Wave 11 — Ch 13

Polysome

Multiple ribosomes on 1 mRNA.

Bacterial ribosomes: masses of subunits and full ribosome

Small subunit: 30S, large subunit: 50S, full ribosome: 70 S (When the subunits come together, there is a change in shape to become more compact to form the 70 S as the entire ribosome. The larger the S value, the mass is larger, but it is not always linear because shape also has to do with the separation that this unit is based off of). The S unit is called the Svedberg and it is based off of sedimentation.

What drives ribosomes to come together in bacterial translation?

mRNA. Otherwise the subunits are apart from one another.

30 S subunit

Made of 21 proteins, S1-S21, and 16S rRNA molecule.

Shine Dalgarro sequence and 16S rRNA

the 16S rRNA has a 9 nuc. Sequence complementary to the Shine Dalgarro sequence (which is also referred to as RBS or ribosomal binding site). The RBS is in the 5’ of the UTR of the mRNA and without it the efficiency of translation drops dramatically. The role of this is for alignment so mRNA can bind to small subunit. The complementary to RBS sequence on the rRNA also has decoding function—> if the wrong charged tRNA molecule comes in during translation, the 16S rRNA will kick it out.

50S subunit

34 proteins, 23S rRNA, 5S rRNA.

23S rRNA is also called and has function…

Peptidyl transferase. This rRNA is a ribozyme involved in formation of peptide bond. Transfers peptides chain in P site to the A site in translstaion.

E P A sites stand for respectively…

Exit site, peptidyl transferase site, amino acyl site

E site

Leftmost site. Where uncharged/used tRNAs leave translation process here.

A site

Right most site. Location of the formation of the peptide bond via formation of acyl group. Where the second tRNA until the last tRNA in translation enters initially from.

P site

Middle site. Where the first tRNA initially enters in.

3 phases of translation

Initiation, elongation, termination

IF1 (initiation factor 1)

Initially in A site before kicked out when IF2 binds charged tRNA. Prevents 50S subunit from joining too early.

IF3

Initially in E site before getting kicked out due to IF2 binding charged tRNA. Prevents 50S subunit from joining too early.

IF2

Carries charged tRNA called initiator tRNA molecule, which is fmet.tRNA^fmet Also carries GTP to couple energy for docking.

EF-Tu

Carries and delivers charged tRNA molecules to A site and requires energy in form of GTP. Doesn’t release GDP after hydrolyzing GTP, but an exchange must be made to get another GTP from EF-Ts

Ribosome movement direction.

Left to right—>slides down 3 bases at a time and requires energy and help from translocase

EF-G (translocase)

Helps slide ribosome by 1 codon in 5’-3’ direction and uses GTP to couple for energy.

EF-Ts

Exchange factor to replace GDP—>GTP just for EF-Tu.

RF1 (release factor 1)

Binds to stop codons UAA and UAG instead of a tRNA to terminate translation and dissociate the ribosomes. The protein shapes of the release factors look like tRNA in that they have clover leaf like shape.

RF2

Binds to UAA and UGA instead of tRNA and terminates translation.

RF3

Just assists, doesn’t bind stop codon.

what marks the end of initiation and start of elongation?

When the mRNA is there, the A site is empty, both ribosomal subunits have bound, and fmet.tRNA^fmet is in the P site.

There are ribosomes in…

Cytoplasm, rough ER, and in chloroplasts and mitochondria! The ribosomes in the organelles are not identical to those in cytoplasm.

Eukaryotic ribosomes Svedberg values

Small subunit = 40S, large subunit is 60S, and whole ribosome = 80 S. Eukaryotic ribosomes are more complex

Assembled bacterial ribosome: how many proteins total?

55

How to denote if an translation factor is in eukaryotic or prokaryotic?

You add an “e” to the start of it if its in eukaryotes. For example: IF2 is prokaryotic, while eIF2 is eukaryotic.

How do eukaryotes bind ribosomes if they don’t have Shine Dalgarro sequence?

eIF4 —> binds to G7 cap to recruit 40S subunit.

Kozak rules for translation in eukaryotic mRNA: How do you recognize AUG in the right reading frame?

Optimal AUG to start translating at is when you see…

What are stop codons also called?

Nonsense codons