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Biology 1113 Ch. 8,9,10 Notes

by: Emily Notetaker

Biology 1113 Ch. 8,9,10 Notes Biology 1113

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Biology 1113
Dr. Ball and Dr. Weinstein
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Date Created: 10/10/16
Energy Flow and Life's Needs Wednesday, September 28, 2016 9:16 AM • Concepts 8.1-8.5 • Learning Outcomes ○ Successful students will be able to.  Explain how different forms of energy are utilized by biological systemsand the laws of thermodynamicsthat govern them.  Explain how ATP is able to provide the energy necessary for cellular functions  Describe the role that enzymes play in biological reactions and the mechanisms used to control their activity Ch. 8 Lecture Notes Wednesday, September 28, 2016 9:18 AM Metabolism • All of the chemical reactions that occur within an organism that are necessary for the maintenance of life ○ Catabolic reactions = breakdown complex moleculesand release energy  Exergonic reaction: Spontaneous reactions (do not require an input of energy)  ΔG<0 ○ Anabolic reactions = use energy to build complexmolecules (adding energy)  Endergonic reaction: Nonspontaneousreactions  ΔG>0 Energy • The capacity to cause change • Different forms ○ Kinetic  Heat - kinetic energy associated with random movementof molecules ○ Potential  Chemical - potential energy available for release in a chemical reaction (i.e. the breakdown of food) Energy Transformation • Thermodynamics= study of the energy transformationsthat occur in a collectionof matter ○ 1st Law = energy can be transferred/transformedbut no destroyed  Principle of Conservationof Energy ○ 2nd Law = Everyenergy transformationof transfer increases the entropy of the universe  Entropy = measure of disorder/randomness  Does the increasing complexity seen in biological systemscontradict the 2nd Law? □ No, the closed system of the body increases entropy as each step of energy transfer is done  Free energy o= portion of a system'senergy that can performwork How is Work done in a cell? • Cells do 3 main types of work: ○ Chemical (i.e. building of polymers) ○ Transport (i.e. pumping moleculesacross the membrane) ○ Mechanical (i.e. muscle contractions) • Energy Coupling ○ Use of exergonic reactions to drive endergonic reactions ○ ATP acts a s immediatesource of energy to power cellular work Adenosine triphosphate (ATP) • Bonds between phosphate groups can be broken by hydrolysis • Exergonic reaction ATP + H 2 -----> ADP + Pi ΔG = -7.3 kcal/mol(-13 kcal/molunder cellular conditions) ○ Chemical work: ATP used to create a phosphorylated intermediatewhich is unstable Regeneration of ATP • Reverse reaction must be endergonic ADP + P i-----> ATP + H2O ΔG = +7.3 kcal/mol • Reverse reaction must be endergonic ADP + P i-----> ATP + H2O ΔG = +7.3 kcal/mol • Exergonic reactions provide necessary energy ○ Cellular respiration ○ Light energy • If ATP could not be regenerated we would use up out body weight in ATP each day ○ Working muscle cell = 10 million moleculesof ATP consumed and regenerated per second Energy and Enzymes • Just because a reaction is spontaneous does not mean it occurs quickly • Enzymes are proteins (mostly)which act as catalysts and speed up reactions ○ Not consumed by the reaction ○ Act by lowering the activation energy (E A ○ Cannot make an endergonic reaction exergonic  Can only hasten reactions will occur anyway • Starting molecules generally have to be contortedinto an unstable form for reaction to occur ○ Reactants absorb energy from their surroundings to reach state where bonds can change  Activation Energy ○ Enzymes catalyze reactions by lowering E A • Enzyme Specificity ○ Substrate = reactant acted on by the enzyme ○ The reaction catalyzed by a particular enzyme is very specific  Active Site = region that actually bind the substrate  Only specific substrate can fit in active site ○ Binding of substrate causes the enzyme to slightly change in shape = induced fit  Brings chemical groups of active site into optimal position to catalyze reactions • Factors that Affect Enzyme Activity ○ Proteins function best under specific conditions  Temperature □ What happens as you increase temp?  It will be more likely for the substrate to collide with the active site, but there is a critical temperature (too high of temperature)where the enzyme becomesdenatured. □ What is optimal?  The best temperaturefor an enzyme in a human being is body temperature.But depending on the organism, the optimal temperaturewill be different for their enzymes.  pH □ What is the optimal pH for enzymes found in humans?  It depends on the enzyme also, like the stomach, you want an acidic pH. In the intestines, you want a basic pH.  Cofactors □ Non-protein helpers □ Can be:  Inorganic (i.e. Zn, Cu, Fe) - need to be bound to work  Organic (coenzymes) ◊ Vitamins (i.e. folic acid, vitamin c, B vitamins)  Inhibitors □ Competitive= resemble substrate and competefor active site □ Noncompetitive= bind to enzyme somewhereother than active site and cause a conformationalchange which decrease activity □ Toxins and poisons often act as enzyme inhibitors □ Toxins and poisons often act as enzyme inhibitors  Sarin gas = binds to active site or acetylcholinesterase (acetylcholineis one of our major neurotransmitters)- will screw up how the nervous system works  Penicillin = blocks active site of enzyme necessary for cell wall formationin bacteria (a good form of toxin) • Enzyme Regulation ○ Metabolic pathways are tightly regulated by controlling when and where enzymes are active  There are things that can turn them off and turn them on ○ Allosteric regulation  Binding of a regulatory molecule at one site affects the activity at a separate site □ Can either stimulate or inhibit activity □ Cooperativity- talking about the substrate itself binding  Still considered allosteric, because when it binds to one active site, it increases the affinity at other sites because of the many subunits (Hemoglobin) ○ Feedback inhibition (feedback