Asam Nukleat

28-1

Asam Nukleat (Nucleic Acid)

Asam Nukleat: material bersifat asam yang ditemui

pada setiap sel hidup (inti sel/nuklei)
Merupakan biopolimer dengan monomer: Nukleotida
Nukleotida terdiri atas gula, basa dan fosfat

Basa

nukleotida

PO4
Gula
nukleosida

28-2

Ada dua macam asam nukleat:

- DNA (deoxyribose nucleic acid)
- RNA (ribose nucleic acid)

28-3

Gula
HOCH2 O

OH

OH

OH

ribose
RNA

HOCH2 O

OH

OH

(no O)

deoxyribose
DNA
28-4

Basa Purin/Pyrimidin

Senyawa amina aromatik heterosiklik

DNA: Adenine, Guanine, Cytosine, Thymine
RNA: Adenine, Guanine, Cytosine, Uracil

HN

N
N9

H
Purine

H
Thymine (T)

H
Cytosine (C)
O

NH2

CH3

HN

H
Uracil (U)

Pyrimidine

NH2

H
Adenine (A)

HN
H2N

H
Guanine (G)

28-5

Nukleosida

Nukleosida: pembangun asam nukleat yang terdiri atas D-ribosa atau 2deoksi-D-ribosa berikatan dengan basa amina aromatik heterosiklik
dengan ikatan glikosida
uracil O
HN

-D-riboside
5'

a -N-glycosidic
bond

HOCH2 O
1'
H
H
4'
H
2 ' H anomeric
3'
carbon
HO
OH
Uridine

28-6

Nukleosida pada DNA

Basa
Adenine (A)
Guanine (G)
Cytosine (C)
Thymine (T)

Gula
Nukleosida
DeoxyriboseAdenosine
DeoxyriboseGuanosine
DeoxyriboseCytidine
DeoxyriboseThymidine

28-7

Nucleosides in RNA
Base
Adenine (A)
Guanine (G)
Cytosine (C)
Uracil (U)

Sugar
ribose
ribose
ribose
ribose

Nucleoside
Adenosine
Guanosine
Cytidine
Uridine

28-8

Nukleotida

Nukleotida: molekul nukleosida yang teresterkan oleh asam fosfat pada

-OH monosakaridanya
NH2
N
O
-

5'

O P O CH2
-

N
N

H
OH
OH
Adenosine 5'-monophosphate
(AMP)

Acyclovir & AZT

(Antiviral)

HN
H2 N
HOCH2
H

N
N

N
HOCH2

O
H H

CH3

HN

N3

Acyclovir
Azidothymidine (AZ T)
(drawn to show its
structural relationship
to 2-deoxyguanosine
28-9

28-10

Struktur Asam Nukleat

Polimer dari empat nukleotida

Dihubungkan dengan ikatan gula-fosfat (fosfodiester)

base

sugar
Pnucleotide

base

nucleotide
sugar
P

base

base

P
P sugar
nucleotide
sugar nucleotide
28-11

Struktur Primer DNA - 1

DeoxyriboNucleic Acids (DNA)

Kerangka 2-deoxy-D-ribose dan fosfat dimana gugus 3-OH dan 2deoxy-D-ribose terhubung dengan ikatan fosfodiester dengan gugus
5-OH pada unit 2-deoxy-D-ribose yang lain
Struktur Primer: urutan basa sepanjang backbone pentosephosphodiester pada molekul DNA atau RNA
Pembacaan dari ujung 5 ke ujung 3
phosphorylated
5' end
HN

O
CH3

O
5'
O
N
O-P-O-C H2
O
O
H
H
H
H
O
O=P O
O-

O
N

NH

H
CH2
H

H
free 3' end 3'
OH

O
H

NH2

28-12

Struktur Sekunder DNA - 2

Hadiah Nobel Bidang Fisiologi atau Kedokteran 1962
untuk penemuan struktur asam nukleat dan perananya pada transfer
infromasi pada materi hidup (1953)

Francis Harry
Compton Crick
United Kingdom
Institute of Molecular Biology
Cambridge, United Kingdom
b. 1916

James Dewey
Watson
USA
Harvard University
Cambridge, MA, USA
b. 1928

Maurice Hugh
Frederick Wilkins
United Kingdom
University of London London,
United Kingdom
b. 1916

28-13

DNA Double Helix

DNA terdiri atas dua untai

nukleotida
Ikatan hidrogen (antar basa)
menghubungkan dua untai dalam
struktur double-helix structure
Struktur helix mirip dengan
tangga spiral
Basa selalu berpasangan antara
AT dan G-C
Kedua basa saling
berkomplemen dalam kedua
untai

