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by: Abhishek Mishra

Notes RUSS 0090

Abhishek Mishra
GPA 3.83
Russian Fairy Tales
Dr. Robert Chip Crane

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Russian Fairy Tales
Dr. Robert Chip Crane
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This 27 page Bundle was uploaded by Abhishek Mishra on Friday January 16, 2015. The Bundle belongs to RUSS 0090 at University of Pittsburgh taught by Dr. Robert Chip Crane in Fall. Since its upload, it has received 176 views. For similar materials see Russian Fairy Tales in Russian at University of Pittsburgh.

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Date Created: 01/16/15
23 Chemical reactions energy and chemical evolution Tuesday August 26 2M4 234 PM Proponents of chemical evolution contend that simple molecules participated in chemical reactions that led to more complex organic molecules Two environments where these reactions are thought to have occurred are The atmosphere which was probably dominated by gases ejected from volcanoes Water vapor carbon dioxide and nitrogen are the dominant gases ejected by volcanoes today small amount of molecular hydrogen and carbon monoxide may also be present Deep sea hydrothermal vents where extremely hot rocks contact deep cracks in the sea floor In addition to gases such as CO2 and H2 certain deep sea vents are also rich in mineral containing reactive materials such as nickel and Iron When gases like CO2 N2 H2 and C0 are put together and allowed to interact on their own very little occurs They do not suddenly link together to create large complex substances like those found in cells Instead their bonds remain intact What is energy Energy is the capacity to do work it is either stored as potential or as an active motion When stored in chemical bonds potential energy is called chemical energy Kinetic energy is energy of motion the transfer of thermal energy is called heat What makes chemical reactions spontaneous Reactions are considered spontaneous when they can proceed on their own without any continuous external influence such as added energy Reactions tend to be spontaneous when the product molecules are less orderly than the reactant molecules Reactions tend to be spontaneous when the products have lower potential energy than the reactants If the electrons in the reaction products are held on more tightly higher electronegativity Module 4 Page 1 How do chemical reactions happen The initial or reactant molecules are shown on the left and the resulting reactions the products are shown on the right The physical state of each reactant and product is indicated as gasg liquidl solids or in an aqueous solutionaq Chemical equilibrium is when the quantities of products and reactants remains constant 2nd law of thermodynamics Entropy disorder always increases in a closed system Physical and chemical processes proceed in the direction that results In increased entropy and lower potential energy 81 What Happens to Energy in Chemical Reactions Sunday November 9 Z 14 431 PM Free energy The amount of energy available to do work There are two kinds of energy 1 Kinetic energy of motion a Called thermal energy at the molecular level 2 Potential energy associated with position or configuration a Called chemical energy and stored in the positions of electrons Chemical Reactions Involve Energy Transformations Energy is not locked into either kinetic or potential Energy is often transformed from one type to another Potential energy of an electron is based on its position relative to other electrons and the protons in the nuclei of nearby atoms Electron releases kinetic energy when going down electron levels First law of thermodynamics 1LoT Energy cannot be created or destroyed but only transferred and transformed Total energy of a molecule is referred to as its enthalpy H EndothermicExothermic When the products have released heat energy products have less potential energy Exo When the products take up heat energy products have higher potential energy Endo Second law of thermodynamics 2LoT Total entropy always increases in an isolated system SpontaneousNonspontaneous To determine whether a reaction is spontaneous or not you must combine changes in heat and disorder AGAHTAS H heat energy 5 entropy T temperature Kelvin SpontaneousExergonic reactions are when AG is less than zero NonspontaneousEndergonic reactions are when AG is greater than zero When AG is equal to zero reactions are at equlibrium Temperature and Concentration Affect Reaction Rates For reactions to proceed one or more chemical bonds have to be broken for others to form For this to happen the substances involved must collide at specific orientations that brings the electrons involved near each other 0 When concentration is high more collisions should occur and reactions should occur more quickly Module 4 Page 2 0 When temperature is high reactants should move faster and collide more frequently Module 4 Page 3 82 Nonspontaneous Reactions May Be Driven Using Chemical Energy Sunday November 9 ZDM 6z PM Energetic coupling between exergonic and endergonic reactions allows chemical energy to be released from reaction to drive another Occurs in one