IB Biology SL: Theme B - Form & Function
B2.2 - Organelles & Compartmentalization
Specialized Structures: The Cellular Division of Labor
🔬 Introduction to Cell Compartmentalization
One of the most fundamental differences between prokaryotic and eukaryotic cells is the presence of membrane-bound organelles in eukaryotic cells. These organelles create distinct compartments within the cell, each specialized for specific functions.
Organelles are discrete, membrane-bound structures within cells that perform specific functions. Think of them as the "organs" of the cell—each has a unique role, but they all work together to keep the cell alive and functioning efficiently.
Compartmentalization is the division of the cell into separate regions (compartments) by membranes. This organization allows eukaryotic cells to carry out complex processes simultaneously without interference, making them far more efficient and sophisticated than prokaryotic cells.
🧩 What are Organelles?
Definition
Organelles are discrete subunits of cells that are adapted to perform specific functions. They are typically surrounded by membranes that separate them from the rest of the cytoplasm.
The term "organelle" means "little organ"—just as organs perform specific functions in the body, organelles perform specific functions within cells.
📝 Important Distinction: What IS and IS NOT an Organelle
✓ ARE Organelles
- Nucleus
- Mitochondria
- Chloroplasts
- Endoplasmic Reticulum (ER)
- Golgi Apparatus
- Lysosomes
- Vacuoles
- Vesicles
- Peroxisomes
- Ribosomes*
*Ribosomes are considered organelles even though they lack membranes
✗ NOT Organelles
- Cell wall
- Cytoskeleton
- Cytoplasm
- Cytosol
- Plasma membrane
- Nucleoplasm
- Chromatin/Chromosomes
These are cellular structures or components, but not discrete, functional subunits
🔑 Key Characteristics of Organelles
1. Discrete Structure
Organelles are distinct, separable units that can be identified and isolated from the rest of the cell
2. Specific Function
Each organelle has a specialized role in cellular metabolism and function
3. Adapted Structure
The structure of each organelle is adapted to its specific function (structure-function relationship)
4. Membrane-Bound (Usually)
Most organelles are surrounded by membranes that create separate compartments (exception: ribosomes)
✨ Advantages of Compartmentalization
Compartmentalization is one of the key features that allows eukaryotic cells to be more complex and efficient than prokaryotic cells. By dividing the cell into specialized compartments, eukaryotes can perform multiple complex processes simultaneously without interference.
Think of it like a well-organized factory: Different departments (organelles) handle different tasks efficiently, rather than having all workers doing everything in one large room.
🎯 Six Main Advantages
1. Concentration of Enzymes and Substrates
Why It Matters:
By confining enzymes and their substrates to specific organelles, cells can increase reaction rates dramatically. Higher concentrations mean more frequent collisions between enzymes and substrates, leading to faster reactions.
🔍 Example:
In mitochondria, enzymes for cellular respiration are concentrated in the matrix and inner membrane. This localization makes ATP production much more efficient than if these enzymes were scattered throughout the cytoplasm.
2. Optimal Conditions for Different Reactions
Why It Matters:
Different biochemical reactions require different conditions (pH, ion concentrations, temperature). Compartmentalization allows each organelle to maintain its own optimal internal environment.
🔍 Example:
Lysosomes maintain a highly acidic pH (~4.5-5.0) perfect for digestive enzymes, while the cytoplasm stays near neutral pH (~7.2). This prevents lysosomal enzymes from digesting the entire cell.
3. Protection from Harmful Substances
Why It Matters:
Some cellular processes produce toxic byproducts or involve dangerous chemicals. Compartmentalization isolates these hazards, protecting the rest of the cell from damage.
🔍 Examples:
- Lysosomes: Contain powerful digestive enzymes that would destroy the cell if released
- Peroxisomes: Safely break down hydrogen peroxide (H2O2), a toxic byproduct of metabolism
- Phagocytic vacuoles: Isolate ingested bacteria and viruses from the cytoplasm
4. Separation of Incompatible Reactions
Why It Matters:
Some metabolic pathways would interfere with or reverse each other if they occurred in the same location. Compartmentalization keeps opposing processes apart.
🔍 Example:
Fatty acid synthesis (anabolic) occurs in the cytoplasm, while fatty acid breakdown (catabolic) occurs in mitochondria. This separation prevents a futile cycle where fatty acids are simultaneously built and broken down.
5. Increased Surface Area for Reactions
Why It Matters:
Internal membranes of organelles dramatically increase the total membrane surface area available for biochemical reactions. Many important enzymes and proteins are embedded in or attached to membranes.
