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BCH311 > Translation > Flashcards

Translation Flashcards

1
Q

Three sites present in ribosome

A

A site (aminoacyl)
P site (peptidyl)
E site (exit)

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2
Q

What does A site stand for?

A

aminoacyl

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3
Q

What does P site stand for

A

peptidyl

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4
Q

What does E site stand for?

A

exit

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5
Q

Function of small ribosomal subunit

A

interact with mRNA

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6
Q

Function of large ribosomal subunit

A

catalyze peptide bond formation

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7
Q

What are synonyms in genetic code?

A

codons specifying the same aa

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8
Q

Featurs of most synonyms

A

different in the last base of triplet

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9
Q

Who got the nobel prize for elucidating the genetic code?

A

R. Holley
G. Khorana
M. Nirenberg

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10
Q

How did ppl elucidate the genetic code?

A

first made UCC –> Phe,
then tested out other codons

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11
Q

how many stop codons are there?

A

3 (UAA, UAG, UGA)

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12
Q

Most synoyms present for one aa

A

6 for both serine and leucine

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13
Q

What enzymes are invovled in forming aminoacyl-tRNA from tRNA?

A

Aminoacyl-tRNA synthetase

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14
Q

least synoyms present for one aa

A

Met, Trp

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15
Q

What direction does polypeptide growth occur?

A

from N to C terminal

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16
Q

chemicals needed for aminoacyl-tRNA formation (generic sense)?

A

i) ATP (power source for reaction)
ii) Mg2+
iii) tRNA

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17
Q

Function of methylation in tRNA structure or function

A

i) prevent base pairing from happening
ii) provide hydrophobicity for interacting with synthetase

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18
Q

Structural features of tRNA

A

i) L-shaped
ii) CCA extend from one end of L-shape
iii) anticodon loop at the other end of L-shape
iv) bases in non-helical regions participate in H bond interactions

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19
Q

Which bases pariticipate in H bond interactions in tRNA?

A

non helical regions

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20
Q

What powers the formation of aminoacyl-tRNA?

A

ATP hydrolysis

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21
Q

Steps in synthesis of aminoacyl tRNA with class I synthetases

A

i) 2’OH of AMP on tRNA attack carboxyl group on aa
–> Class I aminoacyl tRNA synthetase
ii) AMP released, forming 2’O aminoacyl tRNA (aa linked to 2’OH of tRNA)
iii) carboxyl on aa attack 3’OH on tRNA
–>3’O aminoacyl tRNA

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22
Q

What happens in transesterification step for class I aminoacyl tRNA synthetase?

A

carboxyl group of aa attack 3’OH on tRNA
–> now aa connected to 3’OH of tRNA

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23
Q

Difference between class I and class II aminoacyl tRNA synthetase

A

i) only class I has transesterification rxn
ii) in class I, 1st nucleophilic attack from 2’OH of tRNA
in class II, 1st nucleophilic attack from 3’OH of tRNA
iii) Class I bind to front of tRNA, while class II binds to the side of tRNA
iv) Class I is monomeric, class II is dimeric

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24
Q

How much ATPs are needed for making one aminoacyl-tRNA?

A

one ATP for synthetase
one for regenerating AMP to ADP
(ATP +AMP –> 2 ADP)

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25
Q

Similarities between class I and class II aminoacyl tRNA synthetase

A

i) AMP released
ii) final product is 3’-O aminoacyl-tRNA
iii) use nucleophilic attacks to connect aa to tRNA

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26
Q

nonmenclature for aminoacyl-tRNA synthetase

A

add certain aa to tRNA
(e.g. Threonyl-tRNA synthetase)

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27
Q

Naming for aminoacyl tRNA

A

for alanine
Alanyl-tRNA or tRNA^Ala

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28
Q

Naming for wrong aa incorporation into tRNA

A

e.g. serine added to tRNA for ala
Y-tRNA^Ala or Serinyl-tRNA^Ala

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29
Q

What lower the chances of valine incorrectly incorporating into tRNA^Thr?

A

H bond forming between OH of Thr and Asp
–> valine cannot form H bond with methyl grp

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30
Q

How does cells remove Serinyl-tRNA^Thr?

A

with help of aaRS, which recognizes it and hydrolyzes
–> ignores Threonyl-tRNA^Thr

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31
Q

How does aminoacylation proofreading work?

A

it accepts smaller aa in editing site
–> then hydrolyze them

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32
Q

How does tRNA move from synthetic domain to editing domain on synthetase?

A

similar to how DNA polymerase did
–> without dissociation from synthetase, moving to editing domain

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33
Q

What does activation site (synthesis) of aminoacyl synthetase select for?

A

rejects large aa like Tyr and Phe, accepting activation sites

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34
Q

Unique feature of Thr-tRNA synthetase?

