Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

Biochemistry > Biochem 6 > Flashcards

Biochem 6 Flashcards

1
Q

krebs cycle/tricarboxylic acid/citric acid

A
  • one substrate- acetyl CoA
  • one product- CO2
  • its not get a way to oxidize acetyl CoA or make ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

only a small amount of energy available in glucose is captured in glycolysis

A
  • complete oxidation only using the glycolytic path only generates pyruvate acid from glucose and a certain amount of free energy to make ATP
  • complete oxidation of glucose (glycolysis and krebs) -> makes a lot more free energy and ATP
  • amount per glucose is not the important part -> you can upregulate
  • 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)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

in eukaryotes, stages 2 and 3 are localized to the mitochondria

A
  • glycolysis occurs in the cytoplasm
  • citric acid cycle occurs in the mitochondrial matrix
  • mitochondrial matrix has high concentration of enzymes (soluble)
  • oxidative phosphorylation occurs in the inner membrane
  • there are proteins/enzymes in the inner membrane -> carriers for the ETC
  • succinate dehydrogenase -> enzyme participates in the krebs cycle and ETC
  • proteins in the inner membrane transport protons
  • matrix is proton poor compared to cytosol (proton rich)
  • proton movement from the cytosol to the matrix through the ATP synthase -> synthesis of ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

respiration: stage 2: acetyl-CoA oxidation

A
  • krebs cycle
  • generates more NADH, FADH2, and one GTP
  • substrate level phosphorylation converts GDP -> GTP
  • acetyl-CoA was synthesized from pyruvate
  • amino acids (glutamic acid and glutamine) can also enter the krebs cycle -> important role when the cycle is serving to be the first step of gluconeogenesis
  • remaining carbon atoms from carbohydrates, amino acids, and fatty acids are released during stage 2
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

respiration: stage 3: oxidative phosphorylation

A
  • generates the vast majority of ATP in well oxygenated well perfused tissues during catabolism
  • inner membrane
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

sequence of events in oxidative decarboxylation of pyruvate

A
  • enzyme 1:
  • step 1- decarboxylation of pyruvate to an active aldehyde
  • step 2- oxidation of aldehyde to a carboxylic acid
  • electrons reduce lipoamide and form a thioester
  • enzyme 2:
  • step 3- formation of acetyl-CoA (product 1)
  • enzyme 3:
  • step 4- reoxidation of the lipoamide cofactor
  • step 5- regeneration of the oxidized FAD cofactor -> forming NADH (product 2)
  • repeat
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

citric acid cycle: overall cycle

A
  • acetyl-CoA is condensed with oxaloacetic acid (alpha and beta carboxylic acid)
  • claisen condensation via citric synthase -> methyl group of acetyl-CoA appears as a methylene group in citric acid (the product)
  • citrate is dehydrated via aconitase to the enzyme bound product cis-aconitate (cis-aconitic acid)
  • cis-aconitic acid is transferred to the next enzyme -> isocitrate dehydrogenase
  • isocitrate- rehydrated product of cis-aconitic acid -> its hydroxyl group is move from the beta to the alpha -> alpha hydroxycarboxylic acid
  • isocitrate dehydrogenase converts isocitrate to alpha-ketoglutarate -> loss of a CO2 (first loss of a carbon) -> decarboxylation
  • alpha-ketoglutarate is oxidatively decarboxylated via alpha-ketoglutarate dehydrogenase complex -> forms succinyl-CoA (identical to pyruvate oxidative decarboxylation rxn)
  • production of succinate from alpha-ketoglutarate passes through high energy mixed anhydrides and thioester
  • succinyl-CoA synthetase (succinyl thiokinase) -> produces GTP by substrate level phosphorylation (from high energy mixed anhydrides and thioester)
  • succinate is dehydrogenated on the inner membrane by succinate dehydrogenase (falvin dependent enzyme) -> produces fumarate
  • fumarate (has a double bond) is hydrated to malate via fumarate
  • malic acid is dehydrogenated by malate dehydrogenase (NAD dependent) -> forms oxaloacetate
  • oxaloacetate is ready to participate in another round of cycle
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

first half vs second half of krebs

A
  • first half involves decarboxylation’s -> we lose 2 carbons
  • second have is rehydration and dehydrations
  • 2nd half is anabolic
  • 2nd half is found in cancer cells
  • the only decarboxylation in cancer cells during the krebs cycle is the alpha-ketoglutarate dehydrogenase step
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

anaplerotic reactions

A
  • nothing is made or destroyed -> intermediates are extracted though
  • oxaloacetate can be extracted for gluconeogenesis
  • glutamic acid can be converted to alpha-ketogluteric acid and supplement the species in the krebs cycle
  • anaplerotic rxns deplete or enrich the krebs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

summary of sequence of events in the citric acid cycle

A
  • step 1- C-C bond formation between acetate (2C) and oxaloacetate (4C) to make citrate (6C)
  • step 2- isomerization via dehydration/rehydration
  • steps 3-4- oxidative carboxylations to give 2 NADH
  • step 5- substrate level phosphorylation to give GTP
  • step 6 - dehydrogenation to have FADH2
  • step 7- hydration
  • step 8- dehydrogenation to give NADH
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

citric acid cycle: step 1: C-C bond formation by condensation of acetyl-CoA and oxaloacetate

A
  • condensation of oxaloacetate and acetyl-CoA via citrate synthase
  • acetyl-CoA- thioester (high energy) -> instead of being used to make an ATP it goes into a condensation rxn and uses the energy to drive the rxn
  • huge -ΔG -> -32.2 kJ/mol
  • highly thermodynamically favorable/irreversible
  • pushes the entire kreb cycle in one direction
  • this is the only rxn with C-C bond formation
  • uses acid/base catalysis
  • carbonyl of oxaloacetate is a good electrophile
  • methyl of acetyl CoA is a not a good nucleophile unless activated by deprotonation
  • this is the rate limiting step
  • activity largely depends on oxaloacetate
  • product is citrate
  • regulated by substrate availability and product inhibition -> bc oxaloacetate has other fates (gluconeogenesis or making malate which is more favored)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

induced fit in the citrate synthase (step 1 enzyme)

A
  • conformational change occurs upon binding oxaloacetate
  • ordered bisubstrate rxn
  • avoid unnecessary hydrolysis of thioester in acetyl-CoA
  • open conformation- binds oxaloacetate very well but free enzyme does not have a binding site for acetyl-CoA
  • closed conformation- binding of OAA created binding for acetyl-CoA -> reactive carbanion is protected
  • the idea that the enzyme cannot bind the second substrate until the first substrate is bound -> bisubstrate rxn with obligate binding order
  • analog of acetyl-CoA is an uncompetitive inhibitor for oxaloacetate
  • conformational change protects the product from premature hydrolysis
  • enzyme hides substrates from water
  • oxaloacetate binds to bottom of a site that creates an anchor for acetyl CoA to then finally enter the binding site
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

citric acid cyce: step 2: isomerization by dehydration/rehydration

A
  • hydroxyl group is moved from 2 position to 1 position
  • citrate is converted to isocitrate via aconitase enzyme
  • small ΔG
  • not favored one way or another -> more unfavorable/reversible
  • product concentration kept low to pull forward rxn
  • isocitrate is active product -> L-isocitrate
  • elimination of H2O from citrate gives cis double bond -> lyase
  • citrate (tertiary alcohol) is a poor substrate for oxidation
  • isocitrate (secondary alcohol) is a good substrate for oxidation
  • addition of H2O to cis-aconitate is stereospecific
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

iron sulfur center in aconitase

A
  • water removal from citrate and subsequent addition to cis-aconitate are catalyzed by the iron-sulfur center -> sensitive to oxidative stress
  • only make L-isocitrate (optically active) from inactive citrate
  • aconitase has iron sulfur center
  • holds citrate in a specific conformation to define the dehydration of citrate to form cis-aconitate
  • enzyme is asymmetric and can only bind in one orientation
  • citrate is a prochiral molecules -> noramlly optically inactive but replacement of either -CH2COO- groups would make the central C chiral -> active
  • aconitase is stereospecific
  • augstin 3 point attachment model -> if the enzyme can bind to optically inactive substrate (citrate) at at least 3 points the product will be stereospecifically defined (L-isocitrate)
  • possible to induce a center of chirality by binding a optically inactive substrate at at least 3 points
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

citric acid cycle: step 3: oxidative decarboxylation by isocitrate dehydrogenase

A
  • isocitrate is easily dehydrated via isocitrate dehydrogenase
  • isocitrate dehydrogenase is a mitochondrial enzyme that makes use of NAD
  • allosteric site for ATP -> inhibits mitochondrial enzyme
  • ATP is the product of oxidative decarboxylation -> negative feedback
  • oxalosuccinate is an enzyme bound intermediate -> beta keto acid -> spontaneously decarboxylate
  • forms a 5 carbon dicarboxylic acid -> alpha-ketoglutarate (similar to alpha-keto acid pyruvate)
  • forms NADH for ETC
  • alpha-ketoglutarate is the product -> imported from glutamine or exported to glutamate -> regulation
  • highly favorable and irreversible (but it is reversible in the cytosol with NADP -> cancer cells)
  • some alpha-ketoglutarate is converted back to isocitrate
  • cytosolic isocitrate dehydrogenase makes use of NADP -> this enzyme may run the rxn in the opposite direction in cancer cells -> produces isocitrate and then citrate -> citrate leaves into cytosol and carries out biosynthetic rxns
  • catalyzes a rate limiting step -> speeds up the entire krebs in presence of ADP and Ca
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

citric acid cycle: step 4: final oxidative decarboxylation by alpha-ketoglutarate dehydrogenase

