PROTEIN SYNTHESIS

DEPARTEMEN BIOKIMIA
FAKULTAS KEDOKTERAN UNSOED
 REFERENSI

• J. W. Baynes and M. H. Dominiczak, Medical

biochemistry.
•P. Ronner, “Netter’s Essential Biochemistry,” 2018.
TUJUAN PEMBELAJARAN

1. Mahasiswa mampu menjelaskan struktur dan fungsi DNA

dan RNA, kromosom
2. Mahasiswa mampu menjelaskan perbedaan DNA, gen, dan
genome beserta perannya
3. Mahasiswa mampu menjelaskan dogma sentral biologi
molekuler
4. Mahasiswa mampu menjelaskan proses replikasi,
transkripsi, translasi
5. Mahasiswa mampu menjelaskan pengaruh mutasi dna
terhadap ekspresi gen
Deoxyribonucleic Acid (DNA)

DNA is the blueprint for life

• DNA is a polymer of
nucleotides
• Nucleic acids are one of
the major organic
compound
• Each nucleotide
composed of a sugar,
phosphate, and 1. Phosphate Group
2. 5-Carbon Sugar
nitrogenous base (Dexoyribose or Ribose)
3. Nitrogen Base
Nucleotides

Adenine A
Purines
Guanine

N base

Thymine
Pyrimidines
Cytosine
DNA: Complimentary base pairing

• Adenine always bonds with thymine. A = T

• Cytocin always bonds with Guanine. C = G

The lines between the bases represent hydrogen bonds

DNA STRUCTURE

• The structure of
DNA consists of two
polynucleotide
strands wrapped
around each other
in a double helix
Structure and Formation DNA
Double Helix
 Double Helix
• Each strand of the
double helix is
oriented in the
opposite direction
NUCLEUS

• Feature 1
• Feature 2
• Feature 3
Slide Title
Eukaryotic Prokaryotic
RiboNuleic Acid (RNA )

• RNA is also a nucleic acid

– RNA has a slightly different sugar
– RNA has U instead of T

• RNA is a single stranded nucleic acid

made up of monomers called
nucleotides
• RNA have function to Carries DNA’s
message code and helps to make
protein
RNA Nucleotides
A - Sugar (ribose)
B - Phosphate
C - Nitrogen base
Rules for Base Pairing
Cytosine pairs with Guanine

C = G

Adenine pairs with Uracil

A = U

Notice that RNA has Uracil

(not thymine)
RNA STRUCTURE
DIFERENCES RNA AND DNA
TYPES OF RNA
Three Types of RNA
.

 Messenger RNA (mRNA) copies DNA’s

code & carries the genetic information
to the ribosomes
 Ribosomal RNA (rRNA), along with
protein, makes up the ribosomes
 Transfer RNA (tRNA) transfers amino
acids to the ribosomes where proteins
are synthesized
 Other???

Biokimia/Sintesis Protein
 Messenger RNA

• Long Straight chain

of Nucleotides
• Made in the Nucleus
• Copies DNA & leaves
through nuclear
pores
• Contains the
Nitrogen Bases A, G,
C, U ( no T )
Biokimia/Sintesis Protein
Messenger RNA (mRNA)

 Carries the information for a specific

protein
 Made up of 500 to 1000 nucleotides
long
 Sequence of 3 bases called codon
 AUG – methionine or start codon
 UAA, UAG, or UGA – stop codons

Biokimia/Sintesis Protein
Ribosomal RNA (rRNA)

 rRNA is a single strand 100 to

3000 nucleotides long
 Globular in shape

 Made inside the nucleus of a

cell
 Associates with proteins to
form ribosomes
 Site of protein Synthesis
Biokimia/Sintesis Protein
Transfer RNA (tRNA)

• Clover-leaf shape
• Single stranded molecule with
attachment site at one end
for an amino acid
• Opposite end has three
nucleotide bases called the
anticodon

Biokimia/Sintesis Protein
Transfer RNA
amino acid
attachment site

U A C
anticodon
Codons and Anticodons

• The 3 bases of an
anticodon are
complementary to
the 3 bases of a
codon UGA
• Example: Codon ACU
Anticodon UGA ACU
The Genetic Code

• A codon designates an amino

acid
• An amino acid may have more
than one codon
• There are 20 amino acids,
but 64 possible codons
• Some codons tell the ribosome
to stop translating

Biokimia/Sintesis Protein
The Genetic Code

•Use the code by

reading from the
center to the
outside
•Example: AUG
codes for
Methionine

Biokimia/Sintesis Protein
Name the Amino Acids

• GGG?
• UCA?
• CAU?
• GCA?
• AAA?

