Biology Final Notes PDF

Biology Final Notes (For Figures, check Canvas) ***Chapter 5: Membrane transport and cell signaling*** Overview: Life at the Edge Plasma membrane: The essential boundary separating the living cell from its external environment. Selective permeability: This property allows some substances (like s...

Biology Final Notes (For Figures, check Canvas) ***Chapter 5: Membrane transport and cell signaling*** Overview: Life at the Edge Plasma membrane: The essential boundary separating the living cell from its external environment. Selective permeability: This property allows some substances (like small nonpolar molecules) to cross the membrane more easily than others (e.g., large polar molecules or ions). \- The plasma membrane controls the exchange of materials, which is crucial for maintaining cellular homeostasis. **Concept 5.1: Cellular Membranes Are Fluid Mosaics of Lipids and Proteins** **Phospholipid Structure and Membrane Composition** Phospholipids: \- Most abundant lipids in membranes. \- Have amphipathic properties: 1- Hydrophilic (water-loving) head: Consists of a phosphate group and faces the aqueous external and internal environments. 2- Hydrophobic (water-fearing) tail: Comprised of fatty acids, faces inward, shielded from water. A phospholipid bilayer forms a stable boundary between two aqueous regions (e.g., the intracellular cytoplasm and extracellular fluid). Membrane Proteins: \- Most proteins in the membrane are also amphipathic, with hydrophilic portions exposed to water and hydrophobic regions interacting with the lipid core. Fluid mosaic model: Describes the membrane as a fluid structure with proteins embedded in or attached to a bilayer of phospholipids. \- Proteins and lipids can move laterally within the layer. \- Some proteins and lipids are associated in specific regions or \"rafts,\" forming specialized functional patches. **Fluidity of Membranes** Lateral movement of phospholipids and proteins: \- Lipids move rapidly, while proteins move more slowly. Some proteins move in a directed fashion, others drift, and some are anchored in place by cytoskeletal attachments. Temperature effects: \- As temperature drops, Membranes switch from a fluid state to a more solid state. The exact temperature depends on lipid composition: \- Saturated fatty acid tail: Pack tightly, making the membrane more viscous (less fluid). \- Unsaturated fatty acid tails: Have kinks (double bonds) that prevent tight packing, enhancing fluidity at lower temperatures. Cholesterol's role: \- At high temperatures (e.g., 37°C), Cholesterol reduces membrane fluidity by restricting phospholipid movement. \- At low temperatures: Cholesterol prevents close packing of phospholipids, helping the membrane remain fluid and preventing solidification. Membranes must maintain a certain level of fluidity to function, similar to the consistency of olive oil, ensuring that membrane proteins can function properly. **Membrane Proteins and Their Functions** The membrane is a collage of proteins embedded in the phospholipid bilayer, each type performing a specific function. 1- Integral proteins: \- Penetrate the hydrophobic core of the lipid bilayer, often spanning the entire membrane (transmembrane proteins). 2- Peripheral proteins: \- Loosely bound to the surface of the membrane, typically to exposed parts of integral proteins or to the cytoskeleton or ECM. **Six major functions of membrane proteins:** 1\. Transport: (Integral proteins) \- Channel proteins form hydrophilic channels that allow the passage of specific molecules or ions across the membrane. \- Carrier proteins change shape to shuttle substances across the membrane, sometimes using energy (ATP) to actively pump substances (active transport). 2\. Enzymatic activity: (Peripheral proteins) / (Integral proteins) \- Membrane-bound enzymes carry out sequential steps in metabolic pathways. \- Enzyme active sites are exposed to substrates in the adjacent solution. 