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stupid orgo > set 5 > Flashcards

set 5 Flashcards

1
Q

do bacteria, archaea, and eukaryote have the same number and sequence of rRNA molecules and number and type of proteins

A

no

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2
Q

what measures ribosomesl subunit size

A

svedberg units (S)

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3
Q

what structures does rRNA fold into

A

secondary and tertiary structures

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4
Q

three tasks of ribosomes

A
  1. bind to mRNA and locate start codon
  2. facilitate complementary base pairing of mRNA codons and the corresping tRNA anticodons (decoding center)
  3. catalyze formation of peptide bonds between amino acids on the growing polypeptide chain (peptidyl-transferase centre)

which is the first two steps in protein synthesis (initiation and elongation)

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5
Q

how many and what are the binding sites in ribosomes for tRNA

A

A- binds aminoacyl-tRNA
P- binds peptidyl tRNA
E- binds empty/ uncharged tRNA

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6
Q

what are the two regions in ribosomes which are critical for protein synthesis

A
  1. peptidyl-transferase centre

2. decoding centre

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7
Q

where is the start codon

A

corresponds to the N terminus of the protein

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8
Q

where is the stop codon

A

immediately after the codon for the final amino acid

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9
Q

what positions the ribosomes in bacteria

A

a special sequence 5-8 nt upstream (shine-dalgarno sequence and ribosome binding site)

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10
Q

shine-dalgarno sequence

A

purine rich sequence of about six nucleotides 5-8 nucelotides upstream of the start codon

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11
Q

what binds with the shine-dalgarno sequecne on the mRNA

A

the 3’ end of the 16S rRNA base pairs which positions the start codon in the correct place in the P site

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12
Q

what produces polysictronic mRNAs

A

operons which share a single promoter

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13
Q

what do polycistronic mRNAs lead to

A

the synthesis of several different proteins

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14
Q

how do the proteins encoded by operons and the genes function

A

the operons function in the same metabolic pathway and the genes are regulated as a unit

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15
Q

cistron

A

old name for gene

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16
Q

what do polycistronic mRNAs contain

A

multiple polypeptide producing segments with a translation initiating region

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17
Q

what does the translating initiation region in polycistronic mRNAs contain

A

a ribosome binding site (RBS) or (Shine dalgarno sequence) and start stop codons for each reading frame

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18
Q

monocistronic mRNA

A

RNA that directs synthesis one polypeptide

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19
Q

what produces monocistronic mRNA

A

each polypeptide producing gnee in eukaryotes

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20
Q

does eukaryotic mRNA contain shine dalgarno sequences

A

no

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21
Q

how does translation initiate

A

speperate two halves of ribosome and keep them apart
place mRNA so that the start codon is correctly positioned
place first tRNA in the P sire
rejoin the two halves of the ribosome

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22
Q

what keeps two halves of ribosomes apart

A

IF3

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23
Q

what places mRNA so that the start codon is correclty positioned by base pairing with the 3’ end ofco 16S rRNA

A

shine dalgarno sequence

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24
Q

what prevents tRNA from going to the inccorect site (A site)

A

IF1

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25
Q

what guides the initiatior tRNA into the correct site (P site)

A

IF2

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26
Q

what do we need to initiate translation in bacteria E coli

A

the messenger mrna
the small and large subnunti
the initiation tRNA

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27
Q

initiatior tRNA

A

special tRNA used to start translation

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28
Q

codon for methionine

A

AUG

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29
Q

what is the special form of methionine stART CODON

A

tRNAfMEt instead of tRNAMet

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30
Q

what is the initiator tRNA charged with

A

formylmehtionine (gMet)

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31
Q

what is the charged initiator tRNA

A

fMettRNAfMet

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32
Q

what does the initiator tRNA base pair with

A

the start codon

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33
Q

when do the initiation factors F1,2,3, dissociate

A

at the same time when the 70S initiation complex is formed

34
Q

what accompanies the release of IF2 and the joining of two subunits

A

GTP

35
Q

what is the eukaryotic equivalent of IF3

A

eIF1

36
Q

eukaryotic equivalent of IF2

A

eIF2

37
Q

eukaryotic equivalent for IF1

A

eIF1A`

38
Q

what recognizes the 5’ end of the mRNA in eukaryotes? bacteria?

