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Flow of genetic information BIOL2010 > protein translation > Flashcards

protein translation Flashcards

1
Q

What is translation?

A

the process of which the genetic message encoded in the sequence of RNA bases of the mRNA is expressed in the form of an amino acid seqeunce in a protein using the 20 amino acids.

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2
Q

what is the general structure of a ribosome?

A

has small and large subunits.
3 sites for tRNA carrying amino acids to occupy.
mRNA slides through a channel which is on the small subunit.

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3
Q

What are the sites on a ribosome?

A

E-P-A.

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4
Q

What is the first step of translation?

A

initiation. uses initiaiton factors (IFs) which position the small ribosomal subunit and first tRNA at the initiation codon.

joining of the large ribosomal subunit makes the whole ribosome. initiation is the slowest step and therefore limits the rate of translation. the point of the most translational control.

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5
Q

What occurs at the elongation step of translation?

A

uses elongation factors (EFs/eEFs) to ensure correct aa is added sequentially to the growing protein chain by pairing tRNA to the mRNA.

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6
Q

What occurs in the termination of translation?

A

uses release factors (RFs/eRFs) which release the complete polypeptide when the stop codon is reached.
No tRNA coresponds to the stop codon so it brings in a factor to release the whole polypeptide.

The ribsomal subunits separate and can be recycled to be used again for another round of translation.

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7
Q

What tRNA binds in the initiation of bacterial protein synthesis at the P site?

A

formylmethionine-tRNA. is special as is the only AA-tRNA to enter ribosome at the P (peptidyl) site.

also binds with the 30S subunit and initation factors 1-3 and GTP.

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8
Q

What initiation factors bind where in bacterial protein translation inititation and what do they do?

A

IF1 binds to A site. prevents elongator tRNA entering.
IF2 binds the GTP and the fMet-tRNA
IF3 prevents association with the 50S to help ensure fidelity of the initiaiton codon.

these give the initiation complex.

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9
Q

how do ribosomes locate the initiation codon in bacterial protein translation?

A

prokaryotic mRNA possess a Shine-Dalgarno sequence that base pairs to the 3’ end of the 16s rRNA. this places the start codon AUG at the ribosome P site about 10 bases 3’ of the S-D sequence.

this is followed by binding of the 50S subunit and dissasociation of IF1 and 3.

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10
Q

how does the 70s ribosome form to get ready for elongation?

A

once the IF1 and 3 dissosocate when the 30s is at the initiation codon there is the binding of the 50s subunit and the hydrolysis of the GTP bound to the IF2 which causes IF2 to also dissasociate. this gives rise to the 70s ribososme for elongation with the first tRNA in the p site and the A site empty ready for the next tRNA.

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11
Q

What is different in eukaryotic mRNA?

A

it has a cap and a poly(A) tail.
no Shine Dalgarno sequence

also 5’ and 3’ UTRs may contain several features that help regulate protein expression/ mRNA stability/localisation.

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12
Q

how does initiation for protein translation occur in eukaryotes?

A

eIF2 + small 40s ribosome subunit + methionyl-tRNA +GTP bind to eachother.

40s binds to mRNA with other initiation factors bound to the cap and polyA tail regions

40s scans the mRNA looking for the AUG start codon.

eIFs dissasociate and then the 60s binds.

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13
Q

what are similar between prokaryotic and eukaryotic protein translation inititation?

A

eIF2 bound to GTP and brings in the first tRNA.

eIF3 and eIF1 ensure accuracy of initiation and prevent association of the 60s large subunit.

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14
Q

what is a chaperone?

A

they prevent illicit liaisons between proteins.

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15
Q

what should happen to malfolded proteins?

A

hopefully rapidly degraded as misfolding in the ER can be a serious problem and PERK exists to couple protein folding to protein synthesis.

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16
Q

What does PERK do?

A

regulates unfolded proteins response. Normally BiP binds to PERK to keep it inactive in a monomeric state.

When ER is under stress BiP dissasociates to bind to unfolded proteins causing PERK dimers to activate.

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17
Q

What is Wolcott Rallison disease?

A

a loss of PERK function. paitents tend to develop T1 diabetes, growth retardation, and multiple other effects.

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18
Q

What does it mean by that the genetic code is degenerative?

A

means that more than one codon may specify a given amino acid. the degeneracy helps allow for silent mutations in DNA/mRNA

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19
Q

What is tRNA

A

transfer RNA. carries the activated amino acid to the ribosome. have a highly conserved tertiary strucutre. the tRNA posesses an anticodon that recognises teh mRNA codon by antiparallel base pairing.

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20
Q

What is BiP

A

a chaperone protein that is usually bound to PERK

21
Q

what is the tRNA strucuture made of?

A

acceptor stem
D loop
anticodon loop
T pseudouridine C loop.

22
Q

what is pseudouridine?

A

an isomer of the nucleoside uridine in which uracil is attached via a carbon carbon bond instead of nitrogen carbon glycosidic bond.

has more possibilities for H bonding and more rigidity.

23
Q

What enzymes are used to ensure amino acids are linked to its corrected tRNA only?

A

acyl-tRNA synthetases

they catalyse the reaction of the terminal adenine ribose with the amino acid carboxyl group.

there are two types of synthetases. class I and II.

24
Q

how is the amino acid activated?

A

its a 2 step process.

  1. amino acid + ATP + enzyme > enzyme-AMP-amino acid + PPi

this is the formation of an activated intermediate. then

  1. enyzme-AMP- amino acid + tRNA > aminoacyl-tRNA + AMP + enzyme.
25
Q

how is amino acid activation proof read?

