Cell Compartmentalization: Study Guide (Biology 2.9)

A cell needs separate rooms

A eukaryotic cell carries out thousands of different chemical reactions at the same time. Some of them work against each other. One set of enzymes builds fatty acids while another breaks them down. Digestive enzymes that destroy worn-out proteins must not meet the new proteins the cell has just made. Some enzymes work best in acid, others near neutral pH.

A house solves a similar problem with rooms: you cook in the kitchen and sleep in the bedroom. A eukaryotic cell uses membranes as walls. Membranes and membrane-bound organelles divide the cell into compartments. Each compartment holds its own enzymes, its own substrates and its own conditions. This is compartmentalization.

The membrane-bound structures of a eukaryotic cell

Structure	Membranes	What it keeps in its own space
Nucleus	double nuclear envelope with pores	DNA, copying of DNA and making of RNA; ribosomes that make proteins stay outside
Rough endoplasmic reticulum (ER)	network of membrane sheets with ribosomes on the outside	proteins being made for membranes, for lysosomes or for export, kept apart from cytosol proteins
Smooth ER	network of membrane tubes, no ribosomes	lipid synthesis and detoxification enzymes
Golgi complex	stack of flattened membrane sacs	enzymes that modify, sort and package proteins and lipids
Vesicles	small single-membrane sacs	cargo moving between compartments or to the plasma membrane
Lysosomes	single membrane with proton pumps	hydrolytic (digestive) enzymes in an acidic interior
Vacuoles	single membrane	water, ions and stored materials (one large central vacuole in plant cells)
Mitochondria	outer membrane plus a folded inner membrane	two spaces (intermembrane space and matrix) for the stages of aerobic respiration that follow glycolysis
Chloroplasts	double envelope plus internal thylakoid membranes	light-capturing reactions on the thylakoids; carbon-fixing reactions in the fluid around them

The plasma membrane is a compartment boundary too. It separates the whole cell from its surroundings. Ribosomes are not membrane-bound, so they are not compartments, but many of them work on the surface of the rough ER.

Idea 1: compartments keep competing reactions apart

A membrane stops enzymes and substrates mixing freely. That gives the cell three advantages.

1. Opposing processes can run at the same time. Building a molecule and breaking it down would cancel out, and waste energy, if the two sets of enzymes shared one space. Separating them lets the cell control each pathway on its own.
2. Each compartment can keep its own conditions. The best example is pH. Proton pumps in the lysosome membrane use ATP to move H⁺ ions into the lysosome. The inside reaches about pH 4.5–5, while the cytosol stays near pH 7.2. Lysosomal enzymes work best in that acid. Remember that pH is a logarithmic scale: each step of 1 pH unit is a tenfold change in H⁺ concentration.
3. Dangerous enzymes and products stay contained. Lysosomal enzymes can digest proteins, lipids, nucleic acids and carbohydrates. Kept inside a membrane, they only attack material delivered to them. If a few leak out, they meet the near-neutral cytosol, where they work poorly. This is a second line of protection. (Background: peroxisomes are a further example. They make hydrogen peroxide, a harmful by-product, and break it down in the same compartment.)

A small compartment also concentrates its enzymes and substrates. The same number of molecules in a smaller volume means more frequent collisions, so reactions run faster than they would if the molecules were spread through the whole cell.

Idea 2: folded membranes add surface area

Many reactions do not happen in solution. They happen on proteins embedded in a membrane. In a mitochondrion, the proteins of the electron transport chain and the enzyme ATP synthase sit in the inner membrane. In a chloroplast, the light-capturing proteins sit in the thylakoid membranes. The amount of membrane limits how many of these proteins the organelle can hold.

Folding solves this. The inner membrane of a mitochondrion folds into cristae. The thylakoids of a chloroplast are stacked into piles called grana. The ER is a large network of membranes that fills much of the cytoplasm. Each of these packs a large membrane area into a small volume.

The two membranes of a mitochondrion do a second job as well. They create two spaces with different contents. In Unit 3 you will see that the cell pumps H⁺ ions from the matrix into the intermembrane space, and that this difference across the inner membrane is what drives ATP synthase. Without a closed compartment, the ions would simply spread out and the difference would be lost.

Worked example 1: how much area do cristae add?

Question. A model mitochondrion is a box 2.0 µm long, 0.5 µm wide and 0.5 µm high. Each crista is modelled as a flat fold 0.4 µm deep and 0.5 µm wide. A fold has two faces, both made of inner membrane.

(a) Calculate the area of the outer membrane and the volume of the model. (b) The inner membrane has 24 cristae. Calculate its total area, taking the unfolded part to have the same area as the outer membrane. (c) A mitochondrion of the same size in a very active cell has 48 cristae. Compare its inner membrane area with (b).

(a)

1. A box has six faces: area = 2 × (L × W + L × H + W × H).
2. Area = 2 × (2.0 × 0.5 + 2.0 × 0.5 + 0.5 × 0.5) = 2 × (1.0 + 1.0 + 0.25) = 4.5 µm².
3. Volume = 2.0 × 0.5 × 0.5 = 0.5 µm³.