Biokimia/Sintesis Protein
Remember the
Complementary Bases

On DNA:
A-T
C-G
On RNA:
A-U
C-G
Biokimia/Sintesis Protein 30
DNA, GEN, GENOME ?
DNA; GEN; GENOME

DNA contains genes, the information needed to

synthesize functional proteins

DNA : is a nucleic acid, made of long chains of nucleotides

GEN : sequences of nucleotide bases. These Genes code for

polypeptides (proteins)

GENOME ???
DNA - GEN
DOGMA CENTRAL
 Dogma Central

• alir materi genetik dari DNA ke urutan asam amino (protein)

• merupakan konsep dasar sifat menurun yang menentukan
ciri khas suatu spesies
• Cara suatu spesies mempertahankan cir khas materi
genetiknya supaya tetap sama
Dogma Central
Replikasi DNA

• Proses pembentukan
DNA baru di dalam
kromosom

• Replikasi DNA
dibutuhkan setiap
pembelahan
sel/terbentuknya sel
baru
Dogma Central
THREE MODEL OF DNA REPLICATION
Replikasi DNA Model Semikonservatif
Meselson & Stahl (1958)
• Menyimpulkan bahwa
mekanisme replikasi DNA
adalah model
semikonservatif

Setiap molekul untai ganda DNA anakan terdiri atas satu

untai tunggal DNA induk dan satu untai tunggal DNA
hasil sintesis baru.
REPLIKASI DNA
Tahapan Umum Replikasi
Tahap 1: Pemisahan kedua untai DNA

Tahap 2: Pengisian dengan komplemen nukleotida

 Tahapan Umum Replikasi
Tahap 3: Komplemen nukleotida berikatan dan terbentuknya rangka
gula-gugus fosfat baru

Tahap akhir : Setiap molekul DNA mengandung 1 untai DNA

asli/induk dan 1 untai DNA baru/anak
MEKANISME REPLIKASI

• Proses replikasi DNA diawali

dengan pemutusan
(denaturasi) ikatan antara
untai DNA yang satu dengan
untaian komplementernya
(secara enzimatis).
• Denaturasi awal terjadi
pada bagian DNA yang
dikenal sebagai ori (origin of
replication) atau titik awal
replikasi.
Untaian DNA membuka membentuk
struktur yang disebut sebagai garpu
replikasi (replication fork).
Membukanya double helix ini
disempurnakan oleh kerja enzim DNA
helicase. Daerah membukanya double
helix DNA ini, terlihat dengan mikroskop
electron seperti gelembung (bubble),
replication bubble.
Bubble ini akan mengalami peningkatan
ukurannya sejalan dengan bergeraknya
replication fork pada DNA helix dalam dua
arah
Fragmen Okazaki  celah fragment  ditutup oleh DNA Polimerase I
(eksonuklease)

diikat oleh DNA Ligase

Arah Replikasi

• Untai DNA baru selalu

disintesis dalam arah
5’ ke 3’.
• 5’ triphosphate hanya
dapat ditambahkan ke
gugus 3’ OH dari
deoxyribose
Leading and Lagging Strand

• Pembatasan oleh arah sintesis DNA yang hanya dari

5’ ke 3’
• Terdapat 2 strand DNA yang digunakan secara
berbeda pada replication fork
•Leading strand digunakan untuk sintesis DNA
secara kontinu
•Lagging strand digunakan untuk sintesis DNA
secara bertahap (diskontinu)
Lagging Strand Synthesis
Enzim-enzim dalam replikasi DNA

1.Topoisomerase:
• bertanggung jawab dalam proses dimulainya pembukaan double heliks DNA.
Tegangan ikat pada struktur gulungan double heliks DNA dapat dipatahkan
dengan penorehan (nicking) salah satu untai DNA tunggal (topoisomerase I).
Topisomerase II menoreh untai DNA dua-duanya. Topoisomerases I dan II tetap
berikatan dengan DNA setelah nicking.

