Mechanisms of using L-handed amino acids and R-handed DNAs in protein synthesis and homochiral organism structuring and relation with transcription

 Mechanisms of using L-handed amino acids and R-handed DNAs in protein synthesis and homochiral organism structuring and relation with  transcription 

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.

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.

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                 

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. (1)

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.

 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

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-hands palmar side

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.

References

(1)Alan Brown, Sichen Shao, Jason Murray, Ramanujan S Hegde , V Ramakrishnan. Structural basis for stop codon recognition in eukaryotes. Nature. 2015 Aug 5;524(7566):493–496. doi: 10.1038/nature14896. . Author manuscript; available in PMC: 2016 Feb 27.