Okay. Since our lecturer fancies himself a Kage, I did a quick sketch of what I think the forehead protectors for our Biochem Village might look like.
My drawing skills are really rusty, but I think you get the idea (once you’re otaku).
Enjoy, my fellow Biochemians.
This video visually demonstrates how endosymbiosis is thought to have occurred. I wanted to critique a video that was not so good, and here, there are quite a bit of downfalls that I would like to note.
This video is COMPLETELY RELIANT on the viewer having some knowledge in Biology and some familiarity of this theory.
The maker of the video should have included a bit about evidence supporting this theory. You can see the origin of the double membrane, but you would not be able to pick up on that if you had not been familiar with the topic.
The use of the caption “turns it into a mitochondrion” and “turns it into a chloroplast” I do not like. It sounds as if some magical process happened. The creator of this video could have given a lot more detail. This video would not be suitable for persons who are completely clueless on the topic as it uses words such as “prokaryote” and “aerobic”, again, making the video suited to persons who are familiar with this theory. The explanation of the meaning of the word “Symbiosis” would have also helped persons unfamiliar with biology.
One the plus side, once YOU ARE familiar with the topic, the visual representation is clear and simple. The video is short and to the point.
Which of the following is NOT an enzyme class?
a.) Isomerase
b.) Hydrolase
c.) Lyase
d.) Redoxidoase
e.) Transferase
Choose ONE answer.
The black mamba (Dendroaspis polylepis) is a carnivorous, lethally venomous snake that inhabits southern and eastern Africa. These snakes can grow up to fourteen (14) feet in length – Africa’s longest venomous snake – and weigh up to three and a half pounds (3.5 lbs). Before the advent of antivenin (medicine containing antibodies against the snake’s venom), the black mamba’s bite was thought to be hopelessly fatal within about twenty minutes, making it one of the world’s most dangerous snakes.
Researchers (who published their paper in “Nature” on October 25th) have discovered uses in medicine for this snake’s highly potent venom as a pain killer.
The experiments began with purification of the venom, after which active fractions were collected and partial amino acid sequences used to clone complementary DNA (cDNA). The researchers then identified two 57-amino acid isopeptides, consisting of eight cysteine residues, in the black mamba’s venom, which they named mambaglin-1 and mambaglin-2 (Diochot, 2012). Mambaglin-1 and mambaglin-2 only differ by one residue in position at four (4). These peptides have been found to inhibit ASIC (acid-sensing ion channels) which are proton-activated cation channels, found in both central and peripheral neurons that play a major role in pain perception (Alder, 2012).
Mambaglins (see Image 2) represent less than 0.5% of the protein content in the snake’s venom and exhibits a strong positive electrostatic potential that is thought to contribute to its ability to bind to negatively charged ASIC channels. They show not only tremendous potency in blocking homomeric ASIC1a and heteromeric ASIC1a + ASIC2a or ASIC1a + ASIC2b channels (all ASIC channel subtypes), but the effects of mambaglin are also rapid.
These mambaglins were tested on mice and were non-toxic (i.e. none of the typical neurotoxic effects consistent with this snake’s venom were presented) and produced very powerful analgesic effects comparable with that of morphine. However, unlike morphine and other opioid compounds, the mambaglin peptides did not show any side-effect of respiratory depression or nausea. It was also discovered that they do not pose the threat of addiction or drug abuse. Mambaglin-1 was also found to considerably minimize acute and inflammatory pain when various tests were conducted.
Clearly, mambaglin shows much potential as a replacement to morphine, which is prone to habit formation and other possibly addicting painkillers. Further testing is required to determine if these results can be replicated in humans.
Our lecturer always has some interesting facts to give us about the great men and women that contributed to the topics we are studying. Take Glycolysis for example. Three names come to mind: Embden, Meyerhof and Parnas (hence the Embden-Meyerhof-Parnas pathway or the EMP pathway).
