lec 3: control of gene expression Flashcards
1
Q
receptive regions
A
dendrites
2
Q
biosynthetic center
A
cell body
3
Q
impulse generating and conducting region
A
axon
4
Q
sheath of schwann
A
neurilemma
5
Q
one internode
A
schwall cell
6
Q
terminal branches
A
telodendria
7
Q
the cell types in a multicellular organism become different from one another because what?
A
they synthesize and accumulate different sets of RNA and protein
8
Q
different cell types contain the same what?
A
DNA
9
Q
Differentiated cells retain the ability to _______
A
dedifferentiate
10
Q
is the process by which cells grow reversely from a partially or terminally differentiated stage to a less differentiated stage within their own lineage
A
cell dedifferentiation
11
Q
some RNAs and proteins are abundant in _________ cells in which they function and cannot be detected elsewhere
A
specialized
12
Q
true or false: many processes are common to all cells, and any two cells in a single organism therefore have many gene products in common
A
true
13
Q
this gene is expressed in liver but not in most other tissues, which breaks down tyrosine in food
A
tyrosine aminotransferase
14
Q
virtually every cell in your body contains a complete set of genes, but they are not all turned on in every tissue
A
gene regulation
15
Q
eaech cell in your body expresses only a small subset of genes at any time
A
gene regulation
16
Q
during development, different cells express different sets of genes in a precisely regulated fashion
A
gene regulation
17
Q
controlling when and how often a given gene is transcribed
A
transcriptional control
18
Q
controlling the splicing and processing of RNA transcripts
A
RNA-processing control
19
Q
selecting which completed mRNAs are exported from the nucleus to the cytosol and determining where in the cytosol they are localized
A
RNA transport and localization control
20
Q
selecting which mRNAs in the cytoplasm are translated by ribosome
A
translational control
21
Q
selectively destabilizing certain mRNA molecules in the cytoplasm
A
mRNA degradation control
22
Q
selectively degrading specific protein molecules
A
protein degradation control
23
Q
activating, inactivating, or localizing specific protein molecules
A
protein activity control
24
Q
a group of genes that are transcribed at the same time
A
operon
25
they usually control an important biochemical process
operons
26
they are rare in eukaryotes
operons
27
give the three people for their discoveries concerning genetic control of enzyme and virus synthesis
Jacob
Monod
Lwoff
28
give the two genes in an operon model
repressible genes
inducible genes
29
genes whose expression is turned off by the presence of some substance
repressible genes
30
what do you call this substance that turns off the expression of a gene
co-repressor
31
______ represses the trp genes
tryptophan
32
this is typically the end product of the pathway in repressible genes
co-repressor
33
what kind of pathway do repressible genes express?
biosynthetic pathway
34
when E. coli is swimming in tryptophan (milk & poultry), it will absorb the ______ from the media
amino acids
35
when tryptophan is not present in the media, then the cell must what?
manufacture its own amino acids
36
E. coli uses several proteins encoded by a cluster of ______ genes to manufacture the amino acid tryptophan
5 genes
37
these genes are arranged in a cluster on the chromosome and are transcribed from a single promoter as one long mRNA molecule; such coordinately transcribed clusters are called ____
operons
38
each of these clusters is called an operon because its expression is controlled by a cis-regulatory sequence called ____
operator
39
give the genes of Trp operon
trpE
trpD
trpC
trpB
trpA
40
give the regulatory gene of Trp operon
trpR
41
transcription regulator of trp operon is known as?
tryptophan repressor
42
cis-regulatory sequence of trp operon is known as?
tryptophan operator
43
tryptophan repressor is an ______ protein
allosteric protein
44
complete the scenario when trp is absent:
____ repressor
genes are ____
rna polymerase ____
tryptophan is _____
inactive
on
binds
synthesized
45
complete the scenario when trp is present:
____ repressor
genes are ____
rna polymerase ____
tryptophan is _____
active
off
cannot bind
not synthesized
46
genes whose expression is turned on by the presence of some substance
inducible genes
47
_______ induces expression of the lac genes
lactose
48
_____ induces the expression of a resistance gene
antibiotic
49
what kind of pathway do inducible genes express?