loop)  End product of a pathway can bind to an enzyme that acts earlier in the pathway and inhibit it  Preventscell from wasting energy to make excess product ○ Localization of Enzymes  Enzymes can be compartmentalizedor assembled into multi-enzyme complexes Top Hat Questions Wednesday, September 28, 2016 9:31 AM How do living organisms create macromolecules,organelles, cells, tissues, and complex higher-order structures? a. The laws of thermodynamicsdo not apply to living organisms b. Living organisms create order by using energy from the sun c. Living organisms create order locally, but the energy transformationgenerate waste heat that increases the entropy of the universe How might an amino acid change at a site distant from the active site of the enzyme alter the enzyme's substrate specificity? a.An amino acid change away from the active site cannot alter the enzyme's substrate specificity b.By changing the enzyyme's stability c.By changing the enzyme's pH optimum d.By changing the shape of the protein e.By changing the enzyme's location in the cell Protein kinases are enzymes that catalyze phosphorylation of target proteins at specific sites, whereas protein phosphatases catalyze removal of phosphate(s) from phosphorylated proteins. Phosphorylation and dephosphorylationcan function as an on-off switch for a protein's activity, mostlikely through a. A change in the optimal pH at which a reaction will occur b. A change in the optimal temperature at which a reaction will occur c. The excision of one or more peptides d. The change in a protein's charge leading to a conformationalchange e. The change in a protein's charge leading to cleavage Adenosine monophosphate(AMP) activatesthe enzyme phosphofructokinase (PFK) by binding at a site distinct from the substrate binding site. This is an example of a. Cooperativeactivation b. Allosteric activation c. Activation by an enzyme cofactor d. Coupling exergonic and endergonic reactions Which of the following metabolicprocesses can occur without a net influx of energy from some other process? a. ADP + Pi -------> ATP + H2O b. C6H12O6 + 6 O2 -------> 6 CO2 + 6 H2O c. 6 CO2 + 6 H2O -------> C6H12O6 + O2 d. amino acids -------> protein e. glucose + fructose -------> sucrose Book Overview (pg. 141 -159) Tuesday, October 4, 2016 10:19 AM Section 8.1 | Metabolism • Metabolism - the totality of an organism's chemical reactions; transformsmatter and energy; manages the material and energy resourcesof the cell Organization in Metabolic Pathways • Metabolic pathway - thousands of chemical reactions that occur in a cell ○ Begins with a specific molecule that is altered and results in a product ○ Each step of the pathway is catalyzed by a specific enzyme ○ Catabolic pathways - Release energy be breaking down complex moleculesto simpler ones  "Downhill" avenues of metabolism  Ex: cellular respiration: breaks down sugar glucose and other organic fuels in the presence of oxygen to carbon dioxide, water, and energy ○ Anabolic pathways (biosyntheticpathways) - consume energy to build complicated moleculesfrom simpler ones  "Uphill" avenues of metabolism  Ex: Synthesis of amino acid from simpler molecules and the synthesis of a protein from amino acids Forms of Energy • Energy - the capacity to cause change ○ Kinetic energy - the relative motion of objects  Thermal energy - kinetic energy associated with the random movementof atoms or molecules □ Heat - Thermal energy in transfer from on object to another ○ Potential energy - energy that matter possesses because of its location or structure  Chemical energy - potential energy available for release in a chemical reaction Laws of Energy Transformation • Thermodynamics- The study of the energy transformations(PE to KE) that occur in a collectionof matter ○ Isolate system - is unable to exchange either energy or matter with its surroundings ○ Open system - energy and matter can be transferred between the system and its surroundings  Organisms are open systems • First Law of Thermodynamics ○ The energy of the universe is constant: "Energy can be transferred and transformed, but it cannot be created or destroyed" ○ As the Law of Conservationof Energy • Second Law of Thermodynamics ○ Every energy transfer or transformationincreases the entropy of the universe ○ Entropy - a quantity of disorder or randomness when energy is transfered or transformed  You can observed increased entropy in the physical disintegration of a system's organized structure  Entropy takes the form of increasing amounts of heat and less ordered forms of matter □ If a process leads to an increase in entropy, then that process can proceed without and input of energy (Spontaneous process)  Energetically favorable □ If a process leads to a decrease in entropy, then that process will only happen if energy is supplied (nonspontaneous process)  The usage of energy in a nonspontaneousprocess leads to an increase in entropy • Biological Order and Disorder • Biological Order and Disorder ○ Living systemsincrease the entropy of their surroundings  Breaking down starch, proteins, and other complexmolecules from food Section 8.2 | Free - energy change • Free energy - the portion of a system'senergy that can perform work when temperatureand pressure are uniform throughout the system ○ How do we determine the free-energy change that occurs when a system changes like during a chemical reaction? ΔG = ΔH - TΔS Where ΔH is the change in the system'senthalpy, ΔS is the change in the system's entropy, and T is the absolute temperature(Kelvin)  When ΔG<0, the process is spontaneous  When ΔG >0 or =0, the proces is nonspontaneous Free Energy, Stability, and Equilibrium • ΔG also represents the difference between the free energy of the final state and the free energy of the initial state ○ The process can only be spontaneous when there is a loss of free energy during the change from initial state to final state ○ When the system has less free energy, the system in its final state is less likely to change and is thereforemore stable than it was