OCR (A) Biology A-Level Topic 5.2 - Energy for Biological Processes Study Notes

Photosynthesis: Overview and Chloroplast Structure

• Photosynthesis is a chemical reaction in which light energy is utilized to break the strong bonds in water molecules through photolysis, combining hydrogen with carbon dioxide to produce glucose fuel.

• Chemical Waste Product:

  • Oxygen is generated as a waste product of photosynthesis and released directly into the atmosphere.

• Controlling Factors:

  • The overall rate of photosynthesis is determined by three main environmental factors: carbon dioxide concentration, light intensity, and temperature.

• Chloroplast Adaptations:

  • The chloroplast is the specialized organelle where photosynthesis takes place. It possesses specific adaptations:

  • Grana: Stacks of thylakoid membranes containing photosynthetic pigments (such as chlorophyll) organized into functional photosystems.

  • Stroma: The fluid environment surrounding the grana, containing all necessary enzymes required for the light-independent stage of photosynthesis.

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7 → / Stages of Photosynthesis

• Light-Dependent Reaction:

  • Occurs within the thylakoid membranes of chloroplasts.

  • Photons of light are trapped by chlorophyll molecules, exciting electrons to a higher energy level.

  • Excited electrons pass down an electron transport chain via a series of electron carriers.

  • This movement of electrons generates ATP from ADP and inorganic phosphate ($P_i$) through photophosphorylation.

  • Reduced NADP ($\text{NADPH}$) is simultaneously generated as electrons and protons ($H^+$) are transferred to $\text{NADP}^+$.

  • Both ATP and reduced NADP are subsequently transferred to and used in the light-independent stage.

• Light-Independent Reaction (Calvin Cycle):

  • Takes place in the stroma of the chloroplast and uses ATP (as an energy source) and reduced NADP (as reducing power) to form glucose.

  • Step 1 (Carbon Fixation): Ribulose bisphosphate ($\text{RuBP}$) combines with carbon dioxide ($CO_2$) in a reaction catalyzed by the enzyme RUBISCO.

  • Step 2: The molecule converts into two glycerate 3-phosphate ($\text{GP}$) molecules.

  • Step 3: Reduced NADP and ATP are consumed to convert glycerate 3-phosphate ($\text{GP}$) into triose phosphate ($\text{TP}$).

  • Step 4: A portion of the triose phosphate ($\text{TP}$) molecules are used to produce glucose, which is then converted into essential organic compounds including polysaccharides, lipids, amino acids, and nucleic acids.

  • Step 5: The remaining triose phosphate ($\text{TP}$) molecules are used to reform ribulose bisphosphate ($\text{RuBP}$) with the help of ATP.

Limiting Factors of Photosynthesis

• Definition:

  • A limiting factor is an environmental factor present at its lowest or least favorable supply, thereby restricting the maximum rate of a physiological reaction.

• Light Intensity:

  • When light intensity is in short supply, the light-dependent reaction slows down, leading to lower amounts of ATP and reduced NADP ($\text{NADPH}$) being created.

  • Consequently, the conversion of glycerate 3-phosphate ($\text{GP}$) to triose phosphate ($\text{TP}$) in the Calvin cycle is affected.

  • Concentration changes: Level of $\text{GP}$ will rise, while levels of $\text{TP}$ and $\text{RuBP}$ will fall.

• Carbon Dioxide Concentration:

  • When carbon dioxide ($CO_2$) is in short supply, the light-independent reaction slows down.

• Temperature:

  • Low temperatures reduce the kinetic energy of Rubisco and other participating molecules, slowing enzyme-controlled reaction rates.

Cellular Respiration: Glycolysis and Link Reaction

• Overview of Respiration:

  • Aerobic Respiration: Splitting of the respiratory substrate to release carbon dioxide ($CO_2$) as a waste product, accompanied by the reuniting of hydrogen with atmospheric oxygen ($O_2$) with the release of a large amount of energy.

  • Anaerobic Respiration: Occurs in the total absence of oxygen.

  • Respiration is a multi-step process where each step is controlled and catalyzed by a specific intracellular enzyme.

• Glycolysis:

  • Location: Cytoplasm of the cell. First process of both aerobic and anaerobic respiration.

  • Process: A molecule of glucose is phosphorylated to produce $2$ molecules of pyruvate.

  • Net Output per Glucose: $2$ molecules of pyruvate, $2$ molecules of reduced NAD ($\text{NADH}$), and a net production of $2$ molecules of ATP.

• Link Reaction:

  • Location: Mitochondrial matrix.

  • Process: Each pyruvate molecule is converted to an acetyl group.

