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.

Tuesday, July 26, 2016


Albumin is a globular protein consisting only of amino acids. It is soluble in water, sparingly soluble in concentrated salt solutions and undergoes denaturation when exposed to excessive heat. It is the most abundant protein in human blood plasma. Its synthesis occurs in the liver (hepatocytes) and the speed of the process depends on the amount of proteins ingested (negative feedback regulation). It has a molecular weight of about 66KDa and a half-life between 15 and 19 days. The normal concentration of albumin in the blood varies between 3.5 and 5.0 g / dL. The catabolism of this protein takes place preferably in organs with high metabolic rates (liver, spleen and kidney). There are some types of albumins, whose name varies, depending on where they are most prevalent: serum albumin (present in blood plasma), ovalbumin (main protein from egg white), and lactalbumin (present in milk, is composed of high amounts of essential amino acids and, therefore has a high nutritional value). It is used in treatment of burns, hemorrhages and recovery operations, being also useful to reduce edema. It is essential for maintaining the osmotic pressure of blood (it accounts for 75-80% of the osmotic effect of plasma). Albumin has the function of transport and storage of various usually poorly soluble compounds in water with low molecular weight. For example, albumin is essential for the transport of unconjugated bilirubin to the liver and long chain fatty acids to extrahepatic tissues, and also the thyroid hormones, fat-soluble hormones and calcium ions. This protein is also responsible for the control of blood pH and blood viscosity. It also has an important role in lipid metabolism. Deficiencies in this protein concentration can trigger conditions such as hyperalbuminemia (excess albumin in the blood) and hypoalbuminemia (albumin deficit in blood). In the first case, the symptoms are most pronounced in conditions of severe dehydration, being a rare condition with a neglected diagnosis in most cases. Hypoalbuminemia results from reduction of protein synthesis, which may be caused by liver diseases (causing decreased protein production), malnutrition, malabsorption (due to, e.g., intestinal disorders), infections, excessive excretion thereof and in rare cases, genetic disorders. If the concentration of the protein decreases, the osmotic pressure of the blood decreases. Consequently, the plasma tends to seep into the intercellular spaces, causing edema, hence that administration of albumin after surgery is responsible for the reduction of swelling.

Text written by:
Mariana Rebelo
Marta Duarte
Rafael Honório
Sara Silva

Cartoon - Pepetide bond

Sunday, July 24, 2016

Isoelectric point (aminoacids and proteins)

Amino acids are, as mentioned in other posts, molecules that have an amino group and a carboxylic group. These two groups are ionizable, ie, they may undergo protonation/deprotonation. Moreover, the side chains of various amino acids may present additional ionizable groups. This means that amino acids are molecules that can display positive, negative, or neutral charge. What influences the overall charge of each amino acid in a given context is:
1. Chemical composition of the amino acid and the molecule where it is inserted (if that is the case ...). The presence of certain atoms/functional groups in a molecule alters the distribution of its electron cloud, making some covalent bonds stronger and other weaker. The weakening of the bonds involving hydrogen atoms turn easier the occurrence of deprotonation.
2. The pH of the solution in which the amino acid is inserted. As is logical, functional groups will present a state of protonation that is influenced by the pH, that means, if the pH is lower than its pKa, the functional group tends to be protonated, and if it is greater than the pKa, it tends to be deprotonated.
Therefore, based on the characteristics of each amino acid, and the environment where it is, it is possible to obtain different total charges.
The isoelectric point is defined as the pH value for which the total charge of the amino acid is zero. Note that this does not mean that there are no charges on the amino acid, because in reality there are charges, indeed. This means is that when subjected to this pH, total positive charges equal the total negative charges. At this point, the amino acid solubility decreases. When an amino acid is placed in a solution with a pH below its isoelectric point, it acquires positive charge as the functional groups tend to be protonated (gain H+). If the pH is above the isoelectric point, total charge is negative, because the functional groups tend to be predominantly deprotonated (lose H+).
In the case of proteins, it applies exactly the same concept. However, in this case one must consider the total of ionizable groups present in the molecule, and the isoelectric point is defined as the pH value for which the total charge of the protein is zero. 
Again, at this value the solubility of the protein is zero, and it tends to precipitate. This is explored in the laboratory by means of a technique called isoelectric focusing.