A

there is the acylation site and hydrolysis site on the enzyme. if a smaller amino acid enters the tRNA synthetase acylation site then it gets misacylated and then enters the second site the hydolysis site and gets hydrolysed. if it is the correct amino acid it wont be able to fit into the hydrolysiss site.

26
Q

in eukaryotes where are ribosomes assembled?

A

In the nucleolus.

27
Q

What subunits are the eukrayotic ribosomes made of??

A

40s and 60s to make 80s.

28
Q

what subunits are the bacterial ribosomes made of?

A

30s and 50s to make 70s.

29
Q

what are key features of the 30s subunit?

A

16S rRNA and proteins S1-S19.
contains a decoding centre
the A and P tRNA binding sites are made by the helix 44 of the 16S rRNA.
3’ of 16S rRNA complements the shine dalgarno.

30
Q

what are key features of the 50s subunit?

A

23S and 5S rRNAs. has proteins L1-L31.
23S rRNA forms 6 domains.
contains a peptidyl transferase centre. (PTC)
contains the peptide Exit tunnel.

31
Q

what is a Ribozyme?

A

an RNA comelcule that is capable of acting as an enzyme.

32
Q

how is the peptide bond formed in the ribosome?

A

the NH of the incoming amino acid which is attached to the tRNA attacks the CO of the growing polypeptide which is still attached to the tRNA. ends up with extended polypeptide.

it is a nucleophillic attack. ester bond between the amino acid and tRNA is broken.

33
Q

what elongation factor aids the binding of the next aminoacyl-tRNA to the A site?

A

EFTu.GTP

34
Q

what occurs to EFTu.GTP when there is the correct codon:anticodon pairing and how is it recycled?

A

if correct anticodon:codon gets hydrolysed to EFTu.GDP.

is recycled by EFTu.GDP + GTP -> EFTu.GTP + GDP

35
Q

why is tRNA always base paired with mRNA?

A

prevents frame-shifting, ensures accuracy, shows why code is read triplet by triplet (need to maintain the triplets or the code will shift)

36
Q

how is misfolding as the peptitide chain leaves the exit tunnel slowed?

A

TF (trigger factor) is a chaperone at the exit tunnel that slows the misfolding and coordinates it.

37
Q

what are the eukaryotic equivalents to EFTu other factors involved?

A

eEF1A is the equivialent to EFTu. aiding binding of aminoacyltRNA to the A site.

eEF1B is the EFTs (GEF for recycling of eFT1A)

eEF2 = EFG. needed for translocation

phosphylation of eEF2 (in response to rise in AMP, rise in Ca2+, reduces elongation rate.

38
Q

how does termination of protein synthesis occur?

A

elongation occurs unitl a termination codon occupies the A site.

ribosome fails to find cognate AA-tRNA.
release factors RF1 or RF2 and RF3 bind ( the RF1/2 mimic tRNA)

the final amino acyl tRNA ester link is hydrolysed by a reaction with H2O and the peptide is released from the ribosome.

mRNA and ribsoomal subunits seperate

RRF recycles the subunits.

39
Q

how does the antibiotics chlormaphenicol, Erythommycin, and tetracycline affect the bacterial ribosome?

A

Chloramphenicol blocks peptidyl transferase
Erythromycin blocks elongation by binding to the 23S rRUAN tunnel
Tetracycline- prevents amino acyl tRNA binding.

40
Q

how does aminoglycoside antibiotics such as streptomycin work?

A

bind to decoding centre and induce errors in translation.

41
Q

what is puromycin?

A

its a cross kingdom antibiotic. it is an analouge of tyrosyl aminoacyl tRNA and causes premature peptide chain termination.

they cna be used as tags to assay protein synthesis.

42
Q

In eukaryotes what recycles the subunits after they seperate from the mRNA?

A

ABCE1.

43
Q

after splicing of exons what is added?

A

Exon junction complex (EJC) is deposited during splicing and is placed 20-24 nucleotides upstream of each splice site. contains various proteins. most important is UPF3.

EJC is swept off after being passed by first ribosome.

44
Q

What is nonsense mRNA?

A

mRNA that has a stop codon more than 50-55 nucleotides upstream from most 3’ exon junctions. these are recognised as premature.

45
Q

when a ribosome cannot reach the EJC (exon junction complex) downstream of premature termination codon what complex is recruited?

A

SURF

SMG1 (kinase)
UPF1 (RNA and atp dependent helicase)
eRFs (translation termination factors)

UPF1 interacts with UPF2 bridging SURF complex to EJC

46
Q

what does the recruitment of the SURF complex do when with the EJC?

A

causes the formation of a DECID complex. causes aberrant termination.

decapping and 5’ to 3’ decay.
enonuclease attack near the PTC (premature termination codon)
deadenylation of the poly-A tail and 3’ to 5’ decay.

47
Q

How is it identified that there is somthing wrong such as no stop codon? and what occurs?

A

when reaches the polyA tail and keeps on going creates a Poly(Lys) nascent chain.

the poly(Lys) chain is identified which lets the ribosome know somthing is wrong so a protein called A site Pelota that recruits the degregation machinery to get rid of the mRNA.

48
Q

What is the purpose of using rare codons for a particular amino acid and what is the issue with using them too frequently.

A

some codons for particular amino acids are more common than others. when a rare one is used it can cause pausing in the translation. this is useful to stop ribosomes from accelerating too quickly at the start of an ORF and give protein enough time to fold.

excessive pausing can cause No Go decay.

Flow of genetic information BIOL2010 (4 decks)

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