Biology (9700) | Energy and respiration

A-LEVEL BIOLOGY (9700): Energy and Respiration (Topic 12)

Welcome to one of the most fundamental topics in A-Level Biology! This chapter is all about how living things capture, convert, and use energy. Think of it as studying the powerhouse of the cell—the complex mechanisms that allow you to move, think, and grow.
Understanding energy (ATP) and respiration is crucial because these processes underpin almost every other biological activity, from DNA replication to active transport. Don't worry if the cycles seem complex; we will break them down step-by-step!

12.1 Energy: The Universal Currency (ATP)

The Need for Energy

All living organisms require a constant supply of energy to drive essential processes. If the energy supply stops, the cell dies. The main needs for energy include:

• Active Transport: Moving substances against their concentration gradient (e.g., uptake of nitrates by root hairs).
• Movement: Muscle contraction, movement of cilia or flagella.
• Anabolic Reactions: Synthesis of complex molecules from simpler ones (e.g., building proteins during protein synthesis, replicating DNA, and synthesising starch).
• Nerve Impulses: Maintaining resting potential and generating action potentials.

Adenosine Triphosphate (ATP)

ATP is the universal energy currency of the cell. It is an immediate source of energy, making it much more suitable than glucose for energy transfer.

Structure of ATP

ATP is a phosphorylated nucleotide. It consists of:

• Adenine (a nitrogenous base).
• Ribose (a pentose sugar).
• Three Phosphate Groups (linked in a chain).

Features of ATP that make it suitable

Think of ATP as the cell's rechargeable battery. It has features that make it ideal for quick energy transfer:

1. Immediate Energy Release: The bonds linking the phosphate groups (especially the last one) are highly unstable and easily broken by hydrolysis.
2. Rapid Rechargeable: The hydrolysis reaction is reversible (ATP synthesis is fast).
3. Small Energy Packets: It releases small, manageable bursts of energy, enough for a single reaction, minimising energy waste (loss as heat).
4. Universal: Used by all cells in all organisms.

Analogy: Glucose is like a large £50 note—it holds a lot of value, but you can't use it easily everywhere. ATP is like a handful of £1 coins—small, immediate, and universally accepted for single, specific transactions.

Synthesis of ATP

ATP is primarily synthesised by two main methods:

1. Transfer of Phosphate in Substrate-Linked Reactions: (Also called Substrate-level phosphorylation). This happens directly in the cytoplasm (during glycolysis) and in the mitochondrial matrix (during the Krebs cycle). An enzyme transfers a phosphate group from a substrate molecule directly to ADP.
2. Chemiosmosis: This is the major source of ATP. It involves the flow of protons down a concentration gradient across membranes, coupled with ATP synthase activity. This occurs in the inner membrane of mitochondria (during respiration) and in the thylakoid membranes of chloroplasts (during photosynthesis).

Respiratory Substrates and Energy Yields

Cells break down energy-rich molecules to release energy. These molecules are called respiratory substrates.

The relative energy values of substrates depend on the amount of hydrogen they contain compared to oxygen (the H:O ratio). The more hydrogen, the more reduced NAD and FAD can be formed, leading to more ATP via oxidative phosphorylation.

• Lipids: Highest energy value. They have very low oxygen content and a high H:O ratio (lots of potential for $\text{H}$ transfer).
• Carbohydrates (Glucose): Intermediate energy value.
• Proteins: Similar to carbohydrates, but they must first be broken down into amino acids, and the amino group ($\text{NH}_2$) must be removed (deamination), forming urea (a waste product).

The Respiratory Quotient (RQ)

The Respiratory Quotient (RQ) is a way to determine the type of substrate being respired.

