Cell Biology Lecture Notes
Cell Biology Lecture Notes BS3514
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Date Created: 11/07/15
Cell Biology 01/13/2015 ▯ ▯ Lecture 1: Chapter 1 ▯ Cell Theory All organisms consist of one or more cells The cell is the basic unit of structure for all organisms All cells arise only from preexisting cells ▯ ▯ Hooke- looked at cork through a microscope and noticed the boxlike structures that make up cork; he then called these boxes cells; however cork is actually dead cells but he was on the right track ▯ Van Leeuwenhoek- produce a more magnifying microscope lens and became the first person to see living cells ▯ ▯ Areas of cell biology Cytology- concerned primarily with cellular structure Biochemistry- concerned with cellular structure and function Genetics- deals with the genetic code ▯ ▯ See page 7 for examples of images from different types of microscopes Magnify- make it larger Resolution- make it clearer ▯ ▯ Lecture 2: Chapter 2 ▯ Pass easily through a membrane- small, uncharged may be small and polar ▯ Difficulty passing through a membrane- all ions (+ or -), large, large polar ▯ Even small ions are unable to diffuse across a membrane (H+) ▯ ▯ Lecture 3: Chapter 3 (lab quiz 1 is over this) ▯ Proteins ▯ Classes of proteins ▯ The monomers are amino acids ▯ Table 3-1 pg. 42 ▯ Amino acids ▯ Figure 3-1, figure 3-2 ▯ Classes of R groups ▯ The polymers are peptide bonds ▯ Peptide bonds ▯ Directionality ▯ Polypeptide ▯ Monomeric and multimeric proteins ▯ Conformation ▯ Disulfide bonds ▯ Noncovalent bonds and interactions rd ▯ Primary, secondary, tertiary, and quaternary structures table 3-3 (3 column not important) ▯ Figure 3-6 ▯ Fibrous proteins, globular proteins ▯ DNA and RNA ▯ Fatty acids ▯ Saturated, unsaturated ▯ ▯ Lecture 4: Chapter 4 (lab quiz 2 will be over this) ▯ Cells and Organelles Three domains of life o Archaea- have prokaryotic cells (no nucleus no organelles) strange monolayer plasma membrane different cell wall are very different from bacteria o Bacteria- Common everyday average bacteria prokaryotes o Eukarya- Include protists, fungi, plants, and animals eukaryotes prokaryotes- have no true nucleus and lack organelles eukaryotes- have a nucleus and organelles ▯ Table 4-1 comparing three domains of life pg. 76 Main point: each of the three main cell types has a unique set of properties ▯ Limitations on cell size Cell size is limited by: (she said this will be on test) o The need for adequate surface area relative to volume (fg 4-1 p 77); Example: intestinal mucosal cells (fg 4-2) o Smaller cells have larger surface area to volume ratios than larger cells. This means that materials can rapidly diffuse in or out of the entire cell. Specific cells can be specialized to make the surface area even greater o Cytoplasmic streaming (cyclosis in plants) involves moving the cytoplasm and helps to maintain high concentration differences for effective diffusion o Having small cells helps to maintain appropriate concentration of enzymes and reactants where they are needed The rates at which volume can diffuse The need to maintain adequate local concentrations of substances required for necessary cellular functions ▯ Parts of cells Cell membrane (phospholipid bilayer) Ribosomes- make proteins Prokaryotic cells- have a nucleoid region where the DNA is found ▯ ▯ Eukaryotic cells- bound by a nuclear envelope (membrane); contains chromatin (DNA tightly complexed with proteins) Nucleolus- a structure that stains as a dark spot in the nucleus that contains structures for synthesizing and assembling RNA and protein components for ribosomes Cytoplasm- the inside of the cell except the nucleus Cytosol- the semifluid material around the organelles Mitochondria- important for cellular respiration Chloroplasts- sites of photosynthesis ▯ Endosymbiont theory- proposes that eukaryotic cells evolved from a symbiotic association between prokaryotic cells Endoplasmic reticulum is part of the endomembrane system Endoplasmic reticulum has a lumen and o Cisternae- flattened sacs Rough endoplasmic reticulum- has attached ribosomes that make proteins; there proteins are often intended for export for the cell There are also ribosomes loose in the cytoplasm; these often make proteins for use within the cell Smooth endoplasmic reticulum- makes lipids and membrane components; important for detoxification ▯ Golgi complex or Golgi apparatus Package material into vesicles for export from the cell Secretory vesicles- carry materials from the Golgi apparatus to the cell membrane for export from the cell through exocytosis ▯ Need to know these paths through the cells ▯ ▯ Lysosomes- contain digestive enzymes; important for breaking things down and contain hydrolases which break things down using water Peroxisomes- contain enzymes; they are found in plant, animal, fungal, protozoan, and algal cells; they can generate and degrade hydrogen peroxide Catalase is the major enzyme for breaking down hydrogen peroxide; they can also be involved in detoxifying other materials and in breaking down fatty acids Plants can have specialized peroxisomes called glyoxysomes that are important in converting fat to carbohydrates Vacuoles- used for storage o Plant cells generally have a large central vacuole Vesicles- small, membrane bound compartments ▯ Cytoskeleton- helps to maintain cell shape, helps to position organelles, used to move materials and organelles, used in cell movement, etc. ▯ ▯ Microtubules ▯ Microfilaments ▯ Intermediate filaments ▯ - all make up the type of cell ▯ ▯ extracellular matrix- every thing outside the cell membrane cell wall – technically outside of the cell in animal cells, collagen and proteoglycans are especially important in making up the extracellular matrix plant cell walls are made largely of cellulose microfibrils along with other materials bacterial cell walls generally consist of peptidoglycan there are connections between cells Plasmodesmata- connect neighboring plant cells ▯ ▯ Viruses- consist of genetic material and a protein capsid; may have additional components ▯ Viroids- small circular RNA molecules ▯ Prions- proteinacious infectious particles; passed through consumption Prion diseases include o Bovine spongiform encephalopathy (mad cow disease) o Variant Creutzfelt Jakob disease (vCJD) o Chronic wasting disease o Scrapie o Fatal familial insomnia o Kuru ▯ ▯ Bioenergetics: lecture 5 (McMan taught Chapter 5) Types of work o Work- when energy is transferred from one thing to another, where a gain in energy is positive work and a loss of energy is negative work Ex. when