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Molecular Biology > Gene expression I from gene to RNA > Flashcards

Gene expression I from gene to RNA Flashcards

1
Q

what’s a UTR?

A

an untranslated region

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2
Q

what’s a spacer?

A

region of non-coding DNA between genes (introns are non-coding within genes)

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3
Q

what’s a cistron?

A

sections of DNA or RNA molecule that codes for a specific polypeptide in protein synthesis in prokaryotic DNA– same as a gene

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4
Q

what is RNA polymerase?

A

an enzyme that synthesizes RNA on a DNA or RNA template

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5
Q

what’s a promoter?

A

nucleotide sequence, upstream of a gene, to which RNA polymerase binds to initiate transciption

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6
Q

define intron

A

a non coding region within a discontinuous gene in eukaryotes

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7
Q

define exon

A

a coding region within a discontinuous gene in eukaroytes

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8
Q

define genome

A

the entire genetic sequence of a living organism

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9
Q

what’s the sense strand?

A

DNA strand directed in the 3’ to 5’ direction and is not transcribed into RNA (it has the same nucleotide sequence to RNA but with T instead of U)

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10
Q

what’s the antisense strand?

A

DNA strand directed in the 5’ to 3’ direction which is transcribed into RNA (contains the complementary nucleotide sequence to RNA)

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11
Q

what is a gene?

A

a genetic unit containing information to make a functional product (RNA and/or protein)

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12
Q

what 4 bits of information does a gene contain?

A
  • structural
  • temporal
  • positional
  • inducible
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13
Q

what’s structural information?

A

coding DNA

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14
Q

what’s temporal information?

A

when genes should be on or off

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15
Q

what’s positional information?

A

where genes should be on or off

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16
Q

what’s inducible information?

A

when gene is responsive to external stimuli e.g. environmental

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17
Q

what type of genetic information is in all organisms?

A

structural and inducible

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18
Q

what type of genetic information is in more developed/ multicellular organisms?

A

structural
temporal
positional
inducible

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19
Q

is it true that more complex/ developed organisms have more genes?

A

yes– to an extent

not always true e.g. humans have less genes than pieris japonica (a plant)

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20
Q

what components are seen in a prokaryotic gene?

A 
transcription start
promoter 
leader
coding regions (cistrons)
spacers 
transcription termination
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21
Q

are transcription start/stop sites the same as translation start/stop sites?

A

no

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22
Q

what is a leader?

A

apparently useless part of DNA

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23
Q

where are spacers found?

A

between cistrons

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24
Q

what’s lost during transcription? (in prokaryotes)

A

promoter

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25
Q

what’s lost during translation? (in prokaryotes)

A

leader
promoter
terminator

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26
Q

what does the promoter contain?

A

TATA boxes (A-T rich)

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27
Q

what components are seen in a eukaryotic gene?

A 
enhancer
introns
promoter
transciption start 
exons 
transcription termination
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28
Q

what word describes enhancers and promoters?

A

they’re regulatory

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29
Q

where are UTRs found?

A

at the end of each section of mature mRNA

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30
Q

what is mature mRNA?

A

mRNA which has had introns spliced out

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31
Q

where does mature mRNA go?

A

transported out of the nucleus and into the cytoplasm to make proteins

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32
Q

what 2 factors affect the direction in which the polymerase travels?

A
  • promoter

- directionality of the sequence

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33
Q

what’s the transcription bubble?

A

section of unwound DNA found during transcription

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34
Q

what happens at the transcription bubble?

A

RNA polymerase binds to DNA
melts double strand
polymerase polymerises from template strand in the 5’ to 3’ direction

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35
Q

how does the polymerase know where and when to bind to DNA, start transcription, stop transcription etc.?

A

it’s all in the gene

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36
Q

what is TBP?

A

TATA binding Protein- a component of the transcription factor TEIID with ancillary roles in the recognition of the TATA box

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37
Q

how many subunits is the Prokaryotic RNA polymerase made up of?

A

6

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38
Q

which subunits and how many is prokaryotic RNA polymerase made up of?

A 
1 sigma (O)
2 alpha (a)
2 beta (B)
1 omega (w)
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39
Q

what is sigma in prokaryotic RNA polymerase for?

A

promoter recognition

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40
Q

what is alpha in prokaryotic RNA polymerase for?

A

involved in assembly and activation

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41
Q

what is beta in prokaryotic RNA polymerase used for?

A

catalysis and termination of transcription

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42
Q

what is omega in prokaryotic RNA polymerase used for?

A

involved in assembly and folding of some genes

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43
Q

which is the largest part of prokaryotic RNA polymerase?

A

betas

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44
Q

what’s an enzyme called when it has all of its subunits?

A

Holoenzyme

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45
Q

is prokaryotic RNA polymerase fairly large?

A

yes- covers around 70bp of DNA

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46
Q

which subinit can polymerase function without?

A

omega

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47
Q

what does the polymerase do first on DNA?

