Category Archives: Biochemistry

Green Fluorescent Protein: the Art and the Science

This summer I took a course at Rutgers University in New Jersey called GFP: the Art and the Science. It was taught by a biochemistry professor, Dr. William Ward (who had started his own company, Brighter Ideas Inc., to help others realize the potential of GFP), and supposed to be quite difficult. I gleaned this by the topics we were required to write about to get into the program. A lot of them weren’t things that normal students would know off the top of their heads, and questions often had terms like ‘chromophore’ and ‘cyclic tripeptide’ in them. We were supposed to be investigating GFP, a relatively new protein.

Our task was to use biochemistry purification techniques to purify a crude sample of GFP. Dr. Ward and his assistants had inserted the gene for GFP production into e. coli, produced numerous bacteria colonies and put the colonies in to a blender. The result was a green, cloudy, viscous mixture of dead, disembodied bacteria, DNA, other proteins, and ribosomes, etc. These were referred to as ‘contaminants’. Because we only wanted the GFP this meant that we would have to get rid of everything else, which would be difficult. One of the techniques used was chromatography, which is a method for separating substances based on certain criteria, such as charge, polarity, hydrophobicity, density, size, shape, affinity, and solubility. We used ammonium sulfate precipitation, hydrophobic interaction chromatography (HIC), ion exchange chromatography (IEX), and high pressure liquid chromatography (HPLC) to purify the crude GFP sample. After each round of purification we used a spectrophotometer to measure the purity of our sample. We ended up purifying the crude sample, which was only about 25% GFP, to a sample that was nearly 100% GFP. But how to these purification techniques that we used work? Why are they so effective?

GFP

Nearly pure GFP on a UV light

GFP2

samples of the purest GFP

GFP3

collecting samples of GFP as it elutes from the chromatography column

Ammonium sulfate precipitation is a method used to purify GFP by altering its solubility. It solidifies GFP into a mass that does not easily dissolve in water. Therefore, when the crude GFP sample is centrifuged, the GFP separates from the more soluble contaminants by forming a pellet on the bottom. HIC purifies the sample by resulting in only the molecules that have a similar hydrophobicity. IEX purifies the sample by resulting in only molecules with a similar charge. Hydrophobicity and charge are two important characteristics of GFP. By purifying the crude GFP sample using by using these two criteria, a high level of success was ensured.

However, you may be asking yourself why GFP is important. If scientists are interested in purifying it, this must mean that it is worth isolating for further study or for further applications in real life. GFP is special simply because it glows green when exposed blue light. It first came to the public knowledge when a Japanese organic chemist and marine biologist, Osamu Shimamura, decided to investigate what allowed aequorea victoria jellyfish to glow green. He was the first person to isolate GFP from the jellyfish and find out which “part of GFP was responsible for its fluorescence” (Zimmer, Marc). He, along with Roger Tsien and Martin Chalfie won the Nobel Prize in Chemistry in the year 2008 for the “discovery and development of the green fluorescent protein GFP” (nobelprize.org, 2008), which only demonstrates the level of interest it has created in the scientific community. GFP can be modified for a large number of uses – it has been used to create glowing animals/pets, used as a marker in a cancer cell to track the activity of cancer in certain situations, and used in brains to create fluorescent multicolored neutrons which result in beautiful rainbow pictures of brain activity. It is even possible for GFP to be manipulated to express different colors. However, in order for GFP to be used in this fashion GFP must first be isolated, purified and studied, which is why the success of our purification was so important. Only by purifying it can the true potential of GFP be realized.

Works Cited

  1. “Martin Chalfie – Autobiography”. Nobelprize.org. 24 Jul 2011 http://nobelprize.org/nobel_prizes/chemistry/laureates/2008/chalfie.html
  2. Zimmer, Marc. “Green Fluorescent Protein – GFP History – Osamu Shimomura.” Connecticut College: Home Page. Web. 24 July 2011. <http://www.conncoll.edu/ccacad/zimmer/GFP-ww/shimomura.html>.
  3. Zimmer, Marc. “Green Fluorescent Protein – Cool Uses.” Connecticut College: Home Page. Web. 24 July 2011. < http://www.conncoll.edu/ccacad/zimmer/GFP-ww/cooluses0.html>.

Some pictures:

The rainbow of GFP colors

The rainbow of GFP colors

brainbow1

A “brainbow”

300px-GloFish

glofish – genetically modified pet fish

Image Sources

  1. http://www.conncoll.edu/ccacad/zimmer/GFP-ww/cooluses0.html
  2. google images
  3. Green Fluorescent Protein: Wikipedia.org page

Iron Absorption!

At a recent checkup, my doctor informed me that my blood iron levels were once again below the minimum healthy threshold and that I am anemic, even though I had been taking iron pills for almost a year. The doctor said that this was a serious problem, as iron is essential in the successful completion of many vital body functions, notably the production of hemoglobin, which is responsible for carrying oxygen throughout the bloodstream

Needless to say, I was pretty worried. The doctor then proceeded to tell me that my problem with iron absorption might as simple as that I was eating too much of certain foods that are known to block iron absorption, and that I would need to limit the amount of those foods that I ate. He also told me to increase my intake of foods that would facilitate and “enhance” iron absorption, helping my iron levels return to normal.

So what are these “blocking” and “enhancing” foods?

