Metabolism: Cytochrome C in Humans Compared to

Other Species Using Bioinformatics

We live in a human-centric world.

Human Metabolism

Sugar +

OxygenEnergy!

Aerobic respiration

1. Glycolysis2. Citric acid cycle3. Electron transport

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

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

Cytochrome C in eukaryotic mitochondria and bacteria

helps transfer electrons from one carrier to another.

Eukaryote Bacteria

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

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)

Amino Acids Sequences Make Up Cytochrome C Protein

MGDIEKGKKIFVQKCAQCHTVEKGGKHKTGPNLHGLFGRKTGQAVGFSYTDANKNKGITWGEETLMEYLENPKKYIPGTKMIFAGIKKKSERADLIAYLKKATNE

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?

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

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