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Biochem > Translation lecture 2 > Flashcards

Translation lecture 2 Flashcards

1
Q

what is bound to the p site at the initiation of transcription

A

in prokaryotes, methyl-tRNA

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2
Q

what is the sequence of the codon that codes for methonine ? sequence of the complementary anti-codon ?

A

AUG, UAC

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3
Q

whats the second step in the elongation phase ?

A

an aminoacyl-tRNA binds to the A site and a peptide bond is formed

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4
Q

what provides the energy for the formation of the peptide bond ?

A

hydrolysis of the peptidyl-tRNA linkage

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5
Q

when does translation initiation occur in bacteria

A

as soon as the 5’ end of the mRNA is synthesised. transcription is coupled with translation in prokaryotes

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6
Q

how can large mRNA molecules be translated simultaneously >

A

by polyribosomes or polysomes

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7
Q

describe the elongation phase

A
  1. aminoacyl-tRNA is positioned in the A site
  2. following the synthesis of the peptide bond, the newly formed peptide-tRNA is partly in the A site and partly in the P site
  3. translocation shifts the peptide-tRNA completely into the P site, leaving the A site empty and ejecting the deamino-acylated tRNA from the E site.
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8
Q

what are the three release factors in e.coli ? are they proteins

A

yes, RF1 and RF2 - bind to stop codons in the A site.
RF3-GTP - enhances effect of RF1 and RF2. proofreads to ensure stop codon was correctly recongised and stimulates release of RF1 and RF2
these release factors mimic the tRNA.

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9
Q

does the polypeptide grow from the c terminus to the n terminus

A

no its the opposite

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10
Q

what are the three termination codons ?

A

UGA, UAG or UAA

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11
Q

how is the polypeptide hydrolysed in prokaryotes ?

A

when the release factors recognise a termination codon, they cause hydrolysis of the peptide-tRNA. Release of the completed polypeptide is probably accompanied by GTP hydrolysis, providing energy for dissociation of the release factors from the ribosome.

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12
Q

what is the name of the elongation factor that docks an aminoacyl-tRNA in the A site

A

EF-Tu-GTP. Hydrolysis, release of factor, aminoacyl-tRNA remains in the A site where it is positioned for peptide bond formation. elongation factors maintain the processtivity .

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13
Q

what are the two subunits of prokaryotic ribosomes ?

A

50s + 30s to give 70s

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14
Q

what are the two subunits of eukaryotic ribosomes ?

A

60s and 40s to give 80s non-linear scale based on centrifugation

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15
Q

what catalyses peptide bond formation

A

peptide transferase, this enzymatic activity is localised in the large ribosomal subunit

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16
Q

what does peptide bond formation involve ?

A

physically transferring the polypeptide attached to the p site tRNA onto the amino terminus of the amonoacyl-tRNA bound in the ribosome’s A site

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17
Q

what are the three steps in the chain elongation microcycle ?

A
  1. elongation factors dock an aminoacyl-tRNA in the A site
  2. peptide transferase catalyses peptide bond formation
  3. translocation moves the ribosome by one codon
18
Q

describe the ribosome

A

nucleic acids buried in the inside of the ribosome where catalytic activity is localised. alpha helices on the outside surface

19
Q

describe the function of the initiation factors 1A and 3 in eukaryotes

A

1A blocks the A site
1 and 3 block the E site stoping large subunit from binding
P site is left vacant - only site that can be occupied

20
Q

describe mRNA in eukaryotes

A

5’ end is capped. 3’ end is polyadenylated. secondary structure of mRNA is regulatory of translation.

21
Q

function of eIF2-GTP.

A

eIF2 is a GTPase. binds to Met-tRNA to form a ternary complex. the complex then binds to the vacant p site. The binding isn’t finalised. remember the other two sites are blocked. - a 43s preintiation complex is formed.

22
Q

components of eIF4 complex

A

subunits 4E, 4G, 4A and 4B

23
Q

role of subunit 4e of eIF4 complex

A

recognises the 5’ end methyl cap

24
Q

role of subunit 4b, 4a of eIF4 complex

A

4a is a helicase. 4b has hydrolytic capacity for ATP to ADP. can also stimulate and activate the helicase.

