IB Biology HLOrganelles & CompartmentsPaper 1 & 2~13 min read
Organelles in Protein Synthesis
Take one protein — insulin, say — and follow it from the gene that codes for it to the moment it leaves the cell. Four organelles handle it on the way, each doing one job and passing it on. This page is that journey.
📚 What you need to know
The nucleus is separated from the cytoplasm by a double membrane, the nuclear envelope, studded with nuclear pores.
Pores let mRNA and ribosomes travel out, and enzymes such as DNA polymerase and signalling molecules travel in.
The outer nuclear membrane is continuous with the endoplasmic reticulum. Sections with ribosomes are rough ER; sections without are smooth ER.
During mitosis and meiosis the nuclear membrane breaks into vesicles at prophase and reforms at telophase.
Ribosomes are the site of protein synthesis. They have a large and a small subunit made of protein and rRNA, with three tRNA binding sites and one mRNA binding site.
Free ribosomes make proteins for use inside the cell; membrane-bound ribosomes make proteins for secretion or for lysosomes.
A signal sequence at the start of the growing polypeptide, recognised by a signal recognition protein, is what sends a ribosome to the ER.
The Golgi apparatus receives vesicles at its cis face, modifies and packages proteins and lipids, and sends them out from its trans face.
The nucleus and its envelope
The nucleus is present in all eukaryotic cells and is relatively large. Its double membrane creates an area where the DNA and everything that acts on it can be kept apart from the rest of the cell.
A sealed compartment would be useless, though, so the envelope is studded with nuclear pores. These are channels, not holes: they control traffic in both directions.
Out: mRNA carrying the message to the cytoplasm, and ribosome subunits assembled in the nucleolus.
In: enzymes such as DNA polymerase, and signalling molecules that switch genes on or off.
The outer membrane of the nuclear envelope does not stop at the nucleus. It is continuous with the endoplasmic reticulum, so mRNA leaving through a pore emerges right next to the machinery that will use it. Where ribosomes are attached to that membrane it is called rough ER; where they are not, it is smooth ER.
The nuclear envelope is not permanent. During prophase of mitosis and meiosis it breaks up into vesicles so the chromosomes can be separated, and at telophase it reassembles around each new set. Membranes are fluid, which is exactly what makes that possible.
Ribosomes
A ribosome is the site of protein synthesis, and it is not an organelle in the strict sense because it has no membrane. It is built from two subunits:
a large subunit and a small subunit, each made of protein and ribosomal RNA (rRNA)
the protein gives the ribosome its structure
the rRNA holds the mRNA and tRNA in place and catalyses the formation of peptide bonds between amino acids
Each ribosome has three tRNA binding sites and one mRNA binding site. The mRNA sits in a groove between the two subunits, and the ribosome moves along it, adding one amino acid at a time and leaving a growing polypeptide behind.
An enzyme that is not a protein. The rRNA catalysing peptide bond formation makes the ribosome a ribozyme — a catalyst made of RNA rather than protein. Worth remembering as a counterexample if you are ever asked whether all enzymes are proteins.
Free or bound: two destinations
Every ribosome starts free in the cytoplasm. What happens next depends on the protein it turns out to be making.
The ribosome does not choose. The signal sequence at the start of the polypeptide it is building is what sends it to the ER.
🧩 How a ribosome ends up bound to the ER
Translation begins on a free ribosome in the cytoplasm, like every other protein.
A signal sequence appears at the beginning of the growing polypeptide chain, coded for by the mRNA.
A signal recognition protein binds to that sequence, which pauses translation.
The ribosome binds to a receptor protein on the ER membrane. That patch of ER is now rough ER.
Translation restarts and the polypeptide chain is fed into the ER as it is made.
The signal sequence is removed and the finished protein is carried onward in a vesicle.
The Golgi apparatus
The Golgi apparatus is a stack of flattened membrane sacs called cisternae, which is why it looks similar to rough ER. Its role is to modify proteins and lipids and then package them into Golgi vesicles for delivery.
