Biology Midterm 2 PDF

[Midterm 2] \[3.3→ 6.3b\] 1\. Enzyme Inhibition - Definition:      [Types of Inhibition: ]   Competitive Inhibition:   - The inhibitor competes directly with the substrate for the enzyme\'s active site.   - Prevents substrate binding by occupying the active site.   Noncompetitive...

[Midterm 2] \[3.3→ 6.3b\] 1\. Enzyme Inhibition - Definition:      [Types of Inhibition: ]   Competitive Inhibition:   - The inhibitor competes directly with the substrate for the enzyme\'s active site.   - Prevents substrate binding by occupying the active site.   Noncompetitive Inhibition: - The inhibitor binds to a site other than the active site (allosteric site).   - This alters the enzyme\'s structure, reducing its ability to catalyze the reaction. 2\. Feedback Inhibition [Definition:  ] - The product of an enzyme-catalyzed pathway acts as a regulator for the reaction, typically by binding to an allosteric site.   -  This is a form of allosteric regulation. [Purpose:  ] - Conserves cellular resources by halting the pathway when sufficient product is formed. 3\. Effects of Temperature and pH on Enzyme Activity [Optimal Conditions: ] -  Each enzyme has specific optimal temperature and pH values for maximum efficiency.   -  Typically:   -  Temperature: Often matches the physiological temperature of the organism.   -  pH: For intracellular enzymes, near neutral pH (\~7). For extracellular enzymes, the pH optimum may vary.   [Effects of Deviations from Optimum:]  - pH Changes:   - Affects the charged groups in the amino acids of the enzyme.   - Can alter enzyme structure and reduce activity.   - Temperature Changes:  - Below Optimum:Reaction rates increase as temperature rises toward the optimal level.   - Above Optimum: High temperatures cause denaturation of the enzyme (loss of structural integrity), decreasing reaction rates.   [4. Specific Temperature Effects on Enzyme Activity] Heat-Sensitive Enzymes:   -   Example: Enzymes controlling melanin production.   -   In warmer body regions, these enzymes may denature, leading to visible effects such as temperature-sensitive pigmentation. Illustrative Figures (Referenced): Figure 3.26:A diagram of a method of enzyme reaction Description automatically generated with medium confidence Demonstrates feedback inhibition in a metabolic pathway.    Figure 3.27: Shows how pH changes affect charged groups in enzyme amino acids.   Figure 3.28: Depicts the relationship between temperature and enzyme activity, including denaturation at high temperatures. A diagram of a curve with Gateway Arch in the background Description automatically generated 1\. Selectively Permeable Membranes   Functions:   - Separate internal and external environments.   -  Selectively exchange molecules and ions.   - Permeable to water but impermeable to most other molecules.   - Components:  - Phospholipids, glycolipids, sterols (cholesterol, ergosterols, phytosterols).   - Membrane proteins: integral (transmembrane) and peripheral. 2\. Fluid Mosaic Model  - Membranes are fluid lipid bilayers where proteins float.   Key Properties of Membranes:   - Fluidity dependent on lipid composition and temperature.   - Unsaturated fatty acids increase fluidity (due to kinks).   - Sterols buffer membrane fluidity by:   - Preventing excessive movement at high temperatures.   - Preventing tight packing at low temperatures. 3\. Properties of Water and Phospholipids  Water:   - Polar molecule, forms hydrogen bonds.   - Excellent solvent for hydrophilic (polar) molecules.   - Hydrophobic molecules (e.g., lipids) disrupt water structure, driving membrane formation.   Phospholipids: -  Amphipathic with hydrophilic heads and hydrophobic tails.   - Form bilayers in aqueous solutions.   Passive Transport   - Driven by diffusion, requiring no energy.   - Simple Diffusion:  -   - Movement from high to low concentration directly across the membrane.   -   - Small, uncharged molecules (e.g., O₂, CO₂) move easily.   -   - Large or charged molecules face significant barriers.   1\. Types of Passive Transport   - Facilitated Diffusion:  - Requires transporter proteins (e.g., channels or carriers).   - Moves substances down their concentration gradient.   - Stops when concentration gradient = 0.   - Osmosis:  - Diffusion of water across a selectively permeable membrane.   - Water moves from hypotonic (low solute) to hypertonic (high solute) solutions.   2\. Active Transport   -  Moves molecules against concentration gradients using energy (ATP).   Primary Active Transport:  -  Transport protein hydrolyzes ATP directly (e.g., Na⁺/K⁺ pump).   -   Maintains electrochemical gradients.   Secondary Active Transport:  -   Uses gradients created by primary transport.   -   Includes symport (same direction) and antiport (opposite directions). 3\. Bulk Transport   Exocytosis:   - Vesicles fuse with the plasma membrane to secrete substances.   Endocytosis:  -   - Internalization of external materials via vesicles.   Types:   - Pinocytosis: Non-specific uptake of fluids (\"cell drinking\").   - Phagocytosis: Uptake of large particles (\"cell eating\").   - Receptor-Mediated Endocytosis: Specific uptake via receptor-clathrin interactions. - Cell Signaling   Key Steps:  - Reception: Signal molecule binds to receptor.   - Transduction: Signal relayed via intracellular cascades (e.g., phosphorylation).   - Response: Cellular activity altered (e.g., enzyme activation, gene expression).   - Termination: Signal turned off after response.   Signaling Pathways:   -   Amplification occurs as one signal activates multiple downstream molecules.   - Involves kinases (add phosphates) and phosphatases (remove phosphates).   5\. Signal Transduction Examples  Epinephrine (Adrenaline): - Triggers glycogen breakdown in liver cells, increasing blood glucose levels.   - Demonstrates amplification via second messengers (e.g., cAMP).   - Physiological Responses to Adrenaline:\*\*   - Increased heart rate, energy burst, dilated pupils, and gene expression changes. Notes on Oxidation, Reduction, and Cellular Respiration Oxidation Definition: The partial or full loss of electrons from a substance. - The substance that loses electrons is called the \*\*electron donor\*\* and is \*\*oxidized\*\*. - Example: In glucose metabolism, the carbon atom has partially lost electrons because oxygen is more electronegative, leading to the oxidation of carbon. - Representation: Dark shading indicates increased electron density around atoms. Reduction - Definition: The partial or full gain of electrons by a substance. - The substance that gains electrons is the \*\*electron acceptor\*\* and is reduced. - Example: Oxygen gains electrons (reduced) in a reaction with hydrogen atoms. Redox Reactions - Coupled Reactions: Oxidation and reduction occur simultaneously in redox reactions. - Example: Combustion and cellular respiration are redox reactions.    Electron Carriers - NAD+ (Oxidized form): Accepts 2 electrons and 1 proton to become NADH (Reduced form). - FAD (Oxidized form): Accepts 2 electrons and 2 protons to become FADH2 (Reduced form). Example of Redox Reactions Reduction: - NAD+ + 2e⁻ + H⁺ → NADH - FAD + 2e⁻ + 2H⁺ → FADH2 - Oxidation\*\*: - NADH → NAD+ + 2e⁻ + H⁺ - FADH2 → FAD + 2e⁻ + 2H⁺ Cellular Respiration (C6H12O6 + 6O2 → 6CO2 + 6H2O + energy) - Stage 1: Glycolysis (in the cytosol) - Stage 2: Pyruvate oxidation and citric acid cycle (in mitochondria) - Stage 3: Oxidative phosphorylation (in mitochondria) Combustion vs. Cellular Respiration Notes on the Citric Acid Cycle and Oxidative Phosphorylation Citric Acid Cycle (Krebs Cycle or Tricarboxylic Acid Cycle) - Function: Acetyl groups are completely oxidized to CO2, with electrons removed in a series of oxidation reactions. Electron Carriers: Electrons are accepted by NAD+ and FAD, reducing them to NADH and FADH2. ATP Production: Some ATP is produced by substrate-level phosphorylation.    