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: 12q22-q24.2 and the molecular
location on the chromosome 12 is base pairs 102,838,321 to 102,917,603 (Homo sapiens
Annotation Release 107, GRCh38.p2)

Based on the figure above the PAH gene is located on the long (q) arm of chromosome 12
between 22 and 24.2 which is more precisely at base pair 102,838,321 to base pair
102,917,603 at chromosome 12.
In order to identify the DNA coding sequence of the Homo sapiens phenylalanine
hydroxylase (PAH) gene we use the restriction enzyme of Nocardia corallina (NcoI) to
identify the restriction site that can be recognized in the PAH sequence which we listed the
whole PAH sequence in figure below.

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

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

gccctggttcccaagaaccattcaagagctggacagatttgccaatcagattctcagctatggagcggaactgga
base pairs
cgggaccaagggttcttggtaagttctcgacctgtctaaacggttagtctaagagtcgatacctcgccttgacct
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

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

tgatgccaaggagaaagtaaggaactttgctgccacaatacctcggcccttctcagttcgctacgacccatacac
base pairs
actacggttcctctttcattccttgaaacgacggtgttatggagccgggaagagtcaagcgatgctgggtatgtg
1651 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

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

ccagtatcattttccaattaattatcaagtctgttttgggaaacactttgaggacatttatgatgcagcagatgt
base pairs
ggtcatagtaaaaggttaattaatagttcagacaaaaccctttgtgaaactcctgtaaatactacgtcgtctaca
2476 to 2550

tgactaaaggcttggttggtagatattcaggaaatgttcactgaataaataagtaaatacattattgaaaagcaa
base pairs
actgatttccgaaccaaccatctataagtcctttacaagtgacttatttattcatttatgtaataacttttcgtt
2551 to 2625

atctgtataaatgtgaaatttttatttgtattagtaataaaacattagtagttta
tagacatatttacactttaaaaataaacataatcattattttgtaatcatcaaat

base pairs
2626 to 2680

Table by Enzyme Name

Enzyme
name
NcoI
info

No. Positions
cuts of sites
2
979 1834

Recognition
sequence
c/catgg

More

Every enzyme analyzed cuts this sequence.

Table by Site Position
Cut
site
979
info
1834
info

Enzyme
name
NcoI

No. Positions
cuts of other sites
2
1834

Recognition
sequence
c/catgg

More

NcoI

c/catgg

More

979

Based on the table shows that position of the cutting site of the restriction enzyme NcoI is
at the recognition sequence of CCATGG at the position site of 979 and 1834 which total
number of cut in this PAH sequence is two.

REFERENCE
1. PAH phenylalanine hydroxylase [ Homo sapiens (human) ]
http://www.ncbi.nlm.nih.gov/gene/5053
2. Homo sapiens phenylalanine hydroxylase (PAH), mRNA
http://www.ncbi.nlm.nih.gov/nucleotide?
cmd=Retrieve&dopt=GenBank&list_uids=4557818
3. Restriction enzyme NcoI http://www.thelabrat.com/restriction/NcoI.shtml
4. PAH gene http://ghr.nlm.nih.gov/gene/PAH