A different perspective on the positions and orientations of R-handed DNA and L-handed amino acids in cells of the right and left body parts
The right and left body halves of the cat are different. In all cats, the right and left body halves are still different, but not as distinct as the cat in the picture. In all animals and humans, the right and left body parts are not completely symmetrical and are different. It should be difficult to explain these differences by the genes being dominant or recessive. This difference may be due to the location and position of the same genes in the right and left halves of the body, which are reverse mirror images of each other.
The handed structure of molecules or objects cannot be changed without any external intervention, but their directional positions can be changed. Right gloves or hands are always R-Handed, when rotated 180 degrees, their directional positions can be changeable in the opposite direction.
R-handed DNA and L-handed amino acids may be in reversed mirror image positions of each other in the cells of the right-left body parts. Reversed mirror-image localization of the R-handed DNA and the L-handed amino acids on the right and left parts of the body cells may ensure of building R/L body homochiral asymmetric structure. This model may also explain why left-handed amino acids are always used in the protein synthesis of living structures.
In 1848, French chemist Louis Pasteur discovered that some molecules essential for life exist in mirror image forms, much like our L and R- hands. Today, we know biology chooses just one of these “chiral” forms: DNA, RNA, and their building blocks are all right-handed, whereas amino acids and proteins are all left-handed. (1)
The R -hand or R-glove always have R-handed and its structure and handedness cannot be changeable, but directional positions can be changed.
When explaining chirality, the chiral structure of our R/L hands is one of the most frequently used examples. In the mirror, we see our R- hand as if it were our L- hand, but what we see is our R- hand. The direction of the R- hand in the mirror has changed, but R-handedness cannot change. The similarity between molecular chirality and multicellular chirality is the best demonstrated by our R/L hands.
If we extend our hands forward with palms facing down, the R-hand thumb points to the L-direction, and the L- thumb points to the R-direction. When the palms are open upwards, the R-hand thumb points to the R- direction, and the L- thumb points to the L-direction. (Figure 1) R/L handedness does not change but the directions change oppositely. The palmar side of the R-hand may be likened to the localization where base pairs are attached to the backbone of DNA formed by sugar-phosphate molecules. (Figure 2)
Here, the mechanism of opposite directional asymmetric homochiral structuring in living things has been tried to explain.
Figure3. All the hands are palmar side of the R- hand in this figure. The two hands at the top of the figure points mirror image in reversed position of DNA in R/L body parts. The leading strand is blue, and the lagging strand is red. R- blue hand thumb and L-red hand thumb point to strands directions in the L/R body parts and they show directional changing of the strands.
When the R- DNA in the cells on the R-half of the body parts is rotated 180 degrees down to up in vertical position, the R-handedness cannot change but the directionality can be changed in opposite direction. DNA strands are located reverse mirror-image positions of each other in DNA structure. Direction of the DNA strands has also changed in the opposite direction in the R/L body parts. If the leading strand may be positioned in the 5'-3' direction in the R- body half, it is in the 3'-5'opposite direction in the L- body half. A single strand is copied in protein synthesis. When the mRNA is transcribed from the leading strand, it must be oriented oppositely positioned in the R/L body halves.
The mirror image reversed localization of DNA in the R/L body halves may create a R/L asymmetric mirror image homochiral body structuring. This phenomenon may provide an explanation for the always use of L-handed amino asides in protein synthesis.
Bilateral homochiral asymmetrical structuring in animals
Although several theories have been proposed, the biophysical mechanisms underlying LR asymmetry are still unclear, especially the role of cell chirality, the LR asymmetry at the cellular level, on organ asymmetry. (4) In multicellular organisms, cell properties, such as shape, size and function are important in morphogenesis and physiological functions. Recently, 'cellular chirality' has attracted attention as a cellular property because it can cause asymmetry in the bodies of animals. (5)
Homochiral molecules are always in a single-handed form as R-handed DNA and L-handed amino acids in living things structures.
