A-Level Biology (9700): Comprehensive Study Notes on Respiration

Hello future Biologists! This chapter, Respiration and Energy, is absolutely vital. Everything a living cell does—from building proteins to moving muscles—requires energy, and respiration is the process that unlocks that energy.

Don't worry if the names (Glycolysis, Krebs Cycle, Oxidative Phosphorylation) look intimidating. We will break down this complex energy pathway into simple, sequential steps. By the end, you'll see respiration not just as an equation, but as a beautiful, efficient metabolic machine!

12.1 Energy - ATP: The Universal Energy Currency

What is Energy Needed For?

Every living process in organisms requires a constant supply of energy, which cells obtain by hydrolyzing adenosine triphosphate (ATP).

Key processes needing energy (ATP) include:

  • Active Transport: Pumping ions or molecules across membranes against a concentration gradient.
  • Movement: Muscle contraction, movement of cilia, and flagella.
  • Anabolic Reactions: Building larger molecules from smaller ones (e.g., DNA replication, protein synthesis).
  • Nerve Impulse Transmission: Maintaining resting potentials via sodium-potassium pumps.

The Features of ATP

Think of ATP as the cell's immediately accessible cash. While glucose is a great long-term bank account, ATP is quick and easy to spend.

ATP is a phosphorylated nucleotide (related to RNA) consisting of:

  1. Adenine (Nitrogenous base)
  2. Ribose (Pentose sugar)
  3. Three Phosphate groups (The energy is stored in the bonds between these groups).

When the terminal phosphate bond is broken by hydrolysis (catalyzed by ATP hydrolase), energy is released, forming ADP (adenosine diphosphate) and an inorganic phosphate ($P_i$).

$$ATP + H_2O \rightarrow ADP + P_i + \text{Energy}$$

Features that make ATP suitable as a universal energy currency:

  • It releases energy in small, manageable bursts, preventing the cell from overheating.
  • It is soluble, allowing easy movement throughout the cell.
  • It can be rapidly reformed (condensed) from ADP and $P_i$ (a reversible reaction).

How is ATP Synthesised?

There are two main methods of ATP production during respiration:

  1. Transfer of Phosphate in Substrate-linked Reactions:

    A phosphate group is directly transferred from a phosphorylated intermediate molecule (a 'substrate') to an ADP molecule, usually catalyzed by a kinase enzyme. This occurs during Glycolysis and the Krebs Cycle.

  2. Chemiosmosis:

    This is the major method, producing the most ATP. It involves the flow of protons (H+) down a concentration gradient across a membrane, driving the enzyme ATP synthase. This happens on the inner membranes of mitochondria (respiration) and chloroplasts (photosynthesis).

Quick Takeaway 12.1: ATP is the cell's essential, readily available energy molecule. It is produced either directly (substrate-linked) or via the large-scale method, chemiosmosis, within the mitochondria.

12.1 Respiratory Substrates and the Respiratory Quotient (RQ)

Relative Energy Values

Cells can respire carbohydrates, lipids, and proteins. The energy yield depends on the proportion of hydrogen atoms present in the molecule, as these atoms are the source of electrons for the most profitable stage of respiration (Oxidative Phosphorylation).

  • Lipids: Highest energy value per gram. Lipids contain many C-H bonds and require the most oxygen for complete oxidation, thus yielding the most reduced NAD/FAD.
  • Carbohydrates (Glucose): The primary and preferred substrate.
  • Proteins: Used only when carbohydrate and lipid supplies are low. Proteins must first be broken down into amino acids, and the amino groups ($\text{NH}_2$) are removed (deamination) before the remaining skeleton can enter the respiratory pathway (usually the Krebs cycle).

Calculating the Respiratory Quotient (RQ)

The Respiratory Quotient (RQ) is a ratio used to estimate the type of substrate being respired.

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

An RQ value is calculated from the overall chemical equation for the respiration of a specific substrate.

RQ Values for Different Substrates:

  • Carbohydrates: RQ = 1.0 (e.g., Glucose: $\text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O}$). Since 6 moles of $\text{CO}_2$ are produced and 6 moles of $\text{O}_2$ are consumed, RQ = 6/6 = 1.0.
  • Lipids: RQ $\approx$ 0.7. Lipids have less oxygen atoms relative to carbon and hydrogen. They require significantly more $\text{O}_2$ to break down, making the denominator larger, and hence the ratio smaller.
  • Proteins/Amino acids: RQ $\approx$ 0.8 to 0.9.

