BSCI105 Review Study Guide Exam 2
BSCI105 Review Study Guide Exam 2 BSCI105
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Chapter 7- Membrane Structure and Function Plasma membrane- boundary that separates the living cell from its surroundings - Controls traffic into and out of cell by selective permeability – allows some substances in and others not - Made up of mostly fluid with bilayer of lipids- lipids and proteins, mostly phospholipids, because of the amphipathic structure- has hydrophobic and hydrophilic components - Membrane proteins reside in the phospholipid bilayer with the hydrophilic regions protruding- maximize contact of hydrophilic regions of proteins and phospholipids with water in the cytosol and extracellular fluid, matching up the hydrophobic parts of each- the proteins are embedded into the bilayer - Asymmetrical arrangement of proteins, lipids, and carbohydrates in plasma membrane is determined as membrane is being built by ER and Golgi apparatus Fluidity of Membrane- should be fluid to work properly - Held together by hydrophobic interactions- weak bonds - Lipids can pass each other in the line- like someone pushing through a crowd- super quick- 10 times per second - Rare, but happens when a molecules flips from one side of the bilayer to the other- like a summersault- because hydrophilic must pass hydrophobic - Proteins seem to be immobile attached to cytoskeleton or ECM except for those that are most likely driven by motor proteins along cytoskeletal fibers - Membrane is fluid until temperature decreases and phospholipids solidifies in a closely packed arrangement, depending on types of lipids o Unsaturated hydrocarbons (because of double bonds and kinks) and rich in phospholipids- needs lower temp/harder to solidify - Steroid- wedged into phospholipid, but different effects on the membrane o Fluidity buffer- resists changes in membrane fluidity that can be caused by changes in temperature o at really high temperatures, cholesterol makes membrane less fluid by restraining phospholipid movement- it lowers temperature required for membrane to solidify because it stops the close packing of phospholipids - when membrane solidifies- permeability change and enzymatic proteins in membrane can become inactive if activity requires them to move within membrane, but too fluid, then can’t support protein function. Membrane Proteins and Their Functions - Membrane is a collage of different proteins (like mosaic) that is clustered in grouped embedded into the fluid matrix of lipid bilayer- proteins determine the membranes functions - Integral Proteins- penetrate hydrophobic interior of lipid bilayer o most are transmembrane proteins- span the membrane, but some just span some of the hydrophobic interior. Consists of nonpolar amino acids (clearly) with alpha helices. o Some have hydrophilic channel through the center to allow hydrophilic parts to pass - Peripheral Proteins- additions loosely bounded to surface of membrane, not embedded into the bilayer. o Usually exposed to integral proteins - Inside (cytoplasmic side)- some proteins are held by attachment to cytoskeleton or ECM- giving plasma membrane strong framework - Protein Functions on plasma membrane- transport- channel, or changes shape to help move substance along (ATP sometimes) o Enzymatic activity- active site is exposed and acts like an enzyme, sometimes work as a team with others with same goal o Signal transduction- binds with a substance which can cause the protein to change shape and relay the message inside the cell o Cell cell recognition- acts as an identification tag that helps other membranes of other cells recognize it and binds to cell for short time Cells recognize other cells by binding to molecules (often with carbohydrates-short chains) on extracellular surface of plasma membrane Carbohydrates bounded to lipids form glycolipids (glycol=presence of carbohydrates), but most are covalently bonded to proteins forming glycoproteins o Intercellular joining- help bind cells together such tight or gap junctions (long time) o Attachment to cytoskeleton and ECM- microfilaments or other parts of cytoskeleton may be noncovalently bound to membrane proteins, a function that helps maintain cell shape and stabilizes location of membrane proteins. Proteins that can bind to ECM molecules can coordinate extracellular and intracellular changes. Permeability of Lipid Bilayer- nonpolar molecules are hydrophobic and can dissolve and pass through the lipid bilayer easily, without help of membrane proteins. - Polar/hydrophilic molecules have an issue- because the lipid bilayer only allows certain things to go through (selective permeability), so proteins help with that - Transport Proteins- help hydrophilic substances get across the lipid bilayer- specific to the substance it helps get across the bilayer o Some, called channel proteins, have hydrophilic channels that some molecules/ions use as a tunnel through the membrane Aquaporins- tunnels that help millions of water molecules get through the lipid bilayer every second- help in kidneys o Some, called carrier proteins, hold onto substance and change the shape that helps them shuttle them across the membrane Passive Transport- diffusion of substance across a membrane with no energy investment - Diffusion- movement of molecules of any substance so that they spread out evenly into the available space because of thermal energy which is caused by motion- no work, spontaneous process. o One side is more concentrated than other, so the pores would be large enough for the solute to pass through until there is equal concentrations (equilibrium) of solute and solvent throughout the solution- substance goes from more concentrated to less concentrated, or diffuse down own electrochemical concentration gradient- region along which the density of chemical substance increases or decreases, represents potential energy and drives diffusion o Facilitated diffusion- speeds transport of solute- transport proteins help bring substances down concentration gradient Ion channels- channel proteins that transport ions, some function as gated channels- open and close in response to stimuli (some it is electrical, or when substance other than the one that is being transported binds to the channel) Carrier proteins undergo subtle change in shape that somehow translocate the solute binding site across the membrane- change can be triggered by binding/release of transported molecule. Cystinuria- disease that is caused because of absence of carrier protein - Osmosis- diffusion of water across a selectively permeable membrane o Movement of water across cell membrane, and balance