B2.2 Organelles and compartmentalization

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Educerie · IB Diploma · Biology

Theme B Form and function · B2.2 Organelles and compartmentalization

Level: SL and HL. Sections 5 to 10 are HL only. If you are SL, skip them; nothing in your papers tests them.
Themes (key concepts): form and function, at the level of cells. An organelle is a compartment built for one job, and its shape is the job written in membrane: folded where it needs area, small where it needs concentration, sealed where it needs separation.
The question this unit answers: how are organelles in cells adapted to their functions, and what are the advantages of compartmentalization?
Where it is examined: Paper 1A multiple choice (which structures count as organelles, which organelle does what); Paper 1B data on cell fractionation or on electron micrographs, including magnification calculations (3–6 marks); Paper 2 short answers such as "explain one advantage of compartmentalization" (2–3 marks); and at HL, Paper 2 Section B parts such as "explain how the structure of the mitochondrion is adapted to its function" or "outline the production and secretion of a protein" (4–7 marks).

What you must be able to do

You must be able to	Level	What it looks like in the exam
Define an organelle and sort structures into organelles and non-organelles	SL, HL	Paper 1A: "Which of the following is not an organelle?"
Explain how cell fractionation made the study of organelles possible	SL, HL	Paper 1B data on fractions, or a nature-of-science question (2–3 marks)
Explain the advantage of separating the nucleus from the cytoplasm	SL, HL	"Explain one advantage of the nuclear membrane" (2–3 marks)
Explain the advantages of compartments in the cytoplasm, using lysosomes and phagocytic vacuoles	SL, HL	"Explain why the enzymes of lysosomes are kept inside a membrane" (3 marks)
Explain how the mitochondrion is adapted for aerobic respiration	HL only	Annotated drawing or "Explain…" (4 marks)
Explain how the chloroplast is adapted for photosynthesis	HL only	Annotated drawing or "Explain…" (4 marks)
Explain the benefits of the nuclear double membrane, its pores, and its breakdown in division	HL only	"Outline the functions of nuclear pores" (2 marks)
Contrast free ribosomes with ribosomes on the rough ER	HL only	"Distinguish between…" (2–3 marks)
Outline the role of the Golgi apparatus in processing and secreting protein	HL only	Part of a secretion sequence question (3–5 marks)
Describe the structure and roles of vesicles, including clathrin	HL only	Multiple choice, or "Outline how a vesicle forms" (2–3 marks)

Before you start

You need the cell structures from A2.2: what a nucleus, mitochondrion, chloroplast, ribosome and endoplasmic reticulum look like in an electron micrograph, and the difference between prokaryotic and eukaryotic cells. You need B2.1: membranes are phospholipid bilayers that stop most solutes, and vesicles form and fuse because membranes are fluid. It helps to know that transcription makes mRNA from DNA and translation makes a polypeptide from mRNA (D1.2 covers both).

1The idea in one paragraph

A eukaryotic cell is not one open bag of chemicals. It is divided by membranes into compartments, each an organelle built for one function. The nucleus keeps the DNA, and the making of mRNA, apart from the ribosomes in the cytoplasm, so the mRNA can be edited before it is used. Lysosomes and phagocytic vacuoles keep powerful digestive enzymes away from the rest of the cell. Mitochondria and chloroplasts pack the enzymes and membranes of respiration and photosynthesis into small, folded spaces where they work fast. The rough ER, the Golgi apparatus and vesicles form a production line that makes proteins, finishes them and ships them out of the cell. Two advantages run through all of it: compartments concentrate the enzymes and substrates of a process, and they separate processes that would otherwise interfere with each other.

2What counts as an organelle

An organelle is a discrete subunit of a cell that is adapted to perform a specific function. "Discrete" means it is a distinct, separate unit, with a boundary. The guide draws the line in a particular place, and Paper 1A tests it.

Figure 1 · Organelle or not?

