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Everything is okay… In moderation.

I want to teach you about an interesting little molecule called 2,4-dinitrophenol that is capable of uncoupling the most important cellular process in your body.

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2,4-dinitrophenol is a compound that was discovered in the 1930 and for a brief time was sold as a diet pill due to its weight loss effects. When DNP is ingested orally, it finds its way into the mitochondria, positioning itself in the Inner Mitochondrial Membrane. The hydrogen of the phenol is easily deprotonated, the molecule essentially acts as a proton shuttle, moving protons from the intermembrane space to the mitochondrial matrix, by constantly getting protonated and deprotonated. This action is absolutely devastating for the cell because it is effectively uncoupling the Electron Transport Chain from Oxidative Phosphorylation.

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For those of you who may need a small refresher, cellular respiration starts with the breakdown of glucose into electron carriers, which enter the mitochondria to get oxidized in the Electron Transport Chain, causing protons to be pumped into the IMS, creating a proton gradient. These protons are the driving force for the enzyme complex ATP synthase, which ultimately converts ADP to ATP in the matrix. If there is no gradient in the IMS, ATP synthase won’t be able to generate energy for the cell.

When an individual consumes DNP, the reason they lose weight is that as cellular respiration becomes less and less efficient (due to the loss of the proton gradient), the body starts burning more and more fuel in an effort to meet the energy demands of the cell, causing weight loss. So what’s the downside? Well, all the energy that should be going into ATP production ends up being lost as heat, which raises the internal core temperature to lethal levels.

Interestingly, as bad as this sounds for you, the body actually has its own version of this molecule, which is crucial in the thermoregulation of newborns. All mammals have a type of cell called Brown Adipose Tissue (BAT) present mostly in newborns and hibernating animals, but adults also have a small quantity in their bodies. Brown fat is brown due to an increased number of mitochondria, which contain a special protein called thermogenin, located on the inner mitochondrial membrane.

Thermogenin is an uncoupling protein because its function is to uncouple the ETC from oxidative phosphorylation much in the same way DNP does. By opening a proton leak channel in the membrane and decreasing the proton gradient, heat is generated and the core temperature increases. It is especially important for the thermoregulation of infants because they don’t have any other mechanisms at their disposal to regulate their own temperature. They have little hair, not very much skeletal muscle for shivering and of course they can’t just put on a sweater!

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Thermogenin (UCP1) and the role of BAT on metabolic rate are being explored as a possible treatment or therapy for obesity. 

BPA-free Doesn’t Mean Estrogenic-free

Attribution: Flickr Commons

Before the 1990’s, when researchers began publishing papers on the harmful health effects of Bisphenol A (BPA), hard plastic polycarbonate consumer products were mostly made with the chemical monomer. Scientists uncovered that BPA, in similar structure to the estrogen, estradiol, interacts with estrogen receptors in the body, disrupting the endocrine system. This estrogenic activity can cause infertility, heart disease, cancer, neurobehavioral deficits, and more. After public demand, numerous countries began banning BPA, mainly in food and drink containers and baby products.

Estradiol (Top) and Bisphenol A (Bottom). Attribution: Wikimedia Commons and Wikimedia Commons.

Flash forward to now and our water bottles say “BPA-free”; however, this gives us a false sense of safety for, while our water bottles are free of Bisphenol A, the alternative resins used by plastic manufacturers are similar in structure and, as research shows, in negative health effects. Chemicals such as Bisphenol S (BPS) and Bisphenol F (BPF) are used as BPA alternatives in the production of PC plastic bottles and their chemical structures appear just, if not more, like estradiol than BPA. 

Bisphenol F (Top) and Bisphenol S (Bottom). Attribution: Wikimedia Commons and Wikimedia Commons.

