### **1. Pigments, Photosystems, and Leaf Color**
* **Light Perception:** Sunlight consists of colors in the visible spectrum (**ROY G BIV**). We only see **reflected light**, not absorbed light.
* **Pigments:**
* **Chlorophyll A:** Main photosynthetic pigment; absorbs violet, blue, and red light while **reflecting green light**.
* **Chlorophyll B:** Accessory pigment; absorbs blue, orange, and red light while **reflecting green light**.
* **Carotenoids:** Accessory pigments; absorb blue and green light while **reflecting yellow, orange, and red light**.
* **Autumn Leaf Color Changes:** In spring, carotenoids are masked by abundant chlorophyll. In autumn, shorter days reduce sunlight, causing chlorophyll to break down and reveal carotenoids; thus, orange/yellow/red light is **reflected**.
* **Photosystem Structure:** Photosystems are located on the **thylakoid membrane** and consist of proteins, chlorophyll A, chlorophyll B, and carotenoids.
* **Antenna Complex:** Contains chlorophyll B, carotenoids, and proteins. It captures photons and passes solar energy around, but **does not donate electrons**.
* **Reaction Center:** Contains a pair of **Chlorophyll A** molecules. It absorbs solar energy to excite low-energy electrons and **donates high-energy electrons** to the primary electron acceptor.
* **Redox in Photosystems:** When the reaction center donates high-energy electrons, it becomes **oxidized**; the electron acceptor gains them and becomes **reduced**. The lost electrons are replenished by an **electron donor** that donates low-energy electrons and becomes oxidized.
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### **2. Light-Dependent Reactions & Electron Transport Chain**
* **Location:** Occurs on the **thylakoid membrane**.
* **Photosystem II (PS II) vs. Photosystem I (PS I):**
* **PS II:** Absorbs sunlight at **\\(680\text{ nm}\\)**. Its electron donor is **water (\\(\text{H}_2\text{O}\\))**, which is split/oxidized into \\(2\text{ e}^-\\), \\(2\text{ H}^+\\), and oxygen gas (\\(\text{O}_2\\)) inside the thylakoid space. PS II uses electron energy to drive **ATP synthesis**.
* **PS I:** Absorbs sunlight at **\\(700\text{ nm}\\)**. Replaces its lost electrons directly from **Plastocyanin (PC)**. PS I uses re-excited electrons to make **NADPH**.
* **Sequential Electron Order:** \\(\text{H}_2\text{O} \rightarrow \text{PS II (680 nm)} \rightarrow \text{Plastoquinone (PQ)} \rightarrow \text{B}_6\text{f complex} \rightarrow \text{Plastocyanin (PC)} \rightarrow \text{PS I (700 nm)} \rightarrow \text{Ferredoxin (FD)} \rightarrow \text{NADP}^+\text{ reductase} \rightarrow \text{NADP}^+ \rightarrow \text{NADPH}\\).
* **Mobile Electron Carriers:** Light reactions use **3 mobile carriers**:
* **Plastoquinone (PQ):** Accepts electrons from PS II and delivers them to the \\(\text{B}_6\text{f}\\) complex.
* **Plastocyanin (PC):** Carries electrons with the **lowest energy**.
* **Ferredoxin (FD):** Carries electrons with the **highest energy** because its electrons were re-excited by \\(700\text{ nm}\\) light at PS I.
* **Proton Pump & Chemiosmosis:**
* The **\\(\text{B}_6\text{f}\\) complex** is the single proton pump in photosynthesis. It uses electron energy to actively pump \\(\text{H}^+\\) ions from the stroma into the thylakoid space, making the thylakoid space **more acidic (lower pH, higher \\(\text{H}^+\\) concentration)**.
* \\(\text{H}^+\\) ions rush back into the stroma through **ATP synthase** down their concentration gradient via **facilitated diffusion (passive transport)**, synthesizing ATP (chemiosmosis).
* **Products & Energetics:** Produces **\\(\text{O}_2\\)** (in thylakoid space), **ATP**, and **NADPH** (both in stroma). Because ATP is produced, light-dependent reactions are **exergonic**.
* **Final Electron Acceptor:** **\\(\text{NADP}^+\\)**, which is reduced to NADPH by the enzyme \\(\text{NADP}^+\\) reductase.
---
### **3. Photosynthetic ETC vs. Mitochondrial ETC**
* **Mobile Carriers:** Photosynthesis uses **3** (PQ, PC, FD); mitochondria use **2** (Ubiquinone, Cytochrome C).
* **Proton Pumps:** Photosynthesis uses **1** (\\(\text{B}_6\text{f}\\) complex); mitochondria use **3** (\\(\text{NADH}\\) dehydrogenase, \\(\text{BC}_1\\) complex, cytochrome oxidase complex). *(Do not confuse \\(\text{B}_6\text{f}\\) in thylakoids with \\(\text{BC}_1\\) in mitochondria!)*.
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### **4. Light-Independent Reactions (Calvin Cycle / \\(C_3\\) Pathway)**
* **Location & Energetics:** Takes place in the **stroma** of chloroplasts (or cytoplasm of cyanobacteria). It is an **endergonic** process (\\(\Delta G > 0\\), non-spontaneous) that consumes ATP and NADPH.
