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DNA replication and transcription - Briefly.

By Helen Gavaghan. Posted 9th May 2019.

1. To enable DNA replication (known also as duplication) the double helix of DNA opens, allowing in enzymes needed to facilitate creation of new DNA polymers on both parent strands of a double-stranded DNA.

2. Each individual strand of a DNA or RNA polymer has a 5' (prime) and 3' (prime) end. At the 5' end of the DNA or RNA polymer there is a phosphor. At the three-prime end, there is a ribose (sugar). The nomenclature of three prime and five prime is, actually, related to the locations in the polymer molecules of the phosphor atom and OH molecule, but because of phosphor's valence state I always think of phosphor as being at the "5 end" of the polynucleotide. I am essentially correct, but a chemist would use different language. To see representations of the actual numbering schemes of DNA and RNA and the the atoms and molecules attached to its furanose rings, which gives rise to the terminology five prime or three prime, I would be tempted to explore the website of the Royal Society of Chemistry, where I imagine one can find the rationale of the numbering scheme explained.

3. DNA replication starts on one of the parent strands of DNA at that parent strand's three-prime end. The newly forming DNA strand builds up from its 5' end, which is why replication is said to proceed in the 5' to 3' direction. The parent strand of DNA running from three prime to five prime is the sense strand (known also as the coding strand or positive strand). The first replicated strand of a DNA double helix is the leading strand. The partner parent strand also replicates, but in the opposite direction. That newly replicating strand is the lagging strand - though given the speed at which events happen the lag is minimal and nominal. Understanding the biochemisty of how complete replication of the lagging strand was possible generated a Nobel Prize in Physiology or Medcine1.

4. The main enzyme in replication is DNA polymerase. An RNA primer is needed to start the process of DNA polymerisation of a new DNA strand. Primase facilitates formation of the RNA primer. DNA polymerase and primase are each enzymes and proteins. When a chemical moeity in a biological system ends with the letters "ase" it is an enzyme and a protein.

5. Energy to drive creation of a new strand of DNA during replication in vivo is released concurrently with creation of a new phosphodiester bond when pyrophosphate is released from deoxyribonucleoside (nucleoside not nucleotide) triphosphate when it bonds with the OH on position 3 of the furanose ring at the 3' end of the parent strand of DNA.

6. It is chemistry which determines that the replication starts with addition of a deoxyribonucleoside triphosphate at the three-prime end of the DNA molecule, and after an RNA primer has been added. The DNA polymerase needs the RNA primer.

7. In transcription, which is when the DNA's message is copied into RNA prior to embarking on a biochemical journey to become protein, the DNA double helix opens over a short stretch of bases to enable access by the necessary enzymatic and regulatory molecules and deoxyribonucleoside. The helix closes behind the transcription. Transcription also proceeds from the three prime end of a DNA polymer.

The seeming simplicity of this science note belies a fascinating complexity on the border where biology encounters chemistry and vice versa, and both encounter biochemistry.

1. https://www.nobelprize.org/uploads/2018/06/szostak_lecture.pdf [Nobel Prize Lecture.]

Online sources which I would trust if I did not have a science degree, postgrad research experience in the history of science, technology and medicine, and 40 professioal years in international science writing, and journalism would be related to Science or Nature. I have written for both publications about science policy and international science. I am not denigrating other sources, but Nature and Science are international peer-reviewed magazines whose pre-eminence in the world of science has been known to annoy some people. So they are a good place to start. If you want to have some fun, look up words online like DNA topoisomerases (relieving torsional stress), helicase, gyrase, primase to name but a few, and see where the unwinding string leads you! It will show how much more complicated the process of replication is than what I have written above.

Words, layout and code, Helen Gavaghan© All rights reserved

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