MCAT Biochemistry - Carbohydrate Metabolism II: Aerobic Respiration

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citric acid cycle / Krebs cycle / tricarboxylic acid (TCA) cycle

oxidation of acetyl-CoA to CO2 and H2O in the mitochondrial matrix; produces the high-energy electron-carrying molecules NADH and FADH2; most substrates and products of the cycle are reused over and over again; will not occur anaerobically

Acetyl-CoA

obtained from the metabolism of carbohydrates, fatty acids, and amino acids; key molecule in the crossroads of many metabolic pathways; high-energy thioester; negative feedback on own production

pyruvate dehydrogenase complex

multienzyme complex located in the mitochondrial matrix

1. pyruvate dehydrogenase (PDH)

2. dihydrolipoyl transacetylase

3. dihydrolipoyl dehydrogenase

   1. ^ convert pyruvate to acetyl-CoA

4. pyruvate dehydrogenase kinase

5. pyruvate dehydrogenase phosphatase

   1. ^ regulate the actions of PDH

inhibited by an accumulation of acetyl-CoA and NADH

free energy of conversion of pyruvate to acetyl-CoA

exergonic - ΔG∘= −33.4 kJ mol

coenzyme A (CoA)

thiol; covalent attachment of the acetyl group to the thiol group → acetyl-CoA = thioester

pyruvate dehydrogenase complex enzymes needed to catalyze acetyl-CoA formation

1. pyruvate dehydrogenase (PDH)

2. dihydrolipoyl transacetylase

   1. dihydrolipoyl dehydrogenase

Pyruvate dehydrogenase (PDH)

Pyruvate is oxidized, yielding CO2, while the remaining two-carbon molecule binds covalently to thiamine pyrophosphate; requires Mg2+

thiamine (pyrophosphate, TPP) / vitamin B1

water-soluble vitamin; coenzyme held by noncovalent interactions to PDH

Dihydrolipoyl transacetylase

two-carbon molecule bonded to TPP is oxidized and transferred to lipoic acid, which acts as an oxidizing agent, creating the acetyl group via thioester linkage

catalyzes the CoA−SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA; lipoic acid is left reduced

lipoic acid

coenzyme that is covalently bonded to the enzyme

Dihydrolipoyl dehydrogenase

uses FAD to reoxidise lipoic acid; FAD is reduced to FADH2

Flavin adenine dinucleotide (FAD)

coenzyme in order to reoxidize lipoic acid;

Fatty acid oxidation (β-oxidation)

removes two-carbon fragments from the carboxyl end of acyl-CoA

Carnitine

molecule that can cross the inner membrane with a fatty acyl group in tow; carry the acyl group from a cytosolic CoA to a mitochondrial CoA

activation (β-oxidation)

in cytosol, causes a thioester bond to form between carboxyl groups of fatty acids and CoA; fatty acyl group is transferred to carnitine via transesterification

Amino acid catabolism

Certain amino acids can be used to form acetyl-CoA via transamination

transamination

transfers an amino group to a ketoacid to form new amino acids; responsible for the deamination of most amino acids

ketogenic amino acids

amino acids that can be metabolised into ketone bodies and subsequently into acetyl-CoA

Ketones catabolism

ketones can turn into acetyl-CoA; reversible

alcohol dehydrogenase

facilitate the interconversion between alcohols and aldehydes or ketones with the reduction of nicotinamide adenine dinucleotide (NAD+) to NADH in cytosol; buildup of NADH can inhibit Krebs cycle

excess alcohol metabolism

CYP2E1 catalyzes the buildup of NADH to NAD+

acetaldehyde dehydrogenase

catalyze the conversion of acetaldehyde into acetyl-CoA; often follows alcohol dehydrogenase; used primarily to synthesize fatty acids

Acetaldehyde + NAD+ + Coenzyme A ↔ Acetyl-CoA + NADH + H+

Citrate Formation

first step of Krebs cycle

1. acetyl-CoA and oxaloacetate undergo a condensation reaction to form citryl-CoA

