Chemistry Seminar & Literature

Depression is a widespread form ofmental illness. The disease has been associated with hormonal imbalances affecting normal functional brain chemistry.Besides a loose familial correlation, there have been few identified causes or predispositions for depression.Recent research at Columbia University Medical Center has shed new light on a potential cause of this life altering condition.

In the April online edition of the Proceedings of the National Academy of Science (PNAS) researchers report that patients proven to have high risk of depression exhibit a 28% thinning of the right cortex of the brain.These findings were extremely surprising.This significant decrease in size is comparable to that found in more serious conditions such as Alzheimer’s disease.Depression is a much more subtle and mild condition, and such a stark difference in brain mass was startling.Because this cortex mass change predisposes people to the illness, it can be assumed that this more likely a contributing cause rather than an effect of full-on depression.This distinction was important for the researchers, as past studies had not been able to separate cause from effect.

The researchers suggest that the thinning of the right cortex could contribute to decreased social and emotional intelligence.Patients with a smaller right cortex may not pick up on certain social cues or emotions as readily as those whose cortex is fully developed.

This research provides new angles for the diagnosis and treatment of depression.Diagnoses can now be based on analysis of brain size and shape.Previous treatment had centered around chemical cures.If the right receptors are stimulated at the right times, the chemical nature of depression can be combated.Social training, however, could alleviate the development of depression in those with this predisposition in a more natural way.

Information from “Early Brain Marker for Familial Form of Depression:Structural Changes In Brain’s Cortex” in ScienceDaily (Mar. 26, 2009)

In modern times, physicists have taught us that the universe began with the Big Bang and began expanding uniformly in all directions. From this assumption, thye also stated that the universe was slowing down as it expanded. This postulate was accepted for many years and physicists were happy, until now.

When a supernova occurs, it gives off light of a very specific wavelength. However, as this light travels through expaning space its wavelength is altered ever so slightly, a phenomenon known as “red-shift”. Red shift is the technique used by cosmologists to determine how far away a supernove is from Earth. About 11 years ago, by using red-shift techniques, scientists realized that the supernova that they were examining were getting firther and further away, suggesting that the universe was actually expanding faster now than ever, not slowing down.

It has been postulated that this phenomenon is caused by something called “Dark Energy”. Dark energy is some form of repulsive energy that is causing the universe’s expansion to accelerate, rather than decelerate. However, no one knows what dark energy is.

A more probable cause for the red-shift phenomenon has recently been proposed. The universe is filled with matter, and matter exerts a force upon other matter known as gravity, which pulls things together. If we consider this fact, we can assume that maybe our galaxy is in a part of the universe with less matter than in others. Therefore, since there is less matter near us, our part of the universe is expanding faster than others, causing the red-shifts from supernova from other parts of the universe, especially those that have a lot of matter, to appear greater than we would expect.

By this theory, there is no need to consider dark energy. The universe is decelerating, it is just doing so unevenly due to the inhomogeneity of the universe.

4/29/09

This week’s seminar was a presentation by Veronica Casina, who is working towards a PhD in the WFU Chemistry Department under Dr. Rebecca Alexander. Veronica’s presentation did not regard the research for her PhD, but instead presented continued work from an unfinished, unpolished undergraduate research in Dr. Alexander’s lab. This research involved the mutational and kinetic analysis of an aminoacyl-tRNA synthetase, designed to uncover the efficiency and dynamics of this pretranslational enzyme. An aminoacyl-tRNA molecule is the key to translation from mRNA to protein and carries a specific amino acid to be attached to a forming protein on a ribosome. The aminoacyl-tRNA synthetase is the enzyme designed to bring the necesarry amino acid to the correct tRNA. As both substrates are specific to each other, there are specific aminoacyl-tRNA sythetases for differing tRNA and amino acid combinations. The aminoacyl-tRNA used in this experiment was MetRS and was specific to binding the amino acid methionine to its correct tRNA. MetRS catalyzes the formation of the methionine-tRNA bond by first binding ATP, then it binds the methionine at the N terminus and creates a phosphodiester bond with the ATP at the C terminus. The enzyme then finds the appropriate t-RNA and sidles up to the t-RNA, with the last nucleotide sitting in the binding site close to the other substrate. The reaction occurs in an area of the protein known as the Rossman catalytic fold. The enzyme then completes the reaction and attaches the amino acid to the last nucleotide, catalyzing a substitution reaction where the 2′ OH group of the nucleotide attacks the C-terminus of the amino acid.