  • Coenzyme Action: The acetyl group binds to Coenzyme A ($\text{CoA}$) to form Acetyl-CoA. In this process, NAD is reduced to $\text{NADH}$ and $CO_2$ is produced as pyruvate is decarboxylated.

The Krebs Cycle

• Function and Yield:

  • Coenzyme A delivers acetyl to the Krebs cycle, where glucose is oxidized, and carbon dioxide ($CO_2$), ATP, reduced NAD ($\text{NADH}$), and reduced FAD ($\text{FADH}$) are produced.

  • Turns per Glucose: Each glucose molecule causes the cycle to turn twice.

  • Yield per Glucose Molecule in Krebs Cycle:

  • $4$ molecules of $CO_2$

  • $4$ molecules of reduced NAD ($\text{NADH}$)

  • $2$ molecules of reduced FAD ($\text{FADH}$)

  • $2$ molecules of ATP (produced via substrate-level phosphorylation)

Oxidative Phosphorylation

• Definition and Location:

  • Oxidative phosphorylation is the process in which ATP is synthesized in the electron transport chain in mitochondria. This process generates the majority of ATP in aerobic respiration and occurs on the inner mitochondrial membrane.

• Process Mechanism:

  • Hydrogen Carrier Delivery: Reduced coenzymes ($\text{NADH}$ and $\text{FADH}$) carry hydrogen ions ($H^+$) and electrons to the electron transport chain on the inner mitochondrial membrane.

  • Redox Reactions: Electrons are carried from one electron carrier to another in a series of redox reactions; the electron carrier which passes the electron on is oxidized, whereas the electron carrier which receives it is reduced.

  • Proton Pumping: Energy provided by the electrons to the electron carriers is used to move hydrogen ions ($H^+$) across the inner membrane into the intermembrane space, resulting in a high concentration of hydrogen ions in the intermembrane space.

  • Membrane Impermeability: The inner mitochondrial membrane is impermeable to $H^+$.

  • Chemiosmosis: Hydrogen ions ($H^+$) diffuse into the mitochondrial matrix down their electrochemical gradient through the ATPase enzyme. ATP is produced on stalked particles using ATP synthase.

  • Formation of Water: Hydrogen atoms are produced from hydrogen ions and electrons, which then combine with oxygen to produce water ($H_2O$).

  • Final Electron Acceptor: Oxygen ($O_2$) acts as the final electron acceptor.

• ATP Yield Considerations:

  • Theoretical Maximum Yield: $38$ ATP molecules per glucose molecule.

  • Actual Realized Yield: Rarely achieved in real life due to:

  • The inner mitochondrial membrane being "leaky" to $H^+$, meaning not all $H^+$ move through the ATPase.

  • The pyruvate made during glycolysis in the cytoplasm needing active transport to move into the matrix, which uses ATP.

Respiratory Substrates and Respiratory Quotient (RQ)

• Substrate Energy Content:

  • Respiratory substrates include carbohydrates, lipids, and proteins, which release varying amounts of energy depending on the number of hydrogens in the structure that are oxidized to water.

  • For instance, the number of hydrogens is greater in fatty acids than in carbohydrates.

• Respiratory Quotient (RQ) Formula:   $\text{RQ} = \frac{\text{carbon dioxide produced}}{\text{oxygen consumed}}$

• Standard RQ Values:

  • Carbohydrates: $1.0$

  • Proteins: $0.9$

  • Lipids: $0.8$

• Significance: Measuring RQ determines which respiratory substrate is being used and indicates whether an organism is undergoing anaerobic respiration.

Anaerobic Respiration Pathways

• Overview:

  • Occurs when the concentration of oxygen is low.

  • ATP production cannot occur via oxidative phosphorylation due to the lack of oxygen acting as the final electron acceptor.

  • Anaerobic respiration allows glycolysis to continue, maintaining a net production of $2$ ATP molecules per glucose molecule.

• Lactate Fermentation (Mammals):

  • Pyruvate is converted to lactate.

  • Pyruvate acts as the hydrogen acceptor to enable $\text{NADH}$ to be reoxidized to $\text{NAD}^+$, which can then be used to continue glycolysis.

  • Lactate is converted back to pyruvate in liver cells when oxygen levels rise again.

• Alcoholic Fermentation (Yeast and Plants):

  • Step 1: Pyruvate is decarboxylated to ethanal, producing $CO_2$. Because $CO_2$ is produced, this reaction is irreversible.

  • Step 2: Ethanal is reduced to ethanol, reoxidizing $\text{NADH}$ to $\text{NAD}^+$ in the process. Ethanal acts as the hydrogen acceptor.