Biology (9700) | Energy

Welcome to the Energy Chapter!

Hello future Biologists! This chapter is arguably one of the most fundamental in all of A Level Biology. Why? Because every single living process—from thinking to running to growing—requires energy. We are going to dive deep into how cells capture light energy (Photosynthesis) and how they release stored chemical energy from food (Respiration) to fuel all their amazing activities.

Don't worry if the detailed pathways seem complex at first. We will break them down step-by-step using clear language and plenty of helpful analogies. Let’s get started on understanding the universal currency of life!

Section 1: ATP – The Universal Energy Currency

1.1 Why We Need Energy (12.1.1)

All organisms constantly need energy for vital processes. Think of energy as the fuel that keeps the cellular engine running. Key processes requiring energy include:

• Active Transport: Moving substances across cell membranes against the concentration gradient (e.g., sodium-potassium pump).
• Movement: Muscle contraction, cilia and flagella beating.
• Anabolic Reactions: Building larger molecules from smaller ones (e.g., synthesizing proteins from amino acids, DNA replication, photosynthesis itself!).

1.2 Adenosine Triphosphate (ATP) (12.1.2)

ATP is the molecule that acts as the immediate, accessible energy source for the cell. It's often called the universal energy currency—like cash, it can be spent anywhere instantly.

Structure of ATP:

ATP is a phosphorylated nucleotide made up of three parts:

1. Adenine (a nitrogen-containing base).
2. Ribose (a pentose sugar).
3. Three Phosphate Groups (linked in a chain).

Energy Release (Hydrolysis)

Energy is stored in the bonds between the phosphate groups. When the cell needs energy, water is used to break the bond connecting the terminal phosphate group (the third one).

The reaction is called hydrolysis (lysis = splitting, hydro = water):
ATP + H₂O \(\rightarrow\) ADP + P_i + Energy
(\(P_i\) is inorganic phosphate.)

This reaction is exergonic (releases energy) and is coupled to the cell's energy-requiring (endergonic) reactions.

Energy Synthesis (Phosphorylation) (12.1.3)

To recharge this currency, ADP and P_i must be rejoined, a process called phosphorylation. This requires energy input (an endergonic reaction).

ADP + P_i + Energy \(\rightarrow\) ATP + H₂O

ATP is synthesized in cells by two main mechanisms:

1. Substrate-linked phosphorylation: Direct transfer of a phosphate group from a high-energy intermediate molecule (substrate) to ADP. (This occurs during glycolysis and the Krebs cycle).
2. Chemiosmosis: ATP synthesis powered by the movement of protons (\(H^+\)) across a membrane through an enzyme called ATP synthase. (This is the main mechanism in mitochondria during respiration and in chloroplasts during photosynthesis).

Section 2: Respiration – Fueling the Cell

2.1 Respiratory Substrates and Energy Values (12.1.4)

Respiration is the process that transfers energy from organic molecules (like glucose) into ATP.

The primary substrate is usually glucose (a carbohydrate), but cells can also use lipids and proteins.

Relative Energy Values:

Lipids have a much higher energy value per gram than carbohydrates or proteins.

• Lipids (Fatty acids and glycerol): Highest energy yield. They have fewer oxygen atoms relative to carbon and hydrogen (a lower H:O ratio), meaning they are more highly reduced. This allows them to yield more reduced coenzymes (NAD and FAD) during the breakdown stages, leading to more ATP generation later.
• Carbohydrates (Glucose): Intermediate yield. The most common substrate.
• Proteins (Amino acids): Lowest yield. Used only when carbohydrate and lipid supplies are low, after being converted into pyruvate or Krebs cycle intermediates.

2.2 The Respiratory Quotient (RQ) (12.1.5, 12.1.6)

The Respiratory Quotient (RQ) tells us what kind of fuel an organism is primarily respiring.

Definition: The ratio of the volume of carbon dioxide produced (\(CO_2\) out) to the volume of oxygen consumed (\(O_2\) in) during respiration.