2.Helikase;
• menyempurnakan proses membukanya double heliks, setelah gulungan
supercoil dihilangkan oleh topoisomerase. Dua untai DNA ini secara alami ingin
berikatan satu sama lain karena adanya afinitas ikatan hidrogen, dengan
demikian, aktivitas helikase memerlukan energi dalam bentuk ATP untuk
memisahkan menjadi dua untai DNA.
Enzim-enzim dalam replikasi DNA

3.DNA polymerase:
• mengkatalisis pembentukan ikatan hidrogen antara nukleotida baru yang akan
membentuk untai baru dengan nukleotida pada untai DNA lama yang berfungsi
sebagai pencetak (template strand).
• mengkatalisis reaksi antara 5' phosphate pada nukleotida baru dan 3' OH bebas pada
polinukleotida yang sedang dibentuk (ikatan phosphodiester). Sebagai hasilnya, untai
baru DNA hanya dapat bertambah panjang pada arah dari 5' ke 3‘. Sekali lagi, untuk
diketahui bahwa ikatan phosphodiester dibentuk antara gugus 3' OH pada gula
dengan gugus 5' phosphate dari nukleotida yang baru.
• Terdapat beberapa bentuk polymerase DNA; DNA polymerase III bertanggungjawab
dalam proses sintesis untai DNA baru.
• DNA polymerase adalah kelompok yang terdiri dari beberapa sub-unit protein yang
berbeda (disebut holoenzyme). Enzim ini memiliki aktivitas proofreading, yaitu dapat
memastikan bahwa enzim ini menyisipkan basa nitrogen yang tepat, dan memiliki
aktivitas sebagai 3'à 5' exonuclease (excision of nucleotides) dengan demikian enzim
ini dapat memotong bila terjadi kesalahan.
Enzim-enzim dalam replikasi DNA

4.Primase, adalah bagian dari agregat protein yang disebut primeosome.

Enzim ini berfungsi menempelkan primer RNA pendek ke untai tunggal/
single-stranded DNA untuk bertindak sebagai pengganti 3'OH bagi DNA
polymerase sebagai tempat darimana memulai sintesis. Primer RNA ini
pada akhirnya akan dibuang oleh RNase, dan gap/ tempat lowong ini akan
diisi oleh kerja DNA polymerase I.
5.Ligase: mengkatalisis pembentukan ikatan phosphodiester antara 3'OH dan
5'phosphate yang berdekatan. Enzim ini dapat menyambung gap yang tidak
tersambungketika RNA primer dibuang dan kemudian digantikan.
6.Single-stranded binding proteins: sangat penting untuk menjaga stabilitas dari
replication fork. Single-stranded DNA adalah sangat labil, atau tidak stabil,
oleh karena itu protein ini akan berikatan dengannya ketika masih dalam
keadaan untai tunggal (single stranded) dan menjaganya agar tdk
terdegradasi.
Replikasi Prokariota vs Eukariota
GEN; PROTEIN

• Gen ??
• Proteins consist of amino acids, which join into polypeptides
by forming peptide bonds through dehydration synthesis.

• A protein’s three-dimensional shape is vital to its function.

• A denatured protein has a ruined shape.

