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CMCB Fall > #24 Protein Translation 1 10.22.12 > Flashcards

#24 Protein Translation 1 10.22.12 Flashcards

1
Q

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

A

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

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2
Q

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

A

RNase P

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3
Q

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

A

IT is universal!!!

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4
Q

Is the RNAse P an endonuclease or exonuclease?

A

Endonuclease!

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5
Q

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

A

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

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6
Q

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

A

CCA

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7
Q

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

A

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

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8
Q

why is CCA-adding enzyme unusual?

A

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

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9
Q

how are Poly III introns removed?

A

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

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10
Q

In bacteria, what releases teh mature 3’ end>

A

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

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11
Q

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

A

10%

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12
Q

What is INOSINE (I)

A

Deaminated A

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13
Q

What do modifications contribute?

A
  1. to proper folding of tRNA

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

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14
Q

What other types o fRNA ar emodified after transcription?

A

including rRNA

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15
Q

What is the pairing rules for INOSINE (I)

A

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

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16
Q

If codon is 5’AUG what is the anticodon?

A

5’ CAU anticodon Which

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17
Q

Which position can ribosomes tolerate a mismatch (wobble)

A

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

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18
Q

how does ribosome recognize shape of WC pairs

A

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

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19
Q

When does ribosme allow peptride bond fomatino to occur?

A

only when teh correct geometry is recognized

20
Q

What happens to non WC codon anticodn interactions -

A

do not ahve the correct distance and are reject

20
Q

“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”

A

absolute

21
Q

What about the thrid position of the codon?

A

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

21
Q

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

A

absolve

22
Q

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

A

48 different anticodons to recognize 61 codons

23
Q

Bacteria can get b with as fewa as 31 different tRNAs

A

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

24
Q

What are the two steps of Aminoacyt-tRNA synthetase

A
  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
25
Q

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

A

ATP and it costs 2 phosphate equivalents to do this

26
Q

what side of teh amino acid is attackked

A

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

27
Q

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

A

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

28
Q

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

A

yup

29
Q

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

A

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

30
Q

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

A

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

31
Q

How much does editing raise the overall accuracy?

A

1 mistake in 40,000 couplings

34
Q

How many ribosomes make up site of translation?

A

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

35
Q

what are the names of the subunits for eukaryotic ribosomes?

A

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

36
Q

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

A

two subunits of ribosome are dissocaited

37
Q

HOw fast/accurate is the process of translation?

A

Speed is 2 aa persecond for euk and 20 amino acids/sec for prokayrotes

Accuraty is 1 error/10,000 amino acids

38
Q

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

A

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

39
Q

What doe sthe LSU (large subunit) do?

A

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

40
Q

What are the three binding sites for the tRNA

A

A- binds to incoming Aminoacytl tRNA

P. 0 binds ot the Peptidyl -tRNA

E sites- binds to the Exiting deacylated tRNA

41
Q

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

A

Large sutunit

42
Q

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

A

the 2 rRNA G nucleotides and the 2Cs of CCA

43
Q

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

A

yep

44
Q

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

A

yep

45
Q

All fucntional tRNA molecules have the ….sequence at the 3’ end

A

CCA

CMCB Fall (17 decks)

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