Translation

Translation involves
“decoding” a mRNA (genetic
TRANSCRIPTION DNA
mRNA
Ribosome
TRANSLATION

code) and using its Polypeptide

information to build a Amino

Polypeptide acids
polypeptide, or chain of amino
tRNA with
acids. amino acid
Ribosomeattached

Gly

tRNA

A AA
Anticodon
U GG U U U G G C

5 Codons 3
mRNA
 The genetic code
• Genetic information is encoded as a sequence of
nonoverlapping three tnucleotides known as codons

• The gene determines the sequence of bases along the

length of an mRNA molecule

DNA Gene 2
molecule
Gene 1
Gene 3

DNA strand 3 5
(template) A C C A A A C C G A G T

TRANSCRIPTION

U G G U U U G G C U C A
mRNA 5 3
Codon
TRANSLATION

Protein Trp Phe Gly Ser

Amino acid
 The genetic code

Codon: Instructions for making a protein AUG codon: Activates the

ribosome (start codon)
• Each mRNA codon matches with 1 of
20 amino acids
UAA or UAG or UGA codon:
deactivates the ribosome
• Ribosome reads codons 1 at a time
(stop codon)
 The Genetic Code
 Codons: 3 base code for the production of a specific amino acid,
sequence of three of the four different nucleotides

 Since there are 4 bases and 3 positions in each codon, there are
4 x 4 x 4 = 64 possible codons

 64 codons but only 20 amino acids, therefore most have more

than 1 codon

 3 of the 64 codons are used as STOP signals; they are found at

the end of every gene and mark the end of the protein

 One codon is used as a START signal: it is at the start of every

protein

 In translation, the codons of an mRNA are read in order

(from the 5' end to the 3' end) by molecules called transfer
RNAs, or tRNAs.
 Transfer RNA
 Consists of a single RNA strand that is only about 80 nucleotides
long
 Each carries a specific amino acid on one end and has an
anticodon on the other end
 A special group of enzymes pairs up the proper tRNA molecules
with their corresponding amino acids.
 tRNA brings the amino acids to the ribosomes,
3
A
Amino acid C
attachment site C
A 5
The “anticodon” is the set of 3 RNA bases C G
G C
that binds to a matching 3 bases of the C G
U G
mRNA codon on the molecule. U A
A U
U C A U
* C A C AG UA A G *
G * C U C
G U G U * G
*
C C G A G
(a) Two-dimensional structure. The four base- * * U C * A G G
* G AG C
paired regions and three loops are characteristic G C Hydrogen
U A bonds
of all tRNAs, as is the base sequence of the * G
A
amino acid attachment site at the 3 end. The A* C
* U
A
anticodon triplet is unique to each tRNA type. A G

}
Anticodon
 Building a Molecule of tRNA
 A specific enzyme called an aminoacyl-tRNA synthetase
joins each amino acid to the correct tRNA

Amino acid Aminoacyl-tRNA

synthetase (enzyme)

P P P Adenosine
1 Active site binds the
amino acid and ATP.
ATP

2 ATP loses two P groups

and joins amino acid as AMP.
P Adenosine

Pyrophosphate P Pi

Pi
Pi
Phosphates
tRNA
3 Appropriate
tRNA covalently
Bonds to amino
Acid, displacing P Adenosine
AMP. AMP
4 Activated amino acid
is released by the enzyme.

Aminoacyl tRNA
(an “activated
amino acid”)
 Ribosomes
 Ribosomes facilitate the specific coupling of tRNA anticodons
with mRNA codons during protein synthesis

 The 2 ribosomal subunits are constructed of proteins and RNA

molecules named ribosomal RNA or rRNA

TRANSCRIPTION DNA

RIBOSOMES INFRASTRUCTURE mRNA

Ribosome

FOR THE m-RNA,t- RNA & A.A TRANSLATION

Polypeptide
Exit tunnel
Growing
TO INTERACT WITH EACH polypeptide
OTHER FOR TRANSLATION. tRNA
molecules
Large
subunit
E
80S IN EUKARYOTES P A

& 60S IN PROKARYOTES. Small

subunit

5
LARGER 60S (50S) SUBUNIT 3
mRNA
(a) Computer model of functioning ribosome. This is a model of a
bacterial ribosome, showing its overall shape. The eukaryotic ribosome is
SMALLER 40S (30S) SUBUNIT roughly similar. A ribosomal subunit is an aggregate of ribosomal RNA
molecules and proteins.
 Ribosome binding site (RBS)
Shine-Dalgarno sequence

• In Prokaryotes binds to ribosome to the mRNA to initiate protein

synthesis by aligning the ribosome with the start codon.

