Integrative Assignment
Part I
Give a description of your organism.
Homo sapiens is the primate species to which all modern humans belong.
The closest relatives are chimpanzees from which they are distinguished by greater size, a peculiar
distribution of hair, and a larger carbon footprint.
Humans are primarily terrestrial animals and can be found on all continents. They are possibly the
most thoroughly studied organism although mice, E. coli, and Drosophila are also in the running.
(Kibak, Personal Communication).
We study humans because we are self-obsessed.
Domain: Eukaryota
Kingdom: Metazoa
Superphylum: Deuterostomia
Phylum: Chordata
Subphylum: Craniata
Superclass: Euteleostomi
Class: Mammalia
Subclass: Eutheria
Superorder: Euarchontoglires
Order: Primates
Suborder: Haplorrhini
Superfamily: Catarrhini
Family: Hominidae
Genus: Homo
Species: sapiens
Figure above is from the National Geographic Genographic Project.
Use an initial upper-case letter with the Genus name, initial lower-case
letter with the species name. BOTH (and all foreign words) are italicized.
Why organisms are studied:
A. Ease of rearing or culture (e.g. Tribolium Red Flour Beetle, mouse,
Arabidopsis, E. coli, Drosophila)
B. Important in agriculture (Potato, Cow, Gibberella zeae)
C. Important in medicine or disease (Penicillium marneffei ,Aedes
aegypti, Ixodes scapularis)
D. Important in industry (Kluyveromyces lactis, Yarrowia lipolytica)
E. Extremist in some way (Emperor Penguin, Elephant Seal, Canis lupus
familiaris)
F. Ideal for one type of question for some reason (Sea Urchin,
Neurospora, Danio rerio, Mytilus spp. )
Where in the cell is Cytochrome c found?
What does Cytochrome c do?
Cytochrome c diffuses back and forth between Complexes III and IV, being reduced by
electrons from Complex III and oxidizing Complex IV as it offloads the electrons. See
texbook, (Freeman, Biological Science).
Cytochrome c is also a key protein in the
regulation of apoptosis (Jiang & Wang,
2004)
Cytochrome c (pink)
Outer Mitochondrial Membrane
Inter-membrane space
Inner Mitochondrial
Membrane
Mitochondrial Matrix – Krebs Cycle
Image courtesy of Research Collaboratory for Structural Bioinformatics “Molecule of the Month!”
Cytochrome c is a peripheral
membrane protein found on the
inner mitochondrial membrane as
a part of the Electron Transport
Chain.
Cytochrome c accepts electrons
from Cytochrome c1 of Complex
III and transfers them to
Cytochrome a of Complex IV
(also known as Cytochrome c
oxidase).
• Using the amino acid single letter code,
write the primary structure of the
Cytochrome b found in your organism.
(citation)
• How many amino acids are contained in
Cytochrome b from your organism?
To Answer Those Questions You Could:
Google “cytochrome
c” amino acid sequence Aedes
aegypti to find information or use Google Scholar:
But you will probably find too much advanced material to wade through…
NCBI
• Instead of using Google and the web, a better
approach is to use the National Center for
Biotechnology Information (NCBI) website.
• NCBI is essentially “Google” for DNA and
Protein sequences.
Directions to Find the Cytochrome c for
Your Organism
•
Google NCBI
•
In the NCBI’s front page search box type in species name and Cytochrome c
•
To the right, in the drop down menu, switch from “all databases” to “protein” and then
click search.
•
Look through the search results starting at the top. You need to find a cytochrome C
that is about 105aa long. It will say near the top of each article. Your protein WILL
NOT BE “Cytochrome c Oxidase” – you will also have to retrieve that one for this
assignment, but a bit later.
•
Once you find the right protein (about 100-120 aa’s long and correct species), switch
GenPept to FASTA, you now have a more useable format.
•
Copy and paste to a notebook document. Save this file for for later. Copy and past
the nicely formatted courier font sequence into your WORD document.
This is a good one
This one is too short
FASTA is the format you want for your analysis.
Note that all Cytochromes c
have 95-120 amino acids.
So here is the human Cytochrome c amino acid sequence…
You need to do the same for your organism.
This is the FASTA format for human Cytochrome c.
It is displayed in a non-proportional font called “courier.”
