MCAT Biochemistry Chapter 10: Metabolism II, Aerobic Respiration

Krebs Cycle

• Occurs in the mitochondria 

• Oxidizes acetyl-CoA to CO₂ and H₂O 

• Produces high energy electron carrying molecules NADH and FADH₂

Methods of Forming Acetyl-CoA

1. Pyruvate Dehydrogenase complex 

2. Fatty acid oxidation (beta-oxidation) 

3. Amino Acid catabolism

4. Ketones 

5. Alcohol 

Formation of Acetyl-CoA

• catalyzed by the transfer of a thiol from coenzyme A (written as CoA-TH) to form a thioester

• Thioster is high energy bond whose hydrolysis can drive other reactions forwards in metabolism 

Pyruvate Dehydrogenase Complex

•  executes reactions to form acetyl-CoA  in mitochondrial matrix

• Inhibited by an accumulation of acetyl-CoA and/or NADH

• Made up of five enzymes 

  • First 3 work in context to convert pyruvate to acetyl CoA

    • Pyruvate dehydrogenase 

    • Dihydrolipoyl transacetylase

    • Dihydrolipoyl dehydrogenase  

  • Last 2 regulate the actions of PDH

    • Pyruvate dehydrogenase kinase 

    • Pyruvate dehydrogenase phosphatase

Concert Pyruvate to Acetyl CoA

• Pyruvate dehydrogenase 

• Dihydrolipoyl transacetylase

• Dihydrolipoyl dehydrogenase  

Pyruvate Dehydrogenase Enzyme

1. Oxidizes pyruvate, yielding CO₂

2. Rest of two carbon molecule binds to TPP

Dihydrolipoyl Transacetylase Enzyme

1. TPP and the carbon molecule are transferred to lipoic acid, a coenzyme, 

2. Lipoic acid’s disulfide group acts as oxidizing agent, creating acetyl group via thioester linkage

3. catalyzes the CoA-SH interaction with thioester link

   1.  causes transfer of an acetyl group to form Acetyl-CoA 

Fatty Acid Oxidation (beta-oxidation)

• Forms thioester bond between carboxyl groups of fatty acids and CoA-SH

Carnitiine (transport shuttle)

• used to transfer fatty acyl aCoA across inner mitochondrial membrane (fatty acyl group cannot cross on its own) for beta oxidation

  • Fatty acyl group is transferred to carnitine via transesterification reaction

  • Same reaction occurs to transfer the group from a cytosolic CoA-SH to a mitochondrial CoA-SH

Amino Acid Catbolism

• After transamination  (rids of amino group), remaining carbon skeletons can form ketones (see formation of acetyl-CoA from ketones)

acetyl-CoA formation from ketones

• The reverse reaction of forming acetyl-CoA from ketones

Acetyl-CoA formation from Alcohols

• Occurs via Alcohol dehydrogenase and acetaldehyde dehydrogenase

  • Accompanied by NADH buildup which inhibits Kreb-cycle

    • acetyl-CoA formed is usually to synthesize fatty acids

Reactions of the Citric Acid Cycle

• Begins with coupling of a molecule of acetyl-CoA with an oxaloacetate molecule 

• Because of NADH and FADH₂  buildup; cannot occur anaerobically

Citric Acid Cycle: Reactions

1. citrate formation

2. citrate isomerized to isocitrate

3. alpha ketoglutaraet and CO₂ formation

4. succinyl-CoA and CO₂ formation

5. Succinate Foramtion

6. Fumurate Formation

7. Malate Formation

8. Oxaloacetate

Citrate Formation

• acetyl-CoA and oxaloacetate undergo condensation reaction to form citryl-CoA 

• Hydrolysis of citryl-CoA yields citrate and CoA 

  • Energetically favorable, moves cycle forward

Citrate Isomerized to Isocitrate

• Achiral citrate is isomerized to one of four possible isomers of isocitrate

• Necessary to facilitate subsequent oxidative decarboxylation 

  

