Date: Lecture 3 | Source: BIO 203 Lecture 3 Objectives, Ch. 3 Tags: organelles, cytoskeleton, cell junctions, nucleus, mitochondria, microfilaments, microtubules, intermediate filaments, tight junctions, desmosomes, gap junctions, adherens junctions, pemphigus, chromatin, chromosomes, nuclear pore
Difficulty: Intermediate
Prerequisites: Part 1 of these notes (Cell Differentiation, Components, and Plasma Membrane). You should already understand the basic layout of a cell, the four categories of cell components, and the structure of the plasma membrane before tackling organelle functions, the cytoskeleton, and junctions.
This second set of notes from Lecture 3 goes deeper into the cell's interior machinery. You will learn what each organelle does (and be expected to describe those functions on an exam), how the cytoskeleton gives the cell its shape and enables movement, how cells connect to one another through four types of junction, and the internal architecture of the nucleus. This material builds directly on your knowledge of the plasma membrane and cell components from Part 1. Understanding these structures is essential for later topics on tissue organisation, cell division, and membrane transport.
Organelles are the specialised compartments inside a cell, each with a distinct job: mitochondria generate ATP, lysosomes digest waste, peroxisomes neutralise toxins, and the ER and Golgi handle protein and lipid processing. The cytoskeleton (microfilaments, microtubules, intermediate filaments) provides structural support and enables cell movement. Four types of junction (tight, adherens, desmosome, gap) hold cells together and allow communication. The nucleus stores DNA as chromatin, which condenses into chromosomes during division, and nuclear pores regulate traffic between nucleus and cytoplasm.
Cristae
The folds of the inner mitochondrial membrane. They increase the surface area available for the enzymes and electron transport chain complexes that produce ATP.
Think of it as shelving inside the power station, creating more workspace for energy production.
Mitochondrial matrix
The fluid-filled interior space enclosed by the inner mitochondrial membrane. Contains enzymes for the citric acid cycle, mitochondrial DNA, and ribosomes.
In simple terms, this is the innermost compartment of the mitochondrion where key metabolic reactions take place.
Lysosomes
Membrane-bound organelles containing digestive enzymes (hydrolases) that break down worn-out organelles, ingested bacteria, and cellular debris. Sometimes called the cell's "recycling centre."
Think of it as the cell's waste disposal unit.
Peroxisomes
Small, membrane-bound organelles that use oxygen to detoxify harmful substances (including alcohol and free radicals) and break down fatty acids. They produce and then decompose hydrogen peroxide in the process.
In simple terms, peroxisomes are the cell's detox crew.
Glycogen granules
Stored clusters of glycogen (a polysaccharide of glucose) found in the cytoplasm, particularly abundant in liver and muscle cells. They serve as an energy reserve.
Think of it as the cell's pantry: stored glucose ready to be broken down when energy is needed.
Lipid droplets
Cytoplasmic inclusions that store triglycerides (fats) as an energy reserve. Especially prominent in adipocytes (fat cells).
In simple terms, these are the cell's long-term fuel tanks.
Cilia
Hair-like projections on the cell surface that move in coordinated, wave-like motions. They are longer than microvilli and contain a core of microtubules arranged in a 9+2 pattern. Found, for example, lining the respiratory tract, where they sweep mucus upward.
Think of it as tiny oars that row in unison to move substances along the cell's surface.
Flagellum (plural: flagella)
A long, whip-like projection used for cell locomotion. Structurally similar to cilia but much longer, and typically present as a single structure. In humans, the only flagellated cell is the sperm cell.
In simple terms, a flagellum is the cell's propeller.
Cytoskeleton
An internal network of protein filaments and tubules that gives the cell its shape, provides mechanical support, and enables intracellular transport and cell movement. Composed of three types of fibre: microfilaments, microtubules, and intermediate filaments.
Think of it as the cell's scaffolding and transport rail system combined.
Microfilaments (actin filaments)
The thinnest cytoskeletal fibres, made of the protein actin. They are involved in cell shape, muscle contraction, cell division (cleavage furrow), and supporting microvilli.
In simple terms, actin filaments are the cell's muscles and structural cables.
Microtubules
Hollow tubes made of the protein tubulin. They form the mitotic spindle during cell division, provide tracks for intracellular transport, and form the structural core of cilia and flagella.
Think of it as the cell's railway tracks, along which molecular motors carry cargo.
