The Nucleus and the Endomembrane System
Follow a protein from the gene that codes for it, through the ER and Golgi, to its destination, and meet the lysosome clean-up crew.
Quick answer: The nucleus stores the cell's DNA and controls gene activity, while the endomembrane system builds, folds, sorts and ships proteins and lipids. A secreted protein is made on the rough ER, modified and packaged in the Golgi apparatus, and sent to the cell surface in vesicles. Lysosomes digest worn-out material.
What you will learn
- Describe the structure of the nucleus and the role of the nuclear pores.
- Distinguish rough ER from smooth ER.
- Trace the path a secreted protein takes through the cell.
- Explain what lysosomes do and why white blood cells rely on them.
The nucleus: the genome's vault
The nucleusNucleusThe membrane-bound organelle of eukaryotic cells that holds most of the cell's DNA and is the site where genes are copied into RNA. is usually the largest organelle in an animal cell, about 5 to 10 µm across. It holds nearly all of the cell's DNADNA (deoxyribonucleic acid)The molecule that stores genetic information as a sequence of four chemical bases (A, T, G, C) along a double helix., keeps it safe, and controls when each gene is used.
Three features are worth knowing:
- The nuclear envelopeNuclear envelopeThe double membrane around the nucleus. It is perforated by nuclear pores that control which molecules enter and leave. is a double membrane. It is dotted with thousands of nuclear pores, channels that let messenger molecules out and regulatory proteins in, while keeping the DNA itself inside.
- Inside, the DNA is wound around proteins to form chromatinChromatinDNA wrapped around proteins, as it appears in the nucleus when the cell is not dividing.. When a cell is not dividing, chromatin is spread out so genes can be read.
- A dense region called the nucleolus assembles the parts of ribosomesRibosomeA molecular machine made of RNA and protein that reads messenger RNA and links amino acids together to build a protein. It is found in all cells..
For a labelled diagram of these parts, open the topic The Cell Nucleus.
The endomembrane system
Most proteins and lipids the cell exports, or builds into its membranes, go through a connected network of compartments called the endomembrane systemEndomembrane systemThe connected set of membrane-bound compartments in eukaryotic cells: the nuclear envelope, endoplasmic reticulum, Golgi apparatus, lysosomes, and the vesicles that shuttle between them.. Think of it as a factory with a post office attached.
Endoplasmic reticulum: the factory floor
The endoplasmic reticulumEndoplasmic reticulum (ER)A network of membrane tubes and sheets continuous with the nuclear envelope. Rough ER, studded with ribosomes, makes proteins for export; smooth ER makes lipids and detoxifies chemicals. (ER) is a maze of flattened sacs and tubes that is directly joined to the nuclear envelope. It comes in two types:
- Rough ER is studded with ribosomes. Proteins made here are threaded into the ER interior as they are built. It is especially large in cells that secrete a lot of protein.
- Smooth ER has no ribosomes. It makes lipids, helps break down toxins in liver cells, and stores calcium ions.
Golgi apparatus: sorting and shipping
Proteins leave the ER wrapped in small vesiclesVesicleA small membrane-bound bubble that carries cargo between compartments, to the plasma membrane, or into the cell. and travel to the Golgi apparatusGolgi apparatusA stack of flattened membrane sacs that modifies, sorts, and packages proteins and lipids received from the ER, then sends them to their destinations in vesicles., a stack of flattened membrane sacs. Inside, enzymes trim, tag, and modify them, such as by adding sugar chains. At the far face, the finished products are packaged into new vesicles with a destination label.
A protein's journey
Here is the route a protein takes when the cell is going to secrete it, for example an antibody or a digestive enzyme:
- The gene is copied into messenger RNA in the nucleus.
- The mRNA leaves through a nuclear pore, and a ribosome on the rough ER builds the protein.
- A transport vesicle carries the protein to the Golgi.
- The Golgi modifies and sorts it into a secretory vesicle.
- The vesicle moves to the plasma membrane and releases its contents by exocytosisExocytosisA process in which a vesicle fuses with the plasma membrane and releases its contents outside the cell..
Where are proteins that will be exported from the cell first made?
Which organelle modifies, sorts, and packages proteins into vesicles for delivery?
Lysosomes: the recycling center
A lysosomeLysosomeAn acidic, membrane-bound organelle filled with digestive enzymes that breaks down worn-out cell parts and material the cell has engulfed. is a small, acidic vesicle filled with about 50 different digestive enzymesEnzymeA protein that speeds up a specific chemical reaction without being used up.. It does two jobs: it digests material the cell has taken in, and it recycles the cell's own worn-out parts.
The acid inside is a safety feature. The enzymes only work well at low pH, so if a lysosome leaks into the neutral cytoplasm, they are mostly inactive and the cell is not digested from within.
White blood cells make heavy use of lysosomes. A neutrophil engulfs a bacterium in a vesicle, which then fuses with lysosomes. The invader is broken down inside a sealed compartment, where it cannot harm the cell.
Why can lysosomes digest material without harming the rest of the cell?
Key takeaways
- The nuclear envelope has pores that control traffic between the nucleus and the cytoplasm.
- Rough ER carries ribosomes and makes proteins; smooth ER makes lipids and helps detoxify.
- Secreted proteins travel ER, then Golgi, then a vesicle, then the plasma membrane.
- Lysosomes hold digestive enzymes, which is why white blood cells use them to destroy engulfed microbes.
Sources
- Biology 2e, Chapter 4: Cell Structure (OpenStax) Concepts adapted and rewritten; no text reproduced verbatim.
- NIH 3D: Animal cell model
Last reviewed October 1, 2026