2. hydrolysis of citryl-CoA by citrate synthase yields citrate and CoA

   1. energetically favoured step

   2. citrate synthase does not require energy input

Citrate Isomerized to Isocitrate:

second step of Krebs cycle

1. (achrial) citrate binds at three points to the enzyme aconitase

2. dehydration yields cis-aconitate

3. hydration to form (chiral) isocitrate

   1. four possible isomers

aconitase

metalloprotein that requires Fe2+; Achiral citrate is isomerized to one of four possible isomers of isocitrate via switching of a hydrogen and a hydroxyl group

α-Ketoglutarate and CO2 Formation

third step of Krebs cycle

1. Isocitrate oxidized to oxalosuccinate by isocitrate dehydrogenase

   1. rate-limiting step

   2. first NADH produced from intermediates in the cycle

2. oxalosuccinate is decarboxylated to produce α-ketoglutarate and CO2

   1. first of the two carbons from the cycle is lost here

isocitrate dehydrogenase

rate-limiting enzyme of the citric acid cycle; oxidises isocitrate to oxalosuccinate

activated by ADP and NAD+ (allosteric activators)

inhibited by ATP and NADH

Succinyl-CoA and CO2 Formation

fourth step of Krebs cycle

1. α-ketoglutarate and CoA come together and produce cuccinyl-CoA and carbon dioxide with α-ketoglutarate dehydrogenase complex

   1. second and last carbon lost from the cycle

   2. Reducing NAD+ produces another NADH

α-ketoglutarate dehydrogenase complex

α-ketoglutarate and CoA come together and produce cuccinyl-CoA and carbon dioxide using thiamine, lipoic acid, Mg2+

stimulated by ADP and calcium ions

inhibited by succinyl-CoA, NADH and ATP

Succinate Formation

fifth step of Krebs cycle

1. Hydrolysis of the thioester bond on succinyl-CoA yields succinate and CoA by succinyl-CoA synthetase

   1. coupled to the phosphorylation of GDP to GTP

   2. require energy input

nucleosidediphosphate kinase

catalyzes phosphate transfer from GTP to ADP, thus producing ATP; only time in the entire citric acid cycle that ATP is produced directly

Fumarate Formation

fifth step of Krebs cycle

1. succinate undergoes oxidation by succinate dehydrogenase to yield fumarate

   1. FAD is reduced to FADH2

   2. occurs in inner mitochondrial membrane

Succinate dehydrogenase

flavoprotein; integral protein on the inner mitochondrial membrane; also part of electron transport

flavoprotein

covalently bonded to FAD, the electron acceptor

Substrates of Citric Acid Cycle Mnemonic

Please, Can I Keep Selling Seashells For Money, Officer?

(Pyruvate

Citrate

Isocitrate

α-Ketoglutarate

Succinyl-CoA

Succinate

Fumarate

Malate

Oxaloacetate)

Malate Formation

seventh step of Krebs cycle

1. fumarase catalyzes the hydrolysis of the alkene bond in fumarate, thereby giving rise to malate

   1. L-malate only

Oxaloacetate Formed Anew

eighth step of Krebs cycle

1. malate dehydrogenase catalyzes the oxidation of malate to oxaloacetate

   1. third and final molecule of NAD+ is reduced to NADH

Final products of Krebs cycle

4 NADH, 1 FADH2, 1 GTP

NADH ATP conversion

2.5 ATP

FADH2 ATP conversion

1.5 ATP

GTP ATP conversion

1 to 1

pyruvate dehydrogenase kinase

regulation of citric acid cycle via phosphorylation of PDH in response to high ATP; inhibits acetyl-CoA production

pyruvate dehydrogenase phosphatase

PDH dephosphorylated and reactivated in response to high ADP

Citrate synthase

inhibited by citrate, succinyl-CoA, NADH and ATP

electron transport chain

final common pathway that utilizes the harvested electrons from different fuels in the body; proton gradient it generates ultimately produces ATP

Aerobic metabolism / Oxidative phosphorylation

most efficient way of generating energy in living systems

laregely dependent on ADP/ATP and O2

mitochondrion

organelle that compleetes aerobic components of respiration

cristae

inner mitochondrial membrane is assembled into folds; maximize surface area; proton-motive force generated across it

proton-motive force

electrochemical proton gradient generated by the complexes of the electron transport chain essential for generating ATP

