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Chapter 8, Metabolism Flashcards

IB Bio (HL)

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8695811221MetabolismSum total of all reactions that occur within an organism in order to maintain life0
8695823212Metabolic pathwaysSeries of reactions in cells controlling chemical changes through specific enzymes1
8695843557Examples of metabolic chainsGlycolysis (in cell respiration), coagulation cascade (in blood clotting)2
8695845443Examples of metabolic cyclesKrebs cycle (in cell respiration), Calvin cycle (in photosynthesis)3
8695851156Activation energy (EA)Certain amount of energy required for chemical reactions to proceed4
8695856041Enzyme purposeLowers activation energy5
8695860149Process of enzyme catalysis1) Enzyme binds to substrate, stressing and destabilizing its the bonds in the substrate 2) Resulting in reduced overall energy level of substrates transitionary state6
8695879267Types of enzyme reactionsExergonic and endergonic7
8695881850Exergonic reactionReactants contain more energy than products, free energy is released into system - Usually catabolic, as energy is released from broken bonds within a molecule8
8695882806Endergonic reactionReactants contain less energy than products, free energy is lost to system - Usually anabolic, as energy is required to synthesise bonds between molecules9
8695914577Enzyme inhibitorMolecule that disrupts the normal reaction pathway between an enzyme and a substrate - Competitive / non-competitive, depending on their mechanism of action10
8695934744Types of Enzyme Inhibition- Normal enzyme reaction - Competitive Inhibition - Noncompetitive Inhibition11
86959384202 Examples of Enzyme Inhibition- Relenza (Competitive Inhibitor) - Cyanide (Noncompetitive Inhibitor)12
86959416015 steps of Normal Enzyme Reaction1) Substrate binds to enzyme (via the active site) to form an enzyme-substrate complex 2) Shape and properties of the substrate and active site are complementary, resulting in enzyme-substrate specificity 3) Active site undergoes conformational change to optimally interact with the substrate (induced fit) 4) This change destabilised substrate chemical bonds substrate, lowering activation energy 5) Substrate is converted into product at an accelerated rate13
8695956025Normal enzyme reaction diagram14
8695959363Competitive InhibitionMolecule, other than the substrate, binding to the enzyme's active site15
86959607863 steps of Competitive Inhibition1) Molecule (inhibitor) is structurally and chemically similar to substrate (--> able to bind to active site) 2) Competitive inhibitor blocks active site and thus prevents substrate binding 3) As inhibitor competes with substrate, its effects can be reduced by increasing substrate concentration16
8695973281Noncompetitive InhibitionMolecule binding to a site other than the active site (allosteric site)17
8695980457Competitive Inhibition diagram18
86959743043 steps of Noncompetitive Inhibition1) Binding of inhibitor to allosteric site causes conformational change to enzyme's active site 2) Resulting in active site and substrate no longer sharing specificity, (substrate cannot bind) 3) As inhibitor isn't competing with substrate, increasing substrate levels cannot mitigate the inhibitor's effect19
8695982642Noncompetitive Inhibition diagram20
8695991512An example of a use for a competitive inhibitorTreatment of influenza via the neuraminidase inhibitor, Relenza21
8695994697Example of a use for a non-competitive inhibitorUse of cyanide as a poison (prevents aerobic respiration)22
8696009481Relenza (Competitive Inhibitor)Synthetic drug designed by Australian scientists to treat individuals infected with the influenza virus23
86960141563 steps of Relenza's inhibition1) Release of Virions from infected cells when viral enzyme neuraminidase cleaves docking protein (haemagglutinin) 2)Relenza competitively binds to neuraminidase active site, preventing cleavage of docking protein 3) --> virions aren't released from infected cells, preventing spread of influenza virus24