Intermediate filaments
Rope-like fibres made of various proteins (e.g. keratins, vimentin, neurofilaments). They provide tensile strength and mechanical stability, particularly in cells subject to physical stress.
In simple terms, intermediate filaments are the cell's guy-wires, holding everything firmly in place.
Tight junctions (zonula occludens)
Junctions that seal the space between adjacent cells, preventing leakage of molecules between them. Found at the apical surface of epithelial cells.
Think of it as waterproof sealing between tiles, stopping anything from leaking through the cracks.
Adherens junctions (zonula adherens)
Junctions that connect actin filament bundles in adjacent cells, providing mechanical attachment. Located just below tight junctions in epithelial cells.
In simple terms, these are actin-linked clasps that hold neighbouring cells together.
Desmosomes (macula adherens)
Very strong, spot-like junctions that connect intermediate filaments in adjacent cells. They provide resistance to mechanical stress, especially in skin and cardiac muscle.
Think of it as rivets or spot welds between cells, built to withstand stretching and pressure.
Gap junctions
Communicating junctions made of connexin proteins that form channels (connexons) between adjacent cells. They allow small molecules and ions to pass directly between cells, enabling metabolic and electrical coupling.
In simple terms, gap junctions are tiny tunnels that let neighbouring cells share molecules and electrical signals.
Pemphigus
An autoimmune condition in which the body produces antibodies against its own desmosomal proteins (cadherins). This destroys desmosomes, causing epithelial cells to separate from one another, resulting in blistering of the skin and mucous membranes.
Think of it as the immune system attacking the rivets that hold skin cells together, causing them to fall apart.
Nuclear envelope
A double membrane surrounding the nucleus, continuous with the rough endoplasmic reticulum. It separates nuclear contents from the cytoplasm and is perforated by nuclear pores.
In simple terms, this is the wall around the control centre, with doors (pores) that regulate what goes in and out.
Nuclear pore
A large protein complex spanning the nuclear envelope that regulates the transport of molecules (mRNA, proteins, ribosomal subunits) between the nucleus and cytoplasm.
Think of it as a security checkpoint at the nuclear border.
Nuclear matrix
A network of fibrous proteins inside the nucleus that provides structural support, organises chromatin, and serves as a scaffold for DNA replication and gene expression.
In simple terms, the nuclear matrix is the skeleton inside the nucleus.
Chromatin
The complex of DNA and histone proteins found in the nucleus during interphase (the non-dividing state). It is a loosely organised, dispersed form of the genetic material.
Think of it as unspooled thread: the DNA is accessible for reading (gene expression) because it is spread out.
Chromosomes
Highly condensed, tightly coiled structures of chromatin that become visible during cell division (mitosis and meiosis). Humans have 46 chromosomes (23 pairs).
In simple terms, chromosomes are chromatin wound up tightly for transport during cell division, like thread wound onto a bobbin.
Mitochondria: produce ATP via aerobic respiration. Structure: outer membrane, inner membrane (folded into cristae to increase surface area), matrix (contains enzymes for the citric acid cycle, plus mitochondrial DNA and ribosomes).
Peroxisomes: detoxify harmful substances (alcohol, free radicals) using oxidative enzymes. Produce and then break down hydrogen peroxide.
Lysosomes: digest worn-out organelles, ingested material, and cellular debris using hydrolytic enzymes. Active in phagocytic cells such as macrophages.
Glycogen granules: stored glucose polymer; an energy reserve, especially in liver and muscle cells. These are inclusions, not membrane-bound organelles.
Lipid droplets: stored triglycerides for long-term energy. Also inclusions, not organelles. Prominent in adipose tissue.
Ribosomes: sites of protein synthesis. Found free in the cytoplasm (make proteins for internal use) or attached to rough ER (make proteins for export or membrane insertion).
Centrosomes: organise microtubules; contain two centrioles arranged at right angles. Important during cell division for forming the mitotic spindle.
Microvilli are short, finger-like projections that increase surface area for absorption. They do not move. They are supported by actin microfilaments. Found on absorptive cells (e.g. intestinal lining).
Cilia are longer, hair-like projections that beat in coordinated, wave-like motions to move substances along the cell surface. They contain a 9+2 microtubule arrangement. Found lining the respiratory tract and fallopian tubes.
Flagella are much longer than cilia and are used for cell locomotion. Same 9+2 microtubule structure but typically only one per cell. In humans, only sperm cells have a flagellum.