Organelles: the nucleus, ribosomes, vesicles and the plasma membrane, as well as mitochondria, chloroplasts, the endoplasmic reticulum, the Golgi apparatus, lysosomes and vacuoles. Note that ribosomes count even though they have no membrane: they are discrete units with one function, making proteins. The plasma membrane counts because it is a distinct structure with its own functions.
Not organelles: the cell wall, which is outside the plasma membrane and made by the cell rather than part of its working interior; the cytoskeleton, a network of protein fibres spread through the whole cell, not a separate unit; and the cytoplasm, which is the whole region the organelles sit in.

How organelles were studied (nature of science). Seeing an organelle in an electron micrograph tells you its shape, not what it does. To find out what mitochondria do, you need a tube full of mitochondria and nothing else. That became possible only once the ultracentrifuge had been invented, a centrifuge fast enough to throw organelles out of suspension, and methods of cell fractionation had been developed to use it. Figure 2 shows the method, called differential centrifugation.

Figure 2 · Cell fractionation by differential centrifugation

Tissue is broken up in a blender (homogenised) in a solution that is cold, isotonic and buffered. Cold slows enzymes, especially those released from broken lysosomes, that would otherwise digest the organelles. Isotonic means the solution has the same solute concentration as the organelles, so they neither swell and burst nor shrink by osmosis. Buffered keeps the pH steady so proteins are not denatured.
The homogenate is spun at low speed. The largest, densest structures, the nuclei, settle into a pellet at the bottom.
The liquid above (the supernatant) is spun again, faster and for longer. Mitochondria (and chloroplasts in plant tissue, and lysosomes) settle.
Faster still, fragments of ER and ribosomes settle. What is left is the fluid part of the cytoplasm, the cytosol.

Each pellet can then be tested to see which enzymes and reactions it contains. This is how the functions of organelles were mapped: in the 1950s cell fractionation revealed the lysosome, a new organelle nobody had recognised in micrographs, because one fraction held a set of digestive enzymes. The guide's general point is that progress in science often follows the development of a new technique.

3The nucleus: keeping transcription and translation apart

In a eukaryotic cell the DNA is inside the nucleus, and the ribosomes are outside it, in the cytoplasm. So the two stages of making a protein happen in different compartments, shown in Figure 3.

Figure 3 · Why a nucleus helps: transcription and translation kept apart

Transcription, making mRNA from a gene, happens in the nucleus.
Translation, making a polypeptide from the mRNA, happens on ribosomes in the cytoplasm.

The advantage is time and space between the two. Newly made mRNA can be modified before it meets any ribosome: this is post-transcriptional modification. The main example is the removal of stretches of the mRNA that do not code for the protein, with the remaining pieces joined together (D2.2 at HL covers the details). Only the finished mRNA leaves through the nuclear pores to be translated.

In a prokaryote there is no nucleus. Ribosomes can attach to an mRNA and start translating it while the other end of it is still being transcribed from the DNA. There is no gap in which to modify the mRNA, so it is used exactly as it was copied.

4Compartments in the cytoplasm: lysosomes and phagocytic vacuoles

The cytoplasm of a eukaryotic cell is itself divided up by membranes. The guide asks for two advantages.

Concentrating metabolites and enzymes. A reaction goes faster when its enzyme and its substrates meet often, which happens when they are concentrated. Enclosing the enzymes of one process, and its substrates, in a small compartment keeps their concentrations high instead of letting them spread through the whole cell.

Separating incompatible processes. Some processes would damage others, or undo them, if they shared a space. A membrane keeps them apart.

The guide's examples show the second advantage most clearly.

Lysosomes are small vesicles containing hydrolytic enzymes, digestive enzymes that break down proteins, lipids, carbohydrates and nucleic acids. Loose in the cytoplasm these enzymes would digest the cell's own structures. Inside a lysosome they are safe, and the lysosome also keeps its contents acidic, which is the pH at which these enzymes work best. So digestion can happen inside a cell without the cell digesting itself: lysosomes break down worn-out organelles and material brought into the cell.

Phagocytic vacuoles form when a phagocyte, a white blood cell that engulfs pathogens, takes in a bacterium by endocytosis. Figure 4 follows the sequence.

