Dissimilation – Respiration

Overview of Respiration as a Dissimilation Pathway

In biological systems, respiration is a central dissimilatory process: energy-rich organic compounds are broken down and the released energy is converted, in a controlled way, into biologically usable forms, especially ATP.

Respiration is characterized by:

• Stepwise oxidation of substrates (most commonly glucose, but also fatty acids and amino acids).
• Use of an electron transport chain (ETC).
• A terminal electron acceptor (in aerobic respiration: $O_2$).
• Coupling of electron flow to ATP formation via oxidative phosphorylation.

In contrast to fermentation, respiration:

• Completely (or almost completely) oxidizes the substrate to small, highly oxidized molecules (e.g. $CO_2$, $H_2O$).
• Yields substantially more ATP per substrate molecule.
• Requires functional electron carriers and membrane compartments (e.g. inner mitochondrial membrane, bacterial plasma membrane).

This chapter focuses on the chemical logic and main reaction sequences of biological respiration.

Aerobic Cellular Respiration: The Big Picture

Standard aerobic cellular respiration of glucose can be summarized overall as:

$$
\mathrm{C_6H_{12}O_6 + 6\,O_2 \rightarrow 6\,CO_2 + 6\,H_2O}
$$

This reaction is strongly exergonic. In cells, it does not occur in a single step; instead, it is divided into linked partial processes:

1. Glycolysis (in the cytosol)
2. Pyruvate oxidation (link reaction)
3. Citric acid cycle (Krebs cycle, tricarboxylic acid cycle; in the mitochondrial matrix or analogous bacterial compartment)
4. Respiratory chain (electron transport chain, ETC) and oxidative phosphorylation (at an energy-transducing membrane)

In each stage, characteristic redox reactions, rearrangements, and group transfers occur. The chemical energy from oxidation steps is captured in:

• ATP (substrate-level phosphorylation)
• Reduced cofactors (e.g. NADH, $FADH_2$), which then drive ATP formation in the ETC.

Glycolysis as the Entry Pathway

Glycolysis converts one molecule of glucose into two molecules of pyruvate. It proceeds through 10 enzyme-catalyzed steps, which can be grouped into an energy investment phase and an energy payoff phase.

Energy Investment Phase

Here ATP is consumed to activate glucose:

• Phosphorylation of glucose to glucose-6-phosphate (hexokinase reaction).
• Isomerization to fructose-6-phosphate.
• Second phosphorylation to fructose-1,6-bisphosphate (phosphofructokinase reaction).

Key features:

• The neutral glucose molecule is converted into a more reactive, doubly phosphorylated intermediate.
• Phosphate esters “trap” glucose-derived intermediates inside the cell and “prime” them for subsequent cleavage.

Cleavage and Isomerization

Fructose-1,6-bisphosphate is split into two triose phosphates:

• Glyceraldehyde-3-phosphate (G3P)
• Dihydroxyacetone phosphate (DHAP), which is isomerized to a second molecule of G3P

After this point, all subsequent reactions occur twice per original glucose molecule.

Energy Payoff Phase

Here ATP and NADH are generated:

1. Oxidation of G3P to 1,3-bisphosphoglycerate
• G3P is oxidized; NAD⁺ is reduced to NADH.
• A high-energy acyl phosphate is formed (mixed anhydride).
2. First substrate-level phosphorylation
• 1,3-bisphosphoglycerate transfers a phosphate group to ADP → ATP.
• The high-energy acyl phosphate bond is converted to a carboxylate (3-phosphoglycerate).
3. Rearrangements and dehydration
• 3-phosphoglycerate is converted to 2-phosphoglycerate, then to phosphoenolpyruvate (PEP).
• PEP contains a high-energy phosphoenol bond.
4. Second substrate-level phosphorylation
• PEP transfers its phosphate to ADP → ATP.
• Pyruvate is formed.

Overall glycolysis balance (per glucose):

• ATP: 2 used, 4 formed → net 2 ATP (substrate-level phosphorylation).
• Redox: 2 NAD⁺ + 4 e⁻ + 2 H⁺ → 2 NADH.
• Carbon: 1 glucose (6 C) → 2 pyruvate (2 × 3 C).

Glycolysis can proceed under both aerobic and anaerobic conditions. Under aerobic conditions, pyruvate is further oxidized in the mitochondrion (or equivalent structure).

