All living organisms require a continuous supply of energy to carry out essential life activities like absorption, transport, movement, reproduction, and even breathing. This energy is obtained by oxidizing macromolecules called 'food'.

Green plants and cyanobacteria are unique in their ability to produce their own food through photosynthesis, converting light energy into chemical energy stored in the bonds of carbohydrates (glucose, sucrose, starch). This food is then used for energy production through respiration.

Even in green plants, only cells containing chloroplasts perform photosynthesis. Non-green parts (roots, non-photosynthetic tissues) need food supplied to them for respiration. Animals obtain food from plants (directly or indirectly), and saprophytes get it from dead matter. Ultimately, the energy used for life processes originates from photosynthesis.

Cellular respiration is the process of breaking down food materials within cells to release energy, which is then trapped in the form of ATP (adenosine triphosphate).

• Photosynthesis occurs in chloroplasts (in eukaryotes).
• Respiration (breakdown of complex molecules) occurs in the cytoplasm and mitochondria (in eukaryotes).

Respiration involves the breaking of C-C bonds of complex organic compounds through oxidation within cells. This releases a considerable amount of energy.

The compounds oxidized during respiration are called respiratory substrates. Carbohydrates are the most common respiratory substrates, but fats, proteins, and organic acids can also be used under certain conditions.

Energy Release: All energy contained in respiratory substrates is not released in a single step or given out as heat. It is released gradually in a series of enzyme-controlled, stepwise reactions. This allows some of the released energy to be captured as chemical energy in ATP.

ATP acts as the energy currency of the cell. Energy trapped in ATP is used to power various energy-requiring processes. The carbon skeletons produced during respiration also serve as building blocks (precursors) for synthesizing other molecules in the cell.

Do Plants Breathe?

Plants require O$_2$ for respiration and release CO$_2$, similar to animals. However, they do not have specialized respiratory organs like lungs.

Gas exchange in plants occurs primarily through:

• Stomata: Pores on the surface of leaves and sometimes stems.
• Lenticels: Lens-shaped openings in the bark of woody stems and roots.

Plants do not need specialized respiratory organs for several reasons:

1. Each plant part handles its own gas exchange needs; there is minimal gas transport between different parts.
2. Plants have much lower demands for gas exchange compared to animals; respiration rates are generally lower. During photosynthesis, gas exchange is high, but leaves are well-adapted to meet their own needs.
3. The diffusion distance for gases is relatively small even in larger plants. Living cells are located close to the surface (e.g., thin layers under bark, loose packing of parenchyma creating air spaces).

Cellular respiration is the process where glucose (C$_6$H$_{12}$O$_6$) is completely oxidized in the presence of oxygen to produce CO$_2$ and H$_2$O, releasing energy:

C$_6$H$_{12}$O$_6$ + 6O$_2$ $\rightarrow$ 6CO$_2$ + 6H$_2$O + Energy (as heat and ATP)

The cell needs to release this energy in a controlled, stepwise manner to synthesize ATP effectively, rather than releasing it all as heat in a single combustion step.

While aerobic respiration requires oxygen, some organisms and cells can perform respiration without it. The initial stage of glucose breakdown, glycolysis, occurs in all living organisms and does not require oxygen.

Glycolysis

Glycolysis (from Greek 'glycos' = sugar, 'lysis' = splitting) is the partial oxidation (breakdown) of glucose into two molecules of pyruvic acid. It is also known as the EMP pathway, named after Gustav Embden, Otto Meyerhof, and J. Parnas.

Glycolysis is a universal pathway, occurring in the cytoplasm of all living organisms, both aerobic and anaerobic.

In plants, glucose for glycolysis is derived from sucrose (end product of photosynthesis) or stored carbohydrates. Sucrose is converted to glucose and fructose by the enzyme invertase. Both glucose and fructose enter the glycolytic pathway after phosphorylation.

