Protein Synthesis (Translation)

Ilos:
1. Define genetic code
2 List its characters
3. Outline the steps of protein synthesis (translation)
The genetic code
The term genetic code refers to the set of 3-base code words (codons) in mRNA
that represent the 20 amino acids in proteins.
If 3 Bases encode 1 AA: consists of 64 triplet codons (A, G, C, U) 43 = 64
3 are stop signals and the 61 Remainder code for 20 amino acids
• all codons are used in protein synthesis
• 20 amino acids
• 3 termination (stop) codons: UAA, UAG, UGA
• AUG (methionine) is the start codon (also used internally)
• multiple codons for a single amino acid = degeneracy
• 3 additional amino acids (Arg, Leu, and Ser) are specified by six
different codons
Characters of genetic code
1. Triplet
2. Continuous
3. Non-overlapping
4. Start/stop signals
5. Universal (almost)
6. Degenerate
7. 3rd position “wobble”
• The Triplet Code: The genetic code is a set of three-base code words, or
codons. In mRNA, codons instruct the ribosome to incorporate specific
amino acids into a polypeptide
• Code is non-overlapping
– Each base is part of only one codon
• Devoid of gaps or commas
– Each base in the coding region of an mRNA is part of a codon
• The genetic code is nearly universal
– Shared by organisms from the simplest bacteria to the most complex animals
– Genetic code is NOT strictly universal
– Certain eukaryotic nuclei and mitochondria
– UGA Codons cause termination in standard genetic code can code for amino
acids Trp in mitochondria.
• Redundant (degenrate) – More than one codon for all amino acids except
Met and Trp
• Non-ambiguous or specific
– A given codon specifies one and only one amino acid
– UUU code for phenylalanine not any other A.A
– tRNA is an “adapter molecule between nucleotide “language” and amino
acid “language”
Wobble Hypothesis
Unusual Base Pairs between Codon and Anticodon
• Degeneracy of genetic code is accommodated by:
• Isoaccepting species of tRNA: bind same amino acid, but recognize different
codons
 • Wobble, the 3rd base of a codon is allowed to move slightly from its normal
position to form a non-Watson-Crick base pair with the anticodon
• Wobble allows same aminoacyl-tRNA to pair with more than one codon

Translation
• Three stages
– Initiation
– Elongation
– Termination
The direction of polypeptide chain is formed from the amino terminal to the
carboxyl terminal
The mRNA is translated from the 5 end to the 3 end
mRNA
The Shine – Dalgarno sequence (SDS)
mRNA binding to bacterial ribosomes:
E. coli lac z mRNA 5’...AGGAAACAGCUAUG...3’ end
16S rRNA 3’ end... UCCUCCA...5’
Complementary regions: 3’ end of 16S rRNA and 5’ untranslated leader of mRNA
(Note position of initial codon); AG rich
Stronger interactions promote more frequent translation

Structure of Ribosome:
Polysomes:

A polysome is an mRNA in the process of translation - it has a number of

ribosomes bound to it. Protein synthesis starts by the binding of the ribosomal
subunits at (in eukaryotes) or near (in prokaryotes) the 5' end of the mRNA. In
eukaryotes, the subunits initially bind the 5' cap. In prokaryotes the subunits
assemble at the AUG initiation codon. Translation then proceeds down the mRNA
in a 5' to 3' direction until the ribosomes reach the termination codon (here shown
as UGA). At this point, the completed protein is released from the ribosome and
the subunits dissociate. Protein synthesis starts at the amino (N) terminus and
proceeds to the carboxyl (C) terminus.
Ribosomes: Facilitate the specific coupling of tRNA anticodons with mRNA
codons during protein synthesis
Initiation
First initiating codon in human is AUG that code for methionine but Met f in
bacteria
Ribosome in human formed of 2 subunit 40 S and 60 S
 Ribosomal dissociation
This divided into 2 subunit by IF (initiation factor) 1, 3
 Formation of 43S preinitiation complex
This require IF2 which form complex with GTP and methionine tRNA,
 Formation of 48S initiation complex
IF4+mRNA+ 43S preinitiation complex+ATP
 Formation of 80S initiation complex
48S initiation complex + 60 S 80 S complete ribosome
GTP GDP+P+IF2,
The reaction is promoted by peptidyl transferase of the 23S rRNA of the large
ribosomal subunit of the prokaryotic large ribosomal subunit; therefore, it is
probably within the 28S rRNA in eukaryotes
The 23S rRNA may be considered a "ribozyme".
Aminoacyl-tRNA synthetase
a) binds amino acid + ATP to yield enzyme-bound adenylated amino acid
b) tRNA binds to the adenylated a.a.- synthetase complex and the amino acid is
transferred to the 2’ or 3’ OH of the 3’-terminal residue of the tRNA
Elongation Step
1. Codon Recognition: The anticodon of an incoming aminoacyl tRNA base-
pairs with the complementary mRNA codon in the A site. Hydrolysis of
GTP increases the accuracy and efficiency of this step.
2. Peptide bond formation: by peptidyl transferase
3. Translocation, next step, moves mRNA and peptidyl-tRNA one codon’s (3
steps) length through the ribosome
1. Places peptidyl-tRNA in the P site
2. Ejects the deacylated tRNA
3. Process requires elongation factor EF-G which hydrolyzes GTP after
translocation is complete
• energy for elongation is provided by the hydrolysis of two GTPs:
• one for translocation
• one for aminoacyl tRNA binding
Termination
• Finally ribosome encounters a stop codon
– Stop codon signals time for last step
• Three codons are the natural stop signals at the ends of coding regions in
mRNA
– UAG
– UAA
– UGA
• Mutations can create termination codons within an mRNA causing
premature termination of translation
– Amber mutation creates UAG
– Ochre mutation creates UAA
– Opal mutation creates UGA
Releasing Factors
• Prokaryotic translation termination is mediated by 3 factors:
– RF1 recognizes UAA and UAG
– RF2 recognizes UAA and UGA
– RF3 is a GTP-binding protein facilitating binding of RF1 and RF2 to
the ribosome
• Eukaryotes has 2 release factors:
– eRF1 recognizes all 3 termination codons
– eRF2 is a ribosome-dependent GTPase helping eRF1 releasing the
finished polypeptide
Post translation modification (processing) of protein:
1- Triming (conversion of inactive protein ((zymogen) to active one)
Ex. Trypsinogen Trypsin
2- Glycosylation (addition of carbohydrate): cell membrane
3- Hydroxylation (addition of OH)
Proline & lysine by Vit. C to hydroxyProline & hydroxylysine
4- Phosphrylation (addition of P)
Glycogen phosphrylase are active with phosphate
5- Acylation
Acyl group added to N terminal of protein during synthesis
6- Methylation: by SAM
7- Sulfation: by PAPS
8- Vitamin K dependant modification
Vit. K + CO2 Gama Carboxy Glutamate (activate prothrombin)