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BIOL2010 - Flow of Genetic Information > Translation > Flashcards

Translation Flashcards

1
Q

Define translation?

A

Process by which the genetic message, encoded by RNA bases, is expressed in the form of an amino acid sequence in a protein using the 20 amino acids

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2
Q

What is required for protein synthesis

A 
template - mRNA
building blocks - amino acids
a way to assemble a chain - ribosomes
rules on decoding - aminoacyl tRNAs
energy - ATP x 4 for aa
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3
Q

Outline ribosome structure?

A

Small and large subunits need to join together to form 3 sites for tRNA to occupy.
mRNA slides through a channel which is on small subunit.
Composed of rRNA and proteins.
Ribozyme.

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4
Q

Outline translation initiation?

A

Initation factors - pro IFs euk eIFs
Positioning of the small ribosomal subunit and first aminoacyl tRNA at the initiation codon.
Join large subunit
Slowest step - limits rate of translation

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5
Q

Outline translation elongation?

A

Brings the next tRNA, joins together. Expels first tRNA, cycle repeats.

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6
Q

How fast is translation?

A

10-40 aa s-1

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7
Q

error rate of translation?

A

1 in 10,000

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8
Q

Outline translation termination?

A

Release factors - pro RFs euk eRFs
Release the completed polypeptide when stop codon is reached - no tRNA corresponding to the stop codon
Brings in a factor to release the completed polypeptide

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9
Q

What factors release the completed polypeptide?

A

pro RRF

euk ABCE1

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10
Q

prokaryote ribosomal subunits?

A

30S, 50S = 70S

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11
Q

How is the prokaryotic initiation complex formed?

A

30S subunit binds to mRNA (binds a special formylmethionine tRNA) at the P site using initiation factors IF1, IF2, IF3 and GTP

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12
Q

IF1?

A

binds in A site, prevents elongator tRNAs from entering

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13
Q

IF2?

A

binds GTP and fMet-tRNA

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14
Q

IF3?

A

prevents association with the 50S, ensuring fidelity of the initiation codon selection

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15
Q

what is the Shine Dalgarno sequence?

A

on prokayotic mRNA.

base pairs to the 3’ end of 16S rRNA. Places the start codon (AUG) at the P site, about 10 bases 3’ of the S-D sequence

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16
Q

what does the Shine Dalgarno sequence allow?

A

the ribsomal subunit can stay attached and look for next sequence in polycistronic mRNAs

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17
Q

what follows the binding of Shine Dalgarno sequence?

A

followed by binding of 50S subunit and dissociation of IF1 and IF3. binding causes hydrolysis of the GTP on IF2, causing it to also dissociate.

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18
Q

differences in eukaryotic mRNA for initation?

A

a cap and poly(A) tail

no S-D sequence

5’ and 3’ UTRs contain several sequences that help regulate protein expression/mRNA stability & localisation

mRNA is circularised

complexity adds several opportunities for control

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19
Q

what is eIF3?

A

binds to the cap effectively

binds eIF4G (which is cap bound) and 40S subunit

13 subunits

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20
Q

what is eIF4G?

A

acts as a link between poly(A) binding protein (PABP) and the cap binding protein

21
Q

stages of eukaryotic initiation?

A

eIF2 + 40S + met-tRNA + GTP bind

40S binds to mRNA with other eIFs which are bound to cap and poly(A) tail

40S scans the mRNA looking for AUG codon

22
Q

what makes codon searching more efficient?

A

If its within Kozak Consensus

23
Q

what happens after codon is found?

A

eIFs dissociate and 60S subunit binds

24
Q

initiation similarities?

A

eIF2 is bound to GTP and brings in first tRNA

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

25
Q

when is most protein produced?

A

when both a cap and tail are on the mRNA

more than cap + tail so must be synergism

makes it circularised so easier for ribosome to find the mRNA again

26
Q

control of eIF4E availability?

A

4E-4G interaction is required to allow the ribosome to attach to mRNA

4E-BP1 has a similar sequence motif to the eIF4G.

If lots of growth and nutrition factors –> mTORC1 (kinase) is active so can phosphorylate 4E-BP1 so can’t bind to 4E

27
Q

control of eIF2 availability?

A

Brings in tRNA. Key control point.

When translation is initiated, GTP –> GDP + Pi. eIF2B phosphorylates the GDP back to GTP.

When there are stresses on the cell, eIF2B gets blocked. Kinase gets activated and phosphorylates the alpha. stops translation

28
Q

activation of PKR?

A

Virus infected cells release interferon. Induced PKR expression in neighbouring cells.

PKR = Protein Kinase RNA dependent

When PKR is expressed, dsRNA is expressed. PKR dimer autophosphorylates and then phosphorylates eIF2a. Reduces protein synthesis, reducing further infection

29
Q

protein folding?

A

some proteins require assistance from chaperone. Prevent illicit liasions between proteins.

Misfolded are rapidly degraded.

PERK sits on ER and connects to cytoplasm. Can block protein processing.

Normally BiP binds to PERK, keeping it in an inactive monomeric state. BiP dissociates and binds to unfolded proteins which activates PERK dimers. Inhibits translation until the folding issue is sorted.

30
Q

Wolcott Rallison disease?

A

loss of PERK function

31
Q

codon usage bias?

A

preference to decode certain codons

32
Q

how could you make bacteria more effective at producing human proteins?

A

tweak the codons in the transformed DNA so the codons are what the bacteria prefers

could introduce human tRNAs into the bacteria

33
Q

describe the adapter molecule?

A

tRNA
70-90 bases
L shape

3’ terminus ends in CCA with each amino acid linked as an ester to 3’OH

anticodon that recognises the codon through antiparallel base pairing

34
Q

wobble?

A

ability of the first base of an anticodon to base pair with more than one codon.

allows an aminoacyl-tRNA to dock with more than one codon

35
Q

what can U bind with?

A

G

36
Q

what can inosine bind with?

A

A, U or C

looks like guanosine without an amino group but is made by deamination of adenine

37
Q

which direction are proteins synthesised in?

A

amino –> carboxyl

38
Q

features of 30S subunit?

A

16S rRNA and proteins S1-19

Contains decoding centre.

Helix 44 of rRNA forms A and P tRNA binding sites

3’ of rRNA complements the Shine Dalgarno sequence

39
Q

features of 50S subunit?

A

23S rRNA (forms 6 domains) and 5S rRNA and proteins L1-31

Contains peptidyl transferase centre and exit tunnel

40
Q

A site?

A

aminoacyl-tRNA

41
Q

P site?

A

peptidyl-tRNA

42
Q

E site?

A

deacylated tRNA

43
Q

how is peptide bond created?

A

NH of incoming amino acid (tRNA) to attack CO on the growing polypeptide which is also still attached to tRNA

have to break the ester bond between the amino acid and tRNA. Nucleophilic attack by the amino group of incoming aminoacylated tRNA

tRNAs do the attacking and formation

44
Q

how do ribosomes work?

A

decrease the activation energy needed for peptide bond formation, don’t work by chemical catalysis

45
Q

EFTu?

A

Aids aminoacyl tRNA binding. If correct then GTP is hydrolysed

46
Q

EFTs?

A

GEF that recycles EFTu.GDP to EFTu.GTP

47
Q

EFG?

A

Drives translocation step, requires GTP hydrolysis

48
Q

Ribosome exit tunnel?

A

Protects new chain from inappropriate interactions, can sample multiple conformations

BIOL2010 - Flow of Genetic Information (4 decks)

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