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A detailed explanation of cellular respiration and gluconeogenesis, two fundamental metabolic processes. It covers the key steps, enzymes, and regulatory mechanisms involved in both pathways. The document also includes numerous questions and answers, making it an excellent resource for students studying biochemistry or related fields.
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3 stages of cellular respiration - ANSWERS1. Glycolysis (glusoce, FA, AA oxidized to acetyl group of acetyl-CoA. NAD reduced)
redox rxns, accepts hydride ion (H-) Niacin (vit b3) pellagra preparatory phase of glycolysis - ANSWERSphosphorylation of glucose and its conversion to glyceraldehyde 3 phosphate step 1 of glycolysis - ANSWERSphosphorylation of glucose to G6P irreversible keeps glucose in cell 1st rate controlling rxn hexokinase undergoes _____ upon _____ - ANSWERSinduced fit upon substrate binding prevents wasteful ATP hydrolysis 4 different hexokinase enzymes - ANSWERS<0.5 Km in brain (1), skeletal muscle (2), and kidney(3) ~10 Km in liver and pancreas (4) allosteric G6P regulation in all except liver and pancreas hexokinase 4 differ from other 3 hexokinases - ANSWERS1,2 and 3 follow michaelis menton kinetics glucokinase (4) shows slight cooperativity hexokinase 4 - ANSWERSsequestered in liver when glucose concentration is low, store glucos when fed, release when starved step 2 of glycolysis - ANSWERSconversion of G6P to F6P reversible enzyme: phosphohexose isomerase isomerization mechanism involves - ANSWERSenediol intermediate, general acid-base catalysis step 3 glycolysis - ANSWERSphosphorylation of F6P to F16BP irreversible 2nd rate controling step
enzyme: phosphoglycerate kinase 2,3BPG is an ____ of 1,3 BPG a ______ - ANSWERSisomer, glycolysis intermediate step 8 glycolysis - ANSWERSconversion of 3PG to 2PG reversible enzyme: phosphoglycerate mutase phosphoglycerate mutase uses a ____ mechanism - ANSWERS2 step addition/elimination general acid/base catalysis step 9 glycolysis - ANSWERSdehydration of 2PG to PEP reversible 2nd high energy bond forming step (enol phosphate) enzyme: enolase step 10 glycolysis - ANSWERStransfer of phosphoryl group from PEP yeilding Pyruvate and ATP fnal irreversible rxn 3rd rate limiting step substrate level phosphorylation enzyme: pyruvate kinase pyruvate kinase is - ANSWERSallosterically regulated what happens to pyruvate after glycolysis - ANSWERSanabolic fates (gluconeogenesis is low glucose, some AA) catabolic fates (citrate cycle aerobic, fermentation anaerobic) fermentation: energy yeilding anabolic breakdown of a nutreint molecule, regenerate NAD+ so glycolysis can continue in anaerobic conditions conversion of pyruvate to lactate catalyzed by - ANSWERSlactate dehygrogenase fermentation of glucose to lactate yeilds - ANSWERSno net change of NAD+, regenerates it for use in anaerobic glycolysis lactate produced in muscle converted back to glucose in the liver via - ANSWERScori cycle
cancer cells rely on enhanced rates of - ANSWERSglycolysis. the warburg effect. glucose uptake 10x faster in cancer cells, lactate fermentation, increased resilience to hypoxic conditions, increased expression of glucose transporters inhibition of mitochondrial functions. positron emission tomography - ANSWERSPET scan, diagnose cancer cells, inject glucose derivative into patient, observe via body scan (brain bladder and cancer visible) ethanol fermentation converts - ANSWERSglucose to ethanol via 2 steps enzymes: pyruvate decarboxylase turns pyruvate into acetaldehyde alcohol dehydrogenase turns acetaldehyde into ethanol thiamine pyrophosphate - ANSWERSTPP, coenzyme that help catalyze cleavage bonds next to carbonyl carbon. coenzyme derived from thiamine (vit B1) B1 deficiency? Beriberi Gluconeogenesis pathway synthesizes - ANSWERSglucose from simple precursors