MCB 102 Exam 2

bioenergetics

-quantitative study of energy transformations that occur in living cells, including the nature and function of chemical processes -2 laws of thermo: conservation of energy, entropy -conservation of energy: energy may change form or be transported but cannot be created or destroyed -entropy: in all natural processes, the entropy of the universe increases

rates of biochem rxns

-rates of biochem rxns depend on many factors: conc of reactants vs products, activity of enzyme (conc, amount of enzyme or enzyme activity) -can control abundance (amount) or existing enzyme (activity) -conc (amount) of enzyme: transcription (DNA → mRNA), turnover (mRNA → nucleotides or enzyme → AA), translation (mRNA → enzyme), rate of transcription and translation vs rate of degradation, localization (sequestration) -enzyme activity: environment (pH, T, ionic environment (eg Mg2+)), allosteric effectors, post-translational covalent modification (eg phosphorylation), associated regulatory protein, covalent modification (eg P of serine) -life time of an enzyme min to days. Cells regulate their metabolism by variety of mechs over a time scale ranging from less than a ms to days. -slowest method for regulating enzyme: increased expression of a transcription factor that increases enzyme synthesis (make transcription factor, bind promoter, make mRNA, has to be translated - lots of steps take time) -transcription factor: nuclear proteins, bind specific DNA regions near a gene's promoter and activates or represses transcription of that gene -turnover: synthesis followed by degradation

chemiosmotic theory

-reduced substrate (fuel) donates e-. e- carriers pump H+ out as e- flow to O2. energy of e- flow stored asa electrochemical potential. ATP synthase uses electrochemical potential to synthesize ATP -chemical potential delta pH (inside alkaline) + electrical potential delta psi (inside negative) --> ATP synthesis driven by proton-motive force -almost all energy from respiration conserved and used for ATP synthesis -mitochondrial ATP synthase complex: Fo rotates, F1 catalyzes ADP + Pi --> ATP. rotational catalysis. 4 protons drive synthesis of 1 ATP (3 for rotational catalysis to turn Fo, 1 to bring Pi to mitochondrial matrix) -adenine and phosphate translocases: transport substrates in and product out. adenine nucleotide translocase (antiporter) pushes ATP4- out (intermembrane space) and ADP3- in (matrix). phosphate translocase (symporter) pushes both H2PO4- and h+ in. exchange by proton negative 1- to negative side --> proton translocation. -antiport and symport are both favored by transmembrane proton gradient - antiport moves - charge out, symport moves H+ in -10 protons pumped out for NADH, 6 for FADH2 (doesn't use complex 1). need 4 protons for 1 ATP (3 for rotational catalysis, 1 for P-exchange), get 2.5 ATP per NADH (per 2 e- transported) and 1.5 ATP per FADH2 (per 2 e- transported) -What 2 factors are important in calculating deltaG associated w mitochondrial e- transport: delta pH (chem potential, proton gradient across membrane) and delta psi (electrical potential, charge gradient across membrane)

Citric acid cycle stage 2: acetyl-CoA oxidation

-regenerate oxaloacetate at very low conc -2C in, add 4C to get 6C -happens in mitochondria. 8 rxns, 7 enzymes soluble, 1 membrane-bound. C2 compounds enters, 2C released as CO2. purpose is to reduce e- carriers. also intermediates C4/C5 can be used for synthesis -summary production: 3 NADH, 1 FADH2, 1 GTP, release of CO2 -8 e- are transferred to e- carriers after one turn of CAC (3 NADH gives 6 e-, 1 FADH2 gives 2 e-) -CAC is a hub of metabolism, w catabolic pathways leading in and anabolic pathways leading out. acetate groups (acetyl-coA) from catabolism of various fuels used in synthesis of metabolites like AA, FA, and sterols. breakdown products of many AA and nucleotides are intermediates of cycle, and can be fed in or siphoned off as needed by cell.

regulation of citric acid cycle

-regulate at steps where there are large -delta Gs: 1 (citrate synthase), 3 (isocitrate dehydrogenase), 4 alpha-ketoglutarate dehydrogenase, pyruvate dehydrogenase complex -central role of CAC in metabolism requires it be regulated in coordination w other pathways. regulation occurs by both allosteric and covalent mechs that overlap and interact to achieve homeostasis. -exercise (muscle): Ca2+, ADP/AMP -regulation by: substrate availability, direct product inhibition, allosteric feedback -pyruvate dehydrogenase complex: inhibited by ATP, acetyl-CoA, NADH, fatty acids. activated by AMP, CoA, NAD+, Ca2+. -citrate synthase: inhibited by NADH, succinyl-CoA, citrate, ATP. activated by ADP -isocitrate dehydrogenase: inhibited by ATP, activated by Ca2+ and ADP. -alpha-ketoglutarate: inhibited by succinyl-CoA and NADH, activated by Ca2+ -intermediates that can be pulled off for synthesis of other compounds: citrate, alpha-ketoglutarate, succinyl-CoA, malate, oxaloacetate. these are intermediates that aren't channeled.

oxidation-reduction rxns

-result in flow of e- from one compound to another. There is a change in oxidation state. One compound is oxidized and one is reduce -enzymes: oxidases, dehydrogenases, reductases -complete oxidation of reduced compounds is very strongly favorable -e- donating molecule is reducing agent or reductant, e- accepting molecule is oxidizing agent or oxidant -biological oxidation-reduction rxns can be described in terms of 2 half-rxns, each w a characteristic standard reduction potential, Eo' -deltaG^o' is very negative, highly favorable

carbon assimilation (Calvin cycle) rxn 1: carboxylation (rubisco)

-rubisco = ribulose 1,5-bisphosphate carboxylase/oxygenase -ribulose 1,5-bisphosphate + CO2 + H2O --> (rubisco) 2 3-phosphoglycerate -rubisco: 50% of enzymes in plants. fixes CO2. has carboxylase and oxygenase activity (CO2 favored). is a very slow enzyme; solution is to make more of it. most abundant enzyme in world, represents huge N-sink. has been extensively studied. efforts to improve rubisco carboxylase activity has not yielded much progress. -regulation: rubisco is activated by covalent modification (carbamoylation - addition of CO2 to Lys). inhibited by natural transition state analog (rises in dark)

Common categories of biochemical rxns

-rxns that make or break C-C bonds -internal rearrangements, isomerizations, and eliminations (important for variation of molecule to be recognized by an enzyme adds specificity, places double bonds in right position, etc.) -free-radical rxns -group transfers -oxidation-reductions

carbon assimilation (Calvin cycle) stage 3: regeneration

-similar to regeneration of ribulose-5-phosphate in PPP pathway -5 C3s to 3 C5s -use ATP and NADPH, CO2, H2O -6 G3P made, 1 taken off, other 5 used to regenerate ribulose 5-phosphate -P enters from triose phosphate antiporter to keep cycle going -for each ribulose 5-phosphate, release of 2 P in cycle and utilization of 3 ATPs -sum: 3 CO2 + 9 ATP + 6 NADPH + 6 H+ --> triose-P + 8 Pi + 9 ADP + 6 NADP+

NAD/NADP

-soluble e- carriers, associate w enzyme during and after rxns, recycled -in a typical biological oxidation rxn, hydride is transferred to NAD+ (or NADP+), giving NADH or NADPH -NAD typically used in oxidative (catabolic) rxns, NADP typically used in synthesis (anabolic rxns) -composed of 2 nucleotides joined through their phosphate groups by a phosphoanhydride bond -+ sign reverse to amide (oxidation state), not overall charge (actually - overall) -in NADP+, hydroxyl on sugar is esterified w phosphate

glycogen

-storage form of glucose. glucose can be stored for later use as glycogen. Sugar storage in animals/bacteria. -starch in plants (similar structure but less branches = even less soluble) -branched polymer of alpha(1→ 4) linked glucose w alpha(1→ 6) linkages every 12-14 glucose units. Up to 55,000 glucose residues (packed into granules) -degraded to glucose units for use in energy production -can be made from excess blood glucose or recycling of glucogenic metabolites like lactate or certain AA -storage in granules and as glycogen maintains low osmolarity so cell doesn't lyse from large osmolarity -liver (10% weight) - reservoir for brain. Muscle (1-2% weight) - energy storage for activity. -nonreducing ends vs reducing ends (free anomeric C) - allows for efficient degradation since enzyme can work on multiple nonreducing ends at the same time

cytochrome b6f complex links PS II and I and translocates protons into lumen

-structurally and functionally similar to complex III in ETC -protons are removed from PQH2 as it is oxidized -PQ cycle is similar to Q cycle in ETC -e- are funneled to plastocyanin, a single e- carrier, soluble (similar to cyt c in ETC), that carries e- to PS I -PQ cycle: e- in cyt b6, go to PQ, add 2 H+ to become PQH2, e- sent to hemes and to plastocyanin, PQ regenerated.

