Adapted from College Boards Investigation 3 Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST What we know so far We already know that DNA can be used to identify animal species at a genetic level ID: 712139
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Slide1
Using BLAST to Identify Species from Proteins
Adapted from College Board’s “Investigation 3: Comparing DNA Sequences to Understand Evolutionary Relationships with BLAST”Slide2
What we know so far...
We already know that DNA can be used to identify animal species at a genetic level
According to the Central Dogma of Biology, DNA is transcribed into RNA and translated into proteins
If DNA is not present in a bone specimen, other biological material can be acquired to identify a fossilSlide3
Today’s Goal
Become acquainted with BLAST for protein analysis
Identify the relation of extinct dinosaurs to modern species and where dinosaurs fit in on a family tree
Understand how phylogenetic trees depict evolutionary relationships Slide4
What you will need to know
What is BLAST, and how is it used?
Why is BLAST important?
What is a phylogenetic tree?What are orthologs?
How can proteins be used to identify evolutionary relationships?Slide5
What is BLAST?
B L A S T
Basic
Search
Local
Alignment
ToolSlide6
Why is BLAST useful?
BLAST makes it easy to search databases that contain many millions of partial, full, and potential gene sequences
It can be used to compare sequences from one species to another to identify similarities or differences
Knowing the identity of gene sequences from many species allows scientists to track evolutionary heritage of those speciesSlide7
What is a phylogenetic tree?
Diagram that depicts the evolutionary relatedness of species or groups of closely related species
Each endpoint of a branch represents a group of organisms
The closer two branches on a tree are, the more related the groups areSlide8
What are orthologs?
Orthologs are genes in different species that evolved from a common ancestral gene
Basically, they are genes with the same or similar functions in different species
Ex. Human and mouse genesSlide9
How can proteins be used to identify genetic relationships?
Proteins are composed of different combinations of amino acids
The genetic code (DNA/RNA) is used to identify each amino acid to then add on to a growing chain (protein)
There are 20 amino acids and 64 possible combinations of RNA building blocks- some amino acids are repeated!
We can examine differences in protein sequences between species to infer evolutionary relationshipsSlide10
Activity: Identify Evolutionarily Related Protein Sequences
You are a member of a scientific team that has discovered 3 well preserved bone fossil specimens
T. rex
, mastodon, and hadrosaurSmall amounts of tissue have been removed from the fossil
Unusual in such ancient specimens
Amino acid sequences have been extracted from protein fragments
First time this has ever happened!Slide11
Activity: Identify Evolutionarily Related Protein Sequences
Use BLAST to compare these amino acid sequences to protein sequences from other species
Then, create a phylogenetic tree to explore where these extinct species might branch off from the evolutionary treeSlide12
Step 1
Form an initial hypothesis as to where and why you think the three extinct species (
T. rex
, hadrosaur, mastodon) belong on the phylogenetic treeSlide13
Step 2
Locate and download the protein fragment files for the fossilized bone specimensSlide14
Step 3
Upload the sequence into BLAST
Go to BLAST homepage:
https://blast.ncbi.nlm.nih.gov/Blast.cgi Click on “Protein BLAST” Slide15
Step 3
Under “Enter Query Sequence,” paste the first amino acid sequence from “Protein #1”
Do not change any of the settings on the rest of the page
Scroll down and hit “BLAST”Slide16
Step 4
The results page has 2 sections
The first is a graphical display of the matching sequencesSlide17
Step 4
Scroll down to the section titled “Sequences Producing Significant Alignment”
The species in this list are the ones with sequences identical to or most similar to the amino acid sequence of interest
The most similar sequence is listed first
If you click on a result listed, you will get a full report of the species Slide18
Step 4Slide19Slide20
Now that you have this information...
Follow the PDF instructions for the BLAST search of the fossilized
T. rex
bone amino acid sequenceIf you still have time at the end of class and want to practice and explore more, repeat the activity for the hadrosaur and mastodon fossil specimens