Chemistry Lesson Plan

 

Limiting reagents cause focused attention in dark brown, hazel, and blue eyes

 Laws of thermodynamics gather shades of brown, olive, yellow, tan, and white

 Oxidation number rules are quickly, carefully transcribed

 By Papermate pencils tightly gripped by fingernail-chewed hands,

 How do I convince them that they are brilliant

 That they shine when they solve, explain, and share with each other

 How do I help them decimate their low confidence and troubling anxieties

 Their capabilities extend as far as they can see themselves where they want to be

 How do I lure them into believing they are diamonds in the rough

 Not walking wounded

 But able-bodied, neuroplastic, thermodynamic, electo-kinetic, spontaneous

 Emissions of power, knowledge, and potential

A Healthier French Fry? Simplot Says So

How many of us have munched on a plate of fries or chips and wondered about the health consequences? Recently, giant potato company Simplot has generated a potato that contains less of an amino acid that leads to a potential carcinogen called acrylamide. 

Image of fries from http://www.simplotfoods.com/Recipe/18433

Acrylamide (right) has amide and alkene functional groups.

What is this amino acid that causes concern? It is asparagine and is

found to be of highest concentration in french fries and in smaller amounts in baked goods, batter-fried fish and chicken, and even in coffee powder and beer.

From a food safety report about the health implications of acrylamide.

http://www.who.int/foodsafety/publications/acrylamide-food/en/

Asparagine is an amino acid which can change during high temperature cooking into a potential carcinogen acrylamide. Chiral center, carboxylic acid, and amine functional groups are highlighted.

According to a 2007 report from the U.S. Food and Drug Admin-istration, acrylamide typically found in commercial applications such as packaging and in scientific research. Its appearance in food comes from high-temperature cooking such as baking, roasting, and frying where the Maillard Reaction converts naturally occurring asparagine into acrylamide. This often occurs in the presence of sugars found in foods. Acrylamide has been detected in plant-based foods, such as French fries and potato chips. It has also been found in cookies, crackers, breakfast cereals, and bread. The FDA esti- mates that the average amount of acrylamide ingested each day is 0.4 microgram/kilogram of body weight.

In a paper by C.M. Rommens, H. Yan, K. Swords, C. Richael, and J. Ye published in Plant Biotechnology Journal, they were able to create a potato with a lower amount of asparagine by silencing two asparagine synthetase genes using a technique called RNA interference.

Here is a cool video describing the process of RNA interference

Being able to specifically enhance or silence certain genes within the cells of the plant has also enabled researchers to control the potato’s ability to resist black spot bruise, something that can sig- nificantly affect productivity and amount of sellable product to market.

According to Simplot, up to 28% of potatoes like this in the United States are thrown away.

 image from https://www.agric.wa.gov.au/potatoes/improve-potato-quality-minimising-mechanical-damage

Black spot bruising occurs during transportation of potatoes where bumping can cause damage to cells underneath the skin. Often the way to see this is by cutting open the tuber.

The chemical question a curious student may ask is how asparagine changes to acrylamide. A detailed mechanism can be an interesting exercise for an organic chemistry student. Here is one proposal:

For more information:

*Ask the Regulators: Acrylamide, Furan, and the FDA
*Low-acrylamide French fries and potato chips, by C.M. Rommens, H. Yan, K. Swords, C. Richael, and J. Ye
*Innate technology by Simplot
*Acrylamide is formed in the Maillard reaction, by D.S. Mottram, B.L. Wedzicha, and A.T. Dodson

How Green Tomatoes Preserve Muscles During Aging

One thing people notice as they age is the loss of muscle mass and strength. This can be accelerated by factors such as lack of exercise, fasting, or an extended stay in a hospital where one is confined to a bed for long periods of time. A recent discovery by a University of Iowa professor of internal medicine and his team may shed some light on the molecular mechanisms of aging and propose two naturally occurring compounds that can help mediate the negative effects of age-related muscle weakness and atrophy.

An old mouse (front) already displaying some physical limitations. Muscle atrophy can be accelerated due to long periods of inactivity. 
(image from Jeff Miller, University of Wisconsin-Madison)

In a paper published in The Journal of Biological Chemistry this past October, senior author Dr. Chris Adams and his colleagues (including Michael Dyle, Steven Bullard, Jason Dierdorff, Daryl Murry, Daniel Fox, Kale Bongers, Vitor Lira, David Meyerholz, Scott Ebert, and John Talley) went through a compound library of 1,309 compounds to look for small molecule candidates that might have potential in mediating muscle atrophy resulting from fasting or spinal cord injury. Life events such as these are major factors leading to muscle atrophy.

Left to right are CM Adams, JJ Talley, and SM Ebert who are co-authors of the paper explaining how they discovered tomatidine and ursolic acid as small molecules that would mediate age-related skeletal muscle weakness. They are now 3 of the 4 key people in a new company called Emmyon, a "biotechnology company that discovers and develops natural and pharmaceutical compounds that improve muscle mass, strength, exercise capacity, and metabolism." (image from Emmyon site)

Tomatidine is a naturally occurring compound found in green tomatoes and green apples. Up to 0.5 g of tomatidine can occur per kilogram of fresh green tomato. The compound itself is a steroid as well as an alkaloid.