you charge up a phone o Energy can be thought of as the capacity to make things happen (i.e. to do work). It is like money in that you cannot create or destroy it, but you can move it around and change its form. When you move it around (i.e. do work) things tend to happen Some types of work o Synthetic work (biosynthesis) (i.e. build things like complex molecules) o Mechanical work o Concentration work (ex. pump something into an area of higher concentration) o Electrical work o Heat o Bioluminescence o Living things can do these kinds of work Some terminology associated with energy and living things (where living things get energy to do work) o Autotrophs- they can make their own food, meaning that they can make organic molecules from inorganic molecules These food molecules can then be utilized as a source of energy (liberated by cellular respiration) and carbon for building other organic molecules Heterotrophs- they have to eat food o This means that they have to eat organic molecules for their carbon and energy Chemotrophs- obtain energy from chemical reactions Phototrophs- obtain energy from light ▯ Now lets combine some of therse terms Chemoheterotrophs- uses chemical reactions to obtain energy, but it has to consume organic molecules Photoautotroph- ex. a plant, makes its own food using light as an energy source Chemoautotrophs- make organic molecules from inorganic molecules, using chemical reactions as an energy source ▯ Other chemistry terminology Oxidation- electrons are lost o In biochemical systems, oxidation is often accomplished by losing one or more hydrogen atom (which has an electron) and gaining oxygen Reduction- electrons are added o It is the opposite of oxidation. o In biochemical systems reduction typically means gaining H and losing oxygen o Living things release energy by oxidizing organic compounds, often making that energy available for the living thing to use Oxidation energy releases energy Reduction requires an input of energy No physical process (ex. chemical) process occurs with 100% efficiency, so heat is always liberated from the process Thermodynamics- the study of energy transformations o In thermodynamics you might study a comparison between the starting state and ending state of a system, and see whether energy flows into it, out of it etc. Kinetics- is the study of reaction rates and mechanisms Bioenergetics- the thermodynamics of living systems System- the thing that you study Surroundings- everything that is outside of the system An open system- exchanges materials with its surroundings (ex. energy, other materials etc.) A closed system- nothing is exchanged with its surroundings Living things are open systems Energy is often defined in units such as calories, kilocalories, and joules ▯ Laws of thermodynamics and related concepts First Law of Thermodynamics o In every physical or chemical change, the total amount of energy in the universe remains constant, even though the form of energy may change o Energy cannot be created or destroyed o The total amount of energy can only change in an open system o Energy = E o ΔE= E products - E reactants i.e. if the system gains energy then the products have more energy than the reactions o H refers to enthalpy which can be thought of as heat content (heat is a form of energy) o H= ΔE+ΔPV where PV is the pressure and V is the volume o In living things pressure and volume do not change in most chemical reactions o ΔH= Δ + change in PV o For living things we can assume that ΔH is equal to Delta o ΔH=ΔE o ΔH=H products-H reactants o –ΔH – the reaction is exothermic (had heat so its going away) o +ΔH – the reaction is endothermic (heat is coming in) ▯ Bioenergetics: lecture 6 (APat finished Chapter 5) Second law of thermodynamics o All reactions increase the entropy (disorder or randomness) of the universe Gibbs free energy o ΔG= ΔG products – ΔG reactants (when temperature and pressure are constant) o – ΔG means the reaction is exergonic (spontaneous) – releasing to the environment o +ΔG then the reaction is endergonic (nonspontaneous) o ΔG= -RTlnKeq+RT[C]c[D]d/[A]a[B]b (R is gas constant times temp) (small letters on the right are all raised) If the C and D are greater than A and B then it will be greater than one and go left Keg=[C1][D]y/[A]1[B]2 aA=bB yield cC + dD o ΔG = ΔH – TΔS H- enthalpy S- entropy o An input of energy (activation energy)is required to start even spontaneous reactions o ΔG° = free energy at standard conditions 25° C (298K), 1 atm, and 1 M concentrations of all materials o In living systems water is generally vastly more abundant than other reactants or products (approx. 55.5M) o Even if some water is produced or consumed, the amount is generally negligible. Therefore water is an exception to the 1M concentration requirement at standard state o In living systems, reactions often occur at or near a pH of 7. At a pH of 7, the concentration of hydrogen ions is 1x10 to the -7 and the concentration of hydroxide ions is 1x 10 to the -7 o ΔG prime means that the reaction is at a pH of 7 (with the concentration described above for H+ and OH-) o ΔG°prime means that the reaction is at standard conditions with a pH of 7 o A living cell is often in a steady state but you rarely see all reactions at an equilibrium of zero because that often causes death ▯ Chapter 6 Enzymes as biological catalysts: lecture 7 Enzymes- catalysts in living systems; most are proteins but not all of them o Ribozymes are RNA enzymes Catalysts speed up reactions but are not consumed by the reaction They make it possible for reactions to occur in living systems by lowering the activation energy required for the reaction to proceed Metastable state ▯ Active site- place on an enzyme where the substrate binds ▯ Holoenzyme- an enzyme with protein and non-protein components ▯ Apoenzyme- the protein portion of an enzyme ▯ Cofactor- the non-protein component of an enzyme ▯ Prosthetic group- is a cofactor that is firmly attached ▯ Coenzyme- is a cofactor that is loosely attached (often a vitamin) ▯ Specificity- most enzymes work with a particular substrate or small group of substrates ▯ Group specificity- enzymes work with more varied substrates that have some similar components ▯ ▯ Lock and key model- just says it fits like a lock and key ▯ Induced fit model-(more modern and accurate); there is a shape change as the enzyme binds to the substrate ▯ ▯ Enzyme nomenclature- most end in -ase Table -1 pg. 135 shows the major classes of enzymes we need to know Temperature- Reaction rate increases up to an optimal temperature then the reaction rate begins