A

zinc that coordinates with Thr recognition

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35
Q

How does zinc interacts with theronine in Thr-tRNA synthetase?

A

amino grp and OH grp

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36
Q

important residues within Thr-aminoacyl synthetase that help with recognition

A

i) His *2
ii) Asp (interact with OH to form H bond)
iii) Cys

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37
Q

How to identify nucleotides important for aminoacylation specificity in tRNA?

A

conducting mutation studies
–> see if specificity constant (kcat//Km) is reduced–> efficiency of synthetase

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38
Q

important regions in tRNA^Asp for recongition by synthetase?

A

i) acceptor stem
ii) anticodon (rlly important)
iii) D loop

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39
Q

What region is used for recongition by alanyl-tRNA synthetase?

A

G:U at the microhelix region
–> not including the anticodon region

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40
Q

Regions that are recognized by all tRNA synthetases?

A

nope
anticodon not always recognized (e.g. in alanyl-tRNA synthetase)

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41
Q

What supported the finding of anticodon not needed for recognition of tRNA^Ala?

A

Did a mutation study on tRNA^Cys on 3:70 to G:U
–> able to recognize as tRNA^Ala

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42
Q

Differences between binding configuration of class I and II tRNA synthetases?

A

Class I bind to the front
Class II binds to the side

43
Q

Crucial step before aa can be incorporated into the correct tRNA

A

aa is first adenylated

44
Q

Structural differences between class I and II tRNA synthetases

A

class I: monomer
class II: dimer

45
Q

What are isoacceptor tRNAs?

A

diff. tRNAs that attach to the same aa
–> tRNA with different anticodons but code for same aa

46
Q

Difference between prokaryotic and eukaryotic ribosomes

A

i) size: prokaryote – 70S, eukaryote – 80S
ii) more proteins attached to each subunit in eukaryotes
iii) smaller subunit: 30S in pro, 40S in eu
iv) larger subunit: 23S rRNA in pro, 5.8, 28S rRNA in eu

47
Q

Where does ribosome function as polysome?

A

both prokaryotes and eukaryotes

48
Q

What does prokaryotic ribsome recognizes?

A

Shine-dalgarno sequences

49
Q

Which region recognizes the shine dalgarno sequence?

A

3’ end of 16S rRNA

50
Q

Features of shine dalgarno sequence

A

purine rich

51
Q

Features for initial tRNA in prokaryotes targeting Met

A

i) has formyl grp attached

52
Q

What helps with transformylation of methionyl-tRNAi ^ fMet?

A

Met-tRNA fMet i formyl transferase

53
Q

What is prokaryotic ribosome made of?

A

50S and 30S subunit

54
Q

Which site does the initiator tRNA in prokaryotes enter?

A

P site

55
Q

Major steps in prokaryotic translation

A

i) initiator tRNA connected to Met enter P site, then another tRNA enters A site
ii)peptide bond formed
iii) translocation to next site is driven by GTP hydrolysis
–> help from elongation factor G
iv) tRNA at E site leaves ribosome

56
Q

Function of elongation factor G

A

help catalyze translocation of mRNA and ribosome in prokaryotes

57
Q

What determines the protein sequence?

A

mRNA sequence
–> nothing to do with aa on tRNA

58
Q

Who proposed the wobble hypothesis for codon:anticodon pairing?

A

Francis Crick

59
Q

What base in anticodon can pair with the most codons?

A

Inosine –> U,C,A

60
Q

what base can inosine pair with in codon?

A

U,C,A

61
Q

What base in anticodon can pair with the least codons?

A

A,C
–> can only do Watson crick pairing

62
Q

Residues responsible for checking base pairing between codon and anticodon

A

A1493,A1492
G530
–> form H bond with them

63
Q

Why only the third position in codon can do wobble pairing?

A

no residues in ribosome to check codon:anticodon pairing
–> more flexibility

64
Q

What happens if codon:anticodon pairing is wrong in first two positions of codon?

A

unable to form H bonds with residues
–> leave the ribosome

65
Q

Where does IF1 bind to?

A

near A site on 30S subunit in prokaryotes

66
Q

Function of IF-3 in translation

A

prevents premature binding of 50S

67
Q

Function of IF-2

A

associates with tRNAfMet
–> GTP bound
Stimulates association of 50S to complex

68
Q

How does translation initiation occur in prokaryotes?

A

i) IF-3, IF-1 binds to 30S subunit, prevent 50S from binding
ii) GTP bound- IF2 binds to initiator tRNA for Met
iii) brings it to mRNA with shine dalgarno sequence
iv) with GTP hydrolysis, IFs dissociates form complex and 50S binds

69
Q

Function of IF-1

A

Direct IF-2 bound initiator tRNA to P site

70
Q

What are the targets for EF-Tu?