28-14

Pasangan basa
Dua ikatan H untuk A-T
Tiga ikatan H untuk G-C

15

28-15

DNA Double Helix

28-16

Bentuk-bentuk DNA

B-DNA
Bentuk dominan dalam larutan encer
right-handed helix
Ketebalan 2000 pm dengan setiap 3400 pm mengandung 10 pasangan
basa
minor groove : 1200pm dan major groove : 2200 pm
A-DNA
right-handed helix, lebih tebal dari B-DNA
2900 pm mengandung 10 pasang
Z-DNA
left-handed double helix

28-17

28-18

Struktur tersier DNA 3

Struktur Tersier : penataan tiga dimensi molekul DNA,

supercoil
DNA siklis: DNA untai ganda dimana ujung 5 dan 3
tergabung dalam ikatan phosphodiester
Histone: protein, kaya asam amino lysine dan arginine,
yang berikatan dengan molekul DNA
Chromatin: terdiri atas molekul DNA terikat disekitar
histon membentuk struktur seperti partikel bulat

28-19

28-20

28-21

28-22

Problem
Tulis urutan komplemen potongan DNA :
-A-G-T-C-C-A-A-T-G-C

23

28-23

Jawaban

-A-G-T-C-C-A-A-T-G-C

-T-C-A-G-G-T-T-A-C-G-

24

28-24

Ribonucleic Acids (RNA)

RNA mirip dengan DNA tetapi berbeda dalam hal:

Gula pentosa pada RNA merupakan -D-ribose tidak seperti
DNA yang menggunakan -2-deoxy-D-ribose
Basa pyrimidine pada RNA adalah uracil dan cytosine
bukan thymine dan cytosine
RNA merupakan untai tunggal (single stranded)
stranded bukan
double stranded

28-25

Klasifikasi RNA

Klasifikasi molekul RNA berdasarkan struktur dan fungsi

Type

Molecular Weight
Range (g/mol)

mRNA
tRNA
rRNA

25,000 - 1,000,000
23,000 - 30,000
35,000 - 1,100,000

Number of Percentage
Nucleotides of Cell RNA
75 - 3,000
73 - 94
120 - 2904

2
16
82

Ribosomal RNA (rRNA): RNA yang ditemukan pada ribosom, tempat sintesis
protein
O

Transfer RNA (tRNA): RNA yang

membawa asam amino tertentu ke
tempat sintesis protein di ribosom

Base
tRNA-O-P-O-CH2
O
H
H
OH
H
amino acid, bound
O
OH
as an ester to its
specific tRNA
C=O
C
NH3 +
H
R

28-26

Messenger RNA (mRNA): RNA yang membawa kode genetik dari DNA ke
ribosom untuk sintesis protein
Jumlahnya sedikit dan waktu keberadaannya singkat
single stranded
Disintesis berdasarkan informasi yang dikode DNA
Untai komplemen mRNA disintesis sepanjangn satu untai DNA, mulai
dari ujung 3
Proses sintesis mRNA dari DNA disebut transcription

DNA template
3'-A-G-C-C-A-T-G-T-G-A-C-C-5'
5'-U-C-G-G-U-A-C-A-C-U-G-G-3'
mRNA

28-27

Replikasi, Transkripsi, Translasi

Tinjauan Singkat

28-28

Replikasi DNA

DNA in the chromosomes replicates itself

every cell division
Maintains correct genetic information
Two strands of DNA unwind
Each strand acts like a template
New bases pair with their complementary base
Two double helixes form that are copies of
original DNA
29

28-29

DNA Unwinds

G-C
A-T
C-G
T-A

G
A
C
T

C
T
G
A

30

28-30

DNA Copied with Base Pairs

TwocopiesoforiginalDNAstrand
GC
AT
CG
TA

GC
AT
CG
GA

31

28-31

28-32

28-33

28-34

The Genetic Code

U
UUU
UUC
UUA
UUG
CUU
CUC
CUA
CUG

AUU
A AUC
AUA
AUG*
G

GUU
GUC
GUA
GUG

Phe
Phe
Leu
Leu

C
UCU
UCC
UCA
UCG

A
Ser UAU
SerUAC
Ser UAA
Ser UAG

G
Tyr UGU
Tyr UGC
StopUGA
StopUGG

Cys U
Cys C
Stop A
Trp G

Leu
Leu
Leu
Leu

CCU
CCC
CCA
CCG

Pro
Pro
Pro
Pro

CAU
CAC
CAA
CAG

His
His
Gln
Gln

CGU
CGC
CGA
CGG

Arg
Arg
Arg
Arg

U
C
A
G

Ile
Ile
Ile
Met

ACU
ACC
ACA
ACG

Thr
Thr
Thr
Thr

AAU
AAC
AAA
AAG

Asn
Asn
Lys
Lys

AGU
AGC
AGA
AGG

Ser
Ser
Arg
Arg

U
C
A
G

Val
Val
Val
Val

GCU
GCC
GCA
GCG

Ala
Ala
Ala
Ala

GAU
GAC
GAA
GAG

Asp
Asp
Glu
Glu

GGU
GGC
GGA
GGG

Gly
Gly
Gly
Gly

U
C
A
G

*AUG also serves as the principal initiation codon.

