1What lives where

Every one of these is bounded by a membrane, and the membrane controls what enters and leaves (2.4 to 2.8). That control is what lets each compartment hold different contents from the cytosol around it.

2Benefit one: keeping competing reactions apart

If every enzyme in a cell were mixed together in the cytosol, many would get in each other's way.

• Destructive enzymes would attack the cell. Lysosomal enzymes hydrolyse proteins, nucleic acids, lipids and carbohydrates. Inside a lysosome they digest only what is delivered to them. Loose in the cytosol they would break down the cell's own molecules.
• Opposite pathways would cancel out. A cell that builds a molecule in one pathway and breaks it down in another would waste energy if both ran in the same space at once. Putting them in different compartments lets the cell control each separately.
• Different reactions need different conditions. Lysosomal enzymes work best at about pH 5, which is maintained inside the lysosome; the cytosol is close to pH 7.2. A compartment can hold the conditions its enzymes need without forcing them on the whole cell. That separation is also a safeguard: if a lysosome leaks a little, its enzymes are far less active at the cytosol's pH.
• Reactants are concentrated. Enzymes and their substrates are packed into a small space, so they meet more often and reactions run faster.

Compartments keep reactions that would interfere with each other apart, and give membrane-bound reactions more room.

3Benefit two: more membrane, more reactions

Many reactions happen on membranes, because the enzymes or carrier molecules involved are embedded in them. The more membrane a cell has, the more of these reactions it can run at once.

Figure 1 shows a mitochondrion. It has two membranes, so it has two compartments of its own: the narrow intermembrane space between the membranes, and the matrix inside the inner membrane. The inner membrane is folded into cristae. The ATP-producing proteins of respiration sit in the inner membrane, and the folds pack far more of it, and far more of those proteins, into the same small organelle.

Chloroplasts do the same with stacks of internal membrane sacs, where the light-capturing pigments sit. The endoplasmic reticulum's network of sheets and tubes gives a huge area for ribosomes and for lipid-making enzymes.

This is the 2.2 idea working inside a cell: folding raises surface area without raising volume.

4The costs

Compartments are not free.

• Everything that must move between compartments has to cross a membrane, which needs transport proteins and often energy.
• Making and maintaining all those membranes uses lipids, proteins and energy.
• A cell that depends on compartments can be disrupted by damage to any one of them.

For a eukaryotic cell, much larger than a prokaryote (2.2), the benefits outweigh the costs: it could not organise its chemistry in one open space.

5Predicting the effects of disruption

AP asks you to predict the effects of a change in one part of a system. Follow the chain: which compartment is affected → which process does it enclose → what happens to that process → what does the cell lose?

• Leaky lysosome membranes. Hydrolytic enzymes escape into the cytosol. Their activity there is lower, because the pH is near 7.2, but if many lysosomes break they can damage the cell's own molecules, and material inside lysosomes is no longer digested properly.
• Fewer or smaller cristae. Less inner membrane, so fewer ATP-producing proteins: less ATP per mitochondrion, and active transport, protein synthesis and other energy-using processes slow.
• A leak in the inner mitochondrial membrane. The different conditions on its two sides cannot be kept, and ATP production falls (Unit 3 explains why).
• Damage to the nuclear envelope. The nucleus can no longer separate DNA and RNA processing from the cytosol.

An invented data set links structure to output:

The more inner membrane, the more ATP; the ratio of ATP to membrane area stays at about 2.4 relative units per µm² in all three, which supports the claim that ATP output depends on the area of inner membrane.