Merry Christmas!

I wish to all the readers of World of Biochemistry a Merry Christmas! :)

Famous quote (27)

For me, this is the "main law" of science... :)
“Somewhere, something incredible is waiting to be known.” ― Carl Sagan

Metabolic map about the ceramide signalling pathway

Song "The Science Love Song"

Dedicated to those who think that science cannot be romantic... :)

Thank you for the input Suely! :)

Video about sickle cell disease

Thank you for another contribution Vasco! :)

The Organic Chemistry of life...

There is a sentence that I say sometimes in my classes that define my interpretation of what is life ...
"We are no more than a set of molecules that interact and therefore know how to organize themselves into more complex structures."
It is an objective point of view, some might classify it as a cold perspective, but it's my interpretation of what we really are. Of course there are many factors, many variables that we do not know yet, and therefore we do not control.
Astronomy recently took another step in the elucidation of the relationship between chemical, physical and biological sciences, with the probe Philae. For those interested or just curious, here is more information on the subject:
http://www.iflscience.com/space/explainer-what-philae-did-its-60-hours-comet-67p

 
Thank you Vasco for the input!

Amino acids (general considerations)

Amino acids are molecules that, from a chemical point of view, are characterized by the presence of two different functional groups. The name itself refers to them: an amine group and a carboxylic group (that is the most relevant acid group in biochemistry). Although normally when we hear the word “amino acid” we think in proteins, actually any molecule that presents these two functional groups is an amino acid.

From a functional standpoint, the amino acids play many important functions in our body. All our proteins are formed from different combinations of a set of 20 different amino acids, the so-called "standard amino acids". 

This is actually the best known function of the amino acids, they are the building blocks of the thousands of proteins and peptides that exist in nature. However, to summarize all the functions in this one is a very narrow perspective. The amino acids play many other important physiological functions, such as: they are the donors of nitrogen atoms for the synthesis of several molecules, such as nitrogen bases, other amino acids, polyamines, heme group, ...; they are present in the composition of certain lipids, such as phosphatidylserine; they perform the function of neurotransmitters (glutamate and glycine, for example) or are used as precursors in the synthesis of other neurotransmitters (GABA, for example); they function as carriers of nitrogen in the blood stream, with glutamine and alanine with a particular relevant role in this function.

In their chemical composition, the standard amino acids have a common structure among the majority of their constituents. All have a central carbon, designated a-carbon, to which there are attached the amine group and the carboxylic group, to define them as amino acids. As these groups are bonded to a-carbon are often referred as a-amine and a-carboxylic acid, and amino acids are referred to as a-amino acids. In addition to these groups, there is also a hydrogen atom bonded to the central carbon. The 4th substituent is designated by R group or side chain and it is this group that defines the identity of the amino acid, since all other components are common to the 20 standard amino acids. Soon I will talk in more detail about the properties of this R group...

Animation about embrionary development

Download the animation here
.

Famous quote (26)

If we knew what it was we were doing, it would not be called research, would it? 

Albert Einstein

T-shirt - Diffusion

Tattoo - Physics (2)

Video about epimers and anomers

Metabolic map about myocardial infarctation

Cartoon - Water

Trypsin

Trypsin is a digestive protease produced in the pancreas (it is a component of pancreatic juice, which is released in the duodenum during digestion). Its function is to cleave dietary proteins, and for this it recognizes amino acids with basic side chains (lysine and arginine) and cleave peptide bonds in which they are involved. In order to be inactive in the cells that produce it (if this were not the case it would begin to degrade our own proteins), it is synthesized as trypsinogen. Trypsinogen is the zymogen of trypsin, an inactive form of an enzyme, characterized by having more amino acids than those that are required for the enzyme to be in its functional form. The idea is that these additional amino acids block the catalytic activity (e.g., preventing access of substrate to the active site). 

Once in the intestine, trypsinogen is proteolytically cleaved by the action of an enzyme called intestinal enteropeptidase. From the moment that a molecule becomes active trypsin, itself can begin to activate (by proteolytical cleavage) all other zymogens, not only trypsin but also chymotrypsin, carboxypeptidases and aminopeptidases. Thus, trypsin has a central role in the activation of digestive proteases, so it is necessary to ensure that any molecule, under normal conditions, will not become catalytically active inside the cells. The first line of protection is the synthesis of the enzyme in the form of trypsinogen. Additionally, cells which produce pancreatic trypsin also have a second line of defense, which involves the production of an inhibitory protein called pancreatic trypsin inhibitor. Therefore, even if spontaneously one trypsinogen acquires activity inside the cells, the presence of this inhibitor will prevent it to exerts its function and consequently, avoiding the cell to begin to cleave and activate other zymogens proteins.

Tattoo - Microscope (3)

Pencil case - DNA

Animation about DNA transcription

Download the animation here
.

