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有機化學 25 PDF
有機化學 25 PDF
有機化學乙
蔡蘊明 教授
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Chapter 25 Nucleic acids
−
H2O HO
Nucleic acid nucleotides nucleoside + H3PO4
enzyme H2O
(β)
2-deoxy-D-ribose
◎ The base
NH2 O O
3 H3C
N N NH NH
N N1 O N O N O
H H H
pyrimidine cytosine uracil (RNA) thymine (DNA)
NH2 O
7 6
5 N
N N N NH
N1
9 N N N N N N NH2
4
H 3
H H
NH2 NH2
3
N N N
1
N O N N
1 9
HO 5' HO
β-configuration
O O
4' 1'
3' 2'
OH OH
+
H
H2O
HO
OH
O + Base
OH
◎ The nucleotides
O
−
O P O Base
O− O
at pH 7 OH
dianion
5'-monophosphate
H2O HO−
HO O
B −
O + O P OH
O−
OH
Nomenclature
dCMP
monophosphate
2’-deoxy
cytosine
2’-Deoxycytidine-5’-monophosphate
— adenosine—
— thymidine—
— guanosine—
— uridine —
※ Structure of DNA
Primary structure
read from the 5’ end to the 3’ end
5'-end P
O A
B
O P
T
P
O C
-O P O P
O C
B
O
G
O OH
3'-end
◎ Secondary structure The double helix
A/T (1:1 ratio) and G/C (1:1 ratio) in DNA
The Watson-Crick model
A T
G C
(U for T in RNA)
N HN H O CH3
N N H N
sugar
N N
O sugar
A T
N O H NH
N N H N
sugar
N N
HN H O sugar
G C
20 Å
Minor
groove
6Å
34 Å
Major
groove
12 Å
Top view
◎ Tertiary structure
supercoiled
COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B)
AND 146 BP LONG DNA FRAGMENT
Crystal structure of the nucleosome core particle at 2.8 A resolution (1997)
Nature 389: 251-260
http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=1aoi
※ RNA
1. β-D-Ribose
2. A=U, G≡C
U for T
3. Single strand
RNA is less stable
5'-end
O O
B B
O O
O O OH
-O P O -O P O
O O
B B
O O
O O OH
3'-end
※ Function
transcription translation
DNA RNA Protein
replication
DNA
※ Replication of DNA
5'
P P
A A
3' dTTP
P P
G G
P OH P OH
A T O O O A T
−
P HO O P O P O P O P P
T A O− O− O− T A
3'
P P
5'
Enzyme used: DNA polymerase
Serves as a template
5' 3'
3' 5'
5' 3'
latter joined by DNA ligase
※ Transcription
Grow from 5’ to 3’
The template
5'
O CHR
NH2
Phenylalanyl tRNA (yeast)
Data retrieved from: http://www.rcsb.org/pdb/101/motm_disscussed_entry.do?id=4tna
G1
A76
3’-end
Carries AA
細菌的核糖體(70S)是由一個小的30S單元與一個
大的50S單元所組成
30S的分子量為800,000
50S的分子量為1,500,000
Ala Arg
基於Steitz發表的50S結構
The mechanism of peptide bond formation on the ribosome. The α-amino
group of aminoacyl-tRNA in the A site (blue) attacks (black arrow right to left)
the ester bond of the peptidyl-tRNA in the P site (red). A proton is shuttled via
the OH’ group of A76 in peptidyl-tRNA in the P site (black arrows left to right),
aided by an H-bond network (Trobro and Åqvist, 2005) established with the
help of 23S rRNA bases and water molecules (not shown).
精準度的問題
OH O
-
O P O
(dTTP)
O
T
O
OH
O
B
PPPO O
T
O
O
-
O P O
(ddTTP)
O
T
O
A G C T
larger fragments Θ 3'
A
T This sequence is
G complimentary to
C
the DNA template
T
A
smaller fragments
⊕ 5'
• PCR requires:
• A sample of the DNA to be copied
• The enzyme DNA polymerase
• A short ‘primer’ sequence complimentary to the
template DNA
• A supply of A, C, G, and T nucleotide triphosphate
monomers
• A simple device for thermal cycling during the reaction
sequence
one cycle
1) denature DNA
90 oC, ~1 min polymerase repeat
2) annealing 70 oC, 2 min
50-60 oC, 45 s
(primers)
20-60 times
millions of copies