Fibre type | Protein component | Key functions |
|---|---|---|
Microfilaments | Actin | Cell shape, muscle contraction, cell division (cleavage furrow), support microvilli |
Microtubules | Tubulin | Mitotic spindle, intracellular transport, structural core of cilia and flagella |
Intermediate filaments | Mixed proteins (keratins, vimentin, etc.) | Tensile strength, mechanical stability, resist stretching |
Epithelial cells are held together and communicate through four types of junction, arranged from the apical (top) surface toward the basal (bottom) surface:
1. Tight junctions (zonula occludens)
Located at the apical surface.
Seal the space between adjacent cells.
Prevent molecules from leaking between cells (paracellular pathway).
2. Adherens junctions (zonula adherens)
Located just below tight junctions.
Connect actin filament bundles in adjacent cells.
Provide mechanical attachment.
3. Desmosomes (macula adherens)
Very strong, spot-like junctions.
Connect intermediate filaments in adjacent cells.
Provide resistance to mechanical stress.
Abundant in skin and cardiac muscle.
4. Gap junctions
Communicating junctions formed by connexin proteins.
Allow small molecules and ions to pass directly between cells.
Enable metabolic and electrical cell-to-cell coupling.
Important in cardiac muscle (coordinated contraction) and smooth muscle.
Pemphigus
An autoimmune disease where antibodies target desmosomal cadherins.
Desmosomes are destroyed, causing epithelial cells to lose adhesion.
Results in blistering of the skin and mucous membranes.
Bounded by the nuclear envelope, a double membrane continuous with the rough ER.
Nuclear pores perforate the envelope. They are large protein complexes that regulate transport of mRNA (out), proteins (in), and ribosomal subunits (out) between nucleus and cytoplasm.
Contains the nucleolus (site of rRNA synthesis and ribosomal subunit assembly).
Contains chromatin (DNA + histone proteins), which is the dispersed, accessible form of genetic material during interphase.
The nuclear matrix is a fibrous protein scaffold inside the nucleus that organises chromatin and supports DNA replication and transcription.
Chromatin is the loose, uncoiled form of DNA and histones present during interphase, when genes are being read.
Chromosomes are the tightly condensed form of chromatin, visible only during cell division (mitosis/meiosis). Humans have 46 chromosomes (23 pairs).
The two terms describe the same material in different states of packing.
Pemphigus is a real clinical condition treated by dermatologists. Understanding that it targets desmosomes explains why the blistering occurs in tissues subject to mechanical stress (skin, mucous membranes). Immunosuppressant drugs are used to reduce the autoimmune attack.
Cilia dysfunction causes primary ciliary dyskinesia (Kartagener syndrome), where patients suffer chronic respiratory infections because the cilia lining the airways cannot sweep mucus upward. This directly connects the 9+2 microtubule structure to a clinical outcome.
Mitochondrial diseases arise from mutations in mitochondrial DNA. Because mitochondria are inherited maternally, these diseases follow a maternal inheritance pattern, which is a concept you will revisit in genetics.
Students often confuse microvilli and cilia. Microvilli are short, non-motile, actin-supported projections for absorption. Cilia are longer, motile, microtubule-based projections that move substances. They are structurally and functionally different.
Students sometimes think chromatin and chromosomes are two different things. They are the same material (DNA + histones) in different states of condensation. Chromatin is loose (interphase); chromosomes are condensed (division).
Students often mix up the four junction types. A useful mnemonic: Tight seals, Adherens clasps actin, Desmosomes anchor intermediate filaments, Gap lets things through.
Students frequently forget that the nuclear envelope is a double membrane continuous with the rough ER, not a standalone wall.
Be able to draw and label a mitochondrion (outer membrane, inner membrane, cristae, matrix).
Know the three cytoskeletal fibre types, their protein components, and at least two functions each. This is a high-frequency exam question.
Be able to name and describe all four junction types, their structural proteins, and where each is found relative to the apical and basal surfaces.
Know what pemphigus is and which junction it targets (desmosomes).
Understand the distinction between chromatin and chromosomes.
Be able to describe the structure and function of nuclear pores.
Fill in the blank: The folds of the inner mitochondrial membrane are called ______.
Cristae.
True or False: Microvilli contain microtubules arranged in a 9+2 pattern.
