Humboldt State University ® Department of Chemistry

Richard A. Paselk

Chem 432


Spring 2009

Lecture Notes: 27 February

© R. Paselk 2006


DNA, RNA, & Nucleic Acid Structure

The nucleic acids are made up of polymers of four different nucleotide residues each. RNA uses AMP, CMP, GMP, and UMP, while DNA use the deoxy forms: dAMP, dCMP, dGMP, and dTMP. Note that the two nucleic polymers differ by both the 2'functional group (-OH or -H) and the use of either uridine or thymine as the fourth base. The structures of the bases are shown in the table below.

Nucleotide Structure (monophosphate) Nucleotide Base
Adenosine monophosphate (AMP) Adenine
Guanosine monophosphate (GMP) Guanine
Cytidine monophosphate (CMP) Cytosine
Uridine monophosphate (UMP) Uracil
Deoxythymidine monophosphate (dTMP) Thymine

In synthesizing a nucleic acid polymer from individual monomers, the 3'-hydroxyl group of one nucleotide attacks the alpha-phosphate of a nucleotide triphosphate, displacing a pyrophosphate with the cleavage of an anhydride bond:

Note that this reaction should have a somewhat negative enthalpy since an anhydride bond is replaced by an ester bond, which is generally of lower energy. However, the reaction energy is not going to be sufficient to ensure it goes to completion, a necessity for an organism's success. Fortunately, the resulting pyrophosphate can be hydrolyzed, removing one of the products from the equilibrium, and thus driving the reaction by one ATP of energy.

The polymer resulting form this reaction when repeated will have a particular polarity, with new monomers added to a growing 3' end, as shown in the RNA trinucleotide below:

Of course the key structural feature of the nucleic acids for their role in biological information storage and processing is their inherent ability to be replicated via complementary base-pairing in a double helix:

image of DNA double helix

(see also animation on Lecture slides). The two base pairs, AT and GC, found in DNA are shown below.

A-T base-pair

G-C base-pair

Note that these are the most stable of the various base-pairs, so that these two base pairings will tend to occur more commonly than others on energetic grounds. In addition, these two base pairs have essentially identical dimensions within the double helix structure of DNA. That is the distance between the C1' carbons of the deoxyriboses of each base pair is 1.1 nm in each case (1.11 nm for the AT pair and 1.08 nm for GC). This means that these are also the only two base pairs which will properly fit into the double helix, that is the outside diameter of the double helix will be uniform over its length. In addition the resulting molecule will fit properly and thus be recognized by the active site groove of the polymerases which assembles these molecules, allowing for additional specificity.

Finally we should note that the G-C base-pair has three vs. two hydrogen bonds and thus is more stable. This shows up in greater stability and higher melting points for G-C rich regions of DNA.

DNA Structure and Folding

DNA exists as a double-stranded, anti-parallel, double helix (both strands wrap together, like a ribbon, around a common axis). There are three different DNA structures, as seen last time (below left to right, A, B & Z forms) and in Figures 8-19, p 284 of your text.

image of DNA A,B and Z forms

Their "ideal" properties are:

As demonstrated in the Meselson and Stahl experiment, DNA replication is semi-conservative (see Figure 25-2, p 950 of your text).

Pathway Diagrams

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Last modified27 February 2009