MCB/EEB372
Exam 1 (take
home, return by March 29)
An electronic copy of this exam is available on the MCB372 - homepage
1) Assume that the following protein sequence were
obtained from the translation of a putative ORF of a thermophilic
bacterium:
>ORF
with unknown function
MIALILSREAIAGSCGGLRDVKQRRLILELPSDNICYMNPAGSSIHYKGRKLPHAVFDIPRIGVDGPLRDTAALRQFEMLGSYPLNESVAIARARDKLRSMQLLARQGIDLPVTGIAHSPDDTSDLIDMVGGAPLVVKLVEKGTGIGVVLAETRQAAESVIDAFQEYRGLNAHILVIKEAQGCDIRCVSGDTPVLLDAGERRIGDLFMEAIRPKERGEIGQNEEIRVLHDWRIYSGSMVETVEIVSIYHVKIGNAHGKSVRTENGREVRVTPVHKLFNAIVNSVIERPASEVNEGDEIAWPSVSENGDSQTVTTTFLVLDRVVSEMKHSGVFDVYDLMVPDYGYNFIGGNGLIVLHNCLVVGDEVVGCYARNIPPNDFRSNLNIGGAASVASITPQEREIAIAVGRTMALDVAGVDIVLMENDRAGNGPPGILVSLETTGGEKIAIDGKMIRYWITRHETTEAGLGCK
What might be the catalytic activity or function(s) of this protein?
Is
there a common
functional or structural feature among the homologous proteins? What does this tell you
about the protein encoded by this ORF?
Which catalytic activities would you expect for the encoded protein?
Briefly describe how you went about to find homologues to this sequence.
2) Background information: The Pyrococcus A-ATPases have been sequenced as part of
three different genome projects. In all
cases an additional sequence, an intein, was found inserted into the A
subunits. The A-ATPase A-subunit is
homologous to the F-ATPase beta subunits.
Where is the intein located in the Pyrococcus
A-ATPase A-subunits?
Utilizing the homology to the F-ATPases, determine which place of the F1-ATPase structure
(1bmf) corresponds to the intein integration point.
Your
short written answer should include a short description of the tools you used to address this question, and a picture of
the F1-ATPase with the residues homologous to the intein integration point
indicated.
It is
sufficient to use a pen and to draw an arrow pointing to the integration points
in this picture.
3) The following file (here)
contains sequences of several vacuolar ATPase A-subunits and prokaryotic
V/A-ATPase catalytic subunit. Using the
tools of bootstrapping, ml-mapping and/or ml ratio tests address the following
questions:
Do all of the bacterial sequences (Chlamydia,
Chlamydiophila, Enterococcus, Thermus, Deinococcus, Treponema and
Borrelia) form a monophyletic group?
Can one confidently exclude this possibility? Would the answer change, if
one only considers the sequences from Chlamydia, Chlamydiophila, Treponema and
Borrelia?
To incorporate among site rate variation into your model, use a Gamma
distribution with 8 categories and a shape parameter alpha of 0.6. Good starting point to design hypotheses are
the following (names truncated to 10 characters):
A completely resolved tree calculated via neighbor joining from pairwise distances
(((Deinococcu,Thermus),((Enterococc,(((Archaeoglo,(BMethanosa,MMethanosa)),(Haloferax,Halobacter)),
(Thermoplas,(((Thermococc,Desulfuroc),(aPyrococcu,hPyrococcu)),(jMethanoco,Methanobac))))),
((1Treponema,(Aeropyrum,(aSulfolobu,sSulfolobu))),((Chlamydia,Chlamydoph),(2Treponema,Borrelia))))),
(Giardia,(Plasmodium,((Entamoeba,((Dictyostel,((Ascidia,(Bos1,Manduca)),(Nosema,(Saccharomy,
Neurospora)))),(Cyanidium,(Arabidopsi,(2Acetabula,Scherffeli))))),(Trypanosom,Trichomona)))));
A tree that has all branches collapsed that were not significantly positive is the following:
(((Deinococcu,Thermus),(Enterococc,(Archaeoglo,(BMethanosa,MMethanosa),(Haloferax,Halobacter)),
Thermoplas,((Thermococc,Desulfuroc),(aPyrococcu,hPyrococcu)),(jMethanoco,Methanobac),(1Treponema,
(Aeropyrum,(aSulfolobu,sSulfolobu)),((Chlamydia,Chlamydoph),(2Treponema,Borrelia))))),(Giardia,
(Plasmodium,Trichomona,Trypanosom,Entamoeba,((Dictyostel,((Ascidia,Bos1,Manduca),(Nosema,(Saccharomy,Neurospora)))),(Cyanidium,(Arabidopsi,(2Acetabula,Scherffeli)))))));