before. • Free energy can be a measure of a system's instability ○ Unstable systemshave a higher G ○ Stable systems have a lower F ○ There is maximum stability at equilibrium, G is at its lowestpossible value in that system  A system at equilibrium cannot spontaneouslychange, it cannot do work Free Energy and Metabolism • Exergonic and endergonic reactions in metabolism ○ An exergonic reaction proceeds with a net release of free energy in a chemical reaction  G will decrease and ΔG will be negative  Exergonic reactions always occur spontaneously ○ An endergonic reaction is one that absorbs free energy from its surroundings  G will increase and ΔG is positive  Endergonic reactions will always be nonspontaneous  Rememberthat it requires energy to break bonds • Equilibrium and Metabolism ○ Reactions in an isolated system will eventually reach equilibrium, and then can do no more work  The chemical reactions of metabolism could also reach equilibrium □ If they do, that cell will be dead because it can do no work  The constant flow of materials in and out of the cell keeps the metabolic pathways from ever reaching equilibrium Section 8.3 | ATP • A cell does three main kinds of work: ○ Chemical work  The pushing of endergonic reactions that would not occur spontaneously,such as the synthesis of polymers from monomers ○ Transport Work  The pumping of substances across membranes against the direction of spontaneous movement ○ Mechanical work  The beating of cilia, the contraction of muscle cells, and the movementof chromosomesduring cellular reproduction chromosomesduring cellular reproduction • How do cells manage their energy resources? ○ Energy coupling - the use of an exergonic process to drive an endergonic one  ATP is responsible for mediating energy coupling in cells and acts as the source of energy that powers cellular work The Structure and Hydrolysis of ATP • ATP contains ribose, nitrogenous base adenine, and a chain of three phosphate groups ○ The bonds between the phosphate groups can be broken through hydrolysis  When one phosphate leaves ATP, it becomesADP  This reaction is exergonic and releases 7.3 kcal of energy per mole  The high release of energy during the hydrolysis of ATP comesfrom the chemical change of the system to a state of lower free energy, not from the phosphate bonds themselves ○ ATP is useful because the energy it releases during hydrolysis of one of the phosphates is greater than the energy from other molecules How does the hydrolysis of ATP performwork? • When a person is shivering, the body uses ATP hydrolysis during muscle contraction to warm the body ○ Howevermost of the time the heat generation of ATP hydrolysis is inefficient • The cell's proteins harness the energy released during ATP hydrolysis to do the three kinds of work: ○ Chemical work, transport work, and mechanical work • Chemical Work ○ In order to couple exergonic and endergonic reactions, the formationof a phosphorylated intermediateis needed  Phosphorylatedintermediate - the recipient molecule with the phosphate group from ATP covalentlybonded to it  A phosphorylatedmolecules is morereactive and less stable than the original molecule • Transport work ○ ATP phosphorylatestransport proteins • Mechanical work ○ ATP binds non-covalentlyto motorproteins and then is hydrolyzed The Regeneration of ATP • ATP is a renewable resource that can be regenerated by the addition phosphate to ADP ○ Free energy must be spent to make it occur ○ Catabolic pathways like cellular respiration provide the energy for the process ○ Plants use light energy to provide the energy for the process Section 8.4 | Enzymesin Metabolic Reactions • Enzyme - a macromoleculethat acts as a catalyst, a chemical agent that speeds up a reaction without being consumed by the reaction The Activation Energy Barrier • Activation energy - the energy required to contort the reactant moleculesso the bonds can break ○ Think of it as the amount of energy need to push the reactants to the top of an energy barrier (uphill) ○ Supplied by thermal energy that reactants absorb from surroundings  Causes moleculesto collide more often and forcefully ○ Once the bonds break, the reactants are in an unstable condition called the transition state How Enzymes Speed Up Reactions • Heat can speed up the process of SOME reactions, but in a biological system,high temperatures can denature proteins which will kill cells • Enzymes are instead used in the biological systemsas catalysts, which lower the activation energy so that the reactants can reach the transition state moreeasily Substrate Specificity of Enzymes • Substrate - the reactant an enzyme acts on • Enzyme-substratecomplex - when an enzyme binds to the substrate(s) ○ The catalytic action of the enzyme then converts the substrate to the product Example: • An specific reaction will only be catalyzed by the specific enzyme ○ An enzyme will recognize only its substrate (even among like-compounds)  This is because most enzymes are proteins which are very specific in shape and amino acid sequence ○ Active site - the restricted region of the enzyme where the molecule binds to the substrate  Usually a pocket or grooveon the surface of the enzyme  The specificity of an enzyme and substrate can be attributed to the fit of the two moleculesat the site  The active site is not rigid, it will form around the substrate in order to enhance the ability of the enzyme to catalyze the chemical reaction Catalysis in the Enzyme's Active Site • The enzyme catalyzes a substrate into a product, and then the product departs from the active site, the enzyme is then free to catalyze another substrate ○ It is a very fast moving catalytic cycle ○ Enzymes emerge from the reactions in their original form • Metabolic reactions are reversible ○ Enzymes can catalyze both the forward and reversereaction • How enzymes lower the activation energy ○ Providesa template for substrates to orient themselvescorrectly ○ Distorts and stretches the shape of the substrate until bonds break, which helps it approach the transition