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MOLBIO > PHILLIPS CH11 > Flashcards

PHILLIPS CH11 Flashcards

(68 cards)

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1
Q

anticodon

A

on tRNA

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2
Q

codon

A

on mRNA

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3
Q

aminoacyl-tRNA synthetase

A

attach amino acids to tRNA (require ATP)
recognize both AA and rRNA, one for each AA

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4
Q

2 subunits of ribosomes

A

small subunit deciphers mRNA
large subunit mediates chemical bond formations

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5
Q

rate of protein synthesis

A

15 AAs

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6
Q

translation factors

A

often GTPases, associate with ribosomes and help with translation

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7
Q

4 regions of tRNA structure

A

acceptor stem and 3 stem-loops (D-loop, T-loop, anticodon loop)

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8
Q

D-loop

A

contains dihydrouridine (D)

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9
Q

T-loop

A

contains ribothymidine (T) and pseudouridine

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10
Q

anticodon loop

A

contains a hypermodified purine (H) after the anticodon to prevent this from base-pairing with mRNA codon

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11
Q

acceptor stem

A

5’ and 3’ ends base pair, 3’ CCA tail binds the AA

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12
Q

draw structures of dihydrouridine, pseudouridine, inosine

A

see notes

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13
Q

discovery of triplet code

A

three insertions or three deletions restores function

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14
Q

number of codons

A

61 sense codons (AA)
3 antisense codons (stop/nonsense - end of protein)

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15
Q

wobble pairing

A

non Watson-Crick base pairing
can occur on the third position of codon
(e.g. UUC and UUU can pair with AAG)
each codon does not need own tRNA

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16
Q

isoacceptors

A

different tRNAs that carry the same amino acids

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17
Q

how do aminoacyl-tRNA synthetases recognize tRNAs?

A

by sequence and structural features called identity elements, often found n anticodon loop or acceptor stem

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18
Q

EFTu

A

protect highly-reactive aminoacyl-tRNAs and deliver to ribosome A site

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19
Q

size exclusion

A

keeps non-cognate AAs that are too big out of the aminoacylation site

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20
Q

editing site

A

site on aminoacyl-tRNA synthetase that accomodates similar or smaller non-cognate AAs to prevent errors in aminoacylation
pre- or post- transfer
(essentially gives another site for wrong AAs to go)

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21
Q

process of aminoacyl-tRNA synthetase adding a correct AA

A

via ATP, AA enters aminoacylation site, tRNA attaches to it, AA cannot enter the editing site, remains attached to tRNA

