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UNL / Management / MNGT 120 / what is the direct source of energy for phototrophs

what is the direct source of energy for phototrophs

what is the direct source of energy for phototrophs

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∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to convert ADP +Pi to ATP?




o What happens after glycolysis and the citric acid cycle?




∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum number of ATP molecules that could be made through substrate­level phosphorylation?



Chapter 8: Photosynthesis (Lecture 1) ∙ Autotrophs o Producers—generated organic molecules from CO2 and inorganic moWe also discuss several other topics like What are the processes involved in the oxidation of alcohol?
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lecules o Photoautotrophs—use sunlight to make organic molecules from  H2O and CO2 ∙ Heterotrophs o Obtain organic material from other organisms o Consumers—depend on photoautotrophs for food and O2 o Depend on autotrophs ∙ UNL is a major research site for biofuels ∙ Almost all energy to power life comes from the sun ∙ Mostly, photosynthetic organisms are the base of the food chain ∙ Photosynthesis creates sugar from sunlight and then breaks that down  into ATP ∙ Anatomy of photosynthesis o Mesophyll o Veins o Stomata o 30-40 chloroplasts per cell o chlorophyll-in thylakoid membranes  where all the action is taking place  harvests light energy ∙ Photosynthesis as a Redox Process o H2O is oxidized and CO2 is released  Creating sugars  Uphill reaction…positive DeltaG…requires energy o 6 CO2 + 12 H2O + Energy → C6H12O6 + 6 O2 + 6 H2O  o CO2 + 2H2O + Energy → [CH2O] + O2 + 1 H2O  o CO2 + 2H2S + Energy → [CH2O] + 2S + 1 H2O  o H2O is split to provide a source of electrons from H+, releasing O2 as the byproduct ∙ Evolution of Photosynthetic Prokaryotes o Early cells that used light to make CHOs from CO2 oxidized H2S  or Fe compounds o Break-through came with splitting of H2O for organic compound  synthesis o Amount of oxygen in atmosphere controls body size of organisms  Ex. Giant dragon flies lived at an oxygen rich era ∙ Two Stages of Photosynthesis: A Preview o Light reactions (the “photo” part)  Occurs in thylakoids (green pancakes)  Split H2O and released O2  Uses light energy to ∙ Reduce NADP+ to NADPH ∙ Generate ATP by photophosphorylation o Calvin cycle (the “synthesis” part)  Occurs in stroma  Uses ATP and NADPH to carry out carbon fixation—converts CO2 to CH2O ∙ PHOTOSYNTHESIS: 1. Chlorophyll in thylakoid membranes absorbs light energy a. Splitting water 2. Light energy captures H+ and electrons from water to make ATP and  reduce NADPH a. Oxygen is released 3. CO2 enters the stroma and is fed into Calvin cycle—long term storage  section a. ATP and NADPH provide energy to synthesize sugars from CO2 4. Carbon from CO2 is fixed into sugars ∙ The biomass (dry weight) of a tree comes primarily from  o Air o Because trees are made of cellulose (sugar), sugars are made  of carbon, carbon is made from air ∙ Which of the following sequences correctly represents the flow of  electrons during photosynthesis? o H20—>NADPH—>Calvin cycle ∙ Photosynthetic Pigments: The light receptors o Pigments absorb visible light—electromagnetic  Different pigments absorb different wavelengths o Wavelengths not absorbed are reflected and transmitted o Chlorophyll reflects and transmits green light  Chlorophyll a ∙ Primary photosynthetic pigment  Chlorophyll b ∙ Accessory pigments broaden spectrum  Carotenoids ∙ Absorb excessive light that can damage  chlorophyll ∙ A spectrophotometer measures pigments ability to absorb various  wavelengths o Sends light through pigments and measures amount of/which  type of light is being absorbed or transmittedo ∙ an absorption spectrum is a graph plotting a pigment’s light  absorption versus wavelength ∙ the absorption spectrum of chlorophyll a suggests that violet-blue  and red light work best for photosynthesis ∙ An action spectrum profiles the relative effectiveness of different  wavelengths of radiation in driving a process o The action spectrum of photosynthesis was first demonstrated in 1883 by Theodor W. Engelmann o In his experiment, he exposed different segments of a  filamentous alga to different wavelengths o Areas receiving wavelengths favorable to photosynthesis  produced excess O2 o He used the growth of aerobic bacteria clustered along the  alga as a measure of O2 production ∙ Chlorophyll a is the main photosynthetic pigment ∙ Accessory pigments, such as chlorophyll b, broaden the spectrum  used for photosynthesis ∙ Accessory pigments called carotenoids absorb excessive light that  would damage chlorophyll∙ Citric acid cycle overview o Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms citrate (6C) o 7 steps decompose citrate (6c) back to oxaloacetate (4C)­CO2 is released o ATP, NADH, FADH2 are energy products o Generated 1 ATP, 3 NADH, 1 FADH2 per turn o REVIEW TCA FOR EXAM ∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum  number of ATP molecules that could be made through substrate­level phosphorylation? o 1 ∙ carbon skeletons for amino acid biosynthesis are supplied by intermediates of the citric  acid cycle. Which intermediate would supply the carbon skeleton for synthesis of a five carbon amino acid? o Alpha­ketoglutarate ∙ During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis o What happens after glycolysis and the citric acid cycle?  NADH and FADH2 account for most of the energy extracted from food  Electron carriers donate electrons to the electron transport chain, which  powers ATP synthesis via oxidative phosphorylation o NADH and FADH2 convert electrons into ATP energy  We make a ton more ATP a lot faster with this cycle ∙ Cellular respiration involved controlled release of NADH stored energy to produce ATP  o Electrons are passed to the electron transport chain o O2 pulls electrons down the chain o Energy­yielding tumble o Energy used to regenerate ATP  345 lbs./day ∙ Electron transport chain o Protein complexes (I­IV)  Cristae of inner mitochondrial membrane  Prosthetic groups assist electron transport o Carriers alternated reduced and oxidized states  Accept and donate electrons to gradually release energy o Energy drop  NADH to O2­53 kcal/mol  Energy decreases as it goes down the chain o Complex 1  1st Redox reaction ∙ flavomononucleotide (FM) accepts 2 electrons from NADH­gets  reduced ∙ FMN re oxidized when electron passes to (Fe­S) ∙ 2 electrons to ubiquinone (CoQ) o Complex 2 FADH released 2 electrons  Lower energy­produces less ATP o Complex 3 and 4  Cytochromes  Heme­iron atom that accepts/donates electrons  Cyt a2 pass 2 electrons to O2  O2 most electron negative  2 H+ combine to from H2O  electrons now in low energy state o also a Hydrogen ion pump  protein complexes of ET chain function as H+ pump ∙ electron fall down and release energy ∙ H+ pumped across inner mitochondrial membrane ∙ Inner membrane space fills with H+ o Creates chemiosmotic/electrochemical gradient o Both pH and electric potential difference  Produces a proton motive force ∙ End result: an electrochemical gradient ∙ DeltaG is about 50% electrical, 50%  chemical gradient  o Chemiosmosis—the energy coupling mechanism  Electron transfer causes proteins to pump H+ from mitochondrial matrix  to the intermembrane space  H+ moves back across the membrane, through channels in ATP synthase  Exergonic flow of H+ drives phosphorylation of ATP – uses energy of the  ion gradient  Bacteria do something almost identical to this, it’s just on inner surface of  membrane o ATP synthetase  Multisubunit proton pump  Molecular rotary motor  Inner mitochondrial membrane  Prokaryote plasma membrane  1. H+ flow down gradient into anchored stator  2. H+ bind rotor altering shape so it spins  3. H+ leaves rotor after 1 full spin  4. Rotor turns a rod that extends into knob below  5. Catalytic site on turning knobs drive ATP ∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to  convert ADP +Pi to ATP? o Energy released from movement of protons through ATP synthesis ∙ Fermentation and anaerobic respiration produce ATP without use of oxygen o Glycolysis can produce ATP without O2o Oxidation under anaerobic conditions  ATP generated by substrate level phosphorylation  NADH is made & used to regenerate NAD+,  e­ donated to an electron acceptor o Types of anaerobic respiration  Fermentation – ethanol acceptor (yeast)  Fermentation ­ lactic acid acceptor (muscle cells)  Prokaryotes ­ reduce sulfates to H2S   Prokaryotes ­ reduce sulfates to H2S  o Aerobic respiration ­ 38 ATP/glucose o Fermentation ­ 2 ATP/ glucose  Pyruvate ­ fork in the metabolic road   ­ leads to alternative catabolic routes  “Glycolysis flareup” ∙  rapid muscle use consumes ATP ∙  stresses O2 delivery ∙  lactic acid pathway kicks in o Alcohol fermentation  pyruvate converted to ethanol  release of CO2  used by yeast in brewing, winemaking, and baking o Lactic acid fermentation o Pyruvate reduced to NADH o Lactate end product ­ no release of CO2  Fungi and bacteria ∙ cheese & yogurt  Muscle cells  ∙ lactic acid fermentation generates ATP when O2 is scarce o Gycolysis and the citric acid cycle are major intersections to both catabolic and  anabolic pathways o Catabolic pathways  Glucose from starch, glycogen & carbs feed in  Proteins feed in as amino acids & amino groups (deamination)  Fats produce 2x ATP per gm as sugars ∙ Beta oxidation breaks fatty acids ∙ yields NADH & FADH2 ∙ 2 C fragments enter at acetyl CoA o Anabolic Pathways  Glycolysis & citric acid cycle intermediates feed into most major synthesis pathways o Regulation of Cellular Respiration via Feedback mechanisms  Feedback inhibition is the most common mechanism for control ∙ ATP low ­ respiration increases∙ ATP high ­ respiration slows down  Control of catabolism  ∙ Regulate enzyme at strategic points in the catabolic pathway  Allosteric enzymes occur throughout   Set pace of respiration and energy generation o Phosphofructokinase  Allosteric enzyme complex  Activated by AMP  Inhibited by ATP & citrate ∙ FOR EXAM o Understand processes  Not so much structures o TCA Cycle  Why this is so central to biology?  