A study published in Environment Canada found BPA-free consumer water bottles that leach BPA-like chemicals, causing the same effects to the endocrine system. The Austin, Texas private lab, CertiChem, measured the estrogenic activity of various plastic consumer bottles including black and blue CamelBak, blue and green Nalgene, Topaz, and Zeonor reusable plastic bottles. By exposing breast cancer cells, that multiply when their estrogen receptors activate in the presence of estrogen-like chemicals, to the plastic water bottles, and stressing the bottles using UV light, they determined whether these bottles were leaching estrogenic activity such as that of BPS and BPF. Their study confirmed that CamelBak and Nalgene bottles excreted Estrogenic chemicals, while Topaz and Zeonor reusable bottles remained intact even during stressed conditions.

So, if this news is as alarmingly shocking to you as it was for me and you are on the lookout for another water bottle, CertiChem‘s paper suggests that purchasing Topaz or Zeonor products is a better choice than Nalgene and CamelBak; of course, if you remain unsure, non-plastic stainless steel bottles may be the best choice for you. I just bought one at Manna.

For more information, watch the following video.

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-Lori Waugh

Chemicals; The Root of All Evil

All over the media we see advertisements saying things like “chemical-free” or “all natural” when describing some product that they are marketing, and it is definitely working. I frequently have to remind my own mother that everything is made up of ‘chemicals’, and that anyone trying to sell you something that claims otherwise doesn’t know what they’re talking about. But then why does it work?

I believe it is because people automatically assign the word ‘chemicals’ another meaning, such as ‘poisonous’ or ‘toxic’, and as a result they don’t want anything to do with the stuff. As Dr. Mark Lorch, an academic chemist, mentions in an article by BBC defending chemistry “We use phrases like ‘it’s chock-full of chemicals’ to imply something is artificial or bad for you”. I can honestly say that I’ve been told this from my mother to get me to stop drinking Coca-Cola. This means that not only do people not understand what they are saying, but they use the association of ‘chemicals’ with ‘toxic substance’ to justify how they live their life! This comes up in other news articles like one I found about fast food packaging containing the dreaded ‘chemicals’.

The article uses numerical data and chemical jargon such as “fluorinated chemicals” (so specific) to scare its uninformed audience into thinking fast food packaging will hurt them. What do they have to gain from this? Is “chemicals are bad for you” going to be the next “You won’t believe these 17 crazy weight loss techniques!!”?

It’s not even bad enough that the click bait industry is preying upon uninformed audiences to terrify them into reading articles, but they have no shame in who they target. This article from a website called Grandparents.com is entitled “5 Scary Chemicals Lurking in Your Favourite Foods”. Seriously? How do they even know what my favourite foods are? And why are they lurking in the food like some monster? This title is written with the sole intention of scaring the audience into reading it, because it gets you thinking “what if I eat my favourite pasta and it has these scary chemicals hiding in it?”. My grandparents have enough trouble understanding how to get their tablets to work without throwing this pseudo-information at them.

To circumvent this, I believe that either some media authority (such as the Advertising Standards Authority) needs to increase their efforts to stamp out these blatant click bait scares utilizing chemophobia at their core, or people need to have a more rudimentary education concerning ‘chemicals’. From personal experience, I know that once I explained to my little brother that water is a chemical and how it forms the basis for life as we know it, he drank it up like crazy. Understanding is key. As Stephen Hawking said (or at least is credited with saying), “The greatest enemy of knowledge is not ignorance, it is the illusion of knowledge.”

Jake Medeiros

New Plan for Seeking Life on Mars

Written by: Jake Wong, Sept. 24th

Many have wondered whether our neighbor planet, Mars, contains life outside of what we know of here on Earth. It would make sense, as Mars is within the proper distance away from the Sun to sustain life. However, enough research has been done to know that the stereotypical humanoid green “Martian” does not exist. Therefore, researchers are switching targets to find life: fossilized microorganisms, or “microfossil”.

Geology professor Craig Marshall and his team recently released a paper discussing how the detection of vanadium can lead to detecting life. The technique makes use of Raman spectroscopy, which reveals the cellular composition of a sample. Previously, researchers had been using Raman spectroscopy to see if a sample contains carbon chains, which all living things are made of. However, there are a lot of artificial carbon samples that may visually look like a fossil without actually being previously alive. Therefore, a new identifying factor was required, which Marshall’s team believes to be vanadium.

