FOODMIC LE3 Notes PDF

MICROBIAL METABOLISM -free energy -multi-subunit complex of atp -which organelle will house the enzymes -passive diffusion: co2, o2, h2, h2o, uncharged (mitochondria- eukaryotic) molecules are permeable to the membrane -whe...

MICROBIAL METABOLISM -free energy -multi-subunit complex of atp -which organelle will house the enzymes -passive diffusion: co2, o2, h2, h2o, uncharged (mitochondria- eukaryotic) molecules are permeable to the membrane -where to locate the atp synthase -atp synthase is in cytoplasmic membrane for prokaryotic Free energy (G) - the energy released during a chemical reaction that is available to do work, -Catabolism in prokaryotic cells measured in kilojoules (kj) -fermentation, glycolysis, cac delG - change in free energy during a reaction at standard conditions RECAP ON BIOENERGETICS (-)- exergonic release of energy (+)- input of energy is required for the reaction to -Metabolism: sum of all chemical reactions in an proceed endergonic organism (EUKAR/PROKAR) -Catabolic reactions: provides energy (YIELDS ENERGY) and building blocks for anabolism ACTIVATION ENERGY: energy required to bring -full oxidation of glucose -> Co2 (CATABOLIC) all molecules in a chemical reaction into reactive -glucose into pyruvate to enter CAC and enter state electron transport chain and drive synthesis of atp -a catalyst is usually required to breach activation energy barrier -Anabolic: uses energy and building blocks to -high activation energy puts stress on prokaryotic -glucose can be a source of energy in prokaryotic cell and eukaryotic cells -enzymes would lower activation energy in order for -glucose to G6P precursor to form biomolecules chemical reactions to proceed immediately or -building blocks transformed into marcomolecules simultaneously **The products of catabolism serve as precursor molecules that serve as the building blocks of ENZYMES molecules -biological catalysts -peptidoglycan-NAM-NAG -typically proteins (some RNAs) that drive chemical -nucleotides form the acids reactions -amino acids become building blocks of proteins -highly specific -catabolic and anabolic form cell -generally larger than substrate -typically rely on weak bonds Ex. H-bonds, Van der -transport mechanism of glucose in prokaryotic cell: Waals, hydrophobic glucose is a large sugar molecule porosity doesnt -Active Site: region of enzyme that binds substrate allow means to uptake glucose from the environment- from PEP phosphorylation G6P in 1) Substrate is bound to enzyme active site (beta 1- (PHOSPHOTRANSFERASE SYSTEM)- glucose 4 substrate is a sugar) goes in cytoplasm then g6p immediately 2) Enzyme-substrate complex forms -conservation of energy as result of catabolic 3) Strain is placed on bond, enzyme changes reaction conformation and catalyzes the reaction, break b 1- 4 linkage (enzyme: breaks cell wall in bacteria but -eukaryotic cell: GLUT1 integral membrane protein not archea LYSOZYME) embedded in plasma membrane has binding site 4) Products are released specific for glucose -it faces the cytoplasm glucose converted into G6P PROSTHETIC GROUPS via hexokinase -bind tightly to enzymes -usually bind covalently and permanently (e.g. heme group in cytochromes) ELECTRON CARRIERS -NAD+/NADH- most common in prokayotic cells COENZYMES -pyruvate becomes reducing substance -loosely bound to enzymes -NADH+ reduced form = -0.32V tendency to donate -most are derivatives of vitamins electrons (e.g. NAD+/NADH) -NADP+- instead of OH its phosphate group -adcantage: cells can use multiple electron donors and acceptors// compounds used by the cells) -EX: Glucose to -> G6P to biphosphoglyceric acid ELECTRON CARRIERS and NAD/NADH cycling -electron donor and acceptor as an advantage of -NAD+/NADH facilitate redox reactions without prokaryotic cell being consumed; they are recycled