Understand diagram  2 cycles per glucose  Key enzymes & steps  Inputs & outputs  Cellular locationChapter 7 ∙ Feedback inhibition-when the end product of a pathway shuts down the pathway o Helps regulate levels of substance within cells ∙ Cellular respiration o Fundamental metabolic pathways function and connect o Conversion of light energy into chemical energy o Glycolysis first step in cytoplasm ∙ Redox-transfer of electrons ∙ Leo says Ger o L-lose o E-electrons o O-oxidation o G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2 ∙ phosphoglucoisomerase o glucose converted to isomer o form can accept another phosphate ∙ phosphofructokinase (PFK)o fructose phosphorylated  o 6 carbon sugar has two phosphate o allosterically regulated step by ATP feedback inhibition   very important for cell health  “lysis’ part of glycolysis ∙ molecule is energetic and wants to pull itself apart ∙ aldolase o cleaves one 6C to two 3C sugars ∙ isomerase o interconverts two forms o G­3­P quickly processed  Triose phosphate dehydrogenase (Dehydrogenases­enzymes that transfer  H+) ∙ H+ evolved, NAD reduced, REDOX ∙ Phosphate added  ∙ Highly exergonic ∙ Highly reactive product  Phosphoglycerokinase ∙ Exergonic­creates 2 ATP/glucose ∙ First ATP payoff  ∙ Substrate level phosphorylation ∙ Product is an organic acid  Phosphoglyceromutase ∙ Phosphate is rearranged o Destabilizes molecule product further   Enolase  ∙ Creates double bond in substrate ∙ PEP is a high energy product o –DeltaG is 10 kcal  Pyruvate kinase ∙ PEP converted to pyruvate ∙ 2 more ATP generated/glucose ∙ 2nd substrate level phosphorylation ∙ pyruvate to TCA cycle if O2 is present ∙ pyruvate into fermentation if no O2 is present ∙ Substrate­level phosphorylation accounts for approximately what percentage of the ATP  formed by the reactions of glycolysis? o 100% ∙ Which statement about glycolysis is true? o It occurs in the cytoplasm ∙ When a glucose molecule loses a hydrogen atom as a result of an oxidation­reduction  reaction, the molecule becomes o Oxidized  ∙ Citric acid cycle o Aerobic respiration­require O2 o Further breakdown of pyruvate and release of CO2 o Pyruvate enters mitochondrion­transport protein o Pyruvate dehydrogenase­3 enzyme complex o COO gp is released as CO2; NADH is produced o Coenzyme is coupled­high energy Acetyl CoA o Lose Co2, left with 2 C  Coenzyme A (Vitamin B) is a temporary holding molecule for the bond  transfer o Overview   Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms  citrate (6C)  7 steps decompose citrate (6C) back to oxaloacetate (4C)­CO2 is released ∙ recycling  ATP, NADH, FADH2 are energy products  Generated 1 ATP, 3 NADH, 1 FADH2 per turn ∙ 1. 2C acetyl gp added to 4C oxaloacetate –DeltaG is ­7.7 kcal o 4C becomes 6C citrate o citrate synthetase­key regulatory enzyme o follow the fate of C’s  o cirtrate­3 carboxylates  ∙ 2. Citrate converted to a new form ∙ 3. Isocitrate­oxidized NAD, reduced CO2, released ∙ 4. Co2 released, substrate oxidized, NAD reduced, CoA group is  coupled o 2C’s gone, protons and electrons retained ∙ 5. CoA replaced by phosphate, coupled to make GTP, then ATP  energy is stored o regeneration of starting substrate follows o substrate level phosphorylation ∙ 6. Succinate oxidized and FAD reduced to FADH2 ∙ 7. H2O rearranges substrate ∙ 8. Malate oxidized, NAD reduced, oxaloacetate regenerated ∙ Energy yield: o 1 ATP o 3 NADH o 1 FADH2 o per turn o 2x for each glucose∙ KNOW FOR TEST: What’s going in, what’s coming out? Where  and when? Study pathway well. Understand diagram, key  enzymes and steps, inputs and outputs, cellular location, does it require O2 to be present? NoEnergy investment phase Glucose 2 ADP + 2P 2 ATP used Energy payoff phase 4 ADP + 4P 4 ATP formed 2 NAD+ + 4 e– + 4 H+ 2 NADH+ 2 H+ 2 Pyruvate + 2 H2O Glucose 2 Pyruvate + 2 H2O Net 4 ATP formed – 2 ATP used 2 ATP 2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+ ∙ Citric acid cycle overview o Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms citrate (6C) o 7 steps decompose citrate (6c) back to oxaloacetate (4C)­CO2 is released o ATP, NADH, FADH2 are energy products o Generated 1 ATP, 3 NADH, 1 FADH2 per turn o REVIEW TCA FOR EXAM ∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum  number of ATP molecules that could be made through substrate­level phosphorylation? o 1 ∙ carbon skeletons for amino acid biosynthesis are supplied by intermediates of the citric  acid cycle. Which intermediate would supply the carbon skeleton for synthesis of a five carbon amino acid? o Alpha­ketoglutarate∙ During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis o What happens after glycolysis and the citric acid cycle?  NADH and FADH2 account for most of the energy extracted from food  Electron carriers donate electrons to the electron transport chain, which  powers ATP synthesis via oxidative phosphorylation o NADH and FADH2 convert electrons into ATP energy  We make a ton more ATP a lot faster with this cycle ∙ Cellular respiration involved controlled release of NADH stored energy to produce ATP  o Electrons are passed to the electron transport chain o O2 pulls electrons down the chain o Energy­yielding tumble o Energy used to regenerate ATP  345 lbs./day ∙ Electron transport chain o Protein complexes (I­IV)  Cristae of inner mitochondrial membrane  Prosthetic groups assist electron transport o Carriers alternated reduced and oxidized states  Accept and donate electrons to gradually release energy o Energy drop  NADH to O2­53 kcal/mol  Energy decreases as it goes down the chain o Complex 1  1st Redox reaction ∙ flavomononucleotide (FM) accepts 2 electrons from NADH­gets  reduced ∙ FMN re oxidized when electron passes to (Fe­S) ∙ 2 electrons to ubiquinone (CoQ) o Complex 2  FADH released 2 electrons  Lower energy­produces less ATP o Complex 3 and 4  Cytochromes  Heme­iron atom that accepts/donates electrons  Cyt a2 pass 2 electrons to O2  O2 most electron negative  2 H+ combine to from H2O  electrons now in low energy state o also a Hydrogen ion pump  protein complexes of ET chain function as H+ pump ∙ electron fall down and release energy ∙ H+ pumped across inner mitochondrial membrane∙ Inner membrane space fills with H+ o Creates chemiosmotic/electrochemical gradient o Both pH and electric potential difference  Produces a proton motive force ∙ End result: an electrochemical gradient ∙ DeltaG is about 50% electrical, 50%  chemical gradient  o Chemiosmosis—the energy coupling mechanism  Electron transfer causes proteins to pump H+ from mitochondrial matrix  to the intermembrane space  H+ moves back across the membrane, through channels in ATP synthase  Exergonic flow of H+ drives phosphorylation of ATP – uses energy of the  ion gradient  Bacteria do something almost identical to this, it’s just on inner surface of  membrane o ATP synthetase  Multisubunit proton pump  Molecular rotary motor  Inner mitochondrial membrane  Prokaryote plasma membrane  1. H+ flow down gradient into anchored stator  2. H+ bind rotor altering shape so it spins  3. H+ leaves rotor after 1 full spin  4. Rotor turns a rod that extends into knob below  5. Catalytic site on turning knobs drive ATP ∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to  convert ADP +Pi to ATP? o Energy released from movement of protons through ATP synthesis ∙ Fermentation and anaerobic respiration produce ATP without use of oxygen o Glycolysis can produce ATP without O2 o Oxidation under anaerobic conditions  ATP generated by substrate level phosphorylation  NADH is made & used to regenerate NAD+,  e­ donated to an electron acceptor o Types of anaerobic respiration  Fermentation – ethanol acceptor (yeast)  Fermentation ­ lactic acid acceptor (muscle cells)  Prokaryotes ­ reduce sulfates to H2S   Prokaryotes ­ reduce sulfates to H2S  o Aerobic respiration ­ 38 ATP/glucose o Fermentation ­ 2 ATP/ glucose  Pyruvate ­ fork in the metabolic road   ­ leads to alternative catabolic routes “Glycolysis flareup” ∙  rapid muscle use consumes ATP ∙  stresses O2 delivery ∙  lactic acid pathway kicks in o Alcohol fermentation  pyruvate converted to ethanol  release of CO2  used by yeast in brewing, winemaking, and baking o Lactic acid fermentation o Pyruvate reduced to NADH o Lactate end product ­ no release of CO2  Fungi and bacteria ∙ cheese & yogurt  Muscle cells  ∙ lactic acid fermentation generates ATP when O2 is scarce o Gycolysis and the citric acid cycle are major intersections to both catabolic and  anabolic pathways o Catabolic pathways  Glucose from starch, glycogen & carbs feed in  Proteins feed in as amino acids & amino groups (deamination)  Fats produce 2x ATP per gm as sugars ∙ Beta oxidation breaks fatty acids ∙ yields NADH & FADH2 ∙ 2 C fragments enter at acetyl CoA o Anabolic Pathways  Glycolysis & citric acid cycle intermediates feed into most major synthesis pathways o Regulation of Cellular Respiration via Feedback mechanisms  Feedback inhibition is the most common mechanism for control ∙ ATP low ­ respiration increases ∙ ATP high ­ respiration slows down  Control of catabolism  ∙ Regulate enzyme at strategic points in the catabolic pathway  Allosteric enzymes occur throughout   Set pace of respiration and energy generation o Phosphofructokinase  Allosteric enzyme complex  Activated by AMP  Inhibited by ATP & citrate ∙ FOR EXAM o Understand processes  Not so much structureso TCA Cycle  Why this is so central to biology?  Understand diagram  2 cycles per glucose  Key enzymes & steps  Inputs & outputs  Cellular locationChapter 8: Photosynthesis (Lecture 1) ∙ Autotrophs o Producers—generated organic molecules from CO2 and inorganic molecules o Photoautotrophs—use sunlight to make organic molecules from  H2O and CO2 ∙ Heterotrophs o Obtain organic material from other organisms o Consumers—depend on photoautotrophs for food and O2 o Depend on autotrophs ∙ UNL is a major research site for biofuels ∙ Almost all energy to power life comes from the sun ∙ Mostly, photosynthetic organisms are the base of the food chain ∙ Photosynthesis creates sugar from sunlight and then breaks that down  into ATP ∙ Anatomy of photosynthesis o Mesophyll o Veins o Stomata o 30-40 chloroplasts per cell o chlorophyll-in thylakoid membranes  where all the action is taking place  harvests light energy ∙ Photosynthesis as a Redox Process o H2O is oxidized and CO2 is released  Creating sugars  Uphill reaction…positive DeltaG…requires energy o 6 CO2 + 12 H2O + Energy → C6H12O6 + 6 O2 + 6 H2O  o CO2 + 2H2O + Energy → [CH2O] + O2 + 1 H2O  o CO2 + 2H2S + Energy → [CH2O] + 2S + 1 H2O  o H2O is split to provide a source of electrons from H+, releasing O2 as the byproduct ∙ Evolution of Photosynthetic Prokaryotes o Early cells that used light to make CHOs from CO2 oxidized H2S  or Fe compounds o Break-through came with splitting of H2O for organic compound  synthesis o Amount of oxygen in atmosphere controls body size of organisms  Ex. Giant dragon flies lived at an oxygen rich era ∙ Two Stages of Photosynthesis: A Preview o Light reactions (the “photo” part)  Occurs in thylakoids (green pancakes)  Split H2O and released O2  Uses light energy to ∙ Reduce NADP+ to NADPH ∙ Generate ATP by photophosphorylation o Calvin cycle (the “synthesis” part)  Occurs in stroma  Uses ATP and NADPH to carry out carbon fixation—converts CO2 to CH2O ∙ PHOTOSYNTHESIS: 1. Chlorophyll in thylakoid membranes absorbs light energy a. Splitting water 2. Light energy captures H+ and electrons from water to make ATP and  reduce NADPH a. Oxygen is released 3. CO2 enters the stroma and is fed into Calvin cycle—long term storage  section a. ATP and NADPH provide energy to synthesize sugars from CO2 4. Carbon from CO2 is fixed into sugars ∙ The biomass (dry weight) of a tree comes primarily from  o Air o Because trees are made of cellulose (sugar), sugars are made  of carbon, carbon is made from air ∙ Which of the following sequences correctly represents the flow of  electrons during photosynthesis? o H20—>NADPH—>Calvin cycle ∙ Photosynthetic Pigments: The light receptors o Pigments absorb visible light—electromagnetic  Different pigments absorb different wavelengths o Wavelengths not absorbed are reflected and transmitted o Chlorophyll reflects and transmits green light  