to decrease. As the temperature increases beyond the optimal temperature, denaturation occurs. pH- there is an optimal pH for each enzyme and the reaction rate decreases as you go above or below it. As you go too high or too low denaturation occurs changes in substrate concentration and changes in enzyme concentration also affect reaction rate ways that enzymes actually work By positioning the substrate to from bonds (right orientation) by stretching bonds, making it easier for the bonds to break, and by having the correct microenvironment ▯ Bond distortion- refers to stretching a bond ▯ Proton transfer- accepting or donating protons ▯ Electron transfer- accepting or donating electrons ▯ ▯ Enzyme kinetics- (VERY IMPORTANT) Velocity refers to the rate of change in product concentration per unit time Vmax- maximum velocity Saturation- enzymes are working as quickly as they can and increasing the substrate concentration no longer increases the reaction rate Km- the concentration of substrate that gives half the Vmax Km- is the Michaelis constant V=(Vmax[S])/(Km+[S]) ▯ ▯ Kcatt is the turnover number (the rate at which substrate molecules are converted to product by a single enzyme working at maximum velocity) Kcat=Vmax/[Et] ▯ ▯ We focus on the initial velocity because we know that the concentration of the products is 0 at the start ▯ ▯ michaelis – menton plot ▯ Lineweaver- Burk plot (allow you to calculate Vmax and Km) ▯ Eadie- Hofstee plot (allows you to calculate Vmax and Km) ▯ ▯ Enzyme inhibitors ▯ Reversible ▯ Irreversible ▯ ▯ Substrate analogues ▯ Transition state analogues ▯ ▯ Competitive inhibitors bind to the active site of the enzyme and prevent the normal substrate from binding ▯ Non competitive inhibitors bind elsewhere on the enzyme not at the competitive site ▯ ▯ Regulation of enzyme ▯ Allosteric enzyme- activity is modulated by molecules that bind somewhere other than the active site (allosteric site) ▯ Allosteric effectors- small organic molecules that regulate the activity of an enzyme for which they are neither the substrate nor the immediate product ▯ Allosteric activator- activates the enzyme ▯ Allosteric inhibitor- inhibits the enzyme ▯ ▯ Cooperativity- where binding to one site influences binding at other sites ▯ Positive cooperativity- binding at one site on the enzyme increases affinity for binding at other sites ▯ Negative cooperativity- binding at one site decreases affinity for binding at other sites ▯ ▯ Covalent modification ▯ Phosphorylation/dephospohrylation ▯ Protein kinases- enzymes that catalyze phosphorylation ▯ Protein phosphatases- enzymes that catalyze dephosphorylation ▯ ▯ Proteolytic cleavage ▯ A proteolytic enzyme cuts the enzyme into a functional form ▯ Zymogens- inactive forms of enzymes ▯ ▯ Ribozymes- RNA enzymes ▯ Chapter 7 Membranes ▯ Membranes Plasma membrane (cell membrane) Intracellular membranes ▯ ▯ Signal transduction is the specific mechanism used to transmit signals from the outer surface of cells to the interior ▯ Some materials pass through the membrane (ex. steroid hormones) others bind to receptors and cause changes in the cell ▯ ▯ Membrane proteins can be on the surface, imbedded in the protein and attached to lipids ▯ ▯ Cadherins- membrane proteins that are important in forming cell-cell contacts; stimulate adhesion ▯ Adhesive junctions ▯ Tight junctions form tight barriers ▯ Anykrin- point of attachment for the cytoskeleton ▯ ▯ Gap junctions are opening in animal cells that allow them to function ▯ Plasmodesmota are similar in plants ▯ ▯ Fluid mosaic model- says the membrane has proteins that move in fluid lipid layer ▯ Integral proteins are deeply imbedded within the membrane and ▯ Peripheral proteins on the surface of the membrane ▯ Lipid-anchored proteins ▯ Transmembrane proteins cross the membrane ▯ Lipid rafts- dynamic microdomains (small specialized region) that are complexes of lipids and protein ▯ ▯ Lipids classes ▯ Phospholipids ▯ Glycolipids- second part is most important ▯ Sterols (ex. cholesterol) ▯ Phospholipids – most abundant membrane lipids; includes phosphooglycerides and sphingolipids ▯ ▯ Glycolipids include glycosphingolipids ▯ Cerebrosides ▯ Ganglioside ▯ ▯ Sterols Cholesterol is the main sterol in animal membranes Phytosterols and some cholesterol are found in plant membranes Ergosterols are found in fungal membranes ▯ Most prokaryotes have hopanoids which are similar to cholesterol ▯ Mycoplasma bacteria have no cell walls and have sterols ▯ ▯ Thin layer chromatography- technique used to study lipids and other things; move different distances depending on polarity ▯ ▯ Fatty acids- vary in the presence and number of double bonds ▯ Generally have 12 to 20 carbon atoms ▯ 16 and 18 carbon atom chains are especially common ▯ ▯ transverse diffusion- phosphate goes through the membrane to the other side; hard because its actual flipping ▯ rotation ▯ lateral diffusion ▯ flippases can allow transverse diffusion (phospholipid translocation) ▯ ▯ Tm- transition temperature, temperature at which the membrane melts ▯ Long chain fatty acids have higher transition temperatures than short chain fatty acids ▯ The amount of unsaturation can affect the transition temperature ▯ Cis double bonds (most common double bonds in natural fatty acids) don’t pack as tightly as saturated fatty acids (with no double bonds) and increase fluidity ▯ Transdouble bonds don’t allow as much fluidity ▯ Sterols insert themselves between the fatty acids and make the membrane less fluid at higher temperatures but slow stiffening as the temperature gets lower ▯ Organisms regulate fluidity as needed (homeoviscous adaptation) ▯ Sterols also decrease permeability ▯ ▯ Lipids rafts ▯ Microdomains ▯ Thicker, less fluid ▯ ▯ Caveolae- contain caveolin which is a cholesterol binding protein ▯ ▯ Freeze fracturing- used to freeze and break the membrane and lets you look inside of it ▯ -membranes are frozen then broken open and examined using electron microscopy. This is extremely useful in looking at proteins ▯ ▯ types of membrane proteins ▯ integral membrane proteins- embedded deeply within the membrane ▯ integral monotopic proteins- embedded into the lipid layer but only protrude on one side ▯ transmembrane proteins extend across the membrane ▯ single pass proteins cross the membrane once ▯ multipass proteins cross the membrane multiple times ▯ multisubunit proteins- proteins with multiple polypeptide chains ▯ transmembrane proteins have hydrophobic regions ▯ ▯ peripheral membrane proteins -are proteins that are found on the surface of the membrane; studied particularly in