mitochondrial ETC complex II

-succinate dehydrogenase (also a membrane bound TCA cycle enzyme - only membrane-bound enzyme in CAC). so TCA cycle and oxidative phosphorylation happening in parallel here. -prosthetic groups: FAD, Fe-S -FAD is bound to complex II -QH2 from complex I --> QH2 at complex II -e from FADH2 enters here, feeds into complex III -succinate --> furamate (FADH2 --> FAD) donates 2 e- --> FE-S --> Q --> QH2 -total protons pumped: 0

metabolism

-sum of all rxns in cell. Sum of anabolism (synthesis) and catabolism (degradation) -converging catabolism, cyclic pathway, diverging anabolism -autotrophs: Greek "self nourishment" use CO2 as sole C source. Producers: plants, algae, photosynthetic bacteria -heterotrophs: Greek "nourishment from others" grow on organic. consumers: animals, bacteria -cycle: sun → photosynthetic autotrophs → O2, organic products → heterotrophs → CO2, H2O → photosynthetic autotrophs

types of enzymes

-synthase: catalyzes condensation rxns w no NTP required -synthetase: condensation rxns that require ATP or another NTP as energy source for rxn -oxidase: catalyzes oxidation rxn in which O atoms don't appear in oxidized product -oxygenase: used if one or both O do appear in oxidized product (eg as new hydroxyl or carboxyl group) -kinase: transfers a phosphoryl group from a NTP to an acceptor molecule -phosphatase: release of phosphoryl group from its parent molecule -dehydrogenase: catalyzes oxidation-reduction rxns in which NAD+ is e- acceptor. remove 2 H atoms from their substrates. one is transferred as hydride ion to NAD+, other is released as H+. always uses NADPH or NADH. -phosphatase: no ATP, Pi coming off -isozymes: diff enzymes that catalyze same rxn. isozymes could be differentially regulated by allostery (one isozyme might be allosterically regulated bu product while other isn't), transcriptional regulation (one isozyme induced in response to condition, other transcribed at low level), diff activity for substrate (diff Km - one mighty have low Km and make product at low [substrate], while other might have high Km and make product at high [substrate])

mitochondrial ETC complex III

-ubiquinone:cytochrome c oxidoreductase -prosthetic groups: hemes, Fe-S -e- are transported from QH2 to Cyt c with H+ transport -2 stages. first stage: cyt b, QH2 --> 1 e- goes to 2Fe-2S, then Cyt c1 and heme c1, then cyt c, other e- goes to Q --> 'Q-. second stage: another QH2 --> 1 e- goes to cyt c, other e- goes to 'Q- --> QH2. 2H+ into intermembrane space (P side) -2 e- transported to Q, 2 e- transported to cyt c (can only take 1 at a time). -cyt c is soluble, can move and bring e- with it (carries 1 e- at a time). after its heme accepts an e- from complex III, cyt c moves in intermembrane space to complex IV -Q cycle: as e- move from QH2 to complex III, QH2 is oxidized w release of protons on one side of membrane, while at other site Q is reduced and protons are taken up. product of one catalytic site thus becomes substrate at second site, and vice versa. one e- given to cyt c1, other e- goes to unreduced ubiquinone, turns into free radical. need another QH2, donates 1 e- to cyt c, other e- reduces free radical to QH2. QH2 goes back to complex III and recycles (all Qs are recycled to become radical in III or to I or II to accept more e-) -purpose of Q cycle: allows for passage of e- from QH2 to cyt c passing them 1 at a time, while also releasing protons to intermembrane space -total protons pumped: 4

ATP

-usually provides energy via group transfer (phosphoryl) to an enzyme or substrate. -ATP-dependent rxns are not driven by hydrolysis of ATP (just liberates heat, which cannot drive chem process). Covalent attachment of phosphoryl group raises free-energy (ATP participates covalently in enzyme-catalyzed rxns to which it contributes free energy) -ATP-dependent rxns (don't see in product) are usually 2-steps but often shown as 1. Ex: glutamine synthetase (indicates ATP-dependent); glutamate + NH3 + ATP → enzyme-bound glutamyl phosphate (has good phosphate LG now) + ADP + NH3 → glutamine + Pi (carboxylate → amide) -phosphoryl transfer from ATP to make higher energy phosphate esters: results in substrate having a phosphate group (eg glucose conversion to glucose-6-phosphate). Resulting molecules are higher energy. Kinase - puts on phosphate group (ex: hexokinase in glycolysis). Phosphatase - removes P group from phosphate ester (eg FBPase-1 in glycogenesis) -free energy released by hydrolysis of phosphate compounds does not come from specific bond that is broken; it results form products of rxn having a lower free-energy content than reactants

inhibitors/drugs on oxidative phosphorylation

-when e- transfer is blocked, carriers before block become more reduced and those beyond block become more oxidized. -rotenone blocks transfer of e- from NADH to Q. only blocks e- transfer from NADH (but not from FADH2). -antimycin A blocks transfer of e- from cyt b to cyt c1. inhibits e- flow from all sources -CN or CO blocks transfer of e- to O2 (all carriers reduced) -O2 exhausted: all carriers reduced -NADH exhausted: all carriers oxidized (limits e- availability) -abundant NADH and O2: mirrors typical conditions for mitochondria in aerobic environment. early carriers are reduced (NADH, Q), later carriers are oxidized (cyt b, cyt c1, cyt c, cyt a, O2)

ethanol fermentation

-yeast, some bacteria, not mammals -release CO2 -pyruvate (+ Mg2+ + TPP) → (pyruvate decarboxylase) acetaldehyde + CO2 + NADH + H+ → (alcohol dehydrogenase) ethanol + NAD+ -common ex: bubbles in champagne, dough rising in bread making (seen as CO2 is released)

FAD

-+ sign reverse to amide (oxidation state), not overall charge (actually - overall) -in NADP+, hydroxyl on sugar is esterified w phosphate -can accept 1 or 2e- and can form semiquinone (radical) -associates very tightly w proteins, sometimes covalently bonded -reduction potential is very dependent on environment -flavin cofactors allow single e- transfers. Flavin cofactors are tightly bound to proteins. Reduction potential depends on context - eg particular enzyme that it is bound to. -Permits the use of O2 as an ultimate e- acceptor (flavin-dependent oxidases)

regulation of pentose phosphate pathway

-6-G-P can be used in glycolysis or pentose phosphate pathway -if NADPH is used, eg fatty acid synthesis or detoxification eg of radicals, PPP will be preferred over glycolysis. When demand for NADPH slows, level of NADP+ drops, pentose pathway slows, and glucose 6-phosphate is instead used to fuel glycolysis -product feedback inhibition: NADPH inhibits pentose phosphate pathway (by inhibiting glucose-6-phosphate dehydrogenase) and conversion of glucose-6-phosphate → 6-phosphogluconate

glycolysis vs gluconeogenesis

-7 of 10 rxns of glycolysis are reversible. 3 are irreversible: hexokinase, PFK-1, pyruvate kinase (have very -deltaG) -wherever there are irreversible steps, there are bypasses that are controlled to regulate entry and exit. -bypass steps 1 and 3 happening in diff organelles to distinguish from glycolysis in cytosol -gluconeogenesis bypass steps: pyruvate to PEP (pyruvate carboxylase, PEP carboxykinase), fructose 1-6-bisphosphate to fructose 6-phosphate (fructose 1,6-bisphosphatase-1), glucose 6-phosphate → glucose (glucose 6-phosphatase) -glycolysis: produce 2ATP, 2NADH + 2H+ -gluconeogenesis cost: consume 4 ATP, 2GTP, 2NADH + 2H+ (very expensive) -overall rxn glycolysis + GNG: cost 4 ATP/glucose -glycolysis and gluconeogenesis are reciprocally regulated to prevent wasteful operation of both pathways at the same time -if both enzymes run simultaneously, have futile cycle: only consumption of ATP. but heat production (bumble bees use to warm up in morning). -to limit substrate recycling between glycolysis and gluconeogenesis, two pathways are under reciprocal allosteric control, mainly achieved by opposing effects of fructose 2,6-bisphoshate on PFK-1 and FBPase-1

oxidation of fatty acids: 1) conversion to fatty acid-CoA

-ATP + fatty acid --> (fatty acyl-CoA synthetase, adenylation) fatty acyl-adenylate + PPi --> (fatty acyl-CoA synthetase) fatty acyl-CoA + AMP -PPi --> (inorganic pyrophosphatase) 2 Pi -highly exergonic/irreversible -adenylation step: cost is similar to 2 ATPs

regulation of PFK-1

-ATP can be both substrate and inhibitor of PFK-1. ATP is substrate in active site, but also allosteric binding of ATP changes conformation of PFK-1 (decreasing activity at active site) -how ATP levels regulate glycolysis: feedback inhibition. High ATP (product) make it unnecessary to keep going through glycolysis, so ATP = allosteric inhibitor of PFK-1 -why is inhibition of PFK-1 by ATP diminished when ADP conc is high: adenylate kinase catalyzes rxn 2 ADP → AMP + ATP. ADP and AMP are both + allosteric effectors of PFK-1, which will work against inhibition of PFK-1 by ATP. high conc of ADP/AMP would indicate below ATP conc. This activates glycolysis to produce more ATP. PFK-1 activity would be regulated by ratio of ADP (+ effector) to ATP (allosteric inhibitor). Is likely ADP completes w ATP an allosteric site wheen ADP conc gets high

mitochondrial ETC complex I

-NADH dehydrogenase or NADH:ubiquinone oxidoreductase -prosthetic groups: FMN, Fe-S -intermembrane space: P side, matrix: N side -4 protons pumped across intermembrane for 2 e-s donated by NADH (start establishing H+ gradient) -e- come from NADH --> FMN --> series of Fe-S centers --> N-2 --> Q --> QH2. QH2 diffuses throughout membranes -NAD is not bound to complex I -e- from NADH enters here -total protons pumped: 4

lactate fermentation

-animal tissues, muscles, erythrocytes -happens in low/no oxygen environments and in RBC which don't have mitochondria needed for oxidation of pyruvate -deltaGo'= -25.1 kJ/mol -rxn equilibrium strongly favors lactate formation -lactate can be transported to liver and metabolized back to glucose -when do you do lactic acid fermentation? Rapid movements, like during exercise -alligators use lactic acid fermentation for their rapid movements. Requires long periods of recovery (require hours of rest and extra O2 consumption to clear excess lactate from blood and regenerate muscle glycogen) -glycogen → glucose + ATP → pyruvate → lactic acid (with NADH/NAD+ recycled) -common breakfast food is result of lactic acid fermentation: yogurt -Lactate formed by active skeletal muscles (or by erythrocytes) can be recycled; is carried in blood to liver, where it is converted to glucose during recovery from strenuous muscular activity. -even at resting state, conc of lactate isn't 0 because equilibrium strongly favors lactate formation. so even at very low conc of NADH and pyruvate, there is a significant conc of lactate

effect of substrate conc on enzyme activity

-at low conc, slope (ie change in velocity over conc) increases drastically -at high conc, slope increases more slowly

