Unit 3: Cells and Subcellular Organelles — Interactive Notes
In 1665, English scientist Robert Hooke examined thin slices of cork from an oak tree under a microscope. He observed that the cork was made up of many little boxes, which he named "cellulae" (cells), meaning small rooms. Later, Anton van Leeuwenhoek observed living cells (bacteria, protozoa) using his own microscopes. In 1838-39, Matthias Schleiden and Theodor Schwann proposed that all plants and animals are composed of cells. Rudolf Virchow later added that all cells arise from pre-existing cells.
Cell theory can be validated by: (i) visualizing cell structure under microscope, (ii) live cell imaging and genetic studies, (iii) studying DNA sequencing and metabolic pathways, (iv) experiments such as cell culture studies and tissue engineering.
a) Viruses — not made of cells, cannot carry out life processes independently.
b) Prions and viroids — show properties of living organisms but are not composed of cells.
c) Muscle cells in vertebrates (multinucleated).
d) Multinucleated organisms like certain fungi and algae.
e) Self-replication of organelles like mitochondria and chloroplasts.
f) Plasmodesmata — cells of higher plants are not truly independent since they are physically connected via plasmodesmata.
Light Microscope: Uses visible light to make the image of an object. Resolution ≈ 0.2 μm; a light microscope can resolve details down to approximately 250 nm. Magnification up to about 1500X.
Electron Microscope: Uses a beam of electrons instead of light. Resolution ≈ 0.2 nm, can magnify objects up to 250,000 times.
Magnification refers to a microscope's ability to enlarge the image of an object. It is denoted by "X". Total magnification is determined by multiplying the magnification of all lenses (e.g., a 10X lens can enlarge a 1 μm object to 10 μm).
Resolution refers to a microscope's ability to distinguish between two points that are close together. The greater the resolution, the finer the detail observed. The naked human eye has a resolution of about 0.1 mm.
| Feature | TEM | SEM |
|---|---|---|
| Purpose | Views internal structure of cells | Views surface details/topology |
| Mechanism | Transmits electron beam through a thin specimen | Surface coated with metal; reflected electrons form image |
| Magnification | Up to 250,000X | Up to 100,000X |
Confocal microscopy: laser scanning + fluorescence for sharp, detailed membrane images. Total internal reflection fluorescence microscopy: high-resolution images of membrane-cytoskeleton interactions. Atomic force microscopy: topographical images at high resolution. X-ray crystallography: determines the atomic structure of membrane proteins. Lipidomics: comprehensive analysis of membrane lipids via mass spectrometry. Fluorescence recovery after photobleaching (FRAP): studies mobility/dynamics of membrane proteins and lipids.
Protoplast: When the cell wall is removed using cell wall degrading enzymes, the remaining components of the cell are called a protoplast.
Primary wall: The actual cell wall of the cell, composed of polysaccharides — cellulose, hemicellulose, and pectin. Cellulose microfibrils are aligned at angles held together by hydrogen bonds; many proteins are also present.
Secondary wall: Formed between the protoplast and primary wall after maturation in some plant cells. Composed of lignin, cellulose and hemicellulose — more rigid than the primary wall due to lignin.
Plasmodesmata: Small channels that directly connect the cytoplasm of neighbouring plant cells, penetrating both primary and secondary walls — important in cellular communication (and are an exception debated in cell theory).
Diatoms: A group of algae that synthesize cell walls from silicic acid, polymerized inside cells then extruded — requires less energy, giving diatoms higher growth rates.
| Organism | Cell Wall Composition |
|---|---|
| Algae | Cellulose and a variety of glycoproteins |
| Fungi | Chitin (same carbohydrate as insect exoskeletons) |
| Prokaryotes (bacteria, cyanobacteria) | Peptidoglycan — single large polymer of amino acids and sugar |
| Archaebacteria | Different polysaccharides and proteins, no peptidoglycan |
Plasma membrane's basic foundation is a lipid bilayer of phospholipids, with hydrophobic tails oriented inward and hydrophilic phosphate heads outward. A collection of proteins floats within this bilayer.
The hydrophobic interior of the lipid bilayer repels water-soluble molecules; proteins provide passageways across the membrane.
Glycocalyx: Glycoproteins and glycolipids on the outer surface act as identification marks recognized by other cells — crucial for tissue/organ sorting in embryos and immune recognition of foreign cells.
