Advertisement

Spreadsheets in Molecular Biology

Abstract

The central dogma of biology is that deoxyribonucleic acid (DNA) makes ribonucleic acid (RNA) makes protein (Alberts et al. 1994; Lodish et al. 1995). The DNA molecule is a simple linear chain each link of which contains one of four different chemicals called bases. These bases are adenine, thymine, guanine and cytosine and are usually abbreviated as A, T, G and C respectively. Since any one of these bases can be found at each link in the chain the potential informational content of even short lengths of DNA is enormous. For example, a modest twenty base DNA segment can be constructed in 420 different ways, corresponding to 1.099 x 1012 combinations. In living cells segments of DNA generate complementary RNA molecules with the same information content. Certain of these RNA molecules are used to direct the production of proteins. Appropriate parts of the RNA sequence are read in sets of three bases, called codons. The 64 (4*4*4) possible codons each have a specific meaning, resulting in the addition of one specific amino acid to a growing protein or the ending of that chain. Like nucleic acids, proteins are also linear chains, with each link in the chain being represented by one of twenty different types of amino acid. The potential informational content of protein sequences is even greater than nucleic acid sequences. For example there are 2010 = 1.024 * 1013 possible 10-amino acid peptides. The specific nucleic acid sequence is therefore decoded into a specific protein sequence, which in turn defines the folded three-dimensional structure and positioning of chemically reactive amino acid side chains on this structure, both of which determine the function of the protein.

Keywords

Nucleic Acid Sequence Coiled Coil Spreadsheet Program Membrane Span Region Radar Plot 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson J (1994) Molecular Biology of the Cell, 3rd edn. Garland, New YorkGoogle Scholar
  2. Argos JK, Rao M, Hargrave PA (1982) Structural Prediction of membrane-bound protein. Eur J Biochem 128:565–575CrossRefGoogle Scholar
  3. Breslauer KJ, Frank R, Blocker H, Marky LA (1986) Predicting DNA duplex stability from the base sequence. Proc Natl Acad Sci USA 83:3746–3750CrossRefGoogle Scholar
  4. Bult CJ, White O, Olsen GJ, et al (1996) Complete genome sequence of the methananogenic Archaeon, Methanococcus jannaschii. Science 273:1058–1078CrossRefGoogle Scholar
  5. Chou PY,Fasman GD (1978) Empirical predictions of protein conformation. Ann Rev Biochem 47:251–276CrossRefGoogle Scholar
  6. Eckerskorn C, Jungblut P, Mewes W, Klose J, Lottspeich F (1988) Identification of mouse brain proteins after two-dimensional electrophoresis and electroblotting by microsequence analysis and amino acid composition analysis. Electrophoresis 9:830–838CrossRefGoogle Scholar
  7. Ferscht A (1977) Enzyme Structure and Mechanism. Freeman, Reading San FranciscoGoogle Scholar
  8. Fleischmann RD, Adamis MD, White O, et al (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae. Science 269:496–512CrossRefGoogle Scholar
  9. Fraser CM, Gocayne JD, White O, et al. (1995) The minimal gene complement of Mycoplasma genitalium. Science 270:397–403CrossRefGoogle Scholar
  10. Freier SM, Kierzek R, Jaeger JA, Sugimoto N, Carruthers MH, Neilson T, Turner DH (1986) Proc Natl Acad Sci USA 83:9373–9377CrossRefGoogle Scholar
  11. Lodish H, Baltimore D, Berk A, Zipursky SL, Matsudaira P, Darnell J (1995) Molecular Cell Biology, 3rd edn. Scientific American books, New YorkGoogle Scholar
  12. Lupas A, Dyke MV, Stock J (1991) Predicting coiled coils from protein sequences. Science 252:1162–1164CrossRefGoogle Scholar
  13. Mahler HR, Cordes EH (1966) Biological Chemistry. Harper and Row, New YorkGoogle Scholar
  14. Maizel JV Jr, Lenk RP (1981) Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proc Natl Acad Sci USA 78:7665–7669CrossRefGoogle Scholar
  15. Shaw G (1991) Neurofilament proteins. In:Burgoyne RD (ed) The Neuronal Cytoskeleton. Alan Liss, New York, pp 185–214Google Scholar
  16. Shaw G (1993) Rapid identification of proteins. Proc Natl Acad Sci USA 90:5138–5142CrossRefGoogle Scholar
  17. Shaw G (1995) Protein sequence interpretation using a spreadsheet program. Biotechniques 19:978–983Google Scholar
  18. Van Heijne G (1987) Sequence analysis in molecular biology. Academic Press, San DiegoGoogle Scholar
  19. Williams N (1996) Yeast genome sequence ferments new research. Science 272:481CrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 1998

Authors and Affiliations

  • G. Shaw

There are no affiliations available

Personalised recommendations