Biochem 5 Flashcards

Question

brief cancer cell overview in metabolism

Answer 1

- cancer cells are growing -> want to make more of themselves - importance of the NADP (oxidizing) step in glycolysis is overshadowed by the branch pathway that is responsible for making NADPH (reducing agent) - use of different cofactors can control whether were in the energy generating direction or biosynthetic direction (energy consumptive)

Answer 2

- a means of regeneration NAD - if you combine glycolysis with homolactic fermentation you can generate ATP at the substrate level without an accumulation of NADH

Answer 3

- energy source for biosynthetic rxns - collection of phosphoanhydride bonds between the gamma and beta and between the beta and alpha linkages - phosphoester bond- involving ANP - *most cells dont change their ATP concentration regardless of how active or sluggish they may be metabolically -> what changes a lot are the levels of ADP and ANP (regulatory agents) - bc ATP may be a goal for degradation but its not a regulatory compound

Answer 4

- nicotinamide adenine dinucleotide - oxidizing agent in glycolysis - redox reagent - mobile 2 e- carrier - carries 2e- in the form of hydride ion: H+ +2e- -> H- - usually involved in oxidation of primary alcohol to carbonyl - R-CH2-OH + NAD+ -> R-CH=O + NADH + H+ - derived from niacin (vitamin B3) - has an adenine ring, ribose, nicotinamide ring* (oxidized and reduced form) - phosphorylated to NADP+ -> changes which enzyme uses which redox reagent - not a high energy intermediate in glycolysis

Answer 5

-preparatory to the substrate level phosphorylations (one involving oxidation and the other involving ketoenol totonermization)

Answer 6

- excellent fuel - yields good amount of energy upon oxidation (-2840 kJ/mol glucose) - can be efficiently stored in the polymeric form - many organisms and tissues can meet their energy needs on glucose only - glucose is a versatile biochemical precursor - many organisms can use glucose to generate: - all the amino acids - membrane lipids - nucleotides in DNA and RNA - cofactors needed for the metabolism

Answer 7

- glucose is used for biosynthesis and energy (degradation) -> these pathways do double duty- know which ways to activate and inactive for different purposes - storage: - can be stored in the polymeric form (starch, glycogen) - used for later energy needs - energy production: - generates energy via oxidation of glucose - short term energy needs - production of NADPH and pentoses: - generates NADPH for use in relieving oxidative stress and synthesizing fatty acids - generates pentose phosphates for use in the DNA/RNA biosynthesis - structural carbohydrate production: - used for generation of alternate carbohydrates used in cell walls of bacteria, fungi, and plants

Answer 8

-used for biosynthetic rxns

Answer 9

-oxidation of glucose

Answer 10

- extracellular matrix and cell wall polysaccharides (synthesis of structural polymers) - glycogen, starch, sucrose (storage) - ribose-5-phosphate (oxidation via pentose phosphate pathway - pyruvate (oxidation via glycolysis)

Answer 11

- way of avoiding excess increase in osmotic pressure in a cell - if we stored glucose as glucose the cytosolic environment would be hypertonic - when we polymerize into glycogen -> its fine - versatile - means we need a way to break down to get glucose

Answer 12

- sequence of enzyme-catalyzed rxns by which glucose is converted into pyruvate - pyruvate can be further aerobically oxidized - pyruvate can be used as a precursor in biosynthesis - some of the free energy is captured by the synthesis of ATP and NADH - important for energy and equally important for biosynthesis (especially neoplastic rapidly dividing cells) - research of glycolysis played a large role in the development of modern biochemistry: - understanding the role of coenzymes - discovery of the pivotal role of ATP - develop of methods for enzyme purification - inspiration for the next generations of biochemists

Answer 13

- phosphorylation of C6 of glucose - hexose rxn -> clever way of trapping glucose inside cells - hexokinase- first priming rxn - kinases- enzymes that transfer Pi from ATP to a substrate - hexokinase also phosphorylates mannose and fructose - glucose + ATP -> glucose-6-phosphate (G6P) + ADP + H+ - stays in the cytosol - its much easier to put the P onto the C6 than to C1 -> makes a phosphoester - harder to put on C1 bc its apart of a hemiacetal - example of a coupled rxn - this rxn is energy consuming -> ATP is the phosphate donor and the energy is used to put the phosphate on C6

Answer 14

- product of step one of glycolysis - there are a lot of phosphatases inside cells - its always a risk making phosphorylated compounds bc a phosphatase can come around and take the phosphate off - the trick to avoid this is to: keep water away - hydrophobic interior of the enzyme helps - ATP and glucose are bound in a deep cleft that excludes water -> eliminates risk of hydrolysis of the phosphate group off - glucose binding causes a large conformational shift, excluding water and bring the 6'-OH close to the ATP - this is not unique to hexokinase (common strat)

Answer 15

- most cells have hexokinase that has a high affinity (low Km) for glucose -> easy for glucose to be saturating the enzyme within the interior of the cell - liver is self-less -> not worried about acquiring glucose for its own needs - in the liver glucokinase is a regulator of blood glucose - the regulator glucose-6-phosphatase undoes the selective protection of the phosphate in the liver (untraps) - glucose-6-phosphatase takes the phosphate off and glucokinase puts the phosphate on -> rate of phosphate transfer to glucose by glucokinase is dependent on the concentration of glucose - phosphorylation of glucose is trapping it in the liver (low blood glucose) and de-phosphorylation is releasing it (high blood glucose) - the Km for glucokinase is close to the normal physiological levels of glucose - hypoglycemia (low blood glucose) -> rate of phosphorylation of glucose decreases - hydrolysis of glucose-6-phosphate by glucose-6-phosphatase rapidly maintains and makes sure that free glucose is released by the liver during hypoglycemia - during hyperglycemia the rate at which glucokinase phosphorylates glucose increases -> lowers the blood glucose levels - hexose is inhibited by the product (G6P) of its rxn where glucoinase isnt

Answer 16

- in the liver we can break it down back to glucose (liver stores glucose as glycogen) - can become acetyl-CoA (2 carbons) -> this is the product of pyruvate (made in glycolysis) - acetyl-CoA is a precursor for fatty acids, phospholipids, cholesterol

Answer 17

- glucose-6-phosphate is converted to fructose 6-phosphate (F6P) - converts C1-OH to a simple hydroxyl (not a hemiacetal) - *now it will be easy to phosphorylate C1 of fructose-6-phosphate - catalyzes reversible isomerization using acid-base catalysis with an enediol intermediate - phosphoglucose isomerase facilitates this conversion - important intermediate: enediol - enediol is a good way to move a single carbonyl group - converts the 6 membered aldose (glucose-6-phosphate) to the 6 member ketose (fructose-6-phosphate) - equilibrium rxn -> no regulation - enediol mechanism

Answer 18

- committed step -> key to regulatory site - second priming rxn - coupled rxn - irreversible in cells - biphosphate: 2 phosphates not linked to one another - fructose-6-phosphate + ATP -> fructose-1,6-biphosphate (FBP) + ADP + H+ - phosphate is now on C1 and C6 - often not at equilibrium - PFK1- consumes ATP

Answer 19

- PFK is regulated - PFK- a dimer, two binding sites, two allosteric type binding sites on each subunit (4) - similar to NWC model of hemoglobin - binding of negative allosteric effectors results in decrease in affinity of PFK for its substrate F6P (fructose-6-phosphate) - PFK is negatively regulated by binding of ATP in the allosteric site (ATP in the normal binding site facilitates phosphorylation of F6P) - K type allosteric enzyme- what changes is not the catalytic constant -> rather the affinity - recall: ATP concentration is relatively constant... - under normal conditions PFK is negatively regulation by the constant high levels of ATP - if there is a lot of metabolic activity some ATP will be converted to ADP and ANP - ANP is a positive allosteric effector for PFK -> bound with greater affinity than ATP - ANP turns the affinity of PFK for F6P up -> F6P is bound with greater affinity when ANP levels rise - if glycolysis is a way of making ATP the cell knows its going to need more ATP when it encounter high levels of ANP (this means cell is using a lot of ATP) -> this allows the cell to make more ATP by binding to F6P and committing to glycolysis

