Unit 3 VCE Biology: Photosynthesis and Cellular Respiration exhaustive Notes

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Chapter 5: Photosynthesis Key Knowledge

Overview of Biochemical Pathways

This chapter explores the general structure of the biochemical pathways in photosynthesis and cellular respiration, tracking the progression from initial reactants to final products.

Photosynthesis in $C_3$ Plants

• Light-dependent stage: Focuses on inputs, outputs, and locations within the chloroplast.

• Light-independent stage: Focuses on inputs, outputs, and locations (specific biochemical pathway mechanisms are not required for assessment).

General Role of Enzymes and Coenzymes

• Enzymes and coenzymes are explored as facilitators for the various steps within photosynthesis and cellular respiration.

• Rubisco: A pivotal enzyme in photosynthesis. Adaptations in $C_3$, $C_4$, and CAM plants are examined to understand how plants maximize photosynthetic efficiency.

Factors Affecting Rate of Photosynthesis

• Light availability

• Water availability

• Temperature (including enzyme denaturation)

• Carbon dioxide concentration ($CO_2$)

Enzyme Function and Inhibitors

• Factors impacting enzyme function: temperature changes, $pH$ levels, concentration variations.

• Inhibitors: Competitive and non-competitive enzyme inhibitors in the context of photosynthesis and respiration.

Agricultural Applications of CRISPR-Cas9

• Uses of CRISPR-Cas9 technologies to improve photosynthetic efficiencies and increase crop yields.

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5A: The Process of $C_3$ Photosynthesis

Defining Photosynthesis

• Photoautotroph: An organism capable of undertaking photosynthesis.

• Photosynthesis: The biological process where photoautotrophs capture light energy from the sun and convert it into chemical energy (glucose).

Prerequisites and Future Applications

• Autotrophs: Plants convert light energy into chemical energy.

• Chloroplasts: Highly specialized organelles that enable photosynthesis.

• Enzymes/Coenzymes: Crucial for reaction catalysis.

• Adaptations: $C_4$ and CAM plants have evolved to maximize photosynthesis.

• Chapter 6 Connection: Photosynthesis and cellular respiration are Capable of occurring in the same plant, sharing many similarities.

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Theory Details: Overview of Photosynthesis

The Biological Process

Plants, algae, and photosynthetic cyanobacteria are photoautotrophs. Unlike animals, they do not consume food but create their own energy via photosynthesis to survive. Photosynthesis harnesses light energy to produce glucose, which is the plant's energy source.

Inputs and Outputs

Photosynthesis utilizes two primary inputs: carbon dioxide ($CO_2$) and water ($H_2O$). Sunlight is required to energize the reaction.

The Chemical Equations

• Full Equation:     $6\,CO_2 + 12\,H_2O \xrightarrow{\text{sunlight}} C_6H_{12}O_6 + 6\,O_2 + 6\,H_2O$

• Simplified Equation:     $6\,CO_2 + 6\,H_2O \xrightarrow{\text{sunlight}} C_6H_{12}O_6 + 6\,O_2$     (Water is subtracted from both sides as it is both an input and an output).

Fate of Glucose

Glucose ($C_6H_{12}O_6$) is used for:

• Immediate energy via cellular respiration.

• Storage as starch.

• Growth and structural maintenance as complex molecules like cellulose.

Plant Structures

• Leaves: The primary site of photosynthesis, featuring large surface areas to maximize light capture.

• Mesophyll Cells: Specialized plant cells found in leaves containing high populations of chloroplasts.

• Chloroplast: A membrane-bound organelle (found in plants and photoautotrophs) that acts as the site for both stages of photosynthesis.

• Chlorophyll: A pigment in the thylakoids responsible for absorbing and being energized by light energy.

• Stomata (sing. Stoma): Tiny pores on surface leaves that regulate gas exchange ($CO_2$ in, $O_2$ and water vapour out). They close to prevent water loss in dry conditions.

• Xylem: Vascular tissue that transports water and minerals from the roots to the leaves.