Pyruvate Oxidation (Link Reaction)

Pyruvate oxidation connects glycolysis to the citric acid cycle. In eukaryotes, this multi-enzyme complex (pyruvate dehydrogenase complex) is located in the mitochondrial matrix.

Per pyruvate, the main transformations are:

1. Decarboxylation
• Pyruvate (3 C) loses $CO_2$ → a 2‑carbon fragment remains (an acetyl group).
2. Oxidation and attachment to Coenzyme A
• The 2‑carbon fragment is oxidized; NAD⁺ is reduced to NADH.
• The acetyl group is attached to coenzyme A, forming acetyl-CoA (a thioester with high group-transfer potential).

Overall reaction (per pyruvate):

$$
\mathrm{Pyruvate + CoA + NAD^+ \rightarrow Acetyl{-}CoA + CO_2 + NADH + H^+}
$$

Per original glucose, 2 pyruvate molecules are processed, producing:

• 2 $CO_2$ (oxidation).
• 2 NADH (reduced cofactor).
• 2 acetyl-CoA (entry substrates for the citric acid cycle).

Citric Acid Cycle (Krebs Cycle)

The citric acid cycle is a cyclic pathway that completes the oxidation of acetyl units from acetyl-CoA to $CO_2$. It operates in the mitochondrial matrix (or bacterial cytosol in conjunction with the plasma membrane).

Central Chemical Features

1. Condensation of acetyl-CoA with oxaloacetate
• Acetyl-CoA (2 C) + oxaloacetate (4 C) → citrate (6 C) + CoA.
• This step regenerates CoA and initiates the cycle.
2. Isomerization
• Citrate is converted to isocitrate, preparing for subsequent oxidative decarboxylation.
3. Two oxidative decarboxylations
• Isocitrate → $\alpha$-ketoglutarate + $CO_2$ (NAD⁺ reduced to NADH).
• $\alpha$-ketoglutarate → succinyl-CoA + $CO_2$ (NAD⁺ reduced to NADH).
• Two carbons are released as $CO_2$—stoichiometrically matching the acetyl input.
4. Substrate-level phosphorylation
• Succinyl-CoA (a high-energy thioester) transfers the succinyl group to GDP (or ADP) via a phosphorylated intermediate.
• GTP (or ATP) is formed, and succinate is produced.
5. Regeneration of oxaloacetate via redox steps
• Succinate → fumarate ($FAD$ reduced to $FADH_2$).
• Fumarate → malate (hydration).
• Malate → oxaloacetate (NAD⁺ reduced to NADH).

Oxaloacetate is thus regenerated and can condense again with another acetyl-CoA, closing the cycle.

Stoichiometry per Acetyl-CoA

For each acetyl-CoA oxidized:

• 2 $CO_2$ released (complete oxidation of the 2-carbon acetyl unit).
• 3 NADH produced.
• 1 $FADH_2$ produced.
• 1 GTP (or ATP) produced by substrate-level phosphorylation.

Per glucose (2 acetyl-CoA):

• 4 $CO_2$ (from the cycle) + 2 $CO_2$ (from pyruvate oxidation) → 6 $CO_2$ total.
• 6 NADH + 2 $FADH_2$ from the cycle, plus 2 NADH from pyruvate oxidation and 2 NADH from glycolysis.

The citric acid cycle is not only catabolic (dissimilation) but also amphibolic, providing intermediates for biosynthetic pathways. Their withdrawal is balanced by anaplerotic reactions that refill the cycle; these aspects link respiration to metabolism more broadly.

Respiratory Chain and Oxidative Phosphorylation

The reduced cofactors from glycolysis, pyruvate oxidation, and the citric acid cycle (NADH, $FADH_2$) do not directly yield ATP. Instead, they donate their electrons to the respiratory chain, a sequence of redox-active protein complexes and mobile carriers embedded in a membrane (inner mitochondrial membrane; bacterial plasma membrane).

Electron Transport Chain (ETC): Redox Cascade

Key principles:

• Electrons flow from NADH/$FADH_2$ via a series of carriers with increasingly positive standard redox potentials.
• Typical carriers include:
• Flavin mononucleotide (FMN) or flavin adenine dinucleotide (FAD).
• Iron–sulfur (Fe–S) centers.
• Ubiquinone (coenzyme Q).
• Cytochromes containing heme groups.
• The terminal electron acceptor in aerobic respiration is $O_2$:
• $O_2 + 4 e^- + 4 H^+ \rightarrow 2 H_2O$.

The large free energy drop associated with transferring electrons from NADH/$FADH_2$ to $O_2$ is not released in one step but divided among several complexes, each performing redox work.

