Gene expression I from gene to RNA Flashcards
(142 cards)
1
Q
what’s a UTR?
A
an untranslated region
2
Q
what’s a spacer?
A
region of non-coding DNA between genes (introns are non-coding within genes)
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
4
Q
what is RNA polymerase?
A
an enzyme that synthesizes RNA on a DNA or RNA template
5
Q
what’s a promoter?
A
nucleotide sequence, upstream of a gene, to which RNA polymerase binds to initiate transciption
6
Q
define intron
A
a non coding region within a discontinuous gene in eukaryotes
7
Q
define exon
A
a coding region within a discontinuous gene in eukaroytes
8
Q
define genome
A
the entire genetic sequence of a living organism
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)
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)
11
Q
what is a gene?
A
a genetic unit containing information to make a functional product (RNA and/or protein)
12
Q
what 4 bits of information does a gene contain?
A
- structural
- temporal
- positional
- inducible
13
Q
what’s structural information?
A
coding DNA
14
Q
what’s temporal information?
A
when genes should be on or off
15
Q
what’s positional information?
A
where genes should be on or off
16
Q
what’s inducible information?
A
when gene is responsive to external stimuli e.g. environmental
17
Q
what type of genetic information is in all organisms?
A
structural and inducible
18
Q
what type of genetic information is in more developed/ multicellular organisms?
A
structural
temporal
positional
inducible
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)
20
Q
what components are seen in a prokaryotic gene?
A
transcription start promoter leader coding regions (cistrons) spacers transcription termination
21
Q
are transcription start/stop sites the same as translation start/stop sites?
A
no
22
Q
what is a leader?
A
apparently useless part of DNA
23
Q
where are spacers found?
A
between cistrons
24
Q
what’s lost during transcription? (in prokaryotes)
A
promoter
25
what's lost during translation? (in prokaryotes)
leader
promoter
terminator
26
what does the promoter contain?
TATA boxes (A-T rich)
27
what components are seen in a eukaryotic gene?
```
enhancer
introns
promoter
transciption start
exons
transcription termination
```
28
what word describes enhancers and promoters?
they're regulatory
29
where are UTRs found?
at the end of each section of mature mRNA
30
what is mature mRNA?
mRNA which has had introns spliced out
31
where does mature mRNA go?
transported out of the nucleus and into the cytoplasm to make proteins
32
what 2 factors affect the direction in which the polymerase travels?
- promoter
| - directionality of the sequence
33
what's the transcription bubble?
section of unwound DNA found during transcription
34
what happens at the transcription bubble?
RNA polymerase binds to DNA
melts double strand
polymerase polymerises from template strand in the 5' to 3' direction
35
how does the polymerase know where and when to bind to DNA, start transcription, stop transcription etc.?
it's all in the gene
36
what is TBP?
TATA binding Protein- a component of the transcription factor TEIID with ancillary roles in the recognition of the TATA box
37
how many subunits is the Prokaryotic RNA polymerase made up of?
6
38
which subunits and how many is prokaryotic RNA polymerase made up of?
```
1 sigma (O)
2 alpha (a)
2 beta (B)
1 omega (w)
```
39
what is sigma in prokaryotic RNA polymerase for?
promoter recognition
40
what is alpha in prokaryotic RNA polymerase for?
involved in assembly and activation
41
what is beta in prokaryotic RNA polymerase used for?
catalysis and termination of transcription
42
what is omega in prokaryotic RNA polymerase used for?
involved in assembly and folding of some genes
43
which is the largest part of prokaryotic RNA polymerase?
betas
44
what's an enzyme called when it has all of its subunits?
Holoenzyme
45
is prokaryotic RNA polymerase fairly large?
yes- covers around 70bp of DNA
46
which subinit can polymerase function without?
omega
47
what does the polymerase do first on DNA?
opens up DNA at the transcription site
48
what happens to the sigma once the polymerase begins to polymerise?
it is lost/ discarded
49
why is the sigma discarded?