Example of a microfossil from Earth taken by Craig Marshall. Source

It has been previously shown that vanadium on Earth is present in things like crude oil and fossilized plants, both of which are similar to what would indicate life on Mars. This also shows that the vanadium can still be detected after extremely long periods of time and potentially under great pressure. In order to detect vanadium, Marshall is testing a technique called synchrotron micro-X-ray fluorescence, which focuses on the elemental presences in a sample.

So, if a sample has the physical characteristics of a microfossil, is shown to contain carbon material through Raman spectroscopy, and is shown to contain vanadium through synchrotron micro-X-ray fluorescence, then we can conclude that sample contains a microorganism, Marshall states. However, currently all tests on this hypothesis have been on samples from Earth. Soon, we will hopefully see this method being used on actual Martian rocks.

I believe these results are the first steps for mankind to finally make groundbreaking extraterrestrial discoveries. In the past, our testing of Martian samples was highly limited and not extremely targeted for finding life, but with these new ideas and techniques, we may find data that could lead to future colonization of Mars. I have extremely high hopes for this project and the future of our space exploration.

With investigations of Mars continuing and a Rover planned to be sent to Mars in 2020, we may find soon that we are not as alone in the solar system as we once thought.

An artist’s rendition of the Rover to land on Mars in 2020
Credit: NASA/JPL-Caltech

Read Marshall’s paper here.

Driving with Lemon

Climate change has been the most discussed topic for the past decade. The world is feeling the effects of global warming and research has shown that the burning of fossil fuel is one of the leading causes. Fossil fuel must be replaced with a clean and sustainable energy source. A novel new research has found an interesting alternative in lemon peel oils.

Imagine that lemon peels, a produce that is often regarded as food wastes, has the potential to power everyday vehicles. Researcher has successfully extracted oils from lemon peels which has the potential to be an environmentally friendly substitute for diesel fuel.

Lemon Peel

The scientists injected the biofuel into a diesel engine and studied its effects. The engine increased in performance and emitted significantly lower emission levels. One of the measurements made was NOx emission levels as NOx (Nitrious Oxide)  is one of the biggest contributors to global warming.

The biofuel was a mixture of lemon peel oil and diesel fuel, but the increases in proportion of lemon oil corresponded to better performance and less emission. Dr. Ashok, the lead researcher, wrote” it is concluded that 50% lemon peel oil could be readily used in diesel engine with comparable performances and improved emission characteristics”. This study was published in the journal Energy Conversion and Management.

The researchers extracted the lemon peel oil with steam distillation. They tested different proportions of lemon peel oil and diesel fuel mixtures in a fully functional diesel engine. The lemon oil’s natural low viscosity and low boiling point allowed it to function in a normal engine.

Lemon and other Citrus Wastes

The research into lemon peel oil and other biofuels can tackle multiple world issues such as the food waste crisis. Examples such as the lemon peel oil biofuel can be produced and implemented cheaply due to its abundancy as food wastes. Dr. Ashok and the team of researcher stated “Overall diesel engine characteristics indicated that lemon peel oil can partially or completely replace the petroleum diesel usage”.

Written by: Harvey Wu

Anyone Wants a Second Skin?

Skin is crucial part of our body, and as a part of the body, it ages. As the skin ages, it loses its ability to recover rapidly and gets damaged easily. Many people get stressed as they look in the mirror every morning, about wrinkles and blemish on their faces, and hope that they can erase them. Unfortunately, it is almost impossible to recover the skin to its full youth state with existing solutions.

Image from Pexels : https://www.pexels.com/photo/black-and-white-crinkles-elder-elderly-258308/

To solve these problems, scientists have developed a ‘second skin,’ which is a clear, flexible polymer that mimics the properties of real skin that can be worn directly to the skin.