Answer 20

- in the liver fructose is converted by fructokinase to fructose-1-phosphate - fructose-1-phosphate is not a substrate for PFK - it is a substrate for the next enzyme (aldolase) - if fructose-1-phosphate can be cleaved by fructose aldolase -> you carryout glycolysis and bypass PFK in the liver - PFK is the regulatory step in glycolysis - if you feed the liver fructose-1-phosphate it can carry out glycolysis in an unregulated way - the more fructose you eat the more fructose-1-phosphate you make and the more glycolysis -> glyceraldehyde-biphosphate and dihydroxyacetone is a byproduct of this and get reduced and converted to glycerol phosphate which is used to drive the synthesis of fats -> fatty liver

Answer 21

- aldose converts fructose-1,6-biphosphate (FBP) to dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (GAP) - reversible aldol condensation - always in equilibrium - efficient - cleavage rxn - change in numbering in this step! - in the liver aldolase cleaves fructose-1-phosphate (bypasses regulatory step of glycolysis)

Answer 22

- aldolase makes use of a schiff base and an aldol condensation - schiffs base formation

Answer 23

- use enediol mechanism to convert the hydroxyacetone phosphate to glyceraldehyde-3-phosphate (an aldose) - moves a carbonyl from the keto position to the aldol position - glyceraldehyde-3-phosphate and dihydroxyacetone phosphate are both trioses - DHAP is the ketose - G3P is the aldose

Answer 24

- glyceraldehyde-3-phosphate (GAP) is converted to 1,3-biphosphoglycerate (1,3-BPG) via glyceraldehyde-3-phosphate dehydrogenase (GAPDH) - 1,3-biphosphoglycerate is a mixed anhydride -> high energy phosphate - dehydrogenases- involved in oxidation/reduction reactions - couples favorable oxidation to unfavorable phosphorylation through covalent intermediate thioester - dihydroxyacetone phosphate (from last step) can easily be converted to glycerol phosphate -> important for adipocyte where it esterifies with fatty acids to make neutral fats

Answer 25

- covalent intermediate (several) - the enzyme has prepositions sulfhydryl group and NAD+ in the pocket (non-covalently bound) - the substrate binding portrays classic michaelis menten behavior - reaction of the carbonyl of gylceraldehyde-3-phosphate with a thiol on the enzyme -> forms a thiohemiacetal (covalently bound) - thiohemiacetal is oxidized by an NAD+ that is bound to the enzyme - NAD+ is reduced to NADH and thiohemiacetal is oxidized to a thioester (high energy) - NADH is loosely bound - phosphorolysis- inorganic phosphate cleaves the thioester forming a mixed anhydride (high energy) between phosphate and the carboxyl of glycerate acid - this conserves energy of the thioester (high energy intermediate) in acyl-phosphate

Answer 26

- capturing the high energy bond that is in a mixed anhydride by reacting it with ADP - use ADP to cleave the mixed anhydride of 1,3-BPG - mixed anhydride phosphorylates ADP - products are ATP and 3-phosphoglyerate (3PG) - substrate level phosphorylation - 1,3-biphosphoglycerate (1,3-BPG) is converted to 3-phosphoglycerate (3PG) via phosphoglycerate kinase (PGK) - highly reversible when coupled (bc were converting a high energy phosphate (mixed anhydride) to another high energy phosphate)

Answer 27

- resembles hexokinase - hides phosphates inside hydrophobic pocket - this is so the 1 phosphate on 1,3-biphosphoglyceric acid is not immediately hydrolyzed by water - PGK catalyzes a coupled reaction - source of ATP at the substrate level

Answer 28

- mutase- subclass of isomerases, moves functional group from one position to another on substrate - moves the 3-phosphate from the 3PG mixed anhydride to the 2 position on glyceric acid - when its on the 1 position its a mixed anhydride when its on the 2 position its not so impressive in energy - mutase does this by making distinct intermediates -> uses enzyme bound 2,3-BPG equal in concentration to the enzyme itself (catalytic quantities - phosphohistidine is used -> requires an ATP to make this sometimes - substrate binds ->2,3-BPG is made using phosphohistidine which phosphorylates the 2nd position -> free histidine is present -> 2,3-BPG re-phosphorylates the histidine with the phosphate from the 3rd position -> forms 2PG-phosphoenzyme

Answer 29

- cannot work with catalytic (micromolar) quantities of 2,3-DPG -> needs millimolar - Rapoport Luebering shunt - the product of GAPDH is 1,3-BPG - in RBC there is a DPG phosphotase and DPG mutase - DPG mutase- is to take 1,3-DPG and convert it to 2,3-DPG - the enzyme becomes more and more active as the pH goes down - lowering the pH is a call to release O2 to the tissues -> elevate 2,3-DPG -> deoxygenation (negative allosteric effector) - can make as much as needed - 2,3-DPG phosphotase- converts 2,3-DPG to 3-phosphoglycerate -> sacrifices an ATP to make this (recall that PGK can make 3-phosphoglycerate without using ATP) - bypasses the chance to make ATP in order to make substrate level 2,3-DPG - wastes an ATP in a cell that doesnt need a lot of ATP

Answer 30

- people who lack hexokinase enzyme -> make lower levels of all the glycolytic intermediates - includes 1,3-DPG making it harder to make 2,3-DPG -> left shifted O2 affinity curve (high affinity) - people who lack the last enzyme in the glycolytic pathway (pyruvate kinase) -> build up glycolytic intermediates - high levels of 2,3-DPG -> right shift -> low affinity for O2

Answer 31

- 2-phosphoglycerate (2PG) gets dehydrated via the enzyme enolase -> forms phosphoenolpyruvate (PEP) - enolase-metal dependent enzyme; converts low energy to high energy phosphate - enolphosphate (highest energy phosphate) - inhibitor for enolase is fluoride -> fluoride prevents the binding of the metal (Mg) that is needed for the rxn - reversible

Answer 32

- substrate level phosphorylation - capture of the energy in the enolphosphate using ADP - similar to PGK rxn - phosphoenolpyruvate (PEP) is converted to pyruvate and ATP via pyruvate kinase (PK) - largest free energy drop in glycolysis (-61.9kJ/mol) pulls entire pathway forward by mass action - not reversible - first product of rxn between ADP and phosphoenol-pyruvate (PEP) is the enol form of pyruvic acid -> highly reversible; however, it immediately tautomerizes into the keto form - keto enol tautomerization drives the overall rxn and prevents the rxn from reversing (coupled) and permits the production of ATP using high energy from PEP - pyruvate kinase is a ATP source at the substrate level

Answer 33

- 1 ATP made at phosphoglycerate kinase - another ATP made at pyruvate kinase - one NADH made at GAPDH - if we dont use the NADH there will be problems bc we need the NAD+ for the next glycolysis cycle -> no glycolysis

Answer 34

- generation of a high energy phosphate compound incorporates inorganic phosphate -> allows for net production of ATP via glycolysis - first energy yielding step in glycolysis - oxidation of aldehyde with NAD+ gives NADH - active site cysteine forms high energy thioester intermediate - subject to inactivation by oxidative stress - thermodynamically unfavorable/reversible -> coupled to next reaction to pull forward

Answer 35

- substrate level phosphorylation to make ATP - 1,3-biphosphoglycerate is a high energy compound -> can donate the phosphate group to ADP to make ATP - kinases are enzymes that transfer phosphate groups between ATP and various substrates - highly thermodynamically favorable/reversible -> is reversible bc of coupling to GAPDH rxn

