CAPE Biology Unit 2: Detailed Study Notes on Photosynthesis, Respiration, and Ecology

Fundamental Concepts of Nutrition and Photosynthesis

• Heterotrophs: Organisms that cannot synthesize their own food and must consume other organisms. Examples include humans, animals, and fungi.
• Autotrophs: Organisms that synthesize their own organic molecules (food) from simple inorganic substances. Examples include green plants.
• Importance of Photosynthesis:     * Transfers light energy into chemical energy.     * Provides food for almost all living organisms.     * Releases Oxygen ($O_2$) into the atmosphere.
• Definition of Photosynthesis: The process by which green plants convert light energy into chemical energy stored in carbohydrates.
• Chemical Equation for Photosynthesis:     * $6CO_2 + 6H_2O \rightarrow C_6H_{12}O_6 + 6O_2$

Structure and Function of the Dicotyledonous Leaf

• Leaf Adaptations:     * Large surface area and thinness of the Lamina: Maximizes light absorption and gas diffusion.
• Tissue Structures and Specialized Functions:     * Cuticle: A waxy layer that reduces water loss.     * Upper Epidermis: Transparent layer that allows light to pass through to the underlying tissues.     * Palisade Mesophyll: The main site of photosynthesis; cells are long, cylindrical, and closely packed with many chloroplasts to maximize light capture. Its vertical arrangement allows light to pass through the thin cell walls and ensures chloroplasts are pushed to the edge for efficient gas exchange.     * Spongy Mesophyll: Characterized by large air spaces that allow for the rapid diffusion of gases ($CO_2$ and $O_2$) between cells.     * Guard Cells: Specialized cells that control the opening and closing of the stomata.     * Stomata: Pores that permit gas exchange between the leaf interior and the atmosphere.     * Xylem: Vascular tissue that carries water and dissolved minerals to the leaf.     * Phloem: Vascular tissue that transports sugars (sucrose) from the leaf to other parts of the plant.

Chloroplast Structure and Photosynthetic Pigments

• Chloroplast Components and Their Functions:     * Double Membrane: Controls the movement of substances into and out of the organelle.     * Thylakoids: Flattened sacs that serve as the site for light-dependent reactions.     * Grana: Stacks of thylakoids that contain photosynthetic pigments.     * Stroma: The aqueous fluid surrounding the grana; the site of the Calvin cycle (light-independent reactions). It contains ribosomes, circular DNA, and starch grains.     * Starch Grains: Serve as carbohydrate storage.     * Circular DNA and Ribosomes: Used for protein synthesis and genetic material storage within the chloroplast.
• Photosynthetic Pigments:     * Chlorophyll a: The primary pigment; it absorbs red and blue light and reflects green light, which is why it appears green.     * Accessory Pigments: Include Chlorophyll b, Carotene, and Xanthophyll.     * Functions of Accessory Pigments: Absorb additional wavelengths of light, transfer that energy to chlorophyll a, and protect chlorophyll from light-induced damage.

