Chapter Notes

Introduction to Respiration

All living organisms, from the smallest microbes to the largest plants, need a constant supply of energy to carry out life processes like growth, movement, transport, and reproduction. This energy comes from the food they consume or produce. Cellular respiration is the process of breaking down food materials within a cell to release energy.

The ultimate source of all food on Earth is photosynthesis. Green plants and cyanobacteria trap light energy and convert it into chemical energy, storing it in the bonds of carbohydrates like glucose. This energy is then released through respiration.

The breakdown of complex molecules happens in a series of controlled, step-by-step reactions. The energy released is not used directly but is trapped in the form of ATP (Adenosine Triphosphate). ATP acts as the energy currency of the cell, providing power for all cellular activities.

Respiratory Substrates

The compounds that are oxidized during respiration to release energy are called respiratory substrates.

• The most common respiratory substrate is glucose.
• Other substrates like proteins, fats, and organic acids can also be used under certain conditions.

Do Plants Breathe?

Yes, plants respire. They take in oxygen ($O_2$) and release carbon dioxide ($CO_2$), just like animals. However, plants do not have specialized respiratory organs like lungs. Instead, they exchange gases through small pores called stomata (on leaves) and lenticels (on stems).

There are several reasons why plants can manage without complex respiratory organs:

1. Each Part for Itself: Every part of the plant—roots, stem, and leaves—takes care of its own gas exchange needs. There is very little transport of gases from one part to another.
2. Low Demand: Plants have a much lower demand for gas exchange than animals. Their respiration rate is significantly lower. The only time large volumes of gases are exchanged is during photosynthesis, and leaves are perfectly adapted for this.
3. Proximity to Air: In most plants, every living cell is located close to the surface. In thick, woody stems, the living cells are organized in thin layers just beneath the bark, near lenticels. The interior cells are dead and only provide support. Additionally, loose packing of parenchyma cells creates a network of air spaces throughout the plant body.

Respiration vs. Combustion

The overall chemical reaction for the complete oxidation of glucose is: $\mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}+6 \mathrm{O}_{2} \longrightarrow 6 \mathrm{CO}_{2}+6 \mathrm{H}_{2} \mathrm{O}+\text{Energy}$

While this looks like a simple combustion (burning) reaction, it is very different in a living cell.

• Combustion releases all the energy at once, mostly as heat.
• Respiration releases energy in a series of slow, enzyme-controlled steps. This allows the cell to capture a significant portion of the energy and store it in ATP molecules, making it useful for cellular work.

Glycolysis

Glycolysis is the first step in cellular respiration, where a glucose molecule is broken down. The term originates from the Greek words glycos (sugar) and lysis (splitting).

• Location: It occurs in the cytoplasm of all living cells.
• Oxygen Requirement: It does not require oxygen and is a common pathway for both aerobic and anaerobic respiration.
• Alternative Name: It is also known as the EMP pathway, named after its discoverers Gustav Embden, Otto Meyerhof, and J. Parnas.

In this process, one molecule of glucose (a 6-carbon sugar) is partially oxidized to form two molecules of pyruvic acid (a 3-carbon compound).

Key Steps of Glycolysis

Glycolysis is a sequence of ten enzyme-catalyzed reactions. Here are the key events concerning energy:

1. Energy Investment Phase: The cell uses ATP to start the process.
   • ATP is used to convert glucose into glucose-6-phosphate.
   • Another ATP is used to convert fructose-6-phosphate into fructose-1,6-bisphosphate.
2. Splitting Phase: The 6-carbon fructose-1,6-bisphosphate is split into two 3-carbon molecules: 3-phosphoglyceraldehyde (PGAL) and dihydroxyacetone phosphate.
3. Energy Generation Phase: The 3-carbon molecules are converted into pyruvic acid, generating ATP and NADH.
   • When 3-phosphoglyceraldehyde (PGAL) is converted to 1,3-bisphosphoglycerate (BPGA), one molecule of $NAD^+$ is reduced to NADH + $H^+$. Since this happens for both 3-carbon molecules, a total of 2 NADH are formed.
   • Energy is released when BPGA is converted to 3-phosphoglyceric acid (PGA). This energy is used to form an ATP molecule. This is called substrate-level phosphorylation.
   • Another ATP is synthesized when phosphoenolpyruvate (PEP) is converted to pyruvic acid.

Net Gain from Glycolysis

For one molecule of glucose:

• ATP Used: 2
• ATP Produced: 4
• NADH Produced: 2
• Net Gain: 2 ATP and 2 NADH

The final product, pyruvic acid, is a key compound that links glycolysis to the next stages of respiration. Its fate depends on the availability of oxygen.

