PROTEIN SYNTHESIS

(TRANSCRIPTION AND TRANSLATION)

Dr. Marhaen Hardjo, M.Biomed, PhD

Bagian Biokimia Fakultas Kedokteran

Universitas Hasanuddin Makassar 1
The Central Dogma

Transcription Translation
DNA RNA PROTEIN
replication

2
Transcription is very similar
to DNA replication but there
are some important
differences:
1.RNA is made of ribonucleotides
2.RNA polymerase catalyzes the
reaction
3.The synthesized RNA does not
remain base-paired to the
template DNA strand
4.Less accurate (error rate: 10-4)
3
5.Transcription selectively copies
only certain parts of the genome
and makes one to several
hundred, or even thousand,
copies of any given section of the
genome. (Replication?)

4
 Transcription bubble

Fig 12-1 Transcription of DNA into

RNA

5
CHAPTER12: Mechanisms of Transcription

Topic 1:

RNA Polymerase and

The Transcription Cycle

6
RNA polymerase and the transcription cycle

RNA polymerases come in

different forms, but share
many features
 RNA polymerases performs
essentially the same reaction
in all cells
 Bacteria have only a single
RNA polymerases while in
eukaryotic cells there are
three: RNA Pol I, II and III

7
 RNA Pol II is the focus of
eukaryotic transcription, because
it is the most studied polymerase,
and is also responsible for
transcribing most genes-indeed,
essentially all protein-encoding
genes
 RNA Pol I transcribe the large
ribosomal RNA precursor gene
 RNA Pol III transcribe tRNA gene,
some small nuclear RNA genes
and the 5S rRNA genes
8
Table 12-1: The subunits of
RNA polymerases

9
The bacterial RNA polymerase
The core enzyme alone synthesizes RNA

b’
a
b

a
w 10
prokaryotic b’ Fig 12-2 RNAP
Comparison
a
b

a The same color

indicate the
w
homologous of
the two enzymes
eukaryotic
RPB2

RPB3

RPB1
RPB11

RPB6 11
“Crab claw” shape of RNAP
(The shape of DNA pol is__)

Active center cleft

12
There are various channels allowing
DNA, RNA and ribonucleotides (rNTPs)
into and out of the enzyme’s active
center cleft

13
RNA polymerase and the transcription cycle

Transcription by RNA
polymerase proceeds
in a series of steps

 Initiation
 Elongation
 Termination

14
 Initiation
 Promoter: the DNA sequence that
initially binds the RNA polymerase
 The structure of promoter-
polymerase complex undergoes
structural changes to proceed
transcription
 DNA at the transcription site
unwinds and a “bubble” forms
 Direction of RNA synthesis occurs
in a 5’-3’ direction (3’-end growing)
15
Fig 12-3-initiation

Binding (closed
complex)

Promoter “melting”
(open complex)

Initial
transcription
16
Elongation
 Once the RNA polymerase has
synthesized a short stretch of RNA
(~ 10 nt), transcription shifts into
the elongation phase.
 This transition requires further
conformational change in
polymerase that leads it to grip the
template more firmly.
 Functions: synthesis RNA, unwinds
the DNA in front, re-anneals it
behind, dissociates the growing
RNA chain
17
 Termination
 Afterthe polymerase
transcribes the length of the
gene (or genes), it will stop
and release the RNA transcript.
 In some cells, termination
occurs at the specific and well-
defined DNA sequences called
terminators. Some cells lack
such termination sequences.
18
Fig 12-3-Elongation and
termination

Elongation

Termination

19
RNA polymerase and the transcription cycle

Transcription initiation
involves 3 defined steps

1. Forming closed complex

2. Forming open complex
3. Promoter escape

20
Closed complex

 The initial binding of

polymerase to a promoter
 DNA remains double
stranded
 The enzyme is bound to
one face of the helix

21
 Open complex

 theDNA strand separate

over a distance of ~14 bp
(-11 to +3 ) around the
start site (+1 site)

