The nucleus, free ribosomes and rough ER

Cells (Form and function) · Organelles and compartmentalization · note 3 of 4

Spec B2.2.6, B2.2.7
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The nucleus, free ribosomes and rough ERSpec B2.2.6, B2.2.7

In short

The nucleus is surrounded by a double membrane, the nuclear envelope, with pores that let mRNA out and proteins in, and it breaks into vesicles during mitosis and meiosis. Free ribosomes make proteins kept inside the cell, while ribosomes bound to the rough endoplasmic reticulum make proteins for transport within the cell or secretion.

The double nuclear membrane

The nucleus is enclosed by two membranes, together called the nuclear envelope. The outer membrane is continuous with the rough endoplasmic reticulum.

  • Separation: DNA and transcription are kept apart from translation and other reactions in the cytoplasm.
  • Nuclear pores: mRNA made by transcription must leave the nucleus, and proteins made in the cytoplasm (such as enzymes for DNA replication and histones) must enter. Pores, where the two membranes join, allow and control this traffic.
  • Breakdown into vesicles: during mitosis and meiosis the nuclear membrane breaks into vesicles so that spindle microtubules can reach and move the chromosomes. Afterwards the vesicles fuse to form new nuclear envelopes around each set of chromosomes.

Free ribosomes and rough ER

Ribosomes are made of rRNA and protein and have no membrane. In eukaryotic cells they are found free in the cytosol or bound to the rough endoplasmic reticulum (rER), a network of flattened membrane sacs called cisternae.

Contrasting free ribosomes and ribosomes on the rER
FeatureFree ribosomesRibosomes on the rER
LocationIn the cytosol, not attached to membranesAttached to the cytoplasmic surface of the rER
Proteins madeProteins for retention in the cell, used in the cytoplasm or in organelles such as mitochondria and the nucleusProteins for transport within the cell (for example to lysosomes) or for secretion
Where the polypeptide goesReleased into the cytosolInto the lumen of the rER, then in vesicles to the Golgi apparatus

Free and rER-bound ribosomes have the same structure, and translation always begins on a free ribosome in the cytosol. If the polypeptide being made begins with a signal sequence (a short stretch of mainly hydrophobic amino acids), the ribosome is guided to the rER and attaches to it. The growing polypeptide is fed through a pore in the rER membrane into the lumen, and the signal sequence is usually cut off. The details of this targeting are not required.

Nucleus with outer and inner nuclear membranes, nuclear pores, chromatin and nucleolus; the outer membrane is continuous with the cisternae of the rough ER, which carry ribosomes; mRNA leaves through a pore, a free ribosome releases its protein into the cytosol, and a protein made on the rER enters the rER lumen. (opens full size in a new tab)
The outer nuclear membrane is continuous with the rER; free ribosomes make proteins for the cytosol, rER ribosomes feed proteins into the lumen.

Written and checked against the IB Biology HL specification · Updated October 2026

Frequently asked questions

Is a ribosome an organelle?

Yes. In IB Biology an organelle is a discrete subunit of a cell adapted to perform a specific function, so ribosomes count even though they have no membrane. Nuclei, vesicles and the plasma membrane are organelles too, but the cell wall, cytoskeleton and cytoplasm are not considered organelles.

What are the advantages of compartmentalization in cells?

Compartments let a cell concentrate enzymes and their substrates in a small volume, so reactions run faster, and keep incompatible processes apart. For example, lysosomes hold hydrolytic enzymes that would digest the cell if free, and the nuclear membrane lets mRNA be modified before it meets ribosomes.

How does cell fractionation separate organelles?

Cell fractionation breaks cells open in a cold, isotonic, buffered solution and then spins the homogenate in a centrifuge at increasing speeds. Large, dense organelles such as nuclei form a pellet first; mitochondria pellet at higher speeds, and the smallest parts, such as ribosomes, need an ultracentrifuge. Each fraction can then be studied.

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