Answer 36

- be able to form high energy phosphate compound - mutases catalyze the (apparent) migration of functional groups - one of the active-site histidines is posttransitionally modified to phosphohistidine - phosphohistidine donates its phosphate to 3-phosphoglycerate at the 2-carbon oxygen before retrieving another phosphate from the 3-carbon oxygen - note that the phosphate from the substrate ends up bound to the enzyme at the end of the rxn - thermodynamically unfavorable/reversible -> reactant concentration kept high by PGK to push forward

Answer 37

- generate a high energy phosphate compound - 2-phosphoglycerate is not a good enough phosphate donor to generate ATP - 2 negative charges in 2-PG are fairly close - but loss of phosphate from 2-PG would give a secondary alcohol with no further stabilization - slightly thermodynamically unfavorable/reversible -> product concentraton kept low to pull forward

Answer 38

- substrate level-phosphorylation to make ATP - net production of up to 2 ATP/glucose (1 ATP per GAP) depending on diversion of DHAP to fat synthesis - loss of phosphate from PEP yields an enol that tautomerizes into ketone - tautomerization effectively lowers the concentration of the rxn product -> drives the rxn towards ATP formation - pyruvate kinase requires divalent metals (Mg++ or Mn++) for activity - highly thermodynamic favorable/irreversible -> regulated by ATP, divalent metals, and other metabolites

Answer 39

- key to keeping the glycolytic pathway going - in RBC that have no mitochondria and muscles - take pyruvate and reduce it to lactic acid - regenerate the NAD+ to keep the NADH running for glycolysis - NAD is made for GAPDH - lactate is the product of anaerobic glycolysis - if there is no O2 to do anything with NADH -> convert pyruvate to lactate - generates a build up of organic acids (lactic acid) -> 2nd best source of protons - in yeast it converts pyruvate to ethanol - lactate dehydrogenase- enzyme that carries this out (highly reversible) - lactate dehydrogenase uses NADH to convert pyruvate to lactate and NAD+ - if there is mitochondria it uses the krebs cycle to convert NAD+ to NADH - this step is not regulated

Answer 40

- oxidize pyruvate to acetaldehyde (compound that reduces a hangover by suppressing ethanol) - decarboxylation of a pyruvate (alpha ketoacid) to acetaldehyde - trick pyruvate to think its like beta keto acid (decarboxylates spontaneously) - conversion to pyruvate to acetaldehyde is dependent on a co-factor -> thiamine pyrophosphate (TPP) - the C=N in TPP is identical to the one found in cyanide - reduction of acetaldehyde to ethanol via alcohol dehydrogenase (highly reversible) -> carbonyl is reduced to a hydroxyl - alcohol dehydrogenase uses and converts NADH to NAD+

Answer 41

- benzaldehyde and shake with cyanide -> 2 carbonyls of benzaldehyde react directly and combine in the presence of cyanide -> form benzaline - condensation product - cyanide reacts with one of the carbonyls -> the product is a cyanohydryl - forms a double bond - carbonyl is moved one carbon away -> now you can carry an aldehol condensation with another carbonyl - Thiamine pyrophosphate is the biological form of cyanide that permits the carbonyls to react directly -> product is a decarboxylation of pyruvate to form acetaldehyde

Answer 42

- regeneration of NAD+ in the absence of O2 or mitochondria | - can be incredibly upregulated in the cell by two orders of magnitude-

Answer 43

-if the flux of the glycolytic pathway can be increased by 2 orders of magnitude -> doesnt matter how many ATP you can get per glucose (as long you have a good amount)

Answer 44

- can spontaneously decarboxylate - trick the pyruvate in ethanol fermentation (yeast) to act like a beta keto acid (pyruvate is an alpha keto acid in this case)

Answer 45

- biological form of cyanide | - permit us to convert a carbonyl to a cyanohydrin -> permits carrying out aldol rxns directly on what was the carbonyl

Answer 46

- glucose -> 2 lactic acid, G=-196kJ/mol - glucose -> 2 CO2 + 2 ethanol, G=-235kJ/mol - 2 ADP +2 Pi -> 2 ATP, G=61kJ/mol - lactic acid fermentation- 31% efficient - ethanol fermentation- 26% efficient - extra energy ensures pathway is irreversible - oxidative phosphorylation- about 38 ATP/glucose - pasteur effect- yeast consumes more sugar when growing anaerobically - fermentation can produce ATP nearly 100 times faster than oxidative phosphorylation

Answer 47

- consists of 3 stages: in which NADPH is produced, pentoses undergo isomerization, and glycolytic intermediates are recovered - provides NADPH for reductive biosynthesis and ribose-5-phosphate for nucleotide biosynthesis in the quantities that the cell requires - a source of pentoses which is required for RNA's and DNA (riboses) - degradative and oxidative -> gives off a CO2 per carbon - in red cells and cancer cells (fast dividing cells) about 60% of cells go through the pentose phosphate pathway -> very important for some cells - no ATP used or made - neutralizing the potential damage caused by free radical formed in the cells

Answer 48

- glycolytic pathway is not always the best pathway in cancer cells - some cancer cells have a mutated form of pyruvate kinase -> M2 isoform - cancer cells under the influence of tyrosine kinases -> the M2 isoform is phosphorylated and slows down A LOT - M2 pyruvate kinase variant has been phosphorylated -> glycolytic intermediates back up - keeps going bc it has a lot of capacity to reverse the entire glycolytic pathway from phosphoenolpyruvate to glucose -> glucose-6-phosphate accumulates - if pyruvate kinases shut down the pentose pathway takes over - converts multiple molecules of glucose-6-phosphate to pentoses and eventually glyceraldehyde-3-phosphate - *if we convert to glyceraldehyde-3-phosphate it means that we bypasses a portion of glycolysis (step 4) including the regulating step

Answer 49

- conversion of glucose-6-phosphate to ribose-5-phosphate via 2 enzymes: glucose-6-phosphate dehydrogenase and 6-phosphogluconate dehydrogenase - important enzymes bc they convert NADP to NADPH - NADPH- essential for many biosynthetic rxns - oxidation until you get 6-phosphoglucanate -> beta-keto acid intermediate -> spontaneously decarboxylation -> gives off 1 CO2 and generates a pentose (ribulose-5-phosphate) - CO2 gets exhaled and ribose is used to build RNA and DNA - ribulose-5-phosphate (Ru5P)- keto pentose -> used a precursor to 2 products: ribose-5-phoshate and xyulose-5-phosphate (Xu5P)

Answer 50

- ribulose-5-phosphate (Ru5P) is produced and used as a precursor for 2 products: ribose-5-phosphate and xylulose-5-phosophate (Xu5P) - Xu5P has no metabolic value - conversion of ribulose to ribose via ribulose-5-phosphate isomerase (similar to enzyme that converts glucose to fructose) -> makes carbonyl from beta to alpha with an enediol intermediate - ribose makes DNA and RNA but also

Answer 51

- takes a piece of xylulose-5-phosphate (top 2 carbons) and puts them on ribose - ribose is an aldo-pentose - C1 of Xu5P is a hydroxyl - C2 of Xu5P is a carbonyl - according to aldol condensation you cant put 2 carbonyls on each other -> so we react this with thiamine pyrophosphate (TPP) - TPP converts the carbonyl of Xu5P to a hydroxyl group -> converts the 2 carbon piece from Xu5P to a cyanohydrin - TPP facilitates the direct formation of a bond between the carbonyl carbons of 2 pentoses - creates a 7 carbon sugar -> sedoheptulose-7-phosphate (S7P) and 3 carbon sugar is left (from Xu5P): glyceraldehyde-3-phosphate (GAP) - GAP is put into glycolysis where it generates high energy phosphate like 1,3-biphosphateglyceric acid - *pentose pathway can directly feed the synthesis of ATP (this is why rbc's and cancer cells like this)