It is first necessary to look at how iron is absorbed into the body. Iron absorption occurs at a place called the duodenum (Does Vitamin C Increase Absorption?). The duodenum is the first section of the small intestine.

duodenum_position

It can be assumed that the duodenum would simply absorb all the available iron in any food that passed through it, and then send the remaining “waste” material on through the digestive system.

This is not so. There are two types of iron that are present in food, heme iron and non-heme iron.

Heme iron is present in meat, and the duodenum absorbs it very well. It is absorbed well because it it is composed of animal hemoglobin and muscle tissue, which is similar in structure to our own bodies, and is also what the body is trying to produce with the iron absorbed (Does Vitamin C Increase Absorption?)

On the other hand, non-heme iron is found in all non-meat food products, such as dark green leafy vegetables. This form of iron is quite difficult for the duodenum to absorb (Non Heme Iron Foods), and only about 1-7% of non-heme iron in a food source is absorbed. This results in extremely little iron being absorbed at all, potentially leading to low iron levels and health problems (like anemia, where there is not enough hemoglobin in blood to carry oxygen, resulting in dizziness, fatigue, and fainting) (Dietary Supplement Fact Sheet: Iron), even though a person might be eating foods that are technically “high in iron”.

But can this low absorption rate be affected by anything else?

Unfortunately, I learned from my doctor that the consumption of a very common food can even further reduce the amount of iron absorbed by the duodenum: tea.

Tea contains chemical compounds called polyphenols (Foods That Block Iron Absorption) They bind to the non-heme iron before and renders it difficult to be absorbed by the duodenum.

However, I also learned that there is also a food that facilitates the absorption of non-heme iron: anything citrus (my doctor recommended orange juice, or just orange)! Citrus fruits contains vitamin C, which is ascorbic acid.

cid_235

When the ascorbic acid bonds with the non-heme iron, the compound, as a whole, becomes more stable, and the entire molecule becomes water soluble (Does Vitamin C Increase Absorption?). The membranes in our body all allow water to pass through.  As the iron has become water soluble, the duodenum’s mucus membrane readily absorbs the dissolved iron and much more iron is delivered into the bloodstream to produce hemoglobin.

Having learned all of this, I, an orange hater, thought to myself “Well why doesn’t everyone who has iron deficiency problems just eat lots of meat then?” I immediately realized that this was a huge bias.

This new knowledge was certainly beneficial for me, but would be even more beneficial to groups of people who do not consume meat because of religious or personal reasons, such as Buddhists or vegetarians.

Although eating meat is certainly not essential to survival, hemoglobin is. As these groups of people do not consume meat, they lose all sources of the easily absorbed heme iron. Thus, it is necessary that they are aware of these “blocking” and “enhancing” foods in order to be healthy.

Also, going back to the beginning of the post, the doctor made a point to tell me that it likely wasn’t any serious medical condition that was causing my anemia, simply a bad combination of food and that the chemistry between the foods was what was to blame. This shows that although medicine is widely considered to be rooting in biology, understanding how to diagnose and cure illnesses requires chemical knowledge as well.

Bibliography

“cid_235.png.” ascorbic acid. Web. 28 Mar 2011. <http://sci-toys.com/scichem/cid_images/cid_235.png>

Davis, Sarah. “Non Heme Iron Foods.” Livestrong. Livestrong, 23 March 2010. Web. 28 Mar 2011. <http://www.livestrong.com/article/87179-non-heme-iron-foods/>.

“Dietary Supplement Fact Sheet: Iron.” Office of Dietary Supplements. National Institutes of Health, n.d. Web. 28 Mar 2011. <http://ods.od.nih.gov/factsheets/iron/>.

“duodenum_position.png.” Duodenum Anatomy, Location, Parts and Pictures. Web. 28 Mar 2011. <http://www.healthhype.com/duodenum-anatomy-location-parts-and-pictures.html>.

Keefer, Amber. “Foods That Block Iron Absorption.” Livestrong. Livestrong, 9 November 2009. Web. 28 Mar 2011. <http://www.livestrong.com/article/32697-foods-block-iron-absorption/>.

McCarty, Kristen. “Does Vitamin C Increase Iron Absorption?.” Livestrong. Livestrong, 5 August 2010. Web. 28 Mar 2011. <http://www.livestrong.com/article/195055-does-vitamin-c-increase-iron-absorption/>.

Salt, seaweed and red wine – A possible cure for radiation poisoning?

110318_china_salt_crowd1.photoblog600

Chinese shoppers crowd a shop in an effort to buy salt in Lanzhou, northwest China’s Gansu province on Thursday.

While food shopping with my mom at Carrefour two weeks ago, in the immediate aftermath of the Japanese Earthquake and the explosions and nuclear meltdown of the Fukushima I Nuclear Power Plant reactors that followed the earthquake, I noticed most of the locals were buying unusual quantities of salt. When I asked her about it, she said that they believed the iodine in the salt would protect them from iodine-131, a radioactive contaminant which can, in sufficient concentrations, “lodge in the thyroid gland and cause cancer”. This piqued my interest as a chemistry student, and through some research I discovered that medical explanation for this is that people with low levels of natural iodine are vulnerable because “their thyroids will absorb any iodine encountered – even the radioactive kind. But when your thyroid is “topped off” with healthy iodine, it will not absorb the radioactive kind.

