Monica Biology Honors Fall Final Exam Review 2024 PDF

Biology Honors Fall Final Exam Review Criteria 2024 Module 7: Cellular Structure and Function ​ Lesson 1: Cell Discovery and Theory ​ Lesson 2: The Plasma Membrane ​ Lesson 3: Cellular Transport ​ Lesson 4: Structures and Organelles ​ Nature of Science: Mitochondria: More...

Biology Honors Fall Final Exam Review Criteria 2024 Module 7: Cellular Structure and Function ​ Lesson 1: Cell Discovery and Theory ​ Lesson 2: The Plasma Membrane ​ Lesson 3: Cellular Transport ​ Lesson 4: Structures and Organelles ​ Nature of Science: Mitochondria: More Than Just a Powerhouse Module 8: Cellular Energy ​ Lesson 1: How Organisms Obtain Energy ​ Lesson 2: Photosynthesis ​ Lesson 3: Cellular Respiration ​ Scientific Breakthroughs: Faster Photosynthesis: The New Frontier of Food Module 9: Cellular Reproduction and Sexual Reproduction ​ Lesson 1: Cellular Reproduction ​ Lesson 2: Meiosis and Sexual Reproduction ​ Scientific Breakthroughs: Cancer and Aging Research Enters New TERRA-tory Discovery of Cells Early Observations and Inventions ​ Microscope Invention: ​ Robert Hooke (1665): ​ Contribution: Developed a simple microscope and observed cork from oak bark. ​ Discovery: Identified small, box-like structures he named "cellulae" (Latin for "small rooms"), later shortened to "cells." ​ Significance: First recorded use of the term "cell," marking the inception of cell biology. ​ Hypothetical Observation of Living Cells: If Hooke had observed living cells, he would have seen dynamic structures including cytoplasm, membranes, vacuoles, and nuclei, highlighting the complexity of living cells compared to the dead, empty cells of cork.  ​ Anton van Leeuwenhoek (Late 1600s): ​ Contribution: Improved microscope design inspired by Hooke. ​ Discovery: Identified "animalcules" (protozoa) in pond water, milk, and other substances. ​ Significance: Revealed the existence of microscopic living organisms, expanding the understanding of life's diversity. Credit for developing cell theory is usually given to two scientists: Theodor Schwann and Matthias Jakob Schleiden. While Rudolf Virchow contributed to the theory, he is not as credited for his attributions toward it. Microscope Technology Timeline of Key Developments ​ 1590: Hans and Zacharias Janssen invent the first compound microscope using two lenses in a tube for magnification. ​ 1665: Robert Hooke publishes Micrographia, documenting cell structures in cork. ​ 1683: Anton van Leeuwenhoek discovers single-celled protozoans. ​ 1830–1855: ​ 1833: Discovery of the cell nucleus. ​ 1839: Proposal that all organisms are made of cells. ​ 1939: Ernest Everett Just publishes Biology of the Cell Surface, enhancing understanding of cell structure. ​ 1981: Development of the Scanning Tunneling Microscope (STM) allows imaging at the atomic level. ​ 2008: Introduction of 3D Structured Illumination Microscopy (3D SIM) enables high-resolution, multi-color 3D cell imaging. Types of Microscopes ​ Optical Microscopes: ​ Compound Light Microscope: ​ Function: Uses visible light and multiple lenses to magnify objects up to ~1,000×. ​ Limitations: Resolution limited by light wavelength, causing blurring beyond 1,000× magnification; often requires staining for enhanced visibility. ​ Non-Optical Microscopes: ​ Transmission Electron Microscope (TEM): ​ Function: Uses electron beams and magnets to image thin, dead, and stained specimens in shaded, black-and-white images. ​ Advantages: Magnifies up to 500,000×.  ​ Disadvantages: Requires specimens to be dead, thin, and stained with heavy metals. ​ Scanning Electron Microscope (SEM): ​ Function: Scans specimen surfaces with electrons to produce three-dimensional images. ​ Disadvantages: Suitable only for non-living specimens. ​ Scanning Tunneling Microscope (STM): ​ Function: Utilizes a charged probe to create atomic-level 3D images, capable of imaging live specimens. ​ Advantages: Provides detailed surface topology at the atomic scale. Cell Theory Contributors and Fundamental Principles ​ Matthias Schleiden (1838): ​ Contribution: Concluded that all plants are composed of cells. ​ Theodor Schwann (1839): ​ Contribution: Reported that animal tissues are also composed of cells. ​ Rudolph Virchow (1855): ​ Contribution: Proposed that all cells arise from pre-existing cells. ​ Fundamental Principles of Cell Theory: ​ All living organisms are composed of one or more cells. ​ Cells are the basic units of structure and function in organisms. ​ All cells arise from pre-existing cells, with genetic material passed on to daughter cells. Basic Cell Types Endosymbiotic Theory ​ Explains the origin of mitochondria and chloroplasts as once free-living prokaryotes engulfed by ancestral eukaryotic cells. ​ Evidence: ○​ Both have double membranes, their own DNA, and reproduce independently. ○​ Similarity of their DNA to bacterial DNA supports this theory. Prokaryotic Cells ​ Characteristics: ​ Simpler structure with no nucleus. ​ Lack membrane-bound organelles. ​ Examples: Bacteria and archaea. ​ Significance: Resemble the earliest life forms on Earth. Eukaryotic Cells ​ Characteristics: ​ Complex structure with a nucleus containing DNA. ​ Possess multiple membrane-bound organelles (e.g., mitochondria, endoplasmic reticulum, Golgi apparatus). ​ Examples: Plants, animals, fungi, and some unicellular organisms like yeast. ​ Size: Typically 1-100 times larger than prokaryotic cells with higher internal complexity. Structure and Function of the Plasma Membrane Phospholipid Bilayer ​ Composition: ​ Two layers of phospholipids with hydrophilic (water-attracting) heads facing outward and hydrophobic (water-repelling) tails shielded from water. ​ Function: Forms a selective barrier separating the cell's internal environment from the external environment. Other Components ​ Cholesterol: ​ Role: Maintains membrane fluidity by preventing fatty acid tails from sticking together. ​ Proteins: ​ Functions: Act as receptors for signal transmission, form channels or transport proteins allowing substance passage, or anchor the membrane to internal structures. ​ Carbohydrates: ​ Role: Attached to proteins or lipids, aiding in cell recognition and communication. Selective Permeability ​ Definition: Controls the entry and exit of substances, maintaining homeostasis. ​ Mechanisms: ​ Diffusion: Movement of particles from high to low concentration. ​ ​ ​ Osmosis: Diffusion of water.  ​ ​ Aquaporins: Channel proteins that facilitate free water movement through the membrane. Transport Mechanisms Passive Transport ​ Characteristics: No energy required; substances move down their concentration gradient. ​ Types: ​ Simple Diffusion: Direct movement of molecules across the membrane. ​ Facilitated Diffusion: Movement via carrier proteins or channels. ​ Osmosis: Water movement through aquaporins. Active Transport  ​ Characteristics: Requires energy (usually ATP) to move substances against their concentration gradient. ​ Example: ​ Na⁺/K⁺ ATPase Pump: Maintains ion concentrations by moving sodium out of and potassium into the cell. ​ A coupled channel in biology is when the movement of one substance is linked to the movement of another across a membrane.  ​ Endocytosis and Exocytosis ​ Endocytosis:  ​ Function: Engulfing large particles or liquids by wrapping the plasma membrane around them to form vesicles. ​ Exocytosis: ​ Function: Expelling substances from the cell by vesicles fusing with the plasma membrane. Cells in Different Solutions Isotonic Solution ​ Definition: Equal solute concentrations inside and outside the cell. ​ Effect: Water moves in and out at the same rate; the cell retains its shape. Hypotonic Solution  ​ Definition: Fewer solutes outside the cell than inside. ​ Effect: ​ Animal Cells: Water enters the cell, causing it to swell or potentially burst. ​ Plant Cells: Water enters, making the cell firm due to turgor pressure; the cell wall prevents bursting. Hypertonic Solution  ​ Definition: More solutes outside the cell than inside. ​ Effect: ​ Animal Cells: Water leaves the cell, causing it to shrink. ​ Plant Cells: Water exits, causing the plasma membrane to pull away from the cell wall, leading to wilting. Cell Structures and Organelles Organelles All Cells Must Have ​ Plasma membrane: Controls entry and exit of substances. ​ Cytoplasm: Jelly-like substance containing cell components. ​ Ribosomes: Protein synthesis. ​ DNA/RNA: Genetic material for cell functions. Plastids ​ Plastids are organelles in plant cells, responsible for: ○​ Chloroplasts: Photosynthesis. ○​ Leucoplasts: Storage of starch, lipids, or proteins. ○​ Chromoplasts: Pigment storage for coloration. Introduction Organelles within both prokaryotic and eukaryotic cells work synergistically to perform essential functions, analogous to departments in a factory. These membrane-bound structures ensure cellular health, functionality, and survival. Key Organelles and Structures ​ Cytoskeleton: ​ ​ Microtubules: ​ Structure: Long, hollow