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Introduction to Biochemistry

by: Dr. Pablo Pollich

Introduction to Biochemistry BIOCHEM 501

Dr. Pablo Pollich
GPA 3.75


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This 13 page Class Notes was uploaded by Dr. Pablo Pollich on Thursday September 17, 2015. The Class Notes belongs to BIOCHEM 501 at University of Wisconsin - Madison taught by Staff in Fall. Since its upload, it has received 11 views. For similar materials see /class/205197/biochem-501-university-of-wisconsin-madison in Biochemistry at University of Wisconsin - Madison.

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Date Created: 09/17/15
Biochem Exam 2 Lecture 12 0 Cells obtain energy by oxidation 0 CC and CH bonds 0 Thermodynamics 0 Net reaction go towards equilibrium 0 G reveals I How far from equilibrium energy available as it moves toward equilibrium I How much energy will be released I Which direction the reaction will move 0 Conditions can be on either side of equilibrium I Standard conditions 0 1M all species at 25 degrees C AG RT aneq For Exams AG 6 logKeq Large AG more reactants than products Small AG more products than Reactants Provides a measure of relative energy 0 Negative AG favorable spontaneous 0 Positive G not favorable Products at lower energy than reactants 0 Can Calculate AG 0 Determining Direction at NonStandard Conditions I AG AG 6 log productsReactants o Gibbs free energy has 2 components I Enthalpy change AH 0 AH AE thus difference in bond energies o Exothermic releases heat negative AH o Endothermic heat input positive AH I Entropy 0 AS change in randomness 0 Increase in AS contributes to negative AG 0 Sign of AG reveals direction 0 Magnitude of AG indicates how far from equilibrium 0 Thermodynamics does not predict rate 0 ATP Universal energy carrier Adenine triphosphate Kinetically stable little nonenzymatic breakdown ATP has a 4 charge which stores lots of energy Phosphate has double bond character ATP hydrolysis I Hydrolysis with relief of charge repulsion o Electrostatic repulsion between 0 00000 Resonance stabilization 0 Of products 0 Partial negative charge on each of the 4 0 attached to the Phosphate Ionization 0 Stabilization and solvation o Proton dissociates from ADP2 to ionize with ADP3 o In Vivo conditions ofATP Hydrolysis o AG of hydrolysis 3 05 kImol 0 ATP in cells are a lot higher than standard conditions 0 Actual AG of hydrolysis in cell is 50 kImol 0 ATP usually provides energy by Group Transfers not by direct hydrolysis o Unfavorable reactions driven by coupling to favorable reactions 0 Phosphoryl group transfer raises to higher energy state makes neXt step more favorable o Phosphate group transfer potentials 0 High energy donate P 0 Low energy receive P 0 ATP must donate and receive P Lecture 13 o Glycolysis o Ubiquitous ancient method of energy story 0 Preparatory Phase Hexokinase catalyzes phosphate transfer from ATP to glucose generating glucose 6 phosphate and ADP 0 Highly favorable with a AG 167 kImol Phosphohexose isomerase catalyzes an isomerization reaction converting a glucose 6 phosphate to a fructose 6 phosphate 0 Isomerizes an aldose to a ketose 0 Close to equilibrium AG 17 kImol Phosphofructokinase PFKl catalyzes phosphate transfer from ATP to Fructose6phosphate generating Fructose16 bisphosphate and ADO o AG 142 kImol o Fru16bisP is committed to glycolysis and will continues to pyruvate Rate limiting step in glycolysis Inhibitors High ATP fatty acid citrate Stimulators High AMP ADP Irreversible in cell 0 ADPATP ratio is very low Aldolase converts Fructose16bisphosphate to dihyroxyacetonePhosphate and Glyceraldehyde3phosphate o AG 238 kImol I Triose phosphate Isomerase TPI converts dihydroxyacetone phosphate to Glyceraldehyde3phosphate o AG 75 kImol o Payoff Phase I Glyceraldehyde3Phosphate dehydrogenase oxidizes glyceraldehyde3phosphate to 13Bisphosphoglycerate and NAD is reduced to NADH 0 Energy is preserved in phosphate bond and NADH o AG 63 kImol actual AG neg 0 Only redox rxn in glycolysis o Dehydrogenase pulls off hydride Phosphglycerate Kinase removes phosphoryl group from 13 bisphosphoglycerate and adds it to ADP to generate 3 Phosphoglycerate and ATP 0 AG 185 kImol Phosphoglycerate Mutase type ofisomerase catalyzes the isomerization of 3phosphoglycerate to 2phosphoglycerate o AG 44 kImol Enolase