The 5’ and 3’ carbons are the important ones. There, the phosphate group is attached. These carbons are used by the enzymes acting on RNA and DNA to read the direction of these molecules. RNA and DNA are assembled in the 5’ to 3’ direction (down in the diagram). RNA and DNA are read in the 5’ to 3’ direction. When biochemists write an RNA or DNA sequence, they write it in the 5’ to 3’ direction.

DNA and RNA are read in only one direction, the 5′ to 3′ direction. Take a close look at the figure to the right. Locate the numbered carbons on the ribose molecule (1′, 2′, 3′, 4′ and 5′).

Now start at the top with the phosphate group at the upper left of the image below. Note that it attaches to the first deoxyribose (orange) at the carbon labeled 5′. Follow the ring around counter-clockwise to 3′. There’s a phosphate group there. Keep following it. Note that it attaches at the 5′ carbon of the next deoxyribose ring (green). Follow that ring around counter-clockwise to 3′. There’s a phosphate group there. It attaches to the 5′ position of the third (purple) deoxyribose. You have just read this molecule in the 5′ to 3′ direction: 5’—TCG—3′.

An important feature of RNA and DNA is their ability to form base pairs between the nitrogenous bases. This is the foundation for everything that these molecules do, from duplicating themselves to coding for proteins to building proteins in ribosomes.

There are two base pairs:

• Adenine and thymine/uracil form two hydrogen bonds, each with one hydrogen donor and one hydrogen acceptor. The hydrogen donor and acceptor atoms (nitrogen and oxygen) are opposite each other, so that adenine cannot hydrogen bond to another adenine: only to thymine (DNA) or uracil (RNA). (That is, the only possible base pairs in this set are A T, A U, T A, or U A.)
• Cytosine and guanine form three hydrogen bonds. Guanine has two hydrogen donors and one hydrogen acceptor. Cytosine has two hydrogen acceptors (a nitrogen and an oxygen) and one hydrogen donor. Again, these are arranged so that C G or G C are the only possible base pairs in this set.

RNA is an inherently unstable, single-stranded molecule (although it may have some double-stranded regions). DNA is an inherently stable, double-stranded molecule. DNA is designed to hold the genetic code for an organism (the genome) for at least 100 years in the case of humans. Because of this, DNA from ancient organisms has been found. The current record for oldest genome is from a horse that died 700,000 years ago.

DNA uses deoxyribose as its sugar; RNA uses ribose as its sugar.

DNA uses thymine as the base which pairs with adenine; RNA uses uracil as the base which pairs with adenine.

DNA forms a double helix. The two backbone helices, consisting of alternating deoxyribose and phosphate, are oriented in an anti-parallel fashion (see diagram). The two helices are held together with hydrogen bonds between paired nitrogenous bases (base pairs).

When hydrogen bonds are disrupted in biological molecules, either by changes in temperature, pH, ionic strength, or other chemical means, denaturation can result. In proteins, this means the 2°, 3°, and 4° structure is lost, and the protein loses its function even though the 1° structure remains. Denaturation may result in a change in the physical properties of a protein as well. A raw egg white is mostly albumin and water. Add a pinch of cream of tartar (potassium bitartrate) and whip it for a while, and a meringue results. Or crack it into a pan and heat it, and you have a white, solid, fried egg.

Similarly, DNA can be denatured by heating to break the hydrogen bonds between the nitrogenous bases. The two single-stranded molecules that result can be built upon (used as a template) for two new strands of DNA, and then the resulting strands can be denatured, built upon, and the cycle repeats itself to create millions or billions of DNA molecules. This is the basis for a polymerase chain reaction (PCR), a chemical reaction sequence that has revolutionized molecular biology.