It has a distinct orientation, and the two sides have names:
the cis face points towards the endoplasmic reticulum, and receives vesicles arriving from it
the trans face points towards the plasma membrane, and is where finished products leave
Proteins passing through the Golgi typically end up in one of three places: exported from the cell (hormones such as insulin), placed into lysosomes (hydrolytic enzymes), or delivered to another membrane-bound organelle.
A useful way to remember cis and trans: cis is the same side as the ER, and in chemistry “cis” means “on the same side”. Trans means “across” — the far side, facing out of the cell.
The whole pathway
Station 3 has a direction: vesicles arrive at the cis face nearest the ER and leave from the trans face nearest the membrane.
Worked examples
WE 1
Predicting the organelles in a cell
Pancreatic cells secrete large quantities of digestive enzymes. Predict two organelles that would be unusually abundant in these cells, and explain why. (4 marks)
Organelle 1Rough endoplasmic reticulum, because enzymes for secretion are made on ribosomes bound to the ER and fed into its lumen.
Organelle 2Golgi apparatus, because the enzymes must be modified and packaged into secretory vesicles before they can leave.
A third, if you have room
Mitochondria would also be abundant, since making and secreting protein requires a great deal of ATP.
rough ER and Golgi — the two stations on the secretory pathwayevery “predict the organelles” question is really asking you to name the pathway
WE 2
Tracing a labelled amino acid
A cell is supplied with radioactively labelled amino acids. Describe the order in which the label would appear in the cell’s organelles as a secreted protein is made. (3 marks)
Step 1: where it starts
The label appears first in the rough endoplasmic reticulum, where the amino acids are joined into a polypeptide.
Step 2: the middle
It then appears in the Golgi apparatus, carried there in transport vesicles, where the protein is modified.
Step 3: the end
Finally it appears in secretory vesicles, and then outside the cell after exocytosis.
rough ER → Golgi → secretory vesicle → outsidethis is a real classic (the Palade experiment) — note the nucleus is not on the list, because amino acids are not used there
WE 3
Explaining the sorting mechanism
Explain how a cell ensures that only proteins destined for secretion are made on ribosomes attached to the endoplasmic reticulum. (3 marks)
Point 1: the tag
Proteins for secretion begin with a signal sequence at the start of the polypeptide chain, coded for by the mRNA.
Point 2: recognising it
A signal recognition protein binds to that sequence and pauses translation.
Point 3: the result
The ribosome is then carried to a receptor on the ER membrane, translation restarts, and the polypeptide is fed into the ER. Proteins without a signal sequence stay on free ribosomes.
a signal sequence in the protein itself directs the ribosome to the ERthe sorting information is in the protein, not in the ribosome — say so explicitly
💡 Exam tips
Learn the pathway as a sequence: nucleus → rough ER → Golgi → secretory vesicle → plasma membrane.
Say cis face for receiving and trans face for despatch. Getting them the right way round is a mark.
Ribosome composition: protein plus rRNA, in two subunits. Both halves of that are examinable.
Remember the numbers: three tRNA binding sites, one mRNA binding site.
Free ribosomes make proteins for inside the cell; bound ribosomes make proteins for secretion or lysosomes.
Name the signal sequence and the signal recognition protein when explaining sorting.
⚠ Common mistakes
Saying protein synthesis happens in the nucleus. Transcription does; translation happens at a ribosome in the cytoplasm.
Describing nuclear pores as simple holes. They are channels that control what moves in and out.
Putting the Golgi before the ER. The ER always comes first.
Saying the Golgi “makes” proteins. It modifies and packages them; it does not synthesise them.
Claiming bound ribosomes are a different type. They are identical to free ones; only their location differs.
Forgetting smooth ER exists. It is the same membrane system without ribosomes, and it handles lipids rather than proteins.
Up next: Vesicle Formation — every arrow in that pathway was a vesicle. Time to find out how a cell actually builds one.
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