cylinders of protein. ​ Functions: Provide structural support, facilitate substance movement within the cell, and form the spindle apparatus during cell division. ​ Microfilaments: ​ Structure: Thin protein threads. ​ Functions: Maintain cell shape, enable movement (e.g., muscle contraction, cytoplasmic streaming). ​ Dynamic Nature: Both microtubules and microfilaments rapidly assemble and disassemble, allowing the cell to change shape, divide, and reorganize organelles. ​ Centrioles and Cilia/Flagella: ​ Centrioles: ​ ​ Structure: Cylindrical structures composed of microtubules, typically in pairs. ​ Function: Organize spindle fibers during mitosis; present in animal cells and some protists but absent in most plant cells. ​ Cilia and Flagella: ​ ​ Cilia: ​ Structure: Short and numerous plasma membrane extensions. ​ Function: Aid in locomotion and moving substances along cell surfaces. ​ Flagella: ​ Structure: Longer and fewer in number compared to cilia. ​ Function: Facilitate cell movement. ​ Composition: Microtubules arranged in a 9+2 configuration (nine pairs surrounding two single microtubules).  ​ ​ Cell Wall: Peptidoglycan ​ A polymer of sugars and amino acids found in the cell walls of bacteria. ​ Provides structural support and prevents the cell from bursting in hypotonic environments. ​ ​ Plant Cells: ​ Composition: Thick, rigid layer made of cellulose. ​ Functions: Provides structural support, protection, and maintains cell shape. ​ Prokaryotic Cells (e.g., Bacteria): ​ Composition: Peptidoglycan-based wall. ​ Functions: Maintains cell shape, protection. ​ Animal Cells: ​ Note: Lack cell walls; rely on the plasma membrane for structural support and communication. ​ Nucleus: ​ ​ Function: Control center containing genetic material (DNA) that directs all cellular activities, including growth, protein production, and division. ​ Structure: Surrounded by a double membrane called the nuclear envelope with nuclear pores for substance exchange. ​ Substructures: ​ Nucleolus: Site of ribosome production. ​ Mitochondria: ​ ​ ​ Function: Convert chemical energy from food into ATP through cellular respiration. ​ Structure: Outer membrane and highly folded inner membrane (cristae) increasing surface area for energy reactions. ​ Chloroplasts: ​ ​ ​ Presence: Found in plant cells and some protists. ​ Function: Perform photosynthesis, converting light energy into chemical energy stored in sugars. ​ Structure: Contain thylakoids with chlorophyll for light absorption; surrounded by stroma where Calvin cycle occurs. ​ Ribosomes: ​  ​ Function: Sites of protein synthesis. ​ Composition: Composed of RNA and proteins. ​ Locations: Freely floating in the cytoplasm or attached to the rough endoplasmic reticulum (ER). ​ Functions Based on Location: ​ Free Ribosomes: Produce proteins functioning within the cytoplasm. ​ Bound Ribosomes: Produce proteins destined for secretion or incorporation into membranes. ​ Endoplasmic Reticulum (ER): ​ Rough ER: ​ ​ Structure: Surface-bound ribosomes. ​ Function: Synthesizes proteins. ​ Smooth ER: ​ ​ Structure: Lacks ribosomes.  ​ Function: Involved in lipid synthesis and detoxification of harmful substances, especially in liver cells. ​ Golgi Apparatus: ​ ​ Function: Modifies, sorts, and packages proteins synthesized in the rough ER. ​ Processes: ​ Glycosylation: Adding sugar groups to proteins. ​ Vesicle Formation: Packages proteins into vesicles for transport to target destinations within or outside the cell. ​ Vacuoles and Lysosomes: ​ Vacuoles: ​ ​ Plant Cells: Large central vacuole maintaining cell shape and storing nutrients. ​ Animal Cells: Smaller, temporary storage vesicles. ​ Lysosomes:  ​ Function: Contain enzymes for digesting excess or worn-out organelles, food particles, and pathogens. ​ Role: Aid in cellular cleaning and recycling, preventing waste buildup. ​ ​ Contain digestive enzymes to break down macromolecules and damaged organelles. ​ Known as "suicide sacs": Can self-destruct a damaged cell through autolysis. Autolysis ​ Autolysis is the process by which a cell self-destructs through the breakdown of its own components. ​ It occurs when lysosomes release their digestive enzymes into the cytoplasm. ​ Functions and significance: ○​ Removes damaged or dying cells. ○​ Plays a role in tissue remodeling during development. ○​ Can occur under pathological conditions, such as in response to injury or disease. Cellular Processes and the Role of Organelles Protein Synthesis and Transport ​ Concept Map: ○​ Nucleus: DNA → mRNA → ○​ Ribosome: mRNA is translated into a protein → ○​ Rough ER: Modifies and folds proteins → ○​ Golgi Apparatus: Processes and packages proteins → ○​ Vesicles: Transport proteins to destinations →  ○​ Plasma Membrane: Proteins are secreted or integrated into the membrane. Energy Production ​ Mitochondria: ​ Process: Cellular respiration converts glucose into ATP. ​ Stages: Glycolysis, Krebs cycle, Electron Transport Chain (ETC). ​ Chloroplasts (Plant Cells): ​ Process: Photosynthesis captures light energy and converts it into chemical energy stored in sugars. ​ Stages: Light-dependent reactions and the Calvin cycle. Cellular Transport and Communication ​ Plasma Membrane: ​ Function: Regulates substance movement, maintaining homeostasis. ​ Endoplasmic Reticulum and Golgi Apparatus: ​ Functions: Synthesize and transport proteins and lipids throughout the cell. Waste Management ​ Lysosomes: ​ Function: Degrade and recycle cellular debris and foreign materials, maintaining cellular cleanliness. Nature of Science Mitochondria Beyond Energy Production ​ Additional Roles: ​ Aging and Disease: Involved in processes linked to aging, autism, and various diseases. ​ Red Blood Cell Formation: Aid in the development of red blood cells. ​ Gene Expression: Influence the expression of genes within the cell. ​ Ongoing Research: ​ Focus: Exploring mitochondria's multifaceted roles to develop better treatments for diseases and understanding cellular longevity. Cellular Energy Reduced and Oxidized ​ Reduced: Gains electrons (e.g., NAD⁺ → NADH). ​ Oxidized: Loses electrons (e.g., NADH → NAD⁺).  ​ These reactions are critical in cellular respiration to transfer energy. Transformation of Energy ​ Cellular Activities: Including macromolecule assembly, transport, and genetic transmission, all require energy. ​ Thermodynamics: Study of energy flow and transformation in biological systems. Laws of Thermodynamics ​ First Law (Law of Conservation of Energy): ​ Statement: Energy cannot be created or destroyed; it can only be transformed from one form to another. ​ Example: Energy stored in food converts to chemical energy and then to mechanical energy during activities like running. ​ Second Law: ​ Statement: Energy conversions result in the loss of usable energy, typically as heat, increasing entropy (disorder). ​ Example: In food chains, usable energy decreases at each trophic level due to energy loss as heat. Autotrophs and Heterotrophs ​ Autotrophs: ​ Function: Create their own food. ​ Types: ​ Chemoautotrophs: Utilize inorganic substances (e.g., hydrogen sulfide) as energy sources. ​ Photoautotrophs: Convert sunlight into chemical energy through photosynthesis. ​ Heterotrophs: ​ Function: Consume other organisms for energy. Scientific Discoveries in Cellular Energy  ​ 1772: Joseph Priestley discovers that plants take in carbon dioxide and emit oxygen. ​ 1844: Hugo von Mohl identifies chloroplasts in plant cells. ​ 1881-1882: Chloroplasts confirmed as sites of photosynthesis. ​ 1937: Hans Krebs discovers the citric acid cycle (Krebs cycle). ​ 1948: Eugene Kennedy and Albert Lehninger link mitochondria to cellular respiration. ​ 1981: Melvin Calvin and colleagues discover the Calvin cycle (light-independent reactions). ​ 2008: Jaime Miquel links mitochondrial breakdown to aging. ​ 2009: Mitochondrial defects connected to diseases like Parkinson’s and Alzheimer’s. Metabolism ​ Definition: All chemical reactions in a cell involving the flow of matter and energy. ​ Pathways: ​ Catabolic Pathways: Break down large molecules, releasing energy (e.g., cellular respiration). ​ Anabolic Pathways: Use energy to build larger molecules (e.g., photosynthesis). ​ Energy Flow Cycle: ​ Photosynthesis: Anabolic process converting sunlight, CO₂, and H₂O into glucose and O₂. ​ Cellular Respiration: Catabolic process converting glucose and O₂ into ATP, CO₂, and H₂O. ATP: The Unit of Cellular Energy ​ Structure: Comprises an adenine base, a ribose sugar, and three phosphate groups. ​ Function: ​ Energy Release: Breaking the bond between the second and third phosphate groups forms ADP (adenosine diphosphate) and a free phosphate group. ​ Energy Storage: ADP gains a phosphate to revert to ATP, storing energy.  ​ Further Conversion: ADP may lose another phosphate to become AMP (adenosine monophosphate), releasing less energy. Key Takeaways: ​ Energy transformations adhere to the laws of thermodynamics. ​ Autotrophs generate energy; heterotrophs consume it. ​ Metabolism consists of energy-releasing catabolic and energy-utilizing anabolic pathways. ​ ATP cycles between ATP, ADP, and AMP, serving as the primary energy carrier. Photosynthesis Core Concept ​ Function: Converts solar energy into chemical energy stored in glucose, adhering to the first law of thermodynamics (energy transformation without creation or destruction). General Reaction 6CO2+6H2O→(light)C6H12O6+6O2 ​ (This represents the conversion of carbon dioxide and water into glucose and oxygen using light energy.) Phases of Photosynthesis ​ Light-Dependent Reactions: ​ Location: Thylakoid membranes within chloroplasts. ​ Process: ​ Light is absorbed by pigments (chlorophyll and carotenoids). ​ ​ Water molecules split into electrons, protons (H⁺), and oxygen (byproduct). ​ Energy is captured in ATP and NADPH. ​ Electron Transport:  ​ ​ Photosystem II: Excites electrons using light energy. ​ Electron Flow: Electrons move through carriers to Photosystem I via ferredoxin. ​ Energy Capture: H⁺ ions flow through ATP synthase, generating ATP via chemiosmosis. ​ NADPH Formation: Ferredoxin transfers electrons to NADP⁺, forming NADPH. ​ Light-Independent Reactions (Calvin Cycle): ​ ​ Location: Stroma of chloroplasts.  ​ ​ Process: ​ Carbon Fixation: CO₂ combines with RuBP (ribulose bisphosphate) to form 3-PGA (3-phosphoglycerate). ​ Energy Transfer: ATP and NADPH convert 3-PGA into G3P (glyceraldehyde-3-phosphate). ​ Glucose Formation: Two G3P molecules combine to form glucose. ​ Regeneration: Remaining G3P regenerates RuBP with the help of the enzyme rubisco. Alternative Photosynthetic Pathways ​ C4 Pathway: ​ Adaptation: Minimizes water loss in hot climates (e.g., sugarcane, corn). ​ Mechanism: CO₂ is initially fixed into 4-carbon compounds in specialized cells, allowing stomata to remain closed during the day, conserving water while still facilitating photosynthesis. ​ CAM Pathway: ​ Adaptation: Reduces water loss in desert plants (e.g., cacti, orchids). ​ Mechanism: CO₂ is absorbed at night, stored as organic compounds, and released during the day for the Calvin cycle, allowing stomata to remain closed during daylight hours to minimize water evaporation. Key Takeaways: ​ Chloroplast pigments convert light into chemical energy. ​ Photosynthesis involves two main phases: ​ Light-Dependent Reactions: Produce ATP and NADPH using light energy. ​ Calvin Cycle: Synthesizes carbohydrates using ATP and NADPH. ​ Adaptive Pathways (C4 and CAM): Enhance photosynthesis efficiency in extreme environments by minimizing water loss. Cellular Respiration Enzymes in Cellular Respiration ​ Enzymes regulate and catalyze each step of cellular respiration. ○​ Hexokinase: Phosphorylates glucose in glycolysis. ○​ Isocitrate dehydrogenase: Catalyzes a key step in the Krebs cycle. ​ Enzymes enhance efficiency and ensure specificity in biochemical pathways. Overview ​ Function: Converts bonds in food molecules (e.g., glucose) and oxygen into ATP, powering cellular activities like muscle contraction while releasing CO₂ and H₂O as byproducts. ​ Energy Utilization: Some energy is also released as heat to maintain body temperature despite energy loss to the environment. Cellular Respiration Equation C6H12O6+6O2→6CO2+6H2O+Energy (ATP) ​ Stages of Cellular Respiration ​ Glycolysis (Anaerobic, Cytoplasm): ​ ​ Process: Glucose is broken down into two 3-carbon pyruvate molecules. ​ Energy Transactions: ​ Input: 2 ATP consumed to phosphorylate glucose. ​ Output: 4 ATP and 2 NADH produced. ​ Net Gain: 2 ATP and 2 NADH. ​ Steps: ​ Phosphorylation: Two phosphate groups from ATP attach to glucose, forming a 6-carbon phosphorylated compound. ​ Splitting: The 6-carbon compound splits into two 3-carbon molecules. ​ Energy Harvesting: Additional phosphates are added, and electrons and H⁺ combine with NAD⁺ to form NADH. ​ Pyruvate Formation: The 3-carbon compounds are converted into pyruvate, producing 4 ATP. ​ Krebs Cycle (Citric Acid Cycle) (Aerobic, Mitochondrial Matrix): ​ ​ Preparatory Reaction: ​ Conversion: Pyruvate reacts with coenzyme A (CoA), producing acetyl-CoA and releasing CO₂. ​ NAD⁺ Reduction: NAD⁺ is reduced to NADH. ​ Cycle Steps: ​ Acetyl-CoA combines with oxaloacetate to form citric acid (6-carbon molecule). ​ Decarboxylation: Citric acid undergoes transformations, releasing 2 CO₂, producing 1 ATP, 3 NADH, and 1 FADH₂ per cycle. ​ Regeneration: Oxaloacetate is regenerated to continue the cycle. ​ Net Yield per Glucose Molecule (2 Turns): ​ 6 CO₂ ​ 2 ATP ​ 8 NADH ​ 2 FADH₂ ​ Electron Transport Chain (ETC) (Aerobic, Inner Mitochondrial Membrane):  ​ ​ Process: ​ Electron Donation: NADH and FADH₂ donate electrons to the ETC. ​ Proton Pumping: Electrons pass through ETC proteins, pumping H⁺ ions into the intermembrane space, creating a proton gradient. ​ Chemiosmosis: H⁺ ions flow back into the mitochondrial matrix through ATP synthase, generating ATP. ​ Final Electron Acceptor: Oxygen accepts electrons and combines with H⁺ to form water. Effect of Oxygen Deprivation ​ Without oxygen: ○​ The electron transport chain (ETC) halts because oxygen is the final electron acceptor. ○​ ATP production shifts to glycolysis, resulting in less ATP. ○​ Animals: Pyruvate is converted into lactic acid, causing muscle fatigue. ​ ATP Yield: ​ Eukaryotes: 3 ATP per NADH and 2 ATP per FADH₂, totaling 32 ATP. ​ Prokaryotes: 34 ATP due to the absence of mitochondrial transport requirements. Anaerobic Respiration (Fermentation)  ​ Function: Regenerates NAD⁺ to sustain glycolysis when oxygen is unavailable. ​ Types: ​ Lactic Acid Fermentation (e.g., in muscles during strenuous exercise): ​ Process: Pyruvate is converted into lactic acid. ​ Outcome: NADH is oxidized back to NAD⁺. ​ Net Yield: 2 ATP. ​ Effect: Lactic acid buildup causes muscle fatigue and soreness. ​ Alcohol Fermentation (e.g., in yeast): ​ Process: Pyruvate is converted into ethanol and CO₂. ​ Outcome: NADH is oxidized back to NAD⁺. ​ Net Yield: 2 ATP. ​ Photosynthesis vs. Cellular Respiration Phosphorylation 1.​ Substrate-level phosphorylation: ○​ ATP is directly generated by transferring a phosphate group from a substrate to ADP. ○​ Occurs during glycolysis and the Krebs cycle. 2.​ Oxidative phosphorylation:  ○​ ATP is synthesized via the electron transport chain (ETC) and chemiosmosis. ○​ Energy from electron carriers (NADH, FADH₂) drives ATP production using ATP synthase. ​ Photosynthesis: ​ Function: Converts light energy into glucose and oxygen. ​ Equation: ​ 6CO2+6H2O→(light)C6H12O6+6O2 ​ ​ Cellular Respiration: ​ Function: Converts glucose and oxygen into ATP, CO₂, and H₂O. ​ Equation: ​ C6H12O6+6O2→6CO2+6H2O+ATP ​ Interdependence: ​ Photosynthesis: Provides O₂ and glucose as reactants for cellular respiration. ​ Cellular Respiration: Produces CO₂ and H₂O as reactants for photosynthesis. Summary of Cellular Respiration ​ Processes: ​ Glycolysis: 2 ATP.  ​ Krebs Cycle: 2 ATP. ​ ETC: 32 ATP (Eukaryotes) or 34 ATP (Prokaryotes). ​ Total ATP: 36 ATP per glucose molecule in eukaryotes. ​ Anaerobic Conditions: Rely on fermentation, yielding a minimal ATP amount. Scientific Breakthroughs ​ Genetic Engineering: ​ Achievement: Enhanced photosynthesis efficiency by disabling protective mechanisms when light decreases. ​ Result: Plants grew 20% larger. ​ Implication: Potential to boost crop yields, supporting sustainable food supply. Cellular Reproduction and Sexual Reproduction Cell Size Limitations ​ Reason for Small Size: ​ Surface Area-to-Volume Ratio: Critical for efficient material exchange (nutrients, oxygen, waste). ​ Mathematical Illustration:  ​ ​ Ratio: 3:1 SA:V ​ Implication: As cells grow, the SA:V ratio decreases, reducing exchange efficiency. ​ Biological Challenges for Large Cells: ​ Transport: ​ Issue: Diffusion is too slow over large distances. ​ Solution Constraints: Motor proteins cannot efficiently move materials throughout large cells. ​ Communication: ​ Issue: Difficulty in signal transmission affects gene expression and protein synthesis. Chromosomes and the Cell Cycle ​ Chromosomes: ​ Prokaryotes: ​ ​ Structure: Single, circular DNA molecule located in the cytoplasm (nucleoid region).  ​ Characteristics: Lack histones; no organized chromosomes. ​ Eukaryotes: ​ ​ Structure: Linear DNA organized into chromosomes. ​ Characteristics: DNA is coiled around histone proteins, forming nucleosomes; chromatin condenses into visible chromosomes during cell division. ​ Cell Cycle Overview: ​ ​ ​ Interphase: ​ G1 Phase (Gap 1): Cell grows, performs normal functions, synthesizes proteins, and organelles. ​ S Phase (Synthesis): DNA replication; each chromosome duplicates into sister chromatids connected at the centromere. ​ G2 Phase (Gap 2): Final preparations for mitosis, DNA error checking, synthesis of materials required for cell division. ​ Mitosis (Nuclear Division): ​ ​ Prophase: Chromosomes condense, spindle fibers form, and the nuclear envelope begins to dissolve. ​ Metaphase: Chromosomes align at the cell's equatorial plate, attached to spindle fibers. ​ Anaphase: Sister chromatids separate and move to opposite poles of the cell. ​ Telophase: Chromatids reach the poles, nuclear envelopes reform, and chromosomes decondense. ​ Cytokinesis (Cytoplasmic Division): ​ Animal Cells: Formation of a cleavage furrow that pinches the membrane into two distinct cells. ​ ​ Plant Cells: Formation of a cell plate that develops into a new cell wall, dividing the cell into two.  ​ ​ Regulation of the Cell Cycle: ​ Regulatory Proteins: ​ ​ Cyclins and Cyclin-Dependent Kinases (CDKs): ​ Function: Cyclins (proteins) bind to CDKs (enzymes), activating them to control progression through different cell cycle stages. ​ Mechanism: Different cyclin-CDK complexes are active at each stage, ensuring timely progression.  ​ ​ Checkpoints: ​ ​ G1 Checkpoint: Verifies cell size and DNA integrity before DNA replication. ​ G2 Checkpoint: Ensures complete and accurate DNA replication before mitosis. ​ Spindle Checkpoint (Metaphase Checkpoint): Confirms proper attachment of chromosomes to spindle fibers, ensuring correct chromosome separation. ​ Abnormalities in the Cell Cycle: ​ Apoptosis (Programmed Cell Death):  ​ ​ Function: Controlled self-destruction of cells. ​ Purpose: Removes damaged or unnecessary cells (e.g., during embryonic development to remove webbing between fingers). ​ Cancer: ​ Cause: Uncontrolled cell division due to failed regulation mechanisms. ​ Triggers: DNA mutations, often from environmental factors like carcinogens (tobacco, UV radiation, chemicals). ​ Progression: Requires multiple mutations for a cell to become cancerous, leading to tumor formation. ​ ​ Summary of Key Points: ​ Cell Size: Smaller cells maintain a higher surface area-to-volume ratio, enhancing exchange efficiency.  ​ Cell Cycle: Comprises interphase (G1, S, G2), mitosis (prophase, metaphase, anaphase, telophase), and cytokinesis to ensure proper growth, DNA replication, and division. ​ Regulation: Cyclins, CDKs, and checkpoints maintain cell cycle accuracy. ​ Abnormalities: Dysregulation can result in apoptosis or cancer. Meiosis, Sexual Reproduction, and the Molecular Basis of Cancer and Aging Introduction to Meiosis and Genetic Variation ​ Meiosis: ​ Function: A type of cell division producing haploid gametes (sperm and eggs) from diploid cells.  ​ Purpose: Reduces chromosome number by half, ensuring gametes carry a single set of chromosomes for sexual reproduction. ​ Genetic Diversity: Promotes variation through mechanisms like crossing over and independent assortment. Detailed Breakdown of Meiosis ​ Meiosis I: Reduction Division  ​ Prophase I: Subdivided into five stages, introducing genetic variation. ​ Leptotene: Chromatin begins condensation into visible thread-like structures. ​ Zygotene: Homologous chromosomes pair up in synapsis, forming tetrads (bivalents). ​ Pachytene: Crossing over occurs between non-sister chromatids, exchanging genetic material. ​ ​ Diplotene: Homologous chromosomes start to separate but remain connected at chiasmata (sites of crossing over). ​ Diakinesis: Further chromosome condensation, chiasmata move to chromosome ends, and the nuclear membrane begins to disintegrate. ​ Metaphase I: ​ Alignment: Tetrads align randomly at the metaphase plate. ​ Independent Assortment: Random orientation ensures diverse genetic combinations. ​ Anaphase I: ​ Separation: Homologous chromosomes are pulled to opposite poles, halving the chromosome number. ​ Telophase I: ​ Conclusion: Separated chromosomes reach poles, and cytokinesis results in two haploid cells, each with one set of chromosomes. ​ Meiosis II: Equational Division ​ Prophase II: ​ Preparation: Chromosomes condense in both haploid cells; nuclear membranes dissolve. ​ Metaphase II: ​ Alignment: Chromosomes align along the metaphase plate in each haploid cell. ​ Anaphase II: ​ Separation: Sister chromatids are pulled to opposite poles. ​ Telophase II: ​ Completion: Nuclear membranes reform, chromosomes decondense, and cytokinesis results in four non-identical haploid daughter cells, each containing a single set of chromosomes. Homologous Chromosomes Definition:​ Homologous chromosomes are pairs of chromosomes in a diploid organism that have the same structure, length, and gene sequence but may carry different alleles of those genes. Key Features: 1.​ Origin: ○​ One chromosome of each homologous pair is inherited from the mother (maternal) and the other from the father (paternal). 2.