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The Light-Dependent Stage (3.2.4.1)

Overview

This stage is dependent on light to split water into oxygen and hydrogen. It occurs on the thylakoid membranes (specifically the grana) of chloroplasts.

Definitions

• Thylakoid: A flattened sac-like structure inside the chloroplast with a chlorophyll-containing membrane enclosing a lumen.

• Granum (pl. Grana): Stacks of thylakoids.

• NADPH: A coenzyme acting as a proton ($H^+$) and electron carrier.

• ATP: Adenosine triphosphate, a high-energy molecule providing energy for cellular processes.

• Photolysis: The process where molecules are broken down by light action.

Inputs and Outputs

• Inputs:     * $12\,H_2O$     * $12\,NADP^+$     * $18\,ADP + P_i$

• Outputs:     * $6\,O_2$     * $12\,NADPH$     * $18\,ATP$

The Steps of the Light-Dependent Stage

1. Light Absorption: Light energy excites electrons in chlorophyll. These electrons move along proteins in the thylakoid membrane.

2. H+ Pumping: The energy from the electrons powers the pumping of $H^+$ into the thylakoid lumen.

3. Photolysis: To replace electrons leaving chlorophyll, water is split into $O_2$ and two $H^+$ ions.

4. Oxygen Release: Oxygen is released either for environnemental diffusion through stomata or for use in aerobic cellular respiration.

5. Coenzyme Production: $H^+$ ions are used to generate $NADPH$ ($NADP^+ + H^+ \rightarrow NADPH$). The movement of $H^+$ down its concentration gradient (via ATP synthase) generates $ATP$ ($ADP + P_i \rightarrow ATP$).

6. Transition: $ATP$ and $NADPH$ move to the light-independent stage.

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Summary of Energy Conversion in the Thylakoid

The thylakoid effectively turns $12\,H_2O$, $12\,NADP^+$, and $18\,ADP + P_i$ into $6\,O_2$, $12\,NADPH$, and $18\,ATP$.

Summary Points:

• Sunlight excites electrons in chlorophyll.

• Water from root hairs is split during photolysis to donate electrons to chlorophyll.

• Excited electrons and $H^+$ ions lead to the production of high-energy coenzymes ($NADPH$ and $ATP$).

• Oxygen is released as a byproduct.

Exam-Specific Guidance (VCAA):

• Light is not an input molecule; it is a requirement.

• $NADP$ is a valid shorthand for $NADP^+$, but "NAD" is not acceptable for photosynthesis.

• $ADP + P_i$ are required inputs (though listing just $ADP$ is sometimes acceptable, both are needed).

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Enzymes and Coenzymes in Photosynthesis

Enzyme Catalysis

Enzymes ensure reactions are controlled and efficient. For example, ATP synthase catalyses the reaction $ADP + P_i \rightarrow ATP$ using energy from the $H^+$ gradient. Another key enzyme, Rubisco, facilitates the light-independent stage.

Coenzyme Cycling

$NADPH$ and $ATP$ cycle through both stages. They are produced in the light-dependent stage and donate energy/protons in the light-independent stage. They then return to the light-dependent stage as "unloaded" $NADP^+$ and $ADP + P_i$.

The Light-Independent Stage (3.2.4.2)

Overview

Also known as the Calvin cycle, the dark stage, or light-independent reactions. This stage produces glucose from $CO_2$, $NADPH$, and $ATP$ in the stroma (the fluid interior of the chloroplast).

Inputs and Outputs

• Inputs:     * $6\,CO_2$     * $12\,NADPH$     * $18\,ATP$

• Outputs:     * $C_6H_{12}O_6$     * $6\,H_2O$     * $12\,NADP^+$     * $18\,ADP + P_i$

Functional Roles of Coenzymes

• NADPH: Transfers hydrogen ions.

• ATP: Transfers energy.

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The Steps of the Light-Independent Stage

1. Carbon Fixation: $CO_2$ enters the cycle. The carbon combines with a five-carbon molecule (RuBP) and then splits into 2x three-carbon molecules (3-PGA).