of two ways 0 Transfer of electrons 0 Transfer of phosphate group Redox Reactions Transfer Energy via Electrons Chemical reactions that involve the loss or gain of one or more electrons are called reductionoxidation reactions quotOiL RiGquot O Oxidation is loss 0 Reduction is gain Oxidation events are always paired with a reduction 0 Oxidation is exergonic halfreaction 0 Reduction is endergonic halfreaction Energy lost by oxidized molecule is gained by reduced molecule During a redox reaction an electron can be transferred completely from one atom to another or an electron can simply shift its position in a covalent bond Another Approach When an electron is donated it is sometimes accompanied by a proton H which results in the addition of a neutral hydrogen H to the electron acceptor O Molecules tend to gain potential energy from this because CH bonds contain equally shared electrons OgtNgtC2H O The electron donor tends to lose energy because instead of CH bonds CO bonds are formed which contain much less potential energy 0 Reduction quotadds Hsquot Oxidation quotremoves Hsquot Examples FAD gt FADHz D FAD is a electron receptor that is reduced by two electrons accompanied by two protons D FADHz readily donates its highenergy electrons to other molecules and thus has quotreducing powerquot NAD gt NAHD D Like FAD NAD receives two electrons but only one proton 0 It releases the other to the environment All redox reactions involve the transfer of electrons but they do not always involve the transfer of hydrogens ATP Transfers Energy via Phosphate groups ATP contains four negative charges in a small area High potential energy created through likecharge repulsion ATP Hydrolysis Releases Free Energy When ATP reacts with water during hydrolysis the bond between the outermost phosphate group and its neighbor is broken This results in the formation of ADP and HzPO4 inorganic phosphate Pi Module 4 Page 4 U Release of 73 kcal per mole ATP ATP hydrolysis is exergonic because there is much less potential energy when it is broken down into ATP and Pi D Electrons from ATP are now spread on two molecules meaning that there is less electrical repulsion In addition more effective interaction with partial positive charges of water helps stabilize the electrical charges more than on the clustered ATP How Does ATP Drive Endergonic Reactions Energy released when ATP is hydrolyzed may be used to transfer the cleaved phosphate to a target molecule substrate The addition of a phosphate group to a substrate is called phosphorylation When the phosphate group is added to a substrate is activated increases the potential energy and creates a critical point where a endergonic reaction is now exergonic When reactant molecules in an endergonic reaction are phosphorylated the free energy released during phosphorylation is coupled to an endergonic reaction to make the combined reaction exergonic Module 4 Page 5 83 How Enzymes Work Sunday November 9 2 14 845 PM Reactions do not occur at the speed required for life without the support of enzymes Enzymes are catalysts They bring substrates together in an orientation that makes reactions more likely Enzymes Help Reactions Clear Two Hurdles 1 Reactants need to collide in a precise orientation Enzymes Bring Substrates Together Bring substrate molecules together in the enzymes active site Enzymes are generally very large and globular active site is a cleft or cavity within the globular shape Enzymes are flexible and dynamic and undergo significant conformation when reactant molecules bind III Induced fit Degree of interaction between enzyme and substrate reach maximum at the transition state III This is the quotlockingquot stage Energy required to reach the transition state is activation energy How do enzymes clear the activation energy hurdle 2 Have enough kinetic energy to overcome repulsion between electrons that come into contact as a bond forms Enzymes Lower the Activation Energy Reactions happen when reactants have enough kinetic energy temperature to reach the transition state During transition state free energy is highest because bonds of substrate are unstable due to interaction with the enzyme The more unstable the transition state the higher the activation energy and the less likely a reaction will occur Reaction rates depend on kinetic energy temperature and the activation energy of the reaction free energy of the transition state If enzymes don39t raise temperature then they must lower activation energy I How Interaction with the Rgroups of the enzyme help to stabilize the transition state and thus lower the activation energy III Presence of acidicbasic Rgroups allow for reactants to losegain protons more readily III May form short lived covalent bonds that assist with the transfer of atoms or groups of atoms from one reactant to another III Induced fit stretches bonds of substrates to break them more easily Enzymes can speed up reaction by factors of millionTRILLIONS Enzyme is not consumed during reactions Composition remains the same Enzyme catalysis can be analyzed as a threestep process 1 Initiation a Instead of reactants occasionally colliding in a random fashion enzymes orient reactants precisely as they bind at