L15: Ribosome and the mechanisms of translation

roles of ribosome during translation

• codon-anticodon recognition

• transpeptidation

• reads mRNA 5’-3’ while synthesizing polypeptide from N-C terminus

transpeptidation

formation of peptide bond between the growing polypeptide chain and the new aa that is to be added

ribosome structure

made of large and small subunits

large subunit

• forms A,P,E site to hold tRNAs

• enzymatic catalyst for transpeptidation

small subunit

• forms the A,P,E site to hold tRNAs

• forms the channel to hold mRNA

• performs codon-anticodon recognition to judge if they correctly match

A-site

• amino-acyl tRNA site

• entrance of amino-acyl tRNA during elongation

• location of codon-anticodon recognition

P-site

• peptidyl-tRNA site

• location of transpeptidation

E-site

• exit site

• exit site for uncharged tRNA after transpeptidation

• loosely holds the tRNA

• tRNA falls off ribosome once it enters the E site

what is the bacterial large subunit called

• 50S subunit

• 23S rRNA + 5S rRNA + lots of proteins

what is the bacterial small subunit called

• 30S subunit

• 16S rRNA + lots of proteins

what is a fully assembled bacterial ribosome called

• 70S ribosome

• 50S subunit + 30S subunit = 70S subunit

sedimentation rates

• back then sedimentation rate was a common way to analyze diff organelles and macromolecules 

• some molecules were named after their sedimentation rates

what does sedimentation rate measure

how fast a particle settles in solution

svedberg unit

• S, where 1S = 10^-13 seconds

• reps sedimentation rates of biological molecules

what are sedimentation rates affected by

• mass

• size

• shape 

• SA

• this is why 50S and 30S do not perfectly add up

how many rRNAs are in each subunit

1-3

what are rRNAs named after

their individual sedimentation rates

conserved sequences in ribosome structure

• 16S rRNA and 18S rRNA

• gold standards for molecular phylogeny in bacteria and eukaryotes

proteins during initiation in bacteria

initiation factors (IF)

proteins during elongation in bacteria

elongation factors (EF)

proteins during termination in bacteria

release factors (RF)

goal of initiation in bacteria

assemble the 70S ribosome onto the start codon

what does a successful initiation look like

• 70S ribosome is bound to mRNA

• AUG is on the P site

• an initiator tRNA with the corresponding aa is placed in the P site, coupled with the start codon

• A site is ready to accept incoming aminoacyl-tRNA for the 2nd codon

initiator tRNA

fMet-tRNA^Ini

2 major steps to assemble ribosome

1. formation of 30S initiation complex (30SIC)

2. formation of 70S initiation complex (70SIC)

formation of 30S initation complex

• 30S ribosomal subunit is loaded onto the mRNA

• placed AUG inside the incomplete P site along with its anticodon

• P site is incomplete cuz the 50S subunit is missing

formation of 70S initiation complex

• 50S joins the 30S initiation complex

• 70S is now fully assembled with A,P,E sites ready for translation