 Replication bubble forms

22
RNA polymerase and the transcription cycle

Stable ternary complex

 The enzyme escapes
from the promoter
 The transition to the
elongation phase
 Stable ternary complex
=DNA +RNA + enzyme

23
CHAPTER12: Mechanisms of Transcription

Topic 2

The transcription
cycle in bacteria

24
The transcription cycle in bacteria

2-1 Bacterial promoters

vary in strength and
sequences, but have
certain defining features

25
Holoenzyme=
 factor + core enzyme

Figure 12-4

In cell, RNA polymerase initiates

transcription only at promoters.
Who confers the polymerase binding
specificity?
, 26
 Promoters recognized
by E. coli  factor
 The predominant  factor in E.
coli is 70.
 Promoter recognized by 70
contains two conserved
sequences (-35 and –10
regions/elements) separated by
a non-specific stretch of 17-19 nt.
 Position +1 is the transcription
start site.
27
70 promoters contain recognizable
–35 and –10 regions, but the
sequences are not identical.
The distance is conserved

Fig 12-5a: bacterial promoter 28

Comparison of many different promoters
derives the consensus sequences
reflecting preferred –10 and –35 regions

29
• Promoters with sequences closer to
the consensus are generally
“stronger” than those match less
well.

• The strength of the promoter

describes how many transcripts it
initiates in a given time.

30
 Fig 12-5b bacterial promoter
Confers additional specificity

UP-element is an additional DNA

elements that increases
polymerase binding by providing
the additional interaction site for
RNA polymerase

31
 Fig 12-5c bacterial promoter

Another class of 70 promoter lacks a

–35 region and has an “extended –
10 element” compensating for the
absence of –35 region

32
 2-2 The  factor mediates
The transcription cycle in bacteria

binding of polymerase to
the promoter
 The 70 factor comprises four
regions called  region 1 to 
region 4.

33
 Fig 12-6: regions of 

Region 4 recognizes -35 element

Region 2 recognizes -10 element
Region 3 recognizes the extended –10
element 34
Binding of –35 Two helices within
region 4 form a common DNA-binding
motif, called a helix-turn-helix motif
One helix inserts
into the DNA major
groove interacting
with the bases at the
–35 region. The
other helix lies
across the top of the
groove, contacting
the DNA backbone

Fig 5-20* Helix-turn-

helix DNA-binding
motif 35
Interaction with –10 is more
elaborate (精细) and less understood

 The -10 region is within DNA

melting region
 The a helix recognizing –10 can
interacts with bases on the
non-template strand to
stabilize the melted DNA.

36
UP-element is recognized by
a carboxyl terminal domain of the a-
subunit (aCTD), but not by  factor

Fig 12-7  and a subunits recruit RNA

pol core enzyme to the promoter
37
 2-3 Transition to the open
The transcription cycle in bacteria

complex involves structural

changes in RNA polymerase
and in the promoter DNA

This transition is called

Isomerization (异构化)

38
For 70 –containing RNA
polymerase, isomerization is a
spontaneous conformational
change in the DNA-enzyme
complex to a more
energetically favorable form.
(No extra energy requirement)

39
Change of the promoter DNA

 theopening of the DNA

double helix, called “melting”,
at positions -11 and +3.

40
The striking structural
change in the polymerase
 1. the b and b’ pincers down
tightly on the downstream DNA
 2. A major shift occurs in the N-
terminal region of  (region 1.1)
shifts. In the closed complex, 
region 1.1 is in the active center;
in the open complex, the region
1.1 shift to the outside of the
center, allowing DNA access to
the cleft 41
 NTP uptake
channel is in the
back

DNA entering
channel

Fig 12-8 channels into and out of the

open complex 42
 Transcription is initiated by
The transcription cycle in bacteria

RNA polymerase without

the need for a primer

Initiation requires:
 The initiating NTP (usually an A)
is placed in the active site
 The initiating ATP is held tightly
in the correct orientation by
extensive interactions with the
holoenzyme
43
 RNA polymerase
The transcription cycle in bacteria

synthesizes several short

RNAs before entering the
elongation phase

Abortive initiation: the

enzyme synthesizes and
releases short RNA
molecules less than 10 nt.