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

We can calculate RQ from the balanced equation of respiration for different substrates:

• Carbohydrates (e.g., Glucose): RQ = 1.0 (Since the equation for glucose is C₆H₁₂O₆ + 6O₂ \(\rightarrow\) 6CO₂ + 6H₂O, the ratio is 6/6 = 1.0)
• Lipids: RQ is typically 0.7. Lipids require significantly more oxygen to break down because they are highly reduced. (More \(O_2\) consumed than \(CO_2\) produced).
• Proteins: RQ is typically 0.8 or 0.9.

Section 3: Aerobic Respiration (The Major ATP Producer)

3.1 Overview and Location (12.2.1)

Aerobic respiration requires oxygen and involves four main stages in eukaryotic cells:

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: Occurs on the Inner Mitochondrial Membrane (cristae).

Analogy: Think of aerobic respiration as a complex factory line where glucose is disassembled step-by-step, and its energy (in the form of hydrogen/electrons) is packaged into ATP.

3.2 Stage 1: Glycolysis (12.2.2)

Glycolysis means "sugar splitting" and happens in the cytoplasm. It does NOT require oxygen.

The process:

1. Phosphorylation: Glucose (6C) is phosphorylated (uses 2 ATP) to form Fructose 1,6-bisphosphate.
2. Splitting: Fructose 1,6-bisphosphate splits into two Triose Phosphate (3C) molecules.
3. Oxidation: Each Triose Phosphate is further oxidised to Pyruvate (3C). This involves dehydrogenation (removing hydrogen atoms).

Products per Glucose molecule:

• Net gain of 2 ATP (by substrate-linked phosphorylation).
• 2 reduced NAD (NADH).
• 2 Pyruvate molecules.

3.3 Stage 2: The Link Reaction (12.2.3, 12.2.4)

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

The process (per pyruvate):

1. Decarboxylation: A carbon atom is removed as \(CO_2\).
2. Dehydrogenation: Hydrogen is removed, reducing NAD to reduced NAD.
3. The remaining 2-carbon group (acetyl group) combines with Coenzyme A to form Acetyl coenzyme A (Acetyl CoA).

Products per Glucose molecule (2 pyruvates):

• 2 Acetyl CoA (enter Krebs cycle).
• 2 \(CO_2\) (released as waste).
• 2 reduced NAD.

3.4 Stage 3: The Krebs Cycle (12.2.5, 12.2.6, 12.2.7)

Also known as the Citric Acid Cycle, it takes place in the mitochondrial matrix.

The process (Cyclic pathway):

1. Acetyl CoA (2C) joins with the 4-carbon compound Oxaloacetate (OAA) to form the 6-carbon compound Citrate.
2. Citrate then goes through a series of small steps involving:
   • Decarboxylation: Releasing \(CO_2\) (2 carbons released per cycle).
   • Dehydrogenation: Releasing hydrogen atoms.
3. The hydrogen atoms released are immediately picked up by the coenzymes NAD and FAD, forming reduced NAD and reduced FAD.
4. Substrate-linked phosphorylation occurs once, producing 1 ATP (per cycle).
5. The OAA (4C) is regenerated to accept another Acetyl CoA, completing the cycle.

Products per Glucose molecule (2 cycles):

• 6 reduced NAD
• 2 reduced FAD
• 2 ATP (by substrate-linked phosphorylation)
• 4 \(CO_2\)

Note: The primary purpose of the Krebs cycle is not to make ATP, but to generate vast quantities of reduced NAD and FAD to fuel the next stage!

3.5 Stage 4: Oxidative Phosphorylation and Chemiosmosis (12.2.8, 12.2.10)

This is where the vast majority of ATP is produced, using the reduced coenzymes generated in the previous stages. It occurs on the inner mitochondrial membrane (cristae).

Structure-Function Link (12.2.9): The inner membrane is highly folded (cristae), significantly increasing the surface area available for the electron transport chain (ETC) and ATP synthase enzymes.

