Biochem 501 - Unit 3 Metabolic Pathways

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97 Terms

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exergonic

reactants to products

releases energy

-G

<p>reactants to products</p><p>releases energy</p><p>-G</p>
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endergonic

products to reactants

input of energy

+G

<p>products to reactants</p><p>input of energy</p><p>+G</p>
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exothermic

bonds formed and heat released

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endothermic

bonds broken and heat absorbed

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net reactions

go towards equilibrium and energy is available as equilibrium is approached

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prepatory phase of glycolysis

phosphorylation of glucose and its conversion to glyceraldehyde 3-phosphate

-endergonic

-Uses (-2ATP)

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payoff phase of glycolysis

Oxidative conversion of glyceraldehyde 3-phosphate to pyruvate and the coupled formation of ATP and NADH

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dehydrogenase reaction glycolysis

produces 2NADH by oxidation, only redox reaction in glycolysis

step6

<p>produces 2NADH by oxidation, only redox reaction in glycolysis</p><p>step6</p>
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products of glycolysis

2 ATP, 2 NADH, 2 pyruvate

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reactants of glycolysis

glucose, 2 ATP, 2 NAD+

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NADH formation

NAD+ must be oxidized and is a transfer of 2e- and 2H+

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ATP as a substrate and inhibitor

binds to both the active site of the enzyme and to the separate allosteric site.

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enzymes catalyze irreversible steps

this avoids futile cylcing

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fermentation

ways to regenerate NAD+ from NADH w/out O2 to maintain glycolysis to produce ATP

<p>ways to regenerate NAD+ from NADH w/out O2 to maintain glycolysis to produce ATP</p>
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Pyruvate to Lactate

lactate dehydrogenase

NADH to NAD+

<p>lactate dehydrogenase</p><p>NADH to NAD+</p>
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Depleted NAD+

stops glycolysis

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pyruvate to ethanol

Pyruvate is catalyzed by pyruvate decarboxylase and H+ to acetaldehyde and CO2 which is then catalyzed by alcohol dehydrogenase and NADH to Ethanol and NAD+

<p>Pyruvate is catalyzed by pyruvate decarboxylase and H+ to acetaldehyde and CO2 which is then catalyzed by alcohol dehydrogenase and NADH to Ethanol and NAD+</p>
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pyruvate dexarboxylation

only found in yeast cells

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aerobic fate of pyruvate

pyruvate is oxidizied into Acetyl-CoA by pyurvate dehydrogenase complex and NADH and CO2 is produced

<p>pyruvate is oxidizied into Acetyl-CoA by pyurvate dehydrogenase complex and NADH and CO2 is produced</p>
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pyruvate dehydrogenase complex

enzymes that convert pyruvate into acetyl-CoA

E1.E2.E3 subunits

involved in regulation

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reduced form

NADH and FADH2 (carries electrons)

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thiolester bond

acetyl-CoA bond that holds energy

<p>acetyl-CoA bond that holds energy</p>
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Dehydrogenase

An enzyme that catalyzes a chemical reaction during which one or more hydrogen atoms are removed from a molecule.

Performs redox reactions

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more energy when fully oxidized

more C-C and C-H bonds (contain more energy)

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pyruvate DH: E2 reaction

oxidation

lipoic acid on site E2 gains e- and is reduced

<p>oxidation</p><p>lipoic acid on site E2 gains e- and is reduced</p>
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pyruvate DH: E3 reaction

electron shuttling

the e- transfer from lipoic acid to NAD+ which enables PDH to go another round

<p>electron shuttling</p><p>the e- transfer from lipoic acid to NAD+ which enables PDH to go another round</p>
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pyruvate DH: E1 reaction

decarboxylation

<p>decarboxylation</p>
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citric acid cylce

completes the breakdown of glucose

central point of lipid, carb, and protein breakdown

in mitochondria

intermediates recylced

<p>completes the breakdown of glucose</p><p>central point of lipid, carb, and protein breakdown</p><p>in mitochondria</p><p>intermediates recylced</p>
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CAC step 1

Citrate synthase adds an acetyl group ( 2 carbons) to oxaloacetate

Enzyme: citrate synthase

∆G= favorable (hydrolysis of Co-A bond)