The Light-Dependent Stage of Photosynthesis

• Location: Occurs within the thylakoid membranes.
• Main Processes: Light absorption, photoactivation, electron transport, ATP formation, photolysis of water, and reduction of NADP.
• Photosystems:     * Photosystem I (PSI): Involved in both cyclic and non-cyclic photophosphorylation; produces ATP and is involved in the final reduction of NADP.     * Photosystem II (PSII): Involved in non-cyclic photophosphorylation; associated with the photolysis of water and the production of ATP.
• Photophosphorylation: The formation of ATP from ADP and inorganic phosphate ($P_i$) using light energy.     * $ADP + P_i \rightarrow ATP$
• Cyclic Photophosphorylation:     * Uses PSI only.     * Electrons leave chlorophyll in PSI, become excited by light, enter electron carriers, and eventually return to PSI.     * Energy released during electron movement produces ATP.     * No oxygen is produced; no reduced NADP is produced.
• Non-Cyclic Photophosphorylation (The Z-Scheme):     * Features: Uses both PSI and PSII; produces ATP, reduced NADP (NADPH), and oxygen.     * Step 1: Light Absorption by PSII: Light energy excites electrons in chlorophyll, causing them to leave the molecule.     * Step 2: Electron Transport Chain: Electrons move through carriers, releasing energy to pump hydrogen ions ($H^+$) into the thylakoid lumen and generate ATP.     * Step 3: Photolysis of Water: Light activates enzymes in PSII to split water: $2H_2O \rightarrow 4H^+ + 4e^- + O_2$. Electrons replace those lost from PSII. Oxygen is released as a waste product (all oxygen from photosynthesis comes from water).     * Step 4: Light Absorption by PSI: Electrons from the transport chain reach PSI and are re-energized by light.     * Step 5: Reduction of NADP: Re-energized electrons combine with hydrogen ions and NADP to form reduced NADP: $NADP^+ + 2e^- + H^+ \rightarrow \text{reduced NADP}$.
• Chemiosmosis and ATP Formation:     * $H^+$ ions accumulate in the thylakoid lumen, creating a concentration gradient and electrochemical potential energy.     * $H^+$ ions diffuse back into the stroma through the enzyme ATP synthase.     * The energy released by this movement drives the synthesis of ATP.

The Light-Independent Stage (Calvin Cycle)

• Location: Occurs in the stroma of the chloroplast.
• Purpose: Uses ATP and reduced NADP from the light-dependent stage to convert carbon dioxide into carbohydrates.
• Phase 1: Carbon Fixation:     * $CO_2$ combines with Ribulose Bisphosphate (RuBP), a 5-carbon compound.     * The reaction is catalyzed by the enzyme Rubisco.     * $CO_2 + RuBP \rightarrow \text{Unstable 6C intermediate} \rightarrow 2 \text{ molecules of GP (Glycerate-3-Phosphate)}$.     * GP is also known as phosphoglyceric acid (PGA).
• Phase 2: Reduction of GP:     * GP is converted into Triose Phosphate (TP).     * This requires energy from ATP and hydrogen from reduced NADP.     * Importance of TP: It is the first carbohydrate formed. It is used to synthesize glucose, fructose, sucrose, starch, cellulose, amino acids, and lipids.
• Phase 3: Regeneration of RuBP:     * Most TP molecules are recycled to regenerate RuBP so the cycle can continue.     * This regeneration requires ATP.

Limiting Factors in Photosynthesis

• Definition: A factor in shortest supply that restricts the rate of a process.
• Light Intensity: Initially, increasing intensity increases the rate; eventually, it levels off (light saturation) as another factor becomes limiting.
• Carbon Dioxide: Rate increases with $CO_2$ concentration until it levels off due to other limitations.
• Agricultural Applications:     * Artificial lighting: Increases light intensity.     * $CO_2$ enrichment: Increases carbon fixation rates.     * Temperature control: Optimizes enzyme (Rubisco) activity.     * Irrigation: Ensures water supply for photolysis and cell turgidity.     * Pros/Cons: Results in faster growth and year-round production, but is expensive and energy-intensive.

Cellular Respiration and ATP Synthesis

• Definition: The stepwise breakdown of glucose to release energy used to make ATP.
• ATP as Energy Currency: ATP transfers small, usable amounts of energy. Hydrolysis releases energy: $ATP + H_2O \rightarrow ADP + P_i + \text{energy (approx. } 30.5\,kJ\,mol^{-1})$.
• Stages of Aerobic Respiration:     * Glycolysis: Cytoplasm; Glucose split into pyruvate.     * Link Reaction: Mitochondrial matrix; Pyruvate converted to Acetyl CoA.     * Krebs Cycle: Mitochondrial matrix; Oxidation and decarboxylation reactions.     * Oxidative Phosphorylation: Inner mitochondrial membrane; Large-scale ATP production.