8696025300Cyanide (Noncompetitive Inhibitor)Poison which prevents ATP production via aerobic respiration, leading to eventual death25
86960644873 steps of Cyanide inhibition1) Binds to allosteric site on cytochrome oxidase 2) By changing the shape of the active site, cytochrome oxidase can no longer pass electrons to the final acceptor (oxygen) 3) --> electron transport chain cannot continue to function and ATP is not produced via aerobic respiration26
8696075097Cytochrome oxidaseA carrier molecule that forms part of the electron transport chain27
8696086095End-product inhibition (or feedback inhibition)Form of negative feedback by which metabolic pathways can be controlled, where the final product in a series of reactions inhibits an enzyme from an earlier step in the sequence28
8710827965Two steps of end-product inhibition (or feedback inhibition)1) Product binds to allosteric site and temporarily inactivates enzyme (via non-competitive inhibition) 2) As enzyme can't function, reaction sequence is halted and rate of product formation decreases29
8710839795End-product inhibition (or feedback inhibition) functionEnsure levels of an essential product are always tightly regulated30
8710849908How End-product inhibitions (or feedback inhibition) regulate levels of essential products- Product levels build up, product inhibits reaction pathway --> decreasing rate of product formation - Product levels drop, reaction pathway proceeds unhindered --> rate of product formation increases31
8710863702End-Product Inhibition diagram32
8710868716Isoleucine1 Essential amino acid, (is not synthesised by human body --> and must be ingested)33
8710876067Food sources rich in isoleucineEggs, seaweed, fish, cheese, chicken and lamb34
87108890613 steps of Isoleucine production in plants and bacteria1) Threonine converted into intermediate compound by an enzyme (threonine deaminase) 2) Isoleucine can bind to allosteric site on this enzyme, functioning as a non-competitive inhibitor 3) As excess production of isoleucine inhibits further synthesis, it functions as an example of end-product inhibition35
8726740102Distinguishing different types of inhibition from graphs at specified substrate concentrations36
8726751772MalariaDisease caused by parasitic protozoans of the genus Plasmodium37
8726769822How new anti-malarial drugs and medications can be producedBy targeting enzymes for inhibition, which coordinate the development of the parasite in both human and mosquito.38
8726819084How scientists have identified potential targets for inhibition1) Sequenced genome of Plasmodium and used it to determine the parasite's proteome 2) Identified enzymes involved in parasitic metabolism from the proteome 3) screened enzymes against bioinformatic databases of chemicals to identify potential enzyme inhibitors 4) Chemically modified promising compounds to improve binding affinity and lower its toxicity. (Or by rational drug design)39
8726874721Rational drug designUsing computer modelling techniques to invent compound that will function as an inhibitor: - Using combinatorial chemistry, a compound is synthesised that is complementary to the active site of the target enzyme40
8726955481Adenosine triphosphate (ATP)High energy molecule that functions as an immediate power source for cells41
8726972285How ATP stores energyThe three covalently bonded phosphate groups per molecule store potential energy in their bonds42
8727044409How ATP releases energyWhen ATP is hydrolyzed (--> ADP + Pi) energy stored in phosphate bond is released for cell use43
8727052206ATP energy release diagram44
8727059566Two key functions of ATP within cell- Energy currency of cell by releasing energy when hydrolysed to ADP (powers cell metabolism) - May transfer released phosphate group to other organic molecules, rendering them less stable and more reactive45
8727095892Two sources of energy from which ATP is synthesized from ADPSolar energy and oxidative processes46
8727103738How solar energy provides energy for ATP synthesis from ADPConverts light energy into chemical energy that is stored as ATP47
8727109320How oxidative processes provide energy for ATP synthesis from ADPCell respiration breaks down organic molecules to release chemical energy that is stored as ATP48
