Question

in looking at the structure of DNA, we learned that a strand of DNA possesses an inherent polarity; it has a 5’ end and a 3’ end and that the two strands in a DNA duplex have opposite polarities – they run antiparallel to on another. But why? … why are the two strands always and only antiparallel? (think of the H-bonds that hold the two strands together by complementary base pairing)

Answer 1

DNA is double stranded were they are aligned antiparallel to each other. One strand run from 5’ to 3’ and the other strand from 3’ to 5’.

5’ and 3’ indicate the carbon number in the DNA sugar backbone. 5’ end of the DNA has phosphate group, 3’ end of DNA has OH – hydroxyl group.

DNA polymerase enzyme acts on the DNA strands from 5’ to 3’ for the replication to take place because the 3’ end has the OH group which is used to extend the strand by forming phosphodiester bond with the next nucleotide.

Nucleotide base at one position in the DNA strand is complementary to the other strand of DNA. Because of this complementarity the genetic information is carried from one generation to another by DNA replication.

• Nucleotide is made of a 5 carbon sugar, with a phosphate group, and a nitrogenous base.
• Nitrogenous base are 2 types purines and pyrimidines.
• Adenine and guanine is purine and thymine and cytosine are pyrimidine.
• In RNA thymine is replaced with urasil

Base paring rule:

• Purine always pairs with pyrimidine by hydrogen bonding
• Adenine always pairs with thymine and guanine always pairs with cytosine.
• There are 2 hydrogen bonds between adenine and thymine and 3 hydrogen bonds between cytosine and guanine.
• Thus when the sequence of one strand is known the sequence of other strand can be easily known based on the complementary base paring.

Hydrogen bond:

Hydrogen bond is the type of electrostatic interaction between 2 polar groups, when a hydrogen atom bonds with the highly electronegative atom such as nitrogen, oxygen or fluorine.

For a hydrogen bond to be formed one group donates the hydrogen so it is called hydrogen donor, other group accepts the hydrogen and that is called as the hydrogen acceptor.

Antiparallel orientation of DNA strands makes the complementary base pairing between the nucleotides and forms the stable structure. This antiparallel orientation is important in replication, one strand acts as leading strand and the other the lagging strand both strands act as template forming two new identical DNA strands.