GNG 1st bypass: pyruvate to PEP

-bicarbonate + pyruvate + ATP (+ biotin) → (pyruvate carboxylase) oxaloacetate + ADP + Pi + GTP → (PEP carboxykinase) phosphoenolpyruvate (PEP) + GDP + CO2 -biotin coenzyme helps facilitate rxn -same CO2 is added and lost -pyruvate is first transported from cytosol into mitochondria or is generated from alanine within mitochondria by transamination, in which alpha amino group is transferred from alanine (leaving pyruvate) to an alpha-keto carboxylic acid. -deltaGo'= -25 kJ/mol -facilitate rxn by adding CO2 and then taking it off -pyruvate carboxylase is stimulated by acetyl-CoA (increasing rate of gluconeogenesis when cell has adequate supplies of other substrates) for energy production

utilization of hexokinase in cancer detection

-cancer cells have high glycolytic activity -use 18F tag (2-fluoro-2-deoxyglucose) Fdg + ATP → (hexokinase) 6-phospho-2-fluoro-2-deoxyglucose (6-phospho-FdG) + ADP. this product is trapped and can't be metabolized, can image -anti-tumor target: blocking of hexokinase specifically in tumors. -no ATP synthesis → tumor cells die -more aggressive tumor = greater its rate of glycolysis -payoff phase: steps w ATP are substrate-level phosphorylation, get 2ATP (net) and 2NADH

photosystem II

-donates e- from H2O -4 e- donated, 4 photons required -e- are passed one at a time. e- are transferred to plastoquinones (PQ). PQ are structurally and functionally similar to Q in mitochondria. -lumen (P side), stroma (N side) -e- from H2O --> special pair of chlorophylls (rxn center) --> Pheo --> PQA --> PQB --> PQH2 -how is H2O able to donate e- to photosynthetic rxn center of PS II and then pass e- to pheophytin: photon excites an e- in photosynthetic rxn center exciting it to a level where it passes e- to e- acceptor pheo creating a charge separation that is filled by an e- from e- donor H2O.

GNG 3rd bypass: G-6-P to glucose

-glucose-6-P + H2O → (glucose-6-phosphatase) glucose + Pi - Go= -13.8 kJ/mol -bypass of hexokinase. Here - again hydrolysis of Pi - no ATP involved -this enzyme occurs only in certain tissues (eg liver) which supply glucose to blood (eg hepatoctes). Active site is in ER lumen so separated from glycolysis in cytosol

glucagon impact on glucose metabolism

-increase glycogen breakdown: glycogen phosphorylase activated by phosphorylation from glycogen phosphorylase b kinase (through cAMP cascade) -decrease glycogen synthesis: phosphorylation of glycogen synthase -decrease glycolysis: phosphorylation of PFK-2/FBPase-2 -increase gluconeogenesis: phosphorylation of PFK-2/FBPase-2

role of citric acid cycle in anabolism

-intermediates that aren't channeled can be pulled off for anabolism -citrate --> FA, sterols -alpha-ketoglutarate --> amino acids -succinyl-CoA --> porphyrins, heme -pyruvate can make malate (malic enzyme) -oxaloacetate --> GNG (glucose), AA

how are fatty acids stored?

-lipid bodies w triacylglycerols (TG, TAG) -humans only store 100g of glycogen, suffice for 24 hours. fats more important - 100kg person, stores 35 kg TAG, suffice for 18 weeks -95% of available energy is in long-chain fatty acid. glycerol backbone doesn't contribute much to energy. glycerol is pretty oxidized (has OH on each C) whereas FA have long hydrocarbon chains and aren't very oxidized. -fatty acids: form lipid bodies. inert, low osmolarity. very insoluble so have to be emulsified or bound to protein for transport.

Km vs metabolite conc

-many enzymes have a Km that is near or greater than physiological conc of their substrate (especially those utilizing ATP or NAD(H)) -so if you know Km, can guess what [S] is -Km - useful general predictor of physiologically relevant substrate conc

regulation of glycogen breakdown

-mostly at glycogen phosphorylase. Covalent P, hormones, allosteric -glucagon/epinephrine signaling pathway. Starts phosphorylation cascade via cAMP, activates glycogen phosphorylase by promoting phosphorylation. -glycogen phosphorylase cleaves glucose residues off glucogen, generating G-1-P. -glucagon (low blood sugar, liver) and epinephrine (stress hormone, muscle) activate phosphorylase b kinase, which activates phosphorylase a (by phosphorylating it). -high Ca2+ and high AMP also activate phosphorylase b kinase to increase phosphorylase a. -active muscle contraction results in increased AMP-phosphoprotein phosphatase 1 (PP1) converts phosphorylase a (active) to phosphorylase b (less active), dephosphorylating it. -regulation of glycogen phosphorylase by glucose (liver) - allostery and phosphorylation. High blood glucose binds to phosphorylase and promotes inactivation. Glc binds allosteric site, exposes phosphate groups. More accessible for PPi, becomes less active. Slows glycogen breakdown when high blood sugar -insulin activates PP1

pyruvate dehydrogenase complex (oxidative decarboxylation of pyruvate to acetyl-CoA)

-pyruvate - CO2 --> hydroxyethyl TPP, acyl lipoyllysine, + CoA-SH, reduced lipoyllysine, FAD --> FADH2, NAD+ --> NADH + H+ -E1: pyruvate dehydrogenase (bound cofactor TPP). catalyzes first decarboxylation of pyruvate. -E2: dihydrolipoyl transacetylase (bound lipoyl group). ccatalyzes transfer of acetyl group to coenzyme A, forming acetyl-CoA -E3: dihydrolipoyl dehydrogenase (cofactors FAD and NAD). catalyzes regeneration of disulfiide (oxidized) form of lipoate, e- pass first to FAD and then NAD+ -lipoyllysine similar to cysteine-bridge -reduced lipoyllysine needs to be oxidized to cycle back. use FAD reduction to couple. this is then coupled to NAD+ reduction -another ex of susbtrate channeling: intermediates never leave enzyme surface. are tethered by lipoyl arm. arm swings from active site of E1 to E2 to E3, tethering intermediates to enzyme complex to allow substrate channeling

carbon assimilation (Calvin cycle) stage 2: reduction

-reversal of glycolysis oxidation but NADPH instead of NADH -3-phosphoglycyerate + ATP <--> (3-phosphoglycerate kinase, Mg2+) 1,3-bisphosphoglycerate + ADP. 1,3-bisphosphoglycerate + NADPH + H+ <--> (NADP-glyceraldehyde-3-phosphate dehydrogenase) glyceraldehyde 3-phosphate + NADP+ + Pi -thermodynamically unfavorable. high conc of NADPH and ATP in stroma (after light rxns) makes these 2 rxns favorable

protein phosphorylation

-why Ser, The, Tyr: these 3 residues can be phosphorylated because they have OH groups -OH + ATP → (protein kinase) phosphate + ADP. Phosphate + H2O → (phosphoprotein phosphatase) OH + Pi

rxns of TCA cycle

-1) acetyl-CoA + oxaloacetate + H2O --> (citrate synthase) citrate + CoA-SH. deltaG'^o = -32.2 kJ/mol, irreversible. this rxn happens in context of a protein, side chains help facilitate rxn. -2) citrate <--> (aconitase) cis-aconitate + H2O <--> (aonitase) isocitrate. deltaG^o' = 13.3 kJ/mol. iron sulfur complex stabilized by Cys residues helps facilitate rxn -3) isocitrate + NAD+ --> (isocitrate dehydrogenase) alpha-ketoglutarate + CO2. deltaG^o' = -20.9 kJ/mol. Mn2+ helps stabilize intermediates. -4) alpha-ketoglutarate + COA-SH + NAD+ --> (alpha-ketoglutarate dehdyrogenase complex) succinyl-CoA + NAD + CO2. deltaG'^o = -33.5 kJ/mol. energy is conserved in thioester bond, similar to pyruvate dehydrogenase (common evolutionary ancestor). also requires 5 cofactors (TPP, lipoate, FAD, NAD, CoA-SH) and also E1, E2, E3 -5) succinyl-CoA + GDP + Pi <--> (succinyl-CoA synthetase) succinate + GTP + CoA-SH. deltaG'^o = -2.9 kJ/ol. energy (thioester) drives formation of GTP -6) succinate --> (succinate dehydrogenase) furamate + FADH2 -7) furamate + H2O <--> (furamase) L-malate. deltaG'^o = -3.8 kJ/mol. -8) L-malate + NAD+ <--> (malate dehydrogenase) oxaloacetate + NADH + H+. deltaG'^o = 29.7 kJ/mol. equilibrium to left, so constant removal of product and oxaloacetate conc in cell very low (< 1 uM) helps push forward

acetyl-CoA production

-AA, FA, and glucose can make acetyl-CoA -pyruvate dehydrogenase complex in mitochondrial matrix (eukaryotes) -pyruvate --> (pyruvate dehydrogenase complex (E1 + E2 + E3)) acetyl-CoA -5 co-factors/3 enzymes: CoA-SH, NAD+, TPP, lipoate, FAD -deltaG^o' = -33.4 kJ/mol (irreversible) -CoA: helps w specificity in interactions. has pantothenic acid (vitamin), 3'-phosphoadenosine diphosphate and reactive thiol group. thioester hydrolysis: delta G'^o = -31.4 kJ/mol. acetyl-CoA is activated form of acetate -acetyl-CoA is starting material for FA synthesis