of water between cell and environment are crucial to organisms Tonicity- the ability of a surrounding solution to cause a cell to gain or lose water- depends concentration of solutes that cannot cross the membrane relative to that inside the cell Higher concentration of nonpenetrating solutes in the surrounding solution, then water will tend to leave the cell and vice versa Cell with no cell wall is in isotonic environment, then no net movement of water across plasma membrane- water diffuses at same rate across the membrane. Solution that is hypertonic to cell- more solutes outside- so cell will lose water, shrivel up and die. Hypotonic- less solute in solution than inside- too much water enters the cell and cell lyse/bursts. o Osmoregulation- control of solute concentrations and water balance, organisms that lack cell walls need it- certain vacuole or something to help control/adapt o With cell walls, when the cell is placed in a hypotonic solution, the cell will swell and then the walls will exert pressure on cell- turgor pressure- that opposed water uptake. The cell is turgid- very firm- which is healthy for plant cells. However, in isotonic solutions, the plant cells become flaccid- weak- because there is no net tendency for water to enter. In hypertonic solution, the cell will still shrink since water will go out of cell. As it shrivels, the plasma membrane pulls away from the wall- plasmolysis Active Transport- uses energy to move solutes against their gradients, bring solutes to more concentrated- all carrier proteins - Enables cell to maintain internal concentrations of small solutes that differ from concentrations in its environment o An animal cell ahsd much higher concentration of potassium ions and lower concentration of sodium, and plasma membrane helps maintain this by pumping sodium out and potassium in. - ATP supplies energy for most active transport- transfers terminal phosphate group to transport protein, which will change the protein’s shape and allow a different substance to be transported- like the sodium potassium pump- pumps three sodium ions out and two potassium ions in- net transfer of one positive charge to extracellular fluid- stores energy as voltage. - Membrane potential- voltage across membrane- ranges from -50 to 200 mV. Cytoplasmic side’s charge is negative relative to extracellular side because of unequal distributions of anions and cations on the two sides. o acts like a battery, energy source that affects traffic of all charged substances across the membrane. o Electrochemical gradient- Cell likes passive transport of cations into cell and anions out of cell; therefore, two forces drive diffusion of ions across membrane- chemical force (ion’s concentration gradient) and electrical force (effect of the membrane potential on ion’s movement) Electrogenic pump- transport protein that generates voltage across membrane- sodium potassium pump is main Help store energy that can be tapped for cellular work Proton pump- main in plants, fungi, and bacteria- transports protons out of cell Important for ATP synthesis during cellular respiration Cotransport- coupled transport by membrane protein - A single ATP-powered pump that transports a specific solute can indirectly drive the active transport of several other solutes - Substance that has been pumped across membrane can do work as it diffuses back- one thing causes the other to happen Bulk Transport- too big for diffusion or transports - Exocytosis- cell secretes molecules by fusion of vesicles with plasma membrane o Transport vesicle from golgi moves along microtubules of cytoskeleton to plasma membrane and then when they are in contact, specific proteins rearrange the lipid molecules of two bilayers so two membranes fuse and content of vesicles spill out of cell while vesicle becomes part of membrane. (insulin from pancreas, neurotransmitters) - Endocytosis- cell takes in molecules and particulate matter and form new vesicles o Small part of membrane sinks inwards and forms a pocket and pinches in forming a vesicle with content that was outside. o Phagocytosis- cell engulfs a particle by wrapping pseudopodia around it and packing it in a food vacuole and then is digested by lysosome o Pinocytosis- cell gulps droplets of extracellular fluid into tiny vesicles- molecules dissolved in the droplets are needed by cell- not specific to substances it transports o Receptor mediated endocytosis- enables cell to get bulk quantities of specific substance- embedded in membrane are prteins with specific receptor sites exposed to extracellular fliud to which ligands (specific substances) bind. Receptor proteins cluster in regions of membrane called coated pits, which are lined on cytoplasmic side by fuzzy layer of coat proteins. Then, each coated pit forms a vesicle contained the ligand molecule- more bound molecules inside vesicle. After ingested material is freed from vesicle, the emptied receptors are recylcled to the plasma membrane by same vessicel Chapter 8- Introduction to Metabolism Cellular Respiration- drives cellular economy by getting the energy stored in sugars and other fuels Metabolism- totality of organism’s chemical reactions - Arises from orderly interactions between molecules - Manages the material and energy of cell o Transforms matter and energy Organization of the Chemistry of Life into Metabolic Pathways - Metabolism is like a road map of chemical ractions in a cell, with metabolic pathways- begins with a specific molecules and then it is changed by many steps which then results in a new product. o Each step of the way, the molecule is catalyzed by a specific enzyme o Mechanisms that regulate enzymes balance metabolic supply and demand (like traffic lights) - Catabolic Pathways- break down complex molecules and make simpler ones, so by doing that energy is released (i.e. cellular respiration) - Anabolic Pathways (also known as bio synthetic)- build complex molecules from simple ones, so they need to consume energy (i.e making proteins) o the energy released from catabolic can be used for anabolic (downhill and uphill) Energy- capacity to cause change, ability to rearrange matter o Work- move matter against opposing forces o Life depends on it- cells use it to transform energy from one to another o Kinetic Energy- energy associated with motion o Heat/ Thermal Energy- kinetic energy associated with the random movement of molecules o Potential Energy- energy that matter possess because of location or structure o Chemical Energy- refers to potential energy available for release in a chemical reaction Biochemical pathways (in cellular structures) allow us to release chemical energy from