Protein Synthesis by mRNA translation Flashcards
In which direction is the polypeptide chain growing?
N -> C
What type of amino acids form the core?
Neutral, hydrophobic amino acids
Which amino acids form salt bridges?
Acidic bases
Which amino acids can form disulfide bridges?
Cysteine
Bacterial ribosome
70S (50S,16S)
Eukaryotic ribosome
80S (60S, 40S)
What is the function of the large subunit in the ribosome?
Peptide bond formation, peptidyl transferase center
What is the function of the small subunit in the ribosome?
Decoding interaction, find shine-dalgarno seq (bacterial), mRNA binding site
EF-Tu
GTPase, brings the aa-tRNA. Hydrolysis of GTP makes EF-Tu release aa-tRNA in A-site. Also masks amino acid in tRNA so it doesnt react
EF-G
Guides translocation of ribosome, also GTPase.
What is wobble base-pairing
Third codon doesnt have to have correct watson-crick pairing
Important sites of tRNA
Acceptor arm with exposed 3’ end (CCA) which is the amino acid attachment site
anticodon loop - basepairs to mRNA
How does charging work?
Addition of AMP to tRNA by aatRNA synthase provides the high energy bond needed to create an ester linkage between AMP-tRNA and aa-tRNA
aa tRNA synthase
Two classes depending which OH (2’ or 3’) they primarily attach aa group to. Has hydrolytic editing as proofreading; incorrect aa moves to editing site
Protein synthesis initiation in bacteria
Shine-Dalgarno seq upstream of start codon. IF3 binds to E site in small subunit. IF2, IF1 and GTP binds to A-site, mRNA, f-Met to P-site. IF3 leaves so that large subunit can dock (IF2 in GTP form as signal to large subunit), IF2 hydrolyse and leave with IF1.
IF1
Small initiation factor that help IF2 and 3. Blocks A-site.
IF2
GTPase, looses affinity when in GDP state. Provides energy and works as signal molecule for large subunit to come in. Blocks A-site. Also binds to f-Met-tRNA to help it dock
IF3
Large, blocks large subunit from binding to 30S initiation complex. Binds to E-site
Protein synthesis initiation in eukaryotes
preinitiation-complex loops mRNA until it finds start codon, prompting eIF2 to hydrolyze GTP causing some eIFs to disappear. eIF5-GTP binds to A-site, which is signal for large subunit to come in. eIF5 hydrolyze GTP causing all remaining eIFs to leave.
Which is the human homolog for IF2 in bacteria?
eIF5B
Selection in ribosome
Small subunit stabilize mRNA+anticodon loop if its the correct pairing, so that EF-Tu is in the correct position to be hydrolyzed, if wrong aa-tRNA just leaves
Proof-reading in ribosome
tRNA has to be rotated to into peptidyl transferase center. Incorrect tRNAs disappear - only correct base pairing can stand the strain?
Explain peptide bond formation
NH2 in A site attacks CO in P-site, transferring the entre polypeptide chain to the tRNA in the A-site
Peptide release in bacteria
RF1 and R2 release peptide from ribosome. RF3 releases RF1-2. RF3 hydrolyses and releases from ribosome.
Which is the eukaryotic homolog for RF2
eRF1
How does RFs work
Molecular mimicry, looks like tRNA so can go into A-site.
What is ribosome recycling?
Removing the empty tRNAs, removing the mRNA and splitting the ribosome into its subunits so that it can participate in another round of protein synthesis. Done by RRF and EF-G.
What is the primary determinant of secondary structure in a protein?
Hydrogen bonding [between backbone atoms]
Aminoacyl-tRNA
tRNA covalently attached to aa at the 3’ end of tRNA
Chloramphenicol mechanism
Inhibits peptidyl transferase by binding to large subunit
What are the start and stop codons for protein synthesis?
Start: AUG
Stop: UAG
Which eukaryotic initiation factor is homologous to bacterial IF3?
eIF1A
Why is tRNA adenylated in tRNA charging?
To add a high energy bond
What is special about glycine?
Is not chiral; more conformational freedom
What is special about proline?
Less conformational freedom, cant really participate in secondary structures
Which direction is alpha-helixes?
Right handed
What is a possible way to regulate translation in prokaryotes?
High complimentary to 16S RNA (shine-dalgarno seq.), and proper spacing to start codon
How is the ribosome recruited to eukaryotic mRNA?
It recognizes the 5’ cap
How does the polypeptide tunnel limit the conformation of the polypeptide chain?
It can only big enough for alpha helix, no beta or tertiary structures
What is the GGQ?
A motif on class I release factors that stimulate polypeptide release from ribosome.
