Organelles and compartmentalization
🎯What you need to be able to do
- Define an organelle, and state which cell structures are and are not organelles.
- Outline how cell fractionation with an ultracentrifuge made the study of organelles possible.
- Explain the advantage of separating transcription in the nucleus from translation in the cytoplasm.
- Explain the advantages of compartments in the cytoplasm, using lysosomes and phagocytic vacuoles.
- AHL Explain how mitochondria and chloroplasts are adapted for ATP production and photosynthesis.
- AHL Explain the benefits of the nuclear double membrane and its pores, and what happens to it in division.
- AHL Contrast free ribosomes with those on rough ER, and outline the roles of the Golgi apparatus, vesicles and clathrin.
📚The biology
What an organelle is
An organelle is a discrete subunit of a cell that is adapted to perform a specific function — the cell’s equivalent of an organ. Deciding what counts is a matter of definition, and the syllabus draws the line like this:
nucleus, mitochondria, chloroplasts, endoplasmic reticulum, Golgi apparatus, vesicles and vacuoles (including lysosomes), ribosomes, and the plasma membrane.
the cell wall (outside the cell and not a discrete functional unit of the living cell), the cytoskeleton (a network extending throughout the cell) and the cytoplasm (the medium the organelles sit in).
Note that ribosomes count as organelles even though they have no membrane.
Studying the function of individual organelles only became possible after the invention of the ultracentrifuge and the development of cell fractionation. Cells are broken up in a cold, isotonic, buffered solution, and the mixture is spun at increasing speeds. The largest and densest organelles settle out first into a pellet at low speed; smaller ones need higher speeds. Each fraction can then be tested to see what reactions it performs. It is a clear case of scientific progress following the development of a new technique.
nuclei (and in plants, chloroplasts)
mitochondria (and lysosomes)
fragments of ER and other membranes
ribosomes
The advantage of a nucleus
In eukaryotes, the nucleus separates transcription (making mRNA from DNA, inside the nucleus) from translation (making polypeptides on ribosomes, in the cytoplasm).
The benefit is time and space for post-transcriptional modification: the initial RNA transcript can be processed — for example by removing introns (D1.2) — before it leaves the nucleus and meets any ribosomes. Only finished mRNA is translated.
In prokaryotes there is no nucleus, so this is not possible: ribosomes can attach to mRNA and begin translating it while it is still being transcribed.
Compartments in the cytoplasm
Dividing the cytoplasm into membrane-bound compartments has two main advantages:
- Concentration of metabolites and enzymes. Enzymes and their substrates can be kept together at high concentration in a small volume, so reactions happen much faster than if they were spread through the whole cell. Conditions such as pH can also be kept optimal for those particular enzymes.
- Separation of incompatible processes. Reactions or substances that would harm each other, or the cell, can be kept apart.
Lysosomes are the clearest example. They contain hydrolytic enzymes that would digest the cell’s own proteins, nucleic acids and membranes if they were free in the cytoplasm. Inside the lysosome membrane they are kept safely separate, at a high concentration, and at the acidic pH at which they work best. When a phagocyte engulfs a bacterium, the bacterium is held in a phagocytic vacuole; lysosomes fuse with it and release their enzymes, so digestion happens inside a compartment without damaging the rest of the cell.
Mitochondria: adapted for aerobic respiration AHL
The electron transport chain pumps protons from the matrix into the intermembrane space. Because this space is very small in volume, a steep proton gradient builds up quickly from relatively few protons, driving ATP synthesis by chemiosmosis.
The inner membrane is folded into cristae, greatly increasing the area available for the electron transport chain and ATP synthase molecules, so more ATP can be made.
The enzymes and substrates of the link reaction and Krebs cycle are concentrated in the matrix, next to the inner membrane where the reduced NAD they produce is used.
The details of respiration are in C1.2.
Chloroplasts: adapted for photosynthesis AHL
Thylakoids are flattened membrane sacs, many stacked into grana. Their membranes hold the photosystems, electron carriers and ATP synthase, so a large area means more light absorbed and more light-dependent reactions.
Protons are pumped into the thylakoid space, and because its volume is very small, a steep proton gradient forms rapidly for ATP production by chemiosmosis.
The enzymes and substrates of the Calvin cycle, including rubisco, are concentrated in the stroma, surrounding the thylakoids that supply ATP and reduced NADP.
The details are in C1.3.
The nuclear double membrane AHL
The nucleus is enclosed by a double membrane, the nuclear envelope, which separates DNA and the processes of transcription from the reactions of the cytoplasm and protects the DNA.
- Nuclear pores are needed because materials must pass in both directions: mRNA and ribosome subunits must leave the nucleus, and proteins such as RNA polymerase, histones and transcription factors, together with nucleotides, must enter. The pores are large, regulated protein complexes that control this traffic.