​ Similarities: ○​ Same gene loci (locations of genes). ○​ Similar size and shape. ○​ Carry genes for the same traits, but alleles may differ (e.g., one may have the allele for brown eyes, the other for blue eyes). 3.​ Difference from Sister Chromatids:  ○​ Sister chromatids are identical copies formed after DNA replication. ○​ Homologous chromosomes are not identical; they come from different parents. 4.​ Role in Meiosis: ○​ During meiosis I, homologous chromosomes pair up (synapsis) and exchange genetic material (crossing over). ○​ This leads to genetic variation in gametes. Example: In humans: ​ A diploid cell contains 23 pairs of homologous chromosomes (46 total). ​ Autosomes: 22 pairs. ​ Sex chromosomes: 1 pair (XX in females, XY in males). Homologous chromosomes are essential for proper segregation during meiosis and genetic diversity. Sexual Reproduction ​ Fusion of Gametes: ​ Process: Sperm and egg (haploid gametes) fuse to form a diploid zygote. ​ Outcome: Zygote contains a full set of chromosomes, combining genetic material from both parents. ​ Genetic Diversity: ​ Mechanism: Unique genetic combinations arise from the combination of maternal and paternal genes, enhancing population adaptability. Karyotypes ​ Definition: Karyotypes are visual representations of an organism’s chromosomes arranged in decreasing size during metaphase of mitosis. ○​ Chromosomes are stained, highlighting banding patterns to identify homologous chromosomes. ○​ ○​ In humans, karyotypes show 23 pairs of chromosomes, comprising 22 autosomes and one pair of sex chromosomes: ​ Female: Two X chromosomes (XX). ​ Male: One X chromosome and one Y chromosome (XY). Cellular Differentiation and Stem Cells 1.​ Cellular Differentiation: ○​ Process: An unspecialized cell becomes a specialized cell with a specific structure and function. ○​ Importance: Differentiation creates tissues, organs, and organ systems essential for the organism's survival. ○​ Example: Signals during development direct some cells to become skin cells, others to form muscles, etc. 2.​ Stem Cells: ○​ Definition: Cells capable of self-renewal and differentiation into specialized cell types. ○​ Types of Stem Cells: ​ Embryonic Stem Cells: ​ Found in embryos with 100–150 cells. ​ Not specialized and can develop into any cell type. ​ During embryonic development, these cells differentiate to form tissues, organs, and organ systems. ​ Controversy: Ethical concerns due to their source (from embryos). ​ Adult Stem Cells: ​ Found in adult tissues and even in newborns. ​ Can repair and maintain the tissue where they are located. ​ Applications: Used in treatments with less ethical concerns since they can be obtained with donor consent. ​ Example applications: Repairing cardiac tissue post-heart attack, treating diabetes, restoring vision, or reversing paralysis. Nondisjunction  ​ Definition: ○​ An error during cell division where sister chromatids fail to separate properly. ○​ Occurs in meiosis I or meiosis II, leading to gametes with an abnormal number of chromosomes. ○​ Fertilization of such gametes results in offspring with chromosomal abnormalities. ​ Consequences: ○​ Trisomy: Three copies of a chromosome (e.g., Trisomy 21, causing Down syndrome). ○​ Monosomy: Only one copy of a chromosome. ○​ Such abnormalities often lead to serious or fatal disorders. Autosomes ​ Non-sex chromosomes (22 pairs in humans). ​ Carry genes unrelated to sex determination (e.g., height, metabolism). Telomeres  ​ Protective caps at chromosome ends made of DNA and proteins. ​ Prevent genetic loss during cell division. ​ Shorten with aging; linked to cancer via telomerase enzyme. Binary Fission ​ Asexual reproduction in bacteria and some protists. ​ Process: DNA replication → Cell growth → Division into two identical cells. ​ Quick and requires no mate. Scientific Breakthroughs ​ Telomerase and Telomeres: ​ Function: Telomerase repairs telomeres, allowing continuous cell division in stem and cancer cells. ​ Impact: Telomere shortening limits cell lifespan; TERRA molecules regulate telomerase activity. ​ Research Implications: Potential treatments for cancer and aging-related conditions through manipulation of telomere and telomerase mechanisms. ​ Checkpoints and Cancer: ​ Normal Cells: Use checkpoints regulated by cyclins and CDKs to control cell cycle progression. ​ Cancer Cells: Often bypass checkpoints, leading to uncontrolled division and tumor growth. ​ Checkpoint Inhibitors: Therapeutic agents that block cancer cells' ability to bypass regulatory mechanisms, thereby halting their uncontrolled growth.