DNA structure: There are two types of nucleic acids, ribonucleic acid or RNA and deoxyribonucleic acid or DNA used by modern cells. 

Nucleic acids are polymers; their basic building blocks are nucleotides.  

Nucleotides assemble into polymers through condensation reactions coupled to with ATP hydrolysis reactions.

A new triphosphate add to the 3' OH group of a nucleic acid molecule.

A nucleotide consists of three distinct chemical groups, a 5-carbon sugar, a nitrogen-rich base and a phosphate.

In RNA, the sugar is ribose; in DNA, the sugar is deoxyribose.

The nitrogenous base, either a purine (adenine or guanine), or a pyrimidine (thymine, uracil or cytosine), is attached to the 1' carbon of the sugar.

A second difference between RNA and DNA is that RNA uses the pyrimidine uracil
while DNA uses thymine.

Both purines and pyrimidines are flat in the ring plane. The upper and lower surfaces of the rings are hydrophobic, while the edges are hydrophilic.

This means that the same forces that favor the assembly of lipids into membranes are involved in nucleic acid structure.

To minimize their interactions with water, the interactions between hydrophobic surfaces and water need to be minimized.

At the same time, each nucleotide has two very hydrophilic groups:  a negatively charged phosphate and a sugar group.

Both form H-bonds and will interact strongly with water. 

How can the conflicting "molecular desires"  of the nucleotide be satisfied: by stacking the hydrophobic surfaces of the bases in the center of the molecule and positioning the sugars and phosphates at the periphery, in contact with water.

A "bases-inward"  organization was the basis of the Watson and Crick double-helical model for DNA structure.

At the same time, each base has a hydrophilic edge, with -C=O and -N-H groups that can act as H-bond acceptors and donors.

How are these hydrophilic groups arranged in the hydrophobic interior?

An critical clue came from the work of Erwin Chargaff.  He found that the relative amounts of G, C, T and A varied between organisms but were the same for organisms of the same type or species.

On the other hand, the ratios of A to T and G to C were always equal to 1, no matter where the DNA came from.

Knowing these rules, Watson and Crick built a model of DNA that fit the molecular and structural data.

Their result was a double helical structure in which the strands ran anti-parallel to one another and the bases were stacked upon one another in the center.

Their model was for what is now known as B-form DNA.  Under different conditions, DNA can form two other double helical forms, known as the A and Z forms.

A and B forms of DNA are "right-handed" helices, the Z-form of DNA is a left-handed helix.

This has important structural implications.  Most importantly, the structure of a DNA molecule is not altered by the sequence of base pairs along its length.

Any possible sequence can be found, at least theoretically, in a DNA molecule.  This means that DNA can be used to encode information in the sequence of nucleotides along its length.

Second, the sequence of base pairs along one strand of a DNA molecule is the complement of the base pair sequence on the other. The two strands are informationally redundant.

If you know the sequence of one strand of a double-stranded DNA molecule, you automatically known the sequence of the other, anti-parallel strand. This has important implications for the replication of hereditary information.

• Which do you think is stronger (and why) and AT or a GC base pair?  How might you measure the relative base composition of a DNA molecule?
• Why does the ratio of A to G differ between organisms?
• Why is the ratio of A to T the same in all organisms?
• What does it mean that the two strands of a DNA molecular are anti-parallel?  

RNA structure:  RNA differs from DNA in that it uses the sugar ribose instead of deoxyribose and the base uracil rather than thymine.

While DNA is almost always double-stranded, RNAs are generally single-stranded.  This removes a major constraint on their structural diversity.

Once thought of as passive transmitters of information from DNA to proteins (mRNAs), it is now clear that RNAs play many different functions within the cell.

These diverse functions are possible because RNAs (unlike double stranded DNAs) can fold in complex three dimensional shapes.

As in the case of DNA, in water the single-stranded RNA molecule will minimize the interaction between water and the hydrophobic surfaces of the nucleotide bases, and maximize the interactions between water and the hydrophilic phosphates and sugars.

This is accomplished by folding the RNA strand back upon itself, and often leads to the formation of double-stranded stems that end in single-stranded loops.

Regions within a stem that do not base pair will bulge out.

RNAs fold into complex structures that can perform structural or catalytic functions.

The ability of RNA to both encode information in its base sequence and to mediate catalysis through its three dimensional structure has lead to the RNA world hypothesis.

This hypothesis states that instead of DNA and proteins, early organisms relied on RNAs, or more likely simpler RNA-like molecules, to both store genetic information and to catalyze reactions.

According to this view, it was only later in the evolutionary process that organisms develop more specialized DNA-based systems for genetic information storage and proteins for catalysis and other structural functions. 

There are many problems associated with a simplistic RNA world view, the most important being the complexity of RNA subunits and their abiogenic synthesis.

Nevertheless, it is becoming well established that catalytic RNAs played a key role in modern cells, and early evolution as well.   Take the ubiquitous ribosome, which is involved in protein synthesis; its catalytic activity is based on a ribozyme.

• If polypeptides have alpha-helices and beta-sheets, RNAs have ...?