Translation + PTMs

Translation
(transkripsi) (translasi)
DNA------------------ RNA-------------------Protein
Translation: From Messenger RNA to Protein
•The information encoded in DNA is transferred to

messenger RNA and then decoded by the ribosome to
produce proteins.
•The major molecules involved in translation are:

-Messenger RNA (mRNA)
-Transfer RNA (tRNA)
-Ribosomes
-Enzymes, energy sources, other factors
5’-ATGCCTAGGTACCTATGA-3’
======================== DNA
3’-TACGGATCCATGGATACT-5’
Transcription
5’-AUGCCUAGGUACCUAUGA-3’ mRNA
decoded as
(start) (stop)
5’-AUG CCU AGG UAC CUA UGA-3’ (codons)
Translation
N-MET-PRO-ARG-TYR-LEU-C Protein
Messenger RNA
• Carries information copied from

DNA in nucleus to ribosomes in
cytoplasm
• Will become associated with
ribosomes
• Will direct protein synthesis,
putting amino acids in the proper
order on the growing chain
Transfer RNA
• Carrier molecule which transfers amino acids to the protein chain
• tRNA is made in the nucleus from a DNA template
• Each tRNA is specific to carry one of the 20 amino acids used to
make proteins
• tRNA’s sit attached to their specific amino acids in a pool in the
cytoplasm
• tRNA are about 80 nucleotides long, are folded uniquely, due to
hydrogen bonding
• Are recyclable, can be used again and again……
Generalized tRNA
clover leaf shape
Ribosomes
• Very small particles (25nm) that are key
components in protein synthesis
• Made up of 2 subunits, a large and a small.
• Are found as subunits in the cytoplasm and
attached to ER. They assemble on the
mRNA when translation begins
What Ribosomes Look Like
What Ribosomes Look Like
Getting Started: The Genetic Code
– The bases of DNA code for the placement of amino acids
on a growing chain
– 20 different amino acids must be coded for:
• How long is the code?
– a.) If code is 1 base long – only code for 4 amino acids
– b.) If code is 2 bases long – only 16 amino acids can be coded for
– c.) *If code is 3 bases long – 64 amino acids can be coded for*
– This means the code is a triplet. The 3 mRNA bases are
known as the codon, the 3 tRNA bases that match up are
the anti-codon
A 1
U 2
G 3
C 4
A U G C
A 1 2 3 4
U 5 6 7 8
G 9 10 11 12
C 13 14 15 16
Getting Started: The Genetic Code
– Facts about the code:

• It is continuous (no comma’s)
• It is non-overlapping
• It is almost universal
• It shows degeneracy – with 2 exceptions, most
amino acids have more than one codon
– this degeneracy is a built in guard against point mutations
– The code has start and stop signals
degenerate code: a code in which several code words have the
same meaning
The Genetic Code
Note: AUG is the start codon

How Translation Works
– tRNA becomes “charged” by picking up an amino acid.

– This is done by the enzyme “amino-acyl tRNA synthetase”
- One synthetase for each amino acid
- A single synthetase may recognize multiple tRNAs for the
same amino acid
– 5’ end of mRNA comes together with 2 ribosome subunits:
Steps in Translation
• Once the tRNA is charged, translation can begin
• It will occur in 3 steps:
1. initiation
2. elongation
3. termination
1. Initation
• needs energy (GTP) + proteins called initiation factors
• “AUG” is always first codon added. tRNA binds to “p-site” (has
anticodon “UAC”)
GTP: guanosine triphosphate
Three tRNA binding sites:

A site = amino-acyl tRNA
binding site
P site = peptidyl-tRNA
binding site
E site = exit site

UCC-UCC
In addition to the APE sites:
there is an mRNA binding groove that holds onto the message
being translated
2. Elongation
• Amino acid binds to A-site

• 2 amino acids undergo peptide-
bond synthesis; catalyzed by
the enzyme peptidyl transferase
• Dipeptide is attached to A-site,
empty t-RNA shifts to e-site,
called translocation; requires
the enzyme translocase.
3. Termination
is triggered by stop codons:
UAA
UAG
UGA
When a stop codon is reached, the

following happens:
1. protein chain is released
2. mRNA + ribosomes separate
(ribosome splits into subunits)
requires “release factors” + GTP
Release of the protein causes
the disassociation of the
ribosome into its constituent
subunits.
Next step is PTMs
Post translation modifications:
• Proteins maturation
• Proteins becomes functionale
Post Translational Modifications
“Protein” hasil translasi masih dalam bentuk tidak

aktif/fungsional.
Protein harus diproses setidaknya satu dari empat
tipe pemrosesan, yaitu:
1.Chemical modification (modifikasi kimia)