2. Energy Injection: $NADPH$ donates $H^+$ ions and electrons, and $ATP$ breaks into $ADP + P_i$ to release energy, facilitating changes to the carbon molecules.

3. Glucose Contribution: Carbon molecules rearrange. One three-carbon molecule (G3P) leaves the cycle for glucose formation. Six $CO_2$ must enter to produce one six-carbon glucose.

4. Water Production: Leftover oxygen atoms from $CO_2$ combine with $H^+$ from $NADPH$ to create water ($H_2O$).

Summary Points:

• $CO_2$ is collected via stomata.

• Carbon reactions are powered by $ATP$ and $NADPH$.

• The final outcome is the conversion of sunlight energy into chemical energy stored in the bonds of glucose.

• Glucose is transported for cellular respiration or conversion into carbohydrates like starch/cellulose.

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Theory Summary Tables

Comparing Stages

Mars Constraints Revisited

• Light: Mars is $80\text{ million } km$ further from the sun; light energy is low. Dust storms further obscure sunlight.

• Result: Plants on the surface cannot perform the light-dependent stage and would die.

• Solution: Artificial greenhouses with controlled light and climate.

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Questions & Discussion

Chemoautotrophy and Deep Ocean Ecosystems (Case Study)

• Chemoautotroph: Organisms that turn inorganic chemical compounds into usable energy to make food (chemosynthesis) in the absence of light.

• Context: In the deep ocean, bacteria use nutrient-rich hot springs. Land plants cannot survive here because light availability is zero, making the light-dependent stage impossible.

Sea Slug Photosynthesis (Case Study: Elysia chlorotica)

• Mechanism: This sea slug eats algae, acquires their chloroplasts, and stores them in its cells.

• Requirement: It can survive on "solar power" via photosynthesis if it has been fed algae to acquire the necessary machinery. It even acquired essential genes from the algae via horizontal gene transfer.

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5B: Rubisco in $C_3$, $C_4$, and CAM Photosynthesis

Overview of Rubisco

Rubisco (ribulose bisphosphate carboxylase-oxygenase) is a pivotal enzyme in the light-independent stage. It can facilitate photosynthesis (by binding $CO_2$) or a wasteful process called photorespiration (by binding $O_2$).

Prerequisite Review

• Light-dependent: splitting water into hydrogen and oxygen (Grana).

• Light-independent: converting $CO_2$ into organic molecules using $ATP/NADPH$ (Stroma).

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The Role of Rubisco

Rubisco controls the initial reaction of the Calvin cycle.

• Mechanism: Rubisco uses $3 \times CO_2$ and $3 \times \text{five-carbon RuBP}$ to produce $6 \times \text{three-carbon 3-PGA}$.

• Conversion: $ATP$ and $NADPH$ convert 3-PGA into $6 \times \text{three-carbon G3P}$.

• Exit/Recycle: One G3P leaves to make glucose ($6\,CO_2$ needed for one glucose). The remaining five G3P are recycled to regenerate RuBP.

• Cycle Turn: The cycle must turn twice to produce one glucose molecule.

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Stages of the Calvin Cycle

1. Carbon Fixation: Inorganic $CO_2$ is fixed into an organic compound (3-PGA) by Rubisco.

2. Reduction: $NADPH$ donates electrons (reduces) carbon molecules to produce G3P.

3. Regeneration: RuBP is reproduced to restart the cycle.

The Problem with Rubisco: Photorespiration

Rubisco has a major flaw: it can use $O_2$ as a substrate instead of $CO_2$.

• Photorespiration: A wasteful process initiated when Rubisco binds to $O_2$.

• Impact: Photosynthesis is disrupted. Energy is wasted, and no glucose is produced, negatively impacting growth and survival.

• Note: Photorespiration is not cellular respiration.

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Factors Influencing Rubisco Substrate Choice

1. Substrate Concentration: Plants maximize $CO_2$ exposure via stomata. If stomata close (to save water), $O_2$ from the light-dependent stage builds up, increasing photorespiration.

