Biochemistry
II Bioinformatics extra credit problem set
Answers
Due
April 20th in class.
Hand in your answers to the following questions on this page. You will need to give us feedback about the
web site in order to qualify for extra credit.
Use the links and their instructions from the Applications
section to help answer the following questions. More than one application may need to be used at a time. Hint: Keep all results from the applications open
until problem set is complete, you will most likely need them more than once.
1. (3 pts)Find the most probable origin for the
following protein sequence. Give the name of the gene, the organism it comes
from, and what protein it encodes?
MSSIVNKSGT RFAPKVRPRR AATGGTPTPK PRTPQLFIPE
SKEIEEDNSD NDKGVDENET
AIVEKPSLVG ERSLEPFTLT GTNGHDNEIG DEGPIDASTQ
NPKADVIEDN VTLKPAPLQT
HRDQKVPRSS RLASLSKDNE SRPSFKPSFL DSSSNSNGTA
RRLSTISNKL PKKIRLGSIT
ENDMNLKTFK RHRVLGKPSS SIVSKISPPT AMTDSLDRNE
FSSETSTSRE DENENYVISK
VKDIPKKVRD GESAKYFIDE ENFTMAELCK PNFPIGQISE
NFEKSKMAKK AKLEKRRHLR
ELRMRARQEF KPLHSLTKEE QEEEEEKRKE ERDKLLNADI
PESDRKAHTA IQLKLNPDGT
MAIDEETMVV DRHKNASIEY PRPSYTDPWT VEEMIKFYKA
LSMWGTDFNL ISQLYPYRSR
KQVKAKFVNE EKKRPILIEL ALRSKLPPNF DEYCCEIKKH
HMKEIEEAKN TAKEEDQTAG
RLNDANLNKK GSGGIMTNDL KVYRKTEVVL GTIDDLKRKK
LKERNNDDNE DNEGSEEEPE
IDQ
Should use single sequence alignment
tool, find out gene is TFC5 Yeast
protein product is TFIIIB90 from
Saccaromyces Cerevisiae.
2. (3 pts)Compare the sequence given in problem
one with the full sequence of the answer to problem one. What percent identity do they share?
Should use the following sequence,
and compare with the sequence given
in problem one.
MSSIVNKSGT RFAPKVRQRR AATGGTPTPK
PRTPQLFIPE SKEIEEDNSD NDKGVDENET
AIVEKPSLVG ERSLEGFTLT GTNGHDNEIG
DEGPIDASTQ NPKADVIEDN VTLKPAPLQT
HRDQKVPRSS RLASLSKDNE SRPSFKPSFL
DSSSNSNGTA RRLSTISNKL PKKIRLGSIT
ENDMNLKTFK RHRVLGKPSS AKKPAGAHRI
SIVSKISPPT AMTDSLDRNE FSSETSTSRE
ADENENYVIS KVKDIPKKVR DGESAKYFID
EENFTMAELC KPNFPIGQIS ENFEKSKMAK
KAKLEKRRHL RELRMRARQE FKPLHSLTKE
EQEEEEEKRK EERDKLLNAD IPESDRKAHT
AIQLKLNPDG TMAIDEETMV VDRHKNASIE
NEYKEKVDEN PFANLYNYGS YGRGSYTDPW
TVEEMIKFYK ALSMWGTDFN LISQLYPYRS
RKQVKAKFVN EEKKRPILIE LALRSKLPPN
FDEYCCEIKK NIGTVADFNE KLIELQNEHK
HHMKEIEEAK NTAKEEDQTA QRLNDANLNK
KGSGGIMTND LKVYRKTEVV LGTIDDLKRK
KLKERNNDDN EDNEGSEEEP EIDQ
Compare using aligning two sequences
program from NCBI
Should get 90 OR 91% identical
depending on alignment program used.
3. (3 pts)Using the full amino acid sequence,
determine the DNA sequence of the gene.
How many nucleotides in length is it?
Give the first and last ten nucleotides of the sequence.
Should use Backtranslation applet
from Entelechon and get 1782 nucleotides.
first ten ATG TCG TCG A
last ten A ATT GAT CAG
Due to degeneracy of codons,
different nucleotide sequences are possible.
4. (3pts)Which of the following restriction
enzymes cut the DNA and at what base pairs, using the complete DNA sequence
from your answer to question 3 (not just the 20 nucleotides you wrote
down).
ApaI, ClaI, EcoRI, BglI, HaeIII.
ClaI cuts 2x at 806 and 1121
HaeIII cuts 2x at 895 and 1081
ApaI, EcoRI, and BglI do not cut the
sequence.
Due to degeneracy of codons,
different answers are possible.
5. (3pts)Using the literature retrieval links,
find a paper describing a human homologue to this protein, and give a full
citation. (Hint: you may have to use
something other than PubMed)
Example answer from Web of Science
Different human TFIIIB activities direct RNA polymerase III
transcription from TATA-containing and TATA-less promoters
Schramm L, Pendergrast PS, Sun YL, Hernandez N
GENES & DEVELOPMENT
14 (20): 2650-2663 OCT 15 2000
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