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Biochem Final UWGB Dr Heyrman
Questions & Answers
3 stages of cellular respiration - ANSWERS1. Glycolysis (glusoce, FA, AA oxidized to acetyl group of acetyl-CoA. NAD reduced)
- Krebs Cycle (further oxidize acetyl groups, reduce NAD and FAD)
- Electron Transport Chain (oxidation of NAD, FAD. electron transfer to O2, majority of ATP generated) central molecule of metabolism - ANSWERSglucose GLucose - ANSWERSfuel source, full oxidation to CO2 and H2O. precursor molecule for other cell processes. Glycolysis - ANSWERSbreakdown of 1 glucose into 2 pyruvate molecules glycolysis is a __________ process - ANSWERScytosolic phases of glycolysis - ANSWERS2 phases, preparatory and payoff products of glycolysis - ANSWERSenergy (ATP) reducing power (NAD) pyruvate net equation for glycolysis - ANSWERSGlucose + 2NAD++ 2ADP + 2Pi→ 2 pyruvate + 2 NADH + 2H++ 2 ATP + 2H2O role of phosphorylation in glycolysis - ANSWERSkeep glycolysis metabolites inside cell high energy phosphate compounds used to make ATP contribute to delta G regulate enzyme activity NAD is a - ANSWERSwidely used water soluble electron carrier co-enzyme
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
- OH- 2) H+ --> reversible stereospecific enzyme (trans only) Step 8 of Citric Acid Cycle - ANSWERSL-Malate <--> Oxaloacetate Uses malate dehydrogenase enzyme NAD+ <--> NADH reversible 3rd and final NADH forming step Net Rxn of Citric Acid Cycle - ANSWERSacetyl coa-> coa 2 h2o-> 2 co 3NAD+->3NADH 3H+ FAD->FADH NDP Pi-> NTP Triglycerides - ANSWERSenergy storing lipids monoglyceride - 1 FA esterified to glycerol diglyceride-2FA esterified to glycerol where do fatty acids come from - ANSWERSdiet stored in adipocytes synthesized in liver dietary lipids are absorbed - ANSWERSin the small intestine and delivered to target tissues in chylomicrons chylomicrons are aggregates of - ANSWERStriglycerols, phospholipids, cholesterol, and apolipoproteins apolipoproteins - ANSWERSlipid binding proteins facilitate transport of lipids between organs recognize by cell surface receptors lipolysis - ANSWERSlipid droplets in adipocytes mobalize FA to target tissue in response to hormones FA in cytosol are activated before - ANSWERStransport into the mitochondria
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
