Translation

• The genetic code is, in fact, a nonoverlapping, commafree, degenerate, triplet code

• The code is read in a sequential manner starting from a fixed point in the gene. The insertion or deletion of a nucleotide shifts the frame (grouping) in which succeeding nucleotides are read as codons (insertions or deletions of nucleotides are therefore also known as frameshift mutations). Thus the code has no internal punctuation that indicates the reading frame; that is, the code is comma free.

• 3. The code is a triplet code.• 4. All or nearly all of the 64 triplet codons code

for an amino acid; that is, the code is degenerate.

• THE BIG RED FOX ATE THE EGG

• The deletion of the fourth letter, which shifts the reading frame, changes the sentence to

• THE IGR EDF OXA TET HEE GG

• THE IGR EDX FOX ATE THE EGG

• THE BXI GYR EDZ FOX ATE THE EGG

Nature of Genetic Code

• The code is highly degenerate.

• The arrangement of the code table is nonrandom.

• UAG,UAA and UGA are stop codons

• AUG and GUG are chain initiation codons

The “Standard” Genetic Code is not universal

Transfer RNA and its aminoacylation

Two Classes of Aminoacyl–tRNASynthetases

Class I

• Arg

• Cys

• Gln

• Glu

• Ile

• Leu

• Met

• Trp

• Tyr

• Val

Class II

• Ala

• Asn

• Asp

• Gly

• His

• Lys

• Pro

• Phe

• Ser

• Thr

(b) Acartoon comparing the positions of the 3. end of tRNA Ile in itscomplex with Ile RS in its synthetic mode (left) and in its editingmode (right).Note that there is a cleft running between the editing and synthetic sites and that the 3. end of the tRNA continues its A-form helical path in the editing mode butassumes a hairpin conformation in the synthetic mode

• The overall reaction catalyzed by Glu-AdToccurs in three stages:

(1) Glutamine is hydrolyzed to glutamate and the resulting NH3 sequestered;

(2) (2) ATP reacts with the Glu side chain of Glu–tRNAGln to yield an activated acylphosphateintermediate and ADP; and

(3) the acylphosphate intermediate reacts with the NH3 to yield Gln–tRNAGln + Pi

The N-formylmethionine residue (fMet) already has an amide bond and can therefore only be the N-terminal residue of a polypeptide. The tRNA that recognizes the initiation codon, tRNAf Met, differs from the tRNA that carries internal Met residues, tRNAmMet, although they both recognize recognize the same codon In E. coli, uncharged (deacylated) tRNAf Met is first aminoacylated with methionine by the same MetRS that charges tRNAm Met.The resulting Met–tRNAf Met is specifically N-formylated to yield fMet–tRNAf Met in an enzymatic reaction that employs N10-formyltetrahydrofolate as its formyl donor. The formylation enzyme does not recognize Met–tRNAm Met.

• The process begins with the binding of eIF3 (which in mammals consists of 13 different subunits) and eIF1A (a monomer and homolog of bacterial IF-1) to the 40S subunit in the inactive 80S ribosome (which had terminated elongation in its previous elongation cycle) so that it releases the 60S subunit.

• 2. The ternary complex of eIF2 (a heterotrimer), GTP, and Met-tRNAi met binds to the 40S ribosomal subunit accompanied by eIF1 (a monomer) to form the so-called 43S preinitiation complex. Here the subscript “i” on tRNAiMet distinguishes this eukaryotic initiator tRNA, whose appended Met residue is never N-formylated, from that of prokaryotes; both species are, nevertheless, readily interchangeable in vitro.

• Eukaryotic mRNAs lack the complementary sequences to bind to the 18S rRNA in the Shine–Dalgarno manner. Rather, they have an entirely different mechanism for recognizing the mRNA’s initiating AUG codon. Eukaryotic mRNAs, nearly all of which have an m7G cap and a poly(A) tail, are invariably monocistronic and almost always initiate translation at their leading AUG. This AUG, which occurs at the end of a 5’-untranslated region of 50 to 70 nt, is embedded in the consensus sequence GCCRCCAUGG, with changes in the purine(R) 3 nt before the AUG and the G immediately following it reducing translational efficiency by 10-fold each and with other changes having much smaller effects. In addition, secondary structure (stem–loops) in the mRNA upstream of the initiation site may affect initiation efficiency.

• The recognition of the initiation site begins by the binding of eIF4F to the m7G cap. eIF4F is a heterotrimeric complex of eIF4E, eIF4G, and eIF4A (all monomers), in which eIF4E (cap-binding protein) recognizes the mRNA’s m7G cap and eIF4G serves as a scaffold to join eIF4E with eIF4A.

• eIF4B (an RRM-containing homodimer) and eIF4H (a monomer) join the eIF4F–mRNA complex where they stimulate the RNA helicase activity of eIF4A to unwind the mRNA’s helical segments in an ATP-dependent process.

• The eIF4F–mRNA–eIF4B–eIF4H complex joins the 43S preinitiation complex through a protein–protein interaction between eIF4G and the 40S subunit-bound eIF3.

• eIF5 (a monomer) joins the growing assembly. The 43S preinitiation complex then translocatesalong the mRNA, an ATP-dependent process called scanning, until it encounters the mRNA’s AUG initiation codon, which is optimally in the sequence GCC(A/G)CCAUGG. This yields the 48S preinitiation complex. The recognition of the AUG occurs mainly through base pairing with the CUA anticodon on the bound Met-tRNAiMet , as was demonstrated by the observation that mutating this anticodon results in the recognition of the new cognate codon instead of AUG. This explains why the initiator tRNA must bind to the small subunit before the mRNA.

• The formation of the 48S preinitiation complex induces eIF2 to hydrolyze its bound GTP to GDP + Pi, which results in the release of all the initiation factors, thereby leaving the Met-tRNA iMet in the small subunit’s P site.The hydrolysis reaction is stimulated by eIF5, acting as a GAP.

• The 60S subunit then joins the mRNA-bound Met–tRNAiMet 40S subunit complex in a GTPasereaction mediated by eIF5B (a monomer and homolog of bacterial IF-2), thereby yielding the 80S ribosomal initiation complex. Thus eukaryotic translation initiation consumes two GTPs versus one for prokaryotic initiation

• What remains is to recycle the eIF2 GDP complex by exchanging its GDP for GTP. This reaction is mediated by eIF2B (a heteropentamer), which therefore functions as eIF2’s GEF (guanine nucleotide exchange factor.