Alpha ketoglutarate and CO₂ formation 

• Isocitrate is oxidized to oxalosuccinate to by isocitrate dehydrogenase 

• Oxalosuccinate is decarboxylated to produce an alpha ketoglutarate and CO₂

• isocitrate is rate limiting enzyme of the citric acid cycle 

• First NADH produced from intermediates in the cycle

  

Succinyl-CoA and CO₂ formation

• Carried out by the alpha-ketoglutarate dehydrogenase complex 

  • succinyl-CoA and, alpha-ketoglutarate and CoA come together and produce a molecule of carbon dioxide

  • Represents the second and last carbon lost, producing another NADH+

Succinate Formation

• Hydrolysis of the thioester bond on succinyl-CoA is coupled to phosphorylation of GDP to GTP 

  • Catalysed by succinyl CoA synthetase

• Nucleosidediphospohate kinase catalyzes phosphate transfer from GTP to ADP, producing ATP 

  • Only time in citric acid cycle that ATP is produced directly 

Fumarate Formation

• Only step of citric acid cycle that doesn’t take place in the mitochondrial matrix, occurs on inner membrane 

• Succinate oxidized to fumarate; catalyzed by succinate dehydrogenase 

  • Succinate acts as flavoprotein, allowing FAD to be reduced to FADH₂

Malate Formation

• Enzyme fumarase catalyzes hydrolysis of alkene bond in fumarate, giving rise to malate

Oxaloacetae Formed

• Malate dehydrogenase catalyses oxidation of malate to oxaloacetate 

  • A third and final molecule of NAD+ is converted to NADH

Net Resulta and ATP Yield (PDC complex + citric acid cycle)

• Pyruvate Dehydrogenase complex + citric acid cycle

  • 4 NADH → 10 ATP (2.5 ATP per NADH)

  • 1 FADH₂ → 1.5 ATP (1.5 ATP per FADH₂) 

  • 1 GTP → 1 ATP 

• Total: 12.5 ATP per pyruvate = 25 ATP per glucose 

Pyruvate Dehydrogenase Kinase

• Phosphorylation of PDC

  • Inhibits PDH and acetyl CoA production

  • activated by high levels of Acetyl-CoA and NADH;

    (signals high levels of ATP)

Pyruvate Dehydrogenase Phosphatase

• Dephosphorylation of PDH f

  • activativates PDC

  • Occurs in response to high levels of ADP and low levels of Acetyl-CoA

    • high levels of NAD+ indicates lack of ATP

Citric Acid Cycle Regulation

• When considering inhibitors of the citric acid cycle, consider energy carriers and ATP 

• ex: an inhibitor of isocitrate dehydrogenase would be an inhibitor of the Krebs cycle

  • These would be ATP, NADH, FADH₂

Control Points of Citric Acid Cycle

• Three essential checkpoints that regulate the citric acid cycle from within; allosteric activators and inhibitors regulate all of them 

  • citrate synthase

  • isocitrate dehydrogenase

  • 𝞪-Ketogluturate dehydrogenase complex

Citrate Synthase: control point

• ATP and NADH (reaction products)  function as allosteric inhibitors of citrate synthase 

• Citrate inhibits directly 

Isocitrate Dehydrogenase: control point

in the citric acid cycle. It catalyzes the conversion of isocitrate to alpha-ketoglutarate, producing CO2 and NADH

• ADP and NAD+ function as allosteric activators for the enzyme and enhance its affinity for substrates 

𝞪-Ketogluturate dehydrogenase complex

of the citric acid cycle, converting 𝞪-ketoglutarate to succinyl CoA

• Succinyl CoA and NADH (reaction products) function as inhibitors 

• ATP is inhibitory and slows the rate of thecycle when the cell has high levels of ATP 

Electron Transport Chain

aerobic components of eukaryotic respiration harvested in mitochonderia  

• Proton gradient ultimately forms ATP from this mechanism 

• NADH and FADH₂ transfer electrons to carrier proteins located along the inner mitochondrial membrane