catalyzes dehydration of 2phosphoglycerate to phosphoenolpyruvate releasing a water as a product 0 AG 75 kImol Pyruvate Kinase removes a phosphate group from phosphoenolpyruvate to ADP producing ATP and an enol pyruvate which can be isomerized to pyruvate o AG 314kmol 0 Overall AG 85 kImol o Glycolysis is irreversible Lecture 14 Fates of Pyruvate 0 High OZ levels 0 2 AcetylCoA o Fermentation Anaerobic o 2 Lactate o 2 ethanol 0 Other fermentations o Fermentations 0 Ways to anaerobically regenerate NAD from NADH I Pyruvate to lactate o Glucose 9 pyruvate lactate dehydrogenase uses NADH to drive reaction to Produce lactate and NAD I Pyruvate to ethanol Yeast o Glucose uses NAD to undergo glycolysis to produce NADH and Pyruvate o Pyruvate decarboxylase removes C02 to produce acetyl aldehyde 0 Alcohol dehydrogenase uses NADH to produce NAD and ethanol 0 Motochondria site of oxidations 0 Inner membrane ATP Synthesis 0 Matrix I Citric acid cycle I Fatty acid oxidation I Pyruvate oxidation 0 Pyruvate Dehydrogenase complex 0 Enzyme 1 rxns I Thiamine Pyrophosphate TPP forms covalent bond with Pyruvate I H is added which results in decarboxylation of pyruvate giving off C02 to generate hydroxyethylTPP 0 Enzyme 2 rxn oxidation I The hydroxyethyl group acylates the lipoate I coASH attacks the central carbon on acylated lipoate producing acetyl CoA and fully reduces thio groups on the lipoate 0 Enzyme 3 I The FAD removes the lipoate Hydrogens to produce FADH on E3 and Lipoic acid on E2 I FADH then hydrolyses NAD to produce free oating NADH and H and bound FAD on enzyme 0 Overall I Pyruvate CoASH NAD 9 NADH C02 acetyl CoA I AG 334 kImol Lecture 15 o Citric Acid Cycle 0 Citrate synthesis I Acetyl CoA reacts with Oxaloacetate to produce CoASH an Citric Acid citrate o Aconitase catalyzes the isomerization of citrate to isocitrate Dehydration of citrate yields cis Aconitate The addition ofwater to cisaconitate yields isocitrate I AG 133 kImol o Isocitrate dehydrogenase catalyzes isocitrate to otketogluterate and the hydrogenation of NAD to NADH and H 0 0L ketoglutarate dehydrogenase complex I Same 5 cofactors as PDll similar to E1 and E2 identical E3 s I Aketogluterate dehydrogenase complex removes C02 and adds CoASll to aketoglutarate while hydrogenation of NAD to produce NADH and SuccinylCoA I AG 335 kImol O O Succinyl CoA synthetase catalyzes SuccinylCoA and GDP Pi to Succinate and GTP CoA I AG 29 kImol Succinate dehydrogenase oxidizes Succinate to Fumerate and reduces FAD to FADH2 I AG 0 Fumerase catalyzes hydration reaction of fumerate to Lmalate I AG 38 kImol Malate dehydrogenase catalyzes oxidation of Lmalate to oxaloacetate and reduces NAD to NADH and H I Highly endergonic I AG 297 kImol 0 Regulation of Citric Acid Cycle 0 OOO PDC is inhibited by ATP acetylCoA NADH fatty acids Citrate synthase is inhibited by NADH SuccinylCoA Citrate ATP Isocitrate dehydrogenase is inhibited by ATP AKetoglutarte dehydrogenase complex is inhibited by succinylCoA NADH 0 Why ATP NAD FAD CoA 0 000 O Reactive region just a small fraction of the molecules Early life RNA for both information and catalysis Ribozymes RNA enzymes NAD FAD CoA have one end to carry electrons or chemical units to base pair at the active site ofa ribozyme All life has cofactors Lecture 16 Energy From lipids o Lipids O O O Triacylglycerols energy storage lipid Digestion of Dietary Fats I Bile salts are detergents emulsification break down dietary fats Lipases hydrolysis to fatty acids which are the form transported across the plasma membrane I Small intestine 0 Fatty Acid Cycling 0 OO O O Bile salts emulsify dietary fats in the small intestine forming mixed micelles Intestinal lipases degrade triacyglycerols Fatty acids and other breakdown products are taken up by the intestinal mucosa and converted into triacyglycerols Triacylglycerols are incorporated with cholesterol and apolipoproteins into chylomicrons Chylomicrons move through the lymphatic system and bloodstream to tissues o Lipoprotein lipase activated by apoCII in the capillary converts triacyglycerols to fatty acids and glycerol 0 fatty acids enter cells 0 fatty acids are oxidized as fuel or reesterified for storage 0 Fatty Acid Oxidation 0 Activation fatty acid joined to Coenzyme A I Enzymes on outer mitochondrial membrane I AcyCoA synthetases on the outer membrane of the mitochondria