Cartoon about lipids and carbohydrates

Glycogenin

The glycogenin is a protein whose main function is to be the initiator molecule of glycogen synthesis (glycogenesis), a process that allows the storage of glucose residues in the form of a polysaccharide. Glucose residues are added to glycogenin through α-1,4 bonds. The first step in the glycogen synthesis is indeed the synthesis of this protein. Each glycogen molecule is linked to a glycogenin by a glycosidic linkage which involves the first glucose residue of the chain and a tyrosine residue of glycogenin. The glycogenin designation stems from the fact that this protein is involved in the genesis of glycogen, by functioning as a primer in the formation of a new glycogen molecule.The glycogenin through its glucosyltransferase activity, binds covalently to itself a glucose molecule (from UDP-glucose - the active form of glucose). Then, the glycogenin forms a compact complex with glycogen synthase, the enzyme responsible for glycogen synthesis. After the addition of up to 7 more glucose residues (from UDP-glucose) mediated again by the activity of glucosyltransferase of glycogenin. Finally, glycogen synthase and branching enzyme enter in action, being glycogenin covalently linked to the unique reducing end of the glycogen molecule.
In humans there are two isoforms of glycogenin which can be expressed as glycogenin-1, having a molecular weight of 37 kD, and encoded by the GYG gene that is expressed mainly in muscle, or as glycogenin-2 having a molecular weight of 66 kDae encoded by GYG2 gene which is expressed mainly in the liver, cardiac muscle and other types of tissues except skeletal muscle

Disability glycogenin-1 (GYG1) - Mutation of the gene GYG1
A glycogenin-1 deficiency was detected in its gene, GYG1, which revealed a nonsense mutation in one allele and a missense mutation in another allele. A missense mutation results from inactivation of the autoglycosilation of glycogenin-1, which is required for the initiation of glycogen synthesis in muscle. The glycogenin-1 autoglycosilation occurs at Tyr195 by the action of glucose-1-O-tyrosine. A missense mutation of this residue results in inactivation of the autoglycosilation. However, it was also demonstrated that missense mutations affecting other residues of glycogenin 1-cause problems on autoglycosilation.
Phenotypic characteristics of skeletal muscle in a patient with this disorder are muscle glycogen depletion, mitochondrial proliferation and marked predominance of slow twitch amd oxidized muscle fibers. Mutations in glycogenin-1 gene GYG1 are also causes of cardiomyopathy and arrhythmia.

Text written by:

Daniela Marinheiro

Carla Marty

Maria Rocha

Marta Rodrigues

Rita Osório

.

Video about reducing sugars

Metabolic map about NO signalling pathway

Enolase

Enolase is an enzyme, more particularly, an active metalloenzyme. This enzyme belongs to the family of lyases, the hydro-lyases, breaking the carbon-oxygen bonds, and is present in all tissues and organisms involved in glycolysis or fermentation. The optimal pH of this enzyme is 6.5 in humans.Its main function is to intervene in the 9th step of glycolysis (the penultimate step in this metabolic pathway), a step in which occurs the dehydration of 2-phosphoglycerate (2-PG) in phosphoenolpyruvate (PEP), a product that will be used in the next and final step for the production of energy (ATP).
Enolase has three different isoforms: the ENO1 or alpha-enolase (in muscle tissue); ENO2 or gamma-enolase or neuro specific enolase (in neurons); ENO3 or beta-enolase (in skeletal muscle cells). Enolase has a molecular weight of about 100000 Daltons (depending on the isoform). In humans, the α-enolase has two antiparallel subunits, which have two domains that establish hydrophobic interactions. The subunits interact via salt bridges, involving arginine and glutamate.
The specific enolase to neurons is released in a wide variety of diseases, such as multiple sclerosis or stroke, or myocardial infarction.
In several medical experiments, it was employed enolase concentrations in samples in an attempt to diagnose certain conditions and its severity. Several studies demonstrated that different levels of enolase may also be associated with tumor growth or with the occurrence of myocardial infarction or stroke, so it was inferred that the levels of enolase serve as an indicative of the prognostic evaluation of victims of cardiac arrest.
Enolase inhibitors have been utilized in health care for the treatment and prevention various diseases, such as anti-trypanosome drugs and more recently as anticancer agents. Enolase can be inhibited by fluoride ion (F-). The fluoride forms a complex with magnesium and phosphate, which binds to the active center of the enzyme rather than the substrate 2-PG, preventing the conversion of 2-PG into PEP, decreasing the production of PEP and, consequently, ATP.
Intake of fluoride-containing water inhibits the catalytic activity of enolase of bacteria present in oral cavity (highly dependent on glycolysis due to the anaerobic environment), interrupting glycolysis and, thus, bacterial fermentation (decreased acid production), preventing the formation of dental caries.

Text written by:
Inês Carvalho
Junjie Lin
Maria Alves
Susana Pinto
.

Cartoon - carbohydrates

Video about carbohydrates biochemistry

Carbohydrates (main functions)

Carbohydrates play a variety of functions in nature. Because of this, they are indispensable elements for living beings. The main functions of carbohydrates are:

- Metabolic fuel – various monosaccharides may be used as a source of chemical energy through its catabolism. Logically, the main carbohydrate used as metabolic fuel is glucose. However, there are several other monosaccharides that can also be used as metabolic fuel (more information on this subject here), such as fructose, mannose or galactose;

 

- Nucleotide components– this function is performed by two different pentose, ribose and deoxyribose. Actually, only one of these carbohydrates is a “pure” monosaccharide (ribose), the other is a derivative of monosaccharide (deoxyribose). Soon, I will write a post about this... Both ribose and deoxyribose are pentoses, that means, they are monosaccharides with 5 carbons. Ribose enters in the composition of ribonucleotides (and consequently RNA) while deoxyribose takes part of the composition of deoxyribonucleotides (and hence the DNA);

- Metabolic fuel reserve - some polysaccharides play the function of metabolic fuel reserve. In this context, there are two molecules that deserve a highlight: starch and glycogen. Both are composed of a single type of monosaccharide, glucose. Starch is the reserve polysaccharide of glucose in plant cells, while glycogen is the reserve polysaccharide in animal cells;

 

- Structural function - some polysaccharides play structural functions, including cellulose and peptidoglycan. The first is the main component of cell walls of plant cells, while the latter is the main component of the cell wall of prokaryotes;

 

- Protection - some polysaccharides play a protective function, such as chitin, which is the main component of the exoskeleton of insects;

- Lubrication and hydration - due to their rich composition in hydrophilic functional groups, carbohydrates have the ability to interact with a large number of water molecules. Because of this feature, various polysaccharides form viscous and highly hydrated mixtures. These polysaccharides are referred to as glycosaminoglycans and are essential for the skin, joints, etc.

 

- Recognition and cell adhesion - there are several molecules involved in cell adhesion and recognition. These molecules are found on the cell surface and have carbohydrate components, being called glycoproteins or glycolipids.

.

Metabolic map about oxidative stress and gene expression

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

Cartoon about hydrophobic substances

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.

.

Video about protein structure

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

.

Metabolic map about ketogenic and glucogenic amino acids

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.