The Mechanism:

1. Hydrogen Transfer: Reduced NAD and reduced FAD travel to the inner membrane and release their hydrogen atoms (\(H\)). These split into protons (\(H^+\)) and energetic electrons (\(e^-\)).
2. Electron Transport Chain (ETC): The energetic electrons pass along a series of carrier molecules (proteins) embedded in the inner membrane. As electrons move from one carrier to the next, they release energy in small, manageable amounts.
3. Proton Pumping: The energy released by the electrons is used to actively pump the protons (\(H^+\)) from the matrix into the intermembrane space. This creates a high concentration gradient—a proton gradient.
4. Chemiosmosis: The protons flow back down their concentration gradient, through specific channels provided by the enzyme ATP synthase. This facilitated diffusion of protons provides the energy necessary to combine ADP and P_i, synthesizing ATP.
5. Final Acceptance: At the end of the ETC, oxygen acts as the final electron acceptor. Oxygen combines with the electrons and protons to form metabolic water (\(H_2O\)). If oxygen is absent, the ETC stops, and aerobic respiration halts.

Section 4: Anaerobic Respiration (Respiration without Oxygen)

When oxygen is unavailable, the electron transport chain stops because there is no final electron acceptor. This means reduced NAD and FAD cannot be re-oxidised back into NAD and FAD.

However, cells must continue to make *some* ATP to survive. They achieve this by carrying out fermentation, which relies only on glycolysis.

4.1 The Role of Anaerobic Respiration

The crucial step in fermentation is regenerating NAD from reduced NAD, allowing glycolysis (which requires NAD) to continue running and produce its minimal yield of 2 ATP (12.2.10).

4.2 Anaerobic Respiration in Mammals (Lactate Fermentation)

During intense exercise, muscle cells may run out of oxygen (become anaerobic).

The Process:

1. Glycolysis produces pyruvate.
2. Pyruvate accepts hydrogen from reduced NAD.
3. Pyruvate is converted into Lactate (lactic acid).
   Pyruvate + reduced NAD \(\rightarrow\) Lactate + NAD

The NAD produced is reused immediately in glycolysis. Lactate build-up causes muscle fatigue.

4.3 Anaerobic Respiration in Yeast (Ethanol Fermentation)

This process is used in brewing and baking.

The Process:

1. Glycolysis produces pyruvate.
2. Pyruvate is converted to Ethanal (releasing a molecule of \(CO_2\)).
3. Ethanal accepts hydrogen from reduced NAD.
4. Ethanal is converted into Ethanol.
   Ethanal + reduced NAD \(\rightarrow\) Ethanol + NAD

4.4 Energy Yield Comparison (12.2.11)

The energy yield from aerobic respiration (up to 32 ATP per glucose) is vastly greater than the energy yield from anaerobic respiration (2 ATP per glucose).

Why? In anaerobic conditions, the respiratory substrate (glucose) is only partially broken down (only glycolysis occurs), meaning most of the potential energy remains locked in the final products (lactate or ethanol). Aerobic respiration achieves complete oxidation (breakdown to \(CO_2\) and \(H_2O\)).

Section 5: Photosynthesis – Capturing Light Energy

5.1 Overview and Chloroplast Structure (13.1.1, 13.1.3)

Photosynthesis is the process by which light energy is captured and converted into chemical energy (sugars) in plant cells.

In eukaryotes (plants/algae), photosynthesis occurs in chloroplasts.

• Thylakoids: Flattened sacs arranged in stacks called Grana. These are the site of the Light-Dependent Stage. The membranes provide a large surface area and hold the pigments and ETC carriers.
• Stroma: The fluid surrounding the thylakoids. This is the site of the Light-Independent Stage (Calvin Cycle). The stroma contains enzymes (like Rubisco) needed for carbon fixation.

5.2 Light-Dependent Stage (LDR) (13.1.2)

The LDR converts light energy into chemical energy (ATP) and reducing power (reduced NADP).

Pigments and Light Absorption (13.1.4, 13.1.5)

Chloroplasts contain pigments that absorb light, including Chlorophyll a, Chlorophyll b, Carotene, and Xanthophyll.

• Absorption spectra show which wavelengths of light are absorbed by specific pigments.
• Action spectra show the overall rate of photosynthesis at different wavelengths. They closely match the absorption spectra of the photosynthetic pigments.

Photophosphorylation (13.1.7, 13.1.10)

This process uses light to generate ATP (similar to oxidative phosphorylation in mitochondria, but driven by light). It involves two key photosystems, PSII and PSI, which contain pigments.

Non-Cyclic Photophosphorylation (13.1.9)

This is the main LDR pathway and involves both PSII and PSI.

