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Protein and Nucleic acid > Transcription Regulation of gene > Flashcards

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

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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

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3
Q

nucleosomes represses

A

gene
expression

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4
Q

only those Blank by
specific positive regulatory
mechanisms are transcribed

A

genes activated

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5
Q

large, complex multimeric proteins
(500 to 700 kDa), consisting of Blank or
more types of subunit

A

10

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6
Q
  • localized to the nucleolus
  • transcribes the major rRNA genes
A

RNA polymerase I

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7
Q
  • transcribes most noncoding RNA
    genes and all protein-encoding genes
  • responsible for the synthesis of mRNA
A

RNA polymerase II

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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

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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’

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10
Q

the 3 classes of RNA polymerase
can be distinguished by their
sensitivity to

A

a-amanitin

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11
Q
  • a bicyclic octapeptide produced by
    the poisonous mushroom Amanita
    phalloides (destroying angel
    mushroom)
  • blocks RNA chain elongation
A

a-amanitin

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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

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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

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14
Q
  • RNA polymerase III interacts with
    transcription factors Blank, Blank, Blank
A

TFIIIA, TFIIIB, TFIIIC

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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

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15
Q

both yeast and human RNA
polymerase II consist of Blank different
polypeptide

A

12

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16
Q
  • essential to RNA polymerase II
    function
A

C-terminal domain (CTD)

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17
Q

True or False
only RNA polymerase III whose CTD
is not phosphorylated can initiate
transcription

A

False: RNA polymerase II

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18
Q

proceeds only after protein phosphorylation
within the CTD

A

transcription elongation

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19
Q

triggers the conversion of an initiation complex
into an elongation complex

A

phosphorylation

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20
Q

also plays a prominent role in
orchestrating subsequent events in
the transcription process

A

CTD

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21
Q

4 stages of transcription in eukaryotes

A
  • promoter recognition and RNA
    polymerase II binding
  • initiation
  • elongation
  • termination
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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

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22
Q

all this coordinated regulation takes
place in Blank with a large quantity
and sequence diversity of DNA

A

cells

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23
Q

a typical mammalian cell has Blank as
much DNA as an E. coli cell

A

1500 x

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24
Q

gene expression in eukaryotes is
precisely regulated in a blank and blank

A

time-specific
and cell-specific fashion

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25
Q
  • proteins that bind to specific CREs
A

transacting factors

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26
Q

over Blank gene-specific transacting
factors are known

A

1600

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27
Q
  • 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)
A

Locations of CREs

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28
Q

2 distinct CRE sequences in which
efficient transcription of a protein
coding gene by RNA pol II depends

A
  • promoters (sequences at or near
    the TSS)
  • enhancers or silencers (more
    distantly located)
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28
Q

the promoters of eukaryotic
protein-encoding genes are quite
Blank and blank

A

complex and variable

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29
Q
  • their location is defined by the core
    promoter, Blank to blank DNA
    sequence within which lies the TSS
A

a 50- to 100-bp

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30
Q

the assembled apparatus is
megadaltons in size and occupies
more than Blank bp around the TSS

A

100

31
Q

about half of the core promoters
for human protein-coding genes
have an Inr element, about Blank
have a TATA box

A

20%

32
Q
  • 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
A

Inr element

33
Q

is usually located at
position −31 from the TSS
* a feature of tissue-specific genes

A

TATA box (consensus sequence T-A
T-A-A-T/A-A/T-A/G)

34
Q

the Blank nature of the TATA box
facilitates promoter melting and
access of the transcription
apparatus to the template strand

A

A:T-rich

35
Q
  • embedded in the coding region,
    positioned at +28 to +33 relative to
    the TSS
A

DPEs

36
Q
  • genes that encode proteins
    commonly present in all cells and
    essential to normal function
  • transcribed at more-or-less steady
    levels → constitutive expression
A

housekeeping genes

37
Q

short nucleotide sequences called
Blank found near
the promoter (the promoter
proximal region)

A

response elements (REs)