• Consensus seq is AGG AGG

 Ribosome binding site (RBS)
In Eukaryotes

• 5' cap of mRNA

• Translation initiation happens following recruitment of the

ribosome, at the start codon (underlined) found within the
Kozak consensus sequence ACCAUGG.
 Ribosome
 The ribosome has three binding sites for tRNA

 The P site
 The A site
 The E site
P site (Peptidyl-tRNA
binding site)
A site (Aminoacyl-
tRNA binding site)
E site
(Exit site)
Large
subunit
E P A

mRNA
binding site Small
subunit
Schematic model showing binding sites. A ribosome has
(b) an mRNA binding site and three tRNA binding sites, known
as the A, P, and E sites. This schematic ribosome will appear
in later diagrams.
 Building a Polypeptide
Amino end Growing polypeptide

Next amino acid

to be added to
polypeptide chain

tRNA

mRNA 3

Codons
5

(c) Schematic model with mRNA and tRNA. A tRNA fits into a binding site when its anticodon base-
pairs with an mRNA codon. The P site holds the tRNA attached to the growing polypeptide. The A
site holds the tRNA carrying the next amino acid to be added to the polypeptide chain. Discharged
tRNA leaves via the E site.
Translation Details
 Translation begins when the mRNA codon “AUG” is
read by a ribosome
 Ribosome reads one codon at a time

AUG = methionine
GCU = alanine
 tRNA carries over the proper amino acid

 tRNA anticodon matches with the mRNA codon

 Prevents delivery of wrong amino acid

 One by one, amino acids are linked together

 Translation ends when a “stop” codon is reached

 What just happened?: A ribosome made a protein

Translation Overview

Process of making a proteins:

 mRNA enters ribosome
 Ribosome reads one mRNA codon at a time
 tRNA delivers amino acids until a protein is created
Translation into three stages

1. 2. 3.
Initiation Elongation Termination
Translation: Initiation

 mRNA binds to a ribosome,

and the transfer RNA
corresponding to the START
codon binds to this complex.
Ribosomes are composed of
2 subunits (large and small),
which come together when
the messenger RNA attaches
during the initiation process.
 Elongation of the Polypeptide Chain
 In the elongation stage, amino acids are added one
by one to the preceding amino acid
1 Codon recognition. The anticodon
TRANSCRIPTION DNA
Amino end of an incoming aminoacyl tRNA
mRNA
of polypeptide base-pairs with the complementary
Ribosome
TRANSLATION mRNA codon in the A site. Hydrolysis
Polypeptide
of GTP increases the accuracy and
E efficiency of this step.
mRNA 3
Ribosome ready for P A
next aminoacyl tRNA 5 site site
2 GTP
2 GDP

E E

P A P A

2 Peptide bond formation. An

GDP
3 Translocation. The ribosome rRNA molecule of the large
GTP
subunit catalyzes the formation
translocates the tRNA in the A
of a peptide bond between the
site to the P site. The empty tRNA
new amino acid in the A site and
in the P site is moved to the E site, E
the carboxyl end of the growing
where it is released. The mRNA
polypeptide in the P site. This step
moves along with its bound tRNAs,
P A attaches the polypeptide to the
bringing the next codon to be
tRNA in the A site.
translated into the A site.
 Termination of Translation
 The final step in translation is termination. When the ribosome reaches
a STOP codon, there is no corresponding transfer RNA.
 Instead, a small protein called a “release factor” attaches to the stop
codon.
 The release factor causes the whole complex to fall apart: messenger
RNA, the two ribosome subunits, the new polypeptide.
 The messenger RNA can be translated many times, to produce many
protein copies.
Release
factor
Free
polypeptide

5
3 3
3
5 5
Stop codon
(UAG, UAA, or UGA)
1 When a ribosome reaches a stop 2 The release factor hydrolyzes 3 The two ribosomal subunits
codon on mRNA, the A site of the the bond between the tRNA in and the other components of
ribosome accepts a protein called the P site and the last amino the assembly dissociate.
a release factor instead of tRNA. acid of the polypeptide chain.
The polypeptide is thus freed
from the ribosome.
 Protein Structure
Proteins
 Make up about 15% of the cell
 Have many functions in the cell
 Enzymes
 Structural

 Transport

 Motor

 Storage

 Signaling

 Receptors

 Gene regulation

 Special functions
 Overview
 Primary Structure
 Secondary Structure
 Tertiary Structure
 Quaternary Structure
 Primary Structure
 Polypeptide chains 
Amino Acids
 Largest polypeptide chain
approx has 5000AA but
most have less than
2000AA
 Amino Acid Basic
Structure H2N-CH-COOH
 Arrangement of the 20
amino acids in the
polypeptide is the amino
acid sequence which National Genome Research Institute
composes the primary genome.gov

structure of the protein

Secondary Structure
 Alpha Structure
Features
• 3.6 residues per turn

• 5.4 angstroms in length per turn

• carboxyl group of residue i hydrogen

bonds to amino group of residue i+4
 Beta-Sheets
• Beta-sheets formed from
multiple side-by-side beta-
strands.

• Orientation and hydrogen

bonding pattern of strands
gives rise to flat or twisted
sheets

• Can be in parallel or anti-

parallel configuration

• Anti-parallel beta-sheets
more stable
Bonds holding the tertiary structure of
Proteins
 Tertiary structure

• Defines the three

dimensional conformation
of an entire peptide chain
in space

• Determined by the primary

structure

• Modular in nature
 Motifs and Domains

 Motif – a small structural domain that can be

recognized in a variety of proteins

 Domain – Portion of a protein that has a

tertiary structure of its own. In larger proteins
each domain is connected to other domains by
short flexible regions of polypeptide.
 Quaternary Structure
 Not all proteins have a
quaternary structure
 A composite of

multiple poly-peptide
chains is called an
oligomer or
multimeric
 Hemoglobin is an

example of a tetramer
 Globular vs. Fibrous
The Four Levels of Protein Structure