Protein synthesis Flashcards
What do ribosomes comprise of?
RNA and protein.
What are the two types of ribosomes?
- Free in cytosol (the aqueous component of the cell, within which various organelles and particles are suspended).
- Bound to the endoplasmic reticulum.
Where in the ribosomes does proteins synthesis occur?
Protein synthesis occurs in the cleft between the small and the large subunit.
How many amino acids are added to the polypeptide chain per second?
20 amino acids per second.
What are the two subunits in mammalian ribosomes? And why is it not 100S?
- It consists of 40S and 60S which together form the 80S ribosome.
- Its 80S and not 100S because S stands for Svedberg which is a unit for the sedimentation rate (not linear).
- The 40S subunits have 18S rRNA (1900 nucleotides) and ~33 different proteins.
- The 60S subunits have 3 RNAs in eukaryotes which comprise of 5S, 5.8S and 28S (120, 160 and 4700 nucleotides) and ~49 different proteins.
What are the three sites formed when the larger (60S) subunit and smaller (40S) subunit join together within the cleft?
When then larger(60S) subunit and small (40S) subunit join together they form 3 separate sites within the cleft. They are:-
a. Aminoacyl tRNA binding site
b. Peptidyl binding site
c. Exit site
APE sites
What is a UTR (untranslated region)?
- It is a region on either side of the coding sequence on a strand of mRNA.
- It can be a 5’ UTR (leader sequence) or a 3’ UTR (trailer sequence) depending on where it is found.
- Its still a part of the exon as mature mRNA does not contain introns as they are cut out during splicing.
What does the 5’ UTR do?
It determines the rate at which the protein is synthesised.
What does the 3’ UTR do?
It affects the stability of the RNA (how long it can stay in the cell without being degraded).
How many possible codons are there?
Three bases form a codon (triplet codon) and we have 4 possible bases (A, T, C, G) which means we can have 4 x 4 x 4 = 64 different codons.
If all RNA is extracted from a cell what percentage of each type of RNA will there be?
Explain translation (initiation).
- The cap binding protein associates with the cap and the poly A binding protein associates with the poly A tail.
- eIF3 (eukaryotic initiation factor 3) binds to the E site on the 40S subunit and eIF1 blocks the A site on the 40S subunit.
- The blocking of the E and A site allows the first P site to interact with eIF2 that is carrying met-tRNAi. eIF2 has GTP bound to it.
- The 40S subunit with the tRNA, and eIF factors 1,2 and 3 form the 48S pre-initiation complex.
- eIF4 binds to the cap structure at the 5’ cap end of the mRNA.
- The 48S pre initiation complex then binds to the cap structure.
- The complex scans for start codons AUG (mediated by initiation factors).
- As the 48S subunit translocates along the RNA, ATP is used. 1 ATP molecule is used up when scanning 1 base (1 triplet codon).
- eIF2 hydrolysis the GTP to form GDP and phosphate.
- Now the 60S subunit can bind to the complex.
- Once it binds all other eIF factors are released (like eIF3, eIF1).
- The 60S subunit, the 40S subunit, the tRNA, and the mRNA is what forms the translation initiation complex (80S ribosome).
NOTE:- Met-tRNAi is only found in initiation bound to eIF2. In elongation it is aminoacyl-tRNA
Explain translation (elongation).
- There is an aminoacyl-tRNA (tRNA which is bonded to amino acids) bonded to the P site. It is known as the initiator tRNA.
- The EF1 (elongation factor) brings an aminoacyl-tRNA to the A site.
- Once the P and A sites are filled, the enzyme peptidyl transferase catalysis the formation of a peptide bond between the amino acids on the P and A sites.
- When the peptide bond is formed the amino acid detaches from the tRNA in the P site.
- The ribosome complex moves three nucleotides in the 5’ to 3’ direction along the mRNA. This process needs 1 GTP, the enzyme translocase and EF2.
- This moves the tRNA in the P site to the E site and it relocates the tRNA carrying the growing polypeptide into the P site.
- Once the tRNA moves into the E site, it is then expelled out of the ribosome complex to be reacharged by aminoacyl tRNA synthase to form aminoacyl-tRNA, AMP and pyrophosphate.
- Once the A site is empty the process can repeat itself to add another amino acid. This continues until the polypeptide chain is complete.
Explain translation (termination).
- There’s a stop codon that signals termination. If the ribosome reads either UAA, UGA or UAG a protein called release factor will bind to the A site.
- The terminal peptidyl-tRNA will be hydrolysed. This will ultimately cause the polypeptide chain to break off of the tRNA in the P site.
- The ribosome complex will then dissociate and this will end termination.
How energetically expensive is all the processes of translation?
How are bacterial and eukaryotic ribosomes different?