Glycolysis: Detailed Process

• Location: Cytoplasm. Does not require oxygen.
• Step 1: Phosphorylation: Glucose is activated by ATP to form Glucose-6-phosphate. ATP is invested here to make the molecule reactive and trap it in the cell.
• Step 2: Isomerisation: Glucose-6-phosphate becomes Fructose-6-phosphate.
• Step 3: Second Phosphorylation: Another ATP is used to create Fructose bisphosphate.
• Step 4: Lysis: The 6C sugar splits into two 3C Triose Phosphates (TP).
• Step 5: Oxidation: TP is oxidized as hydrogen is removed and accepted by NAD to form reduced NAD (NADH).
• Step 6: ATP Production: ATP is produced via substrate-level phosphorylation.
• Net Yield from One Glucose Molecule:     * 2 Pyruvate molecules.     * 2 Net ATP ($4 \text{ produced} - 2 \text{ used}$).     * 2 Reduced NAD.

Mitochondrion Structure and Function

• Outer Membrane: Controls entry/exit of materials.
• Inner Membrane: Contains the electron transport chain (ETC) and ATP synthase (ATPase).
• Cristae: Folds of the inner membrane that increase surface area for more electron carriers and ATPase enzymes, enhancing ATP production.
• Matrix: Contains enzymes for the Krebs cycle and Link reaction.
• Intermembrane Space: Site where $H^+$ ions accumulate to form a gradient.
• High-Energy Cells: Muscle, liver, and sperm cells contain many mitochondria with extensive cristae.

The Link Reaction and Krebs Cycle

• The Link Reaction:     * Occurs in the matrix. Pyruvate (3C) undergoes oxidative decarboxylation.     * $CO_2$ is removed (decarboxylation).     * Hydrogen is removed to reduce NAD (oxidation).     * The remaining 2C compound combines with Coenzyme A to form Acetyl CoA.
• The Krebs Cycle:     * Acetyl CoA (2C) + Oxaloacetate (4C) $\rightarrow$ Citrate (6C).     * Oxidation: Hydrogen is removed and accepted by NAD (forming 3 reduced NAD) and FAD (forming 1 reduced FAD).     * Decarboxylation: Two $CO_2$ molecules are released per turn.     * Substrate-Level Phosphorylation: 1 ATP is made directly per turn.     * Yield Per Glucose: Since there are 2 pyruvates, the cycle turns twice, yielding 2 ATP, 6 reduced NAD, 2 reduced FAD, and 4 $CO_2$.

Oxidative Phosphorylation

• Location: Inner mitochondrial membrane (cristae). Requires oxygen.
• Process:     1. Reduced NAD/FAD donate electrons to the ETC.     2. Electrons move through carriers, releasing energy.     3. This energy pumps $H^+$ ions into the intermembrane space, creating an electrochemical gradient.     4. Chemiosmosis: $H^+$ ions diffuse back into the matrix through ATPase, driving the production of ATP ($ADP + P_i \rightarrow ATP$).     5. Oxygen's Role: Oxygen is the final electron acceptor. It combines with protons and electrons to form water: $O_2 + 4H^+ + 4e^- \rightarrow 2H_2O$.
• Total ATP Yield: Approximately $32\,ATP$ per glucose molecule.

Anaerobic Respiration

• Lactic Fermentation (Animals):     * Pyruvate is converted to Lactate.     * Reduced NAD is oxidized back to NAD so glycolysis can continue.     * Yield: Only $2\,ATP$ per glucose.     * Oxygen Debt: After exercise, lactate is sent to the liver, converted back to pyruvate; this requires extra oxygen (heavy breathing).
• Alcoholic Fermentation (Yeast):     * Pyruvate is converted to Ethanol and Carbon Dioxide.     * Used in brewing, baking, and wine production.

Ecosystem Dynamics: Habitat and Niche

• Habitat: The physical location where an organism lives (e.g., a coral reef crest for elkhorn coral Acropora palmata at depths less than $6\,m$).
• Ecosystem: The interaction between biotic (living) and abiotic (non-living) factors. (e.g., coral reef including fish, algae, seawater, and sunlight).
• Ecological Niche: The specific role of an organism, including its diet, habitat use, and impact on other species (e.g., queen parrotfish grazing on algae to help reef recovery).