supplies glucose to body when fasting or during exercise when glucose is low hepatocytes renal cortex small intestines gluconeogenesis is not - ANSWERSglycolysis backwards 3 irreversible steps to bypass enzymes located in cytosol, mitochonria, endolasmic reticulum structure of mitochonria - ANSWERSdouble membrane organelle, outer=free movement of small molecules, inner=no free movement of small molecules, matrix= space insid einner membrane First bypass - ANSWERSconversion of pyruvate to PEP requires cytosolic and mitochondrial enzymes two routes: dictated by starting molecule
irreversible under cellular conditions FBPase-1 is ______ regulated in a_____ - ANSWERSallosterically regulated in a reciprocal manner to PFK fructose 2,6 bisphosphate levels controlled by - ANSWERSPFK2 and FBPase F2,6BP allosterically - ANSWERSstimulates PFK1 in glycolysis inhibits FBPase1 in gluconeogenesis PFK2 and FBPase 2 - ANSWERSone bifunctional enzyme hormone regulation: insulin stimulates PFK2 activity (make more pyruvate and ATP) glucagon stimulates FBPase2 activity (make more glucose) glucagon signal transduction pathway is just like - ANSWERSepinephrine signaling third bypass - ANSWERSconversion of G6P to glucose enzyme: glucose 6 phosphatase hydrolysis of C^-phosphoryl bond irreversible under cellular conditions glucose 6 phosphatase is located - ANSWERSin the lumen of the endoplasmic reticulum G6Pase and hexokinase in different compartments only expressed in hepatocytes, renal cells, and epithelium of small intestines glycolysis and gluconeogenesis also regulated by - ANSWERSgene expression in response to hormone signaling. example: insulin glycolytic genes upregulated (kexokinase, PFK1, pyruvate kinase, PFK2/FBPase2) gluconeogenesis genes downregulated (pyruvate carboxylase, PEP carboxykinase, glucose 6-phosphatase) net equation for gluconeogenesis - ANSWERSconsumption of 6 high energy bonds and 2 NADH 2 Pyruvate + 4ATP + 2GTP + 2NADH + 2H++ 6H2O→ Glucose + 4ADP + 2GDP + 6Pi+ 2NAD+
the pentose phosphate pathway oxidizes - ANSWERSglucose 6 phosphate to pentose phosphate 2 phase of PPP - ANSWERSoxidative and nonoxidative the PPP - ANSWERScytosolic pathway rapidly dividing cells, pentoses used to synthesize nucleic acids and coenzymes cells directly exposed to oxygen, NADPH used t oprotect form oxidative damage lipid synthesizing cells, NADPH used for reductive biosynthesis the PPP generates - ANSWERS60% of NADPH in humans why both NAD and NADP? seperation of catabolic and anabolic pathways NAD+ more abundant than NADH NADPH more abundant thatn NADP+ NADPH protects cells from - ANSWERSoxidative damage via reduction of glutathione disulfide NADPH indirectly helps prevent degradation of H2O2 to hydroxyl free radicals the oxadative phase of PPP produces - ANSWERSphosphates and NADPH 4 steps regulation of PPP - ANSWERS[NADPH]/[NADP+] determines the path of glucose 6 phosphate high NADPH favors glycolysis low NADPH favors PPP, NADP+ allosterically activates G6P dehydrogenase summarize oxidative phase - ANSWERSNADPH and Ribose 5 phosphate are important products, NADPH prevents oxidative damage and provides reducing power for biosynthetic rxns ribose 5 phosphate is a precursor for nucletides and coenzymes. nonoxidative phase - ANSWERSrecycles pentose phosphate to glucose 6 phosphate