8727157382Cell respirationControlled release of energy from organic compounds to produce ATP49
8727164030Anaerobic respirationIncomplete breakdown of organic molecules for a small yield of ATP (no oxygen required)50
8727168360Aerobic respirationComplete breakdown of organic molecules for a larger yield of ATP (oxygen is required)51
8727181697Processes via which the breakdown of organic molecules occur- Direct combustion of sugar - Stepwise oxidation of sugar (cell respiration)52
8727231185Diagram of Energy Conversions in Sugar Breakdown (Direct Combustion vs Cell Respiration)53
8727240290Redox ReactionsReduction of one chemical species and the oxidation of another (redox = reduction / oxidation)54
8727250132Reductiongain of electrons / hydrogen or the loss of oxygen55
8727250133Oxidationloss of electrons / hydrogen or the gain of oxygen56
8727318938What carries the energy released by oxidation reactions to the cristae of the mitochondria?NAD and FAD57
8727323527Energy Transfer via Hydrogen Carriers diagram58
8727336997Why is cell respiration a oxidation reactionCell respiration breaks down organic molecules and transfers hydrogen atoms and electrons to carrier molecules (NAD and FAD)59
8727364858Carrier molecules of cellular respiration nicknamesHydrogen carriers or electron carriers60
8727376341Most common hydrogen carrierNAD+61
8727386426NAD + is reduced toNADH62
8727392322FAD is reduced toFADH263
8727381647A less common hydrogen carrierFAD64
8727396098CristaeSite of electron transport chain, which uses energy transferred by the carriers to synthesize ATP65
8727417515What respiration can generate ATP from hydrogen carriersAerobic, as electron transport requires oxygen to function66
8727461544Why does aerobic respiration unlock more energy stored in the organic molecules and produce more ATP?Because Oxygen is required for electron transport67
8726980264PhosphorylationProcess making molecules less stable, which for example breaks down the ATP bonds, which are readily reactive.68
8726696482Isoleucine production in plants and bacteria diagram69
8728364779Organic compounds that can be used in cell respirationLipids, Proteins but mainly Carbohydrates70
8728371136Reason why lipids are not preferentially usedThey are harder to transport and digest (Although they yield more energy)71
8728376987Reason why proteins are not preferentially usedThey release potentially toxic nitrogenous compounds when broken down72
8728434976GlycolysisBreakdown of a hexose sugar (6C) into 3 pyruvate molecules (3C)73
87284434414 Key events of Glycolysis1) Phosphorylation 2) Lysis 3) Oxidation 4) ATP formation74
8728484902Phosphorylation in GlycolysisHexose sugar is phosphorylated by two molecules of ATP (to form a hexose bisphosphate) (makes molecule less stable and more reactive, and prevents diffusion out of the cell)75
8728498160Lysis in GlycolysisHexose bisphosphate (6C sugar) is split into two triose phosphates (3C sugars)76
8728503876Oxidation in GlycolysisRemoval of hydrogen atoms from each of the 3C sugards (via oxidation) to reduce NAD+ to NADH (In total 2 molecules of NADH are produced)77
8728503877ATP formation in GlycolysisSome energy released from the sugar intermediates is used to directly make ATP (In total 4 molecules of ATP are generated)78
8728549337Overview of Glycolysis79
8728580483Glycolysis occurs inThe cytosol80
8728585709Is Glycolysis aerobic or anaerobicAnaerobic, as no oxygen is required81
8728616518Fermentation- If no oxygen is present, the pyruvate remains in the cytosol and is converted into lactic acid (animals) or ethanol and CO2 (Plants and yeast) - A reduction reaction that oxidises NADH allows small amounts of ATP to be produced w.out oxyten82
8728667323Anaerobic Respiration (Fermentation)83
8728941509First stage of aerobic cell respirationLink reaction84
8728944965Link reactionTransports pyruvate into the mitochondria85
