Do Plants Breathe?

Yes, plants do require oxygen for respiration and release carbon dioxide, just like animals. However, unlike animals, plants lack specialized respiratory organs like lungs. Instead, they have structures like **stomata** (on leaves and stems) and **lenticels** (on woody stems and roots) for gaseous exchange (uptake of O$_2$ and release of CO$_2$).

Several reasons allow plants to manage without specialized respiratory organs:

• Each plant part (root, stem, leaf) handles its own gas-exchange needs with minimal transport of gases between parts.
• Plants have relatively low demands for gas exchange compared to animals, respiring at slower rates.
• During photosynthesis, O$_2$ is produced within the cells, ensuring local availability.
• Each living cell in a plant is generally located close to the plant's surface, facilitating diffusion. In woody stems and roots, living cells are in thin layers, and lenticels provide openings.
• Loose packing of parenchyma cells throughout the plant creates an interconnected network of air spaces, aiding gas diffusion to internal living cells.

The complete combustion of glucose (C$_6$H$_{12}$O$_6$) in a single step releases a large amount of energy as heat. Cells, however, break down glucose in several small, enzyme-controlled steps. This allows the energy released at some steps to be coupled to ATP synthesis, trapping usable energy rather than losing it all as heat.

While the combustion of glucose requires oxygen, some organisms live in environments where oxygen is limited or absent (anaerobic conditions). All living organisms possess the enzymatic machinery for the initial breakdown of glucose without oxygen, a process called **glycolysis**.

Glycolysis

**Glycolysis** is the initial metabolic pathway in respiration, where glucose (a six-carbon molecule) is partially oxidized to form **two molecules of pyruvic acid** (a three-carbon molecule). The name comes from Greek words for sugar (glycos) and splitting (lysis). It is also known as the **EMP pathway** (after Embden, Meyerhof, and Parnas). Glycolysis is a universal pathway, occurring in the **cytoplasm** of all living organisms, and is the sole process of respiration in anaerobic organisms.

In plants, glucose for glycolysis is derived from sucrose (end product of photosynthesis) or stored carbohydrates. Sucrose is converted to glucose and fructose by invertase, which then enter the pathway. Glucose and fructose are phosphorylated to glucose-6-phosphate and fructose-6-phosphate, respectively, which then proceed through the same subsequent steps.

Glycolysis involves a series of ten enzyme-controlled reactions (as depicted in Fig 12.1 in text). Key energy changes during glycolysis:

• **ATP Utilisation:** ATP is consumed at two steps: conversion of glucose to glucose-6-phosphate, and conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.
• **ATP Synthesis (Substrate-Level Phosphorylation):** ATP is directly synthesised at two steps: conversion of 1,3-bisphosphoglycerate (BPGA) to 3-phosphoglyceric acid (PGA), and conversion of phosphoenolpyruvate (PEP) to pyruvic acid. Since two molecules of BPGA and two of PEP are formed per glucose molecule, a total of 4 ATP molecules are synthesised at these steps.
• **NADH + H$^+$ Formation:** One molecule of NADH + H$^+$ is formed from NAD$^+$ when 3-phosphoglyceraldehyde (PGAL) is converted to 1,3-bisphosphoglycerate (BPGA). Since two molecules of PGAL are formed per glucose, a total of 2 NADH + H$^+$ molecules are formed. These represent stored chemical energy (reducing power).

Net ATP gain in glycolysis from one glucose molecule is 4 ATP synthesised - 2 ATP utilised = **2 ATP**.

The key product of glycolysis is **pyruvic acid**. Its metabolic fate depends on the organism and the availability of oxygen.

Fermentation

**Fermentation** is an anaerobic process (occurs in the absence of oxygen) where pyruvic acid is converted into other products. It is the main mode of respiration in many prokaryotes and unicellular eukaryotes, and occurs in muscle cells during oxygen deprivation.

Two major types of fermentation:

• **Alcoholic Fermentation:** Occurs in organisms like yeast. Pyruvic acid is converted into **ethanol** and **carbon dioxide**. Enzymes involved are pyruvic acid decarboxylase and alcohol dehydrogenase.
• **Lactic Acid Fermentation:** Occurs in some bacteria and animal muscle cells. Pyruvic acid is reduced to **lactic acid** by lactate dehydrogenase. The reducing agent (NADH + H$^+$) produced during glycolysis is reoxidised to NAD$^+$ in both alcoholic and lactic acid fermentation.

