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BLAST Lab
By Hana, Grace, Christina, and Ana
Overview
Overview
- Part A - Getting Started
- Part B - Structured Inquiry
- Part C - Guided Inquiry
- Part D - Open Inquiry
- Function
- Organism Relationships
- Gene Evolution
- Use of DNA sequencing and other characteristics in study of evolutionary relationships
- Goal and Data
- Conclusion - Cladogram
What is BLAST?
Basic
Local
Alignment
Search
Tool
BLAST LAB
Part A - Getting Started
Part A - Getting Started
- Develop basic understanding of cladograms & their construction
- Expression of genes in different organisms
Constructing a cladogram based on phenotypic traits
Constructing a cladogram based on phenotypic traits
Flowering plants
Pine trees
Ferns
Flowers
Mosses
Seeds
Vascular tissue
Why is the percentage similarity in the gene lower th...
Why is the percentage similarity in the gene lower than that in the protein?
Species
Gene % similarity
Protein % similarity
Cimpanzee (Pan Troglodytes) 99.6% 100%
Dog (Canis lupis familiaris) 91.3% 95.2%
Fruit fly (Drosophila melanogaster) 72.4% 76.7%
Roundworm (Caenorhabditis elegans) 68.2% 74.3%
- Difference in gene may still code for same codon sometimes
- Protein would be more similar, but gene would not
Cladogram based on genetic sequence
Humans
Chimpanzee
Dog
Fruit fly
Roundworm
What did T. rex taste like?
What did T. rex taste like?
- Folder 1
- taught all living things are related to a common ancestor
- Folder 2
- lineages show that animal species have their own history
- also share common ancestry (a part of their history)
- Folder 3
- explained how to draw a cladogram
- cladograms illustrate evolutionary relationships based upon shared features
Part B - Structured Inquiry
- Initially thought the fossil specimen was a rodent
- had a tail so it must be a vertabrate
- After collecting data we formed a new hypothesis
BLAST DATA
BLAST DATA
Sequence 1:
- Gallus Gallus (Chicken)
- Collagen Type V Alpha 1
- function: codes for alpha chain of the fibrillar collagen
- found in humans, birds, crocodiles
Sequence 2:
- Drosophila melanogaster (fruit fly)
- Shaker gene
- function: operation of potassium ion channels
- found in fruit flies
Sequence 3:
- Taeniopygia guttata (zebra finch)
- Ubiquitin conjugating enzyme
- function: catalyzes attachment of ubiquitin to other proteins
- found in humans, birds, turtles
Sequence 4:
- Alligator sinensis (Chinese alligator)
- Mitochondrion genome
- function: produces ATP in eukaryotic cells
- found in birds, crocodiles, turtles
Most important
Least important
Shaker gene
- only found in fruit flies
Collagen type V alpha chain
- forms collagen to support bones
Mitochondrion complete genome
- mitochondrion produce ATP and is necessary for eukaryotes
Ubiquitin conjugating enzyme
- ubiquitin can change and control the function of all other proteins
Hypothesis after using BLAST
Hypothesis after using BLAST
Crocodilians
Birds
Great Apes
Opposable Thumbs
Palatal valve
Feathers
Rodents
Fur
Based on our BLAST data, the 3/4 sequences were found in birds and crocodiles
Vertebrae
Part C - Guided Inquiry
Part C - Guided Inquiry
Genes sequences placed in BLAST:
- ATP Synthase
- Catalase
- GAPDH
- Keratin
- Myosin
- Pax1
- Ubiquitin
ATP Synthase
Function: Creates the energy of protons into ATP for eukaryotes
- ATP - adenosin triphosphate is the main energy source for metabolism
ATP Synthase
ATP molecule
Catalase
- Catalyzes the decomposition of hydrogen peroxide into hydrogen and water
- Found in all living organisms that are exposed to oxygen
Catalase
O
H
O
+
2
GAPDH
- Part of glycolysis, breaks down glucose to energy
- First step of cellular respiration
GAPDH
Keratin
- Present in epithelial cells (cells that make up the skin)
- Forms long strands - anchor cells to each other
- prevents cells from pulling apart
- called an intermediate filament
- Function
- form epidermis, hair and nails
- line internal organs
- form a barrier
Myosin
- Motor protein that plays a role in muscle contractions and cell contraction
Myosin
Pax1
- Important for the development of the vertebral column in fetuses
- Mutations may lead to abnormalities in the spine
Pax1
View inside spinal column from the top
Function of Ubiquitin
Part D: Ubiquitin
- Ubiquitination: the process of a ubiquitin molecule binding to other proteins and changing its outcome.
- Helps in the regulation of proteins using apoptosis
Apoptosis
Apoptosis
Organism Relationships
- Ubiquitin can be found in
- almost all human cellular tissues
- Eukatyote organisms
Organism Relationships
Can the same gene be found in 2 different organisms, b...
Can the same gene be found in 2 different organisms, but not the protein produced from that gene?
Yes
- A specific gene may be present in two different organisms
- Expression depends on the sites in which the pre-mRNA sequence is cut to make mRNA - splicing
- this alternative splicing could be caused by mutations - possibly have led to evolution of one species into another
Gene evolution
If you found the same gene in all organisms you test, what does this suggest about the evolution of this gene in the history of life on earth?
Gene
Evolution
This would suggest that all the organisms that have this gene share an early ancestor that they inherited the gene from.
Use of DNA sequencing and other characteristics in study of evolutionary relationships
Use of DNA sequencing
Does the use of DNA sequences in the study of evolutionary relationships mean that other characteristics are unimportant in such studies?
No, the use of DNA sequences doesn't mean that other characteristics are unimportant. While the DNA may be more reliable because you can't compare genes with more accuracy, other forms of analysis can still be very useful, just not as reliable as the DNA sequencing.
Goal
Data
- To compare human ubiquitin to other organisms' ubiquitin
- Using whole sequences of ubiquitin C (one of the sources of ubiquitin in humans)
Data
Data
Species with most similar genomes of ubiquitin C
- Macaca fascicularis (Crab eating macaque), score: 3387
- Macaca mulatta (Rhesus monkey), score: 3371
- Pan troglodytes (Chimpanzee), score: 3367
- Pongo abelii (Sumatran orangutan), score: 3330
- All e values of 0.0
Note that they are all primates, this tells us that:
- human's common ancestor is primates
- primates and humans have very similar ubiquitin genes
Conclusion - Cladogram
Homo sapiens (Human)
Pongo abelii (Sumatran orangutan)
Cladogram
Pan troglodytes (Chimpanzee)
Macaca mulatta (Rhesus monkey)
Macaca fascicularis (Crab eating macaque)