Answer 52

- products of the pentose pathway generate ATP through feeding to glycolysis - shunt - carrying out the synthesis of sedoheptulose-7-phosphate -> generates a glyceraldehyde-3-phosphate (GAP) - glyceraldehyde-3-phosphate is used to make ATP at the substrate level in glycolysis - GAP makes 1,3-biphsopahteglyceric acid which is a high energy phosphate molecule - fructose-6-phosphate is also made and fed to glycolysis

Answer 53

- use a transaldolase enzyme- takes the top 3 carbons from sedoheptulose-7-phosphate and react them with glyceraldehyde-3-phosphate (there is a pool) - react the alpha carbon to the carbonyl of sedoheptulose-7-phosphate with the carbonyl of GAP - aldolcondensation - forms a 4 carbon sugar -> arythrose-4-phosphate and fructose-6-phosphate - fructose-6-phosphate can also be fed through the glycolytic pathway makes ATP! - transaldolase forms a covalent intermediate (schiffs base) -> carbonyl carbon from the substrate reacts with lysine of the enzyme -> froms a schiffs base covalent intermediate - schiffs base carries out the aldol condensation in reverse - final product: fructose-6-phospahte derived by the condensation of GAP with a 3 carbon sugar and GAP itself - transketolase catalyzes a carbonyl carbon-to-carbonyl carbon condensation wheras transaldolase catalyzes a condensation in which the carbonyl carbons are separated by a non-carbonyl carbon

Answer 54

- glutathione (GSH) aka gamma-L-glutamyl-L-cysteinylglycine - GSH- reduced - GSSG- oxidized - has a sulfhydryl group on it - very reactive - primaquine is a drug used for malaria therapy -> makes oxygen species - malaria parasite is oxidizing everything -> damage - oxygen species are free radical and can damage cells - use glutathione reductase to control these oxygen species - glutathione (GSSG)- oxidized disulfide - *NADPH will reduce GSSG to from two free thiols - reactive oxygen species catalyzes the oxidation of reduced glutathione to oxidized glutathione - use the NADPH to re-reduce oxidized glutathione to have increased supply of the free thiol - if you dont have an supply of the reduced free thiol your RBC's can get infected with a malarial parasite -> generates many free radicals -> cells lyse -> G6PD deficiency - bc 60% of RBC glucose is taken care of by pentose pathway there is a lot of NADPH to scavenge the damaging molecules that are produced from malaria -> limits RBC lysis (hemolytic anemia)

Answer 55

a shunt | -used when you need a lot of ribose (when cells are dividing fast) or NADPH (generating reactive oxygen species)

Answer 56

- most cells can carry out up to the point of glucose-6-phosphate - liver is able to take pyruvate and convert all the way to free glucose in the blood - during interfeeding (when youre not eating) there is still a need for glucose - liver becomes important for supplying that glucose

Answer 57

- can store glucose in the form of glycogen -> convenient to generate free glucose - unique in its ability to convert glucose-6-phosphate to glucose - we take pyruvate and all the metabolites that can be converted to pyruvate and use them to make glucose in liver -> supplies other peripheral organs

Answer 58

- glycolytic pathway is not easily reversed on its own - pyruvate kinase, phospho-fructokinase, and hexokinase- have large -ΔG and cannot be easily reversed - we need another pathway (which most cells have the enzymes for up to glucose-6-phosphate) -> only the liver can take pyruvate and convert it all the way back to glucose (reverse) - irreversible rxn of glycolysis must be bypasses in gluconeogenesis - GAPDH- phosphoglycerate kinase -> reversible

Answer 59

- opposing pathways that are both thermodynamically favorable - both are quasi-irreversible - operate in opposite direction - end product of one is the starting compound of the other - reversible rxns are used by both pathways - irreversible rxn of glycolysis must be bypasses in gluconeogenesis - bypass rxns themselves are largely irreversible - no ATP generated during gluconeogenesis (highly consumptive rxn) - different enzymes in the different pathways - differentially regulated to prevent a futile cycle (would be extremely consumptive of ATP and wouldnt give desired products)

Answer 60

- these steps are quasi-irreversible - requires 2 energy consuming steps - 1st step- pyruvate carboxylase converts pyruvate to oxaloacetate - carboxylation using a biotin cofactor - requires transport into the mitochondria where the enzyme resides - the product (oxaloacetate) can make its way back to the cytosol after (not directly but after conversion to malate) - uses ATP and CO2 for the carboxylation - oxaloacetate can be used for krebs or converted to PEP or malate to be moved to cytosol and used for gluconeogenesis - 2nd step- phosphoenolpyruvate carboxykinase (PEPCK) converts oxaloacetate to phosphoenolpyruvate (PEP) - phosphorylation from GTP to carbonyl of oxaloacetate (enol form) and decarboxylation -> PEP - CO2 that was put on during carboxylation in step 1 is taken off with a high energy phosphate from GTP - occur in mitochondria or cytosol depending on organism - during this conversion the same carbon is added and immediately removed from the structure

Answer 61

- 5 membered ring - has a long valerate side chain (carboxylic acid) that is covalently attached to pyruvate carboxylase - lys forms an amide bond to biotin - biotin ring (2 rings) can bounce between to sites on the enzyme (pyruvate carboxylase) - 1 site to react with CO2 -> forms carboxy biotin - 2nd site uses carboxy biotin to carboxylate pyruvate -> forms oxaloacetate - long valerate side chain allows it to move between sites

Answer 62

- a beta keto acid that can spontaneously decarboxylate (also and alpha) - PEPCK takes advantage of this to phosphorylate the transient intermediate enol form of pyruvate that is left after decarboxylation

Answer 63

- inner mitochondrial membrane is selectively permeable: malate (formed from oxaloacetate), PEP and pyruvate are permeable, while oxaloacetate cannot escape - oxaloacetate can be utilized in the citric acid cycle (krebs) if needed - oxaloacetate can be converted to PEP or malate to allow transport to cytosol for gluconeogenesis

Answer 64

- catalyze reverse rxn of opposing step in glycolysis - are virtually irreversible themselves (Based on ΔG) - reversal of phosphofructokinase by fructose-1,6-bisphosphotase: - fructose 1,6-biphosphate forms -> fructose-6-phosphate (via fructose 1,6-bisphosphotase) - reverses PFK1 - catalyzed by fructose biphosphatease-1 - coordinately/oppositely regulated with PFK - cleaves a sugar phosphate with water - DOES NOT generate ATP - releases inorganic phosphate - Reversing hexokinase rxn: - glucose-6-phosphate -> glucose - via glucose-6-phosphatase - segregated in the ER - cleaves a sugar phosphate ester with water - generates inorganic phosphate - DOES NOT generate ATP

Answer 65

- 2 pyruvate + 4 ATP + 2GTP +2NADH + 2H+ + 4H2O -> glucose + 4ADP + 2GDP + 6Pi +2 NAD+ - costs 4 ATP, 2 GTP, and 2 NADH - yield of ATP from glycolysis is not matched by the consumption of ATP in gluconeogenesis (it uses more than it can generate) - if we lose ATP why do we do this? -> we mobilize glucose to supply tissues like the brain which are vital - physiologically necessary- brain, nervous system, and RBC generate ATP ONLY from glucose which they cannot make themselves - allows generation of glucose when glycogen stores are depleted - during starvation - during vigorous exercise - can generate glucose from most amino acids, but not fatty acids

Answer 66

- PFK1 and hexokinase - fructose-1,6-bisphosphotase and glucose-6-phosphotase do not generate ATP -> release inorganic phosphotase - pyruvate kinase - in gluconeogenesis: pyruvate carboxylase + PEPCK

