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Stephen Peng

5 October 2014

AP Biology; Period 4

Ms. Lenz

Introduction:

In this lab, we wish to research the function of ubiquitin in humans, and investigate the

presence of ubiquitin in other primates. Specifically, our protein was Ubiquitin C, or UBC in short.

Ubiquitin is a regulatory protein, so named because it is found in most eukaryotic cells. This protein is

extremely interesting due to its ubiquitous presence in eukaryotes, the discovery of lysine chains that

link this regulatory protein to other proteins lead to a Nobel Prize in 2004. Also, the consistency of its

makeup across species is fascinatinghuman and yeast ubiquitin are, shockingly, 96% similar. Ubiquitin

functions primarily to signal protein degradation (a process called ubiquitination). It also regulates

activity within the cell, changes the location of the protein, and regulate protein interactions.

Methods:

We used the NCBI resource page to find the DNA sequences of UBC in Homo sapiens (humans),

Pan troglodytes (common chimpanzees), and Pongo abelii (Sumatran orangutans), and copied the FASTA

files for each. Then, we used the NCBI BLAST programs Nucleotide BLAST function to compare the

UBC gene in each species to the other two (3 comparisons total). First, the Homo sapiens UBC sequence

was compared to the Pan troglodytes UBC; then, Homo sapiens UBC and Pongo abelii UBC were

compared. Finally, we compared Pan troglodytes UBC with Pongo abelii UBC. Since the NCBI belongs to

the National Library of Medicine, run and maintained by the government, we considered it to be an

indubitably reliable source.

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Results:

Phylogenetic Tree

Homo sapiens vs. Pan troglodytes

Max Score 3553

Total Score 31825

Identicality 96%

Pongo abelii vs. Pan troglodytes Homo sapiens vs. Pongo abelii

Max Score 2883 Max Score 2982

Total Score 27869 Total Score 25544

Identicality 95% Identicality 95%

Using the indenticality scores found when we used the NCBI BLAST program to compare the

sequences, we drew a phylogenetic tree with the assumption that humans were closer to chimpanzees

than orangutans (since the indenticality score between humans and chimpanzees was higher than those

of humans and orangutans, and chimpanzees and orangutans). Upon further research, we discovered
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that humans were, in fact, more closely related to chimpanzees than orangutans, confirming the data

we collected with the BLAST program.

Discussion:

Since ubiquitin is such a highly conserved gene, the authors of Purifying selection and birth-

and-death evolution in the ubiquitin gene family discuss the possibility that the gene evolved as a result

of birth-and-death, rather than concerted evolution. According to the article, multigene families

associated with immune response or disease resistance are generally subject to birth-and-death

evolution, and this mode of evolution is important in generating a set of diversified member genes to

cope with different pathogens (Nei, 2000). Upon reading this article, and numerous other ones that

discussed the possibility of concerted evolution, I decided it was necessary to research birth-and-death

evolution and concerted evolution of genes.

Additionally, it appears that other ubiquitin-like proteins are beginning to evolve in certain

organisms. According to Mark Hochstrassers paper Origin and function of ubiquitin-like proteins,

these evolutions can offer biologists a glimpse of how ubiquitin evolvedcurrently, a popular theory is

that it ubiquitin-like proteins evolved from prokaryotic sulphurtransferase systems or related enzymes.

Evidence for this includes the fact that these sulphurtransferase systems were widespread before the

first common ancestor of eukaryotes, suggesting that these ubiquitin-like proteins did not evolve in

eukaryotes. (Hochstrasser, 2009).

In this lab, I was able to witness firsthand the direct correlation between gene similarity and

evolutionary relationships. I was astounded by the ability that technology is able to give us regarding

biological phenomena. The inquiry also taught me a lot about the evolutionary relationship between

humans and other types of primates, which helps me understand our evolutionary history a lot better

than my previous assumption that humans evolved from monkeys.

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References

Hochstrasser, M. (2009). Origin and Function of Ubiquitin-like Proteins. Nature, 458.

Nei, M. (2000). Purifying Selection and Birth-and-Death Evolution in the Ubiquitin Gene Family.
Proceedings of the National Academy of Sciences of the United States of America, 97(20).