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Molecular Biology > Gene expression II: from RNA to protein > Flashcards

Gene expression II: from RNA to protein Flashcards

1
Q

what does RNA stand for?

A

Ribonucleic acid

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2
Q

what is RNA?

A

the product of transcription from a DNA template

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3
Q

how much more RNA in a cell than DNA?

A

10x more

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4
Q

what 3 general factors make DNA and RNA different?

A
  • different chemical structure
  • different physical structure
  • different biological role
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5
Q

what’s different chemically about RNA to DNA? (2)

A
  • ribose contains 2-OH, whereas deoxy contains 2-H (deOXY)

- the base uracil is used instead of thymine

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6
Q

how does the oxygenated ribose as opposed to deoxygenated DNA affect stability?

A

it’s less stable (RNA)

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7
Q

what’s the difference between thymine and uracil?

A

uracil doesn’t have a CH3 group that thymine does have

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8
Q

what are the biological roles of RNA?

A
  • transfer of information from DNA to protein (mRNA)
  • synthesis of proteins (rRNA and tRNA)
  • processing of messenger RNA (snRNA)
  • processing and modification of ribosomal RNA (snoRNA)
  • catalytic RNA (self-splicing introns)
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9
Q

how much RNA does a single cell contain?

A

10pg/ 10^-11g

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10
Q

what proportion of RNA in cells is ribosomal?

A

80-85%

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11
Q

what proportion of RNA in cells is low molecular weight RNA e.g. snRNAs, tRNAs etc.?

A

10-15%

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12
Q

what proportion of RNA in cells is messenger?

A

1-5%

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13
Q

what are the physical properties of RNA?

A
  • single stranded

- can base pair with itself to fold into complex structures which depends on its sequence

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14
Q

the regulation of the amount or useage of certain RNAs is important for their function, what is this regulation controlled by? (3)

A
  • synthesis
  • regulated degradation
  • translation efficiency
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15
Q

when iron binds to transferrin what happens?

A

it’s transported into cells via a receptor

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16
Q

what is iron uptake regulated by?

A

degradation of transferrin receptor mRNA

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17
Q

what structures are found within the transferrin receptor mRNA?

A

AU rich loop

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18
Q

what does this Au rich loop act as?

A

binding site for IRE-BP (iron response element binding protein)

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19
Q

what 3 processes does mRNA go through to become mature?

A

capping
cleavage/polyadenylation
splicing

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20
Q

which end of RNA is modified by capping?

A

5’

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21
Q

what happens during capping?

A

the 5’ end of GTP molecule joins the 5’ end of the RNA and 1 phosphate is lost
methylation at the 2’ position of first 2 nucleotides and on the added G

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22
Q

what is the purpose of capping? (5)

A
  • increases the stability of mRNA
  • required for efficient splicing
  • nuclear export (leaving the nucleus)
  • translation initiation (translation can’t start without capping)
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23
Q

what does GTP stand for?

A

Guanosine TriPhosphate

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24
Q

how is RNA modified on the 3’ end?

A

3’ cleavage and polyadenylation

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25
Q

what signals cleavage/ polyadenylation? (2)

A

AAUAAA

G/U or just U rich sequence

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26
Q

what are the steps for 3’cleavage and polyadenylation?(3)

A
  • cleavage and polyadenylation specificity factor (CPSF) binds to AAUAAA
  • cleavage stimulatory factor (CstF) binds to G/U- recruits cleaving factors and poly-A polymerase (PAP)
  • cleavage and addition of polyA
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27
Q

what is PolyA tailing linked to?(2)

A

termination of transcription

stability and translation efficiency

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28
Q

what signals are required for pre-mRNA splicing?

A

conserved sequences at the
5’ splice site, 3’ splice site
and branchpoint region

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29
Q

does splicing happen in 1 or several stages?

A

several

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30
Q

what do splicing sites (5’ donor site and 3’ acceptor site) do?

A

tell apparatus where to cut the RNA

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31
Q

what does the branch point contain?

A

an A in the sequence

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32
Q

how many steps in the splicing mechanism?

A

2

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33
Q

what happens in the first step of the splicing mechanism?

A

cleavage at the 5’ splice site and lariat formation at branchpoint sequence- RNA is cut after exon 1 and the GU of the sequence joins to the A in the branch point (the free 2’ Hydroxyl of A joins to the phosphate of GU)

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34
Q

what happens in the second step of the splicing mechanism?