Glycolysis involves a sequence of ten enzyme-controlled reactions (Figure 14.1).

Key points regarding ATP and NADH during glycolysis:

• ATP Utilisation: ATP is consumed in two steps:
  • Conversion of glucose to glucose-6-phosphate.
  • Conversion of fructose-6-phosphate to fructose-1,6-bisphosphate.
• ATP Synthesis (Substrate-level phosphorylation): ATP is directly synthesized in two steps:
  • Conversion of 1,3-bisphosphoglycerate (BPGA) to 3-phosphoglyceric acid (PGA). Two molecules of ATP are produced per glucose (since 2 BPGA are formed).
  • Conversion of phosphoenolpyruvate (PEP) to pyruvic acid. Two molecules of ATP are produced per glucose (since 2 PEP are formed).
• NADH + H$^+$ Formation: One step involves the reduction of NAD$^+$ to NADH + H$^+$. This occurs during the conversion of 3-phosphoglyceraldehyde (PGAL) to 1,3-bisphosphoglycerate (BPGA). Two molecules of NADH + H$^+$ are produced per glucose (since 2 PGAL are formed).

Net ATP gain in glycolysis: 4 ATP produced - 2 ATP utilized = Net gain of 2 ATP molecules per glucose molecule.

Net NADH + H$^+$ gain in glycolysis: Net gain of 2 NADH + H$^+$ molecules per glucose molecule.

The end product of glycolysis is pyruvic acid (pyruvate). The fate of pyruvate depends on the availability of oxygen and the organism's metabolic needs.

Three major metabolic fates of pyruvate:

1. Lactic acid fermentation
2. Alcoholic fermentation
3. Aerobic respiration (Krebs' cycle)

Fermentation occurs under anaerobic conditions, while aerobic respiration requires oxygen.

Fermentation

Fermentation is a type of anaerobic respiration where glucose is incompletely oxidized without the use of oxygen. It occurs in many prokaryotes and unicellular eukaryotes under anaerobic conditions (Figure 14.2).

Types of Fermentation:

• Alcoholic Fermentation: Performed by organisms like yeast. Pyruvic acid is converted into carbon dioxide (CO$_2$) and ethanol. Enzymes involved are pyruvic acid decarboxylase and alcohol dehydrogenase. The NADH + H$^+$ from glycolysis is reoxidized to NAD$^+$.
• Lactic Acid Fermentation: Performed by many bacteria and in animal muscle cells during strenuous exercise when oxygen is insufficient. Pyruvic acid is reduced to lactic acid by the enzyme lactate dehydrogenase. The NADH + H$^+$ from glycolysis is reoxidized to NAD$^+$.

Characteristics of Fermentation:

• Occurs under anaerobic conditions.
• Incomplete oxidation of glucose.
• Very little energy is released (<7% of the energy in glucose), resulting in a net gain of only 2 ATP molecules per glucose (produced during glycolysis).
• The end products (acid or alcohol) can be toxic to the organism (e.g., yeast dies at $\sim 13\%$ alcohol concentration).
• The primary purpose (besides ATP production) is to reoxidize NADH + H$^+$ to NAD$^+$, which is necessary to keep glycolysis running.

Alcoholic beverages with higher alcohol content than $\sim 13\%$ are produced by distillation after natural fermentation.

For organisms requiring significantly more energy, complete oxidation of glucose through aerobic respiration is necessary.

Aerobic Respiration

Aerobic respiration is the process of complete oxidation of organic substances (like glucose) in the presence of oxygen, releasing CO$_2$, water, and a large amount of energy. In eukaryotes, it takes place within the mitochondria.

Steps in Aerobic Respiration (after glycolysis):

1. Oxidative Decarboxylation of Pyruvate: Pyruvate (produced in the cytoplasm during glycolysis) is transported into the mitochondrial matrix. It undergoes oxidative decarboxylation, where a carbon atom is removed as CO$_2$, and the remaining 2-carbon unit is attached to Coenzyme A, forming Acetyl CoA. This reaction is catalyzed by the enzyme complex pyruvic dehydrogenase and requires NAD$^+$ and Coenzyme A.