Chlorophyll a ∙ Primary photosynthetic pigment  Chlorophyll b ∙ Accessory pigments broaden spectrum  Carotenoids ∙ Absorb excessive light that can damage  chlorophyll ∙ A spectrophotometer measures pigments ability to absorb various  wavelengths o Sends light through pigments and measures amount of/which  type of light is being absorbed or transmittedo ∙ an absorption spectrum is a graph plotting a pigment’s light  absorption versus wavelength ∙ the absorption spectrum of chlorophyll a suggests that violet-blue  and red light work best for photosynthesis ∙ An action spectrum profiles the relative effectiveness of different  wavelengths of radiation in driving a process o The action spectrum of photosynthesis was first demonstrated in 1883 by Theodor W. Engelmann o In his experiment, he exposed different segments of a  filamentous alga to different wavelengths o Areas receiving wavelengths favorable to photosynthesis  produced excess O2 o He used the growth of aerobic bacteria clustered along the  alga as a measure of O2 production ∙ Chlorophyll a is the main photosynthetic pigment ∙ Accessory pigments, such as chlorophyll b, broaden the spectrum  used for photosynthesis ∙ Accessory pigments called carotenoids absorb excessive light that  would damage chlorophyllEXAM 2 REVIEW • The Calvin cycle uses ATP and NADPH to convert CO2 to sugar – Calvin cycle regenerates starting material – Calvin cycle regenerates starting material • Photorespiration – In most plants (C3 plants), initial fixation of CO2, via rubisco,  forms a three-carbon compound (3-phosphoglycerate) – In photorespiration, rubisco adds O2 instead of CO2 in the Calvin  cycle, producing a two-carbon compound – Photorespiration consumes O2 and organic fuel and releases CO2 without producing ATP or sugar – Stoma closure occurs to preserve water – CO2 uptake decreases – O2 conc. increases inside leaf – Calvin cycle is “starved” – Rubisco captures O2 creating 2C products – consume ATP & releases CO2 – C3 plants - rice, wheat & soybean – lose up to 50% of fixed carbon – Evolutionary relic  – Rubisco evolved at a time when the atmosphere had far  less O2 and more CO2 • C4 Plants – Adapted to warm climates – 19 families of grasses – corn, sugarcane, mycanthus – use 4C molecule  • C4 plants spatially separate photosynthesis – Incorporate CO2 into four-carbon not 3C compounds before  entering Calvin cycle  – Physically separate chambers that have more oxygen in them  from the ones that don’t – Do it my anatomy of the leaf  • Mesophyll cells on outside fix CO2 • Bundle sheath on inside house Calvin cycle – CO2 incorporated into 4-carbon oxaloacetate in mesophyll cells – PEP carboxylase – higher affinity for CO2 than rubisco – fix CO2 at low conc – 4C malate exported to bundle-sheath cells – CO2 released into Calvin cycle – Spatial organization – Pyruvate returned to mesophyll cell at expense of 1 ATP • CAM Plants– Adapted to hot, dry climates  – Cacti, succulents & epiphytes – Crassulacean acid metabolism (CAM) – Open stomata at night – Incorporate CO2 into organic acids like C4 at night – Close stomata during day to save water – CO2 is released from organic acids to the Calvin cycle during day – Temporal regulation • Chemiosmosis in Chloroplasts and Mitochondria – ATP is generated in both by chemiosmosis – Mitochondria – H+ pumped into intermembrane space – drives ATP synthesis by diffusing back into matrix – Chloroplasts – H+ pumped into thylakoid space – drives ATP synthesis by diffusing back into the stroma CLICKER QUESTIONS—REVIEW FOR EXAM!!!!! • Why is ATP an important molecule in metabolism? – It provides energy coupling between exergonic and endergonic  reactions • Which of the following statements regarding enzymes is true? – Enzymes increase the rate of a reaction by lowering the  activation energy barrier • The molecule that functions as the reducing agent (electron  donor) in a redox or oxidation reduction reaction – Loses electrons and loses potential energy • The primary role of oxygen in cellular respiration is to  – Act as an acceptor for electrons and hydrogen, forming water • Why is glycolysis considered to be one of the first metabolic  pathways to have evolved? – It does not involve organelles or specialized structures, does not  require oxygen, and is present in most organisms • When oxygen is released as a result of photosynthesis, it is a  direct by-product of  – Splitting water molecules • Which of the following statements best describes the  relationship between photosynthesis and respiration? – Photosynthesis stores energy in complex organic molecules,  whereas respiration releases it • The oxygen atoms in H2O broken down during photosynthesis  end up in  – Molecular O2 released during photosynthesis• What is the term for metabolic pathways that release stored  energy by breaking down complex molecules? – Catabolic pathways • During glycolysis, for each mole of glucose oxidized to pyruvate,  – 2 moles of ATP are used, and 4 moles of ATP are produced • In chemiosmotic phosphorylation, what is the most direct  source of energy that is used to convert ATP + Pi to ATP? – Energy released from movement of protons through ATP  synthase • What carbon sources can yeast cells metabolize to make ATP  from ADP under anaerobic conditions? – Glucose • The biomass (dry weight) of a tree comes primarily from – CO2 (air) • Which of the following sequences correctly represent the flow  of electrons during photosynthesis? – H2O NADPH  Calvin Cycle • In thylakoids, protons travel through ATP synthase from the  thylakoid space to the stroma. Therefore, the catalytic “knobs” of ATP synthase would be located – On the outside of the membrane • Assume a thylakoid is somehow punctured so that the interior  of the thylakoid is no longer separated from the stroma. This  damage will have the most direct effect on which of the  following processes? – The synthesis of ATPLIFE120 LECTURES-(clicker questions and answers in red) CHAPTER 6 ∙ Catabolic pathways-releasing energy, breaking down complex  molecules o Cellular respiration o Harvest energy from bonds (electrons) in food ∙ Anabolic pathways-consume energy, build complex molecules,  synthesis of proteins from amino acids ∙ Forms of energy o Potential-diver at the top of the platform o Thermal-hitting the water, releasing energy as heat o Kinetic-diving off the board o Chemical o Organisms are islands of low entropy in an increasingly random  universe! ∙ Biological Order/Disorder o Cells create ordered structures (anabolic) o Organisms alter matter and energy to less ordered forms  (catabolic) o Energy flows in as light and exits as heat  Transferring energy to create local order ∙ Are chemical reactions at equilibrium in living cells?  o No ∙ Thermodynamics-Laws of Energy Transformation o Energy of universe is constant o First law of thermodynamics  Energy can be transferred and transformed, but it cannot  be created or destroyed (kinetic, heat, potential, chemical) o Second law of thermodynamics  Every energy transfer increases the entropy (disorder) of  the universe ∙ To occur spontaneously, processes occur without  energy input…to occur spontaneously, it must  increase disorder of the universe ∙ Organisms use energy to create more order ∙ Entropy may decrease in an organism o Releasing heat sends entropy into the universe  Heat is the motion of molecules ∙ Organisms are islands of low entropy in an increasingly random  universe! ∙ How do living organisms create macromolecules, organelles, cells,  tissues, and complex higher-order structures?o Living organisms create order locally, but the energy  transformations generate waste heat that increases the entropy  of the universe.  ∙ Free energy o Measure of living systems free energy  Gibb’s Free Energy-energy available to do work when  temperature and pressure are uniform, as in a living cell  ∙ DeltaG=DeltaH-TDeltaS o DeltaG is free energy o DeltaH is enthalpy o T is temperature in Kelvin o DeltaS is entropy ∙ Change in energy tells us whether a process is  spontaneous or not o Enthalpy-total energy of a system  Change in DeltaH o Entropy-measure of disorder in a system  Change in disorder of DeltaS o Change in free energy is related to the change in enthalpy,  entropy, and temperature in Kelvin o Processes with negative DeltaG, reactions are spontaneous (they  go downhill) o Spontaneous processes can be harnessed to perform work  Give off heat ∙ Fireworks o Exergonic-releases energy (spontaneous)  Dissolving of slat in water  o Endergonic-requires energy (nonspontaneous)  Hand warmers for football games o Free Energy, Stability, Equilibrium  Free energy-measures a system’s instability  During spontaneous change, free energy decreases,  stability increases  Equilibrium is achieved-state of maximum stability ∙ Reactions in closed system reach equilibrium, can’t  do work ∙ Reactions in open systems never reach equilibrium,  work continuously o Cells of open systems never in equilibrium  where products of reaction are removed!  Metabolism never at equilibrium-GOOD!! ∙ Anabolic-stores free energy o DeltaG= +686 kcal/mol o Photosynthesis (chloroplasts)∙ Catabolic-releases free energy o DeltaG= -686 kcal/mol o Respiration (mitochondria)  Coupling exergonic reactions ∙ Cell does three kinds of work o Chemical-synthesis of polymers o Transport-pumping ions across membranes o Mechanical-movement ∙ Energy coupling by ATP o Used for most cell work o Larger –DeltaG reactions drives smaller  +DeltaG reaction o Net free energy less than zero o Structure and Hydrolysis of ATP  ATP (adenosine triphosphate)- cell’s energy shuttle  Composed of 3 ribose (a sugar), adenine (a nitrogenous  base), 3 phosphate groups ∙ Bonds between phosphate groups broken by  hydrolysis ∙ Energy released when terminal Pi bond broken ∙ Highly exergonic ∙ Metabolism is never at equilibrium-defining feature of life o Anabolic- (positive DeltaG)  Stores free energy  DeltaG= +686 kcal/cal  Building sugars, all work, costs energy o Catabolic- (negative DeltaG)  Releases free energy  Burning sugars, consumer side   DeltaG= -686 kcal/mol ∙ Gibbs Free Energy Change  o Change in free energy (DeltaG) is related to change in enthalpy  and entropy  Processes with negative DeltaG are spontaneous ∙ Hydrolysis of ATP is spontaneous reaction o Bonds between phosphate groups broken by hydrolysis  o Energy released when terminal Pi bond broken o EXERGONIC ∙ ATP powers cellular work by coupling exergonic reactions to endergonic reactions o Coupling ATP  Used for most cell work  Larger –DeltaG reaction drives smaller +DeltaG reaction ∙ Energy coupling using Hydrolysis of ATPo Endergonic reactions-+DeltaG, not spontaneous o Coupled exergonic reaction  ATP phosphorylates glutamic acid-less stable  o Free energy exchange overall is negative   ATP drives endergonic reactions ∙ Think about all of the activity in your cells right now o A lot of it costs energy, a lot of it makes energy o Have to maintain functions ∙ ATP is a renewable source o Regenerated by Pi addition to adenosine diphosphate (ADP) o Phosphorylation energy comes from cellular catabolic reactions ∙ When ATP releases free energy, it also releases inorganic phosphate.  