Reflections On “Breaking Bad”

Sep 18, 2012.  Updated August 10, 2013 and August 15, 2014 and July 17, 2018.

Advertisements

Chirality Beyond Breaking Bad

Thanks to a couple of Breaking Bad episodes from seasons 1 and 4, it’s possible that more people know about enantiomers than ever before. If you’re not a fan of the show or if you have forgotten a bit of organic chemistry, enantiomers are molecules that are non-superimposable mirror images of one another. As Walter mentions before losing his chemistry-teaching job, enantiomers are like a left and right hand. Try to wear a left glove on your right hand, and it does not fit. This is relevant to chemistry because although enantiomers share the same properties in a non-chiral environment, only one molecular version will bind to something like a neural or nasal receptor. Like gloves, these three dimensional structures discriminate against things which have the same components but are on the wrong side.

In the chilling episode, The Box Cutter, Walter asks, “And if our reduction is not stereospecific, then how can our product(metamphetamine) be enantiomerically pure?”.

This question pertained to his special cooking procedure, but applied generally, it’s also an intriguing one from a biochemical perspective, which we’ll explore later. Methamphetamine has a chiral center, meaning that the molecule contains a carbon atom attached to four different atoms or groups at about 104o from each other. In addition, the molecule has only one chiral center; if it had a pair of centers along with an internal plane of symmetry, it would not be an enantiomer. The dextrorotatory(+) form of metamphetamine shown on the right affects the central nervous system by releasing dopamine, serotonin and norepinephrine, but its levorotatory(-) enantiomer merely acts as a rarely diagnosed nasal decongestant. (Experimentally derived, the (+) designation refers to the ability of such a sample to rotate a plane of polarized light clockwise. The (-)compound rotates the plane in the opposite direction.)

In the second episode Walter told his students about thalidomide. What’s often pointed out when using this drug as an example of an optically active molecule is that only one version is teratogenic. Less known, however, is the fact that even enantiomerically pure thalidomide partially converts into the dangerous form in a living system, so that it is impossible to give just one form to a patient. Of course, this is not the case with metamphetamine or with many other enantiomers.

In nature, one or more species will almost always biosynthesize a single enantiomerically pure compound while the mirror image can be produced by a different organism. For example, the green-head ant, oriental fruit moth and the ochratoxin A-secreting mold Aspergillus ochraceus found in salted foods, grains and soil all produce the beneficial compound (-)-mellein. The latter has both antibacterial properties and the ability to inhibit hepatitis C. But (+)-mellein from the marine fungus Helicascus kanaloanus has no such properties. Similarly A. ochraceus also produces the anti-cancer alkaloid (+)-stephacidin A, but the (-)-A stephacidin from the Arctic mold  A. versicolor lacks such properties. In the odd case where both versions of a chiral molecule are produced by the same species, one predominates. Caraway seeds produce a 49-1 ratio of  (+)-limonene (smells like oranges and has insecticidal properties) to (-)-limonene(smells like lemon and turpentine).

How can the cell’s biochemistry exclusively favor one molecule over the other when they are almost identical? Three different enantiomers of a class of natural products known as monoterpenes (responsible for many flavors and aromas of herbs, spices, citrus and conifers) are derived from a common precursor molecule. At some point, glove-like enzymes will produce chiral intermediates, which then go on to become an enantiomer like (+)-limonene. Investigators labeled the common precursor geranyl diphosphate with tritium and then treated it with an enzyme extracted from Valencia oranges. Only labeled (+)-limonene was obtained. But if the same experiment  was repeated with an enzyme extract from peppermint, the other enantiomer was produced. The caraway enzyme which did not yield an enantiomerically pure limonene might represent some evolutionary intermediate. Or there may be some unknown mechanism that produces the minor enantiomer.

A special class of enantiomeric alkaloids with antitumour and insecticidal properties are produced by Aspergillus and Penicillium species. Key Diels-Alder enzymes involved in creating these enantiomers turn out to have similar amino acid sequences, suggesting that a minor change in the enzyme’s active site is responsible for controlling chirality. (A Diels-Alder reaction, fundamental in both human and non-human laboratories, creates a cyclic compound from linking a reactant with a pair of conjugated double bonded carbons (diene) to a dienophile, one with an affinity for the pair of reaction centers.)