These men all made great contributions to science, especially in our understanding of Glycolysis. So, I was thinking, instead of typing a paragraph about them, why not make what I think the “About” pages of their Facebook profiles would have looked like…
So I did!
I made one for both Embden and Meyerhof. I’ll write a bit about Parnas at the end, because his story is a tad bit more interesting than Embden’s or Meyerhof’s.
——————————————————————————————
Now, the third guy, Jakub Karol Parnas, was a Jewish-Polish-Soviet biochemist. He was born on January 16, 1884.
Jakub Parnas
He became a soviet activist after annexation of Western Ukraine in 1939. He was quite popular an had made many scientific achievements (including, of course, discoveries in the glycolytic pathway). When he lived in Moscow, he was frequently a guest to many Western embassies. He was in continuous contact with scientists all over the world for all his life, so he did not realize how dangerous this was under the regime in Moscow.
Jakub Karol Parnas was arrested by the KGB (The Soviet Union’s main security agency) and falsely accused of being a spy of the West on January 28th, 1949. This happened during the Doctor’s Plot. This plot alleged conspiracy of prominent Soviet medical specialists to murder leading government and party officials; the prevailing opinion of many scholars outside the Soviet Union is that Joseph Stalin intended to use the resulting doctor’s trial to launch a massive party purge. (The trial and the rumoured purge that was to follow did not occur because the death of Stalin (March 5, 1953) intervened.) A day later – January 29th, 1949 – it was said that Parnas died during interrogation in Lubyanka, an infamous Moscow prison, “from a heart attack”. Most believe he was murdered, which I think is a very fair assumption. (I did some extra research on the “Doctor’s Plot” and found that Stalin would instruct his interrogators to “Beat, beat and beat again” in order to obtain confessions.)
He died at age 65.
References:
A new allele linked to alcohol sensitivity identified in Trinidadians? When our Biochemistry lecturer mentioned this I just had to look into it!
The paper I am focusing on in this post (referenced above) was about the discovery of a new allele in Indo-Trinidadians. This allele codes for an enzyme called aldehyde dehydrogenase (ALDH1A1). Research links this enzyme to alcohol dependence and alcohol sensitivity. It is found in the cystosol of the cells of various tissues of the body, with the highest incidence of this enzyme being in the liver. This enzyme has been found to be important in the elimination of ethanol.
Prior to this paper, there were three known polymorphisms of this allele: ALDH1A1*1 (the normal allele), ALDH1A1*2 (this allele has been identified in various ethnic groups including Asian, Caucasian, Jewish and African American) and ALDH1A1*3 (this allele has so far only been discovered in Afro-Americans). Â The novel allele is called ALDH1A1*4 – named according to nomenclature rules.
I bet you’re wondering, “How did the researchers make this discovery?”…
The researchers collected whole blood samples for genotyping from both alcohol dependent and non-alcohol dependent individuals (162 Indo-Trinidadians and 85 Afro-Trinidadians). Control subjects were also recruited and matched by age, sex and ethnicity to the alcohol-dependent subjects.
A slightly different sized allele was detected in one of the subjects. This subject was of Indo-Trinidadian decent and the size exhibited on the autoradiogram was slightly smaller than the ALDH1A1*3 allele and slightly bigger than the ALDH1A1*1 allele. Further investigation confirmed that this was a new allele and the name ALDH1A1*4 given to it. This new allele was not found in any of the Afro-Trinidadian subjects, however.
 
Unfortunately, this is as far as the research goes – the discovery of a new allele, and thus, a new enzyme. Â The frequency of this allele and if it is present in other populations is not yet known.
It would be quite fascinating to see what implications this allele has on the body! I am actually looking forward to reading about it (which is something I never thought I’d say).
Cover Glycolysis in Under 2 Minutes
Here is a quick animation on Glycolysis (the conversion of glucose to pyruvate).
There are also a few questions at the bottom of the page that you can use to test how much you picked up from the animation.