A

opens up DNA at the transcription site

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48
Q

what happens to the sigma once the polymerase begins to polymerise?

A

it is lost/ discarded

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49
Q

why is the sigma discarded?

A

it allows the polymerase to bind to the promoter site, however after this the polymerase has no use for it and needs to be able to bind to other sequences

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50
Q

where does the lost sigma go?

A

to join up with another polymerase

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51
Q

what is the polymerase called when the sigma has gone?

A

the core enzyme (aaBBw)

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52
Q

how many type of RNA polymerase do prokaryotes have?

A

1

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53
Q

How many types of RNA polymerase do eukaryotes have?

A

3

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54
Q

what are the 3 eukaryotic RNA polymerases?

A

polymerase I
polymerase II
polymerase III

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55
Q

what does polymerase I transcribe? (1)

A

ribosomal RNA genes (rRNA)

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56
Q

what does polymerase II transcribe?(2)

A

protein coding genes (mRNA)

small nuclear RNA (snRNA)

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57
Q

what does polymerase III transcribe? (3)

A 
transfer RNA (tRNA)
ribosomal RNA (rRNA)
Small nuclear RNA (snRNA)
58
Q

which eukaryotic RNA polymerase are simple?

A

I and III

59
Q

which eukaryotic RNA polymerase are complex?

A

II

60
Q

Genes which make different types of RNA have: (3)

A
  • different architecture
  • use different RNA polymerases
  • each type of RNA polymerase needs a distinct set of accessory factors
61
Q

what is meant by genes having different architecture?

A

different promoter and coding regions

62
Q

what is meant by each type of RNA polymerase needing a distinct set of accessory factors?

A

needs other factors to work as well as their main subunits

63
Q

what are the first subunits of the RNA polymerase II to bind to the DNA to be transcribed?

A

TFIID (Transcription Factor Polymerase II D)
TFIIA
TFIIB

64
Q

what does TFIID do?

A

recognises a specific region of the promoter

acts as a saddle for another set of factors- TBP (TATA Binding Region)

65
Q

what is TFIID?

A

a TATA (region of DNA) Binding Protein (TBP)

66
Q

what is TBP similar to?

A

the sigma factor in Prokaryotic RNA polymerase

67
Q

what part of the DNA is the TBP associated with?

A

minor-groove

68
Q

what part of the DNA do most DNA proteins interact with?

A

major-groove

69
Q

What does TFIIA do?

A

helps TFIID to bind to DNA

70
Q

what was TFIIB do?

A

sets distance from TATA element to start site

71
Q

how many subunits make up the entirety of RNA polymerase II?

A

10

72
Q

what are the important subunits of RNA polymerase II?(8)

A 
TFIID
TFIIA
TFIIB
TFIIF
TFIIE
TFIIJ
TFIIH
Pol II
73
Q

What do TFIIE, F, H, J and K do? (6)

A

interact with D-A-B complex
blocks non-specific binding of polymerase II (like sigma factor)
promoter clearance- (helping the polymerase move of the promoter and start transcribing the gene)
Helicase activity (unwinding DNA)
Processivity/ elongation- (Polymerase will polymerise a section then stop, but the other factors alllow the polymerase II to keep going for longer)
transcription- coupled DNA repair

74
Q

what sort of RNA do the genes that RNA polymerase II transcribe make?

A

rRNA

74
Q

what sort of RNA do the genes that RNA polymerase II transcribe make?

A

rRNA

75
Q

generally, what is the apparatus and promoter sequence of the RNA polymerase I like?

A

simple

75
Q

generally, what is the apparatus and promoter sequence of the RNA polymerase I like?

A

simple

76
Q

RNA polymerase I cannot access DNA without specific…

A

accessories

76
Q

RNA polymerase I cannot access DNA without specific…

A

accessories

77
Q

what is the polymerase I promoter made up of?

A

2 sequences- core and UCE

77
Q

what is the polymerase I promoter made up of?

A

2 sequences- core and UCE

78
Q

in RNA polymerase I, what is SL1?

A

another general factor, like TFIID, multi subunit protein, containing TBP

78
Q

what is TFIIIB made up of?

A

TBP (TATA Binding Protein) + 2 polymerase III specific TAFs

79
Q

what is the upstream binding factor in RNA polymerase I?

A

factor that binds to UCE and core element in DNA

79
Q

what is the upstream binding factor in RNA polymerase I?

A

factor that binds to UCE and core element in DNA

80
Q

when is transcription started in RNA polymerase I?

A

when RNA polymerase I binds to the complex

80
Q

when is transcription started in RNA polymerase I?

A

when RNA polymerase I binds to the complex

81
Q

in RNA polymerase III, where is the promoter?

A

within the coding region

82
Q

what happens at RNA polymerase III for initiation?

A
  • TFIIIC binds to the B box
    then recruits TFIIIB
    once TFIIB is recruited, TFIIIC is dispensable
    RNA polymerase III is rectruited and initiates transcription
83
Q

what is TFIIIB made up of?

