Lecture 4 Summary

Text highlights: Nucleic acids can be studied by biotechnological and chemical methods. Tools and methods for nucleic acids research include restriction enzymes, gel electrophoresis, chemically-modified and fluorescently-tagged nucleotides. The sequencing of DNA by the chain-terminator method makes use of the latter, and many whole genomes have been sequenced to date, thanks to the development of automated, high-throughput versions of the methods. The complete 3.2 Gb human genome was available in first-draft form in 1995, and continues to be studied, augmented, and analyzed. (3: 50-59)

Recombinant DNA technology (3: 59-70)

Nucleic acids are one the major classes of biological macromolecules. The nucleic acids DNA and RNA are the carriers of information in living cells and viruses. DNA (deoxyribonucleic acid) is the physical realization of the genes and genomes of cellular organisms, while RNA (ribonucleic acid) in most cases mediates expression of the genetic information stored in DNA. Nucleic acids are typically long polymers built up of repeating units called nucleotides. A nucleotide is a combination of a base with a sugar (usually ribose or deoxyribose) and phosphate that include the ribonucleotides and deoxyribonucleotides of RNA and DNA, respectively. A nucleoside is the base and sugar part of a nucleotide, making the latter a phosphate ester of a nucleoside.

Nucleotides can be joined together in a series of phosphodiester linkages to form a nucleotide polymer, or polynucleotide. The 3' hydroxyl of one nucleotide forms an ester with the phosphate attached to the 5' hydroxyl group of another to form a dinucleotide. The chain can be extended to arbitrary length by formation of additional phosphodiester bonds with more nucleotides. There is a directionality to the chain that is specified notationally as the 5'→3' or 3'→5' directions, by reference to the 5' position (hydroxymethylene group exo to the aldopentose ring of ribose or deoxyribose) and the 3' position (3' OH attached directly to the ring) of the sugar part of the backbone. By convention, a polynucleotide sequence can be represented by the single letter symbol for a base, with the first letter listed the 5' end and the last letter listed the 3' end.

Left: Structural drawing of a polyribonucleotide, along with symbolic representations of the four common bases of ribonucleotides and RNA molecules. The directionality of the chain is indicated.

Double-stranded DNA

When two polynucleotide sequences show reverse complementarity, they can form an extended stretch of a perfectly base-paired double-stranded structure held together by many hydrogen bonds. There are three stereochemically distinct types of regular double-stranded helical polynucleotide structures. These are A-form, B-form, and Z-form. The B-form is the most common for DNA.

Diversity in the RNA world

RNA molecules show great diversity in structure and function. A single-stranded polyribonuclotide can fold back upon itself to form a variety of hairpin and stem-loop structures containing antiparallel, double-stranded helical regions featuring the canonical, Watson-Crick base pairs shown above. The favored confomation for an RNA helix is the A-form. This pattern of base-paired and loop regions can be thought of as RNA secondary structure (by analogy to protein structural hierarchy).

A ribozyme is an RNA molecule that catalyzes a chemical reaction. Examples include the self-splicing Group I intron from Tetrahymena, the "hammerhead" ribozyme, and the hairpin ribozyme. The RNA components of the ribosome could also be included, as biochemical, genetic, and structural evidence shows that the RNA, and not the protein components, catalyze the reactions of protein synthesis. The catalytic repertoire of ribozymes is limited mainly to phosphoryl transesterification and hydrolysis reactions.

Nucleic acids and disease

Untranslated RNA species are now being implicated in disease, in which mutant forms of these RNAs occur. A host of diseases, such as Huntington's disease, Fragile X mental retardation syndrome , and myotonic dystrophy, are due to expansion of nucleotide repeats.

Learning objectives

• Become familiar with the structures and nomenclature of the eight common nucleotides (VVP3e).
• Describe and recognize in detail the covalent structure of polynucleotides (nucleic acids).
• Describe the structural features of the Watson-Crick (canonical B-form) DNA double helix

Page updated 08-04-2010

References

1. Donald Voet, Judith G. Voet, Charlotte W. Pratt Fundamentals of Biochemistry (3rd edition) Ch.3, pp.51-70.
2. Berg, Tymoczko, and Stryer. Biochemistry (BTS): 6th edition (2007, Freeman) pp.27-38.
3. Bloomfield VA, Crothers DM, Tinoco I, Jr. Nucleic Acids: Structures, Properties, and Functions (2000, University Science Books)
4. Judson HF. The Eighth Day of Creation: Makers of the Revolution in Biology (Cold Spring Harbor Laboratory Press, 1979)
5. Doherty EA, Doudna JA. (2000) "Ribozyme Structures and Mechanisms" Annu Rev Biochem 69: 597-615.