Figure 4 · A phagocytic vacuole and lysosomes: digestion kept in a compartment

The bacterium is enclosed in a membrane-bound vacuole. Lysosomes fuse with the vacuole and release their enzymes into it. The bacterium is digested inside the vacuole, and useful products are absorbed into the cytoplasm. At no point do the digestive enzymes meet the phagocyte's own cytoplasm, and both advantages are at work: the enzymes are concentrated around their target, and digestion is kept separate from everything else the cell is doing.

5HLThe mitochondrion, adapted for aerobic respiration

SL students can skip to section 11.

Aerobic respiration makes most of its ATP in the mitochondrion, and its structure is adapted to that in three ways the guide names, all labelled in Figure 5.

Figure 5 · The mitochondrion, adapted for aerobic respiration (HL)

A double membrane with a small volume of intermembrane space. The inner membrane pumps protons (H⁺) from the matrix into the space between the two membranes, and ATP is made as they flow back (C1.2). Because that space is so small, pumping relatively few protons builds a steep proton concentration gradient quickly.
A large surface area of cristae. The inner membrane is folded into cristae, which greatly increases its area. The proteins of the electron transport chain and the ATP synthase enzyme sit in this membrane, so more area means more of them, and more ATP made per mitochondrion.
Compartmentalisation of the Krebs cycle in the matrix. The matrix, the fluid inside the inner membrane, holds the enzymes and substrates of the Krebs cycle (and the link reaction) together at high concentration, so these reactions run quickly, and their products are right beside the inner membrane that uses them.

Mitochondria also have their own small circular DNA and 70S ribosomes, which is part of the evidence for their origin by endosymbiosis (A2.1 at HL).

6HLThe chloroplast, adapted for photosynthesis

The chloroplast is the mitochondrion's counterpart, and its adaptations follow the same logic. Figure 6 labels them.

Figure 6 · The chloroplast, adapted for photosynthesis (HL)

A large surface area of thylakoid membranes with photosystems. Inside the double membrane is a system of flattened membrane sacs, the thylakoids, many of them stacked into grana. The photosystems, the complexes of pigment and protein that absorb light, are in the thylakoid membranes. A large membrane area holds many photosystems, so more light is absorbed and the light-dependent reactions run faster.
Small volumes of fluid inside the thylakoids. Protons are pumped into the space inside each thylakoid during the light-dependent reactions. The volume is tiny, so a steep proton gradient builds quickly, and ATP synthase uses it to make ATP, exactly as in the mitochondrion.
Compartmentalisation of the Calvin cycle in the stroma. The stroma, the fluid around the thylakoids, holds the enzymes of the Calvin cycle (including the carbon-fixing enzyme, Rubisco) and their substrates together. The ATP and reduced NADP made on the thylakoid membranes are released straight into it.

Starch grains in the stroma store the sugar made. Like mitochondria, chloroplasts contain their own DNA and 70S ribosomes.

7HLThe double membrane of the nucleus

The nucleus is surrounded by a nuclear envelope of two membranes, the outer one continuous with the endoplasmic reticulum. Figure 7 shows the two things the guide asks you to explain about it.

Figure 7 · The double membrane of the nucleus (HL)

Pores. A barrier that let nothing through would be useless: mRNA must get out to the ribosomes, and proteins made in the cytoplasm (the enzymes that copy and transcribe DNA, the proteins that package it) must get in. So the envelope is crossed by nuclear pores, each a large protein complex where the two membranes join, which control what passes in each direction. The envelope keeps the DNA separate from the cytoplasm; the pores make the separation selective rather than total.

Breaking into vesicles for division. In mitosis and meiosis the chromosomes must be pulled apart by spindle microtubules that form in the cytoplasm. The envelope is in the way, so at the start of division it breaks down into small vesicles, and the spindle can reach the chromosomes. At the end of division the vesicles fuse again around each set of chromosomes to re-form two nuclear envelopes. Because membranes are fluid, this can happen quickly and repeatedly (B2.1).

8HLFree ribosomes and the rough endoplasmic reticulum

All ribosomes are the same, made of RNA and protein, and all translate mRNA into polypeptides. What differs is where they sit, and that decides where their product goes. Figure 8 shows both routes.