3\. Signal transduction (Peripheral proteins) \- Membrane proteins, like receptors, have binding sites for specific signaling molecules (e.g., hormones). \- Binding induces a shape change in the protein, transmitting a signal inside the cell, typically through binding to cytoplasmic proteins. 4\. Cell-cell recognition (Integral proteins) \- Glycoproteins serve as identification tags for other cells, facilitating short-lived cell interactions. 5\. Intercellular joining: (Integral proteins) \- Proteins form permanent connections between cells (e.g., gap junctions, tight junctions), which allow cells to function as a unit. 6\. Attachment to the cytoskeleton and extracellular matrix (ECM): (Integral proteins) \- Proteins anchor the cell by binding to cytoskeletal elements or ECM molecules, stabilizing the cell's shape and ensuring positional stability for certain membrane proteins. **The Role of Membrane Carbohydrates in Cell-Cell Recognition** Membrane carbohydrates Play a crucial role in cell recognition by attaching to lipids (forming glycolipids) or proteins (forming glycoproteins). These carbohydrates vary between species, individuals, and even cell types, giving cells a unique surface identity that enables recognition and interaction with other cells. **Synthesis and Sidedness of Membranes** Asymmetrical distribution: Proteins, lipids, and carbohydrates are distributed asymmetrically between the two faces of the membrane. Membranes are synthesized in the ER and modified in the Golgi apparatus, which determines the final orientation and distribution of membrane components. **Concept 5.2: Membrane Structure and Selective Permeability** Selective permeability: Membranes regulate the passage of molecules and ions across them, essential for maintaining the internal conditions of the cell. **Lipid bilayer permeability:** 1. Hydrophobic molecules (e.g., hydrocarbons, CO₂, O₂) dissolve in the lipid bilayer and pass through easily. 2. Hydrophilic molecules (e.g., ions, polar molecules) do not pass through the bilayer as easily. Even water crosses the membrane less efficiently than hydrophobic molecules. **Transport Proteins** Transport proteins: Facilitate the passage of hydrophilic substances (e.g., ions, polar molecules) that cannot pass through the lipid bilayer on their own. Channel proteins: \- Form hydrophilic tunnels allowing certain molecules/ions to move across the membrane. \- Aquaporins: Specialized channel proteins that facilitate the passage of water molecules. Carrier proteins: \- Bind to molecules and change shape to shuttle them across the membrane. \- These proteins are specific for the substance they transport. **Concept 5.3: Passive Transport/ Concept 5.4: Active transport uses energy to move solutes against their gradients** Concentration Gradient: The difference in concentration between two regions. **Passive Transport** Passive transport: No energy is required; particles move down their concentration gradient (diffusion and osmosis fall into this category). High to Low. 1. Diffusion: Molecules spread out evenly into available space due to random motion; particles move from high to low concentration. Example: A synthetic membrane with pores allows dye molecules to diffuse down their concentration gradient. 2. Osmosis (Water Balance): Osmosis: The diffusion of water across a selectively permeable membrane. - Importance: Regulates water flow and helps maintain homeostasis. Water moves from a region of low solute concentration (high water concentration) to a region of high solute concentration (low water concentration). Water movement continues until the solute concentration is equal on both sides. Tonicity and Water Balance in Cells: Tonicity: The ability of a surrounding solution to cause a cell to gain or lose water. Isotonic Solution: Flaccid - Concentration: Equal inside and outside the cell. - Effect: Cells retain