Energy Flow and Trophic Levels

• Direction: One-way flow (Sun $\rightarrow$ Producer $\rightarrow$ Consumer $\rightarrow$ Decomposer $\rightarrow$ Heat loss).
• Food Chain vs. Food Web:     * Food chain: Simple linear energy transfer (e.g., Grass $\rightarrow$ cricket $\rightarrow$ white-lipped frog $\rightarrow$ Puerto Rican boa $\rightarrow$ broad-winged hawk).     * Food web: Interconnected chains. Better because they show real feeding relationships, multiple trophic levels for one species, and alternative food sources.
• Energy Transfer Efficiency: Usually only $10\%$ or less is passed to the next level.     * Losses: Respiration (heat), movement, uneaten parts (bones/wood), undigested food (faeces).     * Photosynthesis Inefficiency: Plants convert less than $3\%$ of sunlight because light misses leaves, is reflected, or is of the wrong wavelength.     * Endotherms: Mammals and birds lose more energy maintaining body temperature.

Biological Pyramids

• Pyramid of Numbers: Counts organisms. Can be inverted (e.g., one large tree supporting many insects).
• Pyramid of Biomass: Measured in $g\,m^{-2}$. Accounts for organism size. Can be inverted in aquatic systems where phytoplankton reproduce very quickly despite low standing biomass.
• Pyramid of Energy: Measured in $kJ\,m^{-2}\,year^{-1}$. Always upright and most accurate, but hard to measure.

The Nitrogen Cycle

• Nitrogen Fixation: Conversion of $N_2$ gas into ammonia ($NH_3$) or ammonium ($NH_4^+$).     * Rhizobium: Bacteria in legume root nodules. They use the enzyme nitrogenase. Legumes provide sugars and leghaemoglobin (to maintain anaerobic conditions).     * Lightning: Forms nitrogen oxides that enter soil via rain.     * Haber Process: Industrial fertilizer production.
• Assimilation: Plants absorb nitrate ($NO_3^-$) to make amino acids/proteins.
• Ammonification: Decomposers (bacteria/fungi) break down dead matter into ammonia.
• Nitrification: Done by nitrifying bacteria in well-aerated soil.     * Nitrosomonas: $NH_4^+ \rightarrow NO_2^-$ (nitrite).     * Nitrobacter: $NO_2^- \rightarrow NO_3^-$ (nitrate).
• Denitrification: Conversion of nitrate back to $N_2$ gas by denitrifying bacteria in waterlogged/anaerobic soils.

Biodiversity and Conservation

• Types of Biodiversity:     * Species Diversity: Number of different species (Species richness). High in tropical rainforests.     * Genetic Diversity: Variation of genes within species. Example: Zostera marina seagrass with more genotypes survive grazing better.     * Ecosystem Diversity: Variety of habitats in a region (e.g., mangroves, coral reefs, savannas).
• Importance of Maintaining Biodiversity:     * Intrinsic Value: Species have inherent value and right to exist.     * Direct Economic Value: Food, timber, and medicine. Example: Vincristine from the rosy periwinkle (Madagascar) is used to treat leukaemia.     * Indirect Value: Ecosystem services like water purification and oxygen production.     * Tourism: Ecotourism revenue.
• Ecosystem Stability: High biodiversity leads to complex food webs and resistance/recovery after disturbance (e.g., Minnesota grassland study showed high diversity plots resisted drought better).
• Conservation Methods:     * In Situ: Protection in the natural habitat (e.g., Pacuare Nature Reserve for leatherback turtles). Includes national parks and controlling invasive species.     * Ex Situ: Protection outside the natural habitat. Includes zoos (captive breeding of Scimitar-horned oryx), botanic gardens, seed banks (e.g., Millennium Seed Bank at $-20^{\circ}C$), and sperm/embryo banks ($-196^{\circ}C$ in liquid nitrogen).