This phenomenon is not pertinent to just China but other countries as well – “Russian authorities have reported a run on red wine and seaweed”, chemists in Bulgaria are seeing shortages in iodine tablets. Panic buying in China is now so common that many supermarkets are sold out of salt, and there have even been reports of hoarding. False rumors have only fuelled the panic, resulting in “long lines and mob scenes in major cities”. The drastic measures taken by these shoppers begs the question- do these remedies really work, or are they just old wives’ tales?

Alternative treatments have been used by citizens to block radiation in the past, such as in the aftermath of the 1986 Chernobyl disaster in Ukraine, when “the former Soviet government recommended seaweed” (which contains iodine) and red wine (which contains tannin).  It appears that this trend is continuing in present as well, as Japanese authorities are distributing potassium iodide tablets to people living near the Fukushima plant. However, scientists nowadays are questioning these methods. Some cite that iodized salt is not effective enough in blocking radiation (an “adult would need to swallow 6.6 lb to prevent radiation poisoning”) while others say that China “faces no imminent threat of radiation contamination from the Fukushima plant”, due to its distance from China. Most experts recommend that people take potassium iodide tablets if concerned, as they contain higher concentrations of iodine and are US FDA approved for that specific purpose.

The behavior of the Chinese may seem irrational, but are actually quite understandable. People are very concerned when it comes to their health or the health of their loved ones, especially in times like these where they lack a full scientific understanding about what is going on, and are being constantly fed contradictory information from the government and the media. They feel very vulnerable and want to do something to protect themselves from the possibility of danger, and will usually take the safest route to do so, even when they’re not sure why. This is exactly what the Chinese are doing when buying salt – they are reacting to the danger and taking the safer route by buying something they are familiar with which contains low levels of iodine as more of a precaution than an actual remedy. From a sociological standpoint the panic buying is occurring because it is the collective behavior – extraordinary activities carried out by groups of people- of the Chinese.  Therefore the implications of this event are that in times of danger, it is usually best to seek a scientific understanding before one takes action, as then you can better assess the situation and decide on your own solution, rather than getting swayed by the crowd into something futile.

600 words (not including image captions)

If you are more interested in this topic here is a good webpage to go to:

“Fallout Foods” That Block Radiation – worldblog.msnbc.msn.com

Bibliography

Copilon. “Potassium Iodide.” Wikipedia, the Free Encyclopedia. 24 Sept. 2011. Web. 28 Mar. 2011. <http://en.wikipedia.org/wiki/Potassium_iodide>.

Healthy, Jim. “”Fallout Foods” That Block Radiation – Healthy Living on Shine.” Shine: Fashion and Beauty, Healthy Living, Parenting, Sex and Love, Career and Money, Food, and More – Shine on Yahoo! 28 Mar. 2011. Web. 28 Mar. 2011. <http://shine.yahoo.com/channel/health/quot-fallout-foods-quot-that-block-radiation-2466286>.

Johnson, Karen. “Tannin.” Wikipedia, the Free Encyclopedia. 14 July 2002. Web. 28 Mar. 2011. <http://en.wikipedia.org/wiki/Tannin>.

Pierson, David. “China: China Gripped by Panic Salt Buying amid Radiation Fears – Latimes.com.” Los Angeles Times – California, National and World News – Latimes.com. 18 Mar. 2011. Web. 28 Mar. 2011. <http://www.latimes.com/news/la-fg-china-iodine-salt-20110318,0,4281601.story>.

Rayner, Gordon. “Japan Nuclear Plant: Panic Buyers Seek out Salt, Seaweed and Red Wine as Rumour Fuels Fallout Fears – Telegraph.” Telegraph.co.uk – Telegraph Online, Daily Telegraph and Sunday Telegraph – Telegraph. 18 Mar. 2011. Web. 28 Mar. 2011. <http://www.telegraph.co.uk/news/worldnews/asia/japan/8389478/Japan-nuclear-plant-Panic-buyers-seek-out-salt-seaweed-and-red-wine-as-rumour-fuels-fallout-fears.html>.

Image citation

Chinese Shoppers Crowd a Shop in an Effort to Buy Salt in Lanzhou, Northwest China’s Gansu Province on Thursday. 2011. Photograph.

Getty Images.

Why Does Ice Float?

For every fieldtrip, activity day at school, I freeze a plastic water bottle. When I was about to put my bottle into the freezer, my mom would tell me “Don’t fill your bottle up to the brim.” In the morning I always found it amazing to  how the plastic waterbottle had stretched out and bloated like a balloon.

After learning about thermodynamics and states of matter, I was taught that a solid was the most dense form of a substance and that as temperature decreased, so did an atom’s kinetic energy and thus its volume. This however was different from what I had observed with water bottles.

It turns out that water is a very special substance that does not abide by the rules mentioned above. Water contracts untill it reaches 4ºC. This is when water is the most dense – 4 degrees celcius. As the temperature gets lower below 4ºC, water actually begins to expand and gets less dense.

Density of Pure Water
How the density of pure water changes with temperature. This graph shows that pure water has its highest density at 4 oC when it is still a liquid. Author: Lucinda Spokes.