AMPK

-AMP conc is even more sensitive indicator of a cell's energetic state than [ATP]. When someone processes (say muscle contraction) consume ATP, AMP is produced in 2 steps. First, hydrolysis of ATP produces ADP, then rxn catalyzed by adenylate kinase produces AMP: 2 ADP --> AMP + ATP. -AMPK responds to increase in [AMP] by phosphorylating key proteins and regulating their activities. -Rise in [AMP] may be caused by a reduced nutrient supply or by increased exercise. AMPK slows glycogen synthesis by phosphorylating and inhibiting enzyme glycogen synthase. All of changes affected by AMPK serve to raise [ATP] and lower [AMP] -active AMPK in muscle: shifts metabolism in tissues away from energy-consuming processes (like synthesis) and shifts metabolism to use FA as fuel. AMPK in muscle increases FA and glucose uptake and oxidation

nucleotide sugars

-G-1-P + UTP → (UDP Glc pyrophosphorylase) PPi + UDP glucose -activated sugar: UDP-glucose. Formation is irreversible (making PPi hydrolysis has high energy release)l nucleotide can interact non-covalently w other AA residues in protein. UMP/UDP like AMP/ADP is an excellent LG facilitating glycosyl transfer. Nucleotide group can "tag" sugar for a special purpose -formation of Pi from PPi in products is irreversible, pulls rxn -net rxn: sugar phosphate (G-1-P) + NTP (UTP) → NDP-sugar (UDP-glucose) + 2 Pi -Many of the rxns, in which hexoses are transformed or polymerized involve sugar nucleotides, compounds in which anomeric C of sugar is activated by attachment to a nucleotide through a phosphate ester linkage -group trasnfer rxns (glycosyl group): attachment of a good LG to a metabolic intermediate to activate intermediate of subsequent rxn. nucleotidyl group (eg UDP) is an excellent LG, facilitating nucleophilic attack by activated sugar carbon to which it is attached

glycolysis and flux

-Hexokinase has biggest contribution to flux -measure experimentally, change conc of enzyme, see how impacts rate of formation of pathway product. Glycolysis rate: conversion of glucose to pyruvate -hexokinase IV (in liver) has greatest flux control coefficient (C = 0.79), PFK-1 (C = 0.21), phosphohexose isomerase (C = 0.0). Hexokinase most influential in setting flux through glycolysis -some regulated enzymes change flux through pathway (hexokinase IV). other regulated enzymes rebalance to maintain homeostasis (PFK-1). -how to alter amount of (active) enzyme? In vitro (amount you add), genetically (change amount made, extra copy of gene, or amount expressed), specific inhibitors or activators, sequestration (alter effective conc)

group transfer rxns

-acyl group, glycosyl group, phso hotel group. Transferred from one nuc to another -general theme in metabolism: attachment of a good LG to a metabolic intermediate to activate intermediate for a subsequent rxn -ATP: used for phosphoryl group transfer and energy transfer

Pasteur effect

-addition of O2 --> convert from fermentation to oxidative phosphorylation --> don't need as much glucose for energy -aerobic respiration produces far more ATP per glucose than fermentation, so cells in aerobic conditions need to consume far less glucose to meet energy demands than it would for fermentation -ATP rises and inhibits PFK-1, thus slowing rate of glucose entry into glycolytic pathway

rxns that make or break C-C bonds

-aldolases (aldol condensation, carbanion attacks carbonyl, form tetrahedral molecule, ketone → alcohol). Common way to form a C-C bond -often coA-SH involved (claisen ester condensation, carbanion attacks thiol → ketone). Carbanion is stabilized by carbonyl of an adjacent thioester -thioesters undergo much less resonance stabilization than do O esters; diff in free energy between reactant and its hydrolysis products, which are resonance stabilized, is greater for thioesters than for comparable O esters. Thioesters have high free energies of hydrolysis -dehydrogenase (decarboxylation of a beta keto acid, CO2 removed)

regulatory enzymes - hexokinase

-all glycolysis enzymes in cytosol. All gluconeogenesis enzymes in cytosol except for glucose 6-phosphatase (in ER lumen) and pyruvate carboxylase (mitochondria) → compartmentalization or sequestration -note glucose 6-phosphatase is in ER lumen, not cytosol. Highly expressed in liver - dominant site of gluconeogenesis. -HK IV in liver (high Km, can function in higher [glucose] environments, not inhibited by G-6-P, increases flux through glycolysis, high C -HK I in all tissues, HK IV only in liver -kinetic properties of HK I vs HK IV: HK I has Km = 0.2 mM, HK IV (glucokinase) has Km = 10 mM (able to respond based on high [glucose]) -muscle is responsible for using glucose to make TP necessary for movement. muscle HK has a lower Km so it can use glucose at low conc. liver is responsible for sensing and maintaining blood glucose levels. liver HK has a higher Km so it can modulate its response based on blood glucose levels, and continue to increase its activity even at high [glucose] -relative enzyme activity: HK I (muscle) has allosteric regulation and G-6-P inhibition. Already at Vmax when at fasting blood glucose conc. HK IV (glucokinase, liver) has regulation by increased enzyme expression w insulin, responsive to substrate conc - blood glucose, glucose transporter, sequestration -HK IV conc in liver (cytosol) is controlled by sequestration. HK IV binds to regulatory protein when F-6-P is high, is moved to nucleus (glycolysis slows down). Buildup of F-6-P: this will positively regulate association of HK IV w regulatory protein, move to nucleus, now unable to go through glycolysis - During fast, when blood glucose drops below 5 mM, fructose 6-phosphate triggers inhibition of hexokinase IV by regulatory protein, so liver does not compete w other organs for scarce glucose. -release of HK IV from nucleus allows for a rapid response to increased glucose levels -when glucose conc in cytosol rises, equilibrates w glucose in nucleus by transport through nuclear pores. Glucose causes dissociation of regulatory protein, and HK IV enters cytosol to begin phosphorylating glucose -after a meal, blood glucose increases. This favors: glycolysis, movement of dissociated HK IV into cytosol -circumstances that call for greater energy production (low ATP, high AMP, vigorous muscle contraction) or greater glucose consumption (high blood glucose) cause increased transcription of HK IV gene

Chemical properties of carbonyl groups

-carbonyl group C as elec -carbanion (nuc) stabilized by adjacent carbonyl group allowing its formation. (ex: isomerization of G-6-P to F-6-P happens 2 steps before cleavage rxn. what does this accomplish? moves carbonyl from C1 to C2, setting up a C-C bond cleavage between C3 and C4.) -imines function like carbonyl groups to facilitate e- withdrawal. Allow carbanion as nuc -metals and general acids can facilitate carbonyl group function

metabolic regulation vs metabolic control

-cell is in dynamic steady state -homeostasis: intermediates are formed and consumed at same rate -all pathways are interconnected -metabolic regulation: processes that serve to maintain homeostasis -metabolic control: process that leads to a change in flux through metabolic pathway. # of molecules going through pathway is more.

CO2 assimilation in plants (Calvin cycle)

-chloroplast stroma -stage 1: fixation. ribulose 1,5-bisphosphate + CO2 --> (rubisco) 2 3-phosphoglycerate. -stage 2: reduction. 3-phosphoglycerate + ATP + NADPH + H+ --> glycyeraldehyde 3-phosphate + ADP + NADP+ + Pi. glyceraldehyde 3-phosphate used for energy production via glycolysis; starch or sugar synthesis -stage 3: regeneration of acceptor. glyceraldehyde 3-phosphate + ATP --> ribulose 1,5-bisphosphate + ADP -products that can accumulate: 3-phosphoglycerate, glyceraldehyde 3-phosphate, ribulose 1,5-bisphosphate -net product from CO2 fixation: 1 G-3-P

biochemical anatomy of a mitochondrion

-consists of 2 membranes -outer membrane: freely permeable to small molecules and ions (due to porins) -inner membrane: impermeable to most small molecules and ions, including H+. contains respiratory e- carriers (complexes I-IV), ADP-ATP translocase, ATP synthase (FoF1), other membrane transporters --> 10,000 sets. -matrix: contains pyruvate dehydrogense complex, CAC enzymes, fatty acid beta-oxidation enzymes, AA oxidation enzymes, DNA, ribosomes, many other enzymes, ATP, ADP, Pi, Mg2+, Ca2+, K+, many soluble metabolic intermediates -does not contain glycolysis enzymes - cytosol

pentose phosphate pathway (PPP)

