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Date Created: 07/03/14
BIOL 1107 Test 2 Study Guide Today in class Dr Story told us what to expect on the test 70 questions all MC except for one short essay short essay will be on ZScheme we will be given a picture study the worksheets the main things to know from ch 10 are zscheme and calvin cycle Questions she asked us in class today as review What are the products for 1 turn of the Kreb s cycle 1 ATP 2 C02 3 NADH and 1 FADH2 What about 2 turns 2 ATP 4 C02 6 NADH and 1 FADH2 How many CO2 are needed to produce 1 G3P the 3carbon intermediate 3 How many CO2 are needed to produce a glucose molecule 6 If an endergonic process is occurring what would be the values of each thermodynamic property AG AS and AH AG would be positive AS would be negative and AH would be positive Chapter 7 Membrane Structure and Funtion Intro Basically the plasma membrane is really important It controls traffic into and out of the cell through selective permeability some substances can cross more easily than others this property is fundamental to life 71 cellular membranes are fluid mosaics of lipids and proteins staple ingredients of membranes lipids mostly phospholipids proteins carbohydrates kind of not as important as the other two phospholipids are amphipathic it has both a hydrophilic region and a hydrophobic region fluid mosaic model the membrane is a fluid structure with various proteins either embedded in or on a double layer of phospholipids bilayer Hugh Davson and James Danielli proposed the Sandwich Model 1935 the membrane is coated on both sides with hydrophilic proteins SJ Singer and G Nicolson proposed the fluid mosaic model 1972 membrane proteins protrude from the phospholipid bilayer with their hydrophilic regions protruding the membrane is a mosaic of protein molecules bobbing in a fluid bilayer of phospholipids membranes are primarily held together by hydrophobic interactions which are weaker than covalent bonds because of this most of the lipids and some of the proteins can move laterally phospholipids switch positions with their neighbors about 10 times per second thats really freakin fast phospholipids are fluid until the temperature is low enough to make them settle into a closely packed arrangement this causes them to solidify think bacon grease turning into lard they solidify at a lower temperature the richer they are in phospholipids with unsaturated hydrocarbon tails this is because of the kinks in the tails they cannot pack as closely as saturated tails cholesterol steroid makes the membrane less fluid at higher temperatures by blocking phospholipid movement but it also lowers the temperature required for the membrane to solidify when a membrane solidifies the enzymatic proteins in it can become inactive variations in composition of the cell membrane have been an evolutionary change fish that live in cold water have a lot of unsaturated hydrocarbon tails in their bilayers allowing them to remain fluid there are also some organisms that can change their lipid composition depending on the temperatures proteins are what determine the membrane s functions integral proteins embedded in the interior of the bilayer most are transmembrane proteins which go all the way through peripheral proteins do not penetrate the bilayer at all they are loosely attached to the surface of the membrane often to exposed parts of integral proteins main functions of membrane proteins see pg 129 for pictures transport enzymatic activity signal transduction cellcell recognition intercellularjoining attachment to the cytoskeleton and ECM some proteins help outside agents invade their cell studying these has helped develop HIV treatments cellcell recognition helps sort cells into tissues and organs reject the immune system reject foreign cells cells recognize other cells by binding to molecules often carbohydrates on the surface of the plasma membrane some membrane carbohydrates bind to lipids forming glycolipids most membrane carbohydrates bind to proteins forming glycoproteins the two lipid layers may differ in specific lipid composition both sides of the bilayer don t have to match each protein has directional orientation in the membrane 72 membrane structure results in selective permeability a steady traffic of molecules move across the plasma membrane in both directions because these membranes are selectively permeable only certain substances can cross them and different substances cross at different rates nonpolar molecules are hydrophobic and can dissolve in the lipid bilayer crossing it easily ions and polar molecules which are hydrophilic cannot pass as easily due to the hydrophobic interior of the bilayer transport proteins aid hydrophilic substances in crossing the membrane by helping them avoid contact with the membrane channel proteins provide a hydrophilic tunnel ex aquaporins allow massive amounts of water through the membrane carrier proteins hold onto their substances and change shape to shuttle them across the membrane transport proteins are specific for the substance it moves 73 passive