A

cleavage at 3’ splice site. Removal of intron region and exon ligation (join up)- the introns are cut out and exons are kept

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35
Q

what carries out splicing?

A

small nuclear ribonucleoprotein particles (snRNPs/ snurps) and protein splicing factors

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36
Q

what makes snRNPs?

A

snRNA + small nuclear RNA

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37
Q

which snRNPs are involved in splicing?

A

U1, U2, U4, U5 and U6

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38
Q

which snRNPs form the spliceosome?

A

U2
U5
U6

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39
Q

What are the steps of the spliceosome assembly pathway? (5)

A
  • exon 1 and intron boundry recognised by U1 and U2
  • U4, U5 and U6 are recruited
  • complex is called the spliceosome
  • U4, U5 and U6 displace U1- still associated but is pushed away
  • to join the 2 exons together, they must be brought close together and have intron RNA removed- which is done by U2,U5 and U6
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40
Q

what’s alternative splicing?

A

exon inclusion/inclusion to alter a protein sequence

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41
Q

give an example of alternative splicing use:

A

1 from:

  • sex determination in fruit flies
  • control of flowering time
  • olfactory receptor diversity
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42
Q

what’s the purpose of alternative splicing?

A

to produce different proteins with different functions from a single gene

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43
Q

what’s the technical term for protein synthesis?

A

translation

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44
Q

during translation mRNA–>

A

protein

45
Q

how many Amino acids are there?

A

20

46
Q

how was the genetic code broken?

A

polynucleuotides e.g. UUUUUUUU were looked at to see which amino acids they made, then more varying polynucleotides were looked at e.g. UAUAUAU

47
Q

do some AAs have more than one codon?

A

yes e.g. 6 different codons code for Leucine

48
Q

what’s a reading frame?

A

the sequence of codons from a specific start codon to a specific stop codon

49
Q

what codon does almost every protein chain initiate with?

A

AUG (methionine)

50
Q

what are the 3 stop codons?

A
  • UAA
  • UGA
  • UAG
51
Q

are all methionine codons start codons?

A

no

52
Q

what is the role of the 3’ end of tRNA?

A

acceptor arm, covalently bonds to AA

53
Q

what is on the opposite side of tRNA to the AA?

A

anti-codon

54
Q

what’s an anti-codon?

A

a codon which recognizes the codon sequences of the mRNA that’s the same as the AA on the tRNA acceptor arm (complementary)

55
Q

what’s the function of tRNA?

A

to specifically link to a particular amino acid and to recognise a codon in mRNA (ensures amino acid-codon match)

56
Q

what pairs tRNA to amino acids?

A

aminoacyl-tRNA synthetases

57
Q

each synthetase is specific for …

A

amino acid and tRNA

58
Q

can some tRNAs recognise more than one codon?

A

yes- some AAs have more than one codons

59
Q

what does wobble allow?

A

unconventional base pairing between third base in codon and first base in anticodon - allows one tRNA to recognise more than one codon

60
Q

what are the 3 stages of translation?

A
  • initiation
  • elongation
  • termination
61
Q

what are ribosomes?

A

organelles where protein synthesis/ translation takes place

made of RNA skeleton with sites where proteins can build

62
Q

How many svedbergs in prokaryotic ribosome?

A

70S

63
Q

what are the subunits of prokaryotic ribosome?

A

50S

30S

64
Q

what are the subunits of ribsomes made of?

A

difference species of rRNA and proteins

65
Q

how many svedbergs is a eukaryotic ribosome?

A

80S

66
Q

what are the subunits of a eukaryotic ribosome?

A

60S

40S

67
Q

what is a Svedberg?

A

a measure of the sedimentation rate of suspended particles centrifuged under standard conditions
S=size, not mass

68
Q

what’s the 2D structure of rRNA like?

A

elaborate made up of 40 or more stem loops

69
Q

what does the 3D structure of rRNA contain? (3)

A

ridges
crevices
holes

70
Q

what’s the purpose of the holes in rRNA?

A

may be for interaction with mRNA or tRNAs to slot in with an AA

71
Q

how are amino acids activated?

A

by ATP which esterifies it to form an AMP- amino acyl, AA

AA+ATP= AA-AMP (monophosphate) +PP(2 phosphates

72
Q

How do amino acids join to tRNA?

A

the 3’OH group of tRNA acts as an acceptor arm for the activated AA, they join and AMP is released
(AA-AMP+ tRNA–> AA-tRNA+AMP)

73
Q

what is an amino-acyl?