state while reducing the amount of free energy required ○ The enzyme can contain an environmentthat is more conducive to the reaction ○ The amino acids of the enzymes will sometimesbond covalentlywith the substrate • The rate at which an enzyme convertsa substrate is correlated to the concentrationof the substrate ○ The more substrate, the faster and more frequently it can enter the active site  Howevertoo much substrate can be added, and all active sites will be engaged while there is substrate not being catalyzed □ This is called saturated □ This is called saturated □ More enzyme would need to be added to speed up the reaction in this case Effects of Local Conditions on Enzyme Activity • Temperatureand pH ○ 3-D structures of proteins are sensitive to their environment,thereforesome work better under certain conditions (optimal conditions) ○ Above a certain temperature,the speed of an enzymatic reaction will drop sharply  The high temperature disrupts the hydrogen bonds, ionic bonds, and other interactions that stabilize the enzyme □ The protein moleculewill eventually denature  There is an optimal temperature for each enzyme where there are the greatest number of molecular collisions □ Human enzymes optimal temperature:35-40 °C ○ Each enzyme has a pH at which it is most active  Usually optimal pH is from 6-8 □ Pepsin (a digestive enzyme in the stomach)works best at 2 • Cofactors ○ Cofactors- non-protein helpers for catalytic activity  Can either be bound tightly to the enzyme permanently,or bound looselynon- permanently  Coenzyme - if the cofactoris an organic molecule □ Vitamins are coenzymes • Enzyme Inhibitors ○ Bind to the enzyme by weak interactions  Is reversible  Competitiveinhibitors - reduce the productivityof enzymes by blocking substrates from entering active sites □ Can be overcomeby increased concentration of substrate  Noncompetitiveinhibitors - do not competewith substrate to bind to the enzyme active site □ Impede enzymaticreactions by binding to another part of the enzyme  Causes enzyme to change shape so that the active site is non-effectiveat catalyzing a substrate ○ Toxins and poisons are however,irreversible inhibitors  Sarin - binds covalentlyto R group on amino acid serine in acetylcholinesterase (important in nervous system) The Evolution of Enzymes • Mutation - a permanent change in a gene, can result in a protein with one or more changed amino acids ○ This can cause an enzyme to bind to a different substrate, or becomeinactive Section 8.5 | Regulation of enzyme activity Allosteric Regulation of Enzymes • Allosteric regulation - when a protein's function at one site is affected by the binding of a regulatory moleculeto a separate site ○ Can result in inhibition of stimulation of an enzyme's activity Allosteric Activation and Inhibition • Enzymes that are allosterically regulated are composedof a polypeptide chain with an active site which oscillates between being catalytically active and inactive • In allosteric regulation: ○ An activating or inhibiting regulatory moleculebinds to a regulatory site where (often) subunits join  If it is an activator,it stabilizes the functional form of the site  If it is an activator,it stabilizes the functional form of the site  If it is an inhibitor, it stabilizes the inactive form of the site ○ One interaction of an inhibitor or activator can affect all of the regulatory sites subunits • ATP binds allostericallyto catabolic enzyme in order to inhibit their activity • ADP binds allostericallyto catabolic enzymes as an activator ○ Allosteric enzymes control the rates of reaction in metabolic pathways • Cooperativity- amplifies the response of enzymes to substrates ○ One substrate moleculeprimes an enzyme to act on additional substrate moleculesmore readily ○ The binding of the substrate in one active site affects catalysis in another active site Feedback Inhibition • A metabolicpathway is halted by the inhibitory binding of its end product to an enzyme that acts early in the pathway ○ Cells can use it to prevent itself from making moreproducts than are necessary Localization of Enzymes Within the Cell • The cell is compartmentalizedinto specific structures ○ This allows for each enzyme to reside in a specific environmentwithin the cell Cellular Respiration Friday, September 30, 2016 9:39 AM • Concepts 9.1 - 9.6 • Learning objectives ○ Successful students will be able to:  Explain the role that redox reactions play in cellular respiration  Explain how glucose is utilized for energy  Identify the reactants and products of each stage of respiration (glycolysis,CAC and oxidative phosphorylation)  Explain how diffusion plays a role in ATP synthesis  Compare and contrast the conditions and products of respiration and fermentation Lecture Notes Friday, September 30, 2016 9:57 AM Overviewof Cellular Respiration • Potential energy is stored in food due to the arrangement of the electronsin the bonds • Must be broken down to release energy • Two main pathways ○ Aerobic respiration ○ Anaerobic respiration (fermentation) • Energy harvested used to regenerate ATP Role of Redox Reaction • Transfer of electrons releases energy stored in organic molecules • Redox reactions = oxidation - reduction reactions ○ Oxidation = loss of electrons(LEO) ○ Reduction = gain electrons(GER)  Adding electrons REDUCES the amount of positive charge of an atom Energy is harvested in a stepwise manner • If glucose was oxidized all at once too much energy would be lost • Electrons are stripped from glucose at key steps in the process ○ e- do not travel alone … travel with a proton = hydrogen atom • Hydrogen atomsare not transferred directly to oxygen ○ Passed to an electron carrier = NAD+ (NADH reduced) Stages of Cellular Respiration 1. Glycolysis Glucose + 2ATP + 2NAD+ ------> 2 Pyruvate+ 4 ATP (2 NET) + 2 NADH 2. PyruvateOxidation and the Citric Acid Cycle Pyruvate+ CoenzymeA + NAD+ -----> Acetyl CoA + CO2 + NADH Acetyl CoA + H2O + 3 NAD+ + FAD ------> 2CO2 + H2O + 3 NADH + FADH2 + GTP (ATP) 3. Oxidative Phosphorylation NADH + FADH2 + 1/2 O2 + ADP + P ------> ATP + H2O + NAD+ + FAD • Glycolysis ○ Takes place in the cytosol ○ Splits glucose into 2 molecules of pyruvate ○ Requires input of 2 ATP but yields 4 ATP (Net yield = 2 ATP)  Need to know - what goes into it, it splits, what both halves form • Pyruvateoxidation ○ Pyruvateenters the mitochondria through active transport ○ 3 reactions take place  COO is removedand given off as CO2  COO is removedand given off as CO2  Remaining 2-carbon molecule is oxidized □ NADH formed  CoenzymeA is added to form acetyl CoA (high potential energy) • Citric Acid Cycle (Krebs/TCA Cycle) ○ Series of 8 steps, each catalyzed by a specific enzyme  Redox reactions ○ Occurs in the mitochondrial matrix ○ 1 cycle produces  2 CO2  1 GTP (ATP)  3 NADH  1 FADH2 □ How many products are produced per glucose molecule?  