Hydrogen Bonding and DNA

~ Chromoscience

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Two images are shown. The first lies on the left side of the page and shows a helical structure like a twisted ladder where the rungs of the ladder, labeled “Base pair” are red, yellow, green and blue paired bars. The red and yellow bars, which are always paired together, are labeled in the legend, which is titled “Nitrogenous bases” as “adenine” and “thymine,” respectively. The blue and green bars, which are always paired together, are labeled in the legend as “guanine” and “cytosine,” respectively. At the top of the helical structure, the left-hand side rail, or “Sugar, dash, phosphate backbone,” is labeled as “3, prime” while the right is labeled as “5, prime.” These labels are reversed at the bottom of the helix. To the right of the page is a large Lewis structure. The top left corner of this structure, labeled “5, prime,” shows a phosphorus atom single bonded to three oxygen atoms, one of which has a superscripted negative charge, and double bonded to a fourth oxygen atom. One of the single bonded oxygen atoms is single bonded to the left corner of a five-membered ring with an oxygen atom at its top point and which is single bonded to an oxygen atom on the bottom left. This oxygen atom is single bonded to a phosphorus atom that is single bonded to two other hydrogen atoms and double bonded to a fourth oxygen atom. The lower left of these oxygen atoms is single bonded to another oxygen atom that is single bonded to a five-membered ring with an oxygen in the upper bonding site. The bottom left of this ring has a hydroxyl group attached to it while the upper right carbon is single bonded to a nitrogen atom that is part of a five-membered ring bonded to a six-membered ring. Both of these rings have points of unsaturation and nitrogen atoms bonded into their structures. On the right side of the six-membered ring are two single bonded amine groups and a double bonded oxygen. Three separate dotted lines extend from these sites to corresponding sites on a second six-membered ring. This ring has points of unsaturation and a nitrogen atom in the bottom right bonding position that is single bonded to a five-membered ring on the right side of the image. This ring is single bonded to a carbon that is single bonded to an oxygen that is single bonded to a phosphorus. The phosphorus is single bonded to two other oxygen atoms and double bonded to a fourth oxygen atom. This group is labeled “5, prime.” The five-membered ring is also bonded on the top side to an oxygen that is bonded to a phosphorus single bonded to two other oxygen atoms and double bonded to a fourth oxygen atom. The upper left oxygen of this group is single bonded to a carbon that is single bonded to a five-membered ring with an oxygen in the bottom bonding position. This ring has a hydroxyl group on its upper right side that is labeled “3, prime” and is bonded on the left side to a nitrogen that is a member of a five-membered ring. This ring is bonded to a six-membered ring and both have points of unsaturation. This ring has a nitrogen on the left side, as well as an amine group, that have two dotted lines leading from them to an oxygen and amine group on a six membered ring. These dotted lines are labeled “Hydrogen bonds.” The six membered ring also has a double bonded oxygen on its lower side and a nitrogen atom on its left side that is single bonded to a five-membered ring. This ring connects to the two phosphate groups mentioned at the start of this to form a large circle. The name “guanine” is written below the lower left side of this image while the name “cytosine” is written on the lower right. The name “thymine” is written above the right side of the image and “adenine” is written on the top right. Three sections are indicated below the images where the left is labeled “Sugar, dash, phosphate backbone,” the middle is labeled “Bases” and the right is labeled “Sugar, dash, phosphate backbone.”
Figure 1. Two separate DNA molecules form a double-stranded helix in which the molecules are held together via hydrogen bonding. (credit: modification of work by Jerome Walker, Dennis Myts)

Deoxyribonucleic acid (DNA) is found in every living organism and contains the genetic information that determines the organism’s characteristics, provides the blueprint for making the proteins necessary for life, and serves as a template to pass this information on to the organism’s offspring. A DNA molecule consists of two (anti-)parallel chains of repeating nucleotides, which form its well-known double helical structure, as shown in Figure 1.

