Publication 2:Dead Enzymes Show Signs of Life

Reference:
Leslie, Mitch. “Dead Enzymes Show Signs of Life.” Science 340, no.6128 (2013): 25-27. Accessed April 10th, 2013. http://sciencemag.org/content/340/6128/25.full

One of the topics which have been taught from the inception of science classes in primary school is enzymes. Enzymes are reviewed in each class from secondary school to college and at the final level of university. The contents of this topic are very basic and sometimes repeated continuously at each level. Enzymes are defined as biological catalysts which allow a reaction to occur at a faster rate by lowering the activation energy. In biochemistry enzymes are very noble molecules which allow reactions to occur over 10000000 times faster than the normal reaction. Enzymes remain unchanged at the end of the reaction and they are very specific. From all of this content the idea of an enzyme which did not catalyze a chemical reaction seemed very foreign. A decade ago it was discovered that there are enzymes which did not take part in chemical reaction and appeared to have lost their function. They are described as “pseudoenzymes”.

Psuedoenzymes were discovered as biochemist aimed to identify all genes which coded for protein kinase. Out of 518 proteins, 10% appeared to lack the essential amino acids which were needed to catalyze their reactions. This was a surprise as the human body rarely produced molecules which were not needed, as this would be a waste of energy. However, after much more research it was found that these pseudoenzymes played a very important role in the human body.

The structure of the pseudoenzyme closely resembles that of the active enzyme. These enzymes also have the ability to bind to substances. From this the roles of these enzymes in the body have been identified. One of the main functions of pseudoenzymes is to regulate active enzymes. The binding of the pseudoenzymes to active enzymes adjust the activity of the active enzymes. In addition, the binding of a pseudoenzyme to an active enzyme may change the shape of an active enzyme to promote binding of the substrates. Other pseudoenzymes are attached to cell membranes and act as receptors. Some pathogens even utilize pseudoenzymes to increase the activity of the parasites key metabolic enzymes up to 3000 times. An example of a parasite which uses the pseudoenzymes for this purpose is Trypanosoma brucei which causes the African sleeping sickness.

From these features pseudoenzymes seem like the perfect candidates to act as drugs in the human body. One of the main ways in which drugs control diseases in the human body is by inhibiting enzymes which aid in producing key symptoms of the diseases. Chronic myelogenous leukemia is controlled by the inhibition of kinase by Gleevec. As pseudoenzymes have the ability to regulate active enzymes, they may be used in order to reduce the activity of enzymes. However a problem arises as many enzymes have similar active sites, so that drugs which are capable of affecting one enzyme may also affect another. From this side effects arise. Research is still ongoing in ways to overcome this problem.

Pseudoenzymes were a very interesting topic for me. It changed my general outlook on enzymes, as I thought that all enzymes in the human body are used to catalyze chemical reactions. This highlighted that enzymes are so very essential to human life as they are not restricted to one aspect of the functioning of the human body. It was funny that the scientist named the enzymes pseudoenzymes as the prefix pseudo means false. They seem to look at these enzymes as impressionist and intruders.

I look forward to further research on these “false enzymes”

Publication:Dialister pneumosintes Associated with Human Brain Abscesses

Reference:
Rousée, J. M. et al. “Dialister pneumosintes Associated with Human Brain Abscesses.” Journal of Clinical Microbiology 40, no. 10(2013): 3871–3873. Accessed April 11th,1023.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC130909/

It is amazing when scientist discover that the smallest bacterium present in the earth is responsible for deadly diseases in the human population. The Dialister Pneumosintes is the smallest bacteria known to mind kind. The size of the bacteria is approximately 0.5×0.5×1.6 µm. The bacterium is a nonfermentative, anaerobic, gram-negative rod which grows with small, circular, transparent, shiny, smooth colonies on blood agar. The bacteria cannot be identified by morphological and traditional methods and therefore is identified by sequencing of the 16S rRNA gene. A few years ago the bacteria was isolated from two patients by way of a blood culture and from a brain abscess in the brain.