-conversion of 6-phosphogluconate → ribulose 5-phosphate + CO2 is coupled to NADP+ → NADPH. NADPH → NADP+ coupled to reductive biosynthesis of precursors → fatty acids, sterols. etc. -regeneration: produce more NADPH, NADPH required to make FA and sterols and for detoxifying drugs, etc. (detoxification of radicals, ionizing drugs, radiation). In some tissues the essential product of PPP is NADPH for reductive biosynthesis or countering damaging effects of oxygen radicals. By maintaining a reducing atmosphere (a high ratio of NADPH to NADP+ and a high ratio of reduced oxidized glutathione), such cells can prevent or undo oxidative damage to proteins, lipids, and other sensitive molecules -very active in rapidly dividing cells: bone marrow, skin, tumors -net result: NADPH (reductant for biosynthetic rxns) and ribose 5-phosphate (precursor for nucleotide synthesis) -occurs in cytosol -runs when NADPH is low, nucleotides are low (needed for rapid cell division and cancer), need to make FA, or for detoxification

mitochondrial ETC complex IV

-cytochrome c oxidase -prosthetic groups: hemes; CuA, CuB -pass e- through centers, pass to O2, converted (reduced) to H2O, pumping out H+ -1/2O2 --> H2O in matrix, 2H+ pumped across. 3 subunits, heme a3, heme a, CuB, CuA, Fe-Cu enter, 2 cyt c -total protons pumped: 2

oxidation of fatty acids: 2) entry into mitochondrion

-cytosol: acyl-CoA, strip off CoA-SH, coupled to carnitine transport, go through carnitine acyltransferase I. go through intermembrane space, carnitine transport in and out, carnitine removal by carnitine acyltransferase II is coupled to CoA-SH added back on (from diff pool of mitochondrial matrix coA-SH), get fatty acyl-CoA in matrix. -why shuttle? major regulation point. cytosol has synthesis, mitochondria has oxidation (energy)

bioenergetics equations to know

-deltaG = deltaH - TdeltaS -deltaH: change in enthalpy (heat content of rxn, reflects # and kinds of chem bonds in reactants and products) -delta G < 0 exergonic, deltaG > 0 = endergonic -exothermic (-): heat energy is released. endothermic (+): heat energy is taken up -deltaG'^o: rxn at pH 7, 25 C, H2O 55.5 M, Mg2+ 1 mM, rxn at 1 M -deltaG'^o = -RTlnK'eq (++watch out for units and signs, put all conc in M) -when K'eq is less than 1, deltaG'^o is +, rxn proceeds in reverse direction -free energy released in sequential rxns is additive (similar reactants cancel out to make full rxn). -deltaG = deltaG'^o + RT ln ([products]/[reactants]) -free-energy change for a rxn is independent of pathway by which rxn occurs. delta G occurs under real physiological conditions. -deltaG^o' = -nF deltaE^o'. when solving don't switch signs of E^o' values, just use as given in table -adding a catalyst will not affect deltaG. catalysts help a rxn reach equilibrium more quickly by lowering EA, not deltaG -deltaG'^o for ATP: -30.5 kJ/mol

How does NADH from glycolysis (cytosol) get to matrix (N side) for use in ETC? (inner mitochondrial membrane impermeable to NADH and NAD+)

-diff routes depending on tissue -malate-aspartate shuttle (liver/kidney/heart): 2.5 ATP per NADH (no cost for shuttle). NADH --> NAD coupled to DHAP --> glycerol 3-phosphate. this is coupled to FAD --> FADH2, gives e- to QH2 to go to complex III. complex I not involved (less H translocation). NADH reduces oxaloacetate to form malate and NAD+, malate enters mitochondrion via malate-alpha-ketoglutarate. if blocked, NADH accumulates (forces glycolysis to operate anaerobically, reoxidizing NADH via lactate dehydrogenase rxn, oxygen consumption slows, lactate accumulates, AT synthesis decreases) transporter. -glycerol-3-phosphate shuttle (muscle/brain): 1.5 ATP per NADH. cost of 1 ATP. malate dehydrogenase: get NAD+, malate goes through malate-alpha-ketolguatare transporter, get NADH again, oxaloacetate, aspartate aminotransferase, aspartate, go through glutamate-aspartate transporter. net effect: NADHp --> NADHN. delivers reducing equiv from NADH through FAD in glycerol 3-phosphate dehydrogenase to ubiquinone and thus into complex III, not complex I ---> 1.5 ATP per 2e- -so final ATP from glycolysis NADH is 3 or 5 depending on shuttle (2.5 ATP per NADH from malate shuttle, 1.5 ATP per NADH for glycerol-3-P shuttle)

regulation of oxidative phosphorylation

-direct product inhibition can be in active site or allosteric -regulation at irreversible steps -feedback inhibition by ATP, NADH. positive regulation by AMP, and or Pi -oxidative phosphorylation and ATP synthesis are coupled. require substrate availability: NADH and ADP/Pi, O2. need ETC to fully function to establish proton and charge gradient. need ATP synthase to function. if ETC disrupted, so is ATP synthase. if ATP synthase is inhibited, ETC is impacted (NADH, ADP/Pi buildup, 1/2O2 not reduced). -inhibitor of F1 ATPase. IF1: prevents ATP hydrolysis when O2 is low, connects ATP synthase activity to ETC function. -if oxidative phosphorylation is inhibited, NADH accumulates, get feedback inhibition cascade -hexokinase: G-6-P inhibits (direct product inhibition), Pi activates. -PFK-1: AMP and ADP activate, ATP and citrate inhibit. -pyruvate kinase: ADP activates, ATP and NADH inhibit. -pyruvate dehydrogenase complex: AMP, ADP, NAD+ activate, ATP, NADH, and acetyl-CoA (direct product inhibition) inhibit -citrate synthase: ADP activate, ATP, NADH, citrate (direct product inhibition) inhibit -isocitrate dehydrogenase: ADP activate, ATP inhibit -alpha-ketoglutarate dehydrogenase: ATP, NADH, succinyl-CoA (direct product inhibition) inhibit -whenever ATP consumption increases, rate of e- transfer and oxidative phosphorylation increases -in photosynthesis: if ATP synthase inhibited: protons can no longer cross thylakoid membrane and oxygen evolution ceases. uncoupling agent provides route for H+ to move trough thylakoid membrane, allows for continued production of O2 by splitting of water

fatty acid catabolism

-fatty acids provide 80% of energy to heart and liver. lipids store lots of energy! -FA can also be used to generate energy in muscle -not brain - brain needs glucose -fatty acid catabolism and glycolysis convert quite diff starting materials into same product (acetyl-CoA). e- carried from oxidative rxns of these pathways and of CAC are carried by common cofactors (NAD, FAD) to mitochondrial respiratory chain leading to oxygen, providing energy for ATP synthesis by oxidative phosphorylation -evolution selects for chem mechs that make useful rxns more energetically favorable. in breakdown of FA we see activation of a carboxylic acid by its conversion to a thioester (as we saw w acetyl-CoA in CAC). to break C-C bonds in long chain of relatively inert -CH2-CH2 groups in fatty acids, a carbonyl group is created adjacent to -CH2- group. -allosteric mechs and post-translational regulation coordinate metabolic processes within cell. hormones and growth factors coordinate metabolic activities among tissues and organs. reciprocal regulation and anabolic pathways prevents inefficiency of futile cycling -step 1: make fatty acid-CoA (takes energy). step 2: transport from cytosol to mitochondria. step 3: beta oxidation, break down 2Cs at a time

lollipop apparatus used by Calvin et al. Berkeley

-feeding exp w 14CO2 -use algae to get everything synchronized -make single layer of algal cells, expose all to light at same time, follow rxns (a single layer of photosynthetic organism that could respond to light at the same time) -compounds with the 14C label were detected by spots using a film. First spot to appear was first stable compound. audioradiograms showed label C compounds, 1st product was 3-phosphoglycerate

consumption of alcohol results in hypoglycemia. first rxn is oxidation of ethanol to acetaldehyde (alcohol dehydrogenase). how doe this rxn inhibit transformation of lactate to pyruvate?

-first step in synthesis of glucose from lactate in liver is oxidation of lactate to pyruvate, requires NAD+. consumption of alcohol forces a competition for ND+ between ethanol and metabolism and GNG, reducing conversion of lactate to glucose leading to hypoglycemia. problem is compounded by strenuous exercise and lack of food because theses conditions also decrease level of glucose in blood.

GNG 2nd bypass: F-1,6-BP to F-6-P

-fructose-1,6-bisP + H2O → (fructose-1,6-bisphosphatase) fructose-6-P + Pi -deltaGo= -16.3 kJ/mol (irreversible) -bypass of PFK-1. Here note hydrolysis of Pi - no ATP involved

fermentation

-general term for anaerobic degradation of glucose or other organic nutrients to obtain energy -lactate fermentation: muscles, some bacteria -ethanol fermentation: yeast, some bacteria, plants -extract energy (as ATP) but do not consume oxygen or change conc of NAD+ or NADH -need NAD+ to be recycled (failure to regenerate NAD+ would leave cell w no e- acceptor for oxidation of glyceraldehyde). need NAD+ for glycolysis to continue -fermentation upregulated by NADH

carbon labeling practice questions

-glucose label at C-1 produces DHAP and pyruvate labeled at C-3, becomes C-2 on ethanol -to make sure all 14C is liberated as 14CO2 during ethanol fermentation, 14C has to be on C1 of pyruvate (C3 and C4 of glucose) -labeled C-1 on bicarbonate: cleaved off as CO2 in GNG -pyruvate labeled at C-1 would be on C3 and C4 of glucose -C-1, C-2, and C-3 from FBP yield DHAP and C-4, C-5, and C-6 yield G3P -labeled C-2 on oxaloacetate is labeled on C-2 and C-5 on glucose (through GNG)

major pathways of glucose utilization

-glucose → (oxidation via glycolysis) pyruvate → ATP, AA -glucose → (storage/transport) glycogen, starch, sucrose -glucose → (synthesis of structural polymers) extracellular matrix and cell wall polysaccharides (eg cellulose is most abundant polymer of C) -glucose → (oxidation via pentose phosphate pathway) ribose 5-phosphate -glucose conc so low in cell because it is rapidly converted to G-6-P

fatty acid catabolism - entry of glycerol into glycolysis

-glycerol provides only 5% of energy from TAG breakdown -glycerol + ATP --> (glycerol kinase) ADP --> glycerol 3-phosphate + NAD+ --> (glycerol 3-phosphate dehydrogenase) DHAP + NADH <--> (triose phosphate isomerase) glyceraldehyde 3-phosphate --> glycolysis -1 glycerol to 1 GA3P: cost is 1 ATP, produced 1 NADH. -now goes into payoff stage of glycolysis (2 ATP made, 1 more NADH made). net: 1 ATP produced, 2 NADH produced