Thursday, July 21, 2016


Vasopressin (væsoʊprɛsən / vaso + -in + pressure), also known as antidiuretic hormone (ADH) has a molecular weight of 1228 kDa and is formed by the following sequence of nine amino acids: cysteine ​​- tyrosine - phenylalanine - glutamate - aspartate - cysteine ​​- proline - arginine - glycine. The presence of a disulfide bridge between the cysteines in position 1 and 6, gives it a ring-shaped structure. In most species, the 8th position of the molecule is occupied by arginine and due to that, ADH is therefore also called arginine vasopressin or argipressin (AVP). Lysine vasopressin has a lysine in the traditional arginine position. In 1955, Du Vigneaud won the Nobel Prize in Chemistry, in part, by the discovery of vasopressin and oxytocin, a hormone related to vasopressin. In kidney, vasopressin increases the permeability of the renal tubule cells to water. As a result, it allows the body to retain water, increasing urine concentration and decreasing its volume. For this reason it is called antidiuretic hormone (ADH). 
Also, it promotes arteriolar vasoconstriction, increasing consequently the peripheral resistance and blood pressure. For this reason it is also called vasopressin. It also has other functions such as regulation of circadian rhythms, homeostasis and different social behaviors.This hormone is produced by the neurohypophysis, but can also be produced by the hypothalamus at the supraoptic and paraventricular levels of the core. The production of vasopressin begins with the activation of the gene responsible for its biosynthesis. This gene is located on chromosome 20 and has 3 exons separated by 2 introns. Each exon codes for one of the three domains of the precursor molecule of vasopressin.
Under enzymatic action, this precursor loses the signal peptide and is stored in vesicles at the Golgi complex, and then is transported from the cell body of the neuron to the nerve endings. This transport takes approximately 12 to 24 hours. During this time, several cleavages occur, giving rise to ADH molecules, neurophysin and copeptin. ADH is excreted by the neurohypophysis briefly in response to decreases in plasma volume (detected by barorrecetores), potential increases in osmotic plasma (detected by osmorecetores veins, arteries, and other vessels) and also in response to cholecystokinin (excreted by small intestine).
The diseases associated with vasopressin normally give a deficiency or excess in its production or in its effect. Disability can cause polyuria, excessive excreted urine which is hypotonic and when combined with hypernatremia (excess sodium in the blood) may be a sign of diabetes insipidus. The term diabetes refers to water loss, which is insipidus due to the absence of sweetnessin the urine. Diabetes insipidus arises from the lack of production of the hormone ADH. The excess of ADH is characterized by fluid retention and can lead to hyponatremia. It often happens in drops in blood pressure, reduced blood volume (amount of circulating blood) or dehydration. The excess of ADH also occurs by inadequate secretion of vasopressin syndrome, caused by disorders in the central nervous system, cancer, lung disease, and HIV medications and not by pressure drops and any of the other factors.

Text written by:
Luís Alves
Pedro Silva
Ricardo Praia
Tiago Fernandes
Tiago Borges

Wednesday, July 20, 2016

Monday, July 18, 2016

Standard and non-standard amino acids

Amino acids are molecules that, from a chemical standpoint, are characterized by the presence of an amine group and a carboxylic group (acid), and hence its name: amino acid. Its main function is to serve as monomers for the synthesis of peptides and proteins. Of all the amino acids in nature, there is a set of 20 amino acids which are designated by standard amino acids, and that are used as building blocks for most of the proteins produced by any living being. These amino acids are widely studied and have been the central elements in my last posts. Just to remember, the standard amino acids are:

- glycine
- alanine
- proline
- valine
- leucine
- isoleucine
- methionine
- phenylalanine
- tyrosine
- tryptophan
- serine
- threonine
- cysteine
- asparagine
- glutamine
- lysine
- arginine
- histidine
- aspartate
- glutamate
However, besides the standard amino acids, there are many others that are found in some proteins and are called non-standard amino acids. The idea of ​​using these non-standard amino acids is simple to understand. By having a composition different from the standard amino acids, they present different physicochemical properties. Therefore, when it is necessary to introduce in a protein a local with certain properties, if they cannot be provided by the standard amino acid, it is incorporated in the sequence a non-standard amino acid. With regard to translation, in these cases, at these sites are introduced standard amino acids, which suffer post-translation covalent modifications to give amino acids with other features. I would like to highlight something that I think it is important. How you will notice below, several of the non-standard amino acids are found in the extracellular matrix proteins. As the extracellular matrix is a very complex structure, establishing numerous interactions with many different molecules (extracellular and cellular molecules), it is necessary that the proteins that make up the matrix may present a high versatility in the interactions that they establish, hence the need to specifically include some amino acids that have different characteristics. Some non-standard amino acid examples include:
- Cystine, desmosine and isodesmosine, which are amino acids found in extracellular matrix proteins such as elastin;


- Hydroxyproline and hydroxylysine, found in the most abundant protein of  the extracellular matrix – collagen;


- Gamma-carboxyglutamate, found in osteocalcin which is an extracellular matrix protein of bone, but also in the pro-thrombin, which is important for the coagulation cascade;
- Phosphoserine, phosphothreonine and phosphotyrosine, which are found in many different proteins, as protein phosphorylation is the most common post-translational modification, and always involves amino acids with hydroxyl groups in their side chains;

- N-acetillysine, which is fundamental to the structure of histones:
- Methyllyisine, which is found in myosin, a motor protein of our cytoskeleton, more specifically of actin filaments.

Friday, July 15, 2016

Amino acids with acidic side chains

This is the latest group of standard amino group that I will describe. It consists of 2 amino acids, glutamate (also called glutamic acid) and aspartate (also called aspartic acid). Both have a carboxylic group in its side chain, which, being a weak acid group, confers acidic properties to the side chain. In other words, these side chains tend to have a negative charge as a result of deprotonation of the carboxylic group. They are, therefore, very important amino acids to establish ionic interactions with amino acids with alkaline side chains (more information on these amino acids here), and these forces may also be called salt bridges. In order to avoid confusion in the nomenclature of the carboxylic group of the side chain and the carboxylic group attached to the alpha carbon, the side chain group is typically referred to as gamma-carboxylic. The difference between glutamate and aspartate is just a methylene group -CH2 -. Indeed, glutamate has one more carbon (in the form of methylene group) than aspartate. Both can be obtained from intermediates of the Krebs cycle (glutamate from alpha-ketoglutarate and aspartate from oxaloacetate), and besides being building blocks for protein synthesis, they are also used as neurotransmitters. Glutamate also plays a very important role in terms of the sense of taste, and is also important as a donor of amino groups in several reactions of biosynthesis of nitrogenous molecules.