In this colored image of tomatidine, chiral centers are blue and the steroid part is red. The alkaloid part is on the far right and is classified based on the piperidine carbon and nitrogen skeleton.

Zebra tomatoes are naturally green when ripe and are a good source of tomatidine. 

Tomatidine is a product of hydrolysis from tomatine, a larger molecule that also includes some sugars. This larger compound is thought to play a protective role in tomato plants against fungi, bacteria, viruses, and insects.

Tomatine has been studied for its potential role against fungi, bacteria, viruses, and insects. Can you see which bond breaks in its hydrolysis to get tomatidine?

(image by Edgar181 (Own work) [Public domain], via Wikimedia Commons)

Another compound that the Iowa research team studied for its potential to reduce muscle atrophy is ursolic acid, a compound containing 5 hydrocarbon rings and is known as a triterpenoid. As a triterpenoid, this molecule is made from 6 isoprene units.

 

Ursolic acid, chiral carbons are blue

In a plant, biochemical pathways take 6 isoprene molecules and turn them into a pentacyclic ursolic acid compound.  

(image from http://www.mdpi.com/2072-6651/2/10/2428/htm)

  

 

The peels of Fuji and Granny Smith apples are common sources of ursolic acid.

 (Images by Taken by fir0002 | flagstaffotos.com.auCanon 20D + Sigma 150mm f/2.8 - Own work; by Takeaway - Own work. Licensed under CC BY-SA 4.0)

So what did C. M. Adams and his team discover when adult (6 month) and senior-age (22 month old) mice ingested tomatidine (0.05%) or ursolic acid (0.27%) in their diet? Both had similar effects in that the mice gained skeletal muscle weight by 9-10%, increased the size of type IIb or fast-twitch muscle fibers in the quadriceps, and improved forelimb grip strength by 10-12%. 

The researchers in another paper suggest that these observations may may due to the inhibitory effect of tomatidine and ursolic acid on ATF4, a transcription factor known to activate several cell stress responses and may be responsible for muscle atrophy. More research is being done.

 

In this fake commercial for Nolan's Cheddar, John Nolan (the animatronics wiz of Where the Wild  Things Are) created a workout for this rat empowered after eating some of the cheese. There is no known publication on the effect of cheese on muscle strength. The video clip is for inspiration.  (image from https://vimeo.com/12106387).

For More Information:

*Identification and Small Molecule Inhibition of an Activating Transcription Factor 4 (ATF4)-dependent Pathway to Age-related Skeletal Muscle Weakness and Atrophy; SM Ebert, MC Dyle, SA Bullard, JM Dierdorff, DJ Murry, DK Fox, KS Bongers, VA Lira, DK Meyerholz, JJ Talley, and CM Adams; Journal of Biological Chemistry; vol. 290, no. 42, pp 25497-25511.

*Systems-based Discovery of Tomatidine as a Natural Small Molecule Inhibitor of Skeletal Muscle Atrophy; MC Dyle, SM Ebert, DP Cook, SD Kunkel, DK Fox,
KS Bongers, SA Bullard, JM Dierdorff, and CM Adams; Journal of Biological Chemistry; vol. 289, no. 21, pp 14913-14924.

The Yin Yang of Venoms

In warmer parts of our planet, a snake bite can be traumatic and even fatal without available or cost-effective medical treatment. According to a recent article in Reuters, ~52,000 people have died annually from snake bites in India and Bangladesh, and another ~80,000 people havebeen conservatively estimated in TheAmericas and the Carribean. The highest rate documented is in sub- Saharan Africa where ~100,000 people have died. This statistic focuses on snakes alone and does not includes the insects, frogs, scorpions, lizards, and other venomous creatures people have encountered.

According to the Global Snakebite Initiative, ~2.7 million people in India have been bitten. The lack of educational resources and control programs among poor communities continue to bespeak the need to address this as a global health issue.  

(Image of an Indian cobra from The Global Snakebite Initiative)

Some of the most venomous creatures reside on land and in water:

(Images from https://sciencebasedlife.wordpress.com/2011/04/12/the-most-poisonousvenomous-animals-in-the-world/)

(Images from http://listverse.com/2007/12/16/top-10-animals-you-didnt-know-were-venomous/)

Despite the high incidence of these debilitating and often deadly encounters, there are vastly inadequate or unavailable medical resources. Besides the difficulty of obtaining venom directly from a snake, companies like Sanofi Pasteur which produces the most effective antivenom in Africa typically injects it into sheep and horses. After allowing time for the animals to develop antibodies, researchers extract enough blood and filter out antibodies to the venom and eventually create the antivenoms.

 How To Make Antivenom by Popular Mechanics

 

The time and process involved lend to the high cost of treatment – up to $500, an amount most African citizens cannot afford. Because the noted antivenom Fav-Afrique is not profitable for the company, Sanofi Pasteur discontinued manufacturing it last year, and the limited supply of vials is expected to run out some time in June 2016.