87289660284 stages of the Link reaction1) Pyruvate is transported from cytosol into mitochondrial matrix by carrier proteins on mitochondrial membrane 2) Pyruvate loses a carbon atom (decarboxylation), which forms a carbon dioxide molecule 3) The 2C compound then forms acetyl group when it loses hydrogen atoms via oxidation (NAD+ is reduced to NADH + H+) 4) Acetyl compound combines with coenzyme A to form acetyl coenzyme A (acetyl CoA)86
8728995091How often per molecule of glucose does the link reaction occur?Twice, due to glucose being split into two pyruvate molecules87
8729005880Link reaction product per reactionAcetyl CoA (2x) + H+ (2x) + CO2 (2x)88
8729014257Diagram of the Link Reaction89
8729026144Second stage of aerobic respirationThe Krebs cycle90
8729029584The Krebs cycle occurs inThe matrix of the mitochondria91
8729084768The KrebsTransfer of acetyl group to a 4C compound to make a 6C compound - Coenzyme A is released and can return to the link reaction to form another molecule of acetyl CoA92
87291457643 steps of 6C compound breakdown to form the original 4C compound1) Two C atoms are released via decarboxylation to form two molecules of carbon dioxide (CO2) 2) Multiple oxidation reactions result in the reduction of hydrogen carriers (3 × NADH + H+ ; 1 × FADH2) 3) One molecule of ATP is produced directly via substrate level phosphorylation93
8729166773How many times does the Krebs cycle occur per molecule?Twice, as the link reaction produces two molecules of acetyl CoA (1 per pyruvate)94
8729174328Krebs cycle product per cycle4 × CO2 ; 2 × ATP ; 6 × NADH + H+ ; 2 × FADH295
8729182391The Krebs Cycle diagram96
8729208365Final stage of aerobic respirationElectron transport chain97
8729211183Electron transport chain occurs inThe inner mitochondrial membrane98
8729221496Electron transport chainRelease of energy stored within reduced hydrogen carriers in order to synthesise ATP99
8729234126Oxidative phosphorylationEnergy to synthesise ATP is derived from the oxidation of hydrogen carriers during the electron transport chain.100
87292420573 steps of Oxidative phosphorylation1) Generating a Proton Motive Force 2) ATP Synthesis via Chemiosmosis 3) Reduction of Oxygen101
8729282350Generating a Proton Motive Force (Oxidative phosphorylation)1) hydrogen carriers are oxidised and release high energy electrons and protons 2) electrons transfer to electron transport chain, made of several transmembrane carrier proteins 3) Electrons moving through the chain lose energy, which is used by the chain to pump protons (H+ ions) from the matrix 4) Accumulation of H+ ions within intermembrane space creates electrochemical gradient102
8729282351ATP Synthesis via Chemiosmosis (Oxidative phosphorylation)1) Proton motive force causes H+ to move down their electrochemical gradient and diffuse back into matrix (chemiosmosis, helped by ATP synthase) 2) As H+ ions move through ATP synthase they trigger the molecule rotation of the enzyme, synthesizing ATP103
8729348174ChemiosmosisDiffusion of protons104
8729351703ATP synthaseEnzyme facilitating chemiosmosis105
8729282352Reduction of Oxygen (Oxidative phosphorylation)1) Removal of de-energized electrons, so the chain can continue to function by oxygen 2) Oxygen also binds with free protons in matric to form water, removing matrix protons maintains hydrogen gradient 3) Without oxygen, hydrogen carriers cannot transfer energised electrons to chain and ATP production is halted106
8729461508Three types of aerobic respiration reactionsDecarboxylation, oxidation and phosphorylation107
8729470566Decarboxylation in cellular respirationCarbon atoms are removed from the organic molecule (glucose) to form carbon dioxide108
87294915284 steps of Oxidation in cellular respiration1) Electrons and hydrogen ions are removed from glucose and taken up by hydrogen carriers 2) Hydrogen carriers are oxidised at electron transport chain (where energy is used for ATP) 3) Electrons and hydrogen ions are then taken up by oxygen (reduction) to form water 4) 12 hydrogen carriers are produced and six oxygen molecules are required109
8729491529Phosphorylation in cellular respiration1) Energy released from glucose breakdown is used to phosphorylate ADP to make ATP 2) Net total of four ATP molecules produced directly via substrate level phosphorylation 3) Remaining ATP is produced indirectly via electron transport chain110
