Name: Dr. Schacht
Directions
Unless you are copying a picture, sequence, or gene/disease name EVERY answer should be typed in
your own words. Each question has a total point value next to it. There are 150 points possible for the
entire exam. Every place an answer is needed is highlighted. For standard questions they are each in
yellow. Each question also has a blue highlighted section, where you will put what website(s) you used
to complete the problem.
Practical Exam – Online Portion
1. (10 pts) Find the closest chicken homolog to the following protein sequence. Synembryn-A What
percent of the protein overlaps the homolog? 88% How many of the amino acids in that section
are exact matches? 24% What website(s) did you use to get this information? BLAST
MASIGVSGPAKLQAVTTLIHKLTEDLKSTSLSPEERDKALEELKVYGRDPRNADPIFTKQGIETLTKHAFDSPSETTSRNALRVLCNAMLLIPETRQRFV
DLGYESKACEKLKNDNWDDEFLATRVIFFSTYGTTVDLAKLIDEHHLAESMVANLARHASRISEHAKNKTKPDPMELMALGETLRLLFNVTSKCPSKLDC
FTAAVPHIVTLLLSLDIPPPKGTPPLESPLSPLVNALMNLKLDSEEARSCLYPKDAPSSLAEKLITLLDLSLKAYSDQELDATVTPLVCIISSIYENAPA
DSPVRDFIRKSLLPSEEERNKVLGKGDTLPAKLLANMTNPIAPEFARAVSHLLFNVSDKDANKFVENIGYGYASGFLFQNNIPVPEGLGGDAEKGESSQA
GQSSRRAVNPITGQFLDTETFPDMPEMTMEEKEREAERLFVLFERARKLGIVNVENPVAKAVQEGRFEELPDDYEEDSD
2. (7.5 pts) Align the protein given in question 1 with the following protein. What are your
observations about the similarity between these two proteins? Low similarity, especially in the
N-terminus What website(s) did you use to get this information? MUSCLE
__Paste_Alignment_Here__
MDVVLESLKCLCNLVLSSPVAQMLAAEARLVVKLTERVGLYRERSFPHDVQFFDLRLLFLLTALRTDVRQ
QLFQELKGVRLLTDTLELTLGVTPEGNPPPTLLPSQETERAMEILKVLFNITLDSIKGEVDEEDAALYRH
LGTLLRHCVMIATAGDRTEEFHGHAVNLLGNLPLKCLDVLLTLEPHGDSTEFMGVNMDVIRALLIFLEKR
LHKTHRLKESVAPVLSVLTECARMHRPARKFLKAQVLPPLRDVRTRPEVGEMLRNKLVRLMTHLDTDVKR
VAAEFLFVLCSESVPRFIKYTGYGNAAGLLAARGLMAGGRPEGQYSEDEDTDTDEYKEAKASINPVTGRV
EEKPPNPMEGMTEEQKEHEAMKLVTMFDKLSRNRVIQPMGMSPRGHLTSLQDAMCETMEQQLSSDPDSDPD
3. (7.5 pts) Find the structure of the Human ADH1A. The N-terminus of the protein is composed
mainly of what secondary structure(s)? -sheet The C-terminus of the protein is composed
mainly of what secondary structure(s)? Mixed/ -helix What website(s) did you use to get this
information? PDB
__Paste_
_Here__
Name: Dr. Schacht
4. (10 pts) Human RIC8A is known to interact with Guanine Nucleotide (GN) binding proteins.
Which ones interact with it? __GNAQ, GNAI1, GNAO1, GNAS, GNAI3, __ Of the hits which are
attested by more than 1 experiment, which hit or hits would you consider less interesting for
further study? __UBC__ Why? __Interacts with everything__ What website(s) did you use to get
this information? __BioGRID___
5. (5 pts) Lactose intolerance is a disease that affects over 10% of the US population. Find a picture
of the pathway which is mutated in lactose intolerant individuals and paste it below. What
website(s) did you use to get this information? ___KEGG__
__Lactose_Intolerance_Pathway___
6. (10 pts) An important metabolic disease is PKU. What does PKU stand for? __Phenylketonuria__
How is it inherited? ___autosomal recessive__ What chromosome is the mutation located on?
___12__ What are the symptoms if untreated? ____ What is the treatment? __Altered diet___
What website(s) did you use to get this information? ___OMIM__
7. (5 pts) What is the protein sequence for hexokinase A isoform C in model fly? What website(s)
did you use to get this information? _____
Name: Dr. Schacht
__Paste_sequence_here___
8. (10 pts) What Chromosome is mouse adh1 on? __3_ How many alleles are there of this gene?