food molecules ad use the energy to power life processes Movement can change certain energy- i.e from kinetic to potential because of height Thermodynamics- study of energy transformations that occur in matter - Open system- energy and matter can be transferred between the system and surroundings- organisms - Isolated system- energy and matter cannot be exchanged between system and surroundings - First law of thermodynamics- energy can be transferred or transformed, but it cannot be created or destroyed (some becomes unavailable to do work)- principle of conservation of energy - System can only put heat to work when there is a temperature difference that results in heat flowing from a warmer location to a cooler one. If temperature is uniform, then only use for heat energy is to make body warmer (like in humans) - Second law of thermodynamics- every energy transfer or transformation increases the entropy of the universe- unstoppable trend to randomness. For a process to occur spontaneously, the must increase the entropy of the universe. o Entropy- measure of disorder/randomness, causes much of the loss of usable energy during an energy transfer. Living systems increase entropy of surroundings- take organized form of energy and replaces it with less ordered forms- when breaking down complex molecules, it releases carbon dioxide and water, which are smaller molecules that possess less chemical energy than the food and then accounted by heat during metabolism. Spontaneous Process- process that occurs without input of energy (spontaneous means energetically favorable. Nonspontaneous Process- process that will only happy if energy is added to the system. Water moves downhill spontaneously, but uphill with an input of energy. Free Energy Change G - Free energy- portion of system’s energy that can perform work when temperature and pressure are uniform throughout the system- during chemical reaction mostly. o G=H-TS o H= change in system’s enthalpy- total energy in system- when negative, that means it gives up enthalpy, so H decreases o S= change in system’s entropy o T= absolute pressure in Kelvin, which is 273+Celcius o Once we know G- we can tell if the process will be spontaneous, which will only happen when G is negative. Either H or TS must be negative, or both, in order to be spontaneous o G= G final stainitial statese less free energy, the system in final state is less likely to change and therefore more stable than it was previously. o Can think of it as measure of instability (tendency to change to more stable state)- unstable= higher G and more stable=lower G o Equilibrium- maximum stability. Chemical equilibrium is when forward and backward reaction occur at same rate, and no net charges in concentration of reactants and products When it goes toward equilibrium, the free energy of reactants and products decrease- free energy increases when it is pushed away from equilibrium. Any change from equilibrium G will be positive and will not be spontaneous because work will have to be input- a process is spontaneous and can perform work only when it is moving toward equilibrium Free Energy Applied to Metabolism - Exergonic Reaction- energy outward- net release of energy o G is negative because it loses free energy o occur spontaneously o magnitude of G for an exergonic reaction represents the maximum amount of work the reaction can perform- greater decrease of free energy, the more work that can be done o cellular respiration- turning glucose and O in2o water and CO 2 - Endergonic Reaction- one that absorbs free energy from surroundings o Essentially stores free energy in molecules (G increases), G is positive o Nonspontaneous o G represents amount of energy needed for reaction to occur Equilibrium and Metabolism - at equilibrium in an isolated system, there is no work. Chemical reactions of metabolism are reversible and would reach equilibrium if they were in isolated system. o A cell that reaches metabolic equilibrium is dead because they can’t do work o Constant flow in and out, so metabolic pathway never reach equilibrium, because it is an open system. - Some reversible reactions are pulled in one direction, making it impossible to reach equilibrium- product does not accumulate, rather it just becomes reactant in next step (it is steps and used in next reaction) o Occurs because there is a huge free energy difference between glucose and oxygen at top of energy hill and bottom of energy hill- cells have to have a constant supply of glucose and O an2 expel waste products in order for metabolic pathways never reach equilibrium and continue with work Cell Does Three Kinds of Work- - Chemical work- endergonic reactions - Transport work- pumping substance across membrane against direction of spontaneous movement - Mechanical work- contraction of muscle cells, cilia beating… Energy Coupling- - Manner in which cell manages energy resources to do work - Use of exergonic process to drive endergonic process o ATP is responsible for mediating and many times it is source of energy that powers cellular work - ATP o Contains ribose sugar, adenine as nitrogenous base, and 3 phosphate groups- bond between phosphate can be broken by hydrolysis, which it then becomes ADP, which is exergonic reaction and releases 7.3 kcal per mole of ATP hydrolyzed. G=- 7.3- under standard conditions, but cells are not in standard conditions, so G in cells is around -13 kcal/mol. o Release of energy in hydrolysis comes from chemical change to a state of lower free energy, not from the breaking of phosphate bond- it releases more energy than most other molecules o When hydrolyzed, release of energy releases heat and cells intake it to perform their work, which helps with endergonic reactions. If G of an endergonic reaction is less than the amount of energy released by ATP (exergonic), then they can be coupled to be a complete exergonic reaction-this usually involves transfer of phosphate from ATP to another molecule (possibly the reactant)- phosphorylated intermediate- one that gets the phosphate, which is usually more reactive/less stable. ATP can lead to change in protein shape and can bind with other molecules (phosphorylated intermediate helps) o We use ATP all the time, and just by adding a P to ADP, it is regenerated- the free energy required to phosphorylate ADP comes from the exergonic breakdown reactions (catabolism) in cell. ATP Cycle- couples cell’s exergonic to exergonic reactions Works really fast Regeneration of ATP from ADP and P is endergonic ATP hydrolysis to ADP and P yields energy which is used for work, then energy from catabolic pathways is used and ADP and P are now ATP. Enzymes - Macromolecule that acts as a catalyst- chemical agent that speeds up a reaction without being consumed by reaction - Has specific locations within cell- has compartments - Reactant molecules must absorb energy to reach the state where bonds can change- once new bonds of product molecules form, energy is released and molecules return to stable shapes with lower energy than contorted state- have to change starting molecule to unstable state for reaction to begin. - Activation Energy E - enArgy required to contort reactant molecules so bonds can break, or initial investment of energy for starting reaction. Amount of energy needed to push reactants to top of hill in order to be able to go down (their goal). o Can be in form of heat- molecules collide more often and making bonds break more easily, but not in organisms, because it can be dangerous since it speeds up all reactions and kills many others - Transition state- when molecules have absorbed enough energy for bonds to break and reactants are in unstable condition- they are activated already. o After, when they are rearranging to new bonds, more energy is being released than E hAd. - Enzyme is used in organisms and lower the E barrAer- allows reactant to absorb less energy to reach the transition state o Will not change G for reaction o Makes it possible for cell to have a dynamic metabolism o Specific for reactions they catalyze, so determine what will happen when - Substrate- reactant enzyme acts one- enzyme binds to substrate at active site (pocket or something similar on face of enzyme) forming enzyme-substrate complex- held there by weak interactions. Then once this happens, enzyme converts reactant to product. o very specific because of the amino acid sequence it is made of- has a compatible fit for substrate o enzyme is not set to one shape in equilibrium with slight differences in free energy for each position o Induced fit- as substrate enters active site, enzyme changes shape because chemical changes occur when it binds to it- bring chemical groups of active site into position that enhance ability to catalyze chemical reaction- interactions of side chains. Enzyme hugs the substrate more this way. o Very small amount of enzyme can have a huge impact in catalytic cycle o Can catalyze either reverse or forward reaction- depending on which direction has negative G. - Mechanisms that lower E - aAtive site provides template on which substrates come together in proper orientation o Active site of enzyme clutches the bound substrate- may stretch molecule toward transition state form so it goes quicker, which stresses and breaks the critical chemical bonds that must break during reaction. o Active site can provide a microenvironment that is favorable to that reaction o Active site can provide covalent bonding between substrate and side chain of enzyme. o The more substrate molecules that are available, the more frequently they access the active sites of the enzyme At some point, the concentration of substrate will be high enough that all enzyme molecules have their active sites engaged. When this happens, the enzyme is called saturated, and the rate is determined by speed at which the active site converts substrate to product. Only way to increase rate then is to add more enzyme. - Activity of enzyme is effected by environment- pH, chemicals, and temperature. o Optimal conditions- conditions under which the specific enzyme works best in o Up to a point- rate of enzyme increases with increasing temperature- because substrates collide with enzyme more, but above that temp, the speed of the enzymatic reaction drops significantly because the thermal energy would disrupt all the bonds that stabilize the stability of the enzyme (then denature) Most human enzymes have optimal temp of 35-40 C Optimal pH of 6-8 in humans usually- pepsin in stomach has pH of 2 - Cofactors- non protein that helps the enzyme catalyze o Can be attached to enzyme o If organic- it is known as coenzyme- vitamins provide this - Enzyme inhibitors- certain chemicals that stop the enzyme from working properly o if it covalently bonds to the enzyme, it is irreversible o some bond to enzyme with weak interactions, it is reversible Competitive Inhibitors- mimic the normal substrate and compete to bind to active site, so it reduces productivity. Can be overcome by increasing concentration of substrate, so it would have a better chance of entering the active site. Noncompetitive Inhibitors- bind to another part of enzyme, which changes enzymes shape, so active site is less effective. - Regulation of Enzyme Helps Control Metabolism o Allosteric Regulation- when a protein’s function at one site is affected by binding of a regulatory molecule to a separate site, which can cause inhibition or stimulation- can work like a noncompetitive inhibitor Chaos would occur if all metabolic pathways worked at the same time, so the enzymes are there to regulate and control it. Constructed from two or more subunits usually (polypeptide chain and own active site) that switch between an active and inactive form Simplest- activating molecule binds to a regulatory/allosteric site, which stabilizes shape of functional active sites, when the inhibitor stabilizes inactive form of enzyme. When subunit binds and changes the shape of one active site, all the other active site’s shape change to that shape. EX- ATP binds to catabolic enzymes- lowering affinity for substrate which inhibits activity. However, ADP is an activator of same enzymes- logical because catabolism generates ATP. Cooperativity- substrate molecule binds to multi-subunit enzyme which trigger shape change in all subunits, which increases activity at other active sites. (ex- hemoglobin, even though it is not an enzyme) Increases response of enzymes to substrate- one substrate primes an enzyme to act on more substrate molecules more readily. Hard to isolate because bind to enzyme at low affinity Very high specificity o Feedback inhibition- metabolic pathway is switched off by inhibitory binding of end product to an enzyme that acts early in pathway (ATP allosterically inhibits an enzyme in an ATP generating pathway) and it saves the cell from producing unnecessary chemicals Chapter 9- Cellular Respiration and Fermentation Catabolic Pathways and Production of ATP- - Cell degrades the complex molecules into simpler ones to use the potential energy in bonds- energy is used as work or heat - Fermentation- catabolic process that degrades sugars or organic fuels without the use of oxygen - Cellular Respiration- includes both of the following o Aerobic respiration- catabolic pathways where oxygen is consumed with other fuels