4.2 Respiration in Plants

Introduction to Respiration

Respiration is a metabolic process that occurs in all living organisms, including plants, to release energy from organic molecules (like glucose) for various cellular activities. This energy is primarily stored in the form of ATP (adenosine triphosphate).

Exchange of Gases

In plants, the exchange of gases (oxygen and carbon dioxide) primarily occurs through:

Stomata: Small pores on the surface of leaves, regulated by guard cells.
Lenticels: Pores on the bark of woody stems and roots.
General surface of roots: Younger roots can absorb oxygen from the soil.

Plants respire throughout the day and night. During the day, photosynthesis produces oxygen, some of which is used for respiration. At night, only respiration occurs, leading to a net release of carbon dioxide.

Types of Respiration

Respiration can be broadly classified into two types based on the presence or absence of oxygen:

Aerobic Respiration: Occurs in the presence of oxygen. It is a complete oxidation of organic substances, releasing a large amount of energy.
Anaerobic Respiration (Fermentation): Occurs in the absence of oxygen. It is an incomplete oxidation of organic substances, releasing a smaller amount of energy.

Cellular Respiration: An Overview

Cellular respiration is a complex process that involves several stages:

Glycolysis: Occurs in the cytoplasm.
Krebs Cycle (TCA Cycle): Occurs in the mitochondrial matrix.
Electron Transport System (ETS) / Oxidative Phosphorylation: Occurs on the inner mitochondrial membrane.

Glycolysis (EMP Pathway)

Glycolysis (from the Greek glycos for sugar and lysis for splitting) is the first stage of cellular respiration, occurring in both aerobic and anaerobic pathways. Discovered by Gustav Embden, Otto Meyerhof, and Jakub Karol Parnas, it is also known as the EMP Pathway.

The Universal Start Glycolysis is the common pathway for every living cell on Earth. Because it happens in the cytoplasm and doesn't require oxygen, it is thought to be one of the most ancient metabolic processes in evolution.

Location: Cytoplasm (Cytosol)

The Ten Chemical Steps of Glycolysis

Glycolysis is a sequence of ten enzyme-catalyzed reactions divided into two distinct phases:

Preparatory Phase (Energy Investment): Steps 1 to 5, where glucose is phosphorylated and cleaved, requiring an investment of 2 ATP.
Pay-off Phase (Energy Harvesting): Steps 6 to 10, where energy is captured in the form of ATP and NADH, resulting in a net gain.

Phase I: Preparatory Phase (Energy Investment)

First Phosphorylation (Irreversible):
- Reaction: $\text{Glucose} + \text{ATP} \overset{\text{Hexokinase, Mg}^{2+}}{\longrightarrow} \text{Glucose-6-phosphate} + \text{ADP}$
- Enzyme: Hexokinase (requires $\text{Mg}^{2+}$ as a cofactor).
- Significance: Traps glucose inside the cell as the charged phosphate group prevents it from crossing the plasma membrane.
Isomerization (Reversible):
- Reaction: $\text{Glucose-6-phosphate} \rightleftharpoons \text{Fructose-6-phosphate}$
- Enzyme: Phosphohexose Isomerase (Phosphoglucose Isomerase).
- Significance: Converts an aldose (glucose) into a ketose (fructose), preparing the molecule for the next phosphorylation.
Second Phosphorylation (Irreversible):
- Reaction: $\text{Fructose-6-phosphate} + \text{ATP} \overset{\text{PFK-1, Mg}^{2+}}{\longrightarrow} \text{Fructose-1,6-bisphosphate} + \text{ADP}$
- Enzyme: Phosphofructokinase-1 (PFK-1) (requires $\text{Mg}^{2+}$ ).
- Significance: The key rate-limiting, committed, and regulatory step of glycolysis. PFK-1 is allosterically inhibited by high levels of ATP and citrate, and activated by AMP and Fructose-2,6-bisphosphate.
Cleavage (Reversible):
- Reaction: $\text{Fructose-1,6-bisphosphate} \rightleftharpoons \text{Glyceraldehyde-3-phosphate (PGAL)} + \text{Dihydroxyacetone phosphate (DHAP)}$
- Enzyme: Aldolase.
- Significance: Splits the 6-carbon sugar into two 3-carbon isomers.
Triose Phosphate Interconversion (Reversible):
- Reaction: $\text{Dihydroxyacetone phosphate} \rightleftharpoons \text{Glyceraldehyde-3-phosphate}$
- Enzyme: Triose Phosphate Isomerase.
- Significance: Rapidly interconverts the isomers. Since G3P (PGAL) is constantly consumed in the next step, DHAP is continuously converted to G3P. From this step onward, all reactions occur twice per glucose molecule.