44
Structural barrier for the
abortive initiation

 The 3.2 region of  factor lies

in the middle of the RNA exit
channel in the open complex.
 Ejection of this region from
the channel (1) is necessary
for further RNA elongation, (2)
takes the enzyme several
attempts
45
 NTP uptake
channel is in the
back

DNA entering
channel

Fig 12-8 channels into and out of the

open complex 46
 The elongating polymerase
The transcription cycle in bacteria

is a processive machine
that synthesizes and
proofreads RNA

47
Synthesizing by RNA polymerase
1. DNA enters the polymerase
between the pincers
2. Strand separation in the catalytic
cleft
3. NTP addition
4. RNA product spooling out (Only 8-
9 nts of the growing RNA remain
base-paired with the DNA
template at any given time)
5. DNA strand annealing in behind
48
Proofreading by RNA polymerase

 Pyrohosphorolytic （焦磷酸键解）
editing: the enzyme catalyzes the
removal of an incorrectly
inserted ribonucleotide by
reincorporation of PPi.
 Hydrolytic （水解）editing: the
enzyme backtracks by one or
more nucleotides and removes
the error-containing sequence.
This is stimulated by Gre factor,
a elongation stimulation factor.
49
 Transcription is terminated
The transcription cycle in bacteria

by signals within the RNA

sequence
Terminators: the sequences
that trigger the elongation
polymerase to dissociate
from the DNA
 Rho-dependent (requires Rho
protein)
 Rho-independent, also called
intrinsic (内在) terminator
50
Rho-independent terminator
contains a short inverted repeat (~20
bp) and a stretch of ~8 A:T base pairs.

Fig 12-9 51
 Fig 12-10
transcription
termination

Weakest base
pairing: A:U
make the
dissociation easier
52
Rho (r) -dependent terminators
 Have less well-characterized RNA
elements, and requires Rho protein for
termination
 Rho is a ring-shaped single-stranded
RNA binding protein, like SSB
 Rho binding can wrest (夺取) the RNA
from the polymerase-template complex
using the energy from ATP hydrolysis
 Rho binds to rut (r utilization) RNA sites
 Rho does not bind the translating RNA
53
Fig 12-11 the r transcription terminator

RNA tread
trough the
“ring”

Hexamer,
Open ring

54
CHAPTER12: Mechanisms of Transcription

Topic 3:
transcription in
eukaryotes

55
Comparison of eukaryotic and
prokaryotic RNA polymerases

Eukaryotes: Three polymerase

transcribes different class of genes:
Pol I-large rRNA genes; Pol II-
mRNA genes; Pol III- tRNA, 5S
rRNA and small nuclear RNA genes
(U6)
Prokaryotes: one polymerase
transcribes all genes
56
Comparison of eukaryotic and
prokaryotic promoter recognition

Eukaryotes: general transcription

factors (GTFs). TFI factors for
RNAP I, TFII factors for RNAP II
and TFIII factors for RNAP III
Prokaryotes:  factors

57
In addition to the RNAP and GTFs,
in vivo transcription also requires

 Mediatorcomplex
 DNA-binding regulatory proteins

 chromatin-modifying enzymes

58
 RNA polymerase II core
The transcription in eukaryotes

promoters are made up of

combinations of 4 different
sequence elements
Eukaryotic core promoter (~40 nt):
the minimal set of sequence
elements required for accurate
transcription initiation by the Pol
II machinery in vitro

59
Fig 12-12: Pol II core promoter

 TFIIB recognition element (BRE)

 The TATA element/box
 Initiator (Inr)
 The downstream promoter element
(DPE)
60
 Regulatory sequences
The sequence elements other than
the core promoter that are required
to regulate the transcription
efficiency
Those increasing transcription:
 Promoter proximal elements
 Upstream activator sequences
(UASs)
 Enhancers
Those repressing elements: silencers,
boundary elements, insulators (绝缘
体) 61
 RNA Pol II forms a pre-
The transcription in eukaryotes

initiation complex with

GTFs at the promoter
The involved GTFIIs (general
transcription factor for Pol II)
 TFIID=TBP (TATA box
binding protein) + TAFs
(TBP association factors)
 TFIIA, B, F, E, H