specific locations within the active site 2 Transition state facilitation Module 4 Page 6 a Inside active sites molecules are more likely to reach their transition states b Interactions between substrate and Rgroups of the enzyme39s active site lowers the activation energy i Thus catalyzed reaction proceeds much more rapidly than an uncatalyzed reaction 3 Termination a Reaction products have less affinity for the active site than the transition state i Binding ends ii Enzyme returns to original conformation iii Products are released What Limits the Rate of Catalysis SaturationKinetics 0 At some point active sites cannot accept substrates any faster no matter how large the concentration of substrates gets 0 Reaction rates level off because all available enzyme molecules are being used Do Enzymes Work Alone Most often No Many enzyme quothelpersquot 1 Cofactors Inorganic ions Zn2 Mg2 Fe2 which reversibly interact with enzymes 2 Coenzymes Organic molecules that reversibly interact with enzymes such as electron carriers NADH FADHz 3 Prosthetic Groups Nonamino acid atoms or molecules that are permanently attached to proteins In many cases these helpers are part of the active site and play a key role in stabilizing the transition state Vitamins important in producing coenzymes Module 4 Page 7 84 What Factors Affect Enzymes Function Sunday November 9 2 14 845 PM Sensitive to conditions that alter protein shape The activity of an enzyme often changes drastically as a function of temperature pH interactions with other molecules and modifications of its primary structure Enzymes Are Optimized for Particular Environments Temperature affects the folding and movement of an enzyme as well as the kinetic energy of its substrates The concentration of protons in a solution as measured by pH also affects enzyme structure and function 0 pH affects the charge on carboxyl and amino groups in residue side chains 0 pH affects the active site39s ability to participate in reactions that involve the transfer of protons or electrons Temperature affects the movement of the substrates and enzyme pH affects the movement of the substrates and enzyme pH affects the enzymes shape and reactivity Most Enzymes Are Regulated Although temperature and pH affect the activity of enzymes they are not often used as means of regulating enzyme function Other molecules often change the enzyme39s structure in some way and their activity activatesinactivates the enzyme Regulating Enzymes via Noncovalent Modifications Many molecules that regulate enzyme activity bind noncovalently to the enzyme to either activate or inactivate it Since this reaction does not change the enzyme39s primary structure it is a quotReversiblequot modification Reversible modifications affect the enzyme function in one of two ways 1 The regulatory molecule is similar in size and shape to the enzyme39s natural substrate and inhibits catalysis by binding to the enzyme39s active site i This event is called competitive inhibition because the molecule involved competes with the substrate for access to the enzyme39s active site 2 The regulatory molecule bonds at a location other than the active site and changes the shape of the enzyme i This type of regulation is called allosteric different structure regulation because the binding event changes the shape of the enzyme in a way that makes the active site available or unavailable Both strategies depend on the concentration of the regulatory molecule the more regulatory molecule present the more likely it will bind to an enzyme and affect its activity Regulating Enzymes via Covalent Modifications In some cases the function of an enzyme is altered by a chemical change in its primary structure Module 4 Page 8 This change may be reversible or irreversible depending on the type of modification I Irreversible changes often result from the cleavage of peptide bonds that make up the primary structure of the enzyme III eg The protein trypsin is not functional until a small section of the protein is removed by a specific protease I The most common modifications of enzymes is the addition of one or more phosphate groups similar to activated substrates However in this case the enzyme is phosphorylated as opposed to a substrate III When phosphorylation adds a negative charge to one or more amino acid residues in a protein the electrons in that part of the protein change configuration The enzyme39s conformation usually changes as well which may activate or inactivate its function Module 4 Page 9 85 Enzymes Can Work Together in Metabolic Pathways Sunday November 9 2 14 845 PM Metabolic Pathways Are Regulated When an enzyme in a pathway is inhibited by the product of the reaction sequence feedback inhibition occurs 0 This is a convenient way for pathways to shut themselves down when their activity is no longerneeded 0 As the concentration of the product molecule becomes abundant it quotfeeds backquot to stop the reaction sequence By inhibiting a step early in the pathway the amount of initial substrate is not depleted unnecessarily allowing it to be stored or used for other reactions Metabolic Pathways Evolve While many enzymes are extraordinarily specific some can catalyze a range of reactions