Vmax of enzyme glycogen phosphorylase in skeletal msucle vs liver

-glycogen phosphorylase catalyzes release of G1P from terminal alpha-1,4 glycosidic bonds at nonreducing ends -in skeletal muscle: releases G1P form glycogen to be metabolized for energy by glycolysis (or lactic acid fermentation). formation of ATP by glycolysis requires higher glycogen phosphorylase activity for G1P release. Vmax higher in muscle enzyme to allow for rapid production of large amounts of ATP by glycolysis (have high catalytic efficiency). -in liver: regulates glycogen breakdown in response to blood glucose levels. G6P released by glycogen phosphorylase in liver is converted back into glucose and transported elsewhere. large amounts of ATP aren't required in liver, so Vmax of glycogen phosphorylase can be lower

glycogen breakdown

-glycogen phosphorylase, glycogen branching enzyme, phosphoglucomutase. Go through glycolysis -cleaving alpha 1→ 4: removes glucose from nonreducing end. Glycogen chain + pyridoxal phosphate → (glycogen phosphorylase) G-1-P + glycogen shortened by one residue → successive rxns -Pyridoxal phosphate is an essential cofactor in glycogen phosphorylase rxn; its phosphate group acts as a general acid catalyst, promoting attack by Pi on glycosidic bond -branch points: glycogen phosphorylase works on nonreducing ends until it reaches 4 residues from an (alpha1→ 6) branch point. Debranching enzyme transfers a block of 3 residues to nonreducing end of chain. Debranching enzyme cleaves single remaining (alpha1→ 6) linked glucose, which becomes a free glucose unit (not G-1-P). Enzyme has transferase and glucosidase activity. -have as many free glucose as you have alpha1→ 6 linkages, rest are G-1-P (ex: for glycogen w 4 alpha1→ 6 linkages, how many glucose would be released from debranching? 4) -G-1-P must be isomerized to G-6-P for metabolism. Phosphoglucomutase performs this rxn via a mech similar to phosphoglycerate mutase. G-1-P + P (Ser) → glucose 1,6-bisphosphate + OH (Ser) → G-6-P + P (Ser). G-6-P can then do a lot of things: glycolysis (phosphohexose isomerase), PPP (Glc-6-P dehydrogenase), gluconeogenesis (Glc-6 phosphatase) -primary regulation at glycogen phosphorylase

glycogenin

-glycogenin: facilitates formation of glycogen, remains buried -Glycogenin is both primer on which new chains are assembled and enzyme that catalyzes the assembly -each tier has 2 branches.. Each chain has 12-14 glucose units. All at same time can be degraded to release G-1-P

glycolysis

-greek "sweet" "splitting" -done in every organism -overall net rxn: glucose (C6) + 2 NAD+ + 2 ADP + 2 Pi → 2 pyruvate (C3) + 2 NADH + 2 ATP + 2 H2O -10 enzymes, in cytosol -payoff: 2 ATP (put 2 ATP in, get 4 ATP out) -deltaG= -72 kJ/mol. but 2840 kJ total for complete oxidation of glucose, so long way to go. Still have energy in pyruvate, energy stored in NADH and ATP -prepratory phase: phosphorylation of glucose and its conversion to G3P. make F-6-P to have symmetric molecule so it can be cleaved into 2 interconvertible 3C molecules -phosphorylation retains compounds in cell

substrate channeling

-helps couple 2 rxns -sequential action of 2 separate enzymes: product of first enzyme (1,3-bisphosphoglycerate) diffuses to second enzyme. Avoidance of intermediate diffusion speeds up rxn. Results in limited product conc for first rxn and increased reactant conc for second rxn - lowers actual physiological delta G's -Substrate channeling through a functional complex of 2 enzymes: intermediate (1,3-bisphosphoglycerate) is never released to solvent. -coupling of the rxns allows for - deltaG'o

principles of regulation

-homeostasis vs metabolic control -flow of metabolites through pathways is regulated to maintain homeostasis. Homeostasis occurs when conc of metabolites are kept at a steady state in the body. When perturbed, transient alteration and return to steady state. -sometimes, levels of metabolites must be altered very rapidly. Eg need to increase capacity of glycolysis during action. Metabolic control: altering flux through a pathway -regulation is important to keep cells away from equilibrium when they have rxns w large equilibrium constants (need cell to not be at equilibrium to do important rxns). Rxns that are far from equilibrium are typically points of regulation of overall pathway -to maintain steady state, all enzymes operate at the same rate -if net rate changes dramatically, changes flux

energetics of some common rxns

-hydrolysis rxns tend to be strongly favorable (spontaneous. Have -deltaGo'). Recognize a hydrolysis rxn when water is a reactant. -isomerization rxns have smaller free-energy changes -complete oxidation of reduced compounds is strongly favorable. In biochem, oxidation of reduced fuels w O2 is stepwise and controlled

regulation of CO2 assimilation enzymes by light

-in light: pH stroma 7 to 8 (enzymes more active at pH 8), Mg2+ from 2-5 mM --> increases enzyme kinetics. reduced thioredoxin reduces disulfide bonds of proteins --> activates protein. no rubisco allosteric inhibitor (only have inhibitor in dark) --> does not inhibit rubisco. -light affects pH and conc of MgCl2 -thioredoxin-regulated enzymes: reduction phase - glyceraldehyde 3-P dehydrogense. regeneration phase - ribulose 5-phosphate kinase, fructose 1,6-bisphosphatase, seduheptulose 1,7-bisphosphatase. (anything regulated by thioredoxin has 2 disulfide bonds). these enzymes are activated by light-driven reduction of disulfide bonds, oxidized disulfide bonds (in dark) are inactive. -transition state inhibitor of rubisco that increases in dark is not there to inhibit in light

metabolic enzymes controlled by insulin (high blood glucose)

-increased expression: hexokinase II, hexokinase IV, PFK-1, PFK-2/FBPase-2, pyruvate kinase, glucose 6-phosphate dehydrogenase, 6-phosphogluconate dehydrogenase, ATP-citrate lyase, pyruvate dehydrogenase, acetyl-CoA carboxylase, fatty acid synthase complex → more expression for glycolysis, TCA cycle, and FA synthesis. -Decreased expression: PEP carboxykinase (PEPCK), glucose 6-phosphatase → less expression for gluconeogenesis

Favism (disease caused by deficiency in G-6-P dehydrogenase)

-ingredient in falafel -degradation causes accumulation of toxic oxidant (eg H2O2). Usually detoxified by NADPH from PPP (need G-6-P dehydrogenase to generate NADPH to detoxify) -oxidants disrupt membranes (eg erythrocytes) → anemia (favism) -however, people w this deficiency are more resistant to malaria - plasmodium falciparum (causes malaria) is sensitive to oxidative stress -this mutation is common in parts of the world where malaria is common (as high as 25% of pop) -poll question: some pesticides can result in production of toxic oxidants. If you work in those fields, what genetic background would favor your health? Enhanced Glc-6-P dehydrogenase activity

prosthetic groups of cytochromes

-iron protoporphyrin IX: in b-type cytochromes. tightly bound, can dissociate -heme c: in c-type cytochromes. has sulfur Cys residues. covalently bound -heme a: in a-type cytochromes, tightly bound, can dissociate. has long acyl chain and aldehyde in left lower corner. -cytochrome c is soluble, other cytochromes are in inner mitochondrial membrane. carries 1 e- at a time -major point: reduction potential depends on specific protein interactions - different for each cytochrome (E^o' depends on context in protein). for ex, diff iron-sulfur cluster conformations allow for diff E values

rearrangements, isomerizations, eliminations

-isomerase, mutase -rearrangements, isomerizations, and eliminations (intramolecular rearrangement with no change in overall oxidation state of the molecule) tend to have small free energy changes -mutase = enzyme that catalyzes transfer of a functional group from one position to another in same molecule. Are subclass of isomerases (enzymes that interconvert stereoisomers or structural or positional isomers)

ubiquinone (Q)

-isoprenoid chain - allows association w membrane, but can move, freely diffusible. can also associate w a protein -able to transfer e- and protons. able to accept one or two -is lipid soluble, can diffuse through membranes -contrast w FAD: FAD tightly associated w protein - active site (flavoprotein) - not freely diffusible

organization of photosynthetic machinery in thylakoid membrane

-journey of e-: H2O --> 1/2 O2 --> e- to P680 --> excited by light --> PheO --> PQA --> PQB --> cyt b6f complex --> plastocyanin --> P700 --> excited by light --> A0 --> A1 --> Fe-S --> Fd --> Fd: NADP+ oxidoreductase --> NADP+ --> NADPH. ATP synthase -PQ = protein bound plastoquinone -A1 = phylloquinone (Qk) -6 protons mobilized into lumen per H2O, 12 per 2 H2O --> yield is 3 ATP (need 4 H+ to make 1 ATP from ATP synthase). -proton-motive force across thylakoid membrane drives synthesis of ATP. little charge differential (more just conc gradient). -synthesis of ATP has same 3 H+ per 1 ATP cost (rotational) as in oxidative phosphorylation. plus 1 for Pi exchange so 4 total H+ per ATP made.