__6__ What Phenotypes are associated with the knock-out alleles? ___abnormal homeostasis,
growth, mortality__ What website(s) did you use to get this information? ___MGI__
9. (20 pts) Find the closest human hit for each of the best 2 interactors of yeast protein SNF4.
What website(s) did you use to get this information? ___SGD, BLAST__
Interactor 1: __SIP2, ___
Human hit of interactor 1: ___5’AMP-activated protein kinase subunit beta-2__
Interactor 2: __SNF1, __
Human hit of interactor 2: __5’AMP-activated protein kinase catalytic subunit alpha-2___
Which human hit is more likely to be a homolog? ___SNF1 or alpha-2__
10. (20 pts) Tay Sachs is a devastating disease similar to the lesser known Sandhoff disease. What is
the genetic difference between the two diseases? ___which subunit of hexosaminidase is
mutated__ Find the structure of the human protein that is affected by each disease (choose the
crystal structure for each that is not complexed with anything. Hint: don’t search for the 3-4
letter symbol, but the whole gene name)
Tay Sachs gene involved: __hexosaminidase A__
Name: Dr. Schacht
___Paste Tay_Sach_Protein_Structure_Here____
Sandhoff gene involved: __hexosaminidase B__
Name: Dr. Schacht
___Paste_Sandhoff_Protein_Structure_Here____
What website(s) did you use to get this information?
__OMIM, PDB___
11. (25 pts) Align the homologs of human rhodopsin (sequence below) to its homologs (if they exist)
in mouse, fruit fly, zebra fish, Arabidopsis, and rice.
MNGTEGPNFYVPFSNATGVVRSPFEYPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
PLNYILLNLAVADLFMVLGGFTSTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
KPMSNFRFGENHAIMGVAFTWVMALACAAPPLAGWSRYIPEGLQCSCGIDYYTLKPEVNNESFVIYMFVV
HFTIPMIIIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIAFLICWVPYASVAFYIFTHQG
SNFGPIFMTIPAFFAKSAAIYNPVIYIMMNKQFRNCMLTTICCGKNPLGDDEASATVSKTETSQVAPA
Give the protein sequences of the best hits here in FASTA format:
>mouse
MNGTEGPNFYVPFSNVTGVVRSPFEQPQYYLAEPWQFSMLAAYMFLLIVLGFPINFLTLYVTVQHKKLRT
PLNYILLNLAVADLFMVFGGFTTTLYTSLHGYFVFGPTGCNLEGFFATLGGEIALWSLVVLAIERYVVVC
KPMSNFRFGENHAIMGVVFTWIMALACAAPPLVGWSRYIPEGMQCSCGIDYYTLKPEVNNESFVIYMFVV
HFTIPMIVIFFCYGQLVFTVKEAAAQQQESATTQKAEKEVTRMVIIMVIFFLICWLPYASVAFYIFTHQG
SNFGPIFMTLPAFFAKSSSIYNPVIYIMLNKQFRNCMLTTLCCGKNPLGDDDASATASKTETSQVAPA
Name: Dr. Schacht
>fruit fly
MASLHPPSFAYMRDGRNLSLAESVPAEIMHMVDPYWYQWPPLEPMWFGIIGFVIAILGTMSLAGNFIVMY
IFTSSKGLRTPSNMFVVNLAFSDFMMMFTMFPPVVLNGFYGTWIMGPFLCELYGMFGSLFGCVSIWSMTL
IAYDRYCVIVKGMARKPLTATAAVLRLMVVWTICGAWALMPLFGWNRYVPEGNMTACGTDYFAKDWWNRS
YIIVYSLWVYLTPLLTIIFSYWHIMKAVAAHEKAMREQAKKMNVASLRNSEADKSKAIEIKLAKVALTTI
SLWFFAWTPYTIINYAGIFESMHLSPLSTICGSVFAKANAVCNPIVYGLSHPKYKQVLREKMPCLACGKD
DLTSDSRTQATAEISESQA
>zebrafish
MNGTEGPNFYVPMSNRTGLVRSPFEEPQYYLAEPWQFSLLAAYMLFLILGSFPINALTLYVTVQHKKLRT