- During mitosis and meiosis, the nuclear membrane must break down into vesicles so that spindle microtubules can reach and move the chromosomes. At the end of division, the vesicles fuse again to form new nuclear envelopes around each set of chromosomes (D2.1). A membrane that can break into vesicles and re-form is what makes this possible.
Free ribosomes and rough ER AHL
Suspended in the cytoplasm. Synthesize proteins that are retained in the cell and used in the cytoplasm — for example the enzymes of glycolysis.
Bound to the membranes of the ER. Synthesize proteins that are transported within the cell (to lysosomes or membranes) or secreted. The growing polypeptide passes into the ER lumen, where it folds and is carried away in vesicles.
Free and bound ribosomes are identical; where a ribosome ends up depends on the protein it is making. A short signal sequence at the start of a polypeptide destined for secretion directs its ribosome to attach to the ER.
The Golgi apparatus AHL
The Golgi apparatus is a stack of flattened, curved membrane sacs (cisternae). Vesicles carrying proteins from the rough ER fuse with the Golgi on one side. Within the Golgi the proteins are processed — for example by adding carbohydrate chains to make glycoproteins — and sorted. On the other side, vesicles bud off carrying the finished proteins towards the plasma membrane for secretion by exocytosis.
Cells that secrete a great deal of protein, such as pancreatic cells making digestive enzymes or plasma cells making antibodies, have an extensive rough ER and a large Golgi apparatus.
Vesicles and clathrin AHL
Vesicles are small membrane-bound sacs that carry materials within the cell, between the ER, the Golgi, lysosomes and the plasma membrane, and into or out of the cell by endocytosis and exocytosis.
Clathrin is a protein that helps vesicles form. Clathrin molecules have three legs and assemble on the cytoplasmic side of a membrane into a cage-like lattice of hexagons and pentagons. As the lattice grows it bends the membrane into a pit, which deepens into a bud and finally pinches off as a coated vesicle. The clathrin coat is then removed so the vesicle can fuse with its target.
✏️Worked example
contained most of the cell’s DNA
highest rate of oxygen uptake when pyruvate was added
membrane fragments with attached ribosomes
(b) Explain why the solution was cold, isotonic and buffered.
(c) Suggest why pellet 2 also contained high levels of hydrolytic enzyme activity.
(d) Explain the advantage to the cell of keeping those hydrolytic enzymes in a separate compartment.
(a) Pellet 1: nuclei. The nucleus is the largest and densest organelle, so it sediments at the lowest speed, and it contains most of the cell’s DNA. Pellet 2: mitochondria. They sediment at medium speed, and oxygen uptake with pyruvate indicates the link reaction, Krebs cycle and electron transport chain, all of which happen in mitochondria.
(b) Cold slows the activity of enzymes, including hydrolytic enzymes released from damaged lysosomes, which would otherwise digest the organelles. Isotonic prevents water moving into or out of organelles by osmosis, so they neither burst nor shrink. Buffered keeps the pH constant, so proteins are not denatured.
(c) Lysosomes are similar in size and density to mitochondria, so they sediment at a similar speed and end up in the same fraction.
(d) Hydrolytic enzymes would digest the cell’s own proteins, lipids and nucleic acids if free in the cytoplasm. Inside lysosomes they are separated from the rest of the cell, kept at high concentration where they are needed, and at the acidic pH at which they work best. They can then be delivered to phagocytic vacuoles to digest engulfed material safely.
📝Practise
Work through these on paper, then reveal the answer. Questions 4–6 are AHL.
1. State whether each of these is an organelle: ribosome, cell wall, vesicle, cytoskeleton, plasma membrane.
2. Explain the advantage to eukaryotes of transcription and translation happening in separate compartments.
3. Outline two advantages of compartmentalization in the cytoplasm, using lysosomes as an example.
4. AHL Explain how the structure of a mitochondrion is adapted for ATP production.
5. AHL Contrast the proteins made by free ribosomes with those made by ribosomes attached to the rough endoplasmic reticulum.
6. AHL Outline the pathway by which a protein for secretion is produced and released, including the role of clathrin in vesicle formation.
🔗Go deeper — other people’s work
These are external resources, not mine. If one stops working, tell me and everything above it on this page still stands.
- The Cell Image Library — electron micrographs of mitochondria, chloroplasts, rough ER and the Golgi, for practising identification.
- XVIVO / Harvard BioVisions, The Inner Life of the Cell — an animation of vesicle traffic and organelles at work.
- RCSB Protein Data Bank, Molecule of the Month — clathrin, showing the cage structure that shapes vesicles.