Phase II: Pay-off Phase (Energy Harvesting)

Oxidation & Phosphorylation (Reversible):
- Reaction: $2 \times \text{Glyceraldehyde-3-phosphate} + 2\text{NAD}^+ + 2\text{P}_i \rightleftharpoons 2 \times \text{1,3-Bisphosphoglycerate} + 2\text{NADH} + 2\text{H}^+$
- Enzyme: Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH).
- Significance: G3P is oxidized and phosphorylated using inorganic phosphate ( $\text{P}_i$ ) (not ATP). High-energy electrons are transferred to $\text{NAD}^+$ , forming $\text{NADH}$ .
First Substrate-Level Phosphorylation (Reversible):
- Reaction: $2 \times \text{1,3-Bisphosphoglycerate} + 2\text{ADP} \overset{\text{Phosphoglycerate Kinase, Mg}^{2+}}{\longrightarrow} 2 \times \text{3-Phosphoglycerate} + 2\text{ATP}$
- Enzyme: Phosphoglycerate Kinase (requires $\text{Mg}^{2+}$ ).
- Significance: Direct transfer of a high-energy phosphate group from 1,3-BPG to ADP, generating 2 ATP (which recovers the 2 ATP invested in Phase I).
Phosphate Group Shift (Reversible):
- Reaction: $2 \times \text{3-Phosphoglycerate} \rightleftharpoons 2 \times \text{2-Phosphoglycerate}$
- Enzyme: Phosphoglycerate Mutase.
- Significance: Shifts the phosphate group from carbon-3 to carbon-2, preparing the molecule for dehydration.
Dehydration (Reversible):
- Reaction: $2 \times \text{2-Phosphoglycerate} \rightleftharpoons 2 \times \text{Phosphoenolpyruvate (PEP)} + 2\text{H}_2\text{O}$
- Enzyme: Enolase (requires $\text{Mg}^{2+}$ or $\text{Mn}^{2+}$ as cofactors).
- Significance: Removes water to introduce a double bond, creating the highly unstable and energy-rich Phosphoenolpyruvate (PEP).
Second Substrate-Level Phosphorylation (Irreversible):
- Reaction: $2 \times \text{Phosphoenolpyruvate} + 2\text{ADP} \overset{\text{Pyruvate Kinase, Mg}^{2+}, \text{K}^+}{\longrightarrow} 2 \times \text{Pyruvate} + 2\text{ATP}$
- Enzyme: Pyruvate Kinase (requires $\text{Mg}^{2+}$ and $\text{K}^+$ ).
- Significance: Generates another 2 ATP and produces 2 molecules of Pyruvic acid (Pyruvate). This step is highly exergonic and regulated.

Net Products of Glycolysis (per glucose molecule):

2 molecules of Pyruvate ( $C_3H_4O_3$ )
2 molecules of ATP (Net gain: 4 produced - 2 consumed)
2 molecules of NADH (to be utilized in ETS for further ATP generation)

Competitive Edge: SLP vs. Oxidative Phosphorylation In glycolysis, the ATP is produced directly by Substrate-Level Phosphorylation (SLP), where a phosphate group is transferred directly from a substrate to ADP. This is distinct from Oxidative Phosphorylation (which happens later in the mitochondria using oxygen and the electron transport chain).

Fermentation (Anaerobic Respiration)

Fermentation occurs when oxygen is not available after glycolysis. Pyruvate is converted into different products to regenerate NAD+ from NADH, allowing glycolysis to continue.