Did you know? Measuring the RQ of a person or organism can indicate what they are primarily metabolizing. An RQ near 0.7 suggests heavy fat burning (like during sustained moderate exercise).

Practical Investigation using Respirometers

A simple respirometer measures the volume changes in gases during respiration (usually of germinating seeds or small invertebrates like blowfly larvae).

Setup principle:

  1. Organisms are placed in a container connected to a manometer.
  2. A chemical absorbent, usually potassium hydroxide (KOH), is included to absorb the $\text{CO}_2$ produced.
  3. As $\text{O}_2$ is consumed but the resulting $\text{CO}_2$ is absorbed, there is a net decrease in gas volume, causing the manometer fluid to move. This movement measures the $\text{O}_2$ consumption.

To determine the RQ, the experiment must be repeated without the $\text{CO}_2$ absorbent to measure the $\text{CO}_2$ production (or the difference in readings taken with and without KOH can be used).

Quick Takeaway 12.2: Lipids yield the most energy but have the lowest RQ because they need more oxygen to be fully oxidized. The RQ helps determine the primary fuel source.

12.2 Aerobic Respiration: The Four Stages

Aerobic respiration is the release of a large amount of energy from glucose or other organic molecules using oxygen. It is split into four sequential stages.

Stage Locations in Eukaryotic Cells

Understanding where each stage happens is critical, especially when relating function to the structure of the mitochondrion.

  1. Glycolysis: Cytoplasm
  2. Link Reaction: Mitochondrial Matrix
  3. Krebs Cycle (Citric Acid Cycle): Mitochondrial Matrix
  4. Oxidative Phosphorylation (OP): Inner Mitochondrial Membrane (including the cristae)

Mitochondrial Structure and Function

Mitochondria are often called the 'powerhouses' because they host the final three, most productive stages of respiration.

  • Outer Membrane: Controls entry/exit of molecules.
  • Inner Membrane (Cristae): Highly folded to increase the surface area, maximizing the space for the electron transport chain (ETC) components and ATP synthase required for oxidative phosphorylation.
  • Matrix: The fluid interior containing enzymes needed for the Link Reaction and the Krebs Cycle, as well as 70S ribosomes and small circular DNA.
  • Intermembrane Space: The narrow space between the inner and outer membrane, crucial for building up a high concentration of protons (H+) during oxidative phosphorylation.

Stage 1: Glycolysis

Glycolysis is the initial stage and occurs in the cytoplasm of the cell. It does not require oxygen.

The Process:

  1. Phosphorylation: Glucose (6C) is phosphorylated (two ATP are used!) to form fructose 1,6-bisphosphate (6C). This makes the molecule unstable and prevents it from leaving the cell.
  2. Splitting: The 6C sugar splits into two molecules of triose phosphate (3C).
  3. Oxidation and ATP Production: Each 3C molecule is oxidized (loses hydrogen atoms) and converted into pyruvate (3C). This oxidation involves the reduction of $\text{NAD}$ to reduced $\text{NAD}$. Four ATP molecules are produced via substrate-linked phosphorylation.

Net Products per Glucose Molecule:

  • 2 Pyruvate (3C)
  • 2 Net ATP (4 produced - 2 used)
  • 2 Reduced NAD

Analogy: Glycolysis is like taking a crisp £20 note (Glucose) and getting it changed into smaller change (Pyruvate) and some immediately usable cash (2 ATP).

Stage 2: The Link Reaction (Aerobic conditions only)

If oxygen is available, the pyruvate moves from the cytoplasm, through the outer mitochondrial membrane, and into the mitochondrial matrix.

The Process (occurs twice per glucose molecule):

  1. Decarboxylation: Pyruvate (3C) loses a carbon atom as $\text{CO}_2$.
  2. Dehydrogenation: Pyruvate loses hydrogen atoms, reducing $\text{NAD}$ to reduced $\text{NAD}$.
  3. The remaining 2C group (an acetyl group) combines with Coenzyme A ($\text{CoA}$) to form Acetyl $\text{CoA}$.

