Post on 07-Jul-2018
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Question 2
The DNA sequence of phenylalanine hydroxylase known as PAH gene are presence in the
Homo sapiens gene which it produces the enzyme PAH for processing the phenylalanine for building the block of amino acid which obtained through the diet and this can be found in all
proteins content and some in artificial sweeteners. The phenylalanine hydroxylase is
responsible for the conversion of the phenylalanine into another amino acid which is tyrosine.
This enzyme carries out the function with a molecule called tetrahydrobiopterin known as
BH4 to carry out its chemical reaction.
The PAH gene can be found and located cytogenetic location !"q""#q"$." and the molecular
location on the chromosome !" is base pairs !%"&'('&("! to !%"&)!*&+%( (Homo sapiens
Annotation Release 107, GRCh38.p2)
,ased on the figure above the PAH gene is located on the long -q arm of chromosome !"
between "" and "$." which is more precisely at base pair !%"&'('&("! to base pair
!%"&)!*&+%( at chromosome !".
/n order to identify the DNA coding sequence of the Homo sapiens phenylalaninehydroxylase - PAH gene we use the restriction enzyme of Noa!"ia o!allina (No#) to
identify the restriction site that can be recognized in the PAH sequence which we listed the
whole PAH sequence in figure below.
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Homo sapiens phenylalanine hydroxylase (PAH), mRNA
2680 base pairs
cagctgggggtaaggggggcggattattcatataattgttataccagacggtcgcaggcttagtccaattgcaga
base pairs
gtcgacccccattccccccgcctaataagtatattaacaatatggtctgccagcgtccgaatcaggttaacgtct
1 to 75
gaactcgcttcccaggcttctgagagtcccggaagtgcctaaacctgtctaatcgacggggcttgggtggcccgt
base pairs
cttgagcgaagggtccgaagactctcagggccttcacggatttggacagattagctgccccgaacccaccgggca
76 to 150
cgctccctggcttcttccctttacccagggcgggcagcgaagtggtgcctcctgcgtcccccacaccctccctca
base pairs
gcgagggaccgaagaagggaaatgggtcccgcccgtcgcttcaccacggaggacgcagggggtgtgggagggagt
151 to 225
gcccctcccctccggcccgtcctgggcaggtgacctggagcatccggcaggctgccctggcctcctgcgtcagga
base pairs
cggggaggggaggccgggcaggacccgtccactggacctcgtaggccgtccgacgggaccggaggacgcagtcct
226 to 300
caagcccacgaggggcgttactgtgcggagatgcaccacgcaagagacaccctttgtaactctcttctcctccct
base pairs
gttcgggtgctccccgcaatgacacgcctctacgtggtgcgttctctgtgggaaacattgagagaagaggaggga
301 to 375
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agtgcgaggttaaaaccttcagccccacgtgctgtttgcaaacctgcctgtacctgaggccctaaaaagccagag
base pairs
tcacgctccaattttggaagtcggggtgcacgacaaacgtttggacggacatggactccgggatttttcggtctc
376 to 450
acctcactcccggggagccagcatgtccactgcggtcctggaaaacccaggcttgggcaggaaactctctgactt
base pairs
tggagtgagggcccctcggtcgtacaggtgacgccaggaccttttgggtccgaacccgtcctttgagagactgaa
451 to 525
tggacaggaaacaagctatattgaagacaactgcaatcaaaatggtgccatatcactgatcttctcactcaaaga
base pairs
acctgtcctttgttcgatataacttctgttgacgttagttttaccacggtatagtgactagaagagtgagtttct
526 to 600
agaagttggtgcattggccaaagtattgcgcttatttgaggagaatgatgtaaacctgacccacattgaatctag
base pairs
tcttcaaccacgtaaccggtttcataacgcgaataaactcctcttactacatttggactgggtgtaacttagatc
601 to 675
accttctcgtttaaagaaagatgagtatgaatttttcacccatttggataaacgtagcctgcctgctctgacaaa
base pairs
tggaagagcaaatttctttctactcatacttaaaaagtgggtaaacctatttgcatcggacggacgagactgttt