erythrocytes which have spectrin, ankyrin, and band 4.1 protein ▯ ▯ lipid anchored proteins ▯ fatty acid anchored proteins ▯ isoprenylated membrane proteins ▯ GPI anchored proteins ▯ ▯ SDS-PAGE ▯ Isolation of membrane protein ▯ SDS – sodium dodecyl sulfate (an anionic detergent so a charged detergent) ▯ This surrounds the proteins and provides a negative charge ▯ The proteins are then run in an electrophoresis gel, separating them by size ▯ ▯ 2 SDS-PAGE ▯ separates base on charge and size ▯ ▯ western blotting- where proteins on a gel are transferred to a nylon or nitrocellulose membrane, exposed to label antibodies, and then the antibodies are allowed to bind to the proteins of interest ▯ ▯ xRay crystallography ▯ hydropathy analysis- where you look at the hydrophobic regions pg. 179 ▯ ▯ glycosylation the addition of a carbohydrate side chain to a protein ▯ N-linked glycosylation- the carbohydrate group is attached to the nitrogen atom of an amino group ▯ O-linked glycosylation- the carbohydrate is attached to the oxygen of a hydroxyl group ▯ ▯ Glycocalyx is a surface coat of a cell made from plasma membrane ▯ Glycoproteins and glycolipids that protrude ▯ ▯ Chapter 8: Transport across membranes ▯ ▯ For ATP you need three sodium per 2 potassium in order to work ▯ Know difference between hypertonic (more), hypotonic (less), isotonic (same) ▯ Simple diffusion ▯ facilitated diffusion ▯ active transport ▯ ▯ when molecules go down their concentration gradient (high to low), energy is release (-ΔG) spontaneous ▯ ▯ however when molecules go up their concentration (low to high) energy is absorbed (+ΔG); non spontaneous ▯ ▯ electrochemical potential- the sum of the concentration gradient and the charge gradient ▯ V m membrane potential ▯ Most cells have a negative V which means that theremis an excess of negatively charged solutes within the cell ▯ ▯ Simple diffusion ▯ Works for gases, nonpolar molecules, and small polar molecules ▯ Three main factors affect the diffusion of solutes: size, polarity and charge ▯ Smaller materials pass through more quickly ▯ Charged materials have a shell of hydration and this must be removed for the material to pass through the membrane ▯ ▯ Rate of simple diffusion is directly proportional to the concentration gradient ▯ V inward =PΔS ▯ Represents the diffusion of substances from the outside to the inside ▯ P is the permeability coefficient ▯ ▯ Facilitated transport ▯ Carrier proteins (transporters, permeases): bind to molecules and then undergo a conformational change (shape change that moves molecule inside cell) ▯ Channel proteins (porins and ion channels) simple provide a passageway (operate more quickly) ▯ ▯ Carrier proteins have similarities to enzymes Specificity – react with particular substrate Saturation inhibition(point where they cant go any faster) Competitive inhibition (something else is trying to bind) Vmax, Km ▯ Carrier proteins Uniport carrier proteins transport a single solute Coupled transport occurs when two solutes are transports simultaneously o Symport- two solutes move in the same direction o Antiport- two solutes move in opposite directions ▯ Active transport Has directionality Two categories o Direct active transport- accumulation of solute molecule is coupled directly to an exergonic reaction (most common hydrolysis of ATP) o Transport proteins driven by the hydrolysis of ATP is called ATPases or ATP pumps o Indirect active transport- requires energy but depends on the simultaneous transport of two solutes; the favorable transport of one solute down its concentration gradient drives the unfavorable movement of other solutes up its concentration gradient Synport Antiport ▯ In most cases, one of the two solutes is an ion that moves exergonically down its electrochemical gradient; NA+ is most commonly used in animals and H+ is most commonly used in other organisms ▯ ▯ Direct active transport depends on four types of ATPases (pumps) P-type ATPases o Most are found in or near plasma membrane o Proteins that are reversibly phosphorylated by ATP o Sensitive to VO - inh4bition o P1 ATPases are mainly responsible for transporting heavy metals o P2 ATP ases- responsible for maintain gradients of ions (e.g., Na+/K+ pump) o P3 ATPases- H+ ATPases that pump protons out o P4 ATpases pump hydrophobic molecules o P5 ATPases transport cations ▯ V- type ATPases are the ones that pump protons into organelles such as lysosomes endozomes and the Golgi apparatus ▯ F- type ATPases- found in bacteria mitochondria and chloroplasts Function in revers and ATP synthases ▯ ABC type ATPases are importers and exporters ▯ ▯ Most cells continuously pump either sodium or hydrogen out of the cell which maintains a relatively high concentration of sodium ions outside of the cell that can act as a driving force for the uptake of other materials (e.g. sugars and amino acids); can also be used for export ▯ ▯ Na+/K+ pump (figure 8-2, 8-11) 3 NA+ are pumped out and 2 K+ are pumped in for each ATP ▯ be familiar with active transport systems sodium dependent glucose transporters bacteriodopsin (light energy) Sodium potassium pump ▯ ▯ Energetics If you have uncharged solutes then only the concentration gradients are important in determining energetic If the solutes are charged then both concentration gradients and electrical potential are important ▯ [S] outside [S] inside ▯ ΔG=ΔG°+ RTln([S] inside /[S] outside R= 1.987 cal/(molK) ▯ ▯ K ieq1 because the solute concentrations are the same at equilibrium ▯ ΔG=RTlnK =-RTln1=0 eq ΔGinward = RTln([S]outside/[S]outside) ▯ ▯ ▯ If [S] inside is less than [S]outside, then ΔG is negative If [s]inside is greater than [S]outside then ΔG is positive ▯ ▯ ▯ For charged solutes, ΔG depends on the electrochemical potential as well ▯ Vm for animal cells is -60 to -90 mV ▯ Vm for bacterial cells is -15- mV Vm for plants is -200 mV ▯ ▯ Typically the inward movement of cations is favored ▯ ΔGinward=RTln([S]inside/[S]outside)+zFVn ▯ ▯ Sz is a solute with charges z ▯ Z is the charge F is the faraday constant (23,062 cal/molV) ▯ ▯ ▯ ΔGinward= -ΔGoutward ▯ ▯ Do questions by Friday ▯ Chapter 8, numbers 3,5,7,8 ▯ ▯ Chapter 9: Chemotrophic energy metabolism (not emphasized as much on exam) ▯ ▯ Chemotrophic energy metabolic Substrate level phosphorylation- pairing an exergonic reaction with an endergonic reaction to make ATP Oxidative phosphorylation- using an electron transport chain to make ATP Photophosphorylation- using light energy to make ATP ▯ ATP is a good energy currency Intermediate phosphate group transfer potential When a phosphate group leaves, oxygen’s with