Net Products per Glucose Molecule:

  • 2 Acetyl $\text{CoA}$ (2C)
  • 2 $\text{CO}_2$ (waste product)
  • 2 Reduced $\text{NAD}$

Stage 3: The Krebs Cycle (Citric Acid Cycle)

This cycle occurs in the mitochondrial matrix and is the main source of reduced coenzymes ($\text{NAD}$ and $\text{FAD}$).

The Process (occurs twice per glucose molecule):

  1. Citrate Formation: The 2C acetyl group from Acetyl $\text{CoA}$ combines with a 4C molecule, oxaloacetate, to form a 6C molecule, citrate. (Oxaloacetate is the acceptor molecule).
  2. Decarboxylation and Dehydrogenation: The 6C citrate is broken down in a series of small, enzyme-catalyzed steps, involving:
    • Release of $\text{CO}_2$ (decarboxylation).
    • Removal of hydrogen atoms (dehydrogenation), reducing coenzymes $\text{NAD}$ and $\text{FAD}$.
  3. Oxaloacetate Regeneration: Eventually, the 4C oxaloacetate is regenerated, ready to accept another acetyl group, keeping the cycle turning.

Net Products per Glucose Molecule (after two turns):

  • 4 $\text{CO}_2$
  • 6 Reduced $\text{NAD}$
  • 2 Reduced $\text{FAD}$
  • 2 ATP (via substrate-linked phosphorylation)

Quick Review Box: The Hydrogen Carriers

The Link Reaction and the Krebs Cycle don't produce much ATP directly. Their most important function is to harvest hydrogen atoms (and their energetic electrons) by reducing NAD and FAD. These reduced coenzymes will deliver the hydrogen to the final stage.

Stage 4: Oxidative Phosphorylation (OP)

This is the stage where the vast majority of ATP is produced, using the energy carried by the reduced coenzymes. It occurs on the inner mitochondrial membrane (cristae).

The Mechanism: Chemiosmosis and the Electron Transport Chain ($\text{ETC}$)

Step-by-Step Breakdown:

  1. Delivery: Reduced $\text{NAD}$ and reduced $\text{FAD}$ deliver their hydrogen atoms to the protein carriers embedded in the inner mitochondrial membrane.
  2. Splitting: The hydrogen atoms are split into protons ($\text{H}^+$) and energetic electrons ($\text{e}^-$).
  3. Electron Transport Chain (ETC): The electrons pass along the chain of protein carriers. At each transfer step, they lose a little energy.
  4. Proton Pumping: The energy released by the electrons moving through the $\text{ETC}$ is used to actively transfer the $\text{H}^+$ protons from the matrix into the intermembrane space.
  5. Creating a Gradient: This pumping action creates a high concentration of $\text{H}^+$ in the intermembrane space (a proton gradient). The combination of a concentration gradient and an electrical gradient is called the electrochemical gradient.
  6. Chemiosmosis: The protons cannot diffuse back into the matrix easily. They return by facilitated diffusion through specific channels associated with the enzyme ATP synthase.
  7. ATP Synthesis: The flow of protons through $\text{ATP}$ synthase provides the kinetic energy needed to join ADP and $P_i$ to form ATP.
  8. Final Acceptance: At the end of the $\text{ETC}$, the less energetic electrons and the protons combine with Oxygen. Oxygen acts as the final electron acceptor, forming water ($\text{H}_2\text{O}$).

Crucial Role of Oxygen: If oxygen is absent, the electrons cannot leave the $\text{ETC}$. The chain backs up, proton pumping stops, and ATP synthesis ceases. This highlights why aerobic respiration is dependent on $\text{O}_2$.

Quick Takeaway 12.3: The vast energy difference between aerobic and anaerobic respiration comes from Oxidative Phosphorylation, which is only possible because of the $\text{ETC}$, chemiosmosis, and oxygen's role as the final electron acceptor.

12.2 Anaerobic Respiration (Fermentation)

When oxygen is scarce or absent, pyruvate cannot enter the mitochondria to undergo the Link Reaction or Krebs Cycle. Only Glycolysis can run, but it quickly runs into a problem: it needs $\text{NAD}$ to accept hydrogen atoms (Step 3 of Glycolysis). If the $\text{ETC}$ is backed up (due to lack of $\text{O}_2$), reduced $\text{NAD}$ cannot drop off its hydrogens and regenerate free $\text{NAD}$.

