#24 Protein Translation 1 10.22.12

Question 1

Why is tRNA transcribed with extra sequences at both its 5’ end and 3’ end?

Answer 1

Extra b/c polymerase is sloppy at beginning and end ; Transcription just adds a little junk

Question 2

What catalytic RNA or ribozyme is the site specific endonuclease that generates the mature 5’ end of ALL tRNAs

Answer 2

RNase P

Question 3

is the RNase processing of the 5’ end for euk or prok?

Answer 3

IT is universal!!!

Question 4

Is the RNAse P an endonuclease or exonuclease?

Answer 4

Endonuclease!

Question 5

In bacteria, what kind of enzymes release the mature 3’ end?

Answer 5

a combination of exo- and endo- nucleases release the mature 3’ end

Question 6

what is the universl code at the mature 3’ end of all tRNAs of bacteria

Answer 6

CCA

Question 7

Do euk genes code for CCA? If not, how is CCA added?

Answer 7

no! CCA is added by CCA-adding enzyme after trimming iwth an endonuclease

Question 8

why is CCA-adding enzyme unusual?

Answer 8

it doesn’t use a template (like poly A polymerase)

Question 9

how are Poly III introns removed?

Answer 9

unlike Pol II (coding genes), Pol III introns are removed by a PROTEIN BASED NON-SPLICEOSOMAL PATHWAY

Question 10

In bacteria, what releases teh mature 3’ end>

Answer 10

a combination of exo and endo nucleases releases the mature 3’ end, which contains universal CCA, which is coded for in teh tRNA gene

Question 11

How many (%) of all nucleotides in mature tRNA have been chemically modified after transcritpion?

Answer 11

10%

Question 12

What is INOSINE (I)

Answer 12

Deaminated A

Question 13

What do modifications contribute?

Answer 13

1. to proper folding of tRNA

2. to recognition of tRNA by the ribosome and by enzymes that must interact with teh tRNA

Question 14

What other types o fRNA ar emodified after transcription?

Answer 14

including rRNA

Question 15

What is the pairing rules for INOSINE (I)

Answer 15

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

Question 16

If codon is 5’AUG what is the anticodon?

Answer 16

5’ CAU anticodon Which

Question 17

Which position can ribosomes tolerate a mismatch (wobble)

Answer 17

at teh third position of the codon (which corresponds to teh first position of the anticodon)

Question 18

how does ribosome recognize shape of WC pairs

Answer 18

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

Question 19

When does ribosme allow peptride bond fomatino to occur?

Answer 19

only when teh correct geometry is recognized

Question 20

What happens to non WC codon anticodn interactions -

Answer 20

do not ahve the correct distance and are reject

Question 20

“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”

Answer 20

absolute

Question 21

What about the thrid position of the codon?

Answer 21

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

Question 21

“使无罪，解除责任：free from, guilt, exculpate”

Answer 21

absolve

Question 22

Because wobble positions allow non-WC pairings, humans only use ……. different anticodons to recognize …..codons

Answer 22

48 different anticodons to recognize 61 codons

Question 23

Bacteria can get b with as fewa as 31 different tRNAs

Answer 23

Humans have 497 tRNA genes, but theese represent ony 48 different anticodons

Question 24

What are the two steps of Aminoacyt-tRNA synthetase

Answer 24

1. ATP reacts with amino acid to make an adenylated amino acid (AMP linked through a high energy phosphate linkage to aa) 2. the amino acid is transferred onto the 3' OH of hte 3' end of th tRNA

Question 25

How much eneryg does the aminoacyl-tRNA syntehtase reaction use?

Answer 25

ATP and it costs 2 phosphate equivalents to do this

Question 26

what side of teh amino acid is attackked

Answer 26

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

Question 27

What does the large interface (between teh tRNA moleucle and teh aminoactyl-tRNA synthetase) help?

Answer 27

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

Question 28

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

Answer 28

yup

Question 29

what do synthetatses do to discriminate between very similar amino acids (like val and isoleucine)

Answer 29

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

Question 30

What happens when a correclty cahrged aminacytl-tRNA docks inot he editing site

Answer 30

It is neither recognized nor hydrolyzed, and as a result --> dissociates as a correclty charged amionacyl-tRNA.

Question 31

How much does editing raise the overall accuracy?

Answer 31

1 mistake in 40,000 couplings

Question 34

How many ribosomes make up site of translation?

Answer 34

2 subunits- small subunit and large subunit (not additive)

Question 35

what are the names of the subunits for eukaryotic ribosomes?

Answer 35

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

Question 36

what association do subunits have when they are not synthesizing protein?

Answer 36

two subunits of ribosome are dissocaited

Question 37

HOw fast/accurate is the process of translation?

Answer 37

Speed is 2 aa persecond for euk and 20 amino acids/sec for prokayrotes Accuraty is 1 error/10,000 amino acids

Question 38

What is the SSU (small subunit)'s function?

Answer 38

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

Question 39

What doe sthe LSU (large subunit) do?

Answer 39

binds to the CCA ends of tRNAs and houses the peptidyl transferase enter where peptide bond formation is catalyzed by rRNA

Question 40

What are the three binding sites for the tRNA

Answer 40

A- binds to incoming Aminoacytl tRNA P. 0 binds ot the Peptidyl -tRNA E sites- binds to the Exiting deacylated tRNA

Question 41

Universal rRNA contacts to teh CCA end of the tRNA in aht ....

Answer 41

Large sutunit

Question 42

in the A site of the LSU, WC pairs form between....

Answer 42

the 2 rRNA G nucleotides and the 2Cs of CCA

Question 43

in the P site of the LSU, WC pair forms between an rRNA G nucleotide and the 2nd C of the CCA

Answer 43

yep

Question 44

In the E-site of the LSU, non WC rRNA contacts regnozes the A of CCA.

Answer 44

yep

Question 45

All fucntional tRNA molecules have the ....sequence at the 3' end

Answer 45

CCA