Reactive oxygen species
Reactive oxygen species (ROS) include oxygen ions,  free radicals and peroxides both inorganic and organic. They are generally very small molecules and are highly reactive due to the presence of unpaired valence shell electrons.
ROSs form as a natural byproduct of the normal metabolism of oxygen and have important roles in cell signaling. However, during times of environmental stress ROS levels can increase dramatically, which can result in significant damage to cell structures. This cumulates into a situation known as oxidative stress.

# Damaging effects
Cells are normally able to defend themselves against ROS damage through the use of enzymes such as superoxide dismutases and catalases.   Small molecule antioxidants such as ascorbic acid (vitamin C), uric acid, and glutathione also play important roles as cellular antioxidants.   Similarly, polyphenol antioxidants assist in preventing ROS damage by scavenging free radicals.   In contrast, the antioxidant ability of the extracellular space is relatively less--e.g., the most important plasma antioxidant in humans is probably uric acid.
The effects of ROS on cell metabolism have been well documented in a variety of species. These include not only roles in programmed cell death and apoptosis, but also positive effects such as the induction of host defence genes and mobilisation of ion transport systems. This is implicating them more frequently with roles in redox signaling or oxidative signaling. In particular, platelets involved in wound repair and blood homeostasis release ROS to recruit additional platelets to sites of injury. These also provide a link to the adaptive immune system via the recruitment of leukocytes.
Reactive oxygen species are implicated in cellular activity to a variety of inflammatory responses including cardiovascular disease.  They may also be involved in hearing impairment via cochlear damage induced by elevated sound levels, ototoxicity of drugs such as cisplatin, and in congenital deafness in both animals and humans.  Redox signaling is also implicated in mediation of apoptosis or programmed cell death and ischaemic injury.  Specific examples include stroke and heart attack.
Generally, harmful effects of reactive oxygen species on the cell are most often:
- damage of DNA
- oxidations of polydesaturated fatty acids in lipids
- oxidations of amino acids in proteins

# Internal production
Free radicals are also produced inside (and also released towards the cytosol) organelles, such as the mitochondrion. Mitochondria convert energy for the cell into a usable form, adenosine triphosphate (ATP).  The process in which ATP is produced, called oxidative phosphorylation, involves the transport of protons (hydrogen ions) across the inner mitochondrial membrane by means of the electron transport chain. In the electron transport chain, electrons are passed through a series of proteins via oxidation-reduction reactions, with each acceptor protein along the chain having a greater reduction potential than the last. The last destination for an electron along this chain is an oxygen molecule. Normally the oxygen is reduced to produce water; however, in about 1-2% of all cases, the oxygen is instead reduced to give the superoxide radical,O2-. Superoxide needs an additional electron to make it more stable, so it steals an electron from the nearest source, such as: mitochondrial DNA, the mitochondrial membrane (called lipid peroxidation), or from protein, or from reductants such as Vitamins C or E, or, from non enzymatic antioxidants such as glutathione or thioredoxin. If too much damage is caused to its mitochondria, a cell undergoes apoptosis or programmed cell death.
Bcl-2 proteins are layered on the surface of the mitochondria, detect damage, and activate a class of proteins called Bax, which punch holes in the mitochondrial membrane, causing cytochrome C to leak out. This cytochrome C binds to Apaf-1, or apoptotic protease activating factor-1, which is free-floating in the cells cytoplasm. Using energy from the ATPs in the mitochondrion, the Apaf-1 and cytochrome C bind together to form apoptosomes. The apoptosomes binds to and activates caspase-9, another free-floating protein. The caspase-9 then cleaves the proteins of the mitochondrial membrane, causing it to break down and start a chain reaction of protein denaturation and eventually phagocytosis of the cell.

# Cause of aging
According to the Free Radical Theory of Aging, aging occurs (via a loss of energy producing cells) either when mitochondria begin to die out because of free radical damage or when fewer functional mitochondria remain within these cells. The focus of the projectTemplate:Vague is to neutralize the effect of these free radicals with antioxidants. Antioxidants neutralize free radicals by donating one of their own electrons. The antioxidant nutrients themselves dont become free radicals by donating an electron because they are stable in either form.

# Superoxide dismutase
Superoxide dismutase (SOD) is present in two places naturally in the cell. SOD that is present in the mitochondria contains manganese (MnSod). This SOD is transcribed in the nucleus and has a mitochondrial targeting sequence, thereby localizing it to the miotchondrial matrix. SOD that is present in the cytoplasm of the cell contains copper and zinc (CuZnSod). The genes that control the formation of SOD are located on chromosomes 21, 6, and 4. When superoxide dismutase comes in contact with superoxide, it reacts with it and forms hydrogen peroxide. The stoichiometry of this reaction is that for each 2 superoxide radicals encountered by SOD, 1 H2O2 is formed.  This hydrogen peroxide is dangerous in the cell because it can easily transform into a hydroxyl radical (via reaction with Fe2+: Fenton chemistry), one of the most destructive free radicals. Catalase, which is concentrated in peroxisomes located next to mitochondria but formed in the rough endoplasmic reticulum and located everywhere in the cell, reacts with the hydrogen peroxide and forms water and oxygen. Glutathione peroxidase reduces hydrogen peroxide by transferring the energy of the reactive peroxides to a very small sulfur containing protein called glutathione. The selenium contained in these enzymes acts as the reactive center, carrying reactive electrons from the peroxide to the glutathione.  Peroxiredoxins also degrade H2O2, both within the mitochondria, cytosol and nucleus. .