(b)

1. Area of one crista = 2 faces × 0.4 µm × 0.5 µm = 0.40 µm².
2. Area added by 24 cristae = 24 × 0.40 = 9.6 µm².
3. Total inner membrane = 4.5 + 9.6 = 14.1 µm².
4. Compared with the outer membrane: 14.1 ÷ 4.5 = 3.1 times as much.
5. Membrane area per unit volume rises from 4.5 ÷ 0.5 = 9.0 µm⁻¹ to 14.1 ÷ 0.5 = 28.2 µm⁻¹. The volume has not changed.

(c)

1. Area added by 48 cristae = 48 × 0.40 = 19.2 µm².
2. Total = 4.5 + 19.2 = 23.7 µm², which is 23.7 ÷ 14.1 = 1.7 times the area in (b).

Interpretation. If each square micrometre of inner membrane holds the same number of ATP synthase molecules, the 48-crista mitochondrion can hold about 1.7 times as many and can make ATP faster, all in the same volume. A common slip is to compare only the added area (9.6 ÷ 4.5 = 2.1); the unfolded part of the inner membrane counts too. Real cristae are curved and vary in size, so treat the numbers as a model, but the conclusion holds: folding raises the area without raising the volume.

Worked example 2: predicting the effect of disrupting a compartment

Question. A researcher measures the activity of a lysosomal enzyme (enzyme L) at different pH values. The data are fictional.

pH	4.5	5.0	5.5	6.0	6.5	7.2
Activity / % of maximum	100	92	70	45	24	6

In untreated cells, the lysosome interior is at pH 4.8. Two hours after adding a drug that blocks the proton pumps in the lysosome membrane, it is at pH 6.4.

(a) By what factor did the H⁺ concentration inside the lysosomes change? (b) Estimate the activity of enzyme L before and after the drug. (c) Predict the effect on the cell, and predict what would happen to enzyme L if lysosomes burst.

(a)

1. The pH rose by 6.4 − 4.8 = 1.6 units.
2. Each unit is a factor of 10, so the H⁺ concentration fell by a factor of 10¹·⁶ ≈ 40.

(b) Read between the data points (assume a straight line between neighbouring points).

1. pH 4.8 is 0.3 units above 4.5, which is 0.3 ÷ 0.5 = 0.6 of the way to 5.0: 100 − 0.6 × (100 − 92) = 100 − 4.8 ≈ 95%.
2. pH 6.4 is 0.4 units above 6.0, which is 0.4 ÷ 0.5 = 0.8 of the way to 6.5: 45 − 0.8 × (45 − 24) = 45 − 16.8 ≈ 28%.
3. The activity falls by about 67 percentage points, a loss of about 70% of its previous value (67 ÷ 95 ≈ 0.70).

(c) Prediction. The pumps keep the compartment acidic, and they need ATP. Without them, H⁺ ions leak out until the lysosome is close to the cytosol’s pH. Enzyme L then works at under a third of its previous rate. Material sent to the lysosomes for digestion (old organelles, engulfed particles) would be broken down slowly and would build up, so the lysosomes would swell. The cell would also recycle fewer amino acids and other building blocks from that material.

If lysosomes burst, enzyme L would enter the cytosol at pH 7.2, where its activity is only about 6% of maximum. A few broken lysosomes would do little harm. That is the protective value of keeping digestive enzymes in an acidic compartment. Large-scale bursting, however, releases so much enzyme that the cell can be damaged.

How confident? The prediction assumes the drug acts only on the pumps and that enzyme L behaves inside a cell as it did in the test tube. A good next experiment would measure undigested material in treated and untreated cells.

Common misconceptions

• “The cytoplasm is one well-mixed soup.” In a eukaryotic cell, membranes divide it into many spaces with different enzymes and conditions.
• “Membranes are just walls.” They are also work surfaces. Many enzymes, pumps and ATP synthase are embedded in membranes.
• “Cristae make the mitochondrion bigger.” Folding increases membrane area while the volume stays the same.
• “Compartments are sealed off from each other.” Material moves between them in vesicles and through transport proteins. Compartments control traffic; they do not stop it.
• “Lysosomal enzymes would destroy the cell the moment one leaks.” They work poorly at the near-neutral pH of the cytosol, which limits damage from small leaks.
• “The nucleus makes the cell’s proteins.” The nucleus holds the DNA and makes RNA. Proteins are made on ribosomes outside it, in the cytosol or on the rough ER.
• “A higher pH means more H⁺ ions.” The opposite: higher pH means fewer H⁺ ions, by a factor of 10 for each unit.

Where this leads

Topic 2.10 asks where compartments came from, and compares the internal organization of prokaryotic and eukaryotic cells: go to Origins of Cell Compartmentalization. In Unit 3 you will use the idea of separate spaces and folded membranes to explain photosynthesis and cellular respiration. Test yourself now with the practice questions, then use the revision notes and the checklist to consolidate. If you need to review pumps and active transport first, see Mechanisms of Transport.