Pyruvic acid (3C) + CoA + NAD$^+$ $\xrightarrow{\textsf{Pyruvate dehydrogenase}}$ Acetyl CoA (2C) + CO$_2$ + NADH + H$^+$

Since two pyruvate molecules are produced per glucose, two molecules of Acetyl CoA and two molecules of NADH + H$^+$ are formed in this step.

2. Tricarboxylic Acid Cycle (TCA cycle) or Krebs' Cycle: Acetyl CoA enters a cyclic pathway in the mitochondrial matrix (Figure 14.3).

Key events in one turn of the TCA cycle (for one Acetyl CoA):

• Acetyl CoA (2C) condenses with Oxaloacetic acid (OAA, 4C) to form Citric acid (6C).
• Through a series of reactions, Citric acid is oxidized and decarboxylated (CO$_2$ removed) twice, generating 5-carbon ($\alpha$-ketoglutaric acid) and 4-carbon (succinyl-CoA) compounds.
• Oxidation continues, regenerating OAA to keep the cycle going.
• For each Acetyl CoA entering the cycle:
  • 2 molecules of CO$_2$ are released.
  • 3 molecules of NADH + H$^+$ are produced.
  • 1 molecule of FADH$_2$ is produced.
  • 1 molecule of ATP is produced via substrate-level phosphorylation (as GTP, which is readily converted to ATP).

Since two Acetyl CoA molecules are formed from one glucose molecule, the TCA cycle runs twice per glucose. Therefore, for one glucose molecule, the TCA cycle yields: 4 CO$_2$, 6 NADH + H$^+$, 2 FADH$_2$, and 2 ATP.

3. Electron Transport System (ETS) and Oxidative Phosphorylation: This stage occurs on the inner mitochondrial membrane (Figure 14.4). It utilizes the energy stored in the NADH + H$^+$ and FADH$_2$ molecules generated during glycolysis and the TCA cycle to synthesize a large amount of ATP.

Key events in ETS and Oxidative Phosphorylation:

• Electrons from NADH + H$^+$ are transferred through a series of electron carriers (Complex I to IV) embedded in the inner mitochondrial membrane.
• Electrons from FADH$_2$ enter the chain at a later point (Complex II).
• As electrons move through the chain, energy is released. This energy is used to pump protons (H$^+$) from the mitochondrial matrix into the intermembrane space, creating a proton gradient across the inner membrane.
• Oxygen (O$_2$) acts as the final electron acceptor at the end of the chain (Complex IV). Oxygen accepts electrons and combines with protons to form water (H$_2$O). The presence of oxygen is essential to keep the electron flow going.
• The proton gradient across the inner membrane represents potential energy. Protons flow back from the intermembrane space into the matrix through specific channels in the ATP synthase enzyme (Complex V) (Figure 14.5).
• The energy released by this proton flow drives ATP synthase to catalyze the synthesis of ATP from ADP and inorganic phosphate. This process is called oxidative phosphorylation because ATP synthesis is coupled to the oxidation of electron carriers (NADH, FADH$_2$) and the presence of oxygen.

ATP yield from ETS: Oxidation of one molecule of NADH + H$^+$ yields approximately 3 molecules of ATP. Oxidation of one molecule of FADH$_2$ yields approximately 2 molecules of ATP.

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The Respiratory Balance Sheet

Calculating the exact number of ATP molecules produced during aerobic respiration of one glucose molecule is complex due to various factors in a living system (simultaneous pathways, substrate withdrawal/entry, ATP utilization). However, a theoretical maximum yield can be estimated based on certain assumptions (sequential pathways, complete oxidation, no intermediate use, only glucose as substrate).