Products of Citric Acid Cycle (Per Acetyl Group) - 2 CO2 - 1 ATP - 3 NADH - 1 FADH2 Summary of Citric Acid (Kreb) Cycle Reaction: - 1 acetyl-CoA + 3 NAD+ + 1 FAD + 1 ADP + 1 Pi + 2 H2O   - 2 CO2 + 3 NADH + 1 FADH2 + 1 ATP + 3 H+ + 1 CoA At the End of the Citric Acid Cycle (for 2 Acetyl-CoA molecules): 2 ATP 6 NADH 2 FADH2 Electron Transport Chain and Oxidative Phosphorylation - - Flow of Energy in Cellular Respiration: - Stage 1 (Glycolysis): Glucose is oxidized to produce ATP and reduced electron carriers (NADH). - Stage 2 (Pyruvate Oxidation and Citric Acid Cycle): Acetyl-CoA enters the citric acid cycle, producing more NADH, FADH2, and ATP. - Stage 3 (Oxidative Phosphorylation): NADH and FADH2 donate electrons to the electron transport chain, leading to ATP synthesis. Notes on Fermentation, Anaerobic Respiration, and Oxygen\'s Role Fermentation - Occurs in eukaryotic cells under low oxygen levels. - Pathway of respiration that oxidizes fuel molecules in the absence of oxygen - Types of Fermentation:    1\. Lactate Fermentation:  - Electrons from NADH are transferred to pyruvate, producing lactic acid and NAD+. - Occurs in animals and bacteria.    2\. Alcoholic Fermentation: - Electrons from NADH are transferred to pyruvate, producing ethanol and NAD+. - Occurs in plants and fungi. Fermentation yields only 2 ATP because products (lactic acid, ethanol) are not fully oxidized, retaining chemical energy. Pathways of Pyruvate Metabolism - Aerobic Conditions: - Pyruvate → Acetyl-CoA → Citric Acid Cycle → Electron Transport Chain (ETC). - Anaerobic Conditions -  Pyruvate is metabolized via fermentation pathways (lactic acid or ethanol fermentation). Anaerobic Respiration - Performed by bacteria and archaea lacking mitochondria. - Use alternative terminal electron acceptors like sulfate, nitrate, or ferric ion. - Generates ATP without O2. Lifestyles Dictated by Oxygen - Strict Anaerobes: Cannot grow in oxygen\'s presence. - Strict Aerobes: Require oxygen for growth. - Facultative Aerobes: Can grow with or without oxygen (can switch to fermentative pathways). Paradox of Aerobic Life - Oxygen is required for electron transport but is inherently dangerous. - Produces \*\*reactive oxygen species (ROS) like superoxide and hydrogen peroxide, which are strong oxidizing agents and harmful to cells. Defence Against Reactive Oxygen Species Enzymatic Defenses: - Superoxide dismutase: Converts superoxide to hydrogen peroxide. - Catalase: Converts hydrogen peroxide to water and oxygen. - Non-Enzymatic Defenses:   Antioxidants like vitamin C and vitamin E neutralize ROS. Reduction of Oxygen to Water - O2 is reduced stepwise to water during electron transport, forming intermediate ROS, which are potentially harmful if not neutralized. Electron Transfer System and Oxidative Phosphorylation Overview   - Electron Transport Chain (ETC): Converts potential energy in NADH and FADH2 into a proton-motive force.   - Proton gradient drives ATP synthesis via ATP synthase.   Electron Carriers   - Stages 1-2: Glucose is oxidized, producing NADH and FADH2.   - Stage 3 (Oxidative Phosphorylation): NADH and FADH2 donate electrons to the ETC, leading to large-scale ATP production.   Electron Transport Chain (ETC) Components   - Protein Complexes:   - Complex I: Accepts electrons from NADH.   - Complex II: Accepts electrons from FADH2.   - Complex III: Transfers electrons to cytochrome c.   - Complex IV: Reduces oxygen to form water.   Shuttle Carriers:   - Coenzyme Q (CoQ): Transfers electrons between complexes I/II and III.   - Cytochrome c: Transfers electrons to complex IV.   