IRREVERSIBLE

Co-A recycled cofactor

<p>Citrate synthase adds an acetyl group ( 2 carbons) to oxaloacetate</p><p>Enzyme: citrate synthase</p><p>∆G= favorable (hydrolysis of Co-A bond)</p><p>IRREVERSIBLE</p><p>Co-A recycled cofactor</p>
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CAC step 2

Aconitase isomerizes citrate to isocitrate (C-OH bond moved)

Enzyme: aconitase

∆G= 0/+

Aconitate is intermediate between these 2

<p>Aconitase isomerizes citrate to isocitrate (C-OH bond moved)</p><p>Enzyme: aconitase</p><p>∆G= 0/+</p><p>Aconitate is intermediate between these 2</p>
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CAC step 3

Isocitrate dehydrogenase releases the first CO2

Enzyme: isocitrate dehydrogenase

∆G= favorable

IRREVERSIBLE

Isocitrate to α-ketoglutarate, make an NADH, and lose a CO2 (from oxaloacetate)

<p>Isocitrate dehydrogenase releases the first CO2</p><p>Enzyme: isocitrate dehydrogenase</p><p>∆G= favorable</p><p>IRREVERSIBLE</p><p>Isocitrate to α-ketoglutarate, make an NADH, and lose a CO2 (from oxaloacetate)</p>
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oxidative decarboxylation

COOCH into CO2

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CAC step 4

α-Ketoglutarate dehydrogenase releases the second CO2

Enzyme: α-Ketoglutarate Dehydrogenase Complex (α-KDHC)

IRREVERSIBLE

LOSE CO2 and MAKE NADH

-CO2 came from oxaloacetate (has not lost acetyl group from acetyl-CoA)

Succinyl CoA

conserved energy in thioester in NADH

<p>α-Ketoglutarate dehydrogenase releases the second CO2</p><p>Enzyme: α-Ketoglutarate Dehydrogenase Complex (α-KDHC)</p><p>IRREVERSIBLE</p><p>LOSE CO2 and MAKE NADH</p><p>-CO2 came from oxaloacetate (has not lost acetyl group from acetyl-CoA)</p><p>Succinyl CoA</p><p>conserved energy in thioester in NADH</p>
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CAC step 5

Succinyl-CoA synthetase catalyzes substrate level phosphorylation

Enzyme: succinyl-CoA synthetase

Need to kick off CoA

1st substrate level phosphorylation

Make GTP

Take phosphate off a substrate and put it on GDP to make GTP

<p>Succinyl-CoA synthetase catalyzes substrate level phosphorylation</p><p>Enzyme: succinyl-CoA synthetase</p><p>Need to kick off CoA</p><p>1st substrate level phosphorylation</p><p>Make GTP</p><p>Take phosphate off a substrate and put it on GDP to make GTP</p>
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CAC step 6

Succinate dehydrogenase generates ubiquinol

Enzyme: Succinyl dehydrogenase

Enzyme participates in krebs cycle (TCA) and in electron transport (ETC)

Only enzyme that sits in INNER MEMBRANE of mitochondria (enzyme cannot move)

-(rest of enzymes float around in inner membrane space)

Succinate -> fumarate, make FADH2 -> passes e- to coenzyme Q

Electrons taken off of succinate added to FAD

FADH2 passes e- to coenzyme Q to make QH2 (very important for ETC)

<p>Succinate dehydrogenase generates ubiquinol</p><p>Enzyme: Succinyl dehydrogenase</p><p>Enzyme participates in krebs cycle (TCA) and in electron transport (ETC)</p><p>Only enzyme that sits in INNER MEMBRANE of mitochondria (enzyme cannot move)</p><p>-(rest of enzymes float around in inner membrane space)</p><p>Succinate -&gt; fumarate, make FADH2 -&gt; passes e- to coenzyme Q</p><p>Electrons taken off of succinate added to FAD</p><p>FADH2 passes e- to coenzyme Q to make QH2 (very important for ETC)</p>
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CAC step 7

Fumarase catalyzes a hydration reaction

Enzyme: fumarase

Fumarate -> malate (happens fast)

Fumarate considered catalytically perfect

<p>Fumarase catalyzes a hydration reaction</p><p>Enzyme: fumarase</p><p>Fumarate -&gt; malate (happens fast)</p><p>Fumarate considered catalytically perfect</p>
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CAC step 8