Complex I (NADH-CoQ oxidoreductase)

transfer of electrons from NADH to coenzyme Q (CoQ)

1. NADH transferring its electrons over to FMN → NAD+ and FMNH2

2. flavoprotein becomes reoxidized while the iron–sulfur subunit is reduced

3. reduced iron–sulfur subunit donates electrons to coQ → CoQH2

FOUR protons moved to intermembrane space

flavin mononucleotide (FMN)

coenzyme to flavoprotein in Complex I

coenzyme Q (ubiquinone)

recieves electrons from Complex I & II

Complex II (Succinate-CoQ oxidoreductase)

transfers electrons from succinate to coenzyme Q

1. succinate from the citric acid cycle is oxidized by reducing FAD covalently bonded to the complex → fumarate and FADH2

2. FADH2 gets reoxidized to FAD as it reduces an iron–sulfur protein

3. reoxidizes the iron–sulfur protein as coenzyme Q is reduced

NO protons pumped

Complex III (CoQH2-cytochrome c oxidoreductase / cytochrome reductase)

transfer of electrons from coenzyme Q to cytochrome c via Q cycle

FOUR protons pumped

cytochromes

proteins with heme groups in which iron is reduced to Fe2+ and reoxidized to Fe3+

Q cycle

1. two electrons are shuttled from a molecule of ubiquinol (CoQH2) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitochondrial matrix

2. Another two electrons are attached to heme moieties, reducing two molecules of cytochrome c, assisted by iron-sulfur carrier

Complex IV (cytochrome c oxidase)

transfer of electrons from cytochrome c to oxygen, the final electron acceptor; includes subunits of cytochrome a, cytochrome a₃, and Cu2+ ions

1. cytochrome oxidase gets oxidized as oxygen, becomes reduced, and forms water

TWO protons

electrochemical gradient

gradient that has both chemical and electrostatic properties

shuttle mechanisms

transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane from the cytosol; explains variation in amount of ATP in cells (30-32)

Glycerol 3-phosphate shuttle

cytosol contains one isoform of glycerol-3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate (DHAP)

outer face of the inner mitochondrial membrane exists another isoform of glycerol-3-phosphate dehydrogenase that is FAD-dependent → reduced and transfers electrons to ETC via Complex II

Malate–aspartate shuttle

Cytosolic oxaloacetate, which cannot pass through the inner mitochondrial membrane, is reduced to malate by cytosolic malate dehydrogenase → oxidation of cytosolic NADH to NAD+

mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH

pass along its electrons to the ETC via Complex I and generate 2.5 ATP per molecule of NADH

Recycling the malate requires oxidation to oxaloacetate, which can be transaminated to form aspartate, which crosses into the cytosol, and can be reconverted to oxaloacetate to restart the cycle

mitochondrial DNA

only encoded 13 of 100 polypeptides necessary for oxidative phosphorylation; mutation rate nearly ten times higher than that of nuclear DNA

chemiosmotic coupling

allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, thus forming ATP

ATP synthase

harness proton-motive force to form ATP from ADP and an inorganic phosphate

F₀ portion (ATP synthase)

ion channel for protons to travel along gradient

ΔG^∘ − 220 kJ mol

F₁ portion (ATP synthase)

utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP; reminiscent of a turbine, spinning within a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding

conformational coupling

suggests that the relationship between the proton gradient and ATP synthesis is indirect; ATP is released by the synthase as a result of conformational change caused by the gradient

Uncouplers

compounds that prevent ATP synthesis without affecting the ETC, thus greatly decreasing the efficiency of the ETC/oxidative phosphorylation pathway; as ADP builds up and ATP synthesis decreases, the body responds to this perceived lack of energy by increasing O2 consumption and NADH oxidation; energy produced from the transport of electrons is released as heat

respiratory control

coordinated regulation of O2, ADP/ATP, NAD+/NADH, FAD/FADH2, citric acid pathways