activate fatty acids by producing a thioester fatty acylCoA Transport across inner mitochondrial membrane into mitochondrial matrix I MalonylCoA inhibits carintine acyltransferase I o Boxidation conversion of fatty acid into acetylCoA units in mitochondrial matrix I Dehydration 0 Fatty AcylCoA dehydrogenases catalyzes oxidation of fatty acylCoA to TransAZ enoylCoA I Hydration o Enoyl CoA hydratase catalyzes the addition ofwater to TransAZ enoylCoA to yield LBhydroxyacyl CoA I Dehydration o BhydroxyacylCoA dehydrogenase catalyzes the oxidation of LBhydroxyacylCoA to BketoacylCoA and reduces NAD to NADH and H I Thiolytic Cleavage o Thiolase converts BketoacylCoA to acetylCoA and a fatty acylCoA o Repetitive removal of AcetylCoA I nAcetylCoAs formed from n1 oxidations I c2 acetyl CoA generated Lecture 17 using Amino Acids as fuels 0 The 20 amino acids are converted to acetate or citric acid cycle intermediates 0 Transamination o Aminotransferase enzyme transfers amino group 0 Deaminating alanine converts it to pyruvate o Aspartate can be transaminated to oxaloacetate o Transdeamination o Occur only in liver mitochondria Aamino acid is transaminated to aketo acid by aminotransferase Aketogluterate is transaminated to glutamate by aminotransferase Glutamate is deaminated by glutamate dehydrogenase to a ketogluterate and NAD is reduced to NADH and an ammonia is released 0 PKU phenylketonuria 0 OOO O O O Inability to digest phenylalanine Untreated results in severe brain impairment treated by diet Amino acids must lose amino group in order to be metabolized o Serine and cysteine can be used as energy sources 0 How to deal with toxic NH4 O 0 Brain is first affected High NH4 might drive glutamine synthetase resulting in depletion of glutamate and glutamine in the brain might increase to the point of osmotic swelling 0 Urea Cycle 0 O O O OO O O O OO Glutamine and Glutamate are entry points into mitochondria matrix Glutamine can be converted to Glutamate and ammonia by glutaminase Glutamate is deaminated by glutamate dehydrogenase to a ketogluterate and NAD is reduced to NADH and an ammonia is released Oxaloacetate is converted to aspartate using aspartate aminotransferace in mitochondria matrix Aspartate diffuses out of mitochondria to cytosol Synthesis of Carbamoyl Phosphate I Bicarbonate is phosphorylated by ATP to carbonicphosphoric anhydride and ADP Ammonia group displaces phosphate on carbonicphosphoric anhydride to produce carbamate Carbamate is phosphorylated by ATP to produce carbamyl phosphate Carbamoyl phosphate reacts with ornithine to form citrulline and release a free oating phosphate Citrulline reacts with ATP to generate citrullylAMP intermediate Intermediate then interacts with aspartate to get argininosuccinate I The amino groups that are going to form urea are attached to same carbon Argininosuccinate loses fumerate to get arginine Arginine is reacted with water and arginase to yield urea and ornithine o Urea cycle takes place in cytosol and mitochondria 0 Synthesis of carbamoyl phosphate and aspartate take place in mitochondria Lecture 18 Electron Transport and ATP production 0 Energy benefits of oxidative phosphorylation O O 3 2 ATPglucose in aerobic only 4 ATP of the 32 ATPglucose from glycolysis o ReductionOxidation Redox Chemistry 0 E reduction potential affinity for electrons I Tendency to become reduced or oxidized E values can be measured relative to hydrogen quothalf cell reference 0 Force that drives spontaneous ability to use e AE always positive in spontaneous direction electrons ow to higher reduction value 0 AE expresses AG for redox reactions I AG nFAE o N number of electrons 2 o F965 kjmol I Spontaneous direction has AG and AE In eukaryotes e from NADH and FADHZ to 02 occurs in the mitochondria via an electron transport chain 0 Outer membrane freely permeable to small molecules and ions I Porin channels on the outside 0 Inner membrane impermeable to most small molecules and ions including H 0 Matrix contains pyruvate dehydrogenase complex citric acid cycle enzymes fatty acid Boxidation enzymes amino acid oxidation enzymes DNA ribosomes Complexes and mobile carriers provide an electrontransfer circuit from NADH and FADHZ to 02 0 As electrons ow to 02 H pumped across inner membrane at complexes 1 II III amp IV Electron Transport Chain 0 Happens on inner membrane 0 NADH is