Chapter 12

Translation
The biochemistry department of SYMC

Translation
The synthesis of protein molecules
using mRNA as the template, in other
word, to translate the nucleotide
sequence of mRNA into the amino acid
sequence of protein according to the
genetic codon.

Section 1
Protein Synthetic System

Protein synthesis requires multiple elements

to participate and coordinate.

mRNA, rRNA, tRNA

substrates: 20 amino acids
Enzymes and protein factors:
initiation factor (IF), elongation
factor (EF), releasing factor (RF)
ATP, GTP, Mg2+

Three kinds of RNAs different functions

during translation
template: mRNA
direction of translation 5-3
peptide chain synthesis from N to C

carrier(adaptor): tRNAs

Genetic codon
Three adjacent nucleotides in the 53 direction on mRNA constitute a
genetic codon, or triplet codon.
One genetic codon codes for one
amino acid.

Genetic codon

Universal
The genetic codons for amino acids
are always the same with a few
exceptions of mitochondrial mRNA.
Cytoplasm
AUA: Ile
AUG: Met, initiation
UAA, UAG, UGA:
termination

Mitochondria
AUA: Met, initiation
UGA: Trp
AGA, AGG:
termination

Activated amino acid

Ala-tRNAAla
Ser-tRNASer
Met-tRNAMet

1.2 Ribosomes
Ribosome is the place where protein
synthesis takes place.
A ribosome is composed of a large
subunit and a small subunit, each of
which is made of ribosomal RNAs
and ribosomal proteins.

Molecular components of ribosome

of prokaryotes

Three sites on ribosomes

location

function

Aminoacyl site
(A site)

Composed by
large and small
subunit

Accepting an
aminoacyl-tRNA

Peptidyl site
(P site)

Composed by
large and small
subunit

Forming the
peptidyl bonds

Exit site
(E site)

Only on large
subunit

Releasing the
deacylated tRNA

Section 2
Protein Synthetic Process

General concepts
The direction of the protein
synthesized : N-terminalC-terminal
The direction of template mRNA: 5
3end
The process of Protein :
initiation
elongation
termination

2.1 Initiation
Prokaryotic initiation
Four steps:
Separation between 50S and 30S
subunit
Positioning mRNA on the 30S subunit
Registering fMet-tRNAimet on the P site
Associating the 50S subunit

Three initiation factors: IF-1, IF-2 and

IF-3.

Initiation 1-1

IF-3

IF-1

Initiation 1-2
The IF-1 and IF-3
bind to the 30S
subunit, making
separation
between 50S and
30S subunit.
The mRNA then
binds to 30S
subunit.

Alignment of 16S rRNA

The 3end of 16s rRNA has consensus

sequence UCCUCCA which is complementary
to AGGAGGU in S-D sequence (also called
ribosomal binding site).

Shine-Dalgarno (S-D) sequence

-AGGAGGU .AUG purine rich of 4-9 nts long

8-13 nts prior to AUG

Initiation 3

The complex of
the GTP-bound
IF-2 and the
fMet-tRNA
enters the P
site.

Initiation 4
The 50S subunit
combines with this
complex.
GTP is hydrolyzed
to GDP and Pi.
All three IFs depart
from this complex.

Pi
GTP
IF-2 -GTP
GDP

5'

3'

AUG

IF-3

IF-1

One GTP is consumed in initiation

course

2.2 Elongation
Three steps in each ribosome cycle:
Positioning an aminoacyl-tRNA in the A
site--- Entrance
Forming a peptide bond---Peptide bond
formation
Translocating the ribosome to the next
codon---Translocation

Elongation factors (EF) are required.

Step 1: Entrance
An AA-tRNA occupies the empty A site.
Registration of the AA-tRNA consume
one GTP.
The entrance of AA-tRNA needs to
activate EF-T.

GTP
Tu Ts

Ts
Tu GDP
5'

AUG

3'

Step 2: Peptide bond formation

The peptide bond formation occurs at
the A site.
The formylmethionyl group is
transferred to NH2 of the AA-tRNA
at the A site by a peptidyl transferase.

Peptide bond formation 1

Peptide bond formation 2

Step 3: Translocation
EF-G is a translocase.
GTP bound EF-G provides the energy
to move the ribosome one codon
toward the 3 end on mRNA.
After the translocation, the
uncharged tRNA is released from the
E site.

Translocation

fMet
fMet

Tu GTP
5'

AUG

3'

2.3 Termination
Prokaryotes have 3 release factors:
RF-1, RF-2 and RF-3.
RF-1 and RF-2: Recognizing the
termination codons
RF-3: GTP hydrolysis and coordinating
RF-1/RF-2 and rpS

Eukaryotes have only 1 releasing

factor: eRF.

Termination 1

The peptidyl
transferase is
converted to an
esterase.

Termination 2

The uncharged
tRNA, mRNA, and
RFs dissociate
from the
ribosome.

COORF
5'

UAG

3'

Polysome

Proteins are synthesized on a single

strand mRNA simultaneously, allowing
highly efficient use of mRNA.

Section 3
Interference of Translation

Antibiotics
streptomycin and
karamycin

Tetracycline

5'

3'

P site A site

Puromycin

chloromycetin

cycloheximide

Antibiotics
name

target

function

tetracycline

30S

block the A site to prevent

binding of AA-tRNA with 30S

streptomycin

30S

repress the translocase

chloromycetin

50S

block the peptidyl

transferase, and inhibit the
elongation

cycloheximide

60S

repress the translocase,

inhibit the elongation

puromycin
Erythromycin

ribosome of P
and E
50S

release the prematured

peptide
Inhibit the translocase

Puromycin
It has a similar
structure to TyrtRNA.
It works for both
prokaryotes and
eukaryotes.