and are able to interact with a family of related substrates Research suggests this flexibility allowed new enzymes to evolve Pathway Evolution Would have started with enzymes that make the building blocks of life out of readily available substrates such as small organic compounds If the original substrate were depleted natural selection would favor the evolution of a new enzyme to make more of it from other existing molecules The process of creating a new reaction to produce the original substrate now an intermediate is referred to as retroevolution Patchwork Evolution As early pathways emerged early enzymes may have been recruited to new pathways where they evolved new catalytic activities that performed new tasks Pathways that break down molecules for sources of energy and carbon building blocks are called catabolic pathways Pathways that use energy and carbon building blocks to synthesize molecules are called anabolic pathways Module 4 Page 10 91 An Overview of Cellular Respiration Sunday November 9 Z 14 845 PM Cells on average have enough ATP in reserve for 30 secondsfew minutes ATP is unstable and not stored Cells are making ATP all the time Storage carbs like starch glycogen save chemical and convert to ATP in times of need Glucose is used to produce ATP through one of two general processes 0 Cellular respiration O Fermentation I The primary difference between these processes lies in the degree to which glucose is oxidized What Happens When Glucose Is Oxidized When glucose goes through uncontrolled oxidation burning it releases massive amounts of its energy as heat However glucose is not burned in cells 0 Glucose is oxidized through a series of small carefully controlled redox reactions Instead of releasing energy as heat redox allows for the energy to be used to make ATP 0 Used to synthesize ADP and Pi into ATP Oxidation v Fermentation O Respiration results in the complete oxidation of glucose 0 Fermentation does not fully oxidize glucose and releases small organic molecules as waste The complete oxidation of glucose via cellular respiration can be thought of as a fourstep process 0 Each step consists of chemical reactions 0 Each step has a distinctive starting molecule 0 Each step has a characteristic set of products 1 Glycolysis One 6carbon molecule of carbon is broken down into 2 molecules of threecarbon pyruvate 2 ATP used 4 ATP created net gain of 2 ATP 2 NADH formed from NAD THE FOLLOWING REACTIONS HAPPEN TWICE ONCE FOR EACH PYRUVATE 2 Pyruvate processing 1 Cycle Releases one molecule of C02 Remaining 2 carbons are used to make acetyl CoA One more NADH made from NAD 3 Citric Acid Cycle 1 Cycle Acetyl CoA is oxidized to two molecules of C02 One GTP or ATP 3 NADH produced 1 FADHz 4 Electron transport and oxidative phosphorylation Electrons from NADH and FADHz move through a series of proteins called the electron transport chain ETC Energy released in this chain of redox reactions is used to create a proton gradient across a membrane Link between the phosphorylation of ADP with the oxidation of NADH and FADHz results in name oxidative phosphorylation Module 4 Page 11 Cellular respiration is any suit of reactions that uses electrons harvested from highenergy molecules to produce ATP via an ETC Two fundamental requirements of cell are energy carbon 0 Energy Need a source of highenergy electrons for generating chemical energy in the form of ATP 0 Carbon Source of carboncontaining molecules that can e used to synthesize DNA RNA proteins fatty acids and other molecules Cellular Respiration Plays a Central Role in Metabolism Sets of reactions that break down molecules are called catabolic pathways 0 Harvest stored chemical energy to produce ATP Sets of reactions that synthesize larger molecules from smaller components are called anabolic pathways 0 Often use energy in the form of energy Catabolic Pathways Break Down a Variety of Molecules 0 Using enzymecatalyzed reactions cells can produce glucose from glycogen starch and most simple sugars Glucose and Fructose can then be processed in glycolysis O Fats can be broken down to release the glycerol and convert the fatty acids into acetyl CoA molecules I The glycerol can be further processed and enter glycolysis I Acetyl CoA enters the citric acid cycle 0 Proteins can also be catalyzed and broken down to produce ATP I Hydrolyzed into constituent amino acids I Enzymecatalyzed reactions remove the amino groups NH2 through urine I The remaining carbon compounds are converted to pyruvate acetyl CoA and other intermediates in glycolysis and the citric acid cycle Catabolic Intermediates Are Used in Anabolic Pathways Where do cells get the precursor molecules required to synthesize amino acids RNA DNA phospholipids and other cell components I The answer often involves intermediates in carbohydrate metabolism Half the required amino acids can be synthesized from molecules siphoned from the citric acid cycle Acetyl CoA is the starting point for anabolic pathways that result in the synthesis of fatty acids Fatty acids can then be used to build phospholipid membranes or fats Intermediates in glycolysis can be oxidized to start the synthesis of the sugars in ribonucleotides and deoxyribonucelotides