Download What is the function of DNA

Use Biology Workbench (http://workbench.sdsc.edu) and your textbook to answer the
following questions.
1. What is the function of DNA?
2. What is the function of mRNA?
3. What is the function of proteins?
4. Here is a gene sequence (alcohol dehydrogenase):
1
61
121
181
241
301
361
421
481
541
601
661
721
781
841
901
961
1021
1081
1141
1201
1261
1321
1381
1441
1501
1561
1621
1681
1741
1801
1861
1921
1981
2041
ctgagcatca
atgggcactg
cccttctcca
attttggcca
aagtttccag
gtgactacag
tgcaatgctt
ggagtactgg
atgaacacca
gatgatgcag
ggcgctgctg
ggaggagttg
gggattgacc
atcagtccca
aacgtgggat
tcctgccaca
ctcacctatg
ggtttgaaaa
gacctggacc
ctgctcaatt
gaggtctgtg
catgtatctg
tataaagaat
taataacaat
aaaacataca
tgcagatata
agtaatattc
tttaaacact
catattactg
cgattaagaa
caaggctatt
ataaacatag
gaattgcaag
gtgtttttag
attcttaaga
gtcagaaaaa
ctggaaaagt
ttgaggaaat
caggaatctg
tgattgtggg
tgaaaccagg
gtcgcaaccc
ctgatggcac
gtacatttac
ctcctcctga
ttaaaactgg
gcctgtcagt
tcaacaaaga
aggactctac
acacctttga
tgaactatgg
acccgatgtt
gcagagatga
agttgataac
caggacaaag
ttgtcatggt
tctcacaaat
tattaacctt
gttaatattt
cttggatttc
taactcaaaa
acttaacaca
tgttatgagt
gattagatta
tcatcattac
tgccagcata
agctagagtc
tccctaagtc
tttttaacaa
aaatt
gtctatgttt
tattaaatgc
agaagttgcc
tcgcacagat
acatgaggca
tgacaaagtc
agatggcaac
caccagattt
cgagtacaca
gaaagtctgt
caaggtcaaa
catcatgggc
caaatttgag
caaacccatc
agttattggg
gaccagcgtg
gctcttcact
tgtcccaaaa
tcatgtttta
cattcgaacg
gaactggagt
acaagcataa
tataaacatt
ttgatttaca
tatgttgaaa
cagatatagc
ttgaaactat
taacttggat
agaaagacag
ataacttggt
tattaatatt
atattatcat
cctattcact
ctacactgat
gcagaaatac
aaagcagctg
ccaccaaaga
gaccatgtga
actgggattg
atccctctct
ctttgcatta
acatgcaagg
gtggtggatg
ttaattggct
cctggttcca
tgtaagtcag
aaggccatgg
agtgaggtgc
catcttgaaa
gttgtaggag
ggacgcacat
ctagtgactg
ccatttaaaa
gtcctgacgt
ttctcttgtg
gtagaagatt
taaagtcttg
ttttgtaagg
tggagatttt
gtataaagat
tattttttag
tacattttga
aaaagattaa
gaaactgaaa
ttagaaaata
acttatcata
gtgcttagta
gtatctatat
5. Does the sequence represent DNA, mRNA, or protein?
6. How can you tell?
agatccaaga
tgctttggga
ctaaagaagt
taaaaggaac
tagagagcat
ttctgccaca
ggagcgatat
gcaaaccagt
aatcttctgt
gtgggttttc
cttgcgtcgt
ctggtgcatc
ctgtaggtgc
tgtcagaaat
ccatgattga
ttcctccatc
ggaagggatg
agttcctggc
aaatcagtga
tttgagatcc
agagttccct
tgttgaagac
tgagcacctg
ctataattgt
taagagtttt
atagtaaatg
atttgaatat
aatcagttca
gggacgggca
aagtatatca
ttccttttgt
atgttcaatt
gtgactccat
atatctataa
caaagacagg
gcagaagcaa
tcgcattaag
aatggtgtcc
tggagaagga
atgtagagaa
tactggtcgt
ccaccacttc
tgctaagatt
cactggatat
ctttggcctg
taggatcatt
cactgagtgt
gacaggcaac
tgccctggca
agccaagatg
tgtctttgga
aaagaaattt
aggatttgag
aaagtggcag
catctgaaat
atagaaccct
ggaattagta
atcttttaag
aaccagctgc
catctcctag
aaatgtattt
ttccatgatg
catttttcaa
tatgggtaca
aatactgaat
tgatacagta
ttaataaaaa
catgttaaaa
7. What form of this gene sequence (DNA, mRNA, or protein) has activity in the
cell?
8. If two genes have a similar nucleotide sequence, what will you expect with
regards to the activity of the protein the gene codes for? Why?
9. Using a BLASTN search, list genes that have a similar nucleotide sequence and
their functions, if available.
10. What can you hypothesize regarding the function of the protein coded for by the
sequence above?
11. What is the protein sequence of the gene? You may need to determine the open
reading frame first. Use SIXFRAME to find the sequence without interrupting
stop codons.
12. What are the levels of protein structure?
13. Which level of protein folding shows activity?
14. Use secondary structure predictor to determine the secondary structure of the
protein. Use GOR4 to do this.
15. What does the overall active protein look like? Is it round, long, angular (you
describe it)? You can find it on the “Molecule of the Month” list at the PDB
website.
16. How does the predicted secondary structure compare to the actual secondary
structure found in the active protein?
Describe the shape of protein (in more detail than above):
17. How many chains?
18. How many helices?
19. How many beta sheet chains?
20. What other molecules does this protein interact with?
21. Where is the active site of this protein?
22. What cells is this protein found in?