A
  • alpha-ketoglutarate (5 carbon dicarboxylic acid) converted to succinyl-CoA via alpha-ketoglutarate dehydrogenase complex
  • this complex is very similar to pyruvate dehydrogenase complex -> all the same cofactors
  • E1 and E2 are different to accommodate different sized substrates but E3 are identical
  • favorable -> irreversible
  • regulated by product inhibition
  • oxidative decarboxylation of an alpha-keto acid -> TPP
  • last oxidative decarboxylation
  • net full oxidation of all carbons of glucose after 2 turns of the cycle
  • carbons not directly from glucose bc carbons lost come from oxaloacetate, not acetate
  • succinyl-COA is another higher energy thioester bond
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

alpha-ketoacids making use of TPP

A
  • alpha-ketoacids that are oxidatively decarboxylated used same mechanisms using TPP
  • seen in pyruvate dehydrogenase complex -> acetyl-CoA
  • citric acid cycle -> step 4 -> succinyl-CoA
  • oxidation of isoleucine (leucine, valine) -> branched amino acids -> produces alpha-methylbutyryl-CoA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

alpha-ketoglutarate dehydrogenase complex

A
  • three enzymes
  • 5 cofactors
  • E1- alpha-ketoglutarate dehydrogenase (TPP)
  • E2- dihydrolipoyl transsuccinylase (lipoamide, CoA)
  • E3- dihydrolipoyl dehydrogenase (NAD+, FAD)
  • E3 from pyruvate dehydrogenase complex is identical to E3 from alpha-ketoglutarate dehydrogenase complex
  • alpha-ketoglutarate reacts with TPP -> forms hydroxyethyl-TPP complex -> forms active succinyl intermediate
  • active succinyl intermediate is transferred to lipoic acid to produce succinyl hydrolipoic acid
  • succinyl hydrolipoic acid reacts with CoA -> forms succinyl-CoA (thioester) and dihydrolipoic acid
  • E3=E3 of pyruvate dehydrogenase
  • dihydrolipoic acid is reoxidized by disulfide -> forms an internal dithiol -> reoxidized by FAD -> which is reoxidized by NAD -> produces a NADH and reoxidized lipoic acid to repeat
  • long lipollysyl arm transfers intermediates from one active site to another
  • this rxn is abnormally low in people suffering from beriberi (deficiency of thiamine)
  • 2 different coenzymes with sulfhydryl groups participate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

origin of C-atoms in CO2

A
  • carbons from acetate are red
  • all CO2 generated during the citric acid cycle is produced before succinyl-CoA is made
  • in one turn of the citric acid cycle, neither of the red carbons is lost
  • both CO2 molecules lost were present on the oxaloacetate used to begin the cycle
  • citrate -> isocitrate -> alpha-ketoglutarate -> succinyl-CoA (6 carbons to 4 carbons)
  • citrate is made from 4 carbon oxaloacetate and 2 carbons from acetyl-CoA
  • the 2 carbons from acetyl-CoA are NOT the carbons released until we convert succinyl-CoA to succinate -> in this step the molecule loses it selectivity and structure
  • carbons from acetyl-CoA are retained from conversion to citrate to succinyl-CoA
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

citric acid cycle: step 5: generation of GTP through thioester

A
  • substrate level phosphorylation by succinyl-CoA synthetase
  • succinyl-CoA synthetase- going from succinate to succinyl-CoA (reverse)
  • succinyl thiokinase- going from succinyl-CoA to free succinate (forward)
  • conversion of succinyl-CoA to succinate
  • free thiol of succinyl-CoA comes from CoA (thiol came from the enzyme itself from glyceraldehyde-3-dehydrogenase)
  • it makes a phosphoenyzme and a mixed anhydride
  • succinyl-CoA reacts with inorganic phosphate and the enzyme succinyl thiokinase -> forms an enzyme bound mixed anhydride -> uses this to make a phosphohistidiene on the enzyme -> phosphohistidyl enzyme
  • succinate is released (symmetrical and inactive)
  • phosphohistidiene is used to phosphorylate GDP to make GTP
  • sulfhydryl is not contributed by the enzyme -> rather CoA
  • similar to the way thioester was used by glyceraldehyde-3-phosphate dehydrogenase and diphosphoglycerate kinase -> made a mixed anhydride
  • for the enzyme diphosphoglycerate kinase direct phosphorolysis succinyl-CoA by inorganic phosphate to make ATP -> but in this rxn the enzyme succinyl thiokinase puts the phosphate onto a histidine and then onto GTP (substrate level phosphorylation)
  • acyl phosphate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

citric acid cycle: step 6: oxidation of an alkane to alkene by succinate dehydrogenase

A
  • succinate converted to fumarate via succinate dehydrogenase
  • succinate is optically inactive -> origin of the carbons become scrambled
  • succinate dehydrogenase part of the mitochondrial inner membrane
  • highly reversible (near equilibrium
  • product concentration kept low to pull forward
  • this enzyme is special bc its also an intermediate step in the electron transport chain -> acts as complex II in the ETC
  • flavin dependent enzyme
  • succinate reduced FAD - FADH2
  • succinate itself becomes oxidized -> fumarate
  • reduced of alkane to alkene requires FADH2
  • reduction potential of carbon-hydrogen bond is too low for production of NADH
  • FAD is covalently bound (unusual)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

citric acid cycle: step 7: hydration across a double bond

A
  • addition of water to fumarate (fumaric acid) to L-malate (malic acid) via fumarase
  • malate is chiral (optically active)
  • fumarate is optically inactive -> converted to L-malate
  • somewhat similar to 3 point model of aconitase
  • slightly thermodynamically favorable -> highly reversible
  • product concentration kept low to pull rxn forward
  • fumarase is stereospecific
  • addition of water to fumarate is always trans and forms L-malate
  • OH- adds to fumarate -> then H+ adds to the carbanion
  • cannot distinguish between inner carbons -> so either can gain the OH-
  • if you give fumarase D-malate it will attempt to make maleate (maleaic acid) -> cis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

citric acid cycle: step 8: oxidation of alcohol to a ketone and regeneration of oxaloacetate by malate dehydrogenase

A
  • L-malate is oxidized to oxaloacetate via L-malate dehydrogenase
  • L-malate is capable of diffusing out of the mitochondrial membrane -> implications for gluconeogenesis
  • unfavorable -> reversible
  • citrate synthase has a low delta G -> favorable -> therefore this rxn is winning -> free oxaloacetate concentration is low in mitochondria -> pulls rxn forward
  • final step of the krebs
  • regenerates oxaloacetate for citrate synthase
  • NAD reduced to NADH
  • malate dehydrogenase helps overcome the impermeability of oxaloacetate to the mitochondrial membrane -> mitochondrial and cytosolic catalyze malate/oxaloacetate interconversion that are part of malate-oxaloacetate shuttle
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

Net result of the citric acid cycle

A

acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O -> 2CO2 + 3NADH + FADH2 + GTP + CoA + 3H+

  • net oxidation of 2 carbons to CO2 -> equivalent of 2 carbons of acetyl-CoA -> but NOT the exact same carbons
  • energy captured by electron transfer to NADH and FADH2
  • generates 1 GTP -> can be converted to ATP
  • completion of cycle
  • source of GTP (ATP), CO2, and reducing equivalents (substrates for ETC -> ATP)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

CAC intermediates are amphibolic

A
  • amphibolic- both catabolic and anabolic functions
  • catabolic- oxidation of acetate to CO2
  • anabolic- intermediates serve as precursors to other molecules
  • depletion of intermediates for anabolic pathways creates a problem for catabolism -> slows CAC
  • depletion come from biosynthesis in the cell
  • beginning of an anabolic path for the cancer cell
  • some intermediates can go in and out of mitochondria
  • krebs cycle is amphibolic -> some rxns feed the cycle and some deplete the cycle
  • glutamine is used by the mitochondrion of many cancer cells and converted to glutamate and then to alpha-ketoglutarate (alpha-ketoglutarate can leave the mitochondria)
  • cancer cells rely heavily on glutamine to run the second half of the krebs cycle
  • involving multiple forms of isocitrate dehydrogenase we can run the first half of the krebs cycle backwards up to citrate
  • citrate can leave the mitochondria -> citrate is a powerful inhibitor of glycolysis -> especially a potent inhibitor for glyceraldehyde-3-phophsate dehydrogenase
  • malic acid can go in and out of the mitochondria
  • oxaloacetate leaves the mitochondria by being converted to malic acid to be used but is also used inside the mitochondria for other purposes
  • oxaloacetate is the keto acid that is formed from aspartic acid
  • alanine (amino acid) is formed from pyruvate (keto acid)
  • many amino acids can be converted to glucose -> glucogenic amino acids
  • some amino acids can only be converted to kreb cycle intermediates -> ketogenic
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

cataplerotic reactions

A
  • empty the citric acid cycle
  • depletion
  • use of citrate in metabolism
  • aspartyl aminotransferase converts oxaloacetate + alanine aspartate + pyruvate -> enzymes leak out when liver is damaged
  • glutamate dehydrogenase converts alpha-ketoglutarate +NADH + H+ + NH4 glutamate + NAD+ + H2O
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

anaplerotic reactions

A
  • fill the citric acid cycle
  • doesnt provide the substrate acetyl-CoA -> provides intermediates
  • pyruvate carboxylase is rxn that creates oxaloacetate (kreb cycle intermediate)
  • amino acid breakdown
  • odd-chain fatty acid breakdown
  • pyruvate + CO2 + ATP + H2O -> oxaloacetate + ADP + Pi
  • acetyl-CoA activates pyruvate carboxylase, makes more oxaloacetate and then permits pyruvate to be used as a source of both substrate and intermediate for krebs cycle
  • intermediates in the CAC can be used in biosynthetic pathways (removed from cycle)
  • must replenish intermediates in order for cycle and central metabolic path to continue
  • 4-carbon intermediates are formed by carboxylation of 2-carbon precursors
  • involves fixation of CO2
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

pyruvate carboxylase: anaplerotic reaction

A
  • pyruvate + CO2 + ATP + H2O -> oxaloacetate + ADP + Pi
  • liver and kidney
  • replenish krebs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

