Metabolism: Cytochrome C in Humans Compared to Other Species Using Bioinformatics.
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Transcript of Metabolism: Cytochrome C in Humans Compared to Other Species Using Bioinformatics.
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Metabolism: Cytochrome C in Humans Compared to
Other Species Using Bioinformatics
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We live in a human-centric world.
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Human Metabolism
Sugar +
OxygenEnergy!
Aerobic respiration
1. Glycolysis2. Citric acid cycle3. Electron transport
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Human Metabolism
Cytochrome C: protein in the e- transport chain that transports electrons to oxygen
H+
2 H +1/2O2
+Pi H+
H+
e– 4 H +
H2O
2
3
H+
ATPsynthaseFirst pump
Intermembranespace
Secondpump
Thirdpump
2 H+
ADP
ATP
Matrix
NAD+4 H+
NADH
1
1
Inner mitochondrialmembrane
Outer mitochondrialmembrane
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Life exists outside our box.
Subtitle
Text
Shock & Holland (2007)
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For example, there is life deep down on the ocean floor.
C-DEBI (Center for Deep Energy Biosphere Investigations)
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Do these different organisms all metabolize in the same way?
No!• Some are aerobic or anaerobic• Some use oxygen or sulfur, iron, nitrogen • Some are faster or slower
BUT ….
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Cytochrome C suggests similarities in metabolism
Cytochrome C in eukaryotic mitochondria and bacteria
helps transfer electrons from one carrier to another.
Eukaryote Bacteria
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Purpose of today is to
1. Understand and use bioinformatics.
2. Compare and contrast sequences.
3. Relate sequences from various species to genome evolution and protein function.
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Hypotheses
1. Shared ancestry common amino acid sequences in cytochrome C
2. Similar metabolism function common amino acid sequences in cytochrome C
3. Genetic disease of cytochrome C protein different amino acid sequences of cytochrome C
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Our Subjects
2 bacteria: prokaryotes that live in the deep ocean
Pseudonoma: aerobic, cold artic
Caldithrix abyssi: anaerobic, uses nitrogen (not oxygen), hot thermal vents
Homo Sapiens 1(healthy)
Pan Troglodytes
Apis mellifera
4 eukaryotes: 2 humans, chimps and bees
Homo Sapiens 2 (disease)
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Amino Acids Sequences Make Up Cytochrome C Protein
MGDIEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAVGFSYTDANKNKGITWGEETLMEYLENPKKYIPGTKMIFAGIKKKSERADLIAYLKKATNE
Cytochrome C Species
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Start Comparing Sequences!Three exercises (watch posted youtube videos)
1. BLAST: identify accuracy of given amino acid sequences (figure out unknown)
2. BLAST: compare amino acid sequences for cytochrome C between species
3. Sea View: visually align cytochrome C amino acid sequences for all 6 species
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Results
Exercise 1: Identify with BLAST
BLAST is accurate at identifying cytochrome C protein and the organism.
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Results
Exercise 2: Compare species with BLAST
What does this table tell you about genome evolution?
We are more closely related to eukaryotes than bacteria.
Cytochrome C Homo Sapiens 2
Pan troglodytes
Apis mellifera
Pseudonomas Caldithrix abyssi
Homo Sapiens 1 100 94 75 43 30
Table 2. Amino Acid Identity Table for Cytochrome C
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Results
Exercise 3: Visually align cytochrome C sequence with Seaview
Cytochrome C has conserved regions across species due to its common functions as an electron transporter.
Cytochrome C differs the most in an anaerobic organism because electron is transported to nitrogen and not oxygen.
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Discussion
• Do you support your hypotheses?
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Summary
• Humans and other organisms share some common amino acid sequences for cytochrome C with both eukaryotes and bacteria suggesting a common ancestry.
• If amino acid sequences for cytochrome C are more similar, then there is more similarity in metabolism function.
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TOOLKIT CREDITS: Developed by Angela Gee, (Los Angeles Trade Tech Community College, CA) and Marissa Pantastico-Caldas, Los Angeles Trade Tech Community College (CA) with data and guidance by John Kirkpatrick (University of Rhode Island, RI) with and support by the rest of the C-DEBI Collaborative Toolkit Team. WEBSITE: http://www.coexploration.org/C-DEBI/toolkits_biology.html