2.Protein folding (pelipatan protein)
3.Proteolytic cleavage (pemotongan proteolitik)
4.Intein splicing (pembuangan intein)
(Murray, Robert K.,dkk. 2006. BIOKIMIA HARPER EDISI 27 . Jakarta : EGC)
1. Chemical modification (modifikasi kimia)
Polipeptida dimodifikasi melalui penambahan gugus kimia baru, seperti:
a. Fosforilasi
Penambahan gugus fosfat.
b. Modifikasi Lipofilik
Penambahan komponen lipid.
c. Metilasi
Penambahan gugus metil pada residu asam amino, misal pada aspartat dan
lisin.
d. Penambahan gugus prosteotik (bagian enzim, nonprotein).
e. Pembentukan ikatan sulfida, misalnya pada insulin.
e. Glikosilasi
Penambahan komponen gula.
Tipe umum glikosilasi:
a) O-glikosilasi: penempelan gula pada gugus hidroksil serin atau
threonin.
b) C-glikosilasi: penempelan gula pada gugus amino asparagin.
2. Protein folding (pelipatan protein)
Urutan asam amino pada protein menentukan proses pelipatannya.

Banyak protein yang membutuhkan bantuan untuk:
a. Mencegah salah pelipatan (misfolding) sebelum sintesis selesai
b. Terlipat secara tepat
Begitu diperoleh kondisi yang sesuai, kebanyakan polipeptida akan segera
melipat menjadi struktur tersier yang tepat, karena konformasi/bentuk ini
memiliki energi yang paling rendah.
Namun protein folding sering dimediasi oleh protein lain dan dapat
diinduksi oleh stres pada sel.
Molekul protein yang membantu proses folding adalah chaperon:
(1) mengikat dan (2) menstabilkan protein yang belum terlipat; sehingga
tidak beragregat dengan protein lain dan (3) akan menghasilkan konformasi
pelipatan yang tepat.
3. Proteolytic cleavage (PC) (=pemotongan proteolitik)
Pemotongan protein oleh protease, membuang segmen-segmen dari satu
atau kedua ujung polipeptida.
Hasil pemotongan berupa:

1. fragmen protein aktif yang lebih pendek, atau
2. Fragmen-fragmen protein yang seluruhnya aktif atau hanya beberapa
fragmen protein saja yang aktif.
Fungsi PC pada pemrosesan paska translasi:
a. membuang potongan pendek dari ujung daerah N dan atau C dari
polipeptida, meninggalkan suatu molekul tunggal yang pendek yang
melipat menjadi protein yang aktif.
b. memotong poliprotein menjadi bagian‐ bagian dengan semua atau
beberapa diantaranya adalah protein yang aktif.
Contoh PC: menghilangkan residu terminal metionin dan peptida signal,

konversi prekursor inaktif menjadi aktif.
4. Intein splicing (pembuangan intein)
Intein merupakan bagian protein yang mengkatalisis pemisahannya
sendiri dari protein yang panjang.
Intein merupakan urutan penyela pada beberapa protein, mirip intron pada
mRNA.
Intein harus dibuang (splicing) dan potongan protein disambung (exteins)
menjadi protein aktif.
Tahapan sintesis protein selesai
Protein telah menjadi bentuk fungsional

Translation + PTMs

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Translation + PTMs

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Translation

•The information encoded in DNA is transferred to

•The major molecules involved in translation are:

• Carries information copied from

– Facts about the code:

Note: AUG is the start codon

– tRNA becomes “charged” by picking up an amino acid.

Three tRNA binding sites:

E site = exit site

• Amino acid binds to A-site

When a stop codon is reached, the

“Protein” hasil translasi masih dalam bentuk tidak

1.Chemical modification (modifikasi kimia)

Urutan asam amino pada protein menentukan proses pelipatannya.

Hasil pemotongan berupa:

Contoh PC: menghilangkan residu terminal metionin dan peptida signal,

Tahapan sintesis protein selesai

Protein telah menjadi bentuk fungsional

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