Figure 8 · Free ribosomes, rough ER and Golgi: two destinations for proteins (HL)

Free ribosomes are loose in the cytosol. They make proteins that are retained in the cell and work in the cytosol, such as the enzymes of glycolysis, and proteins destined for the nucleus, mitochondria or chloroplasts.

The rough endoplasmic reticulum (RER) is a network of flattened membrane sacs (cisternae) with ribosomes attached to its outer surface. As each membrane-bound ribosome makes its polypeptide, the chain is threaded through the membrane into the space inside the RER. These proteins are the ones for transport within the cell and for secretion: proteins to be released from the cell, such as digestive enzymes and hormones, proteins for lysosomes, and proteins for the plasma membrane.

How does a ribosome know where to go? Every ribosome starts in the cytosol. If the first stretch of the polypeptide it is making is a particular signal sequence, the ribosome is guided to the ER and attaches there. So the destination is written into the protein itself.

The contrast the guide wants, in one sentence: free ribosomes make proteins for use inside the cell; ribosomes on the RER make proteins for transport through the cell's membrane system and for secretion out of it.

9HLThe Golgi apparatus

The Golgi apparatus is a stack of flattened, curved membrane sacs, also called cisternae, but not joined to each other as the ER's are. It has two faces: vesicles from the RER arrive at one face, and vesicles leave from the other. The guide limits its role to the processing and secretion of protein.

Receiving. Proteins made on the RER leave it in small transport vesicles, which fuse with the receiving face of the Golgi.
Processing. As the proteins move through the stack, they are modified. The main change is the addition or trimming of carbohydrate chains, which turns many of them into glycoproteins. Some are also cut or folded into their final form.
Sorting and packaging. At the far face, the finished proteins are sorted by destination and packed into vesicles that bud off.
Secretion. Secretory vesicles move to the plasma membrane, fuse with it, and release their contents outside the cell by exocytosis (B2.1).

So a secreted protein, such as a digestive enzyme leaving a pancreas cell, follows one route: ribosome on the RER, into the RER, transport vesicle, Golgi apparatus, secretory vesicle, exocytosis. That route is a favourite extended-response question; learn it in order.

10HLVesicles, and the role of clathrin

A vesicle is a small sac of membrane with fluid inside. Vesicles are the cell's delivery vans: they carry materials between the ER, the Golgi, lysosomes and the plasma membrane, into the cell by endocytosis and out by exocytosis. Because membranes are fluid, a vesicle can bud off one membrane and fuse into another without either one leaking.

Budding does not happen by chance. A flat membrane has to be bent into a sphere, and the guide names the protein that does much of the bending: clathrin. Figure 9 shows how it works.

Figure 9 · Clathrin pulls a patch of membrane into a vesicle (HL)

Clathrin molecules, each shaped like a three-legged star, gather on the cytoplasm side of a patch of membrane, often where receptor proteins have bound the particles to be carried.
The clathrin units lock together into a curved lattice, a cage of pentagons and hexagons, and as the cage grows it pulls the membrane into a pit.
The pit deepens until it pinches off as a clathrin-coated vesicle containing its cargo. The coat is then removed, so the vesicle can fuse with its target.

Clathrin-coated vesicles form in endocytosis at the plasma membrane and when vesicles bud from the Golgi towards lysosomes.

11Where marks are lost

Calling the cell wall or the cytoskeleton an organelle. The guide excludes both, along with the cytoplasm. It includes ribosomes, vesicles, the nucleus and the plasma membrane.

"Ribosomes are not organelles because they have no membrane." The guide counts them. An organelle is a discrete subunit adapted to a function; a membrane is not required.

Saying the nucleus "protects the DNA" and stopping there. The advantage the guide wants is that transcription and translation are separated, so mRNA can be modified before translation. Protection alone scores little.

Saying compartments "keep things organised". Name the actual advantage: enzymes and substrates concentrated, or incompatible processes, such as digestion, kept apart.

Mixing up the order of the pellets. Largest and densest settle first, at the lowest speed: nuclei, then mitochondria, then ER fragments and ribosomes.

(HL) "The intermembrane space is large, so it can hold many protons." It is small, so a steep gradient builds with few protons. Size of space and steepness of gradient are inversely related.