Answer 67

- pyruvate conversion to PEP is associated with formation of ATP from ADP -> energetically favorable rxn bc the enol form of pyruvate is so disfavored over the keto form - reversal of this rxn requires the expenditure or 2 nucleoside triphosphates to overcome the thermodynamic challenge - reversal requires 2 enzymes, 2 different high energy phosphate, and an essential cofactor (biotin) - an enzyme that synthesizes an active form of CO2 in an ATP-dependent step can also use that activated CO2 to convert pyruvate to oxaloacetate, and a second enzyme that can convert oxaloacetate to phosphoenolpyruvate in a GTP-dependent step

Answer 68

- when biotin gets carboxylated in site 1 -> forms carboxy biotin - valeric acid is covalently linked to the pyruvate carboxylase enzyme

Answer 69

- pyruvate carboxylase converts pyruvate to oxaloacetate - carboxylation using a biotin cofactor - requires transport into the mitochondria where the enzyme resides - the product (oxaloacetate) can make its way back to the cytosol after (not directly but after conversion to malate) - uses ATP and CO2 for the carboxylation - oxaloacetate can be used for krebs or converted to PEP or malate to be moved to cytosol and used for gluconeogenesis - 1. ATP and biocarbonate convert pyruvate to carboxyphosphate at site 1 - ATP is used to make an activated form of CO2 -> carboxyphosphate - 2. carboxyphosphate is used to carboxylate biotin -> forms carboxybiotin (site 1) - 3. pyruvate reacts with carboxy biotin -> forms the keto form of pyruvic acid - 4. pyruvate donates a proton to the biotinyl group -> forms enol form (pyruvate enolate) -> biotin is stabilizing the enol form - 5. nucleophilic attack by enolate on CO2 -> forms oxaloacetate (dicarboxylic acid)

Answer 70

-irreversible

Answer 71

- go glycolysis if AMP is high and ATP is low - go gluconeogenesis if AMP is low - K type- increases the affinity of the substrate for the enzyme - affinity for the enzyme for fructose-6-phosphate is under regulation by positive and negative allosteric effectors - AMP is a positive allosteric effector for PFK - ATP is a negative allosteric effector of PFK - alter the affinity of the enzyme for F6P - ADP is a positive allosteric effector but not bound as strong as AMP - citric acid is a negative allosteric effector of PFK1 - AMP potent allosteric activator of PFK1 is a negative allosteric effector for fructose-biphosphotase -> enzyme that takes the phosphate off is inhibited while the enzyme that puts the phosphate on is activated - classic positive and negative allosteric effectors that regulate the PFK/F-1,6-bPase step in glycolysis and gluconeogenesis - regulatory allosteric effector, F-2,6-biP, has a prominent role in the liver

Answer 72

- most potent of the allosteric effectors of PFK1 and FBPase especially in the liver - beta-D-fructose-2,6-bisphosphate (F2,6P) - NOT a glycolytic intermediate, only a regulator - produced specifically to regulate glycolysis and gluconeogenesis - activates phosphofructokinase (glycolysis) - inhibits fructose-1,6-bisphosphate (gluconeogenesis)

Answer 73

- k-type allosteric effecotr - potent and positive allosteric effector for PFK1 - increases the affinity of PFK1 for its substrate F6P -> left shift - potent negative allosteric effector for FBPase (fructose-1,6-bisphosphotase) - fructose-6-phosphate is bound with lower affinity in the presence of F2,6P -> right shift

Answer 74

- produced from fructose-6-phosphate using another phosphofructokinase-2 (in liver) - we break it back down to fructose-6-phosphate with a fructose bisphosphotase-2 (FBPase-2) - 2 activities in a single bifunctional enzyme complex - regulated by a different system than the allosteric effector mechanism - this mechanism is turned on by dephosphorylation - phosphotase activity that removes the 2-phosphate and converts it back to fructose-6-phosphate is activated by phosphorylation - kinase dependent phosphorylation and phosphotase dependent dephosphorylation is important for regulation in liver

Answer 75

- in the presence of a kinase produced when the liver is driven to carry out gluconeogenesis -> PFK2 and FBPase-2 gets phosphorylated - PFK2 is inactivated by phosphorylation - FBPase-2 is activated by phosphorylation -> results in removal of fructose-2,6-bisphosphate from the cytosol of the liver -> this removes the activation of PFK1 and activates fructose-1,6-bisphosphotase - active fructose-1,6-bisphosphatase and inhibited PFK1 -> glycolysis is inhibited and gluconeogenesis is stimulated - insulin activates a phospho-protein phosphotase -> results in removal of the phosphate form the bifunctional enzyme complex -> PFK2 is active -> PFK1 can be activated bc fructose-2,6-bisphosphate can be made - PFK1 results in stimulation of glycolysis - gluconeogenesis (associated with inhibition of PFK1 and activation of fructose-1,6-bisphosphotase) is activated when there is very little fructose-2,6-bisphosphate around - phosphorylation of the bifunctional enzyme activates gluconeogenesis and inhibits glycolysis - deactivation of the bifunctional enzyme allows for the synthesis of fructose-2,6-bisphosphate and inhibits gluconeogenesis

Answer 76

- hormone that stimulates the release of blood glucose - activates gluconeogenesis - we want to get glucose in the blood under these conditions - when glucagon is low glycolysis is inhibited and gluconeogenesis is stimulated

Answer 77

- produced after you eat - we dont want to make more glucose in the liver - we like to store glucose and use glucose by organs like brain (requires glycolytic pathway) - under insulin stimulation glycolysis is increased - gluconeogenesis is inhibited

Answer 78

- low blood glucose stimulates the release of - > increase glucagon secretion -> increases cAMP -> increases enzyme phosphorylation -> activates FBPase-2 and inactivates (lowers levels) PFK-2 -> decreases F2,6P -> inhibits PFK-1 and activates FBPase -> increases gluconeogenesis - supplies glucose back to blood

Answer 79

- reverse hexokinase (first step) glycolysis rxn -> irreversible - a lot of glucose-6-phosphatase in the liver (converts glucose-6-phosphate to glucose) - glucose-6-phosphate is made in gluconeogenesis in lots of cells -> but in most cells it cant be hydrolyzed (glucose-6-phosphate is used only by the cell that made it) - ex. muscles cells use glucose-6-phosphate and store it as glycogen - liver can hydrolyze glucose-6-phosphate in the ER of the hepatocyte - glucose-6-phosphate enters the ER from the cytosol via the G6P transporter (T1) - G6P is dephosphorylated by glucose-6-phosphatase - glucose then leaves the hepatocyte through transporters (T2 and T3) and passes through the plasma membrane (via glucose transporter (GLUT2) and enters the blood - use of concentration gradients for glucose and glucose-6-phosphate to control flux out of liver - deficiency of this enzyme (glucose-6-phosphatase) results in low blood glucose (even when liver has stored a lot of glycogen) - people without glucose-6-phosphatase have no glucose during interfeeding (between meals) -> brain suffers - there is also a build up of glucose-6-phosphate -> stimulates the formation of glycogen -> glycogen storage disease

Answer 80

- epinephrine (muscle) - glucagon (liver) - catalyze the breakdown of molecules -> glycogen and glycolytic pathway - inhibit glycogen synthesis by inhibiting the conversion of inactive glycogen synthase to active

Answer 81

- insulin - tends to increase the synthesis of things -> glycogen - activates the dephosphorylation of glycogen synthase -> activates

Answer 82

- large molecules - glucose polymer - branched -> offers multiple points of degradation by cleavage of glucose units from each nonreducing end - mostly glucose-1,4 linkages - 4 hydroxyl is linked to the 1 hydroxyl - there are some 1,6 linkages - provides a way to store large amounts of glucose in the liver - prevents high concentrations of glucose -> high osmotic pressure - when glycogen is broken down to form glucose-1-phosphate and then glucose-6-phosphate and then finally glucose -> this glucose is exported out of liver into blood - there is a single reducing end and a lot of non-reducing ends