What purpose does this serve (if any) in the cell? o The phosphate may be incorporated into many different  molecules ∙ Enzymes speed up reactions but aren’t consumed in them ∙ Catalyst-a chemical agent that speeds up a reaction without being  consumed o Metals ∙ Enzyme-catalytic protein ∙ Activation of the energy barrier o Chemical reaction between molecules involves bond breaking  and bond forming   AB + CD  AC +BD o Activation energy (Ea) o Free energy of activation  Initial energy needed to start reaction  Heat-chemical reactions  Cells can’t be heated or they die! ∙ Everything will become denatured ∙ Energy profile of an exergonic reaction—SLIDE 15, lecture 2 o DeltaG is unaffected by the enzyme ∙ The reaction has a DeltaG of -5.6 kcal/mol. Which of the following  would most likely be true? o The reaction would result in an increase in entropy (S) and a  decrease in the energy content (H) of the system  ∙ Enzyme temperatures—SLIDE 19 ∙ Competitive inhibitors o Bind active site and compete with substrate o Competing for substrate spot in active site ∙ Noncompetitive inhibitors o Bind to other part of enzyme, alter shape of active site less  effective  o Inhibitor binds somewhere away from active site Enzyme is inactive and can’t bind substrate anymore ∙ Allosteric regulation-may either inhibit or stimulate an enzyme’s  activity o Occurs when a regulatory molecule binds to a protein at one site  and affects the protein’s function at another site Chapter 7 ∙ Feedback inhibition-when the end product of a pathway shuts down the pathway o Helps regulate levels of substance within cells ∙ Cellular respiration o Fundamental metabolic pathways function and connect o Conversion of light energy into chemical energy o Glycolysis first step in cytoplasm ∙ Redox-transfer of electrons ∙ Leo says Ger o L-lose o E-electrons o O-oxidation o G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2∙ phosphoglucoisomerase o glucose converted to isomer o form can accept another phosphate ∙ phosphofructokinase (PFK) o fructose phosphorylated  o 6 carbon sugar has two phosphate o allosterically regulated step by ATP feedback inhibition   very important for cell health  “lysis’ part of glycolysis ∙ molecule is energetic and wants to pull itself apart ∙ aldolase o cleaves one 6C to two 3C sugars ∙ isomerase o interconverts two forms o G­3­P quickly processed  Triose phosphate dehydrogenase (Dehydrogenases­enzymes that transfer  H+) ∙ H+ evolved, NAD reduced, REDOX ∙ Phosphate added  ∙ Highly exergonic ∙ Highly reactive product  Phosphoglycerokinase ∙ Exergonic­creates 2 ATP/glucose ∙ First ATP payoff  ∙ Substrate level phosphorylation ∙ Product is an organic acid  Phosphoglyceromutase ∙ Phosphate is rearranged o Destabilizes molecule product further   Enolase  ∙ Creates double bond in substrate ∙ PEP is a high energy product o –DeltaG is 10 kcal  Pyruvate kinase ∙ PEP converted to pyruvate ∙ 2 more ATP generated/glucose ∙ 2nd substrate level phosphorylation ∙ pyruvate to TCA cycle if O2 is present ∙ pyruvate into fermentation if no O2 is present ∙ Substrate­level phosphorylation accounts for approximately what percentage of the ATP  formed by the reactions of glycolysis? o 100%∙ Which statement about glycolysis is true? o It occurs in the cytoplasm ∙ When a glucose molecule loses a hydrogen atom as a result of an oxidation­reduction  reaction, the molecule becomes  o Oxidized  ∙ Citric acid cycle o Aerobic respiration­require O2 o Further breakdown of pyruvate and release of CO2 o Pyruvate enters mitochondrion­transport protein o Pyruvate dehydrogenase­3 enzyme complex o COO gp is released as CO2; NADH is produced o Coenzyme is coupled­high energy Acetyl CoA o Lose Co2, left with 2 C  Coenzyme A (Vitamin B) is a temporary holding molecule for the bond  transfer o Overview   Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms  citrate (6C)  7 steps decompose citrate (6C) back to oxaloacetate (4C)­CO2 is released ∙ recycling  ATP, NADH, FADH2 are energy products  Generated 1 ATP, 3 NADH, 1 FADH2 per turn ∙ 1. 2C acetyl gp added to 4C oxaloacetate –DeltaG is ­7.7 kcal o 4C becomes 6C citrate o citrate synthetase­key regulatory enzyme o follow the fate of C’s  o cirtrate­3 carboxylates  ∙ 2. Citrate converted to a new form ∙ 3. Isocitrate­oxidized NAD, reduced CO2, released ∙ 4. Co2 released, substrate oxidized, NAD reduced, CoA group is  coupled o 2C’s gone, protons and electrons retained ∙ 5. CoA replaced by phosphate, coupled to make GTP, then ATP  energy is stored o regeneration of starting substrate follows o substrate level phosphorylation ∙ 6. Succinate oxidized and FAD reduced to FADH2 ∙ 7. H2O rearranges substrate ∙ 8. Malate oxidized, NAD reduced, oxaloacetate regenerated ∙ Energy yield: o 1 ATP o 3 NADHo 1 FADH2 o per turn o 2x for each glucose ∙ KNOW FOR TEST: What’s going in, what’s coming out? Where  and when? Study pathway well. Understand diagram, key  enzymes and steps, inputs and outputs, cellular location, does it require O2 to be present? Noo G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2 ∙ phosphoglucoisomerase o glucose converted to isomer o form can accept another phosphate ∙ phosphofructokinase (PFK) o fructose phosphorylated  o 6 carbon sugar has two phosphate o allosterically regulated step by ATP feedback inhibition   very important for cell health  “lysis’ part of glycolysis ∙ molecule is energetic and wants to pull itself apart ∙ aldolase o cleaves one 6C to two 3C sugars ∙ isomerase o interconverts two forms o G­3­P quickly processed  Triose phosphate dehydrogenase (Dehydrogenases­enzymes that transfer  H+)∙ H+ evolved, NAD reduced, REDOX ∙ Phosphate added  ∙ Highly exergonic ∙ Highly reactive product  Phosphoglycerokinase ∙ Exergonic­creates 2 ATP/glucose ∙ First ATP payoff  ∙ Substrate level phosphorylation ∙ Product is an organic acid  Phosphoglyceromutase ∙ Phosphate is rearranged o Destabilizes molecule product further   Enolase  ∙ Creates double bond in substrate ∙ PEP is a high energy product o –DeltaG is 10 kcal  Pyruvate kinase ∙ PEP converted to pyruvate ∙ 2 more ATP generated/glucose ∙ 2nd substrate level phosphorylation ∙ pyruvate to TCA cycle if O2 is present ∙ pyruvate into fermentation if no O2 is present ∙ Substrate­level phosphorylation accounts for approximately what percentage of the ATP  formed by the reactions of glycolysis? o 100% ∙ Which statement about glycolysis is true? o It occurs in the cytoplasm ∙ When a glucose molecule loses a hydrogen atom as a result of an oxidation­reduction  reaction, the molecule becomes  o Oxidized  ∙ Citric acid cycle o Aerobic respiration­require O2 o Further breakdown of pyruvate and release of CO2 o Pyruvate enters mitochondrion­transport protein o Pyruvate dehydrogenase­3 enzyme complex o COO gp is released as CO2; NADH is produced o Coenzyme is coupled­high energy Acetyl CoA o Lose Co2, left with 2 C  Coenzyme A (Vitamin B) is a temporary holding molecule for the bond  transfer o Overview  Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms  citrate (6C)  7 steps decompose citrate (6C) back to oxaloacetate (4C)­CO2 is released ∙ recycling  ATP, NADH, FADH2 are energy products  Generated 1 ATP, 3 NADH, 1 FADH2 per turn ∙ 1. 2C acetyl gp added to 4C oxaloacetate –DeltaG is ­7.7 kcal o 4C becomes 6C citrate o citrate synthetase­key regulatory enzyme o follow the fate of C’s  o cirtrate­3 carboxylates  ∙ 2. Citrate converted to a new form ∙ 3. Isocitrate­oxidized NAD, reduced CO2, released ∙ 4. Co2 released, substrate oxidized, NAD reduced, CoA group is  coupled o 2C’s gone, protons and electrons retained ∙ 5. CoA replaced by phosphate, coupled to make GTP, then ATP  energy is stored o regeneration of starting substrate follows o substrate level phosphorylation ∙ 6. Succinate oxidized and FAD reduced to FADH2 ∙ 7. H2O rearranges substrate ∙ 8. Malate oxidized, NAD reduced, oxaloacetate regenerated ∙ Energy yield: o 1 ATP o 3 NADH o 1 FADH2 o per turn o 2x for each glucose ∙ KNOW FOR TEST: What’s going in, what’s coming out? Where  and when? Study pathway well. Understand diagram, key  enzymes and steps, inputs and outputs, cellular location, does it require O2 to be present? NoEnergy investment phase Glucose 2 ADP + 2P 2 ATP used Energy payoff phase 4 ADP + 4P 4 ATP formed 2 NAD+ + 4 e– + 4 H+ 2 NADH+ 2 H+ 2 Pyruvate + 2 H2O Glucose 2 Pyruvate + 2 H2O Net 4 ATP formed – 2 ATP used 2 ATP 2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+ ∙ Citric acid cycle overview o Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms citrate (6C) o 7 steps decompose citrate (6c) back to oxaloacetate (4C)­CO2 is released o ATP, NADH, FADH2 are energy products o Generated 1 ATP, 3 NADH, 1 FADH2 per turn o REVIEW TCA FOR EXAM ∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum  number of ATP molecules that could be made through substrate­level phosphorylation? o 1 ∙ carbon skeletons for amino acid biosynthesis are supplied by intermediates of the citric  acid cycle. Which intermediate would supply the carbon skeleton for synthesis of a five carbon amino acid? o Alpha­ketoglutarate∙ During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis o What happens after glycolysis and the citric acid cycle?  NADH and FADH2 account for most of the energy extracted from food  Electron carriers donate electrons to the electron transport chain, which  powers ATP synthesis via oxidative phosphorylation o NADH and FADH2 convert electrons into ATP energy  We make a ton more ATP a lot faster with this cycle ∙ Cellular respiration involved controlled release of NADH stored energy to produce ATP  o Electrons are passed to the electron transport chain o O2 pulls electrons down the chain o Energy­yielding tumble o Energy used to regenerate ATP  345 lbs./day ∙ Electron transport chain o Protein complexes (I­IV)  Cristae of inner mitochondrial membrane  Prosthetic groups assist electron transport o Carriers alternated reduced and oxidized states  Accept and donate electrons to gradually release energy o Energy drop  NADH to O2­53 kcal/mol  Energy decreases as it goes down the chain o Complex 1  1st Redox reaction ∙ flavomononucleotide (FM) accepts 2 electrons from NADH­gets  reduced ∙ FMN re oxidized when electron passes to (Fe­S) ∙ 2 electrons to ubiquinone (CoQ) o Complex 2  FADH released 2 electrons  Lower energy­produces less ATP o Complex 3 and 4  Cytochromes  Heme­iron atom that accepts/donates electrons  Cyt a2 pass 2 electrons to O2  O2 most electron negative  2 H+ combine to from H2O  electrons now in low energy state o also a Hydrogen ion pump  protein complexes of ET chain function as H+ pump ∙ electron fall down and release energy ∙ H+ pumped across inner mitochondrial membrane∙ Inner membrane space fills with H+ o Creates chemiosmotic/electrochemical gradient o Both pH and electric potential difference  Produces a proton motive force ∙ End result: an electrochemical gradient ∙ DeltaG is about 50% electrical, 50%  chemical gradient  o Chemiosmosis—the energy coupling mechanism  Electron transfer causes proteins to pump H+ from mitochondrial matrix  to the intermembrane space  H+ moves back across the membrane, through channels in ATP synthase  Exergonic flow of H+ drives phosphorylation of ATP – uses energy of the  ion gradient  Bacteria do something almost identical to this, it’s