Peter John M.Phil, PhD Atta-ur-Rahman School of Applied Biosciences (ASAB) National University of Sciences & Technology (NUST)

Genetic Code Genetic code: The relationship between a sequence of DNA and the sequence of the corresponding protein. The genetic code is read in groups of three nucleotides, each group representing one amino acid. Codon: Each trinucleotide sequence is called a Codon.

Genetic Code The triplets are nonoverlapping and are read from a fixed starting point. Mutations that insert or delete individual bases cause a shift in the triplet sets after the site of mutation. Combinations of mutations that together insert or delete 3 bases (or multiples of three) insert or delete amino acids but do not change the reading of the triplets beyond the last site of mutation.

Genetic Code Three types of RNAs: mRNA: messenger RNA Contains 3 bases ( codon) rRNA: ribosomal RNA Comprises the 70 S ribosome tRNA: transfer RNA Transfers amino acids to ribosomes for protein synthesis Contains the anticodon (3 base sequence that is complimentary to codon on mRNA)

Genetic Codes The seq of coding strand DNA start in 5’---3’ direction It consist of NT triplet called codons, which represent one AA Four NT (A, T, G, C) makes 64 possible codons 61 codons are involve in protein synthesis, 3 are terminating codons

Condon & Amino Acids Sixty one of the sixty four possible triplets code for twenty amino acid Three codons don’t represent amino acids and cause termination Most amino acids are represented by more than one codon

Condon & Amino Acids Multiple codons for an amino acid are usually related Related amino acids often have related codons, minimizing the effect of mutation Identical set of codon assignments is used in bacteria and eukaryotic cytoplasm By this mRNA from one species can translated invitro/vivo by protein synthetic apparatus of other species

Genetic Codes

Codon & Anticodon The meaning of the codon is determined by tRNA that correspond to it The assignment of the AAs to the codon is not random, but shows a relationship b/w codon & anti codon

Related Codon represent related AAs There are more codons than AAs, as a result all AAs are represented by more than 1 codon Only 2 AAs Met & Trp have single set of codon & are called “ synonymous” Codon representing the same AA have same seq only with the diff at position at 3, this is called “ third base degeneracy”

Ribosome This codon/anticodon interaction is stabilized by the environment of the ribosomal “A’ site. Then ribosome control the environment & pairing occur b/w first 2 bases & additional reactions are permitted at third base.

Third base degeneracy The third base degeneracy reduce the effect of mutation b/c no change in AA occur The three codons, UAA, UAG, UGA are stop/terminating codons mark the end of gene

Codons in other species The same set of genetic code is used in bacteria and eukaryotic cytoplasm Thus codon use in one specie have the same meanings for the ribosome of the other specie Any change in the genetic code result in the disruption of the protein

Meanings of Codons in other species Sometimes change in the meanings of the codons are different in different species, e.g. In mycoplasma: UGA (stop)------ code for Trp In certain ciliates: UAA & UAG (stop)------ code for Glutamine

Wobble Base Pairing All codons differ at position 3 There are 8 codon families (32 codons) sharing the first 2 bases, but differ at position 3 There are 7 codon pairs in which either Purine may be present, changing the AA 3 codons with unique meanings AUG (Met) UGG (Trp) UGA (Stop)

Wobble Base Pairing C & U never have unique meanings at position 3, and “A” never signify a unique AA Codon/Anti codon are complementary 5’ ACG ‘3 (codon) 3’ UGC ‘5 (anticodon) Anti codon is written in 5---3 direction 5’ CGU ‘3

Wobble Base Pairing

Wobble Base Pairing tRNA can recognize more than one codon, so base in the first position of the anticodon must be able to accommodate base at 3rd position First 2 base follow the normal pairing rule but tRNA permit flexibility at position 3, where, G can pair with U A with U/G C with G/U

Wobble Base Pairing

tRNA structure All tRNAs have similar sequences of 73 to 93 nucleotides 3' end always terminates with the sequence CCA, with the 3' hydroxyl of the ribose of the terminal A being the point of covalent attachment of the amino acid

tRNA Processing A mature tRNA is generated by processing a precursor. The 5' end is generated by cleavage by the endonuclease RNAase P. The 3' end is generated by cleavage followed by trimming of the last few bases, followed by addition of the common terminal trinucleotide sequence CCA.

tRNA Processing tRNA synthesized as precursor molecule and the processes by endonucleolytic & exonucleolytic activities All tRNAs have CCA seq at 3 end 5 end is generated by the cleavage action of Ribonuclease P (RNAase P) 3 end is trimmed by endonuclease activity & CCA is added

tRNA Processing Different models to add CCA at 3 end A single enzyme add CCA Single enzyme have different active sites In some organism different enzymes are responsible for adding C & A tRNA which is not properly processed is degraded, so this have no effect on protein synthesis

tRNA Processing

Structure of tRNA

Condon/Anti Codon Pairing

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