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[Biochemistry](https://durgical.com/en/biochemistry/) · Topic

# Cell organelles and their metabolism

Each organelle has its own metabolic job: mitochondria make ATP, lysosomes recycle, peroxisomes oxidise, and the ER and Golgi build.

Updated 2026-11-01

## Key facts

- Cytosol: glycolysis, pentose phosphate pathway, fatty acid synthesis, part of gluconeogenesis and of the urea cycle.
- Mitochondrion: Krebs cycle, β-oxidation, respiratory chain, ketogenesis and the first steps of urea and haem synthesis; it has its own DNA (maternal inheritance).
- Lysosome: acid hydrolases (pH ≈ 5) that break down macromolecules; marker enzyme, acid phosphatase.
- Peroxisome: β-oxidation of very-long-chain fatty acids, plasmalogen and bile acid synthesis; catalase as marker.
- Rough ER: secretory and membrane protein synthesis; smooth ER: lipids, steroids and detoxification (cytochrome P450). Golgi: modifies, sorts and tags (mannose 6-phosphate).

## In detail

- 1. Nucleus: DNA replication and transcription; the nucleolus makes ribosomes.
- 2. Proteins with a signal peptide enter the rough ER while being made, are glycosylated on asparagines and move to the Golgi in vesicles.
- 3. In the cis-Golgi, lysosomal hydrolases receive mannose 6-phosphate; in the trans-Golgi they are sorted to lysosomes, membrane or secretion.
- 4. Mitochondrial and peroxisomal proteins are made in the cytosol and imported afterwards using their own signals (mitochondrial presequence, PTS1/PTS2).
- 5. The urea cycle, gluconeogenesis and haem synthesis use both the mitochondrion and the cytosol.
- 6. Classic marker enzymes: succinate dehydrogenase (inner mitochondrial membrane), glucose 6-phosphatase (ER), galactosyltransferase (Golgi), catalase (peroxisome), acid phosphatase (lysosome).

## Memory aid

Split mitochondria–cytosol pathways: "HUG" (Haem, Urea, Gluconeogenesis).

**Also called**
Compartments of the cell

## Clinical notes

- Mitochondrial diseases (MELAS, Leigh syndrome): the organs that use the most energy, brain and muscle, fail.
- Peroxisomal diseases (Zellweger syndrome, X-linked adrenoleukodystrophy): very-long-chain fatty acids accumulate.
- Lysosomal diseases (Gaucher, Tay–Sachs, Hurler, I-cell disease): lysosomes fill with undegraded material.

## Pathways

- [Krebs cycle (citric acid cycle)](https://durgical.com/en/biochemistry/pathways/krebs-cycle/)
- [Fatty acid β-oxidation](https://durgical.com/en/biochemistry/pathways/fatty-acid-oxidation/)
- [Glycolysis](https://durgical.com/en/biochemistry/pathways/glycolysis/)

## Related conditions

- [Zellweger syndrome (Zellweger spectrum)](https://durgical.com/en/conditions/zellweger-syndrome/)
- [MELAS (mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes)](https://durgical.com/en/conditions/melas/)
- [Pompe disease (glycogen storage disease type II)](https://durgical.com/en/conditions/pompe-disease/)
- [I-cell disease (mucolipidosis II)](https://durgical.com/en/conditions/i-cell-disease/)

## Related

- [Membrane structure](https://durgical.com/en/biochemistry/topics/membrane-structure/)
- [Lysosomal storage diseases](https://durgical.com/en/biochemistry/topics/lysosomal-storage-diseases/)
- [Mannose 6-phosphate tagging (sending enzymes to the lysosome)](https://durgical.com/en/biochemistry/topics/mannose-6-phosphate-tagging/)
- [Peroxisomal oxidation (β- and α-oxidation)](https://durgical.com/en/biochemistry/topics/peroxisomal-oxidation/)
- [Electron transport chain and oxidative phosphorylation](https://durgical.com/en/biochemistry/pathways/electron-transport-chain-and-oxidative-phosphorylation/)
- [Catalase](https://durgical.com/en/biochemistry/enzymes/catalase/)

## Test yourself

Think of the answer, then tap the question to see it.

## In which organelle are very-long-chain fatty acids β-oxidised?

In the peroxisome; the mitochondrion then finishes oxidising the shorter products.

## Which marker enzyme identifies peroxisomes?

Catalase, which breaks down the hydrogen peroxide they produce.

## Why are mitochondrial DNA diseases inherited from the mother?

The embryo's mitochondria come from the egg; those of the sperm are eliminated.

## Which pathways use both the mitochondrion and the cytosol?

The urea cycle, gluconeogenesis and haem synthesis.

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Educational information, not medical advice. For any symptom, see a health professional.

Sources: [Membrane Trafficking](https://reactome.org/PathwayBrowser/#/R-HSA-199991) (Reactome, 2026); [Mitochondrial protein import](https://reactome.org/PathwayBrowser/#/R-HSA-1268020) (Reactome, 2026); [Peroxisomal protein import](https://reactome.org/PathwayBrowser/#/R-HSA-9033241) (Reactome, 2026); [Transport to the Golgi and subsequent modification](https://reactome.org/PathwayBrowser/#/R-HSA-948021) (Reactome, 2026); Textbook of Biochemistry for Medical Students, 6th ed. (Jaypee Brothers Medical Publishers (Vasudevan DM, Sreekumari S, Vaidyanathan K), 2011).

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Representative model, for educational purposes only.

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License: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/). Cite as: DurgiPedia (durgical.com), https://durgical.com/en/biochemistry/topics/cell-organelles-and-their-metabolism/