Answer 83

- requires 2 enzymes: phosphorylase and debranching enzyme - phosphorylase cleaves 1-4 linkages (glycosidic bonds) from nonreducing ends by phosphorolysis - branching enzyme- takes care of the 1,6 branch points - phosphorylase can mobilize glucose from these polymers efficiently by attacking multiple nonreducing ends at the same time

Answer 84

- classic kinase (phosphorylation) cascade ex - amplify mechanisms - important in regulation of pathways and cell signaling - phosphorylating enzymes- kinases - phosphatases can removes phosphates -> phosphoprotein phosphatase-1 - reversible - phosphorylase uses inorganic phosphate while the kinases use high energy phosphate (ATP) - at the top of the cascade -> protein kinase A -> activated by nucleoside phosphate -> doesnt phosphorylate it just regulates -> 3-5 cyclic AMP - protein kinase A phosphorylates phosphorylase kinase -> becomes more active - phosphorylase kinase targets/phosphorylates the enzyme glycogen phosphorylase a -> active (the less active form (unphosphorylated) is called glycogen phosphorylase b)

Answer 85

- phosphorylation is catalyzed by protein kinases - dephosphorylation is catalyzed by protein phosphatases or can be spontaneous -> less specific in targeting - typically, proteins are phosphorylated on the hydroxyl groups of Ser and Thr or Tyr

Answer 86

- phosphoprotein phosphatase is attached to glycogen via the Gm subunit -> less active form - while phosphoprotein phosphatase-1 is linked to glycogen via the Gm subunit -> if the Gm subunit is phosphorylated -> more active form -> decreased phosphorylation -> increased glycogen synthesis - further phosphorylation of the Gm subunit (2 phosphates) will cause phosphoprotein phosphatase-1 to dissociate -> inactive form -> increased phosphorylation -> increased glycogen breakdown - insulin regulates by stimulating a protein kinase -> phosphorylates the Gm subunit -> active form - epinephrine regulates by stimulating protein kinase a (PKA) -> inactive form

Answer 87

- puts phosphates on - puts an inorganic phosphate on glycogen to cleave glycogen -> releases glucose-1-phosphate - phosphorylase has a cofactor -> pyridoxal-5'-phosphate (PLP) - PLP stabilizes and activates inorganic phosphate to cleave glycogen (does NOT donate its own phosphate or directly participate in chemical mechanism) - PLP is a vitamin cofactor that plays a major role in amino acid metabolism as well

Answer 88

- with assistance of PLP inorganic phosphate can cleave glycogen at a nonreducing end (1,4 linkage) -> Releases the terminal glucose as an oxonium ion intermediate (transition state) - inorganic phosphate that cleaved will now react with oxonium ion (half chair) -> produces glucose-1-phosphate - glycogen that was attacked can be released -> then rebinding - continues until phosphorylase encounters a glucose residue that is 3-4 residues removed from a 1-6 branch -> at this point phosphorylase falls off the branch and cant attack -> this stud branch is called a limit branch - debranching enzymes takes the limit branch (except for the last glucose that is attached to the main chain by 1,6 linkage) and transfers it to the end of the main chain -> elongates - now phosphorylase can attack the main chain ag until it reaches a limit branch point - the last glucose that the debranching enzyme didnt touch is removed by simple hydrolysis

Answer 89

- glucogon/epinephrine signaling pathway - starts phosphorylation cascade mediated by cAMP activation of protein kinase a (PKA) - protein kinase a is activated by cyclic AMP - cyclic AMP is generated by epinephrine (muscle) and glucagon (liver) via the enzyme adenylyl cyclase - adenylyl cyclase requires a g-protein coupled receptor - activates glycogen phosphorylase through action of phosphorylase kinase (PK) - requires phosphorylation of phosphorylase kinase by protein kinase a - glycogen phosphorylase cleaves glucose residues off glycogen, generating glucose-1-phosphate - removal of phosphates from active phosphorylase a is catalyzed by phosphoprotein phosphatase (PP1 -> activated by kinase cascade involving insulin) - insulin dephosphorylates phosphorylase through phosphoprotein phosphatase - epinephrine and glucagon phosphorylate phosphorylase via protein kinase a and phosphorylase kinase

Answer 90

- glucagon and epinephrine activate adenylyl cyclase which produces cAMP (g protein coupled receptors) - cAMP binds to protein kinase a (PKA) -> activates by causing dissociation of regulatory subunit - PKA phosphorylates phosphorylase kinase -> activates - phosphorylase kinase converts the less active glycogen phosphorylase b to glycogen phosphorylase a (active) - activates glycogenolysis - glycogen phosphorylase a degrades glycogen -> releases glucose-1-phosphate

Answer 91

- phosphoglucomutase phosphorylates serine - phosphoserine is used to make an enzyme bound diphospho-intermediate with enzyme bound glucose-1,6-bisphosphate - present in enzyme level concentrations (less than substrate level) - each intermediate is used to convert glucose-1-phosphate to glucose-6-phosphate with rephosphorylation of the serine - has inorganic phosphate attached to a serine in the enzyme - phosphoglucomutase has similar function/mechanism to phosphoglycerate mutase (uses histidine)

Answer 92

- same process of glucose-6-phospate that is made from gluconeogenesis - G6P enters ER from cytosol via G6P transporters (T1) - glucose-6-phosphatase dephosphorylates G6P - glucose and phosphate exit via glucose (T2) and phosphate transporters (T3) - from the cytosol to the blood glucose is transported via GLUT2 - lack of glucose-6-phosphatase -> low blood glucose and build up of G6P

Answer 93

- conversion of glucose-6-phosphate to glycogen - key player- involves UDP glucose (activated form) -> has a phosphoanhydride linkage (high energy) - glycogen is made from a glucose that is attached to a protein (glycogenin) - there are 7 glucoses that are then added to the glycogenin until the protein has an octasaccharide unit - octasaccharide tail is used as a primer to form more glucose in the form of UDP glucose to synthesize glycogen using the enzyme glycogen synthase - glycosylated by glycogen synthase and UDP glucose -> adds hexose oxonium ions by their reducing ends to grow the glycogen chain - does NOT occur with breakdown simultaneously and at high rates

Answer 94

- use of G6P to make glucose-1-phospahte via phosphoglucomutase (highly reversible and low G) -> rapid equilibrium - activation of glucose-1-phopshate to make UDP glucose - use of UDP glucose to polymerize glucose moiety's on glycogenin (already had 8 glucose on it) -> catalyzed by glycogen synthase - branches on glycogen that have to be introduced in order to be an efficient source of free glucose when its broken down - degradation made us a phosphorylase and inorganic phosphate - synthesis and degradation paths are different

Answer 95

- converting a high energy phosphate (UTP- has many high energy phosphoanhydride linkages) to another high energy phosphate (UDP-glucose - glucose-1-phopshate is the substrate - UMP moiety of UTP is transferred to glucose-1-phosphate to make UDP glucose (UDPG) - rxn has small delta G -> reversible - inorganic pyrophosphate is released by the enzy - me (UDPG pyrophosphorylase) which makes UDPG - inorganic pyrophosphatase has a very high negative delta G -> hydrolyzes pyrophosphate to inorganic monophosphate - this highly negative delta G rxn coupled to the relatively neutral equilibrium pyrophosphate rxn -> drives the synthesis of UDPG in one direction - inorganic pyrophosphate efficiently destroys one of the products of the synthetic rxn in order to drive synthesis UDPG in the direction of the product

Answer 96

- involves making use of the UDP glucose high energy phosphoanhydride to attack the nonreducing end of glycogen - nonreducing end of glycogen is attacked by cleaving UDP glucose and releasing UDP - the sugar nucleoside on UDP glucose is released as an oxonium ion - oxonium ion can attack the terminal glucose of glycogen to create a 1,4-linkage - glycogen synthase releases UDP from UDP glucose - the reactive form of the terminal sugar -> the oxonium ion (half chair) -> attacks the terminal sugar on glycogen -> forms a new 1,4-linkage - glycogen synthase grows the glycogen chain one glucose at a time on the nonreducing end by releasing UDP