As shown in the graph on the left, water’s density is at its maximum at around 4°C. The density of liquid water is 1g/mL while the density of ice is 0.92g/mL. (Wikipedia)

Now why does water behave like this? It is because of its unique shape and bond. H2O, water, forms strong hydrogen bonds, so water molecules are mixed very close to one another in its liquid state. The negative oxygen atom attracts the positive hydrogen atom in another molecule, resulting in a tight intermolecular bond.

This shows the polarity of the water molecule with a relatively negative charged Oxygen and two positively charged hydrogens. The dotted lines on the diagram on the right shows the hydrogen bonds that are formed.
This shows the polarity of the water molecule with a relatively negative charged Oxygen and two positively charged hydrogens. The dotted lines on the diagram on the right shows the hydrogen bonds that are formed.

At 4°C, water molecules are as tightly packed as they can get. As water cools below 4°C, each molecule rearrages itself into a more stable crystalline structure and forms a stable solid, ice, at 0°C. It is during this process of rearrangement, when the volume of the water increases for its molecues to move around. Its mickymouse shaped molecules neatly stack on top of each other , and trap air bubbles in the process. This creates more space inbetween the water molecules in its solid form than in its liquid state. The round, bent structural shape of the water molecule also begin repelling each other once they get too close.

This is why ice floats in water. If ice was not less dense than water, icebergs would not exist. We would not be able to skate on a frozen pond, nor enjoy a lemonade with floating ice. Situations similar to my fozen water bottle example, happen in everyday life. Water pipes freeze and burst in unheated houses.

One particularly interesting thing I realized when I researched the properties of water was its relavent to our current IB Chemistry topic on Bonding. Hydrogen bonding, and the existence of a permanent dipole, which we had just learned a couple of days ago, was crucial to understanding anomaly. These properties of water also confliced with the laws of thermodynamis and rules about kinetic energy. Although theories and models are good general explanations of things, this example of water provided us an example of limitation of simplfying assumptions, and how models do not fit in evey reallife applications.

Once again, we should be glad that ice is less dense than liquid water. “If water froze from the bottom up, much of Earth’s water would solidify in winter, and life might be impossible.” (Wollard)

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Bibliography

-Helmenstine, Anne Marie. “Why Does Ice Float?” About.com. Web. 14 Nov. 2010.

-Lunar and Planetary Institute. “An Expanding Ice.” Lunar and Planetary Institute (LPI). Web. 14 Nov. 2010.

-Max Plank Institute. “Properties of Water.” Atmospheric Chemistry. Web. 14 Nov. 2010.

-U.S. Geological Survey. “Water Properties: Water Science for Schools: Physical and Chemical Water Properties.” USGS Georgia Water Science Center – Home Page. Web. 14 Nov. 2010.

-Wikipedia contributors. “Properties of water.” Wikipedia, The Free Encyclopedia. Wikipedia, The Free Encyclopedia, 13 Nov. 2010. Web. 14 Nov. 2010.

-Wollard, Kathy. “Why Does Water Expand When It Cools?” The Word Detective. Web. 15 Nov. 2010.

Solids, Liquids, and Gas masks

The development of gas masks had been a huge part of chemical warfare, especially in the two World Wars. However, the gas mask had humble beginnings from way back in 1847, when they were just moist filters meant to keep out dust. It was not until 1854 that John Stenhouse discovered that powdered charcoal had the ability to effectively protect people from toxic gases (“The Invention of the Gas Mask“). The primary function of a gas mask is to protect its wearer from harmful pollutants in the air, which can range from simple paint fumes to the highly poisonous phosgene. But how does a simple mask such as the one below filter out these chemicals?

A Typical Gas Mask
A Typical Gas Mask

The answer is simple–it does so through a filtering process which usually includes adsorption by activated carbon.

But I have no idea what either of those things are!

According to the Rensselaer Polytechnic Institute, “Adsorption [is] the binding of molecules or particles to a surface, [and] must be distinguished from absorption, the filling of pores in a solid.” The particles bind to the surface of the adsorbent through the attraction of van der Waals forces (Kvech).  In the case of many gas masks, poisonous molecules are bound to the surface of activated carbon within them, which is a solid with an amazing surface area:volume ratio (1 gram of it has around 100 square meters of surface area, according to Kvech). Since the toxic particles are bound to the activated carbon, they are taken out of the air, allowing the wearer to breathe freely. This process is illustrated in the following diagram.

Particles binding to an absorbent.
Particles binding to an adsorbent.

The development of adsorption technology has impacted the world’s technologies in many areas other than surviving chemical attacks in wars. Activated carbon, in particular, is so versatile as an adsorbent that it is used even in water purification and filtration systems. The way it works is that activated carbon causes particles with an odor of color to bind more strongly to itself than substances with no odor or color (e.g. water). As a result, the water is left nearly tasteless, and nearly odorless (which is an important quality of drinking water).  Just as with the removal of toxic airborne particles, it can also be used to remove toxic particles in water.

Space technology has also been significantly impacted, as the same principles used in gas masks and water filtration have also been used to filter air (specifically, carbon dioxide) in the life support systems of astronauts (“A Life-preserving Suit.“) .

Adsorbent technology has had a great impact on the purification technologies of today, and perhaps in the future, it could be developed to a point where purifying drinkable water becomes trivial.

Bibliography:

“A Life-preserving Suit.” Canadian Space Agency. 08 Feb. 2004. Web. 09 Nov. 2010. <http://www.asc-csa.gc.ca/eng/educators/resources/spacesuit/functions.asp>.