• 20 different amino acids exist

 Amino Acid and Polipeptides

Amino Acid Structure polypeptides

• Feature 1
• Feature 2
• Feature 3

 Amino acid chains are called

polypeptides
Slide Title
Molecular tools
Machines
Enzymes
Structural cables
Hormones
Regulator
contractile filaments
antibodies,
form blood clots,
transport substances
Dogma Central
• Didalam genome suatu jasad hidup terdapat rangkaian gen yang
menyusun genotipe jasad tersebut
• Genome : kumpulan lengkap informasi genetik suatu organisme/
jasad hidup
• Genotipe adalah potensi - potensi genetik yg dimiliki oleh suatu
jasad hidup yg jika diekspresikan akan memunculkan sifat fisiologis
atau kenampakan morfologis yang secara umum disebut Fenotipe.
• Fenotip : karakteristik (baik struktural, biokimiawi, fisiologis, dan
perilaku) yang dapat diamati dari suatu organisme yang diatur oleh
genotipe dan lingkungan serta interaksi keduanya
• Pemunculan suatu fenotip merupakan hasil ekspresi banyak gen melalui
rangkaian proses pengaturan yang komplek.
• Ekspresi genetik dilakukan melalui proses transkripsi gen tertentu menjadi
RNA (mRNA, tRNA, dan rRNA ) selanjutnya mengalami proses translasi
menjadi protein
atau enzim.
• Transkripsi adl proses penyalinan kode kode genetik yg
terdapat pada molekul DNA.
• Proses translasi memerlukan molekul rRNA untuk menyusun ribosom, serta
molekul tRNA yg membawa
asam asam amino spesifik yang akan dirangkaikan
menjadi molekul protein
DNA BEGIN THE PROCESS

• DNA is found inside the

nucleus
• Proteins, however, are made
in the cytoplasm of cells by
organelles called ribosomes
• Ribosomes may be free in the
cytosol or attached to the
surface of rough ER
 DNA ‘s code must be copied
and taken to the cytosol
 In the cytoplasm, this code
must be read so amino acids
can be assembled to make
polypeptides (proteins)
 This process is called
PROTEIN SYNTHESIS
Roles of RNA and DNA

• DNA is the MASTER

PLAN

• RNA is the
BLUEPRINT of the
Master Plan
Biokimia/Sintesis Protein 67
 Protein Synthesis

 The production or synthesis

of polypeptide chains
(proteins)

 Two phases:
Transcription & Translation

 mRNA must be processed

before it leaves the nucleus
of eukaryotic cells
Biokimia/Sintesis Protein 68
Transcription

 The process of
copying the sequence
of one strand of
DNA, the template
strand
 mRNA copies the
template strand
 Requires the enzyme
RNA Polymerase
Biokimia/Sintesis Protein 69
Question:

 What would be the

complementary RNA strand
for the following DNA
sequence?

DNA 5’-GCGTATG-3’

Biokimia/Sintesis Protein 72
Answer:

 DNA 5’-GCGTATG-3’
 RNA 3’-CGCAUAC-5’

Biokimia/Sintesis Protein 73
Transcription

• During transcription, RNA

polymerase binds to DNA and
separates the DNA strands
• RNA Polymerase then uses
one strand of DNA as a
template to assemble
nucleotides into RNA

Biokimia/Sintesis Protein 74
 Synthesis of an
RNA Transcript
Promoter
Transcription unit
5 3
3 5
DNA
Start point
RNA polymerase 1 Initiation. After RNA polymerase binds to
the promoter, the DNA strands unwind, and
the polymerase initiates RNA synthesis at the
start point on the template strand.
5 3
3 5

• The stages of Unwound RNA

Template strand of
DNA

transcription are DNA transcript

2 Elongation. The polymerase moves downstream, unwinding the
– Initiation DNA and elongating the RNA transcript 5  3 . In the wake of
transcription, the DNA strands re-form a double helix.
Rewound
– Elongation RNA

– Termination 5
3
5
3
3
5

RNA
transcript
3 Termination. Eventually, the RNA
transcript is released, and the
polymerase detaches from the DNA.