Fermentation

Under anaerobic conditions (without oxygen), many organisms use fermentation to process the pyruvic acid produced during glycolysis. Fermentation is the incomplete oxidation of glucose. The main purpose is to regenerate $NAD^+$ from the NADH produced in glycolysis, allowing glycolysis to continue producing a small amount of ATP.

There are two main types of fermentation:

Alcoholic Fermentation

• Organisms: Carried out by organisms like yeast.
• Process: Pyruvic acid is first converted into acetaldehyde and $CO_2$. The acetaldehyde is then reduced by NADH to form ethanol (alcohol).
• Enzymes: The reactions are catalyzed by pyruvic acid decarboxylase and alcohol dehydrogenase.

Lactic Acid Fermentation

• Organisms: Carried out by some bacteria and also in animal muscle cells during strenuous exercise when oxygen supply is inadequate.
• Process: Pyruvic acid is directly reduced by NADH to form lactic acid.
• Enzyme: The reaction is catalyzed by lactate dehydrogenase.

Energy Yield of Fermentation

Fermentation is not very efficient.

• It releases less than 7% of the energy stored in a glucose molecule.
• The net gain is only 2 ATP molecules per glucose (from glycolysis).
• The end products (alcohol or acid) can be hazardous to the cells.

Aerobic Respiration

In the presence of oxygen, organisms can carry out aerobic respiration to completely oxidize glucose and extract a much larger amount of energy.

• Location: This process takes place inside the mitochondria.
• Process: Pyruvic acid from the cytoplasm is transported into the mitochondria for the final stages of respiration.

The crucial events in aerobic respiration are:

1. The complete oxidation of pyruvate, removing all its hydrogen atoms and leaving three molecules of $CO_2$. This occurs in the mitochondrial matrix.
2. The passing of electrons (from the hydrogen atoms) to molecular oxygen ($O_2$), leading to the formation of water and the synthesis of ATP. This occurs on the inner mitochondrial membrane.

Oxidative Decarboxylation (The Link Reaction)

Before entering the main cycle, pyruvate undergoes a transition step in the mitochondrial matrix.

• Reaction: Pyruvic acid is converted into Acetyl CoA (a 2-carbon molecule).
• Products: This reaction releases one molecule of $CO_2$ and reduces one $NAD^+$ to NADH.
• Enzyme: The reaction is catalyzed by the enzyme complex pyruvic dehydrogenase.

The equation for one molecule of pyruvic acid is: $\text{Pyruvic acid} + \text{CoA} + \text{NAD}^{+} \xrightarrow[\text{Pyruvate dehydrogenase}]{\mathrm{Mg}^{2+}} \text{Acetyl CoA} + \mathrm{CO}_{2} + \mathrm{NADH} + \mathrm{H}^{+}$ Since one glucose produces two pyruvic acid molecules, this step yields 2 Acetyl CoA, 2 $CO_2$, and 2 NADH.

Tricarboxylic Acid Cycle (Krebs' Cycle)

The acetyl CoA then enters a cyclic pathway in the mitochondrial matrix called the Tricarboxylic Acid (TCA) Cycle or Krebs' Cycle, named after its discoverer, Hans Krebs.

1. First Step: The cycle begins when the acetyl group (2C) from Acetyl CoA combines with oxaloacetic acid (OAA) (4C) to form citric acid (6C).
2. Cyclic Reactions: The citric acid then goes through a series of reactions, losing two carbon atoms as $CO_2$ and regenerating the starting molecule, OAA.
3. Energy Harvest: For each molecule of Acetyl CoA that enters the cycle, the following are produced:
   • 3 molecules of NADH + $H^+$
   • 1 molecule of $FADH_2$
   • 1 molecule of GTP (which is equivalent to 1 ATP)

Since one glucose molecule produces two Acetyl CoA molecules, the Krebs' cycle turns twice. The total yield from one glucose molecule via the Krebs' cycle is: 6 NADH, 2 $FADH_2$, and 2 ATP.

The summary equation for the breakdown of one pyruvic acid molecule in the mitochondrial matrix is: $\text{Pyruvic acid} + 4\text{NAD}^{+} + \text{FAD}^{+} + 2\text{H}_{2}\text{O} + \text{ADP} + \text{Pi} \rightarrow 3\text{CO}_{2} + 4\text{NADH} + 4\text{H}^{+} + \text{FADH}_{2} + \text{ATP}$

Electron Transport System (ETS) and Oxidative Phosphorylation

This is the final stage of aerobic respiration, where the energy stored in NADH and $FADH_2$ is converted into ATP.

