Difficulty: Introductory | Prerequisites: None, though a basic understanding of biological molecules (proteins, lipids, nucleic acids) is helpful.
Cell structure is the foundation of all biology. Every living organism, from the simplest bacterium to the most complex animal, is built from cells, and understanding how cells are organised is the first step toward understanding how life works. This topic covers the two major categories of cells (prokaryotic and eukaryotic), the organelles that carry out specific functions within them, and how the endomembrane system connects several of those organelles into a coordinated network. If you are coming into this cold, the core idea is straightforward: cells are compartmentalised, and each compartment has a job.
Cells come in two flavours: prokaryotic (no nucleus, simpler) and eukaryotic (membrane-bound nucleus, compartmentalised organelles). Eukaryotic cells use an interconnected set of organelles called the endomembrane system to build, modify, and ship proteins and lipids. Both cell types share a plasma membrane and ribosomes, but eukaryotes have far more internal structure.
Prokaryote
An organism whose cells lack a membrane-bound nucleus and other membrane-bound organelles. Divided into two domains: Bacteria and Archaea. In simple terms, these are the smaller, simpler cells. Their DNA floats freely in the cytoplasm.
Eukaryote
An organism whose cells contain a clearly defined, membrane-bound nucleus housing well-defined chromosomes. Think of it as the "upgraded" cell type, with internal compartments (organelles) that each handle specific tasks.
Plasma membrane
A selectively permeable membrane found in all cells that separates the cell's interior from the outside environment. It is the boundary of every cell. Nothing gets in or out without passing through or being approved by this membrane.
Ribosome
An RNA-containing structure in the cytoplasm that binds messenger RNA (mRNA) and transfer RNA (tRNA) to synthesise polypeptides and proteins. Think of it as the cell's protein-building machine. Both prokaryotes and eukaryotes have them.
Endoplasmic reticulum (ER)
A network of membranes within the eukaryotic cell that produces proteins and lipids for the rest of the cell. Comes in two forms: smooth ER (no ribosomes, makes lipids, detoxifies, stores calcium) and rough ER (studded with ribosomes, synthesises proteins and phospholipids). In simple terms, the ER is the cell's factory floor, split into two wings with different jobs.
Golgi apparatus
A membrane-bound organelle that receives products from the ER, modifies and sorts them, and manufactures certain macromolecules. Think of it as the cell's post office: it packages, labels, and ships proteins to their correct destinations.
Lysosome
A membrane-bound organelle with an acidic interior, filled with digestive enzymes that break down macromolecules (proteins, fats, nucleic acids, polysaccharides) into their component parts via hydrolysis. The cell's recycling centre. It digests worn-out parts and foreign material.
Circular DNA
DNA that forms a closed loop with no free ends, characteristic of prokaryotic cells. Prokaryotic chromosomes are rings, not the long linear strands you see in eukaryotes.
Endomembrane system
The collective term for the interconnected network of organelles (ER, Golgi apparatus, lysosomes, vesicles, plasma membrane) that work together to synthesise, process, and transport proteins and lipids within the cell. It is the supply chain that runs through a eukaryotic cell, connecting production to delivery.
The most fundamental division in cell biology is between prokaryotes and eukaryotes. Know the overlaps and differences cold; this comparison appears on virtually every introductory biology exam.
What they share (both cell types)
Plasma membrane (acts as a container)
Semifluid aqueous interior called cytosol
Chromosomes made of DNA (carry inheritance information)
Ribosomes (help make proteins)
Prokaryote-only features
One chromosome of circular DNA
DNA located in an unbound "nucleoid" region, not inside a membrane
Always have a cell wall
Some have a capsule (extra protective layer outside the cell wall)
Some have flagella or fimbriae for movement or attachment
No membrane-bound organelles
Eukaryote-only features
Two or more chromosomes of linear DNA
DNA housed inside a membrane-bound nucleus
Do not always have a cell wall (animal cells lack one; plant and fungal cells have one)
Have membrane-bound organelles (ER, Golgi, mitochondria, lysosomes, etc.)
Plants and animals share most of the same organelles. The key differences: plant cells have a cell wall and chloroplasts; animal cells do not.
The plasma membrane is universal: every cell has one. It separates the cell's interior from the external environment and controls what enters and exits.
In bacterial and plant cells, a rigid cell wall sits outside the plasma membrane, providing structural support.
Animal cells have no cell wall, only the plasma membrane.
The membrane is selectively permeable, meaning it allows certain molecules through while blocking others.
This distinction matters when comparing cell types. "Does it have a cell wall?" is one of the quickest ways to sort prokaryotes from animal cells on an exam.
The endomembrane system is a network of organelles that work together to synthesise, modify, package, and transport proteins and lipids. This is a eukaryote-only feature.
Ribosomes
Found in both prokaryotes and eukaryotes, but in eukaryotes they can be free in the cytoplasm or attached to the rough ER.
Function: bind mRNA and tRNA to synthesise polypeptides (proteins).
They are not membrane-bound, so they are technically not organelles, but they are essential to the system.
Smooth endoplasmic reticulum (smooth ER)
No ribosomes on its surface.
Functions:
Lipid synthesis
Detoxification of poisons and drugs
Calcium ion (Ca²⁺) storage
Particularly abundant in liver cells (detoxification) and muscle cells (calcium storage for contraction).
Rough endoplasmic reticulum (rough ER)
Studded with ribosomes on its cytoplasmic surface, giving it a "rough" appearance.
Functions:
Protein synthesis (secretory proteins and membrane proteins)
Phospholipid production
Makes components of the endomembrane system itself
Proteins made here are threaded into the ER lumen, folded, and sent to the Golgi in transport vesicles.