A

any aminoacyl-tRNA with correct codon:anticodon pairing
–> excluding fMet-tRNAf

71
Q

Function of EF-Tu

A

i) protects ester linkage in tRNA from hydrolysis
ii) bring aminoacyl tRNA to A site of ribosome

72
Q

Why GTP hydrolysis is needed after EF-Tu binds aminoacyl tRNA?

A

as a confirmation for the correct codon:anticodon pairing

73
Q

Function of EF-T

A

help regenerate EF-Tu that is bound to GTP, instead of GDP

74
Q

How is EF-Tu regenerated?

A

i)EF-Tu with GDP is replaced with EF-T that removes GDP
ii) GTP joins in and EF-T leaves EF-Tu

75
Q

How does translocation occur in prokaryotes?

A

i) GTP bound EF-G bind to 50S
ii) GTP hydrolysis lead to conformational change in EF-G
iii) causes mRNA and tRNA to move by one codon
iv) EF-G dissociates to allow ribosome to accept another aminoacyl tRNA

76
Q

Where does EF-G bind to prokaryotes?

A

A site of 50S ribosome

77
Q

Function of RF-3 in prokaryotes

A

mediate interaction between RF-1, RF02 and ribosome

78
Q

What compounds have similar structure to EF-G with tRNA?

A

EF-Tu binding to aminoacyl tRNA

79
Q

What recognizes stop codons?

A

release factors (RFs)

80
Q

Function of RF-1 in prokaryotes

A

recognizes UAA, UAG

81
Q

Function of RF-2 in prokaryotes

A

recognizes UAA, UGA

82
Q

which RFs are GTP-bound?

A

RF-3

83
Q

How does termination occur in prokaryotes?

A

i) Once stop codon is at A site, GTP-bound RF-3 with RF-1/2 binds at A site
ii) H2O from RF led to hydrolysis of ester linkage in polypeptide chain
iii) GTP hydrolysis of RF3 + GTP-RRF
–> ribosomal complex dissociates

84
Q

What proteins are GTP bound within prokaryotic translation?

A

IF2, EF-Tu, EF-G
RF-3, RRF (ribosomal release factor)

85
Q

What does eIF4E bind to?

A

methyl cap

86
Q

Function of eIF2

A

similar to IF2, it binds to initiator tRNA and 60s ribosome

87
Q

Steps for eukaryotic translation

A

i) eIF4E in eIF4F complex bind methyl cap
ii) 43S ribosome complex (initiator tRNA, GTP-eIF2, 40S subunit) joins eIF4F complex
iii) starts to scan for start codon (AUG) with help of ATP hydrolysis
iv) 60S subunit joins in with eIF5B
+ all other eIFs dissociated
v)80S ribosome complex formed

88
Q

Function of eIF3

A

i) prevents 60S recruited in absence of initiation complex
ii) promote initiator tRNA and mRNA binding

89
Q

what binds to poly A tail?

A

PABP (poly A binding protein)

90
Q

Translocation part of eukaryotes

A

i) instead of EF-Tu, EF1alpha brings in aminoacyl tRNA plus GTP to A site
ii) EF1alpha is regenerated with help of EF1betagamma
iii) mRNA and tRNA moves with help of EF2 (similar to EF-G)

91
Q

Function of EF1alpha

A

brings in aminoacyl tRNA plus GTP to A site

92
Q

Function of EF1betagamma

A

regenerates EF1alpha

93
Q

Function of EF2

A

mRNA and tRNA moves by one codon

94
Q

Termination of eukaryotes

A

carried out by one RF, which recognizes stop codon
–> hydrolysis removes polypeptide chain from ribosome
—>GTP hydrolysis lead to dissociation of ribosomal complex

95
Q

How does puromycin interrupts with translation?

A

act as analog of aminoacyl tRNA
–> lead to pre-mature termination

96
Q

In what organisms is puromycin effective in?

A

prokaryotes and eukaryotes

97
Q

Why does puromycin lead to pre-mature termination?

A

NH2 in puromycin attackes carboxyl grp in aa of P site
–> forms a peptide bond + cannot carry out nucleophilic attack at 3’OH

– later dissociates

98
Q

How does streptomycin interupts translation?

A

inhibits intiation in prokaryotes with the highly basic properties

99
Q

In what organisms is streptomycin effective in?

A

prokaryotes

100
Q

Function of B fragment in diptheria toxin

A

allow A to enter cytoplasm of cells

101
Q

Function of A fragment in diptheria toxin

A

catalyze covalent modifications

102
Q

How does diptheria toxin stops translation?

A

i) first cleaved into A and B after entry
ii) A catalyzes covalent modification with NAD+
iii)this blocks EF2 function, stops protein synthesis

103
Q

How does ricin stop translation?

A

A chai removes a conserved residue (A4324) in 28SrRNA
–> doesn’t allow EF to bind

103
Q

configuration of ricin

A

heterodimeric A and B
–> A is catalyic

BCH311 (4 decks)

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