676 to 750
catcatcaagatcttgaggcatgacattggtgccactgtccatgagctttcacgagataagaagaaagacacagt
base pairs
gtagtagttctagaactccgtactgtaaccacggtgacaggtactcgaaagtgctctattcttctttctgtgtca
751 to 825
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gccctggttcccaagaaccattcaagagctggacagatttgccaatcagattctcagctatggagcggaactgga
base pairscgggaccaagggttcttggtaagttctcgacctgtctaaacggttagtctaagagtcgatacctcgccttgacct
826 to 900
tgctgaccaccctggttttaaagatcctgtgtaccgtgcaagacggaagcagtttgctgacattgcctacaacta
base pairs
acgactggtgggaccaaaatttctaggacacatggcacgttctgccttcgtcaaacgactgtaacggatgttgat
901 to 975
NcoI
ccgccatgggcagcccatccctcgagtggaatacatggaggaagaaaagaaaacatggggcacagtgttcaagac
base pairs
ggcggtacccgtcgggtagggagctcaccttatgtacctccttcttttcttttgtaccccgtgtcacaagttctg
976 to 1050
tctgaagtccttgtataaaacccatgcttgctatgagtacaatcacatttttccacttcttgaaaagtactgtgg
base pairs
agacttcaggaacatattttgggtacgaacgatactcatgttagtgtaaaaaggtgaagaacttttcatgacacc
1051 to 1125
cttccatgaagataacattccccagctggaagacgtttctcaattcctgcagacttgcactggtttccgcctccg
base pairs
gaaggtacttctattgtaaggggtcgaccttctgcaaagagttaaggacgtctgaacgtgaccaaaggcggaggc
1126 to 1200
acctgtggctggcctgctttcctctcgggatttcttgggtggcctggccttccgagtcttccactgcacacagta
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base pairs
tggacaccgaccggacgaaaggagagccctaaagaacccaccggaccggaaggctcagaaggtgacgtgtgtcat
1201 to 1275
catcagacatggatccaagcccatgtatacccccgaacctgacatctgccatgagctgttgggacatgtgccctt
base pairs
gtagtctgtacctaggttcgggtacatatgggggcttggactgtagacggtactcgacaaccctgtacacgggaa
1276 to 1350
gttttcagatcgcagctttgcccagttttcccaggaaattggccttgcctctctgggtgcacctgatgaatacat
base pairs
caaaagtctagcgtcgaaacgggtcaaaagggtcctttaaccggaacggagagacccacgtggactacttatgta
1351 to 1425
tgaaaagctcgccacaatttactggtttactgtggagtttgggctctgcaaacaaggagactccataaaggcata
base pairs
acttttcgagcggtgttaaatgaccaaatgacacctcaaacccgagacgtttgttcctctgaggtatttccgtat
1426 to 1500
tggtgctgggctcctgtcatcctttggtgaattacagtactgcttatcagagaagccaaagcttctccccctgga
base pairs
accacgacccgaggacagtaggaaaccacttaatgtcatgacgaatagtctcttcggtttcgaagagggggacct
1501 to 1575
gctggagaagacagccatccaaaattacactgtcacggagttccagcccctgtattacgtggcagagagttttaa
base pairs
cgacctcttctgtcggtaggttttaatgtgacagtgcctcaaggtcggggacataatgcaccgtctctcaaaatt
1576 to 1650
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tgatgccaaggagaaagtaaggaactttgctgccacaatacctcggcccttctcagttcgctacgacccatacac
base pairs
actacggttcctctttcattccttgaaacgacggtgttatggagccgggaagagtcaagcgatgctgggtatgtg1651 to 1725
ccaaaggattgaggtcttggacaatacccagcagcttaagattttggctgattccattaacagtgaaattggaat
base pairs
ggtttcctaactccagaacctgttatgggtcgtcgaattctaaaaccgactaaggtaattgtcactttaacctta
1726 to 1800
NcoI
cctttgcagtgccctccagaaaataaagtaaagccatggacagaatgtggtctgtcagctgtgaatctgttgatg
base pairs
ggaaacgtcacgggaggtcttttatttcatttcggtacctgtcttacaccagacagtcgacacttagacaactac
1801 to 1875
gagatccaactatttctttcatcagaaaaagtccgaaaagcaaaccttaatttgaaataacagccttaaatcctt
base pairs
ctctaggttgataaagaaagtagtctttttcaggcttttcgtttggaattaaactttattgtcggaatttaggaa
1876 to 1950
tacaagatggagaaacaacaaataagtcaaaataatctgaaatgacaggatatgagtacatactcaagagcataa
base pairs
atgttctacctctttgttgtttattcagttttattagactttactgtcctatactcatgtatgagttctcgtatt
1951 to 2025
tggtaaatcttttggggtcatctttgatttagagatgataatcccatactctcaattgagttaaatcagtaatct