“Adsorption.” Rensselaer Polytechnic Institute. 26 Feb. 2000. Web. 09 Nov. 2010. <http://www.rpi.edu/dept/chem-eng/Biotech-Environ/Adsorb/adsorb.htm>.

Kvech, Steve, and Erika Tull. “Activated Carbon.” The Charles Edward Via, Jr. Department of Civil and Environmental Engineering. 24 Feb. 1998. Web. 09 Nov. 2010. <http://www.cee.vt.edu/ewr/environmental/teach/wtprimer/carbon/sketcarb.html>.

Miles, Wyndham D. “The Velvet-Lined Gas Mask of John Stenhouse.” Armed Forces Chemical Journal (1958): 24-25. Brinkster.com. Web. 09 Nov. 2010. <http://www33.brinkster.com/iiiii/gasmask/stenhouse.html>.

“The Invention of the Gas Mask.” Brinkster.com. Web. 09 Nov. 2010. <http://www33.brinkster.com/iiiii/gasmask/page.html>.

Images:

Gas Mask. Digital image. Wikimedia Commons. 13 Mar. 2009. Web. 09 Nov. 2010. <http://commons.wikimedia.org/wiki/File:Gas_mask.svg>.

Langmuir Izoterma. Digital image. Wikimedia Commons. 05 Sept. 2009. Web. 09 Nov. 2010. <http://commons.wikimedia.org/wiki/File:Langmuir_izoterma.png>.

Science: a matter of life (and death!)

Regardless of whether there is an after life or not, the fact that our physical bodies decompose remains. With the coming of Halloween, my research on spooky facts led my trail of thoughts to the morbid topic of decomposition after death. This got me started on thinking about my prior knowledge on the topic – our heart and brain shuts down, the body turns cold and stiff (according to the movies) and the body starts to decompose, the soil and maggots lending a helping hand in process. Finally, the body would completely disintegrate, ceasing to exist. Or at least that’s what I thought.

Decomposing Pig
Decomposing Pig

I became curious on whether or not what I knew was true. What really breaks our body down? It turns out that our own bodily processes help. Even when we’re well and alive, our body contains many decomposing enzymes and microorganisms. Bacteria in the large intestines helps to digest food when we are alive, but they also help break down dead cells in your body. Upon death, these enzymes start to break down the body itself, a process called autolysis, or self- digestion. Ever thought of why bodies stink? Well, this process is also the main contributor to the smells of a decaying body; when the body is being broken down, chemical reactions occur, producing gases. Hydrogen sulfide and methane are the two primary gases involved, and both carry a pungent odor. As these gases build up in the body they increase the body’s pressure from within, causing liquids to starts to seep from its openings! In addition, exothermic reactions occur; so really, in the initial stages, the body starts to heat up before turning stone cold!

Over the recent school break, I got to watch the movie “Dead Snow“, a movie that plays with the idea of Nazi zombies. As the media has always portrayed zombies with inflexible, rigid movements, it was much to my surprise that the body doesn’t actually stay rigid- it is only temporary. At the initial stages of decomposition, rigor mortis begins. A little bit of explanation here is required – muscle fibers have connections between them that cause contractions and relaxations of the muscle, this dependent on the presence of calcium ions. “The concentration of calcium ions is higher in the fluid surrounding muscle cells that inside the cells, so calcium tends to diffuse into the cell” (Australian Museum). Therefore, if the calcium level is higher within the cell, the muscle remains contracted. It is only through expelling of the calcium ions from the cell can the muscle be relaxed; however, this requires energy, energy that cannot be produced upon death.

Relax, rigor mortis goes away. Although cells in the body don’t ‘die’ immediately, instead taking anywhere from a few minutes to hours before they stop working, muscle cells would be lacking of oxygen, becoming unable to producing energy. Thus, the muscles are forced to remain contracted, until approximately 72 hours after death, when the muscle proteins would be broken down, causing the rigid cell connections to break down altogether.

Although I have only listed the first of many chemical processes that our corpses goes through, I hope that this post has satisfied your burning curiosity of some questions regarding this topic. Do keep in mind that everything mentioned above didn’t weigh in factors such as environment, temperature and climate – even the food in the stomach would affect the rate of decomposition! Nevertheless, this is enough ‘dead’ talk for me for the day. Why focus on the science of life, when, even in death, chemistry is with us?

Works Cited:

Decomposition – Body Changes – Australian Museum.” Australian Museum – Nature, Culture, Discover – Australian Museum. Australian Museum. Web. 24 Oct. 2010.

Decomposition.” Wikipedia, the Free Encyclopedia. Wikimedia Foundation, Inc., 21 Oct. 2010. Web. 24 Oct. 2010. .

Decomposition.” World of Forensic Science. Ed. K. Lee Lerner and Brenda Wilmoth Lerner. Gale Cengage, 2006. eNotes.com. 2006. 24 Oct, 2010 .

Asian Glow?

We’ve all seen it (or at least heard of it), whether it be in movies, stories from friends, or *shock* in real life! Becoming tipsy after just a sip of drink, the reddening of the face….what is this often humiliating and always frustrating problem that so many Asians have?

