Chapter 15 - Translation Flashcards
At what speed does translation take place
20 amino acid per second.
What is the composition of the ribosome? What are the functions of those subunits?
A large subunit that contain the peptide transferase centre, which is responsible for the formation of peptide bonds. The small subunit contains the decoding centre in which charged tRNAs read to “decode” the codon units of the mRNA.
What is the sedimentation velocity of the ribosomal subunits?
In bacteria, 70 & 30 Svedbergs. The intact ribosomes is referred to as 70S. In eukaryotic ribosomes, 60S and 40s that together form 80S.
What are the rRNA called in the different subunits?
In bacteria, the 50S contains a 5S rRNA and a 23S rRNA, whereas the 30S subunit contains a single 16S rRNA. In eukaryotic ribosome, the 60S subunit is composed of 5.8S, 5S and 28S rRNA. The 40S subunit is composed of 18S rRNA.
What is the ribosome cycle?
The small and large subunit of the ribosome associate with each other and the mRNA, translate the target mRNA, and then dissociates after completing synthesis of the protein.
Translation begins with the binding of the mRNA and initiation tRNA to a free, small subunit of the ribosome. The small subunit-mRNA-initiatior-tRNA complex the recruits a large subunit to create an intact ribosome with the mRNA sandwiched between the two subunits. Protein synthesis is initiated in the next step, connecting at the start codon at the 5’ end of the message and progressing towards the 3’ end of the mRNA. As the ribosome translocate from the codon to codon, one charged tRNA after another is slotted into the decoding and peptidyl transferase centers of the ribosome. When the elongating ribosome encounters a stop codon, the now completed polypeptide chain is released, and the ribosome dissociates from the mRNA as separate large and small subunits.
What is a polyribosome or a polysome?
A mRNA bearing multiple ribosomes. Although a ribosome can synthesise only one polypeptide at a time, each mRNA can be translated simultaneously by multiple ribosomes.
Which chemical reaction does a ribosome catalyse? And where does it occur?
The formation of a peptide bond. This occurs between the amino acid residue at the carboxyl-terminal end of the growing polypeptide and the incoming amino acid added to the chain. Both the growing chain and the incoming amino acid are attached to tRNAs; as a result, during peptide-bond formation, the growing polypeptide is continuously attached to a tRNA.
What is the substrate for each round of amino acid addition? And where are they attached?
Two charged species of tRNAs –> an aminoacyl-tRNA and a peptidyl-tRNA. The aminoacyl-tRNA is attached at its 3’end to the carboxyl group of the amino acid. The peptidyl-tRNA is attached in exactly the same manner (at it’s 3’ end) to the carboxyl terminus if the growing polypeptide chain.
Which bond is broken during the formation of the next peptide bond?
The bond between the peptidyl-tRNA and the growing polypeptide chain is broken as the growing chain is attached tot he amino group of the amino acid attached to the aminoacyl-tRNA to form a new peptide bond.
Explain the peptidyl transferase reaction.
The 3’ end of these two tRNA are brought into close proximity by the ribosome. The resulting tRNA positioning allows the amino group of the amino acid attached to aminoacyl-tRNA to attack the carbonyl group of the most terminal amino acid attached to the peptidyl-tRNA. The result of this nucleophilic attack is the formation of a new peptide bond between the amino acids attached to the tRNAs and the release of the polypeptide chain from the peptidyl tRNA.
What are the three binding site of the ribosome? And what are their function?
the A-, P- and E-site. The A-site is the binding site for the amincoacylated-tRNA, the P-site is the binding site for the peptidyl-tRNA, and the E-site is the binding site for the tRNA that is released after the growing polypeptide chain has been transferred to the aminoacyl-tRNA.
How does mRNA enter and exit (polypeptide chain) the ribosome?
The mRNA enters and exits the decoding center through two narrow channels in the small subunit. The channel is only wide enough for the unpaired RNA to pay through. In between the two channels is a region that is accessible to tRNA and where adjacent condons can bind to the aminoacyl-tRNA and peptidyl-tRNA in the A-and P-site, respectively.
The second channel provides an exit path for the newly synthesised polypeptide chain.
Which 3 events must occur for translation to be successful?
- The ribosome must be recruited.
- A charged tRNA must be be placed into the P-site of the ribosome.
- The ribosome must be precisely positioned over the start codon.
What mediates the association between the small subunit and the mRNA?
Base-pairing interaction between the RBS and the 16S rRNA.
What is the role of initiator tRNA?
Binds to the P-site without previously occupying the A-site. Initiator tRNA base-pairs usually with AUG or GUG.
Which charged group is aded to initiator tRNA?
Initiator tRNA is first charged with a methionine, then a formyl group is rapidly added to the methionine amino group by a separate enzyme (Met-tRNA transformylase) –> coupled to N-formyl methionine. The charged initiator tRNA is referred to as fMet-tRNA.
What is the task of deformylase?
This enzyme removes the formyl group from he amino terminus during or after synthesis of the polypeptide chain.
Which three factors catalyses the initiation prokaryotic translation? And what are their function and where do they bind?
IF1 - Assists in binding of IF3 to the 30S subunit. Prevents tRNA from binding to the portion of the small subunit that will become part of the A-site.
IF2 - Is a GTPase that interacts with three key components of the initiation machinery: the small subunit, IF1, and the charged initiator tRNA. By interacting with the small subunit and prevents other charged tRNAs from associating with the small subunit.
IF3 - bind the small subunit and blocks it from reassociating with the large subunit. Because initiation requires a free small subunit, the binding of IF3 is crucial for a new cycle of translation. IF3 becomes associated with the small subunit at the end of a previous round of translation when it help to dissociate the 70S ribosome into its large and small subunit.
IF1 binds directly to the portion of the small subunit that will become the A-site. IF2 binds to IF1 and reaches over the A-site into the P-site to contact the fMet-tRNA. IF3 occupies the part of the small subunit that will become the E-site.
How does the large subunit bind to create the 70S initiation complex?
When the start codon and fMet-tRNA altered conformation results in the release of IF3. In absence of IF3, the large subunit is free to bind to the small subunit with its cargo of IF1, IF2, mRNA and fMet-tRNA. In particular, IF2 acts as an initial docking site of the large subunit, and this interaction subsequently, stimulates the GTPase activity of IF2-GTP.IF2 bound to GDP has reduced affinity for the ribosome and the initiator tRNA, leading to the release of IF2-GDP as well as IF1 from the ribosome.
How does initiation in eukaryotes differ from prokaryotes?
Eukaryotes use a fundamentally distinct method to recognise the mRNA and the start codon. In eukaryotes the small subunit is already associated with an initiator tRNA when it is recruited to the capped 5’ end of the mRNA. It then “scans” along the mRNA in a 5’–> 3’ direction until it reaches the first 5’-AUG-3’, which it recognises as the start codon.
What are the 4 steps of initiation in eukaryotes?
- Binding of the initiator tRNA to the small subunit always precedes association with the mRNA.
- A separate set of auxiliary factors mediates the recognition of the mRNA.
- The small ribosomal subunit bound to the initiator tRNA scans the mRNA for the first AUG sequence.
- The large subunit of the ribosome is recruited after initiator tRNA base-pairs with the start codon