Nucleotides in turn are building blocks used in RNA and DNA synthesis f ATP is abundant pyruvate and lactate can be used in the synthesis of glucose Excess glucose maybe be converted to glycogen or starch and stored Module 4 Page 12 92 Glycolysis Processing Glucose to Pyruvate Sunday November 9 2014 845 PM Glycolysis Is a Sequence of 10 Reaction In both eukaryotes and prokaryotes all 10 reactions of glycolysis occur in the cytosol 1 Glycolysis starts out by using ATP not producing it 2 Once the energy investment phase is complete the subsequent reactions represent an energypayoff phase For each molecule of glucose processed the net yield is two molecules of NADH two ATP and two pyruvate 3 Reactions 7 and 10 involve the movement of phosphate groups onto ADP molecules forming ATP These ATP are produced by substratelevel phosphorylation How is Glycolysis Regulated Note At step 3 an enzyme called Phosphofructokinase catalyzes the synthesis of fructose16 biphosphate from fructose6phosphate This step is crucial because at this point glycolysis cannot be revered There are two binding sites for ATP on Phosphofructokinase the one with higher affinity is used to phosphorylate fructose6phosphate the one with lower affinity turns off the enzymes activity At step 3 ATP can act as a regulatory molecule on Phosphofructokinase via feedback inhibition This means that when ATP concentration are high the cell will save its stores of glucose for when ATP is scarce Module 4 Page 13 m imamquotWWquot a iycolysh Handout Hose 150 can 39 2398 1 qu 1 IL AH M 1 tUf MAL o i x 0 Ml j 397 Amp mb 93 Processing Pyruvate to Acetyl CoA Sunday November 9 2014 845 PM In Eukaryotes pyruvate produced by glycolysis is transported from the cytosol to mitochondria Pyruvate is moved across the mitochondria39s outer layer through pores and then through the inner membrane into the matrix Inside the mitochondrion pyruvate reacts with a compound called coenzyme A CoA O CoA acts as a coenzyme by accepting and then transferring an acetyl groups COCH3 to a substrate This reaction occurs inside the enormous pyruvate dehydrogenase complex n eukaryotes this is located in the mitochondrial matrix n bacteria and archaea this is located in the cytosol As pyruvate is processed one of the carbons in the pyruvate is oxidized to C02 and NAD is reduced to NADH O The remaining twocarbon acetyl unit is transferred to CoA Pyruvate processing is under both positive and negative control 0 Large supplies of ATP Acetyl CoA NADH use feedback inhibition to stop slowdown the pathway 0 Large supplies of NAD CoA or AMP indicator for low ATP speed up reactions catalyzed by pyruvate dehydrogenase CH3 Pyruvate NADH Acetyl 60A 0 2011 Pearson taxamn lrc Module 4 Page 14 94 The Citric Acid Cycle Oxidizing Acetyl CoA to C02 Sunday November 9 ZOM 845 PM tetyI Citrate One rotation of TCACItrIc ACIdKrebs cycle produces 3 NADH r 1 FADHz mma tme Esotitrate 1ATPorGTP 39 O ATPGTP production depends on what cell respiration is occurring in x L Mala Ef l aa etog utarate n Eukaryotes occurs in mitochondrial matrix In bacteria and archaea occurs in cytosol Occurs twice for each molecule of glucose processed 0 Because of two Acetyl CoA L Elmaimam 39 Howls the Citric Acid Cycle Regulated 39 The citric acid cycle can be turned off at multiple points via several different mechanisms of feedback inhibition Reaction rates are high when ATP is scarce reactions rates are low when ATP is abundant Fumamte Ezucxcilwltoi What Happens to the NADH and FADHz Electrons from NADH and FADHz which oxidizes them to NAD and FAD are transferred to oxygen which is then reduced to water In effect glycolysis pyruvate processing and the citric acid cycle transfer electrons from glucose to NAD and FAD to form NADH and FADHz Oxygen then accepts the electrons from these reduced molecules to form water What happens to the energy that is released as electrons are transferred from NADH and FADH 2 to oxygen atoms Module 4 Page 15 95 Electron Transport and Chemiosmosis Building a Proton Gradient to Produce ATP Sunday November 9 26314 845 PM The Electron Transport Chain ETC As electrons are passed from one molecule to another in the chain the energy released by the redox reactions is used to move protons across the inner membrane of mitochondria Key Points 0 Most of the molecules are proteins that contain distinctive cofactors and prosthetic groups where the redox events take place They include ironsulfur complexes ringcontaining structures called flavins or ironcontaining heme groups called cytochromes Each of these groups is readily reduced or oxidized O The inner membrane of the mitochondrion also contains a molecule called ubiquinone CoQ CoQ is lipid soluble and moves efficiently throughout the hydrophobic interior of the inner mitochondrial membrane 0 The molecules involved in processing NADH and FADHz differ in electronegativity Some molecules will pick up a proton along with the electron forming an hydrogen atom while others obtain just electrons Because Q and the ETC proteins can cycle between a reduced and oxidized state and because they differ in electronegativity it should be possible to organize them into order Electrons would pass from a molecule with