Protein Synthesis: Translation

of the Genetic Message

1
Outline
• Translating the genetic message
• The genetic code
• Amino acid activation
• Prokaryotic translation
• Stages

© 2018 Cengage Learning. All Rights Reserved.

Translating the Genetic Message
• Protein biosynthesis is a complex process requiring:
• Ribosomes
• Messenger RNA (mRNA) + transfer RNA (tRNA)
• Bound to the ribosome in the course of protein synthesis
• Responsible for the correct order of amino acids in the
growing protein chain
• Protein factors

© 2018 Cengage Learning. All Rights Reserved.

Steps Involved in Protein Biosynthesis
• Amino acid is activated
• Activated: Process by which an amino acid is
covalently bonded to tRNA, forming an aminoacyl-
tRNA
• Involves tRNA + aminoacyl-tRNA synthetases

© 2018 Cengage Learning. All Rights Reserved.

Figure 12.1 - Steps in Protein Biosynthesis

Polypeptide chains are formed:

• Chain initiation: Binding of the 1st

aminoacyl-tRNA to the start site of
the ribosome
• Chain elongation: Formation of
peptide bonds between successive
amino acid residues
• Chain termination: Release of a
newly formed protein from the
ribosome

© 2018 Cengage Learning. All Rights Reserved.

Nature of the Genetic Code
• Triplet code
• Sequence of 3 bases (codon) is needed to specify
one amino acid
• Genetic code must translate the language of the DNA,
which contains 4 bases, into the language of the 20
common amino acids found in proteins
• No codon can encode more than one amino acid

© 2018 Cengage Learning. All Rights Reserved.

Overlapping vs. Nonoverlapping code

• Nonoverlapping
• No bases are shared between consecutive codons
• Ribosome moves along the mRNA three bases at a time rather than
one or two at a time

© 2018 Cengage Learning. All Rights Reserved.

Figure 12.2 - Theoretically Possible Genetic
Codes

© 2018 Cengage Learning. All Rights Reserved.

Nature of the Genetic Code (continued 1)
• Commaless
• No intervening bases between codons exist
• 64 possible triplets of the 4 bases occur in RNA
• All 64 codons have assigned meanings
• 61 codons → amino acids
• 3 termination signals

© 2018 Cengage Learning. All Rights Reserved.

Table 12.1 - The Genetic Code

© 2018 Cengage Learning. All Rights Reserved.

Nature of the Genetic Code
• Degenerate code
• More than one triplet
can encode the same
amino acid
• Degeneracy of the
code acts as a buffer
against deleterious
mutations

© 2018 Cengage Learning. All Rights Reserved.

Nature of the Genetic Code
• Universality of the code
• Code is the same in all organisms
• Can be observed in viruses, prokaryotes, eukaryotes
• e.g. of an exception - Some codons seen in
mitochondria are different from those seen in the
nucleus

© 2018 Cengage Learning. All Rights Reserved.

Determination of the Code
• Experiment
• Messenger used - Synthetic polyribonucleotides
• When homopolynucleotides are used as a synthetic
mRNA, homopolypeptides are produced
• e.g. When poly U is the messenger, the product is
polyphenylalanine
• When an alternating copolymer is the messenger, the
product is an alternating polypeptide
• Only 1 reading frame is possible in a triplet code
• Reading frames: Starting points for reading genetic
messages

© 2018 Cengage Learning. All Rights Reserved.

Codon–Anticodon Pairing
• Codon can form base
pairs with a
complementary anticodon
of a tRNA when an amino
acid is incorporated
during protein synthesis
• Anticodon: Sequence of
3 bases in tRNA that H-
bonds with the mRNA
triplet that specifies a
given amino acid

© 2018 Cengage Learning. All Rights Reserved.

Codon–Anticodon Pairing + Wobble
• Some tRNAs bond to one codon exclusively, but
many tRNAs can recognize more than one codon
because of variations in allowed patterns of hydrogen
bonding
• Variation is called wobble, + it applies to the first base
of an anticodon

© 2018 Cengage Learning. All Rights Reserved.

Wobble Base Pairing
• Wobble base of the anticodon
hydrogen-bonds to the 3rd
base of the codon
• Base in the wobble position of
the anticodon can base-pair
with several bases in the
codon

© 2018 Cengage Learning. All Rights Reserved.

Figure 12.5 - Various Base-Pairing Alternatives

© 2018 Cengage Learning. All Rights Reserved.

Wobble Base Pairing Hypothesis
• Provides insight into some aspects of the degeneracy
of the code
• In many cases, the degenerate codons for a given
amino acid differ only in the 3rd base
• Fewer different tRNAs are needed because a given
tRNA can base-pair with several codons
• Existence of wobble minimizes the damage that can
be caused by misreading the code
• If a Leu codon, CUU, were misread as:
• CUA or
• CUG during transcription of mRNA…?

© 2018 Cengage Learning. All Rights Reserved.

© 2018 Cengage Learning. All Rights Reserved.
Amino Acid Activation + the Formation of
Aminoacyl-tRNA
• Both are catalyzed by aminoacyl-tRNA synthetase
• Take place in 2 separate steps
• Step 1
• Amino acid forms a covalent bond to an adenine
nucleotide, producing an aminoacyl-AMP
• Free energy of hydrolysis of ATP provides energy for bond
formation

© 2018 Cengage Learning. All Rights Reserved.

Amino Acid Activation + the Formation of
Aminoacyl-tRNA
• Both are catalyzed by aminoacyl-tRNA synthetase
• Take place in 2 separate steps
• Step 1
• Step 2
• Ester linkage is formed between the amino acid + either
the 3′-hydroxyl or the 2′-hydroxyl of the ribose at the 3′
end of the tRNA

© 2018 Cengage Learning. All Rights Reserved.

Aminoacyl-tRNA Synthetases
• Two classes appear to be unrelated + indicate a
convergent evolution
• Class I loads the amino acid onto the 2′ OH
• Class II loads the amino acid onto the 3′ OH
• Specificity of the enzyme contributes to the accuracy of the
translation process

• Primary function is to assure

that the right amino acid
pairs up with the right tRNA

© 2018 Cengage Learning. All Rights Reserved. © 2002, Bruce Alberts et al.
Second Genetic Code
• Extra level of proofreading by aminoacyl-tRNA
synthetases
• Two-stage amino acid activation reaction allows
selectivity at 2 levels
• Amino acid
• Aminoacyl-AMP remains bound to the enzyme
• Binding of the correct amino acid is verified by an editing
site in the tRNA synthetase
• tRNA
• Specific binding sites exist on tRNAs + are recognized
by aminoacyl-tRNA synthetases

© 2018 Cengage Learning. All Rights Reserved.

Figure 12.8 - Ribbon Diagram of the tRNA Tertiary
Structure
Secondary structure of tRNA Early model of aminoacyl tRNA function
3
Amino acid
3 Binding site for
amino acid
5 5

Binding site for

Serine anticodon mRNA codon
5 3
mRNA
Serine codon

Revised model incorporating tertiary structure of tRNA

5
3

3
Anticodon

Codon
5 mRNA

© 2018 Cengage Learning. All Rights Reserved.

Stages in Prokaryotic Translation

Chain Chain Chain

initiation elongation termination

© 2018 Cengage Learning. All Rights Reserved.

Bacterial Ribosome Yeast Ribosome

© 2018 Cengage Learning. All Rights Reserved.