Malate dehydrogenase regenerates oxaloacetate

Enzyme: malate dehydrogenase

Malate -> oxaloacetate, make NADH

After this goes back to step 1 and keeps going

-Highly endergonic +∆G= unfavorable

<p>Malate dehydrogenase regenerates oxaloacetate</p><p>Enzyme: malate dehydrogenase</p><p>Malate -&gt; oxaloacetate, make NADH</p><p>After this goes back to step 1 and keeps going</p><p>-Highly endergonic +∆G= unfavorable</p>
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desaturation

C-C to C=C

C-H to C-C

(also oxidation)

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regulation of the citric acid cylce

inhibitors: Increases energy (ex: atp produced)

stimulators: decreases energy (ex: amp, adp)

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reactants in citric acid cylce

glucose/2pyruvate

NAD+ ,FAD, H20, ADP

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products in citric acid cylcle

CO2, NADH, FADH2, ATP

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replenishing anaplerotic reaction

pyruvate + HCO3- and ATP

adds CO2 to oxaloacetate

enzyme: pyruvate carboxylase (biotin)

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Fatty acid oxidation

the metabolic breakdown of fatty acids to acetyl CoA; also called beta oxidation.

<p>the metabolic breakdown of fatty acids to acetyl CoA; also called beta oxidation.</p>
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FA oxidation step 1

Activation: Fatty acid join to Co-A

-enzymes on outer mitochondrial membrane

<p>Activation: Fatty acid join to Co-A</p><p>-enzymes on outer mitochondrial membrane</p>
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FA oxidation step 2

Transport: across inner mitochondrial membrane into mitochondrial matrix

-carnitine carrier system separates cytosolic and mitochondrial pools

<p>Transport: across inner mitochondrial membrane into mitochondrial matrix</p><p>-carnitine carrier system separates cytosolic and mitochondrial pools</p>
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FA oxidation step 3

Beta Oxidation: conversion of fatty acid into Co-A units in mitochondrial matrix

-Splitting fatty acid chain into 2-cabon sections

-4 step process

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B-oxidation step 1

Dehydrogenation: C-H bonds into C=C bond

FAD to FADH2

Enzyme: Fatty Acyl-CoA dehydrogenases

<p>Dehydrogenation: C-H bonds into C=C bond</p><p>FAD to FADH2</p><p>Enzyme: Fatty Acyl-CoA dehydrogenases</p>
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B-oxidation step 2

Hydration: C=C bond to C-OH and C-H bond

addition of H2O

<p>Hydration: C=C bond to C-OH and C-H bond</p><p>addition of H2O</p>
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B-oxidation step 3

dehydration again

<p>dehydration again</p>
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B-oxidation step 3

Thiolytic cleavage: the formation of the 2-carbon sections formed and the s-CoA is bonded.

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overall B-oxidation

8 acetyl-CoA + 7 FADH2 + 7NADH

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# of acetyl-CoA

n-1 B-oxidations

(n= # of 2C-atom segments)

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Fatty acids in mitochondria

in mitochondria: fatty acids broken down

Cytosol: fatty acids produced in excess carbohydrates

ETC keeps pools separate

<p>in mitochondria: fatty acids broken down</p><p>Cytosol: fatty acids produced in excess carbohydrates</p><p>ETC keeps pools separate</p>
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Malonyl CoA

Fatty Acid Metabolism

Acts as an inhibitor to Carnitine Acyltransferase I (CAT-1)

also known as Carnitine Palmitoyl Transferase I

Thus preventing the transport of Fatty-Acyl-CoA via the Carnitine shuttle to the mitochondria.