🔍 Examples:
- Mitochondrial cristae: Folded inner membrane provides huge surface area for ATP synthase enzymes
- Chloroplast thylakoids: Stacked membranes maximize light-capturing photosystems
- Rough ER: Extensive membrane network allows massive protein synthesis
6. Simultaneous Processes Without Interference
Why It Matters:
Compartmentalization allows the cell to carry out multiple different processes at the same time without the products or intermediates of one reaction interfering with another.
🔍 Example:
A cell can simultaneously: synthesize proteins (ribosomes/ER), produce ATP (mitochondria), digest materials (lysosomes), transcribe DNA (nucleus), and modify proteins (Golgi)—all without these processes interfering with each other.
🎯 Summary: Compartmentalization = Efficiency
Compartmentalization transforms eukaryotic cells into highly organized, efficient systems where specialized "departments" (organelles) work together harmoniously while maintaining their unique environments and functions.
🔬 Major Organelles: Structure & Function
🧬 Nucleus: The Control Center
Structure
- Nuclear envelope: Double membrane (two phospholipid bilayers) with nuclear pores
- Nuclear pores: Protein-lined channels that control movement of materials in/out
- Nucleoplasm: Gel-like substance inside the nucleus
- Chromatin: DNA wrapped around histone proteins; condenses into chromosomes during division
- Nucleolus: Dense region within nucleus (not membrane-bound); site of ribosome synthesis
Functions
1. Stores Genetic Information
Houses DNA (genes) that contain instructions for making proteins and controlling cell activities
2. Controls Gene Expression
Regulates which genes are transcribed into mRNA (transcription occurs here)
3. Ribosome Assembly
Nucleolus produces ribosomal RNA (rRNA) and assembles ribosomal subunits
4. Protects DNA
Nuclear envelope separates DNA from potentially damaging cytoplasmic enzymes
🔑 Structure-Function Correlation:
The double membrane with pores allows selective transport: mRNA exits to the cytoplasm for translation, while proteins needed for transcription enter. This separation of transcription (nucleus) from translation (cytoplasm) is a key difference from prokaryotes.
⚡ Mitochondria: The Powerhouse
Structure
- Double membrane: Outer membrane (smooth) and inner membrane (highly folded)
- Cristae: Infoldings of inner membrane; increase surface area dramatically
- Matrix: Fluid-filled space inside inner membrane; contains enzymes, ribosomes, and mitochondrial DNA
- Intermembrane space: Gap between outer and inner membranes
- Size: 1-10 μm in length; rod-shaped or spherical
Functions
1. ATP Production (Cellular Respiration)
Primary function: Generate ATP through aerobic respiration (Krebs cycle in matrix, electron transport chain on cristae)
2. Energy Currency Production
Converts energy from glucose, fats, and proteins into ATP (adenosine triphosphate)—the cell's energy currency
3. Metabolic Functions
Site of fatty acid oxidation, amino acid metabolism, and other metabolic pathways
4. Apoptosis Regulation
Plays key role in programmed cell death (releasing cytochrome c to trigger apoptosis)
🔑 Structure-Function Correlation:
The highly folded inner membrane (cristae) provides enormous surface area for ATP synthase enzymes and electron transport chain proteins. This maximizes ATP production.
⚡ Cells with high energy needs (muscle cells, liver cells, sperm) have MORE mitochondria—sometimes thousands per cell!
🧬 Special Feature: Semi-Autonomous Organelle
Mitochondria contain their own DNA and ribosomes (70S, like bacteria). They can replicate independently of the cell. This supports the endosymbiotic theory—mitochondria were once free-living bacteria that were engulfed by ancestral eukaryotic cells.
🌿 Chloroplasts: Solar Energy Converters (Plant Cells Only)
Structure
- Double membrane: Outer and inner membranes (similar to mitochondria)
- Stroma: Fluid-filled space inside chloroplast; contains enzymes, DNA, ribosomes
- Thylakoids: Flattened membrane sacs containing chlorophyll and photosystems
- Grana (plural) / Granum (singular): Stacks of thylakoids
- Thylakoid space/lumen: Interior space within thylakoid membranes
- Size: 5-10 μm in diameter; disc or lens-shaped
Functions
1. Photosynthesis
Primary function: Convert light energy into chemical energy (glucose) through photosynthesis
2. Light-Dependent Reactions (Thylakoids)
Capture light energy and convert it to ATP and NADPH; produce oxygen as byproduct
3. Light-Independent Reactions / Calvin Cycle (Stroma)
Use ATP and NADPH to fix CO2 and produce glucose (sugar synthesis)
4. Energy Foundation for Ecosystem
Provide organic molecules and oxygen for nearly all life on Earth
🔑 Structure-Function Correlation:
Stacked thylakoids (grana) maximize surface area for light absorption. Chlorophyll and photosystems are embedded in thylakoid membranes to capture maximum light energy. The separation of light reactions (thylakoids) from the Calvin cycle (stroma) allows efficient compartmentalization of the two stages of photosynthesis.