2. Temperature: At high temperatures, Rubisco's affinity for $O_2$ increases. The enzyme's 3D shape "loosens" at high heat, favoring oxygen binding. Extreme heat leads to denaturation.

Summary of Hot/Dry Impacts

Hot/dry conditions $\rightarrow$ water loss $\rightarrow$ stomata close $\rightarrow$ $O_2$ trapped $\rightarrow$ Rubisco binds $O_2$ $\rightarrow$ More photorespiration, less photosynthesis.

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$C_3$, $C_4$, and CAM Adaptation Strategies

$C_3$ Plants

• Status: "Normal" plants (approx. 85% of Earth's plants).

• Mechanism: No adaptations to fight photorespiration. The entire Calvin cycle occurs in a single mesophyll cell.

• Examples: Trees, cereals (wheat, rice), nuts, fruits.

$C_4$ Plants

• Adaptation: Spatial separation. Initial carbon fixation and the Calvin cycle occur in different cells.

• Site 1 (Mesophyll Cell): Initial fixation produces a four-carbon molecule.

• Site 2 (Bundle-Sheath Cell): Location of the remainder of the Calvin cycle.

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Mechanism of $C_4$ Photosynthesis

1. PEP Carboxylase: $CO_2$ enters mesophyll cells and is fixed by PEP carboxylase into oxaloacetate (4-C). This enzyme has no affinity for $O_2$.

2. Malate Transport: Oxaloacetate is converted to malate and transported into bundle-sheath cells.

3. $CO_2$ Release: In bundle-sheath cells, malate breaks down to release $CO_2$, maintaining a high $CO_2$ concentration for Rubisco.

4. Recycling: Pyruvate returns to the mesophyll and is converted back to PEP using $ATP$.

• Cost: Uses more $ATP$ than $C_3$.

• Advantage: Outperforms $C_3$ in hot environments where photorespiration is high.

• Examples: Corn, sugarcane, switchgrass.

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CAM Plants

• Crassulacean Acid Metabolism: Temporal separation of steps.

• Night Time: Stomata open to collect $CO_2$. Fixed into oxaloacetate by PEP carboxylase, then converted to malate and stored in vacuoles.

• Day Time: Stomata close to prevent water loss. Malate is transported out of vacuoles and broken down to release $CO_2$. This $CO_2$ enters the Calvin cycle while Rubisco is protected from high $O_2$.

• Cost: High $ATP$ requirement.

• Advantage: Extreme resistance to water loss. Best for very hot, dry areas.

• Examples: Cacti, pineapples, vanilla, orchids.

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Comparison Table

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5C: Factors Affecting the Rate of Photosynthesis

Light (3.2.6.1)

The Relationship

Light intensity directly determines the reaction rate by exciting electrons in chlorophyll.

• Graph: Photosynthesis rate increases with light intensity until it reaches a plateau.

• Plateau Causes:     1. Saturation Point: Enzymes within chloroplasts are operating at full capacity.     2. Limiting Factor: Another input (like $CO_2$ or temperature) is in short supply, acting as the "weakest link."

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Light Wavelength (Colour)

• Optimal Colours: Violet and Red (highest photosynthesis rate).

• Lowest Rate: Green (most green light is reflected).

Temperature and pH (3.2.6.2)

Temperature

• Graph: Increasing rate up to the optimal temperature (more collisions). Above the optimum, a steep drop-off occurs due to enzyme denaturation.

• Adaptation: $C_4$ and CAM plants generally have higher optimal temperatures than $C_3$ plants.

pH

• Optimal pH: Enzymes function best at a specific $pH$. Above or below, they denature.

• Thylakoid Note: Enzymes in the thylakoid lumen must function at $pH\,4$ due to concentrated protons.

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Carbon Dioxide (3.2.6.3)

Concentration Effects

• Graph: Rate increases as $CO_2$ concentration increases until it plateaus (saturation of enzyme systems).

• Photorespiration Link: Low $CO_2$ levels encourage Rubisco to bind $O_2$, debilitating $C_3$ plants. $C_4$ and CAM plants are less affected by low environmental $CO_2$.