Organic compounds + O yields CO +Water+ Energy 2 2 C6H 12+66O yie2ds 6H O + 2nergy (ATP + heat) Glucose is fuel for cells. Breakdown is exergonic= free change of -686kcal o Anaerobic respiration- makes chemical energy without O - 2 prokaryotes do it Redox Reactions - Transfer of one or more elections fro one reactant to another - Loss of electrons from one= oxidation, addition of electrons to one= reduction o Xe + Y yields X + Ye - X becomes oxidized when Y becomes reduced (more negative) Electron donor= reducing agent and electron acceptor= oxidizing agent Therefore, it always goes together Energy state of electron changes as hydrogen (with electrons) are transferred to oxygen Oxidation of glucose transfers electrons to lower energy state, liberating energy that becomes available for ATP synthesis - Can be in covalent reactions- doesn’t have to involve complete transfer of electrons- just more negative or more positive. - The more electronegative, the more energy you need to for redox reaction to occur o Redox reaction that moves electrons closer to oxygen releases chemical energy that can be put to work Activation energy holds back the electron flood from energy yielding foods to lower energy state energy being released all at once is not conducive for work- so glucose and other organic molecules are broken down by steps- at key steps, electrons are stripped from glucose along with a proton (all together a hydrogen atom), which are then passed to an electron carrier (coenzyme NAD+) - NAD+ - can easily be oxidized (NAD+) or reduced (NADH) making it the perfect carrier. o As an electron acceptor, NAD+ acts as an oxidizing agent. o Traps electrons from glucose and other organic molecules through enzymes of dehydrogenases- which removes a pair of hydrogen atoms (2 e- and 2 protons) from substrate (glucose), which oxidizes it. One proton is released as H ion into surrounding solution and 2 e- and one proton is delivered by the enzyme to NAD+, which then neutralizes it and becomes NADH (which stores some energy to make ATP when electrons fall down energy gradient from NADH to oxygen). The electrons lose very little of their potential energy during this transfer Electron Transport Chain (ETC)- number of molecules (proteins usually) in the inner membrane of mitochondria used to break the fall of electrons into several energy releasing steps. Top is high energy (from NADH) and bottom is low energy (going to O wi2h addition of H to make water). Creates an exergonic reaction of -53 kcal/mol by steps Preview of Cellular Respiration Harvesting of energy from glucose by three metabolic stages (catabolic)- - Glycolysis- in cytosol o Begins the process of breaking down glucose into two pyruvate - Pyruvate oxidation and citric acid cycle o in mitochondria for eukaryotes (cytosol for prokaryotes) o the pyruvate is brought there and is oxidized by Acetyl CoA, which then enters citric acid cycle where glucose is then turned into CO 2represents oxidized fragments of oxidized molecules) o some redox reactions occur- making NAD+ into NADH via dehydrogenases - Oxidative phosphorylation (electron transport chain and chemiosmosis) o Accepts electrons from breakdown of products of first stages and passes them from molecule to next- and at the end the they are combined with molecule O and H2 ions making water o Energy released is stored in mitochondria and is used to make ATP from ADP, which is called oxidative phosphorylation (powered by redox reactions of ETC) o Inner membrane is site of ETC and chemiosmosis in eukaryotes, but in plasma membrane for prokaryotes- processes that together make oxidative phosphorylation- accounts for 90% of ATP synthesis in respiration Glycolysis and citric acid cycle can make ATP through substrate level phosphorylation- enzyme transfers a phosphate group from substrate molecule (organic molecule generated as an intermediate during catabolism of glucose) to ADP, instead of adding inorganic phosphate to ADP like oxidative phosphorylation. - For every glucose molecule made into CO and H 2- cell 2akes up to 32 molecules of ATP (each with 7.3 kcal/mol of free energy), Glycolysis- - In cytosol/cytoplasm - Harvest chemical energy by oxidizing glucose into 2 pyruvates- 6 C is split up into 2 3C sugars, and are oxidized/rearranged to form two pyruvates - Energy investment stage- 2 ADP + P makesi2 ATP, which is used to start reaction - Energy payoff stage- 4 ATP is produced by substrate level phosphorylation and 2NAD+ is reduced to 2NADH by glucose acting as the reducing agent (giving up electrons) - Occurs even when O is 2ot there - Net- glucose yields 2 pyruvate +2H O 2 o 4ATP form- 2ATP used yields 2 ATP o 2 NAD+ +4e- +4H+ yields 2NADH +2H+ Citric Acid Cycle (Krebs Cycle) - In mitochondria - One pyruvate enters the cycle at a time, so double results at end two get cellular respiration of one glucose molecule - Oxidation of pyruvate to acetyl coenzyme A (Acetyl CoA)- before citric acid o Pyruvate’s carboxyl group (COO ) is oxidized and is given off at CO 2 o NAD+ turns into NADH because of the electrons from acetate - (the remains of pyruvate- CH COO 3 o CoA contains sulfur and attaches to acetate forming acetyl CoA, which will give the acetyl group to citric acid cycle and joins with oxaloacetate to form citrate in first step - For each acetyl group- o Pyruvate is broken down to 3 CO (inclu2ing the one from before) o 1 ATP is produced by substrate level phosphorylation (or GTP) o 3 NAD+ is reduced to 3NADH, which is energy also o 1 FAD is reduced to FADH , whi2h is energy also Oxidative Phosphorylation (Chemiosmosis and Electron Transport Chain) - Electron Transport Chain- in inner membrane of mitochondria o NADH and FADH enter2 and goes from protein to proteins and lets out free energy after each drop- the proteins go between reduced and oxidized as they accept and free electrons- reduced when NADH or FADH come 2o them but as they let them go they are oxidized again. (FADH ent2rs at a lower point because it holds less energy.) They let out H+ and form and H+ gradient. o Last electron acceptor of the chain is O whic2 picks up pair of hydrogen ions and forms H O. 2 - Chemiosmosis- turns the free energy into ATP o In the inner membrane of the mitochondria, there are a lot of ATP synthase (enzyme that makes ATP from ADP and P)- works i like reverse ion pump. It uses energy from existing ion gradient to power ATP synthesis- power source for it is the difference in the concentration if H+ in opposite sides of inner mitochondrial membrane- flow of H+ through this enzyme powers ATP generation. It is a rotor motor (spins and makes the product) The H+ has tendency to move back