The idea of artificial skin came with scientists’ interest in creating autonomous intelligent robots among with other applications, leading to development of electronic hand with sensors since 1974. A lot of research has been conducted then to enhance the function of electronic skin and to make it resemble that of human. Inspired from scientific fictions, researchers have developed flexible and active-matrix electronic skin in 2004. However, there was still a long journey left to catch up with the complicated, real skin.

Finally in recent studies, Daniel Anderson, an associate professor in Chemistry Engineering in MIT, and his research team along with Harvard University developed a ‘second skin,’ called XPL. This wearable skin, an elastic polymer layer, has the properties of real skin and can be applied on human skin as a cream, instantly without use of heat or light-mediated activation.

Application of platinum catalyst to polysiloxane compound. Image credit : Olivo Labs

The second skin works in two-step process, where polysiloxane compounds, followed by platinum catalyst, is applied. The platinum catalyst enables the polymer to be attached to the skin for up to 24 hours, resisting washing and rubbing. The platinum catalyst does this by creating a strong layer on top of the polysiloxane compounds and adhering strongly to the skin.

To see the applicability of this material, Anderson has observed the visual impact when it is worn, tested on durability by twisting the skin with XLP on top, by wearing it over 24 hours, and by washing and rubbing under running water. The result was amazing. The ‘second skin’ was found to be ‘wearable, moisturizing, safe, well tolerated, and provides enhanced mechanical integrity to the underlying skin’ (Anderson, 2016).

“So the goal was to really create something that was totally invisible, breathable, could coat the skin, protect it, perhaps deliver drugs to it, and also perhaps even make it look better,” Anderson says.

Not only does it hide the wrinkles which many people get stressed about, it also protects our skin from UV radiation, the well-known main cause of skin cancer.

 

While further research will be continued to create more ideal products in the future, the ability to deliver drugs, to protect the underneath skin layer, and its invisibility gives hope to the people with diseases or wounds on their skin. Also, this could make our life easier by replacing cosmetics!

 

-Diana Kim-

Roast Your Own Perfection

In three minutes, you will learn how to perfect your cup of coffee – just the way you like it.

To do this, we have to talk about chemistry!

Seven years ago, German food chemists researched how the bitterness of coffee changes depending on how long you roast the beans.

They confirmed what Trugo and Macrae found in 1984: the more you roast coffee beans, the more bitter the coffee tastes because organic compounds called chlorogenic acids are degrading.

 

Structure of one chlorogenic acid: 5-O-caffeoylquinic acid.

Wikimedia Commons: Ed. https://commons.wikimedia.org/wiki/File:Neochlorogenic_acid.svg

Then, what makes this 2010 study different?

Well, these German scientists used evolved technology.

In 1984, those researchers used High Pressure Liquid Chromatography (HPLC), a technique that separates the components of coffee in a solvent. In 2010, however, the German researchers used the evolved form of HPLC: HPLC-MS/MS and HPLC UV/Vis. The combination of HPLC with mass spectrometry (MS, another analytical technique) enabled these researchers to figure out how much there is of each compound as you increase the roasting temperature.

An HPLC-MS Diagram. 

Wikimedia Commons: Daniel Norena-Caro. https://en.wikipedia.org/wiki/File:Liquid_chromatography_tandem_Mass_spectrometry_diagram.png

With this advanced tool, they tracked the concentration of three classes of compounds:

  • Caffeoylquinic acids (CQAs), a chlorogenic acid, gives the non-bitter taste;
  • Monocaffeoyl quinides (MCQs), also a chlorogenic acid, gives a pleasant bitter taste;
  • And oligomers (Os), a newly discovered class of compounds in coffee, gives a harsh bitter taste

And found that as roasting temperature increases from 190°C to the maximum 280°C, the concentration of CQAs decrease exponentially, MCQs increase then decrease, and Os increase exponentially. So, the presence of each compound is different at different roasting temperatures.

With this knowledge, you can personalize the bitter taste of your coffee.

For example, if you prefer a pleasant tasting brew, set your oven at 235°C and roast your coffee beans for less than 20 minutes. Watch as your beans change from green to brown and crack twice.

