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molekylær biologi > chapter 31 protein synthesis > Flashcards

chapter 31 protein synthesis Flashcards

1
Q

which error frequency is intolerable

A

10^-2

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2
Q

the error frequency must not exceed 10^-4 to effectively produce large proteins

A

10^-4

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3
Q

where are amino acids attached in tRNAs

A

to 3’ end to 3’ hydroxyl group of an adenosin

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4
Q

why are certain bases unusually methylated in tRNAs

A

so that they don’t form base pairs and to be accessible for other interaction.
The methylations also give a hydrophobic character that can be used when interacting with certain proteins

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5
Q

about ….. of the bases are paired in tRNAs

A

50 %

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6
Q

tRNA which form of helix does it have

A

A form

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7
Q

Components of tRNA

A 
5-phosphorylated terminus 
DHU loop (dihydrouracil)
anticodon loop 
extra arm variable loop 
Tpsi C loop (ribothymine pseudouracil-cystosine)
CCA arm
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8
Q

what is I in anticodons

A

purine base inosin

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9
Q

How is inosin formed

A

deamination of adenosine after the synthesis of the primary transcript

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10
Q

what checks if the codon-anticodon duplex is correct in bacteria

A

the 30s subunit with 16s that form hydrogen bonds with the first two correct nucleotides in the anticodon but not with the wrong ones

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11
Q

why must aminoacids be activated

A

because peptide formation between free aminoacids is not thermodynamically favourable

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12
Q

where are ATPs consumed when activating aminoacids

A

the first one is in the formation of ester bond in aminoacyl-tRNA and the other is considered in driving the reaction forward

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13
Q

how do aminacyl-tRNA synthetases correctly remove or accept the correct amino acid?

A

through acylation sites rejecting ones that are larger than the correct one
hydrolytic sites
cleaving ones that are smaller than wanted

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14
Q

Which parts of tRNAs interact extensively with amino-acyl synthetase

A

acceptor stem and anticodon loop

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15
Q

How many classes of synthetases and the differences?

A

1- CCA is helical in II and hair pin in I
2- I 2’ and II 3’
3- bind ATP in different conformations
4- I monomeric and II dimeric

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16
Q

which subunit is mRNA being translated bound to in bacteria ? what about tRNA?

A

30s subunit
in contact with both
30s and 50s

17
Q

the consensus of shine dalgarno sequence in prokaryotes

A

AGGAGG

18
Q

Factors determining the start of protein synthesis

A

pairing of 3’ of 16s to initiation sites

pairing of anticodon to codon

19
Q

initiation codons for bacteria

A

AUG GUG UUG

20
Q

which tRNA initiates protein synthesis in bacteria

A

tRNAf with N-formylmethionine

21
Q

when is N-formylmethionine removed

A

when 10 aminoacids have been synthesized

22
Q

What enzyme formylates methionin

A

transformylase

23
Q

what is the rate limiting step in protein synthesis in bacteria

A

the formation of 70s initiation complex

24
Q

what is the highly conserved site that interacts with EF-TU in subunit 50s is called? function?

A

sarcin ricin loop interacts with EF-Tu complex and causes the hydrolysis of its GTP releasing EF-Tu-GDP

25
Q

what is accomodation in protein synthesis in bacteria

A

when structural changes happen moving the aminoacyl-tRNA closer to p-site in subunit 50s

26
Q

which factor recognises and interacts with tRNAf

A

IF2

27
Q

polyribosome /polysome

A

Multiple ribosomes translating an mRNA simultaneously

28
Q

tRNAs and stop codons?

A

They don’t exist

29
Q

what recognises stop codons

A

RFs

30
Q

RF1 and RF2 and RF3

A

RF 1 : UAA UAG
RF2 : UAA UGA
RF3: removes the other ones when the protein synthesized is released

31
Q

what does RFs interact with and how?

A

The peptidyl transferase center on the 50s subunit using a highly conserved loop containing GGQ with glutamine being methylated
promoting water molecule attacks on the ester linkage between tRNA and the polypeptide chain

32
Q

How is the 70s complex entirely dissociated

A

through the hydrolysiss of GTP by binding to EF-G and RRF (ribosome release factor)

33
Q

the initiation factor in eukaryotes?

A

eIFs

34
Q

when are internal ribosome entry sites are used? The function ?

A

when there are no 5’caps. They faciltate the association of subunit 40s to mRNA

35
Q

the eukaryotic counterparts of elongation factors in eukaryotes
EF-G
release factors

A

EF1alpha
EF1Betagamme EF1By
EF2
eRF1 and eRF3 to accelerate the activity of eRF1

36
Q

antibiotics that inhibit protein synthesis in eukaryotes?

and how do they operate and what do they affect?

A

ricin a-sarcin and diptheria
they all inhibit elongation
ricin and a-sarcin covalently modify rRNA and diptheria covalently modify the elongation factor EF2

37
Q

secretory pathway

A

cotranslation of a protein directed towards the endoplasmic reticulum

38
Q

a ribosome in eukaryotes remain free in …… unless directed to the …..ER

A

cytoplasm, ER

39
Q

the components of translocation across endoplasmic reticulum

A

1- signal sequence

2- signal recognition particle (SRP)

3- SRP receptor (SR)

4- Translocon

molekylær biologi (14 decks)

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