Thursday, August 25, 2016

Metabolic map about oxidative stress and gene expression


Sunday, August 21, 2016

Cytochrome c

Cytochromes were first described in 1884 by MacMunn as respiratory pigments. Later, in 1920, Keilin rediscovered these respiratory pigments and gave them the name of Cytochrome, classifying these heme proteins based on the lowest level of the cytochrome energy absorption position.Cytochrome c is a small protein with 104 amino acids located in the intermembrane space of mitochondria of all living beings who do aerobic respiration. Part of its chain is separated by a matrix protease when the polypeptide is inserted into the inner membrane, being anchored in a proper orientation.It is a heteroprotein (protein composed of amino acids and other chemical elements), which besides amino acids, has a heme group (cofactor)that is bound to the cysteines 14:17.It is a hydrophilic protein, highly soluble in water (solubility ~100g /L).The percentage of each type of amino acid present in the protein varies, depending on the species and it is related to their evolutionary proximity. The variation in the primary structure in different species, indirectly reveals their genetic differences since the code for the protein is written in the genes. This protein plays an important role in cellular respiration as it is an electron carrier between complexes III and IV, displacing them to an oxygen molecule (final acceptor), thereby converting molecular oxygen to two molecules of water. In this process, it occurs translocation of protons to the intermembrane space, which help the formation of a chemiosmotic potential used by the ATP synthase for the formation of ATP. It is also responsible for stimulating programmed cell death, or apoptosis, by activating the intrinsic pathway of the process. This leads to activation of caspase 9, which in turn activates caspases 3 and 7, and the target cell  dies by apoptosis. Finally, it also promotes the release of calcium stored in the endoplasmic reticulum, increasing the ion concentration in the cytosol.Regarding the formation of cytochromes, they suffer reversible changes in the iron oxidation number, changing between +2 and +3 in a cyclical process. There are three main groups of cytochromes, denominated by the letters a, b and c. They differ in the structure of the prosthetic group (side chain), leading to different absorption spectra, wherein the cytochrome c absorbs the shorter wavelengths.

Text written by:
Ana Ribeiro
João Esteves 
Maria Correia
Maria Melo

Monday, August 15, 2016

Carbohydrates (general characteristics)



Carbohydrates, also referred to as sugars, are a class of biomolecules characterized by the presence of many polar groups in its composition. The building block of the carbohydrates are the monosaccharides, since any carbohydrate has one, or more than one, monosaccharide. Consequently, they can be grouped into different classes, namely, monosaccharides, oligosaccharides and polysaccharides.
When only one or a few monosaccharides are present, usually the carbohydrate has a sweet taste and is therefore referred to as sugars. In fact, when looking for a label of a food product, it is common an information like "Carbohydrates of which sugars". This information may cause some confusion, because in fact there is some ambiguity in the designation of sugar. If some people call sugars to carbohydrates, there are those who use this designation only to carbohydrates that are sweet.
Carbohydrates are the most abundant class of biomolecules in nature, being also the most abundant class of biomolecules in our food, and should correspond to 45-75% of total energy intake.
Carbohydrates exist in a free form, i.e. without being linked to other types of molecules. In this case, they are referred to as poly-hydroxyaldehydes or poly-hydroxyketones, since they present several hydroxyl groups and one carbonyl group which can be aldehyde or ketone, respectively (if you have any questions about these functional groups, you can find more information about them HERE and HERE). 

If carbohydrates are combined with other molecules, the resulting molecule is referred to as a glycoconjugate, being the most well-known glycoconjugates the glycoproteins and glycolipids.
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Thursday, August 11, 2016

Catalase

Catalase, or hydroperoxidase, is an intracellular enzyme found in most organisms. This protein is found in the peroxisomes, glyoxisomes (plant peroxisome) and in the cytoplasm of prokaryotes. Catalase is an oxidoreductase, since it uses hydrogen peroxide (H2O2)both as an acceptor of electrons and as an electronic donor, decomposing it accordingly to this chemical reaction: 2H2O2 → 2H2O + O2.Although there are various known forms of this enzyme, it is commonly found in the form of a tetramer of 240 kDa, having four polypeptide chains in a quaternary structure. Each polypeptide chain binds a heme group that has an iron ion, which reacts with the hydrogen peroxide, decomposing the molecule. However, there are also some non-heme catalases, that is, instead of havin heme groups, they have one binuclear manganese center.
The toxic H2O2 is a product of the metabolism of our cells, produced, for example, during the peroxisomal β-oxidation of fatty acids, which requires a rapid conversion of it into a chemical species that is harmless the organism. Catalase has the highest known turnover number (kcat): the enzymes is able to decompose 40000000 H2O2 molecules per second! Catalase is also important for certain invading microorganisms, which is used as a defense system against some cells of our immune system whose action rely in the production of H2O2 as an antibacterial agent. Finally, this enzyme is associated with delayed aging mechanism connected to oxidative stress.
The reaction catalyzed by this enzyme is a dismutation reaction, i.e., the substrate acts as both reductant and oxidant agent. It is known that it occurs in two basic steps: H2O2 + Fe (III)-E → H2O + O = Fe (IV)-E and H2O2 + O = Fe (IV)-E → H2O + Fe (III)-E + O2. 

Fe-E represents the iron ion of the heme group, bound to the enzyme. Catalase is also capable of catalyzing the oxidation of other molecules such as formaldehyde, formic acid and certain alcohols. H2O2 + H2R → 2H2O + R, where R is the oxidized form of the molecule that undergoes the reaction. Metal ions (especially copper (II) and iron (II)) are non-competitive inhibitors, and cyanide and curare behave as competitive inhibitors.
Catalase is used also used in the textile industry to remove H2O2 from the tissues, and in some contact lens cleaning products, acting as an antibacterial agent. Currently, it has also been used in beauty masks, combining the enzyme with H2O2 to increase cellular oxygenation of the upper layers of the epidermis.
The so-called Catalase Test is used in microbiology and consists in the detection of catalase in bacteria, serving essentially to distinguish staphylococci and streptococci. In this test, peroxide is put in contact with a liquid microorganism culture to be tested if it appears bubbles (oxygen); if so, the organism is catalase-positive (has catalase if staphylococci), otherwise, it is designated catalase-negative (streptococci).

Text written by:
Ana Araújo
Inês Oliveira
Mariana Pires
José Cardoso
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Friday, July 29, 2016

Amino acids as neurotransmitters



In addition to being used as building blocks for protein synthesis, amino acids play many other important physiological functions. One is undoubtedly the fact that there are several amino acids that play neurotransmitter functions:
- Glutamate is the main excitatory neurotransmitter in the central nervous system. It plays central roles in terms of rapid nerve transmission (i.e. rapid response to a stimulus), cognition, memory, movement and sensation. It is recognized by two classes of receptors: ionotropic receptors, which are receptors that when activated allow ion flow across the membrane; and metabotropic receptors, which when activated stimulate the production of secondary messengers.

 - Aspartate, it is also an excitatory neurotransmitter of the central nervous system. Due to biochemical similarities between glutamate and aspartate (more on this subject here), the actuation mechanism and effects are identical between them (although glutamate is, from a quantitative point of view, more important than aspartate).

 


- Glycine is the simplest amino acid, and has inhibitory functions in the central nervous system, with particular emphasis on the spinal cord, brain stem and in the retina. In addition to its role as a neurotransmitter, it also plays immunomodulatory functions, anti-inflammatory and cytoprotection (cell protection). The activation of its receptors allows influx of chloride ion.