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Water (3.2.6.4)

Water Stress

Water is not usually a limiting factor in chemical volume but influences the state of stomata.

• Mechanism: Water loss $\rightarrow$ stomata close $\rightarrow$ $CO_2$ entry stops $\rightarrow$ $O_2$ cannot exit $\rightarrow$ photorespiration increases $\rightarrow$ photosynthesis rate decreases.

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Enzyme Inhibition (3.2.3.6)

Definitions

• Competitive Inhibitor: Blocks the active site.

• Non-competitive Inhibitor: Binds to an allosteric site, changing the active site shape.

• Reversible vs Irreversible: Based on bond strength.

Impact

Inhibitors lower the rate. Competitive reversible inhibition can be overcome by increasing substrate concentration. Irreversible/non-competitive inhibitors reduce the maximum possible reaction rate regardless of substrate levels.

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5D: Agricultural Applications of CRISPR-Cas9

CRISPR-Cas9 Technology (3.2.10.1)

• CRISPR: Sequences of DNA acting as an adaptive immune system in prokaryotes.

• Cas9: An endonuclease that cuts DNA at specific sites designated by guide RNA.

• Genetic Modification: Manipulation of an organism's DNA, creating Genetically Modified Organisms (GMOs).

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Improving Crop Yields

By 2050, agricultural productivity must double to meet global demand. Arable land is exhausted. CRISPR allows for precise editing to:

• Bypass Photorespiration: Mimicking $C_4$ and CAM mechanisms in $C_3$ crops.

• Modify Rubisco: Improving its efficiency and $CO_2$ affinity.

• Chloroplast Efficiency: Targeting organelles to capture light better.

• Stomatal Adjustment: Editing stomata to reduce water stress impact.

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Potential Targets and Real-World Experiments

• Physical Tolerance: Drought, frost, and heat stress tolerance.

• Chemical Resistance: Resistance to herbicides and pesticides.

• Bioactive Compounds: Longer shelf life (e.g., browning-resistant mushrooms), improved nutritional value, and gluten-free wheat.

• Research Example: Rice yield was increased by $25\text{--}30\%$ by manipulating genes related to the hormone abscisic acid.

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6A: Aerobic Cellular Respiration

Overview of Cellular Respiration (3.2.1.1)

Cellular respiration is the process of creating usable energy ($ATP$) from glucose. It occurs via two pathways:

1. Aerobic Cellular Respiration: Requires oxygen. Produces $30$ or $32\,ATP$ per glucose.

2. Anaerobic Fermentation: Occurs without oxygen. Produces only $2\,ATP$ and harmful byproducts.

The $1000 Bill Metaphor

• Glucose: A $1000 bill (high energy, but not useful for day-to-day transactions).

• ATP: A $10 bill (more useful for the cell's daily "purchases").

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The Aerobic Equation

$C_6H_{12}O_6 + 6\,O_2 \rightarrow 6\,CO_2 + 6\,H_2O + 30\text{ or }32\,ATP$

Mitochondrial Structure

• Mitochondrial Matrix: Interior space inside the inner membrane. Site of the Krebs Cycle.

• Cristae: Folds of the inner membrane. Site of the Electron Transport Chain.

• Cytosol: Site of Glycolysis.

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Glycolysis (3.2.7.1)

• Location: Cytosol.

• Process: Breakdown of 6-carbon glucose into 2x three-carbon pyruvate.

• Inputs: $1\text{ Glucose}$, $2\,ADP + 2\,P_i$, $2\,NADP^+ + 2\,H^+$.

• Outputs: $2\text{ Pyruvate}$, $2\,ATP$, $2\,NADH$.

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The Krebs Cycle (3.2.7.2)

• Location: Mitochondrial Matrix.

• Link Reaction: Pyruvate is converted into acetyl-CoA, releasing $CO_2$ and producing $NADH$.

• Inputs (for 2 acetyl-CoA): $2\text{ acetyl-CoA}$, $2\,ADP + 2\,P_i$, $6\,NAD^+ + 6\,H^+$, $2\,FAD + 4\,H^+$.