negative charges are separated The inorganic phosphate that is removed from ATP to make ADP has resonance making it very stable When ATP is broken down to ADP, Pi, entropy increases because you go from one molecule to two ▯ Metabolism- all of the reactions in a living organism ▯ Catabolic reactions are reactions that break things down ▯ Anabolic reactions are reactions that build things up ▯ ▯ NAD+, NADH ▯ ▯ Obligate aerobes require oxygen ▯ Obligate anaerobes require an oxygen free environment ▯ Facultative anaerobes can survive with or without oxygen but do better with oxygen ▯ ▯ Cellular respiration Glycolysis generally occurs in the cytoplasm In glycolysis one glucose molecule is split into two molecules of pyruvate. Two ATP are consumers; 4 ATP and 2 NADH are produced This gives a net gain of 2 ATP and 2 NADH (KNOW NUMEBRS) ▯ In some organism NADH donates its electrons to an organic molecule such as pyruvate in order to regenerate NAD+ and allow glycolysis to continue this is called fermentation ▯ ▯ Gluconeogenesis (forming glucose; reverse of glycolysis with several different steps) ▯ There are three irreversible steps of glycolysis that are important in regulation. Gluconeogenesis has different reactions to replace them ▯ ▯ Glycolysis is used to break down many molecules not just glucose ▯ Different molecules enter at different parts of the pathway ▯ ▯ Fatty acids are broken down by B-oxidation. This produces acetyl-coA that can enter the Krebs cycle ▯ ▯ NADH from glycolysis is converted back to NAD+ Aerobic respiration- NADH donates its electrons to an electron transport chain with oxygen as the terminal electron acceptor Anaerobic respiration- NADH donates its electron to an electron transport chain with a different molecule as the terminal electron acceptor; this term is also used to mean any respiration without oxygen Fermentation is where NADH donates its electron to an organic molecule such as pyruvate ▯ ▯ In eukaryotic cells pyruvate is moved into the mitochondrion ▯ Pyruvate is converted to acetyl-coA (one carbon is lost as CO2) ▯ acetyl-coA enters the Krebs cycle in to mitochondrial matrix ▯ the Krebs cycle is also known as the tricarboxylic acid and as the citric acid cycle ▯ ▯ Acetyl-coA combines with oxaloacetate to form citrate and begin the Krebs cycle. The Krebs cycle produces NADH, FADH2, CO2, and GTP ▯ The electron transport chain takes place on the inner mitochondrial membrane. NADH and FADH2 donate electrons to electron acceptors ▯ The electrons move from one acceptor to another. The energy produced is used to move H+ across the inner mitochondrial membrane and into the intermembrane space. The H+ move down their concentration gradient from high concentration in the intermembrane space to low concentration in the matrix by passing through ATP synthase, producing ATP ▯ ▯ In prokaryotes these processes take place on the infoldings of the plasma membrane ▯ ▯ Chapter 10 ▯ Aerobic vs anaerobic ▯ Know figure 10-1 ▯ Mitochondria and parts of mitochondria Inner and outer membrane ▯ Table 10-1 overview of what mitochondrion actually does ▯ Pg. 259 TCA cycle ▯ Pg. 273 Figure 10-15 Electron transport chain overview ▯ Pg. 274 Table 10-3 she usually uses name in parenthesis ▯ Pg. 275 figure 10-16 ▯ Pg. 276 Evidence for chemiosmotic model 7 subtitles underneath this ▯ something about maximum theoretical yield ▯ ▯ photosynthesis consists of light reactions Calvin cycle- light independent reaction ▯ light reactions convert light energy to chemical energy noncyclic photophosphorylation- produces ATP and NADPH cyclic photophosphorylation produces ATP and involves photosystem 1 ▯ Goes In: light energy, ADP Pi (phosphate), NADP+, H2o ▯ Goes Out: ATP NADPH O2 ▯ ▯ Calvin cycle – uses the energy produced by the light reactions to make sugars ▯ In: CO2, ATP, NADH ▯ Out: sugars, ADP Pi (phosphate), NADP+ ▯ ▯ Ribulose bisphosphate carboxylate oxygenase (RUBISCO) is the enzyme responsible for adding carbon dioxide which begins the Calvin cycle ▯ ▯ Photorespiration- when it reacts with oxygen instead of CO2 ▯ ▯ C3 plants (everyday ordinary plants) ▯ C4 and CAM plants are capable of reducing photorespiration ▯ C4- separate the Calvin cycle from O2 in the atmosphere spatially ▯ CAM- separate the Calvin cycle from O2 temporally (in time) ▯ ▯ Succulents (like cacti) are CAM plants ▯ ▯ Figure 11-17 pg. 319 ▯ ▯ Chapter 12 Endomembrane system ▯ ▯ Pg. 325 figure 12-1 ▯ ▯ Transport vesicle takes something into cell ▯ Secretory vesicle is taking something out of the cell ▯ Retention tag ▯ Retrieval tag ▯ Mano6 phosphate tag ▯ Constitutive secretion-continually being secreted; not turned on or off ▯ Clathrin ▯ LDL- bad cholesterol ▯ Ligand- anything that binds ▯ Lysosomes ▯ Peroxisomes- not part of the membrane system ▯ ▯ The endomembrane system is an interconnected system of membranes The endoplasmic reticulum, lysosomes, endosomes, and golgi apparatus ▯ ER Cisternae- sacs that make up the ER ▯ Lumen- interior opening ▯ Rough ER-has ribosomes on the cytostolic side of the membrane ▯ Transitional elements are important in forming transition vesicles that move from the ER to the golgi apparatus ▯ ▯ Microsomes- are sealed vesicles formed from broken ER ▯ ▯ RER makes proteins processes proteins; ex. may add carbohydrate groups to make glycoproteins; participates in protein folding and removes misfolded proteins. Has enezymes that help in forming protein structure ▯ ▯ Er- associated degradation- the process by which proteins that are not properly assembled or folded are exported for degradation ▯ ▯ SER Makes membrane components drug detoxification carbohydrate metabolism (breaking down of glycogen) calcium storage steroid biosynthesis sarcoplasmic reticulum- specialized smooth endoplasmic reticulum that stores calcium in muscle cells golgi apparatus- has cisternae forming golgi stacks Cis side of the golgi apparatus faces the ER (known as cis Golgi network CGN) Trans side of the golgi apparatus- side that faces outside of cell (trans Golgi network TGN) Medial cisternae- form the middle Stationary cisternae model- says that materials move through stationary cisternae Cisternai maturation model- cisternae move from one side to the other Anterograde transport- transport from ER to Golgi to outside of cell Retrograde transport- opposite direction ER and Golgi are both involved in glycosylation Materials are labeled so they get to the right place and stay Signal tags- general tags used to localize something (ex. sort amino acid sequences. Oligosaccharide side chains, hydrophobic domains, etc.) Lipids are generally tagged