catabolic pathway
50
this enzyme hydrolyses lactose into glucose and galactose
β-galactosidase
51
promotes RNA polymerase binding in β-galactosidase
CAP (catabolite activator protein)
52
blocks RNA polymerase binding in β-galactosidase
repressor
53
give the genes of lac operon
lacZ
lacY
lacA
54
E. coli can use either ____, which is a monosaccharide, or _____, which is a disaccharide
glucose
lactose
55
however, _______ needs to be hydrolysed (digested) first
lactose
56
so E. coli prefers to use ____ when it can
glucose
57
when lactose is absent:
repressor protein is continuously _____
it sits on an _____ site
the repressor protein blocks the ____ site where the RNA polymerase settles before it starts transcribing
synthesized
operator
promoter
58
when lactose is present:
repressor protein is _____ by ______ from the _____
repressor _____ on the operator
removed by allolactose from the operator site
can no longer sit
59
in the absence of glucose (the cell’s favorite energy source), the bacterium makes _____, which activates _____ to switch-on genes that allow the cell to utilize alternative sources of carbon—including lactose
cAMP
CAP
60
the Lac operon in E. coli, for example, is controlled by both the ______
Lac repressor
CAP activator
61
when lactose is present, a small amount of sugar called _____ is formed within the cell
allolactose
62
allolactose fits onto the repressor protein at another active site called ____
which this causes the repressor protein to chage its shape (______)
allosteric site
conformational change
63
when glucose and lactose are present, RNA polymerase can sit on the promoter site but it is ______ and it _________
unstable
keeps falling off
64
when glucose is absent and lactose is present:
another protein is needed which is the _____
CAP (catabolite activator protein)
65
this protein stabilizes RNA polymerase
CAP (catabolite activator protein)
66
the activator protein only works when glucose is _____
absent
67
+ glucose
+ lactose
lac operon:
CAP:
off because CAP is not bound
68
+ glucose
- lactose
lac operon:
CAP:
off because lac repressor bounds and CAP does not bound
69
-- glucose
-- lactose
lac operon:
CAP:
off because repressor bounds, but CAP bounds
70
- glucose
+ lactose
lac operon:
CAP:
on because repressor does not bound and CAP bounds
71
Four situations are possible
1. When glucose is present and lactose is absent the E.
coli ______ β-galactosidase
2. When glucose is present and lactose is present the
E. coli ______ β-galactosidase
3. When glucose is absent and lactose is absent the E.
coli ______ β-galactosidase
4. When glucose is absent and lactose is present the E.
coli ______ β-galactosidase
does not produce
doest not produce
does not produce
produces
72
how does a cell determine which of its thousands of genes to transcribe?
transcription factors
chromatin modifications
regulatory elements
73
recognize specific sequences of DNA cis-regulatory sequences
transcription regulators
74
the region of the chromosome must be opened up in order for enzymes and transcription factors to access the gene
chromatin remodeling
75
give the process that starts with chromatin remodeling
chromatin remodeling
transcription
rna processing
translation
post-translational modification
76
what are the post-translational modifications?
folding
transport
activation of protein
77
elements of transcriptional control
1) RTF recruit chromatin remodeling complex and HATs
2) DNA and promoter are exposed
3) RTF recruit proteins of basal transcription complex to promoter
4) RNA pol and BTC join to form initiation complex
78
nucleosomes contain how many proteins?
8 proteins
79
what is wrapped around each nucleosome?
DNA
80
tightly wrapped around histones (no transcription and genes turned off)
DNA packing as gene control
81
two types of chromatin
heterochromatin
euchromatin
82
darker DNA, tightly packed
heterochromatin
83
highly condensed transcriptionally inactive region
heterochromatin
84
lighter dna, lesser coiled
euchromatin
85
transcriptionally active region which can be easily accessed by RNA polymerase
euchromatin
86
telemores are traditionally considered as?