Answer 97

-growing glycogen chains are subject to branching enzyme rxns -bc the chain is coming off a preexisting branch point it is subject to attack by the branching enzyme -> it is transferred to the main chain to create a new branch point -1,4-linkage on the growing branch point is transferred to the main chain to create a new branch point -> 1,6-linkage -

Answer 98

- control of glycogen synthesis - increases glucose import (uptake) into muscle - glucose-6-phosphate especially in muscle - stimulates the activity of muscle hexokinase - activates glycogen synthase - increased hexokinase activity enables activation of glucose - glycogen synthase makes glycogen for energy storage - in muscles the glycogen synthesized is made/stored solely for that owns muscle cells use -> take care of themselves but also depend on liver when they run out of glycogen - in the liver the glycogen is released into the blood in the form of free glucose to feed other organs like the brain - insulin can activate a pathway for removal of phosphates that have been put on proteins activated by glucagon

Answer 99

- insulin facilitates uptake of glucose - glucose transporters are stimulated by insulin - traps glucose via the hexose rxn -> phosphorylates -> glucose-6-phosphate - activates glycogen synthase

Answer 100

- 2 forms: phosphorylated glycogen synthase b (inactive) and dephosphorylated glycogen synthase a (active form) - active form is subject to inactivation by a kinase -> glycogen synthase kinase (GSK3) - GSK3 is inhibited by insulin - protein phosphatase-1 (PP1) can attack glycogen synthase b (inactive) and remove the phosphates on the serines -> releases them as inorganic phosphates - insulin, glucose-6-phosphate, and glucose activate PP1 - phosphorylase kinase can phosphorylate PP1 -> activates synthesis of glycogen when we have also activated the breakdown of glycogen - lacking the glucose-6-phosphatase enzyme causes accumulation of glucose-6-phosphate -> activates glycogen synthase -> accumulation of glycogen -> peripheral organs will be lacking glucose

Answer 101

- insulin stimulated - PKB stimulated - PP1 stimulated - hexokinase stimulated - decrease in GSK-3 - glycogen phosphorylation is decreased - high glycogen synthesis - increase glycolysis (in muscle) - decrease glycogen breakdown

Answer 102

- high glucagon - high cAMP - high PKA - high phosphorylase kinase - low glycogen synthase - low PFK-1 - low F26BP - high FBPase - low PFK-2 - low pyruvate kinase L - low glycolysis (in muscle) - low glycogen synthesis - high glycogen breakdown

Answer 103

- MUSCLE: - uses its own glycogen and breaks it down to glucose-6-phosphate -> goes to glycolysis -> makes pyruvate - glycolysis and glycogenolysis is stimulated by epinephrine in muscle - IN LIVER: - (also glucagon hormone) - glycogen is broken down to glucose-6-phosphate - pyruvate is converted to glucose-6-phosphate via gluconeogenesis path - glycolysis is inhibited (regulation by fructose-2,6-bisphosphate - glucose-6-phosphate is primarily released into the blood as free glucose

Answer 104

- activates the degradative phosphorylase path - inhibits the glycogen synthase path - dephosphorylation activates the synthase path and inhibits the phosphorylase path - regulates the metabolism of glycogen

Answer 105

-gluconeogenesis or glycogenolysis

Answer 106

- conversion of pyruvate and all glycolytic intermediates (not acetyl CoA) can be converted to glucose - requires bypass of pyruvate kinase (with carboxylase and PEPCK), PFK (with F1,6diPase), and HK (with G6Pase) - all these bypass rxns are highly regulated - PFK/F1,6diPase cycle is regulated by F2,6diP and the HK/G6Pase cycle is regulated, not at the levels of enzyme activity but by liver and kidney specific expression of G6P

Answer 107

- breakdown of glycogen by phosphorylase and conversion of G1P to G6P - requires active (phosphorylated) phosphorylase, activated (phosphorylated) phosphorylase kinase, and cAMP-dependent protein kinase A, and debranching enzyme

Answer 108

-bridges the rxns in the cytosol involving glycolysis and gluconeogensis to the rxns in the mitochondria (krebs and ETC)

Answer 109

- occupies a central role in metabolism - 2 molecules of pyruvate contain 95% of potential energy is 1 molecules of glucose - generated by the glycolytic path - depleted by the gluconeogenic path - generated by breakdown of some amino acids - breakdown of neutral fats (triacylglycerols/tryiglycerides) -> fatty acids cannot be cannot be converted to pyruvate easily - glycerol can easily be converted to dihydroxyacetone phosphate (precursor for pyruvate) - various fates of pyruvate in cytosol- converted back to glucose-6-phosphate and then back to glucose in the gluconeogenesis path - in the mitochondrial inner membrane pyruvate pyruvate dehydrogenase (enzyme complex) converts pyruvate to acetyl-CoA -> feeds mitochondria with its unique substrate - acetyl-CoA is the effectively only converted to one product -> CO2 - pyruvate dehydrogenase produces the sole substrate for the krebs cycle

Answer 110

- pyruvate dehydrogenase produces the sole substrate for the krebs cycle -> acetyl-CoA - oxidative decarboxylation - takes a 3 carbon substrate pyruvate and converts it to a 2 carbon product (acetyl) - this rxn is irreversible- ΔG = -33.4 kJ/mol - cannot go back to glucose from acetyl-CoA - 3 enzymes with 5 cofactors - complex speeds overall rate of rxn bc products are not allowed to diffuse away from enzyme

Answer 111

- triglycerides - fatty acids of triglycerides can be converted to acetyl-CoA but cant be converted to pyruvate - cannot make carbohydrates from fats!

Answer 112

- one true substrate- acetyl-CoA | - one product- CO2

Answer 113

- can enter in 2 different ways - pyruvate can be converted by pyruvate dehydrogenase to acetyl-CoA - pyruvate can also be converted to oxaloacetate in the first step of the gluconeogenesis path -> pyruvate carboxylase - pyruvate is carboxylated - regulation so that the levels of acetyl-CoA and oxaloacetate are matched upon entry

Answer 114

- main substrate for the krebs cycle - its not only a product of fatty acid breakdown -> it is also the initial substrate for fatty acid synthesis - these rxns are independent of the rxns involving the various carbohydrates

Answer 115

- 3 enzymes within complex and 5 cofactors: - E1- pyruvate dehydrogenase/decarboxylase -> cofactor thiamine pyrophosphate (TPP) for decarboxylase activity and lipoamide (lipoic acid) for dehydrogenase activity - lipoamide is covalently attached to E2 but stuck into E1 - E2- dihydrolipoyl transacetylase -> cofactors: lipoamide and CoA - CoA- receives the product of E1 - E2- transfers the acetyl group from E1 lipoamide to CoA on E2 via transthioesterfication - E3- dihydrolipoyl dehydrogenase (NAD+, FAD) - E3- dihydrolipoic acid is converted back to lipoate - NAD- not tightly bound - FAD- tightly bound - complex speeds overall rate of rxn bc products are not allowed to diffuse away from enzyme -> combines them all together

Answer 116

- bound to E1 - decarboxylates pyruvate - yielding a hydroxyethyl-TPP carbanion - biologically safe form of cyanide - reacts with carbonyl groups and converts them to cyanohydrin analogs - TPP permits the reaction of two carbonyls

Answer 117

- covalently linked to a lys on E2 (lipoamide) through amide linkage called lipoamide - accepts the hydroxyethyl carbanion from TPP as an acetyl group - like heme -> prosthetic group - 8 carbons- 3 participate in an internal disulfide -> reactive end - two functions: fixed 2e- carrier (as 2 H atoms) and acyl group carrier (forms thioester like CoA) - long alkyl chain acts like crane, carries substrate from one active site to another - reactive disulfide end can be reduced -> forms dihydrolipoic acid with 2 sulfhydryl groups on it - oxidized form (lipoamide) reacts with a activated form of acetaldehyde (rxn that occurs on E1) - long tail is what allows lipoic acid to swing into E1

