#24 Protein Translation 1 10.22.12 Flashcards
Why is tRNA transcribed with extra sequences at both its 5’ end and 3’ end?
Extra b/c polymerase is sloppy at beginning and end ; Transcription just adds a little junk
What catalytic RNA or ribozyme is the site specific endonuclease that generates the mature 5’ end of ALL tRNAs
RNase P
is the RNase processing of the 5’ end for euk or prok?
IT is universal!!!
Is the RNAse P an endonuclease or exonuclease?
Endonuclease!
In bacteria, what kind of enzymes release the mature 3’ end?
a combination of exo- and endo- nucleases release the mature 3’ end
what is the universl code at the mature 3’ end of all tRNAs of bacteria
CCA
Do euk genes code for CCA? If not, how is CCA added?
no! CCA is added by CCA-adding enzyme after trimming iwth an endonuclease
why is CCA-adding enzyme unusual?
it doesn’t use a template (like poly A polymerase)
how are Poly III introns removed?
unlike Pol II (coding genes), Pol III introns are removed by a PROTEIN BASED NON-SPLICEOSOMAL PATHWAY
In bacteria, what releases teh mature 3’ end>
a combination of exo and endo nucleases releases the mature 3’ end, which contains universal CCA, which is coded for in teh tRNA gene
How many (%) of all nucleotides in mature tRNA have been chemically modified after transcritpion?
10%
What is INOSINE (I)
Deaminated A
What do modifications contribute?
- to proper folding of tRNA
2. to recognition of tRNA by the ribosome and by enzymes that must interact with teh tRNA
What other types o fRNA ar emodified after transcription?
including rRNA
What is the pairing rules for INOSINE (I)
A pairs with U; in mRNA where A has been edited via deamination to I, I pairs with C
IC pair is isosteric with Watson-Crick paris and recognized as cognate codon-anticodion bae par at the first 2 position fo the codon
At the wobble position of bacteria, I can pair with either A, C, or U (
I is like a G
Eukaryotic ribosomes are a little more precise
If codon is 5’AUG what is the anticodon?
5’ CAU anticodon Which
Which position can ribosomes tolerate a mismatch (wobble)
at teh third position of the codon (which corresponds to teh first position of the anticodon)
how does ribosome recognize shape of WC pairs
use non WC interactions between the 1st and 2nd bases
ribosomes use a “deoding” ruler to measure the distance between the 2’ hyroxyl group of the first 2 codon/anticodon base pairs
When does ribosme allow peptride bond fomatino to occur?
only when teh correct geometry is recognized
What happens to non WC codon anticodn interactions -
do not ahve the correct distance and are reject
“专制的：unconstrained; 无限的unqualified; 完美的，纯净不惨杂的：free from imperfection, mixture; 不容置疑的，确凿的：unquestionable”
absolute
What about the thrid position of the codon?
designated the wobble position, is not recongnized as teh precisely as the ribosomes –> allowing it to accept both WC and some no n WC base pairs
“使无罪，解除责任：free from, guilt, exculpate”
absolve
Because wobble positions allow non-WC pairings, humans only use ……. different anticodons to recognize …..codons
48 different anticodons to recognize 61 codons
Bacteria can get b with as fewa as 31 different tRNAs
Humans have 497 tRNA genes, but theese represent ony 48 different anticodons
What are the two steps of Aminoacyt-tRNA synthetase
- ATP reacts with amino acid to make an adenylated amino acid (AMP linked through a high energy phosphate linkage to aa)
- the amino acid is transferred onto the 3’ OH of hte 3’ end of th tRNA
How much eneryg does the aminoacyl-tRNA syntehtase reaction use?
ATP and it costs 2 phosphate equivalents to do this
what side of teh amino acid is attackked
amino acid is attached to 3’ end of tRNA. It is the carboxyl group of the aa that is attached, so the amion gorup is available to attack the carboxyl group at teh C-terminal end of the growing peptide
What does the large interface (between teh tRNA moleucle and teh aminoactyl-tRNA synthetase) help?
Helps recognize distinctive features of its cognate tRNA
Synthetases have evolved to preferentially bind the correct tRNA and the corresponding cognate aa by matching the size, shape and chemical properties of both substrates
Aminoacylt tRNA charging reaction catalyzed by synthetases my not be 100% accurate when discriminating between two highly similar amion acids - valine and isoleucine differe by only a single methyl gorup
yup
what do synthetatses do to discriminate between very similar amino acids (like val and isoleucine)
in this subset of synthetatses, aminoacyl charging occurs at the active site and editin occurs at a nearby eidint site, which has a high affinity for the “wrong” amion acid
When wrong aa is attached to active site the flexibitly of the CCA end of the tRNA allwos this misharged aminoacyl group to dock into the editing site–> wrong aa recognized and removed by hydrolysis
What happens when a correclty cahrged aminacytl-tRNA docks inot he editing site
It is neither recognized nor hydrolyzed, and as a result –> dissociates as a correclty charged amionacyl-tRNA.
How much does editing raise the overall accuracy?
1 mistake in 40,000 couplings
How many ribosomes make up site of translation?
2 subunits- small subunit and large subunit (not additive)
what are the names of the subunits for eukaryotic ribosomes?
large subunit is about 49 proteins, plus three rRNA moleucles with sizes 5S, 5.8S, and 29S respectively
Small subunit is made up of ~33 proteins plus an 18S rRNA
what association do subunits have when they are not synthesizing protein?
two subunits of ribosome are dissocaited
HOw fast/accurate is the process of translation?
Speed is 2 aa persecond for euk and 20 amino acids/sec for prokayrotes
Accuraty is 1 error/10,000 amino acids
What is the SSU (small subunit)’s function?
binds t the message and the aanticodon end of the tRNA
SSU is in charge for decoding the message (ensurign tehat the codon and anticodon bp properly
What doe sthe LSU (large subunit) do?
binds to the CCA ends of tRNAs and houses the peptidyl transferase enter where peptide bond formation is catalyzed by rRNA
What are the three binding sites for the tRNA
A- binds to incoming Aminoacytl tRNA
P. 0 binds ot the Peptidyl -tRNA
E sites- binds to the Exiting deacylated tRNA
Universal rRNA contacts to teh CCA end of the tRNA in aht ….
Large sutunit
in the A site of the LSU, WC pairs form between….
the 2 rRNA G nucleotides and the 2Cs of CCA
in the P site of the LSU, WC pair forms between an rRNA G nucleotide and the 2nd C of the CCA
yep
In the E-site of the LSU, non WC rRNA contacts regnozes the A of CCA.
yep
All fucntional tRNA molecules have the ….sequence at the 3’ end
CCA