Then make your coffee as usual: grind the beans in a filter, then pour hot water through.

(By the way, why should you roast your coffee beans? It’s easy and tastes much better!)

And so for YOU who’s a keen coffee-drinker, I also note that water percolation or “pouring hot water through” the coffee beans makes a difference in how much of these compounds there are in the end as well! Not that much of a difference, but if you really want that perfect brew, look into this study in the Journal of Agricultural and Food Chemistry.

As for me, I don’t like bitterness anyway; so I’ll just stick to water.

-Ivy Wu

Skin-deep tattoo woes: study confirms presence of tattoo ink nanoparticles in lymph nodes

A compelling study published last Tuesday in Nature‘s Scientific Reports has confirmed that tattoo ink nanoparticles dangerously circulate the body. In this groundbreaking study, scientists from the European Synchrotron Radiation Facility (ERSF) have demonstrated overwhelming evidence for the movement and long-term deposition of toxic elements in tattoo pigments in tissues which lead to inflammation as well as other side effects upon tattooing.

Think before you ink; experts believe there are long-term safety concerns in tattoo inks. Untitled (c) Dan Prado.  CC BY-NC-SA 2.0

Whether it be a daring drunken escapade or a meaningful memento, getting a tattoo in Western societies has long been culturally accepted and not particularly novel. Tattoos have been around for millennia, the earliest artifacts dating to 1200 BC. Due to the recent popularity of tattoos, however, some began to ponder safety concerns of this seemingly innocuous trend.

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Concerns for tattoo ink safety are rising.

 

When it comes to the safety of tattoos, people are generally worried about the sterilization of needles, and rightly so, as infectious diseases like methicillin-resistant Staphylococcus aureus (widely known as MRSA) and HIV are known to spread through improper sanitation. However, the authors of the study believe that the chemical compounds of the inks pose an equivalent, if not greater risk for customers.

“People should be aware of the unknown risks that might come along with tattooing, rather than presuming that the colours are safe,” explains Ines Schreiver, first author of the study.

Currently, the toxicological data for individual ink ingredients are accessible, but the specific in vivo (Latin for “within the living”) interaction of tattoo compounds with cells are uncertain. So, researchers from the ERSF decided to not only to characterize the specific compounds within the dyes, but also quantify the size range of the molecules and qualify biomolecular changes in the affected tissues.

A key objective of the study was to show that organic dyes, inorganic compounds and metallic elements from tattoo particles were able to translocate from the skin to the lymph nodes in nano form, which means the particles are on the magnitude scale of 10-9 meters. Tissue samples were collected from deceased donors, and photographic evidence from comparing lysed skin and lymph nodes showed that the lymph nodes became tinged with the colour of the tattoo on the skin. Using spectroscopic techniques, the scientists were then able to identify compounds as well as quantify metal content such as Nickel and Chromium, which are linked to carcinogenicity.

Synchrotron X-ray fluorescence measurements allowed the researchers to pinpoint compounds at the micro and nano scale. Most particles detected were found at the micro scale, but the smaller particles on the nano scale had the pesky ability to migrate to the lymph nodes and induce enlargement which can lead to a myriad of other health issues.

If this finding has changed your mind about tattoos, keep an eye out for related studies. The authors of this paper will likely go ‘skin-deep’ in further research.

Frances Gu

CRISPR: A Future with Super-humans?

Researchers at Jennifer Doudna’s lab in the University of California have potentially found the cure to all forms of diseases. With the help of CRISPR and gene editing, which was only part of a dream a few decades ago has now become a reality. Research on Escherichia coli bacteria back in the 1980’s has allowed scientists to finally pin down the Cas 9 protein which enables the bacteria to survive virus attacks. When a virus attacks a bacterium, it inserts its RNA into the organism which leads to the virus using the bacteria as a factory and it eventually hijacks the entire cell. However, with E -coli and its Cas 9 protein, the RNA is recognized by the bacteria and allows it to destroy it. When a virus inserts a copy of RNA that is not recognizable by the bacteria, the Cas 9 protein is able to read the RNA and insert it into its memory where it will know which virus is attacking it.