heterochromatic
87
heterochromatin have ____ DNA
methylated/deacetylated
88
euchromatin have ____ DNA
unmethylated/acetylated
89
chromatin remodelling __________ and facilitate the binding of RNA polymerase and the general transcription factors
increase the accessibility of DNA
90
blocks transcription factors (genes are turned off)
dna methylation
91
attachment of methyl groups (-CH3) to cytosine
dna methylation
92
histone methylation is the addition of methyl groups that can _____ chromatin
condense
93
are genomic regions that contain a high frequency of CG dinucleotides
CpG islands
94
CpG islands particularly occur at or near the transcription ____ site of _____ genes
start site of housekeeping
95
a gene involved in basic functions is required for the sustenance of the cell
housekeeping gene
96
true or false: housekeeping genes are constitutively not expressed
false, they are expressed
97
give example of a housekeeping gene
enzymes in metabolic cycle
98
are those coding for specialized functions synthesized (usually) in large amounts in particular cell types
they are only transcribed if needed
luxury gene
99
example of luxury genes
insulin (beta cells)
serum albumin gene (liver cells)
100
histone acetylation ______ DNA
unwinds
101
attachment of acetyl groups (-CoCH3) to histones
acetylation
102
conformational change in histone proteins
transcription factors have easier access to genes
acetylation
103
enzyme for deacetylation
HDAC/histone deacetylase
104
enzyme for acetylation
HAT/histone acetyltransferase
105
histone tails protrude _____ from a nucleosome
outward
106
acetylation of histol tails promotes ____ chromatin structure that ____ transcription
loose
permits
107
active (open) chromatin
unmethylated cytosines
acetylated histones
gene switched on
108
silent (condensed) chromatin
methylated cytosines
deacetylated histones
gene switched off
109
enzyme for methylation
HMT/histone methyltransferase
110
enzyme for demethylation
HDM/histone demethylase
111
_________ may be located many _____ away from the promoter they regulate
DNA transcription control elements
kilobases
112
these proteins bind to genes at sites known as ______ and speed the rate of transcription
activators
enhancers
113
these proteins bind to selected sets of genes at sites known as _____ and thus slow transcription
repressors
silencers
114
these adapter molecules integrate signals from activators and repressors
coactivators
115
in response to injunctions from activators, these factors position RNA pol at the start of transcription and initiate the transcription process
basal transcription factors
116
it masks the activation surface
repressor
117
binds to the activation domain of the activator protein thereby preventing it from carrying out its activation functions
repressor
118
binds tightly to the activator without having to be bound to DNA directly
repressor
119
what happens to repressor?
1) masks the activation surface
2) competitive dna binding
3) directs integration with the GTFs
4) recruits CRC
5) recruits HDAC
6) recruits HMT
120
interacts with an early stage of the assembling complex of general transcription factors, blocking further assembly
repressor
121
can direct histone deacetylation at specific genes
repressor
122
repressor that is expressed preferentially in the developing kidney
wilms' tumor (WT1) gene
123
children that produce ________ protein, invariably develop kidney tumors
no functional WT1
124
regulates development of kidneys, gonads, etc.
WT1 gene
125
a tumor repressor gene but also acts as an oncogene
WT1 gene
126
a post-transcriptional regulator that is involved in RNA metabolism
WT1 gene
127
capping at the 3’ end and addition of poly-A tail
posttranscriptional control
128
this promotes translation in oocytes
cytoplasmic polyadenylation
129
what is CPEB?
cytoplasmic polyadenylation element binding protein
130
a highly conserved RNA-binding protein that promotes the elongation of the polyadenine tail
CPEB
131
addition of more poly-a-tail in oocytes happend during _____ but is dormant, so it is only activated during _____
meiotic arrest
transcription
132
provides a point where the expression of a gene can be controlled
RNA splicing
133
exons can be spliced together in different ways
RNA splicing
134
this allows a variety of different polypeptides to be assembled from the same gene
RNA splicing
135
______ is common in insects and vertebrates, where 2 or 3 different proteins are produced from one gene
alternate splicing
136
RNA short transcript has what splice site?
5' splice site (donor)
137
RNA long transcript has what splice site?
5' splice site (donor)
3' splice site (acceptor)
138
what is the end product of long rna transcript?
terminal hydrophobic peptide
139
what is the end product of short rna transcript?
terminal hydrophilic peptide
140
in short rna transcript, intron sequences are not removed because of what reason?
acceptor splice junction is missing
141
long repeats of serine adn arginine amino acid residues
SR proteins
142
RNA-binding proteins that bind to exonic splicing enhancer sequences in exons
SR proteins
143
mediate cooperative binding between ubiquitin and spliceosome
SR proteins
144
critical in defining exons in the large pre-mRNAs of higher organisms.