The first patient from which the bacterium was isolated had various flu-like symptoms. Along with a high fever, a left temporal head ache and paralysis to an arm, there was also swelling of lymph nodes. Doctors passed this off as symptoms of a normal fever and treated it with antibiotics. However, as time went by the condition of the patient became worst. This lead to a CT scan which revealed an empyma compressing the frontal lobe .The empyma was evacuated and the frontal sinus drained and examined. Colonies of Streptococcus angrinosus were isolated. These are recognized as normal flora which if present in excess can lead to brain abscess. However the Streptoccus angrinosus were present in small amounts. Further examination of the empyma isolated Dialister pneumosintes. All other blood cultures tested negative for the presence of other bacteria.

The second patient displayed a variety of symptoms. He was admitted to the hospital for right-side tonic-clonic seizures. When examined the patient did not have a fever but was postictal and had a right side hemiparesis . A craniotomy was performed on the patient and green pus was drained from the frontal brain tissue. Examination of the sample revealed numerous Streptoccocus cells, gram positive rods and rare cultures of Diaslister pneumonsintes.

Before these two cases the bacteria was suspected to be involved in the formation of brain infections. This was never confirmed because of poor results of phenotypic characterization from the sequencing of the 16s rRNA. Doctors firmly believe that the two cases afore mentioned link Dialister pneumosintes with brain infections. In the first patient this was proved by the identification of the bacteria by the gram staining results and microscopic examination. The bacterium was believed to be the source of the infection in the frontal lobe. In the second patient the culture from the brain proved the involvement of the bacteria with the abscess. The scientists believe that the gram-positive stain was only achieved because of inadequate decolorization of the gram stain. From previous phenotypic characterization from gene sequencing the bacteria was expected to be present in oral cavities,nasopharyngeal and vaginal flora. It is believed that the bacterium is also responsible for gingivitis. From this it has been concluded that Diaslister pneumosintes in mixed flora can act as a deadly pathogen.

The findings of the research are very fascinating. However I find that two patients are not enough to confirm the involvement of the bacterium with brain infections. It is my belief that the doctors should continue to look for new ways to identify the organism. The fact may be that the infections were caused by other bacteria which were not identified by the cultures or even the Streptococcus bacteria which were identified. To be absolute positive that the Dialister pneumosintes caused the infection, a lot more research needs to be done.

Chemiosmotic Theory pt 2

Hey so I am back again. To finally do what I want to do. Talk about inhibition! Okay maybe this is weird that I like talking about inhibition. However lets go on with the explanations:

There are three substances which affect the electron transport system; cyanide, 2,4-DNP and rotenone. So we will leave the best for last. Cyanide and Rotenone can be grouped as they both work by inhibiting one of the four complex in the inner membrane. While 2,4-DMP is an example of an uncoupler.

2,4-DMP separates one of the processes from the other. Therefore one process happens in the absence of the other. Whether it is that the complex transport protons from the matrix to the inter-membrane or the ATP synthase transporting protons from the inter-membrane to the matrix. All the uncouplers are hyhdrophobic and have the ability to release protons. 2,4-DMP binds the protons on one side of a membrane and drifts to the opposite side of the membrane where it will release the proton. Because of this it is impossible to maintain a proton gradient and hence inhibits the ETC.

Cyanide is a very toxic substance. Cyanide inhibits complex IV (cytochrome c oxidase) of the ETC. Cyanide prevents the transport of the electrons from the matrix to the inter-membrane space.

Rotenone is a competitive inhibitor and inhibits complex I. Rotenone inhibits the transfer of the electrons from the iron sulfur centers in complex I. This can interfere with NADH during the creation of ATP.

Please note that neither Cyanide or Rotenone interferes with ATP synthase. Also once one complex is inhibited it affects all the other complexes.
tumblr_lwk5nf0kp91r4z4of

So enjoy people!