across the membrane by diffusing down its gradient, and the ATP synthase is the only place where they can do so and it uses the exergonic flow of H+ to drive the phosphorylation of ADP. Energy in H+ gradient across membrane couples the redox reactions of ETC to ATP synthesis (the H+ gradient is called proton motor force). o It is an energy coupling mechanism that uses energy stored in the form of an H+ gradient across a membrane to drive cellular work. - Makes between 26-28 ATP - Without pull from O a2 end of oxidative phosphorylation, it would cease. Production of ATP without O 2 - Anaerobic Respiration- ETC is used o It uses other very electronegative molecules in place of O , and 2 then it can build up, which then builds up a proton-motive force to produce ATP and then H S is2produced instead of H O 2 - Fermentation- harvests chemical energy without cellular respiration o Extension of glycolysis because it generates little ATP without oxygen, rather it uses substrate level phosphorylation Must be sufficient supply of NAD+ to accept the electrons during the oxidation step of glycolysis, otherwise it would deplete because there would be no oxidizing agent Transfer electrons from NADH to pyruvate, instead of transferring electrons to ETC o Alcohol Fermentation- pyruvate converted to ethanol in two steps Releases carbon dioxide from pyruvate, which is converted to 2C compound acetaldehyde That is then reduced by NADH to ethanol, which generates supply of NAD+ needed for glycolysis o Lactic Acid Fermentation- pyruvate is reduced directly by NADH to form lactate, with no release of CO 2 Muscle cells make ATP through this when O is sca2ce Excess lactate goes into liver where it is converted back to pyruvate o Only 2 molecules of ATP are produced (just like glycolysis) - Obligate anaerobes- only fermentation of anaerobic respiration, can’t survive with O 2 - Facultative anaerobes- can make enough ATP to survive on just fermentation - Pyruvate is needed in all processes Glycolysis and Citric acid cycle are major intersections of the cell’s catabolic and anabolic pathways. - Catabolic- breaks down and uses for energy - Anabolic- helps with molecules structure- not everything is used for energy, and comsume ATP o Helps convert some kinds of molecules to others that we need Intermiediate compounded generated by glycolysis- Dihydroxyscetone phosphate can be converted to one of the major precursors of fats- if we eat too much than diet can hold, then we store it as fat Feedback really helps with cellular respiration - The anabolic pathways that creates certain things will be switched off if there is too much of it. o The end product of anabolic pathway inhibits the enzyme that catalyzes an earlier step in the pathway o Catabolism as well- if cell is working hard and ATP concentrations begins to drop, respiration speeds up. When there is plenty of ATP, respiration slows down, allowing the organic molecule to focus on the other functions Phosphofructokinase is considered a peacemaker because it is the enzyme that catalyzes the third step in glycolysis, which commits the substrate to finishing the the glycolytic pathway- can speed up or slow down based on the feedback It is an allosteric enzyme with receptor sites for inhibitors or activators- inhibited by ATP, but activated by AMP, which is derived from ADP. Becomes active when ATP is being converted to ADP faster than the synthesis of ATP. Also inhibited by citrate (first step in citric acid cycle) Chapter 10- Photosynthesis Preview- - Photosynthesis in a nutshell- chloroplasts of plants capture light energy and convert it to chemical energy that is stored in sugar and other organic molecules. – - Nourishes entire world o Organism gets organic compound it uses for energy and carbon skeleton by one of 2 ways Autotrophs- self feeders- sustain themselves without eating other things that are derived from other living things, but can be a source for others. Produce their organic molecules from CO and 2ther raw inorganic materials from the environment Plants are because they just get water and nutrients from the soil and CO f2om air- specifically photoautotrophs because they use light also to synthesize organic molecules Heterotrophs- get organic compounds from other organisms; consumers Animals eat other living things Dependent on photoautotrophs for food and O 2 (byproduct of photosynthesis) Photosynthesis probably originated from bacteria’s molecules in plasma membrane, which is now known as a chloroplast in a eukaryotic cell. Chloroplasts- site of photosynthesis - Make the plant green from chlorophyll (in the thylakoid) and found mostly in mesophyll- leaf’s interior tissue o CO en2ers leaf and O exits2by pores called stomata, and water is absorbed through veins of leaf - Stroma- liquid in chloroplast, thylakoids- separates the stroma from the thylakoid space within these sacs, each stack of sacs is called granum. - Light energy absorbed by chlorophyll drives the synthesis of the organic molecules Process of Photosynthesis- - 6CO +212H O +2light energy yields C H O + 66 12 6 2+ 6H 2 - Opposite of cellular respiration - O given off from plants is derived from H O, not CO - chloroplast splits 2 2 2 the water into H and oxygen Redox Reaction- - 6CO (2xidizing agent) becomes reduced into C H O 6 12 6 - 6H 2 (reducing agent) is oxidized to 6O 2 - Electrons increase potential energy as they move from water to sugar- it requires energy, which means it is endergonic, and this energy is provided through light Preview of Photosynthesis - It is two processes- light reactions (photo part) and Calvin cycle (synthesis part) - Light reactions- water is split, providing H ions and giving of O as a 2y- product. Light absorbed by chlorophyll causes transfer of electrons and H ions to NADP+ (acceptor- extra phosphate in this compared to NAD+). Use solar power to reduce NADP+ to NADPH by adding a pair of electrons with H+. generate ATP by photophosphorylation (adding a P to ADP)- light energy is now converted to chemical energy in form of NADPH and ATP o Occurs in thylakoids o On outside of thylakoids, NADP+ and ADP pick up electrons and phosphate, and then NADPH and ATP are released into stroma - Calvin cycle (can be referred to as dark reaction- don’t need light)- CO 2 from air into organic molecules present in chloroplast (carbon fixation). Reduces fixed carbon to carbohydrate by addition of electrons, and this reducing power is provided by NADPH. The ATP and NADPH is needed for the synthesis to occur. o Occurs in stroma Nature of Sunlight- - Light is electromagnetic energy that travels in waves o Distance between the two crests is called wavelength (from less than a nm to more than a km) and the entire range is known as electromagnetic spectrum o Visible light- between 380nm and 750 nm- can be recognized o Photons- discrete particles in light, the shorter the wavelength, the greater energy of each photon - Pigment- substances that absorb visible light and each absorb different wavelength o If it absorbs all colors, it appears black. If it reflects all colors, it appears white. o The color you see is reflected back, while the pigment absorbs the shorter wavelengths o Light can perform work in chloroplasts only if it is absorbed there What happens when chlorophyll and other pigments absorb light? - is elevated to an orbital where it has more potential energy, which went from ground state Colors with absorbed wavelengths disappear, but energy cannot disappear. When a molecule absorbs a photon, one molecules electrons to excited state. (the only photons absorbed are those whose energy is exactly equal to the energy difference between ground and excited state, making each pigment have a unique absorption spectrum) - The electron can’t remain in excited state for long since it is unstable and generally drop right back down to ground state, releasing excess energy as heat/photons. o When photons are given off, there is an afterglow (fluorescent) Photosystem- - A reaction center complex associated with light harvesting complexes, Chlorophyll and other organic molecules are organized into a photosystem, converts light energy into chemical energy - Reaction center complex- organized association of proteins holding a special pair of chlorophyll a molecule. o Contains a molecule capable of accepting electrons and becoming reduced (primary electron acceptor)- pair of chlorophyll a molecules are special because of their environment- able to use energy from light to boost electron to higher energy but also to transfer it to the primary electron acceptor. - Light harvesting complex- various pigment molecules (chlorophyll a, chlorophyll b, carotenoids) bound to proteins o Number and variety of pigment molecules helps photosystem harvest light over bigger surface area and act as antenna for reaction center complex o When pigment molecule absorbs light, the photon is passed along from molecule to molecule until it is passed into reaction center complex. - Transfer of photon from reaction center chlorophyll a pair to primary electron acceptor is first step of light reactions. Excited then primary electron acceptor catches it which happens in structured environment of chloroplast (redox reaction). - Thylakoid is populated by two types of photosystems that cooperate in the light reactions of photosynthesis- photosystem II and photosystem I. o Reaction center of chlorophyll a in PSII is known as P680 because it is best at absorbing light with wavelength of 680. o Chlorophyll at reaction center complex of PSI is known as P700 because it is best at absorbing light with wavelength of 700. o They have different proteins associations which effects electron distribution which accounts for slight differences in light absorbing properties Linear Electron Flow - Light drives synthesis of ATP and NADPH by energizing the two photosystems, but a flow of electrons through the photosystems and other components in thylakoid is necessary. - Steps- - 1. Photon hits pigment in PSII and an e- is boosted to higher energy level and as this falls another e- in a nearby pigment is excited- repeats until it reaches P680, and an electron pair of chlorophylls is excited - 2. E- is transferred from excited P680, which is now known as P680 + (strongest oxidizing agent), to primary electron acceptor - 3. Enzyme catalyzes split of water into H+, 2 e-, and O atom. The e- are supplied one by one to P680, H+ go into thylakoid lumen, and O combines with another O to make O 2 - 4. Each photoexcited electron is passed from primary electron acceptor of PSII to PSI via ETC made up of proteins, which is exergonic. - 5. ETC provides energy for synthesis of ATP, and H+ are pumped into thylakoid lumen, helping with proton gradients that is used in chemiosmosis. - 6. Light energy has been transferred via light harvesting complex pigments to the PSI reaction center complex, exciting an electron of the P700 pair of chlorophyll a, which was then transferred to PSI’s primary electron acceptor, making it P700+ (a hole/missing something), allowing it to act as an electron acceptor, accepting an electron that reaches the bottom of the ETC (gets more electronegative as it gets toward bottom and source for electrons is water) from PSII. - 7. Redox reactions occur when pass from primary acceptor down second ETC through protein Fd (no proton gradient, so no ATP) - 8. NADP+ reductase (enzyme) catalyzes transfer from Fd to NADP+ and made into NADPH by two electrons. NADPH is higher energy than water and e- more readily available for Calvin cycle. Removes H+ from stroma Cyclic Electron Flow - only uses PSII in certain cases o electrons cycle back from Fd to cytochrome complex (which makes ATP via chemiosmosis) and then to P700 no production of NADPH, no release of O , but 2t generates ATP Comparison of chemiosmosis in mitochondria and chloroplasts is explained in picture Summary of light reaction- - electron flow pushes electron from water (low state of energy) to NADPH (stored as high state of energy) and this current drives production of ATP. O i2 byproduct Calvin Cycle - uses chemical energy of ATP and NADPH to reduce CO to sugar 2 - anabolic- builds carbohydrates from smaller and consumes energy - Carbon enters in form of CO and2leaves as sugar. Spends ATP as energy source and consumes NADPH as reducing power for adding high energy electrons to make sugar. - Carbohydrate produced directly is glyceraldehyde 3-phoshphate G3P- for synthesis of one, Calvin cycle must happen three times (fixing 3 CO 2olecules) - Phase 1- Carbon Fixation- gets each CO molecules2by attaching it to five carbon sugar RuBP, which is catalyzed by rubisco (most abundant protein), which makes a very unstable 6C which then splits in half forming two 3-phosphoglycerate (for each CO ) 2 - Phase 2- Reduction- each 3-phosphoglycerate gets phosphate group from ATP, making it 1, 3-bisphoglycerate; then a pair of electrons from NADPH reduces that and makes it lose a phosphate group, which then becomes G3P (same sugar from glycolysis when glucose is split). So, 6 G3P are formed for all three CO 2 - Phase 3- regeneration of the CO acceptor2(RuBP)- the carbon skeleton of five molecules of G3P are rearranged into three molecules of RuBP by spending three more molecules of ATP and RuBP is now prepared for more CO 2 - Net synthesis