5 3
3 5

5 3
Completed RNA
transcript
Synthesis of an RNA Transcript - Initiation

TRANSCRIPTION DNA 1 Eukaryotic promoters

RNA PROCESSING Pre-mRNA
mRNA

• Promoters signal the initiation of TRANSLATION Ribosome

RNA synthesis
Polypeptide
Promoter

• Promoters are regions on

5 T A T A A AA 3
3 AT AT T T T 5
TATA box
DNA that show where RNA
Start point Template
DNA strand

Polymerase must bind to 2 Several transcription

factors
begin the Transcription of Transcription
factors
RNA 5 3

• Called the TATA box

3 5
3 Additional transcription
factors

• Transcription factors help

eukaryotic RNA polymerase
recognize promoter sequences RNA polymerase II
Transcription factors

5 3
3 5 5
RNA transcript
Transcription initiation complex
 Synthesis of an RNA Transcript - Elongation

• RNA polymerase synthesizes a single strand of RNA against the DNA template strand (anti-sense
strand), adding nucleotides to the 3’ end of the RNA chain

• As RNA polymerase moves along the DNA it continues to untwist the double helix, exposing about
10 to 20 DNA bases at a time for pairing with RNA nucleotides

Elongation Non-template
strand of DNA
RNA nucleotides
RNA
polymerase

T C C A A T
A T
3 C U
3 end
T
A U G G
C AE G C A A G
C
5 A
T A G G T T A

Direction of transcription
5 Template
(“downstream”)
strand of DNA

Newly made
RNA
Synthesis of an RNA Transcript -
Termination

• Specific base sequences act as signals

to stop Called the termination signal

• When one of these is encountered by

the polymerase, the RNA transcript is
released from the DNA and the double
helix can zip up again.
mRNA Processing

 After the DNA is

transcribed into RNA,
editing must be done to
the nucleotide chain to
make the RNA functional
 Introns, non-functional
segments of DNA are
snipped out of the chain
Biokimia/Sintesis Protein 80
RNA Processing Reaction

1.Addition of a 5′ cap
2.Addition of a poly(A) tail
3.Intron removal

Biokimia/Sintesis Protein 81
1. RNA Capping

methylation (addition of a methyl group), which partially

accumulates at the 5' end of mRNA. This structure came
to be known as the mRNA cap(mRNA cap), in the form of a
7-methylguanosine (m7G) molecule
Function :
1. protects mRNA from degradation
2. improve mRNA translation efficiency
3. increase the transport of mRNA from the nucleus to
thecytoplasm
4. improve the efficiency of the mRNA splicing process
2. Polyadenylation

• the poly-A chain is added post-transcriptionally

becauseno part of the gene encoding the A
• addition is done using activity of poly(A)-polymerase
enzyme
• Function:
improve mRNA stability so mRNA has a lifespanwhich
is longer than the mRNAdoes not have poly-A
3. Splicing
Result of Transcription
mRNA Transcript

•mRNA leaves the nucleus

through its pores and goes to
the ribosomes

Biokimia/Sintesis Protein 86
Transcription

Translation

Biokimia/Sintesis Protein 88
Translation

 Translation is the process

of decoding the mRNA into
a polypeptide chain
 Ribosomes read mRNA
three bases or 1 codon at
a time and construct the
proteins

Biokimia/Sintesis Protein 89
Ribosomes
• Made of a large and small
subunit
• Composed of rRNA (40%)
and proteins (60%)
• Have two sites for tRNA
attachment --- P and A

Biokimia/Sintesis Protein 90
Ribosomes

Large
subunit
P A
Site Site

mRNA

A U G C U A C U U C G
Small subunit
Biokimia/Sintesis Protein 91
Step 1- Initiation

• mRNA transcript
start codon AUG
attaches to the
small ribosomal
subunit
• Small subunit
attaches to large
ribosomal subunit

mRNA transcript
Biokimia/Sintesis Protein 92
 Initiation
aa2
aa1

2-tRNA
1-tRNA

anticodon
G A U
U A C
hydrogen A U G C U A C U U C G A
bonds codon mRNA
Biokimia/Sintesis Protein 93
Step 2 - Elongation
• As ribosome moves, two tRNA with
their amino acids move into site A and
P of the ribosome
• Peptide bonds join the amino acids