Brief Idea of Fermentation:

Alcoholic Fermentation: Occurs in yeast and some bacteria. Pyruvate is converted to acetaldehyde, and then to ethanol, releasing CO₂. Pyruvate → Acetaldehyde + CO₂ Acetaldehyde + NADH → Ethanol + NAD+
Lactic Acid Fermentation: Occurs in some bacteria and animal muscle cells under anaerobic conditions. Pyruvate is directly converted to lactic acid. Pyruvate + NADH → Lactic Acid + NAD+

Energy Yield: Fermentation yields very little energy (only the 2 ATP from glycolysis) compared to aerobic respiration.

The Link Reaction (Transition Reaction / Gateway Step)

Before entering the Krebs cycle, the pyruvate generated in glycolysis (cytoplasm) must be transported into the mitochondrial matrix. This transport is mediated by the Mitochondrial Pyruvate Carrier (MPC) across the inner membrane.

Once inside the matrix, pyruvate undergoes oxidative decarboxylation in a process known as the Link Reaction or transition reaction. This reaction is irreversible and catalyzed by a multi-enzyme system called the Pyruvate Dehydrogenase Complex (PDC).

The Pyruvate Dehydrogenase Complex (PDC)

The PDC is a macromolecular assembly consisting of three enzymes:

Pyruvate Dehydrogenase ( $E_1$ ): Performs decarboxylation of pyruvate.
Dihydrolipoyl Transacetylase ( $E_2$ ): Transfers the acetyl group to Coenzyme A.
Dihydrolipoyl Dehydrogenase ( $E_3$ ): Regenerates the electron carrier cofactors.

Five Essential Cofactors

The reaction requires five distinct cofactors to function:

TPP (Thiamine Pyrophosphate): Derived from Vitamin $B_1$ .
Lipoic acid (Lipoamide): Serves as a swinging arm within $E_2$ .
Coenzyme A (CoA-SH): Derived from Vitamin $B_5$ .
FAD (Flavin Adenine Dinucleotide): Derived from Vitamin $B_2$ .
$\text{NAD}^+$ (Nicotinamide Adenine Dinucleotide): Derived from Vitamin $B_3$ .

Note: Magnesium ions ( $\text{Mg}^{2+}$ ) are also required to activate the complex.

Chemical Equation:

$\text{Pyruvic Acid (3C)} + \text{CoA-SH} + \text{NAD}^+ \overset{\text{PDC, Mg}^{2+}}{\longrightarrow} \text{Acetyl-CoA (2C)} + \text{CO}_2 \uparrow + \text{NADH} + \text{H}^+$

Net Products of the Link Reaction (per glucose molecule, i.e., 2 Pyruvates):

2 molecules of Acetyl-CoA (which enter the Krebs cycle)
2 molecules of $\text{CO}_2$ (released as waste)
2 molecules of NADH (transported to the ETS)

Krebs Cycle (TCA Cycle / Citric Acid Cycle)

Also known as the Tricarboxylic Acid (TCA) Cycle or Citric Acid Cycle, this cyclic pathway was discovered by Sir Hans Adolf Krebs. It takes place in the mitochondrial matrix and represents the terminal pathway for the complete oxidation of carbohydrates, lipids, and proteins.