of one G3P- consumes 9 molecules of ATP and 6 NADPH, but light reaction regenerates ATP and NADPH. G3P made from Calvin cycle is string material for for metabolic pathways that synthesize other organic compounds. Importance of Photosynthesis - from photons to food - light reaction capture solar energy and make ATP and transfer electrons from water to NADP+ to form NADPH. The Calvin cycles uses the ATP and NADPH to produce sugar and carbon dioxide. Energy that enters chloroplasts as sunlight becomes sotred as chemical energy in organic compounds. - Sugar gives entire plant chemical energy and carbon skeleton for production of organic molecules in cell- half of organic material is consumed as fuel for cellular respiration - Responsible for oxygen in atmosphere Makes billions and billions o Chapter 10- Photosynthesis Preview- - Photosynthesis in a nutshell- chloroplasts of plants capture light energy and convert it to chemical energy that is stored in sugar and other organic molecules. – - Nourishes entire world o Organism gets organic compound it uses for energy and carbon skeleton by one of 2 ways Autotrophs- self feeders- sustain themselves without eating other things that are derived from other living things, but can be a source for others. Produce their organic molecules from CO and oth2r raw inorganic materials from the environment Plants are because they just get water and nutrients from the soil and CO fr2m air- specifically photoautotrophs because they use light also to synthesize organic molecules Heterotrophs- get organic compounds from other organisms; consumers Animals eat other living things Dependent on photoautotrophs for food and O 2 (byproduct of photosynthesis) Photosynthesis probably originated from bacteria’s molecules in plasma membrane, which is now known as a chloroplast in a eukaryotic cell. Chloroplasts- site of photosynthesis - Make the plant green from chlorophyll (in the thylakoid) and found mostly in mesophyll- leaf’s interior tissue o CO en2ers leaf and O exits 2y pores called stomata, and water is absorbed through veins of leaf - Stroma- liquid in chloroplast, thylakoids- separates the stroma from the thylakoid space within these sacs, each stack of sacs is called granum. - Light energy absorbed by chlorophyll drives the synthesis of the organic molecules Process of Photosynthesis- - 6CO +212H O + 2ight energy yields C H O + 66 12 6 2+ 6H 2 - Opposite of cellular respiration - O 2iven off from plants is derived from H O, not2CO - chloro2last splits the water into H and oxygen Redox Reaction- - 6CO (2xidizing agent) becomes reduced into C H O 6 12 6 - 6H 2 (reducing agent) is oxidized to 6O 2 - Electrons increase potential energy as they move from water to sugar- it requires energy, which means it is endergonic, and this energy is provided through light Preview of Photosynthesis - It is two processes- light reactions (photo part) and Calvin cycle (synthesis part) - Light reactions- water is split, providing H ions and giving of O as a 2y- product. Light absorbed by chlorophyll causes transfer of electrons and H ions to NADP+ (acceptor- extra phosphate in this compared to NAD+). Use solar power to reduce NADP+ to NADPH by adding a pair of electrons with H+. generate ATP by photophosphorylation (adding a P to ADP)- light energy is now converted to chemical energy in form of NADPH and ATP o Occurs in thylakoids o On outside of thylakoids, NADP+ and ADP pick up electrons and phosphate, and then NADPH and ATP are released into stroma - Calvin cycle (can be referred to as dark reaction- don’t need light)- CO 2 from air into organic molecules present in chloroplast (carbon fixation). Reduces fixed carbon to carbohydrate by addition of electrons, and this reducing power is provided by NADPH. The ATP and NADPH is needed for the synthesis to occur. o Occurs in stroma Nature of Sunlight- - Light is electromagnetic energy that travels in waves o Distance between the two crests is called wavelength (from less than a nm to more than a km) and the entire range is known as electromagnetic spectrum o Visible light- between 380nm and 750 nm- can be recognized o Photons- discrete particles in light, the shorter the wavelength, the greater energy of each photon - Pigment- substances that absorb visible light and each absorb different wavelength o If it absorbs all colors, it appears black. If it reflects all colors, it appears white. o The color you see is reflected back, while the pigment absorbs the shorter wavelengths o Light can perform work in chloroplasts only if it is absorbed there What happens when chlorophyll and other pigments absorb light? - is elevated to an orbital where it has more potential energy, which went from ground state Colors with absorbed wavelengths disappear, but energy cannot disappear. When a molecule absorbs a photon, one molecules electrons to excited state. (the only photons absorbed are those whose energy is exactly equal to the energy difference between ground and excited state, making each pigment have a unique absorption spectrum) - The electron can’t remain in excited state for long since it is unstable and generally drop right back down to ground state, releasing excess energy as heat/photons. o When photons are given off, there is an afterglow (fluorescent) Photosystem- - A reaction center complex associated with light harvesting complexes, Chlorophyll and other organic molecules are organized into a photosystem, converts light energy into chemical energy - Reaction center complex- organized association of proteins holding a special pair of chlorophyll a molecule. o Contains a molecule capable of accepting electrons and becoming reduced (primary electron acceptor)- pair of chlorophyll a molecules are special because of their environment- able to use energy from light to boost electron to higher energy but also to transfer it to the primary electron acceptor. - Light harvesting complex- various pigment molecules (chlorophyll a, chlorophyll b, carotenoids) bound to proteins o Number and variety of pigment molecules helps photosystem harvest light over bigger surface area and act as antenna for reaction center complex o When pigment molecule absorbs light, the photon is passed along from molecule to molecule until it is passed into reaction center complex. - Transfer of photon from reaction center chlorophyll a pair to primary electron acceptor is first step of light reactions. Excited then primary electron acceptor catches it which happens in structured environment of chloroplast (redox reaction). - Thylakoid is populated by two types of photosystems that cooperate in th
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