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Gene Sequencing Lab
Your Goal:: In this lab you will learn how to use the Genbank database and BLAST website search tool to search for and
compare nucleotide sequences in a particular gene between different species.
You will first need to watch the 10 minute tutorial. It then shows you step-by-step how to use the databases to
compare the nucleotide sequence of the gene coding for actin (a muscle protein) in different species. Please note that
during the first 4 minutes of the video, you will be given an overview on Evolution; while this information is not
completely necessary for today’s lab since we have not yet studied Evolution, it will help you to better understand
what you are doing.
Note: While you will work with a partner to complete the following assignment, EACH INDIVIDUAL STUDENT MUST
COMPLETE AND SUBMIT THEIR OWN WORK INDIVIDUALLY.
How will you hand in this assignment?
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You must finish the lab in class on TUESDAY. If needed, you may finish the conclusion for homework.
Print out your work. Then, print out the PSOW page found on Blackboard. Put your work in your lab folder,
and staple the PSOW to the front. Then, hand in what you’ve done to your teacher. This is all due on
THURSDAY.
TUTORIAL LINK: Comparing DNA Sequences - YouTube
NOTE: Sequencing of the human genome shows that all humans share the vast majority of their base sequences but
also that there are many single nucleotide polymorphisms that contribute to human diversity. This is why you will see
more than one result for “Homo sapien” in each search, for each gene. Ref: IB Biology Syllabus 2014, pp 49.
Part I: Understanding how to use the databases (questions to answer while watching the tutorial)
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What can the differences between nucleotide sequences be used for/ to show or create?
What are the names of the TWO databases you need to use in this tutorial?
What is the name of the protein that is being used in this example?
What does this protein do?
What chromosome is the actin gene located on in humans?
How many different “hits” come back when you search for the actin nucleotide sequence in BLAST?
Which species has actin that is MOST similar to humans (Homo sapiens)?
Which species has actin LEAST similar to humans?
What is the species who has an actin gene transcript that is 96% similar to the human actin gene transcript?
Part II: Genetics Review
1. Either write a definition or sketch an image of each of the following genetics terms: gene, nucleotide, base,
chromatid, chromosome.
2. What is a mutation?
3. What does each gene code for?
4. What does the term base sequence mean?
5. A part of a human gene has the following base sequence: ATCGGCGCATGGG. If you are given the base
sequences of 3 different species for that same gene, how will you know which species is most closely related
(evolutionarily) to humans?
6. What does the term locus mean?
7. How many chromosomes do humans have?
8. Where are chromosomes found?
9. Explain what a SNP means.
Part III: Using the databases to compare the Cytochrome C gene between different species.
Use the directions given in the tutorial to start a new search: Search for the “Human Cytochrome C” nucleotide
sequence, scroll down until you reach “NCBI reference sequence” and then click on the FIRST blue hyperlink under the
“mRNA and Protein” heading. Scroll down and copy the entire sequence. Paste this into the BLAST search engine.
1. First, research on your own the answer to the following question: What is Cytochrome C, and where would
you find this protein in the cell? What does this protein do?
2. What chromosome is the cytochrome c gene located on (in humans)?
3. How many different “hits” come back when you search for the Cytochrome C nucleotide sequence in BLAST?
4. Which species has actin that is MOST similar to humans?
5. What is the % similarity between this species and humans for the cytochrome C gene?
6. Which species has a cytochrome C gene transcript 85% similar to humans, and is LAST on the list? What is the
% similarity between this species and humans for the cytochrome C gene?
Part IV: Additional Genes
Research 5 of the following genes found in the following list: Actin, GAPDH, Pax1, ATP synthase, Keratin, Ubiquitin,
Catalase, Myosin, Zinc Finger.
For each gene:
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What is the function of the gene? What does the protein it codes for do?
How many hits come back when you search for this gene in BLAST?
Which chromosome is this gene located on in humans?
Which species has this gene that is the most similar to humans?
Part V. Conclusion
Write a 1 page (typed, double spaced, Times New Roman Font) conclusion to the lab. In your conclusion, include:
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A summary of what you did in the lab
Overall what you learned from doing this lab/What was the purpose? (Be clear and detailed).
Any challenges that you faced or questions you still have based on the lab
Ideas for extension
Mini-Lab Rubric:
____ All parts of the lab were completed in class (10 points)
____ All reflection questions are answered in a clear and detailed way that demonstrates the student’s understanding
of the material (30 points)
____ Student worked independently with a partner during class time, carefully reading instructions and consistently
on task (10 points)
____ Conclusion is clear, detailed, and organized and demonstrates a strong understanding of the course material (40
points)
____ All sources used are cited with APA formatting. (10 points)