Picture 1

“asian_glow_cmyk-300×191.jpg.” Esophageal Cancer and the ‘Asian Glow’. Web. 21 Oct 2010. <asian_glow_cmyk-300×191.jpg>.

Studies have shown that up to 50% of Asians suffer from “alcohol flush reaction” (deCODEme), colloquially known as “Asian glow”, a reference to the fact that, indeed, it is mostly Asians that have this problem. This reaction to alcohol entering the bloodstream causes facial flushing, nausea, an accelerated heartbeat, headaches, bloodshot eyes, and very rarely, seizures and loss of consciousness. 540 million in total in the entire world have this condition, and it is commonly acknowledged that that group of people is comprised of mainly Asians. But why?

First of all, it is necessary to understand what is supposed to happen to the alcohol upon ingestion by a human being. The alcohol would be ingested, reach the liver, and then undergo a series of complex chemical reactions, involving the deprotonation of alcohol, and the release of the product acetaldehyde.

At this point, enzymes called alcohol dehydrogenases would break the ethanol (CH3CH2OH) into acetaldehyde (CH3CHO) through oxidation. Then,  “acetaldehyde dehydrogenase”, or ALDH would then break down the toxic acetaldehyde into harmless acetic acid (think vinegar) which would then be absorbed by the body (Zbeda)

zbeda_equation_cmyk-300x115

“asian_glow_cmyk-300×191.jpg.” Esophageal Cancer and the ‘Asian Glow’. Web. 21 Oct 2010. <http://dujs.dartmouth.edu/wp-content/uploads/2009/11/zbeda_equation_cmyk.jpg>.

This enzyme, ALDH, is responsible for the plight of those who have the aforementioned condition, “alcohol flush reaction”

Many Asians carry a mutated form of the ALDH2 gene, manifesting as a result of a dominant allele passed from their parents. The most common theories seem to embrace the idea that either 1) the allele calls for the encoding of a slow-metabolizing form of ALDH2, resulting in large amounts of acetaldehyde circulating through the bloodstream, causing the symptoms mentioned above as a result of the toxicity of the product, or 2) a deficiency of the enzyme, also causing slow metabolizing within the body

But why Asians? Why not Europeans, or Australian aboriginals, or Inuits from the Arctic Circle, to name a few?

As the first organized civilizations began to emerge, communities needed to be able to find ways to attain clean drinking water if they were not near enough to a potable water source. Europeans, who were familiar with grains such as wheat and barley, fermented the plants into alcoholic drinks, which thus rendered the liquid antiseptic. Alcohol became readily available and common, as entire cultures were calibrated with alcohol in mind. As a result, their inborn acetaldehyde Dehydrogenase enzymes were frequently used, and thus carried through from generation to generation, causing modern-day Europeans and ancestors of Europeans  to almost always be able to tolerate alcohol.

On the other hand, in Asia, the Chinese had figured out a different way to purify their water: boiling. This method of purification soon spread to other areas around East Asia, and the level of alcohol consumed by Asians was very little compared to the Europeans. After centuries of disuse, evolution simply rendered the enzyme inactive, or extremely weak.

But big deal! So what? Getting a bit red in the face and experiencing some mild discomfort is a small price to pay for a fun night out, right?

Not so. Long term effects of this weakened/mutated enzyme can lead to up to a 1000% chance increase in risk of esophageal cancer! Acetaldehyde circulating through the body, not getting broken down, is what causes this risk to skyrocket, as acetaldehyde is a well-known and dangerous carcinogen (Blisstree).

But, having alcohol flush reaction comes with an advantage as well. It, intuitively, appears to suppress alcoholism rates in those who have the condition, as the side effects are often more than enough to deter them from drinking at all, let alone in excess (deCODEme). Furthermore, Asians are the most prone to alcohol flush reaction, and also are one of the races least prone to dependence upon alcohol, or alcoholism.

For real alcoholics, doctors often prescribe a drug called Disulfram, which essentially creates the same effects as the faulty ALDH2 enzyme. It works by preventing the oxidization of the acetaldehyde, resulting in the acetaldehyde circulating through the body, causing the “flush” reaction to occur, and thus discouraging the patient from drinking (“Flexyx”)

As AFR is, in Asian populations, a relatively common condition, measures should be taken to spread awareness about the huge amount of dangers associated with drinking with this condition, such as the possibility of becoming rapidly inebriated, and as a result, incapacitated, or eventually contracting esophageal cancer.

There currently is no “cure” for this “problem”, or some might say “blessing in disguise”. But might there be in the near future?

Works Cited:

“Alcohol Flush Increases Cancer Risk in Asia « Blisstree.” Blisstree. Web. 01 July 2010. <http://blisstree.com/geneticsandhealth/alcohol-flush-increases-cancer-risk-in-asia/>.

“Alcohol Flush Reaction Risk – Genetic Testing for Alcohol Flush Reaction Risk | DeCODEme.” Genetic Testing for Diseases, Common Conditions and Health | Trace Your Ancestry | Explore Your DNA with a Genetic Test | DeCODEme. DeCODEme. Web. 01 July 2010. http://www.decodeme.com/alcohol-flush-reaction.

“Flexyx: Esperal (Generic name – Disulfiram).” Flexyx. Flexyx, n.d. Web. 21 Oct 2010. <http://www.flexyx.com/E/Esperal.html>.