PEP carboxykinase: anaplerotic rxn

A
  • phosphoenolpyruvate + CO2 + GDP -> oxaloacetate + GTP
  • heart and skeletal muscle
  • replenish krebs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

PEP carboxylase: anaplerotic rxn

A
  • phosphoenolpyruvate + CO2 -> oxaloacetate + Pi
  • higher plants, yeast, and bacteria
  • replenish krebs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

malic enzyme: anaplerotic rxn

A
  • pyruvate + CO2 + NAD(P)H -> malate + NAD(P)
  • widely distributed in eukaryotes and bacteria
  • both in mitochondria and cytosol
  • involves biotin
  • 3-carbon -> 4- carbon
  • replenish krebs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

regulation of citric acid cycle

A
  • regulated at highly thermodynamically favorable and irreversible steps -> PDH, citrate synthase, IDH, and KDH
  • activated by substrate availability
  • inhibited by product accumulation
  • overall products of krebs (NADH and ATP) affect all regulated enzymes
  • inhibitors- NADH and ATP
  • activators- NAD+, ADP and AMP
  • pyruvate dehydrogenase to make acetyl-CoA -> can be phosphorylated at E1 -> ATP inhibits -> inhibits krebs
  • acetyl-CoA is a potent feedback inhibitor of pyruvate dehydrogenase as well
  • fatty acids dont directly inhibit pyruvate dehydrogenase but they are metabolized to acetyl-CoA -> inhibits
  • citrate synthase is feedback inhibited by citrate and also inhibited by succinyl-CoA
  • isocitrate dehydrogenase is very sensitive and inhibited by ATP -> stimulated by ADP -> therefore the reducing equivalents will be convert ADP to ATP -> inhibits
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

regulation of pyruvate dehydrogenase

A
  • regulated by reversible phosphorylation of E1: phosphorylation -> inactive and dephosphorylation -> active
  • PDH kinase and PDH phosphatase (a form of phosphoprotein phosphatase) are part of mammalian PDH complex
  • kinase is activated by ATP
  • high ATP -> phosphorylated PDH -> less acetyl-CoA
  • low ATP -> kinase is less active and phosphatase removes phosphate from PDH -> more acetyl-CoA
  • regulation of PDH is somewhat similar to regulation of glycogen synthase/glycogen phosphorylase system by protein kinase cascade and phosphoprotein phosphatase
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

regulation of citrate synthase

A
  • -citrate synthase is feedback inhibited by citrate and also inhibited by succinyl-CoA
  • alpha-ketoglutarate is an important branch point for amino acid metabolism
  • succinyl-CoA communicates flow at this branch point to the start of cycle
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

regulation of isocitrate dehydrogenase

A
  • controls citrate levels
  • very sensitive and inhibited by ATP -> stimulated by ADP -> therefore the reducing equivalents will be convert ADP to ATP -> inhibits
  • aconitase is reversible
  • inhibition of IDH leads to accumulation of isocitrate and reverses aconitase
  • accumulated citrate leaves mitochondria and inhibits phosphofructokinase in glycolysis
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

krebs, glycolysis, and cancer

A
  • cancer cells accumulate succinate (from succinyl thiokinase) and fumarate (from fumarase) as a result of loss of function of fumarase and succinic dehydrogenase (mutated)
  • excess succinate chemically modifies enzymes involved in DNA and histone methylation -> succinylation
  • cancer cells have NADP-dependent isocitrate dehydrogenase isozymes (in cytosol) with elevated activity leading to accumulation of alpha-hydroxyglutarate (2-HG)
  • inhibition of alpha-ketoglutarate-dependent oxygenases by 2-HG results in extensive epigenetic modification to DNA in cancer
  • cancer cells accumulate glutamine -> convert it to alpha-ketoglutarate, malate, pyruvate, and finally lactate, which is secreted in high amount by cancer cells
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

isocitrate dehydrogenase in cancer cells

A
  • cytosolic
  • take alpha-ketoglutarate and reduce it to alpha-hydroxyglutarate
  • NADP-dependent rxn
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

alpha-hydroxyglutarate

A
  • produced from isocitrate dehydrogenase in the cytosol for cancer cells
  • methylates DNA and RNA
  • methylates histones
  • alter the functional properties of cancer cells associated with loss of contact inhibition
  • alters the extracellular matrix in cancer cells
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

cancer cells take up glucose and glutamine

A
  • cancer cells can do things with malic acid that is formed from the glutamine they take up -> export it to make pyruvate and lactate
  • accounts for high levels of high lactic acid production in cancer cells
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

warburg effect

A
  • even though cancer cells may have a lot of O2 available -> they still tended to convert (ferment) glucose into lactate
  • the glucose that is being metabolized through the glycolytic pathway up to a certain point -> pyruvate kinase
  • lactate is not a product of synthesis of pyruvate by the cancer cells -> rather the lactate is a product of the malate that is carrying second part of krebs forward
  • the reason the pyruvate is converted to lactate cant be derived all from glucose is that -> in the step that converts phosphoenolpyruvate to pyruvate -> many cancer cells have a M2 variant of pyruvate kinase -> sluggish
  • PEP accumulates or relys of glycolysis and all the glycolytic intermediates accumulate
  • PEP can be used to make the phosphoglycerate mutase that converts 3-phosphoglyerate to 2-phosphosphoglycerate
  • PEP continuously converts 3PG to 2PG by donating a phosphate group to the histidine of phosphoglycerate mutase (rather than ATP)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

M2 isoform

A
  • people tried to make activators for M2 isoform of pyruvate kinase to proceed through glycolysis and make pyruvate for krebs
  • cancer arnt interesting in feeding their mitochondria with glycolytic intermediates -> they want to use glycolysis to make more intermediates for biosynthetic rxns
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

malaria

A
  • parasite (plasmodium falciparum) can be eliminated by red cells that have undergone structural changes as a consequence of -> ex. hemoglobin S disease of glucose-6-phosphate dehydrogenase deficiency
  • plasmodium falciparum does not carryout synthesis of acetyl-CoA for krebs cycle efficiently uses pyruvate and pyruvate dehydrogenase (unlike cancer cells) -> it feeds its krebs cycle with alpha-ketoglutarate (like cancer cells) from glutamic acid and glutamine
  • uses the acetly-CoA to make amino sugars
  • one it has made alpha-ketoglutarate and put it in the krebs -> it will secrete malate (like cancer cells)
  • runs the second half of the krebs cycle in the forward direction up to the point of malate -> exports that malate
  • uses the other isoform of isocitrate dehydrogenase to run the first half of krebs backward
  • second half of krebs is a dehydrogenation pathway -> makes reduced products/equivalents -> if we run the 1st half of krebs backward we need to oxidize the ETC intermediates
  • NO net gain of oxidation or reduction of ETC intermediates in malarial parasites -> no significant oxidation phosphorylation (ATP)
  • this is ok bc it doesnt really have mitochondria it does krebs cycle in cytosol (makes minimal ATP in mitochondrion)
  • mimics the metabolic events in a mammalian cancer cells -> conversion of pyruvate to lactate and running of the krebs by feeding it with alpha-ketoglutarate
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

ETC overview

A
  • intermediates have been reduced
  • intermediates capture electrons for redox rxns
  • generates a proton motor force -> generated by movement of electrons along the ETC
  • equal distribution of proton on either side of the inner membrane is responsible for synthesis of ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

energy from reduced fuels are used to synthesize ATP in animals

A
  • carbohydrates, lipids, and amino acids are the main reduced fuels for the cell -> get oxidized
  • electrons from reduced fuels are transferred to reduced cofactors NADH or FADH2 -> drive ETC
  • generate a proton gradient -> used to make ATP
  • in oxidative phosphorylation, energy from NADH and FADH2 is used to make ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

chemiosmotic theory

A
  • ADP + Pi -> ATP is a highly thermodynamically unfavorable
  • phosphorylation of ADP is not a result of a direct rxn between ADP and some high energy phosphate carrier
  • energy needed to phosphorylate ADP is provided by the flow of protons down the electrochemical gradient -> driving force
  • distributed unequally
  • energy released by ETC is used to transport protons against the electrochemical gradient
  • captures a series of oxidations of the reduced cofactors -> provides energy to establish unequal distribution of proton across the inner membrane
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

chemiosmotic energy coupling requires membranes

A
  • proton gradient needed for ATP synthesis can be stably establish across inner membrane that is impermeable to ions
  • membrane must contain proteins that couple the downhill flow of electron in the electron transfer chain with the uphill flow of proton across the membrane
  • membrane must contain a protein that couples the subsequent downhill of protons to the phosphorylation of ADP
  • intermembrane transporters have the ability to move electrons from their reduced state to oxidized state
  • vectorial protons
  • movement of vectorial protons -> membrane bhor effect
  • proteins of ETC that bind or release protons (chemical/scalar protons) themselves through oxidation and reduction -> stochiometric
  • proteins undergo conformational changes -> allows proteins to move protons from the matrix through the intermembrane to the intermembrane space
  • vectorial and scalar protons are generated as a result of the movement of the electron down the ETC -> proton gradient is used to drive the ATP synthase (dissipates gradient)
  • ATP synthase is induced to undergo conformational changes that causes phosphorylation of ADP -> ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