In fermentation, glucose is only **incompletely oxidized**. Very little energy is released compared to aerobic respiration (less than 7% of glucose energy). The net gain of ATP from fermentation of one glucose molecule (through glycolysis) is **2 ATP**.

Fermentation processes produce hazardous end products like acid (lactic acid) or alcohol (ethanol). Yeast dies when alcohol concentration reaches about 13%. Alcoholic beverages with higher alcohol content are obtained by distillation.

Aerobic Respiration

**Aerobic respiration** is the process that leads to the **complete oxidation** of organic substances in the **presence of oxygen**, releasing CO$_2$, water, and a large amount of energy. In eukaryotes, aerobic respiration occurs within the **mitochondria**.

For aerobic respiration, pyruvate (product of glycolysis in the cytoplasm) is transported into the mitochondrial matrix. Crucial events:

1. Complete oxidation of pyruvate by removing hydrogen atoms, releasing CO$_2$.
2. Transfer of electrons removed from hydrogen atoms to molecular O$_2$, leading to H$_2$O formation and simultaneous ATP synthesis (oxidative phosphorylation).

The first process (oxidation of pyruvate and CO$_2$ release) takes place in the **mitochondrial matrix**, while the second process (electron transport and oxidative phosphorylation) occurs on the **inner mitochondrial membrane**.

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Tricarboxylic Acid Cycle (TCA Cycle or Krebs' Cycle)

Before entering the TCA cycle, pyruvate undergoes **oxidative decarboxylation** in the mitochondrial matrix, converting it to **acetyl CoA**. This reaction is catalysed by pyruvic dehydrogenase and requires coenzymes like NAD$^+$ and Coenzyme A. CO$_2$ is released, and NADH + H$^+$ is produced.

Pyruvic acid $\xrightarrow{\text{Pyruvate dehydrogenase}}$ Acetyl CoA + CO$_2$ + NADH + H$^+$

Since two pyruvic acid molecules are produced from one glucose, two molecules of acetyl CoA are formed, and two NADH + H$^+$ are produced in this step.

The **TCA cycle** (also called Citric Acid Cycle or Krebs' Cycle) is a cyclic pathway occurring in the **mitochondrial matrix**. It begins with the condensation of acetyl CoA with a 4-carbon molecule, **oxaloacetic acid (OAA)**, to form a 6-carbon molecule, citric acid. Through a series of reactions, citric acid is oxidised, releasing CO$_2$ and generating reducing power (NADH + H$^+$, FADH$_2$) and ATP (by substrate-level phosphorylation).

Key products of one turn of the TCA cycle (from one Acetyl CoA): **2 CO$_2$, 3 NADH + H$^+$, 1 FADH$_2$, 1 ATP** (via GTP). Since two Acetyl CoA molecules enter the cycle per glucose molecule, these products are doubled for complete oxidation of glucose.

Summary equation for the oxidation of pyruvate to CO$_2$ via the TCA cycle (per pyruvate):

Pyruvic acid + 4NAD$^+$ + FAD$^+$ + 2H$_2$O + ADP + Pi $\to$ 3CO$_2$ + 4NADH + 4H$^+$ + FADH$_2$ + ATP

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Electron Transport System (ETS) And Oxidative Phosphorylation

The **Electron Transport System (ETS)** is a metabolic pathway located on the **inner mitochondrial membrane**. Its function is to release and utilize the energy stored in NADH + H$^+$ and FADH$_2$ (produced during glycolysis and the TCA cycle) for ATP synthesis. Electrons are passed from one carrier to another in the ETS, and are finally transferred to oxygen.

Process:

1. Electrons from NADH (from mitochondrial matrix) are oxidised by Complex I (NADH dehydrogenase) and transferred to ubiquinone (located in the inner membrane).
2. Ubiquinone also receives electrons from FADH$_2$ (from succinate oxidation in TCA cycle) via Complex II.
3. Reduced ubiquinone (ubiquinol) is oxidised, transferring electrons to cytochrome c via Complex III (cytochrome bc$_1$ complex).
4. Cytochrome c (a mobile carrier) transfers electrons from Complex III to Complex IV. Complex IV (cytochrome c oxidase) contains cytochromes a and a$_3$ and copper centers.
5. As electrons move through Complexes I, III, and IV in the ETS, protons (H$^+$) are pumped from the mitochondrial matrix to the intermembrane space. This creates a proton gradient across the inner mitochondrial membrane.