normal shape; water movement is balanced. Hypotonic Solution: Turgid - Concentration: Lower outside than inside. - Effect: Water enters the cell, causing swelling (in plant cells, this increases turgor pressure, making them firm). Hypertonic Solution: Plasmolysis - Concentration: Higher outside than inside. - Effect: Water exits the cell, causing it to shrink (in plant cells, this causes plasmolysis---membrane shrinks from the wall). Plant Cells and Water Balance: - Turgid: A plant cell in a hypotonic solution becomes swollen as the cell wall prevents excessive intake of water. - Flaccid: In an isotonic environment, the plant cell does not gain water and may become limp. - Plasmolysis: In hypertonic solutions, plant cells lose water, causing the membrane to pull away from the wall, which can be lethal. 3. Facilitated Diffusion: A type of passive transport where transport proteins help molecules move across the membrane without energy input. - Channel Proteins: Provide passageways for molecules like water (aquaporins) or ions (ion channels). - Carrier Proteins: Change shape to transport molecules across the membrane. Active transport moves substances against their concentration gradients, requiring energy (usually ATP). Low to High Sodium-Potassium Pump: A specific example of active transport, where 3 Na+ ions are pumped out of the cell and 2 K+ ions are pumped in, maintaining concentration differences essential for cell functions. Transport of Large Particles: 1. Endocytosis: Engulfs material from outside into a vacuole within the cell. - Phagocytosis: \"Cell eating\" (engulfing large particles). - Pinocytosis: \"Cell drinking\" (engulfing fluids). - Receptor-mediated endocytosis: Specific uptake of molecules after binding to cell surface receptors. 2. Exocytosis: Vesicles fuse with the plasma membrane to expel contents from the cell (e.g., in secretory cells). ***Chapter 7: Cellular Respiration & Fermantion*** **Definition:** Cellular respiration is a series of metabolic reactions that convert biochemical energy from nutrients into ATP (adenosine triphosphate), releasing waste products such as CO₂ and H₂O. This process is essential for providing energy to fuel cellular activities. **General Equation:** C6​H12​O6​+6O2​→6CO2​+6H2​O+Energy (36-38 ATP) **Types of Cellular Respiration:** 1. **Aerobic Respiration**: C6​H12​O6​+6O2​→6CO2​+6H2​O+Energy (36-38 ATP) - Requires oxygen. - Produces 36-38 ATP per glucose molecule. 2. **Anaerobic Respiration**: - Occurs without oxygen. - Includes processes like fermentation. C6​H12​O6​→2C2​H5​OH+2CO2​+Energy (2 ATP) - Produces 2 ATP per glucose molecule. **Why Do You Need to Breathe?** Breathing supplies the oxygen necessary for aerobic cellular respiration. Without oxygen: - The electron transport chain (ETC) cannot function, halting ATP production. - Cells must resort to fermentation, which provides significantly less energy (only 2 ATP per glucose molecule). Breathing also removes carbon dioxide, a waste product of respiration, preventing it from accumulating to toxic levels. **Why is ATP Important?** - ATP powers various cellular processes such as active transport (e.g., pumping ions like Na⁺ and K⁺ across membranes), muscle contraction, and biosynthesis of molecules. - ATP acts like a rechargeable battery: when cells use energy, ATP is converted to ADP, which is then recharged back to ATP during cellular respiration. **Stages of Cellular Respiration** 1. **Glycolysis: The First Stage** - **Definition:** Glycolysis is the first step in breaking down glucose (a 6-carbon sugar) into two molecules of pyruvate (3-carbons each). - **Location:** Occurs in the cytoplasm. - **Details of Phases:** 1. **Energy Investment Phase:** - Two ATP molecules are used to phosphorylate glucose, making it more reactive. - Glucose is split into two 3-carbon molecules, glyceraldehyde-3-phosphate (G3P). 