Chapter 6: Protein synthesis
What are the names of the most abundant rRNAs found in the small ribosomal subunits of bacteria and eukaryotes, respectively?
16S rRNA in bacteria, 18S rRNA in eukaryotes.
Which direction does the ribosome 'read' the mRNA?
3' to 5'.
What is the Shine-Dalgarno sequence of bacterial mRNA?
A hexamer polypurine sequence found <10 bp upstream of the initiation codon that base pairs with a sequence in the 30S ribosomal subunit and leads to binding of the mRNA.
What is the mechanism by which the ribosome forms the nascent polypeptide chain?
A initiator tRNA binds via its anticodon, to the initiator codon AUG at the P site of the ribosome. The next aa-tRNA then enters the A site and a peptide bond is formed between met and the incoming amino acid. In this process the nascent polypeptide chain is transferred to the tRNA in the A site. The ribosome then moves along the mRNA 1 codon (3 bp) in the 5' direction and the 'empty' tRNA in the P site exits the ribosome and the tRNA previously occupying the A site is transferred to the P site. The cycle continues until a stop codon is reached.
What is the main initiation codon in bacteria and eukaryotes?
AUG (codes for methionine, which can be formylated in bacteria).
What is the role of EF-Tu?
Facilitates entry and loading of the the aminoacyl-tRNA into the A site of the ribosome in a process that requires hydrolysis of GTP.
What is the third bacterial initiation factor to aid in the process of initiation and what is its mechanism of action?
IF1 binds to region of the 30S-mRNA that corresponds to the A site and prevents premature entry of aminoacyl-tRNAs.
What are the 3 translation initiation factors found in bacteria?
IF1, IF2 and IF3.
What is the second bacterial initiation factor to aid in the process of initiation and what is its mechanism of action?
IF2 binds to the initiator tRNA (Met-tRNA) in the cytoplasm and controls its binding to the initiator codon as part of the 30S-mRNA.
What intrinsic activity does IF2 possess and how does this aid in initiation of translation?
IF2 possess intrinsic GTPase activity, which upon binding of the met-tRNA bound 30S ribosomal subunit, leads to hydrolysis of GTP that causes a conformational change in the ribosome and formation of the mature 70S ribosome.
What is the first bacterial initiation factor to aid in the process of initiation and what is its mechanism of action?
IF3 binds to free 30S ribosomal subunits in the cyotosol and causes association with the ribosome binding site of the mRNA.
What are the 3 stages of protein synthesis?
Initiation, elongation and termination.
What is the mechanism of action of the antibiotic puromycin?
Puromycin resembles an aromatic aminoacyl-tRNA, except the amino acid is joined via an amide linkage to a single adenine nucleotide. Upon entry into the ribosome, the amide nitrogen performs a nucleophilic attack on the carboxyl carbon of the amino acid joined to the aminoacyl-tRNA int he P-site. Formation of this bond transfers the nascent polypeptide chain to puromycin, which then dissociates.
What are the 2 proteins involved in the elongation phase of eukaryotic protein synthesis?
The G-protein EF-Tu and the accessory protein EF-Ts.
Which species of RNA is used to supply amino acids to the ribosome during protein synthesis?
The aminoacyl-tRNAs.
What is the name of the assembled bacterial ribosome and what are the names of its constituent subunits?
The bacterial ribosome is the 70S and is formed of the 50S (large) and 30S (small) ribosomal subunits.
What is the name of the assembled eukaryotic ribosome and what are the names of its constituent subunits?
The eukaryotic ribosome is the 80S and is formed of the 60S (large) and 40S (small) ribosomal subunits.
How does translation initiation in eukaryotes differ from bacteria?
There is no extensive base pairing between the mRNA and the small ribosomal subunit (18S) in eukaryotes.
What are the 3 main stop codons?
UAA, UAG and UGA.