The most important building blocks in living things are L-amino acids and proteins. They build the body according to the DNA genes expression. The DNA and L-amino acids position and orientation in the cell nuclei of the R/L- body parts might be in a reversed mirror image position of each other. (Figure 3) If the DNA is the R-handed-R-directional in the R- body half, it may be R-handed and L-directional positioned due to the 180-degree rotation in the L- body half. In this position and orientation, same genes expression may be a bit different in the R/L body parts of the body. This orientation and location model can be able to build R/L asymmetric homochiral body structuring.
Figure 4. Bilateral homochiral positions of organs and cells in the human body. Everything in living things is built by R-handed DNA and L-handed proteins. The red arrows symbolize the direction of the organs on the R- half of the body parts. All the organs are R-handed - L-directional on the R-body part and on the L- body part, they should be L-handed and R-directional.
All the dual organs in the R/L body parts must be homochiral structures, just like our hands. They are positioned as mirror images of each other in the R/L body parts. The direction and position of the organs is opposite to the body part direction where they are located. R- kidney points to the L-direction and the L- kidney points to the R-direction. The possible direction of the cells in the R/L body parts is also shown on this figure. R- brain controls the L-half of the body, while the L-brain- controls the other side. This location pattern may create a polarity difference between the R/L brains and can facilitate brain’s function. Reverse mirror image positioning of all the genes and L-amino acids in the R/L body parts might create a homochiral body structuring as mirror image of each other. Bidirectional opposing homo chiral structuring can be a basic rule of advanced being alive.
The human body appears anatomically as a bilateral structure where the R / L half of the body meet at the exact midline. R/L - hands are homochiral structures but also R/L- brain hemispheres, eyes, lungs, kidneys, testis, ovaries and foots are also homochiral. The R/L body half parts are homochiral mirror images of each other, like our L /R hands but not completely symmetrical. All the cells, tissues, and organs in the R/L body parts except for single organs must be homochiral structured mirror image of each other like our hands. Figure 4. There may be specific genes for single structured organs like liver and spleen.
All the structures in the L- body half can be R-handed and R-directionality and on the R-body half, R-handed and L-directionally .All the sperms produced in the R-testicle should be R-handed L-directional and those in the L-testicle sperms should be R-handed R-directional, like the positions of the palmar sides of our R/L hands .Figure4. The same position may be valid for the ovum.
The basic body plan of the mammalian embryo is established through gastrulation, a pivotal early post implantation event during which the three major germ layers (endoderm, ectoderm, and mesoderm) are specified with cellular and spatial diversity. Despite its basic and clinical importance, human embryo development from peri-implantation to gastrulation remains shrouded in mystery. (6)
R-handed and L-handed snail shells would be a good example of a type of one handed -chirality or directionality: they are different creatures, and the R-handed ones are more numerous. Homochiral structuring in embryonic development may have begun with the first division of the zygote. One of the two blastomeres formed in the first division of the zygote may be in a position and location like the R-handed -snail position while the other may be in a reversed mirror-image position of the R-handed snail. Blastomeres might be positioned and located in the reverse mirror image of each other in zygote first division.
Until about the ninth-tenth week of embryonic development, the R /L- body parts may have been created as separately and in opposite directions by the relevant genes, like the R-handed snails.
Later, they may merge at the midline as mirror image of each other and form R/L homochiral body structuring of fetus in three months.
Evolution might be managed to combine the R-handed structures of snails as reverse mirror images of each other in advanced living things in R/L body parts.
Reversed mirror-image spatial orientation of each other of R-handed DNA and L-amino acids on the R and L- parts of the body may ensure building R/L body homochiral structuring and explain why only L-handed amino acids are always used in protein synthesis.
Directionality in DNA Replication
The DNA is synthesized in the 5'- 3' direction in replication. The leading strand is synthesized easily since its direction is the same as DNA polymerase direction.
The lagging strand synthesized discontinuously and slowly in small segments because its direction is opposite to the 5' to 3' synthesis direction. The difficulties of performing molecular functions in the opposite direction are seen in the DNA replication.
