What does “3’5′” mean with regard to DNA?
What does it mean when they talk about the direction of DNA replication as “3’5′” or say that “Linear polymers of nucleotides, linked by 3′,5′ phosphodiester linkages”, I get it that it does not have anything to do with feet, as in measurements right. Then what?
Well, as you know, DNA stands for deoxyribonucleic acid, and consists of phosphates, sugars, and bases. The deoxyribose sugar consists of 5 carbons and an oxygen in a ring, and the carbons can be numbered 5′, 4′, 3′, 2′, and 1’. Why the “prime”? The prime means you are talking about the carbons in the deoxyribose RING, and not the carbons of the base; it is just a naming convention. When individual nucleotides link up to make DNA polymers, it is the 3′ hydroxyl (OH) that links up with the 5′ phosphate group to form what is known as a phosphodiester bond. Have a look at this diagram:
So then DNA replication proceeds in the direction of 5′ -> 3′, meaning the new units are added on to the 3′ end, extending it in that direction.
Hope that helps.
3′ and 5′ are read as ‘3 prime’ and ‘5 prime’ and it refers to the locations of carbons on the pentose sugars.
“Linear polymers of nucleotides, linked by 3′,5′ phosphodiester linkages” is just saying that the pentose sugars are linked by the phosphodiesters at the ‘3 prime’ carbon position and the ‘5 prime’ carbon position. take a look at this picture as an example
you can see which carbons in the pentose sugars are called the 3′ and 5′,this is common for every pentose sugar in DNA.
you’ll also notice in the picture that on one side of DNA, the pentose sugars and the phosphate groups appear to be flipped, as compared to the other one. this is because DNA is considered to run ‘anti-parallel’.. notice on the left hand side your starting carbon is a 3′ carbon, and the ending carbon is a 5′ carbon. this is considered the direction of the DNA and you can say that this strand of DNA runs 3′ to 5′. it jsut means that it starts at carbon 3, and ends at carbon 5. on the right hand side, you’ll notice it’s the reverse, and yo can say that this strand runs 5′ to 3′. again, the carbons are used to show the direction. so, when you say the direction of DNA replication is from 3′ to 5′, you can see that DNA replication would occur from bottom to top in the left hand strand, and top to bottom in the right hand strand to fit the ‘running 3′ yo 5” thing. DNA would not be replicated on the right hand side from bottom to top, because this would mean it’s being read in 5′ to 3’ direction.
hope that helped!
3` or 3 prime, and 5` or 5 prime refers to the part of the DNA molecule. the 3` end is the top of the molecule (i.e.by the first phosphate group) and the 5` end is the bottom of the molecule ( by the end of the deoxyribose sugar). A diagram would be useful to show this…google the 5 prime or something)…when they say the direction of DNA replication is in the 3` to the 5` direction, the nucleotides are added from the start of the molecule to the end..
Follow that link and go down to DNA structure and DNA Polymerase and look at the pictures…hope that helps