# Structural Biochemistry/Cell Organelles/Mitochondria/High level of ROS

Reactive oxygen Species and protein mutations
Reactive oxygen species (ROS) cause damaging effects to the mitochondria which contributes to aging and disease. ROS is a leading cause to protein damage because of constantly misfolding and misassembling the proteins. An increase in ROS can generate an overwhelming load of misfolded mitochondrial proteins. ROS are chemically active molecules containing oxygen. When the body is in stress the ROS levels increase tramatically which then causes the proteins to misassemble and misfold causing errors in the mitochondria. These errors in the mitochondria lead to the effect of aging and disease. The mammalian mitochondria is comprised of one thousand to one thousand five hundred proteins. This leaves tons of room for error or mutations. However the cell has a quality control to help regulate and protect against damaged and misfolded proteins. Even under optimal conditions approximately ten percent of newly synthesized proteins are mistranslated. Excess or misfolded subunits are degraded by quality control proteases before it can interact with other proteins and organelle disfunction. When the protein is folding into tertuary structures the use of chaperones and proteases prevent the accumulation of unfolded and singled subunits. A majority of the misflding occurs in the electron transport chain and the inner membrane of the mitochondria. Translation errors and nuclear DNA mutations lead to misfolded proteins which then leads to electron transport chain disfunction which leads to higher doses of reactive oxygen species which then can lead to either more misfolded proteins or mtDNA mutations. All of theses have leading effects to aging. However there are some functions that help protect against the misfolding of proteins. Once a protein is detected to be folded wrongly then the UPRmt is notified which notifies quality control and both of these functions help protect against damaged and misfolded proteins. The electron transport chain is comprised of approximately one hundred proteins, thirteen of which are encoded by the matrix of the mitochondria and inserted in the inner membrane. The rest are translated in the cytoplasm and imported into the mitochondria. The electron transport chain is composed of five different complexes. Complex one is the NADH-ubiquinone oxidoreductase, complex two is the Succinate dehydrogenase, complex three is the Cytochrome bc1, complex four it the Cytochrome oxidase and complex five is the ATP synthesis. The mitochondria needs all these complexes in order to make ATP. Reactive oxygen species is generated primarily by complexes one and three of the electron transport chain during oxidative phosphorylation and can damage proteins in all four mitochondrial compartments.
Mitochondrial Compartments
There are four compartments in the mitochondria where protein folding and assembling takes place. These compartments include the outer membrane (OM), the inner membrane space (IMS), the inner membrane (IM), and the matrix. Below goes into further detail about each.
Outer Membrane (OM)
The outer mitochondrial membrane is the membrane that encomposes the entire mitochondia. This membrane contains numerous integral proteins which contain a relatively large internal channel that is permeable to most molecules. The outer mitochondrial membrane also contains enzymes which are involved in many activities including elongation of fatty acids, oxidation of epinephrine, and the degradation of tryptophan.
Intermembrane Space (IMS)
Since the outer mitochondrial membrane contains channels, the content of the intermembrane space is similar to that of the cytoplasm. When the electrons move down the proteins in the electron transport chain, the electrons lose energy and bring hydrogen ions from the mitochondrial matrix into the intermembrane space. When the concentration gradient of H+ ions forms, a protein called ATP synthase conectects the potential energy of these ions and starts chemiosmosis, where the hydrogen ions reenter the matrix via this enzyme bound to the folds of the inner membrane. ATP is formed by the combining a phosphate group and ADP.
Inner Membrane (IM)
The mitochondria forms two membranes to have greater space for proteins to function efficiently and properly. The inner membrane contains transport proteins that transport metabolites across the membrane in a highly controlled manner. This is also the region where the electron transport chain is located.
Matrix
The matrix contains soluble enzymes that catalyze the oxidation of small organic molecules. This region also contains the mitochondia's DNA and ribosomes. The pH of the matrix is approximately 7.8.
ROS affects DNA
Reactive Oxygen Species (ROS) can be damaging to the DNA because it can break the strands and result in the loss of base. This damage to the DNA leads to aging and neurological disorders. ROS occurs naturally in the body and can be reduced by the quality control. An abundance of the ROS is body for the cells and results in damage to the DNA and proteins. For the misfolding of proteins, the cells have the quality control to fix this but with the strand breaks in DNA the cells have an enzyme polynucleotide kinase/phosphatase (PNKP) to control this.
Polynucleotide Kinase/Phosphatase (PNKP)
PNKP is an important enzyme in cellular processing of strand breaks and participates in many DNA repair pathways. PNKP consists of 5'-kinase and 3'-phosphatase activities which are frequently required for processing single and double strand breaks. PNKP is a multi-domain enzyme that consists of a N-terminal and a C-terminal. PNKP contains two catalytic active sites which are on the same side of the protein. PNKP contains a selective distinct groove for the large, double stranded DNA substrate which consist of two positively charged surfaces. Since the amino acids substitute on the surfaces of kinase activity, it illustrates that the DNA substrates bind across the surfaces in a distinct orientation. Mammal PNKP effortlessly acts on the 3'-phosphate ends. The PNKP goes about repairing the DNA differently depending on the type of damage the DNA has. For instance if the DNA is broken at a single strand, the PNKP will go about repairing this differently than if the DNA had a break in the bases. It will also repair it differently if it had a break in the double strand. PNKP is involved in multiple DNA repair pathways. A mutation in the PNKP can cause a severe neurological autosomal recessive disease characterized by intractable seizures and developmental delays. Researchers are researching PNKP's regulation, physiological role in neurons and other tissues, and interaction with other repair enzymes. Since PNKP is involved in many repair pathways, it is now being thought of a therapeutic target to the treatment of cancer.
References
Baker, M. Brooke and Haynes, M. Cole; Mitochondrial Protein Quality Control During Biogenesis and Aging, pg 254-260.
Weinfeld, Michael; Mani, Rajam S.; Abdou, Ismail; Acetuno, R. Daniel and Glover, J.N. Mark; Tidying up loose ends: the role of polynucleotide kinase/phosphatase in DNA strand break repair, pg. 1-7