🧬 Like Mitochondria: Semi-Autonomous
Chloroplasts also have their own DNA and ribosomes (70S), and replicate independently. This also supports the endosymbiotic theory—chloroplasts evolved from photosynthetic cyanobacteria.
🏭 Endoplasmic Reticulum (ER): The Manufacturing Network
The ER is an extensive network of interconnected membranes forming flattened sacs (cisternae) and tubes. There are two types:
1. Rough Endoplasmic Reticulum (RER)
Structure:
- Studded with ribosomes on the cytoplasmic surface (gives "rough" appearance)
- Network of flattened sacs (cisternae)
- Continuous with the nuclear envelope
Functions:
- Protein synthesis: Ribosomes on RER synthesize proteins destined for secretion, cell membrane, or other organelles
- Protein folding: Helps newly made proteins fold into correct 3D shapes
- Quality control: Checks protein structure; misfold proteins are marked for degradation
- Protein modification: Adds carbohydrate chains to proteins (glycosylation) to make glycoproteins
- Transport packaging: Packages proteins into vesicles for transport to Golgi apparatus
2. Smooth Endoplasmic Reticulum (SER)
Structure:
- NO ribosomes on surface (smooth appearance)
- Network of tubular structures
- Continuous with RER
Functions:
- Lipid synthesis: Produces phospholipids and cholesterol for membranes
- Steroid hormone synthesis: In endocrine cells (testosterone, estrogen, cortisol)
- Detoxification: Breaks down toxins and drugs (especially abundant in liver cells)
- Carbohydrate metabolism: Glucose-6-phosphatase in liver converts glucose-6-phosphate to glucose
- Calcium storage: In muscle cells (sarcoplasmic reticulum), stores and releases Ca2+ for contraction
🔑 Why Two Types?
The separation into rough and smooth ER allows specialized functions: protein synthesis (RER) and lipid synthesis/detoxification (SER) occur in different regions, preventing interference.
📦 Golgi Apparatus: The Shipping Department
Structure
- Flattened membrane sacs (cisternae) stacked on top of each other
- Cis face (receiving side): Faces the ER; receives vesicles from ER
- Trans face (shipping side): Opposite side; releases vesicles to destinations
- Medial region: Middle compartments between cis and trans
- Each compartment has different enzymes for different modifications
Functions
1. Modification of Proteins
Further modifies proteins from ER (adds/removes carbohydrates, phosphate groups, sulfate groups)
2. Sorting and Packaging
Sorts proteins and lipids based on destination (lysosome, membrane, secretion) and packages them into vesicles
3. Tagging Proteins
Adds "address labels" (molecular tags) to direct proteins to correct destinations
4. Lysosome Formation
Packages digestive enzymes into vesicles that become lysosomes
5. Secretion
Produces secretory vesicles that fuse with plasma membrane to release contents (hormones, enzymes, mucus)
🔑 Structure-Function Correlation:
The stacked cisternae structure creates an assembly line: proteins move from cis → medial → trans, undergoing sequential modifications in each compartment. This ensures proteins are processed in the correct order.
🗑️ Lysosomes: The Recycling Center
Structure
- Single membrane-bound vesicles
- Contain hydrolytic (digestive) enzymes (lipases, proteases, nucleases, glycosidases)
- Acidic interior (pH ~4.5-5.0) maintained by proton pumps
- Formed from Golgi apparatus
- Size: 0.1-1.2 μm in diameter
Functions
1. Intracellular Digestion
Break down worn-out organelles, damaged proteins, and other cellular debris (autophagy)
2. Digestion of Engulfed Material
Fuse with phagocytic vesicles to digest bacteria, viruses, and other foreign particles
3. Recycling of Macromolecules
Break down complex molecules into monomers that can be reused by the cell
4. Programmed Cell Death
Participate in apoptosis by releasing enzymes that digest the dying cell
🔑 Structure-Function Correlation:
The acidic pH inside lysosomes is optimal for digestive enzymes. Importantly, if lysosomal membrane ruptures and enzymes leak into cytoplasm (pH ~7.2), they are INACTIVE at neutral pH, protecting the cell from self-digestion.
⚠️ This is a perfect example of compartmentalization protecting the cell from harmful substances!
