Name: __________________
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. _____ What
percent of the protein overlaps the homolog? _____ How many of the amino acids in that
section are exact matches? ____ What website(s) did you use to get this information? _____
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? ____ What website(s) did you
use to get this information? _____
__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)? ______ The C-terminus of the protein is composed
mainly of what secondary structure(s)? _____ What website(s) did you use to get this
information? _____
__Paste_Picture_Here__
4. (10 pts) Human RIC8A is known to interact with Guanine Nucleotide (GN) binding proteins.
Which ones interact with it? ____ Of the hits which are attested by more than 1 experiment,
which hit or hits would you consider less interesting for further study? ____ Why? ____ What
website(s) did you use to get this information? _____
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? _____
__Lactose_Intolerance_Pathway___
Name: __________________
6. (10 pts) An important metabolic disease is PKU. What does PKU stand for? ____ How is it
inherited? _____ What chromosome is the mutation located on? _____ What are the symptoms
if untreated? ____ What is the treatment? _____ What website(s) did you use to get this
information? _____
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? _____
__Paste_sequence_here___
8. (10 pts) What Chromosome is mouse adh1 on? ___ How many alleles are there of this gene?
____ What Phenotypes are associated with the knock-out alleles? _____ What website(s) did
you use to get this information? _____
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? _____
Interactor 1: _____
Human hit of interactor 1: _____
Interactor 2: ____
Human hit of interactor 2: _____
Which human hit is more likely to be a homolog? _____
What website(s) did you use to get this information?
_____
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? _____ 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: ____
___Paste Tay_Sach_Protein_Structure_Here____
Sandhoff gene involved: ____
___Paste_Sandhoff_Protein_Structure_Here____
What website(s) did you use to get this information?
_____
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:
___Best hit of each in FASTA___
Name: __________________
Which species have valid homologs? Which do not?
____
Explain why your observations about homologs makes sense – why should/ shouldn’t each of
these species have rhodopsin?
_____
Make an alignment of the valid homologs of human rhodopsin and include it below:
__Paste_Alignment_Here___
Give your observations about the alignment:
____
What website(s) did you use to get this information?
_____
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: __________________
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
Tree:
A
0
4
12
2
B
4
0
7
8
C
12
7
0
10
D
2
8
10
0