in the process -not only end product is being used -importantly, cells only require a small amount of -coenzymes are involved to drive these reactions NAD+’/NADH because it is recycled EXAMPLES: -co-enzyme can loosely bind to an enzyme -always occurs in two half -substrate can bind towards an active site -all cells need this -binding of NAD+ -energy from redox reaction is used in synthesis of -substrate will donate its electrons to NAD+ energy-rich compounds (ATP) -enzymes are electron carriers -ELECTRON DONOR: substance oxidized -ELECTRON ACCEPTOR: substance reduced THE REDOX TOWER 1) Enzyme 1 reacts with e- donor and oxidized form of coenzyme 2) NADH and reaction product are formed -recycle, hindi naubusan ng enzymes -NADH needs to be reduced -another binding site of NADH -substrate now becomes electron acceptor -reaction facilitate formation of the product NADH now converted to oxidized NAD+ -NAD+ can receive electrons from particular substrates -oxygen is not always the final electron acceptor *In biological systems, the electrons are often -show the position of substances regarding associated with hydrogen atoms REDUCTION POTENTIAL- tendency to donate -biological oxidation are often dehydrogenations electrons the move negative they are -electrons = H+ protons transferred in biological rxn -left molecule oxidized -right molecule reduced -0.5 has tendency to get molecule -chemical energy released in redox reactions is -final electron acceptor is commonly oxygen primarily stored in PHOSPHORYLATED synthesis COMPOUNDS (ATP, PEP, G6P) -microorganisms need to conserve energy -Fermentation: substrate-level phosphorylation; -chemical energy also stored in coenzyme A ATP is directly synthesized from an energy-rich -not all phosphate bonds are energy rich intermediate (1 ADP + PO4- ATP) -PO4 2- is a high energy molecule bonding is high energy bc it is hard to stabilize the bonds- -Respiration: oxidative phosphorylation (pasok hydrolyzing also requires high energy electron carriers); ATP is produced from proton -energy stored in G6P is energy containing but not motive force formed by transport of electrons energy rich -discuss different pathways that make ATP -Glucose -> synthesis of ATP -fully consumed glucose -> pyruvate then oxidized - > CO2 -> ETC (O2 as final electron acceptor) -> ATP -ex. Facultative aerobe can switch to aerobic or anaerobic -glucose can still be consumed but not fully -PEP- glut transferase system- difficult to stabilize (FERMENTATION) – CO2 +EtOH- LAB or gas anhydride bond -RESPIRATION- means of phosphorylation - -ATP- two phosphate molecules linked via process- 1 ADP anhydride bonds -phosphate molecule attached to the sugar is an energy rich bond -linked phosphate by means of anhydride bond -high energy bond -G6P- only linked by ESTER BOND not anhydride bond -molecule gets phosphorylated- ADP -> ATP -energy rich intermediate has phosphate group -CATABOLISM- KREBS- NAD+.NADH- NADPH, FAD+/FADH- enter ETC in cytoplasmic membrane facilitate translocation of protons- MEMBRANE POTENTIAL acts like a batery -energy released by phospho thioester bond is made up of negative charges enough to drive the synthesis of chemical reactions of energy rich phosphate -ENERGIZED MEMBRANE of prokaryotic cell -common in anaerobic -protons lumabas ng cell, ATP is synthesized -transfer of a high-energy PO4- to ADP -two reaction series are linked to energy conservation in chemoorganotrophs: fermentation ADP + P ATP and respiration. They differ in mechanism of ATP 2. Oxiddative phosphorylation -transfer of electrons from one compound to another is used to generate ATP by CHEMIOSMOSIS -transfer makes energy -redox reactions -pyruvate oxidized to carbon dioxide CATABOLISM: FERMENTATION & RESPIRATION -glycolysis and fermentation -Respiration: CAC and glyoxylate cycles -Respiration: electron Carriers STAGE 1 -ETC and PMF -glucose uptake via transport system -Energy Conservation -immediately convert to G6P via hexokinase -addition of phosphate on C6 GLYCOLYSIS AND FERMENTATION -phosphate comes from HYDROLYZED ATP -> -fermented substance is both electron donor and ADP + P acceptor -isomerase converts G6P to F6P -GLYCOLYSIS (Embden-Meyehof Pamas) -F6P to F 1,6P via phosphofructokinase enzyme common pathway for catabolism of glucose phosphate group to C1 and C6 -prokaryotic cells: uptaken via phosphotransferase -aldolase converts to GA3P and dihydroxyacetone system or glut-translocation phosphate-> GA3P (becomes 2) -enzymes of glucose are found in mitochondria END OF STAGE ONE: 2 GA3P GLYCOLYSIS Stage I: Preparatory reaction- not redox reactions STAGE 2 (ENZYMATIC REACTIONS) -start of redox -GA3P converted into 1-3 Biphosphoglycerate Stage II: redox reactions occur, energy conserved (redox) via enzyme Glyceraldehyde 3-P as ATP, and TWO MOLECULLES OF PYRUVATE dehydrogenase and electron carrier NAD+ being & NADH FORMED reduced to NADH (start of energy conservation) -NADH has to be oxidized to NAD+ -oxidative phosphorylation process -another mechanism for oxidation -1-3 biphosglycerate acid tun into 3-P-Glycerate will -cell reuses generate of ATP 1:1 ratio therefore 2 ATP since 2 GA3P Stage III: redox balance achieved through further redox reactions, NADH consumed & fermentation -2 3-P-Glycerate converted to 2 2-P-Glycerate products formed -enolase enzyme turns into PEP (high energy -NADH to be oxidized containing molecule) -needs electron acceptor (PYRUVATE) to be -precursor molecule in compounds reduced and NADH will be oxidized -2 PEP release 2 ATP when converting to pyruvate -obligate aerobe, from pyruvate straight to CAC MOLECULES GINAMIT SUBSTRATE-LEVEL PATHWAY OF GLYCOLYSIS PHOSPHORYLATION STAGE 1: 2 STAGE 2: 4 ATP PRODUCED IN TOTAL NET ATP: 4-2= 2 cell consumed 2 at stage 1 -NAD+ reduced to NADH convert to oxidized to regain balance  -2 molecules of pyruvate first STAGE 3 -pyruvate undergoes decarboxylation (removal -1 molecule of glucose = 2 pyruvate CO2) to form acetyl CoA -NADH re-oxidized so it will donate electrons to -coupled reaction (NAD+ reduced to NADH) pyruvate to become NAD+ -Acetyl CoA is a high energy containing molecule, -by-products of fermentaion: yeast so 2 ethanol and condenses with oxaloacetate to form CITRATE 2 CO2 through citrate synthase -CITRATE-> ACONITATE -> ISOCITRATE – -conservation of energy is not that high (NADP -> NADPH and CO2 gone)) – a- -if cell fully respires is a different story Ketoglutarate via isocitrate-dehydrogenase -other sugars can be utilized by cell but needs to be -becomes Succinyl CoA through another coupling converted into glucose CoA + NAD+ reduced toNADH and CO2 gone -Succinyl CoA to Succinate warrants the synthesis of ATP driven by enzyme synthetase (ADP/GDP + Pi -> ATP/GTP) substrate-level phosphorylation -succinate to fumarate via succinate dehydrogenase (FAD -> FADH2 reduced) -fumarate to malate via fumarase -malate to oxaloacetate using malate dehydrogenase (NAD+ -> NADH reduced) END PRODUCT: OXALOACETATE for synthesis RESPIRATION: CITRIC ACID CYCLE of amino acids -important reaction in carbon metabolism succinyl coa makes cytochromes associated with ATP formation -site of many electron carries that can enter ETC -aka krebs attributed to them -KEY PATHWAY in all cells - 1. Two carbon compound acetyl-CoA condenses CAC with the 4C compound oxaloacetate to form the 6C -pathway pyruvate is completely oxidized to CO2 citrate -initial steps (glucose to pyruvate) same as 2. Oxidations and transformations, citrate becomes glycolysis oxaloacetate then another cycle with addition of -per glucose molecules, 6 CO2 molecules acetyl-CoA added released and NADH and FADH generated 3. Two redox