Mystery Molecule Project, PART II-BIO1001 Fall 2020

Directions:

To complete the remainder of this project and prepare for your presentation, follow the instructions below. Your presentation should include the answers to all questions indicated below. For your final presentation, you are expected to organize your research and present a rehearsed, 10-12 minute presentation using the rubric at the end of this document as a guideline for preparation.


Learning Objectives

At the conclusion of this phase of the mystery molecule project, students will be able to

Effectively navigate sequence databases of the NCBI website
BLAST DNA sequence against the human genome
Analyze alignment data from genomic databases
Identify an unknown gene based on DNA sequence
Use the scientific literature (primary and secondary resources) to analyze gene products, and research the cellular and molecular basis of a disease gene.
Organize scientific content into a coherent presentation.
Communicate research results to a group of peers.
Step 1: BLAST your DNA sequence

Go to:
http://www.ncbi.nlm.nih.gov/

Click on BLAST (under “popular resources” at the right side of the screen)

Choose the nucleotide blast program (under “Web BLAST”)

In the “blastn” tab (on left) enter your DNA sequence into the “enter query sequence” box (obtain your mystery DNA sequences in the Mystery Molecule content area in D2L).

In “choose search set” click the “genomic + transcript databases”
From the drop down menu below, select “Human genomic + transcript (Human G + T)”
Under “program selection” in the next section down, optimize for highly similar sequences (megablast)

Submit query (click on “BLAST” at the bottom of the screen) and wait – this may take up to a few minutes.

A colorized map of sequence alignment scores will appear. Red indicates very good sequence alignment.

Scroll down to descriptions of sequences that produced statistically significant alignments. You should see options for genomic alignments and transcripts. An e-value close to zero, and maximum sequence identity close to 100% are optimal.

Identify your mystery gene/transcript from the description, e-value, and % sequence identity.
Step 2: Analysis of gene product

Click on the reference number (left, in the column labeled, “Accession”) for the mRNA transcript or genomic sequence of your mystery gene. Scroll down; you will see many references (titles, authors, years of publication) describing your gene. Clicking on any one of the PubMed reference numbers will link you directly to the original publication. You will need these publications to characterize your gene for your presentation. Bookmark this page—all your references must be from primary or secondary sources (no google, wikipedia, textbooks, blogs, etc.). You must use a minimum of 7 references that can be found by searching NCBI/PubMed in the completion of your project-note that this may require you to utilize interlibrary loan, so plan ahead.

From these references, the rest of NCBI’s resources (PubMed, genes and disease area of NCBI, etc.), and the knowledge you gained from Part I of this project, you should be able to determine answers to the following questions:

About the Gene:
What is the name of your gene?
Where in the human genome is your gene located (i.e., on which chromosome)?
About the Disease:
What disease is caused by mutation(s) in your gene?
What are the symptoms and signs of the disease?
How prevalent is the disease in the human population (how many people are affected; is it more likely to affect people based on gender/race/nationality; etc.)?
What is the expected outcome for people with this disease? Is it deadly? If so, what is the mortality rate? If not, what treatment is available to people affected by the disease?
What specific mutation(s) destroys the function of the gene product (NOTE: there may be more than one)?
About the Gene Product (RNA and protein):
How long is the mRNA transcript (in bases or kilobases)? Is there a difference between the wild-type and mutant forms?
How many exons are present in the transcript? Is there a difference between the wild-type and mutant forms?
How many amino acids are present in the final, wild-type protein product?
What change(s) in amino acids is(are) present in the mutant allele of this gene? How many amino acids are present in the mutant protein product?
About molecular mechanisms:
How does mutation affect the structure of your protein? How do these structural changes influence the function of your protein (i.e., does the mutation affect an enzyme’s active site or allosteric site? Or perhaps a transmembrane domain?)
What cellular and molecular processes are affected by mutation(s) in your gene? (NOTE: you might want to think of this in terms of major cellular systems, like transport, metabolism, structural proteins, etc.)

Step 3: Preparing an oral presentation

Use the information from your research to prepare an oral presentation. In addition to answering all of the questions from Step 2 above, your presentation should:

Last from 10-12 minutes, including questions.
Make use of visual aids, such as through a PowerPoint presentation.
Be logically organized, clear, and engaging for the audience.
Additional details about the mechanics of the presentation are found in the evaluation rubric below.

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