62
1. TBP in TFIID binds to the
TATA box
2. TFIIA and TFIIB are
recruited with TFIIB
binding to the BRE
3. RNA Pol II-TFIIF complex
is then recruited
4. TFIIE and TFIIH then bind
upstream of Pol II to form
the pre-initiation complex
5. Promoter melting using
energy from ATP
hydrolysis by TFIIH )
6. Promoter escapes after
the phosphorylation of 63the
CTD tail
 Promoter escape
 Stimulated by phosphorylation of
the CTD (C-terminal domain) tail
of the RNAP II
 CTD contains the heptapeptide
repeat Tyr-Ser-Pro-Thr-Ser-Pro-Ser
 Phosphorylation of the CTD “tail” is
conducted by a number of specific
kinases including a subunit of TFIIH

64
 TBP binds to and distorts
The transcription in eukaryotes

DNA using a b sheet

inserted into the minor
groove
 Unusual
(P367 for the
detailed
mechanism)
 The need for
that protein
to distort the
local DNA
structure 65
 A:Tbase pairs (TATA box)
are favored because they
are more readily distorted
to allow initial opening of
the minor groove

66
 The other GTFs also have
The transcription in eukaryotes

specific roles in initiation

 ~ 10 TAFs: (1) two of them

bind DNA elements at the
promoter (Inr and DPE); (2)
several are histone-like TAFs
and might bind to DNA similar
to that histone does; (3) one
regulates the binding of TBP to
DNA

67
  TFIIB: (1) a single polypeptide chain,
(2) asymmetric binding to TBP and the
promoter DNA (BRE), (3)bridging TBP
and the polymerase, (4) the N-terminal
inserting in the RNA exit channel
resembles the 3.2 .

Fig 12-13 TFIIB-TBP-promoter complex 68

 TFIIF: (1) a two subunit factor, (2)
binding of Pol II-TFIIF stabilizes the
DNA-TBP-TFIIB complex, which is
required for the followed factor binding
 TFIIE: recruits and regulates TFIIH
 TFIIH: (1) controls the ATP-dependent
transition of the pre-initiation complex
to the open complex, (2) contains 9
subunits and is the largest GTF; two
functions as ATPase and one is protein
kinase. (3) important for promoter
melting and escape. (4) ATPase
functions in nucleotide mismatch repair,
called transcription-coupled repair.
69
 in vivo, transcription
The transcription in eukaryotes

initiation requires
additional proteins
 The mediator complex
 Transcriptional regulatory
proteins
 Nucleosome-modifying enzymes
To counter the real situation that
the DNA template in vivo is
packed into nucleosome and
chromatin
70
Fig 12-16 assembly of the pre-initiation
complex in presence of mediator,
nucleosome modifiers and remodelers,
and transcriptional activators

71
 Mediator consists of
The transcription in eukaryotes

many subunits, some

conserved from yeast to
human
 More than 20 subunits
 7 subunits show significant sequence
homology between yeast and human
 Only subunit Srb4 is essential for
transcription of essentially all Pol II
genes in vivo
 Organized in modules (模块)
72
Fig 12-17 comparison
of the yeast and
human mediators

73
Eukaryotic RNA Pol II holoenzyme
is a putative preformed complex:
Pol II + mediator + some of GTFs

Prokaryotic RNA Polymerase

holoenzyme:
core polymerase +  factor

74
 A new set of factors
The transcription in eukaryotes

stimulate Pol II
elongation and RNA
proofreading

75
Transition from the initiation to
elongation involves the Pol II
enzyme shedding (摆脱) most of its
initiation factors (GTF and mediators)
and recruiting other factors:
(1) Elongation factors: factors that
stimulate elongation, such as TFIIS
and hSPT5.
(2) RNA processing (RNA 加工) factors
Recruited to the C-terminal tail of the
CTD of RNAP II to phosphorylate the
tail for elongation stimulation,
proofreading, and RNA processing
like splicing and polyadenylation. 76
Fig 12-18 RNA processing enzymes are
recruited by the tail of polymerase