Veronica analyzed the binding kinetics of MetRS, along with multiple mutant variants. These mutant variants were designed to knock out areas of the enzyme that were hypothesized to be key areas for binding the substrate and catalyzing the reaction. Through analysis of the wild type enzyme and mutants, she found that the aspartate 369 and the lysine 295 residues were essential to binding the substrates and catalyzing the reaction. Elimination of the aspartate severely effected the entire catalytic reaction while the lysine residue was essential for binding and attachment of the ATP and methionine residue. It was also found that the enzyme was a model system for long range communication of the enzyme domains, which were up to 50 angstroms. The identification of the essential aspartate and lysine residues imply that these two amino acids are very important to the pre translation process and that these structures within the Rossman catalytic fold are conserved.

This presentation was given relatively quickly but was jam packed with information regarding the experimental process and the subsequent results. This presentation was refreshingly interesting and also an engaging look the dynamics of protein formation.

Whether we think about it or not, there is considerable chemistry involved in the production of essentially all of the food we consume.In some instances, such as the fermentation of beer, leavening of bread, and ripening of cheese, the chemistry is carried out with the aid of microorganisms such as bacteria and yeasts.Thus, while microorganisms have been used for such purposes for much of history, scientists are continually finding new ways to employ them to enrich our food supply.For instance, vanilla flavoring, naturally derived from two species of orchid, Vanilla planifolia and Vanilla tahitensis, is primarily composed of a chemical compound called vanillin.

Due to the rarity of natural vanilla and the wide appeal of vanilla flavoring, scientists have developed numerous ways of synthesizing vanillin artificially.Past methods utilized wood lignin as a substrate and required the use of environmentally toxic chemicals to carry out the reaction.However, a new method developed by University of Copenhagen professor, Birger Lindberg Moller has genetically modified two strains of beer and baker’s yeast to synthesize the compound.Not only is this process much more environmentally friendly, it also uses a more readily available starting material, glucose. By splicing in genes from mold, bacteria, and humans coding for enzymes that catalyze the reactions necessary to transform glucose to vanillin, the researchers were able to develop yeast capable of synthesizing up to 65milligrams of vanillin per liter.

One problem that had baffled researchers in the past was the fact that vanillin is toxic to many organisms at high concentrations.Moller was able to sidestep this complication by adding a gene coding for a plant enzyme which attaches a sugar to the vanillin, eliminating its toxicity and allowing the yeast to synthesize even greater yields of the compound.The addition of the sugar, does not affect the taste or aroma of vanillin.

Interestingly, the uses of vanillin are not confined to the kitchen.For instance, vanillin, along with capsaicin, the compound found in hot peppers, is being researched for potential use as a pain reliever, and vanillin is commonly used in perfumes and aromatherapy products.This new innovative technique provides an excellent example of chemistry bridging the gap between the laboratory and the kitchen.

*Information for this review was obtained from ScienceNews (http://www.sciencenews.org/view/generic/id/43124/title/Yeast_bred_to_bear_artificial_vanilla)

Accessed on April 29,2009

For many years, catalytic converters have been used in cars to reduce environmentally hazardous and toxic chemicals such as carbon monoxide from fuel exhausts in our automotive engines. This technology has successfully been able to reduce air pollution, smog, and other harmful emissions coming from the tailpipe. However, just as the catalytic converter seems to be a scott-free method of making the car industry more environmentally friendly, new evidence indicates that the use of catalytic converters is causing an ironic twist to what seemed to be a totally environmentally friendly endeavor: osmium pollution.

Catalytic converters rely on the use of platinum and palladium to catalytically convert (thus the name) toxic emissions into less dangerous compounds. A newly discovered issue with this process; however, is that platinum and osmium are found in similar ores and that the extraction of platinum ultimately releases osmium into the atmosphere. Though the article states that the atmospheric osmium concentration is too low to pose any significant health problems on human populations, this is still an environmental concern. Osmium is a heavy metal and i believe it is one of the most dense metals on the periodic table if not the most dense. Like all metals, osmium participates in a geochemical cycle and this cycle is being preturbed by human interaction. Whether this presents itself as a significant environmental concern is not clear from the article. If i were to guess i would imagine there are thousands of other environmental issues that are more important, but it is worth mentioning as it is just another example of how human practices have had impacts of natural cycles and how these practices may lead to harmful consequences. I found it ironic that in the effort to reduce harmful emissions, people are ultimately agitating the geochemical cycle of an element and introducing it into the atmosphere. After reading this article, it became even more clear to me that as scientists and engineers set out to develop solutions to current environmental problems, it is important to also develop a means by which no new serious problems develop. Osmium pollution may not seem to be a major issue, but it is an example of how a seemingly good idea (such as reducing harmful emissions) puts the harm elsewhere.