A

CAP binding protein

eIF4E

39
Q

what binds the 3’ end of the mRNA

A

polyA binding protein

40
Q

what recognizes the 3’ end of the mRNA

A

eIF4G

41
Q

kozac sequence

A

5’-ACCAUGG-3’

42
Q

who discovered the kozac sequence

A

marilyn kozac

43
Q

when do the initiation factors dissociate

A

once a match is found for the start codon and the large subunit is recruited

44
Q

what accompanies dissociation of the initiation factors

A

GTP hydrolysis

45
Q

what are the four steps to the formation of a peptide bond

A
  1. match the next tRNA to the codon
  2. move the amino acid into the peptidyl transferase centre
  3. form the peptide bond
  4. shift everything over by one codon/place
46
Q

what inspects the open A site

A

GTP

47
Q

what associates with EF-Tu

A

charged tRNAs

48
Q

what happens if the tRNA base pairs correctly with the codon on the mRNA

A

hydrolysis of GTP, releasing EF-Tu and GTP from the tRNA

49
Q

accomodation

A

the 3’ end of the tRNA which carries the amino acid moves into the peptidyl transferase centre

50
Q

what does the peptidyl transferase activity do

A

catalyzes the formation of a peptide bond between amino acids on the tRNAs at the P and A sites

51
Q

what enters the A site and translocates the ribosome along the mRNA leading to GTP hydrolysis. what does this lead to

A

EF-G. moves tRNA from A site to P site and opens the A site for the next charged tRNA

52
Q

How long does the elongation cycle last

A

until one of the three stop codons enters the A site of the decoding centre

53
Q

is there a tRNA that recognizes the stop codons

A

no

54
Q

what recognizes stop factors in bacteria and eukaryotes

A

RF1 +RF2 in bacteria

eRF1 in eukaryotes

55
Q

what does binding of the release factors lead to

A

hydrolysis and release of the polypeptide bound to the tRNA at the P site

56
Q

can mRNAs that have not yet been fully synthesized be translated in bacteria

A

yes becaues nothing seperates translation and transcription as they are coupled

57
Q

polyribosomes

A

found in bacteria and are groups of ribosomes all actively translation the same mRNA

58
Q

what happens to pre-mRNAs before they are exported to the cytoplasm for translation

A

must be processed

59
Q

what blocks the translocation step

A

cycloheximide

60
Q

what inactivates eEF2

A

diphtheria toxin

61
Q

what is the structural analog of aa-tRNA and triggers the premature release of polypeptide

A

puromycin

62
Q

what blocks elongation step

A

erythromycin

63
Q

what causes misreading during elongation

A

streptomycin

64
Q

what prevents stable binding of EF-Tu*tRNA

A

tetracycline

65
Q

what do the termination sequences found in mRNA include

A

an inverted repeat followed by a string of 6-8 uracils

66
Q

what forms the stem-loop structure called a hairpin

A

the mRNA containing the inverted repeats

67
Q

what does the hairpin followed by 6-8 uracils lead to

A

it causes the RNA polymerase to slow down or pause which leads to instability along with the U A base pairs induces polymerase to release the transcript and to seperate from the DNA

68
Q

what does the rho protein do

A

binds to the nascent mRNA and brings about the separation of the new mRNA transcript from the RNA polymerase

69
Q

what is a rut site

A

a rho utalization site

70
Q

are rho dependant termination sequences well defined

A

no. they have a rut site to wich rho can bind and a stretch of about 50 nucleotides rich in cytosine

71
Q

how many rna polymerases are in eukaryotes

A

at least 3

72
Q

differences in promoter sequences in bacteria and eukaryotes

A

bacteria- promoter sequences act as binding sites for RNA polymerase
euk- promoter sequences act as binding sites for proteins that act to alter the accessibility to RNA polymerases

73
Q

how are genes organized in bacteria and euk

A

bacteria- in clusters called operons

euk- as single transcription units

74
Q

exons

A

expressed

75
Q

introns

A

must be removed from the pre-mRNA before it can be translated into protein (mRNA splicing)

76
Q

what did crick speculate

A

a separate enzyme would be required to join each adapter (tRNA) to its own amino acid

77
Q

what does transcription produce

A

30S pre-RNA

78
Q

what is the nucleotide sequence at the 3’ acceptor end of the tRNA

A

CCA

79
Q

where is the peptidyl transferase center

A

ontop of A and P

80
Q

what is released from the e site

A

deacylated tRNA

81
Q

intercistronic spacers

A

include the dalgarno sequence and some extra nucleotides in between the stop codon of the first polypeptide mRNA and the start codon of the next in polycixtronic mRNAs

stupid orgo (7 decks)

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