Bio 181 Respiration Notes
Bio 181 Respiration Notes BIO 181
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This 25 page Class Notes was uploaded by Ernie on Monday February 22, 2016. The Class Notes belongs to BIO 181 at Arizona State University taught by Chakravadhanula, Farrokh, Konikoff in Winter2015. Since its upload, it has received 67 views. For similar materials see General Biology 1 in Biochemistry at Arizona State University.
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Date Created: 02/22/16
Lecture Notes 2192016 Energy and Respiration Clicker Questions HPPPPPF wgtngtgtmn How Do Cells Make ATP 0 ATP is created with metabolic pathways this means the product of one reaction is the reactant for another Enzymes bind to substrates and release products Enzymes Biological catalysts they are not consumed in reactions they can continue on to other reactions Enzymes bind to reactants due to complementary shape Enzymes lower activation energy and speed up reactions 3 Modules in Respiration 1 Glycolysis 2 Citric Acid Cycle 3 ETC Oxidative PhosphorylationETCChemiosmosis Use ATP Synthase ATP Synthase Forms ATP from ADP and a P has an ion gradient with H39s called Protons Pass protons from outside of Mitochondria to inside Energy from ETC creates the proton gradient Energy is released as electrons are passed between carriers because each carrier has less energy H Protons they lack the electron c As electrons are passed to carriers the energy released is used to pump out protons this helps to create the proton gradient that create ATP Each carrier has a higher af nity for electrons than the previous carrier NADH is where the electron comes from in ETC Oxidation of NADH losses its electron Electrons are usually passed in the form of H Oxidation releases a lot of energy because it release Electron with H Reduction requires an input of energy because it takes an H Nicotinamide Adenine Dinucleotide NADH NADH has one extra H than NAD CH Bonds have potential energy Bio Lecture Notes Cellular Respiration Part III 2262016 Clicker Questions PPHP P PPP wwnmgtwugtm Have not converted Glucose into energy during cellular respiration Oxygen has the most mass in glucose while Hydrogen has the least mass C72 096 H12 Most of the mass in glycolysis goes into Pyruvates because this is where all Carbons go Most of the mass in TCA cycle goes into C02 If cell receives no oxygen then it either 1 Fermentation takes place 2 Dies In fermentation Pyruvate is turned into lactic Acid When this happens NADH is used up and converted back into NAD No ATP is produced after Glucose is not completely oxidized Bio Lecture Notes Respiration part II 2242016 Clicker Questions PHP P PPPE rnn39 gtgtw3939gtgt D 11 D 12 B 13 B Glycolysis Get ATP directly from glycolysis along with NADH Glucose is the electron Donor in Glycolysis NAD gains electrons in glycolysis NAD and ADP gains potential energy in glycolysis When things are reduced they gain potential energy CH and Phosphate Bonds have potential energy ATP NADH amp Pyruvate has lost energy from glycolysis ETC helps to regenerate NAD for another round of glycolysis 3 Inputs for Glycolysis Glucose 2 NAD 2 ADP 2 ATP go into 3 Outputs of Glycolysis 2 Pyruvates has energy amp mass 2 NADH 4 ATP There is a total gain of 2 ATP from glycolysis All C from Glucose goes into the Pyruvates Citric Acid Cycle Substrate Level Phosphorylation 2 Pyruvates from Glucose 8 NADH are made 2 FADH2 are made 2 ATP are made 6 C02 are made Pyruvate is oxidized in pre Kreb Cycle into Acetyl CoA NAD gains electron to make NADH so it is reduced so it gains potential energy due to gaining electrons Cellular Respiration Notes The last bond on ATP is very high energy and when this breaks off this energy is used Condensation reaction Reattach the Phosphate to ADP to make it ATP again Glucose can be broken to produce ATP 1 Glycolysis Make glucose into Pyruvate which produces 2 ATP molecules After this 2 Pyruvates are converted into Acetyl CoA these will go through the Kreb Cycle 2 Kreb Cycle Acetyl CoA goes through and NADH and FADH2 are produced along with C02 NADH and FADH2 assist the mitochondria in creating a proton gradient inside inner membrane of mitochondria this will help with ATP Synthase this takes an ADP and Phosphate group and combines them to create ATP 3 Electron Transport Chain Cellular Respiration Equation C6 H12 06 1 Glucose 602 Six Oxygen D 6C02 Six C02 6H20 6 Water