Difficulty: Introductory | Prerequisites: Basic chemistry (atoms, molecules, bonds), prokaryotic cell structure.
This topic sits at the heart of BIO 101. Every living organism you will study for the rest of the course, from yeast to humans, is built from eukaryotic cells. Understanding what each organelle does, and how they cooperate, is the scaffold for everything that follows: metabolism, genetics, cell division, and disease. You should already be comfortable with the difference between prokaryotes and eukaryotes at a surface level, and with the idea that cells are bounded by membranes. If the word "phospholipid bilayer" means nothing to you, revisit the membrane tutorial first.
Eukaryotic cells are defined by membrane-bound compartments, each performing a specialised job. The nucleus stores and copies genetic information, the endomembrane system (ER, Golgi, lysosomes) manufactures and ships proteins, and mitochondria (plus chloroplasts in plants) handle energy conversion. The endosymbiotic theory explains how mitochondria and chloroplasts were once free-living bacteria that took up permanent residence inside ancestral eukaryotic cells.
Eukaryotic cell
A cell that contains a true nucleus and other membrane-bound organelles. In simple terms, these are the complex cells that make up animals, plants, fungi, and protists.
Prokaryotic cell
A cell that lacks a nucleus and membrane-bound organelles; its DNA sits in a region called the nucleoid. Think of it as the simpler, older cell design, found in bacteria and archaea.
Organelle
A membrane-enclosed structure inside a cell that performs a specific function. Think of organelles as specialised departments in a factory, each handling a different part of the production line.
Nucleus
The double-membrane-bound organelle that houses the cell's DNA and coordinates gene expression. It is the cell's control centre, where genetic instructions are stored and copied.
Ribosome
A molecular machine (made of rRNA and protein) that translates mRNA into polypeptide chains. In simple terms, ribosomes read the genetic recipe and assemble proteins from amino acids.
Endoplasmic reticulum (ER)
A network of membrane-enclosed channels extending from the nuclear envelope. The rough ER (studded with ribosomes) makes and folds proteins destined for membranes or export; the smooth ER synthesises lipids and detoxifies chemicals.
Golgi apparatus (Golgi body)
A stack of flattened membrane sacs (cisternae) that receives proteins from the ER, modifies them (e.g. adds sugar chains), sorts them, and ships them to their final destination. Think of it as the cell's post office.
Lysosome
A membrane-bound vesicle filled with digestive (hydrolytic) enzymes at an acidic pH. It breaks down worn-out organelles, engulfed pathogens, and macromolecules. The cell's recycling centre.
Mitochondrion (pl. mitochondria)
A double-membrane organelle that carries out aerobic respiration, converting glucose-derived molecules into ATP. Often called the powerhouse of the cell.
Chloroplast
A double-membrane organelle found in plant and algal cells that carries out photosynthesis, converting light energy into chemical energy (glucose). Contains its own DNA, like mitochondria.
Cytoskeleton
A network of protein filaments (microfilaments, intermediate filaments, microtubules) that gives the cell shape, enables movement, and organises internal transport.
Endomembrane system
The collective term for the interconnected membrane compartments that work together to modify, package, and transport proteins and lipids: the nuclear envelope, ER, Golgi apparatus, lysosomes, vesicles, and plasma membrane.
Endosymbiotic theory (endosymbiosis)
The theory that mitochondria and chloroplasts originated as free-living prokaryotes that were engulfed by an ancestral eukaryotic cell and became permanent, mutualistic residents. In simple terms, a bigger cell swallowed a smaller one, and instead of digesting it, the two struck a deal.
Vesicle
A small, membrane-enclosed sac that transports materials within the cell or between the cell and its environment.
Plasma membrane (cell membrane)
The phospholipid bilayer that forms the outer boundary of all cells, controlling what enters and exits.
Both are bounded by a plasma membrane (phospholipid bilayer)
Both contain DNA as their genetic material
Both have ribosomes for protein synthesis
Both carry out transcription and translation
Both use ATP as their energy currency
Nucleus: Eukaryotes have a true, membrane-bound nucleus. Prokaryotes have a nucleoid region with no surrounding membrane.
Size: Eukaryotic cells are typically 10 to 100 micrometres across; prokaryotic cells are roughly 1 to 10 micrometres.
Genome structure: Eukaryotic DNA is linear and wrapped around histone proteins, forming chromosomes. Prokaryotic DNA is typically a single circular chromosome, with no histones (in bacteria; archaea do have histone-like proteins).
Membrane-bound organelles: Eukaryotes contain compartmentalised organelles (nucleus, ER, Golgi, mitochondria, etc.). Prokaryotes lack these.
