Hydrogen bonding between bases
An important property of the bases found in DNA is that they pair specifically through the formation of hydrogen bonds. Due to the types of atoms present and their orientation, G and C form three hydrogen bonds and A and T form two (Fig. 9). This property forms the basis of an important property of DNA as a whole: complementarity. Complementarity means that each base on a strand of DNA is partnered on the opposite strand with the complementary base that will form the same number of hydrogen bonds.
Fig. 9 Hydrogen bonds formed between nucleotide pairs. The squiggly lines represent the bonds connecting the bases to the sugars. (Images by Iñaki Silanes from Wikimedia Commons)
The DNA modeling tutorial places the hydrogen bonds in the context of the whole helix. Go to
http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/structure/dna/dna.htm
then scroll about 2/3 of the way down the right frame to the section entitled "Hydrogen bonds". After reading that section, click on each of the links labeled "View Animation".
Fig. 10 Modeling hydrogen bonds in the CPK model set
Organization of the backbone chain
Nucleotide pairs are joined to each other by bonds between the 3' (read as "three prime") hydroxyl group of the deoxyribose on one nucleotide and the phosphate of another nucleotide. This process is described in the 7th paragraph in the DNA modeling tutorial, which begins with " Polymerization of the nucleotides…". After reading that paragraph, click on the “View Animation” link to see how that connection is made.
Fig. 11 Orientation of phosphates and deoxyribose sugars in the backbone chain of DNA
When these bonds are repeated many times, the alternating chain of sugar and phosphate units is called the "backbone" of the DNA molecule (Fig. 11).
A very important feature of the backbone chain is that it has directionality (i.e. a "beginning" and an "end"). The two ends of the backbone are designated as 5' and 3'. You should view the part of the DNA modeling simulation that begins about half way down with "The starting and the ending points…" and which ends with the section on "Hydrogen bonds" that you have already viewed. From that part of the simulation, you should have learned that by convention, the sequence of a DNA molecule is specified by listing the order of bases found on a strand in order from the 5' to the 3' end. Since the two strands are complementary, the sequence of the other strand can always be inferred from the first strand. However, it is important to note that because the two strands run in opposite directions (i.e. are antiparallel), the complementary bases would be written in the reverse order of their mates on the first strand. This maintains the convention of always specifying the sequence from 5' to 3'.