transport is diffusion of a substance across a membrane with no energy investment diffusion is the spontaneous movement of molecules of any substance so that they spread out evenly into the available space the goal is to reach dynamic equilibrium in the absence of other forces a substance will diffuse from where it is more concentrated to where it is less concentrated down the concentration gradient the region along with the density of a chemical substance increases or decreases the diffusion of a substance across a biological membrane is called passive transport osmosis water diffuses across the membrane from the region of lower solute concentration more water to the region of higher solute concentration less water basically water likes to go to places that don t have a lot of it tonicity is the ability of a surrounding solution to cause a cell to gain or lose water for cells without walls animal cells if the cell is immersed in an isotonic environment there is the same amount of stuff outside as there is inside there will be no net movement of water across the plasma membrane if the cell is immersed in a hypertonic environment more solute than is inside the cell the cell will lose water shrivel and die if the cell is immersed in a hypotonic environment less solute than is inside the cell the water will enter the cell faster than it leaves causing it to swell and burst osmoregulation is the control of solute concentrations and water balance by a cell or organism for cells with walls plant cells prokaryotes fungi and some protists when immersed in an hypotonic solution the cell wall helps maintain the cells water balance because it can only swell so much before the wall starts to push back on the surrounding environment at this point the cell is turgid or firm when immersed in a isotonic solution there is no net tendency for the water to come into the cell at this point the cell is flaccid ornot firm when immersed in a hypertonic solution the cell will lose water and shnvel this causes plasmolysis or the plasma membrane pulling away from the wall which leads to wilting and plant death back to transport proteinsfacilitated diffusion is when polar molecules and ions diffuse passively with the help of transport proteins channel proteins that are specifically for ions are called ion channels many of these function as gated channels which open or close in response to a stimulus such as electricity 74 active transport uses energy to move solutes against their gradients facilitated diffusion is passive transport even though it uses proteins because the solute is moving down its concentration gradient active transport type of membrane traffic that pumps solute across a membrane against its gradient requiring work all transport proteins for active transport are carrier proteins sodiumpotassium pumps are a good example of active transport in animal cells there is a much higher concentration of K ions than its surrounding and much lower Na ion concentration the plasma membrane helps maintain the gradient by pumping Na out of the cell and K into the cell ATP can power active transport by transferring its terminal phosphate group to the transport protein causing the protein to change shape three sodium ions are pumped out for every two potassium ions pumped in net transfer of 1 charge from the cytoplasm to the ECM membrane potential the voltage across a membrane cytoplasmic side of the membrane is negative compared to the extracellular side membrane potential favors passive transport of cations postitive into the cell and anions negative out of the cell two forces drive the diffusion of ions across membranes forming the electrochemical gradient chemical force concentration gradient electrical force membrane potential a transport protein that generates voltage across a membrane is called an electrogenic pump in animal cells the sodiumpotassium pump is the major one in plants fungi and bacteria a proton pump is the major one a single ATPpowered pump that transports a specific solute can indirectly drive the active transport of several other solutes in a mechanism called cotransport 75 bulk transport across the plasma membrane occurs by exocytosis and endocytosis large molecules can t move across membranes by diffusion or pumping large molecules such a proteins and polysaccharides as well as larger particles generally cross the membrane in bulk by mechanisms that involve packaging in vesicles exocytosis when the cell expels certain molecules by fusing vesicles with the plasma membrane a transport vesicle that has budded from the Golgi moves along microtubules of the cytoskeleton to the plasma membrane when the vesicle and the membrane come into contact proteins rearrange the lipids of the two bilayers so that they two membranes fuse endocytosis the cell takes in molecules and particulate matter by forming new vesicles from the plasma membrane three types phagocytosis cellular eating pinocytosis cellular drinking receptor mediated endocytosis cellular being merry ligands are any molecule that binds specifically to a receptor site on another molecule pg 