How the Amino Acids Got Their Names

It is the waterloo of biochemistry and premedical students everywhere: memorizing the 20 naturally occurring amino acids along with their respective 1- and 3-letter codes. Unlike most classes of biomolecules, this family does not have a systematic naming system, forcing students to come up with their own creative ways of matching structure to name. So how did the amino acids get their names in the first place? Was there either rhyme or reason behind these choices? And why do some of their codes seem completely arbitrary? In his paper “Amino acid names and parlor games,” Murray Saffran, a biochemist at the Medical College of Ohio, discusses the history of these biomolecules.

A few of the amino acids were named with a rational system in mind, based on their chemical groups and resemblance to existing structures. For example, methionine contains a methyl (meth-) group and a sulfur (thio-) group [1]. Proline’s cyclic structure resembles the chemical pyrrole, while phenylalanine contains a benzene ring (also called a phenyl group) [2]. Some amino acids were mistakenly named for incorrect structures, but the name still stuck: believing that it contained an aldehyde group, scientists named a newly discovered amino acid Alanine, only to find out later that it consisted of only a single methyl group [2].

Figure A: the structures of pyrrole (left) and the amino acid proline (right) are very similar [3,4].

Figure B: the structure of amino acid phenylalanine with its phenyl group highlighted [5].

Many of the other amino acid names originate from Greek words that describe either their physical properties or source of isolation. “Arginine” comes from the Greek word for “silver,” alluding to the shiny, metallic appearance of its crystals [2]. Glycine was named for its sweet taste; the prefix “Gly” comes from the Greek word for “sweet” [1,2]. “Serine” is derived from the Latin word for silk (“sericus”), as it was isolated from a protein involved in silk production [1]. Some amino acid names originate from English words, making them even more memorable: asparagine and aspartic acid were isolated from asparagus, while glutamine and glutamic acid come from gluten [2]. Histidine was found in tissues (the study of which is called histology) while cysteine was first observed in urine (the bladder is sometimes called a “cyst”) [1,2]. 

Arginine (structure on right) was named for its metallic, silvery appearance [6,7].

Serine (structure on left) was first isolated from proteins involved in the production of silk [8,9].

Barring a few exceptions to eliminate redundancy, most of the three-letter codes for the amino acids are simply the first three letters of the amino acid’s name. However, the one-letter codes posed more problems. Only amino acids with unique first letters—cysteine, histidine, valine—could be represented without ambiguity; alanine, arginine, aspartic acid and asparagine cannot all be “A” in shorthand [10]. To solve this problem, scientists came up with new codes phonetically. Alanine remains A; arginine sounds like “R”-ginine, so its 1-letter code is R [10]. Aspar-”D”-ic acid is represented with a D [2]. Glutamine becomes “Q”-lutamine (Q), and phenylalanine is “F”-enylalanine (F) [2]. Some amino acids, while not abbreviated phonetically themselves, are named by their “proximity” to other amino acids. For example, because glutamic acid’s side chain has one more carbon than aspartic acid (D), it is abbreviated as E, the next letter in the alphabet [2]. Because leucine is abbreviated as L, lysine is assigned K [2]. Still other choices are even more ambiguous: tryptophan is abbreviated as W simply because its bulky ring structure is reminiscent of the letter itself [10].

At first, it may seem counterintuitive to use such a complex and unstructured naming system; yet knowing these anecdotes may aid students in memorization. As Saffran points out in his paper, it is much easier to remember “the names and characteristics of 20 relatives and friends” than it is a list of 20 random names [2]. By learning the history behind the amino acid names, you may remember a unique detail that can help you recall the one-letter code or structure when it comes to test time.

References

1. Vickery, H. B. and Schmidt, C. L. A. The History of the Discovery of the Amino Acids. Chemical Reviews 1951, 9 (2), 169-318. https://pubs-acs-org.ezproxy.rice.edu/doi/pdf/10.1021/cr60033a001

2. Saffran, M. Amino Acid Names and Parlor Games: From Trivial Names to a One-Letter Code, Amino Acid Names Have Strained Students’ Memories. Is a More Rational Nomenclature Possible? Biochemical Education 1998, 26 (2), 116–118. https://doi.org/10.1016/S0307-4412(97)00167-2.

