8.1 Metabolism

Developments in scientific research follow improvements in computing—developments in bioinformatics, such as the interrogation of databases, have facilitated research into metabolic pathways.

Bioninformatics is the “Synthesis of molecular biology and computer science that develops databases and computational tools to store, retrieve, and analyze nucleic acid and protein sequence data.” (Pierce, B) and we have encountered it already in 7.3 Translation.

In addition to genes, though, bioinformatics can screen metabolic pathways and protein structures in order to assess potential targets for new drugs. For example, the Malaria Drug Target database allows researchers to search for potential inhibitors and targets in the malarial parasite, based on protein structure and function cross-referenced with genetic sequences. Many of these potential targets are key enzymes within metabolic pathways.  Hasan et al. (2015) used a protein database to investigate the possibility of using the enzyme transketolase as a drug target.  The enzyme is important in the pentose phosphate pathway, which is part of  energy generation and nucleic acid synthesis (Hasan et al.).  Analysis using various databases and computer software allowed the researchers to identify the enzyme, determine its structure and compare it to the human version of the enzyme. The result is a promising avenue for testing drugs to control the spread of Plasmodium falciparum, the malaria parasite.

Hasan , A. et al. Molecular-docking study of malaria drug target enzyme transketolase in Plasmodium falciparum 3D7 portends the novel approach to its treatment. Source Code for Biology and Medicine 2015. 10:7. Web .Accessed April 19, 2016.

Pierce, B. Genetics: A conceptual approach. 2nd Edition. 2005. Web. Accessed April 19, 2016.

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7.3 Translation

Developments in scientific research follow improvements in computing—the use of computers has enabled scientists to make advances in bioinformatics applications such as locating genes within genomes and identifying conserved sequences.

Bioinformatics is the application of computer science to molecular biology, allowing the creation of massive databases of molecular information (proteins, genes, DNA sequences etc.) You might remember from our Crash Course video on replication that one cell contains genetic information equivalent to a stack of single A4 pages nearly 100m high! It is only the advent of powerful (and affordable) computers over the last 25 years that has enabled the collection and synthesis of genetic information on a large scale.

To explore this topic, we will be performing a BLAST search using resources from the European Molecular Biology Lab (EMBL).  We will be searching for information about the Protein PAX6 through a series of databases on the web.  The activity we are doing can be found through the EMBL’s education section, the European Learning Laboratory for Life Sciences.