• Outputs: $4\,CO_2$, $2\,ATP$, $6\,NADH$, $2\,FADH_2$.

• Purpose: Extracting protons and high-energy electrons for the next stage.

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The Electron Transport Chain (3.2.7.3)

• Location: Cristae of mitochondria.

• Inputs: $26\text{ or }28\,ADP+P_i$, $10\,NADH$, $2\,FADH_2$, $6\,O_2$.

• Outputs: $26\text{ or }28\,ATP$, $10\,NAD^+ + 10\,H^+$, $2\,FAD + 4\,H^+$, $6\,H_2O$.

• Mechanism: NADH/$FADH_2$ unload electrons. Energy powers pumping $H^+$ into the intermembrane space. $H^+$ build-up flows through ATP synthase, spinning it to make $ATP$.

• Role of Oxygen: Terminal acceptor for protons and electrons to form water, preventing cell damage.

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6B: Anaerobic Fermentation

Overview (3.2.8.1)

In the absence of oxygen, the Krebs cycle and ETC stall because $NADH/FADH_2$ cannot be unloaded. Fermentation allows for the regeneration of $NADP^+$ so glycolysis can continue.

Anaerobic Pathways (3.2.8.2)

• Animals (Lactic Acid Fermentation):     $\text{Glucose} \rightarrow 2\text{ Lactic Acid} + 2\,ATP$     Occurs in cytosol. Lactic acid is toxic in high amounts (lowers $pH$) and must be converted back to pyruvate when oxygen returns.

• Yeasts (Ethanol Fermentation):     $\text{Glucose} \rightarrow 2\text{ Ethanol} + 2\,CO_2 + 2\,ATP$     Two-step process: Pyruvate $\rightarrow$ Acetaldehyde $\rightarrow$ Ethanol. Ethanol and $CO_2$ diffuse out.

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6C: Factors Affecting Cellular Respiration Rate

Temperature and pH (3.2.9.1)

• Temperature: Highest rate at the enzyme's optimal temperature. Low temperature $\rightarrow$ low kinetic energy. High temperature $\rightarrow$ denaturation.

• pH: Different sites (matrix, cytosol) have specific optimal $pH$ levels. Matrix is approx $pH\,7.8$.

Substrate Concentration

• Glucose (3.2.9.2): Rate increases until enzymes reach saturation point ($V_{\text{max}}$).

• Oxygen (3.2.9.3): Rate increases with oxygen availability for aerobic respiration until enzymatic systems are saturated.

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Enzyme Inhibition (3.2.3.7)

• Cyanide: Lethal because it binds to cytochrome c oxidase (ETC) irreversibly, halting $ATP$ production.

• End-product Inhibition: $ATP$ can non-competitively inhibit phosphofructokinase (glycolysis) to regulate energy production when levels are high.

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6D: Biofuel from Fermentation

Definitions (3.2.11.1)

• Biomass: Organic material (plant/animal) used to make fuel. Renewable and sustainable.

• Fossil Fuel: Formed over millions of years; non-renewable.

• Carbon Neutral: No net increase in atmospheric $CO_2$ because the carbon released was recently absorbed by photosynthesis.

Biofuel Generations

• First-generation: Made from edible crops (corn, wheat). Conflict with food demands (Food vs Fuel debate).

• Second-generation: Made from non-edible agricultural waste/wood. Harder to break down.

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Production Process (Bioethanol)

1. Deconstruction: Physical/chemical/enzymatic breakdown of cell walls to increase surface area.

2. Digestion by Enzymes: Hydrolysis (using water and enzymes like amylase) to turn starch into glucose.

3. Ethanol Fermentation: Yeast converts glucose to ethanol and $CO_2$ anaerobically.

4. Purification: Distillation/dehydration to remove water and refine biofuel.

Implications

• Strengths: Carbon neutral, local energy security, decentralized control.

• Weaknesses: High production cost, food competition, environmental impacts (deforestation/habitat loss for plantations).