SR proteins
145
essential for splicing pre-mRNA
SR proteins
146
results from mutations in a region of the genome containing two closely related genes, SMN1 and SMN2
spinal muscle atrophy
147
what is the meaning of SMN?
survival of motor neurons
148
encodes a protein identical with SMN1, but it is expressed at much lower level
SMN2
149
SMN2 encodes a protein identical with SMN1, but it is expressed at much lower level because a _______ in one exon interferes with the binding of an _____, leading to exon skipping in most of the ____ mRNAs
silent mutation
SR protein
SMN2
150
SMN2 mRNAs that are correctly spliced is sufficient to maintain cell viability during fetal development, but insufficient of ______ in childhood, resulting in their death and associated disease
spinal cord motor neurons
151
mechanism of silencing gene after transcription by causing degradation of some specific mRNA molecules
RNA interference (RNAi)
152
synthetic RNA molecules that can silence specific genes
degrades ssRNA
short hairpin RNA or shRNA
153
dsRNA of 20-25 bp
small interfering RNA (siRNA)
short interfering RNA
154
small non-coding RNAs of 21-22 nucleotide long, that hybridize to the 3’ untranslated regions of specific target mRNAs
microRNA (miRNA)
155
induces degradation of mRNAs
RNA interference
156
an RNAse III nuclease that converts either long dsRNAs or hairpin RNAs into siRNAs
dicer
157
dicer converts either ____
dsRNAs or shRNAs into siRNAs
158
_______ contains argonaute
RNA-induced silencing complex (RISC)
159
it is an endonuclease capable of degrading messenger RNA whose sequence is complementary to that of the siRNA guide strand
argonaute
160
enumerate the RNAi pathway
long dsRNA
drosha
short dsRNA
cytoplasm
dicer
siRNA/miRNA
RISC recruitment
unwinds
protein-RNA complex
bind to mRNA
mRNA cleaved
161
long dsRNA is processed by this RNase enzyme
drosha
162
the shorter dsRNA is exported then binds to this RNase enzyme
dicer
163
RNAi has become an essential tool in _____
C. elegans research
164
_______ can cause a cell to change the expression of its genes
external signals
165
steroid hormones that regulates the metabolism of glucose
glucocorticoid hormone
166
stimulate breakdown of fat
glucocorticoid hormone
167
is released during time of starvation and intense physical activity, stimulating liver cells to increase the production of glucose from amino acids and other small molecules
glucocorticoid hormone
168
enhancer of glucocorticoid
glucocorticoid response element (GRE)
169
is required for maximal initiation of transcription of glucose
GRE
170
when glucocorticoid hormone is absent, the glucocorticoid receptor _____ from DNA
dissociates
171
iron storage protein that stores surplus iron and release it when the body needs it
ferritin
172
iron storage in the _____
liver
173
the most important iron storage protein
ferritin
174
protein synthesized in the liver that serves as the main transporter of iron in the body
transferrin
175
an increase in iron concentration in the cytosol leads to the increase synthesis of _____ that bind to extra iron
also, this decreases the synthesis of _____ receptor in order to import less iron across plasma membrane
mediated by ____ an iron-responsive regulatory protein which can recognize ____ structure
ferritin
transferrin
aconitase
stem loop
176
the binding of aconitase of the ferritin mRNA ______ translation initiation
blocks
177
during iron starvation, where does cytosolic aconitase in the ferritin mRNA?
5' UTR
178
during iron starvation, where does cytosolic aconitase in the transferrin mRNA?
3' UTR
179
during iron starvation, cytosolic aconitase binds to the 3' UTR in the transferrin mRNA, which blocks an ___________ and thereby stabilizes the mRNA
endonuclease cleavage site
180
during excess iron, what happens to the cytosolic aconitase?
it dissociates from the mRNA because the iron binds into it
181
what happens in excess iron?
ferritin is made, transferrin is not made because of its endonucleolytic cleavage
