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Mitochondria are membrane-bound organelles that generate most of the chemical energy a cell needs, storing it in a small molecule called adenosine triphosphate (ATP). They also carry their own small circular chromosome, take part in cell signaling, calcium handling and cell death, and have a built-in quality-control system that can repair mild damage and remove severely damaged organelles.
What are mitochondria and their main functions?
The NHGRI Talking Glossary defines mitochondria as membrane-bound cell organelles that “generate most of the chemical energy needed to power the cell’s biochemical reactions,” with that energy stored in ATP. In cell biology, that is the headline function, and it is why mitochondria are widely called the powerhouse of the cell.
A review of mitochondrial function in development and disease (Europe PMC, PMC8214736) lists the wider job description. Mitochondria are biosynthetic hubs and also take part in signaling, cell death and calcium homeostasis. The membrane potential across the inner membrane “provides the energy required for ATP synthesis,” which links structure directly to the energy function.
Definition and scope
Mitochondria differ from most organelles in one respect: they contain their own DNA. The NHGRI glossary notes that mitochondrial DNA is the circular chromosome found inside the organelle, and that mitochondria, and therefore mitochondrial DNA, are generally inherited only from the mother.
For a broader map of the field this topic belongs to, see our overview of cell biology, and for how it differs from neighbouring disciplines see cell biology vs molecular biology.
How mitochondria are built and how they work
The review describes an outer membrane that envelops the entire organelle and an inner membrane divided into the inner boundary membrane, which lies next to the outer membrane, and the cristae. Cristae protrude into the mitochondrial matrix and expand the surface area of the inner membrane. The space between the outer and inner membranes is the intermembrane space.
The inner membrane carries the machinery that links the membrane potential to ATP synthesis. The human mitochondrial genome is a circular double-stranded DNA molecule of 16,569 base pairs. It encodes 13 proteins, which are subunits of the electron transport chain and ATP synthase, plus transfer and ribosomal RNAs. Most mitochondrial proteins are encoded in the nucleus and imported.
Matrix vs intermembrane space
The matrix and the intermembrane space are two different compartments, separated by the inner membrane. The table summarises what the review reports for each.
| Feature | Matrix | Intermembrane space |
|---|---|---|
| Position | Enclosed by the inner membrane; the cristae protrude into it | Between the outer and inner membranes |
| Contents and quality control | Imported proteins arrive via one of five import pathways; holds the mitochondrial DNA nucleoid; protein folding and quality control take place here | Accumulation of proteins triggers a distinct stress response, the IMS-UPRmt |
Can damaged mitochondria be repaired?
Partly. The review describes a graded quality-control system rather than a single repair step. The response depends on how severe the damage is.
- Mild defects. The mitochondrial unfolded protein response (UPRmt) responds to less severe homeostatic defects, leading to organelle repair.
- Fusion and fission. Mitochondria fuse and divide. Mitofusins 1 and 2 act on the outer membrane, OPA1 on the inner membrane, and DRP1 drives fission.
- Severe damage. Mitophagy engulfs the entire mitochondrion in an autophagosome, followed by degradation in the lysosome.
- Other routes. The review also lists ubiquitin-proteasome degradation and mitochondria-derived vesicles, giving at least four pathways in total.
So damaged mitochondria are repaired when the defect is mild and removed when it is severe.
Mitochondria in plant cells
Plant cells have mitochondria too, and the questions people ask about mitochondria in a plant cell, of a plant cell or on a plant cell all point to the same organelle. Recent plant research reports that plant mitochondria contain additional alternative electron transport pathways. A 2026 study in The Plant Journal (PMC13584256) reports that respiration is essential for converting reducing power into ATP and that disrupting both the alternative oxidase pathway and the cytochrome pathway is lethal in the moss Physcomitrium patens. A 2026 review in New Phytologist (PMC12961250) examines these alternative respiratory pathways during fruit growth and ripening. A 2026 study in Frontiers in Plant Science (PMC13677838) describes plant mitochondrial genomes as structurally dynamic and as contributing to energy metabolism and stress responses.
Where it matters for labs and clinics
Researchers planning mitochondria-related work tend to settle the same few questions first. This checklist ties each one to its source.
| Question to settle | What the sources say |
|---|---|
| Is the target encoded in mitochondrial DNA or the nucleus? | Human mitochondrial DNA is 16,569 base pairs and encodes 13 proteins; most mitochondrial proteins are nuclear-encoded (PMC8214736) |
| Does inheritance matter for your design? | Mitochondrial DNA is generally inherited only from the mother (NHGRI) |
| Is a “mitochondrial” signal really mitochondrial? | Our MTT assay guide notes the signal is attributed to NADH- and NADPH-dependent oxidoreductase activity rather than a single dedicated mitochondrial enzyme |
| Is mitochondrial shape a stress readout? | Our live-cell imaging guide lists mitochondrial fragmentation among cell responses to sustained oxidative stress from imaging light |
| Is the damage mild or severe? | Mild defects can lead to organelle repair through UPRmt; severe damage leads to mitophagy (PMC8214736) |
Common misunderstandings
- “Mitochondria only make ATP.” They are also biosynthetic hubs and take part in signaling, cell death and calcium homeostasis.
- “All mitochondrial proteins come from mitochondrial DNA.” Human mitochondrial DNA encodes 13 proteins; most mitochondrial proteins are nuclear-encoded and imported.
- “Damaged mitochondria are always degraded.” The response is graded: mild defects can lead to repair, severe damage to mitophagy.
FAQ
What are mitochondria and their main functions?
Mitochondria are membrane-bound organelles that generate most of a cell’s chemical energy, stored as ATP. They also take part in signaling, cell death and calcium homeostasis, and they are biosynthetic hubs.
Can damaged mitochondria be repaired?
Mild defects can be repaired through the mitochondrial unfolded protein response, and fusion and fission help maintain the network. Severely damaged mitochondria are engulfed and degraded by mitophagy.
What is the difference between the matrix and intermembrane space in mitochondria?
The matrix is the compartment enclosed by the inner membrane, holding the mitochondrial DNA nucleoid and handling protein folding and quality control. The intermembrane space lies between the outer and inner membranes, and protein accumulation there triggers its own stress response, IMS-UPRmt.
Do plant cells have mitochondria?
Yes. Plant mitochondria are the subject of current research on alternative respiratory pathways, including in fruit ripening and in moss.
Sources
- NHGRI Talking Glossary, Mitochondria (https://www.genome.gov/genetics-glossary/Mitochondria) and Mitochondrial DNA (https://www.genome.gov/genetics-glossary/Mitochondrial-DNA) (checked 2026-10-29).
- Mitochondrial function in development and disease, review, PMC8214736, via Europe PMC (https://europepmc.org/article/PMC/PMC8214736) (checked 2026-10-29).
- Essential mitochondrial activity in Physcomitrium patens relies on complementary cytochrome and alternative oxidase pathways, The Plant Journal, 2026 (abstract checked 2026-10-29).
- Fruit respiration: putting alternative pathways into perspective, New Phytologist, 2026 (abstract checked 2026-10-29).
- Comparative mitogenomics of Roscoea alpina and R. purpurea from contrasting elevations, Frontiers in Plant Science, 2026 (abstract checked 2026-10-29).