ATP synthase

A
  • proton gradient is used to drive the ATP synthase
  • dissipates proton gradient
  • induced to undergo conformational changes in its F0 subunit -> causes phosphorylation of ADP -> ATP
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

structure of mitochondrion

A
  • double membrane leads to 4 distinct compartments
  • outer membrane- relatively porous membrane that allows passage of metabolites
  • intermembrane space (IMS)- similar environment to cytosol and has a higher proton concentration (lower pH)
  • inner membrane:
  • relatively impermeable (even to protons), with proton gradient across it
  • location of ETC complexes (4)
  • convolution called cristae serve to increase the SA
  • matrix: location of the krebs and parts of lipid amino acid metabolism (oxidation) -> lower proton concentration (higher pH)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

FMN and FAD: electron funnels

A
  • FMN and FAD can be covalently bound to proteins and act to funnel and distribute electrons to ETC
  • flavins
  • accept 2 electrons from carrier (NADH and NADPH) that are unstable donated single electrons
  • can donate 1 electron at a time, using a semiquinone-like free radical intermediate to acceptors that can only accept single electrons -> sometimes good sometime risky
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

cytochromes

A
  • all cytochromes are one electron carriers
  • either in ferric or ferrous state
  • contains hemes
  • iron coordination porphoryin ring derivatives
  • feroprotoporphyrin 9 -> in hemoglobin -> this can be oxidized or reduced in the b-type cytochrome
  • a. b, or c differ by ring additions
  • heme A has a long hydrophobic chain that anchors it to the membrane of the last component of the ETC (complex 4)
  • heme C is associated with the c-type cytochromes -> completely soluble and not bound to any membrane
  • although c-type cytochrome has a binding site on the inner membrane
  • cytochrome C1 (a different type) -> we find in complex 3
  • cannot diffuse through (within) membranes but it can bind
  • mobile carrier bc it moves from complex to complex
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

iron sulfur clusters

A
  • one electron carriers
  • iron is coordinated to cysteines in the protein
  • there are multiple iron sulfur centers or clusters each with a distinct arrangement of sulfur atoms coordinated to the iron
  • iron and sulfur (given from cysteine) are holding the clusters together
  • moving electrons to the other one electron carriers like cytochromes
  • participate in some rxns in which the valency is not strict -> mixture of ferous and feric iron -> imperfect stoichiometry’s of electron movement (in general one electron carriers though)
  • many iron-sulfur centers contain multiple irons -> means that the electrons that are carried can move within the centers -> not just redox intermediates -> they are truly carriers that can move electrons through proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

coenzyme Q or ubiquinone

A
  • ubiquinone (CoQ) is a lipid soluble conjugated dicarbonyl compound that readily accepts electrons
  • 2 electron donor
  • hydrophobic -> never leaves the internal bilayer of membranes -> floats within
  • mobile electron carrier -> goes to complex to complex
  • upon accepting 2 electrons, it picks up 2 protons to give an alcohol -> ubiquinol (CoQH2)
  • mechanism acquires protons selectively from one or the other side of the inner membrane
  • reoxidation of ubiquinol to ubiquinone releases the protons selectively to another side of the inner membrane
  • CoQ and CoQH2 can freely diffuse in the membrane, carrying electrons with protons from one side of the membrane to another side
  • CoQ pool is larger than the number of complexes in the ETC
  • Coenzyme Q is a mobile electron carrier transporting electrons from complexes 1 and 2 to complex 3
  • can exist in quinone form (fully oxidized), semi-quinone form (reduced by 1 electron), or quinol (hydroquinone) form (fully reduced by 2 electrons)
  • there is always a ubiquinone available to participate in a redox rxn
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

complex 1 of ETC

A
  • NADH dehydrogenase
  • contains a flavin
  • contains a lot of iron sulfur clusters
  • no cytochromes
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

complex 2 of ETC

A
  • succinate dehydrogenase
  • from krebs cycle (only part of krebs that is membrane bound)
  • iron sulfur clusters
  • FAD
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

complex 3 of ETC

A
  • ubiquinone: cyto
  • b and c type hemes/cytochromes
  • iron sulfur clusters -> rieske center -> one of the irons is coordinated by 2 histidine’s
  • contains histidine and cysteine
  • cytochrome c participates
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

complex 4 of ETC

A
  • cytochrome oxidase
  • contains 2 different kinds of a-type cytochromes
  • 2 copper atoms
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

NADH: Ubiquinone Oxidoreductase (Complex 1)

A
  • one of the largest macromolecular assemblies in the mammalian cell
  • over 40 different polypeptide chains, encoded by both nuclear and mitochondrial genes
  • NADH binding site facing the matrix side
  • noncovalently bound flavin mononucleotide (FMN) accepts 2 electrons from NADH
  • several iron sulfur centers pass 1e- at a time toward the ubiquinone binding site (from NADH) -> forms matrix arm
  • matrix arm does electron transport
  • when the electron reaches the ubiquinone binding site (bound loose) it passes to the ubiquinone one at a time -> makes a semiquinone -> then the ubiquinol (QH2)
  • QH2 picks up 2 protons
  • QH2 stays in the intermembrane bc its so hydrophobic
  • protons are transported by proton wires (membrane bohr effect)
  • transmembrane proteins- responsible of movement of vectorial protons from matrix (N) to intermembrane space (P)
  • bind protons on the matrix side and release them on intermembrane space -> membrane like bhor effect
  • the protons that are moved are bound and released by ionizable amino acids (protonated and deprotonated) within the component of the membrane arm to get a net transfer of a proton from one side of a membrane to another
  • membrane arm move about 4 protons per 2 electrons (or 1 NADH) moved through matrix arm
  • NADH + Q + 5H+ = NAD+ + QH2 + 4H+
  • transmembrane proteins undergo conformational changes -> drives proton pumping mechanism
  • conformational changes alter the pK values of ionizable side chains so that protons are taken up or released as electrons are transferred
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

energy produced by complex 1

A
  • there is enough energy to make an ATP from the reduction of CoQ by NADH
  • ADP cant bind to any of the species therefore it is not made
  • there is more than enough energy captured in the movement of the protons
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

inhibition of complex 1

A
  • inhibited by rotenone or amytal
  • rotenone- rat poison
  • bind to complex 1
60
Q

succinate dehydrogenase: complex 2

A
  • succinate binding site in the matrix
  • succinate is oxidized to fumarate -> 2e- picked up by FAD
  • succinate dehydrogenase is covalently bound to FAD
  • FAD accepts 2e- from succinate and donates 1e- at a time
  • electrons are passed one at a time via iron sulfur centers (and 1 cytochrome b) to ubiquinone which becomes reduced to QH2
  • QH2 goes into the inner membrane -> floating
  • does not transport protons (no membrane arm)
  • free energy from succinate to CoQ is insufficient to drive ATP synthesis -> still important bc it allows relatively high potential e- to enter ETC by bypassing complex 1
  • can move 2e-
  • adds to the pool of reduced ubiquinone
  • succinate dehydrogenase is a single enzyme with dual roles
  • coverts/oxidizes succinate to fumarate in the citric acid cycle (reducing FAD to FADH2)
  • captures and donates electrons in the ETC
  • heme b (nothing to do with e- transport)- scavenges free radicals that might have formed as a result of e- movement such as semi-quinone in FAD
61
Q

complex 1 and 2

A
  • do not operate in series
  • they happen side by side
  • not one after the other
  • both accomplish the same result: transfer of electrons to CoQ from reduced substrate (NADH or succinate)
  • CoQ diffuses in the lipid bilayer among the respiratory complexes and serves as a collection point for electrons
  • CoQ collects electrons from the FADH2 produced by the glycerophosphate shuttle
62
Q

intermembrane space

A

-higher concentration of protons when electrons are allowed to pass through the entire ETC

63
Q

matrix

A

-lower concentration of protons when electrons are allowed to pass through the entire ETC

64
Q

double duty of ETC

A
  • moves electrons down electrochemical gradient

- moves protons

65
Q

ubiquinone: cytochrome c oxidoreductase: Complex 3

A
  • uses 2e- from QH2 to reduce 2 molecules of cytochrome c
  • cytochrome c is not apart of any mitochondrial membrane (floats in intermembrane space)
  • contains iron sulfur clusters, cytochrome b isoforms, and cytochrome c
  • clearance of electrons from the reduced quinones via the Q-cycle results in translocation of 4 additional protons to the intermembrane space
  • cytochrome b(Low) -> contains bL type heme
  • cytochrome b(High) -> contains bH type heme
  • two binding sites for CoQ -> Qp/o and Qn/i
  • Qp/o- pointing towards intermembrane space/positive space (protons here)
  • Qn/i- pointing towards the matrix/
  • rieske center is here- alternatly donate electrons to cytochrome bL or bH or cytochrome c1
  • cytochrome c1 (has heme c1)- has a basket at the top that points into the intermembrane space and binds cytochrome C
66
Q

rieske center

A
  • iron is coordinated to 2 cysteines and histidine’s

- functions to alternating donate electrons to cytochrome bL or bH or cytochrome c1

67
Q

the Q cycle: complex 3

A
  • 4 protons are transported across the membrane per 2 electrons that reach cytochrome c
  • 2 of the 4 protons come from QH2 (from complex 1 or 2) the other 2 come from the matrix
  • Q cycle provides good model that explains how 2 additional protons are picked up from the matrix
  • depleting the matrix of protons
  • 2 molecules of QH2 become oxidized -> releases protons into the intermembrane space
  • one molecule becomes re-reduced -> net transfer of 4 protons per reduced CoQ
  • protons are NOT moved by conformational changes in the proteins here, -> oxidation and reduction of CoQ moves them -> these are chemical or scalar protons
  • 2 molecules of cytochrome C are reduced to the ferrous form
68
Q

