B2.2 Organelles and compartmentalization

A eukaryotic cell is a city of specialised compartments. Rather than letting every reaction happen in one shared space, the cell wraps incompatible processes in their own membranes — a strategy called compartmentalization. This lets the cell run digestion, energy capture and protein manufacture side by side without interference, much as a factory keeps its furnace separate from its packing room. For B2.2 you need to know what each organelle does and, crucially, why separating it from the rest of the cell makes the cell more efficient. Examiners reward answers that explain the advantage of the compartment, not just name the part.

Why compartmentalize?

Compartmentalization is the division of the cell into membrane-bound compartments. It brings several efficiency advantages that the syllabus asks you to explain:

• Incompatible processes are separated. Hydrolytic (digestive) enzymes are kept inside lysosomes, so they cannot break down the rest of the cell.
• Concentrations of reactants and enzymes can be raised locally. Keeping enzymes and substrates together in a small volume speeds reactions.
• Optimum conditions can be maintained. Each compartment can hold a different pH, such as the acidic interior of a lysosome.
• Membranes provide extra surface area for reactions that occur on membranes, such as the light-dependent reactions on thylakoid membranes.
• Toxic or reactive intermediates are contained, protecting the rest of the cell.

The membranes themselves are made of phospholipid bilayers, so the properties from B2.1 explain how each compartment controls its own internal environment.

Organelles of energy and synthesis

The nucleus is bounded by a double membrane (the nuclear envelope) perforated by pores; it stores the DNA and is where transcription occurs, keeping the genetic material separate from the cytoplasm.

Mitochondria carry out aerobic respiration, producing most of the cell’s ATP. They have a double membrane; the inner membrane is folded into cristae that increase the surface area for the reactions of oxidative phosphorylation, and the fluid matrix holds the enzymes of the Krebs cycle.

Chloroplasts (in plants and algae) carry out photosynthesis. Stacks of thylakoid membranes hold chlorophyll and provide surface area for the light-dependent reactions, while the surrounding fluid stroma is where the light-independent reactions fix carbon.

Both mitochondria and chloroplasts contain their own small loop of DNA and 70S ribosomes — evidence for the endosymbiotic origin of eukaryotic cells.

The endomembrane system

Several organelles work together to make, modify and ship proteins:

• Ribosomes synthesise polypeptides. Free ribosomes make proteins for use inside the cell; those on the rough endoplasmic reticulum make proteins for secretion or membranes. Eukaryotic ribosomes are 80S, larger than the 70S of prokaryotes.
• Rough endoplasmic reticulum (rER) is studded with ribosomes and processes and transports newly made proteins.
• Smooth endoplasmic reticulum (sER) lacks ribosomes and synthesises lipids.
• Golgi apparatus modifies, sorts and packages proteins into vesicles for secretion or delivery.
• Vesicles transport materials between organelles and to the membrane.
• Lysosomes contain hydrolytic enzymes for digesting worn-out organelles and engulfed material; their isolating membrane is what makes this safe.

Structures unique to certain cells

Some structures appear only in particular cell types, and the syllabus asks you to compare cells. The cell wall of plants and fungi (cellulose in plants) lies outside the membrane and provides support and prevents bursting. The large central vacuole of plant cells stores sap and maintains turgor pressure. Centrioles in animal cells help organise the spindle during cell division.

It is also useful to contrast eukaryotic with prokaryotic cells: prokaryotes lack a nuclear membrane and membrane-bound organelles, have a single circular DNA molecule in a region called the nucleoid, and have smaller 70S ribosomes. The absence of compartmentalization is a key difference and explains why prokaryotes cannot reach the size and internal complexity of eukaryotes.