just on inner surface of  membrane o ATP synthetase  Multisubunit proton pump  Molecular rotary motor  Inner mitochondrial membrane  Prokaryote plasma membrane  1. H+ flow down gradient into anchored stator  2. H+ bind rotor altering shape so it spins  3. H+ leaves rotor after 1 full spin  4. Rotor turns a rod that extends into knob below  5. Catalytic site on turning knobs drive ATP ∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to  convert ADP +Pi to ATP? o Energy released from movement of protons through ATP synthesis ∙ Fermentation and anaerobic respiration produce ATP without use of oxygen o Glycolysis can produce ATP without O2 o Oxidation under anaerobic conditions  ATP generated by substrate level phosphorylation  NADH is made & used to regenerate NAD+,  e­ donated to an electron acceptor o Types of anaerobic respiration  Fermentation – ethanol acceptor (yeast)  Fermentation ­ lactic acid acceptor (muscle cells)  Prokaryotes ­ reduce sulfates to H2S   Prokaryotes ­ reduce sulfates to H2S  o Aerobic respiration ­ 38 ATP/glucose o Fermentation ­ 2 ATP/ glucose  Pyruvate ­ fork in the metabolic road   ­ leads to alternative catabolic routes “Glycolysis flareup” ∙  rapid muscle use consumes ATP ∙  stresses O2 delivery ∙  lactic acid pathway kicks in o Alcohol fermentation  pyruvate converted to ethanol  release of CO2  used by yeast in brewing, winemaking, and baking o Lactic acid fermentation o Pyruvate reduced to NADH o Lactate end product ­ no release of CO2  Fungi and bacteria ∙ cheese & yogurt  Muscle cells  ∙ lactic acid fermentation generates ATP when O2 is scarce o Gycolysis and the citric acid cycle are major intersections to both catabolic and  anabolic pathways o Catabolic pathways  Glucose from starch, glycogen & carbs feed in  Proteins feed in as amino acids & amino groups (deamination)  Fats produce 2x ATP per gm as sugars ∙ Beta oxidation breaks fatty acids ∙ yields NADH & FADH2 ∙ 2 C fragments enter at acetyl CoA o Anabolic Pathways  Glycolysis & citric acid cycle intermediates feed into most major synthesis pathways o Regulation of Cellular Respiration via Feedback mechanisms  Feedback inhibition is the most common mechanism for control ∙ ATP low ­ respiration increases ∙ ATP high ­ respiration slows down  Control of catabolism  ∙ Regulate enzyme at strategic points in the catabolic pathway  Allosteric enzymes occur throughout   Set pace of respiration and energy generation o Phosphofructokinase  Allosteric enzyme complex  Activated by AMP  Inhibited by ATP & citrate ∙ FOR EXAM o Understand processes  Not so much structureso TCA Cycle  Why this is so central to biology?  Understand diagram  2 cycles per glucose  Key enzymes & steps  Inputs & outputs  Cellular location ∙ Citric acid cycle overview o Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms citrate (6C) o 7 steps decompose citrate (6c) back to oxaloacetate (4C)­CO2 is released o ATP, NADH, FADH2 are energy products o Generated 1 ATP, 3 NADH, 1 FADH2 per turn o REVIEW TCA FOR EXAM ∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum  number of ATP molecules that could be made through substrate­level phosphorylation? o 1 ∙ carbon skeletons for amino acid biosynthesis are supplied by intermediates of the citric  acid cycle. Which intermediate would supply the carbon skeleton for synthesis of a five carbon amino acid? o Alpha­ketoglutarate ∙ During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis o What happens after glycolysis and the citric acid cycle?  NADH and FADH2 account for most of the energy extracted from food  Electron carriers donate electrons to the electron transport chain, which  powers ATP synthesis via oxidative phosphorylation o NADH and FADH2 convert electrons into ATP energy  We make a ton more ATP a lot faster with this cycle ∙ Cellular respiration involved controlled release of NADH stored energy to produce ATP  o Electrons are passed to the electron transport chain o O2 pulls electrons down the chain o Energy­yielding tumble o Energy used to regenerate ATP  345 lbs./day ∙ Electron transport chain o Protein complexes (I­IV)  Cristae of inner mitochondrial membrane  Prosthetic groups assist electron transport o Carriers alternated reduced and oxidized states  Accept and donate electrons to gradually release energy o Energy drop  NADH to O2­53 kcal/mol  Energy decreases as it goes down the chaino Complex 1  1st Redox reaction ∙ flavomononucleotide (FM) accepts 2 electrons from NADH­gets  reduced ∙ FMN re oxidized when electron passes to (Fe­S) ∙ 2 electrons to ubiquinone (CoQ) o Complex 2  FADH released 2 electrons  Lower energy­produces less ATP o Complex 3 and 4  Cytochromes  Heme­iron atom that accepts/donates electrons  Cyt a2 pass 2 electrons to O2  O2 most electron negative  2 H+ combine to from H2O  electrons now in low energy state o also a Hydrogen ion pump  protein complexes of ET chain function as H+ pump ∙ electron fall down and release energy ∙ H+ pumped across inner mitochondrial membrane ∙ Inner membrane space fills with H+ o Creates chemiosmotic/electrochemical gradient o Both pH and electric potential difference  Produces a proton motive force ∙ End result: an electrochemical gradient ∙ DeltaG is about 50% electrical, 50%  chemical gradient  o Chemiosmosis—the energy coupling mechanism  Electron transfer causes proteins to pump H+ from mitochondrial matrix  to the intermembrane space  H+ moves back across the membrane, through channels in ATP synthase  Exergonic flow of H+ drives phosphorylation of ATP – uses energy of the  ion gradient  Bacteria do something almost identical to this, it’s just on inner surface of  membrane o ATP synthetase  Multisubunit proton pump  Molecular rotary motor  Inner mitochondrial membrane  Prokaryote plasma membrane  1. H+ flow down gradient into anchored stator  2. H+ bind rotor altering shape so it spins  3. H+ leaves rotor after 1 full spin 4. Rotor turns a rod that extends into knob below  5. Catalytic site on turning knobs drive ATP ∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to  convert ADP +Pi to ATP? o Energy released from movement of protons through ATP synthesis ∙ Fermentation and anaerobic respiration produce ATP without use of oxygen o Glycolysis can produce ATP without O2 o Oxidation under anaerobic conditions  ATP generated by substrate level phosphorylation  NADH is made & used to regenerate NAD+,  e­ donated to an electron acceptor o Types of anaerobic respiration  Fermentation – ethanol acceptor (yeast)  Fermentation ­ lactic acid acceptor (muscle cells)  Prokaryotes ­ reduce sulfates to H2S   Prokaryotes ­ reduce sulfates to H2S  o Aerobic respiration ­ 38 ATP/glucose o Fermentation ­ 2 ATP/ glucose  Pyruvate ­ fork in the metabolic road   ­ leads to alternative catabolic routes  “Glycolysis flareup” ∙  rapid muscle use consumes ATP ∙  stresses O2 delivery ∙  lactic acid pathway kicks in o Alcohol fermentation  pyruvate converted to ethanol  release of CO2  used by yeast in brewing, winemaking, and baking o Lactic acid fermentation o Pyruvate reduced to NADH o Lactate end product ­ no release of CO2  Fungi and bacteria ∙ cheese & yogurt  Muscle cells  ∙ lactic acid fermentation generates ATP when O2 is scarce o Gycolysis and the citric acid cycle are major intersections to both catabolic and  anabolic pathways o Catabolic pathways  Glucose from starch, glycogen & carbs feed in  Proteins feed in as amino acids & amino groups (deamination)  Fats produce 2x ATP per gm as sugars ∙ Beta oxidation breaks fatty acids ∙ yields NADH & FADH2∙ 2 C fragments enter at acetyl CoA o Anabolic Pathways  Glycolysis & citric acid cycle intermediates feed into most major synthesis pathways o Regulation of Cellular Respiration via Feedback mechanisms  Feedback inhibition is the most common mechanism for control ∙ ATP low ­ respiration increases ∙ ATP high ­ respiration slows down  Control of catabolism  ∙ Regulate enzyme at strategic points in the catabolic pathway  Allosteric enzymes occur throughout   Set pace of respiration and energy generation o Phosphofructokinase  Allosteric enzyme complex  Activated by AMP  Inhibited by ATP & citrate ∙ FOR EXAM o Understand processes  Not so much structures o TCA Cycle  Why this is so central to biology?  Understand diagram  2 cycles per glucose  Key enzymes & steps  Inputs & outputs  Cellular location Chapter 8: Photosynthesis (Lecture 1) ∙ Autotrophs o Producers—generated organic molecules from CO2 and inorganic molecules o Photoautotrophs—use sunlight to make organic molecules from  H2O and CO2 ∙ Heterotrophs o Obtain organic material from other organisms o Consumers—depend on photoautotrophs for food and O2 o Depend on autotrophs ∙ UNL is a major research site for biofuels ∙ Almost all energy to power life comes from the sun ∙ Mostly, photosynthetic organisms are the base of the food chain ∙ Photosynthesis creates sugar from sunlight and then breaks that down  into ATP ∙ Anatomy of photosynthesiso Mesophyll o Veins o Stomata o 30-40 chloroplasts per cell o chlorophyll-in thylakoid membranes  where all the action is taking place  harvests light energy ∙ Photosynthesis as a Redox Process o H2O is oxidized and CO2 is released  Creating sugars  Uphill reaction…positive DeltaG…requires energy o 6 CO2 + 12 H2O + Energy → C6H12O6 + 6 O2 + 6 H2O  o CO2 + 2H2O + Energy → [CH2O] + O2 + 1 H2O  o CO2 + 2H2S + Energy → [CH2O] + 2S + 1 H2O  o H2O is split to provide a source of electrons from H+, releasing O2 as the byproduct ∙ Evolution of Photosynthetic Prokaryotes o Early cells that used light to make CHOs from CO2 oxidized H2S  or Fe compounds o Break-through came with splitting of H2O for organic compound  synthesis o Amount of oxygen in atmosphere controls body size of organisms  Ex. Giant dragon flies lived at an oxygen rich era ∙ Two Stages of Photosynthesis: A Preview o Light reactions (the “photo” part)  Occurs in thylakoids (green pancakes)  Split H2O and released O2  Uses light energy to  ∙ Reduce NADP+ to NADPH ∙ Generate ATP by photophosphorylation o Calvin cycle (the “synthesis” part)  Occurs in stroma  Uses ATP and NADPH to carry out carbon fixation—converts CO2 to CH2O ∙ PHOTOSYNTHESIS: 1. Chlorophyll in thylakoid membranes absorbs light energy a. Splitting water 2. Light energy captures H+ and electrons from water to make ATP and  reduce NADPH a. Oxygen is released 3. CO2 enters the stroma and is fed into Calvin cycle—long term storage  section a. ATP and NADPH provide energy to synthesize sugars from CO2 4. Carbon from CO2 is fixed into sugars∙ The biomass (dry weight) of a tree comes primarily from  o Air o Because trees are made of cellulose (sugar), sugars are made  of carbon, carbon is made from air ∙ Which of the following sequences correctly represents the flow of  electrons during photosynthesis? o H20—>NADPH—>Calvin cycle ∙ Photosynthetic Pigments: The light receptors o Pigments absorb visible light—electromagnetic  Different pigments absorb different wavelengths o Wavelengths not absorbed are reflected and transmitted o Chlorophyll reflects and transmits green light  Chlorophyll a ∙ Primary photosynthetic pigment  Chlorophyll b ∙ Accessory pigments broaden spectrum  Carotenoids ∙ Absorb excessive light that can damage  chlorophyll ∙ A spectrophotometer