Answer 118

- substrate for E2 - accepts the acetyl group from lipoamide - mobile acyl-group carrier - carries acyl groups much like ADP carries phosphate groups - simplest acyl: acetate -> forms acetyl-CoA - acetyl CoA is a thioester (high energy) -> favorable to breakdown - has a reactive thiol that forms a thioester with carboxylic acids - hydrolysis of the thioester is energetically favorable: acetyl-CoA + H2O -> acetate + CoA-SH ΔG = -31.5 kJ/mol - reactive end as the sulfur -> beta-mercaptoethylamine residue -> forms the thioester with acetate - pantothenate is the precursor for CoA

Answer 119

- bound to E3 - reduced by lipoamide - bound tight - fixed 1 or 2 e- carrier - carries 2e- but passes through a 1e- step - remains associated with enzyme -> called flavoenzyme - carries electrons as H-atoms (H+ + e-) - derived from riboflavin (vitamin B2) - flavin carries out all the oxidation and reduction - oxidized form is a quinone -> 2 double bonds - when it is reduced with a single H+ -> forms a semiquinone -> stable free radical -> can react with oxygen and form oxygen free radicals - further reduction of semiquinone -> hydroquinone -> FADH2 (fully reduced)

Answer 120

- substrate for E3 - reduced by FADH2 - not bound tight - releases product NADH - mobile 2e- carrier - carries 2e- in the form of hydride ion: H+ + 2e- -> H- - 2e- are involved in reduction of pyrimidine ring in the nicotinamide portion of NAD+ - usually involved in oxidation of primary alcohol to carbonyl: R-CH2-OH + NAD+ -> R-CH=O + NADH + H+ - derived from niacin (vitamin B3)

Answer 121

- lipoic acid can react with an active form of acetaldehyde -> to form acetyl-hydrolipoate - E2 (transthioacetylase) exchanges the thioester with the sulfhydryl group of CoA to synthesize acetyl-CoA and fully reduce dihydrolipoic acid - both acetylhydrolipoic acid and acetyl-CoA are both thioesters and are both high energy compounds - long arm on lipoic acid (covalently attached to E2) allows for it to swing to E1 and eventually E3

Answer 122

- take benzaldehyde and cyanide and shake them up - benzaldehyde reacts with cyanide -> forms cyanohydrin - cyanohydrin can react with another benzaldehyde -> two carbonyl are essentially reacting together - cyanide can then come off the product -> forms benzoin - reversible - this is the heart of the rxn that allows us to take pyruvate and convert it to active acetaldehyde on E1

Answer 123

- E1 - pyruvate reacts with TPP (safe form of cyanide) - forms hydroxyethyl-TPP (cyanohydrin of acetaldehyde) -> active acetaldehyde intermediate - TPP permits the reaction of two carbonyls - one carbonyl on pyruvic acid and the other (right next to it) on carbonyl of the carboxyl group of pyruvic acid

Answer 124

- E1 - involves the rxn of the active acetaldehyde (hydroxyethyl-TPP) with fully oxidized lipoic acid - internal redox rxn - oxygen is oxidized - sulfur is reduced - produces a thioester with one sulfur reduced to thiol -> acetyl-dihydrolipoic acid (dihydrolipoamide) -> covalently attached to E2 - swing acetyl-dihydrolipoic acid into E2 for the transacetylation

Answer 125

- conversion of one thioester (acetyl-dihydrolipoic acid) to acetyl-CoA and fully reduced dihydrolipoic acid - acetyl lipoate transfers acetyl via a transthioeswterfication to CoA -> forms acetyl-CoA - this is the function of E2 -> transacetylase

Answer 126

- fully reduced dihydrolipoic acid is not capable of reacting again with pyruvate to form active acetaldehyde and acetylhydrolipoate - the rxn on E1 demands fully oxidized lipoic acid - E3 re-oxidizes dihydrolipoic acid back to lipoate so that E1 can react with it to produce another lipoyl acetaldehyde - disulfide exchange reaction -> 2 cysteine that are close to each other on E3 and they are in the form a disulfide -> this disulfide can react with dihydrolipoate to produce -> oxidized lipoate disulfide and a dithiol E3

Answer 127

- E3 has been reduced to the dithiol form -> we must restore the dithiol back to the disulfide - carried out by the tightly bound FAD - FAD oxidizes the dithiol back to the disulfide - FAD is reduced to FADH2 - less tightly bound NAD can re-oxidize FADH to FAD and NADH

Answer 128

- powerful inhibitor of pyruvate dehydrogenase - all forms -> organic arsenicals, pesticides - arsenite reacts with dihydrolipoic acid to produce a arsenic bridged dithiol compound -> stable -> irreversible - lipoic acid is tied up with arsenic

Answer 129

- generates some ATP, NADH, FADH2 - conversion of carbohydrates like glucose to pyruvate via the glycolytic path - use of pyruvate dehydrogenase complex to convert pyruvate to acetyl-CoA - carbohydrates release 1/3 of total potential CO2 during stage 1 - you can get some ATP from this from the substrate level ATP synthesis in glycolysis - substrate level phosphorylation

Answer 130

- generates more NADH, FADH2 and one GTP - remaining carbon atoms from carbohydrates, amino acids, and fatty acids are released - involves the krebs cycles - generates a lot more ATP - generates a lot of reducing equivalents (NADH, FADH2) - oxidative phosphorylation

Answer 131

- depends on if there is a another source of acetyl-CoA in the mitochondria - other *major* source -> is from the oxidation of fatty acids - products of fatty acid oxidation- acetyl-CoA and NADH -> allosteric inhibitors of pyruvate dehydrogenase

Answer 132

- NADH and acetyl-CoA (products of fatty acid oxidation) - NADH- binds to pyruvate dehydrogenase as a negative allosteric effector - acetyl-CoA- regulates pyruvate dehydrogenase (PDH) kinase and PDH phosphatase - pyruvate dehydrogenase kinase phosphorylates E1 -> inactivates - pyruvate dehydrogenase phosphatase dephosphorylates E1 -> activates - acetyl-CoA is a potent allosteric activator of PDH kinase and allosteric inhibitor of PDH phosphatase - fatty acids get catabolized -> make a lot of acetyl-CoA -> acetyl-CoA binds to PDH kinase -> actives PDH kinase and inhibits pyruvate dehydrogenase -> inhibits the oxidation of pyruvate to acetyl-CoA - product inhibition, negative feedback - shuts itself down bc instead of using pyruvate to make more acetyl-CoA you can use pyruvate for anabolic rxns, synthesis of glucose -> YOU CANT MAKE CARBS FROM FATTY ACIDS

Answer 133

- BOTH- phosphoglycerate kinase, aldolase, enolase, phosphoglucose isomerase - GLUCONEOGENESIS- glucose-6-phosphatase - GLUCOLYSIS- hexokinase, PFK1, pyruvate kinase

Answer 134

- an animal fed a large excess of fat in diet will convert any fat not needed for energy production into glycogen to be stored for later use - conversion of fructose 1,6-bisphosphate to fructose 6-phosphate is routinely catalyzed by PFK2 in a bypass rxn - conversion of glucose 6-phosphate to glucose is catalyzed by hexokinase - conversion of phosphoenol pyruvate to 2-phosphoglycerate occurs in 2 steps including carboxylation

Answer 135

-exists in an active (a) form and an inactive (b) form that is allosterically regulated by AMP

Answer 136

- lysine | - it is attached to phosphate, biotin, and pyruvate at some point

Answer 137

- non sugars - lactate - pyruvate - glycerol - amino acids

Answer 138

- 3 ATP | - starting with G6P -> skips hexokinase which uses an ATP

Biochem 5 Flashcards

(164 cards)