It would double the amount of products above ○ CoA and oxaloacetaterecycled • So where are we at energy-wise? ○ Per glucose molecule … - Glycolysis + 2 ATP - Krebs Cycle + 2 ATP TOTAL = Net + 4 ATP ○ So where is most of the energy from glucose? - It's in the NADH • Oxidative Phosphorylation ○ Generates ATP by adding P to ADP ○ Two steps: - Electron Transport Chain - Chemiosmosis Electron Transport Chain • Collection of moleculesembedded in the mitochondrialinner membrane • Electrons are dropped off by NADH and FADH2 ○ Electron carriers alternate between reduced and oxidized states as they accept and donate e- ○ Final e- acceptor is oxygen which also picks up 2H+ ions to form H2O - Still no ATP production Chemiosmosis • Exergonic flow of electrons is used to pump H= across the membrane (into the intermembranespace) ○ Generates a gradient = proton motiveforce • Chemiosmosis= the energy-coupling mechanism that uses energy stored in a H= gradient to drive cellular work • Note: NADH and FADH2 enter the ETC at different complexes = less energy for ATP synthesis when e- come from FADH2 Using the Proton-MotiveForce to Generate ATP • ATP syntahse = uses energy of the H+ gradient to power ATP synthesis ○ Located in the mitochondrialinner membrane • H+ ions flow through ATP synthase down their concentrationgradient ○ Bind to active sites and cause conformationchange = rotor spins ○ Activates catalytic sites that generate ATP How efficient is it? How efficient is it? • Completeoxidation of glucose releases 686 kcal/mol And… ADP ---> ATP stores 7.3 kcal/mol So … (32 ATP x 7.3 kcal/mol)/686kcal/mol= 0.34 34% of the potential energy of glucose in transferred to ATP (the most efficient cars only convert25% of gas to energy) What happens to the rest of the energy? It turns into heat! Anaerobic Respiration • Still uses an electron transport chain but O2 is not the final electron acceptor ○ Other electronegativesubstances can also work • Some marine bacteria use the sulfate ion (SO42-) ○ Produce H2S instead of water • Other substance used include NO3-, CO2, S, Fe, and uranium Fermentation • Processto generate energy with using oxygen or an electrontransport chain • Basically an extension of glycolysis ○ Glycolysis+ a process to regenerate NAD+ • Different types of fermentation ○ Differ in the end products formed ○ Two commontypes: alcohol and lactic acid fermentation Alcohol Fermentation • Pyruvateis reduced to ethanol • Used by somebacteria and yeast • Used to make beer, wine, liquor, and bread Lactic Acid Fermentation • Pyruvateis reduced directly by NADH to form lactate • Used in food industry to make yogurt, cheese and sauerkraut • Muscle cells use this process when supply of oxygen can't keep up with energy demand So what is actually happening when you are deprived of oxygen (suffocated)? If you don't have oxygen, the electrons cannot be pulled off of the electron transport chain, therefore ATP cannot be created, and your body will die because there is no energy. Why can't your cells just switch over to fermentation? Fermentation will not be able to keep up with the amount of energy the body needs. How do we use other moleculesfor energy? • Glucose is not the only moleculethat can be broken down to release energy ○ Other carbs, fats and proteins can also be used A gram of fat produces 2x the ATP generated from 1 g of carbohydrate. Why? Because of their chemical structure and high energy level of their electrons (equally shared between carbon and hydrogen). Why does this make it hard to lose weight? Because so many calories are stockpiled in each gram of fat, and since fat produces more ATP less of it is initially needed and the other fat is fat produces more ATP less of it is initially needed and the other fat is then stored. Biosynthesis • Cells need building blocks to make their own molecules ○ Food provides the carbon skeletons necessary in addition to energy - Amino acids can be incorporated into cell's own proteins - Many intermediatesfrom glycolysis and the Krebs cycle can be used as precursors for molecules the cell requires • Requires energy (anabolic) How is Cellular Respiration Regulated? • Follows principles of supply and demand ○ The cell does not waste energy making more of a particular substance than it needs • Preventscell from wasting energy making something it already has • Main mechanism of control is feedback inhibition ○ The end product of the anabolic pathway inhibits the enzyme that catalyzes an early step of the pathway. • The cell also control its catabolism ○ If the cell is working hard and its ATP concentration begins to drop, respiration speeds up, and if there is plenty of ATP, respiration slows down Book Overview (pg. 162 - 182) Friday, September 30, 2016 9:57 AM Section 9.1 | Catabolic Pathways • Catabolic pathways are metabolic pathways that release stored energy by breaking down complex molecules Catabolic Pathways and Production of ATP • Enzymes systematicallydegrade complexorganic molecules,that contain PE due to the arrangement of electrons in the bonds between their atoms,into simpler waste products that have less energy. ○ The energy taken out is used to do work or be given off as heat • Fermentation- a partial degradation of sugars and other organic fuel that occurs without oxygen (we can call these types of catabolic pathways anaerobic respiration) ○ Not as efficient as aerobic respiration ○ Aerobic respiration - oxygen is consumed as a reactant along with the organic fuels • Cellular respiration ○ Includes both aerobic and anaerobic respiration but refers to aerobic more ○ Food provides the fuel for respiration and then gives out carbon dioxide and water as products  Carbohydrates, fats, and proteins from food can all be used as fuel ○ The degradation of glucose:  This reaction is exergonic which means the products store less energy than the reactants and can happen spontaneously ○ Creates ATP from ADP through oxidation and reduction, ATP drives cellular work like flagella, pumping solutes across membranes,polymerizing monomers Redox Reactions • In cellular respiration, glucose and other moleculesin food are oxidized ○ Transfers electronsto a lower energy state which liberates energy for ATP synthesis ○ Energy yielding foods are carbohydrates and fats • How cells obtain energy in order to make ATP ○ Glucose --> NADH --> electron transport chain --> oxygen  In the electron transport chain, electrons that are removedfrom glucose are shuttled by NADH to the top energy end of the chain and at the bottom,O2 captures electrons and hydrogen in order to form water  This is an exergonic reaction Stages of Cellular Respiration: 1. Glycolysis 2. PyruvateOxidation and Krebs Cycle 2. PyruvateOxidation and Krebs Cycle 3. Oxidative Phosphorylation Energy flows in this sequence: Glucose --> NADH --> electron transport chain --> proton-motiveforce --> ATP Glycolysis: • The glucose moleculeis split into three-carbon sugars that are oxidized into pyruvate ○ Energy investmentphase of glycolysis:  The cell spends 2 ATP ○ Energy payoff phase  ATP is produced by substrate-level phosphorylationand NAD+ is reduced to NADH when electrons are released from the oxidation of glucose  The net energy yield per glucose molecule is 2ATP plus 2NADH • Occurs in the cytosol PyruvateOxidation and Krebs Cycle • In aerobic reactions, the two pyruvate moleculesenter the mitochondrionwhere the oxidation of glucose is completed ○ In the mitochondrionpyruvate is convertedinto an acetyl coenzyme A (acetyl CoA) 1. Pyruvate'scarboxyl group (COO-) is removedand given off as CO2 2. The remaining two-carbon fragment is oxidized and form acetate (CH3COO-), the extracted electrons then are transferred to NAD+ to form NADH 3. Acetyl CoA is formed from a vitamin and acetate • The Citric Acid Cycle (Krebs Cycle) ○ Consumes oxygen ○ Produces carbon dioxide and water as waste products ○ Converts ADP to ATP, produces 2 ATP molecules ○ Takes place in the mitochondria - Oxidative Phosphorylation • Uses energy released by the electron transport chain to power ATP synthesis • Electron Transport Chain - a collectionof molecules embedded in the membrane of the mitochondrionin eukaryoticcells (plasma membrane of prokaryotes) ○ The enfolded membraneis suited for the series of redox reactions • Chemiosmosis:The energy coupling mechanism ○ The process in which energy stored in the form of a hydrogen ion gradient across a membrane is used to drive cellular work and the synthesis of ATP ○ Proton Motiveforce - The H+ gradient that results from the electrontransport chain and drives H+ back across the membrane to ATP synthases The ATP synthase is an enzyme that makes ATP from ADP and inorganic phosphate ○ The ATP synthase is an enzyme that makes ATP from ADP and inorganic phosphate Efficiency of Cellular Respiration: • In some cases it can produce 32 or 30 ATP. The ATP yields vary depending on the oxidative phosphorylationstep. • Hibernation of mammals:it is beneficial to reduce the efficiency of cellular respiration in these cases. ○ When the body is in a state of inactivity during winter, the metabolism is lowered. ○ Their body temps are lower than normal, but still must be kept significantly higher than the external temp ○ Brown fat in these mammals contain an uncoupling protein that allow protons to flow back down the concentrationgradient without creating ATP  This allows for ongoing oxidation of stored fat which generates heat, without ATP production □ If ATP was created, the buildup of it would cause cellular respiration to be shut down and thereforeno heat would be produced causing animals to freeze to death. Section 9.5 | Fermentation and anaerobic respiration Distinction between Fermentationand anaerobic respiration: • The electron transport chain is used in anaerobic respiration but not fermentation ○ The chain is used without an oxygen as a final electron acceptor at the end but with other electronegativesubstances at the end Fermentation: • Alcohol fermentation and lactic acid fermentation Top Hat Questions Friday, September 30, 2016 9:59 AM Cellular respiration can best be described as: a.Endergonic, anabolic, deltaG < 0 b.Endergonic, catabolic, deltaG >0 c.Exergonic, catabolic, deltaG <0 d.Exergonic, anabolic, deltaG >0 A moleculethat is phosphorylated … a.Has less energy than before its phosphorylationand therefore less energy for cellular work b.Has a decreased chemical reactivity;it is less likely to provide energy for cellular work c.Has been oxidized as a result of a redox reaction involving the gain of an inorganic phosphate d.Has an increased chemical potential energy; it is primed to do cellular work e.Has been reduced as a result of a redox reaction involving the loss of an inorganic phosphate What pathways generate reduced electron carriers? a.The citric acid cycle b.Glycolysis c.Pyruvateoxidation d.All of the above e.Glycolysisand the citric acid cycle only During aerobic respiration, electrons travel downhill in which sequence? → citric acid cycle → ATP → NAD+ b.glucose → pyruvate → ATP → oxygen → glycolysis → citric acid cycle → NADH → ATP → NADH → electron transport chain → oxygen e.glucose → ATP → electron transport chain → NADH Which of the following statementsabout the chemiosmoticsynthesis of ATP is correct? a.The energy for