Q cycle: complex 3: cycle 1

A
  • reduced QH2 from complex 1 or 2
  • reaction involving rieske center separates the electrons in QH2 -> converts to fully oxidized CoQ -> diffuses back into bilyaer
  • the 2 protons are unidirectionally diffused into the intermembrane space
  • protons are moved across inner membrane by a lipid soluble carrier (QH2) that occupies 2 sites
  • one of the electrons from QH2 is passed to cytochrome C1 and then to cytochrome C
  • the other electron is passed to cytochrome bL and then to cytochrome bH -> finally transferred to oxidized CoQ
  • oxidized CoQ is converted to a free radical (semiquinone)
  • QH2 + Q + cyt c (oxidized) -> Q + Q- + 2Hp + cyt c (reduced)
69
Q

Q cycle: complex 3: cycle 2

A
  • another fully reduced QH2 enters and is split
  • 2 protons from the QH2 are unidirectionally deposited into the IMS
  • 1 electron is passed to reduced cytochrome c1 and then cytochrome C
  • the other electron is passed to cytochrome bL and cytochrome bH -> then the electron reacts with the free radical (semiquinone) that was generated in the first cycle of Q cycle
  • electron reduces the semiquinone and picks up 2 protons unidirectionally from the matrix
70
Q

inhibitors of complex 3

A
  • antimycin A- binds to the Qi/n site (site that is closest to the mitochondrial matrix)
  • stigmatellin- binds to the Qo/p site (site that binds CoQ that is very close to the intermembrane space)
  • antimycin blocks electron transfer between cytochrome b and c1
71
Q

cytochrome C

A
  • second mobile electron carrier
  • one electron acceptor
  • never enters the membrane
  • soluble heme-containing protein in the intermembrane space
  • heme iron can be either ferrous (oxidized) or ferric (reduced)
  • cytochrome c carries a single electron from the cytochrome bc1 complex in complex 3 to cytochrome oxidase (complex 4)
  • can accept electrons directly from an iron containing heme on one complex to a copper on another complex without any intermediates or cofactors
72
Q

cytochrome c absorbs visible light

A
  • intense Soret band near 400nm absorbs blue light and gives cytochrome c an intense red color
  • cytochromes are named by the position of their longest-wavelength (alpha) peak
73
Q

cytochrome oxidase: complex 4

A
  • mammalian cytochrome oxidase is a membrane protein with 13 subunits
  • contains 2 heme groups: a and a3
  • contains copper ions:
  • CuA: 2 ions that accept electrons from cytochrome C
  • CuB: bonded to heme a3, forming a binuclear center that transfers 4 electrons to oxygen (tyrosine involved in binding)
  • copper ions are held in place by histidine’s and a cysteine -> a tyrosine is involved too for CuB
  • one the protein subunits it capable of moving protons through a membrane type bhor effect -> vectorial/ pumped protons
  • there are also scalar/chemical protons too -> these arnt deposited into the IMS, rather they are depleted from the matrix -> used to reduced oxygen to water
  • hydrogens of the water are obtained specifically from the matrix by scalar protons
74
Q

cytochrome oxidase passes electrons to O2: complex 4

A
  • 4 electrons are used to reduce 1 oxygen molecule into 2 water molecules
  • 4 protons are picked up from the matrix in this process -> chemical/scalar protons
  • 4 additional protons are passed from the matrix to the intermembrane space via membrane bohr effect (conformational changes) -> vectorial/pumped protons
75
Q

electron flow through complex 4

A
  • 4 electrons from cytochrome C and passes them to CuA
  • CuA gives the electrons to heme A
  • electrons then move from heme A to a complex including heme A3 and CuB
76
Q

complex 4: formation of water

A
  • O2 bridges CuB to heme a3 -> splitting of this leads to H2O
  • O2 binds to site with heme iron, non-heme copper, and tyrosine that can form a free radical
  • electrons move from CuA to heme a to the heme a3 and CuB complex
  • iron and copper conspire to split O2 into two O units that can each be protonated by scalar protons
  • coppers go from Cu(1) (cuprous) to Cu(2) (cupric)
  • iron in heme a3 exists in 3 valences -> ferrous, ferric, and ferril (Fe+4)
  • all of the different valences of iron and copper must be achieved to split O2
  • complex 4 carries a series of 1e- rxns involving changes in valency of Cu and Fe atoms
77
Q

alternate donor of electron to complex 4

A
  • rather than just cytochrome C there is tetramethyl-p-phenylenediamine (TMPD)
  • can donate electrons to complex 4 directly
  • we can bypass complex 1, 2, and 3 with TMPD
  • electron pair is initially derived from ascorbic acid (reduces 2 electrons at a time) which reduced TMPD
  • cytochromes involved in complex 3 and 4 are 1 electron redox carriers (problem bc ascorbic is 2e-)
  • TMPD is a mediator -> can carrier 2e- or 1e- at a time
  • combination of ascorbate and TMPD can reduced cytochrome oxidase without the aid of complex 1, 2, and 3
78
Q

summary of ETC transport

A
  • complex 1 -> comple 4
  • 1NADH + 11H+ + 1/2O2 -> NAD+ + 10H+ + H2O
  • complex 2 -> complex 4
  • FADH2 + 6H+ + 1/2O2 -> FAD + 6H+ + H2O
  • difference in number of protons transported relfects differences in ATP synthesized
  • in reality these are rarely truly integral bc the vectorial protons are not participating directly in chemical rxns
  • more protons are moved when complex 1 is the initial source of electrons than when complex 2 is used
79
Q

multiple complexes associate together to forma respirasome

A
  • all the complexes together in a respirasome
  • ensures great efficiency for electron movement from one complex to another
  • not covalently linked -> they are aggerated in a multicomplex structure
80
Q

mitochondria

A
  • couples electron transport using the various intermediates of the ETC
  • also moves the protons
  • protons are the driving force for ATP synthesis in the mitochondria
  • ETC- oxidative part is carried out and reduction of water to O2
  • ATP synthase carries out the phosphorylation part
81
Q

inhibitors of the ETC

A
  • rotenone and amytal inhibits complex 1 -> block it at the conversion of NAD to NADH and the oxidation of NADH reducing CoQ
  • no inhibitors of complex 2
  • antimycin A and stigmatellin inhibits complex 3 -> block the reoxidation of reduced CoQ and the reduction of cytochrome C
  • carbon monoxide (CO) and cyanide (CN-) (like hemoglobin) inhibited complex 4 moves protons using a membrane bohr effect and depletes the matrix of protons to complete the reduction of water to O2
  • cyanide binds to ferric state iron -> irreversible
  • a-type cytochrome heme is sensitive to cyanide
82
Q

proton motive force

A
  • protons in ETC create electrochemical proton gradient by:
  • actively transporting protons across the membrane (complex 1 and 4 -> vectorial protons)
  • chemically removing protons from the matrix (reduction of CoQ in complex 3 and reduction of O2 to water in complex 4 -> scalar or chemical protons)
  • releasing protons into the intermembrane space (oxidation of QH2 in complex 3 -> scalar or chemical protons)
  • intermembrane space becomes positive with protons
  • matrix is depleted and negative relatively (either into the intermembrane or by O2)
  • proton concentration and electrical charge change -> chemical and electrical potential
  • binding of protons from matrix to inner membrane proteins coupled to release of protons from other inner membrane proteins or other domains of membrane spanning protein into the intermembrane space
  • rxn of protons in the matrix with ETC components without subsequent release into IMS
83
Q

chemiosmotic model for ATP synthesis

A
  • electrical potential drops are balanced to the fact that protons are moving from the matrix to the intermembrane
  • electropotential- charge separation
  • chemical potential- proton concentration difference
  • electron transport sets up a proton motive force
  • energy of proton motive force drives synthesis of ATP
84
Q

ATP synthase (complex 5)

A
  • 2 major components: F1 and F0
  • F1- multiprotein component that sticks into the matrix -> can be split off the F0 component
  • F1 is soluble in the matrix
  • F1 individually catalyzes the hydrolysis (phosphorylation) of ADP and inorganic phosphate to ATP
  • F0- anchored (integral) within the inner membrane
  • multisubunit bridge that connects F0 and F1
  • F0 transports protons from IMS to matrix dissipating the proton gradient -> energy is transferred to F1 to catalyze phosphorylation of ADP
  • stalk- attached to the F0 and makes it way through the interior of F1
  • driving force is the passage of protons through proton channel in F0
85
Q

relationship of ETC and ATP synthesis

A
  • ATP synthesis via oxidative phosphorylation requires electron transport
  • electron transport DOES NOT require ATP
  • need for ADP and inorganic phosphate for the coupled preparation of mitochondria to take up O2
  • when we add succinate substrate to ETC we see there is a large uptake of O2 and ATP is synthesized
  • if we add succinate without ADP (substrate for ATP synthase) we see some electron transport and minimal ATP synthesis
  • once ADP is added O2 is consumed and ATP is made
  • when we add an inhibitor of the ATP synthase (oligomycin) -> no ATP is made and little O2 is taken up -> inhibits the entire ETC too!
  • if we add dinitrophenol (DNP) which allows electrons to flow back in the matrix bypassing ATP synthase -> no ATP synthesis but still O2 is taken up -> inhibits ATP synthase but not the ETC
86
Q

uncouplers

A
  • lipophilic weak acids
  • pass through the membrane in either a charged or uncharged state
  • when there are more protons in the IMS than matrix -> protons bind to uncouplers and are moved back into the matrix down the concentration gradient (no channels)
  • allow protons to move back form the intermembrane to the matrix bypassing the ATP synthase
  • collapses a proton gradient -> no driving force for ATP synthase (not essential for ETC)
  • collapsing gradient prevents ATP synthesis but ETC is still carried out
  • no ATP synthesis but still O2 is taken up
  • inhibits ATP synthase but not the ETC
  • DNP- 2,4-dinitrophenol (shoe polish)
  • FCCP
  • CCCP
87
Q

