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Biomed 2 > Genetic information - Translation > Flashcards

Genetic information - Translation Flashcards

1
Q

what determines the rate of translation

A

initiation
-its the slowest step

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2
Q

what tRNA does bacterial mRNA bind to

A

formylmethionine-tRNAf

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3
Q

what is the function of each initiation factor

A

IF1 - binds in A-site, prevents elongator tRNA from binding
IF2 - binds the GTP and fMet-tRNAf
IF3 - prevents association with the 50s subunit, ensure fidelity of the initiation codon selection
forms the initiation complex

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4
Q

what do prokaryotic mRNA possess to help locate the initiation codon

A

a Shine-Dalgarno sequence that base pairs to the 3’ end of the 16s rRNA

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5
Q

where is the start codon (AUG) placed

A

ribosome P-site
about 10 bases 3’ of the Shine-Dalgarno sequence

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6
Q

what happens after the start codon is placed

A

the 50s subunit binds and IF1/3 dissociate

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7
Q

what is eIF3

A

eukaryotic equivalent to IF3
binds eIF4G and the 40s subunit

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8
Q

outline eukaryotic initiation
(long essay awnser)

A

eIF2 + the small 40S ribosome subunit + methionyl-tRNAimet + GTP bind to each other
The 40S subunit binds to mRNA with other initiation factors (eIFs) bound to the cap and poly A tail regions
The 40S ribosome then “scans” the mRNA looking for the AUG initiation codon: usually uses first AUG it encounters
More efficient if this AUG is within the Kozak Consensus
eIFs then dissociate and the 60S subunit binds
Intact cap and tail regions are essential for initiation

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9
Q

what are the similarities of initiation between eukaryotes and prokaryotes

A

eIF2 bound to GTP and brings in first tRNA
eIF3 and eIF1 ensure accuracy of initiation and prevent association of 60S large subunit

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10
Q

why does 4E-BP’s bind to eIF4E

A

4E-BP has a very similar sequence motif to eIF4E binding site of eIF4G

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11
Q

why does does 4E-BP dissociate with eIF4E

A

4E-BP gets hyperphosphorylated

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12
Q

structure of eIF2 and what part binds GTP where specifically is it phosphorylated

A

alpha, beta and gamma subunit
gamma
Ser 51 on alpha subunit

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13
Q

what are the implications for elF2 when it is phosphorylated

A

it cannot bind GTP

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14
Q

in terms of elF2, outline what happens from the point of stress

A

1 - stress
2 - increase in elF2 kinase
3 - increase in elF2-α phosphorylation
4 - general translation is blocked
5 - paradoxical increase in translation of specific mRNA

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15
Q

what do viral-infected cells produce and what does that induce and what does it cause

A

interferons (IFN)
induces protein kinase R (PKR) in neighbouring cells - anti-viral state
causes reduction in protein synthesis in both host and viral mRNA - prevents further infection

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16
Q

function of chaperones

A

heat shock proteins
prevent illicit liaisons between proteins
(interactions between exposed hycrophobic regions)

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17
Q

what keep PERK inactive

A

BiP binds to PERK and keeps it in an inactive monomeric state

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18
Q

how is PERK activated

A

BiP dissociates to bind to unfolded proteins
activating PERK dimers

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19
Q

what is Walcott-Rallison’s disease

A

recessive
Loss of PERK function – patients develop Type I diabetes, growth retardation, multiple other effects

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20
Q

in terms of a modified base in tRNAPhe, what is the function of pseudouridine

A

has more possibilities for H-bonding (a,d), and more rigidity
Better for stability in tertiary structure and interaction with ribosome

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21
Q

what is step 1 of the amino acid activation process

A

Amino acid + ATP + enzyme ==
= enzyme-AMP-(bond)-amino acid + PPi

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22
Q

step 2 of the amino acid activation process

A

enzyme-AMP—amino acid + tRNA =
= Aminoacyl—tRNA + AMP + enzyme

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23
Q

how much ATP is used during the 2 step process of aa activation and what is their purpose

A

2 ATP is used
the second is used to drive the reaction

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24
Q

what happens if an aa acid that is too large tries binding with an incorrect aminoacyl-tRNA transferase

A

if its too large it wont be able to enter the acylation active site

25
Q

what happens if an aa thats too small tries binding with an incorrect aminoacyl-tRNA transferase

A

it can enter the acylation active site but it also enters the hydrolytic active site
so it gets hydrolysed

26
Q

how does the corresponding aa bind to its aminoacyl-tRNA transferase

A

enters acylation site but cannot enter the hydrolytic site
properly acylated tRNA
properly charged tRNA

