What is DNA Made of?

DNA stands for deoxyribonucleic acid. It is a polymer of deoxyribonucleotides. The nucleotide consists of: one sugar, one nitrogenous base, and at least one phosphate.

The structure you have put into the frame at left using the X-spot button is a fragment of double-strand DNA 12 base-pairs long.

The two chains are shown coloured yellow and cyan

(PBD DataBase # 355D; HETATOMS removed
G.G.Hu, X.Shui, L.Isom-McFail, L.D.Williams)
The structures of all the components are introduced below, and then shown together as a strand of DNA.

Sugar

The sugar in DNA is deoxyribose. The sugar in RNA is r ibose. The deoxy- prefix indicates that this form of the sugar contains one less oxygen atom. The 2-carbon of the pentose sugar has two hydrogens attached to it instead of an hydrogen and hydroxyl (-OH).

This is shown in the diagram below, and in the structural images which can be loaded into the frame on the left using the button above. Remember that the rotatable images in the frame on the left do not show the hydrogen atoms.

The positions of the carbon atoms are indicated by the numbers. The apostrophe after the number means 'prime' and denotes the atoms on the sugar, as opposed to an atom in the base. The atoms therefore, read from one-prime through to five-prime. When the sugars are displayed on their own the prime is omitted.

All of the bases are linked to the carbon 1atom of the sugar.

Nitrogenous Bases

PYRIMIDINES

There are three pyrimidine bases, and each consists of a 6-member ring containing both nitrigen and carbon atoms. Two pyrimidines, Thymine and Cytosine , are found in DNA. RNA also contains two pyrimidines, but they are Cytosine and Uracil .

NOTE The images of the bases in the frame to the left DO show the hydrogen atoms.

The pyrimidine is linked via N1 to carbon 1 of the sugar. When this occurs, a nucleoside (either deoxycytosine or deoxythymidine) is formed and the atoms of the sugar are distinguished from the base by the prime designat ion (').

NOTE The hydrogens are NOT shown on the images of the nucleosides in the frame to the left.

Bases are known by their first letter, hence the three pyrimidines are T, C and U.

PURINES

Again, the purines are made from two heterocyclic rings of carbon and nitrogen. This time, a 6-member and a 5-member ring have fused. There are two purines, Adenine and Guanine , and both are found in DNA and RNA.

The purines are joined by their N9 atom to the 1' carbon of deoxyribose. The nucleosides formed are deoxyadenosine and deoxyguanosine. The bases are known as A and G.

Phosphates

The addition of one or more phosphate groups to a nucle oside, transforms it into a nucleotide . This is the base-sugar-phosphate unit which, when polymerised, forms DNA.

The phosphate is bound to t he sugar by means of an ester bond at the 5' carbon. Hence this becomes a 5' nucleotide (e.g. deoxyadenosine 5'-monophosphate - as shown in the frame on the left).

NOTE The phosphate group on the deoxyadenosine 5'-monophosphate only shows t hree of the four oxygen atoms (red) associated with the phosphorous (yellow).

The nucleotides which contain three phosphates (deoxyribonucleotide 5'triphosphates) are the precursors for the synthesis of DNA. The two phosphate groups at the end are lost during DNA synthesis, hence the sequence only contains deoxyribonucleotide monophosphates.

Polymers o f dNTP's

Nucleotides are linked by the phosphates . The 3'-hydroxyl of one nucleotide is linked to the phosphate attached to the 5'-hydroxyl of the next nucleotide in the chain by a phosphate-ester linkage. The phosphorous atoms are the yellow spheres.

This creates a phosphodieste r bridge in which the phosphate is linked by two phosphate-ester linkages to the 3'OH of one nucleoside and the 5'-OH of the next.

The sequence shown would be written pCGTA. Cytosine is the base attached to the sugar which has the free phosphate group on the hydroxyl groupat the 5'-end, and is written first. Adenosine is the base attached to the sugar with the free 3'-hydroxyl, and is written last. Hence DNA s trands have polarity 5' to 3'. This is the conventional way DNA sequences are written.

Once again, you've reached the end of the tutorial. Hopefully you have taken notes, and have all the important facts (all of them) down for later use. If you want to go to the next tutorial, press the NEXT button in the navigational frame. If you want to remind yourself how to manipulate the images in the left hand frames, go to HELP.