2. **Energy Payoff Phase:** - Each G3P is oxidized, transferring electrons to NAD⁺, forming 2 NADH. - Four ATP molecules are produced through substrate-level phosphorylation. - Two pyruvate molecules and two water molecules are the final products. - **Net Yield:** 1. **ATP:** 2 (4 produced - 2 consumed). 2. **NADH:** 2. 3. **Pyruvate:** 2. - **Key Points**: 1. Glycolysis does not require oxygen. 2. NADH carries high-energy electrons to the Electron Transport Chain (ETC). **2. Pyruvate Oxidation (Link Reaction)** - **Definition:** Converts pyruvate into acetyl-CoA, preparing it for the citric acid cycle. - **Location:** Mitochondrial matrix. - **Steps:** 1. Pyruvate (3 carbons) is decarboxylated, releasing one molecule of CO₂. 2. The remaining 2-carbon fragment is oxidized, reducing NAD⁺ to NADH. 3. The oxidized fragment binds to coenzyme A, forming acetyl-CoA. - **Products per pyruvate:** 1. 1 NADH. 2. 1 CO₂. 3. 1 Acetyl-CoA. - **Net Yield per Glucose**: 1. 2 NADH. 2. 2 Acetyl-CoA. 3. 2 CO₂. **3. Citric Acid Cycle (Krebs Cycle)** **Definition:** A cyclic series of reactions that further breaks down acetyl-CoA to generate electron carriers and ATP. - **Location:** Mitochondrial matrix. - **Key Steps:** 1. Acetyl-CoA (2-carbons) combines with oxaloacetate (4-carbons) to form citrate (6-carbons). 2. Citrate undergoes a series of transformations, releasing two CO₂ molecules and regenerating oxaloacetate. 3. Along the way, electrons are transferred to NAD⁺ and FAD, forming NADH and FADH₂. 4. One ATP (or GTP) is generated directly per cycle. - **Yield per acetyl-CoA:** 1. 3 NADH. 2. 1 FADH₂. 3. 1 ATP. 4. 2 CO₂. - **Net Yield per Glucose (Two Turns of the Cycle)**: 1. 2 ATP. 2. 6 NADH. 3. 2 FADH₂. 4. 4 CO₂. - **Detailed Explanation**: 1. The key intermediates include citrate, isocitrate, alpha-ketoglutarate, succinate, fumarate, and malate. 2. NADH and FADH₂ produced here carry electrons to the ETC. **4. Oxidative Phosphorylation** - **Definition:** A series of protein complexes in the inner mitochondrial membrane that use electrons from NADH and FADH₂ to produce ATP. - **Process:** 1. NADH and FADH₂ donate electrons to the ETC. 2. Electrons move through the complexes, releasing energy at each step. 3. This energy pumps H⁺ ions into the intermembrane space, creating a proton gradient. 4. H⁺ ions flow back into the matrix through ATP synthase, driving the production of ATP. 5. Oxygen is the final electron acceptor, combining with electrons and H⁺ to form water. **Chemiosmosis:** - **Purpose**: Uses the proton gradient to drive ATP synthesis via ATP synthase. - **Mechanism**: 1. Protons (H⁺) accumulate in the intermembrane space, creating a high concentration compared to the mitochondrial matrix. 2. This proton gradient represents potential energy, referred to as the proton-motive force. 3. Protons flow back into the mitochondrial matrix through ATP synthase channels. 4. The energy released by this movement drives the conversion of ADP and inorganic phosphate (Pi) into ATP. - **Detailed Explanation**: 1. ATP synthase operates like a rotary engine, with protons driving its rotation. 2. Approximately 3 protons are required to synthesize 1 ATP molecule. - **Net Yield**: 1. 26-28 ATP. **Fermentation** - **Definition**: Fermentation is an anaerobic process that allows cells to generate ATP when oxygen is scarce. It follows glycolysis, which breaks down glucose into pyruvate. Fermentation processes ensure that glycolysis can continue by regenerating NAD⁺, which is needed for the oxidation of glucose in glycolysis. **1. Alcohol Fermentation** - **Process Overview**: - Alcohol fermentation occurs when pyruvate is converted to ethanol (alcohol) and carbon dioxide (CO₂). - This process regenerates NAD⁺, which is required for glycolysis to continue in the absence of oxygen. - **Steps**: - **Decarboxylation of Pyruvate**: - Pyruvate (C₃H₄O₃) is decarboxylated (removal of a CO₂ group), resulting in an intermediate compound called **acetaldehyde** (C₂H₄O). - **Reduction of Acetaldehyde**: - Acetaldehyde is then reduced by NADH (generated from glycolysis) to form **ethanol** (C₂H₅OH). - This step regenerates NAD⁺, enabling glycolysis to continue producing ATP. - **Net Yield**: - **2 ATP** (from glycolysis). - **2 NAD⁺** is regenerated. - **2 Ethanol** and **2 CO₂** are produced per glucose molecule. - **Equation**: - Glucose (C₆H₁₂O₆) is broken down into two glycolysis molecules of pyruvate (C₃H₄O₃). - Pyruvate is then converted to ethanol (C₂H₅OH) and CO₂. - **Yeast**: Used in brewing, winemaking, and baking, where fermentation produces ethanol (alcohol) and CO₂ gas (which causes bread dough to rise). **2. Lactic Acid Fermentation** - **Process Overview**: - Lactic acid fermentation occurs when pyruvate is directly reduced to lactate (lactic acid) without the release of CO₂. - This process also regenerates NAD⁺, which is necessary for glycolysis to continue in anaerobic conditions. - **Steps**: - **Reduction of Pyruvate**: - Pyruvate (C₃H₄O₃) is reduced by NADH (from glycolysis) to form **lactate** (C₃H₆O₃). - This process regenerates NAD⁺, which is then available to be reused in glycolysis. - **Net Yield**: - **2 ATP** (from glycolysis). - **2 NAD⁺** is regenerated. - **2 Lactate** is produced per glucose molecule. **Equation**: Glycolysis C6​H12​O6​\-\-\-\-\-\-\-\-\-\-\-\-- ​2C3​H4​O3​→2C3​H6​O3​+2 ATP - Glucose (C₆H₁₂O₆) is broken down into two pyruvate molecules (C₃H₄O₃) during glycolysis. - Pyruvate is then reduced to lactate (C₃H₆O₃), and NADH is oxidized back to NAD⁺. Example: - Muscle Cells: During intense exercise when oxygen supply is limited (anaerobic conditions), muscle cells undergo lactic acid fermentation to generate ATP. This leads to the buildup of lactate, which is later converted back to pyruvate when oxygen becomes available. The purpose of fermentation is to regenerate NAD⁺ from NADH, which is needed for glycolysis to continue. In the absence of oxygen, fermentation recycles NADH back into NAD⁺, allowing glycolysis to produce ATP anaerobically. A screenshot of a computer Description automatically generated **Redox Reactions:** - **Oxidation**: Loss of electrons. - **Reduction**: Gain of electrons. - **Reducing Agent**: Donates electrons. - **Oxidizing Agent**: Accepts electrons. - Cellular respiration involves oxidation-reduction (redox) reactions. - **Oxidation:** Loss of electrons (e.g., glucose is oxidized to CO₂). - **Reduction:** Gain of electrons (e.g., O₂ is reduced to H₂O). **Electron Carriers:** - **NAD⁺/NADH**: Reduced during glycolysis, pyruvate oxidation, and the citric acid cycle. - **FAD/FADH₂**: Reduced in the citric acid cycle. **Energy Yield Summary:**  **Comparison: Cellular Respiration vs. Photosynthesis** **Similarities:** - Both involve redox reactions and electron transport chains. - ATP synthase functions in both processes. **Differences:** **Feature** **Cellular Respiration** **Photosynthesis** ------------------------- -------------------------- -------------------- Location Mitochondria Chloroplasts Reactants Glucose, O₂ CO₂, H₂O Products CO₂, H₂O, ATP Glucose, O₂ Electron Source NADH, FADH₂ Water (H₂O) Final Electron Acceptor Oxygen NADP⁺ **Lab** ***Enzymes*** **What Are Enzymes?** - **Definition:** Enzymes are proteins that act as biological catalysts, speeding up chemical reactions by lowering the activation energy required for the reaction to proceed. - **Structure:** Enzymes have a tertiary or quaternary structure, giving them a specific shape critical for their function. - **Properties:** - Highly specific for their substrates. - Reusable; not consumed in the reaction. - Often named with an \"-ase\" suffix (e.g., lactase, sucrase, catalase). **Key Definitions in Enzymes and Reactions** 1. **Substrate**: - The **reactant molecule** on which an enzyme acts. - It binds to the enzyme's **active site** to undergo a chemical transformation. - **Example**: - In the reaction catalyzed by amylase, **starch** is the substrate. 