Zbeda, Robert. “Esophageal Cancer and the “Asian Gow”.” The Dartmouth Undergraduate Journal of Science. Trustees of Dartmouth College, 21 Nov. 2009. Web. 21 Oct 2010. <http://dujs.dartmouth.edu/fall-2009/esophageal-cancer-and-the-%E2%80%98asian-glow%E2%80%99>.

Pictures:

“asian_glow_cmyk-300×191.jpg.” Esophageal Cancer and the ‘Asian Glow’. Web. 21 Oct 2010. <http://dujs.dartmouth.edu/wp-content/uploads/2009/11/asian_glow_cmyk.jpg>.

“zbeda_equation_cmyk.jpg.” Esophageal Cancer and the ‘Asian Glow’. Web. 21 Oct 2010. <http://dujs.dartmouth.edu/wp-content/uploads/2009/11/zbeda_equation_cmyk.jpg>.

A Cure All?

Disease has been a plague throughout all of history ranging from the black plague to small that both cripples and kills millions each year. With the constant influx of disease, there has always been a constant search for cures; however, we have yet to find cures for many diseases such as diabetes, Alzheimer’s disease, spinal cord injuries, or strokes. But biological insights over the past years and recent breakthroughs have brought us many steps closer towards a cure for all these diseases and many more. This supposed cure all is none other than the immortal, malleable stem cells.

stem-cells2

Stem cells are unspecialized cells capable of renewing themselves through cell division, sometimes after long periods of inactivity, and under certain physiologic or experimental conditions, they can be induced to become tissue or organ-specific cells with special functions. The beauty of stem cells from a medical standpoint is their potential to develop into any type of cell in the body acting as an “internal repair system” able to theoretically repair any and all organic damage whether it be producing new blood cells to counter blood related disease or even used to replace organs like the heart or lungs.

scientsit

Recently, stem cell research has made great strides despite some controversy and opposition – some view harvesting the stem cells from embryos as murder. In 2007, scientists reported that they were able to cause skin cells from mice to revert back into the embryonic state (into stem cells). Without the need for an embryo, this breakthrough circumvented the controversy enabling stem cell research to proceed without restriction. And then in 2008, another group of researchers discovered a method to derive an entire stem cell line from an embryo without destroying the embryo and then manipulate these cells into blood, muscles, retinal tissue, or even neuronal tissue. Stem cell treatments for many blood related illnesses leukemia or sickle-cell anemia have already become a reality, and future projects will tackle Parkinson’s, Alzheimer’s, even paralysis.

Despite stem cells undeniable potential and swift progress, many obstacles remain. The problem comes when trying to integrate the stem cells into the body; in addition to stem cells and protein scaffolding, the complex array of signaling molecules, molecules that tell the cell which side is left or right, where to become a specific cell, and when to stop growing, are necessary for the regeneration of body parts. One of the most shocking implications of this issue is the ability of stem cells to reproduce over and over. Without knowing how to tell the stem cells to stop growing the stem cells can form clumps of undifferentiated cells that grow out of control – in other words: cancer. Another area of difficulty is the fact that each disease has a set of conditions that must be met in order to cure it. The stem cells must be introduced in the correct order and correct stage. According to Doris Taylor, director of the Center for Cardiovascular Repair at the University of Minnesota

“we don’t understand all the cures, so we can’t control, the outcome, and we aren’t ready to use them without more research in the lab”

Aside from their potential medical usage, stem cells illustrate a key issue of scientific research. The controversy of stem cells reminds us that scientific research is not only subject to the critique or review of other scientists but to the critique of the people as well. On the one hand, these controversial debates corrode the pure and innocent notion of pursing knowledge for the sake of knowledge. On the other hand, these ethical critiques are a beneficial (as evidenced by proactive work to synthesize stem cells) and sometimes necessary element of scientific growth as they push and encourage the powerful adaptability and inventiveness of science.

Sources:

Lenzer, Jeanne. “The Super Cell.” Discover November 2009: 31-36

Dying (your) hair

Hair coloring is the process of changing one’s natural hair color to another. Although this concept has been around for centuries (it was first recorded in print in the book Eighteen books of the secrets of arts and nature which was published in 1661), it has only risen to commercial availability from the beginning of the 20th Century. Coloring one’s hair is a popular option for both men and women today for the many different functions it can be used to serve.

Before investigating how the chemicals in hair coloring agents “color” one’s hair, we need to have an understanding of what hair truly is. Hair is a protein filament that grows through certain layers of the skin. Hair is found exclusively in mammals. However, there are non-mammalian species that have filament-like structures that are similiar to hair. The main component that makes mammalian hair is keratin. Keratin is a family of fibrous structural proteins (also known as scleroproteins)that are characteristic for their toughness. These form into long chains and are insoluble in water due to hydrophobic R groups (learn more about hydrophobic molecules from Kyle’s blog post). More about the chemistry of hair can be found on the following website.

The color of hair is attributed to two types of melanin: eumelanin and pheomelanin. Melanin is a group of compounds that serve as a pigment. Eumelanin colors hair either black or brown, while pheomelanin colors hair red. The more melanin there is in hair, the darker it shall be in color. This medical journal talks about how melanin is delivered to the hair follicles. Hair color is attributed to genetics by several theories, however, none have been confirmed.

