Biology (9610) | Respiration

🔬 Comprehensive Study Notes: Respiration (9610 Syllabus 3.3.3)

Hello Biologists! This chapter is all about how living organisms capture the energy stored in food molecules (like glucose) and convert it into a usable form: ATP (Adenosine Triphosphate). Respiration is essential for life—it powers everything from muscle contraction to DNA replication. Don't worry if the pathways look complicated; we will break them down step-by-step!

💡 Quick Review: Why is ATP important?

ATP is often called the "immediate source of energy" or the "energy currency" of the cell. It's much easier for a cell to break down ATP than to break down glucose directly, making it perfect for rapid energy release for biological processes. ATP is resynthesised (re-made) during respiration (Syllabus Principle).

3.3.3.1 Glycolysis: The Universal Starting Point

Glycolysis is the first stage of respiration and is truly universal, meaning it happens in virtually all organisms (prokaryotes and eukaryotes). It is also unique because it occurs in the absence of oxygen, making it common to both aerobic and anaerobic pathways.

Where does Glycolysis happen?

In the cytoplasm of the cell.

The Process of Glycolysis (Step-by-Step)

This process involves the breakdown of one 6-carbon glucose molecule into two 3-carbon pyruvate molecules.

1. Phosphorylation (Energy Investment): Glucose is first destabilised by adding two phosphate groups (from two separate ATP molecules). This creates a 6-carbon molecule called glucose phosphate. Think of this as spending 2 pounds (ATP) to start a business.
2. Splitting: The unstable glucose phosphate splits into two molecules of 3-carbon triose phosphate (TP).
3. Oxidation and ATP Generation (Energy Payoff): Each triose phosphate molecule undergoes oxidation (loss of hydrogen).
   • The hydrogen is accepted by the coenzyme NAD, reducing it to reduced NAD. This reduced NAD is crucial later for the aerobic stages!
   • In a series of reactions, phosphate groups are directly transferred to ADP to form ATP. This is called substrate-level phosphorylation.
4. End Product: The triose phosphate is converted into pyruvate.

Key Outputs of Glycolysis (Per Glucose Molecule):

• 2 molecules of Pyruvate
• Net gain of 2 molecules of ATP (4 produced - 2 used up = 2 net gain)
• 2 molecules of Reduced NAD

3.3.3.2 Anaerobic Respiration (Fermentation)

When oxygen (O₂) is scarce or absent, organisms cannot proceed with the aerobic stages (Link Reaction, Krebs Cycle, ETC). However, they must keep glycolysis running to produce at least some ATP (the net 2 ATP). To do this, they need to solve one problem: recycling NAD.

The sole purpose of anaerobic respiration is to regenerate NAD from reduced NAD, allowing glycolysis to continue.

1. Alcoholic Fermentation (Yeast and Plants)

This process converts pyruvate into ethanol and carbon dioxide.

Pyruvate is converted to Ethanol and Carbon Dioxide (CO₂) using the reduced NAD.

\( \text{Pyruvate} \xrightarrow{\text{decarboxylase}} \text{Ethanal} \xrightarrow{\text{dehydrogenase}} \text{Ethanol} + \text{NAD} \)

Did you know? This process is fundamental to baking (CO₂ causes bread to rise) and brewing (ethanol is alcohol).

2. Lactate Fermentation (Mammals/Animals)

In muscles during intense exercise, oxygen supply cannot meet demand.

Pyruvate is converted to Lactate (lactic acid) using the reduced NAD. This regenerates NAD so glycolysis can continue, providing rapid (but small amounts of) ATP.

\( \text{Pyruvate} \xrightarrow{\text{lactate dehydrogenase}} \text{Lactate} + \text{NAD} \)

Lactate build-up in muscles causes muscle fatigue and cramps. When oxygen is available later, the lactate is transported to the liver and converted back to pyruvate or glucose (requiring oxygen—this is why you keep breathing heavily after exercise!).

3.3.3.3 Aerobic Respiration: The Main ATP Harvest

If oxygen is present, pyruvate moves into the mitochondria, and the cells can extract much more energy. This stage happens in three steps: the Link Reaction, the Krebs Cycle, and Oxidative Phosphorylation.

Where does Aerobic Respiration happen?

The remaining stages occur inside the mitochondria. Pyruvate enters the mitochondrial matrix via active transport (using carrier proteins and ATP).

A. The Link Reaction (Connecting Glycolysis to the Cycle)

This is a short, intermediate step occurring in the mitochondrial matrix.

1. The 3-carbon pyruvate is oxidised (loses CO₂ and hydrogen). This process is called decarboxylation and oxidation.
2. The hydrogen removed is accepted by NAD, forming reduced NAD.
3. The resulting 2-carbon molecule is called acetate.
4. Acetate combines with coenzyme A to form acetyl coenzyme A (Acetyl CoA).

Since one glucose molecule produced two pyruvate molecules, the link reaction happens twice.

B. The Krebs Cycle (The Central Hub)

The Krebs cycle (also known as the Citric Acid Cycle) takes place in the mitochondrial matrix. Its primary role is to produce vast quantities of reduced coenzymes (reduced NAD and reduced FAD) which carry hydrogen atoms to the final stage.