EnergyATP Cellular Respiration Glycolysis Begins with Glucose 2 NADH is produced 2 Pyruvates are produced Krebs Cycle Pyruvates go into the Krebs cycle The Pyruvates are converted into Acetyl CoA by Pyruvate Dehydrogenase Complex AceTyl CoA has one less C this is how C02 is produced Produce another NADH as we lose Carbons FADH2 is produced 3 NADH39s are produced ETC 4 Protein Complexes in ETC Also ATP Synthase Begins with NADH that was produced from earlier stages NADH loses 2 electrons and becomes NAD the 2 electrons follow the ETC Produces Water While electrons are pumped through they pump out protons outside the membrane The protons follow the gradient through ATP synthase this is because that there is a higher concentration of Protons outside of the Mitochondria so the protons go back into the Mitochondria and joins ADP and a P to create ATP Bio Notes 181 An Overview of Gene Regulation and Information Flow Flow of information from DNA to activation is represented as DNA DmRNAleroteinlectivated protein DNA to mRNA represents Transcription which is the creation of messenger RNAmRNA mRNA to Protein represents Translation which is when ribosomes read the information on the mRNA and use this to synthesize proteins Protein to activated protein represents modi cations to the protein that can change shape and activity Ways to Avoid Producing Unnecessary Proteins 1 Transcriptional Control when regulatory proteins affect RNA polymerase39s ability to bind to a promoter and start transcription Transcription is prevented 2 Translation Control Prevent the mRNA from being translated into protein occurs when regulatory molecules alter the length of mRNA39s life or affect the rst two phases of translation InitiationElongation 3 PostTranslation Control Regulating the activation of proteins All of these occur in bacteria TransciptionControl is the most ef cient since it stops at the earliest possible stage TranslationControl allows cell to make rapid changes in the amounts of different proteins because mRNA is already present and available to be translated PostTranslation Control Gives the most rapid response because only one step is needed to activate a protein All have trade offs with speed and ef ciency Transciption Control is slow but energy ef cient Post Translation Control is fast but very costly as far as energy goes Gene expression is not ALL OR NOTHING there can be varying levels of expression forgenes The E Coli bacteria39s main food supply is glucose it will eat lactose but only if all glucose is gone To eat lactose the E Coli rst transports the sugar into its cell and then has an enzyme break down the cell into glucose that can be used lnducer A small molecules that will trigger the transcription of a certain gene This makes the gene more prominent if induced 183 Negative Control of Transcription Transcription is regulated in 2 ways in principle 1 Negative Control When a quotRepressor proteinquot binds to DNA and stops the process of transcription 2 Positive Control When a quotActivator proteinquot binds to DNA and causes transcription Negative Control Brakes on a car Positive Control Gas Pedal on a car Lactose Unbinds the negative control so it quotreleases the parking brakesquot Operon Set of coordinately regulated bacterial genes that are transcribed into one mRNA lac operon Genes involved with lactose metabolism 3 Hypotheses in Model of lac operon Regulation 1 lacZ lacY amp lacA genes are adjacent and are all transcribed into a single mRNA initiated from the single promoter of the lac operon AKA Cotranscription Causes coordinated expression of the three genes 2 The repressor is encoded by lacl which binds to DNA and prevents transcription of lac operon genes lacZ lacY amp lacA lacl is constantly expressed and repressor binds to a section of DNA in the lac operon called the quotOperatorquot 3 The lnducerLactose binds to a repressor this makes the repressor change shape due to the change in shape the repressor falls off of the DNA it is binded to AKA Allosteric Regulation small molecule binds to a protein and causes the protein to change shape and activity allows transcription to conUnue Glucose has been seen to prevent expression of lac operon lnduce Exclusion Glucose preventing the transport of an inducer Gene Expression Regulated by physical contact between regulator proteins and speci c regulator sites in DNA Repressor Proteins are always produced they39re activity is