energy of the ETC

A
  • there is more than enough energy that is associated with moving electrons from NADH all the way to reduction of H2O to O2
  • enough to make 3 ATP worth but no ATP is made directly by the ETC
  • big delta G
88
Q

structure of ATP synthase complex 5

A
  • base is made up of 10-12 C subunits -> F0 that is anchored in the membrane
  • F0 takes protons that are accumulated in the IMS into the matrix
  • F1 has alpha and beta subunits
  • gamma stalk connects F1 and F0 -> anchored in F0 and travels through the interior of F1 (not covalently attached)
  • oligomycin sensitivity conferring protein (OSCP)- the top of the bridge
  • conformational changes in the bridge are felt by the OSCP -> affects the alpha beta pairs of F1
  • OSCP can cause a slowdown and stoppage of ETC in a well coupled mitochondrion if oligomycin is allowed to bind to complex V -> but ETC can resume if CCCP is then added to mitochondrion
89
Q

rotation of the gamma stalk

A
  • attached to the C subunits of F0 and passes through the interior of F1 alpha beta pairs
  • c subunits can undergo rotation that is structurally coupled to rotation of gamma subunit
  • rotates
  • first event in the synthesis of ATP is for ADP and inorganic phosphate to bind to one of the alpha beta pairs in the loose (L) conformation
  • as the gamma stalk rotates alpha beta subunit pair goes through conformational change to the tight (T) site induced by the rotation of the gamma stalk -> brings the ADP and inorganic phosphate up against each other -> orbital steering (orbits line up)
  • alpha-beta pairs in F1 DO NOT rotate
  • ADP and inorganic phosphate react to form ATP
  • additionally, in this step ATP’s previously made in the tight (T) conformation are now in the open (O) site -> escape of ATP
  • gamma stalk rotates again and the 3rd alpha beta pair participates in binding ADP and inorganic phosphate in loose -> orbital streeing and rxn in the tight -> and release of ATP in the open
  • repeat
  • all of the ATP appears to come from the conformational changes in the alpha beta pairs induced by rotation of the gamma stalk
90
Q

isolated ATP synthase experiment

A
  • F1 is anchored via the bridging peptide sequence -> His tag to an immobilized surface
  • protons are supplied to the C subunits
  • F-actin tail is attached to the C subunits
  • F-actin tail rotates as the C subunits are offered protons
  • the system can be made to rotate backwards by supplying ATP -> ATPase activity of the alpha beta pairs will rotates the entire system backwards
  • proton gradient rotates forward
  • if the complex is isolated so there is no gradient -> ATP can force it to rotate backward
91
Q

transport of ADP and Pi into matrix: substrates

A
  • ATP synthase is driven by proton but it has substrates
  • substrates are ADP and inorganic phosphate
  • IMS and matrix are relatively impermeable
  • ADP makes it way into the matrix from the IMS via an ATP ADP channel (antiporter)
  • once ATP is made by F1 it escapes the matrix into the IMS and ADP is exchanged into the matrix
  • inorganic phosphate is transported via symporter (moves inorganic phosphate and protons to maintain a charge balance)
92
Q

inhibitors of the ATP ADP antiporter

A
  • atractyloside
  • bongkrekic acid
  • if you cant get substrates (ADP) into the matrix the synthase wont work
  • you need both substrates and proton gradient
93
Q

positively charged residues

A
  • responsible for moving the protons from the IMS through the C subunits back into the matrix
  • ex. arg
94
Q

P/O ratios

A
  • how many ATPs are made per O2 consumed by the ETC
  • enough energy going from NADH all the way to reduction of H2O to O2 to make 3 ATP
  • you can short circuit the chain by providing succinate instead of NADH -> fewer protons are moved from the matrix to the IMS -> then only 2 ATPs are made per O2 consumed
  • if we use TMPD which bypassing almost the entire chain except for cytochrome oxidase -> just enough protons are moved by cytochrome oxidase to make 1 ATP (tested by using antimycin A and stigmatellen which inhibit complex 3)
  • P/O ratio is consistent which the extent of rotation of the C subunits by the protons passing through the c subunit channels
  • about 10 protons need to be passed through that channel for the complete rotation of the c-ring and gamma subunit -> makes 3 ATPs
  • if we use succinate there will only be 2/3rds of a rotation -> 2 ATP made
  • if we use ascorbate and TMPD there will only be 1/3rd of a rotation -> 1 ATP
95
Q

inhibiting the ETC by inhibiting the ATP synthase in a well coupled mitochondria

A
  • if you were to inhibit ATP synthesis with oligomycin in a well coupled mitochondrial preparation -> you would no longer be able to allow protons to rotate the c subunits as they try to pass through the ATP synthase
  • oligomycin inhibits by attaching to delta subunits of F1
  • rotation of the c subunits is stopped my oligomycin
  • no protons could pass through c subunits -> proton gradient being made from the ETC will grow bigger and bigger
  • proton gradient is so large from high concentration of the proton in the IMS -> that the entire ETC would stop
  • possible to stop electron transport in a well coupled mitochondria by inhibiting the ATP synthase
  • if we add DNP, DCCP, CCCP -> destroys the gradient and now the ETC will proceed
96
Q

uncouplers: weight loss

A
  • shoe polish- DNP
  • CCCP
  • FCCP
  • used as weight loss strat
  • oxygen is consumed (burn metabolites) in the ETC but no ATP is not made
  • causes toxic problems
97
Q

natural uncouplers in the body

A
  • UCP’s
  • UCP2 and UCP3
  • natural proteins
  • partially in a limited way collapses the proton gradient
  • work the same as CCCP and DNP
98
Q

ATP/ADP and ATP/Pi ratios

A
  • in a well coupled mitochondrial preparation that is well supplied with substrates -> the ATP/ADP ratio and ATP/Pi ratio will be high bc ATP is being made
  • the synthesis of ATP by a well coupled mitochondrial system is dependent on the source of ETC substrates
  • NADH/NAD ratio affects this
  • when NADH is high -> driving force to make ATP
  • when NAD is high -> less ATP is made
  • NADH/NAD ratio controls many steps in carbohydrate metabolism and krebs
  • when NADH/NAD ratio is high -> citrate synthase, isocitrate dehydrogenase, and succinyl thiokinase are activated -> drives krebs to generate reducing equivalents which feed into ETC -> drives ATP synthesis
  • when NADH/NAD ratio is low there are no proton to form the gradient to make ATP
  • NADH/NAD ratio has reciprocal affects to ATP/ADP and ATP/Pi ratios
99
Q

IF1

A
  • regulates ATP synthase
  • at lower pHs IF1 inhibits ATPase activity of F1 by binding -> prevents ATP hydrolysis back to APD and Pi
  • can drive itself into the F1 subunit complex of the ATP synthase
  • regardless of ETC and coupling between the proton transport and ATP synthesis -> if F1 enters the ATP synthase at the alpha beta subunit region the entire system stops
  • if you are making more than enough ATP -> you want to avoid the ATP synthase to reverse itself on its own
  • F1 subunit can hydrolyze ATP back to ADP by itself
  • deprives the cell of its remaining energy resources
  • IF1 protects the entire system from hydrolyzing ATP back to ADP and Pi
100
Q

krebs cycle

A

effective biosynthetic pathway

101
Q

tyrosine kinases

A
  • insulin receptor

- M2 variant in cancer cells

102
Q

warburg effect

A
  • carry out synthesis of lactic acid (homolactic fermentation) even though there is oxygen around
  • cancer cells
  • yeast
103
Q

oncogenes

A
  • p53
  • AKT
  • entore
  • activation of the pathways: aerobic glycolysis, aerobic homolactic fermentation, krebs cycle driven by glutamine and glutamate -> alpha-ketoglutarate, partial activation of krebs to malate and oxaloacetate
  • neoplastic transformation
104
Q

fats

A
  • cancer cell metabolism
  • fatty acid synthase (FASN) tends to be activated
  • drugs inhibit fatty acid synthase are antineoplastic reagents
  • FASN inhibitors are antiproliferative towards tumor cells
  • inhibit proliferative activity
  • orlistat (Xenical) inhibits fatty acid synthase and lipases secreted by pancreas and in the stomach
  • antilipase activity- weight loss
  • antagonism of fatty acid synthase repurposed
  • activator of catabolic rxns in cells -> AMP kinase (AMPK) -> phosphorylates
  • phosphorylation activates regulated steps in breakdown (glycolysis) and inhibits regulated steps in synthesis
  • AMPK sustained activation inhibits tumor growth
  • AMPK activates glycolysis by activating PFK-2 (via phosphorylation) -> makes the F2,6diP -> activates PFK-1
  • AMPK inhibits acetyl-CoA carboxylase (via phosphorylation) -> which inhibits fatty acid synthesis -> lowers levels of malonyl CoA (rate limiting) > relieve inhibition of carnitine acyl transferase (active) -> enhances fatty acid entry into the mitochondria and breakdown to acetyl-CoA
105
Q