139 has diagrams of each Chapter 8 An Introduction to Metabolism Introduction Cells are important and unique and do cool stuff 81 an organism s metabolism transforms matter and energy subject to the laws of thermodynamics metabolism is the totality of an organism s chemical reactions it is an emergent property of life that arises from orderly interactions between molecules metabolic pathways begin with a specific molecule which is then altered in a series of defined steps resulting in a certain product catabolic pathways release energy by breaking down complex molecules ex cellular respiration energy that was stored in the organic molecules becomes available to do work for the cell anabolic pathways consume energy to build complicated molecules energy released from catabolic pathways can be stored and used to drive the reactions of anabolic pathways bioenergetics the study of how energy flows through living organisms energy is the capacity to cause changedo work energy associated with the relative motion of objects is kinetic energy kinetic energy associated with the random movement of atoms or molecules is thermal energy or heat energy that matter possesses because of its location or structure is potential energy the potential energy available for release in a chemical reaction is chemical energy big picture biochemical pathways enable cells to release chemical energy from food and use that energy to power life the study of the energy transformations that occur in a collection of matter is called thermodynamics an isolated system is unable to exchange neither energy nor matter with its surroundings an open system allows for the transfer of energy and matter between the system and its surroundings organisms are open systems first law of thermodynamics energy can be transferred and transformed but it cannot be created or destroyed second law of thermodynamics every energy transfer or transformation increases the entropy of the universe entropy is the measure of disorder or randomness there is an unstoppable trend toward randomization of the universe as a whole a spontaneous process is one that occurs without an input of energy spontaneous processes increase the entropy of the universe the entropy of a particular system such as an organism may actually decrease as long as the total entropy of the universe system surroundings increases 82 the freeenergy change of a reaction tells us whether or not the reaction occurs spontaneously free energy is the portion of a system s energy that can perform work when temperature and pressure are uniform throughout the system as in a living cell equation AG AH TAS AG is the change in free energy AH is the change in the system s enthalpy total energy AS is the change in the systems entropy T is the absolute temperature in Kelvin K C 273 only processes with a negative AG are spontaneous for AG to be negative either AH must be negative or TAS must be positive or both every spontaneous process decreases the system s free energy loss of free energy during the change from the initial state to the final state free energy is a measure of the system s instability higher G means more unstable lower G means more stable a glucose molecule is less stable more likely to break down than the simpler molecules into which it can be split as a reaction goes towards equilibrium the free energy of the mixture of reactants and products decreases systems never spontaneously move away from equilibrium a process is spontaneous and can perform work only when it is moving toward equilibrium an exergonic reaction starts with a net release of free energy AG is negative exergonic reactions are those that occur spontaneously the greater the decrease in free energy the greater the amount of work that can be done remember that the breaking of bonds does not release energyit requires energy an endergonic reaction is one that absorbs free energy from its surroundings AG is positive when a system reaches equilibrium it is at a minimum G value and therefore can do no work so it is dead metabolism as a whole is never at equilibriumthat s what keeps us alive cellular respiration is kept going by the huge free energy difference between glucose and oxygen at the top of the energy hill and carbon dioxide and water at the downhill end 83 ATP powers cellular work by coupling exergonic reactions to endergonic reac ons a cell does 3 main kinds of work chemical work pushing of endergonic reactions transport work pumping of substances across membranes mechanical work beating of cilia contraction of muscles etc energy coupling is the use of an exergonic process to drive an endergonic one the bonds between the phosphate groups of ATP adenosine triphosphate can be broken by hydrolysis a water molecule is added to ATP causing a molecule of inorganic phosphate to leave creating ADP adenosine diphosphate this reaction is exergonic releases energy the release of energy during the hydrolysis of ATP comes from the chemical change to a state of lower free energy phosphorylated intermediate the recipient of a phosphate group which forms a covalent bond the key to coupling exergonic and endergonic reactions is the formation of this which is more reactive than the original unphosphorylated molecule you can regenerate ATP from ADP via phosphorylation the free energy required to phosphorylate ADP comes from the exergonic breakdown reactions in the cell this is an endergonic reaction 84 enzymes speed up metabolic reactions by lowering energy barriers an enzyme is a macromolecule protein that acts as a catalyst a chemical agent that speeds up a reaction without actually being consumed by the reac on the energy required to contort reactant molecules so that the bonds can break is called the activation energy or free energy of activation or EA the bonds have to break in order to change one molecule into another often supplied in the form of thermal energy which is absorbed by the reactant molecules causing them to collide more often and more forcefully when the molecules have absorbed enough energy to break the bonds energy equivalent to EA they are in their transition state after their transition state atoms settle into their new more stable bonding arrangements releasing energy the formation of new bonds releases more energy than was needed to break the old bonds often EA is so high and the transition state is reached so rarely that the reaction won t happen proteins DNA and other complex molecules of the cell have a lot of free energy and can decompose spontaneouslythe laws of thermodynamics favor their breakdown the only reason these molecules persist is that they can t make it over the activation energy hump because the healthy temperature for cells doesn t provide enough thermal energy enzymes catalyze reactions by lowering the EA barrier enabling the reactant molecules to absorb enough energy to reach the transition state even at moderate temperatures a substrate is the reactant on which an enzyme acts the enzyme binds to its substrates forming an enzymesubstrate complex the specificity of an enzyme goes from its shape which is a result of its amino acid sequence the shape of the active site and the shape of its substrate fit together an active site is the region on the surface of any enzyme on which catalysis occurs via the substrate binding to the enzyme not a rigid receptacle for the substrate as the substrate enters the active site the enzyme changes shapeike a hug this is called an induced fit and it makes the active site fit even more tightly around the substrate enzymes can catalyze either forward or reverse reactions this is how enzymes lower EA and speed up the reaction the active site can provide a template on which the substrates can come together the enzyme can stretch the substrate to the form of their transition state the active site can provide a microenvironment that is more conducive to a particular type of reaction than the solution alone would be the active site can participate directly in the chemical reaction enzyme activity is affected by environmental factors like temperature and pH increasing temperature will speed up enzymatic activity up to a certain point above this point the enzyme denatures it s a protein and loses func on there is also an optimal pH for enzyme activity many enzymes require nonprotein helpers for catalytic activity called cofactors an organic cofactor molecule is called a coenzyme certain chemicals can inhibit the action of specific enzymes if the inhibitor attaches to the enzyme covalently the inhibition is irreversible competitive inhibitors reduce the productivity of enzymes by blocking substrates from entering active sites it s like a phony substrate noncompetitive inhibitors do not directly compete with substrates for the active site they bind to another part of the enzyme causing it to change shape 85 regulation of enzyme activity helps control metabolism if all of a ce s metabolic pathways were happening at the same time chemical chaos would ensue allosteric regulation is when a protein s function at one site is affected by the binding of a regulatory molecule to another site the entire enzyme goes back and forth between two shapes one catalytically active and the other inactive the binding of an activator to a regulatory site causes the enzyme to take it s active shape the binding of an inhibitor causes the enzyme to take it s inactive shape there s a lot of stuff about ATP that is confusingbasically ATP can be an allosteric inhibitor for enzymes but ADP can be an activator for those same enzymes more specifically if ATP production starts to lag causing a buildup of ADP the ADP will go and activate the enzyme to produce more ATP lftoo much ATP is being produced it will build up and be like whoa enzyme calm down cooperativity is when a substrate molecule binds to an active site on an multisubunit enzyme that triggers a change in shape of the enzyme s subunits increasing catalysis at the other active sites feedback inhibition is when a metabolic pathway is switched off my the inhibitory binding of it s end produce to an enzyme that acts early in the pathway like the whole ATP thing
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