Chemiosmotic Theory pt 1

Hey good morning. How are you? Yes I am still up and I am tired, but this is what the life is about I guess. So we did the most awesome thing today, a topic which I have always wanted to do: CYANIDE. So we finally did the topic which deals with the juicy stuff, how cyanide affects the human body. My interest for cyanide stems from a crazy room mate that I have who is just in love with cyanide but enough of the yibble yabble and more of bicohemistry.

So there is this process known as the Chemiosmotic theory. For your understanding about cyanide inhibition I would have to break the topic into two part blogs, so you can slowly digest each part. So after reading this blog please go to the Chemiosmotic Theory Part 2.

I am not promising that this explanation for the Chemiosmotic theory is the best, as this is not my strong point. As a matter of fact this is the first topic that is giving me a little trouble understanding. I got advice from a friend saying maybe I should write about it and see if it becomes clearer. So here it goes:

Electrons have a very high energy transfer potential. These electrons pass through the electron transport chain (ETC). The ETC is made up of four complexes.Complex I is NADH dehydrogenase. Complex II is succinate dehydrogenase. Complex III is cytochrome BC1 complex.Complex IV is cytochrome c oxidase. As the electron pass from one complex to the next energy is released. The complex uses this energy to pump electrons from the matrix to the inter-membrane space. However only three complex pump ions. Complex II does not pump protons from the matrix to the inter-membrane space. The word pump is used to put emphasis on the protons moving against the concentration gradient. As the electrochemical gradient builds this causes a force to be set up which try and push the protons back into the matrix. This is causes the proton motive force. However the the protons can not pass through the membrane as the inner membrane is impermeable to the protons. However a channel is located in the inner membrane known as the ATP synthase which allows protons to be transported back to the matrix. As the protons pass through ATP synthase, the ATP synthase undergo a conformational change which allows energy to be released in order to make ATP. ( ADP + Pi —–> ATP)
chemo

Mitochondrial_electron_transport_chain—Etc4.svg

So I hope I got this right. At least partially right on my first try. I am going to try and read the text book again and maybe re post again with a little more clarity. What can I say? I guess you learn from trying! So never give up peeps. Peace out!
keep calm

Titration of Glutamate

Hey good morning. How is everybody doing? So today we actually did some calculations in biochemistry. So thats to show you that it is not all about learning structures and memorizing enzymes ( although it seems that way sometimes). WE BIOCHEMIST KNOW HOW TO USE A CALCULATOR!
chemistry-calculations

So we did the titration of glutamate. Its a pretty straight forward calculations but some of my friends were having problems as they did not have a chemistry back ground. So I am going to post the video and make some general comments.

https://www.youtube.com/watch?v=SDrYBKikcHI

So first of all we know that acids exsit below the pH 7 and alkaline exist above the pH 7. pH 7 is like neutral ground. 7 is also the pH of water. So some definitions are that Lewis acids are substance which are ionized and lose a proton while Lewis bases accepts a proton.

The general way of explaining these two definitions are the following two formulas:
HCl + H2O —–> H3O+ + Cl-

So in the above equation water was added to hydrochloric acid and the acid lost a proton (hydrogen) and the water accepted that proton. So water acts as a base.

NH3 + H2O —–> NH4+ + H2O ——>
So what happens here is that ammonia is acting as the base and water is acting as an acid. Ammonia accepts the proton while water donate the proton.

So basically what is happening in the titration is as pK increases the hydrogen is lost from different groups. Wheter it be the alpha amino group, R group or alpha carboxylic group.

When a proton (hydrogen) is lost from a neutral base the final product has a negative charge hence:
COOH —-> COO- + H+

When hydrogen is lost from a positive substance the product is neutral. Hence:
NH4+——> NH3 + H+

Concerning net charges now:
The net charge is basically the total charge on the amino acid. So COO- has a 1- charge. NH3 has 0 charge and NH4+ has 1+ charge. So lets say that the follwing groups were present on the amino acid:
alpha amino group: NH4+
alpha carboxylic group : COO-
R group: COO-
The net charge will be 1- (1+(-1)+(-1).