AMPK

A
  • catabolic pathway generally
  • activated by phosphorylation by liver Kinase B1 (LKB1)
  • stimulates a catabolic cascade
  • defective AMPK is associated with increase tendency to develop cancer -> mutation in LKB1
  • activation of LKB1 -> antiproliferative signal
  • activator of catabolic rxns in cells -> AMP kinase (AMPK) -> phosphorylates
  • phosphorylates and activates regulated steps in breakdown (glycolysis) and inhibits regulated steps in synthesis
  • AMPK sustained activation inhibits tumor growth
  • AMPK activates glycolysis by activating PFK-2 (via phosphorylation) -> makes the F2,6diP -> activates PFK-1
  • AMPK inhibits acetyl-CoA carboxylase (via phosphorylation) -> which inhibits fatty acid synthesis -> lowers levels of malonyl CoA (rate limiting) > relieve inhibition of carnitine acyl transferase (active) -> enhances fatty acid entry into the mitochondria and breakdown to acetyl-CoA
106
Q

effects of AMPK

A
  • in the heart homolactic fermentation is stimulated by AMPK
  • in skeletal muscles glycogen storage is diminished
  • glycolysis is stimulated
  • catabolism in skeletal muscles includes utilization of pyruvate and fatty acids for catabolic rxns -> krebs cycle and CO2
  • in liver all the biosynthetic rxns (gluconeogenesis, synthesis of steroids and cholesterol from acetyl-CoA) are inhibited
  • ultimate catabolic signaling enzyme
  • shuts down ATP consuming biosynthetic rxns and stimulating oxidative catabolic pathways that lead to increase ATP production
  • proanabolic and anticatabolic signals (insulin) are inhibited by AMPK
  • glycogen synthase is inhibited bc of this
  • the source of insulin (beta cells of pancreas) are inhibited by AMPK too
107
Q

AMPK inhibits synthesis of fatty acids, cholesterol, and glucose in liver

A
  • AMPK phosphorylates and inhibits acetyl-CoA carboyxlase ACC1 and FS -> FA synthesis decreases
  • AMPK phosphorylates and inhibits HMG-CoA reductase -> cholesterol synthesis decreases
  • AMPK phosphorylates and inhibits TORC2 -> inhibits transcription of gene coding PEPCK -> turns off gluconeogenesis to conserve ATP
108
Q

AMPK promotes FA oxidation and glucose uptake, but inhibits glycogen synthesis in skeletal muscle

A
  • AMPK inhibits ACC -> malonyl-CoA decreases -> lifts inhibition or activates carnitine palmitoytransferase -> more fatty acids move into mitochondria for beta-oxidation
  • AMPK increases recruitment of GLUT4 to plasma membrane -> stimulates expression of gene encoding GLUT4 -> facilitates insulin-independent uptake of glucose
  • AMPK inhibits G5 -> inhibits glycogen synthesis
109
Q

overview of signal transductions

A
  • extracellular small molecule (typically hormone) binds to a receptor
  • receptor is coupled to a membrane associated kinase through a g-protein
  • g-protein coupled receptors transfer the extracellular signals to the kinases in order to activate them
  • 3 common forms of receptor mediated g-protein coupled receptor activations: insulin receptor, adenylate cyclase, phosphoinositide
  • g-protein coupled receptors can be activating or inhibitory
110
Q

G-protein coupled receptor: insulin

A
  • tyrosine kinase
  • leads to inflammation as well as tumor cell invasiveness
  • tyrosine kinases are coupled via g-proteins
111
Q

G-protein coupled receptor: phosphoinositide pathway

A
  • triggered by generation of breakdown of the phospholipids in phosphatidylinositol
  • breakdown of phosphatidylinositol generates a bunch of signals inside the cell -> include inositol triphosphate and residue (diacyl glycerol) of the mechanism by which phosphatidylinositol is incorporated into biological membranes
  • when phosphatidylinositol is hydrolyzed diacyl glycerol (DAG) is produced and inositol triphosphate (IP3) (secondary signaling molecules)
  • initiation of the hydrolysis of phosphatidylinositol is achieved via g-protein coupled to phospholipase C that breaks it down
112
Q

g-protein coupled receptor: adenylate cyclase

A
  • activation of the phosphorylating enzyme: protein kinase A
  • receptors detects an extracellular signal
  • glucagon or epinephrine are extracellular signaling molecules -> activate protein kinase A
  • triggers communication to a heterotrimeric g-protein- associated with protein kinase A signal transduction pathway
  • communication is between the receptor of the hormone (glucagon and epinephrine) which activates a membrane bound enzyme -> adenyl cyclase
  • adenyl cyclase makes cyclic AMP -> cyclic AMP activates protein kinase A
  • product of pathway (cyclic AMP) can destroyed before it activates protein kinase A -> hydrolyze cyclic AMP and convert it to AMP
  • enzymes that inhibit phosphodiesterase (hydrolyzes cAMP) are drugs -> Viagra -> vasodilation
  • certain toxins that keep the activating g-protein from dissociating -> keep on all the time -> cholera toxin
  • certain toxins turn off the activity of the (inhibitory) g-protein coupled receptors that would otherwise be activated -> pertussis
113
Q

adenyl cyclase

A
  • membrane bound enzyme that makes cAMP
  • stimulates catabolic pathways
  • multidomain membrane protein complex
  • domains that inhibit adenyl cyclase
  • cAMP is capable of activating the protein kinase A
  • PKA catalytic subunits are activated by dissociation of regulatory subunits upon binding of 2 cAMP to each regulatory subunit -> displace the catalytic subunits that can now bind protein targets
  • protein kinase A can feedback and inhibit adenyl cyclase
  • activating g-proteins -> alpha subunit of the g-protein is responsible for activating adenyl cyclase
  • prevention of alpha subunit of the inhibitory g-protein from being released to reach adenylyl cyclase -> pertussis toxin -> results in activation of adenyl cyclase
114
Q

activating pathway of adenylate cyclase

A
  • receptor for glucagon or epinephrine (specific for activation)
  • g-protein (which is heterotrimeric) -> alpha subunit (binds GDP or GTP) and beta and gamma subunits which are always tightly associated
  • receptor that responds to the extracellular signal causes dissociation of the g-alpha subunit from the g-beta/g-gamma subunits
  • dissociated g-alpha subunit activates or inhibits adenyl cyclase (in this case activate bc glucagon and epinephrine are specific to activation)
  • g-alpha is released from g-beta and g-gamma which turns on adenyl cyclase -> cAMP is generated -> protein kinase A is turned on
115
Q

sequence of events for adenyl cyclase activation and deactivation

A
  • the sequence of events starts with the heterotrimeric protein associating with the receptor GDP bound to the g-alpha subunit
  • heterotrimeric g-protein are capable of shuttling between receptors and adenylate cyclase
  • when the receptor interacts with the heterotrimeric g-protein AND a ligand like glucagon or epinephrine -> there will be an exchange with GDP with GTP -> guanine exchange factor rxn
  • guanine nucleotides bind to Galpha subunit
  • GTP is now bound to g-alpha subunit
  • GTPase activity of Galpha shuts down heterotrimeric g-proteins
  • GTP bound g-alpha subunit dissociates from the receptor -> diffuses and activates adenyl cyclase
  • adenyl cyclase is activated as long as the GTP bound g-alpha subunit is associated
  • hydrolysis of the GTP on the g-alpha subunit favors dissociation of the g-alpha subunit -> turns off activation of adenyl cyclase -> activates protein kinase A
116
Q

protein kinase A

A
  • activated by adenyl cyclase
  • target of cAMP
  • hetertetrameric enzyme
  • 2 regulatory and 2 catalytic subunits
  • favors breakdown (glycolytic and glycogenolytic enzyme)
  • catalytic subunits- activates phosphorylase (chemical modification)
  • phosphorylase is also subject to allosteric regulation (non chemical)
117
Q

breakdown of glycogen

A
  • phosphorylation cascade that favors breakdown of glycogen involves other targets like phosphorylase kinase, cAMP, activating protein kinase A
  • activating protein kinase A is a means for phosphorylation phosphorylase and phosphorylase kinase
  • protein kinase A- catalytic subunit
  • glycogen phosphorylase is activated via protein kinase A
  • phosphorylase is regulated by allosteric effectors and chemical modification through phosphorylation
118
Q

liver adapts to changing metabolic condition

A
  • portal vein carries nutrients to the liver
  • hepatocytes turn nutrients into fuel
  • hepatocyte enzymes turn over quickly
  • enzymes increase or decrease with changes in diet and the needs of other tissues
119
Q

fates for glucose-6-phosphate in the liver

A
  • dephosphorylate to yield free glucose to send to other tissues
  • make into liver glycogen
  • enter glycolysis, make acetyl CoA and then ATP for hepatocytes themselves
  • enter glycolysis, make acetyl CoA to be made into fatty acids and then TAGs
  • enter pentose phosphate pathway to yield NADPH and ribose-5-phospahte
120
Q

muscles (myocytes): two types

A
  • slow-twitch (red muscle):
  • fed by many blood vessels
  • rich in mitochondria (to provide energy via slow and steady oxphos)
  • fast twitch (white muscle):
  • fewer mitochondria and lower O2 delivery
  • uses ATP faster and fatigues faster due to greater demands (more tension) combined with reduced O2 delivery
  • endurance training can increase mitochondria
121
Q

energy source for muscle contraction

A
  • muscle glycogen -> glucose-6-phosphate
  • yields 3 ATP, not 2 (as in glycolysis)
  • glycogen breakdown skips ATP dependent hexokinase rxn
  • pyruvate -> lactate to create NAD+ to enable glycolysis to continue
  • phosphocreatine is another energy source
  • phosphocreatine + ADP -> burst of heavy activity -> creatine + ATP (other way around during rest)
  • acted on by creatine kinase to release ATP
  • during light activity or rest- fatty acids, ketone bodies, blood glucose is used
122
Q

hormonal control of glycogen mobilization

A
  • epinephrine cascade stimulates glycogen phosphorylase

- break down glycogen in muscle and liver

123
Q

O2 debt

A
  • after vigorous exercise, rapid breathing continues
  • used for oxidative phosphorylation to build proton gradient and replenish ATP
  • ATP used for gluconeogenesis to use up lactate and restore muscle glycogen concentration (cori cycle)
124
Q