good energy source because source of quotreducing power it can reduce something else 0 Complex 1 NADH Ubiquinone oxidoreductase I Catalyzes oxidation of NADH and reduction of UQ and quotpumpsquot 4 H oxidoreductase formal for dehydrogenase I NADH drops electrons off on complex 1 to produce NAD 0 Complex II Succinate Dehydrogenase I Catalyzes oxidation of succinate to fumerateand reduction of UQ I only membrane inserted enzyme of Krebs Cycle I No Proton pumping only increases pool of ubiquinol 0 Complex 111 UbiquinoneCytochrome c oxidoreductase I Oxidizes ubiquinol and reduces cyt c1 I quotpumpsquot 4 H per 2e transferred to 2 cyt c1 I quotQ cycle 1 e transfer from 2 e carrier UQ to 1e carrier cyt c1 0 Cytochrome C I Protein shuttles between Complex II and Complex IV I Reduced by 111 I Oxidized by VI 0 Complex IV Cytochrome oxidase I Complex at which is 02 consumed by respiring organisms I Accumulates 4 e from 4 cyt c and reduces 02 to 2 H20 I Designed to preventrelease of toxic partially reduced oxygen species Pumps 2 H per 2 e 4H per 02 0 Accounts for 99 of 02 we use 0 Electrons ow from complex 1 to complex 2 o FADH drops offH at complex 2 o Electrons ow from complex 2 to Q 0 Defense Against reactive oxygen 0 Superoxide dismutase I Takes oxygen radicals and couples it with 2 H to give peroxide and oxygen 0 Reducing power used to make antioxidants like glutathione to deal with toxic byproducts that result from life with 02 Lecture 19 o Chemiosmotic theory ofATP production 0 Electron ow coupled to formation ofa gradient ofH across the mitochondrial inner membrane which is used for ATP synthesis 0 Energy of H gradient called protonmotive force 0 Two contributions I Gradient of anything chemical potential energy I H gradient also has charge difference 0 Electron transport and ATP production are coupled I Protons will not ow through ATP synthase unless ADP and Pi are present I Electron transport and proton pumping does not occur without ATP production I With succinate alone electron transport builds up proton gradient until equilibrium is reached free energy to drive proton transport balances free energy of electron transport I Oligomycin inhibits ATP synthase I Uncoupler dissipates proton gradient and permits electron transport in absence ofATP synthesis 0 Uncouplers I Membrane permeable proton carriers DNP I Uncouplers reduce or prevent ATP synthesis but do not prevent electron transport I Dissipates proton gradient uncouples proton transport 0 Evidence of chemiosmotic theory I Artificially induced proton gradient drived ATP synthesis without substrates redox or electron transport 0 What makes ATP synthase spin 0 3 symmetric active sites for ATP production one on each dimer o Rotational catalysis I Bound ATP formed from ADP and Pi without proton motive force Conformational change to release bound ATP required energy ofproton motive force I Proton gradient used to release ATP from ATP synthase I ATP synthase is a rotary engine 0 Mitochondrial Transport and shuttle systems I Adenine nucleotide translocase antiporter 0 Pumps ATP 4 out of mitochondrial matrix and pumps ADP 3 into mitochondrial matrix 0 Driven by voltage gradient I Phosphate translocase symporter 0 Pumps H2P04 into mitochondrial matrix 0 Pumps protons into matrix 0 Driven by proton gradient 0 Uncoupling in plants via an electron shunt 0 Heat from rapid metabolic ux 0 Free from normal feedback control 0 Bypass sites ofproton pumping quotshort circuit not uncoupling Lecture 20 o Photosynthesis 0 Light reactions I Light energy water 9 chemical energy NADPH ATP 02 0 Dark reactions I Chemical energy NADPH ATP C02 9 Sugars 0 Net light energy H20 C02 9 Sugars o Chloroplasts Structure 0 Has genome protein synthesis divides 0 Triple membrane system 0 Chlorophylls Primary light collectors I Porphyrin ring with complexed Mg2 I Hydrophobic side chain anchors in membrane I Absorption spectrum Chlorophylls a and b differ complementary A range 0 Reaction Center I A complex of chlorophyll and proteins I Accessory pigments expand range of these quotSolar Collectors I Antenna chlorophylls and Carotenoids capture light light bounces until it reaches rxn center 0 Light Reactions 0 PS I and PS 11 ZScheme I PS 11 captures light energy and used to split water into 02 4H and electrons are split off and promoted to high energy state P680 is reaction center