measures pigments ability to absorb various  wavelengths o Sends light through pigments and measures amount of/which  type of light is being absorbed or transmitted o ∙ an absorption spectrum is a graph plotting a pigment’s light  absorption versus wavelength ∙ the absorption spectrum of chlorophyll a suggests that violet-blue  and red light work best for photosynthesis ∙ An action spectrum profiles the relative effectiveness of different  wavelengths of radiation in driving a process o The action spectrum of photosynthesis was first demonstrated in 1883 by Theodor W. Engelmanno In his experiment, he exposed different segments of a  filamentous alga to different wavelengths o Areas receiving wavelengths favorable to photosynthesis  produced excess O2 o He used the growth of aerobic bacteria clustered along the  alga as a measure of O2 production ∙ Chlorophyll a is the main photosynthetic pigment ∙ Accessory pigments, such as chlorophyll b, broaden the spectrum  used for photosynthesis ∙ Accessory pigments called carotenoids absorb excessive light that  would damage chlorophyllLIFE120 CH8 PHOTOSYNTHESIS-(Lecture 2 Notes with Clicker Questions in red) ∙ Chlorophyll (green) is tightly linked in a protein pigment complex with  low energy e- donor (gray) & a high energy e- acceptor (blue) o High energy electrons get transferred to acceptor molecules and  go on down the chain o A low energy electron takes place of the electron that left in  chlorophyll molecule  In center called P680 for photosystem II o Structure of photosystem II:  ∙ Photo system complex: o  transmembrane protein   pigments capture photon  photon funneled to chlorophyll a  excited electron goes to 1ary electron acceptor in reaction  center in complex by energy being pumped through  photons  1st redox reaction ∙ Linear Electron flow through Photosystems I and II o Primary pathway to produce ATP and NADPH using light energy— involved two photosystems Photosystem II (PS II) ∙ Functions first—absorbs 680 nm wavelength ∙ Chlorophyll a double molecule called P680  Photosystem I (PS I) ∙ Absorbs 700 nm wavelength ∙ Chlorophyll a double molecule called P700  ∙ photon hits pigment ∙ energy passed by pigments to P680 ∙ excited electron from P680 transferred to “primary  electron acceptor”  ∙ P680+ (missing electron) is strong oxidizing agent ∙ H2O is split, electron transfer from H atoms to P680+ o P680 now reduced ∙ O2 released as by-product ∙ Electrons fall down electron transport chain from  primary acceptor of PS II ∙ Energy creates a proton gradient across thylakoid  membrane ∙ Diffusion of H+ across membrane drive ATP synthesis ∙ Photosystem I o Light energy excited P700 o Electrons lost to primary electron acceptor o P700+ accepts electrons passed from PS II via  electron transport chain  Electron “falls” from primary electron  acceptor of PS I to ferredoxin (Fd)  Electrons then transfer to NADP+ ∙ Reduce it to NADPH o Cyclic Electron Flow  Used only in photosystem I  Electrons cycle back via ferredoxin ATP produced by chemiosmosis  No NADPH is generated  Evolutionary left over ∙ Purple sulfur bacteria ∙ Cyanobacteria that have PSII ∙ Protective role ∙ H+ Gradient and Chemiosmosis in Thylakoid Membrane o Creating a proton gradient to store energy/make ATP o 1. H2O split by PSII   release electrons and H+ in Tspace o 2. Pq transfers electrons to cytochrome, pulling 4H+ from stroma o 3. H+ removed from stroma when NADPH made ∙ Chemiosmosis in Chloroplasts and Mitochondria o ATP is generated in both by chemiosmosis o Mitochondria  H+ pumped into intermembrane space ∙ Knob points inward  Drive ATP synthesis by diffusing back into matrix o Chloroplasts  H+ pumped into thylakoid space  ∙ Knob points outward   Drives ATP synthesis by diffusing back into the stroma ∙ What does the chemiosmotic process in chloroplasts involve? o Establishment of a proton gradient across the thylakoid  membrane ∙ Assume a thylakoid is somehow punctured so that the interior of the  thylakoid is no longer separated from the stroma. This damage will  have the most direct effect on which of the following processes? o The synthesis of ATP ∙ In thylakoids, protons travel through ATP synthase from the thylakoid  space to the stroma. Therefore, the catalytic “knobs” of ATP synthase  would be located where?’ o On the outside for the thylakoid membrane ∙ The Calvin Cycle uses ATP and NADPH to convert CO2 to sugar o Calvin cycle regenerates starting material o Stores electrons as bonds in sugars o Builds sugar from CO2 o Uses ATP and NADPH generated by light reactions ∙ Overview of Calvin Cycle o Net C in=3 CO2 molecules o Net C out = 1 glyceraldehyde-3-phosphate (G3P)  Net synthesis requires 3 turns of cycle  Phase I-carbon fixation∙ CO2 attached to 5 carbon acceptor RuBP by enzyme  called rubisco (RuBP carboxylase) o Rubisco is most plentiful protein on earth  Phase II-Reduction ∙ ATP phosphorylates & NADPH reduces substrates to  make glyceraldehyde-3-P (3C)  Phase III-Regeneration of the CO2 acceptor ∙ 5 C/2Pi acceptor remade (RuBP – ribulose  biphosphate) o  1. CO2 coupled to RuBP by rubisco ∙ forms 6C intermediate  2. Splits into 2 x 3C molecules of 3-phosphogylcerate  Input CO2 (Entering one 3 at a time) Phase 1: Carbon fixation Rubisco 3 P P Short-lived 3 6 P P P6ATP 6 ADP intermediate Ribulose bisphosphate 3-Phosphoglycerate  (RuBP) Calvin 6P P 1,3-Bisphosphoglycerate 6 Cycle 6 P 66 NADP+ NADPH P i Glyceraldehyde-3-phosphate Phase 2: (G3P) Reduction Output 1 G3P P Glucose and other organic (a sugar) compounds ∙ 2. 3-phosphoglycerate phosphorylated by ATP – more reactive 1,3  biphosphoglycerate  ∙ 3. 1,3 biphosphoglycerate reduced by NADPH with loss of Pi –  produces high energy (3C) G-3-P ∙ 4. 1 x G-3-P gained every 3 turns of cycle ∙ 6. 3 ATPs phosphorylate then rearrange 5 x 3C G-3-P into 3 x 5C  RuBP∙ 5. 5 x 3C G-3-P recycled to re-make RuBPLIFE120 LECTURES-(clicker questions and answers in red) CHAPTER 6 ∙ Catabolic pathways-releasing energy, breaking down complex  molecules o Cellular respiration o Harvest energy from bonds (electrons) in food ∙ Anabolic pathways-consume energy, build complex molecules,  synthesis of proteins from amino acids ∙ Forms of energy o Potential-diver at the top of the platform o Thermal-hitting the water, releasing energy as heat o Kinetic-diving off the board o Chemical o Organisms are islands of low entropy in an increasingly random  universe! ∙ Biological Order/Disorder o Cells create ordered structures (anabolic) o Organisms alter matter and energy to less ordered forms  (catabolic) o Energy flows in as light and exits as heat  Transferring energy to create local order ∙ Are chemical reactions at equilibrium in living cells?  o No ∙ Thermodynamics-Laws of Energy Transformation o Energy of universe is constant o First law of thermodynamics  Energy can be transferred and transformed, but it cannot  be created or destroyed (kinetic, heat, potential, chemical) o Second law of thermodynamics  Every energy transfer increases the entropy (disorder) of  the universe ∙ To occur spontaneously, processes occur without  energy input…to occur spontaneously, it must  increase disorder of the universe ∙ Organisms use energy to create more order ∙ Entropy may decrease in an organism o Releasing heat sends entropy into the universe  Heat is the motion of molecules ∙ Organisms are islands of low entropy in an increasingly random  universe! ∙ How do living organisms create macromolecules, organelles, cells,  tissues, and complex higher-order structures?o Living organisms create order locally, but the energy  transformations generate waste heat that increases the entropy  of the universe.  ∙ Free energy o Measure of living systems free energy  Gibb’s Free Energy-energy available to do work when  temperature and pressure are uniform, as in a living cell  ∙ DeltaG=DeltaH-TDeltaS o DeltaG is free energy o DeltaH is enthalpy o T is temperature in Kelvin o DeltaS is entropy ∙ Change in energy tells us whether a process is  spontaneous or not o Enthalpy-total energy of a system  Change in DeltaH o Entropy-measure of disorder in a system  Change in disorder of DeltaS o Change in free energy is related to the change in enthalpy,  entropy, and temperature in Kelvin o Processes with negative DeltaG, reactions are spontaneous (they  go downhill) o Spontaneous processes can be harnessed to perform work  Give off heat ∙ Fireworks o Exergonic-releases energy (spontaneous)  Dissolving of slat in water  o Endergonic-requires energy (nonspontaneous)  Hand warmers for football games o Free Energy, Stability, Equilibrium  Free energy-measures a system’s instability  During spontaneous change, free energy decreases,  stability increases  Equilibrium is achieved-state of maximum stability ∙ Reactions in closed system reach equilibrium, can’t  do work ∙ Reactions in open systems never reach equilibrium,  work continuously o Cells of open systems never in equilibrium  where products of reaction are removed!  Metabolism never at equilibrium-GOOD!! ∙ Anabolic-stores free energy o DeltaG= +686 kcal/mol o Photosynthesis (chloroplasts)∙ Catabolic-releases free energy o DeltaG= -686 kcal/mol o Respiration (mitochondria)  Coupling exergonic reactions ∙ Cell does three kinds of work o Chemical-synthesis of polymers o Transport-pumping ions across membranes o Mechanical-movement ∙ Energy coupling by ATP o Used for most cell work o Larger –DeltaG reactions drives smaller  +DeltaG reaction o Net free energy less than zero o Structure and Hydrolysis of ATP  ATP (adenosine triphosphate)- cell’s energy shuttle  Composed of 3 ribose (a sugar), adenine (a nitrogenous  base), 3 phosphate groups ∙ Bonds between phosphate groups broken by  hydrolysis ∙ Energy released when terminal Pi bond broken ∙ Highly exergonic ∙ Metabolism is never at equilibrium-defining feature of life o Anabolic- (positive DeltaG)  Stores free energy  DeltaG= +686 kcal/cal  Building sugars, all work, costs energy o Catabolic- (negative DeltaG)  Releases free energy  Burning sugars, consumer side   DeltaG= -686 kcal/mol ∙ Gibbs Free Energy Change  o Change in free energy (DeltaG) is related to change in enthalpy  and entropy  Processes with negative DeltaG are spontaneous ∙ Hydrolysis of ATP is spontaneous reaction o Bonds between phosphate groups broken by hydrolysis  o Energy released when terminal Pi bond broken o EXERGONIC ∙ ATP powers cellular work by coupling exergonic reactions to endergonic reactions o Coupling ATP  Used for most cell work  Larger –DeltaG reaction drives smaller +DeltaG reaction ∙ Energy coupling using Hydrolysis of ATPo Endergonic reactions-+DeltaG, not spontaneous o Coupled exergonic reaction  ATP phosphorylates glutamic acid-less stable  o Free energy exchange overall is negative   ATP drives endergonic reactions ∙ Think about all of the activity in your cells right now o A lot of it costs energy, a lot of it makes energy o Have to maintain functions ∙ ATP is a renewable source o Regenerated by Pi addition to adenosine diphosphate (ADP) o Phosphorylation energy comes from cellular catabolic reactions ∙ When ATP releases free energy, it also releases inorganic phosphate.  