8729556667Aerobic respiration typically produces net total of ... ATP per molecule of glucose consumed2 + 2 + 4 + 6 + 18 + 4 = 36111
8729631740Powerhouse of the cellMitochondrion112
87296472935 ways in which the structure of the mitochondrion is adapted to the function it performs- Outer membrane: Transport proteins enabling shuffling of pyruvate from cytosol - Inner membrane: Electron transport chain and ATP synthase for oxidative phosphorylation - Cristae: Folds which increase the SA:Vol ratio - Intermembrane space: Maximizes hydrogen gradient upon proton accumulation - Matrix: Central cavity containing appropriate enzymes and suitable pH for Krebs cycle113
8729699982Electron tomographyTechnique by which the 3-dimensional internal structure of a sample can be modelled114
87297037583 steps of Electron tomography0) (if biological material: dehydrating or freezing) 1) Repeat imaging of samples using electron microscope 2) After image, sample is tilted to different angle 3) computational reconstruction of 3D representation (tomogram)115
87297570423 observations of mitochondria made using electron tomography1) Cristae are continuous with the internal mitochondrial membrane 2) The intermembrane space is of a consistent width throughout the entire mitochondrion 3) The relative shape, position and volume of the cristae can change in active mitochondria116
8710772709OILRIGOxidation Is Losing electrons (gaining energy) Reduction Is Gaining electrons (losing energy)117
8710780561Gaining energyBreaking bonds between between ADP and creating ATP with breakdown of glucose118
87110866995 steps of respiration1) Glycolysis 2) Link reaction 3) Kreb's cycle 4) Electron transport chain 5) Chemiosmosis119
8711160708Mitochondria drawing120
8723702202GlycolysisSplitting of glucose into pyruvate121
8723706857LysisSplitting122
8723708998Oxydation in glycolisisNADH+ --> NADH + H123
8723710004Glycolysis 6 steps1) Glucose (Hexose, 6C) 2) Phosphorylation 3) Lysis 4) Oxidation 5) ATP formation 6) Pyruvate (2x)124
8723722430The anaerobic cell respirationGlycolysis125
8723724114ATP yield of Glycolysis- 2 ATP + 4 ATP = 2ATTP126
8723768070Glycolysis occurs in ...Cytoplasm127
8723771571Glycolysis summary1) Hexose sugar is phosphorylated using ATP 2) Hexose phosphate is split in 2 triose phosphates 3) Oxidation removes hydrogen 4) Hydrogen is used to reduce NAD to NADH 5) 4 ATP produced resulting in net gain of 2 ATP 6) 2 pyruvate molecules are produced at end128
8723782703Oxidate Decarboxylation diagram129
8723789570Oxidate Decarboxylation Net Yield2 Acetyl CoA per glucose molecule130
8723792542Oxidate Decarboxylation occurs in ...Mitochondria131
8723795614Oxidate Decarboxylation summary1) Pyruvate enters mitochondria matrix 2) Enzymes remove 1xCO2 and H from pyruvate 3) Hydrogen is accepted by NAD to form NADH 4) Removal of hydrogen (oxidation) 5) Removal of carbon dioxide is decarbodylation 6) Link reaction is therefore oxidative decarboxylation 7) Product is acetyl group, reacting w. coenzyme A 8) Acetyl CoA enters Krebs cycle132
8766353883PhotosynthesisProcess by which cells synthesise organic molecules (e.g. glucose) from inorganic molecules (CO2 and H2O) in the presence of sunlight133
8766366410Two steps of photosynthesis1) Light dependent reactions 2) Light independent reactions134
8766379834Light dependent reactions (3 steps)1) Chlorophyll absorbs light and releases energised electrons that are used to produce ATP 2) Carrier molecules (NADP+) gets electrons 3) Photolysis: Water replaces lost electrons in chlorophyll135
8766413580The light dependent reactions occur in theThylakoids136
8766569411The light independent reactions occur in theStroma137
8766415647ThylakoidsIntermembrane space of membranous discs of chlorophyl138
8766383007Light independent reactions (2 steps)1) Transfer of ATP and hydrogen / electrons (Carried by NADPH) to stroma 2) CO2 combines w. H/electrons to form complex organic compounds (Via ATP)139
8766526098StromaFluid-filled interior of the chloroplast140