reactions occur but no CO2, is -plays key role in CATABOLISM AND released from succinate to oxaloacetate BIOSYNTHESIS 4. Oxaloacetate can be made crom C2 compounds -energetics advantage to aerobic respiration by the addition of CO2 **refer to miss sandra’s method Glycolysis: 8 ATP Substrate: 2 ATP Oxidative: 3x2 ATP CAC: 15 ATP (X2 pyruvate) == 30 ATP Substrate: 1 GTP = 1ATP Oxidative: 4 NADH x 3 -> 12 ATP 1 NADH x 2 -> 2 ATP *if electron carriers would go to ETC, 30 ATP will -electron carriers are arranged based on reduction be produced potential (more positive, more right left (-) -> right (+) () Sum overall == 38 ATP per glucose in AEROBIC -COMPLEX I, II, III, IV RESPIRATION (facultative aerobes desire bc of the -complex IV has positively charged electron carriers amount of energy produced) CASE OF -accept electrons rather than donating PROKAYOTIC CELLS -ETC is series of oxidation reduction, transfer of -and conserve more energy electrons occurs GLYOXYLATE CYCLE COMPLEX I -papasok NADH + H+ from oxidative phosphorylation from glycolysis -NADH gives electrons and H protons = extrusion of 4H+ in outer portion of cytoplasmic membrane (not totally outside of the cell) -FMN (flabimononucleotide) donate electrons to Fe/S -Fe/S donates to quinones in complex 2 (small non- protein molecules) C2- acetate COMPLEX II oxaloacetate- needed in a lot of anabolic reactions -FADH2 can donate electrons to the quinones (go -cells should not run out of oxaloacetate thru q-cycle) -Acetyl-CoA -> Citrate -> Isocitrate -> (isocyltrate -electrons donated into CytBC1 complex in lyase) -> Glyoxylate complex 3 -isocitrate can do other steps in CAC, can bypass the cycle, turn into glyoxylate -> malate -> COMPLEX III oxaloacetate -CytB, CytC, Fe/S proteins quinones in complex 2 to complex 3 ELECTRON TRANSPORT CHAIN -flow of electrons CytB -> Fe/S -> CytC1 -Fe3+ in heme ring cytochromes = SITE OF REDOX RXN -Electrons transported to CytC (not part of cytoplasmic membrane- PERIPLASM, acts as shuttle to drive electrons into complex 4) COMPLEX IV -cytochromes act as TERMINAL OXIDASE ENZYMES -drive the reaction in which O2 will be final -when go in, C12 turns like a rotor electron acceptor -torque/ rotational force activates changing the -O2 converted into H2O conformation of the beta-subunit complex in the F1 -protons extruded = 8H+ 0 multi subunit -Beta subunit has specific binding sites for ADP + PROTON MOTIVE FORCE Pi -> as such, ATP catalyzes -acts like a battery -synthesis of ATP is in beta subunit of the synthase -negative and positive charges together -pasok hydrogen, iikot C12 turns, two other -provides potential energy to the cell subunits, conformational changes in F1 multi- -water dissociates to produce neg ions and H+ subunit. In beta subunit and it allows synthesis of -negative inside, positive on the membrane ATP from readily available ADP + Pi HOW IS ATP SYNTHESIZED THEN SUMMARY OF PATHWAYS -driven by proton motive force Glycolysis: formation of pyruvate, it will enter CAC, different electron carriers generated that will enter ATP SYNTHESIS ETC to drive the SYNTHESIS OF ATP coming from -catalyst for conversion of PMF into ATP is a large the energy of the PROTON MOTIVE FORCE membrane enzyme complex called ATP SYNTHASE OR ATPase aka COMPLEX V of ETC MICROBIAL METABOLISM WHEN MICROBES (transporter) FEED ON GLUCOSE AS THEIR CARBON SOURCE 2 PARTS 1) Multi-subunit headpiece F1- cytoplasmic side of membrane 2) Proton-conducting channel F0- spans membrane -F1/F0 complex catalyses reversible reaction between ATP and ADP +Pi -structure of ATPase highly conserved in all domains of life, suggesting very early evolutionary invention -its in the cytoplasmic membrane -F0 facing membrane 57 -F1 facing cytoplasm -outer surface has a lot of H+ papasok since mas marami kesa sa loob (electrochemical gradient)