On April 15^th, Dr. Jeffery Long From UC Berkley gave an impressive seminar entitled “Hydrogen Storage in Metal-Organic Frameworks”. As any modern day chemistry knows, CO₂ emissions from our automobile-dependent culture has had a detrimental effect on our environment and presents itself as a growing concern in terms of global warming and climate change. In the past decade or so, the hydrogen car has been seriously investigated as an alternative method to transportation due to its environmental cleanliness and its reduction of dangerous emissions. While knowledge of a possible hydrogen powered cars has been long known, several issues have hindered its development. One of the main problems is storing hydrogen effectively. In order to be used as a safe and energetically efficient power source, suitable hydrogen storage is an area of concern. Compressed hydrogen gas is both dangerous (due to explosive nature in the presence of oxygen) and inefficient because the storage pressure would be too high and tanks would be too heavy and bulky to be safe and energetically efficient in a vehicle. Similarly liquid hydrogen has also been considered an option, but presents itself as a problem in that it is very expensive and difficult to produce. To sidestep these major problems, Dr. Long’s research is primarily involved in developing metal organic frameworks that are suitable for hydrogen storage. In just one gram of his zinc-based material, there is a an approximate storage area of 5000 square meters. The benefit of an metal organic framework is that the compounds within the framework interact with hydrogen molecules to make storage a thermodynamically favorable process. Having a MOF that has a binding energy to hydrogen is favorable over compression chambers in that more hydrogen can be store at an equal pressure and is much more energetically stable.

Dr. Long’s research with metal organic frameworks aims to satisfy several goals issued by the United States Department of Energy concerning hydrogen storage. His research is quite interesting and has many strong implications in the development of hydrogen powered vehicles. As with anyone interested in an alternative fuel source that is environmentally friendly, I found this research to be quite interesting and I am intrigued by this specific approach to hydrogen storage. Metal organic frameworks appear to be the only feasible option for storage of hydrogen due to safety and energy concerns.

On April 15th, 2009 Jeffery Long of the University of California Berkely visited Wake Forest University to give a seminar entitled “Hydrogen Storage in Metal Organic Frameworks.” Long began his lecture by stating some alarming statistics regarding the environment and our contributions to its deterioration. He pointed out that one of the biggest problems currently facing the environment is the amount of carbon dioxide that is emitted from passenger cars. Approximately one third of all carbon dioxide emissions comes from the cars we drive everyday. In response to this environmental issue Long and his collaborators are working to develop cars using hydrogen gas as their primary fuel source, thus eliminating much of the carbon dioxide emissions.

Hydrogen gas seems like an ideal fuel source because it produces water as a byproduct, but Long quickly pointed out that it too has it drawbacks:

a) Hydrogen gas is extremely reactive and it could be especially dangerous when compacted at high pressures in an automobile. Also, compacting hydrogen gas would add extra weight to the car. Therefore cars would need to be made from extremely lightweight materials. These materials are very expensive, thus the cost of purchasing a hydrogen fueled car would not be in the average consumers budget.

b) Another problem with a hydrogen fueled automobile is the average lifetime of a fuel cell. Currently, fuel cells are extremely expensive and have a very short life span. In order to reduce the cost of a hydrogen powered car and make them more practical for consumers, scientists need to develop a cheaper and longer lasting fuel cell.

c) A final issue concerning Long is the creation of this hydrogen gas. Hydrogen gas can be produced using solar panels or cells but this method is also very expensive and inpractical when considering the general public as a consumer.

These problems with the hydrogen powered car all relate back to the issue of the money and the practicality of the hydrogen car for the general public. There are also problems concerning the storage of high pressured hydrogen gas on board an automobile. Long stated that there are currently four ways to store hydrogen gas. These are:

-As compressed hydrogen gas

-As liquid hydrogen

-As carbon nanotubes

-Through metal hydrides

None of these options are practical storage options for a hydrogen powered automobile. Long and his collaborators are working to solve this storage problem using Metal Organic Frameworks. These Metal Organic Frameworks bind to solvent and give the storage container a much larger available surface area. Although this large surface area is important for storing the hydrogen gas, the Framework can still be reactive to its surroundings such as moist air. Therefore, the Metal Organic Frameworks have their advantages and disadvantages, just as the other forms of hydrogen storage have their strengths and weaknesses. Long is working to develop these Metal Organic Frameworks because he believes that they will eventually be the source of hydrogen gas storage leading to the success of a hydrogen fueled automobile. Long’s work is extremely important as we are beginning to become more aware of environmental issues, carbon dioxide emissions being a big one.

