Name:
Are you a graduate or undergraduate student? Please circle one.
Bioinformatics Take Home Test #4
(This is an open book exam based on the honors system -- you can use notes, lecture notes, online manuals,
and text books.
Teamwork is not allowed on the exams, write down your own answers, do not cut and paste from webpages.
If your answer uses a citation, give the source of the quoted text.)
1. 1pt Which organism have primary plastids, i.e. plastids that evolved directly from a
cyanobacterial endosymbiont?
2. 1pt List at least three groups of organisms that have secondary plastids, i.e. plastids that evolved
form a secondary endosymbiosis with a eukaryotic algae.
3.
1pt Which biomolecule was first used to place microorganisms onto the tree of life?
4.
1pt Mitochondrial Eve" lived around 200000 years ago. Which genes in modern human trace their
ancestry to this person?
5.
1pt Were other humans alive at the same time as "Mitochondrial Eve"? Yes /No
6.
1pt Describe the origin of Mitochondria in less than twenty words.
7.
1pt Do cyanobacteria (also sometimes called blue green algae) have plastids? Yes /No
8.
1pt A group of organisms that is defined be a shared primitive character is
A) monophyletic
B) paraphyletic
C) polyphyletic
9.
2pt According to Hennig a natural taxonomy should be based on (circle all that apply, more than one might
be correct)
- clades,
- monophyletic groups,
- paraphyletic groups,
- shared derived characters,
- synapomorphies,
- symplesiomorphies,
- autapomorphies.
10. 1pt An autapomorphy of a group of organisms is useful in establishing the relation between this group and
other groups. correct / incorrect
11. 1pt If you have an unrooted tree (i.e. you don't know where inside the tree the ancestor is located), can you
define clades using this tree?
Yes /No
12. 3pt Prokaryotes are characterized by the absence of a complex internal membrane system, in particular,
they do not have a membrane system (= nuclear envelope) surrounding their genetic material.
a. Is the absence of the nuclear envelope a sympleisiomorphy or a synapomorphy?
Yes /No
b. Is the group formed by the presence of this character a proper taxonomic category, i.e. monophyletic?
c.
Is there any value in the term Prokaryotes or should it be thrown away?
13. 2pt Archaea and Eukaryotes both have so-called TATA binding proteins, which play an important role in
directing the RNA polymerase to the promoter, whereas bacteria do not have a homologous protein.
Do you consider the presence of a TATA binding protein a shared derived character?
Yes /No
Is this a valid argument to support shared ancestry between Archaea and at least part of the eukaryotic
nucleocytoplasmic component?
Yes /No
14. 1pt In defining protein space JALVIEW uses A) the presence or absence of a conserved sequence motif to define protein space
B) each alignment column as a dimension to define protein space
C) a tree based on percent identity to define a groups that are close to each other in sequence space
15. 2pt What are the three steps clustal performs to align sequences?
16. 1pt Does clustalx2 provide for the possibility to treat gaps inserted at the beginning and end of a sequence
differently from gaps inserted into the middle of a sequence?
Yes /No
17. 1pt Does clustalx2 allow for different gap opening and extension penalties?
18. 1pt A pairwise sequence alignment calculated with the Needleman-Wunch algorithm is the best possible
alignment given the parameters (scoring matrix, gap penalty). A) this alignment is always better in aligning homologous structures than a multiple sequence alignment B) The Needleman-Wunch algorithm provides the single best alignment. C) The alignment is optimal (as measured by the alignment score), but there might be many equally optimal
pathways/traces through the scoring table.
19. 1pt According to the currently favored version of the tree of life, which prokaryotic domain is the closest
relative of the nucleocytoplasm?
Extra credit:
20. 1pt What happened to cause the downfall of the Five Kingdoms of Life? Is this concept totally useless, or is
there some value left to cling to?
21. 1pt Chloroplasts are maintained in the cell as an organelle with the aid of genes horizontally acquired from
Chlamydia, an intracellular parasite. Can you think of any similar mechanism that would allow
mitochondria to be retained as organelles?
22. 1pt Why is it easier to look back into the origins of chloroplasts than it is to look into the origins of
mitochondria?
For Graduate Students: Short essays please.
23. 3pt Why are gaps important in alignments (what would happen to alignment with no gaps and to an alignment
with an infinite number of gaps)? What biological phenomena cause gap in alignments? And how does gap
placement relate back to homology?
24. 3pt Why are synapomorphies useful in defining clades? What is it about these characters that make them better
than other characters? In biology, why is it more useful to study monphyletic grouping than it is to study
paraphyletic groups?