38
Q
  • CREs located quite distant from the
    genes they regulate, ranging from
    several kbp to nearly a megabase
    pair in some human genes
A

enhancers and silencers

39
Q
  • 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
A

enhancer

40
Q

(ENCODE) meaning

A

Encyclopedia of DNA
Elements

40
Q
  • 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
A

silencers

41
Q
  • called upstream activation
    sequences (UASs) in yeast
  • assist transcription initiation
A

enhancers

42
Q
A
43
Q
  • 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
A

enhancers

44
Q
  • 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
A

insulators

45
Q

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

A

False: can act

46
Q

is a tumor response element activated in the
presence of tumor-promoting phorbol esters such as TPA
(tetradecanoyl phorbol acetate)

A

TRE

47
Q
  • 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
A

metallothionein

48
Q

when MTF binds heavy metals such
as blank and blank, it activates
metallothionein gene expression by
binding to the MREs

A

cadmium and zinc

49
Q

in the presence of the stress
hormone cortisol, Blank binds to the metallothionein
gene GRE, activating transcription
*

A

growth hormone
(GR)

50
Q

nearly Blank of human genes have a
GRE

A

30%

51
Q
  • 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
A

PIC (preinitiation complex)

52
Q

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)

A

TFIID

53
Q
  • the first GTF to recognize and bind to
    the promoter
A

TFIID complex

54
Q
  • 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
A

TBP

55
Q
  • stimulates transcription by
    stabilizing the interaction of TFIID
    and the TATA box
A

TFIIA

56
Q
  • serves as a bridge between
    promoter-bound TFIID and RNA pol
    II, positioning the RNA polymerase
    active site over the promoter
A

TFIIB

57
Q
  • the assemblage of RNA polymerase
    II and these other proteins at the
    promoter
A

initiation complex

58
Q

transcription initiation in
eukaryotes also requires Mediator,
which in humans is composed of Blank
subunits, the Med proteins

A

26

59
Q
  • a megacomplex of about 20
    proteins
  • named for its Spt, Ada, and Gen5
    subunits
A

SAGA

60
Q
  • a family of proteins involved in
    gene expression
A

Spt

61
Q
  • a histone acetyltransferase (HAT, a
    histone-modifying enzyme)
A

Ada

62
Q
  • a lysine acetyltransferase (KAT)
A

Gen5

63
Q
  • contains TAF (TBP-associated proteins)
    subunits
  • can recognize TATA boxes
  • required for the expression of most
    RNA pol II-transcribed genes
A

SAGA

64
Q

is critical for
recognition, with AA side chains
providing most of the critical contacts
with DNA

A

hydrogen bonding

65
Q

protein contacts with the bases of
DNA usually occur within the Blank (but not always)

A

major
groove

66
Q

3 kinds of small, distinctive structural
motifs

A
  • helix-turn-helix (HTH)
  • zinc finger (Zn-finger)
  • leucine zipper-basic region (bZIP)
67
Q
  • occurs on DNA in the
    nucleus
A

transcription

68
Q
  • occurs on ribosomes in
    the cytoplasm
A

translation

69
Q

*must be transported
from the nucleus to the cytosol to
be translated

A

transcripts

70
Q
  • alterations that convert the newly
    synthesized RNAs, or primary
    transcripts, into mature mRNAs
  • eukaryotic mRNAs are exclusively
    monocistronic
A

processing

71
Q
  • protein-coding regions of an
    interrupted or split gene
  • sequences that are represented in
    mature RNA molecules
A

exons

72
Q
  • non coding regions
  • intervening nucleotide sequences
    that are removed from the primary
    transcript when it is processed into
    a mature RNA
A

introns

73
Q
  • adding a GMP to the 5’-phosphate
    end
A

capping

74
Q
  • addition of methyl groups on various
    bases and riboses at the 5’-end
A

methylation

75
Q
  • addition of multiple A residues to
    the 3’-end
A

polyadenylylation

76
Q
  • removal of all introns
A

splicing

77
Q
  • 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
A

heterogeneous nuclear RNA (hnRNA)

78
Q
A

Protein and Nucleic acid (9 decks)

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