The DNA molecule, also called Deoxyribose Nucleic Acid, is composed of two complementary strands that twist into a right-handed helix and are held together by hydrogen bonds. Each strand is made of a numerous nucleotides strung together. A nucleotide is the combination of a phosphate, five carbon sugar, and a nitrogen base. The sugar in a DNA molecule is deoxyribose, which means it lacks an OH. Also, the nucleotide strands run antiparallel to each other.
Purines by Allen Gathman, on Flickr
Purine Nucleotides pair with pyrimidines in the DNA structure. What sets the two types of nucleotides apart is the number of rings each base has; Purines have two rings while Pyrimidines only have one. The Purine Nucleotides are Adenine (which forms two hydrogen bonds with Thymine) and Guanine (which forms 3 hydrogen bonds with Cytosine). The reason two Purines cannot pair together is because their hydrogen bonds do not match up; one base requires two while the other requires three.
Pyrimidine nucleotides by Allen Gathman, on Flickr
Pyrimidine nucleotides are nucleotides that contain nitrogen bases with only one cyclic ring. Examples of pyrimidines in nucleotides are the nitrogen bases cytosine and thymine. Uracil is also a pyrimidine, but found only in RNA.
Deoxyribose by Allen Gathman, on Flickr
Picture is of naturally occurring D-Deoxyribose.
Deoxyribose is a type of sugar (ribose) that lacks a hydroxyl group on the 2' end of the cyclic ring. This type of sugar is found in DNA (deoxyribonucleic acid).
Cytidine by Allen Gathman, on Flickr
Cytosine is a pyrimidine base found in DNA structure that hydrogen bonds to the purine base guanine.
Thymidine by Allen Gathman, on Flickr
Thymine is a nitrogenous base that pairs with the base, Adenine. Thymine is known as a pyrimidine, meaning that it has one ring structure present. Thymine is only present in DNA and NOT
Guanosine by Allen Gathman, on Flickr
Guanine is a nitrogenous base that makes three hydrogen bonds with its complementary base pair Cytosine. The nucleotide containing one deoxyribose, guanine, and a phosphate is referred to as Deoxyguanidine monophosphate and is a key component of DNA. Guanine is similar to Adenine in the fact that it is a purine base; its structure consists of a two membered ring.
Adenosine by Allen Gathman, on Flickr
Adenine is a nitrogenous base that binds to Thymine by two hydrogen bonds in DNA. In RNA, Adenine pairs with Uracil. Adenine is a purine, meaning that it has two ring structures present.
Why purines pair with pyrimidines
Why purines pair with pyrimidines by Allen Gathman, on Flickr
If two pyrimidines were lined up across from one another on two different strands of DNA, the hydrogen bonds between them would not occur. This is because they would both be single-ringed structures and the distance between them is too large when you try to bond them across a 2nm gap.
If two purines were lined up across from one another on two different strands of DNA, there would not be enough room for them to be properly fit into place. This is because they would both be two-ringed structures and are simply too large for the 2nm gap.
The only way for two bases to bond across two strands of DNA is if one is a purine and the other is a pyrimidine.
Nitrogenous bases are adenine, thymine, cytosine, guanine, and uracil
A nucleotide consists of a base, a sugar(ex: ribose or deoxyribose), and a phosphate.
A nucleoside is a sugar and base: adenosine, thymidine, cytidine, guanosine, and uridine.
DNA molecule, spacefilling model
DNA by Allen Gathman, on Flickr
The differences in the size of the grooves in DNA double helices is due to the antiparallel base pair of nucleotides. The major grooves then allow for proteins to bind to the DNA.
One turn of the helix spans 3.4nm, which is approximately 10.4 base pairs. Due to the ring structure of purines and pyrimidines, these molecules are planar. Base pairs are tightly stacked inside the double helix and loosely held together by van der Waals interactions. The Major Groove is the right size for a protein alpha helix to bind to it. A protein does not fit properly into a Minor Groove for a bond to form.
The two stranded helical structure of DNA initially caused some debate due to how DNA replicate. Much of this was due to the potential of supercoiling and daughter DNA becoming tangled. Later it was discovered that to alleviate supercoiling in prokaryotes such as E. coli,topiosomerase II cuts both strands while topiosomerase I cuts one strand altering the twisting of the DNA (shown in the figure on the right) by removing one positive twist. In this way gyrase moves ahead of the replication fork studied in the next powerpoint by uncoiling it. It takes 10 base pairs to equal one positive twist of the DNA. This further gives insight into the thoughts of Delbrok in regards to the dispersive theory.
DNA by Allen Gathman, on Flickr
Picture shows structure of DNA with two strands. The strand on the left from 5' to 3' end contains thymine attached to cytosine via phosphodiester linkage. Thymine is hydrogen bound to adenine which is the 3' end of the right stand. Also cytosine has hydrogen bonding with guanine (5' end of right strand) which has a phosphodiester linkage with adenine.
Phosphate group always present at 5' carbon.
Hydroxyl group always present at 3' carbon. This is true when it is at the ends of the strand. If the 3' carbon of the ribose is involved in bonding, the hydroxyl group will not be present.