Theoretical ATP yield per glucose in aerobic respiration:

• Glycolysis: Net 2 ATP (substrate-level) + 2 NADH + H$^+$ ($\rightarrow 2 \times 3 = 6$ ATP via oxidative phosphorylation) = 8 ATP
• Pyruvate to Acetyl CoA: 2 NADH + H$^+$ ($\rightarrow 2 \times 3 = 6$ ATP via oxidative phosphorylation) = 6 ATP
• TCA cycle (2 turns): 2 ATP (substrate-level) + 6 NADH + H$^+$ ($\rightarrow 6 \times 3 = 18$ ATP) + 2 FADH$_2$ ($\rightarrow 2 \times 2 = 4$ ATP) = 24 ATP

Total theoretical maximum ATP yield per glucose molecule = $8 + 6 + 24 = \textbf{38 ATP}$. (Note: some texts use 36 ATP assuming transport of cytoplasmic NADH into mitochondria costs energy).

Comparison of Fermentation and Aerobic Respiration:

• Degradation: Fermentation is partial glucose breakdown; Aerobic respiration is complete degradation to CO$_2$ and H$_2$O.
• ATP Yield: Fermentation yields only 2 net ATP; Aerobic respiration yields up to 38 ATP.
• NADH Oxidation: NADH is slowly oxidized to NAD$^+$ in fermentation; NADH oxidation is rapid and vigorous in aerobic respiration (via ETS).

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Amphibolic Pathway

While traditionally considered a catabolic pathway (breaking down molecules for energy), the respiratory pathway is better described as amphibolic, meaning it involves both catabolism (breakdown) and anabolism (synthesis).

Various respiratory substrates (carbohydrates, fats, proteins, organic acids) enter the pathway at different stages (Figure 14.6).

• Carbohydrates are converted to glucose, entering at glycolysis.
• Fats are broken into glycerol and fatty acids. Glycerol enters after conversion to PGAL. Fatty acids are degraded to Acetyl CoA and enter the TCA cycle.
• Proteins are broken into amino acids (after deamination), entering at various points within glycolysis, pyruvate oxidation, or the TCA cycle depending on their structure.

Crucially, the intermediates produced during respiration are not only used for energy extraction but can also be withdrawn from the pathway to synthesize other molecules.

Example: Acetyl CoA, an intermediate, is produced during fatty acid breakdown (catabolism) and enters the respiratory pathway. However, Acetyl CoA can also be withdrawn from the respiratory pathway to synthesize fatty acids (anabolism).

Similarly, intermediates in the TCA cycle can be used for the synthesis of amino acids or other biomolecules.

Thus, the respiratory pathway is involved in both breaking down substances (catabolism) and providing precursors for synthesis (anabolism), making it an amphibolic pathway.

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Respiratory Quotient

The Respiratory Quotient (RQ) or respiratory ratio is the ratio of the volume of CO$_2$ evolved to the volume of O$_2$ consumed during aerobic respiration.

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

The value of RQ depends on the type of respiratory substrate being used.

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

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

  RQ = $\frac{\textsf{6 CO}_2}{\textsf{6 O}_2} = 1.0$

• Fats: When fats are used as respiratory substrates, the RQ is typically less than 1 because more oxygen is consumed for their complete oxidation compared to the CO$_2$ evolved.

  Example (Tripalmitin): 2(C$_{51}$H$_{98}$O$_6$) + 145O$_2$ $\rightarrow$ 102CO$_2$ + 98H$_2$O

  RQ = $\frac{\textsf{102 CO}_2}{\textsf{145 O}_2} \approx 0.7$

• Proteins: When proteins are used as substrates, the RQ is approximately 0.9.
• Organic Acids: When organic acids are used, the RQ is typically greater than 1 because they are already partially oxidized and require less oxygen for further oxidation compared to the CO$_2$ they release.

In living organisms, a mix of substrates is usually respired, so the measured RQ represents an average value.

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