Transcription Regulation of gene Flashcards
1
Q
although the mechanism of
transcription in bacteria and
eukaryotes is fundamentally similar,
transcription is substantially more
complicated in Blank
A
eukaryote
2
Q
one significant difference is that the
DNA of eukaryotes (and Archaea) is
wrapped around Blank to form
nucleosomes, and the nucleosomes
are further organized into Blank
A
Histones, chromatin
3
Q
nucleosomes represses
A
gene
expression
4
Q
only those Blank by
specific positive regulatory
mechanisms are transcribed
A
genes activated
5
Q
large, complex multimeric proteins
(500 to 700 kDa), consisting of Blank or
more types of subunit
A
10
6
Q
- localized to the nucleolus
- transcribes the major rRNA genes
A
RNA polymerase I
7
Q
- transcribes most noncoding RNA
genes and all protein-encoding genes - responsible for the synthesis of mRNA
A
RNA polymerase II
8
Q
- transcribes tRNA genes, the rRNA
genes encoding 5S rRNA, and a variety
of other small RNAs, including several
involved in mRNA processing and
protein transport
A
RNA polymerase III
9
Q
all possess 2 large subunits (each 140
kDa or greater) having sequence
similarity to the large Blank and Blank
subunits of E. coli RNA polymerase
A
β- and β’
10
Q
the 3 classes of RNA polymerase
can be distinguished by their
sensitivity to
A
a-amanitin
11
Q
- a bicyclic octapeptide produced by
the poisonous mushroom Amanita
phalloides (destroying angel
mushroom) - blocks RNA chain elongation
A
a-amanitin
12
Q
RNA polymerase I is Blank to this
compound, RNA polymerase II is
Blank and RNA polymerase
III is Blank
A
resistant, very sensitive, less sensitive
13
Q
- DNA binding proteins that
recognize and accurately initiate
transcription at specific promoter
sequences - RNA polymerase I templates are
the rRNA genes
A
transcription factors
14
Q
- RNA polymerase III interacts with
transcription factors Blank, Blank, Blank
A
TFIIIA, TFIIIB, TFIIIC
14
Q
- must carry out its function at any
moment only on those genes whose
products are appropriate to the
needs of the cell in its ever-changing
metabolism and growth
A
RNA polymerase II
15
Q
both yeast and human RNA
polymerase II consist of Blank different
polypeptide
A
12
16
Q
- essential to RNA polymerase II
function
A
C-terminal domain (CTD)
17
Q
True or False
only RNA polymerase III whose CTD
is not phosphorylated can initiate
transcription
A
False: RNA polymerase II
18
Q
proceeds only after protein phosphorylation
within the CTD
A
transcription elongation
19
Q
triggers the conversion of an initiation complex
into an elongation complex
A
phosphorylation
20
Q
also plays a prominent role in
orchestrating subsequent events in
the transcription process
A
CTD
21
Q
4 stages of transcription in eukaryotes
A
- promoter recognition and RNA
polymerase II binding - initiation
- elongation
- termination
21
Q
in eukaryotes, metabolic activity,
cell division, complex patterns of
embryonic development and cell
differentiation must be coordinated
through the regulation of Blank
A
gene
expression
22
Q
all this coordinated regulation takes
place in Blank with a large quantity
and sequence diversity of DNA
A
cells
23
a typical mammalian cell has Blank as
much DNA as an E. coli cell
1500 x
24
gene expression in eukaryotes is
precisely regulated in a blank and blank
time-specific
and cell-specific fashion
25
* proteins that bind to specific CREs
transacting factors
26
over Blank gene-specific transacting
factors are known
1600
27
* at or near the transcription start
site (TSS, the nucleotide where
transcription begins)
* many thousands of base pairs away
(distal CREs which include
enhancers, insulators, silencers)
Locations of CREs
28
2 distinct CRE sequences in which
efficient transcription of a protein
coding gene by RNA pol II depends
* promoters (sequences at or near
the TSS)
* enhancers or silencers (more
distantly located)
28
the promoters of eukaryotic
protein-encoding genes are quite
Blank and blank
complex and variable
29
* their location is defined by the core
promoter, Blank to blank DNA
sequence within which lies the TSS
a 50- to 100-bp
30
the assembled apparatus is
megadaltons in size and occupies
more than Blank bp around the TSS
100
31
about half of the core promoters
for human protein-coding genes
have an Inr element, about Blank
have a TATA box
20%
32
* has the consensus sequence: C/G/T
C/G/T- C-A-C/G/T-A/T, with the bold A at
position +1, defining the TSS
* found in housekeeping genes
Inr element
33
is usually located at
position −31 from the TSS
* a feature of tissue-specific genes
TATA box (consensus sequence T-A
T-A-A-T/A-A/T-A/G)
34
the Blank nature of the TATA box
facilitates promoter melting and
access of the transcription
apparatus to the template strand
A:T-rich
35
* embedded in the coding region,
positioned at +28 to +33 relative to
the TSS
DPEs
36
* genes that encode proteins
commonly present in all cells and
essential to normal function
* transcribed at more-or-less steady
levels → constitutive expression
housekeeping genes
37
short nucleotide sequences called
Blank found near
the promoter (the promoter
proximal region)
response elements (REs)
38
* CREs located quite distant from the
genes they regulate, ranging from
several kbp to nearly a megabase
pair in some human genes