  • Electrons are given to oxygen as hyrides 

  • Energy released from transporting electrons proton transport at 3 specific locations 

Aerobic Respiration (eukaryotes vs. prokaryotes)

Eukaryotes: occurs in mitochondria

Prokaryotes: occurs in cytoplasm

ETC Complexes and Electorn Flow

• Formation of ATP is endergonic and electron transport is an exergonic pathway 

• Coupling these reactions yields energy from one reaction to fuel another 

• Electron transport chain is a series of oxidation-reduction reactions amongst various complexes 

NADH: good electron donor; O₂ has high reduction potentia

ETC Complex I (NADH-CoQ oxidoreductase)

• Transfer of electrons from NADH to coenzyme Q (CoQ) is catalyzed here via FMN

  • Flavoprotein subunit uses a coenzyme (flavin mononucleotide (FMN)) to oxidize NADH and take its electrons 

  • An iron-sulfur subunit then takes those electrons (reduced) and the flavoprotein is reoxidized

• Iron sulfur subunit donates electrons to Coenzyme Q; becomes (COQH₂)

  • First of 3 sites where proton pumping occurs 

  • 4 protons moved to intermembrane space

ETC Complex II (Succinate-CoQ oxidoreductase) 

• Transfers electrons to coenzyme Q 

• Succinate oxidized to fumarate upon interaction with FAD (becomes FADH₂) 

• FADH₂ oxidised to FAD as its reduces iron-sulfur complex

  • Coenzyme Q is once again reduced by oxidizing iron-sulfur complex

ETC Complex III (CoQH₂ -cytochrome c oxidoreductase)

• Facilitates the transfer of electrons from coenzyme Q to cytochrome c 

• Involves the oxidation and reduction of cytochrome protein with heme groups (in which iron is reduced) 

• Q-cycle: 2nd location of proton pumping

Q -cycle

• 2nd location of proton pumping 

  • Complex III’s main contribution to proton motive force

  • Shuttles four electrons, displacing four protons to intermembrane spac

As [H+] increases in the intermembrane space….

• pH drop 

• Voltage difference (between intermembrane space and matrix) increases

• These contribute to an electrochemical gradient b

  • ATP synthase: harnesses this energy to form ATP from ADP

NADH Shuttles

• NADH cannot directly cross into mitochondrial matrix and needs shuttles 

• Transfers high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane 

• Depending on the shuttle mechanism, either 1.5 or 2.5 ATP will be produced 

Glycerol-3-phosphate Shuttle

• Glycerol phosphate dehydrogenase oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate 

• Mitochondrial FAD resides on outer face of inner mitochondrial membrane 

  • Once reduced, transfers its electrons to the ETC via complex II (generates 1.5 ATP) 

Malate-Aspartate Shuttle

• Cytosolic oxaloacetate’s conversion to malate allows malate to cross into inner mitochondrial membrane 

• Oxidation of cytosolic NADH to NAD+, 

  • Once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH

  • NADH passes along to ETC via complex I and generates 2.5 ATP

Generation of Proton Motive Force

• [H]+ inrease in intermembrane space generates voltage difference

• NADH shuttles

  • Glycerol-3-phosphate shuttle

  • malate aspartate shuttle

Chemiosmotic Coupling

Predominant method describing ATP synthesis

• Allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP to form ATP 

  • F₀ : portion of ATP synthase that functions as ion channel allowing protons to to flow back into matrix

  • F₁ : utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP 

Conformational Coupling

ther method that describes ATP synthesis that suggests that the relationship between the proton gradient and ATP synthesis is indirect 

• ATP is released by the synthase as a result of the conformational change caused by the gradient 

Regulation of ETC

• : in presence of adequate O₂, rate of oxidative phosphorylation is dependent on the availability of ADP

• If O₂ is limited rate of oxidative phosphorylation decreases, and concentration of NADH and FADH₂ increase 

  • Accumulation of NADH, in turn, inhibits the citric acid cycle

ADP Accumulation

activates ETC

• activates isocitrate dehydrogenase → increasing production of NADH/FADH₂