Nucleus: A prominent structure present in all eukaryotic cells (central in animal cells, pushed to the side in plant cells). Functions: stores hereditary material (DNA); coordinates cell activities (growth, protein synthesis, cell division).
Nuclear envelope: A double membrane, continuous with the endoplasmic reticulum. On its inner side is a protein lining called the nuclear lamina, which binds to chromatin for structural support.
Nuclear pores: Tiny holes in the nuclear envelope, made of a nuclear pore complex with several subunits — annular subunit, column subunit, ring subunit, luminal subunit. Materials that pass through: DNA/RNA building blocks and ATP (in); ribosomal subunits (out).
Nucleoplasm: The semifluid matrix inside the nucleus, containing chromatin that organizes into chromosomes during cell division.
Chromatin — two types: Euchromatin (genetically active, transcribing RNA) and Heterochromatin (genetically inactive DNA).
Chromosome: Made of chromatids and a centromere. DNA wraps around histone proteins to form nucleosomes, which make up chromatin. Inside every human cell's nucleus is a 6-feet-long DNA subdivided into 46 individual molecules (each 1.5 inches long), one for each chromosome.
Nucleolus: Formed at NOR (Nucleolus Organizer Regions) — certain chromosome sites whose DNA encodes ribosomal RNA. Consists of granular components (ribosomal subunits) and fibrillar components (raw materials for ribosome subunits). In cells producing large amounts of protein, the nucleolus is considerable in size; it disappears at the onset of mitosis and reforms from the NORs after division.
The endoplasmic reticulum is physically connected to the nuclear envelope — the ER lumen and the space between the nuclear envelope layers form a single compartment, enabling efficient information sharing between the nucleus and ER.
Rough Endoplasmic Reticulum (RER): Studded with ribosomes on its surface. Function: production and processing of proteins.
Smooth Endoplasmic Reticulum (SER): Lacks ribosomes. Functions: (i) production of lipids, (ii) detoxification of drugs, (iii) storage of calcium and calcium/carbohydrate metabolism.
Definition: Ribosomes are granular structures not bound by any membrane.
Occurrence: Found in all organisms. In eukaryotes, found attached to RER or scattered free in cytoplasm; also found inside mitochondria and chloroplasts (these differ in size/makeup, resembling prokaryotic ribosomes).
Svedberg values: Based on rate of sedimentation in a centrifuge (not simply additive, since sedimentation depends on size and shape, not just mass). Eukaryotic ribosome = 80S; prokaryotic ribosome = 70S.
Function: Protein synthesis (translation, using mRNA, tRNA and rRNA). Proteins synthesized by free ribosomes are for the cell's own internal use; proteins from RER-bound ribosomes are transported outside the cell.
Origin: Millions of years ago, small free-living prokaryotes were engulfed (but not consumed) by larger prokaryotes, developing a symbiotic relationship — the larger organism provided nutrients, the smaller provided ATP (endosymbiotic theory).
Occurrence: Number depends on metabolic requirements (from one to thousands); found in nearly all eukaryotes; large enough to be seen with a light microscope.
1. Outer membrane — smooth boundary.
2. Inner membrane — folded into cristae, increasing surface area; contains F1 particles (knob-like extensions of ATP synthase enzyme) and electron transport chain proteins.
3. Matrix — semi-fluid, contains circular DNA, ribosomes (70S-like), and enzymes for the Krebs cycle.
Mitochondria are the sites of cellular respiration — generating ATP from oxygen and nutrients (chemical energy "currency" of the cell). Enzymes in the matrix catalyse Krebs cycle steps; electron transport chain proteins on the inner membrane generate ATP via ATP synthase (F1 particles).
Types of plastids (in plant/protist cells): Chloroplasts (green, photosynthesis), Chromoplasts (yellow-to-red, colour plant parts), Leucoplasts (colourless, storage).
Ellipsoid-shaped, enclosed by two membranes; the intermembrane space lies between them. A semi-fluid stroma is present inside the inner membrane, containing dissolved enzymes and comprising most of the chloroplast's volume. Two adjacent inner membranes fuse along their periphery forming disc-shaped compartments called thylakoids; thylakoids stack into grana (singular granum); non-green lamellae connect two grana.
Light is absorbed by chlorophyll molecules embedded in thylakoid discs — chlorophyll pigments emit electrons, forming ATP. Using these ATPs, in the stroma, low-energy carbon dioxide is transformed into a high-energy compound like glucose (photosynthesis).