with phosphate groups and other things Retention tags keep something where it is Retrieval tags return something Late endosomes are formed from early endosomes Early endosomes are formed from vesicles from the plasma membrane and from the trans golgi network TGN As an early endosome matures into a late endosome, the pH decreases Constitutive secretion- secretion that is continuous and independent of specific signals; always secreted Regulated secretion- secretion that must be stimulated by some signals Exocytosis- the steps are summarized in figure on pg 342 increases in calcium concentration appear to trigger exocytosis polarized secretion- where secretion occurs on a specific side or specific part of a cell ▯ endocytosis an endocytic vesicle is formed ▯ phagocytosis- ingesting relatively large particle ▯ pinocytosis- ingesting a smaller particle of liquids ▯ receptor-mediated endocytosis ▯ ▯ ligands bing to receptors; they move to a coated pit ▯ clathrin is often involved ▯ coated vesicles are produced ▯ ▯ vesicles formed through receptor mediated endocytosis are uncoated and then fuse with early endosomes ▯ ▯ in some cases the endosome may move to the plasma membrane and release their content through exocytosis. This is called transcytosis ▯ ▯ fluid phase endocytosis ▯ ▯ coat protinss found in coated vesicles clathrin COPI COPII Caveolin ▯ Lysosomes- relatively acidic and contain acid hydrolases which aid in digestion ▯ ▯ Lysosomal enzymes are made in RER and transported to golgi. They are trasported to endosomes in transport vesicles ▯ ▯ Early endosomes develop fro transport vesicles and endocytic vesicles that may fuse ▯ ▯ Early endosomes mature into late endosomes which have acid hydrolases but are not involved in digestive activity ▯ The environment is made more acidic activating the enzymes and the late endosome becomes a lysosome ▯ ▯ ATP dependent proton pumps may pump H+ to make the lumen more acidic or the late endosome may fuse with an existing lysosome ▯ ▯ Heterphagic lysosomes contain substances from inside and outside of the cell ▯ Autophagic lysosomes contain substances from within the cell ▯ ▯ Autophagy ▯ Macrophagy- where an organelles or other large structure becomes engulfed in membrane from ER ▯ Microphagy- the formation of a much smaller autophagic vesicle ▯ ▯ Extracellular digestion can alos be accomplished by lysosmomes releaseing digestive enzymes outside of the cell ▯ ▯ Plants may have acidic vaculose that are involved n digestion (vacuoles also used for storage, pumping water, etc) ▯ ▯ Peroxisomes have single membranes and are not part fo the membrane system. They rare involved in peroxide metabolism some are involved in other processes (glyoxylate cycle, breakdown of fatty acids) ▯ Signal Transduction (how the nervous system works and the endocrine system) Nervous system is used for instantaneous things Endocrine can be used for relatively quick responses but is also involved in slower responses (growth hormone) ▯ Two major types of nervous tissue cells: neurons and glial cells Neurons actually control impulses Glial cells help ▯ Neurons Dendrite, cell body (soma), myelin sheath (waxy covering), nodes of Ranvier (gaps in between), synaptic boutons Be able to diagram neurons Many different types of neurons In peripheral myelin sheath is produced by Schwan cells ▯ Resting membrane potential is the potential you have when there’s an excess of anions in the cell The Vm (membrane potential) is maintained by the balance of ion concentrations on both sides of the membrane K+ Is pumped in and NA+ is pumped out by the sodium potassium pump Some K+ and N+ leaks across the membrane as well When K+ leaks across, it leaves negatively charged molecules ▯ Ion channels exist in several forms Voltage-gated ion channels- stimulated by voltage Ligan-gated ion channels- stimulated by binding of something ▯ Patch clamping You hold constant the charge on the membrane You can do a variety of things to manipulate the membrane ▯ Action potential Once depolarization brings the membrane to a threshold potential, it triggers an action potential Figure pg 376 Studied in squid because they have giant axons Na+ channels open and it rushes into the cell causing depolarization Then the sodium channels close and K+ channels open K+ rushes out of the cell causing repolarization and then hyperpolarization Then all channels close and the resting membrane potential is restored ▯ There is an absolute refractory period when you cant trigger another action potential then a relative refractory period in which triggering an action potential is difficult Action potentials are all or none so you just get a standard You cant make one action potential greater you have to have multiple spaced action potentials ▯ Myelin sheaths allow extremely rapid salutatory (skipping) transmission of the impulse. Oligodendrites form myelin sheaths in the central nervous and Schwann cells form myelin sheaths in the peripheral nervous system. CNS- brain and spinal cord Peripheral- everything else ▯ Propigated action potentials travel rapidly (almost instantaneous) without degradation (don’t get smaller) Amount of depolarization is same at beginning and end ▯ Synaptic transmission Electrical synapses have gap junctions connecting the presynaptic and postsynaptic cells ▯ Chemical synapses use neurotransmitters An action potential reaches the presynaptic boutons. Calcium enters through voltage gated channels triggering the release of neurotransmitters through exocytosis The neurotransmitters bind to receptors on the post synaptic membrane. The may have an inhibitory or excitatory affect. If enough neurotransmitters bind they can trigger an action potential in the postsynaptic neuron ▯ The neurotransmitters are either degraded or taken up Selective serotonin reuptake inhibitors (SSRI’s) Inhibit reuptake and affectively increases neurotransmitter concentration We don’t entirely understand what happens with these ▯ Receptors- something that’s capable of binding a ligand ▯ Signal transduction- converting a signal form one form to another ▯ Second messenger- molecule within a cell involved in signal transduction, carries a message from a molecule that has bound to a receptor ▯ Steroid hormones- generally cross the membrane and act directly ▯ Other types of hormones bind to receptors Are made of lipids that’s why they get through easily ▯ Agonists- activate the receptor to which they bind ▯ Antagonists- inhibit the receptor Endocrine hormones- travel throughout the body and influence cells with the appropriate receptors Go into blood stream, released