You should note:
I bet you read the title, did a double take and went, “Whaaaat?”
Actually, this post is about proteins and enzymes, and one particular enzyme- Luciferase. Sound familiar? This enzyme has nothing to do with a fallen angel, though. “Lucifer” is actually Latin in origin meaning “light bringing” or “light bearer”.  So, you can probably infer that this enzyme brings light, which is pretty much true.
Luciferase works with luciferin (a photoprotein) causing the phenomenon of bioluminescence in some organisms. The most familiar of these organisms has to be the firefly.
Ever wondered how a firefly’s butt lights up? Well, here’s the answer…
(I’ll assume that you are at least a little familiar with how DNA codes for proteins and the processes of translation and transcription…)
First, in the nucleus of the cells in the firefly’s tail, RNA polymerase (another enzyme) locates and the portion of the firefly’s DNA that codes for the LUC gene (which specifies the sequence of amino acids, that will synthesize the luciferase enzyme). Transcription occurs, and mRNA (a copy of the LUC gene) moves from the nucleus to cytoplasm. Ribosomes use the mRNA to synthesize a sequence of amino acids identical to those the LUC gene coded for via a process called translation. This string of amino acids then folds to a three-dimensional structure in order to function as an enzyme – Luciferase.
Luciferase binds to the substrate- the photoprotein luciferin. The enzyme catalyses a reaction of luciferin and oxygen to produce oxyluciferin. Now, this reaction requires energy (in the form of ATP [adenosine triphosphate]), which excites electrons. On releasing this energy (as electrons return to their ground state) light is produced at 560nm. The products of the reaction are AMP and pyrophosphate (which ATP is hydrolyzed to) and carbon dioxide.
Bioluminescent Reaction Catalyzed by Firefly Luciferase
 Fun fact: This light that fireflies (and other bioluminescent organisms) produce generates no heat. References:(Image retrieved from: photobucket)
Hello there! It’s Avagadbro! Coming to you live from a laptop!
Finally, I’m getting to this quick overview on enzyme action. Enzymes are globular proteins (soluble in water) that act as biological catalysts, and our lecturer covered a lot of this topic last week. However, here is the main thing you need to know about enzymes: THEY ARE MAGICAL.
Haha. Well, almost…
There is an enzyme able to make a reaction go up to ten million times faster than they would under normal circumstances (i.e. without a catalyst) and the enzymes themselves are not altered in the process. That sounds pretty magical if you ask me.
Now, how do they perform such amazing feats? Well, they lower the activation energy of reactions, which allows the reaction to proceed at a much lower energy than it would without a catalyst. Enzymes have regions called active sites that the substrate attaches to. This is where the magic happens…
The substrate attaches to the active site forming a complex with the enzyme. Here, the substrate can be broken down or combined with something else, or both to give the end product of the reaction. The active site’s shape is very specific, which basically means each enzyme can only perform one trick – a particular enzyme can convert only a specific substrate to end product.
It is important to note that enzymes perform best at their optimum temperature. This optimum temperature varies from enzyme to enzyme. The same goes for pH – certain enzyme will function best at a certain pH. You could say that enzymes perform their acts best when the environment is right – adoring fans, good lighting…. you get the idea.
The action of enzymes are extremely important. Life would not be able to be sustained without them. For instance, carbonic anhydrase, (an enzyme that removes carbon dioxide from the blood by binding it to water), has a turnover rate of 106. This means that one molecule of the enzyme can cause a million molecules of carbon dioxide to react in one second. Without this enzyme, carbon dioxide would accumulate in the blood, ultimately leading to death. Think enzymes are amazing yet? You should, because this is just one example. There are many other enzymes that keep you going.
Enzymes make life possible.
I guess you can think of enzymes as the “Criss Angel of Biochemistry” – their magic tricks are just real and far, far, far more important.
More on Enzymes soon!
References: Indo Gulf Group – ENZYMES Fact Monster – ENZYME ACTION
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