Further research has allowed scientists to isolate this protein and use it for gene editing by using the protein to recognize faulty DNA nucleotides in the human genome. The Cas 9 protein needs to be able to bind specifically and reversible therefore the interaction is via non covalent bonds.With billions of nucleotides present in an organism this protein is highly accurate and can destroy genetic mutations such as metabolic liver disease, congenital blindness, blood disorders, Huntington’s disease and cystic fibrosis. As Jennifer Doudna has stated “We may be nearing the beginning of the end of genetic diseases”. Moreover, there is more than just curing genetic diseases, you can also go a step further and add desirable traits. Since CRISPR is very efficient in detecting the exact nucleotide sequence, you can replace it with the desired characteristics. You want a blond hair, just replace the DNA strand which codes for blond hair color, you want bigger muscles, just replace the nucleotides, you want to be taller just replace the nucleotides – you get the idea. You can be the most powerful person living with this technology – if yet reached.

The insertion of nucleotides in a genome with the help of Cas 9 protein                                                         (Attribution: ViktoriaAnselm – Own work)                                                                           (https://upload.wikimedia.org/wikipedia/commons/9/93/CRISPR-Cas9_mode_of_action.png )

Replace a strand – get super powers ?                                  Attribution: IMGUR (http://i.imgur.com/LTDKlbm.gif)

 

Researchers are still investigating the full potential of the CRISPR technology and it can lead to artificially selecting humans on birth if used at an early stage. The idea of pre-selecting humans might sound uncomfortable to a few but humans have been artificially selecting for decades from plants to humans. We currently only crop the best type of plant in order to achieve the most desirable traits. In humans , genetic disorders such as down syndrome are undesirable. 88% of people in Europe would undergo an abortion if they found out that their fetus has down syndrome. CRISPR might just amplify the amount of selecting we do, and we have to ask when is enough? I believe that CRISPR is an amazing technology in curing various genetic diseases but using it to select certain traits seems excessive. There are somethings that nature does not want changed. As research continues it is important to keep human rights in our thoughts and as Newton would say “What we know is a drop, what we don’t know is an ocean”. The ocean may be filled with gold or horror.

Garvit Bhatt

CHEM 300 Course Blog

Welcome to the CHEM 300 course blog!

Here are few things to make note of before you get started with your posts. First of all, you should read the blogging resources page under the Create menu. This will help you out a lot if you are brand new to using WordPress. On this page, you will find video tutorials about writing posts on this blog, adding media to your posts, tagging, and categorizing. You will also find a link to the rubric we’ll use to grade your blog posts.

Next, check out the blogging guidelines. Here you will find the answer to the question: “What are we supposed to blog about?” You can also check out one of last term’s blogs for some additional inspiration.

There are a few important things to keep in mind when blogging. Please do not assume that just because something is online, it is OK for you to use it. For example, unless it is explicitly stated, an image on the internet cannot just be copied, saved, and used in your own post without permission to do so. We’ve provided you with a lot more detail about properly using online content, but if you have questions, let us know.

This blog also contains a lot of resources for you. For example, still under the Create menu, you will find a  list of suggested software to use for your projects. We’ve also collected some writing and presentation resources.  Basic audio/visual equipment can be borrowed from CHEM300. Contact the course coordinator for more info.

Under the Explore menu, you will find some sample podcasts and videos, links that may be of interest or assistance, a list of groups and associations related to communicating science as well as a list of local museums and science centres. The Explore menu also contains a library resources page, which you should definitely have a look at. Finally, there is a bookshelf that lists relevant books that are on reserve for you in Woodward Library.

Let us know if you have any questions about the blog or would like to see any other resources made available. Or, if you find something that you think would be useful to the rest of the class, tell us, and we can add it to the resources. Better yet — write a post about it!

Happy blogging!

The CHEM 300 Team