3. luketoboot. (2012, October 8). Pyrrole [Image]. Retrieved from https://www.flickr.com/photos.

4. Stevens, C. (2013, November 7). Proline [Image]. Retrieved from https://www.flickr.com/photos. 

5. Keith&KatieBond. (2011, September 21). Phenylalanine [Image]. Retrieved from https://www.flickr.com/photos/keithkatiebond.

6. Stewart, P. (2007, July 9). Silver coin of Otacilia [Photograph]. Retrieved from https://www.flickr.com/photos/peterstewart. 

7. Kirchoff, B. (2015, October 6). 118 Arginine 9 STR [Image]. Retrieved from https://www.flickr.com/photos/brucekirchoff.

8. Stevens, C. (2013, November 7). Serine [Image]. Retrieved from https://www.flickr.com/photos.  

9. 1sock. (2013, November 10). Silk [Photograph]. Retrieved from https://www.flickr.com/photos/1sock. 

10. IUPAC-IUB Comm. on Biochemical Nomenclature. A One-Letter Notation for Amino Acid Sequences. Tentative Rules. Biochemistry 1968, 7, (8), 2703-2705. https://pubs-acs-org.ezproxy.rice.edu/doi/pdf/10.1021/bi00848a001

The Future of the War Against Viruses: Lung Signaling Lookouts

During flu season, our bodies become a battlefield, with our internal weaponry waging war against perpetually adapting armies of the influenza virus. Like any war, we must be cognizant of our arsenal and our lookouts. The incredible way our body builds up its resistance to disease hinges on the successful functioning of our personal, curated immune systems. But despite these remarkable innate lines of defense, we still get sick. So, how can we help our body fight off its enemies? 

Scientists at Emory University School of Medicine believe that they have found a way. Dr. Jacob Kohleimer and his team have identified two signaling molecules, CXCR6 and CXCL16, that may hold the key to improving our immunity [1]. We know that CD8 T cells recognize epitopes, which are small segments of viral protein, and signal to the body that there is a viral infection. Through the release of cytokines, CD8 T cells can recruit other parts of the immune system and help to kill those infected cells [2]. However, T cells cannot survive long in the lungs due to their low nutrient state, which compromises lung immunity [3]. Through experimentation with mice models, the researchers were able to find populations of CD8 T cells cells in the interstitium, which is the space between the epithelial cells in the lungs and blood vessels. These epithelial cells produce CXCL16, while CXR6 can be found directly on T cells [1]. In reaction to an infection, CXCR6 acts as a homing beacon, enabling the efficient and reliable recruitment of T cells to the lungs and into the airways.

The discovery of these two signaling molecules may revolutionize how we make our vaccines. Currently, vaccines do not account for the directing of CD8 T cells to the airways; they mainly work by introducing pathogenic molecules into the body, teaching the immune system how to react if it were actually attacked [3]. But with the enhancement of these two signaling proteins, vaccines could increase the transport to and longevity of T cells in the lungs, thus decreasing or even eliminating symptoms altogether. As a result, these lookout proteins might just be the soldiers we need to win the war against foreign invaders.

References 

1. Eastman, Q. Immunologists identify T cell homing beacons for lungs.  https://news.emory.edu/stories/2019/09/jem_kohlmeier_tcells_lungs/index.html.

2. Harper, R. T cell homing beacons for lungs identified by researchers. https://www.drugtargetreview.com/news/50299/t-cell-homing-beacons-for-lungs-identified-by-researchers/

3. Emory Health Sciences. Immunologists identify T cell homing beacons for lungs. https://eurekalert.org/pub_releases/2019-09/ehs-iit092719.php.

Boozy Bacteria: A Microorganism Microbrewery

If a patient were diagnosed with liver disease, most people would think of hepatitis, a viral infection of the liver, or cirrhosis, chronic scarring of the liver often associated with heavy alcohol use [1]. However, according to the Mayo Clinic, the most common form of chronic liver disease in the United States is actually non-alcoholic fatty liver disease (NAFLD), which affects between 80 and 100 million people nationwide [2]. Despite the condition affecting around 35% of the US population, its causes remain unknown [3]. 

