In Silico Determination of differences between cytochrome C Oxidase 1 DNA and protein sequences among selected mammalian groups.

Date

4-2011

Degree

Bachelor of Science in Biology

College

College of Arts and Sciences (CAS)

Adviser/Committee Chair

Ivan Marcelo A. Duka

Abstract

PABUAYON, ISAIAH CATALINO MANALO. 2011. In Silico Determination of Differences between Cytochrome C Oxidase 1 (MT-C01) DNA and Protein Sequences among Selected Mammalian Groups. University of the Philippines Los Banos. BS Biology Major in Genetics.

Adviser: Ivan Marcelo A. Duka

ABSTRACT Using bioinformatics tools, differences and similarities in the DNA and protein cytochrome c oxidase 1 sequences of 56 selected mammalian species in ten orders were determined. The main goal of the study sought to find patterns that can define each of the mammalian groups. CLUSTALW alignment in the nucleotide level showed high conservation in every first and second position of the codons found in the sequences. The third nucleotide position showed high variation, which is permitted by the degeneracy of the genetic code. This meant that distinctions between species are probably located in these positions. With the use of TMHMM, highly conserved sequences were observed in the transmembrane domains predicted for the different mammalian species. Since cytochrome c oxidase is a necessary enzyme in the respiratory chain, it is expected to be highly conserved because of its function. This high conservation can be observed in the transmembrane profiles predicted for the organisms, as well as in the secondary structure predictions (PSIPRED) which showed high similarity among all mammals selected. Lastly, the DNA sequences of the organisms were used to create a phylogenetic tree using MEGA, which was compared to and found to be different from the tree of Kriegs et al. based from retrosposed elements. Differences in the placement of organisms, and the order by which the organisms appear in the tree can be observed. However, clustering of organisms in their respective orders was also seen in the tree created. Hence, cytochrome c oxidase I can be used as an identification tool, as it shows high difference among species. There was however, no distinct and definitive pattern in the MT-001 sequence that discerns one group from another. Additional studies with more representative species are recommended to reveal a more distinct pattern in the phylogenetic tree of mammals.

Language

English

Location

UPLB Main Library Special Collections Section (USCS)

Call Number

Thesis

Document Type

Thesis

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