What purpose does this serve (if any) in the cell? o The phosphate may be incorporated into many different  molecules ∙ Enzymes speed up reactions but aren’t consumed in them ∙ Catalyst-a chemical agent that speeds up a reaction without being  consumed o Metals ∙ Enzyme-catalytic protein ∙ Activation of the energy barrier o Chemical reaction between molecules involves bond breaking  and bond forming   AB + CD  AC +BD o Activation energy (Ea) o Free energy of activation  Initial energy needed to start reaction  Heat-chemical reactions  Cells can’t be heated or they die! ∙ Everything will become denatured ∙ Energy profile of an exergonic reaction—SLIDE 15, lecture 2 o DeltaG is unaffected by the enzyme ∙ The reaction has a DeltaG of -5.6 kcal/mol. Which of the following  would most likely be true? o The reaction would result in an increase in entropy (S) and a  decrease in the energy content (H) of the system  ∙ Enzyme temperatures—SLIDE 19 ∙ Competitive inhibitors o Bind active site and compete with substrate o Competing for substrate spot in active site ∙ Noncompetitive inhibitors o Bind to other part of enzyme, alter shape of active site less  effective  o Inhibitor binds somewhere away from active site Enzyme is inactive and can’t bind substrate anymore ∙ Allosteric regulation-may either inhibit or stimulate an enzyme’s  activity o Occurs when a regulatory molecule binds to a protein at one site  and affects the protein’s function at another site Chapter 7 ∙ Feedback inhibition-when the end product of a pathway shuts down the pathway o Helps regulate levels of substance within cells ∙ Cellular respiration o Fundamental metabolic pathways function and connect o Conversion of light energy into chemical energy o Glycolysis first step in cytoplasm ∙ Redox-transfer of electrons ∙ Leo says Ger o L-lose o E-electrons o O-oxidation o G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2∙ phosphoglucoisomerase o glucose converted to isomer o form can accept another phosphate ∙ phosphofructokinase (PFK) o fructose phosphorylated  o 6 carbon sugar has two phosphate o allosterically regulated step by ATP feedback inhibition   very important for cell health  “lysis’ part of glycolysis ∙ molecule is energetic and wants to pull itself apart ∙ aldolase o cleaves one 6C to two 3C sugars ∙ isomerase o interconverts two forms o G­3­P quickly processed  Triose phosphate dehydrogenase (Dehydrogenases­enzymes that transfer  H+) ∙ H+ evolved, NAD reduced, REDOX ∙ Phosphate added  ∙ Highly exergonic ∙ Highly reactive product  Phosphoglycerokinase ∙ Exergonic­creates 2 ATP/glucose ∙ First ATP payoff  ∙ Substrate level phosphorylation ∙ Product is an organic acid  Phosphoglyceromutase ∙ Phosphate is rearranged o Destabilizes molecule product further   Enolase  ∙ Creates double bond in substrate ∙ PEP is a high energy product o –DeltaG is 10 kcal  Pyruvate kinase ∙ PEP converted to pyruvate ∙ 2 more ATP generated/glucose ∙ 2nd substrate level phosphorylation ∙ pyruvate to TCA cycle if O2 is present ∙ pyruvate into fermentation if no O2 is present ∙ Substrate­level phosphorylation accounts for approximately what percentage of the ATP  formed by the reactions of glycolysis? o 100%∙ Which statement about glycolysis is true? o It occurs in the cytoplasm ∙ When a glucose molecule loses a hydrogen atom as a result of an oxidation­reduction  reaction, the molecule becomes  o Oxidized  ∙ Citric acid cycle o Aerobic respiration­require O2 o Further breakdown of pyruvate and release of CO2 o Pyruvate enters mitochondrion­transport protein o Pyruvate dehydrogenase­3 enzyme complex o COO gp is released as CO2; NADH is produced o Coenzyme is coupled­high energy Acetyl CoA o Lose Co2, left with 2 C  Coenzyme A (Vitamin B) is a temporary holding molecule for the bond  transfer o Overview   Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms  citrate (6C)  7 steps decompose citrate (6C) back to oxaloacetate (4C)­CO2 is released ∙ recycling  ATP, NADH, FADH2 are energy products  Generated 1 ATP, 3 NADH, 1 FADH2 per turn ∙ 1. 2C acetyl gp added to 4C oxaloacetate –DeltaG is ­7.7 kcal o 4C becomes 6C citrate o citrate synthetase­key regulatory enzyme o follow the fate of C’s  o cirtrate­3 carboxylates  ∙ 2. Citrate converted to a new form ∙ 3. Isocitrate­oxidized NAD, reduced CO2, released ∙ 4. Co2 released, substrate oxidized, NAD reduced, CoA group is  coupled o 2C’s gone, protons and electrons retained ∙ 5. CoA replaced by phosphate, coupled to make GTP, then ATP  energy is stored o regeneration of starting substrate follows o substrate level phosphorylation ∙ 6. Succinate oxidized and FAD reduced to FADH2 ∙ 7. H2O rearranges substrate ∙ 8. Malate oxidized, NAD reduced, oxaloacetate regenerated ∙ Energy yield: o 1 ATP o 3 NADHo 1 FADH2 o per turn o 2x for each glucose ∙ KNOW FOR TEST: What’s going in, what’s coming out? Where  and when? Study pathway well. Understand diagram, key  enzymes and steps, inputs and outputs, cellular location, does it require O2 to be present? NoEnergy investment phase Glucose 2 ADP + 2P 2 ATP used Energy payoff phase 4 ADP + 4P 4 ATP formed 2 NAD+ + 4 e– + 4 H+ 2 NADH+ 2 H+ 2 Pyruvate + 2 H2O Glucose 2 Pyruvate + 2 H2O Net 4 ATP formed – 2 ATP used 2 ATP 2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+Chapter 7 ∙ Feedback inhibition-when the end product of a pathway shuts down the pathway o Helps regulate levels of substance within cells ∙ Cellular respiration o Fundamental metabolic pathways function and connect o Conversion of light energy into chemical energy o Glycolysis first step in cytoplasm ∙ Redox-transfer of electrons ∙ Leo says Ger o L-lose o E-electrons o O-oxidation o G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2 ∙ phosphoglucoisomerase o glucose converted to isomer o form can accept another phosphate ∙ phosphofructokinase (PFK)o fructose phosphorylated  o 6 carbon sugar has two phosphate o allosterically regulated step by ATP feedback inhibition   very important for cell health  “lysis’ part of glycolysis ∙ molecule is energetic and wants to pull itself apart ∙ aldolase o cleaves one 6C to two 3C sugars ∙ isomerase o interconverts two forms o G­3­P quickly processed  Triose phosphate dehydrogenase (Dehydrogenases­enzymes that transfer  H+) ∙ H+ evolved, NAD reduced, REDOX ∙ Phosphate added  ∙ Highly exergonic ∙ Highly reactive product  Phosphoglycerokinase ∙ Exergonic­creates 2 ATP/glucose ∙ First ATP payoff  ∙ Substrate level phosphorylation ∙ Product is an organic acid  Phosphoglyceromutase ∙ Phosphate is rearranged o Destabilizes molecule product further   Enolase  ∙ Creates double bond in substrate ∙ PEP is a high energy product o –DeltaG is 10 kcal  Pyruvate kinase ∙ PEP converted to pyruvate ∙ 2 more ATP generated/glucose ∙ 2nd substrate level phosphorylation ∙ pyruvate to TCA cycle if O2 is present ∙ pyruvate into fermentation if no O2 is present ∙ Substrate­level phosphorylation accounts for approximately what percentage of the ATP  formed by the reactions of glycolysis? o 100% ∙ Which statement about glycolysis is true? o It occurs in the cytoplasm ∙ When a glucose molecule loses a hydrogen atom as a result of an oxidation­reduction  reaction, the molecule becomes o Oxidized  ∙ Citric acid cycle o Aerobic respiration­require O2 o Further breakdown of pyruvate and release of CO2 o Pyruvate enters mitochondrion­transport protein o Pyruvate dehydrogenase­3 enzyme complex o COO gp is released as CO2; NADH is produced o Coenzyme is coupled­high energy Acetyl CoA o Lose Co2, left with 2 C  Coenzyme A (Vitamin B) is a temporary holding molecule for the bond  transfer o Overview   Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms  citrate (6C)  7 steps decompose citrate (6C) back to oxaloacetate (4C)­CO2 is released ∙ recycling  ATP, NADH, FADH2 are energy products  Generated 1 ATP, 3 NADH, 1 FADH2 per turn ∙ 1. 2C acetyl gp added to 4C oxaloacetate –DeltaG is ­7.7 kcal o 4C becomes 6C citrate o citrate synthetase­key regulatory enzyme o follow the fate of C’s  o cirtrate­3 carboxylates  ∙ 2. Citrate converted to a new form ∙ 3. Isocitrate­oxidized NAD, reduced CO2, released ∙ 4. Co2 released, substrate oxidized, NAD reduced, CoA group is  coupled o 2C’s gone, protons and electrons retained ∙ 5. CoA replaced by phosphate, coupled to make GTP, then ATP  energy is stored o regeneration of starting substrate follows o substrate level phosphorylation ∙ 6. Succinate oxidized and FAD reduced to FADH2 ∙ 7. H2O rearranges substrate ∙ 8. Malate oxidized, NAD reduced, oxaloacetate regenerated ∙ Energy yield: o 1 ATP o 3 NADH o 1 FADH2 o per turn o 2x for each glucose∙ KNOW FOR TEST: What’s going in, what’s coming out? Where  and when? Study pathway well. Understand diagram, key  enzymes and steps, inputs and outputs, cellular location, does it require O2 to be present? NoEnergy investment phase Glucose 2 ADP + 2P 2 ATP used Energy payoff phase 4 ADP + 4P 4 ATP formed 2 NAD+ + 4 e– + 4 H+ 2 NADH+ 2 H+ 2 Pyruvate + 2 H2O Glucose 2 Pyruvate + 2 H2O Net 4 ATP formed – 2 ATP used 2 ATP 2 NAD+ + 4 e– + 4 H+ 2 NADH + 2 H+ ∙ Citric acid cycle overview o Acetyl group of acetyl CoA combines with oxaloacetate (4C) forms citrate (6C) o 7 steps decompose citrate (6c) back to oxaloacetate (4C)­CO2 is released o ATP, NADH, FADH2 are energy products o Generated 1 ATP, 3 NADH, 1 FADH2 per turn o REVIEW TCA FOR EXAM ∙ Starting with one molecule of isocitrate and ending with fumarate, what is the maximum  number of ATP molecules that could be made through substrate­level phosphorylation? o 1 ∙ carbon skeletons for amino acid biosynthesis are supplied by intermediates of the citric  acid cycle. Which intermediate would supply the carbon skeleton for synthesis of a five carbon amino acid? o Alpha­ketoglutarate∙ During oxidative phosphorylation, chemiosmosis couples electron transport to ATP  synthesis o What happens after glycolysis and the citric acid cycle?  