28-35

The Genetic Code

Properties of the Code

only 61 triplets code for amino acids; the remaining 3 (UAA, UAG, and
UGA) signal chain termination
the code is degenerate, which means that several amino acids are
coded for by more than one triplet. Leu, Ser, and Arg, for example,
are each coded for by six triplets
for the 15 amino acids coded for by 2, 3, or 4 triplets, it is only the
third letter of the codon that varies. Gly, for example, is coded for by
GGA, GGG, GGC, and GGU
there is no ambiguity in the code; each triplet codes for one and only
one amino acid

28-36

Sequencing DNA

Restriction endonuclease: an enzyme that catalyzes hydrolysis of a

particular phosphodiester bond within a DNA strand
over 1000 endonucleases have been isolated and their specificities
determined
typically they recognize a set sequence of nucleotides and cleave the
DNA at or near that particular sequence
EcoRI from E. coli, for example, cleaves as shown
cleavage here

5'

G-A-A-T-T-C---3'

EcoRI

5'

Sequencing DNA
following are several more
examples of
endonucleases and their
specificities

G + 5' -A-A-T-T-C---3'

Recognition
Enzyme
Sequence
AluI
AG CT
BalI

TGG CCA

Recognition
EnzymeSequence
HpaII C CGG
Mbol

GATC

FnuDII CG CG

Not I GC GGCCGC

HeaIII GG CC

SacI

GAGCT C

28-37

Sequencing DNA
Polyacrylamide gel electrophoresis: a technique so sensitive that it is
possible to separate nucleic acid fragments differing from one another in
only a single nucleotide
Maxam-Gilbert method: a method developed by Allan Maxam and
Walter Gilbert; depends on base-specific chemical cleavage
Dideoxy chain termination method: developed by Frederick Sanger
Gilbert and Sanger shared the 1980 Nobel prize for biochemistry for
their development of chemical and biochemical analysis of DNA
structure.
Replication
in Vitro

During replication, the sequence of nucleotides in one strand

is copied as a complementary strand to form the second
strand of a double-stranded DNA
Synthesis is catalyzed by DNA polymerase
DNA polymerase will catalyze synthesis in vitro using singlestranded DNA as a template, provided that (1) the four
deoxynucleotide triphosphate (dNTP) monomers and (2) a
primer are present
Primer: an oligonucleotide capable of forming a short section
of double-stranded DNA (dsDNA) by base-pairing with its
complement on a single-stranded DNA (ssDNA)

28-38

Replication in Vitro
Because a new DNA strand grows from its 5' to 3' end, the
primer must have a free 3'-OH group to which the first
nucleotide of the growing chain is added
5'
T

Single-stranded DNA
C
G
A
T
C
T

G
dATP, dTTP, dCTP, dGTP
3'HO
direction of synthesis
catalyzed by DNA polymerase

OH 3'
G

A
C
T
Primer

5'

Dideoxy Chain Termination

the key to the chain termination method is addition to the
synthesizing medium of a 2,3-dideoxynucleotide triphosphate
(ddNTP)
because a ddNTP has no 3-OH, chain synthesis is terminated
where a ddNTP becomes incorporated
-

O
O
O
O-P-O-P-O-P-O-CH2
O- O- OH

Base
H

H
H

A 2',3'-dideoxynucleoside triphosphate
(ddNTP)
28-39

Dideoxy Chain Termination

In this method, the following are mixed

single-stranded DNA of unknown sequence and primer; then
divided into four reaction mixtures
To each reaction mixture is then added
the four dNTP, one of which is labeled in the 5 end with
phosphorus-32
32
15 P

32
16 S

+ Beta particle
+ Gamma rays

DNA polymerase
one of the four ddNTPs
after gel electrophoresis of each reaction mixture
a piece of film is placed over the gel
gamma rays released by P-32 darken the film and create a
pattern of the resolved oligonucleotide
the base sequence of the complement to the original strand is
read directly from bottom to top of the developed film

28-40

Dideoxy Chain Termination

Polyacrylamide gel electrophoresis
A
Larger fragments

3'
A
G
T
T
G

This
sequence
is the
complement
of the DNA
template

C
T
Smaller fragments

A
5'

If the complement of the DNA template

is
5' -A-T-C-G-T-T-G-A-3'
Then the original DNA template must
be
5' -T-C-A-A-C-G-A-T-3'

28-41