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
50
where does the lost sigma go?
to join up with another polymerase
51
what is the polymerase called when the sigma has gone?
the core enzyme (aaBBw)
52
how many type of RNA polymerase do prokaryotes have?
1
53
How many types of RNA polymerase do eukaryotes have?
3
54
what are the 3 eukaryotic RNA polymerases?
polymerase I
polymerase II
polymerase III
55
what does polymerase I transcribe? (1)
ribosomal RNA genes (rRNA)
56
what does polymerase II transcribe?(2)
protein coding genes (mRNA)
| small nuclear RNA (snRNA)
57
what does polymerase III transcribe? (3)
```
transfer RNA (tRNA)
ribosomal RNA (rRNA)
Small nuclear RNA (snRNA)
```
58
which eukaryotic RNA polymerase are simple?
I and III
59
which eukaryotic RNA polymerase are complex?
II
60
Genes which make different types of RNA have: (3)
- different architecture
- use different RNA polymerases
- each type of RNA polymerase needs a distinct set of accessory factors
61
what is meant by genes having different architecture?
different promoter and coding regions
62
what is meant by each type of RNA polymerase needing a distinct set of accessory factors?
needs other factors to work as well as their main subunits
63
what are the first subunits of the RNA polymerase II to bind to the DNA to be transcribed?
TFIID (Transcription Factor Polymerase II D)
TFIIA
TFIIB
64
what does TFIID do?
recognises a specific region of the promoter
| acts as a saddle for another set of factors- TBP (TATA Binding Region)
65
what is TFIID?
a TATA (region of DNA) Binding Protein (TBP)
66
what is TBP similar to?
the sigma factor in Prokaryotic RNA polymerase
67
what part of the DNA is the TBP associated with?
minor-groove
68
what part of the DNA do most DNA proteins interact with?
major-groove
69
What does TFIIA do?
helps TFIID to bind to DNA
70
what was TFIIB do?
sets distance from TATA element to start site
71
how many subunits make up the entirety of RNA polymerase II?
10
72
what are the important subunits of RNA polymerase II?(8)
```
TFIID
TFIIA
TFIIB
TFIIF
TFIIE
TFIIJ
TFIIH
Pol II
```
73
What do TFIIE, F, H, J and K do? (6)
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
what sort of RNA do the genes that RNA polymerase II transcribe make?
rRNA
74
what sort of RNA do the genes that RNA polymerase II transcribe make?
rRNA
75
generally, what is the apparatus and promoter sequence of the RNA polymerase I like?
simple
75
generally, what is the apparatus and promoter sequence of the RNA polymerase I like?
simple
76
RNA polymerase I cannot access DNA without specific...
accessories
76
RNA polymerase I cannot access DNA without specific...
accessories
77
what is the polymerase I promoter made up of?
2 sequences- core and UCE
77
what is the polymerase I promoter made up of?
2 sequences- core and UCE
78
in RNA polymerase I, what is SL1?
another general factor, like TFIID, multi subunit protein, containing TBP
78
what is TFIIIB made up of?
TBP (TATA Binding Protein) + 2 polymerase III specific TAFs
79
what is the upstream binding factor in RNA polymerase I?
factor that binds to UCE and core element in DNA
79
what is the upstream binding factor in RNA polymerase I?
factor that binds to UCE and core element in DNA
80
when is transcription started in RNA polymerase I?
when RNA polymerase I binds to the complex
80
when is transcription started in RNA polymerase I?
when RNA polymerase I binds to the complex
81
in RNA polymerase III, where is the promoter?
within the coding region
82
what happens at RNA polymerase III for initiation?
- 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
what is TFIIIB made up of?