light energy and ATP

-light energy is converted to ATP in plant chloroplasts. light converts H2O to a good e- donor. e- carriers pump H+ in as e- flow to NADP+. energy of e- flow stored as electrochemical potential. ATP synthase uses electrochemical potential to synthesize ATP. not too big of a charge differential in chloroplast -in plants, e- are freed from H2O, which generates O2 and H+. these e- are excited and moved through photosynthetic e- chain. per water, 6 H+ are mobilized into lumen. -when light is turned off, production of ATP and NADPH ceases. chloroplasts can then no longer convert 3-phosphoglycerate to hexoses, because conversion depends on ATP and NADPH. -chloroplast: stroma, stromal thylakoids, grana, thylakoids have membrane. antenna chlorophylls and carotenoids rxn center: photochemical rxn here converts energy of photon into a separation of e- flow, initiating e- flow. -photosystem: ~200 chl, 50 carotenoids

carb metabolism in liver vs muscle

-liver: glycogen → G-6-P → blood glucose. Pyruvate → G-6-P → blood glucose. Need more blood glucose to brain, muscle. Low sugar, glucagon, stress and epinephrine increase glycogenolysis, decrease glycolysis, and increase gluconeogenesis in liver -muscle uses glycogen and glucose to make ATP (via glcycolysis) for muscle contraction. No export of glucose. No gluconeogenesis. Glycogen → G-6-P → pyruvate. Stress and epinephrine in muscle increase glycogenolysis and increase glycolysis -glucagon only regulates liver (muscle cells lack ability to respond to glucagon). Epinephrine regulate both muscle and liver

-control of carbohydrate metabolism in liver

-liver: where GNG happens, balance of sugar in bloodstream. responds to blood glucose levels and can export glucose. -high blood glucose after eating: decrease glycogen breakdown, increase glycogen synthesis, increase glycolysis -high glucose → increase insulin, increase insulin-sensitive protein kinase, increase PP1, decrease glycogen phosphorylase, decrease glycogen breakdown. High PP1 also decrease phosphorylase kinase → decrease glycogen phosphorylase → decrease glycogen breakdown. PPi also increases glycogen synthase, which increases glycogen synthesis. High insulin → high PKB → low GSK-3 → high glycogen synthase → high glycogen synthesis. High insulin → synthesis of HK II, PFK-1, pyruvate kinase → increase glycolysis. High blood glucose → GLUT2 → high glucose inside → increase glycolysis. -PFK-2 active, F-2-BP increase, glycolysis favored. -PP1 removes phosphate from phosphorylase kinase, glycogen phosphorylase, and glycogen synthase. -low glucose between meals/fasting: high glycogen breakdown, low glycogen synthesis, low glycolysis, high gluconeogenesis -low blood glucose → high glucagon → high cAMP → high PKA → low glycogen synthase → low glycogen synthesis. High PKA → high phosphorylase kinase → high glycogen phosphorylase → high glycogen breakdown. High PKA → high FBPase-2 and low PFK-2 → low F-2,6-BP → low PFK-1 → low glycolysis. High PKA → low pyruvate kinase L → low glycolysis. Low F-2,6-BP → high FBPase 1 → high F-6-P → high gluconeogenesis -PKA phosphorylates

reduction potential E

-measure of affinity of e- acceptors for e-; unit = . stronger the tendency to gain e-, the more + the acceptor (strongly + E) -reduction potentials are measured w respect to H electrode, which has reduction potential of 0 at pH 0 -Standard reduction potential: Eo' (25 C, 1M, pH 7) -donors have - Eo', e- acceptors have + Eo'. compounds w more - potentials get oxidized (release e-), compounds w more + potential get reduced (receive e-) -e- will tend to go to half-cell w more + E, and strength of that tendency is proportional to E -E' = E^o' + RT/nF ln [e- acceptor]/[e- donor] -E^o: chem standard reduction potential. T = 25 C, pH = 0, conc = 1M. -E: takes into account actual conc.

elasticity coefficient (epsilon)

-measures responsiveness of an enzyme to changes in substrate conc -E = 1 at low substrate conc, E = 0 at high substrate conc near Vmax -an enzyme w typical Michaelis-Menten kinetics show hyperbolic response to increasing substrate conc. -for allosteric enzymes that show cooperativity, E may exceed 1.0 but cannot exceed its Hill coefficient

regulation of glycogen synthesis in muscle

-metabolic control: insulin increases flux. Transporter GLUT4 guided to plasma membrane, synthesis of hexokinase -metabolic regulation: homeostasis. Covalent modification of glycogen synthase to make it more active (dephosphorylation) -so insulin activates GLUT4 in membranes, hexokinase, and glycogen synthase -regulation of glycogen synthase: high glucose, stimulates glycogen synthase promoting glycogen production. Insulin activates PP1, which converts glycogen synthase b (inactive, phosphorylated) → glycogen synthase a (active, unphosphorylated). G-6-P also activates PP1. glucagon and epinephrine inhibit PP1. -glucagon accounts in liver cells, epinephrine acts in muscle cell, also liver

regulatory enzymes - PFK-1

-metabolic regulation: homeostasis (prevent large changes in metabolite conc when flux through glycolysis increase in response to elevated blood glucose or insulin) -flux control coefficient: relatively low -coordinate regulation of PFK-1 and FBase-1, both enzymes are in cytosol (so one would be used preferentially) → very important to control -F-6-P → F-1,6-BP is committed step in glycolysis -when ATP is a substrate, ATP is also a - effector (do not speed glucose in glycolysis if there is plenty of ATP). PFK-1 activity increases as F-6-P increases at low [ATP], PFK-1 activity kind of increase as F-6-P increases at high [ATP]. when high cellular [ATP] signals that ATP is being produced faster than it is being consumed, ATP inhibits PFK-1 by binding to an allosteric site and lowering affinity of enzyme for its substrate fructose 6-phosphate -F-6-P + ATP → F-1,6-BP + ADP. ATP and citrate inhibit, AMP and ADP and F-2,6-BP activate -go glycolysis if AMP is high and ATP is low. go gluconeogenesis if AMP is low -ATP inhibits PFK-1 (glycolysis), ADP activate PFK-1 (glycolysis), AMP activate PFK-1 (glycolysis) but inhibit FBPase-1 (gluconeogenesis), citrate inhibits PFK-1 (glycolysis) -also F-2,6-BP similar to AMP: not in structure but in how it regulates both enzymes (F-2,6-BP activates PFK-1 and inhibits FBPase-1); not a metabolite, just an allosteric effector. -AMP (acts on PFK-1 and FBPase-1) and F26BP (made my PFK-2/FBPase-2) activate glycolysis and inhibit GNG

oxidative phosphorylation

-mitochondria play central role in eukaryotic aerobic metabolism. ATP production is not only important function; mitochondria play host to CAC, fatty acid beta-oxidation pathway, and pathways of AA oxidation. mitochondria also act in thermogenesis, steroid synthesis, and apoptosis. -mitochondria trace their evolutionary origin back to bacteria. over 1.45 billion yers ago, an endosymbiotic relationship arose between bacteria and a primitive eukaryote. -e- flow from e- donors (NADH, FADH2) (oxidizable substrates) (move to more + electric potentials) through a chain of membrane-bound carriers to final e- acceptor w large reduction potential. final e- acceptor is O2. appearance of O2 in atmosphere some 2.3 billion years ago, and its harnessing in living systems via evolution of oxidative phosphorylation, made more complex life forms possible -last stage: e- used to make ATP. put in 2H+ + 1/2O2 --> H2O. get ATP. -membrane needed to facilitate (driven from proton differential across membrane) -e flow down a reduction gradient. flows from donor (- E^o') to acceptor (+ E^o'). get -220 kJ/mol for 1 NADH (2 e-) -carriers: NAD, ubiquinone, cytochromes a, b, c types -order of e- cascade was identified by inhibitors/drugs. -energy of e- transfer is conserved as a proton gradient. 2 e- --> 10 H+ on P side -free energy made available by "downhill" (exergonic) e- flow is coupled to uphill transport of protons across proton-impermeable membrane. free energy of fuel oxidation is thus conserved as a transmembrane electrochemical potential -transmembrane flow of protons back down electrochemical gradient through specific protein channels provides free energy for synthesis of ATP. this process is catalyzed by a membrane protein complex (ATP synthase) that couples proton flow to phosphorylation of ADP -efficiency: 32 ATP x 30.5 kJ/mol = 976 kJ/mol. theoretical oxidation of glucose = 2840 kJ/mol, so 34% efficiency