Process   Electron Flow:   - Electrons move spontaneously from NADH/FADH2 through the ETC to oxygen.   - Oxygen acts as the final electron acceptor and is reduced to form water.   Proton Pumping:   - Complexes I, III, and IV pump protons (H+) from the mitochondrial matrix to the intermembrane space, creating a proton gradient.   ATP Synthesis:   - Protons flow back into the matrix through ATP synthase, driving the conversion of ADP + Pi to ATP.   Key Molecules and Steps   - NADH and FADH2: Electron donors.   - Oxygen: Final electron acceptor, reduced to H2O.   - Prosthetic Groups: Within protein complexes, cycle between oxidized and reduced states to facilitate electron transfer.   - CoQH2: Transfers electrons from complexes I/II to III.   - ATP Synthase: Uses proton-motive force to produce ATP.   Summary of ETC   - NADH/FADH2 → ETC → O2 → H2O + ATP.   - Proton gradient is the energy source for ATP synthesis. What you need to know: - Where in the cell it takes place - Key inputs (e.g. glucose, ATP, NAD+) - Key outputs (pyruvate, ATP, NADH) - Overall phases - Understand what types of reactions are taking place at different steps of the pathway (e.g. redox, anabolic, catabolic, phosphorylation) - One key enzyme - Phosphofructokinase catalyzes the second ATP-consuming step of the pathway Dependency upon Presence of Oxygen   - In anaerobic respiration, the terminal electron acceptor is not oxygen.   Fermentation   - In eukaryotic cells, low oxygen levels result in fermentation.   - Fermentation is the pathway of respiration that oxidizes fuel molecules in the absence of oxygen.   - Two types of fermentation exist: lactate fermentation and alcohol fermentation.   Paradox of Aerobic Life   - Although many organisms cannot exist without oxygen because it is required for electron transport, oxygen itself is inherently dangerous to all forms of life.   - Reactive oxygen species (ROS) include superoxide and hydrogen peroxide, which are strong oxidizing agents.   Reduction of Oxygen to Water   - The conversion of O2 to water occurs stepwise, resulting in the formation of intermediate ROS, which are potentially harmful.   Defence against Reactive Oxygen Species   - Antioxidant defence system includes:   - Enzymes such as superoxide dismutase and catalase.   - Non Enzymes such as antioxidants like vitamin C and vitamin E.   Chapter 6 - Photosynthesis   Chlorophylls and Carotenoids   - Chlorophylls are the major photosynthetic pigments in plants, green algae, and cyanobacteria.   - Chlorophyll b and carotenoids are accessory pigments that donate excitation energy to chlorophyll a via inductive resonance.   - Light absorbed by carotenoids and chlorophylls drives photosynthesis.   - Absorption spectrum: The amount of light absorbed by a pigment at different wavelengths.   - Action spectrum: Graph showing the effectiveness of each wavelength in driving photosynthesis.   Engelmann's Experiment (1883)   - Theodor Engelmann used a glass prism to project a spectrum of light onto algae with aerobic bacteria.   - Bacteria clustered where algae produced the most oxygen, in areas of blue, violet, and red light.   - Resulted in an action spectrum for photosynthesis.   Two Stages of Photosynthesis   - Light reactions: Capture light energy to synthesize ATP and NADPH.   - Calvin cycle: Uses NADPH and ATP to fix CO2 into carbohydrates.   Major Components of a Photosystem   - Antenna complex: Absorbs light using chlorophyll a, chlorophyll b, and carotenoids; transfers energy to the reaction center via inductive resonance.   - Reaction center: Contains specialized chlorophyll a molecules (P680 in PSII and P700 in PSI).   - Primary electron acceptor: Pheophytin in PSII.   Photosystems I and II   - Photosystems consist of pigments and proteins involved in photoreduction.   - Photosystem II (PSII):   - P680 chlorophyll molecules absorb light and become excited (P680\*).   - P680 is oxidized to P680+ by the primary electron acceptor (Pheophytin).   - Pheophytin transfers electrons to plastoquinone (PQ), which shuttles them to the cytochrome complex.   - P680+ regains an electron from water oxidation in the water-splitting complex, releasing O2 and H+.   - Photosystem I (PSI):   - P700 chlorophyll molecules absorb light and are involved in reducing NADP+ to NADPH.   Photosynthetic Electron Transport Chain   - Links PSII and PSI, enabling electron flow from water to NADP+.   - Provides the energy needed to extract electrons from water and reduce NADP+ to NADPH. - When photons of light hit an object, they can be: reflected, transmitted, or absorbed.   - For light to be used as energy, it must be absorbed. The energy of the photon is transferred to an electron in a molecule.   - Energy transfer moves the electron from its grounded state to an excited state.   Pigments Absorb Photons   - Pigments are molecules that absorb photons of specific wavelengths.   - Key feature for light absorption: a conjugated system of carbon atoms covalently bonded with alternating single and double bonds.   - Differences in the arrangement of conjugated systems and chemical structures determine the wavelengths absorbed by each pigment.   - A pigment's color results from the wavelengths of light it does not absorb.   Pigments   - Pigments are highly efficient at absorbing visible light due to their structure and excitable electrons.   - Example: Chlorophyll is a photosynthetic pigment.   Electromagnetic Spectrum   - High energy to low energy: Gamma rays → X-rays → UV → Visible light → Infrared → Microwaves → Radio waves.   - Visible light spectrum ranges from 400 nm (violet) to 700 nm (red).   Fates of an Excited-State Electron   - The electron returns to its ground state, releasing energy as heat or light of a longer wavelength (fluorescence).   - Energy from the excited electron in one pigment molecule is transferred to a neighboring pigment via inductive resonance.   - The excited-state electron is transferred to a nearby electron-accepting molecule (photoreduction).   All three processes occur following light absorption by photosynthetic pigments.   - Photosynthesis uses light energy to convert carbon from CO2 gas into organic molecules.   - Oxygen is released as a by-product from the oxidation of water (H2O) during the process.   - Photosynthesis provides the source of all food we consume, either directly or indirectly.   Overall Reaction   - CO2 + H2O → O2 + Organic molecules   - Metabolic Classification of Organisms   - Autotrophs: Produce organic molecules from inorganic sources (e.g., CO2, water).   - Photoautotrophs: Use light energy for photosynthesis (e.g., cyanobacteria, vascular plants).   - Chemoautotrophs: Use energy from chemical compounds.   - Heterotrophs: Depend on organic molecules from other organisms for energy.   - Examples: Animals, most bacteria.   Photoautotrophs: Primary Producers of Earth   - Convert sunlight into chemical energy.   - Use energy to assemble complex organic molecules from inorganic materials.   - Organic molecules provide energy for themselves and other organisms.   Two Stages of Photosynthesis   Light Reactions   - Light energy absorbed by pigments is converted into ATP and NADPH.   - Oxygen is released as a by-product of water oxidation.   - Calvin Cycle   - ATP and NADPH from light reactions provide energy and reducing power.   - Fixes carbon from CO2 to synthesize carbohydrates.   - Photosynthesis as a Redox Reaction   - Synthesis of carbohydrates from CO2 requires energy from sunlight.   - Reduction occurs when a molecule gains electrons and energy.   - Oxidation occurs when a molecule loses electrons and releases energy.   Location of Photosynthesis   - In eukaryotes (e.g., higher plants, algae), photosynthesis occurs in chloroplasts.