Ribosomes: Both have them, but they differ in size. Eukaryotic ribosomes are 80S; prokaryotic ribosomes are 70S. (This size difference is clinically important: some antibiotics target 70S ribosomes without harming 80S ones.)
Cell wall: Many prokaryotes have a peptidoglycan cell wall. Plant cells have a cellulose cell wall. Animal cells have no cell wall at all.
Reproduction: Prokaryotes divide by binary fission. Eukaryotes divide by mitosis (and meiosis for sexual reproduction).
The core idea is compartmentalisation. Eukaryotic cells gained efficiency by walling off different chemical reactions inside separate membrane-bound spaces, so that each environment can be independently optimised (pH, enzyme concentration, redox state).
Surrounded by a double membrane called the nuclear envelope. The space between the two membranes is continuous with the lumen of the rough ER.
The nuclear envelope is studded with nuclear pores, large protein complexes that regulate the traffic of molecules (mRNA, ribosomal subunits, proteins) in and out of the nucleus.
Inside, you find chromatin (DNA + histone proteins). During cell division, chromatin condenses into visible chromosomes.
The nucleolus is a dense region within the nucleus where ribosomal RNA (rRNA) is synthesised and ribosomal subunits begin assembly.
The nucleus is where transcription occurs: DNA is read and copied into messenger RNA (mRNA), which then exits through nuclear pores to be translated in the cytoplasm.
The path from gene to working protein follows a clear route:
DNA in the nucleus is transcribed into pre-mRNA.
Pre-mRNA is processed (introns spliced out, a 5' cap and poly-A tail added) to become mature mRNA.
Mature mRNA exits the nucleus through nuclear pores.
In the cytoplasm, ribosomes translate the mRNA into a polypeptide chain.
The polypeptide folds (sometimes with help from chaperone proteins) into a functional protein.
If the protein is destined for secretion or for a membrane, translation begins on free ribosomes in the cytoplasm and then the ribosome-mRNA-polypeptide complex is directed to the rough ER by a signal sequence at the start of the polypeptide.
Made of two subunits (large and small), each composed of rRNA and proteins.
Eukaryotic ribosomes are 80S (60S large + 40S small). Prokaryotic ribosomes are 70S (50S + 30S).
Free ribosomes float in the cytoplasm and typically produce proteins that function within the cytoplasm itself.
Bound ribosomes are attached to the rough ER and produce proteins destined for membranes, for organelles, or for export (secretion) from the cell.
Free and bound ribosomes are structurally identical. The difference is simply where they happen to be working at any given moment.
The endomembrane system is a set of interconnected membranes that divide the cell into functional compartments. Proteins and lipids flow through this system via transport vesicles that bud off one compartment and fuse with the next.
Rough ER: Studded with ribosomes on its cytoplasmic face. Proteins are threaded into the ER lumen as they are translated, where they fold and may receive initial sugar modifications (glycosylation). The rough ER is the starting point for proteins headed to the Golgi, the plasma membrane, lysosomes, or secretion.
Smooth ER: Lacks ribosomes. Functions include lipid synthesis (phospholipids, steroids), carbohydrate metabolism, and detoxification of drugs and poisons. In muscle cells, a specialised form of smooth ER (the sarcoplasmic reticulum) stores calcium ions.
Receives transport vesicles from the ER at its cis face (the side nearest the ER).
Proteins move through the Golgi stack from cis to trans, being further modified at each stage (trimming and adding sugar groups, adding phosphate tags, etc.).
At the trans face, finished products are sorted and packaged into vesicles for delivery to their final destination: lysosomes, the plasma membrane, or secretion outside the cell.
The Golgi also manufactures certain polysaccharides, including components of the plant cell wall.
Contain roughly 50 different hydrolytic enzymes that work best at pH ~5 (the lysosome interior is kept acidic by proton pumps in its membrane).
Functions include: digesting food particles brought in by endocytosis (phagocytosis), breaking down damaged or worn-out organelles (autophagy), and recycling macromolecules into their building blocks.
If a lysosome's membrane ruptures, the enzymes are less active at the cytoplasm's neutral pH, which limits damage, but extensive rupture can trigger cell death.
Transport vesicles bud from one compartment, travel along cytoskeletal tracks (usually microtubules), and fuse with the target membrane.
The direction of flow: ER → Golgi (cis) → Golgi (trans) → plasma membrane or lysosome.
Secretory vesicles fuse with the plasma membrane and release their contents outside the cell (exocytosis). This is how hormones, neurotransmitters, and digestive enzymes are exported.
Endocytic vesicles move material inward, from the plasma membrane to endosomes and eventually lysosomes for digestion.
Found in nearly all eukaryotic cells (a few anaerobic protists have lost them or replaced them with reduced organelles called hydrogenosomes or mitosomes).