🧬 Ribosomes: The Protein Factories
Structure
- NOT membrane-bound (exception to organelle definition)
- Made of ribosomal RNA (rRNA) and proteins
- Composed of two subunits: large subunit + small subunit
- 80S ribosomes in eukaryotes (60S large + 40S small subunit)
- 70S ribosomes in prokaryotes, mitochondria, and chloroplasts
- Very small: ~20-30 nm in diameter
Location & Function
1. Free Ribosomes (in Cytoplasm)
Function: Synthesize proteins for use within the cytoplasm (enzymes, cytoskeletal proteins, proteins for nucleus/mitochondria/chloroplasts)
2. Bound Ribosomes (on Rough ER)
Function: Synthesize proteins for secretion, plasma membrane, or organelles (endomembrane system)
🔑 Primary Function: Protein Synthesis (Translation)
Ribosomes read mRNA sequences and assemble amino acids into polypeptide chains (proteins). They are the sites of translation—the second stage of protein synthesis.
💡 Cells that make lots of proteins (antibody-producing cells, pancreatic cells secreting enzymes) have MILLIONS of ribosomes!
💧 Vesicles & Vacuoles: Transport and Storage
Vesicles
Structure:
Small, membrane-bound sacs that transport materials within cells or to/from cell membrane
Functions:
- Transport vesicles: Move proteins/lipids between ER → Golgi → membrane/secretion
- Secretory vesicles: Store substances for secretion; fuse with membrane to release contents
- Endocytic vesicles: Bring materials into cell via endocytosis
- Phagocytic vesicles: Engulf large particles (bacteria, dead cells)
Vacuoles
Structure:
Large membrane-bound sacs (larger than vesicles). In plant cells, the central vacuole can occupy up to 90% of cell volume.
Functions (especially in plant cells):
- Water storage: Stores water and dissolved substances (ions, sugars, pigments)
- Turgor pressure: When full, exerts pressure on cell wall, keeping plant rigid and upright
- Storage of nutrients: Stores sugars, amino acids, proteins for later use
- Waste storage: Stores toxic waste products isolated from cytoplasm
- Pigment storage: Contains anthocyanins (red/purple/blue pigments in flowers/fruits)
- Defense: Stores toxic compounds that deter herbivores
🌱 In Animal Cells:
Animal cells have small, temporary vacuoles (if any) mainly for temporary storage or digestion (food vacuoles in protists).
📊 Quick Reference: Organelle Summary
| Organelle | Primary Function | Key Structural Feature | Found In |
|---|---|---|---|
| Nucleus | Houses DNA; controls cell activities | Double membrane with pores | All eukaryotes |
| Mitochondria | ATP production (cellular respiration) | Cristae (folded inner membrane) | All eukaryotes |
| Chloroplasts | Photosynthesis (light → chemical energy) | Thylakoids stacked in grana | Plants, algae |
| Rough ER | Protein synthesis and modification | Studded with ribosomes | All eukaryotes |
| Smooth ER | Lipid synthesis; detoxification | No ribosomes; tubular | All eukaryotes |
| Golgi Apparatus | Modifies, sorts, packages proteins | Stacked flattened sacs (cisternae) | All eukaryotes |
| Lysosomes | Digestion; waste removal | Acidic interior (pH ~4.5-5) | Mainly animals |
| Ribosomes | Protein synthesis (translation) | Two subunits (rRNA + protein) | All cells |
| Vacuoles | Storage; turgor pressure | Large central vacuole in plants | Mainly plants |
| Vesicles | Transport; secretion | Small membrane-bound sacs | All eukaryotes |
🎯 Key Concepts Summary
✓ Organelles as Specialized Subunits
Organelles are discrete, membrane-bound structures adapted to perform specific functions. Each has unique structural features that suit its role (structure-function relationship).
✓ Compartmentalization Advantages
Dividing cells into compartments increases efficiency by: concentrating enzymes/substrates, providing optimal conditions, protecting from harmful substances, separating incompatible reactions, increasing surface area, and allowing simultaneous processes.
✓ Energy Production Organelles
Mitochondria (all eukaryotes) produce ATP via cellular respiration. Chloroplasts (plants/algae) convert light energy to chemical energy through photosynthesis. Both have double membranes and their own DNA.
✓ Endomembrane System
ER, Golgi apparatus, lysosomes, and vesicles work together as the endomembrane system: synthesizing, modifying, packaging, and transporting proteins and lipids throughout the cell.
✓ Nucleus: Command Center
The nucleus stores genetic information (DNA) and controls gene expression. The nuclear envelope separates transcription (nucleus) from translation (cytoplasm), allowing regulation of protein synthesis.
✓ Lysosomes: Cellular Cleanup
Lysosomes contain digestive enzymes in an acidic environment (pH ~4.5-5). This compartmentalization protects the cell: if membrane ruptures, enzymes are inactive at cytoplasmic pH (~7.2).
📚 About the Author
Adam
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