Proteomes

Question 1

Ribosome (the decoding centre APE)

Answer 1

A-site -> Next aminoacyl-tRNA loaded with a new amino acid enters through the A-site. This site exposes the mRNA codon representing the next amino acid, where the codon-anticodon interaction takes place
P-site -> Contains the peptidyl-tRNA, a tRNA carrying the growing polypeptide chain. The polypeptide is transferred to the aa carried by the aminoacyl-tRNA in the A-site. Peptide bond catalyzed by large subunit
E-site -> Deacylated tRNA exits the ribosome

Question 2

Initiation of translation in Bacteria

Answer 2

1. rRNA 16S of the small subunit recognizes the RBS. This allows the small subunit + IF-3 + IF-1 to bind to the mRNA over the initiation codon
2. IF-2 GTP binds to the P-site and brings the initiator tRNA-fMET. IF-2 ensures that only tRNA-fMET starts translation
3. IF-1 induces a conformational change in the initiation complex that enables attachment of the large subunit. (requires energy)
4. IF-2 has ribosome-dependent GTPase activity, hydrolyzed a GTP molecule as energy source
5. IFs and GDP are released
6. when translation starts -> initiator tRNA-fMET is removed

Question 3

Initiation of translation in Eukaryotes (Cap-dependent initiation)

Answer 3

1. Small ribosome subunit binds to the 5’methylated cap and moves until the initiation site -> large subunit attaches
2. A complex of initiation factors and initiator tRNA bind to the small ribosomal subunit (40S) -> preinitiation complex
3. A Second group of initiation factors binds to the 5’methylates end of the mRNA to form the cap-binding complex. It binds to the Poly-A binding protein (PABP). -> circular structure
4. Preinitiation complex binds to the 5’ end of the mRNA and scans for the initiation codon
5. IFs dissociate and large subunits attaches

Question 4

Elongation of translation

Answer 4

1. EF-Tu + GTP + aminoacyl-tRNA forms a ternary complex -> binds to the A-site of the ribosome
2. Codon-anticodon interaction stabilized the tRNA binding
3. The 3’ end of the aa-tRNA moves to the A-site of the large subunit
4. EF-Tu hydrolyzes GTP and Ef-Tu-GDP released -> inactive and cannot bind aa-tRNA
5. EF-tu will be activated again with the EF-Ts and GTP

Question 5

Translocation of the ribosome

Answer 5

1. Ribosome advances three nucleotides along the mRNA
2. The deacylarted tRNA exits via E-site, the new peptidyl-tRNA is located in the P-site and a A-site is empty again and contains a new codon -> new aminoacyl-tRNA can enter
3. Elongation cycle is repeated until the STOP codon in reached.

Question 6

Termination of translation in Bacteria

Answer 6

1. Protein release factor (RF1) has a structure that mimics tRNA, enters in the A-site and releases the polypeptide
2. The ribosome recycling factor (RRF) has also a tRNA-like structure. Enters the A and P sites and dissociates the remaining components
3. Dissociation requires GTP hydrolysis

Question 7

Ubiquitination

Answer 7

1. Activation -> Attatched to an activator protein -> uses ATP to bind ubiquitin to a cysteine
2. Conjugation ->
3. Ligation -> Transferred to the lysine of the target protein.