Double membrane: the smooth outer membrane is permeable to small molecules; the highly folded inner membrane (cristae) is where the electron transport chain and ATP synthase sit.
The matrix (the space inside the inner membrane) contains the enzymes of the citric acid cycle (Krebs cycle), as well as the mitochondrion's own circular DNA and 70S ribosomes.
Overall job: aerobic respiration. Pyruvate (from glycolysis in the cytoplasm) enters the mitochondrion, is oxidised through the citric acid cycle, and the resulting electron carriers (NADH, FADH2) feed electrons into the electron transport chain, which pumps protons across the inner membrane to drive ATP synthase. Net yield per glucose: roughly 30 to 32 ATP.
Mitochondria can divide independently of the cell by binary fission, much like bacteria.
Found in plants and algae; absent from animal and fungal cells.
Double outer membrane plus a third internal membrane system: the thylakoid membranes, which are arranged in stacks called grana (singular: granum). The fluid-filled space around the thylakoids is the stroma.
Thylakoid membranes house the photosystems and electron transport components for the light reactions of photosynthesis.
The stroma contains the enzymes of the Calvin cycle (light-independent reactions), which fix CO2 into sugar (G3P).
Like mitochondria, chloroplasts have their own circular DNA and 70S ribosomes, and they divide by binary fission.
Mitochondria and chloroplasts are energy converters working in complementary directions. Chloroplasts capture light energy and store it as glucose; mitochondria break glucose down to release that energy as ATP. In a plant cell, both organelles are present, and the oxygen produced by chloroplasts is consumed by mitochondria.
Microfilaments (actin filaments): Thinnest fibres (~7 nm). Made of actin. Involved in cell shape changes, muscle contraction, cytokinesis (pinching the cell in two), and amoeboid movement.
Intermediate filaments: Medium-diameter fibres (~8 to 12 nm). Made of various proteins (e.g. keratins in epithelial cells). Provide mechanical strength and anchor organelles in place. Not found in all eukaryotes.
Microtubules: Thickest fibres (~25 nm). Made of tubulin dimers (alpha and beta). Form the mitotic spindle during cell division, serve as tracks for vesicle transport (motor proteins dynein and kinesin walk along them), and are the structural core of cilia and flagella.
The centrosome is the main microtubule-organising centre (MTOC) in animal cells. It contains a pair of centrioles, each made of nine triplets of microtubules arranged in a cylinder.
During cell division, the centrosome duplicates and the two copies move to opposite poles of the cell, organising the mitotic spindle.
Plant cells lack centrioles but still form functional spindles.
Both are extensions of the plasma membrane supported by a core of microtubules arranged in a 9+2 pattern (nine doublets around two central singlets).
Cilia are short and numerous; they beat in coordinated waves (e.g. lining the trachea to sweep mucus). Flagella are long and few; they propel the cell (e.g. sperm).
Peroxisomes: Single-membrane organelles that carry out oxidation reactions, including fatty acid breakdown and detoxification of hydrogen peroxide (H2O2) using the enzyme catalase.
Vacuoles: Large, membrane-bound sacs. In plant cells, the central vacuole can occupy most of the cell volume, storing water, ions, pigments, and waste products, and maintaining turgor pressure.
Cell wall (plants, fungi): A rigid layer outside the plasma membrane. In plants it is made of cellulose; in fungi, chitin. It provides structural support and protection.
When an organelle fails, the consequences depend on which cellular process is disrupted.
Lysosomal storage diseases (e.g. Tay-Sachs disease): A missing or defective lysosomal enzyme means the cell cannot break down a specific substrate. The substrate accumulates, eventually damaging cells. In Tay-Sachs, the enzyme hexosaminidase A is missing, so a lipid called GM2 ganglioside builds up in neurons, causing neurodegeneration.
Mitochondrial diseases: Because mitochondria have their own DNA (inherited maternally), mutations in mitochondrial DNA affect energy production. Symptoms typically appear in tissues with high energy demands: brain, muscle, heart. Examples include MELAS (mitochondrial encephalomyopathy, lactic acidosis, and stroke-like episodes) and Leber hereditary optic neuropathy.
Cystic fibrosis (ER and protein folding): A mutation in the CFTR gene produces a misfolded protein that is retained and degraded in the ER instead of reaching the plasma membrane. Without functional CFTR chloride channels, thick mucus accumulates in the lungs and other organs.
Kartagener syndrome (ciliary defects): Mutations in dynein, the motor protein that drives ciliary beating, cause immotile cilia. The result is chronic respiratory infections (cilia cannot clear mucus), male infertility (immotile sperm flagella), and often situs inversus (reversed organ positioning, because cilia-driven fluid flow during embryonic development determines left-right body asymmetry).