77
 Some elongation factors
 P-TEFb:
 phosphorylates CTD
 Activates hSPT5

 Activates TAT-SF1

 TFIIS:
 Stimulates the overall rate of
elongation by resolving the
polymerase pausing
 Proofreading
78
 Elongation polymerase is
The transcription in eukaryotes

associated with a new

set of protein factors
required for various
types of RNA processing
RNA processing:
 Capping of the 5’ end of the RNA
 Splicing of the introns (most
complicated)
 Poly adenylation (多聚腺苷化) of the
3’ end
79
Elongation, termination of
transcription, and RNA
processing are interconnected/
coupled (偶联的) to ensure the
coordination (协同性) of these
events
Evidence: this is an overlap in
proteins involving in those events
 The elongation factor hSPT5 also
recruits and stimulates the 5’
capping enzyme
 The elongation factor TAT-SF1
recruits components for splicing 80
 Function of poly(A) tail
 Increased mRNA stability
 Increased translational
efficiency
 Splicing of last intron

81
 Function of 5´cap
 Protection from degradation
 Increased translational
efficiency
 Transport to cytoplasm
 Splicing of first intron

82
RNA processing 1
5’ end capping
 The “cap”: a
methylated guanine
joined to the RNA
transcript by a 5’-5’
linkage
 The linkage
contains 3
phosphates
 3 sequential
enzymatic reactions
 Occurs early
83
Splicing: joining the
protein coding sequences
 Dephosphorylation of Ser5 within
the CTD tail leads to dissociation of
capping machinery
 Further phosphorylation of Ser2
recruits the splicing machinery

84
 3’ end polyadenylation
 Linked with the termination of
transcription
 The CTD tail is involved in
recruiting the polyadenylation
enzymes
 The transcribed poly-A signal
triggers the reactions
1. Cleavage of the message
2. Addition of poly-A
3. Termination of transcription 85
1. CPSF (cleavage and
polyadenylation specificity
factor) & CstF (cleavage
stimulation factor) bind to
the poly-A signal, leading to
the RNA cleavage
2. Poly-A polymerase (PAP)
adds ~ 200 As at the 3’ end
of the RNA, using ATP as a
substrate

Fig 12-20
polyadenylation 86
and termination
 What terminates
transcription by polymerase?

87
Models to explain the link
between polyadenylation and
termination (see the animation on
your CD)
 Model 1: The transfer of the 3’
processing enzyme to RNAP II
induces conformational change—
RNAP II processivity reduces—
spontaneous termination
 Model 2: absence of a 5’cap on the
second RNA molecule—recognized
by the RNAP II as improper—
terminate transcription
88
 RNA Pol I & III recognize
distinct promoters , using
The transcription in eukaryotes

distinct sets of
transcription factors, but
still require TBP
 Pol I: transcribes rRNA precursor
encoding gene (multi-copy gene)
 Pol III: transcribes tRNA genes,
snRNA genes and 5S rRNA genes

89
Pol I promoter recognition

Upstream control element

UBF binds to the upstream of UCE, bring SL1 to the

downstream part of UCE. SL1 in turn recruits RNAP
I to the core promoter for transcription

Fig 12-21 Pol I promoter region 90

Pol III promoter recognition
1. Different forms, 2. locates
downstream of the transcription site

TFIIIC binds to the promoter, recruiting

TFIIIB, which in turn recruits RNAP III

Fig 12-22 Pol III core promoter 91

Mechanisms of
Translation

92
Alur Genetika

93
 tRNA
 Mengkopi Bagian Spesifik dari
DNA
 Site Amino acid spesifik
 Anticodon

 Terlibat dalam translasi (sintesis

Protein)
 rRNA
 Ribosom tersusun atas dua
subunit
prokariot : 70S = sub unit 50S
+ 30S
eukariot : 80S = sub unit 60S +
40S
 Tiap subunit terdiri dari rRNA
dan protein
 Terlibat dalam translasi
Karakteristik Struktural tRNA dan mRNA.
 KODON