• Both organelles convert energy for the cell.
• Mitochondria perform aerobic respiration — generate ATP by metabolizing sugars, fats and other fuels using oxygen.
• Chloroplasts perform photosynthesis — convert solar energy into biosynthesis of organic nutrients using CO₂ and water.
• Like mitochondria, chloroplasts contain their own DNA and grow/reproduce independently of the cell (both support the endosymbiotic theory).
Discovery: Discovered by Camillo Golgi in 1898 during research on the nervous system using "Golgi staining".
Structure: Consists of five to eight cup-shaped, membrane-covered sacs called cisternae, stacked over each other (some unicellular flagellates may have up to 60 cisternae). Found in plant, animal and unicellular eukaryote cells. Animal cells generally have 10-20 Golgi stacks, usually located near the nucleus. Each stack has a cis face (near the ER) and a trans face (near the plasma membrane).
Golgi apparatus is the distribution/shipping department for the cell's chemical products. Small vesicles containing proteins, carbohydrates, phospholipids and other molecules bud off the ER, reach the cis face, and fuse with it, releasing molecules into the Golgi. Enzymes in the Golgi lumen convert them into glycoproteins and glycolipids. Processed products are released from the trans face in a vesicle, directed to their final destination inside/outside the cell — exported products are called secretions; others return to the ER or become lysosomes. In plant cells, the Golgi apparatus also produces pectin and other polysaccharides for plant structure and metabolism.
Discovery: Discovered by Belgian scientist Christian Rene de Duve, who observed acid phosphatase release from damaged cells during centrifugation studies of carbohydrate metabolism.
Structure: Spherical organelles bound by a single membrane, formed by budding from the Golgi apparatus (enzymes made in ER, modified in Golgi). Contain about 40 different hydrolytic enzymes.
• Digestive compartments — breakdown cellular waste products, fats, carbohydrates, proteins and other macromolecules for re-use.
• Most numerous in disease-fighting cells (e.g., white blood cells) since they must digest bacteria/viruses/foreign invaders.
• Autophagy — breaking down cellular materials that have exceeded their lifetime.
• Selective cell death during development e.g., tadpole tail cells destroyed as it develops into a frog; many brain cells die during development via lysosome rupture.
• Cell safety: Lysosomal matrix is acidic (~pH 4.8) while cytosol is neutral, so even if a lysosome ruptures, its enzymes become inactive and the cell remains uninjured.
Patient lacks one of the hydrolytic enzymes; abnormal lysosomes fill with indigestible substances, interfering with cellular function.
Pompe's disease: lacks glycogen-digesting enzyme — glycogen accumulates in liver cells.
Tay-Sachs disease: lacks lipid-digesting enzyme — lipids accumulate in brain nerve cells, causing mental retardation and early death.
Peroxisomes: Single membrane bound organelles in all eukaryotic cells. Contain oxidative enzymes that rid the cell of toxic substances — e.g., catalase breaks down hydrogen peroxide (a toxic metabolic by-product) into water and oxygen: 2H₂O₂ → 2H₂O + O₂. Liver cell peroxisomes detoxify alcohol and other harmful compounds.
Glyoxisomes: Similar to peroxisomes but found only in plant cells, most abundant in lipid-rich seeds (e.g., castor beans, soybeans). Contain enzymes that convert stored lipids into carbohydrates during seed germination, providing energy for growth.
Together, lysosomes (digestion/recycling of macromolecules), peroxisomes (detoxification via oxidation) and glyoxisomes (lipid-to-carbohydrate conversion) regulate the amount and safety of cellular contents by breaking down or converting materials the cell no longer needs or that would otherwise be harmful.
Definition: Membrane-bound sacs found in both animal and plant cells.
Formation in plant cells: Many small vacuoles fuse during maturation to form one large, single central vacuole, occupying 80% or more of the cell's volume.
Structure: Surrounded by a membrane called the tonoplast; the material inside is called cell sap, which differs markedly from surrounding cytoplasm.
(a) In mature plant cells — structural support, storage, waste disposal, protection, growth.
(b) In animal cells — smaller, used for temporary storage/transport.
(c) Turgor pressure — central vacuole swells with water under optimum conditions, creating high turgor pressure that maintains structural integrity along with the cell wall.
(d) Store pigments — give flower colours that attract pollinators.
(e) Protection — release molecules poisonous to insects/animals.