enzymes that degrade and sythesize glycogen clusters of beta particles are called - ANSWERSalpha rosettes only hepatocytes during well fed states clusters of 20-40 beta particles ______ reversibly interconverts G6P to G1P - ANSWERSphosphoglucomutase activation of glucose 1 phosphate to UDP-glucose by - ANSWERSUDP pyrophosphorylase rationale for sugar-nucleotide - ANSWERSsequesters glucose 1-phosphate metabolically irreversible important substrate for glycogen synthase (next enzyme in pathway) -contributes delta Gb in next step -nucleotidyl is a good leaving group glycogen synthase extends - ANSWERSnonreducing ends of glycogen glycogen branching enzyme - ANSWERSadds branches to glycogen Aka amylo alpha 1->4 to alpha 1->6 transglycosylase transfers 6-7 glucose molecules glycogen elongating and branching - ANSWERSincreased number of non reducing ends increases soluability of glycogen molecule glycogenolysis - ANSWERSglycogen phosphorylase breaks down alpha 1->4 glucose linkages phosphoroylysis conserves some energy from glycosidic bond in phosphate ester bond coenzyme: pyridoxal phosphate (PLP) PLP acts as a ______ during phosphorolysis - ANSWERSgeneral acid debranching enzyme removes - ANSWERSalpha 1->6 branch points
aka oligo alpha1-6 to alpha 1-4 glucantransferase -2 successive reactions (trisaccharide transfer adn alpha 1-6 glucosidase insulin regulates - ANSWERSglucose and glycogen metabolism in well fed state liver: glygogenesis (synthesis) glycolysis FA synthesis glycogenolysis (breakdown) gluconeogenesis muscle: glucose uptake (GLUT4) glycogenesis glycolysis glycogenolysis glucagon regulates - ANSWERSglucose and glycogen metabolism fasting state liver: glycogenolysis (breakdown) gluconeogenesis FA metabolism glycogenesis glycolysis muscle: no receptor for glucagon hepatocyte glycogen phosphorylation regulated by - ANSWERShormones and allosterism liver glycogen phopsphorylase - ANSWERShormone: glucagon epinephrine, insulin allosteric:glucose phosphorylase b kinase - ANSWERShormine: glucagon, epinephrine, insulin allosteric: Ca2+ phosphorylase a phosphate (PP1) - ANSWERShormone: insulin glucagon epinephrine allosteric: glucose 6 phosphate Glycogen Sythase - ANSWERSregulated by hormones and allosterism both hepatocytes and myocytes
affects muscle symptoms: exersice fatigue, cramps during exercise, muscel weakness andersons disease type 4 - ANSWERSbranching enzyme abnormal glycogen affects liver enlarged liver, failure to thrive, immune response destroys liver von gierke disease type 1a - ANSWERSenzyme: G6Pase increased glycogen storage affects liver and kidney enlarged liver and kidney, hypoglycemia during fasting conversion of pyruvate to acetyl-CoA is - ANSWERSthe link between glycolysis and citric acid cycle enzyme: pyruvate dehydrogenase catalyzed by PHD complex, mitochondrial matrix, irreversible, comprised of 3 enzymes, 5 coenzymes/prosthetic groups 2 regulatory enzymes prosthetic group of E2 - ANSWERSlipoate sulfer containing FA derivative electron and acyl carrier provides flexible linker to move acyl between active sites coenzyme of E2 - ANSWERSCoenzyme A (CoA) activated carrier of acyl groups prosthetic group of E3 - ANSWERSflavin adenine dinucleotide (FAD) FAD bound proteins- falvoproteins riboflavin (B2) redox rxn:
-accepts 2 H atoms 3 redox states (FAD, FADH+, FADH2) structure of pyruvate dehydrogenase complex - ANSWERSpyruvate dehydrogenase around outter ring, E2 middle ring, E3 spots in center of E2 ring pyruvate dehydrogenase comlex, 5 consecutive rxns - ANSWERSsubstrate channeling. 1-rate limiting step, decarbox of pyruvate, covalent bond to TPP 2-hydroxyethyl oxidation to acetate, lipoyl group reduced, form acyl lipoyllysine 3-acyl group transfered to CoA, forming acetyl-CoA via thioester bond 4-regerate oxidized lipoyllysine by reduction of FAD 5-regerate oxidized FAD by reducing NAD+ allosteric and covalent modifications - ANSWERSregulate PDH complex pyruvate dehydrogenase kinase -inhibiting PDH complex when ATP is high pyruvate dehydrogenase phosphatase removes phosphate group Overview of Citric Acid Cycle - ANSWERS8 rxns 2 carbon enter as acetyl-coa 2 carbon leave as co important products: 3NADH 1FADH 1GTP (or ATP) Step 1 of Citric Acid Cycle - ANSWERSAcetyl-CoA + Oxaloacetate --> Citrate Uses citrate synthase enzyme H2O --> CoA citrate synthase catalyzes - ANSWERSa claisen condensation from c-c bond between thioester and ketone citrate synthase undergoes 2 conformational changes during - ANSWERSformation of citrate, induced fit mechanism conformational changes induced by -oxaloacetate binding