production of ATP from ADP comesdirectly from a gradient of electrons across the inner mitochondrialmembrane. b.Oxygen participates directly in the reaction that makes ATP from ADP and P. c.The chemiosmoticsynthesis of ATP requires that the electron transport in the inner mitochondrial membrane be coupled to proton transport across the same membrane. d.The chemiosmoticsynthesis of ATP occurs only in eukaryotic cells, because it occurs in mitochondria. e.ChemiosmoticATP synthesis requires oxygen In cellular respiration, the energy for most ATP synthesis is supplied by a.high energy phosphate bonds in organic molecules. a.high energy phosphate bonds in organic molecules. b.converting oxygen to ATP c.generating carbon dioxide and oxygen in the electron transport chain. d.a proton gradient across a membrane. e.transferring electrons from organic molecules to pyruvate Drugs known as uncouplers facilitate diffusion of protons across the membrane. When such a drug is added, what will happen to ATP synthesis and oxygen consumption,if the rates of glycolysis and the citric acid cycle stay the same? a.Both ATP synthesis and oxygen consumption will decrease. b.ATP synthesis will decrease; oxygen consumption will increase. c.ATP synthesis will increase; oxygen consumption will decrease. d.Both ATP synthesis and oxygen consumption will increase e.ATP synthesis will decrease; oxygen consumption will stay the same Why are carbohydrates and fats considered high energy foods? a.They have no nitrogen in their makeup. b.They have a lot of electrons associated with hydrogen. c.They have a lot of oxygen atoms. d.They are easily reduced e.They can have very long carbon skeletons. The purpose of fermentationreactions is a.To regenerate NAD+ so glycolysiscan continue b.To make alcohol or lactic acid that cells can metabolizefor energy under anaerobic conditions c.To make additional ATP when respiration can’t make ATP fast enough d.To slow down cellular oxygen consumptionwhen oxygen is scarce e.To make organic moleculesthat cells can store until oxygen becomes available What is the probable effect on ATP production of a low-caloriediet? a.ATP production would decrease due to a reduction in the availability of fuel molecules. b.ATP production would increase as stored fats are catabolized c.ATP production would increase if mostcalories were provided by fats and decrease if most calories were provided by high-fiber grains. d.ATP production would remain constant as stored fats or other body moleculesare oxidized. e.ATP production would remain constant as long as the exercise level was increased. You have a friend who lost 7 kg (about 15 pounds) of fat on a regimen of strict diet and exercise. How did the fat leave her body? a.It was released as CO2 and H2O. a.It was released as CO2 and H2O. b.It was convertedto heat and then released. c.It was convertedto ATP, which weighs much less than fat. d.It was convertedto urine and eliminated from the body. e.It was broken down to amino acids and eliminated from the body. Photosynthesis Wednesday, October 5, 2016 9:53 AM • Concepts 10.1 - 10.4 • Learning Objectives ○ Successful students will be able to:  Explain how plants are able use energy from the sun to synthesize organic molecules  Identify reactants and products for the light reactions and Calvin Cycle  Explain the differences between the light reactions and the Calvin Cycle  Describe the adaptations plants use to increase carbon fixation in dry hot climates and what characteristic of rubisco makes this necessary Lecture Notes Wednesday, October 5, 2016 9:56 AM The photosynthesisformula backwards is the ATP formula In the process of photosynthesis,plants convert radiant energy from the sun into chemical energy in the form of glucose - or sugar. 6H 2 + 6CO +2radiant energy (sunlight) -----> C 6 12+66O 2 Chloroplasts • Chloroplasts are the reason plants are green in all parts, but the leaves are the major sites of photosynthesisin most plants ○ Carbon dioxide enters the cell through pores called stomata • Chlorophyll resides in the thylakoid membrane Photosynthesisis a Redox Reaction • Water is split and the electron (and H+) are transferred to CO2, reducing it to sugar • Electrons increase in potential energy as they movefrom water to sugar ○ Therefore reaction is endergonic  The energy boost is provided by light Quick Lesson on Light! • Light is a form of energy = electromagneticradiation (energy) ○ Electromagneticwaves are analogous to those created by dropping a pebble in a pond ○ Electromagneticwaves are disturbances of electric and magnetic fields • The entire range of radiation is the electromagneticspectrum ○ What we can detect as various colors = visible light (380 - 750 nm) • Photons = discrete particles with a fixed amount of energy (no mass!) ○ The amount of energy is inversely related to a wavelength of light: the shorter the wavelength = the greater the energy of each photo Why is the sky blue? All of the wavelengths are being absorbed, except the blue wavelength. Why does something appear white? All of the wavelengths are coming at you, none are being absorbed. Black? None of the wavelengths are coming at you, all are absorbed. • When light meets matter,it may be reflected, transmitted,or absorbed • Pigment = substance that absorbs visible light Different pigments absorb different wavelengths of light ○ Different pigments absorb different wavelengths of light ○ Chlorophyll a & b appear green because they do not absorb wavelengths in that part of the spectrum (Violet-blue and red light are absorbed and are the most effectivecolors for photosynthesis)  Chlorophyll a - the key light-capturing pigment that participates directly in the light reactions  Chlorophyll b - the accessorypigment - broadens the spectrum of colors that can be used for photosynthesis  Carotenoids - a separate group of accessorypigments - hydrocarbons that are various shades of yellow and orange because they absorb violet and blue-green light □ Photoprotection- absorb and dissipate excessivelight energy that