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22
Q

16S rRNA

A

mediates interaction between tRNA and mRNA

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23
Q

23S rRNA

A

found in peptidyl transferase center, interacts with tRNAs

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24
Q

3 binding sites in ribosomes for tRNAs

A

A: aminoacyl site
P: peptidyl site
E: exit site

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25
initiation (translation in bacteria)
initiation factors load initiator methionine tRNA into the P site of the small subunit and the large subunit joins
26
elongation (translation in bacteria)
1) elongation factor Tu loads next aminoacyl tRNA into A site of ribosome 2) ribosomal peptidyl transferase catalyzes peptide bond formation 3) elongation factor G (EFG) promotes movement of the mRNA - tRNA complex places next codon into A site
27
termination (translation in bacteria)
class I release factors recognize the stop codon, tRNA releases polypeptide chain, recycling factors promote dissociation of ribosomal subunits from one another
28
ribosome recycling
dissociation of ribosomal subunits and release of tRNA and mRNA
29
polysomes
many ribosomes piled up on the same mRNA (elongates simultaneously) transcription and translation occur simultaneously only in bacteria
30
GTPases
catalyze the hydrolysis of GTP to GDP EFTu, eIF2, EFG
31
EFTu
protects and delivers aminoacyl-tRNA to ribosome A site
32
eIF2
loads tRNA methionine into P site during initiation
33
EFG
promotes directional movement of mRNA-tRNA complex through ribosome binds in A site
34
GAPs
GTPase activating proteins, promote GTP hydrolysis
35
GEFs
guanine-nucleotide exchange factors, promote exchange of GDP to GTP
36
initiator tRNA
distinct from tRNA(met), structure prevents binding by elongation factors tRNA(fMet) in bacteria, tRNAi(Met) in eukaryotes
37
polycistronic
having several open reading frames, each frame has its own start and stop codon (e.g. bacterial mRNAs)
38
Shine-Dalgarno sequence
polypurine tract 6-8 bases upstream of initiator AUG, usually in initiation codons
39
anti-Shine-Dalgarno sequence
polypyrimidine region in the 3' end of the bacterial 16S rRNA, pairs with Shine-Dalgarno sequence pairing guides initiator AUG mRNA into P site
40
initiation factors that guide tRNA(fMet)
IF1, IF2, IF3
41
IF1 and IF3
binds the A and E sites (respectively) of the small ribosomal subunit in the absence of mRNA or tRNA(fMet) direct the initiator tRNA to P side, stops large ribosomal subunit from binding inappropriately
42
monocistronic
mRNA only encoding one protein, eukaryotes
43
AUG recognition in eukaryotes
scanning mechanism for first AUG sensitive to sequence context - kozak sequence
44
kozak sequence
consensus sequence containing AUG, dictates initiation efficiency
45
eIF4E
binds eukaryotic mRNA 5' cap
46
PABP
binds eukaryotic mRNA 3' poly A tail
47
closed loop complex / elF4 complex
eukaryotic mRNA bound by elF4E (on 5' cap) and PABP (3' poly A tail) forms the closed loop, functions as quality control to weed out unfinished/damaged mRNAs
48
pre-initiation complex (translation)
40S ribosomal subunit bound to initiation factors, primed to scan mRNA initiator tRNAi(Met) bound to eIF2
49
eIF5
stimulates GTP hydrolysis on eIF2
50
initiation (translation in eukaryotes)
pre-initiation complex brought to closed loop complex, scans mRNA for AUG
51
eIF4G
brings pre-initiation complex to the closed mRNA loop
52
elongation (in bacteria and eukaryotes)
decoding, peptide bond formation, translocation, tRNA in E site leaves
53
decoding
EFTu loads next charged tRNA into A site cognate, near-cognate, non-cognate matches cognate matches bind strongly with ribosome, stimulates conformational change in ribosome and aminoacyl-tRNA is released to A site
54
peptide bond formation
catalyzed between the amino acid in the P site and A site
55
translocation
mRNA-tRNA through ribosome move the peptidyl-tRNA from A to P site
56
elF4E
binds 5' cap, required to form the closed loop complex
57
hybrid states model
in translocation, tRNAs first move independently, then anti-codon end moves (classic > rotated > classic)
58
class I release factors
recognize stop codons in termination RF1: recognizes UAA and UAG RF2: recognizes UAA and UGA
59
RRF
ribosome recycling factor along with the EFG, acts as a wedge between ribosomal subunits > ribosome disassembly
60
recoding
the genetic code is superseded and an mRNA is read differently than expected
61
nonsense suppression
stop codons are misread and termination fails to occur
62
peptidyl transferase
catalyzes peptide bond formation in growing polypeptide
63
frameshifting
the mRNA shifts so the peptide synthesis proceeds in a different reading frame ribosome moves by a number that is not 3, usually +1 or -1
64
selenocysteine
"21st AA," similar to cysteine but has selenium instead of sulfur, needed in the catalytic site of some enzymes
65
how is selenocysteine loaded?
selenocystein-tRNA matches UGA stop codon, specialized loading protein SelB delivers it (can only deliver when there is a specific hairpin element in RNA)
66
pyrrolysine
modified lysine, found in methyltransferase genes at catalytic sites
67
how is pyrrolysine loaded?
it has its own aminoacyl-tRNA synthetase and tRNA which recognizes UAG stop codon, EFTu helps load
68
programmed frameshifting of RF2 (termination factor)
high RF2: recognizes stop codon low RF2: +1 frameshift so translation continues to produce RF2

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