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DNA BLAST Lab

2013 AP Biology-Ms.Hunt Neeraja N., Alice A.
by

Alice An

on 12 January 2013

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Transcript of DNA BLAST Lab

Background photo by t.shigesa Primary Question: The main objective of this experiment is to place the newly discovered fossil into the right location in the cladogram by comparing gene sequences, which are found in the 4 genes. In this project group identified the main proteins as well their functions which as useful in determining which time period the fossil belonged to as, each species has its own set of traits and characteristics by using the BLAST website. The sequences of gene 4 match to Alligator sinensis and it encodes mtDNA, which is crucial for eukaryotic organisms along with gene 3, which is contained in zebra finch and essential for eukaryotes to regulate cellular processes. Shaker gene from gene 2 proves this organism is evolved from fruit fly. The protein found in Gene 1 support s the hypothesis that the organism is a vertebrate. Looking over the phonological trees of the 4 organisms proved to be useful as well. At the end a conclusion was made that the fossil should fall between insect, crocodile and birds of the cladogram as shown in hypothesis. Introduction Abstract Results DNA BLAST Lab Hypothesis
The newly discovered fossil falls between insects and crocodilians with high chances of it being a vertebrate. Methodology and Experiment Design 1. Download the four gene sequences that are found “blogging4biology.com” and upload then them up on the NCBI Blast site.

2. ‘Blast’ each gene individually and look for the gene sequence with the maximum identity.

3. Click on the gene bank and write down the genus, species, sequence number and common name of the organism obtained from that particular gene sequence.

4. The protein synthesized by the organism is listed next to its name. Google the name of the protein to find out its functions.

5. After noting down the proteins synthesized and its functions for each gene, organize the four organisms (obtained from the four genes respectively) according to its phonological tree.

6. The traits inherited by the organism (found in the fossil) helps categorize it in its proper location in the cladogram.

7. Create analytical tables and charts to support your research and make a conclusion. Conclusion & Interpretation of Results After the experiment is completed, the hypothesis that was made at the beginning of the experiment is supported through the research. This proves by comparing the gene sequences from genes that are found in the fossil. The organisms that match with a specific gene sequences provide information regarding the fossil and the evolutionary history as well.
According to the gene libraries, the sequences of gene 4 match to Alligator sinensis, which is known as chinese alligator that contains mtDNA protein (Mitochondrion DNA). Mitochondrion DNA is necessary for eukaryotic cells to produce ATP. Also, it is involved in signaling, regulating cell cycle and cell growth. The most important part of function is expressed in embryotic stem cells during cell differentiation. This supports that this organism is eukaryotic organism because mtRNA is crucial for especially animals.
The sequences of gene 3 display the organism called Taeniopygia guttata (zebra finch). This organism falls into the category of birds and the protein found in this organism is called ubiquitin-conjugating enzyme E2Q, which exist at transcript level. It targets abnormal proteins for degradation. The enzyme, proteases, is from this special protein, which is ubiquitous and crucial for eukaryotes in order to regulate cellular processes.
Gene 2 was found to belong to a fruit fly (Drosophila Melanogaster) which was the oldest organism found in the phonological tree/cladogram. The organism found in the fossil is most likely to have inherited Shaker genes from the fruit fly. The Shaker genes are necessary for the formation of K-channels in the potassium-ion-pumps (an essential part of cell transportation). Originally these genes were mutants in the Drosophila and eventually, through natural selection they have become a crucial trait which is present in all organisms.The sequences of Gene 1 led to a Gallus Gallus (chicken) as its main organism.
The protein Collagen type 5, alpha 1 produces fibrillar collagens which are extracellular matrix proteins that help in the formation of teeth, bones and tissues. This helps support our hypothesis that the organism is a vertebrate. Neeraja N.
Alice A. Background Context: Literature Cited How can DNA sequences be used to create cladograms that depict evolutionary relationships and how can this be utilized to place an organism in its proper position in its phenological tree? - Learning about the gene sequences allows understanding of the evolutionary changes happened in the past and relationships among organisms.
- By using newly developed technology called BLAST, which displays statistics, mathematical modeling for matching gene sequences, scientists are now able to search entire genome libraries for identical or similar sequences that they are looking for.
- Along with the searching of gene sequences, BLAST also provides information that promotes scientists to construct a cladogram, which is the evolutionary relationships of different species, by comparing several genes.
- The cladogram is treelike visualization that demonstrates a common ancestor among organisms and people can predict evolutionary history of specific organism by observing the cladogram. Observation: - Backbone
- Tail
- Insects
- two parts of limbs
- hole in the skull
- Birds like limbs
- Snout looking feature "Basic Local Alignment Search Tool." BLAST:. N.p., n.d. Web. 11 Jan. 2013.

"Result Filters." National Center for Biotechnology Information. U.S. National Library of Medicine, n.d. Web. 11 Jan. 2013.

"Collagen." Wikipedia. Wikimedia Foundation, 01 Sept. 2013. Web. 11 Jan. 2013.

"Collagen Fibrillar Structure." Collagen Fibrillar Structure. N.p., n.d. Web. 11 Jan. 2013.

"Shaker Gene." Wikipedia. Wikimedia Foundation, 17 Dec. 2012. Web. 11 Jan. 2013.

"FruitFly: Shaker Introduction." FruitFly: Shaker Introduction. N.p., n.d. Web. 11 Jan. 2013. Groleau, Rick. "NOVA Online | Neanderthals on Trial | Tracing Ancestry with MtDNA." PBS: Public Broadcasting Service. N.p., n.d. Web. 12 Jan. 2013. <http://www.pbs.org/wgbh/nova/neanderthals/mtdna.html>.

"UBE2Q1 ubiquitin-conjugating enzyme E2Q family member 1 [Homo sapiens] - Gene - NCBI." National Center for Biotechnology Information. N.p., n.d. Web. 12 Jan. 2013. <http://www.ncbi.nlm.nih.gov/gene/55585>.

"Ubiquitin-conjugating enzyme E2Q-like protein 1 - Homo sapiens (Human)." UniProt. N.p., n.d. Web. 12 Jan. 2013. <http://www.uniprot.org/uniprot/A1L167>.

"Ubiquitin-conjugating enzyme E2Q-like protein 1 - Mus musculus (Mouse)." UniProt. N.p., n.d. Web. 12 Jan. 2013. <http://www.uniprot.org/uniprot/A0PJN4>.

contrast, and the Neandertal genome had an average of 27 +/- 2.2. "Fossil Hominids: mitochondrial DNA."
TalkOrigins Archive: Exploring the Creation/Evolution Controversy. N.p., n.d. Web. 12 Jan. 2013. <http://www.talkorigins.org/faqs/homs/mtDNA.html>. Along the footsteps of Fossil
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