Transcription and translation mechanism and dual opposite directionality
In the simplest sense, expressing a gene means manufacturing its corresponding protein, and this multilayered process has two major steps. In the first step, the information in DNA is transferred to a messenger RNA (mRNA) molecule by way of a process called transcription. During transcription, the DNA of a gene serves as a template for complementary base-pairing, and an enzyme called RNA polymerase II catalyzes the formation of a pre-mRNA molecule, which is then processed to form mature mRNA. The resulting mRNA is a single-stranded copy of the gene, which next must be translated into a protein molecule. A gene is expressed through the processes of transcription and translation. (7) During translation, which is the second major step in gene expression, the mRNA is "read" according to the genetic code, which relates the DNA sequence to the amino acid sequence in proteins. Each group of three bases in mRNA constitutes a codon, and each codon specifies a particular amino acid (hence, it is a triplet code). The mRNA sequence is thus used as a template to assemble—in order—the chain of amino acids that form a protein. (7)
Nucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. (8)
The genetic code is degenerate. Except for two amino acids (Met and Trp), all other amino acid residues are each encoded by multiple, so-called synonymous codons. (9)
Termination of protein synthesis occurs when a translating ribosome encounters one of three universally conserved stop codons: UGA, UAA, or UAG. Release factors recognize stop codons in the ribosomal A site to mediate release of the nascent chain and recycling of the ribosome. Bacteria decode stop codons using two separate release factors with differing specificities for the second and third bases. By contrast, eukaryotes rely on an evolutionary unrelated omnipotent release factor (eRF1) to recognize all three stop codons. The molecular basis of eRF1 discrimination for stop codons over sense codons is not known. (10)
Figure 5. The mRNA might be oriented in the reversed mirror image of each other in the R/L part of the body. When mRNA might be positioned as L-directional on the L part of the body and it must be in R-directional position on the R- body part.
The opposite direction also exists between codon-anti-codon and mRNA and template strand. The codon-anticodons and the opposite orientation of the mRNA to the template strand appear to mimic the position of the DNA strands. Also, mRNA and tRNA are positioned in opposite directions for their functions. In the right body half, if mRNA is positioned in the ribosome in 5-3 directional from right to left, In the other half of the body, the mRNA can be positioned in the ribosome from left to right as 3-5 directional. This reverse positioning of the mRNA in the ribosomes R/L body parts may ensure to build the L-handed amino acids in the R/L body parts in reversed mirror-image positions of each other. The mirror image reversed localization of the DNA and L-amino acids in the R/L body halves may build a R/L asymmetric homochiral body structure
Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a regulator of eukaryotic transcription; however, the modes and mechanisms of this regulation are elusive. (11)
There may be a directional mechanical mechanism in transcription that recognizes the molecules shape and automatically quickly locates it in the appropriate position, together with RNA polymerase and other transcription factors.
The use of uracil instead of thymine in transcription may be very important.
In eukaryotes, the DNA is in the cell nucleus and is protected from external harmful factors. In prokaryotes, it is found in cell cytoplasm. One of the reasons for the T-U change may be that the DNA remains in the nucleus and protects its original structure. In addition, uracil might be played an important function in protein synthesis by location in a specific position in the start and stop codon’s structure. The special codon for tryptophan is UGG. It has a unique and special codon structure with the first letter U and two letter purines (GG). UAA-UAG-UGA are stop codons and there are no anti-codons The localization of purine and pyrimidine bases in the stop codons is remarkable. There is only uracil as a pyrimidine, and it is always located as the first letter in stop codons and the other two letters are always purine. If stop codons UAA-UAG-UGA had anticodon, they would have to be AUU-AUC-ACU. There is no anti-codon whose first letter is Adenine. Stop codons may not be recognized by ribosomes and tRNA due to unusual molecular codon sequence and protein synthesis might be terminated for this reason.
Positions of Adenine and Uracil in mRNA codons may have special importance in the molecular recognition mechanism. 5-fluoro uracil (5FU) is used in cancer treatment. Uracil and 5-Fu is pyrimidine analogue. This fact may also indicate another importance of uracil in cancer treatment.
Transcription has a mechanical component, as the translocation of the transcription machinery or RNA polymerase (RNAP) on DNA or chromatin is dynamically coupled to the chromatin torsion. This posits chromatin mechanics as a regulator of eukaryotic transcription; however, the modes and mechanisms of this regulation are elusive. (11)
There may be a directional mechanical mechanism in transcription that recognizes the molecules shape and automatically quickly locates it in the appropriate position, together with RNA polymerase and other transcription factors.