by endocrine glands, bind to only cells with the receptor ▯ Autocrine signals- act on the cell that produces them ▯ Paracrine signals- act over a short distance ▯ Juxtacrine signals- acts on cells that are in contact ▯ ▯ Table 14.1 pg. 399 shows important functions regulated by cAMP cAMP is an extremely important second messenger molecule ▯ G protein (396)- ▯ ▯ Changes in calcium concentration are often associated with signaling Increases in calcium concentration can be accomplished by opening calcium channels (allowing calcium into the cell) or by releasing stored calcium (e.g. from the sarcoplasmic reticulum) ▯ ▯ Pg 407 examples of growth factors ▯ Types of hormones pg. 415 ▯ Know exactly how the action potential takes place and be able to read that figure ▯ ▯ Cytoskeleton Prokaryotic cells have proteins that act similarly to cytoskeletal proteins in eukaryotic cells MreB protein (actin like) FtsZ (tubulin like) Crescentin (involved in cell shape) ▯ We will focus on the eukaryotic cytoskeleton ▯ KNOW table 15.1 pg. 423 ▯ She gives a list of characteristics of functions from everything in this table except the diameter just know relative size (which is larger) and you have to be able to say if it’s a microtubule or microfilament etc. Know functions, polarity (dynamic), etc. Microtubules Microfilaments Intermediate filaments Microtubules- A-tubulin, B-tubulin are the main monomers that make up the microtubules Protofilaments of A-tubulin and B-tubulin are arranged in a circular structure with a hollow center. It is common to have 13 protofilaments Cytoplasmic microtubules- have a variety of functions within the cytoplasm. They are involved in axon structure and strength. Form mitotic spindles and move and positions organelles etc. Axonemal microtubules- are highly organized to form structures like cilia and flagella Microtubule assembly involves the formation of A-tubulin and B-tubulin heterodimers. These association into oligomers (a collection of these) during nucleation New tubulin monomers are added at both ends to lengthen the microtubules. The plus end grows more rapidly the minus end grows more slowly. Critical concentration- the concentration at which MT assembly is exactly balanced with disassembly This is called Dynamic instability Treadmilling- is that adding and removing thing mentioned above A variety of drugs can affect microtubules Be familiar with these drugs Ex. Taxol (don’t have to know how the work just that they inhibit microtubules and can be studied in cancer) ▯ GTp- helps to stabilize microtubule caps CTp cap The dynamic instability model proposes that there are two populations of microtubules One population grows in length at the plus end while the other population shrinks from depolimerization The population that grows is distinguished by GTP caps The population that shrinks has GDP instead Microtubule organizing centers (MTOCs) help microtubules to be organized microtubules often originate from MTOCs the centrosome is an MTOC found in animal cells associated with two centrioles that appear to help organize the spindle apparatus (although the spindle can still work without them) ▯ ▯ microtubule associated proteins (MAPs) help to stabilize and bundle microtubules ▯ other proteins can have the opposite affect and can destabilize microtubules ▯ ▯ know basic structure, made up of heterodimers, form tubular structure, can be organized into MTOC’s ▯ ▯ microfilaments G-actin is globular actin G-actin monomers polymerize (join together to make a chain) into F- actin microfilaments F-actin microfilaments have plus and minus ends. The plus ends grow more rapidly. The growing ends tend to have ATP-F actin while the bulk of the microfilament has ADP-F-actin ▯ Actin filaments can be regulated and organized ▯ Some proteins favor polymerization ▯ Some proteins (capping proteins) stabilized the filaments (capZ) ▯ Some proteins crosslink the filaments ▯ Some proteins sever the filaments ▯ Other proteins bundle the filaments together ▯ Filaments may also be linked to membranes ▯ ▯ Microvilli contain actin bundles (be familiar) ▯ ▯ Intermediate filaments are very varied ▯ They differ in different cells ▯ Figure 15-4 ▯ They are especially important in providing mechanical strength and elasticity ▯ ▯ Linker proteins between microtubules, microfilaments, and intermediate filaments help to connect their functions ▯ ▯ Cellular movement Microtubule associated motor proteins Table 16-1 Kinesins and dyneins Cytoplasmic dynein- moves materials towards the minus ends of the microtubules Axonemal dynin is found in cilia and flagella Kinesins generally move materials towards the plus ends of microtubules ▯ ▯ These microtubule associated proteins require ATP ▯ Materials can be moved along microtubule tracks (e.g. organelles can be moved, fast axonal transport, etc.) ▯ Know figure 16-5 ▯ Cilia and flagella Sliding microtubule model helps to explain the movement of cilia and flagella The basic structure is: basal body, transition zone, axoneme KNOW THE STRUCTURES Microfilaments Muscle contractions Actin and the protein myosin are critical for muscle contraction Muscle cells are also called muscle fibers Skeletal muscle cells are multinucleate Be very familiar the SARCOMERE STRUCTURE Sarcomere- the contractile unit of a muscle cell BE FAMILIAR with figure 16-10,12,15,16,and 18 16-2 is also good http://www.wiley.com/college/pratt/0471393878/student/animations/actin basic steps of contraction: an impulse reaches the end of an axon (terminal bouton of an axon) at a motor end plate (adjacent to a muscle cell) the impulse triggers the release of a neurotransmitter, acetylcholine into the synaptic cleft the neurotransmitter binds to receptors on the muscle plasma membrane, triggering depolarization of the muscle cell the depolarization spreads rapidly throughout the cell because of the system of T tubules (infoldings of membrane that go deep into the cell) the depolarization triggers the release of calcium from the sarcoplasmic reticulum calcium binds to troponin causing tropomyosin to move and expose the myosin binding sites on actin once the contraction is finished CA2+ ATPases pump calcium back into the sarcoplasmic reticulum to stop contractions see page 465 for a detailed description of what happens within the sarcomere Cardiac muscle One nucleus per cell unlike skeletal muscle which is multinucleate Has a branched appearance Cells are joined by intercalated discs There are many gap junctions between cells ▯ Differences from skeletal muscle (from page 468) Use of fatty acids from adipocytes instead of