It is defined as the ratio of the volume of carbon dioxide produced ($\text{CO}_2$) to the volume of oxygen taken in ($\text{O}_2$) over the same period, as a result of respiration.

\[ \text{RQ} = \frac{\text{Volume of CO}_2\text{ produced}}{\text{Volume of O}_2\text{ consumed}} \]

Calculating RQ Values

We can calculate the RQ from the balanced equation for aerobic respiration:

• Carbohydrate (e.g., Glucose):
  \[ \text{C}_6\text{H}_{12}\text{O}_6 + 6\text{O}_2 \rightarrow 6\text{CO}_2 + 6\text{H}_2\text{O} \]
  RQ = 6 $\text{CO}_2$ / 6 $\text{O}_2$ = 1.0
• Lipid (e.g., Tripalmitin): Lipids require much more $\text{O}_2$ relative to the $\text{CO}_2$ produced because they have less oxygen already. The denominator ($\text{O}_2$ consumed) is large.
  \[ 2\text{C}_{51}\text{H}_{98}\text{O}_6 + 145\text{O}_2 \rightarrow 102\text{CO}_2 + 98\text{H}_2\text{O} \]
  RQ = 102 / 145 ≈ 0.7
• Protein/Amino Acid: RQ value is usually around 0.9.

Key Takeaway: An RQ value of 1.0 indicates carbohydrate respiration. An RQ less than 1.0 (typically 0.7) indicates lipids are being respired. If an organism is starving, the RQ will likely fall below 1.0 as it starts breaking down fats and proteins.

12.2 Respiration: Breaking Down Energy

Aerobic respiration is the process that releases a large amount of energy by completely oxidising respiratory substrates (like glucose) using oxygen.

Stage Locations in Eukaryotic Cells (12.2.1)

Aerobic respiration is a four-stage process:

1. Glycolysis: Occurs in the Cytoplasm.
2. Link Reaction: Occurs in the Mitochondrial Matrix.
3. Krebs Cycle: Occurs in the Mitochondrial Matrix.
4. Oxidative Phosphorylation (OP): Occurs on the Inner Mitochondrial Membrane.

Memory Trick: L-R-K-O (Link, Krebs, OP) are all happening inside the Mitochondria. Glycolysis happens outside (in the cytoplasm).

Stage 1: Glycolysis (12.2.2)

Glycolysis is the anaerobic breakdown of glucose into pyruvate. It doesn't require oxygen, so it is the starting point for both aerobic and anaerobic respiration.

Steps (Outline):

1. Phosphorylation: Glucose (6C) is phosphorylated using ATP (this costs 2 ATP).
2. Splitting: The phosphorylated glucose is converted to fructose 1,6-bisphosphate (6C), which is then split into two molecules of triose phosphate (TP) (3C).
3. Oxidation/ATP production: The two TP molecules are subsequently oxidised (dehydrogenated) and rearranged into pyruvate (3C). This step produces ATP (via substrate-level phosphorylation) and reduces the coenzyme NAD.

Net Results per Glucose molecule:

• 2 Pyruvate (3C)
• Net gain of 2 ATP (4 produced, 2 consumed)
• 2 Reduced NAD ($\text{NADH} + \text{H}^+$)

Stage 2: The Link Reaction (12.2.3, 12.2.4)

If oxygen is present, pyruvate moves from the cytoplasm into the mitochondrial matrix.

Process:

1. Pyruvate (3C) undergoes decarboxylation (loses a $\text{CO}_2$ molecule).
2. Pyruvate is simultaneously dehydrogenated (loses $\text{H}$, reducing NAD).
3. The resulting 2C fragment (Acetyl group) combines with Coenzyme A to form Acetyl coenzyme A (Acetyl CoA).

Net Results per Pyruvate molecule (x2 per glucose):

• 1 Acetyl CoA (2C)
• 1 $\text{CO}_2$
• 1 Reduced NAD

Stage 3: The Krebs Cycle (Citric Acid Cycle) (12.2.5, 12.2.6)

The Krebs cycle takes place in the mitochondrial matrix. Its primary role is to generate massive amounts of reduced NAD and reduced FAD for the final stage.