(HL) Putting the Calvin cycle on the thylakoids. Light-dependent reactions on the thylakoid membranes; Calvin cycle in the stroma. The mitochondrion's parallel: Krebs cycle in the matrix.

(HL) Getting the secretion route out of order. RER, vesicle, Golgi, vesicle, plasma membrane. The Golgi never comes before the ER.

12Draw it right

The guide asks for annotated drawings of organelles, and electron micrograph questions ask you to identify and label them.

Annotate means label plus function. "Cristae" is a label. "Cristae: folds of the inner membrane giving a large area for the electron transport chain and ATP synthase" is an annotation.
Mitochondrion: two membranes drawn as two lines; the inner one folded into cristae reaching into the matrix; the intermembrane space shown as a narrow gap.
Chloroplast: a double envelope; thylakoids drawn as flattened sacs, several stacked as grana, joined by single membranes; stroma around them; starch grains if you like.
Nucleus: a double line with gaps for pores, the outer line meeting the inner line at each pore.
Rough ER: flattened sacs with dots (ribosomes) on the outer surface only. Dots inside the sacs are wrong.
Golgi: a stack of curved sacs, not joined, with vesicles budding from the edges.
Magnification: actual size = image size ÷ magnification. Convert units before dividing (1 mm = 1,000 µm), and give the answer in µm for organelles.

13Try it

Marks in brackets. Answers and marker's notes are at the end.

Q1. Which of the following is an organelle? 1 mark

A. Cell wall

B. Cytoskeleton

C. Ribosome

D. Cytoplasm

Q2. Liver tissue was homogenised and separated by differential centrifugation into three pellets (P1 at the lowest speed, P3 at the highest) and a final supernatant, S. Each fraction was tested for DNA and for two enzymes. The table shows the percentage of the total found in each fraction. The data are invented. 6 marks

Fraction	DNA / %	A Krebs cycle enzyme / %	A glycolysis enzyme / %
P1	92	6	3
P2	5	85	4
P3	2	7	5
S	1	2	88

(a) Identify the fraction containing most of the mitochondria, with a reason. 1 mark

(b) Deduce where in the cell glycolysis takes place. 1 mark

(d) Explain why the tissue was homogenised in a cold, isotonic, buffered solution. 3 marks

Q3. Explain the advantage to a eukaryotic cell of separating the nucleus from the cytoplasm. 3 marks

Q4. Explain how compartmentalization allows a phagocyte to digest a bacterium without damaging itself. 3 marks

Q5 (HL). A mitochondrion measures 36 mm long on an electron micrograph taken at a magnification of ×18,000.

(a) Calculate its actual length in micrometres. 2 marks

(b) Explain how the structure of the mitochondrion is adapted to aerobic respiration. 4 marks

Q6 (HL). Outline the route by which a protein made in a pancreas cell is secreted, contrasting it with the synthesis of a protein that stays in the cytosol. 5 marks

14In one breath

An organelle is a discrete subunit of a cell adapted to one function: nuclei, ribosomes, vesicles and the plasma membrane count; the cell wall, the cytoskeleton and the cytoplasm do not. Organelles could only be studied once ultracentrifuges and cell fractionation existed: homogenise in cold, isotonic, buffered solution and spin faster and faster, so nuclei, then mitochondria, then ER and ribosomes settle out. The nucleus separates transcription from translation, so mRNA is modified before ribosomes read it; in prokaryotes they happen together. Compartments concentrate enzymes and substrates and keep incompatible processes apart, as lysosomes do with digestive enzymes and phagocytic vacuoles do with engulfed bacteria. HL: the mitochondrion has a double membrane with a small intermembrane space for a steep proton gradient, cristae for a large area of membrane, and the Krebs cycle in the matrix; the chloroplast has a large area of thylakoid membrane with photosystems, tiny thylakoid spaces for a steep proton gradient, and the Calvin cycle in the stroma. The nuclear envelope is a double membrane with pores for traffic, and it breaks into vesicles for mitosis and meiosis. Free ribosomes make proteins kept in the cytosol; ribosomes on the rough ER make proteins for transport and secretion, which pass through the Golgi apparatus to be modified and packaged into vesicles, then leave by exocytosis. Clathrin forms a cage on the cytoplasm side that bends membrane into coated vesicles.