Scientists in Europe have genetically enhanced maize, related to corn, to be more nutritious for human consumers.The maize was infused with beta carotene, the precursor of vitamin A, and the necessary precursors to make vitamin C and folic acid.While genetically enhanced food has been common, this experiment represents the first time that a plant has been modified to include multiple vitamins.

The maize was created by inserting metal particles coated with pieces of DNA necessary for the production of the vitamins into the embryos of a variety of maize known as M37W.Once the embryos took up the metal particles, the plant began to produce the vitamins, which lasted for multiple generations according to preliminary studies.The plant is envisioned as a possible solution for the vitamin deficiency commonly found in poor areas, such as Africa.In fact, eating 100-200 g of the maize would be enough to get almost all of the recommended daily intake of vitamin A and folic acid, and nearly 20% of ascorbate, which becomes vitamin C.

Some, however, are skeptical to genetically modified crops.Clare Oxborrow, from the group Friends of the Earth, said “Supporting families to grow green leafy vegetables in their communities can ensure sufficient levels of vitamin A, as well as a host of other nutrients and vitamins that a narrow GM (genetically modified) fix would not even begin to solve.”

Nonetheless, animal studies of the genetically modified maize will begin soon and initial human trials are expected as early as 2010, starting in the United States.Upon successful completion of these preliminary trials, Dr. Paul Christou from the University of Lleida in Spain cites “Once this is done we will be able to have enough data to try in Africa.”

The article in its entirety can be read on BBC, at http://news.bbc.co.uk/2/hi/science/nature/8020925.stm.

Link from Scientific American: http://www.sciam.com/article.cfm?id=algae-biofuel-of-future

Last week, the company Sapphire Energy announced it will be producing 1 million gallons of biodiesel and jetfuel for commercial use by the year 2011. However, this is not the normal ethanol/corn biodiesel which we have heard so much about: it is produced from genetically-altered algae. The fuel produced can be used to run jets and cars that already are in use today so there would be no alterations needed to the machinery we use in order to accommodate this source of energy. It has already been tested by Continental Airlines and has been shown to even have better gas mileage than our current petroleum-based fuels.

Surprisingly (to me at least), our current petroleum crude oils actually are comprised of algae-like microorganisms from millions of years ago. 500 million years ago, the earth contained nearly 18 times the atmospheric CO2 levels that it does today, which allowed the algae to thrive by using this excess of carbon dioxide as a food source. Roughly 100 million years later, these algae died out. The dead organisms, under the pressure and temperature conditions of the next 400 millions, eventually turned into the petroleum crude oils which we use today.

The algae produces fuels by converting carbon dioxide and water into lipids which are essentially biofuels. Therefore, not only are these organisms valuable for producing fuel, but will also reduce CO2 levels in the atmosphere by consuming this harmful biproduct of combustion during fuel synthesis. Coal power plants are already implementing programs to capture their CO2 emissions in order to be reused by companies such as Sapphire Energy in order to offer a more efficient and eco-friendly solution to our oil dependence. Advocates are currently pushing for the implementation of government incentives to coal plants which reuse their CO2 emissions for the production of algae-based biofuels.

Clearly, this technology is invaluable to both our dependence on foreign fuel as well as improving the air quality of our atmosphere. Global warming is a big issue right now and if we are able to reuse the CO2 we dispense into the atmosphere, it would be very good for our environment. It will be interesting to see if these algae-based fuels ever reach the mass production that gasoline has, but Sapphire energy and its affiliates are certainly showing promise.

Article

Structure of Morphine

accessed 4/29/09

Morphine is a common and widely used opiate derived painkiller that has been used in some form for over a hundred years. It does have some side effects and is, most notably, a very additive substance. The addictive nature of morphine is partly because of its nature as an opiate but also due to the fact that most people develop a tolerance to morphine relatively quickly. This tolerance implies that a physcian must constantly increase the dosage of morphine for a patient to give the same general level of pain relief. Researchers at the Hebrew University of Jerusalem have isolated the primary protein responsible for the development of morphine tolerance, interleukin-1. This protein is important for the body as it increased the pain signals produced by an injured area, causing the body to treat the area with care. Taking morphine to manage pain releases additional interleukin-1 over time, increasing the strength of pain signals sent to the brain. The reasearchers, led by Proffessor Yehuda Shavit, designed a morphine treatment in conjunction with an interleukin-1 blocker. This created a more efficient morphine treatment that did not necesitate a large increase in dosage but maintained the same pain relief effect.