Week #16 Scientist: Rosemary Puckett
Week #16 Scientist: Rosemary Puckett
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WE MOVED!!! CLICK HERE:
BioBus Explore! at Home Challenge
BioBus Explore! at Home Challenge
Step 1: Watch the video!
Step 1: Watch the video!
Step 2: Do the challenge! Use the resources and worksheets below to help with your experiment.
Step 2: Do the challenge! Use the resources and worksheets below to help with your experiment.
Step 4: Try another science challenge!
Step 4: Try another science challenge!
We want to know what you discovered when you did the challenge!
We want to know what you discovered when you did the challenge!
We'll feature the research and questions you share!
We'll feature the research and questions you share!
That means other scientists can learn from your work.
That means other scientists can learn from your work.
RESOURCES
RESOURCES
The database we're going to ask BLAST to search inside for this experiment is called the Universal Protein Resource (uniprot.org)
The database we're going to ask BLAST to search inside for this experiment is called the Universal Protein Resource (uniprot.org)
1.) Get on the internet and visit www.uniprot.org to get started.
*. REMEMBER, WE'RE STARTING OUT COMPARING THE PROTEIN SEQUENCES OF OTHER SPECIES TO THE PROTEIN SEQUENCE FROM HUMANS (HOMO SAPIENS), SO WE'LL NEED TO INCLUDE "HUMAN" IN OUR UNIVERSAL PROTEIN RESOURCE SEARCH
2.) Enter your sample protein into the search bar, specifying the species (ex. "Human BDNF") and hit BLAST.
SAMPLE PROTEINS: BDNF, MGLUR, MBP, TIMELESS
SAMPLE PROTEINS: BDNF, MGLUR, MBP, TIMELESS
(BDNF: brain-derived neurotrophic factor; mGluR: metabotropic glutamate receptor; MBP: myelin basic protein; TIMELESS: a circadian clock protein)
3.) When you get your results, click on the ENTRY that matches the protein ("brain-derived neurotrophic factor") and the species ("Homo sapiens") that you want to compare against.
4.) This will bring up the database entry page for that protein sequence in that species. There's a lot of cool info here! To run a BLAST experiment, click on the BLAST button at the top with the wrench icon. (Select "default" and hit Go!)
Now the BLAST is running!
Now the BLAST is running!
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Be patient, it might take a few minutes.
5.) Once you get your results, you can scroll down and observe the identity alignments. Look at how closely the sequence for that particular protein in several different species compares to that protein's sequence in your referral species (in this example, the "referral species" is Homo sapiens).
This list is ordered from the closest alignment at the top (~100%) through more and more distantly aligned as you scroll down.
You could also choose a specific species to compare protein sequences with if you can find its scientific name from All the Organisms in the list on the left.
You could also choose a specific species to compare protein sequences with if you can find its scientific name from All the Organisms in the list on the left.
** Hack the Code - PANTR is their shorthand for "Pan troglodytes" which are chimpanzees ~ our closest living relative! **
For example, here we're comparing the BDNF sequence in a human to the BDNF sequence in an alligator.
They have 91.5% alignment!
BLAST Worksheet
BLAST Worksheet
*. Play around and explore the similarities and differences among different living species.
Fill in all the species that you investigate to compare their protein sequences against your referral species.
FOR EXAMPLE, HERE ARE SOME OF OUR FAVORITES...
Record how aligned the protein sequence is from each of your experimental species when compared to that protein's sequence in humans. Are they similar or different?
What happens if you run the experiment using another species besides human as the one you compare the others against (in other words, what if you change your referral species and do your BLAST experiment again)?
TRY MAPPING THE RELATIONSHIPS OUT and BUILDING AN EVOLUTIONARY TREE
More Resources to Explore
More Resources to Explore
DNA and Proteins
DNA and Proteins
DNA Learning Center
Explore more about DNA, genetics, and biotechnology with online resources from the DNA Learning Center. Check out the Biology Animations featuring stunning visualizations of cellular and molecular processes. Learn more about student research projects using DNA barcoding to study biodiversity with the Urban Barcode Research Program. Find out how these NYCSRMC partners are using genetic tools to investigate our urban environment and natural history.
Genetics and Evolution
Explore the basics of genetics and epigenetics and dive deeper into how genetics influences everything from neuroscience to plants to ecology and beyond with this Learn Genetics resource from the Genetic Science Learning Center at the University of Utah. Investigate more ways to use DNA as a scientific tool.
BioBus Student Town Hall
Watch Dr. Teaster Baird and Dr. Christine Marizzi answer student questions about DNA, inheritance, genetic tools, and the code for genes and proteins in this edition of BioBus's weekly Student Town Hall series. What is inheritance? Can DNA be a helpful tool? How do our genes react in our life? Listen to the scientists discuss these things and more. Find more scientific Student Town Halls at www.biobus.org/townhall and ask YOUR questions to the experts!
DNA Databases and the Recent Evolution of Humans
Read a science article from The Atlantic about what biologists and anthropologists are learning about genes important to recent human evolution using these bioinformatics tools and techniques.
You can also tag @biobus from your social media to show us your challenge activities and get a BioBus Shout-Out!
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