lower electronegativity to a molecule with higher negativity As electrons were moved through the chain they would be held more and more tightly and as a result a small amount of energy would be released in each reactions lowering the potential energy of the successive bonds Role of the Electron Transport Chain What does the ETC do with all of this energy Movement of electrons through the ETC actively transports protons from the mitochondrial across the inner membrane and into the intermembrane space When CoQ accepts electrons from complex I or complex II it picks up protons from the matrix This reduced form of CoQ diffuses through the inner membrane where its electrons are used to reduce a component of complex I near the intermembrane space The protons held by CoQ are now released and the electron proceeds down the ETC Much of the chemical energy originally present in glucose is now accounted for in this electrochemical gradient but if the ETC is not making ATP then what is The Discovery of ATP Synthase Racker created hypothesis of membranebound proton channel essential to ATP synthesis Connection between proton transport and ATP synthesis The Chemiosmosis Hypothesis The real job of the ETC is so pump protons across the inner membrane of mitochondria from the matrix to the intermembrane space After a proton gradient is established an enzyme in the inner membrane like Racker39s ATP synthase would synthesize ATP from ADP Pi ETC39s and ATP synthases are used by organisms throughout the tree of life Module 4 Page 16 96 Fermentation Qunolay November PM Fermentation is the metabolic pathway that regenerates NAD by oxidizing stockpiles of NADH The electrons removed from NADH are transferred to pyruvate instead of an ETC Serves as an emergency backup that allows glycolysis to continue producing ATP even when the ETC is shut down Many Different Fermentation Pathways Exist When oxygen is absent the ETC shuts down and NADH cannot donate its electrons there O In this case pyruvate from glycolysis begins to accept electrons from NADH and fermentation takes place 0 This process is called lactic acid fermentation I Regenerates NAD by forming a product molecule called lactate a deprotonated form of lactic acid O In yeast instead of depositing the electrons from NADH into pyruvate O This process is called alcohol fermentation I Yeast first converts the 3C pyruvate to the 2C acetaldehyde o The CO released causes the bubbles in champagne in beer I Acetaldehyde then accepts electrons from NADH forming the NAD required to keep glycolysis going I The addition of electrons to acetaldehyde forms ethanol Bacteria and Archaea can life off of fermentation exclusively O eg Rumen of cow Fermentation as an Alternative to Cellular Respiration Even though fermentation is widespread it is extremely inefficient compared with aerobic cellular respiration Fermentation produces just 2 ATP for every molecule of glucose metabolized O Respiration produces around 15x more This is because oxygen has a much higher electronegativity than molecules used during fermentation as electron receptors like pyruvate As a result the potential energy drop between the start and end of fermentation is a tiny fraction of the potential energy change that occurs during cellular respiration Module 4 Page 17 Gluoooo l 2 ATP 2 Pvruvoto 34 more ATF fermentation oloohol C02 yeast plants oerooio roopirotion lootato animals 101 Photosynthesis Harnesses Sunlight to Make Carbohydrate Sunday November 9 ZOM 846 PM Photosynthesis is an endergonic suite of redox reaction that produces sugars from carbon dioxide and light energy Cellular respiration is an exergonic suite of redox reactions that produces carbon dioxide and ATP from sugars Photosynthesis Two Linked Sets of Reactions The 02 released during photosynthesis is not from C02 but rather H20 Shows two distinct sets of reactions 0 One uses light to produce 02 from H20 0 One converts C02 into sugars Tldr Photosynthesis consists of two reactions One set is triggered by light the other set the Calvin Cycle requires the products of the lightcapturing reactions The light capturing reactions produce oxygen from water the Calvin cycle produces sugar from carbon dioxide Photosynthesis Occurs in Chloroplasts Chloroplasts contain two membranes 0 Outer 0 Inner I Within the inner membrane stacks of thylakoids are present in granum I Space between inner and granum is called the stoma I Inside of thylakoid is lumen III Lumen contains pigments Module 4 Page 18 102 How Do Pigments Capture Light Energy Sunday November 9 2M4 846 PM Function of Carotenoids Accessory pigments that increase range of wavelengths utilized during photosynthesis Acceptstabilizing unpaired free radicals to protect chlorophyll molecules from harm When Light is Absorbed Electrons Enter an Excited State When a photon strikes a chlorophyll molecule the photons energy can be transferred to an electron in the chlorophyll molecules head region This quotexcitesquot the electron into a higher energy state Energy states are discrete requires exact energy to reach higher energy level If a photon ofthe right energy transfers the right amount of energy in the form of electromagnetic radiation the electron now has