blood glucose for energy Each cell has one nucleus instead of being multinucleate Contraction is stimulated from within the heart rather than from an external signal Sinoatrial node is known as the pacemaker and triggers the heartbeat Atrioventricular node (AV node) helps to spread the impulse ▯ Smooth muscle Each cell has one nucleus Has a smooth appearance instead of a striated appearance Dense bodies have a similar function to Z lines Calcium for contraction comes from outside of the cell The process that causes contraction is slower than the process in skeletal muscle ▯ See figure 16.24 ▯ ▯ Non-muscle motility Filopodia Lamellipodia Amoeboid movement (gel-sol transition) Cytosplasmic streaming Cyclosis (circular flow of cell contracts around the central vacuole) ▯ Chemotaxis- directed movement in response to a chemical signal Positive chemotaxis- moving towards a chemical signal Negative chemotaxis- moving away from a chemical signal Chemo attractants Chemo repellants ▯ ▯ Chapter 17 ▯ Figure 17.7 ▯ Table 17.1 ▯ Table 17.2 ▯ ▯ Cell-cell adhesion receptors ▯ Immunoglobulin superfamily proteins ▯ Cadherins ▯ Selectins ▯ ▯ Hemophilic interactions- between like molecules on different cells ▯ Heterophilic interactions- interaction between different molecules on different cells ▯ ▯ Cell-cell recognition- often mediated by carbohydrate groups ▯ Lectins- carbohydrate binding proteins are important in that ▯ ▯ Human erythrocytes (RBC) have carbohydrates on the surface attached to glycolipids in the membrane; distinguish different blood types ▯ ▯ Cell-cell junctions Adhesive junctions- link cells together Tight junctions- connect cells to form seals Gap junctions- allow communication between cells ▯ Adhesive junctions include adherens junctions, desmosomes, etc. ▯ Focal adhesions and hemidesmosomes are also examples ▯ ▯ Know the differences in functions, basic differences in structures and main components of these ▯ ▯ Also be familiar with (Table 17.2) the main components of extracellular matrix in animals and of the cell wall in plants ▯ Know how the cell wall is formed pg. 499 ▯ Role of lignins too (middle lamella, primary cell wall, secondary cell wall, lignins, etc.) ▯ ▯ II DNA. ▯ DNA is transcribed to RNA in the nucleus and messenger RNA is translated to protein in the cytoplasm ▯ ▯ DNA is generally found as a double helix ▯ Two strands are held together by hydrogen bonds between nitrogen bases ▯ Complementary base pairing rules A with T (U in RNA) C with G ▯ Each nucleotide of DNA contains A phosphate group A deoxyribose sugar (spell) Nitrogenous base ▯ Denaturation- separating the two strands of DNA ▯ Renaturation- causing two strands to come back together ▯ ▯ Genome- entire genetic makeup of an organism ▯ ▯ Restriction enzymes (restriction endonucleases) are used to cut DNA at specific locations ▯ ▯ Electrophoresis separates DNA molecules based on size ▯ DNA moves in an electrical field because of the negative charge on phosphate ▯ It moves toward the positive electrode ▯ Larger pieces move more slowly and travel shorter distances than smaller pieces ▯ Autoradiography and other methods are used to identify the DNA of interest ▯ ▯ Southern blotting- paper (nitrocellulose) is placed against the gel to blot the DNA then the paper is exposed to probes to identify the sequences of interest ▯ Northern blotting- same using RNA ▯ Western blotting- same using proteins ▯ ▯ Restriction mapping- cutting DNA with restriction enzymes and comparing the fragments to make maps ▯ ▯ DNA sequencing Working out the sequence of bases ▯ PCR (polymerase chain reaction) used to make many copies of DNA rapidly ▯ Sanger sequencing ▯ ▯ Bioinformatics using computer tools and analysis in order to get information from data ▯ ▯ Blast- basic local alignment search tool- used to run DNA and find matches ▯ ▯ Polymorphisms- differences in a sequence; helps identify per person ▯ Include single base differences Deletions Additions Insertions Microsatellites (tandem repeats) a repeating sequence AAA AAA AAA Mini satellites – larger tandem repeats Complex haplotypes- sequences that vary in some type of pattern Single nucleotide polymorphisms- Telomeres- sequences on the end of eukaryotic chromosomes Protect DNA from getting shorter ▯ ▯ Plasmids- small circular pieces of DNA; do not contain main essential genes for functioning ▯ ▯ Chromatin- the diffuse mass of chromosomes and protein found within the nucleus of a eukaryotic cell ▯ Chromosomes are DNA; in eukaryotes its tightly wound around proteins ▯ ▯ Heterochromatin – tightly packed DNA not expressed ▯ Constituative heterochromatin- always tightly packed; not expressed ▯ Facultative heterochromatin- tightly packed but can be converted to euchromatin ▯ Euchromatin- loosely packed and can be expressed ▯ ▯ Mitochondria and chloroplasts have their own DNA ▯ ▯ Nucleus ▯ Nuclear membrane or nuclear envelope surrounds nucleus ▯ Nuclear pores are openings in the membrane through which materials pass ▯ Nucleoplasm- material within nucleus ▯ Nucleolus- location in nucleus that stains darkly and is involved in ribosome formation ▯ ▯ ▯ ▯ ▯ ▯ ▯ ▯ Cell cycle ▯ ▯ Cell cycle includes ▯ G1 (growth) ▯ S (synthesis; the DNA is replicated ▯ G2 (preparation for mitosis) ▯ M (mitosis) ▯ ▯ Cells that stay in G1 rather than dividing are said to be in the G0 stage ▯ Stages G1 S and G2 are called interphase (not a stage of mitosis During the S phase, DNA replication occurs DNA replication is semiconservative; each daughter strand has one parental strand and one entirely new strand DNA replication occurs through complementary base pairing Adenine pairs with T and C pairs with G RNA uses Uracil instead of thymine In order for replication to occur, licensing must occur first. In licensing proteins called MCM proteins bind to the replication origin (along with ORC and other proteins) after replication beings the MCM proteins are removed. This prevents the DNA from being replicated again immediately DNA replication involves the following proteins among others Helicases- help to unwind double helix Topoisomerases help to relive super coiling Primases add small RNA primers DNA polymerases add DNA nucleotides Ligases join fragments together Single strand binding proteins help to hold open the double helix ▯ DNA polymerases have restrictions They can only add to a single strand Or to an existing strand Or in a 5’ to 3’ direction ▯ ▯ Steps of DNA replication A replication bubble forms providing single strands Helicases help to unwind the double helix at the forks of the
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