Proton Gradient and Chemiosmotic Coupling

During electron transfer, specific complexes of the ETC pump protons ($H^+$) across the membrane:

• Matrix (or cytosol side) → intermembrane space (or periplasmic side).
• This generates:
• A proton concentration gradient (pH difference).
• An electrical potential difference (charge separation).

Together, these form the proton motive force (PMF), a form of stored electrochemical energy.

ATP synthase, a membrane-embedded enzyme complex, allows protons to flow back down the gradient. The flow of protons drives conformational changes that catalyze:

$$
\mathrm{ADP + P_i \rightarrow ATP}
$$

This process is oxidative phosphorylation, because ATP synthesis is coupled to the oxidation of substrates via the ETC.

Approximate ATP Yields

Exact ATP yields differ between organisms and conditions, but approximate values for aerobic respiration of one glucose are:

• From glycolysis:
• Net 2 ATP (substrate-level phosphorylation).
• ~2 NADH → ~3–5 ATP via oxidative phosphorylation (depending on shuttle systems).
• From pyruvate oxidation:
• 2 NADH → ~5 ATP.
• From the citric acid cycle:
• 2 GTP/ATP (substrate-level phosphorylation).
• 6 NADH → ~15 ATP.
• 2 $FADH_2$ → ~3 ATP.

Total: roughly 30–32 ATP per glucose in eukaryotic cells, significantly higher than the yield from fermentation alone.

Aerobic vs. Anaerobic Respiration

While respiration often refers to aerobic processes using $O_2$ as terminal electron acceptor, some organisms carry out anaerobic respiration:

• Terminal electron acceptors other than $O_2$ are used, such as:
• Nitrate ($NO_3^-$),
• Sulfate ($SO_4^{2-}$),
• Carbon dioxide ($CO_2$) (e.g. methane formation),
• Fumarate, etc.
• An electron transport chain and membrane-bound complexes are still employed.
• ATP is still formed via a proton (or ion) gradient and oxidative phosphorylation.

Anaerobic respiration yields more ATP than fermentation but usually less than aerobic respiration, because alternative electron acceptors generally provide a smaller redox potential difference than $O_2$.

Fate of Different Substrates in Respiration

Although glucose is a central model substrate, other biomolecules can be catabolized via respiration:

Fatty Acids

• Activated as acyl-CoA derivatives.
• Degraded via $\beta$-oxidation:
• Repeated cycles shortening the fatty acid by 2 carbons as acetyl-CoA.
• Each cycle generates 1 NADH and 1 $FADH_2$.
• Acetyl-CoA enters the citric acid cycle; NADH and $FADH_2$ feed into the ETC.
• Fatty acid respiration yields more ATP per molecule than glucose due to greater reduction (more C–H bonds, fewer C–O bonds).

Amino Acids

• First undergo deamination (removal of the amino group).
• Carbon skeletons are transformed into intermediates of:
• Glycolysis (e.g. pyruvate).
• Pyruvate oxidation (e.g. acetyl-CoA).
• Citric acid cycle (e.g. $\alpha$-ketoglutarate, succinyl-CoA, fumarate, oxaloacetate).
• These intermediates are then oxidized through the usual respiratory pathways.

Respiration thus serves as a central convergence point for the breakdown of carbohydrates, fats, and proteins.

Regulation and Physiological Significance

Respiration is tightly regulated to balance energy supply and demand:

• Key control points:
• Glycolysis: hexokinase, phosphofructokinase, pyruvate kinase.
• Pyruvate dehydrogenase complex.
• Citric acid cycle: isocitrate dehydrogenase, $\alpha$-ketoglutarate dehydrogenase.
• Allosteric regulation:
• ATP, ADP, AMP, NADH, and citrate often act as feedback inhibitors or activators.
• Oxygen availability:
• Limited $O_2$ restricts ETC activity; NADH accumulates; oxidative pathways slow; cells may switch partly to fermentation to reoxidize NADH.

Physiologically, respiration:

• Supplies ATP for mechanical work (muscle contraction), active transport, biosynthesis, and signal transduction.
• Generates metabolic intermediates used as precursors for anabolic pathways.
• Produces heat, contributing to thermoregulation in many organisms.

By integrating redox chemistry, proton gradients, and group-transfer reactions, respiration exemplifies how fundamental chemical principles are harnessed in biological systems to convert the free energy of organic molecules into usable biochemical work.