Video about mitochondrial ATP synthase

Metabolic map about bone remodeling

Cartoon about science

Tavistock Tutors

I was surfing on the internet and found a website that provides a very interesting and potentially useful service to many readers of this blog. I am talking about Tavistock Tutors (http://tavistocktutors.com/), which allows students of various levels of education to have access to private tutors in any subject site. This service is mainly conducted ​​in London, but it is also possible to have a tutoring service internationally. It is a company that was founded in 2009 and aims to be the best tutoring company in London. The goal is hard to achieve, but they are in the right way, undoubtedly! It has grown significantly in recent times, having already over 400 tutors and many renowned academic advisors. In fact, it is a company that promises to revolutionize the way we study and how do we have access to knowledge. The extensive tutor database of Tavistock Tutors is able to solve the problem of virtually any student, 365 days a year, 24 hours a day. One key of their success lies in the fact that tutors are carefully selected to ensure the quality of education they provide.

In the case of Biochemistry, Tavistock Tutors has a team of excellent professionals, trained in some of the most respected departments of Biochemistry around the world, such as Cambridge, Oxford and Imperial College London. You can access more detailed information about these tutors in http://tavistocktutors.com/tuition/biochemistry-tutors-london/. The competence of the tutors of Biochemistry, in particular, goes far beyond their knowledge, and the way they link the basic concepts of biochemistry (biology and chemistry) allows students to better understand the subjects and, consequently, achieve better results in their examinations. Do you have questions about the chemistry of biomolecules, on the basis of our metabolism, or on a metabolic pathway in particular? The Tavistock Tutors will surely help you!

So, you know… If you need additional help to better understand biochemistry, if you need someone who can explain you the details behind this science that sometimes is quite complex,visit their website and you can make the request for tutoring through it and you will see that after all the biochemistry is not that hard! :)

Mitochondrial ATP synthase (general characteristics)

The mitochondrial ATP synthase (F-ATP synthase) is an enzyme which is located in the inner mitochondrial membrane whose function is closely related to the mitochondrial respiratory chain. Because of this, some authors call it Complex V, though most do not use this nomenclature. Personally, I also think it should not be called Complex V, since the complexes are, in my opinion, those involved in the transport of electrons, and this process ends in oxygen (in the complex IV). 

As its name suggests, the ATP synthase will catalyze the synthesis of ATP molecules through the process of oxidative phosphorylation. That is, to conduct the phosphorylation of ADP to ATP it is necessary an oxidation, which in this case involves the use of NADH or FADH2 in the mitochondrial respiratory chain.

The general reaction of operation of ATP synthase is:

ADP + Pi → ATP

This reaction is quite endergonic and therefore requires energy to occur. And where does this energy come from? From the H+ gradient created during the operation of the respiratory chain complexes. Therefore, the energy liberated during the transport of electrons is used to create an accumulation of H+ in the intermembrane space, and then these ions will tend to return to the matrix, causing the release of energy. This is the energy that is used to produce ATP.

ATP synthase has two different subunits:

- Fo subunit which is a transmembrane subunit with a pore through which the H+ return to the matrix. As a curiosity, the name is Fo (and not F "zero"), because the "o" derives from the fact that this subunit binds to oligomycin, which is an antibiotic.

- Subunit F1, the catalytic subunit which is responsible for ATP synthesis and is located in association with the matrix side of the inner mitochondrial membrane. Paradoxically, this subunit has an ATPase activity (ATP hydrolysis) when isolated, but when in contact with the inner mitochondrial membrane and specifically to Fo subunit, it has the activity of ATP synthesis.

Tattoo - Maths (4)

Music about the immune system

The music Yankee Doodle inspired Dr. Ahern to create a song about the immune system.

Download the music here

The Immune Tune

Antigen presenting cells
Help to clear infection
And they help your thymocytes
Go through t-cell selection

Endocytose antigen
And then cross-present it
All to slow the illness down
Or possibly prevent it

Activate a CD8
This will help you be well
It will differentiate
To cytotoxic t-cell

Systems of immunity
Fusing with perfection
Thank Adaptive and Innate
For giving such protection!

Video about uncoupling proteins

Metabolic map about circadian rhythms

Cartoon about climatic changes

Uncoupling proteins

The uncoupling proteins (UCPs) are proteins that, as their name indicates, will decouple, that means, separate processes that occur in normal conditions associated with one another. I am talking about the transport of electrons along the mitochondrial respiratory chain, and ATP synthesis. What happens is that, under normal conditions, if one of the processes stops, the other will be blocked. The presence of UCPs allows a process to can occur even in the absence of the other. Basically they are proteins of the inner mitochondrial membrane that will allow the return to the matrix of the H+ accumulated in the intermembrane space without passing through ATP synthase. 

Thus, it will continue to occur the transport of electrons in the respiratory chain, but this process will no longer be solely dependent on the synthesis of ATP. There are different isoforms of UCPs… UCP1, also known as thermogenin serves to produce heat in brown adipose tissue, thereby helping to maintain body heat in newborns and during hibernation, for example. The UCP2 is a protein essentially involved in the production of heat in the muscle; however, recent papers have suggested that this protein may also be important to regulate the levels of reactive oxygen species in mitochondria. The UCP3 is still not as well characterized, but it is thought that it may be related to the regulation of the levels of reactive oxygen species in skeletal muscle and cardiac muscle.