NADH and FADH2 account for most of the energy extracted from food  Electron carriers donate electrons to the electron transport chain, which  powers ATP synthesis via oxidative phosphorylation o NADH and FADH2 convert electrons into ATP energy  We make a ton more ATP a lot faster with this cycle ∙ Cellular respiration involved controlled release of NADH stored energy to produce ATP  o Electrons are passed to the electron transport chain o O2 pulls electrons down the chain o Energy­yielding tumble o Energy used to regenerate ATP  345 lbs./day ∙ Electron transport chain o Protein complexes (I­IV)  Cristae of inner mitochondrial membrane  Prosthetic groups assist electron transport o Carriers alternated reduced and oxidized states  Accept and donate electrons to gradually release energy o Energy drop  NADH to O2­53 kcal/mol  Energy decreases as it goes down the chain o Complex 1  1st Redox reaction ∙ flavomononucleotide (FM) accepts 2 electrons from NADH­gets  reduced ∙ FMN re oxidized when electron passes to (Fe­S) ∙ 2 electrons to ubiquinone (CoQ) o Complex 2  FADH released 2 electrons  Lower energy­produces less ATP o Complex 3 and 4  Cytochromes  Heme­iron atom that accepts/donates electrons  Cyt a2 pass 2 electrons to O2  O2 most electron negative  2 H+ combine to from H2O  electrons now in low energy state o also a Hydrogen ion pump  protein complexes of ET chain function as H+ pump ∙ electron fall down and release energy ∙ H+ pumped across inner mitochondrial membrane∙ Inner membrane space fills with H+ o Creates chemiosmotic/electrochemical gradient o Both pH and electric potential difference  Produces a proton motive force ∙ End result: an electrochemical gradient ∙ DeltaG is about 50% electrical, 50%  chemical gradient  o Chemiosmosis—the energy coupling mechanism  Electron transfer causes proteins to pump H+ from mitochondrial matrix  to the intermembrane space  H+ moves back across the membrane, through channels in ATP synthase  Exergonic flow of H+ drives phosphorylation of ATP – uses energy of the  ion gradient  Bacteria do something almost identical to this, it’s just on inner surface of  membrane o ATP synthetase  Multisubunit proton pump  Molecular rotary motor  Inner mitochondrial membrane  Prokaryote plasma membrane  1. H+ flow down gradient into anchored stator  2. H+ bind rotor altering shape so it spins  3. H+ leaves rotor after 1 full spin  4. Rotor turns a rod that extends into knob below  5. Catalytic site on turning knobs drive ATP ∙ In chemiosmotic phosphorylation, what is the most direct source of energy that is used to  convert ADP +Pi to ATP? o Energy released from movement of protons through ATP synthesis ∙ Fermentation and anaerobic respiration produce ATP without use of oxygen o Glycolysis can produce ATP without O2 o Oxidation under anaerobic conditions  ATP generated by substrate level phosphorylation  NADH is made & used to regenerate NAD+,  e­ donated to an electron acceptor o Types of anaerobic respiration  Fermentation – ethanol acceptor (yeast)  Fermentation ­ lactic acid acceptor (muscle cells)  Prokaryotes ­ reduce sulfates to H2S   Prokaryotes ­ reduce sulfates to H2S  o Aerobic respiration ­ 38 ATP/glucose o Fermentation ­ 2 ATP/ glucose  Pyruvate ­ fork in the metabolic road   ­ leads to alternative catabolic routes “Glycolysis flareup” ∙  rapid muscle use consumes ATP ∙  stresses O2 delivery ∙  lactic acid pathway kicks in o Alcohol fermentation  pyruvate converted to ethanol  release of CO2  used by yeast in brewing, winemaking, and baking o Lactic acid fermentation o Pyruvate reduced to NADH o Lactate end product ­ no release of CO2  Fungi and bacteria ∙ cheese & yogurt  Muscle cells  ∙ lactic acid fermentation generates ATP when O2 is scarce o Gycolysis and the citric acid cycle are major intersections to both catabolic and  anabolic pathways o Catabolic pathways  Glucose from starch, glycogen & carbs feed in  Proteins feed in as amino acids & amino groups (deamination)  Fats produce 2x ATP per gm as sugars ∙ Beta oxidation breaks fatty acids ∙ yields NADH & FADH2 ∙ 2 C fragments enter at acetyl CoA o Anabolic Pathways  Glycolysis & citric acid cycle intermediates feed into most major synthesis pathways o Regulation of Cellular Respiration via Feedback mechanisms  Feedback inhibition is the most common mechanism for control ∙ ATP low ­ respiration increases ∙ ATP high ­ respiration slows down  Control of catabolism  ∙ Regulate enzyme at strategic points in the catabolic pathway  Allosteric enzymes occur throughout   Set pace of respiration and energy generation o Phosphofructokinase  Allosteric enzyme complex  Activated by AMP  Inhibited by ATP & citrate ∙ FOR EXAM o Understand processes  Not so much structureso TCA Cycle  Why this is so central to biology?  Understand diagram  2 cycles per glucose  Key enzymes & steps  Inputs & outputs  Cellular locationLIFE120 LECTURES-(clicker questions and answers in red) CHAPTER 6 ∙ Catabolic pathways-releasing energy, breaking down complex  molecules o Cellular respiration o Harvest energy from bonds (electrons) in food ∙ Anabolic pathways-consume energy, build complex molecules,  synthesis of proteins from amino acids ∙ Forms of energy o Potential-diver at the top of the platform o Thermal-hitting the water, releasing energy as heat o Kinetic-diving off the board o Chemical o Organisms are islands of low entropy in an increasingly random  universe! ∙ Biological Order/Disorder o Cells create ordered structures (anabolic) o Organisms alter matter and energy to less ordered forms  (catabolic) o Energy flows in as light and exits as heat  Transferring energy to create local order ∙ Are chemical reactions at equilibrium in living cells?  o No ∙ Thermodynamics-Laws of Energy Transformation o Energy of universe is constant o First law of thermodynamics  Energy can be transferred and transformed, but it cannot  be created or destroyed (kinetic, heat, potential, chemical) o Second law of thermodynamics  Every energy transfer increases the entropy (disorder) of  the universe ∙ To occur spontaneously, processes occur without  energy input…to occur spontaneously, it must  increase disorder of the universe ∙ Organisms use energy to create more order ∙ Entropy may decrease in an organism o Releasing heat sends entropy into the universe  Heat is the motion of molecules ∙ Organisms are islands of low entropy in an increasingly random  universe! ∙ How do living organisms create macromolecules, organelles, cells,  tissues, and complex higher-order structures?o Living organisms create order locally, but the energy  transformations generate waste heat that increases the entropy  of the universe.  ∙ Free energy o Measure of living systems free energy  Gibb’s Free Energy-energy available to do work when  temperature and pressure are uniform, as in a living cell  ∙ DeltaG=DeltaH-TDeltaS o DeltaG is free energy o DeltaH is enthalpy o T is temperature in Kelvin o DeltaS is entropy ∙ Change in energy tells us whether a process is  spontaneous or not o Enthalpy-total energy of a system  Change in DeltaH o Entropy-measure of disorder in a system  Change in disorder of DeltaS o Change in free energy is related to the change in enthalpy,  entropy, and temperature in Kelvin o Processes with negative DeltaG, reactions are spontaneous (they  go downhill) o Spontaneous processes can be harnessed to perform work  Give off heat ∙ Fireworks o Exergonic-releases energy (spontaneous)  Dissolving of slat in water  o Endergonic-requires energy (nonspontaneous)  Hand warmers for football games o Free Energy, Stability, Equilibrium  Free energy-measures a system’s instability  During spontaneous change, free energy decreases,  stability increases  Equilibrium is achieved-state of maximum stability ∙ Reactions in closed system reach equilibrium, can’t  do work ∙ Reactions in open systems never reach equilibrium,  work continuously o Cells of open systems never in equilibrium  where products of reaction are removed!  Metabolism never at equilibrium-GOOD!! ∙ Anabolic-stores free energy o DeltaG= +686 kcal/mol o Photosynthesis (chloroplasts)∙ Catabolic-releases free energy o DeltaG= -686 kcal/mol o Respiration (mitochondria)  Coupling exergonic reactions ∙ Cell does three kinds of work o Chemical-synthesis of polymers o Transport-pumping ions across membranes o Mechanical-movement ∙ Energy coupling by ATP o Used for most cell work o Larger –DeltaG reactions drives smaller  +DeltaG reaction o Net free energy less than zero o Structure and Hydrolysis of ATP  ATP (adenosine triphosphate)- cell’s energy shuttle  Composed of 3 ribose (a sugar), adenine (a nitrogenous  base), 3 phosphate groups ∙ Bonds between phosphate groups broken by  hydrolysis ∙ Energy released when terminal Pi bond broken ∙ Highly exergonic ∙ Metabolism is never at equilibrium-defining feature of life o Anabolic- (positive DeltaG)  Stores free energy  DeltaG= +686 kcal/cal  Building sugars, all work, costs energy o Catabolic- (negative DeltaG)  Releases free energy  Burning sugars, consumer side   DeltaG= -686 kcal/mol ∙ Gibbs Free Energy Change  o Change in free energy (DeltaG) is related to change in enthalpy  and entropy  Processes with negative DeltaG are spontaneous ∙ Hydrolysis of ATP is spontaneous reaction o Bonds between phosphate groups broken by hydrolysis  o Energy released when terminal Pi bond broken o EXERGONIC ∙ ATP powers cellular work by coupling exergonic reactions to endergonic reactions o Coupling ATP  Used for most cell work  Larger –DeltaG reaction drives smaller +DeltaG reaction ∙ Energy coupling using Hydrolysis of ATPo Endergonic reactions-+DeltaG, not spontaneous o Coupled exergonic reaction  ATP phosphorylates glutamic acid-less stable  o Free energy exchange overall is negative   ATP drives endergonic reactions ∙ Think about all of the activity in your cells right now o A lot of it costs energy, a lot of it makes energy o Have to maintain functions ∙ ATP is a renewable source o Regenerated by Pi addition to adenosine diphosphate (ADP) o Phosphorylation energy comes from cellular catabolic reactions ∙ When ATP releases free energy, it also releases inorganic phosphate.  What purpose does this serve (if any) in the cell? o The phosphate may be incorporated into many different  molecules ∙ Enzymes speed up reactions but aren’t consumed in them ∙ Catalyst-a chemical agent that speeds up a reaction without being  consumed o Metals ∙ Enzyme-catalytic protein ∙ Activation of the energy barrier o Chemical reaction between molecules involves bond breaking  and bond forming   AB + CD  AC +BD o Activation energy (Ea) o Free energy of activation  Initial energy needed to start reaction  Heat-chemical reactions  Cells can’t be heated or they die! ∙ Everything will become denatured ∙ Energy profile of an exergonic reaction—SLIDE 15, lecture 2 o DeltaG is unaffected by the enzyme ∙ The reaction has a DeltaG of -5.6 kcal/mol. Which of the following  would most likely be true? o The reaction would result in an increase in entropy (S) and a  decrease in the energy content (H) of the system  ∙ Enzyme temperatures—SLIDE 19 ∙ Competitive inhibitors o Bind active site and compete with substrate o Competing for substrate spot in active site ∙ Noncompetitive inhibitors o Bind to other part of enzyme, alter shape of active site less  effective  o Inhibitor binds somewhere away from active site Enzyme is inactive and can’t bind substrate anymore ∙ Allosteric regulation-may either inhibit or stimulate an enzyme’s  activity o Occurs when a regulatory molecule binds to a protein at one site  and affects the protein’s function at another site Chapter 7 ∙ Feedback inhibition-when the end product of a pathway shuts down the pathway o Helps regulate levels of substance within cells ∙ Cellular respiration o Fundamental metabolic pathways function and connect o Conversion of light energy into chemical energy o Glycolysis first step in cytoplasm ∙ Redox-transfer of electrons ∙ Leo says Ger o L-lose o E-electrons o O-oxidation o G-gain  o E-electrons o R-reduction ∙ Reducing agent-electron donor ∙ Oxidizing agent-electron receptor  o Oxygen is very electronegative and, thus, a strong oxidizer ∙ Oxidation-lose electrons ∙ Reduction-gain electrons ∙ NAD+  o Battery o Carries a charge o Electron acceptor (oxidizing agent) ∙ NADH o Reduced form of NAD+ ∙ Stages of Cellular Respiration o Glycolysis  “splitting sugar”  cytoplasmic  step 1 ∙ hexokinase—enzyme responsible for phosphorylation o glucose phosphorylated by ATP o destabilizing o traps glucose inside cell—creates sink ∙ kinases o transfer of phosphate to and from ATP  step 2

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