Steps (Outline):

1. Acceptor and Citrate Formation: The cycle begins when oxaloacetate (4C) acts as an acceptor, combining with the 2C fragment from Acetyl CoA to form citrate (6C).
2. Decarboxylation and Dehydrogenation: Citrate is then converted back to oxaloacetate through a series of small steps. These steps involve multiple:
   • Decarboxylation: $\text{CO}_2$ is removed (twice per turn).
   • Dehydrogenation: Hydrogen is removed (used to reduce coenzymes).
3. Coenzyme Reduction: The coenzymes NAD and FAD are essential hydrogen carriers and are reduced during these steps.
4. Substrate-level ATP: A small amount of ATP is produced directly.
5. Regeneration: Oxaloacetate (4C) is regenerated, ready to accept another Acetyl CoA.

Net Results per turn of the cycle (x2 per glucose):

• 2 $\text{CO}_2$
• 3 Reduced NAD
• 1 Reduced FAD
• 1 ATP (or equivalent via substrate-linked reaction)

Stage 4: Oxidative Phosphorylation and Chemiosmosis (12.2.7, 12.2.8)

This is where the majority of ATP is produced, located on the inner mitochondrial membrane (IMM).

1. Delivery and Splitting of Hydrogen

• Reduced NAD and Reduced FAD (the 'payoff' from Glycolysis, Link, and Krebs) deliver their hydrogen atoms ($\text{H}$) to the carriers embedded in the IMM.
• The hydrogen atoms split into highly energetic electrons ($\text{e}^-$) and protons ($\text{H}^+$).

2. Electron Transport Chain (ETC)

• The energetic electrons are passed along a chain of carrier molecules (electron carriers are redox molecules).
• As the electrons move from one carrier to the next, they release energy in a series of small steps. (Details of specific carriers are NOT expected.)

3. Proton Gradient Formation

• The energy released by the electrons is used to actively transfer the protons ($\text{H}^+$) from the mitochondrial matrix into the intermembrane space (the space between the inner and outer mitochondrial membranes).
• This creates a proton gradient (a high concentration of $\text{H}^+$ in the intermembrane space and a low concentration in the matrix). This gradient stores potential energy.

4. Chemiosmosis (ATP Synthesis)

• Protons cannot easily diffuse back across the impermeable IMM, except through special channels linked to the enzyme ATP synthase.
• Protons return to the matrix by facilitated diffusion through the ATP synthase. This flow of protons provides the kinetic energy needed to catalyse the synthesis of ATP from ADP and inorganic phosphate ($\text{P}_i$).

5. Final Electron Acceptor

• At the end of the ETC, the electrons, now low in energy, must be removed.
• Oxygen ($\text{O}_2$) acts as the final electron acceptor.
• Oxygen combines with the depleted electrons and the protons ($\text{H}^+$) that flowed back into the matrix to form water ($\text{H}_2\text{O}$).

Did you know? If oxygen is not available, the ETC stops, the carriers remain reduced, and the whole aerobic process grinds to a halt. This is why oxygen is absolutely vital for aerobic life!

Mitochondrial Structure and Function (12.2.9)

The structure of the mitochondrion is perfectly adapted for aerobic respiration, especially Oxidative Phosphorylation:

• Outer Membrane: Controls entry and exit.
• Inner Mitochondrial Membrane (IMM): Highly folded into structures called cristae, which dramatically increase the surface area available for embedding electron transport chains and ATP synthase enzymes. This maximises the rate of ATP synthesis.
• Intermembrane Space: Small space between membranes where protons ($\text{H}^+$) accumulate, creating a steep, high concentration gradient required for chemiosmosis.
• Matrix: Contains enzymes for the Link Reaction and Krebs Cycle, 70S ribosomes, and small circular DNA.

12.2 Anaerobic Respiration

When oxygen is absent or in short supply, respiration becomes anaerobic. Only Glycolysis can proceed, as the Link Reaction, Krebs Cycle, and Oxidative Phosphorylation all require oxygen, either directly or indirectly.