False. Microvilli are supported by actin (microfilaments). It is cilia and flagella that have the 9+2 microtubule arrangement.
Fill in the blank: The three cytoskeletal fibre types are microfilaments (made of ______), microtubules (made of ______), and intermediate filaments (made of ______).
Actin; tubulin; mixed proteins (e.g. keratins, vimentin).
True or False: Gap junctions seal the space between cells and prevent leakage.
False. That describes tight junctions. Gap junctions allow communication by letting small molecules and ions pass between cells.
Fill in the blank: Pemphigus is an autoimmune condition that targets ______, causing epithelial cells to separate.
Desmosomes (specifically, desmosomal cadherins).
Q: Draw and label a mitochondrion. What are the four structural components you should include?
A: Outer membrane, inner membrane, cristae (folds of the inner membrane), and matrix (the fluid-filled interior). The matrix contains enzymes for the citric acid cycle, mitochondrial DNA, and ribosomes.
Q: Compare microvilli, cilia, and flagella. How do they differ in structure, function, and location?
A: Microvilli are short, non-motile, actin-supported projections that increase surface area for absorption (e.g. intestinal lining). Cilia are longer, motile projections with a 9+2 microtubule core that beat in waves to move substances (e.g. respiratory tract). Flagella are very long, whip-like structures also with a 9+2 core, used for locomotion (e.g. sperm cells). Microvilli do not move; cilia and flagella do.
Q: Name the three types of cytoskeletal fibres, their protein components, and one key function of each.
A: Microfilaments (actin): involved in cell shape and muscle contraction. Microtubules (tubulin): form the mitotic spindle and provide tracks for intracellular transport. Intermediate filaments (mixed proteins): provide tensile strength and resist mechanical stress.
Q: Name the four types of cell junction and describe the function of each.
A: Tight junctions seal space between cells, preventing leakage. Adherens junctions connect actin filaments between adjacent cells for mechanical attachment. Desmosomes connect intermediate filaments between cells for resistance to stress. Gap junctions allow small molecules and ions to pass between cells for communication.
Q: What is pemphigus, and which cell junction is affected?
A: Pemphigus is an autoimmune disease in which antibodies attack desmosomal cadherins, destroying desmosomes. This causes epithelial cells to lose adhesion, resulting in skin and mucous membrane blistering.
Q: Distinguish between chromatin and chromosomes.
A: Chromatin is the loose, dispersed form of DNA and histone proteins found in the nucleus during interphase, when genes are being expressed. Chromosomes are the same material in a tightly condensed form, visible during cell division. They are the same substance in different states of compaction.
Q: Describe the structure of the nucleus and the function of nuclear pores.
A: The nucleus is bounded by a double-membrane nuclear envelope (continuous with the rough ER) perforated by nuclear pores. It contains the nucleolus (makes rRNA and assembles ribosomal subunits), chromatin (DNA + histones), and the nuclear matrix (structural scaffold). Nuclear pores are protein complexes that regulate transport of mRNA, proteins, and ribosomal subunits between the nucleus and cytoplasm.
The cytoskeleton connects to cell division (mitosis): microtubules form the mitotic spindle that separates chromosomes, and actin microfilaments form the cleavage furrow. You will revisit these structures when studying the cell cycle.
Cell junctions are central to epithelial tissue biology. When you study the four tissue types, you will see how tight junctions create barriers in the gut and bladder, and how desmosomes hold cardiac muscle cells together at intercalated discs.
Chromatin, chromosomes, and nuclear pores all reappear in genetics and cell division. Understanding how DNA is packaged and how molecules move through nuclear pores is prerequisite knowledge for gene expression and protein synthesis.
Organelle functions, mitochondria structure, cristae, mitochondrial matrix, lysosomes, peroxisomes, glycogen granules, lipid droplets, ribosomes, centrosomes, centrioles, microvilli, cilia, flagella, 9+2 microtubule arrangement, cytoskeleton, microfilaments, actin, microtubules, tubulin, mitotic spindle, intermediate filaments, keratin, vimentin, tight junctions, zonula occludens, adherens junctions, zonula adherens, desmosomes, macula adherens, gap junctions, connexin, connexons, pemphigus, autoimmune blistering disease, nuclear envelope, nuclear pore, nuclear matrix, chromatin, chromosomes, histone proteins, nucleolus, rRNA, BIO 203, cell biology, anatomy and physiology