base pairs
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accatttagaaaaccccagtagaaactaaatctctactattagggtatgagagttaactcaatttagtcattaga
2026 to 2100
gtcgcatttcatcaagattaattaaaatttgggacctgcttcattcaagcttcatatatgctttgcagagaactc
base pairs
cagcgtaaagtagttctaattaattttaaaccctggacgaagtaagttcgaagtatatacgaaacgtctcttgag
2101 to 2175
ataaaggagcatataaggctaaatgtaaaacacaagactgtcattagaattgaattattgggcttaatataaatc
base pairs
tatttcctcgtatattccgatttacattttgtgttctgacagtaatcttaacttaataacccgaattatatttag
2176 to 2250
gtaacctatgaagtttattttctattttagttaactatgattccaattactactttgttattgtacctaagtaaa
base pairs
cattggatacttcaaataaaagataaaatcaattgatactaaggttaatgatgaaacaataacatggattcattt
2251 to 2325
ttttctttaggtcagaagcccattaaaatagttacaagcattgaacttctttagtattatattaatataaaaaca
base pairs
aaaagaaatccagtcttcgggtaattttatcaatgttcgtaacttgaagaaatcataatataattatatttttgt
2326 to 2400
tttttgtatgttttattgtaatcataaatactgctgtataaggtaataaaactctgcacctaatccccataactt
base pairs
aaaaacatacaaaataacattagtatttatgacgacatattccattattttgagacgtggattaggggtattgaa
2401 to 2475
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ccagtatcattttccaattaattatcaagtctgttttgggaaacactttgaggacatttatgatgcagcagatgt
base pairs
ggtcatagtaaaaggttaattaatagttcagacaaaaccctttgtgaaactcctgtaaatactacgtcgtctaca
2476 to 2550
tgactaaaggcttggttggtagatattcaggaaatgttcactgaataaataagtaaatacattattgaaaagcaa
base pairs
actgatttccgaaccaaccatctataagtcctttacaagtgacttatttattcatttatgtaataacttttcgtt
2551 to 2625
atctgtataaatgtgaaatttttatttgtattagtaataaaacattagtagttta base pairs
tagacatatttacactttaaaaataaacataatcattattttgtaatcatcaaat 2626 to 2680
Table by Enzyme Name
Enzyme No. Positions ecognition
name c!ts o" sites se#!ence
NcoI 2 979 1834 c$catgg %ore
in"o
E&ery enzyme ana'yze( c!ts t)is se#!ence.
Table by Site Position
*!t Enzyme No. Positions ecognitionsite name c!ts o" ot)er sites se#!ence
979 NcoI 2 1834 c$catgg %ore
in"o
1834 NcoI 2 979 c$catgg %ore
in"o
,ased on the table shows that position of the cutting site of the restriction enzyme NcoI is
at the recognition sequence of **+,-- at the position site of )*) and !'($ which total
number of cut in this PAH sequence is two.
http://www.neb.com/rebase/enz/NcoI.htmlhttp://www.neb.com/rebase/enz/NcoI.htmlhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://rna.lundberg.gu.se/cgi-bin/cutter2/rebase?NcoIhttp://www.neb.com/rebase/enz/NcoI.htmlhttp://www.neb.com/rebase/enz/NcoI.html
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R!RN"
!. 0A1 phenylalanine hydroxylase 2 1omo sapiens -human 3
http44www.ncbi.nlm.nih.gov4gene45%5(
". 1omo sapiens phenylalanine hydroxylase -0A1& m6NA
http44www.ncbi.nlm.nih.gov4nucleotide7
cmd86etrieve9dopt8:en,ank9list;uids8$55*'!'
(. Rest!ition en$%me No/ http44www.thelabrat.com4restriction4Nco/.shtml
$. PAH &ene http'&h!.nlm.nih.&o&enePAH
http://www.ncbi.nlm.nih.gov/gene/5053http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.thelabrat.com/restriction/NcoI.shtmlhttp://ghr.nlm.nih.gov/gene/PAHhttp://ghr.nlm.nih.gov/gene/PAHhttp://www.ncbi.nlm.nih.gov/gene/5053http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.ncbi.nlm.nih.gov/nucleotide?cmd=Retrieve&dopt=GenBank&list_uids=4557818http://www.thelabrat.com/restriction/NcoI.shtmlhttp://ghr.nlm.nih.gov/gene/PAH