Biokimia/Sintesis Protein 94
 Elongation
peptide bond
aa3
aa1 aa2

3-tRNA

1-tRNA 2-tRNA G A A
anticodon
U A C G A U
hydrogen A U G C U A C U U C G A
bonds codon mRNA
Biokimia/Sintesis Protein 95
 aa1 peptide bond
aa3
aa2

1-tRNA

3-tRNA
U A C
(leaves)
2-tRNA G A A

G A U
A U G C U A C U U C G A
mRNA

Ribosomes Biokimia/Sintesis
move over one codon
Protein 96
 peptide bonds
aa1 aa4

aa2 aa3

4-tRNA

2-tRNA 3-tRNA G C U

G A U G A A
A U G C U A C U U C G A A C U
mRNA

Biokimia/Sintesis Protein 97
 peptide bonds
aa1 aa4
aa2

aa3

2-tRNA
4-tRNA
G A U
(leaves)
3-tRNA G C U

G A A
A U G C U A C U U C G A A C U
mRNA

Ribosomes Biokimia/Sintesis
move over one codon
Protein 98
 peptide bonds aa5
aa1
aa2
aa4
aa3

5-tRNA

U G A
3-tRNA 4-tRNA

G A A G C U
G C U A C U U C G A A C U
mRNA

Biokimia/Sintesis Protein 99
 aa1 peptide bonds aa5
aa2
aa3
aa4

5-tRNA

3-tRNA U G A
G A A 4-tRNA

G C U
G C U A C U U C G A A C U
mRNA

Ribosomes Biokimia/Sintesis
move over one codon
Protein 100
 aa5
aa4 aa199

aa3 primary aa200 Termination

structure
aa2 of a protein

aa1
terminator
200-tRNA
or stop
codon

A C U C A U G U U U A G
mRNA

Biokimia/Sintesis Protein 101

End Product –The Protein!

• The end products of protein

synthesis is a primary structure of a
protein
• A sequence of amino acid bonded
together by peptide bonds

aa5
aa3 aa4
aa2 aa199

aa1 aa200
Biokimia/Sintesis Protein 102
Messenger RNA (mRNA)

start
codon
A U G G G C U C C A U C G G C G C A U A A
mRNA

codon 1 codon 2 codon 3 codon 4 codon 5 codon 6 codon 7

protein methionine glycine serine isoleucine glycine alanine stop

codon

Primary structure of a protein

aa1 aa2 aa3 aa4 aa5 aa6

peptide bonds
Biokimia/Sintesis Protein 103
Protein Targeting

• mRNAs that encode proteins destined for the cytoplasm or

nucleus are translated primarily on polysomes free in the
cytoplasm,
• whereas mRNAs encoding membrane and secreted proteins are
translated on polysomes attached to the ER
• Proteins destined for export, insertion into membranes, or
specific cellular organelles such as the nucleus, lysosomes, or
mitochondria are distinct from proteins that reside in the
cytoplasm. The distinguishing characteristic of proteins targeted
for these locations that they contain a signal sequence of 20–30
amino acids
Protein Targeting
POST TRANSLATIONAL MODIFICATION

1. Trimming (Perampingan)
Protein dihasilkan sebagai molekul precursor besar
yang tidak berfungsi aktif  Sebagian rantai harus
dipotong oleh endoprotease
POST TRANSLATIONAL MODIFICATION

2. Covalent Alteration :
a) Phosphorylation
b) Glycosylation
c) Hydroxylation
d) Other covalent modifications
POST TRANSLATIONAL
MODIFICATION

3. Protein Folding
POST TRANSLATIONAL
MODIFICATION

4. DEGRADATION
Proteins that are defective or destined
for rapid turnover are often marked for
destruction by ubiquitination attachment
of a small, highly conserved protein,
called ubiquitin.
Proteins marked in this way are rapidly
degraded by a cellular com­ponent
known as the "proteasome", which is a
complex, ATP-dependent, proteolytic
system located in the cytosol
MUTATIONS

• Mutations are changes in the DNA base sequence

– These are caused by errors in DNA replication or
by mutagens
– The change of a single DNA nucleotide causes
sickle-cell disease
TYPES MUTATION