 Kode Triplet yang spesifik untuk

membentuk asam amino
 Terdapat pd mRNA
 20 asam amino
 Start kodon dan Stop kodon
 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Second Base Position

U C A G
UUU
UUC } Phenylalanine
UCU
UCC
Serine
UAU
UAC
} Tyrosine
UGU
UGC } Cysteine
U
C
U
UUA
UUG } Leucine
UCA
UCG
UAA
UAG
} STOP**
UGA
UGG
STOP**
Tryptophan
A
G
CUU CCU CAU
} Histidine
CGU U
First Base Position

CUC CCC CAC CGC C

Third Base Position

C Leucine Proline Arginine
CUA
CUG
CCA
CCG
CAA
CAG } Glutamine
CGA
CGG
A
G
AUU
AUC
Isoleucine
ACU
ACC
AAU
AAC } Asparagine
AGU
AGC } Serine
U
C
A Threonine
AUA
AUG STARTfMethionine*
ACA
ACG
AAA
AAG } Lysine
AGA
AGG } Arginine
A
G

G
GUU
GUC
Valine
GCU
GCC
Alanine
GAU
GAC } Aspartic acid
GGU
GGC
Glycine
U
C
GUA
GUG
GCA
GCG
GAA
GAG } Glutamic acid
GGA
GGG
A
G

* This codon initiates translation.

**For these codons, which give the orders to stop translation, there are no corresponding tRNAs and no amino acids.
Gambaran Kodon dan pasangannya yang membawa
asam amino
Sintesis PROTEIN
(translasi)

 Beberapa faktor yang terlibat dalam

sintesis protein
• mRNA : kodon
• tRNA : site asam amino dan site anti
kodon
• Ribosom : site P & site A, large & small
unit
Interaksi ribosom, tRNA dan mRNA
 Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Interaksi kodon - anti kodon

Leucine

fMet 2

1
A
P
E 2
1

G AC G
Anticodon U AC CUG C CG
A UG
mRNA

Codon
UAG

(a) Entrance of tRNAs 1 and 2

INTERAKSI ANTARA KODON DENGAN ANTI KODON
Ketepatan sintesis protein ditentukan oleh dua system :
1. system ketepatan muatan asam amino pada tRNA
2. pasangan kodon-antikodon

Pasangan kodon-antikodon.
- 61 dari 64 kodon mengkode 20 asam amino, sehingga
diharapkan ada 61 tRNA yang berbeda.
- Faktanya tRNAAla dari Yeast (ragi) dapat berpasangan
dengan 3 dari 4 kodon alanin (GCX) yaitu :
-GCU
O
-GCC
-GCA C N
Antikodon tRNAAla tersebut adalah : 5’-IGC-
H- N 3’ C
I = inosin adalah nukleosida ribosil hipoksantin C-H
H- C C
N N
I dapat berpasangan U,C,A dengan ikatan hydrogen
tetapi tidak sekuat tipe Watson-Crick. Ribosa
Tidak ada antikodon yg dimulai dg 5’A.
Setiap A muncul pd posisi pertama dr tRNA baru hasil
transkripsi, A akan di-deaminasi mjd hipoksantin (basa dr
inosin).
HIPOTESIS WOBBLE (bergoyang)
Hampir semua kodon menunjukkan bhw basa ke-3 tidak
penting
Francis Crick (1965) mengusulkan hipotesis wobble meliputi :
- respon bbrp tRNA thd bbrp kodon
- pola redundancy (kelebihan) sbg respon dari satu antikodon
untuk bbrp kodon
Dalam interaksi kodon-antikodon, standar pasangan tdk spt
pd double helix. Posisi basa ke-3 dari kodon bermain dlm
struktur (permainan ini disebut wobble = goyangan),
memberi peluang tjd pasangan basa yg tdk standar.