just altered when they are needed to be used to represses 183 Negative Control of Transcription Transcription can be regulated in two ways 1 Negative Control When the regulatory protein known as a Suppressor binds to the DNA and shuts down transcription 2 Positive Control Regulatory Proteins known as an Activator binds to DNA and triggers transcription Negative Control Car Brakes Positive Control AccelerationGas Pedal Lactose releases the brake on the suppressor protein Lacl Gene Codes for a repressory protein that uses negative control on LacZ and LacY 101 Photosynthesis Harnesses Sunlight to Make Carbohydrates Photosynthesis is an endergonic suite of redox reactions that produce sugars from C02 and light energy Cellular Respiration Exergonic suite of redox reactions that produces C02 and ATP from sugars Oxygen atoms from 02 come from water Van Niel showed 1 That C02 and H20 do not interact during photosynthesis 2 Showed that 02 in C02 is not released as oxygen in gas H20 was the source of the 02 atoms being released Photosynthesis uses one reaction from light and another reaction to produce 02 from H20 and one that converts C02 into sugars Calvin Cycle Make C02 into Sugars can only occur in the presence of light Photosynthesis is made of 2 reactions 1 Triggered by light 2 Calvin Cycle requires the products of light capturing reactions the light capturing reactions produce 02 from H20 the Calvin cycle produces sugars from C02 The two reactions are linked by electrons that are released when water is split to form oxygen gas During the light capturing reactions these electrons are promoted to a high energy state by light and the transferred through a series of redox reactions to NADP this creates NADPH NADPH works as a reducing unit like NADH in cellular respiration some energy released during this process is used to create ATP In the Calvin Cycle electrons in NADPH and potential energy in ATP are used to make C02 to a carbohydrate The resulting sugars are used in cellular respiration to produce ATP for the cell Plants oxidize sugars in mitochondria and consume 02 in process Photosynthesis Occurs in Chloroplast Chloroplast has outer and inner membrane The interior is dominated by Thylakoids Flattened sac like structures Thylakoids occur in interconnected stacks called Grana Lumen The space inside Thylakoid the interior to any sac like structure Stroma Fluid lled space between thylakoids and inner membrane Thylakoids have large quantities of pigments Pigments Molecules that absorb certain wavelengths of light the other wavelengths are re ectedtransmitted the color in pigment comes from the wavelengths that they do not absorb 102 How Do Pigments Capture Light Energy What is the Role of Carotenoids amp Other Accessory Pigments Carotenoids Absorb light and pass the energy to the chlorophyll Absorb wavelengths of light that are not absorbed by chlorophyll this causes them to extend the range of wavelengths that can drive photosynthesis Plants without Carotenoids lost chlorophyll and die Carotenoids Accept free radicals and stabilize unpaired electrons that free radicals cause this means that they protect chlorophyll from harm When Light is Absorbed Electrons Enter an Excited State Excited Raised to higher energy state Chlorophyll can absorb Red and Blue photons because the difference between ground state and state 1 is equal to energy in a red photon If the difference between possible energy states is the same as the amount of energy in the photon the photon can be absorbed If a pigment absorbs a photon with the right amount of energy energy is transferred to the electron in the form of electromagnetic radiation the electron now has high potential energy Fluorescence When the electron energy produces light electromagnetic radiation in this is lower and a longer wavelength because some of the original photons energy is transferred into heat Antenna Complex In the thylakoid membrane the chlorophyll molecules and accessory pigments are organized in structures Photosystem Antenna Complexes along with molecules that captures and process excited electrons When a redblue photon strikes a pigment molecule in the Antenna Complex the enrgy is absorbed and an electron is excited in response the energy from here is passed to a chlorophyll here another electron is excited in response this is called resonance energy transfer Resonance Energy Transfer is possible only if it is between pigments