would otherwisedamage chlorophyll ○ Why do leaves change colors? We are seeing the wavelengths of light that are reflected by chlorophyll, and as the seasons start to change, the plants will stop making chlorophyll, and then we will be able to see the colors that were already there (the colors are always there or carotenoids). Overviewof Photosynthesis • Photosynthesisis not a single process, but two process, each with multiple steps ○ Light Reactions (The photo part of photosynthesis)  Convert light energy into chemical energy □ H2O is split to provide e- and H+ □ NADP+ reduced to NADPH □ ATP is produced from chemiosmosis □ O2 is given off as a by-product ○ Calvin Cycle (Light independent/dark reactions) (the synthesis part)  Fixes carbon from Co2 into organic molecules  Reduces fixed carbon into sugar using the NADPH and ATP from light reactions Light Reactions Light + H2O -----> NADPH + ATP + O2 • Photosystems(chlorophyll molecules are organized along with other small organic moleculesand proteins into complexes)which capture light are located in thylakoid membrane • Photosystemsare composed of a reaction-centercomplex, surrounded by several light-harvesting complexes: ○ Light harvesting complexes:contain pigment moleculesbound to proteins which absorb light and transfer the energy to reaction-centercomplex (i.e. antenna)  When a pigment moleculeabsorbs a photon, the energy is transferred from pigment moleculeto pigment molecule within a light-harvesting complex until it is passed to the reaction center ○ Reaction-centercomplex: contains a special pair of chlorophyll a moleculeswhich can reduce the primary electron acceptor  The chlorophyll a molecules' location and molecularenvironmentenables them to use  The chlorophyll a molecules' location and molecularenvironmentenables them to use the energy from light to boost on of their electrons to a higher energy level and transfer it to a different molecule(the primary electronacceptor) • The thylakoid membrane contains two photosystems: ○ PhotosystemII - functions first in the light reactions  Contains a chlorophyll a molecule called P680that is best at absorbing light having a wavelength of 680 nm ○ PhotosystemI - functions second  Contains a chlorophyll a molecule called P700that is best at absorbing light having a wavelength of 700 nm ○ Light drives these two photosystemsthrough linear electron flow (a flow of electrons through the photosystemsand other molecular components)  Linear electron flow: □ The light-driven electrons from the pigments flow from water to NADPH • Cyclic electron flow - used by photosystemI to cycle electrons through, does not create NADPH or oxygen, but generates ATP • Summary of light reactions: ○ Electron flow pushes electrons from water (low potential state of energy) to NADPH (high potential state of energy) while simultaneouslyproducing ATP Calvin Cycle • Uses the Chemical energy stored in ATP and NADPH to reduce CO2 to sugar (G3P) • Broken down into 3 phases: ○ Carbon fixation  Rubisco (RuBP carboxylase) attaches CO2 moleculeto ribulose biphosphate (RuBP) ○ Reduction  Carbon intermediate receivedphosphate group from ATP  Reduced by NADPH and loses the phosphate = G3P ○ Regeneration of CO2 acceptor  Series of steps which utilize ATP to rearrange 5 molecules of G3P to regenerate 3 moleculesof RuBP  Very important step so that the cycle can continue and restart • Cycle must occur 3 times to produce 1 net G3P (Fixing 3 CO2) ○ Technically produces 6 G3P moleculesbut 5 must be used to regenerate RuBP ○ For 1 G3P, cycle uses 9 ATP and 6 NADPH What happens to the sugar produced? • 50% is used as fuell for cellular respiration ○ Transported throughout the plant (only green parts of photosynthetic) • Linked together to form • Excess stored as starch • Makes 160 BILLION metric tons of carbohydrate per year ○ Equal to about 60 trillion copes of your textbook Top Hat Questions Friday, October 7, 2016 9:29 AM In the thylakoid membranes, what is the main role of the pigment molecules in a light-harvesting coa. transfer electrons to ferredoxin and then NADPH b. split water and release oxygen to the reaction-centerchlorophyll c. synthesize ATP from ADP and Pi d. concentratephotons within the stroma e. transfer light energy to the reaction-centerchlorophyll The light reactions of photosynthesissupply the Calvin cycle with a. Light energy b. CO2 and ATP c. H2O and NADPH d. ATP and NADPH e. Sugar and O2 When oxygen is released as a result of photosynthesis,it is a direct by-product of a. chemiosmosis. b. splitting water molecules. c. the electron transfer system of photosystem II d. reducing NADP+ e. the electron transfer system of photosystem I How are the light reactions and the Calvin cycle connected? a. The light reactions provide ATP to the Calvin cycle, and the Calvin cycle provide NADPH for the light reactions. b. The light reactions provide ATP and NADPH to the Calvin cycle, and the Calvin cycle returns ADP, Pi, and NADP+ to the light reactions. c. The light reactions provide ATP and NADPH to the Calvin cycle, and the Calvin cycle returns reduced sugars to the light reactions. d. The light reactions provide NADPH to the Calvin cycle, and the Calvin cycle provides RuBP to the light reactions. e. The light reactions provide RuBP to the Calvin cycle, and the Calvin cycle returns G3P to the light reactions. Which of the following does NOT occur during the Calvin cycle? a. Carbon fixation b. Oxidation of NADPH c. Regeneration of the CO2 acceptor d. Consumption of ATP e. Release of oxygen Which process is most directly driven by light energy? a. Creation of a pH gradient by pumping H+ across the thylakoid membrane b. Carbon fixation in the stroma c. Reduction of NADP+ molecules d. Removalof electrons from chlorophyll molecules e. ATP synthesis If you plant a maple seed in your backyard and over the course of many years it grows into a tall maple tree, where did the increase in mass come from? a. soil b. water c. air d. organic fertilizer e. light


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