The final calculation is just the pI value (isoelectric point). For this you just take the pK values on the two sides of the amino acid which has a net charge of zero. You add up these two pK values and divde by 2. Isoeclectric point is the pH at which the amino acis has a net charge of zero.
finally done

So I hope my chemistry insight came in useful to some of you. Enjoy your day and please practice.

Fates of Pyruvate

Good morning everybody, (yes once again I am here) but its all in the name of science.

So a lot of people have this idea that once pyruvate is produced thats it! IT IS FINISHED. Well I would know this as I was one of the person who thought that it just went onto the electron transport cycle.But I learned something completely different in class today and it is called THE FATES OF PYRUVATE-THE EVOLUTION!

So here comes along a glucose molecule and it produces two pyruvate molecules. What happens after this?

Well as in the famous words of JM himself ” First you have to ask yourself the question, is oxygen present or is it missing in action”

If oxygen is present then the linkage reaction takes place. Basically this is where pyruvate is converted to Acetyl-CoA by the enzyme pyruvate dehydrogenase. The cofactors are CoA-SH,NAD+,TPP,Lipotate and FAD.

09_10PyruvateToAcetylCoA_L

If oxygen is missing in action (anaerobic conditions) pyruvate can go through two processes. These are know as fermentation. Pyruvate can be fermented to ethanol and two carbon dioxide and this is normally done by yeast. Pyruvate is first converted to acetaldehyde ( by the enzyme pyruvate decarboxylase) and then to ethanol ( by alcohol dehydrogenase). NADH goes to NAD+ during this conversion. The co factors for this reaction is TPP and Mg2+.
pyr-eth
On the other hand the pyruvate can be fermented to lactate. This occurs in muscle cells. Pyruvate is converted to lactate by the enzyme lactate dehydrogenase. This occurs in mature red blood cells. An interesting fact to note about red blood cells is that they have no mitochondria, so the can not perform the linkage reaction and the RBC depends solely on glycolysis in order to obtain energy.
pyruvate to lactate

The big picture for fermentation is that it replenishes NAD+ in a cell. A cell has limited amounts of NAD+ and this is needed to glycolysis. Without NAD+ glycolysis will not countinue and the cells will not be able to produce ATP! And we all know what that means! NO ENERGY!

death

So I hope I have made it a little clearer for you and summed up the fates of pyruvate in a nice revision blog.Study hard and eat a food people. I out!

How does Viagra

Good morning again,
So one of the things that I have always wondered is how does Viagra work? How did it achieve its function in men. So I went and did a little research and I came up with this:

Viagra was intentionally meant for men who suffered from erectile dysfunction. For examples many diabetes suffer from erectile dysfunction especially pass the age of 45. So what happens is that when a man is aroused and this causes the release of Cyclic Guanosine Monophosphate in the body. These chemicals will relax the muscles of the penis and allow large amounts of blood to enter the penis. Normally blood can not flow to the penis as the blood flow is cut off by constricted muscles. So once these muscles are relaxed blood flows into the penis and allows an erection to take place. The erection is normally reversed by the release of a chemical known as phosphodiesterase type 5 [PDE5]. This chemical breaks down Cyclic Guanosine Monophosphate (stucture is below) which allowsthe muscles to relax. The muscles in the penis will constrict again and blood will leave the penis.
200px-CGMP2.svg

Now viagra works by blocking PDE5. When PDE5 is blocked the chemicals which are responsible for the relaxation of muscles (Cyclic Guanosine monophosphate) are not broken down and hence the penis remains in an erected state for a longer period of time. This has been proven very useful for the male population.
Viagra-spam-emails

So I have officially brought science into a topic which I would not dare talk about in public. The things that science makes you do. Enjoy peeps!
love peace chicken grease