Now, due to a recent study published in Cell Metabolism, we’re closer to solving this mystery. Jing Yuan et al. of Capital Medical University observed an individual with NAFLD and auto-brewery syndrome, a condition in which the body produces alcohol from digested sugars and starches [4]. This syndrome ultimately leads to intoxication without consumption of any alcohol. While many college students would point to this as a key medical discovery for totally-not-parties, the individual presented with an ultra-high blood alcohol content level (BAC) of 400 milligrams per deciliter, or five times the legal limit of .08% [5]. 

Furthermore, Yuan et al. observed a high-alcohol producing strain of the typical gut bacterium Klebsiella pneumoniae in this patient, which they called HiAlc Kpn [4]. The high level of alcohol produced by HiAlc Kpn in this patient and the patient’s symptoms led the researchers to suspect a link between HiAlc Kpn and NAFLD. To test the veracity of the link, they conducted an experiment which compared mice who were exposed to HiAlc Kpn and mice who were fed ethanol, a common alcohol [4]. The mice who were exposed to HiAlc Kpn displayed signs of steatosis, or fat buildup in the liver, a common precursor to non-alcoholic fatty liver disease. The HiAlc Kpn-exposed group of mice also demonstrated elevated levels of CD4 T-cells, macrophages, and neutrophils, all of which suggest that the immune system was activated in response to the fat buildup. This immune response may further damage the liver by causing tissue damage, chronic disease, and cancer [6]. 

However, although these results indicate a strong correlation between HiAlc Kpn and NAFLD, researchers have yet to identify a causal relationship. Since HiAlc Kpn was found in only 61% of a Chinese cohort of patients with NAFLD, it cannot be the sole factor behind NAFLD [4]. That said, this discovery offers insight into auto-brewery syndrome and potential causes for NAFLD. Non-communicable diseases (NCDs) like cancer and NAFLD already account for 71% of annual deaths worldwide [7]. As the burden of NCDs grows, research yielding even the smallest clue becomes invaluable.

References

1. (2018, November 30) Alcoholic hepatitis. Mayo Clinic. Mayo Foundation for Medical Education and Research.

2. Spengler, E. K., and Loomba, R. (2015, September) Recommendations for Diagnosis, Referral for Liver Biopsy, and Treatment of Nonalcoholic Fatty Liver Disease and Nonalcoholic Steatohepatitis. Mayo Clinic proceedings. U.S. National Library of Medicine.

3. (2019, August 22) Nonalcoholic fatty liver disease. Mayo Clinic. Mayo Foundation for Medical Education and Research.

4. Yuan, J. (2019) Fatty Liver Disease Caused by High-Alcohol Producing Klebsiella pneumoniae. Cell Metabolism 30, 675–688.

5. Olena, A. (2019, September 19) Gut Microbe Linked to Nonalcoholic Fatty Liver Disease. The Scientist Magazine®.

6. Kubes, P., and Jenne, C. (2018) Immune Responses in the Liver. Annual Review of Immunology 36, 247–277.

7. (2018, June 1) Non communicable diseases. World Health Organization. World Health Organization.

The Intelligence of Plants

Who is capable of learning? It seems to be humanity’s specialty, but researchers have long been interested in the ability of primates and other mammals to learn and memorize simple tasks and pieces of information. However, scientists have only recently begun to genuinely delve into the concept of plant learning.

What is learning, anyway? As a basic definition, it is a process for acquiring memories as a result of experience and changing resultant behavior to better adapt to whatever circumstances to which the memories apply. Plants may not have the cognitive abilities of animals, but research has strongly indicated that they may be able to habituate their behavior to a new stimulus by identifying common situational similarities. One study published in 2016 used a simple Y-shaped maze, a light source, and the neutral cue of a fan to examine the influence of external cues on the direction of plant growth. The plants changed their growth based on the fan’s repeated indication of which direction the light source would come from rather than their innate phototropism [1]. Their behavior supported the idea that not only are plants capable of associative learning, but also that learning is necessitated by metabolic demands.