Anaerobic respiration (fermentation) is an emergency measure whose main purpose is to regenerate $\text{NAD}$ so Glycolysis can continue and produce small amounts of ATP.

Since the later stages are skipped, the total ATP yield is drastically lower: only the 2 Net ATP produced during glycolysis.

1. Lactate Fermentation (Mammals/Muscle Cells)

In highly active mammalian muscle cells, oxygen demand often exceeds supply, leading to anaerobic conditions.

  • Pyruvate accepts the hydrogen atoms from reduced $\text{NAD}$.
  • This regenerates $\text{NAD}$, allowing glycolysis to restart.
  • The pyruvate is converted into Lactate (lactic acid).

$$Pyruvate + \text{Reduced } NAD \rightarrow Lactate + NAD$$

Lactate accumulates and causes muscle fatigue and cramps. When oxygen is available again (after exercise), the lactate is transported to the liver and converted back to pyruvate for full aerobic respiration.

2. Ethanol Fermentation (Yeast Cells)

This process is utilized in brewing and bread-making.

Step 1: Pyruvate is converted into Ethanal, releasing $\text{CO}_2$ (this is why bread rises and beer is fizzy).
Step 2: Ethanal accepts hydrogen from reduced $\text{NAD}$, regenerating $\text{NAD}$.
Step 3: Ethanal is converted into Ethanol (alcohol).

$$\text{Pyruvate} \rightarrow \text{Ethanal} + CO_2$$ $$\text{Ethanal} + \text{Reduced } NAD \rightarrow \text{Ethanol} + NAD$$

Adaptation of Rice in Submerged Conditions

Rice roots are often submerged in water, which contains very little oxygen. Rice is adapted to cope with these conditions:

  • Aerenchyma: Specialized tissue forms air spaces in the stems and roots, providing a pathway for oxygen transport from the parts above water down to the submerged roots.
  • Ethanol Fermentation Tolerance: Rice roots can perform ethanol fermentation to produce ATP, but unlike most plants, they are tolerant of the toxic buildup of ethanol, allowing them to survive prolonged periods underwater.
  • Faster Stem Growth: The plant may accelerate stem growth to ensure some parts reach the surface quickly to access atmospheric oxygen.

12.2 Practical Investigations into Respiration Rate

We can measure respiration rate using indicators or respirometers, often testing factors like temperature or substrate concentration.

Using Redox Indicators (DCPIP and Methylene Blue)

These investigations commonly use yeast cells. Redox indicators change colour when they accept hydrogen (become reduced).

  • DCPIP: Changes from Blue (oxidized) to Colourless (reduced).
  • Methylene Blue: Changes from Blue (oxidized) to Colourless (reduced).

When yeast respires a substrate (like glucose), it releases hydrogen atoms (dehydrogenation). If the indicator is present, it acts as an artificial hydrogen acceptor, diverting the $\text{H}$ from the normal respiratory pathway.

The rate of respiration is proportional to the rate at which the indicator changes colour (i.e., the time taken for the solution to decolorize).

Common Mistake: Remember that these indicators are measuring the *release* of hydrogen during respiration, not oxygen consumption directly.

Using Respirometers (Effect of Temperature)

As discussed in Section 12.1, a respirometer measures the volume change caused by oxygen consumption.

  • To investigate the effect of temperature, you place identical respirometers containing respiring organisms (e.g., germinating seeds) in water baths maintained at different temperatures.
  • The higher the temperature (up to the optimum), the faster the enzymes work, leading to a higher rate of respiration and faster $\text{O}_2$ consumption (faster manometer fluid movement).

Accessibility Tip: Always include a control tube with non-living material (e.g., glass beads of the same mass/volume) to compensate for changes in the ambient temperature or atmospheric pressure during the experiment.

Chapter Summary: Respiration is a multi-stage process that systematically strips energy (in the form of electrons and protons) from carbon compounds. Glycolysis starts in the cytoplasm, producing a small amount of ATP. The majority of the ATP is synthesized in the mitochondrial inner membrane via chemiosmosis, driven by the proton gradient created by the electron transport chain, which relies entirely on oxygen to keep the system running.