The Universe is Biased For a Specific Molecular Shape
Image credits belong to: geralt | Pixabay
"Looking back on the things I've done.
I was trying to be someone.
I played my part, kept you in the dark.
Now let me show you the shape of my heart."
Do you recognize those Backstreet Boys lyrics from the year 2000? I kept thinking about these lyrics as I wrote about the importance of shape in molecules. Molecules must have a particular shape and orientation to enable the continuation of life. Indeed, if the Backstreet Boys do not have the correct molecular shapes, they will not have a functioning heart to show! The same applies to you and me.
When the Parts are Different from the Whole
19th Century chemists believed that a chemical compound's properties were only alterable if the elements were different. Friedrich Wohler's synthesis of silver cyanide, which shared identical elements but different properties with silver fulminate, dethroned this dogma in 1828. Not long after that, urea and ammonium cyanide were found to be chemically identical but differ in properties. Jons Jakob Berzelius would be responsible for this realization of isomerism (Michael and Gloria Gerald, The Biology Book, pg. 182) [1].
Isomerism is a state in which molecules' atoms are identical in number, type, and formula but have different chemical and physical properties. The word isomer is rooted in Greek, meaning "equal parts." How can chemical compounds have the same parts but a different whole? This is analogous to two bracelets that each have five red and five green beads but vary in their order or combination of colors [2].
In 1848, Louis Pasteur used optical isomers to rotate polarized light (light waves vibrating on a single plane) that passed through a white crystalline organic solution of tartaric acid (used in food, medicines, photography, wine-making, salts, and esters). He discovered light rotating opposite the acid crystals rotating the polarized light in the laboratory. Polarized light moved in the levorotatory (-) or counterclockwise direction while light moved in the dextrorotatory (+) or clockwise direction (Michael and Gloria Gerald, The Biology Book, pg. 182) [1].
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Chirality is the Important Part
When discussing isomers, the subject of chirality is not too far behind. Chirality is about orientation. Meanwhile, isomerism is about uniform molecular formulas and distinct spatial arrangements of bonded atoms [3]. Most biological molecules are chiral, meaning that your molecules are 3-dimensional with mirror images that are non-overlapping and asymmetrical. We get the word chiral from the Greek word 'cheir,' meaning 'hand' [4]. Chirality is imperative to the proper functioning of your amino acids and sugars that are the construction units of your proteins and nucleic acids. Your DNA's helical character (twisting staircase) is also due to chirality. Most of your amino acids are levorotatory, and your sugars are dextrorotatory, fitting you like your right glove belongs on your right hand, and your left glove belongs on your left hand [5]. You are a chiral person on the DNA and protein level.
Chirality has been observed in ciliates (unicellular microorganisms with hair-like structures), metazoans (multicellular eukaryotic organisms of the Animalia kingdom), Drosophila (small fruit flies), and invertebrates such as snails [6]. Ciliates are microorganisms located in nearly every body of water [7]. Chirality is a characteristic we share with them, which is evidenced by our molecules' mirror-images and our motor skills being dominant in one hand over the other (ambidexterity is rare).
Artificial sweeteners such as Tagatose and Natrulose are right-handed because our bodies can only metabolize sugars' right-handedness. Our bodies could not accept these sugars if they were manufactured with the opposite orientation [5].
The chiral compounds that mirror each other are also called enantiomers. Enantiomers all have the same solubility, density, melting point, and boiling point but have different optical properties. Enantiomers that are levorotatory are given a (-) angle, while enantiomers that are dextrorotatory are given a (+) angle. Enantiomers were involved with Pasteur's isomers rotating plane-polarized light [8].
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Which Part Might be Alien?
Despite the abundance of levorotatory amino acids and the rarity of dextrorotatory amino acids in living organisms, a 2016 article from the U.S. National Library of Medicine reported that dextrorotatory amino acids could be found working with an important neurotransmitter receptor in the mammalian brain. Despite the rarity of homochirality's involvement with function, it has been theorized that homochirality has an extraterrestrial origin based on the enantiomeric excesses of left-rotating amino acids that were identified in the meteorite that fell in Australia in 1969 [6].
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Where is Your Center?
Your molecules are chiralized by an atom (usually a carbon atom) acting as a center linking four different groups that make it non-superimposable or non-overlapping. Silicon, nitrogen, and phosphorus can also act as chiral centers, though carbon is the most common chiral center. A mixture of these two mirror-images, called racemic mixtures, is said to exist in equal proportions, rotating polarized light in both directions equally to negate the net rotation [9].
Now, what does that mean for the human body? The two enantiomers of a molecule can determine taste and smell due to their orientation or (+) and (-) forms. For instance, oranges and lemons have different scents because of the (+) and (-) forms of limonene (colorless liquid hydrocarbon) that are present [10].
Image credits belong to: analogicus | Pixabay
The Human Body's Bias and a Drug Story?
The human body is biased toward particular chiral compounds, rendering some effective and others ineffective. The story of Thalidomide and its enantiomeric (chiral) character is relevant. Once upon a time, Thalidomide was sold in stores and used to reduce nausea in people with cancer and reduce morning sickness for pregnant women. Thalidomide was the cause of congenital disabilities in 10,000 infants in the early 1960s. We pulled Thalidomide from the market. After a lack of testing on the isomers, evaluators identified the amine position in the molecule and the S isomer to be the culprits. The catastrophe caused countries to strengthen their preliminary drug evaluations before Thalidomide could regain a better reputation for treating cancer, leprosy, rheumatoid arthritis, and other autoimmune diseases. Its prevention of angiogenesis (blood vessel growth) has seemingly prevented tumor growth; however, the prevention of angiogenesis could have been the cause of infant deformities. All of this drives home the point that normal molecular shapes are imperative to live (Gerald Bergtrom, Basic Cell and Molecular Biology, University of Wisconsin, 2018 pgs. 52-53) [11].