Perhaps the most direct example of associated learning behavior comes from a particularly charismatic organism, Mimosa pudica, the “sensitive plant”. M. pudica exhibits a defensive behavior in which its compound leaves fold rapidly inward upon being disturbed or touched in general. This response requires movement and thus energy from the plant, but is useful if the plant is being threatened. Also in 2016, researchers conducted an experiment on M. pudica’s ability to remember and alter its folding behavior under varying light conditions. Several of the plants were lifted and dropped onto a flat surface, causing them to reflexively fold, and then the drop was repeated several times for each plant. They found that as the process was repeated, the plants stopped folding their leaves each time. These results reveal the presence of plant learning: the plants likely habituated to the drop after realizing that the drop was harmless and that their defensive mechanism was energetically costly [2]. The effect was even more noticeable when light sources for each plant’s habitat was changed and energy was scarcer [3]. 

Plants clearly do not have brains, but we know that they have an intricate cell network of calcium (Ca2+)-signaling, which mimics animal processes and various biological functions in many organisms. Another hypothesis posits that electrical signaling via ion channels in plant cells could work similarly to neural networks in animals [2]. Both theories will need further research to be substantiated, but the concept of plant memory, learning, and intelligence remains a new and exciting field – one that may even encourage us to reconsider the way we think about learning in general.

References

1. Gagliano, M.; Vyazovski, V. V.; Borbely, A. A.; Grimonprez, M.; Depczynski, M. Learning by Association in Plants. Nature. 2016, 6, 38427.

2. Gagliano, M.; Renton, M.; Depczynski, M.; Mancuso, S. Experience teaches plants to learn faster and forget slower in environments where it matters. Oecologia. 2014, 175, 63-72.

3. The Paris Review. The Intelligence of Plants. https://www.theparisreview.org/blog/2019/09/26/the-intelligence-of-plants/?utm_source=pocket-newtab. (Accessed October 2, 2019).

The Camera: What Really Is It?

Some feats of technology are so magical that we users forget to even stop and think about how they work. Photography is one of these feats--especially with the rise of modern smartphone technology, manufacturers do their best to blend the camera as merely a small component of phones. Taking a step back and learning about how cameras work is not only exciting, but may also help you take better photos (even with a smartphone)!

To explore how this device works, let's think of an analogy. Imagine a tap that flows water into a bucket. When you press the button to take a photo, you are turning on the tap for a short amount of time, letting in light into the camera’s sensor (the bucket). Once the light hits the sensor, electronics convert it to electric signals by breaking it up into pixels and storing the information. The amount of light that hits the sensor--or the amount of water in our bucket-- determines what we perceive to be the brightness of the image.

There are three main variables that must be balanced together in order to form a perfectly exposed image. The first is Shutter Speed, which describes the amount of time that the shutter of the camera remains open. The longer the tap is on, the more water that falls into the bucket, making our image brighter. If your image is a little dark, consider bumping up the shutter speed to let more light into the sensor. The next is Aperture, which describes the size of the opening through which light is let in. As you might imagine, the wider the aperture, the more light is let in and the brighter the resulting image. The final variable, ISO,refers to the sensitivity of the sensor to the light. Going back to our analogy, ISO reflects the water pressure from the tap--the greater the pressure, the faster the bucket fills, but the greater the chance of water splashing around. This splashing leads to a granier looking image, so be careful when increasing your ISO.

Exposing is the art of balancing these three elements to capture a photo. If these three elements are so crucial, you may wonder why you’ve never heard of them. Modern smartphone camera technology is able to use algorithms developed to balance these elements and properly expose images. However, this automated exposure technology also takes away artistic control from the user.

Shutter Speed, Aperture, and ISO each have their unique side effects to the resulting photo. Faster shutter speeds are able to capture dynamic shots, while drawn out exposures can be used to produce light trails. Wide apertures shorten the focal plane to create greater subject background isolation, giving photos that classic “portrait look”. Finally, bumping up the ISO can make the imaging grainier. In order to fully take advantage of these effects, you will have to manually expose your shot. Thankfully, phones nowadays let you control these three elements via the default camera app or third-party apps, putting the tools you need to take great photos at your very fingertips!

References:

Unsplash. Veins of Gold | HD photo by Simon Zhu (@smnzhu) on Unsplash.     https://unsplash.com/photos/dlYgicF7u08 (accessed Apr 6, 2019).