that are able to absorb different photon wavelengths Reaction Center When a chlorophyll molecule is excited in the reaction center its excited electron is transferred to an electron acceptor Electromagnetic Energy is turned into chemical energy Energy that is released from electrons can 1 Be emitted in the form of uorescence 2 Be given off as heat 3 Excite an electron in nearby pigment and induce resonance 4 Transferred to an electron acceptor in a redox reaction 103 The Discovery of Photosystems I and II Enhancement Effect Different wavelengths causes photosynthesis to be more productive Because when 2 Photosystems are working together it is more productive Pheophytin ldentical to chlorophyll except it lacks magnesium in the head region the two have very different functions ETC in photosystem II and ETC in mitochondria are similar Plastoquinone Quinone like ubiquinone in ETC of cellular respiration Shuttles electrons form photosystem II to Cytochrome complex Protons in plastoquinone result in a large concentration of protons in thylakoid lumen Photophosphorylation Energy derived from light depends on chemiosmosis like oxidative phosphorylation Photosystem ll Obtains Electrons by Oxidizing Water Light energy from photosystem II splits water When excited electrons leave photosystem II and enter ETC the photosystem becomes so electronegative that enzymes can remove electrons from water leaving protons and oxygen Photosystem II is used to create 02Oxygen How Does Photosystem I Work NADH amp NADPH are electron carriers 1 Pigments in antenna complex absorb photons and pass energy to photosystem I reaction center Electrons are excited in reaction center Chlorophyll molecules Reaction center pigments are oxidized and high energy electrons are pass through carriers in photosystem then to Ferredoxin and then to NADP Reductase 4 NADP Reductase transfers 2 electrons and a proton to NADPH UJN Electrons from photosystem I are used to produce NADPH which is a reducing agent similar to NADH and FADH2 produced in citric acid cycle Electrons from photosystem II are used to create a proton motive force that drives ATP synthesis Together Photosystems l and II produce chemical energy in ATP and NADPH The Z Scheme Photosystems I amp ll Work Together Z Scheme Model for how photosystems l and II interact in a Z shape Plastocyanin When electrons reach the end of the cytochrome complex they are passed into this This is critical because physically links Photosystem l amp ll g Understanding The Enhancement Effect When both photosystems are working at the same time ef ciency is enhanced Noncyclic Electron Flow Between Water amp NADP Noncyclic Electron Flow Electrons pass from water to NADP through a chain of redox reactions in a linear fashion Like in cellular respiration a proton gradient is created amp at the end of the chains electrons are donated to terminal electron acceptors ln chloroplast energy increases through the ETC instead of decreasing like in Mitochondria Cyclic Electron Flow Recycles Electrons amp Drives Photophosphorylation Cyclic Electron Flow Alternative electron path in algae This ow coexists with the Noncyclic electron ow and produces extra ATP the ATP is used to reduce C02 and create sugars Where Are Photosystems I and II Located Both are located in the Thylakoid membrane Photosystem II is located in interior stacked membranes of grana Photosystems l amp ATP synthase are located in exterior unstacked membranes Oxygenic Photosynthesis amp The Evolution of Earth 104 How Is Carbon Dioxide Reduced to Produce Sugars The Calvin Cycle Fixes Carbon Carbon Fixation The addition of Carbon Dioxide to an organic compound This is a redox reaction because the C in C02 is reduced RuBP is the Initial Reactant With C02 RuBP Initial Reactant to make C02 produce 3PGA The Calvin Cycle 1 Fixation Phase C02 reacts with RuBP this xes carbon and produce 2 3PGA 2 Reduction Phase the 3 PGA is phosphorylated by ATP and reduced by electrons from NADPH this produces G3P some of this is used to create Glucose amp Fructose 3 Regeneration Phase The rest of G3P keeps the cycle going by serving as a substrate for the third phase in the cycle reactions that use ATP in regeneration of RuBP A phases occur in stroma of choropast One turn in Calvin Cyce xes 1 Carbon Dioxide Explains how ATP amp NADPH produced by light capturing reactions allow cells to reduce C02 to carbohydrates 0 Each mole of C02 requires 3 moles of ATP amp 2 Moles of NADPH The Discovery of Rubisco Rubisco Found in all photosynthetic organisms most abundant enzyme on earth Very slow process and inef cient 02 amp C02 compete at enzymes active sites which sows C02 reduction This trait of accepting both 02 amp C02 is maladaptive or it hurts tness of the organism Photorespiration Consumes energy amp releases xed C02 this means that it undoes photosynthesis Oxygen amp Carbon Dioxide Pass Through Stomata Stoma An open one allows C02 to enter and be diffused These are opened during the day and closed at night If it is too hot they will close the stoma Mechanisms For Increasing C02 Concentration C4 Pathway Fix C02 and create 4 Carbon molecules Steps 1 PEP Carboxylase xes C02 to a three carbon molecule in mesophyll cells 2 4 Carbon Organic acids are transported to bundle sheath cells via Plasmodesmata 3 4 Carbon Organic Acids release C02 molecule that rubisco uses as a substrate to form 3PGA this starts the Calvin cycle 4 3 Carbon compound remaining after C02 is released is returned to Mesophyll cell to regenerate PEP C4 Pathway acts as a C02 concentrator the reactions that happen in mesophyll cells require energy in the form of ATP however they increase C02 concentration in cells where rubisco is active C4 Pathway improves the ef ency of Calvin Cycle CAM is like the Calvin Cycle except it occurs at a different time CAM occurs in cacti and species that routinely keep their stomata closed on hot dry days at night they open up the stomata C4 amp CAM pathways function as C02 pumps they minimize photorespiration when stomata is closed and C02 cannot diffuse directly In C4 plants the reactions catalyzed by PEP carboxylase and rubisco are separated in space In CAM plants the reactions are separated in time How Photosynthesis Regulated Rate of photosynthesis is nely tuned to use resources ef ciently in response to changes in environmental conditions What Happens to the Sugar That is Produced by Photosynthesis Gluconeogenesis Production of glucose amp fructose Bio Reading Notes 2172016 91 An Overview of Cellular Respiration ATP has very high potential energy so it is not stable and not stored cells contain enough ATP to last 30 seconds to a few minutes Most of the glucose used to make ATP comes from photosynthesis Glucose is not burned in cells it is oxidized in cells through many redox reactions Respiration fully oxidizes Glucose while Fermentation does not Respiration therefor releases more energy than Fermentation Chemical Energy in Glucose to Chemical Energy in ATP is a 4 Step Process 1 Glycolysis One carbon of the glucose is broken into 2 molecules of the 3 carbon compound Pryuvate ATP is produced from ADP and Nicotinamide Adenine Dinucleotide NAD is reduced to create NADH 2 Pyruvate Processing Pyruvate is processed and releases one C02 molecule while the remain 2 carbons from the original 3 in Pyruvate are used to form acetyl CoA oxidizing Pryuvate causes more NAD being reduced to NADH 3 Citric Acid Cycle Aceter CoA is oxidized into 2 molecules of C02 while this is happening more ATP and NADH are created and Flavin Adenine Dinucleotide FAD reduces and forms NADSZ 4 Electron Transport and Oxidative Phosphorylation The electrons from NADH and FADH2 move through ETC Electron Transport Chain the energy released in this chain of redox reactions is used to create a proton gradient across the membrane this ow over the gradient is used to create ATP Cellular Respiration Any suite of reactions that uses electrons harvested from high energy molecules to produce ATP with an electron transport chain A cells require Energy and Carbon They require a source of high energy electrons to generate chemical energy in the form of ATP They also require a source of Carbon containing molecules that can be used to synthesize DNA RNA Proteins Fatty Acids and other molecules Catabolic Reactions Break down molecules these often produce ATP Anabolic Reactions synthesis larger molecules from smaller molecules they use ATP Enzymes normally break down fats to releases glycerol and convert the fatty acids into Acetyl CoA Glycerol can be broken down further and enter glycolysis while Acetyl CoA enters the Citric Acid cycle Proteins can be used to create ATP One molecule can have many different functions in the cell Catabolic and Anabolic pathways are intertwined By a cell regulating key reactions it can maintain homeostasis 92 Glycolysis Processing Glucose to Pyruvate Metabolic processes can occur outside of an organism All 10 reactions of glycolysis occur in the cytosol in both Eukaryotes and Prokaryotes 1 Glycolysis starts by using ATP it uses 2 ATP molecules before producing any 2 Each molecule of glucose produces 2 molecules of NADH and 2 of ATP and 2 Pyruvates 3 Phosphate group moves onto an ADP making it ATP Substrate Level Phosphorylation Enzyme catalyzed reactions that produce ATP 0 Energy to produce ATP comes from phosphorylated substrate not a proton gradient 0 However ATP comes from proton gradient through oxidative phosphorylation Phosphofructokinase Causes the synthesis of fructose In this ATP acts as a regulator Glycolysis 1 Starts with one 6 carbon glucose and ends with 2 3 carbon pyruvate molecules the reaction happens in the cytoplasm and the energy that is released is used to produce 2 ATP and 2 NADH 93 Processing Pyruvate to Acetyl CoA Cristae Sac like structures that ll the interior membrane it is connected to the main part of the membrane by short tubes Mitochondrial Matrix Inside the inner membrane but outside the Cristae Pyruvate moves across mitochondrion39s outer membrane through pores CoA Reacts with pyruvate acts as a coenzyme by accepting and moving Acetyl group Pyruvate reacts with CoA and creates acetyl CoA Pyruvate Dehydrogenase Enzyme complex where pyruvate reacts with CoA and creates Acetyl CoA In eukaryotes this is located in the mitochondrion matrix In Bacteria and Archaea this occurs in Cytosol While Pyruvate is being processed one of the carbons in Pyruvate is oxidized to C02 and NAD is turned into NADH the remaining carbon acetyl unit becomes CoA Pyruvate NAD and CoA go in C02 NADH and Acetyl CoA comes out If ATP is abundant the process will cease Large supplies of a product will slow downstop the Pyruvate process while low supplies of the product and high supplies of the reactants will increase the process 94 The Citric Acid Cycle Oxidizing Acetyl CoA and C02 Carboxylic Acids Redox reactions that oxidize smaII organic acids Energy is released by the oxidation of one molecule of Acetyl CoA is used to create 3 molecules of NADH and one of FADH2 and one of GTPATP ATP or GTP depends on the cell being created In eukaryotes the enzymes for the citric acid cycle are in the mitochondrial matrix Citric Acid Cycle has many regulations at many points Citric Acid Cycle Begins with 2 Carbon Acetyl molecule in the form of Acetyl CoA and ends with the release of 2 C02 the energy that is released by this is used to create 3 NADH 1 FADH2 and 1 ATPGTP for every Acetyl oxidized 95 Electron Transport and Chemiosmosis Building a Proton Gradient to Produce ATP Electron Transport Chain Molecules responsible for oxidation of NADH and FADH2 As electrons are moved the energy released by the redox reactions is used to move protons across the inner membrane of mitochondria Ubiquinone Moves quickly through hydrophobic interior of the inner of the mitochondrial membrane Cytochrome C Acts as a shuttle that transfers electrons between complexes ATP Synthase Enzyme to synthesis ATP ETC Used to pump protons across inner membrane of mitochondria from the matrix to the intermembrane space after the gradient is established an Enzyme ATP Synthase will synthesis ATP Chemiosmosis Use of a proton gradient to drive energy requiring process like the production of ATP ATP production relies on a proton motive force ATP can be produced without a ETC but needs proton motive force ATP synthase can be done in reverse rebuilding a broken proton gradient Glucose can produce 29 ATP Species that need oxygen to accept electrons for respiration are called Aerobic Cells that do not require oxygen to accept electrons are anaerobic Aerobic is more successful in respiration 96 Fermentation Fermentation Metabolic Process that regenerates NAD by oxidizing stockpiles of NADH the electrons that are removed from NADH are moved to pyruvate or a molecule derided from pyruvate instead of an ETC Allows cells to grow without an ETC Lactic Acid Fermentation Regenerates NAD by forming a product molecules called lactate a form of lactic acid Fermentation is very ineffective compared to Aerobic Cellular Respiration due to Oxygens high electronegativity Usually used when Oxygen runs out to produce ATP Faculatitve Anerobes Organisms that are able to switch between Cellular Respiraion and Fermnetation
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