Oxygen (O$_2$) acts as the **final electron acceptor** in the ETS. It accepts electrons and combines with protons to form **water (H$_2$O)**. Oxygen is essential for aerobic respiration as it removes hydrogen from the system, allowing the ETS to continue and drive the entire process.

**Oxidative Phosphorylation:** The process of ATP synthesis using the energy released during the oxidation of NADH + H$^+$ and FADH$_2$ in the ETS. The energy from electron transport is used to create a proton gradient. Protons flow back from the intermembrane space to the matrix through a channel in the **ATP synthase enzyme (Complex V)**. This flow of protons down the electrochemical gradient provides the energy to activate ATP synthase, which catalyses the synthesis of ATP from ADP and inorganic phosphate.

For each molecule of NADH + H$^+$ oxidised, approximately **3 molecules of ATP** are produced. For each molecule of FADH$_2$ oxidised, approximately **2 molecules of ATP** are produced.

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The Respiratory Balance Sheet

Calculating the net gain of ATP molecules from the aerobic respiration of one glucose molecule is a theoretical exercise based on certain assumptions (e.g., ordered pathways, efficient transfer of NADH, no intermediate use, only glucose respiration). While real living systems are more complex and dynamic, these calculations help appreciate the efficiency of energy extraction.

The theoretical net gain of ATP from the complete aerobic respiration of one glucose molecule is approximately **38 ATP** molecules.

Comparison of fermentation and aerobic respiration:

• **Breakdown:** Fermentation is a partial breakdown of glucose; aerobic respiration is complete breakdown to CO$_2$ and H$_2$O.
• **Energy Release/ATP Gain:** Fermentation yields only 2 net ATP per glucose (from glycolysis); aerobic respiration yields many more ATP (theoretically ~38).
• **NADH Oxidation:** NADH is oxidised slowly in fermentation; it is oxidised very vigorously in aerobic respiration (by ETS).

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Amphibolic Pathway

The respiratory pathway has traditionally been considered **catabolic** (breaking down substrates). However, it also involves **anabolic** (synthesis) processes. The compounds that are intermediates in the respiratory pathway are not only products of breakdown but can also serve as precursors for the synthesis of other molecules.

For example, when fatty acids are used as substrates, they are broken down into acetyl CoA, which enters the respiratory pathway. But when the organism needs to synthesize fatty acids, acetyl CoA is withdrawn from the pathway. Similarly, proteins are broken down into amino acids, which can enter the pathway at various stages (e.g., as pyruvate or intermediates in the Krebs' cycle). But for protein synthesis, intermediates can be withdrawn from the pathway and converted into amino acids.

Because the respiratory pathway is involved in both the breakdown (catabolism) of substrates to yield energy and the synthesis (anabolism) of intermediates used for building other molecules, it is better considered an **amphibolic pathway** rather than solely catabolic.

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Respiratory Quotient

The **respiratory quotient (RQ)**, or respiratory ratio, is a value used to determine the type of respiratory substrate being used. It is defined as the ratio of the volume of carbon dioxide (CO$_2$) evolved to the volume of oxygen (O$_2$) consumed during respiration.

$$ \text{RQ} = \frac{\text{Volume of CO}_2 \text{ evolved}}{\text{Volume of O}_2 \text{ consumed}} $$

The RQ value depends on the chemical composition of the respiratory substrate:

• **Carbohydrates:** When carbohydrates (like glucose) are completely oxidised, the volume of CO$_2$ evolved is equal to the volume of O$_2$ consumed.

  C$_6$H$_{12}$O$_6$ + 6O$_2$ $\to$ 6CO$_2$ + 6H$_2$O + Energy

  RQ (Carbohydrate) = $\frac{6 \text{ CO}_2}{6 \text{ O}_2} = 1.0$

• **Fats:** When fats are used as respiratory substrates, they require more oxygen for complete oxidation compared to the CO$_2$ produced.

  Example for Tripalmitin (a common fat): 2(C$_{51}$H$_{98}$O$_6$) + 145O$_2$ $\to$ 102CO$_2$ + 98H$_2$O + Energy

  RQ (Fats) = $\frac{102 \text{ CO}_2}{145 \text{ O}_2} \approx 0.7$ (less than 1)

• **Proteins:** When proteins are used as respiratory substrates, the RQ value is generally around 0.9.
• **Organic Acids:** Some organic acids have an RQ value greater than 1.

In living organisms, respiration often involves a mix of substrates, so measuring RQ can provide insight into the primary substrate being respired.

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