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translation protein synthesis

*Process by which nucleotide sequence of mRNA is used as a template to join the amino acids in a polypeptide chain
*There are 3 types of mRNA involved:
*mRNA: carries genetic information in sets of 3 nucleotide sequences (codons)
*tRNA: deciphers codons in mRNA, each amino acid has its own subset of tRNAs; pair with the codons via their anticodons
*rRNA: forms ribosome in association with proteins; 28S rRNA is a ribozyme that catalyzes the reaction in which the peptide bond is formed
*Ribosomes move along the mRNA and catalyze the assembly of amino acids

the genetic code

*Genetic code: 64 codons for the 20 standard amino acids that are specified by triplets of bases
*Degeneracy: some amino acids are specified by more than one code
*Three codons do not code an amino acid, they are "stop" codons, they tell ribosomes when to stop translation
*AUG codon: codon for Met serves as most common start codon
*There are some exceptions from the universal genetic code (mitochondria, protoozoans)

deviations in genetic code

Most changes involve reading of normal stop codons as amino acids, not an exchange of one amino acid for another. They are probably later evolutionary event

reading frames

There is no division between the codons therefore one mRNA could be translated in 3 reading frames
Most mRNAs can be read in only one reading frame
The reading frame is selected based on the frame in which AUG start codon appear
Triplet codons are read in a non-overlapping, coma-less manner
Very rarely one mRNA will be read in more than one frame

mRNA decoding

Step 1
*Amino acids are attached in ester link to the 3' end of tRNA forming amino acyl-tRNA
*This reaction is driven by ATP and the enzyme catalyzing this reaction is aminoacyl-tRNA synthetase
Step 2
*The amino acid is added to the growing protein chain based on codon:anticodon interactions between mRNA and tRNA

tRNA structure

*70-80 nucleotides long
*Stem loop structure resembles clover leaf
*4 double helical stems
*3 loops 7-8 residues each; one of the loops contains anticodon
*Upper stem also known as acceptor stem ends with CCA 3' in all tRNAs
*Amino acid is attached to the free A residue

3 dimensional model of tRNA reveals L-shaped structure

Codon:anticodon base pairing

*H-bonding between 1st and 2nd position of the codon and the 3rd and 2nd position of the anticodon occur via Watson-Crick base pairing
*Base pairing between the 3rd position of the codon and the 1st position of the anticodon is less constrained (wobble position)
*For example, G, U, and I (inosine) in the wobble position of the anticodon can base pair with C/U, A/G, and C/A/U in the codon, respectively.
*Wobble base pairing reduces the number of tRNA genes that an organism must make to carry out translation.
*It helps protect against mutations that might inactivate tRNA genes

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