2. **Product**: - The **molecule(s)** formed after the enzyme catalyzes the reaction. - The substrate is converted into the product through enzymatic action. - **Example**: - Amylase breaks down starch into **maltose** and other sugars (products). 3. **Active Site**: - The specific **region on the enzyme** where the substrate binds. - It has a **specific shape** and chemical properties that match the substrate, allowing the enzyme to function with **high specificity**. - **Function**: - Facilitates the conversion of substrate into product by lowering the **activation energy** required for the reaction. **How Do Enzymes Work?** 1. **Enzyme-Substrate Interaction:** - The enzyme binds to a specific substrate at its **active site** to form an enzyme-substrate complex. 2. **Activation Energy Reduction: Catalysis** - Enzymes weaken substrates\' chemical bonds, reducing the required activation energy and facilitating faster reactions. 3. **Product Formation:** - The enzyme releases the products and returns to its original state, ready for another reaction. **Enzyme Mechanism Explained:** - **Lock-and-Key Model:** Enzymes and substrates fit together precisely, like a lock and key. - **Induced Fit Model:** The enzyme changes shape slightly to accommodate the substrate more snugly, enhancing the reaction\'s efficiency. - Enzyme denaturation refers to the structural alteration of an enzyme, leading to the loss of its biological activity. This occurs when the enzyme\'s three-dimensional shape is disrupted. **Factors Affecting Enzyme Activity** 1. **Environmental Conditions:** - **Temperature:** The optimal temperature for most human enzymes is 37°C (body temperature). High heat denatures enzymes. - Enzyme activity increases with temperature up to an optimal point. - Excessive heat causes denaturation (loss of shape and function). - **pH Levels:** - Most enzymes work best near a neutral pH (6-8). Extreme pH values can denature enzymes. - **Ionic Concentration:** High salt concentrations can disrupt enzyme ionic bonds, affecting their function. 2. **Cofactors and Coenzymes:** - Non-protein molecules that assist enzymes. - Examples: - **Cofactors:** Inorganic ions like zinc or iron. - **Coenzymes:** Organic molecules like vitamins. 3. **Inhibitors:** - **Competitive Inhibitors:** Bind to the active site, blocking the substrate. - **Non-Competitive Inhibitors:** Bind elsewhere, altering the enzyme\'s shape and functionality. **Optimal pH Levels for Common Enzymes** Enzymes have an optimal pH at which they are most active. Deviations can lead to reduced efficiency or denaturation. Here are the best pH levels for some key enzymes: 1. **Amylase** - **Optimal pH:** 6.7-7.0 - **Function:** Breaks down starch into maltose. - **Location:** Saliva and pancreas. 2. **Pepsin** - **Optimal pH:** 1.5-2.0 - **Function:** Break down proteins into peptides. - **Location:** Stomach. 3. **Trypsin** - **Optimal pH:** 7.5-8.0 - **Function:** Break down proteins into smaller peptides. - **Location:** Pancreas and small intestine. 4. **Lipase** - **Optimal pH:** 8.0 - **Function:** Break down fats into glycerol and fatty acids. - **Location:** Pancreas, active in the small intestine. 5. **Lactase** - **Optimal pH:** 6.0 - **Function:** Break down lactose into glucose and galactose. - **Location:** Small intestine. 6. **Catalase** - **Optimal pH:** 7.0 - **Function:** Break down hydrogen peroxide into water and oxygen. - **Location:** Found in most cells, especially liver and plant tissues. **Comparison of Catalase in Animals vs. Plants** - **Similarities:** - Found in peroxisomes. - Breaks down hydrogen peroxide into water and oxygen. - **Differences:** - **Plants:** Involved in managing photorespiration. - **Animals:** Detoxifies hydrogen peroxide in high-energy tissues like the liver. **Important Graphs**  Exploring Enzymes \| Scientific American