enhancers and silencers
39
* has a highly variable DNA sequence
less than 100-bp-long
* located in a region of chromatin
accessible to DNA-binding proteins
because nucleosomes are sparse
enhancer
40
(ENCODE) meaning
Encyclopedia of DNA
Elements
40
* sequences where transcriptional
repressors bind
* searches through the human
genome by the Encyclopedia of DNA
Elements (ENCODE) Consortium
reveal hundreds of thousands of
putative enhancers and silencers,
far more than the number of
protein-coding gene
silencers
41
* called upstream activation
sequences (UASs) in yeast
* assist transcription initiation
enhancers
42
43
* sequences are bidirectional
* can be removed and then
reinserted in the reverse sequence
orientation without impairing their
function
* represent modules of consensus
sequence
* non-specific
* stimulate transcription from any
promoter that happens to be in
their vicinity
* function is dependent on
recognition by a specific
transcription factor
enhancers
44
* DNA sequences of 0.1–1 kb that act
in 2 ways
✓ to shield regions of chromatin
active in transcription from inactive
regions
✓ to block an enhancer from
stimulating transcription from a
specific promoter
insulators
45
True or False
an insulator sequence cannot act as an
enhancer blocker if it is located
somewhere along the DNA
sequence between the enhancer
and the promoter
False: can act
46
is a tumor response element activated in the
presence of tumor-promoting phorbol esters such as TPA
(tetradecanoyl phorbol acetate)
TRE
47
* a metal binding protein that protects
cells against metal toxicity by binding
excess amounts of heavy metals and
removing them from the cell
* always present at low levels
* its concentration increases in
response to heavy metal ions such as
cadmium or in response to
glucocorticoid hormones
metallothionein
48
when MTF binds heavy metals such
as blank and blank, it activates
metallothionein gene expression by
binding to the MREs
cadmium and zinc
49
in the presence of the stress
hormone cortisol, Blank binds to the metallothionein
gene GRE, activating transcription
*
growth hormone
(GR)
50
nearly Blank of human genes have a
GRE
30%
51
* composed of more than 100
polypeptides
* RNA polymerase II
* a set of general transcription factors
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIH)
* Mediator, a 1.5-megadalton complex
that mediates interactions between
RNA pol II and proteins bound at
distal CREs
PIC (preinitiation complex)
52
consists of the TBP (the TATA
binding protein), which directly
recognizes the TATA box within the
core promoter and a set of TBP
associated factors (TAFs)
TFIID
53
* the first GTF to recognize and bind to
the promoter
TFIID complex
54
* the TATA box-binding protein that
recognizes the promoter core, making
contacts with the DNA minor groove
and distorting and bending the DNA
so that sequences upstream and
downstream of the TAT box come into
closer proximity
TBP
55
* stimulates transcription by
stabilizing the interaction of TFIID
and the TATA box
TFIIA
56
* serves as a bridge between
promoter-bound TFIID and RNA pol
II, positioning the RNA polymerase
active site over the promoter
TFIIB
57
* the assemblage of RNA polymerase
II and these other proteins at the
promoter
initiation complex
58
transcription initiation in
eukaryotes also requires Mediator,
which in humans is composed of Blank
subunits, the Med proteins
26
59
* a megacomplex of about 20
proteins
* named for its Spt, Ada, and Gen5
subunits
SAGA
60
* a family of proteins involved in
gene expression
Spt
61
* a histone acetyltransferase (HAT, a
histone-modifying enzyme)
Ada
62
* a lysine acetyltransferase (KAT)
Gen5
63
* contains TAF (TBP-associated proteins)
subunits
* can recognize TATA boxes
* required for the expression of most
RNA pol II-transcribed genes
SAGA
64
is critical for
recognition, with AA side chains
providing most of the critical contacts
with DNA
hydrogen bonding
65
protein contacts with the bases of
DNA usually occur within the Blank (but not always)
major
groove
66
3 kinds of small, distinctive structural
motifs
* helix-turn-helix (HTH)
* zinc finger (Zn-finger)
* leucine zipper-basic region (bZIP)
67
* occurs on DNA in the
nucleus
transcription
68
* occurs on ribosomes in
the cytoplasm
translation
69
*must be transported
from the nucleus to the cytosol to
be translated
transcripts
70
* alterations that convert the newly
synthesized RNAs, or primary
transcripts, into mature mRNAs
* eukaryotic mRNAs are exclusively
monocistronic
processing
71
* protein-coding regions of an
interrupted or split gene
* sequences that are represented in
mature RNA molecules
exons
72
* non coding regions
* intervening nucleotide sequences
that are removed from the primary
transcript when it is processed into
a mature RNA
introns
73
* adding a GMP to the 5’-phosphate
end
capping
74
* addition of methyl groups on various
bases and riboses at the 5’-end
methylation
75
* addition of multiple A residues to
the 3’-end
polyadenylylation
76
* removal of all introns
splicing
77
* primary transcripts or pre-mRNAs that
serve as precursors to mRNA
* shortly after transcription of hnRNA is
initiated, the 5’-end of the growing
transcript is capped by addition of a
guanylyl residue
heterogeneous nuclear RNA (hnRNA)
78