A

an AA joined to something else

74
Q

is the shine-dalgarno sequence seen in prokayotes or eukaryotes?

A

prokaryotes

75
Q

what is the shine-dalgarno sequence?

A

sequence which defines which is the correct initiation codon- not all methionines are equal (it needs the shine-dalgarno surrounding it)

76
Q

what does the shine-dalgarno interact with?

A

the 16S rRNA of the 30S small subunit to identify the site of initiation of protein synthesis

77
Q

what’s the shine- dalgarno sequence called in eukaryotes?

A

Kozak sequence

78
Q

can initiation occur without methionine?

A

yes sometimes if the kozak/ shine-galdarno sequence is ‘good enough’

79
Q

how many tRNAs are there for methionine?

A

2

80
Q

what is each of the tRNAs for methionine used for?

A

one for initiation (tRNAi)

one for elongation

81
Q

what’s different about prokaryotic methionine as opposed to eukaryotic?

A

it’s formylated

82
Q

what happens in the process of initiation?

A
  • IF2 engages with 30S subunit
  • messenger RNA (mRNA) and 1st methionine join onto the 30S subunit- this forms the ternary complex (ribosome, mRNA and tRNA and IFs)
  • the large subunit is assembled on the ternary complex- it has 2 slots (P and A)
  • initiator methionine is lined up with the P slot
  • IF2 and IF3 are ejected and GTP is hydrolysed to GDP and 2 ATPs are hydrolysed to 2 ADPs
  • initiation complex has been formed
83
Q

what are IFs?

A

initiation complexes

84
Q

what does IF1 do?

A

blocks A site to tRNAi-met, inhibiting premature 30S-50s interaction

85
Q

what does IF2 do?

A

tags tRNAi and regulates entry into ribosome

86
Q

what does IF3 do?(3)

A
  • inhibits premature 30S-50s interaction
  • stabilises free 30S
  • accuracy check for tRNAi-met binding
87
Q

what happens during elongation?

A
  • tRNA-meti is the only tRNA which can bind to the P site
  • the next aminoacyl tRNA comes in and binds to the A site, brought there by EFTu, using energy form the hydrolysis of GTP to GDP
  • AAs join together by peptide bonds and tRNA-meti is ejected from the complex- leaving an occupied A site, not P (as nothing else can bind to it)
  • the ribsosome translocates (moves along) the mRNA so P site is lined up with next codon, where the next tRNA comes in and so on and so forth
88
Q

what are EFs?

A

Elongation Factors

89
Q

what are the 2 EFs?

A
  • EF-Tu

- EF-G

90
Q

what does EF-Tu do?

A

mediates aminoacyl-tRNA entry to the ribosome

91
Q

what does EF-G do?

A

mediates translocation of ribosome

92
Q

what happens at termination?

A
  • RF-GTP binds to A site when the termination codon appears
  • hydrolysis of polypeptide chain from tRNA (the polypeptide is ejected) by RF
  • then there’s dissociation of the tRNA,RF and GTP
93
Q

what’s an RF?

A

release factor

94
Q

how many prokaryotic RFs are there?

A

3

95
Q

what are the RFs?

A

RF1
RF2
RF3

96
Q

What does RF1 do?

A

specific to UUA/UAG stop codons to cause termination when these are reached

97
Q

what does RF2 do?

A

specific to UAA/UGA stop codons to cause termination when these are reached

98
Q

what does RF3 do?

A

helps RF1/2 bind to ribosome

99
Q

what does GTP stand for?

A

Guanosine Triphosphate

100
Q

what does GTP do?

A

provides energy by being hydrolysed

101
Q

what does GTP do in inititation?

A

Adds a large subunit

102
Q

what does GTP do in elongation?

A

adds amino-acyl-tRNA with EF-Tu
peptide synthesis
transloacation

103
Q

what does GTP do in termination?

A

releases the peptide chain and dissociates ribosome from complex

104
Q

which RNA codes for protein?

A

mRNA

105
Q

which RNA is involved in processing mRNA?

A

snRNA

106
Q

which RNA is involved in siting and catalysis of protein synthesis?

A

rRNA

107
Q

which RNA is involved in the processing of ribosomal RNA?

A

snoRNA

108
Q

which bases can I (inosine) bond with?

A

C,A,U — not G

109
Q

which base is inosine most similar to?

A

G

Molecular Biology (4 decks)

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