* **Three Phases:**
1. **Carbon Fixation:** \\(\text{CO}_2\\) (\\(1\text{C}\\)) combines with **RuBP** (\\(5\text{C}\\) sugar), catalyzed by the enzyme **Rubisco**, to form two \\(3\text{C}\\) molecules of **3-phosphoglycerate (3-PG / PGA)**. *(Inorganic carbon becomes fixed into organic compounds)*.
2. **Reduction:** Uses \\(12\text{ ATP}\\) and \\(12\text{ NADPH}\\) to reduce \\(12\text{ PGA}\\) into \\(12\text{ G3P}\\) (glyceraldehyde 3-phosphate). **G3P is the direct product** of the Calvin cycle. Two G3P molecules leave the cycle to form **1 glucose molecule** (indirect product).
3. **Regeneration of RuBP:** Consumes \\(6\text{ ATP}\\) to regenerate RuBP from the remaining 10 G3P molecules so the cycle can continue.
* **Energy Requirements per Glucose:** Requires **6 turns** of the cycle, consuming **\\(18\text{ ATP}\\)** (\\(12\\) in reduction, \\(6\\) in regeneration) and **\\(12\text{ NADPH}\\)** (used only in reduction).
---
### **5. Photorespiration & Plant Adaptations (\\(C_3\\), \\(C_4\\), and \\(CAM\\))**
* **Photorespiration:** Under hot, dry conditions, plants close their **stomata** to prevent water loss, causing internal \\(\text{CO}_2\\) to drop and \\(\text{O}_2\\) to build up. **Rubisco** binds \\(\text{O}_2\\) instead of \\(\text{CO}_2\\) to RuBP, creating a **wasteful anabolic process** that consumes ATP and produces \\(\text{CO}_2\\) and \\(\text{H}_2\text{O}\\).
* **\\(C_3\\) Plants:** Majority of plants. Have chloroplasts and Rubisco **only in mesophyll cells**. Run only the Calvin cycle and consume **\\(18\text{ ATP}\\)** per glucose.
* **\\(C_4\\) Plants (e.g., corn, sugarcane):**
* **Structural Difference:** Have chloroplasts in **both mesophyll cells and bundle-sheath cells**.
* **Spatial Separation:**
* **Mesophyll cells:** \\(\text{CO}_2 + \text{PEP} \rightarrow \text{Oxaloacetate } (4\text{C}) \rightarrow \text{Malate}\\) via **PEP carboxylase**. *(No Rubisco here)*.
* **Bundle-sheath cells:** Malate is transported here and decarboxylated into \\(\text{CO}_2\\) and pyruvate. **Rubisco** uses this concentrated \\(\text{CO}_2\\) in the Calvin cycle (\\(C_3\\) pathway).
* **Energy Cost:** Transporting each \\(\text{CO}_2\\) as malate costs \\(2\text{ ATP}\\) equivalents (\\(12\text{ ATP}\\) total for \\(6\text{ CO}_2\\)). Total energy per glucose = \\(18 + 12 =\\) **\\(30\text{ ATP}\\)**.
* **\\(CAM\\) Plants (e.g., cacti, pineapples):**
* **Temporal Separation:** Run both pathways in **mesophyll cells only** (where Rubisco is located).
* **Night:** Stomata open at night to fix \\(\text{CO}_2\\) into malate (\\(C_4\\) pathway) and store it in central vacuoles.
* **Day:** Stomata close; malate releases \\(\text{CO}_2\\) to drive the Calvin cycle (\\(C_3\\) pathway) during daylight.
* **Energy Cost:** Consumes **\\(30\text{ ATP}\\)** per glucose.
---
### **6. Important Review Points for Exam 2**
* **Final Electron Acceptors:**
* Light-dependent reactions: **\\(\text{NADP}^+\\)** (reduced to \\(\text{NADPH}\\)).
* Aerobic cellular respiration: **Oxygen (\\(\text{O}_2\\))** (reduced to \\(\text{H}_2\text{O}\\)).
* Lactic acid fermentation: **Pyruvate** (reduced to lactate/lactic acid in skeletal muscles, causing muscle fatigue).
* Ethanol/Alcohol fermentation: **Acetaldehyde** (reduced to ethanol, releasing \\(\text{CO}_2\\) in yeast).
* Methanogens: **\\(\text{CO}_2\\)**.
* **Glycolysis Energy & Enzymes:**
* **Initial Phase:** Endergonic (uses \\(2\text{ ATP}\\)).
* **Middle Phase:** Exergonic (produces \\(2\text{ ATP}\\) and \\(2\text{ NADH}\\); uses **kinase** and **dehydrogenase**).
* **Final Phase:** Exergonic (produces \\(2\text{ ATP}\\)).
* **Overall:** Exergonic (net yield of **\\(2\text{ ATP}\\)** per glucose).
* **Krebs Cycle:** Exergonic; produces **\\(2\text{ ATP}\\)** per glucose via **substrate-level phosphorylation** (catalyzed by kinases).
* **Isotope Labeling Experiment:**
* Oxygen labeled in \\(\text{CO}_2\\) ends up in **glucose**.
* Oxygen labeled in \\(\text{H}_2\text{O}\\) ends up in **oxygen gas (\\(\text{O}_2\\))**.
* **Organism Interdependence:** Photoautotrophs can survive without heterotrophs, but heterotrophs cannot survive without photoautotrophs.
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