living enhance contrast of cells unstained cells Fluorescence Light Molecules within a cell Molecules within a can be found using this cell be labelling them with fluorescent dyes or antibodies 3D reconstruction can be created from standard image that is blurry but once out of focus light is excluded it is very clear Uses optical sectioning technique that limits out Confocal Light of focus light to create a single plane of fluorescence in the image Micrographs taken with this show a 3D image of surface of a specimen by beam scanning the surface covered In gold film that Scanning electron Good for vuewrng Electron excuted electrons that microscopy are detected by a surface of cells device that translates the pattern of electron into an electronic signal that is sent to a video screen Profiles a thin section of a specimen Aims electron beam through thin section of specimen that has been stained with atoms of heavy metals Good for viewin Transmission that attach to certain g Electron Internal cellular electron microscopy cellular structures structure enhancing density lmage displays transmitted electrons and uses electromagnets as lenses to bend the path of the electrons Answer concept check 61 question 2 on page 97 in the space below ggll Fractionation technique for studying cell structure and function which takes the cells apart and separates major organelles and other subcellular structures from one another Centrifuge is used to do this 1They are usually just colored with dye and don t change the density of the cell where as the electron microscopes require the use of stains with heavy metal atoms that alter the density of the cell being investigated 2 Phase contrast fer living and scanning electron fer hair surface What is the cytoskeleton What three major molecular structures make up the cytoskeleton What are the major roles of the cytoskeleton Cytoskeleton A network of fibers extending through the cytoplasm lMicrotubules microfilaments and intermediate filaments Roles to give mechanical support the the cell and maintain its shape Balances between opposite fbrces exerted by its elements Provides anchorage fer many organelles and even cytosolic enzyme molecules Can quickly be taken apart in one part of the cell and reassembled in another changing the shape of the cell How do motor proteins interact with the cytoskeleton to achieve cell motility cell motility ability fer the cell as a whole to change shape and movement of cell parts Motor proteins proteins that help with the movement of the cell Which interact with the cytoskeleton to allow who cell walls to move along the fibers outside the cell or fer vesicles and other organelles often use motor proteins to walk along the cytoskeleton fibers How do microtubules change size using the protein tubulin Microtubules are the largest of the three fibers to make up the cytoskeleton microfilaments actin filaments are the thinnest and intermediate filaments are in the middle Microtubules are hollow rods made from globular protein called tubulin Each tubulin protein is a dimer molecule with two subunits that are two slightly different polypeptides alpha and beta tubulin Each end of the tubule grows independently at different rates and can result in one side being thicker than the other since it has a much higher rate What are centrosomes and centrioles See Figure 622 for a microscopic image of these structures What type of microscopy was used to obtain this image Centrosomes where microtubules grow from in an animal cell a region that is often located near the nucleus Centrioles centrosome pair composed of nine sets of triplet microtubules arranged in a ring Light microscope was used to find this photo How do microtubules contribute to the movement of m and flagella How is the motor protein dynein involved Cilia and Flagella microtubule containing extensions that project from eukaryotic cells Microtubules help with the movement by being responsible fer the beating pattern of them the two patterns are different Flagellum undulate while cilia move back and fbrth They are also different in length number per cell and beating pattern But they both have groups ofmicrotubules sheathed in an extension of the plasma membrane Nine doublets of microtubules are arrange in a ring with two single microtubules in its center 3992 pattern The microtubule assembly is anchor in a basal body which is similar to a centriole with microtubule triplets in a 90 order The bending movement of39both flagella and cilia involves the proteins called dyneins that are attached along each outer microtubule doublet and consist of two feet that walk along the microtubule adjacent to it usingATP for energy How are microfilaments involved in muscle cell contraction along with the motor protein myosin amoeboid movement and cytoplasmic streaming Microfilaments are thin solid rods built from molecules of actin and help with muscle cell contraction by acting as a pulling force Cortical membranes help support the cell s shape and gives the outer cytoplasmic layer cortexa gel consistency Actin filaments and myosin filaments interact to cause contraction of muscle cells This same interaction is involved in the amoeboid crawling movement of our white blood cells by extending pseudopodia fake foot and moving toward them Both actin andmyosin interactions in plants lead to cytoplasmic streaming the circular flow of cytoplasm within cells How did intermediate filaments get their name Are intermediate filaments more or less sturdy than microtubules and microfilaments Intermediate filaments are named for their diameter which is in between that of39microfilaments andmicrotubules They are only found in the cells of some animals including vertebrates and are specialized for bearing tension like microfilaments Uhlike them though intermediates are formed from subunits of proteins whose members include keratin and are permanent fixtures of cells It is found that they are exceptionally sturdy Complete the following table to help you organize information about cytoskeleton components See Table 61 for help Made up of Description Diameter Cellular Funcnons what protein of structure nm examples Separation of Hollow rods chromosomes grouped into in cell division Dimer of two centrioles In 25nm wuth shape and subunns 9 sets of 15nmumen support cell Microtubules alpha and Flagella culia triplet 250 nm tracks for beta tubulin microtubule centriole organelles polypetides 5 arranged guide vesncles in a ring from ER to Golgi apparatus Thin solid Provide support rods that is 7nm approx shape Actin a twisted 200nm increases 233510 Microfilaments globular double 92 surface area to g cytoplasmic protein chain of arrangement absorb streaming actin nutrients act as subunits bearing forces Cell shape suppon tension Fibrous bearing Proteins Intermediate proteins anchorage of Dead skin such as 8 12nm filaments conled Into nucleus and cells keratin cables other organelles formation of nuclear lamina


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