25
Q

role of subunit 4g of eIF4 complex

A

binds the poly A tail which is at the 3’ end of the mRNA and circularises the mRNA

26
Q

in eukaryotes, how does the mRNA bind to the preintiation complex

A

the mRNA attaches to the ribosome by binding to eIF3 and 5

27
Q

in eukaryotes, small subunit is bound to the mRNA at the..

A

5’ end not at the AUG codon

28
Q

give an overview of the initiation of translation in eukaryotes . first 4 steps.

A
  1. eIF2 forms ternary complex with tRNA
  2. 43s preintiation complex is formed, 1,3,5 block e site, 1A blocks A site
  3. mRNA is activated by binding of the eIF4 complex to mRNA. This step is coupled to ATP hydrolysis.
  4. mRNA attaches to the ribosome by binding to eIF3 and 5.
29
Q

give an overview of the initiation of translation in eukaryotes . part 2

A
  1. complex translocates along the mRNA from 5’ to 3’ scanning for the initiation codon. The helicase unwinds the the secondary structure of mRNA. the 4e subunit remains bound to the methyl cap
  2. initiation codon recognition, hydrolysis of eIF2-bound GTP and release of Pi. This secures the base pairing between the initiation codon and the anticodon. the initiation codon is positioned in the p site, where it interacts with Met-tRNA. 48s initiation complex is now formed. NOTE the 43s preintiaiton complex is assembled at the 5’ end.
  3. the 60s ribosomal subunit binds to complete the 80s initiation complex and all the initiation factors except 1A dissociate. The dissociation of eIF-2 is accompanied by GTP hydrolysis.
  4. 5B-GTP binds to the A site. the 5B subunit hydrolyses its GTP releasing the two initiation factors. The 80s initiation complex is now assembled.
30
Q

give an overview of the initiation of translation in eukaryotes . part 3

A
  1. the 60s ribosomal subunit binds to complete the 80s initiation complex and all the initiation factors except 1A dissociate. The dissociation of eIF-2 is accompanied by GTP hydrolysis.
  2. 5B-GTP binds to the A site. the 5B subunit hydrolyses its GTP releasing the two initiation factors. The 80s initiation complex is now assembled.
31
Q

initiation complex in eukaryotes recognises..

A

the kozak sequence. AUG is part of that specific sequence. the first AUG sequence usually serves as the initiation codon.

32
Q

give one difference between mRNA in eukaryotes and mRNA in prokaryotes

A

mRNA is polycistronic in prokaryotes, while mRNA molecules in eukaryotes usually encodes only a single polypeptide.

33
Q

what are the three elongation factors that participate in chain elongation in eukaryotes ?

A

EF-1alpha, EF-1beta, and EF2

34
Q

what are the three elongation factors that participate in chain elongation in prokaryotes ?

A

EF-Tu, EF-T, EF-G . EF-Tu and EF-G are GTPases.

35
Q

what is the role of EF-1alpha . ELONGATION FACTOR

A

its activity parallels that of EF-Tu of E.coli; it forms a GTP complex and docks the aminoacyl-tRNA in the A site. If the correct base pairs are formed, the GTP is hydrolysed causing a conformational change in the ribosome, positioning the polypeptide in close proximity with the next amino acid. see diagram for clarification

36
Q

what is the role of EF-1beta . ELONGATION FACTOR

A

acts like EF-Ts, recycling EF-1alpha by exchanging GDP bound to the elongation factor for GTP.

37
Q

what is the role of EF2-GTP. ELONGATION FACTOR

A

activity is similar to that of EF-G, carrying out translocation. EF-G and EF-2 both form complexes with GTP. Translocation is coupled to the hydrolysis of the GTP to GDP.

38
Q

initially, at the very beginning, the growing peptide is in the..

A

A site

39
Q

what are the two termination factors in eukaryotes ?

A

eRF1 and eRF3-GTP.

40
Q

what is the role of eRF1 ?

A

recognises and bind to the stop codon.

41
Q

what is the role of eRF3-GTP ?

A

proofreads that the correct base pairs have been formed.

42
Q

how is the polypeptide released in eukaryotes ?

A

when the release factors recognise a termination codon, they cause hydrolysis of the peptide-tRNA. Release of the completed polypeptide is probably accompanied by GTP hydrolysis. ABCE1 hydrolyses ATP to ADP, providing energy for dissociation of the release factors from the ribosome.

Biochem (7 decks)

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