(f) Store materials useful to humans, e.g., opium, rubber, garlic flavouring.
In animal and most protist cells, centrioles are organelles associated with the assembly and organization of cytoskeleton fibres i.e. microtubules (including spindle fibres). A centriole is made of nine triplets of microtubules.
In eukaryotic cells, centrioles occur in pairs, located at right angles to one another near the nuclear envelope. In ciliated/flagellated cells, centrioles form the basal body that anchors each cilium/flagellum. The cells of plants and fungi lack centrioles and basal bodies — their microtubules and spindle fibres are organized from cytoplasmic structures called MTOCs (microtubule organizing centres).
The cytoskeleton is a network of protein fibres present in the cytoplasm, comprising three types of fibres:
1. Microfilaments — present in all eukaryotic cells; solid rods made of the globular protein actin. They disassemble/reassemble to help cells change shape and move, enable a dividing cell to pinch into two, and (with myosin) help in cellular contraction.
2. Microtubules — straight, hollow cylinders made of subunits of two tubulin proteins (alpha- and beta-tubulin). They give structure/shape to the cell, serve as highways for organelle transport, are major components of cilia and flagella, and form spindle fibres during cell division.
3. Intermediate filaments — found only in some higher animal groups; made of different proteins, most commonly vimentin (keratin in skin cells). They maintain cell shape and rigidity, and anchor organelles including the nucleus.
Cilium (pl. cilia) and flagellum (pl. flagella) are thin, tail-like locomotor appendages protruding from certain cells. Cilia are short and numerous; flagella are longer but fewer. Cilia are rare in plants; many protozoans (ciliates, e.g., Paramecium) possess cilia. In humans, cilia line the trachea, sweeping mucus and dirt out of breathing tubes.
The core of eukaryotic cilia/flagella is called the axoneme. It contains two central microtubules surrounded by an outer ring of nine doublet microtubules ("9+2" arrangement). Dynein arm molecules bridge the gaps between adjacent doublets, enabling movement. A plasma membrane surrounds the entire axoneme. At the base is the basal body (organizing centre) — same structure as the outer ring of the axoneme but with triplets instead of doublets of microtubules; it is actually a modified centriole.
Prokaryotic flagella have a completely different structure, built from the protein flagellin, and lack microtubule triplets — unlike eukaryotic flagella which spin via a rotating basal body motor, prokaryotic flagella rotate like a propeller driven by proton motive force.
Bacteria and archaea are made of prokaryotic cells. Characteristics:
| Characteristic | Eukaryotic Cell | Prokaryotic Cell |
|---|---|---|
| Distinct Nucleus | Present | Absent |
| Chromosomes | More than one | One (not true chromosome; plasmids) |
| Cell Type | Usually multicellular | Usually unicellular |
| Lysosomes/Peroxisomes | Present | Absent |
| Microtubules | Present | Absent or rare |
| ER, Mitochondria, Golgi | Present | Absent |
| Cytoskeleton | Present | May be absent |
| Vacuoles | Present | Present |
| Ribosomes | Larger (80S) | Smaller (70S) |
| Chloroplasts | Present (plants) | Absent; chlorophyll scattered |
| Cell Division | Mitosis/meiosis | Binary fission |
| Flagella | 9+2 microtubules, membrane-bound | Flagellin, not membrane-bound |
| Cell Wall | Cellulose (plants)/chitin (fungi) | Peptidoglycan |
| Cell Size | 10-100 μm | 1-10 μm |
Both have DNA as genetic material, plasma membranes as coverings, and ribosomes for protein synthesis.
Definition: Cell signalling is the ability of cells to respond to stimuli from their environment, producing cellular responses via transmission of signals through molecular events.
1. Signal Reception — a signal molecule (ligand) binds to a receptor on the target cell's membrane (or inside the cell); each receptor is specific to a particular ligand.
2. Signal Transduction — receptor binding causes a conformational change activating an intracellular pathway (signalling cascade) — second messengers like cAMP, calcium ions, and IP3 transmit the signal.
3. Cellular Response — often changes gene expression, leading to cell growth, division, differentiation, or apoptosis; can also affect metabolism, enzyme activity, or ion channels.
(i) Protein/Peptide Signalling: Water-soluble, cannot pass through the plasma membrane. Ligand binds to a specific receptor on the plasma membrane → conformational change activates the receptor → triggers a series of reactions → generates second messengers (e.g., cAMP) → changes in gene expression, metabolism, growth, division or apoptosis.
