II. Post-transcription | 24. The structure of prokaryotic and eukaryotic ribosomes; the ribosome cycle; binding of tRNA to ribosomes

Question 1

1. Basics
   a/ The role of ribosome

Answer 1

Ribosome performs protein synthesis, a complex catalytic machine that serves as the site of biological protein synthesis.

Question 2

1. Basics
   b/ General structure of ribosomes

Answer 2

• Made up from ribosomal RNA (rRNA) and more than 50 different proteins – the ribosomal proteins.
• The ribosomal proteins + rRNA are arranged into 2 ribosomal pieces of different sizes: large subunit + small subunit.
• Ribosomal subunits are built up in the nucleolus.

Question 3

1. Basics
   c/ What does S mean?

Answer 3

S = svedberg units, a parameter sensitive to molecular size and shape

Question 4

1. Basics
   d/ The role of small subunit of ribosome

Answer 4

The small subunit provides the framework on which the tRNAs match to the right codons of the mRNA

Question 5

1. Basics
   e/ The role of large subunit of ribosome

Answer 5

The large subunit catalyzes the formation of the peptide bonds that link amino acids together

Question 6

1. Basics
   f/ When will the ribosome form a complex and dissociate?

Answer 6

• When not actively synthesizing proteins, the two subunits are separate
• Only form a complex during translation

Question 7

2. Prokaryotic ribosomes
   a/ Structure of prokaryotic ribosomes?

Answer 7

• RNA constitute about 60% of the mass of a bacterial ribosome
• Prokaryotic ribosomes are composed of 3 different rRNA molecules and 54 ribosomal proteins organized into a large + small subunit
• Small ribosomal subunit consists of the 16S rRNA molecule => 21 proteins & total size = 30S
• Large ribosomal subunits consists of 23S + 5S rRNA molecule => 34 proteins & total size = 50S
• The assembled ribosome is 70S in bacteria

Question 8

3. Structure of Eukaryotic ribosomes

Answer 8

• RNA constitutes about 50% of the mass of a human ribosome
• Eukaryotic ribosomes are composed of 4 different rRNA molecules & about 80 ribosomal proteins organized into a large + small subunit
• Small ribosomal subunit consists of the 18S rRNA molecule => 33 proteins & total size = 40S
• Large ribosomal subunits consists of 28S, 5.8S, 5S rRNA molecules => 49 proteins & total size = 60S
• The assembled ribosome is 80S in bacteria

Question 9

4. Function of ribosomes
   a/ How does tRNA binds to ribosome?

Answer 9

The ribosome has 3 binding sites for tRNA molecules that span the space between the large and small ribosomal subunits.
=> The sites where tRNAs are bound by ribosomes are:
1) A-site (aminoacyl-tRNA): acceptor for growing of the protein during peptide bond formation
2) P-site (peptidyl-tRNA): binding of tRNA responsible for the growing polypeptide chain
3) E-site (exit): occupied by tRNA on transit out from the ribosome

Question 10

5. Polyribosomes
   a/ What is Polyribosomes?

Answer 10

when mRNA molecules are attached to multiple ribosomes bearing nascent (beginning-to-exist / developing) growing polypeptide chains.

Question 11

5. Polyribosomes
   b/ The role of polyribosomes in prokaryotes

Answer 11

1. Transcription and translation simultaneously
2. Post-translational folding

Question 12

5. Polyribosomes
   c/ The role of polyribosomes in eukaryotes

Answer 12

1. Transcription and translation both spatially and temporally are separated
2. Co-translational folding

Question 13

5. Polyribosomes
   d/ How does polyribosomes in eukaryotes function?

Answer 13

1. multiple copies of the PABP (poly-A-binding protein) interact with both poly-A-tail (mRNA) and the G subunit of eIF4 (eIF4: eukaryotic initiation factor 4)
2. since the E subunit of eIF4 binds to the cap structure on the 5’-end of a mRNA, the two ends of a mRNA molecule are bridged forming a ‘’circular mRNA’’
3. ribosomal subunits that disengage from a stop codon are positioned near 5’-end,
   facilitating re-initiation by interaction of the 40S subunit and its associated initiation
   factors with eIF4 bound to the 5’-cap
4. this circular pathway is thought to engage ribosome recycling and the efficiency of
   protein synthesis

Question 14

6. Ribosome cycle
   a/ How does ribosome cycle occur?

Answer 14

1. Several ribosomes are engaged in protein synthesis as they move along a mRNA molecule, forming a polysome.
2. At the termination codon, the completed polypeptide chain is released and the ribosome leaves the mRNA to become a termination ribosome.
   -> This intermediate of the ribosome cycle is unstable and readily dissociates, yielding pair of free ribosomal subunits.
3. These free ribosomal subunits are short-lived intermediates that can proceed along two different paths: (IF = initiation factor) which are sufficient IF-3 and insufficient IF3

Question 15

6. Ribosome cycle
   b/ What happen if free ribosomal subunits proceed along sufficient IF-3 path?

Answer 15

The small ribosomal subunit binds IF- 3, which results in a pair of stable, native ribosomal subunits

Question 16

6. Ribosome cycle
   c/ What happen if free ribosomal subunits proceed along insufficient IF-3 path?

Answer 16

• Free ribosomal subunits associate with high affinity to form a relatively stable single ribosome = does not function as an intermediate of the ribosome cycle, but can return when it is dissociated into free subunits
  => During one of the steps leading to formation of a new initiation complex on mRNA, initiation factor IF-3 is released and recycled