Download Human Metabolism Compared to Other Species

Metabolism:
Cytochrome C in Humans
Compared to Other Species
Using Bioinformatics
We live in a human-centric world.
Human Metabolism
Aerobic respiration
Sugar +
Oxygen
Energy!
1. Glycolysis
2. Citric acid cycle
3. Electron transport
Human Metabolism
Cytochrome C: protein in the e- transport
chain that transports electrons to oxygen
Outer mitochondrial
membrane
Inner mitochondrial
membrane
2
H+
Intermembrane
space
H+
Second
pump
1
4H+
1
Third
pump
2 H+
First pump
e–
H+
ATP
synthase
H2O
3
2 H 1+/2 O2
ADP
+
Pi H+
ATP
4 H+ NAD+
NADH
Matrix
Life exists outside our box.
Subtitle
Text
Shock & Holland (2007)
For example, there is life deep
down on the ocean floor.
C-DEBI
(Center for Deep Energy Biosphere Investigations)
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 ….
Cytochrome C suggests similarities
in metabolism
Eukaryote
Bacteria
Cytochrome C in eukaryotic mitochondria and bacteria
helps transfer electrons from one carrier to another.
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.
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
Our Subjects
4 eukaryotes: 2 humans, chimps and bees
Homo
Sapiens 1
(healthy)
Homo
Sapiens 2
(disease)
Pan
Troglodytes
Apis
mellifera
2 bacteria: prokaryotes that live in the deep ocean
Pseudonoma: aerobic, cold artic
Caldithrix abyssi: anaerobic, uses nitrogen
(not oxygen), hot thermal vents
Amino Acids Sequences Make Up
Cytochrome C Protein
MGDIEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAVGFSYTDA
NKNKGITWGEETLMEYLENPKKYIPGTKMIFAGIKKKSERADLIAYLKKATNE
Cytochrome C
Species
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
Results
Exercise 1: Identify with BLAST
BLAST is accurate at identifying cytochrome C
protein and the organism.
Results
Exercise 2: Compare species with BLAST
What does this table tell you about genome evolution?
Table 2. Amino Acid Identity Table for Cytochrome C
Cytochrome C
Homo Sapiens 1
Homo
Sapiens 2
100
Pan
Apis
troglodytes mellifera
94
75
Pseudonomas Caldithrix
abyssi
43
30
We are more closely related to eukaryotes than
bacteria.
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.
Discussion
• Do you support your hypotheses?
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.
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