Question

Understand that the nucleotides in DNA contain a base, a sugar and a phosphate. I would ask exactly why a ribose sugar is there and exactly how does it contribute to the maintenance/replication of the molecule. Same question for the phosphate. Guidance sought

Answer 1

Really good question. To begin with one needs to understand that DNA has deoxyribose sugar, which is a 2'H group, while RNA has a ribose sugar which is a 2'OH group. Next, the 2'H is less reactive than the 2'OH, making the DNA more stable as compared to RNA and that is one of the reasons why we have a deoxyribose instead of a ribose sugar in the DNA. Secondly, the DNA has smaller grooves as compared to the grooves in an RNA, making it less vulnerable to enzymes that could attack it. Hence, we have deoxyribose sugar and not ribose sugar, and DNA over RNA. Next, for the phosphate I don't have an exact answer for it but I like to understand it by understanding it with ATP. When ATP is broken down the release of phosphate ion gives energy and similarly, when forming DNA as the nucleotides come in and join in a 5' to 3' way, the 5' dNTP (deoxyribonucleotide) gives away 2 phosphate ions to form a phosphodiester bond with the 3'end of the sugar molecule on the DNA (basically the nucleotide ahead of it) . The release of phosphate ions provides energy for this anabolic activity. And above all, an important thing and a big misconception in biology and one that my biochemistry professor specifically highlighted is that, the only major difference between DNA and RNA that distinguishes them specifically is the deoxyribose sugar and ribose sugar respectively. The common difference about RNA having Uracil and DNA having Thymine can be argued because DNA can very likely have a Uracil in a mutation and still be called a DNA. Hope this helps! :)

Answer 2

Follow up question
Much thanks for the extensive reply. I would want to inquire further about the helix. What is the specific intermolecular interaction that curves the spine of the DNA chain? Is there something about the helix that offers accessibility/protection to the bases? Was DNA always in a helix configuration through time?

Got my bachelors in molecular biology over twenty years ago and may want to get back in the game.

Answer 3

Alright, so now you know that DNA has 1)bases (A,T,C,G) 2)sugar (deoxyribose) 3)Phosphate. Of these, the sugar as well as phosphate are hydrophilic in nature, while the nitrogenous bases are highly hydrophobic. So if you see the structure of DNA, bases are inside, and sugar and phosphate are outside in the double helix. Since cells have huge amount of water content in it, and considering that bases are hydrophobic, they want to stay away from the water. As a result bases go inwards while the sugar and phosphate are present outwards. Similar to how lipids line up in the cell membrane. The hydrophilic stuff towards the outside facing water, while hydrophobic inwards. This doesn't end here. Even though the bases are inwards and sugar and phosphate outwards, they still have to arrange properly so that there are no places for water to sneak in. This leads to the organization into a helix. The complementary base pairing also acts to make a helical structure. Now, the reason why Adenine pairs to Thymine and Cytosine pairs to Guanine is because of their structure. They form maximum number of Hydrogen bonds between one another if they pair up that way hence the complementary pairing. Then, they are anti parallel because it just helps them in the replication process since replication is from 5' to 3' direction. The forces that are present in the DNA are - Hydrogen bonds between the complementary bases and Van der Waals force between the base pairs (as in the stacked base pairs). The chain of bonds basically gives immense strength for the stability of the DNA as well as forms grooves (curves that you see in the DNA) in the DNA for appropriate protein binding as well as protection from unwanted stuff. Hence, the structure of DNA. You can also check out this book - Understanding DNA: the molecule & how it works. I hope this helps! Ignore the spelling mistakes, if there are any. Happy to help! :)