The Eight Chemical Steps of the Krebs Cycle

Condensation (Irreversible):
- Reaction: $\text{Acetyl-CoA (2C)} + \text{Oxaloacetate (4C)} + \text{H}_2\text{O} \overset{\text{Citrate Synthase}}{\longrightarrow} \text{Citrate (6C)} + \text{CoA-SH}$
- Enzyme: Citrate Synthase.
- Significance: Acetyl group condensates with oxaloacetate (OAA) to form citric acid. This step commits carbon to the cycle and is inhibited by ATP, NADH, and Succinyl-CoA.
Isomerization (Reversible):
- Reaction: $\text{Citrate} \rightleftharpoons \text{cis-Aconitate} \rightleftharpoons \text{Isocitrate (6C)}$
- Enzyme: Aconitase (requires $\text{Fe}^{2+}$ as a cofactor).
- Significance: Isomerizes Citrate to Isocitrate through dehydration followed by rehydration.
First Oxidative Decarboxylation (Irreversible):
- Reaction: $\text{Isocitrate} + \text{NAD}^+ \overset{\text{Isocitrate Dehydrogenase, Mn}^{2+}}{\longrightarrow} \alpha\text{-Ketoglutarate (5C)} + \text{CO}_2 \uparrow + \text{NADH} + \text{H}^+$
- Enzyme: Isocitrate Dehydrogenase (requires $\text{Mn}^{2+}$ ).
- Significance: The rate-limiting step of the cycle. Generates the first NADH and releases the first $\text{CO}_2$ . Allosterically activated by ADP and $\text{Ca}^{2+}$ , inhibited by ATP and NADH.
Second Oxidative Decarboxylation (Irreversible):
- Reaction: $\alpha\text{-Ketoglutarate (5C)} + \text{CoA-SH} + \text{NAD}^+ \overset{\alpha\text{-KGDH}}{\longrightarrow} \text{Succinyl-CoA (4C)} + \text{CO}_2 \uparrow + \text{NADH} + \text{H}^+$
- Enzyme: $\alpha$ -Ketoglutarate Dehydrogenase Complex (requires the same 5 cofactors as PDC: TPP, Lipoamide, CoA-SH, FAD, and $\text{NAD}^+$ ).
- Significance: Releases the second $\text{CO}_2$ and generates the second NADH.
Substrate-Level Phosphorylation (Reversible):
- Reaction: $\text{Succinyl-CoA} + \text{GDP/ADP} + \text{P}_i \rightleftharpoons \text{Succinate (4C)} + \text{GTP/ATP} + \text{CoA-SH}$
- Enzyme: Succinyl-CoA Synthetase (Succinic Thiokinase).
- Significance: Thioester bond cleavage drives the phosphorylation of GDP to GTP (in animals) or ADP to ATP (in plants/bacteria).
Dehydrogenation / Oxidation (Reversible):
- Reaction: $\text{Succinate} + \text{FAD} \overset{\text{Succinate Dehydrogenase}}{\longrightarrow} \text{Fumarate (4C)} + \text{FADH}_2$
- Enzyme: Succinate Dehydrogenase.
- Significance: Only membrane-bound enzyme of the cycle, embedded in the inner mitochondrial membrane where it functions directly as Complex II of the Electron Transport Chain. Generates $\text{FADH}_2$ .
Hydration (Reversible):
- Reaction: $\text{Fumarate} + \text{H}_2\text{O} \rightleftharpoons \text{L-Malate (4C)}$
- Enzyme: Fumarase (Fumarate Hydratase).
- Significance: Adds water across the carbon-carbon double bond.
Malate Oxidation / Regeneration of OAA (Reversible):
- Reaction: $\text{L-Malate} + \text{NAD}^+ \rightleftharpoons \text{Oxaloacetate (4C)} + \text{NADH} + \text{H}^+$
- Enzyme: Malate Dehydrogenase.
- Significance: Regenerates Oxaloacetate (OAA), allowing the cycle to repeat, and yields the third NADH.

Net Products of Krebs Cycle (per glucose molecule, i.e., 2 turns of the cycle):

6 molecules of NADH
2 molecules of $\text{FADH}_2$
2 molecules of ATP (or GTP)
4 molecules of $\text{CO}_2$

Electron Transport System (ETS) and Oxidative Phosphorylation

This is the final stage of aerobic respiration, where the majority of ATP is produced.

Location: Inner mitochondrial membrane

Brief Idea of ETS (Flowchart Idea):

NADH and FADH₂ (produced in glycolysis and Krebs cycle) donate their electrons to a series of protein complexes (Complex I, II, III, IV) embedded in the inner mitochondrial membrane.

Electrons move from a higher energy level to a lower energy level through these complexes.

As electrons move, protons (H+) are pumped from the mitochondrial matrix into the intermembrane space, creating a proton gradient.

Oxygen acts as the final electron acceptor, combining with electrons and protons to form water.