Figure 6.L-hand palmar side and reversed mirror image positions of the L-hand palmar side in the R/L body parts. L-handed amino acids and proteins may be positioned reversed mirror image in the R/L body parts. The left gloves or hands can be placed on top of each other in the same direction easily and L- amino acids might be positioned in peptide strands like this way. All amino acids and proteins in the R/ L body parts are L-handed but their directions may change oppositely in R/L- body parts. On the right side of the body, L- amino acids can be in the L-handed and R-directional position. They can be in the L-handed and L-directional position in the L-body part. L-handedness of the amino acids has not changed, but the directions have changed in the opposite direction. Such a localization must be necessary for the building of homochiral R/L body asymmetric structuring as mirror image.
If mRNA is in the ribosome in the R-half of the body in the 5-3 direction, it should be in the ribosome in the L-half of the body in the 3-5 direction. In other words, mRNA must be in the opposite directional position of each other in the R/L body parts. The leading strand may be dominant in DNA functions. The leading strand orientation and position may be in reverse mirror images of each other in R/L body parts. mRNA can be transcribed from the leading strand in both R/L body parts. Figure 5. The mRNA is in the opposite direction from the template strand and in the same direction as the copied strand. The codons and anti-codons are oriented opposite each other and mimicking DNA strands position.
Left glove can be thought of as if the L- hand. Objects with the same handed and directional can be easily sequenced on top of each other. The L- gloves can be placed on top of each other in the same direction easily. L-handed amino acids can be sequenced in the same direction and L-handed position in the peptide chains. Ribosomes can position the L-handed amino acids in L-handed L-directional in the L half of the body and in the L-handed R orientation in the R half. Figure 6. Because of the reversed position of the mRNA in R/L body parts, the ribosome machinery may arrange and locate the L-amino acids in the R and L- body parts in the reversed mirror-image positions of each other together with chemical bonds.
Evolution may have achieved the R-DNA and L- amino acids position reverse mirror image of each other location in the R/L body parts. It is not possible for both L/R body parts to be the same oriented in the same positions in body. That is, both body halves cannot be right-directional or left-directional. If this stage had not occurred in the evolutionary process, there could have been many livings species structure that remained at a level like the R-L handed structuring of snails separately. The mirror image reversed localization of the R handed DNA and L-handed amino acids in the R/L body parts may have to create a homochiral body structuring as mirror image in living things.
Discussion
Chirality may be Universal. Everything from subatomic particles to galaxies can be have “dual opposite directional and polarized, chiral asymmetrical structures". Homochiral, chiral, and handed structures can be analyzed not only in terms of isomeric properties, but also at macro molecular levels localization, positions, and directionality. Any type of dual configuration, directional or opposite directional, may be related to chirality at various levels.
The Milky Way and Andromeda are spiral galaxies. Venus and Earth have similar masses, and Venus rotates in the opposite direction. They may have a kind of chirality.
The directional medications used in treatment may have some different effects due to the opposite orientations of the R and L- half of the body. The best example of the importance of directionality in chiral molecules is thalidomide which has two enantiomers. The (S)-enantiomer is teratogenic (R)-enantiomer is used in medical treatments. D-glucose is used as an energy source in living things, but L-glucose cannot be used. Directional positions of molecules may be an important part of the molecular recognition mechanism.
The R-handed DNA virus genome is in the form of double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA). Over hundreds of millions of years of evolution, one of the DNA virus genomes that is randomly coiled into a half-circle in a prebiotic environment may encounter another DNA half-circle virus genome that is coiled in the opposite direction, creating the prototype of a bacterial genome that is in the shape of a circle.
The development of millions of bacteria species in different areas, their relationships with other bacteria and their evolution, especially the formation of mitochondrial DNA, may be a process of billions of years in the transition to multicellular organisms.
Some bacterial genomes may have begun to mimic the structure of DNA strands at small sizes, by being fragmented from time to time by internal and external factors and by positive mutations. The coincidental positioning of small strands, both right-handed, in opposite directions together with R-handed RNA and bases may be the first seeds of eucaryotic cells.
References
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