Basa ke-3 Basa ke-1 Basa ke-1

Tabel
kodon pasangan
antikodon wobble
antikodon
A U I
G C U
U G I
C G I
Tahapan Sebelum Translasi (Preinisiasi):

: reaksi esterifikasi antara asam amino dg

tRNA

Asam
tRNA
amino

Aminoasil tRNA
 Tahapan TRANSLASI
Inisiasi :
 Ribosom sub unit kecil akan menempel
pada mRNA dekat dengan start codon
(cth. AUG)
 Antikodon tRNA yang mengikat asam
amino pertama (inisiator) akan
menempel pada start codon
 Ribosom sub unit besar bergabung
mbtk kompleks inisiasi
 Tahapan TRANSLASI
Elongasi :
 Ribosom akan bergerak ke kodon
berikutnya (Translokasi), diikuti
dengan tRNA (antikodon) baru yang
melekat pada kodon tersebut dan
menambahkan asam amino tersebut
dengan asam amino sebelumnya
 Ikatan asam amino yang terbentuk
merupakan ikatan peptida atau protein
oleh enzim peptidil transferase
Peptidil
transferase
 Tahapan TRANSLASI
Terminasi :
 Stop codon menghentikan proses
translasi
 Protein lepas dr mesin sintesis
 Ribosom lepas dr mRNA & terdisosiasi
kembali
Proses Translasi.
Animasi protein synthesis
Beberapa cara modifikasi :
1.a. Prokariot
modifikasi f-met pada NH2 terminal asam
amino yaitu
gugus formil dibuang dg enzim deformilase :
f-met metionin
b. Prokariot atau eukariot
f-met, met dan bbrp as. amino
dibuang
enz amino
peptidase
deformilasi
Proses f-met met,
terjadi bila as amino kedua : Arginin, Asparagin,
as.Aspartat, as.Glutamat, Isoleusin dan Lisin
Proses f-met hilang (dibuang),
terjadi bila AA kedua : Alanin, Glisin, Prolin,
2. NH2-terminal as.amino yg baru
terbentuk kadang mengalami
asetilasi
3. Beberapa as. amino dimodifikasi
kolagen: prolin dan lisin
hidroksilasi
bbrp organisme : serin,tirosin,
treonin fosforilasi pd gugus OH
sering OH-bebas dari serin dan
treonin berikatan dg gula
membentuk glikoprotein
4. Dua gugus sulfhidril (-SH) yg jauh
pada 2 sistein mengalami oksidasi
TRANSKRIPSI DAN
TRANSLASI PADA
EUKARYOTA
 Mirip dengan Prokariot, kecuali :
 AUG mengkode methionin dengan bentuk
yang berbeda
 mRNA hanya mengkode satu protein
(monosistronik)
 Transkripsi dan translasi tidak terjadi
secara simultan
 Sebelum mRNA terbentuk terlebih dahulu
berupa Pre-mRNA yg terdiri dari :
• Introns (urutan RNA yang bukan merupakan
penyandi genetik)
• Exons
 Untuk membentuk mRNA dari Pre-mRNA
terjadi Splicing (penghilangan intron).
Eukaryota vs Prokariot
 Animasi

processing of
Welcome Each of You
gene informationto
My Molecular Biology
procaryotes and
eucaryotes Class
PENGHAMBAT SINTESIS
PROTEIN OLEH
ANTIBIOTIK
 Rifampisin : mengikat pada
enzim polimerase RNA bakteri
dan menghambat mRNA
 Eritromisin dan Azitromisin :
mengikat pada ribosome
bakteri, dan menghambat
pelekatan pada mRNA.
 Tetrasiklin : mengikat pada
ribosome bakteri, dan
menghambat translasi mRNA
15.1 Many Genes Encode Proteins
• The One Gene One Enzyme
Hypothesis:

• Genes function by encoding

enzymes, and each gene encodes a
separate enzyme.