8766406484PhotolysisSplitting of water into oxygen and hydrogen141
87668469813 steps of light dependent reactions to convert light energy into chemical energy (ATP and NADPH)1) Excitation of photosystems by light energy 2) ATP Production via an electron transport chain 3) Reduction of NADP+ and the photolysis of water142
8766865755Step 1 of light dependent reaction: Excitation of Photosystems by Light Energy2) When a photosystem absorbs light energy, delocalised electrons in pigments get energised 3) These excited electrons are transferred to carrier molecules within the thylakoid membrane143
8766886895PhotosystemsGroups of photosynthetic pigments (including chlorophyll) embedded within the thylakoid membrane144
8766897151Photosystems are classed according toTheir maximal absorption wavelengths145
8766953638What generates excited electronsAbsorption of light by photosystems146
8766962129Location of Transfer of excited electronsBetween carriers in thylakoid membranes147
8767000545Step 2 of light dependent reaction: Production of ATP via an Electron Transport Chain1) Excited electrons from Photosystem II are transferred to an electron transport chain within the thylakoid membrane 2) As electrons are passed through the chain they lose energy, which is used to translocate H+ ions into the thylakoid 3) Build up of protons in thylakoid creates electrochemical gradient, or proton motive force 4) H+ ions return to stroma via transmembrane enzyme ATP synthase 5) ATP synthase uses passage of H+ ions to catalyse synthesis of ATP (from ADP + Pi) 6) The newly de-energised electrons from Photosystem II are taken up by Photosystem I148
8767041927PhotophosphorylationATP production by the light dependent reactions149
8767060893Is used to contribute to generate a proton gradient in the light dependent reactionExcited electrons from Photosystem II150
8767065820Generates ATP using the proton gradientATP synthase in thylakoids151
8767079327Step 3 of the light dependent reaction: Reduction of NADP+ and the Photolysis of Water1) Excited electrons from Photosystem I may be transferred to a carrier molecule and used to reduce NADP+ --> This forms NADPH 2) The electrons lost from Photosystem I are replaced by de-energised electrons from Photosystem II 3) Electrons lost from Photosystem II are replaced by electrons released from water via photolysis 4) Water is split by light energy into H+ ions and oxygen152
8767120920Two types of PhotophosphorylationCyclic and non-cyclic processes153
8767136840Cyclic photophosphorylationUse of only one photosystem (PS I) and does not involve the reduction of NADP+154
87671617933 steps of Cyclic photophosphorylation1) Light is absorbed by Photosystem I --> excited electron may enter into electron transport chain to produce ATP 2) De-energized electron returns to photosystem, restoring its electron supply155
8767181325Why is water not needed in the cyclic photophosphorylation and why is NADP+ not reducedBecause the electron returns to the photosystem156
87671927233Cyclic photophosphorylationPhotophosphorylation that involves two photosystems (PS I and PS II) and does involve the reduction of NADP+157
87672039453 steps of non-Cyclic photophosphorylation1) Light is absorbed by Photosystem II and the excited electrons enter into an electron transport chain to produce ATP 2) Meanwhile, photoactivation of Photosystem I results in the release of electrons which reduce NADP+ (forms NADPH) 3) The photolysis of water releases electrons which replace those lost by Photosystem II (PS I electrons replaced by PS II158
8767219431Cyclic vs Non-Cyclic Photophosphorylation159
8910080250The light independent reactions occur inStroma (fluid-filled space of chloroplast)160
8910087369Collective name of the light independent reactionThe calvin cycle161
8910091559Three main steps of the calvin cycle/light independent reactions1) Carbon fixation 2) Reduction of GP 3) Regeneration of RUBP162
8910110066Carbon fixation"Carboxylation of ribulose bisphosphate"163
8910113024"Reduction of glycerate-3-phosphate"164
8910116969Regeneration of ribulose bisphosphate165

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