Zellweger syndrome (peroxisome defects): Peroxisomes fail to form properly, so very-long-chain fatty acids cannot be broken down. Severe neurological and developmental impairment results.
The size difference between eukaryotic 80S and prokaryotic 70S ribosomes is the basis of many antibiotics. Drugs like erythromycin and tetracycline target the bacterial ribosome without affecting human ribosomes, selectively killing bacteria.
Understanding vesicle traffic is central to modern drug delivery: researchers design lipid nanoparticles (essentially artificial vesicles) to carry mRNA vaccines and gene therapies into cells.
Lysosomal enzyme replacement therapy is used to treat some storage diseases (e.g. Gaucher disease): the missing enzyme is manufactured and infused into the patient, where it is taken up by cells via endocytosis and delivered to lysosomes.
Students often think that "membrane-bound nucleus" is the only difference between prokaryotes and eukaryotes. The differences extend to genome organisation, organelle compartmentalisation, cell size, ribosome size, and reproduction method.
Students frequently confuse the rough ER and the Golgi. The rough ER is where proteins are first made and folded; the Golgi is where they are modified, sorted, and dispatched. They are sequential stations, not interchangeable.
Many students believe that plant cells have chloroplasts instead of mitochondria. Plant cells have both. They need mitochondria for aerobic respiration at all times, including at night when photosynthesis stops.
Students sometimes think free ribosomes and bound ribosomes are structurally different types. They are identical. A ribosome becomes "bound" when the signal sequence on the polypeptide it is making directs it to the ER membrane.
Know the function of every organelle and be able to link a defect in that organelle to a specific disease or symptom.
Be able to trace the path of a secretory protein from gene to export: DNA (nucleus) → mRNA → ribosome on rough ER → ER lumen → transport vesicle → Golgi → secretory vesicle → plasma membrane → extracellular space.
Understand why compartmentalisation is advantageous (different environments for different reactions).
Be prepared to compare prokaryotic and eukaryotic cells in a table format, covering at least: nucleus, organelles, DNA structure, ribosome size, cell wall, and reproduction.
The endosymbiotic theory and its evidence (covered in Part 2) is a favourite exam topic. Know the four main lines of evidence.
True or false: All eukaryotic cells contain mitochondria. (Answer: Mostly true, but a few anaerobic protists have lost them.)
Fill in the blank: The ______ is the organelle where ribosomal RNA is synthesised. (Answer: nucleolus.)
True or false: The smooth ER is covered in ribosomes. (Answer: False. The rough ER is covered in ribosomes; the smooth ER lacks them.)
Fill in the blank: Lysosomes maintain an internal pH of approximately ______. (Answer: 5, i.e. acidic.)
True or false: Free ribosomes and bound ribosomes are structurally different. (Answer: False. They are identical; their location differs.)
Q: Name three features that eukaryotic cells have but prokaryotic cells lack.
A: A membrane-bound nucleus, membrane-bound organelles (e.g. ER, Golgi, mitochondria), and a cytoskeleton with microtubules, intermediate filaments, and microfilaments.
Q: Trace the pathway of a protein destined for secretion, starting from the gene.
A: Gene in the nucleus is transcribed to mRNA → mRNA exits through nuclear pores → translation begins on a free ribosome → signal sequence directs the ribosome to the rough ER → polypeptide is threaded into the ER lumen and folded → transport vesicle buds off the ER and carries the protein to the Golgi → protein is modified and sorted in the Golgi → secretory vesicle buds off the trans-Golgi → vesicle fuses with the plasma membrane (exocytosis) → protein is released outside the cell.
Q: A patient has a genetic mutation that prevents the production of a specific lysosomal enzyme. What type of disease would this cause, and why?
A: A lysosomal storage disease. Without the enzyme, the substrate it normally breaks down will accumulate inside lysosomes, eventually impairing cell function and causing tissue damage.
Q: Why do mitochondria and chloroplasts have their own DNA and ribosomes?
A: According to the endosymbiotic theory, these organelles descended from free-living prokaryotes that were engulfed by an ancestral eukaryotic cell. They retained some of their original genome and protein-synthesis machinery.
Q: Explain why a mutation in dynein could affect both respiratory health and fertility.
A: Dynein is the motor protein that drives the beating of cilia and flagella. Defective dynein means immotile cilia (leading to chronic respiratory infections because mucus is not cleared) and immotile sperm flagella (leading to male infertility).
This material connects directly to cell membrane structure (the phospholipid bilayer underlies every organelle membrane), to metabolism (mitochondria and chloroplasts are covered in depth in the photosynthesis and cellular respiration chapters), and to genetics (the nucleus, DNA replication, transcription, and translation). Understanding organelle function now will also pay off when you reach cell signalling, cell division (mitosis and meiosis), and disease pathology later in the course.
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