How Did Chirality Get Here?
A May 2020 American Astronomical Society article reports that two scientists, Noemie Globus (New York University and Flatiron Institute) and Roger Blandford (Stanford University and KIPAC) used laboratory-based, lightspeed, high-energy protons and atomic nuclei on bacteria to test the idea that the geometry of life's building blocks was influenced by cosmic rays kindling many rounds of mutagenesis and giving DNA its right-handedness billions of years ago. These are laboratory simulations of cosmic ray particles already known to hurtle into Earth's atmosphere and generate a deluge of secondary particles that contact the Earth's surface. Such a long mutagenesis series would allow abiotic stuff to adapt to their environment and increase their complex survival mechanisms [12] [13].
Pions (subatomic particles with a mass 270 times that of an electron) are the secondary particles quickly decomposing due to the weak force that has mirror symmetry. These pions generate electrons and muons (unstable subatomic particles with a mass 200 times greater than an electron) that share the same chirality as they bounce around and slam into the ground [14].
According to what has been reported about Blandford's interpretation, the mutations were caused by the cosmic ray particles loosening an electron from the helixes that are characteristic of the DNA and RNA that we have in our bodies. For millions of years, millions of cosmic rays were striking free electrons in life-promoting strands that eventually altered the DNA strand letters in such a way that helped our ancestors to outrival the mirror-reversed strands that were antithetical to life [14].
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Admitting that We Do Not Know How It Happened
A January 2020 research article from Plos Computational Biology tells me that scientists are still mystified as to how homochirality in biopolymers (molecules with many repeating subunits in living organisms) could spring from a chemical condition of non-life. Why did the non-life condition favor one type of chirality for monomers, nucleotides, and amino acids, which are all basic units of our makeup? Decades of research have gone by with no answers and no unanimity because of empirical difficulties. How can we know the origins of life if we cannot even be unanimous on the definition of life? Despite the doubts raised by the 2020 research article, it still reports that scientists used computer models to simulate a breakaway from symmetric-chirality in monomers to pave the way for biopolymers to be present at the spark of life [15].
It is stated that DNA and RNA molecules must have a mechanical guide or pattern by which they replicate or make identical copies. Homochirality is integral to that guide or pattern to make everything fold properly. The racemic mixture of two chiral types in the prebiotic chemical world was an obstacle to homochirality but could have been surmounted in an RNA-world where monomers mixing two chiral types could develop polymers that prefer the homochirality. The computer simulation showed that RNA polymerization (the process of forming a large chainlike network) had a preference for homochiral subunits, allowing for a situation called autocatalysis where a product of a chemical reaction will be a cause unto its own reproduction. Autocatalysis made way for the universe's change from racemic preferences to homochirality preferences. In an RNA world, where RNA-enzymes increase the rate of chemical reactions, they also influence the change in chirality-preference by introducing longer homochiral RNA chains that spark more complex RNA-enzymes [15].
The research article's professional doubt also gives me doubt about our understanding of life's origins. I can hear claims about miracles and god-of-the-gaps fallacies whispering in my ear and wanting to become the fallback conclusion. We do not know how it all happened, so it is necessary to assume it was a deity or supernatural event. Right?
A 2016 Evolution News article hopes to be nipping at our heels:
"As it stands, no experimental or theoretical model explains the origin of life's homochirality by natural processes. Some experimenters have produced a slight enantiomeric excess of one hand or the other, but usually with non-biological chemicals, and nothing approaching the purity of life's chiral molecules. Proteins and nucleic acids cannot work with mixed handedness. A single wrong-handed building block is enough to destroy DNA, RNA, and proteins. As we saw last year, checkpoints ensure that life's building blocks remain homochiral" [16].
Leaning on materialists' bewilderment, the author analogizes that the chances of producing long, homochiral polymeric sequences from racemic stuff is equivalent to doing a lot of coin-flipping and always resulting in heads. But I still remember that the clever and tantalizing analogy does not merit a pretense of knowledge after admitting that we do not know how life arose.
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Works cited:
[2] isomerism | Definition, Types, & Examples | Britannica
[4] Chirality - an overview | ScienceDirect Topics
[5] Welcome to The Rowland Institute at Harvard
[6] Cell chirality: its origin and roles in left–right asymmetric development (nih.gov)
[8] Optical Activity - Specific Rotation & Enantiomeric Excess - Stereochemistry - YouTube
[9] Stereochemistry / Isomerism - CHEM 221 - Library Guides at Salisbury University
[10] Chirality in Biochemistry (azolifesciences.com)
[11] BASIC CELL AND MOLECULAR BIOLOGY 3e: WHAT WE KNOW AND HOW WE FOUND OUT (uwm.edu)
[12] Cosmic Rays as the Source of Life’s Handedness (aasnova.org)
[13] The Chiral Puzzle of Life - IOPscience
[14] Cosmic Rays May Explain Life’s Bias for Right-Handed DNA | Quanta Magazine
[15] The origin of biological homochirality along with the origin of life (plos.org)