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Fattay acyl Co-A

cannot be brought into matrix alone, must be converted into carnitine F.A. and brought into matrix and converted back into fatty acyl Co-A

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carnitine

a small, organic compound that transports free fatty acids from the cytosol into the mitochondria for oxidation

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products of burning proteins

CO2 + H2O + (NH4+)

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NH4+ elimination

N-atoms from amino groups are attached to CO2 through urea cycle to produce urea (waste)

<p>N-atoms from amino groups are attached to CO2 through urea cycle to produce urea (waste)</p>
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detoxification

glutamine synthetase adds NH3 to glutamate to glutamine

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extrahepatic

NH4+ is detoxified to liver as glutamine which will not diffuse to the brain

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removal of amino group

Keto acids produced by transaminations which are used for CAC for gluconeogenesis and glutamate for liver

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transaminations

swapping amino groups and catalzyed by aminotransferases

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aminotransferases

transfers amino groups and turns glutamate (amino acids) --> alpha-ketoglutarate

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alanine aminotransferase

Converts Pyruvate to Alanine (a-ketogluatate to glutamate) and is highly reversible (Cycling)

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keto acid

ketone with a COO- attached

<p>ketone with a COO- attached</p>
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N-atoms flow in urea cylce

1) urea via amino acids to glutamine + glutamate

2) NH4 to aspartate

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N-donor

glutamine and glutamate in cytosol give up their N-atoms to mitochondrial liver

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excess amino acids and alanine

end in liver as glutamate via a-ketoglutarates and a-keto acid cylcing (outside mitochondria)

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how does NH4+ form

glutamate/mine form NH4+ by glutaminase/glutamate dehydrogenase

Glu to aspartate by asp aminotransferase

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carbamoyl phosphate

fuel for the urea cycle (uses ATP, HCO3-, and NH4+)

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Urea cycle step 1

ornithine + carbamoyl phosphate --> citrulline

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Urea cycle step 2

Citrulline +Asparate -> Argininosuccinate

2 N-atoms for urea joined to C-atom of CO2

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ATP used

energize/activate citrulline to react with aspartate

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Urea cylce step 3

urea released by arignase

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NH4+ and aspartate

provide N-atoms for urea production

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ketogenic

amino acids converted to acetate

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gluconeogenic

amino acids converted to CAC intermediate

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oxidative phosphorylation

NADH and FADH2 are oxidized and produces ATP

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reducing power

electrons available in NADH and FADH2 are transported to the ETC to O2 (makes H2O) and ATP

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Reduction potential

Eº - affinity for e's (tendency to reduce/oxidize)

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difference in reduction potentials

Delta Eº - electron motive force, "energy in redox reaction"

Delta Eº = (Lower Eº) - (higher Eº)

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more positive Eº

gains electrons (reduced) and oxidized state has higher e- affinity

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more negative Eº

loses electrons (oxidized) and oxidized state has lower e- affinity

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NADH & H20

are reduced and NADH (electron donor)

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O2 & NAD+

are oxidized and NAD+ (electron acceptor)

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spontaneous direction

neg G change and positive E change

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Cytochrome C

protein that shuttles electrons between complexes III and IV (associated with respirasomes)

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Path of energy flow

electron-motive force (reducing power) is converted to a proton-motive force (proton gradient) and then into high energy phosphate bonds (ATP)

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ETC pathway 1

NADH (electrons) to I --> Q --> III ---> Cyt C --> IV --> O2

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ETC pathway 2

Succinate/FADH2 (electrons) to II ---> Q --> III ---> Cyt C ---> IV ---> O2

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Respirasome

moves electrons from ubiquinol (QH2) to oxygen

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ubiquinone

Coenzyme Q that is a soluble membrane mobile carrier

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Complex 1

NADH-ubiquinone oxidoreductase (NADH dehydrogenase)

- catalizes oxidation of NADH and reduction of UQ helps pump 4H+

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Complex 2

Succinate dehydrogenase

- catalyzes the oxidation of succinate and reduction of Ubq

- only membrane inserted enzyme of citric acid cycle

- no pumping of H+ (increases pool of ubiquinol)

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Complex 3

Ubiquinone: cytochrome c oxidoreductase

-oxidizes ubiquinol and reduces Cyt C1

-pumps 4H+ per 2 e- transferred 2Cyt C1

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Complex 4

cytochrome c oxidase

- complex where O2 is consumed

- Accumulates 4e- from 4 Cyt C and reduces O2 = H2O

- pumps 2H+ per 2e- / 4H+ per O2

- evolved to prevent the release of toxic partially reduced oxygen species

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defense against reactive O2

reducing powers (NADPH) used to make glutamine that reduces enzymes. These enzymes then get rid of toxic by-products from O2 reactions