a higher potential energy 0 What happens now I lfthe electron simply returns to its ground state it releases the energy in the form of heat and electromagnetic radiation light D The fluorescence has lower energy and a longer wavelength because some ofthe original energy was released as heat I The majority of excited electrons are used to drive photosynthesis Chlorophyll and accessory pigments are organized by array of proteins to form the antenna complex and the reaction center In conjunction with molecules that capture and process excited electrons form a photosystem The Antenna Complex Location of resonance transfer Moves from highenergy pigments to lowerenergy pigments Moves into center of antenna complex called reaction center The Reaction Center When an exited electron reaches this state it is transferred to an electron acceptor The reduction that results from that accepted electron completes the process of electromagnetic energy being transformed into chemical energy What happens to the highenergy electrons that are transferred to the electron acceptor in the reaction center Specifically how are they used to manufacture sugars Module 4 Page 19 pigments Photosystem s electron acceptor Reaction center chlorophle Photosystem 103 The Discovery of Photosystems and II Sunday November 9 Z 14 846 PM How Does Photosystem Work Converting Light Energy into Chemical Energy 0 Action begins when antenna complex transmits resonance energy to the reaction center Electron carrier Pheophytin accepts the excited electron from the reaction center These reducing electrons are transported through an ETC in the thylakoid membrane Potential used to establish proton gradient Drives process of photophosphorylation 0000 How are electrons from oxidized reaction center replaced Photosystem Obtains Electrons by Oxidizing Water 0 Since oxygen is highly electronegative what supplies the energy necessary to split oxidize it I When excited electrons leave photosystem II and enter the FTC the photosystem becomes so electronegative that enzymes can remove electrons from water leaving protons and oxygen How Does Photosystem Work Instead of using electrons to produce a protonmotive force like photosystem II photosystem I uses the electrons to reduce NADP into NADPH In combination photosystems II and I produce chemical energy stored in ATP and NADPH The 2 Scheme Photosystems II and Work Together Direction of incrcnsing energy of clcmmn 1 L 1 htrnhmitit I39iiiuml imn Lilil39LLr printinr EHE39l F illlquot Ferrudcmjn Til3959 DP rcdlicialsc quotPlumsuqtiinont39 t39luquotir i1l11 tiquot39Larii 113 39 K P 2mm TIii39 ML mi 39 ll lastm39yanin 39 39 r39 3 r n 2e Ing MES 1 W Mm L39ii Hm iii393 r 39539 quotr d quotJ J 3H m Phalua mm T V 7 Ir I 3 u affair I UE39y gE39I39 Evolving L39suinpllt39k 4W I Plliattmy ltm H a EU EHquot From photosystem II When electrons reach the end of the cytochrome complex used to create proton gradient they are passed to plastocyanin Reduced plastocyanin donates electrons to oxidized reaction center in photosystem I These electrons are eventually catalyzed to reduce NADP into NADPH Understanding the Enhancement Effect n red light photosystem II is most efficient In farred light photosystem I most efficient When both wavelengths are available both systems are at max output Where Are Photosystems II and I located Module 4 Page 20 ATP Synthase and Photosystem I located on exterior of thylakoid 0 Makes sense because they need access to substrates that would be difficult to access in the interior Cytochrome Complex and Photosystem located in tightly packed interior The gap between where plastocyanin the link between the two photosystems is reduced the cytochrome complex and where it is oxidized the photosystem I reaction center is very large 0 This physical separation is under intense research Module 4 Page 21 104 Howls Carbon Dioxide Reduced to Produce Sugars Sunday November 9 2014 46 PM The reactions that produce sugar from carbon dioxide are not triggered directly by light instead they 3 GD 39 f depend on the ATP and NADPH produced by the lightdependent reactions of photosynthesis LE Erzphnaphoglyeerata i The Calvin Cycle Fixes Carbon Hi39ml sa Carbon fixation is the addition of carbon dioxide to an organic compound li bl pmspl ala IE TIEbisphnsphoglyperate Fixes C02 to a biologically useful form 39 Carbon fixation is a redox reactionthe carbon atom in C02 is reduced l1quot 3 Hibuloa E Glyceraldenyde RuBP Is the Initial Reactant with C02 SJphosphate Expl l f phate g 5C RuBP has one C from C02 attached to form 2 molecules of 3C 3PGA initial product of carbon 2 2 7 1 l g f mld h l reduction at E Gilyiaaraldahyde E thphal a E Emphosphale The Calvin Cycle Is a ThreeStep Process n E r 1 Fixation Phase a The Calvin cycle beings when C02 reacts with RuBP This phase produces two molecules of 3PGA 2 Reduction phase a The 3PGA phosphorylated by ATP and then reduced by electrons from NADPH The products is the phosphorylated 3C sugar G3P i Some of the G3P is drawn off to manufacture glucose and fructose 3 Regeneration phase a The rest of the G3P keeps the cycle going by serving as the substrate for the third phase in the cycle i Third phase is the regeneration of RuBP from G3P All three phases take place within the stoma of chloroplasts Each turn of the cycle fixes one molecule of C02 Every 3 turns yields one molecule of G3P and fully regenerated RuBP Each turn uses 3 ATP and 2 NADPH or 9 ATP and NADPH per G3P The Discovery of Rubisco Enzyme that fixes C02 onto RuBP Most common protein found in cells that undergo Calvin cycle Very slow to catalyze reactions this could be reason why it is created in such quantities Can catalyze addition of C02 or 02 onto RuBP 0 Competition between C02 and 02 for active sites C3 plants C plants 0 Addition of 02 results in photorespiration I Consumes ATP releases C02 and regenerates 3PGA 1 I Potentially when plants are in HighLight LowC02 systems p D 0xygen and Carbon Dioxide Pass Through Stomata 39 Aquot W 1 39 A39 39v Guard cells Pore Stoma I u A Stomata usually open during day to allow C02 to diffuse in and 02 diffuse out while photosynthesis is quot 3 quot n occurring quot V However on hot and dry clays plants close stomata to reduce risk of dehydration 4 o In this environment photosynthesis slows and photorespiration increases l How do plants prevent dehydration while making sure C02 supplies high enough to avoid A39 39 photorespiration I I j a Hurtn39n Hh A g n5 39 Mechanisms for Increasing C02 Concentration The C4 Pathway In C4 plants two fixation patterns are used 0 PEP carboxylase fixes C02 to a threecarbon molecule C4 0 Rubsico fixes C02 onto a BC to form 2 G3P C3 A four step model can be used to show how C4 pathways feed carbon into the Calvin cycle 1 PEP carboxylase fixes C02 to a three carbon molecule is mesophyll cells 2 The fourcarbon organic acids that are produced as a result are transported to bundlesheath cells via Plasmodesmata 3 The fourcarbon organic acids release a C02 molecule that Rubisco uses as a substrate to form 3PGA This initiates the Calvin Cycle 4 The threecarbon compound remaining is then transported back to the mesophyll cells to regenerate PEP C02 is stored at night and used during the day Pros Concentrates C02 improves efficiency of Calvin cycle Stomata can be open for shorter amounts of time less water loss Cons Requires more energy CAM Plants Extreme environments n E Module 4 Page 22 neqwres more energy 02 CAM Plants Extreme environments Cacti Resembles C4 pathway 0 C02 concentrator 0 However instead of CAM occurring at a different place it occurs at a different time During Day Stomata Closed At Night Stomata opens and large quantities of C02 temporarily fixed for storage 0 The next day this CD is released within the plant to feed he Calvin cycle The C4 and CAM pathways serve as CO pumps They minimize photorespiration when the stomata are closed and C02 is not able to directly diffuse into the cell But while C4 plants stockpile CO by fixing and storing organic acids in cells where rubisco is inactive CAM plants store C02 when rubisco is inactive How Is Photosynthesis Regulated Presence of light triggers production of proteins required for photosynthesis When sugar supplies are high the production of proteins required for photosynthesis is inhibited but the production of proteins required to process ad store sugars is stimulated Rubisco is activated by regulatory molecules that are produces when light is available but inhibited in condition of low CO availability when photorespiration is favored Module 4 Page 23 Study Guide Virus W dm 5day N Vmbr 26 Z 14 1 216 PM Module 4 Page 24 Study Guide Energy W dm 5dayy N Vmbr Z6 Z 14 1 215 PM Module 4 Page 25 Study Guide Respiration T 4 Wednesday November 26 ZOM 1 215 PM Q h 0 Glycolysis One 6 carbon molecule of carbon is broken down into 2 molecules of three carbon pyruvate 2 ATP used 4 ATP created net gain of 2 ATP 2 NADH formed from NAD THE FOLLOWING REACTIONS HAPPEN TWICE ONCE FOR EACH PYRUVATE g Pyruvate processing 1 Cycle Releases one molecule of CO V m W Remaining 2 carbons are used to make acetyl CoA One more NADH made from NAD Citric Acid Cycle 1 Cycle 39 Acetyl CoA is oxidized to two molecules of C02 One GTP or ATP 3 NADH produced 1 FADHz N A Electron transport and oxidative phosphorylation Electrons from NADH and FADHz move through a series of proteins called the electron transport chain ETC Energy released in this chain of redox reactions is used to create a proton gradient across a membrane Link between the phosphorylation of ADP with the oxidation of NADH and FADHz results in name oxidative KN r Wm MOWkn e What Happens to the NADH and FADHz Electrons from NADH and FADHz which oxidizes them to NAD and FAD are transferred to oxygen which is then reduced to water In effect glycolysis pyruvate processing and the citric acid cycle transfer electrons from glucose to NAD and FAD to form NADH and FADHz Oxygen then accepts the electrons from these reduced molecules to form water What happens to the energy that is released as electrons are transferred from NADH and FADHz to oxygen atoms Module 4 Page 26 Study Guide Photosynthesis Wednesday November 262 Z 14 215 PM Calcin Cycle G3P regenerates RuBP H20 and 02 H20 is split to form protons that are pumped in gradient oxygen used as final e acceptor and electrons to rejuvenate ps Module 4 Page 27


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