PLNYILLNLAVADLFMVLGGFTVTLYTALHGYFLLGVTGCNIEGFFATLGGEIALWSLVVLAIERYIVVC
KPMSTFRFGEKHAIIGVGFTWVMALTCAVPPLLGWSRYIPEGMQCSCGIDYYTPKPEVHNTSFVIYMFIL
HFSIPLLIIFFCYSRLLCTVRAAAAQQQESETTQRAEREVTRMVVVMVIAFLVCWVPYASVAWYIFANQG
AEFGPVFMTVPAFFAKSAALYNPVIYIMLNRQFRNCMLSTVCCGKNPLAEDESSSAVSSKTQSSVVSSAQ
VSPA
>Arabidopsis
MQPNSHIFVIITISSLIITVSAYGSTGTIAAAFGENGFFCAIDASGKQEVICWDRGNTNRSLNRPPGEIS
GYSPPMTSLSGGEGFLCAITSNTSRAFCWNLEDPSENLVPRAFQYNSYLQIASGNNHVCAISGLYYSGPD
YGPVHCWEYSDNTNFTSGLLWNSSFHNPYIDSLMFRKIVSGDGFSCGVTKDGDLVCWGPKSNLLNFSNNE
EFEVLASGRNSVCGVSKDSGQLHCFGDETEFGSLPNRPRFIALSAGANHYCGIREDDHGVECWGRNLNSS
SSSSAPNTSGFVAISSSDSTTCGVRELDLVLDCWRVHDSSKADYSPPLELCSPGMCSPRGNCGDGWFAFN
ASILKESELTSLCSFHNLNICLRCGISCLEGYFPSSTCNPNADRVCTPCSLCQNSSCYGICKIRATKSKE
HEQKEQREVRRLVIIIGCSVLGFLVMLIGLSFIPKMTKGSKRDDEERSKMTCCFCFDKNSVEADPDPVPH
QSVLLPTAVSLGETKIFRLSELKDATHGFKEFNELGRGSFGFVYKAVLSDGIHVAVKRANAATIIHSNNR
GFESELEILCKIRHNNIVNLLGYCSEMGERLLVYEYMPHGTLHDHLHGDLSQLDWSMRLKIMLQAARGLD
YLHNEVDPPIIHRDVKTSNILLDGEMCARIADFGLVSSNERDSSNSDREGDVYDFGIVLLEILSGRKAID
RESDPAGIAEWAVPLIRKGKAAAIIDRNICLPRNVEPLLKLAELAELAVRENSNERPNIRNILCFLDLIV
KSGLTF
>Rice
MDSSAASAAAAAAAPVVLVTNDDGIDAPGLRFLVGQLVAARRYRVLVCAPDTDRSGVSHSITWRPALRCK
RVDIDGATAFAASGTPADCASLGISGKLFDGLVPDLAISGINVGNNCGCHVIYSGTVGGAREAFLYGIPS
LAMSYDWVASQSSVNDLKVAAEVVMPLINNVMAEIKNGTYPQGSFLNIDIPTDAAHHKGYKITKQGRYMA
RIGWEQTVYKKPAVESYQTANMDVDSEKDSEVDTSSENDLLFKRVLVRRSYDEEEGDDIDHKCLVDGYIT
VTPLGALSRAEADVIPYYKACLSRL
Which species have valid homologs? Which do not?
__Mouse, Fruit fly, zebrafish__
Explain why your observations about homologs makes sense – why should/ shouldn’t each of
these species have rhodopsin?
__Plants don’t have eyes, while animals do___
Make an alignment of the valid homologs of human rhodopsin and include it below:
__Paste_Alignment_Here___
Give your observations about the alignment:
__small gaps at N-terminus, large at C-terminus, fruit fly least similar__
What website(s) did you use to get this information?
Name: Dr. Schacht
___
__
12. Extra Credit: Visit OMIM and choose a disease not on this test and not heavily covered by this
class (not any form of muscular dystrophy, SCID, or Werner syndrome). For that disease, give
the:
Disease name: ____
Name of 1 gene associated with the disease: ____
Protein sequence coded for by the gene: ____
Name: Dr. Schacht
Practical Exam – Paper Portion
13. (20 pts) How many differences do the two sequences below have?
AGTGACTGCACGTC
AGAGTCTCCACGAC
The grid for the first set of distances has been supplied. Use it to calculate all additional grids,
and ultimately the tree for these 4 organisms.
A
B
C
D
A
0
4
12
2
B
4
0
7
8
AD
C
11
7
0
0
6
11
6
0
7
ADB
C
ADB
0
8.5
C
8.5
0
__|__
__|_
|
_|_ | |
| | | |
A D B C
D
2
8
10
0
B
AD
B
C
Tree:
C
12
7
0
10