The authors of a 2012 review paper* point out that if one chiral-dominant enzyme does not get altered into the other through a single mutation, then the in-between products have to be not only functional but at least benign to the organism. As the pathways and genetics of more natural products become elucidated, there will be more insight gained into molecular evolution. Unfortunately this area of fundamental research has experienced severe budgetary cutbacks in the last few years.

Sources:

*Enantiomeric Natural Products: Occurrence and Biogenesis Jennifer M. Finefield , Prof. Dr. David H. Sherman , Prof. Dr. Martin Kreitman , Prof. Dr. Robert M. Williams

Fun With Elemental Symbols

Since all matter including people consists of elements, it’s nice to see proper names entirely composed of elemental symbols, like , or if you recall the actress who played the part of a sultry James Bond villain,, or if we stick to chemistry .  In the English language alone, there are also thousands of improper nouns with such properties (27192, to be exact), and of course someone wrote a program to generate an exhaustive list. Probably one of the most interesting ones is CHOPS, as in pork chops, because the elements are all actually found in meat and include five of the six most common elements in living matter.

Unfortunately, it’s a hopeless case for any chemical compound’s name ending in ide, but luckily there is CoPPEr CArBONaTe, a substance formerly believed to make up Lady Liberty’s veneer. It’s ironic that more names, relative to inorganic nomenclature, exist for the elements themselves (IrON, CArBON, TiN, NeON, KrYPtON, SiLiCoN, CoPPEr, ArSeNIC, SiLvEr and four others). Silver’s inclusion depends on the synthetic superheavy element  Lv, or livermorium, a name only officially adopted last year after the element was synthesized in 2000 from uniting calcium and curium nuclei. Livermorium is not honoring dead liver but named after the Lawrence Livermore National Laboratory.

In organic chemistry, it should be easy to find names fitting the criteria, given the field’s gargantuan vocabulary. Although there are none among the basic heterocyclics; only AlKYNe among the basic functional groups and the lone VAlINe among the 20 amino acids, there is a sweet spot among alkanes: PrOPaNe, BUTaNe, NoNaNe and gasoline’s HePTaNe and OCTaNe. And turning to astronomy, order in the universe is further restored due to the existence of the MoON, SUN, SAtURn, NePtUNe, URaNUS, at least one asteroid, CeReS, at least a couple of constellations, BOOTeS and CaPrICORnUS, and some of the brightest stars, SIrIUS, AlTaIr and SPICa.

Spica’s name contains two of the alpha ladder elements (Ca and S) produced during helium fusion. The remaining pair, phosphorus and iodine, are formed mostly in type II supernovae, and being a blue giant with 10 solar masses, Spica is a candidate for such a fate.

* This article was coauthored and edited by PINa TeOLi.

A few related riddles:

1. The series Breaking Bad would use a single elemental symbol for each name in its credits. fraserWho was the only regular whose entire real or fictional name can be written with symbols?

2. Which of the elemental symbols in CORnFLaKEs are actual elements found in cereal?

3. Are there any metallic elements among the symbols of IONIC?

4. Which vegetable can be spelled with elemental symbols and also contains every element within its tissues?

Answers:

1. LaURa FrAsEr who played the callous Lydia Rodarte-Quayle in 12 episodes. Notice the poison, As , in her name, but she was killed by ricin, which because of the “r”, cannot be entirely spelled out with symbols  

2. carbon, oxygen and potassium(K).

3. No, but how IrONIC, that the word “ironic” has both metals and nonmetals’ symbols!

4. SPINaCH.  Although not high in the sulfur-containing amino acids methionine and cysteine, spinach does contain some of those compounds along with sulfur containing enzymes and coenzymes.   Phosphorus is in ATP, DNA and other compounds. Spinach is one of the vegetables that’s richest in iodine; it has a little bit of Na: 24 mg of sodium per 30 gram serving; carbon and hydrogen are all over the place in its oils, carbohydrates, vitamins and protein.

And finally, BeNiCe, even if it means bringing together members of different families!

BeNiCe

WordPress.com.

Up ↑