The cycle involves a series of oxidation-reduction reactions:

1. The 2-carbon acetyl coenzyme A enters the cycle. Coenzyme A is released and recycled.
2. The acetyl group (2C) reacts with a 4-carbon molecule (often called oxaloacetate) to form a 6-carbon molecule (citrate).
3. Over a series of steps, the 6-carbon molecule is converted back into the original 4-carbon molecule (oxaloacetate). In this conversion, the molecule is repeatedly decarboxylated (releases CO₂) and oxidised (releases hydrogen).
4. The hydrogen atoms are picked up by NAD and FAD, producing reduced NAD and reduced FAD.
5. A small amount of ATP is produced via substrate-level phosphorylation.

Outputs of one turn of the Krebs Cycle (from one Acetyl CoA):

• 3 Reduced NAD
• 1 Reduced FAD
• 1 ATP (via substrate-level phosphorylation)
• 2 Carbon Dioxide (CO₂)

Remember: Since two acetyl CoA entered from one glucose, these outputs are doubled for a full glucose molecule!

C. Oxidative Phosphorylation (The Energy Grand Finale)

This stage produces the vast majority of ATP and requires oxygen. It occurs on the inner mitochondrial membrane (which is highly folded into cristae to maximise surface area).

This complex process relies on two linked mechanisms: the Electron Transfer Chain (ETC) and Chemiosmosis.

1. The Electron Transfer Chain (ETC):

• Reduced NAD and reduced FAD (which were produced in glycolysis, link reaction, and Krebs cycle) deliver the hydrogen atoms they are carrying to the inner mitochondrial membrane.
• These hydrogen atoms split into protons (\(H^+\)) and electrons (\(e^-\)).
• The high-energy electrons are passed along a chain of protein carriers embedded in the membrane. This is the ETC.
• As the electrons move down the ETC, they release energy.

2. Generating the Proton Gradient:

• The energy released by the electrons is used to actively pump the protons (\(H^+\)) from the mitochondrial matrix into the intermembrane space.
• This creates a high concentration of protons in the intermembrane space—a proton gradient (or electrochemical gradient).

3. Chemiosmosis and ATP Synthesis:

• The high concentration of protons in the intermembrane space creates a strong tendency for them to diffuse back into the matrix.
• Protons can only pass back through special channels associated with the enzyme ATP synthase, which is also embedded in the inner membrane.
• The movement of protons (a flow known as chemiosmosis) down their concentration gradient provides the kinetic energy used by ATP synthase to catalyse the synthesis of ATP from ADP and inorganic phosphate (\(P_i\)).

4. The Role of Oxygen (The Final Electron Acceptor):

• At the end of the ETC, the electrons, which are now low in energy, must be removed.
• Oxygen is vital here; it acts as the final electron acceptor.
• Oxygen combines with the electrons and the protons (\(H^+\)) in the matrix to form water (\(H_2O\)).
  \( 4e^- + 4H^+ + O_2 \rightarrow 2H_2O \)
• If oxygen is absent, the entire chain stops working, leading to anaerobic respiration.

3.3.3.4 Respiratory Substrates and Respiratory Quotient (RQ)

While glucose (a carbohydrate) is the primary fuel we discuss, cells can break down other molecules like lipids (fats) and proteins (amino acids) to generate ATP. These are known as respiratory substrates.

Alternative Substrates

• Lipids: Lipids are first broken down into glycerol and fatty acids. Fatty acids are broken into 2-carbon fragments which are converted to acetyl coenzyme A and enter the Krebs cycle. (They also produce large amounts of reduced NAD/FAD through beta-oxidation, leading to high ATP yield).
• Proteins: Proteins are broken down into amino acids. Amino acids have their amino groups removed (deamination). The remaining carbon skeleton enters respiration at various points—either converted to pyruvate, acetyl CoA, or directly into intermediates of the Krebs cycle.

Because lipids have far more hydrogen atoms than carbohydrates, they require significantly more oxygen to break down and therefore release much more energy per gram.

The Respiratory Quotient (RQ)

The Respiratory Quotient (RQ) is a mathematical measure used to determine what type of substrate an organism is metabolising (i.e., what food source it is using for respiration).

The RQ is calculated using the following ratio:

$$ \text{RQ} = \frac{\text{Volume of } CO_2 \text{ produced}}{\text{Volume of } O_2 \text{ consumed}} $$

Note: The CO₂ and O₂ volumes (or moles) must be measured in the same units (e.g., cm³ or moles) and in quantities proportional to the number of molecules involved.

Interpreting RQ Values

The RQ value tells us which substrate is being oxidised because different substrates require different amounts of oxygen relative to the CO₂ they produce.

• Carbohydrates: RQ is generally 1.0.
  Example: Complete oxidation of glucose: \( C_6H_{12}O_6 + 6O_2 \rightarrow 6CO_2 + 6H_2O \)
  RQ = 6 CO₂ / 6 O₂ = 1.0
• Lipids (Fats): RQ is typically around 0.7.
  Lipids are highly reduced (less oxygen content), meaning they require a lot more external oxygen to be fully oxidised compared to the CO₂ they release.
• Proteins/Amino Acids: RQ is typically around 0.8 - 0.9. (The value depends on which part of the molecule enters the cycle).

Tentative Nature of Conclusions

When you use RQ data, you should always comment on the tentative nature of the conclusion (i.e., that the conclusion is not certain). Why?

• The organism might be respiring a mixture of substrates simultaneously (e.g., 60% carbohydrate, 40% lipid), which would give an intermediate RQ value.
• If the organism is performing anaerobic respiration alongside aerobic respiration (or in addition to), the measured RQ value will be higher than 1.0 (since CO₂ is produced but little O₂ is consumed).