where electrum is kicked up Electron then moves to plastoquinone where they reduce plastoquinone to plastoquinol Plastoquinol then passes electrons to cytochorome complex The cytochrome complex oxidizes plastoquinol and pass protons inside lumen of thylakoid which establishes proton gradient Electrons ow from cytochrome complex to plastocyanin From plastocyanin electrons ow to photosystem I At PS I light energy is harvested to kick electrons backup to high energy state in P700 reaction center Electrons fall into Fd then FAD I Then FAD can reduce NADP to NADPH 0 Provided a mechanism to reduce water to strip electrons off ofwater then kick up electrons to NAD to make NADPH 0 Dark Reactions Calvin Cycle 0 Has to spin 3 times to get one molecule of glyceraldehyde3phophate o Rubulose 15 bisphosphate is phosphorylated by rubisco to generate 6 molecules of 3phosphoglycerate o 3phosphoglycerate needs 6 molecules ofATP to produce 13 bisphosphoglycerate o 13bisphosphoglycerate then uses 6 molecules of NADPH to reduce to glyceraldehyde 3phosphate glyceraldehyde 3phosphate can leave cycle and can be used for other purposes or is regenerated to rubulose 5phosphate o 3 fates of glyceraldehyde 3phosphate 0 Can leave chloroplast and be oxidized in glycolysis 0 Storage in the form of starch 0 Travel as starch in plant Lecture 21 0 Early Earth 0 Organic molecules forming on earth and quotrainingquot from space 0 Lucky that no 02 in atmosphere I Organic molecules could accumulate without being destroyed by oxygen in the harsh conditions of early earth I Inorganics such as H2 Fe2 did not quotrustquot 0 There are many metabolic routes for living systems to obtain energy other than fermentation and 02 based respiration using CC and CH bonds but all routes have common features The earth has undergone several huge changes in climate and metabolic evolution has often been a major force in such changes 0 Current anaerobic respiration quotnon02quot electron acceptor 0 Many anaerobes quotrespirequot with a range of electron acceptors o Nitrate reductase does the same thing as Complex IV in Electron Transport Chain but gives electrons to NO3 rather than 02 O O 0 We would need to consume 15 lbs per day to survive and excrete 15 libs ofNO2 Anaerobes and microbial Fuel cells quotnon O2 electron acceptor 15V same as standard battery Homo sapiens have been here for about 0002 of the entire time on earth Geobiology 0 Evolution and metabolism has effected the atmosphere chemistry climate and geology Ancient example of anaerobic respiration o Methanogens release methane gas into the atmosphere 0 Used components of early atmosphere as both electron donor amp acceptor 0 Also fixed C02 Did methanogens prevent earth from freezing 0 Higher CO2 levels than present 0 Perhaps another major part methanogen s CH4 quotblanketquot CH4 a much more potent greenhouse gas than CO2 Possible effect of evolution ofphotosynthesis o quotSnowball Earth after loss of methane earth may have been covered in a sheet ofice over a mile deep How else did evolution ofphotosynthesis affect the earth 0 The release of oxygen was quotby far the greatest crisis the earth has ever endured but from the crisis came one of the most spectacular and important evolutions in the history of life multicellular organisms Foundation of quotrevolutionquot water as electron donor in photosynthesis o For the first time major source of renewable energy from H20 and sunlight 0 Life no longer dependent on existing energyrich organic molecules minerals and H2 Sunlight adds quotcontinuously to a sum of chemical difference 0 H2O ubiquitous electron donor and Sun is a quotfreequot source of energy large in ux of foodenergy into ecosystems 0 Created an ozone layer colonizing land now favorable How did evolution of photosynthesis affect the Earth 0 Certain prokaryotes evolved the ability to use 02 as electron acceptor 0 Large free energy change from moving electrons from quotfoodquot to 02 o 02 ubiquitous o Diffusible readily crosses membranes tissues can obtain electron acceptor 0 Product of electron accepting H20 is not only harmless but useful no need to dispose Carbon Cycle 0 Light energy is used to break down water and carbon dioxide to sugar and oxygen 0 Sugars and oxygen are broken down by respiration to water and carbon dioxide


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