Cori cycle

-muscle: ATP produced by glycolysis for rapid contraction -liver: ATP used in synthesis of glucose (gluconeogenesis) during recovery. Only place you can make glucose -(muscle) glycogen → ATP + lactate (regenerate NAD+) → blood lactate → (liver) lactate + ATP → glucose → blood glucose → (muscle) glycogen -forming glucose takes time → recovery time. Recovery period after intense exercise (athletes, alligators) -purpose: regenerates NAD+ for continued glycolysis when oxygen is low, which occurs during prolonged strenuous muscle usage

gluconeogenesis

-new formation of sugar (pyruvate → glucose) -pathway for synthesis of glucose from 3-C precursors (pyruvate, acetate, etc.) in liver in mammals -deltaG of gluconeogenesis is -16 kJ/mol (intracellular conditions) -glucose is produced from lactate, pyruvate, oxaloacetate, or any compound (including TCA cycle intermediates) that can be converted to one of these intermediates -energy requiring biosynthetic processes are coupled to breakdown of ATP in such a way to make overall process irreversible (both glycolysis and gluconeogenesis are overall irreversible) -overall rxn: 2 pyruvate + 4 ATP + 2 GTP + 2 NADH + 2 H+ + 2 H2O --> glucose + 2 NAD+ + 4 ADP + 2 GDP + 6 Pi -regulated in ER, mitochondria, and cytoplasm -regulation: pathways are diff from glycolysis (although many rxns are shared, 3 need to be bypassed). pathways are controlled by diff regulatory enzymes or sequestered in space. GNG is coupled to hydrolysis, making it irreversible

fructose 2,6-bisphosphate (F-2,6-BP)

-not a glycolytic intermediate, only an allosteric regulator -glycolysis is not happening in liver unless you have F-2,6-BP -produced in liver -activates PFK-1 (glycolysis), inhibits F-1,6-BPase-1 (gluconeogenesis) -hormones glucagon and insulin control its production -F-2,6-BP is produced from F-6-P. F-6-P + ATP → (PFK-2) F-2,6-BP + ADP. F-2,6-BP → (FBPase-2) F-6-P + Pi -PFK-2 and FBPase-2 are on same enzyme -Insulin - high blood glucose, favors glycolysis. Glucagon - low blood glucose, favors GNG. insulin activates phosphoprotein phosphatase, dephosphorylates enzyme, PFK-2 active and FBPase-2 inactive, high F-2,6-BP. glucagon increases [cAMP], activate cAMP-dependent protein kinase, phosphorylated enzyme, PFK-2 (inactive) and FBPase-2 (active), low [F-2,6-BP], inhibits glycolysis, stimulates gluconeogenesis -knockout of FBPase-2 in liver would increase F-2,6-BP conc (since it usually breaks down this intermediate to F-6-P), which promotes glycolysis, and it slows GNG By by binding FBPase-1 and reducing affinity for substrate) -F26BP present --> FBPase activity decreased, requires more substrate (higher Km) and has a lower Vmax. F26BP absent --> FBPase activity increased, has lower Km and higher Vmax.

flux control coefficient

-not all enzymes have same effect on entire pathway. Some control flux through pathway (change rate through pathway), others regulate steady state conc of metabolites in response to changes in flux -control of metabolic flux is distributed among all enzyme in pathway, but some enzymes have more impact than others (think about contribution of every single enzyme in pathway) -flux control coefficient C is an experimentally determined measure of effect of an enzyme's conc on flux (J) through pathway. Sum of flux control coefficients in a pathway = 1 -characteristic of whole system, not intrinsic to enzyme -ex: formation of D: 0.3 + (-0.2) + 0 + 0.9 = 1.0. C2 w C = 0 → probs an isomerase, still included in calculation and notation -a negative flux control coefficient means it draws intermediates away from branch -factors that contribute to its value: rxn it catalyzes -target enzymes to regulate that have largest coefficients.

anaplerotic "fill-up" rxns in CAC

-once intermediates are removed, need to be replenished (anaplerotic rxns). all cost energy. -pyruvate + HCO3- + ATP --> (pyruvate carboxylase) oxaloacetate + ADP + Pi in liver and kidney -PEP + GDP + CO2 --> oxaloacetate + GTP (heart, skeletal muscle) -pyruvate + HCO3- + NADPH --> (malic enzyme) malate + NADP+ (eukaryotes and bacteria)

fatty acid oxidation

-oxidation of FAs in mitochondrial matrix. no loss due to shuttling -TCA cycle: in mitochondrial matrix -oxidative phosphorylation: in mitochondrial inner membrane -TAGs: get 2 NADH and 1 ATP per glycerol, fatty acids make acetyl-CoA so get 3 NADH, 1 FADH2, and 1 GTP (ATP) for each acetyl-CoA, plus 2.5 ATP/NADH and 1.5 ATP/FADH2

oxidative phosphorylation vs photophosphorylation

-oxidative phosphorylation: in almost every living thing. e- from reduced cofactors NADH and FADH2 are passed to proteins in respiratory chain. in eukaryotes, oxygen is ultimate e- acceptor for these e-. energy of oxidation is used to phosphorylate ADP to ATP. in mitochondria. -photophosphorylation: water is source of e- that are passed via chain of protein transporters to ultimate e- acceptor, NADP+ (requires 2 e- for conversion to NADPH). light energy is used to separate charges on chlorophyll to generate NAPDH and phosphorylate ADP to ATP (reductive phosphorylation because you produce reduced NADPH). oxygen is byproduct of water oxidation. in chloroplast. have light-dependent rxns (H2O --> O2, NADP+ --> NADPH) and carbon-assimilation rxns/Calvin cycle (dark rxns) (ATP --> ADP, CO2 --> triose phosphates, carbs). this is anabolism (synthesis), requires ATP and reductant (NADPH). scientists behind assimilation of CO2 - Melvin Calvin (Nobel prize, UCB) and Andrew Benson -plastocyanin is analogous to cyt c in ETC as they are both soluble e- carriers -plastoquinone is analogous to ubqiuinone in ETC as it is lipid soluble and carries e-s in membrane -thylakoid membrane is site of phosphorylation analogously to mitochondrial inner membrane, site of oxidative phosphorylation -final e- acceptor of photophosphorylation is NADP+, final e- acceptor of oxidative phosphorylation is O2

glycogen synthesis

-phosphoglucomutase, UDP-Glc pyrophosphorylase, glycogen synthase, glycogen-branching enzyme, glycogenin. (G6P → G1P → UDP-glucose → glycogen) -synthesized by glycogen synthase (alpha1→ 4). UDP-glucose + nonreducing end of glycogen chain → (glycogen synthase) elongated glycogen w new nonreducing end + UDP -glycogen synthase: promotes transfer of glucose residue from UDP-glucose to a nonreducing end of a branched glycogen molecule -synthesis of branches in glycogen: when polymer is 11-12 residues long, 6-7 residues are transferred for branching. Makes new nonreducing end. -purpose of branching: increase in nonreducing ends → more efficient degradation. -glycogen branching enzyme catalyzes transfer of 6-7 glucose residues from nonreducing end to a residue at more interior position -primary regulation at glycogen synthase -takes place in all animal tissues but is especially prominent in liver and muscle -casein kinase serves as priming kinase for GSK3; after priming, GSK3 phosphorylates glycogen synthase 3x to deactivate.

pigments harvest light energy

-primary gatherers of energy -phytol side chain anchors to membrane/protein -similar to heme in structure; but Mg2+ instead of Fe2+ in phytochromes -double bonds absorb photons -photopigments absorb diff wavelengths of light. energy is transferred to photosynthetic rxn center -E = hc/lambda (energy is inversely proportional to wavelength) -photosynthetic organisms capture energy from light at variety of wavelengths using accessory pigments and funnel it via excitons to rxn centers.

citric acid cycle

-purpose: provides e- for energy production, provides intermediates for anabolism -makes reduced e- carriers -pyruvate is metabolite that links 2 central catabolic pathways, glycolysis and citric acid cycle. is therefore logical point for regulation that determines rate of catabolic activity and partitioning of pyruvate among its possible uses -rxns of citric acid cycle follow a chemical logic. in its catabolic role CAC oxidizes acetyl-CoA to CO2 and H2O. energy from oxidations in cycle drives synthesis of ATP. chem strategies for activating groups (like CoA making good LG) for oxidation and for conserving energy in form of reducing power and high-energy compounds -look for C oxidized when you see e- released -enzymes have evolved to form complexes to efficiently achieve a series of chem transformations w/o releasing intermediates into bulk solvent. this strategy, seen in pyruvate dehydrogenase complex and metabolons of CAC, ubiquitous in other pathways of metabolism, in respiration, and in many "-somes" that assemble and disassemble informational macromolecules. -in aerobic organisms, CACC is an amphibolic pathway. can serve in catabolic or anabolic role -net equation: acetyl-CoA + 3NAD+ + FAD + ADP + Pi --> 2CO2 + CoA-SH + 3NADH + FADH2 + ATP

regulatory enzymes - pyruvate kinase

-pyruvate carboxylase is in mitochondria, not cytosol -2 isoforms: pyruvate kinase M (all glycolytic tissue including liver, pyruvate kinase L (liver only) -allosterically activated by F-1,6-BP. Increase flow through glycolysis. allosterically inhibited by signs of abundant energy supply (all tissues): ATP, acetyl CoA and long-chain FA, alanine (enough AA) -pyruvate kinase L only inactivated by phosphorylation in response to signs of glucose depletion (glucagon) (liver only). Glucose from liver is exported to brain and other vital organs. Glucagon activates PKA, have inactive pyruvate kinase L. low blood glucose - stop glycolysis. Responding to sugar in blood

glucogenic amino acids

-pyruvate: Ala, Cys, Gly, Ser, Thr, Trp -alpha-ketoglutarate: Arg, Glu, Gln, His, Pro -succinyl-CoA: Iso, Met, Thr, Val -furamate: Phe, Tyr -oxaloacetate: Asn, Asp