Oxidative Phosphorylation:

Definition: The process of ATP synthesis that occurs when the energy released from the oxidation of NADH and FADH₂ (via the electron transport chain) is used to generate a proton gradient, which then drives the synthesis of ATP by ATP synthase.

Mechanism: The proton gradient created by the ETS drives protons back into the mitochondrial matrix through ATP synthase (Complex V). This flow of protons powers the synthesis of ATP from ADP and inorganic phosphate.

Energy Relations: Number of ATP Molecules Generated

The theoretical maximum ATP yield from the complete aerobic respiration of one glucose molecule is approximately 30-32 ATP molecules.

Stage	ATP (Direct)	NADH	FADH₂	ATP from NADH (2.5 ATP/NADH)	ATP from FADH₂ (1.5 ATP/FADH₂)	Total ATP
Glycolysis	2	2	0	5 (or 3 if shuttle costs energy)	0	7-5
Pyruvate Oxidation (2x)	0	2	0	5	0	5
Krebs Cycle (2x)	2 (GTP)	6	2	15	3	20
Total	4	10	2	25	3	30-32

Note: The exact number of ATPs can vary due to different shuttle systems for NADH from glycolysis into the mitochondria and the efficiency of proton pumping.

Amphibolic Pathways

Definition: Metabolic pathways that can function in both catabolism (breakdown of molecules) and anabolism (synthesis of molecules). They are central to metabolism, allowing for the interconversion of different types of molecules.

Brief Idea of Amphibolic Pathway:

Cellular respiration, particularly the Krebs cycle, is a prime example of an amphibolic pathway.

Catabolic Role: The Krebs cycle breaks down Acetyl-CoA to produce ATP, NADH, and FADH₂.
Anabolic Role: Intermediates of the Krebs cycle can be used as precursors for the synthesis of other molecules:
- α-Ketoglutarate: Can be used to synthesize amino acids.
- Oxaloacetate: Can be used to synthesize amino acids and glucose (via gluconeogenesis).
- Succinyl-CoA: Can be used for chlorophyll and heme synthesis.

This dual nature allows the cell to efficiently manage its resources, breaking down molecules when energy is needed and building up molecules when precursors are available.

Respiratory Quotient (RQ)

Definition: The ratio of the volume of carbon dioxide (CO₂) evolved to the volume of oxygen (O₂) consumed during respiration.

RQ = Volume of CO₂ evolved / Volume of O₂ consumed

Significance: RQ values provide information about the type of respiratory substrate being oxidized.

RQ Values of Different Substrates:

Carbohydrates: $\text{RQ} = 1.0$ (equal volume of $\text{CO}_2$ evolved and $\text{O}_2$ consumed). $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} + \text{Energy}$ $\text{RQ} = \frac{6\text{ CO}_2}{6\text{ O}_2} = 1.0$
Fats (e.g., Tripalmitin): $\text{RQ} \approx 0.7$ (fats are oxygen-poor relative to carbon/hydrogen and require more oxygen for oxidation). $2\text{C}_{51}\text{H}_{98}\text{O}_6 + 145\text{O}_2 \rightarrow 102\text{CO}_2 + 98\text{H}_2\text{O} + \text{Energy}$ $\text{RQ} = \frac{102\text{ CO}_2}{145\text{ O}_2} \approx 0.7$
Proteins: $\text{RQ} \approx 0.9$ (complex molecules whose exact value varies depending on the specific amino acids being respired).
Organic Acids: RQ > 1 Organic acids are rich in oxygen, so they require less external oxygen for oxidation, leading to an RQ greater than 1. Example: 4C₂H₂O₅ (Oxalic Acid) + O₂ → 8CO₂ + 4H₂O RQ = 8CO₂ / 1O₂ = 8
Anaerobic Respiration: RQ = Infinity (∞) In anaerobic respiration, CO₂ is evolved but no O₂ is consumed. Example (Alcoholic Fermentation): C₆H₁₂O₆ → 2C₂H₅OH + 2CO₂ RQ = 2CO₂ / 0O₂ = ∞