1. Photoactivation: Light energy hits PSII, exciting electrons within the chlorophyll to a higher energy level.
2. Electron Transport: These energetic electrons pass through an electron transport chain (ETC), releasing energy.
3. Chemiosmosis (ATP synthesis): The energy released is used to pump protons (\(H^+\)) into the thylakoid space, creating a proton gradient. Protons flow back out into the stroma through ATP synthase, generating ATP.
4. Photolysis of Water: PSII replaces the lost electrons by splitting water (catalyzed by the oxygen-evolving complex):
   H₂O \(\rightarrow\) 2\(H^+\) + 2\(e^-\) + \(\frac{1}{2}O_2\)
   Oxygen is released as a byproduct.
5. NADP Reduction: Electrons eventually reach PSI, get boosted again by light, and are used (along with H+ from water) to reduce NADP.
   NADP + 2\(H^+\) + 2\(e^-\) \(\rightarrow\) Reduced NADP

Products: ATP, Reduced NADP, and Oxygen.

Cyclic Photophosphorylation (13.1.8)

This simpler process involves only Photosystem I (PSI). Electrons are excited by light and pass through an ETC, generating ATP via chemiosmosis, but they eventually cycle back to PSI.

Products: ATP only. No reduced NADP or oxygen is produced.

Section 6: Photosynthesis – The Calvin Cycle

6.1 The Light-Independent Stage (13.1.11, 13.1.12)

This stage occurs in the stroma. It uses the ATP (energy) and reduced NADP (reducing power) generated during the LDR to "fix" carbon dioxide into complex organic molecules (sugars).

The three main stages of the Calvin Cycle:

1. Carbon Fixation:
   The 5-carbon compound Ribulose Bisphosphate (RuBP) combines with \(CO_2\). This reaction is catalyzed by the enzyme RuBP carboxylase (Rubisco). This unstable 6-carbon intermediate immediately splits to form two molecules of Glycerate 3-Phosphate (GP), a 3-carbon compound.
2. Reduction:
   GP is converted into Triose Phosphate (TP), which is also a 3-carbon compound. This reduction reaction requires energy from ATP and hydrogen from reduced NADP.
3. Regeneration:
   Most of the TP molecules (5 out of 6 produced) are used to regenerate the initial acceptor molecule, RuBP. This process requires more ATP.

What happens to Triose Phosphate (TP)? (13.1.12)

TP is the crucial final product of the cycle. It can be immediately used by the plant to synthesize:

• Carbohydrates (e.g., glucose, sucrose, starch, cellulose).
• Lipids (fatty acids and glycerol).
• Amino acids (requires the addition of nitrogen/mineral ions).

Section 7: Limiting Factors of Photosynthesis (13.2)

A process is limited by the factor that is nearest its minimum optimum value. The rate of photosynthesis can be limited by any stage, but usually, the LIS is slower than the LDR.

7.1 The Three Main Limiting Factors (13.2.1)

The three environmental factors that most commonly limit the rate of photosynthesis are:

1. Light Intensity
2. Carbon Dioxide Concentration
3. Temperature

7.2 Explaining the Effects (13.2.2)

• Light Intensity:

  At low light intensity, the rate of photosynthesis is directly proportional to intensity. Light is the limiting factor because it controls the rate of the Light-Dependent Reaction (needed for photoactivation and producing ATP/reduced NADP). Once intensity increases past a certain point, the LIS takes over as the limiting factor.

• Carbon Dioxide Concentration:

  \(CO_2\) is required for the Light-Independent Stage (specifically, the fixation step catalyzed by Rubisco). If \(CO_2\) concentration is low, the amount of GP and TP produced decreases, slowing the whole process.

• Temperature:

  Photosynthesis involves many enzyme-controlled reactions, especially in the Light-Independent Stage (e.g., Rubisco).
  - As temperature increases, the rate increases (kinetic energy), up to the optimum.
  - Beyond the optimum (around 40–50°C for many plants), enzymes start to denature, and the rate drops rapidly.

That wraps up the core concepts of Energy, Respiration, and Photosynthesis! Remember these processes are interconnected—Respiration provides the ATP for general cell function, while Photosynthesis provides the complex organic molecules (food) needed for respiration. Keep practicing those reaction locations and the sequence of steps!