All your sequence data MUST BE DISPLAYED in COURIER.
FASTA format has two requirements.
1. The first line has a “>” and contains information.
2. The following lines are sequence.
>gi|11128019|ref|NP_061820.1| cytochrome c [Homo sapiens]
MGDVEKGKKIFIMKCSQCHTVEKGGKHKTGPNLHGLFGRKTGQAPGYSYTAANKNKGIIWGE
DTLMEYLENPKKYIPGTKMIFVGIKKKEERADLIAYLKKATNE
How many amino acids are contained in
Cytochrome c from your organism?
What proportion of these amino acids are
hydrophobic?
Provide the best illustration you can for the
tertiary structure of human Cytochrome c.
Strategy
1. Take the human Cytochrome c sequence and search the structure
(PDB) database in NCBI for similar sequences for which the
structure has been solved.
2. Download Cn3D to display the structure.
3. Export the structure as a PNG file.
1. Select protein blast at NCBI BLAST http://www.ncbi.nlm.nih.gov/BLAST/
2. Paste sequence. 3. Select “Protein Data Bank” 4. Select “blastp”
Be PATIENT! The page will sit here for a while… updating several times until
suddenly the results page appears.
Click on the first structure link and see what it is… If it
makes sense, then click on the S.
First you will see this
page.
Then you will see
this page
If you don’t have
Cn3D installed,
download it. You
won’t need admin
privileges.
It is a lot easier to work with peripheral membrane proteins than integral
membrane proteins. Crystal structures have been solved for Cytochrome
c from many organisms.
http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?db=t&form=6&dopt=s&uid=27574
If link doesn’t work, go to next page…
Just like Cytochrome b,
Cytochrome c has a heme
group that is good at binding
and releasing electrons.
Where in the cell is Cytochrome c Oxidase found?
What does Cytochrome c Oxidase do?
Cytochrome c Oxidase is a protein in
Complex Four of the Electron Transport
Chain… would that make it an integral
membrane protein?
Human Cytochrome c Oxidase
Human mitochondrion http://www.ncbi.nlm.nih.gov/nuccore/251831106?report=graph
>ref|YP_003024028.1 cytochrome c oxidase subunit I Homo sapiens 513aa
MFADRWLFSTNHKDIGTLYLLFGAWAGVLGTALSLLIRAELGQPGNLLGNDHIYNVIVTAHAFVMIFFMV
MPIMIGGFGNWLVPLMIGAPDMAFPRMNNMSFWLLPPSLLLLLASAMVEAGAGTGWTVYPPLAGNYSHPG
ASVDLTIFSLHLAGVSSILGAINFITTIINMKPPAMTQYQTPLFVWSVLITAVLLLLSLPVLAAGITMLL
TDRNLNTTFFDPAGGGDPILYQHLFWFFGHPEVYILILPGFGMISHIVTYYSGKKEPFGYMGMVWAMMSI
GFLGFIVWAHHMFTVGMDVDTRAYFTSATMIIAIPTGVKVFSWLATLHGSNMKWSAAVLWALGFIFLFTV
GGLTGIVLANSSLDIVLHDTYYVVAHFHYVLSMGAVFAIMGGFIHWFPLFSGYTLDQTYAKIHFTIMFIG
VNLTFFPQHFLGLSGMPRRYSDYPDAYTTWNILSSVGSFISLTAVMLMIFMIWEAFASKRKVLMVEEPSM
NLEWLYGCPPPYHTFEEPVYMKS
Source: http://www.rcsb.org/pdb/101/motm.do?momID=36
You can use
wikipedia but
you can’t cite
it.
Citation style = APA (see http://www.library.cornell.edu/resrch/citmanage/apa )
Freeman, S. (2011). Biological Science (4th Ed.). San Francisco: Pearson
Benjamin Cummings.
Jiang X, & Wang X. (2007). Cytochrome C-mediated apoptosis. Annual
Review of Biochemistry, 73, 87-106.
Mitochondrial ATP Synthase
http://classes.csumb.edu/BIO/BIO241-01/campus/Lecture10respiration/ATPase.flv
http://multimedia.mcb.harvard.edu/anim_ATPase_flv.html
http://carbon.cudenver.edu/~bstith/1418m.mov