BIOC 223

We’ve been focusing on the chemical structure of proteins and the effect that these confirmations have on the overall function of the protein and it astounds to believe that proteins can spontaneously refold to their natural  orientation. Obviously, this shows that there is a clear thermodynamically favorable conformation. So this got me wondering, what happens when proteins misfold?

There are neurodegenerative diseases, such as Parkinson’sand Alzheimer’s, that are cause by incorrect protein folding. In particular, Alzheimer’s is caused by the aggregation of amyloid beta proteins in the brain.

In turn, this got me wondering… Do proteins always have one stable conformation or can they have multiple “stable” conformations when at physiological conditions? If so, how does these proteins differ in function?

The semester only started about the month ago and I’m already relying on caffeine more and more to get me through the week. With midterms starting up, I’m sure a lot of you feel the same way! Since I spend most of my time with a cup of coffee or a Diet Coke in my hand, I thought it was time to learn the actual mechanism of caffeine.

Caffeine is a stimulant of the central nervous system. In plants, it’s synthesized from AMP, GMP, and IMP. It’s then converted to xanthosine and then theobromine, which is then converted to caffeine. In the body, it counteracts adenosine, which reduces neural activity. Caffeine is able to easily cross the blood-brain barrier because of its small size and solubility in both water and lipids. It also inhibits phosphodiesterase and activates protein kinase A. It’s also a little basic, with a pKa of around 0.6.

Apparently, it’s also fairly toxic in doses above about 500 mg at a time (which is probably a good thing for me to remember right about now.)

At the beginning of the semester, we all pretty much agreed that one thing we did not want as part of our learning environment was competition. Ironically, competition is my favorite lesson from lecture this week.

I was passing through the campus center earlier today and found myself sneezing uncontrollably. I got to my dorm and my nose and eyes were running non-stop- I do not have a cold. Previous experience has taught me that antihistamines are usually the solution to such problems and so I figured histamine would be the cause. A few  minutes of internet research later I found out histamine an inflammatory mediator is released by antibody bound mast cells when allergens are inhaled and causes sneezing, watery eyes and inflamed nasal passages, basically my symptoms, but even more interesting, histamine’s structure contains a 5 member ring with 2 nitrogens, just like histidine (nature’s economy)!

Moving on to read about anti-histamines taught me that they are ‘inverse agonists’ to the histamine receptor, essentially, they compete with histamine in binding to the receptor and when they do, they do not cause the unfortunate effects that histamine does. I’m really glad competition exists and affects the interactions of biochemical molecules because now I can breath freely!

It seems like more and more people are getting sick recently! This is definitely not a good thing, especially since everyone, including me, has a lot of work coming up. Taking an extra measure to ensure I don’t get catch whatever bacteria or virus is going around, I took a few tablets of Airborne over the last few days. Not surprisingly, it is mostly vitamin C, in fact 1667% of our suggested daily value – perhaps a little much. Vitamin C is also known as L-ascorbic acid (a chiral molecule!) or ascorbate under certain conditions. These conditions depend on pH, so ascorbic acid usually exists as an anion within the body as well.

The reason why vitamin C is so essential to our well-being is because it is a cofactor in enzymatic reactions, which we’ve learned about in class. It is a reducing agent, so it donates electrons in these reactions. In addition to this critical vitamin, Airborne also contains an amino acid blend of L-lysine hydrochloride and L-glutamine. Both are obviously important components to the body’s proteins and promote healthy body functions and immune resistance. They also give the tablets their effervescent property by being pH sensitive. It’s amazing how much our bodies rely on small tweaks of biochemical activity to stay healthy. Like the parts of a well-tuned machine, it is these microscopic amino acids and molecules that guide our bodily functions and ensure that we are running smoothly.