Golgi apparatus
Receives transport vesicles from the ER.
Modifies, sorts, and packages proteins and lipids.
Manufactures certain macromolecules (e.g. polysaccharides).
Works by cisternal maturation: products move through a series of flattened membrane sacs (cisternae) from the cis face (receiving side, near the ER) to the trans face (shipping side, near the plasma membrane).
Lysosomes
Membrane-bound sacs with an acidic interior (low pH), full of hydrolytic (digestive) enzymes.
Break down macromolecules: proteins, fats, nucleic acids, and polysaccharides into their smaller components.
Carry out intracellular digestion via phagocytosis (engulfing material from outside the cell) and autophagy (recycling the cell's own worn-out organelles).
Enzymes are made by the rough ER and processed by the Golgi before delivery to the lysosome.
The flow through the system
Rough ER (protein synthesis) → transport vesicles → Golgi apparatus (modification and sorting) → vesicles → either the plasma membrane (secretion) or lysosomes (digestion). The smooth ER contributes lipids and handles detoxification in parallel.
No formulas in this topic, but two diagrams are worth memorising:
Venn diagram: prokaryote vs eukaryote. Draw three zones (prokaryote-only, shared, eukaryote-only) and fill them from the comparison table above. Being able to reproduce this from memory is a reliable exam skill.
Endomembrane system flow diagram. Sketch the pathway: Rough ER → transport vesicle → Golgi (cis to trans) → vesicle → plasma membrane or lysosome. Place the smooth ER alongside, feeding lipids into the system. Label each organelle with its primary function.
Antibiotics like penicillin target the prokaryotic cell wall, which is why they kill bacteria without harming your own (eukaryotic) cells. This is the direct clinical payoff of understanding the structural differences between the two cell types.
Lysosomal storage diseases (e.g. Tay-Sachs) occur when a lysosome lacks a specific enzyme and cannot break down a particular molecule, causing toxic build-up. Understanding lysosome function explains why these diseases are so damaging.
Students often think all prokaryotes are bacteria. They are not. Archaea are a separate domain of prokaryotes with distinct biochemistry.
Students often confuse the cell wall with the plasma membrane. The cell wall is a rigid outer layer (present in bacteria, plants, fungi). The plasma membrane is the flexible lipid bilayer underneath it. All cells have a plasma membrane; not all have a cell wall.
Students often think the smooth ER is less important because it lacks ribosomes. It handles critical functions: lipid synthesis, detoxification, and calcium storage.
Students sometimes place ribosomes only on the rough ER. Free ribosomes in the cytoplasm also synthesise proteins, particularly those used within the cytoplasm itself.
⚠️ The prokaryote vs eukaryote comparison is one of the most commonly tested topics in introductory biology. Be able to list shared features, prokaryote-only features, and eukaryote-only features from memory.
⚠️ Know the functions of smooth ER vs rough ER. Exams frequently ask you to match each ER type to its specific roles.
⚠️ Understand the flow through the endomembrane system: Rough ER → Golgi → plasma membrane or lysosome. Questions often ask you to trace a protein from synthesis to its final destination.
⚠️ Lysosome function (hydrolysis, phagocytosis, autophagy) is a frequent exam target. Know what happens when lysosomal enzymes are missing or non-functional.
True or False: Prokaryotic cells contain membrane-bound organelles. (False)
Fill in the blank: The ______ ER is studded with ribosomes and is involved in protein synthesis. (Rough)
True or False: Both prokaryotes and eukaryotes have ribosomes. (True)
Fill in the blank: Lysosomes break down macromolecules through a process called ______. (Hydrolysis)
True or False: Animal cells have a cell wall outside their plasma membrane. (False)
Q: Name three features shared by both prokaryotic and eukaryotic cells.
A: Plasma membrane, cytosol, ribosomes, and DNA (chromosomes). Any three of these.
Q: A protein is synthesised on the rough ER. Trace its path to secretion outside the cell.
A: Rough ER (synthesis and folding) → transport vesicle → Golgi apparatus (modification and sorting) → secretory vesicle → plasma membrane → exocytosis (release outside the cell).
Q: What are the three main functions of the smooth ER?
A: Lipid synthesis, detoxification of poisons and drugs, and calcium ion storage.
Q: How do lysosomes contribute to cellular recycling?
A: Lysosomes contain hydrolytic enzymes that break down macromolecules. Through autophagy, they digest the cell's own worn-out organelles and recycle the components. Through phagocytosis, they digest material brought in from outside the cell.
Q: Why do prokaryotes lack an endomembrane system?
A: Prokaryotes have no membrane-bound organelles. The endomembrane system (ER, Golgi, lysosomes, vesicles) requires internal membranes to compartmentalise functions, which is a defining feature of eukaryotic cells only.
This material connects directly to membrane transport (how substances cross the plasma membrane), which builds on the membrane's selective permeability covered here. It also connects to cellular respiration and photosynthesis, because the mitochondria and chloroplasts introduced in the next set of notes are themselves membrane-bound organelles that fit into the broader picture of eukaryotic compartmentalisation. The endomembrane system's protein-trafficking pathway is foundational for understanding the secretory pathway and signal transduction in later units.
Prokaryote, eukaryote, cell structure, plasma membrane, cell membrane, cell wall, ribosome, endoplasmic reticulum, smooth ER, rough ER, Golgi apparatus, Golgi body, lysosome, hydrolysis, endomembrane system, circular DNA, nucleoid, organelle, cytoplasm, cytosol, vesicle, transport vesicle, secretory pathway, autophagy, phagocytosis, cisternal maturation, phospholipid, protein synthesis, BIO 112, intro biology, cell biology basics