While the yin or dark side of venoms highlights may represent their deadliness, it also points to the chemical challenges vaccine manufacturers face in producing these much needed antidotes. Some man-made or synthesized compounds do not last long enough in the body to counteract the venom. In other cases, even venom extracted from the same animal appears differently upon scientific characterization due to the animal’s age, gender, and the environment when it was captured.

  

(image from http://www.ncbi.nlm.nih.gov/pubmed/12955733)

 In the same genus, one can find great variation in venom profiles. These were analyzed by LC/MS (liquid chromatography/mass spectrometry) in the lab of Professor Bryan Fry, aka the Venom Doc, an associate professor at the School of Biological Sciences, University of Queensland.

Then there is the challenge of identifying the molecules or proteins that target specific organs in the victim. These tend to be large (sometimes >65,000 Daltons), compact, and complicated structures tightly held in some cases by disulfide bridges. 

Chlorotoxin is a polypeptide of 36 amino acids with the red alpha helix and blue beta sheet held together by 4 disulfide bridges highlighted in orange. It comes from the death stalker scorpion.  
(image from http://www.mdpi.com/2072-6651/7/4/1079)

The yang side of venoms imparts a different aspect of hope and potential that these compounds may provide medical therapies for debilitating maladies such as diabetes, high blood pressure, chronic pain, and muscular dystrophy. Companies and venom experts collaborate to decipher the complex molecular structures of these peptide molecules and to test their potential for medical application. A few known examples include:

Captopril is used to treat hypertension and congestive heart failure. It comes from the lancehead viper, Bothrops insularis.

 (Top image from https://en.wikipedia.org/wiki/Bothrops_insularis; Left image from https://en.wikipedia.org/wiki/Captopril; Right image from http://www.euvipharm.com/index.php?/en/product/detail/122/captoril)

 

Byetta or exenatide is used in the treatment of diabetes mellitus type 2. It is based on a hormone in the saliva of the gila monster.  

Top left image from http://animals.sandiegozoo.org/animals/gila-monster; top right image from https://commons.wikimedia.org/wiki/File:Byetta_10_mcg.jpg;Bottom image from http://www.polypeptide.com/exenatide-generic-peptides-10.html

Prialt or ziconotide is used to treat chronic pain. 

Ziconotide is very soluble in water. Can you tell why? Look at the number of amine and oxygen-containing functional groups. Also note the S-S bridges that keep this polypeptide together.

 (Top right image from http://www.popsci.com/scitech/article/2005-11/elan-prialt;top left image from http://www.australiangeographic.com.au/news/2014/03/cone-snail-pain-drug-is-non-addictive; bottom image from http://www.mdpi.com/1660-3397/13/8/4967/htm)

Currently, venoms continue to bring hope to those who are personally affected by illnesses with no known treatment. One company, Tonus Therapeutics, was co-founded in 2009 by Jeff Harvey from Buffalo, NY. His grandson J. B. was born with a defective gene leading to Duchenne muscular dystrophy. Without any effective options, Jeff searched online and contacted Frederick Sachs, a professor of physiology and biophysics at SUNY-Buffalo.

Jeff Harvey, co-founder of Tonus Therapeutics

 (image from http://www.buffalo.edu/home/feature_story/good-venom.html)

Why Professor Sachs? He had discovered and had been researching the effect of venoms on mechanosensitive channels. The latter are membrane proteins that respond to mechanical stress and can a significant impact on ion channels in the cell membrane.

 (image from https://www.youtube.com/watch?v=__B5isN07AQ)

Here is a nice video description of how mechanosensitive channels work. Note that alpha helices are part of the secondary structure of a protein and play an active role in controlling the channel's size.

Dr. Sach's research involves a venom peptide known as GsMTx4, and it comes from the Chilean rose tarantula. Dr. Sachs and his research team believe this peptide can close the mechanosensitive ion channel that inhibits the flow of Ca ions which can lead to the breakdown of muscle cells.

Chilean rose tarantula, adult male

(image by Viki, http://creativecommons.org/licenses/by-sa/3.0/, via Wikimedia Commons)

(image from http://www.buffalo.edu/home/feature_story/good-venom.html)

Frederick Sachs, a professor of physiology and biophysics, - See more at: http://www.buffalo.edu/home/feature_story/good-venom.html#sthash.ljyGanMq.dpuf

Frederick Sachs, a professor of physiology and biophysics, - See more at: http://www.buffalo.edu/home/feature_story/good-venom.html#sthash.ljyGanMq.dpuf

What's So Funny About Chemistry...

In a super-serious field like chemistry, I sometimes get inspiration from artists who can inject some humor while still seeming sophisticated. Matthew Diffee is one such artist who is a regular cartoonist for The New Yorker and The Texas Monthly. Besides being a talented individual, he is a down to earth Tex-Yorker-Braugh (now in LA) with a convivial curiosity.

image from http://www.matthewdiffee.com/, photo by Scott Gordon Bleicher

Taking inspiration, I thought to try a hand at this as a break from exam week. Feel free to roll your eyes or groan. Once the illness has passed, we'll return to our normal operations.