Chapter 22 and 23 - Translation Flashcards
steps of translation
initiation
elongation
termination
initiation
The steps of translation up to entrance of the first aminoacyl-tRNA into the A site
elongation
Repeated rounds of polypeptide chain extension
Addition of one amino acid at a time to the growing polypeptide chain
termination
A separate reaction that ends translation by stopping the addition of subunits and stimulating disassembly of the apparatus
a site
aminoacyl tRNA
p site
peptidyl-tRNA
E site
deacetylated tRNA exit
ribozymes
ribosome with catalytic site
all of them!
tRNA
3’ terminus has the sequence 5’-CCA-3’ that serves as the amino acid acceptor stem
Presence of unusual bases in their structure
All created from standard ribonucleotides post-transcriptionally
tRNA structure
Have a characteristic and conserved pattern of single and double stranded regions
Amino acid acceptor arm
ΨU (Pseudouridine) loop
Dihydrouridine (D) loop
Anticodon loop
Variable loop
Often represented as a cloverleaf structure
Actual structure is inverted L-shape
aminoacyl-tRNA synthetase
are the family of enzymes that load tRNAs with the correct amino acid
aminoacyl-tRNA synthetase steps
- An amino acid reacts with ATP to form an aminoacyl adenylate intermediate
Energy of hydrolysis is trapped in the mixed anhydride linkage of the adenylate
Pyrophosphate is released - The 2’-OH or 3’-OH of the terminal 3’ nucleotide in the tRNA attacks the carbonyl carbon of the adenylate
- An aminoacyl-tRNA and AMP is formed
how do the synthetases detect tRNA differences
All tRNAs share the same general tertiary structure, but differ at nucleotide positions of the four arms
Changes in the nucleotide sequences
Subtle differences between the shape of the L-shaped arms
tRNA synthetases discriminate between tRNAs using both direct (nucleotide differences) and indirect (phosphodiester) methods
Most common discriminators are in the anticodon loop and amino acid acceptor arm
how do synthetases detect amino acid differences
Primary discriminator is shape of different amino acids
But amino acids are very small, and some are very similar in structure
Those that are similar in structure have different binding efficiencies and free energies
class I tRNA synthetases
Primarily monomeric
Aminoacylate tRNA at 2’-OH
Bind tRNA in the minor groove of the amino acid acceptor stem and require hairpin formation
Reaction rate is limited by rate of aminoacyl-tRNA release
class II tRNA synthetases
Primarily dimeric
Aminoacylate tRNA at 3’-OH
Bind tRNA in the major groove of the amino acid acceptor stem
Reaction rate is limited by previous chemical steps or active site rearrangement
synthetase kinetic proofreading when correct
tRNAs that match the specific nucleotide sequence combination for the synthetase
Properly align their amino acid acceptor stem with the ATP and amino acid in the active site
Quickly trigger aminoacylation reaction
synthetase kinetic proofreading when incorrect
Misalignment of acceptor stem in active site
Will not quickly trigger aminoacylation reaction
Dissociates much faster than it can react
isoleucyl synthetase chemical proofreading
Isoleucyl-tRNA synthetase cannot effectively distinguish isoleucine from valine using shape of amino acid binding site
Unable to prevent significant levels of valine-tRNAIle synthesis without proofreading
Nine different tRNA synthetases are able to proofread and correct errors once incorrect amino acid has bound to enzyme
Analogous to the 3’to5’ exonuclease proofreading function of DNA polymerases
two forms of chemical proofreading
pre-transfer editing
post transfer editing
pre-transfer editing
Incorrect aminoacyl-AMP is hydrolyzed after tRNA binding but before charging has occurred
post-transfer editing
Amino acid is hydrolyzed from aminoacyl-tRNA after tRNA charging
Uses an editing active site in the synthetase enzyme that is separate from the synthetic/loading active site
post transfer editing sieve analogy
The post-transfer editing pathway can be thought of as an integrated double-sieve
Based on relative sizes of the synthetic and editing sites
The synthetic site is larger than the editing site
The first sieve is the synthetic site
Amino acids larger than correct amino acid will be excluded from the synthetic site
Loading will not occur
The second sieve is the editing site
Amino acids smaller than the correct amino acid will fit into the synthetic site and the editing site
The incorrect amino acid will then be hydrolyzed and removed in the editing site
post transfer editing mechanism
Amino acids larger than correct amino acid will be excluded from the synthetic site
Loading will not occur
Amino acids smaller than the correct amino acid will fit into the synthetic site and the editing site
The incorrect amino acid will then be hydrolyzed and removed in the editing site
The correct amino acid can fit into the synthetic site, but not the editing site
Will be correctly charged and retained in an aminoacyl-tRNA