TBP (TATA Binding Protein) + 2 polymerase III specific TAFs
84
define operon
a cluster of genes transcribed by the same promoter that give rise to polycistronic mRNA (encodes several proteins)- genes usually related
85
define lac operon
a complete genetic unit containing genes for all the enzymes for a particular pathway and gene(s) which regulate it
86
what is the Plac?
promoter
87
what is the Olac?
operator
88
in the lac operon, what are the 3 subunits for a polyamide?
lacZ, lacY, lacA
89
what protein does lacZ translate to?
B- Galactosidase
90
what does B-Galactosidase do?
hydrolyses lactose to galactose and glucose
91
what's the main source of energy for bacteria?
glucose
92
what sort of sugar is lactose?
Disaccharide
93
what monosaccharides is lactose made up of?
Galactose and glucose
94
in what situation is the lac operon activated?
when there's no glucose available but there's lactose available
95
what does the lac repressor tetramer do under normal conditions?
prevents the transcription of the gene required when lactose is present
96
what happens when lactose isn't present?
lac operon repressed
repressor binds to lacO
prevents RNA polymerase from clearing promoter
97
what does lacA translate to?
lactose transacetylase
98
what is lactose in terms of how it affects the operon?
an inducer
99
what happens to the lac operon when lactose runs out
the system will switch off
100
what is the lacI?
lac repressor
101
what does lacY translate to?
lactose permease
102
what does lactose permease do?
facilitates the entry of lactose into cell
103
what does lacA translate to?
lactose transacetylase
104
what does a cis-acting factor do?
regulates DNA it's directly joined to
105
what does a trans-acting factor do?
regulates DNA anywhere
106
is a cis-acting factor dominant or recessive?
dominant
107
is a trans-acting factor dominant or recessive?
recessive
108
what is the CRP?
Catabolite Repression Protein
109
what does a lacOc (constitutive) mutation cause?
the lac operon to be permanently switched on, as the operon isn't repressed
110
is a lacOc mutation dominant or recessive?
dominant
111
is a lacOc mutation cis or trans- dominant?
cis
112
in a lacOc mutation, would adding a repressor make a difference?
no
113
what does a lacI- mutation cause?
the lacI gene be permanently switched on as the repressor is mutated
114
if glucose is low,
cAMP is high, so CRP is active
115
what is catabolite repression?
repression of the lac-operon in the presence of glucose
116
what is CRP?
Catabolite Repressor Protein
117
what is CAP?
Catabolite Activator Protein
118
what does the Trp repressor do?
binds to operator when tryptophan is present- prevents transcription
119
how does the CRP bind?
using cyclic AMP (cAMP)
120
if glucose is high...
cAMP is low, so CRP is inactive
121
if glucose is low,
cAMP is high, so CRP is active
122
is catabolite repression an example of a cis or trans- acting repressor?
trans
123
what is the Trp operon used to make?
Tryptophan
124
what's different about promoters and enhancers positionally?
enhancers are independent of position and orientation, whereas promoters can be affected by these factors
125
what does the Trp repressor do?
binds to operator when tryptophan is present- prevents transcription
126
how is eukaryotic DNA organised?
into chromatin
127
what does DNA coated in chromatin do in terms of transcription factors?
it presents a physical barrier
128
when a gene is transcribed what happens to the chromatin around it?
it changes
129
what's the chain of events in the signal tranduction pathway, starting with the ligand-receptor interaction at the cell plasma membrane?
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
where is the regulatory information situated?
the enhancer
131
what's different about promoters and enhancers positionally?
enhancers are independent of position and orientation, whereas promoters can be affected by these factors
132
in transcription of eukaryotes, how is the issue of a large distance between the enhancer and promoter solved?
they are looped out
133
how does histone acetylation make DNA acceptable for transcription?
changes the lysine tails from positive to negatively charged, causing the histones to be repelled by the negatively changed DNA
134
what do ATP- dependent chromatin modification complexes do?
also make DNA to be transcribed accessible
135
what are signal transduction pathways?
how a signal from outside a cell can interact with the cell and which then interacts with the nucleus and affect transcription factors