• Location: The ETS is a series of protein complexes located on the inner mitochondrial membrane.
• Process: High-energy electrons from NADH and $FADH_2$ are passed along a chain of electron carriers.

The Electron Carriers (Complexes I-IV):

• Complex I (NADH dehydrogenase): Receives electrons from NADH.
• Complex II: Receives electrons from $FADH_2$.
• Ubiquinone: A mobile carrier that transfers electrons from Complex I and II to Complex III.
• Complex III (cytochrome bc1 complex): Passes electrons to cytochrome c.
• Cytochrome c: A mobile carrier that transfers electrons between Complex III and IV.
• Complex IV (cytochrome c oxidase): Transfers the electrons to the final acceptor.

The Role of Oxygen: As electrons move down the chain, they lose energy. At the end of the chain, the electrons are passed to oxygen ($O_2$), which acts as the final electron acceptor. Oxygen then combines with hydrogen ions ($H^+$) to form water ($H_2O$). The presence of oxygen is vital because it pulls electrons through the system, driving the entire process.

Oxidative Phosphorylation: The energy released as electrons move through the ETS is used to pump protons ($H^+$) from the mitochondrial matrix into the intermembrane space, creating a proton gradient. This process of using energy from oxidation-reduction reactions to create ATP is called oxidative phosphorylation.

ATP Synthase (Complex V): The protons flow back into the matrix down their concentration gradient through a channel in an enzyme called ATP synthase. This enzyme has two parts:

• $F_0$: An integral protein that forms the proton channel.
• $F_1$: A peripheral protein headpiece that uses the energy from the proton flow to synthesize ATP from ADP and inorganic phosphate (Pi).

ATP Yield from ETS:

• Oxidation of one molecule of NADH produces 3 molecules of ATP.
• Oxidation of one molecule of $FADH_2$ produces 2 molecules of ATP.

The Respiratory Balance Sheet

We can calculate the theoretical maximum number of ATP molecules produced from one molecule of glucose during aerobic respiration.

• The pathways operate sequentially and in an orderly fashion.
• NADH from glycolysis is efficiently transported into the mitochondria.
• No intermediates are diverted to build other molecules.
• Only glucose is being respired. In reality, the net gain is often lower.

Comparison of Fermentation and Aerobic Respiration

Amphibolic Pathway

Respiration is traditionally considered a catabolic (breakdown) process. However, this view is too simple. The respiratory pathway is also involved in anabolic (synthesis) processes.

• Catabolism: Carbohydrates, fats, and proteins are broken down to release energy.
  • Fats are broken into glycerol (enters glycolysis) and fatty acids (enter as Acetyl CoA).
  • Proteins are broken into amino acids, which can enter the pathway at various points (as pyruvate, Acetyl CoA, or Krebs' cycle intermediates).
• Anabolism: Intermediates from the respiratory pathway can be withdrawn to synthesize other essential molecules.
  • For example, if the body needs to synthesize fatty acids, Acetyl CoA is withdrawn from the pathway.
  • Amino acids can be synthesized from Krebs' cycle intermediates.

Because the respiratory pathway is involved in both breakdown (catabolism) and synthesis (anabolism), it is more accurately described as an amphibolic pathway.

Respiratory Quotient (RQ)

The Respiratory Quotient (RQ), or respiratory ratio, is the ratio of the volume of carbon dioxide evolved to the volume of oxygen consumed during respiration.

$RQ = \frac{\text{volume of } CO_2 \text{ evolved}}{\text{volume of } O_2 \text{ consumed}}$

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

• Carbohydrates: When carbohydrates like glucose are completely oxidized, the RQ is 1.0. $\mathrm{C}_{6} \mathrm{H}_{12} \mathrm{O}_{6}+6 \mathrm{O}_{2} \quad \rightarrow 6 \mathrm{CO}_{2}+6 \mathrm{H}_{2} \mathrm{O}$ $RQ = \frac{6 CO_2}{6 O_2} = 1.0$
• Fats: When fats are used, the RQ is less than 1 (around 0.7). This is because fats require more oxygen for their complete oxidation compared to the amount of $CO_2$ produced. $2(\mathrm{C}_{51} \mathrm{H}_{98} \mathrm{O}_{6}) + 145 \mathrm{O}_{2} \rightarrow 102 \mathrm{CO}_{2} + 98 \mathrm{H}_{2} \mathrm{O}$ $RQ = \frac{102 CO_2}{145 O_2} = 0.7$
• Proteins: When proteins are used as the substrate, the RQ is approximately 0.9.

In living organisms, the respiratory substrate is often a mixture of carbohydrates, fats, and proteins, so the RQ value reflects the overall metabolic activity.