Description of the structure and function of the 60S large ribosomal subunit
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| Roughly what proportion of the ribosome is made up of protein? | 1/3
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| Roughly what proportion of the ribosome is made up of RNA? | 2/3
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| What rRNAs are found in the large ribosomal subunit? Which ones? | 2: 23S and 5s
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| How many proteins are found in the large ribosomal subunit? | 31
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| What is the function of the A site? | Aminoacyl site; binds aminoacyl tRNAs
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| What is the function of the P site? | Peptidyl site; binds peptidyl tRNA
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| What is the function of the E site? | Exit site; binds empty tRNAs
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| What are the 4 stages of translation? | -Initiation
-Elongation
-Release
-Recycling
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| What occurs during the initiation stage of translation? | Recognition and positioning of the ribosome over a START codon
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| What occurs during the elongation stage of translation? | Sequential addition of amino acids to the growing polypeptide chain
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| What occurs during the release stage of translation? | STOP codon recognition and hydrolysis of the polypeptide chain from the final peptidyl tRNA
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| What occurs during the recycling stage of translation? | The ribosome dissociates into its subunits and prepares for another round of synthesis
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| What is modeled in the paper? | -2 rRNA molecules: 23S and 5s
-27 proteins
-4Cd2+
-2MG2+
-1K+
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| Does the structure show the complete large ribosomal subunit? | No. Some nucleotides and some peptides are missing from both rRNAs
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| What is the "crown view"? | It is a specific orientation of the ribosome that positions the 5S rRNA on top of the structure. This view places the surface that bonds with the small subunit toward the viewer.
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| How many domains make up the 23S rRNA? | 6
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| Which proteins are missing from the structure? | L1, L10, L11, L12
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| Where are the proteins located within the structure? | -Mostly on the surface of the complex
-Removed from the catalytic center
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| What seems to be the role of the proteins? | To stabilize the rRNA; to this effect, 4 of the proteins contain zinc finger domains
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| What is shown by the structure in IFFK? | The original structure of the complete 50S ribosome at 2.5 angstrom resolution
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| What is shown by the structure in IFGO? | The structure of 23S domain V in complex with an aminoacyl tRNA analog linked to puromycin
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| What is shown by the structure in IFFZ? | The structure of the 23S domain V in complex with the "CCdA-p-Puro" inhibitor, also called the Yarus inhibitor
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| What is puromyocin? | An antibiotic that mimics an aminoacyl tRNA of tyrosine. It binds to the ribosomal A site and prematurely terminates translation
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| Where is the peptidyl transferase site presumed to be? | At the confluence of the P and A sites
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| How does the Yarus inhibitor inhibit ribosome function? | The Yarus inhibitor contains a tetrahedral PO4 that mimics the transition state tetrahedral carbon at the peptidyl transferase site
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| Where does the c-c-puro inhibitor locate to during inhibition? | The A site
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| Where does the Yarus inhibitor locate to during inhibition? | The peptidyl transferase site between the A and P sites
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| Why do all tRNAs end with a CCA sequence? | Several bases in the P-site hydrogen bond with the CCdA of the Yarus inhibitor
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| Where do the inhibitors bind? | At the bottom of a deep cleft surrounded by nucleotides from the central loop in the 23S rRNA domain V
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| Do the proteins come close to the active site? | No, the closest proteins to the active site are non globular and are about 18 angstroms away
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| What does the position of the proteins relative to the active site tell us about the ribosome? | That the mechanism is carried out exclusively by rRNA and that the ribosome is therefore a ribozyme
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| What is significant about mutations in the ribosome that convey inhibitor resistance? | The nucleotides subjected to these mutations are near the active site, and do not interact with other ribosomal nucleotides
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| What is the first step of the catalytic cycle? | A2486 acts as a general base, deprotonating the alpha amino group from the A-site aminoacyl tRNA
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| What is the second step of the catalytic fcycle? | The amino group of the incoming amino acid nucleophillically attacks the carbonoyl carbon of the last peptide to be incorporated into the polypeptide chain.
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| What is the third step of the catalytic cycle? | The protonated A2486 N3 stabilizes the formation of the oxy anion by hydrogen bonding to it as in the Yarus inhibitor complex structure
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| What is the fourth step of the catalytic cycle? | N3 of A2486 could the subsequently transfer then H+ to the 3' O of the p-site-bound tRNA which is liberated as the peptide shifts to the A-site-bound tRNA
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| What was found when the crystallographic model was compared to a cryo-electron microscopy structure? | The tRNA CCA and 3' OH of the inhibitors align with these elements of the cryo structure
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| How do polypeptides exit the ribosome? | Polypeptides exit via the exit tunnel which is about 100 angstroms long
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| What conformation is the polypeptide found in in the exit tunnel? | The tunnel is not wide enough for a polypeptide in secondary structure to pass. The tunnel is wide enough for an alpha helix, but there is no evidence that this structure is present.
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| Why don't unfolded proteins stick to the sides of the exit tunnel? | There are no patches of hydrophobic residues large enough to which the nascent protein could bind. Electrostatic interactions are discouraged by the large change in entropy this would require.
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| How do proteins interact with the polypeptide chain in the exit tunnel? | Peptides L4 and L22 form a gate in the exit tunnel, but there is not enough evidence to support a function of this gate
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