Each nucleotide contains a (deoxyribose) sugar bound to a phosphate group on one side, and one of four nitrogenous bases on the other. Two of the bases, cytosine (C) and thymine (T), are single-ringed structures known as pyrimidines. The other two, adenine (A) and guanine (G), are double-ringed structures called purines. These bases form complementary base pairs consisting of one purine and one pyrimidine, with adenine pairing with thymine, and cytosine with guanine. Each base pair is held together by hydrogen bonding. A and T share two hydrogen bonds, C and G share three, and both pairings have a similar shape and structure Figure 2.

A large Lewis structure is shown. The top left corner of this structure, labeled “5, prime,” shows a phosphorus atom single bonded to three oxygen atoms, one of which has a superscripted negative charge, and double bonded to a fourth oxygen atom. One of the single bonded oxygen atoms is single bonded to the left corner of a five-membered ring with an oxygen atom at its top point and which is single bonded to an oxygen atom on the bottom left. This oxygen atom is single bonded to a phosphorus atom that is single bonded to two other hydrogen atoms and double bonded to a fourth oxygen atom. The lower left of these oxygen atoms is single bonded to another oxygen atom that is single bonded to a five-membered ring with an oxygen in the upper bonding site. The bottom left of this ring has a hydroxyl group attached to it while the upper right carbon is single bonded to a nitrogen atom that is part of a five-membered ring bonded to a six-membered ring. Both of these rings have points of unsaturation and nitrogen atoms bonded into their structures. On the right side of the six-membered ring are two single bonded amine groups and a double bonded oxygen. Three separate dotted lines extend from these sites to corresponding sites on a second six-membered ring. This ring has points of unsaturation and a nitrogen atom in the bottom right bonding position that is single bonded to a five-membered ring on the right side of the image. This ring is single bonded to a carbon that is single bonded to an oxygen that is single bonded to a phosphorus. The phosphorus is single bonded to two other oxygen atoms and double bonded to a fourth oxygen atom. This group is labeled “5, prime.” The five-membered ring is also bonded on the top side to an oxygen that is bonded to a phosphorus single bonded to two other oxygen atoms and double bonded to a fourth oxygen atom. The upper left oxygen of this group is single bonded to a carbon that is single bonded to a five-membered ring with an oxygen in the bottom bonding position. This ring has a hydroxyl group on its upper right side that is labeled “3, prime” and is bonded on the left side to a nitrogen that is a member of a five-membered ring. This ring is bonded to a six-membered ring and both have points of unsaturation. This ring has a nitrogen on the left side, as well as an amine group, that have two dotted lines leading from them to an oxygen and amine group on a six membered ring. These dotted lines are labeled “Hydrogen bonds.” The six membered ring also has a double bonded oxygen on its lower side and a nitrogen atom on its left side that is single bonded to a five-membered ring. This ring connects to the two phosphate groups mentioned at the start of this to form a large circle. The name “guanine” is written below the lower left side of this image while the name “cytosine” is written on the lower right. The name “thymine” is written above the right side of the image and “adenine” is written on the top right. Three sections are indicated below the images where the left is labeled “Sugar, dash, phosphate backbone,” the middle is labeled “Bases” and the right is labeled “Sugar, dash, phosphate backbone.”
Figure 2. The geometries of the base molecules result in maximum hydrogen bonding between adenine and thymine (AT) and between guanine and cytosine (GC), so-called “complementary base pairs.”

The cumulative effect of millions of hydrogen bonds effectively holds the two strands of DNA together. Importantly, the two strands of DNA can relatively easily “unzip” down the middle since hydrogen bonds are relatively weak compared to the covalent bonds that hold the atoms of the individual DNA molecules together. This allows both strands to function as a template for replication.

Source:

Flowers, P., Theopold, K., Langley, R., & Robinson, W. R. (2019, February 14). Chemistry 2e. Houston, Texas: OpenStax. Access for free at: https://openstax.org/books/chemistry-2e

Published by Chromoscience