A

TBP (TATA Binding Protein) + 2 polymerase III specific TAFs

84
Q

define operon

A

a cluster of genes transcribed by the same promoter that give rise to polycistronic mRNA (encodes several proteins)- genes usually related

85
Q

define lac operon

A

a complete genetic unit containing genes for all the enzymes for a particular pathway and gene(s) which regulate it

86
Q

what is the Plac?

A

promoter

87
Q

what is the Olac?

A

operator

88
Q

in the lac operon, what are the 3 subunits for a polyamide?

A

lacZ, lacY, lacA

89
Q

what protein does lacZ translate to?

A

B- Galactosidase

90
Q

what does B-Galactosidase do?

A

hydrolyses lactose to galactose and glucose

91
Q

what’s the main source of energy for bacteria?

A

glucose

92
Q

what sort of sugar is lactose?

A

Disaccharide

93
Q

what monosaccharides is lactose made up of?

A

Galactose and glucose

94
Q

in what situation is the lac operon activated?

A

when there’s no glucose available but there’s lactose available

95
Q

what does the lac repressor tetramer do under normal conditions?

A

prevents the transcription of the gene required when lactose is present

96
Q

what happens when lactose isn’t present?

A

lac operon repressed
repressor binds to lacO
prevents RNA polymerase from clearing promoter

97
Q

what does lacA translate to?

A

lactose transacetylase

98
Q

what is lactose in terms of how it affects the operon?

A

an inducer

99
Q

what happens to the lac operon when lactose runs out

A

the system will switch off

100
Q

what is the lacI?

A

lac repressor

101
Q

what does lacY translate to?

A

lactose permease

102
Q

what does lactose permease do?

A

facilitates the entry of lactose into cell

103
Q

what does lacA translate to?

A

lactose transacetylase

104
Q

what does a cis-acting factor do?

A

regulates DNA it’s directly joined to

105
Q

what does a trans-acting factor do?

A

regulates DNA anywhere

106
Q

is a cis-acting factor dominant or recessive?

A

dominant

107
Q

is a trans-acting factor dominant or recessive?

A

recessive

108
Q

what is the CRP?

A

Catabolite Repression Protein

109
Q

what does a lacOc (constitutive) mutation cause?

A

the lac operon to be permanently switched on, as the operon isn’t repressed

110
Q

is a lacOc mutation dominant or recessive?

A

dominant

111
Q

is a lacOc mutation cis or trans- dominant?

A

cis

112
Q

in a lacOc mutation, would adding a repressor make a difference?

A

no

113
Q

what does a lacI- mutation cause?

A

the lacI gene be permanently switched on as the repressor is mutated

114
Q

if glucose is low,

A

cAMP is high, so CRP is active

115
Q

what is catabolite repression?

A

repression of the lac-operon in the presence of glucose

116
Q

what is CRP?

A

Catabolite Repressor Protein

117
Q

what is CAP?

A

Catabolite Activator Protein

118
Q

what does the Trp repressor do?

A

binds to operator when tryptophan is present- prevents transcription

119
Q

how does the CRP bind?

A

using cyclic AMP (cAMP)

120
Q

if glucose is high…

A

cAMP is low, so CRP is inactive

121
Q

if glucose is low,

A

cAMP is high, so CRP is active

122
Q

is catabolite repression an example of a cis or trans- acting repressor?

A

trans

123
Q

what is the Trp operon used to make?

A

Tryptophan

124
Q

what’s different about promoters and enhancers positionally?

A

enhancers are independent of position and orientation, whereas promoters can be affected by these factors

125
Q

what does the Trp repressor do?

A

binds to operator when tryptophan is present- prevents transcription

126
Q

how is eukaryotic DNA organised?

A

into chromatin

127
Q

what does DNA coated in chromatin do in terms of transcription factors?

A

it presents a physical barrier

128
Q

when a gene is transcribed what happens to the chromatin around it?

A

it changes

129
Q

what’s the chain of events in the signal tranduction pathway, starting with the ligand-receptor interaction at the cell plasma membrane?

A

there’s then the generation of a 2nd messenger small molecule

this activates protein kinases

causing the regulation of transcription factor activity
charge, structure and protein-protein interactions

DNA binding activation nuclear localisation, degradation

affects DNA activation

130
Q

where is the regulatory information situated?

A

the enhancer

131
Q

what’s different about promoters and enhancers positionally?

A

enhancers are independent of position and orientation, whereas promoters can be affected by these factors

132
Q

in transcription of eukaryotes, how is the issue of a large distance between the enhancer and promoter solved?

A

they are looped out

133
Q

how does histone acetylation make DNA acceptable for transcription?

A

changes the lysine tails from positive to negatively charged, causing the histones to be repelled by the negatively changed DNA

134
Q

what do ATP- dependent chromatin modification complexes do?

A

also make DNA to be transcribed accessible

135
Q

what are signal transduction pathways?

A

how a signal from outside a cell can interact with the cell and which then interacts with the nucleus and affect transcription factors

Molecular Biology (4 decks)

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