27
Q

what plays no role in loading of the correct amino acid onto the tRNA

A

the anti-codon

28
Q

what does tRNA wobble usually involve

A

nucleotides U or inosine (I) at the first position of the anti-codon

29
Q

what is inosine

A

made by deamination of adenine

30
Q

what can I base pair with

A

A, U or C using 2H bonds

31
Q

what are the key features of bacterial 50s ribosome subunit

A

23S and 5S rRNAs + proteins L1– L31
23S rRNA forms 6 domains (I-VI)
Contains the peptidyl transferase centre (PTC)
Contains the peptide exit tunnel

31
Q

what are the key features of the 30s ribosomal subunit of bacteria

A

16S rRNA + proteins S1- S19
Contains the “decoding centre” (DC)
Helix 44 of 16S rRNA forms the A and P tRNA binding sites
3’ of 16S rRNA complements the Shine-Dalgarno

32
Q

what is a ribozyme

A

RNA thats capable of acting as an enzyme

33
Q

what is the evidence to suggest that bacterial ribosomes are ribozymes

A

No ribosomal proteins located in the PTC (peptidyl-transferase centre) – nearest ones are 15-18Å away – too far to take part
Ribosomes that are largely depleted of protein still have peptidyl-transferase activity

34
Q

how is the ester bond broken between amino acid and tRNA

A

nucleophilic attack by amino group of the incoming aminoacyl-tRNA

35
Q

what mutation causes a decrease in the rate of peptide-bond formation

A

Mutation of 2’-OH of A76 of peptidyl-tRNA decreases the rate of peptide bond formation ~million-fold

36
Q

what mutations do not effect the rate peptidyl-transferase reaction and what does this mean

A

mutations of rRNA bases
Therefore ribosome helps to position substrates and water molecules which aids proton transfer and stabilisation of intermediates - basically decreasing necessary activation energy

37
Q

what is the speed and error rate at which ribosomes work

A

10-40aa per second
1 in 10,000 errors

38
Q

why is tRNA always base paired with mRNA

A

prevents frameshifting
ensures accuracy

39
Q

what is trigger factor (TF)

A

coordinates folding/elongation rates

40
Q

purposes of the exit tunnel

A

Nascent chain passes through the ribosome exit tunnel
Protects new chain from inappropriate interactions
Allows it to sample multiple conformations

41
Q

function of chloramphenicol

A

blocks peptidyl transferase

42
Q

function of erthromycin

A

blocks elongation by binding to the 23S rRNA tunnel

43
Q

function of tetracycline

A

prevents amino acyl tRNA binding

44
Q

name two aminoglycoside antibiotics and their function

A

paromomycin
streptomycin
bind to decoding centre (DC) and introduce errors

45
Q

what is puromycin and its functions

A

is an analogue of tyrosyl aminoacyl tRNAtyr and causes premature peptide chain termination - also inhibits protein synthesis in eukaryotes
Can use puromycin analogues as tags to assay protein synthesis

46
Q

what recycles ribosomal subunits

A

ABCE1

47
Q

purpose of mRNA surveillance in terms of nonsense-mediated decay (NMD)

A

mechanism used to detect premature termination codons (PTC) before translation
prevents accumulation of truncated proteins

48
Q

what happens to the pioneer round of translation when it binds to a mRNA with a PTC

A

ribosome does not reach the EJC and cannot displace it

49
Q

where are EJC’s placed on mRNA

A

20-24 nucleotides upstream of each splice site

50
Q

what is considered a PTC

A

Stop codons more than 50-55 nucleotides upstream from most 3’ exon junctions are recognised as premature.

51
Q

what is recruited to a mRNA with a PTC

A

SURF

52
Q

what does SURF contain

A

SMG1 (kinase)
UPF1 (RNA and ATP-dependant helicase)
eRFs (translation termination factors)

53
Q

what brings SURF to the PTC containing mRNA

A

UPF1 interacts with UPF2, bridging SURF complex to EJC

54
Q

function of SMG1

A

Following SURF binding, SMG1 phosphorylates UPF1 and causes dissociation of eukaryotic Release Factors and ribosome.

55
Q

what does phosphorylated UPF1 cause

A

recruits SMG7
decays enzymes

56
Q

what does a SURF + EJC create and cause

A

DECID complex
causes aberrant termination

57
Q

regarding no-go decay (NGD) what happens if the ribosome doesn’t dissociate

A

the reading frame can shift to the +1 frame and then make an aberrant protein

Biomed 2 (18 decks)

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