Hair coloring agents can be classified into four distinct groups: temporary, semi-permanent, demi-permanent and permanent. Each class is based on the amount of time the hair color persists and how much lifting occurs. Lifting, in this context, means how much of the natural hair color is absorbed by the dye.

Temporary hair coloring agents, as the name suggest, are the weakest of the four classes. These may be available in the form of shampoos, gels, sprays and foams. The color particles are adsorbed to the hair shaft, but can be removed through a simple shampooing. Semi-permanent hair coloring agents use smaller molecules that are able to partially penetrate the hair shaft requiring 4-5 shampoos to remove. Semi permanent agents contain low levels of peroxide and ammonia (referred to as ‘developer’). Some agents even contain p-Phenylendiamine (PPD), an aromatic amine which can cause heavy allergic reactions and scarring in some of its users.

Permanent hair coloring agents make use of higher levels of developer, which consists of ammonia and hydrogen peroxide. Ammonia is an oxidizing agent and when it is mixed with hydrogen peroxide, the peroxide becomes alkaline and diffuses through the hair fiber. It reaches the cortex and breaks down the melanin, causes lightening to occur. Upon doing this, it replaces the melanin with its desired pigment. This process can only be reversed through stripping, which can be very damaging to the hair.

Hair coloring is used for a variety of purposes, but I believe a  primary use of it is cosmetic. Hair color and style have often been subject to one’s perception of beauty. My research with hair coloring leads me to ask two questions. The first, how does hair color affect one’s perception of what is beautiful? Is it subject to an individual’s experiences or prejudices, as a certain hair color or style could well be part of another’s social circle, culture or religion? And secondly, what extents do humans go to in order to become beautiful? Hair coloring can be a damaging process as many formulas are potentially toxic or even carcinogenic. Repeated dyeing can truly cause one’s hair to die, and yet people have been known to undergo this process repeatedly. So, is dy(e)ing your hair worth the possibility that you may never be able to dye it once again?

Ribosomes, Ribosomes, Ribosomes Oh My

nobel-prize

New scientific discoveries and breakthroughs are being made every day, and once a year certain scientists are recognized for their outstanding achievements with a Nobel Prize.  The Prizes were recently awarded and this year’s Nobel Prize for chemistrywent to Venki Ramakrishnan, Thomas Steitz and Ada Yonath for their major contributions to understanding the nature of the ribosome. 

Ribosome are small granular structures within cells that synthesize proteins – an extremely important part of the cell considering proteins have a huge range of functions in living organisms from catalyzing reactions to moving substances across cell membranes.  In short, a ribosome translates the instructions for making a protein (found in DNA) into the proper order of amino acids to construct a protein (Click for a more detailed explanation of the function of the ribosome).  Now, this information has been known to biologists since the 1960s, but a deeper understanding of the ribosome could not progress without first understanding the detailed structure of the ribosome.  A task easier said than done considering the ribosome contains hundreds and thousands of atoms.

ribosome-structure 

Well, these three scientists took up the challenge and attempted to visualize the ribosome using X-ray crystallography.  X-ray crystallography is an imaging technique where the diffraction patterns that X-rays passing through a crystal of a substance create are used to determine the crystal’s atomic structure.  Ada Yonath went about the problem by growing crystals a ribosome from the bacteria Geobacillus stearothemophilus which could then be irradiated with X-rays in order to determine the atomic structure.  Yonath succeeded and was able to create the first ribosomal crystals in 1980, a huge step forward as prior to her discovery the task of preparing suitable ribosomal crystals was deemed impossible.  It would take another 20 years before the crystallized ribosomes could diffract enough of the X-rays to construct a detailed atomic model.  Over two decades of investigation ended in success, and the high resolution structures of both ribosomal subunits were published in 2000.  (I’ve only presented a very brief explanation of Venki Ramakrishnan’s, Thomas Steitz’s and Ada Yonath’s studies but much more detailed information can be found here     

Such a discovery has immense positive implications for biomedical research.  Today, 50% of known antibiotics target the ribosomes of bacteria (if a bacteria’s ribosome is shut down, it can no longer synthesize proteins, and thus no longer function).  Looking at the detailed structures and learning precisely how antibiotics interact with the ribosome will provide key data to help the designs of new antibiotics to combat drug-resistant bacteria. 

Additionally, this new understanding of ribosomes has lead to a big leap in the area of evolution.  The function of the ribosome is to synthesize proteins, but at the same time ribosomes are composed of proteins.  So the question arises – did the proteins or the ribosomes come first?  We now know that the ribosomes came before the proteins because the active core of the ribosome is made of RNA, and the proteins present in ribosomes were added later.  Dr. Berg of the National Institute of General Medical Sciences stated that the ribosome is a

 RNA-based machine that evolved the ability to make proteins.

In conclusion, this new understanding has re-defined the way we interpret the world around us.  And, although, our previous lack of knowledge regarding the ribosome highlights the uncertainty of science, this new insight also emphasizes the fact that our scientific understanding is continuously being expanded.  Though, in this case, the idiom “ignorance is bliss” may be appropriate as this new discovery has opened even more possibilities and left even more questions (for example, the ribosome came before proteins, but another key question for evolution emerges – when did RNA base of the ribosome learn to make proteins?)      

Bibliography

Allot, Andrew. “Biology for the IB diploma.” Oxford University Press 2001.