The total energy yield is much smaller in anaerobic respiration compared to aerobic respiration (12.2.11), because only the 2 ATP from Glycolysis are gained; the main energy-producing stages are bypassed.

The Problem and The Solution

The primary issue in anaerobic conditions is the accumulation of reduced NAD. Glycolysis needs a continuous supply of oxidised NAD ($\text{NAD}^+$) to continue. Anaerobic fermentation acts to regenerate $\text{NAD}^+$ so Glycolysis can keep making a small amount of ATP.

1. Lactate Fermentation (Mammals) (12.2.10)

Occurs in muscle cells during intense exercise when oxygen demand exceeds supply.

1. Pyruvate accepts hydrogen atoms from reduced NAD.
2. Pyruvate is converted to Lactate (lactic acid).
3. This regenerates $\text{NAD}^+$, allowing Glycolysis to continue.

\[ \text{Pyruvate} + \text{Reduced NAD} \rightarrow \text{Lactate} + \text{NAD}^+ \]

Lactate builds up, lowering the pH, which causes muscle fatigue. It must be transported to the liver where it is converted back to pyruvate (requiring extra oxygen—the 'oxygen debt').

2. Ethanol Fermentation (Yeast) (12.2.10)

Occurs in yeast cells (used in brewing and baking).

1. Pyruvate is decarboxylated (releases $\text{CO}_2$), forming Ethanal.
2. Ethanal accepts hydrogen atoms from reduced NAD.
3. Ethanal is converted to Ethanol.
4. This regenerates $\text{NAD}^+$, allowing Glycolysis to continue.

\[ \text{Pyruvate} \rightarrow \text{Ethanal} + \text{CO}_2 \] \[ \text{Ethanal} + \text{Reduced NAD} \rightarrow \text{Ethanol} + \text{NAD}^+ \]

Adaptations for Anaerobic Environments: The Rice Plant (12.2.12)

Rice is an unusual crop as it is adapted to grow with its roots submerged in water, an environment severely lacking in oxygen (anaerobic). It uses a combination of structural and metabolic adaptations:

1. Aerenchyma Tissue: The plant develops specialised tissues (air spaces) in the roots and stems. This allows gases ($\text{O}_2$) to diffuse down to the submerged roots, providing some oxygen supply.
2. Ethanol Tolerance: Rice is highly tolerant of the ethanol produced by fermentation in the root cells. Unlike many plants, it can cope with the toxicity.
3. Fast Stem Growth: The stem grows quickly (especially in deep water varieties) to ensure the leaves and gas exchange surfaces reach the air above the water line rapidly, facilitating oxygen uptake.

Practical Investigations in Respiration (12.2.13, 12.2.14)

You need to be familiar with investigations measuring the rate of respiration using:

1. Simple Respirometers

A respirometer measures the rate of $\text{O}_2$ uptake by an organism (e.g., germinating seeds or insects). The setup includes:

• A tube containing the organism and potassium hydroxide ($\text{KOH}$) or soda lime (to absorb the $\text{CO}_2$ produced).
• A capillary tube connected to a manometer (drop of coloured liquid).
• Any decrease in gas volume is due to $\text{O}_2$ consumption, which causes the drop of liquid to move towards the organism.

This apparatus can be used to investigate the effect of temperature on the rate of respiration.

2. Redox Indicators (Yeast Respiration)

Yeast respiration rate can be measured by observing the rate at which redox dyes change colour. These dyes act as alternative hydrogen acceptors instead of NAD/FAD, changing colour when they accept electrons (are reduced).

• Methylene Blue: Changes from blue (oxidised) to colourless (reduced).
• DCPIP: Changes from blue (oxidised) to colourless (reduced).

The time taken for the indicator to become colourless is inversely proportional to the rate of respiration. This method is used to investigate the effects of temperature and substrate concentration (e.g., glucose) on yeast respiration.