In the true spirit of Valentine’s Day, I ate a lot of chocolate (and chocolate chip cookies) today. Cocoa is made from cocoa butter, a lipid, which we briefly touched upon. Making chocolate is a lengthy and complex process. In one of the final steps, tempering, the cocoa buyer is left to freely crystallize into crystals of different sizes. This reminds me of what we did in the second lab when we made salt solutions and looked at some crystals under the microscope. Interestingly, many cocoa crystals are too small for the naked eye. It is these crystals that cause chocolate to have a shiny layer and break sharply. In a solid piece of chocolate, the cocoa butter fats are in a rigid crystalline structure. When heat is added, the rigid structure becomes more fluid as the interactions break. Clearly, biochemistry is responsible for the delicious properties of chocolate, something I don’t usually think about when I’m enjoying it.

Last week, I was walking out of my dorm when I slipped on some freshly fallen snow and skinned my hands and knees. Since then, I’ve been applying Neosporin to help the scrapes heal faster. I began to wonder how exactly it does that. It turns out that Neosporin consists of three active ingredients: bacitracin, neomycin, and polymyxin B. Bacitracin is made up of polypeptides. After looking up its structure, I was surprised to find that I could identify a few of its amino acids. It’s very strange to realize that I’m rubbing the structures we’re studying in class into my skin.

The other compounds are also antibiotics. However, it turns out that Neosporin has actually been proven to cause skin irritations and even promote the growth of certain bacteria! When its primary function is to kill bacteria. This is probably due to its contribution in promoting antibiotic-resistant bacteria, so the strains that do survive are extra deadly. Thanks to this information, I know I definitely wont be using Neosporin from now on.

The top layer of my cell phone cover unfortunately came loose, so I had to use some tacky glue to put it back together. I was curious what was making it stick. When it comes to super glue at least, doesn’t the description below make it sound like hydrogen bonding?

“How Superglue works?

The major constituent of Superglue is a chemical called cyanoacrylate. Its chemical formula is C5H5NO2. What’s so special about Cyanoacrylate is that it is an acrylic resin that forms extremely strong bonds almost immediately. Superglue contains many other chemicals such as zinc oxide, zinconium, and zinc sulphate.

The only thing superglue needs to form these strong bonds is hydroxyl ions found in water. This makes applying superglue easy as almost all surfaces contain traces or a thin layer of water. As Superglue comes in contact with water it forms long, strong chains, which bind the two surfaces together almost immediately.Superglue forms an almost unbreakable, waterproof bond within seconds.”

I just read an article on how in the summer of 2012, a huge space rock hit Mars, creating a 100-ft crater.

We’ve been talking these past two days about bond length and strength, and so this article prompted me to wonder whether those would change in space. Since the force of gravity changes in space, would there also be slight changes in the nanometer range?

I was pleasantly surprised by the Concept Map assignment. Up until 4 weeks ago, I wasn’t actually that familiar with them (although I had of course used them, without knowing what the term was).

Then over Wintersession, while I was here for the Albright Institute, we actually had an entire session on concept maps and paradigms! Professors Dan Brabander and Rob Martello spent time with us discussing effective concept maps, and what makes them understandable, clear, and sometimes clustered, and how they can aid in understanding complex relationships.

Having to make one for Biochem this week I think illustrates pretty well why concept maps are a great tool for visualization of relationships. Biochem is so much about the big picture, that concept maps I’m sure are often more clear in delineating connections than if you tried writing them all out. Understanding cause and effect are crucial. My biostats textbook also starts off with stating how humans are naturally programmed to understand information through images. That statement only adds weight to the effectiveness of concept maps.

Looking at the 3D models with Ramachandran angles set really challenged my knowledge of protein secondary structure. I mean, I knew that proteins existed in 3 dimensions and they filled space and they had to be pretty tough in order to perform all the functions they do but I did not really understand just how complex and well developed they were. All I saw today was a short alpha helix in isolation yet I was in awe of the sturdiness it seemed to possess. To think that a single protein contains not one but many more such structures further strengthened by other interactions simply astounds me- and that they take on so many different forms! I may never again look at hair, or skin, or nails the same.

Just thinking… if tiny tiny atoms can achieve such grandeur by coming together and ‘giving their best’ by bonding and other non bonding interactions, just what can people achieve if they too come together and give their all?