Answers

Q1. C. Ribosomes are discrete subunits with one function, protein synthesis, so they are organelles even without a membrane. The cell wall, the cytoskeleton and the cytoplasm are not discrete subunits of the cell. C only.

Q2. (a) P2, because it contains 85% of the Krebs cycle enzyme, and the Krebs cycle takes place in mitochondria. (b) In the cytosol (the fluid part of the cytoplasm), since 88% of the glycolysis enzyme is in the final supernatant, which contains no organelles. (c) Some cells were not broken open during homogenisation, so their mitochondria settled with the nuclei in P1; or some mitochondria were trapped among the nuclei. (d) Cold slows the activity of enzymes, such as those released from lysosomes, that would otherwise digest or damage the organelles. Isotonic means there is no net movement of water by osmosis into or out of the organelles, so they do not burst or shrink. A buffer keeps the pH constant, so proteins, including the enzymes being measured, are not denatured. (a) 1 for P2 with the Krebs data. (b) 1 for cytosol or cytoplasm, with the supernatant data. (c) 1 for any reasonable suggestion. (d) 1 for each of cold, isotonic and buffered with its reason. A reason that repeats the word ("isotonic so it is isotonic") scores 0.

Q3. Transcription takes place in the nucleus and translation takes place on ribosomes in the cytoplasm, so the two processes are separated. This means mRNA can be modified after transcription, for example by removing non-coding sections, before it leaves through the nuclear pores and reaches ribosomes. In prokaryotes, which have no nucleus, ribosomes translate mRNA as soon as it is made, so it cannot be modified first. 1 for transcription in the nucleus and translation in the cytoplasm, 1 for post-transcriptional modification before translation, 1 for the contrast with prokaryotes or for the modification happening before mRNA meets ribosomes.

Q4. The bacterium is taken in by endocytosis and enclosed in a membrane-bound phagocytic vacuole. Lysosomes, which contain hydrolytic enzymes held inside a membrane, fuse with the vacuole and release their enzymes into it. The bacterium is digested inside the vacuole, so the enzymes are concentrated around it and never come into contact with the phagocyte's own cytoplasm and organelles. 1 for the phagocytic vacuole, 1 for lysosomes with hydrolytic enzymes fusing with it, 1 for digestion kept separate from the cytoplasm. "The lysosome eats the bacterium" scores 0.

Q5 (HL).

36 mm = 36 × 1 000 = 36 000 µm

actual length = 36 000 µm ÷ 18 000 = 2 µm

(b) The inner membrane is folded into cristae, giving a large surface area for the electron transport chain and ATP synthase. The intermembrane space is small, so pumping protons into it builds a steep proton gradient quickly. The matrix holds the enzymes and substrates of the Krebs cycle (and link reaction) together, concentrated in one compartment. The double membrane separates the matrix from the intermembrane space, which is what allows the gradient to exist. (a) M1 for converting to µm or an equivalent correct method, A1 for 2 µm. (b) 1 for each structure linked to its function, up to 4. A structure named with no function scores 0.

Q6 (HL). The secreted protein is made by ribosomes attached to the rough ER, and the polypeptide passes into the RER as it is made. It is carried in a transport vesicle to the Golgi apparatus, where it is modified, for example by adding carbohydrate, and packaged. A secretory vesicle carries it to the plasma membrane, fuses with it and releases the protein by exocytosis. By contrast, a protein that stays in the cytosol is made by free ribosomes in the cytosol and does not enter the ER or the Golgi. 1 for RER-bound ribosomes, 1 for the vesicle to the Golgi, 1 for modification in the Golgi, 1 for secretory vesicle and exocytosis, 1 for the free-ribosome contrast. Stages given out of order lose the mark for the misplaced stage.

Educerie · written from the published IB Diploma Programme Biology guide, first assessment 2025, section B2.2 Organelles and compartmentalization. Original text, examples and questions. Diagrams drawn by Educerie. Last reviewed 25 September 2026.

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