(ii) Steroid Signalling: Steroid hormones are lipophilic and diffuse through the plasma membrane directly. Once inside, they bind specific intracellular receptors (cytoplasm or nucleus), forming an active receptor-hormone complex, which moves into the nucleus (if not already there) and binds specific DNA sequences in target genes, regulating transcription — increasing or decreasing production of specific proteins.
Membrane transport mechanisms are essential for the cell to maintain homeostasis, acquire nutrients, remove waste, and communicate with its environment.
a. Diffusion — net movement of a substance from higher to lower concentration (along the gradient); no energy expended.
b. Facilitated Diffusion — molecules move down their concentration gradient with the help of transport proteins; still no energy used. Main transport protein types: Channel proteins (form hydrophilic channels, gated or non-gated, e.g., ion channels, aquaporins) and Carrier proteins (bind specific molecule, undergo conformational change, can become saturated, e.g., glucose transporters).
| Simple Diffusion | Facilitated Diffusion | |
|---|---|---|
| Mechanism | Directly through lipid bilayer | Through specific transport proteins |
| Energy | None required | None required |
| Molecules | Small, nonpolar (O2, CO2) | Polar/charged (glucose, ions) |
| Rate depends on | Concentration gradient, temperature, permeability | Number/availability of transport proteins (can saturate) |
c. Osmosis — diffusion of water across a selectively permeable membrane, from hypotonic (lower solute) to hypertonic (higher solute) solution. Crucial for cell turgor. Aquaporins facilitate rapid water transport.
Reverse osmosis — external pressure applied to push water through a semipermeable membrane from higher to lower solute concentration (opposite of natural osmosis) — used for water purification/desalination.
Movement of substances against the concentration gradient (low to high), using energy.
1. Active transport through carrier proteins — e.g., the Na⁺-K⁺ pump in nerve cell membranes; spends ATP to actively move Na⁺ out of the cell and K⁺ into the cell.
2. Endocytosis — bulky materials moved into the cell; plasma membrane invaginates, material is enclosed, ends seal to form a vesicle. Two forms: Phagocytosis (solid material, "cell eating") and Pinocytosis (liquid droplets, "cell drinking"). Receptor-mediated endocytosis — specific receptor proteins pick up material (e.g., liver cell receptors take up cholesterol-carrying LDLs from blood).
3. Exocytosis — bulky material packed in a vesicle moves to and fuses with the plasma membrane, releasing contents to the extracellular environment.
Stem cells are unique cells with the remarkable ability to develop into many different cell types. When a stem cell divides, each new cell can either remain a stem cell or become specialized (e.g., muscle, red blood, or brain cell).
1. Totipotent — differentiate into all possible cell types (e.g., zygote and cells from the first few divisions).
2. Pluripotent — turn into almost any cell (e.g., cells of the early embryo).
3. Multipotent — differentiate into a closely related family of cells (e.g., hematopoietic stem cells → RBCs, WBCs, platelets).
4. Oligopotent — differentiate into a few cell types (e.g., adult lymphoid or myeloid stem cells).
5. Unipotent — produce only their own cell type but can still self-renew (e.g., adult muscle stem cells).
1. Embryonic Stem Cells (ESCs) — derived from the inner cell mass of blastocysts; pluripotent, high differentiation potential; ethical concerns (use of embryos, teratoma risk, immune rejection).
2. Adult Stem Cells (ASCs) — found in tissues like bone marrow, fat, blood; multipotent; less ethical controversy, lower immune rejection risk if from patient's own tissue; limited differentiation potential, harder to isolate/culture.
3. Induced Pluripotent Stem Cells (iPSCs) — generated in the lab by reprogramming adult somatic cells to a pluripotent state using specific transcription factors; similar to ESCs.
Advantages: no ethical controversy (no embryo destruction), can be from patient's own cells (minimizing immune rejection), potential for regenerating tissues/organs.
Disadvantages: reprogramming can introduce genetic changes, risk of forming tumours (teratomas), difficult to direct into fully functional cell types.
1. Regenerative Medicine — repair/replace damaged tissues (spinal cord injuries, type 1 diabetes, Parkinson's disease, heart disease).
2. Drug Testing and Development — model human diseases for accurate drug testing, reducing reliance on animal models.
3. Personalized Medicine — derived from a patient's own cells, reducing immune rejection risk, more effective/safer therapies.
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