reversible, only FADH2 formed, integral membrane protein Step 7 of Citric Acid Cycle - ANSWERSFumarate <--> L-Malate Uses fumarase enzyme
step 1- fatty acyl-coa synthetase -activates FA -costs 2 ATP outer mitochondrial membrane protein irreversible fatty acid cains >12 carbons require - ANSWERScarnitine shuttle to enter mitchondria step 2- fatty acyl-coa transesterified to affty acyl-carnitine committed step of beta oxidation inhibited by malonyl-coa stage 1 beta oxidation - ANSWERSmitochondrial matrix successive removal of 2carbon units forming acetyl coa each round of beta oxidation uses - ANSWERS4 enzymes to remove 2 carbons from FA chain. step 1: acyl-coa dehydrogenase, oxidation of fatty acyl-coa, FADH2 produced step 2: hydration, beta carbon hydroxylated step 3: beta-hydroxyacyl-coa dehydrogenase. (oxidation, form NAD+ and H+, inhibited byhigh NADH levels) step 4: thiolase, cleavage between alpha and beta carbons, fatty acyl-coa now 2 carbons shorter, inhibited by acetyl-coa beta oxidation spiral - ANSWERS4 step sequencec repeats until a 4 carob acyl-coa is cleaved to 2 acetyl-coa complete oxidation of Palmitic acid generates - ANSWERS106 ATP Unsaturated fatty acid - ANSWERS(delta 3 delta 2 enoyl-coa isomerase required for monounsaturated fatty acids) reversible isomerization polyunsaturated fatty acids - ANSWERS(2,4-dienoyl-coa reductase and delta 3 delta 2 enoyl-coa isomerase required)
complex contains: FAD Cytochrome b(heme b) 3 iron sulfer centers cytochromes are iron-heme containing - ANSWERSproteins single e- carriers 3 classes in mitochondria (a, b, c) vary in light absorbing properties Complex 3 (cytochrome BC1) - ANSWERSaka ubiquinone: cytochrome c oxidoreductase accepts e- from comlexes 1 or 2 via coenzyme Q proton pump: 4H+ pumped into intermembrane space per 2e- complex contains: 6 heme groups 2 iorn-sulfur centers cytochrome c is a_____ protein - ANSWERSperipheral membrane protein, shuttles single electron between complexes 3 and 4 intermembrane space carries one e- at a time Complex 4 (cytochrome oxidase) - ANSWERS4e- from cytochrome c and 4H+ fromthe matrix react with molecular oxygen (o2) creating 2 h2o molecules proton pump: 4H+ pumped out of matrix per 4 e- complex contains 2 binuclear centers: Cua and Cub 2 cytochromes(heme): a and a repiratory chain creates - ANSWERSproton gradient proton motive force: chemical potential energy electrical potential energy
multiple steps of the ETC can lead to - ANSWERSformation of reactive oxygen species slowing down e- flux thorough ETC increases e- leakages, ROS production large proton motive force high NADH/NAD+ how does NADH from glycolysis enter ETC - ANSWERSMalate aspartate shuttle (liver kidney heart, NADH e- enter ETC in comlex 1=2.5 ATP per 2e-) glycerol 3-phosphate shuttle (skeletal muscle and brain, enters thoruhg FADH2 = only 1.5 ATP per 2e-) Complex 4 ATP synthase uses flow of protons into the matrix to form - ANSWERSATP F-type ATPase 2 complexes -F1 (peripheral membranes protein-ATP sythesis) -F0 (integral membrane protein-proton transport) F0 facilitates H+ movement - ANSWERSacross membrane a subunit (2 half H+ channels to load and unload H+) c ring (8-15 subunits/ring, species specific) c subunits rotate around circle Asp residue undergoes reversible ionization direction of rotatoin depends on H+ gradient Mechanism of ATP formation - ANSWERSH+ passes though c ring, makes y subunit rotate rotation of y subunit causes confomational changes alphabeta pairs (loose=bind ADP + Pi) (tight=bind ATP - stabalize transition state to form ATP) (open= release ATP) 1 full rotation counter clockwise of y subunit=3ATPproduced how many ATP are produced per NADH or FADH2 - ANSWERSP/O ratio (phosphate/oxygen) or p/2e- ratio