the cori cycle

A
  • in skeletal muscle that is capable of bursts of activity there is a process that allows the muscle to receive ATP from aerobic mitochondria or anaerobic catabolism that only uses glycolytic path
  • during anaerobic activity lactate is produced
  • lactate enters the blood and goes to the liver -> uses lactate as a fuel
  • uses ATP in gluconeogenesis to make glucose form lactate (during recovery)
  • glucose leaves liver and returns to the muscle which uses its own glycogenic pathway to build up glycogen for next period of active contraction
  • liver making glucose from lactate
  • muscle making lactate from glucose
  • there is a version of the cori cycle that works in the heart
125
Q

heart muscle versus skeletal muscle

A
  • heart muscle has more mitochondria (50% of cell volume)
  • it is fueled primarily by fatty acids (some ketones, some glucose, some phosphocreatine)
  • uses fatty acids (preferably) as the krebs cycle substrate
  • glycolytic path runs through pyruvate and goes through part of gluconeogenesis to make oxaloacetate and malate -> these are kreb cycle intermediates that can now use the krebs cycle to oxidize acetyl CoA (from fatty acids) all the way to CO2
  • it is an aerobic organ
  • if the O2 supply is cut off, the muscle dies -> myocardial infarction
126
Q

aerobic organ

A
  • makes ATP in mitochondira
  • substrate of choice will be fatty acid oxidation
  • acetyl CoA is the substrate of the krebs (doesnt prefer)
  • acetyl CoA is used for oxidation not used for biosynthetic purposes
127
Q

heart: energy

A
  • three major demands: house keeping functions (you need ATP), ion pumping for contraction, contraction (ATP for movement of myosin heads)
  • energy demands are a lot
  • we must integrate fatty acid catabolism and carbohydrate catabolism to get the energy we need
  • getting fatty acids into the mitochondria is the rate limiting step in fatty acid catabolism
  • carnitine acyl transferase shuttles the fatty acids into the heart
  • once the fatty acids are in they will be catabolized/oxidized all the way to acetyl CoA -> no intramitochondrial regulatory step (this is why regulation at the carnitine acyl transferase is important)
  • carbohydrates are converted via the glycolytic pathway to pyruvate
  • pyruvate can be completely oxidized to acetyl CoA via pyruvate dehydrogenase however if there is enough acetyl CoA from fatty acid catabolism it can chose not to
128
Q

heart: acetyl CoA

A
  • derived from fatty acid catabolism or carbohydrates converted from pyruvate to acetyl CoA via pyruvate dehydrogenase
  • fatty acid oxidation mostly is unregulated
  • fatty acids is the preferred method of making acetyl CoA
  • acyl transferase that make use of carnitine bring fatty acids into the heart -> regulated
  • use a little bit of gluconeogenic pathway to make kreb cycle intermediates in order to make full use of the fatty acid derived acetyl CoA
  • acetyl CoA inhibits pyruvate dehydrogenase -> fatty acid catabolism shuts down carbohydrate metabolism
  • krebs cycle and ETC of mitochondria is supplying the ATP
129
Q

creatine

A
  • if there is more than enough ATP the heart stores glucose and uses it to make glycogen
  • BUT more importantly it can store creatine
  • creatine can be phosphorylated to phosphocreatine
  • phosphocreatine has a high energy phosphate bond -> high energy nitrogen bond that can be used to make ATP
  • phosphocreatine is hydrolyzed and phosphorylates ADP
130
Q

advantage of acetyl CoA from fatty acid catabolism/oxidation: 2 inhibition methods

A
  • two products of fatty acid oxidation that we need to consider: coenzyme A in the form of acetyl CoA and NADH
  • both of these products are regulatory towards pyruvate dehydrogenase -> allosteric negative effectors
  • fatty acid oxidation inhibits the oxidation of pyruvate via pyruvate dehydrogenase to acetyl CoA
  • shut down is not extreme bc the activity of the mitochondria is enough to use up a lot of the NADH in ETC and acetyl CoA in the krebs which slows inhibition
  • if krebs and ETC slow down the allosteric negative effectors accumulate and feedback on to pyruvate dehydrogenase
  • NADH and acetyl CoA can shut down pyruvate kinase through another mechanism (analogous to shut down of PFK2 and F26biP
  • a kinase stimulated by cAMP phosphorylates E1 of pyruvate dehydorgenase -> inhibits
  • phosphatase stimulated by insulin removes the phosphate from E1 -> relieves inhibition
  • excess NADH also tends to slow the glycolytic pathway at other steps (glyceraldehyde-3-phosphate dehydrogenase step) -> shys away from glycolysis while fatty acid catabolism is going on
131
Q

heart: lactate

A
  • heart takes up lactate from skeletal muscle

- extracts lactate from the blood and use it for fuel

132
Q

depletion of O2 to the heart

A
  • when we decrease blood and therefore O2 we decrease mitchondrial metabolism which is necessary for fatty acid catabolism -> glycolysis increases which causes accumulation of lactate, protons (lower pH)
  • atherosclerotic cardiovascular disease
  • blood passes through at a reduced rate (reduced prefusion) -> low O2 and nutrients
  • reduced reduction of blood and O2 will compromise hearts ability to wash out metabolic products of contractile activity
  • the heart may switch over to some modest anaerobic glycolysis -> uses glycogen stores to supplement reduced glucose form reduced blood flow -> generates lactate
  • accumulation of lactate
  • protons form glycolysis and mitochondrial metabolism will decrease pH -> negative effect on glycolysis (PFK is pH sensitive)
  • if you lower pH the muscle cant carry out glycolytic metabolism as well
  • therefore is glycolysis if slowed, and mitochondrial activity is slowed (low oxygen) -> myocardial infarction
  • clots will cause serious problems
133
Q

chronic ischemia

A
  • people who blood supply is not completely cut off
  • function normally by reducing the obligate dependency of the heart on fatty acid catabolism
  • partially inhibit the catabolic pathway
  • do this by using trimetazidine- partial inhibitor
  • trimetazidine inhibits thiolase enzyme (beta-ketoaceyl transferase)
  • trimetazidine is a partial inhibitor meaning that fatty acid catabolism is not completely stopped but significantly reduced
  • partially reduction of fatty acid catabolism -> NADH and acetyl CoA (products) is partially depleted -> pyruvate dehydrogenase is less inhibited
  • heart switches from fatty acid catabolism to glycolytic oxidation (pyruvate dehydrogenase) when under chronic ischemia (slow blood flow)
  • glucose and lactate are used as sources of energy (they are not absolutely dependent on O2) -> can use anaerobic when there is less O2
134
Q

diabetes

A
  • ketone bodies accumulate in blood (ketosis)
  • at risk for elevated levels of acetyl CoA and NADH in the cardiac mitochondria
  • endogenously produced acetyl CoA and NADH from fatty acid oxidation combine with the other acetyl CoA NADH cardiac mitochondria -> reduce the ability of the heart to use glycolysis (inhibits pyruvate dehydrogenase)
  • ketone bodies are sources of acetyl CoA
  • only organ that can make ketone bodies, but also cant use -> liver
  • heart can use ketone bodies -> accumulation of acetyl CoA -> poorly perfused (same as chronic ischemia)
135
Q

maintaining angina (chest pain) due to cardiac ischemia

A
  • give insulin -> helps allow entry of glucose into cardiac muscle
  • insulin also relieves the inhibition of pyruvate dehydrogenase E1 through phosphatase
  • improving blood flood -> nitroglycerin (dilates vessels)
  • inhibit fatty acid oxidation with drugs like trimetazidine
136
Q

chloroacetate

A
  • specific inhibitor of the kinase that inhibits E1 by being phosphorylated
  • drug
137
Q

drugs that inhibit the carnitine acyl transferases

A
  • reduces the levels of fatty acids entering the heart

- allow the heart to rely more on glycolysis and carbohydrate metabolism

138
Q

resting state

A

-flux through krebs is low bc there is low local concentrations of NAD+ if the rate of oxidative phosphorylation is low

139
Q

why is krebs aerobic even though it doesnt use O2

A
  • bc it produces reduced electron carriers that are reoxidized by transferring their electrons to O2
  • without O2 electrons build up -> glycolysis starts producing lactate (instead of pyruvate) -> inhibits krebs
140
Q

NADH

A
  • cannot transport one electron at a time

- FMN, FAD, ubiquinone, and heme can

141
Q

if ascorbate and methylene blue or TMPD are added to a mitochondria that is inhibited with antimycin a or stigmatellin

A

-about 1 ATP can be made per O2 consumed using the proton gradient established in part by selective uptake of protons from the matrix in a sequence of rxns that result in reduction of oxygen to water

142
Q

citrate synthase

A

-catalyzes an unfavorable rxn that is pushed in the forward direction by the concentration of oxaloacetate

143
Q

isocitrate dehydrogenase

A
  • can be found in at least two isozymes
  • one in cytosol that use different redox cofactors
  • one uses NADPH and the other NADH
144
Q

similarities between PDH and alpha-ketoglutarate dehydrogenase

A
  • both employ TPP to convert a carbonyl into a hydroxyl and supply a double bond beta to the carboxyl in order to eliminate it
  • both react an aldehyde with the disulfide form of a cofactor to generate a thiohemiacetal
  • both release a product from their 2nd subunit, E2, that has a high energy bond
  • both use flavin to reduce a nicotinamide
145
Q

GTPase

A

-GTPase activity of alphaG subunit causes it to dissociate from AC -> shuts down cyclase activity

Biochemistry (8 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions