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### **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. --- ### **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!)*. --- ### **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.

Biology Study Guide Complete review of your notes • Vocabulary + concepts to know • No tables This guide covers the vocabulary, nitrogen cycle, phosphorus cycle, water cycle, energy transfer, food chains, organisms, and ecological processes from all your notes. I combined repeated information and clarified a few definitions to help you prepare for tomorrow’s test. Part 1: Vocabulary 1. Ecology and ecosystem organization Ecology — The study of interactions between organisms and their environment. Biosphere — All parts of Earth where life exists. Population — Members of the same species living in the same area. Community — Different populations living and interacting in the same area. Ecosystem — A community of organisms and the nonliving environment they interact with. Biomass — The total mass of living organisms in a particular area or trophic level. Trophic level — An organism’s feeding position in a food chain. 2. Types of organisms Autotroph — An organism that makes its own food using light energy or chemical energy. * Examples: plants, algae and some bacteria. * Autotrophs are also called producers. Heterotroph — An organism that obtains energy and nutrients by consuming or absorbing organic matter from other organisms. - Examples: animals and fungi. Producer — An organism that makes its own organic food. Consumer — An organism that obtains energy by eating other organisms. Herbivore — An organism that eats plants or other producers. Examples: deer, cows and caterpillars. Carnivore — An organism that eats other animals. Examples: lions, hawks and sharks. Omnivore — An organism that eats both plants and animals. Examples: humans, bears and crows. Scavenger — An organism that feeds on dead animals. Example: a vulture. Detritivore — A heterotroph that obtains nutrients by ingesting detritus. Detritus — Dead and decomposing plant and animal material, including organic waste. Decomposer — An organism that breaks down organic matter externally using enzymes and absorbs the released nutrients. - Examples: fungi, mushrooms and bacteria. Phytoplankton — Tiny photosynthetic organisms, including algae, that drift in aquatic environments and form the base of many aquatic food webs. 3. Food and energy vocabulary Food chain — A single pathway showing how energy passes from one organism to another. Food web — A network of interconnected food chains showing feeding relationships in an ecosystem. Energy transfer — The movement of energy from one organism to another. Photosynthesis — The process that uses light energy to make sugars from carbon dioxide and water. Cellular respiration — The process of breaking down molecules such as glucose to release usable energy. Chemosynthesis — The process of using energy from chemical reactions to make organic molecules. 4. Nitrogen cycle vocabulary Nitrogen fixation — The conversion of atmospheric nitrogen gas into usable nitrogen compounds. Assimilation — The process in which plants absorb nitrogen compounds and use the nitrogen to build organic molecules. Consumption — Animals obtain nitrogen and other nutrients by eating plants or other animals. Ammonification — Decomposers convert nitrogen in organic matter into ammonia or ammonium. Nitrification — Bacteria convert ammonium into nitrite and then nitrate. Denitrification — Bacteria convert nitrate into nitrogen gas, returning nitrogen to the atmosphere. Ammonia — A nitrogen-containing compound with the formula . Ammonium — A positively charged nitrogen ion with the formula . Nitrite — A nitrogen-containing ion with the formula . Nitrate — A nitrogen-containing ion with the formula , which plants can absorb. 5. Water cycle vocabulary Evaporation — Liquid water absorbs energy and changes into water vapor. Condensation — Water vapor cools and changes into liquid droplets. Transpiration — The release of water vapor from plants, mainly through their leaves. Precipitation — Water falling from clouds as rain, snow, sleet or hail. 6. Nutrients and other vocabulary Phosphorus — An essential nutrient used to build DNA, RNA, ATP and cell membranes. It also supports plant growth and root development. Limiting nutrient — A nutrient whose limited availability restricts the growth of organisms. Eutrophication — The process in which excess nutrients enter a body of water, promoting excessive algae growth and potentially reducing dissolved oxygen. Amino acids — The building blocks of proteins. Proteins — Molecules made of amino acids that perform many functions in living organisms. Nucleic acids — Molecules such as DNA and RNA that store and transmit genetic information. External digestion — The breakdown of food outside an organism’s cells or body using enzymes, as fungi do. Decomposition — The breakdown of dead organic matter and waste, returning nutrients to the environment. Part 2: Things You Need to Know 1. The nitrogen cycle The nitrogen cycle describes how nitrogen moves between the atmosphere, soil, water and living organisms. Nitrogen is essential for making proteins, amino acids and nucleic acids such as DNA and RNA. Although the atmosphere contains a lot of nitrogen gas, most plants cannot use atmospheric nitrogen gas directly. The main processes 1. Nitrogen fixation Atmospheric nitrogen gas () is converted into usable nitrogen compounds. * Mainly carried out by nitrogen-fixing bacteria. * Lightning also helps convert atmospheric nitrogen into compounds that enter the soil. 2. Assimilation Plants absorb nitrate () or ammonium () from the soil and use the nitrogen to make proteins and nucleic acids. 3. Consumption Animals obtain nitrogen by eating plants or other animals. 4. Ammonification Decomposers break down nitrogen-containing material in dead organisms and waste, releasing ammonia or ammonium into the environment. 5. Nitrification Bacteria convert ammonium into nitrite and then nitrate. NH_4^+ \rightarrow NO_2^- \rightarrow NO_3^- 6. Denitrification Bacteria convert nitrate into nitrogen gas, returning nitrogen to the atmosphere. Important things to remember * Nitrogen fixation starts with atmospheric nitrogen gas, . * Nitrogen fixation is carried out mainly by bacteria, but lightning also contributes. * Plants need nitrogen to build proteins and nucleic acids. * Animals obtain nitrogen through food. * Decomposers recycle nitrogen from dead organisms and waste. * Nitrification produces nitrite and then nitrate. * Denitrification returns nitrogen to the atmosphere. The nitrogen cycle is a cycle, so nitrogen can enter through several pathways. The processes do not always occur in one simple sequence. 2. Nitrogen formulas to memorize * = nitrogen gas * = ammonia * = ammonium * = nitrite * = nitrate Pay special attention to the difference between ammonia, ammonium, nitrite and nitrate. 3. The phosphorus cycle Phosphorus is an essential nutrient that organisms need to survive. How it moves through the environment * Weathering breaks down rocks and releases phosphorus into soil and water. * Plants absorb phosphorus through their roots. * Animals obtain phosphorus by eating plants or other animals. * Waste and dead organisms are broken down by decomposers. * Phosphorus returns to soil and water, where it can be used again. Why phosphorus matters * It is needed to build DNA and RNA. * It is part of ATP, which cells use to transfer energy. * It is a component of cell membranes. * It helps plants grow and develop strong roots. * It is often a limiting nutrient in soils and aquatic ecosystems. Important difference: Unlike the nitrogen cycle, the phosphorus cycle does not have a major atmospheric gas phase. 4. Eutrophication Eutrophication happens when too many nutrients enter a body of water. This can occur when fertilizers or sewage enter lakes and rivers. Know the steps: * Excess nutrients enter the water. * Algae grow rapidly, creating an algal bloom. * Algae die and decomposers break down the dead material. * Decomposers use dissolved oxygen during decomposition. * Oxygen levels decrease, which can harm or kill fish and other aquatic organisms. Remember that the problem is not simply that algae grow. The decomposition of dead algae can use up the oxygen aquatic organisms need. 5. The water cycle The water cycle describes how water moves between Earth’s surface and the atmosphere. The four main processes * Evaporation: Liquid water absorbs heat and becomes water vapor. * Condensation: Water vapor cools and forms liquid droplets, helping create clouds. * Precipitation: Water falls from clouds as rain, snow, sleet or hail. * Transpiration: Plants release water vapor through their leaves. Water also collects in rivers, lakes and oceans, while some infiltrates the soil and becomes groundwater. Make sure you can explain the difference between evaporation and condensation: * Evaporation: liquid to gas. * Condensation: gas to liquid. 6. Photosynthesis, respiration and chemosynthesis Photosynthesis * Uses light energy to produce sugars. * Takes in carbon dioxide and water. * Releases oxygen in typical plant photosynthesis. * Stores energy in chemical bonds. Cellular respiration * Breaks down glucose and other molecules to release usable energy. * Happens in plants, animals and many other organisms. * Most of the energy organisms obtain is eventually released as heat. Chemosynthesis * Uses energy from chemical reactions instead of sunlight. * Allows certain organisms, such as some bacteria, to produce organic molecules. How they differ Photosynthesis uses light energy, cellular respiration releases usable energy from molecules, and chemosynthesis uses chemical energy to make organic molecules. 7. Carbon and energy in ecosystems Your notes include these important ideas about carbon and energy. * Carbon enters the atmosphere through processes such as respiration, decomposition and the burning of fossil fuels. * Vehicles release carbon dioxide when they burn gasoline or other fossil fuels. * Plants remove carbon dioxide from the atmosphere during photosynthesis. * Energy moves through food chains and food webs. * Most energy obtained by organisms is eventually released as heat. * Unlike nutrients, energy does not continuously recycle through an ecosystem; it flows through the ecosystem. 8. Food chains and food webs A food chain shows one pathway of energy transfer, while a food web shows many connected feeding relationships. For example: Grass — Producer Grasshopper — Primary consumer Frog — Secondary consumer Snake — Tertiary consumer Arrows point from the organism being eaten to the organism receiving the energy. Know these facts * Producers make their own food. * Primary consumers eat producers. * Secondary consumers eat primary consumers. * Tertiary consumers eat secondary consumers. * Food webs connect multiple food chains. * Less energy is available at higher trophic levels because energy is used for life processes and much is released as heat. 9. Autotrophs versus heterotrophs Autotrophs: * Make their own organic food. * Use light energy or chemical energy. * Include plants, algae and certain bacteria. Heterotrophs: * Obtain organic food from other organisms or organic matter. * Include animals and fungi. * Depend directly or indirectly on producers for energy. Remember that not every heterotroph eats another living organism. Decomposers, for example, absorb nutrients from dead organic matter. 10. Detritivores, decomposers and scavengers These three types of organisms are easy to confuse. Scavengers eat dead animals. Examples include vultures and some crabs. Detritivores ingest dead organic matter and waste. Examples include earthworms, woodlice and some aquatic organisms. Decomposers break down organic matter externally by releasing enzymes, then absorb the nutrients. Examples include fungi and bacteria. Where they live * Terrestrial means land-based. Examples of detritivores include earthworms and woodlice. * Aquatic means water-based. Some crabs and other aquatic organisms feed on detritus. Why they matter They help recycle nutrients back into the environment, allowing those nutrients to be used by other organisms. 11. Ecosystem organization Know the difference between these four terms: * Population: One species living in a particular area. * Community: Multiple populations living in an area. * Ecosystem: The community and its nonliving environment. * Biosphere: All parts of Earth where life exists. A community consists of different populations. An ecosystem includes both living and nonliving components. 12. Phosphorus transfer through food webs * Plants absorb phosphorus from soil or water. * Heterotrophs obtain phosphorus by eating plants or other animals. * Phosphorus moves between organisms through feeding. * Decomposition and waste return phosphorus to the environment. Phosphorus is important for plant growth and for building molecules that all living organisms need. Part 3: What to memorize before the test If you’re short on time, make sure you can answer these questions without looking at your notes. Final review checklist 0 of 13 Define ecology, biosphere, population, community and biomass. Explain the differences between autotrophs and heterotrophs. Distinguish herbivores, carnivores, omnivores, scavengers, detritivores and decomposers. Explain the nitrogen cycle processes and put them in context. Memorize N₂, NH₃, NH₄⁺, NO₂⁻ and NO₃⁻. Explain the phosphorus cycle and why phosphorus matters. Explain the steps of eutrophication and why oxygen decreases. Define evaporation, condensation, precipitation and transpiration. Compare photosynthesis, cellular respiration and chemosynthesis. Explain the difference between food chains and food webs. Explain why energy decreases at higher trophic levels. Explain how decomposers recycle nutrients. Describe how carbon enters and leaves the atmosphere. My advice for tonight: Study the vocabulary first, draw the nitrogen cycle from memory, and then explain eutrophication and the water cycle out loud. Finish by testing yourself on the checklist. If you can explain each item without looking, you’re in a good position for your test.