• More specific: one gene one

polypeptide hypothesis
 Concept Check 1

Auxotrophic mutation 103 grows on minimal

medium supplemented with A, B, or C. Mutation
106 grows on medium supplemented with A and
C, but not B; and mutation 102 grows only on
medium supplemented with C. What is the order
of A, B, C in a biochemical pathway?
 Concept Check 1

Auxotrophic mutation 103 grows on minimal

medium supplemented with A, B, or C. Mutation
106 grows on medium supplemented with A and
C, but not B; and mutation 102 grows only on
medium supplemented with C. What is the order
of A, B, C in a biochemical pathway?

BAC
 Breaking the Genetic Code

• Codon: a triplet RNA code

 The Degeneracy of the Code

• Degenerate code: Amino acid may be

specified by more than one codon.

• Synonymous codons: codons that

specify the same amino acid

• Isoaccepting tRNAs: different tRNAs

that accept the same amino acid but
have different anticodons

• Wobble hypothesis
 The Degeneracy of the Code

 Sense codons: encoding amino acid

 Initiation codon: AUG

 Termination codon: UAA, UAG, UGA

 Concept Check 2

Through wobble, a single can pair with

more than one .

a. codon, anticodon
b. group of three nucleotides in DNA,
codon in mRNA
c. tRNA, amino acid
d. anticodon, codon
 Concept Check 2

Through wobble, a single can pair with

more than one .

a. codon, anticodon
b. group of three nucleotides in DNA,
codon in mRNA
c. tRNA, amino acid
d. anticodon, codon
15.1 Many Genes Encode Proteins
• The One Gene One Enzyme
Hypothesis:

• Genes function by encoding

enzymes, and each gene encodes a
separate enzyme.

• More specific: one gene one

polypeptide hypothesis
15.2 The Genetic Code Determines How
the Nucleotide Sequence Specifies the
Amino Acid Sequence of a Protein
The Reading Frame and Initiation Codons

• Reading frame: three ways in which

the sequence can be read in groups of
three. Each different way of reading
encodes a different amino acid
sequence.

• Nonoverlapping: A single nucleotide

may not be included in more than one
codon.

• The universality of the code: near

15.3 Amino Acid Are Assembled into a Protein
Through the Mechanism of Translation
 The Binding of Amino Acids to Transfer
RNAs

• Aminoacyl-tRNA syntheses and tRNA

charging

• The specificity between an amino

acid and its tRNA is determined by
each individual aminoacyl-tRNA
synthesis. There are exactly 20
different aminoacylt-tRNA
syntheses in a cell.
 The Initiation of Translation

• Initiation factors IF-3, initiator tRNA

with N-formylmethionine attached to
form fmet-tRNA

• Energy molecule: GTP

 The Initiation of Translation

• The Shine–Dalgarno consensus

sequence in bacterial cells is
recognized by the small unit of
ribosome.

• The Kozak sequence in eukaryotic

cells facilitates the identification of
the start codon.
 Elongation

• Exit site E

• Peptidyl site P

• Aminoacyl site A

• Elongation factors: Tu, Ts, and G

 Concept Check 3

In elongation, the creation of peptide bonds

between amino acids is catalyzed by .

a. rRNA
b. protein in the small subunit
c. protein in the large subunit
d. tRNA
 Concept Check 3

In elongation, the creation of peptide bonds

between amino acids is catalyzed by .

a. rRNA
b. protein in the small subunit
c. protein in the large subunit
d. tRNA
 Termination

 Termination codons: UAA, UAG, and

UGA

 Release factors
 15.4 Additional Properties of RNA and
Ribosomes Affect Protein Synthesis

 The three-dimensional structure of

the ribosome

 Polyribosomes:
 An mRNA with several ribosomes
attached
 15.4 Additional Properties of RNA and
Ribosomes Affect Protein Synthesis

• Messenger RNA surveillance:

• Detect and deal with errors in

mRNA

• Nonsense – mediated mRNA decay:

eliminating mRNA containing
premature termination codons

• The posttranslational modifications of