9.4

Question 1

While, strictly speaking, the term [blank_start]promoter[blank_end]
refers to the DNA sequence that determines where a polymerase
initiates transcription, the term is often used to refer
to both a promoter and its associated [blank_start]promoter[blank_end]-[blank_start]proximal[blank_end]
control elements.

Accepted Answer

promoter

Accepted Answer

promoter

Accepted Answer

proximal

Question 2

There is flexibility in the spacing of promoter-proximal elements and the promoter.

Answer

true

Question 3

As noted earlier, transcription from many eukaryotic promoters
can be stimulated by control elements located thousands
of base pairs away from the transcription start site.
Such long-distance transcription-control elements, referred
to as [blank_start]enhancers[blank_end], are common in eukaryotic genomes but
fairly rare in [blank_start]bacterial[blank_end] genomes.

Accepted Answer

enhancers

Accepted Answer

bacterial

Question 4

The general consensus
now is that a spectrum of control elements regulates transcription
by RNA polymerase [blank_start]II[blank_end]. At one extreme are [blank_start]enhancers[blank_end],
which can stimulate transcription from a promoter tens
of thousands of base pairs away. At the other extreme are
[blank_start]promoter[blank_end]-[blank_start]proximal[blank_end] elements, such as the upstream elements
controlling the HSV-I tk gene, which lose their influence
when moved 30–50 bp farther from the promoter.

Accepted Answer

II

Accepted Answer

enhancers

Accepted Answer

promoter

Accepted Answer

proximal

Question 5

About 70 percent
of mammalian genes are expressed from [blank_start]CpG[blank_end] island promoters,
usually at much lower levels than genes with [blank_start]TATA[blank_end]
box promoters.

Accepted Answer

CpG

Accepted Answer

TATA

Question 6

The various transcription-control elements found in eukaryotic
DNA are binding sites for regulatory proteins
called [blank_start]transcription factors[blank_end].

Accepted Answer

transcription factors

Question 7

In this approach, a DNA
regulatory element that has been identified by the kinds
of mutational analyses described above is used to identify
[blank_start]cognate[blank_end] proteins—those proteins that bind specifically
to it. Two common techniques for detecting such cognate
proteins are [blank_start]DNase I[blank_end] footprinting and the [blank_start]electrophoreticmobility shift assay[blank_end].

Accepted Answer

cognate

Accepted Answer

DNase I

Accepted Answer

electrophoreticmobility shift assay

Question 8

Like activators,
most eukaryotic repressors are modular proteins that
have two functional domains: a [blank_start]DNA-binding[blank_end] domain and a
[blank_start]repression[blank_end] domain.

Accepted Answer

DNA-binding

Accepted Answer

repression

Question 9

Many bacterial repressors are dimeric proteins in
which an α helix from each monomer inserts into the major
groove in the DNA helix and makes multiple, specific interactions
with the atoms there (Figure 9-29). This α helix
is referred to as the [blank_start]recognition helix[blank_end] or [blank_start]sequence-readinghelix[blank_end] because most of the amino acid side chains that contact
bases in the DNA extend from this helix.

Accepted Answer

recognition helix

Accepted Answer

sequence-readinghelix

Question 10

The recognition
helix, which protrudes from the surface of a bacterial
repressor, is usually supported in the protein structure in
part by [blank_start]hydrophobic[blank_end] interactions with a second α helix just
N-terminal to it. This entire structural element, which is
present in many bacterial repressors, is called a [blank_start]helix[blank_end]-[blank_start]turn[blank_end] [blank_start]helix[blank_end]
[blank_start]motif[blank_end].

Accepted Answer

hydrophobic

Accepted Answer

helix

Accepted Answer

turn

Accepted Answer

helix

Accepted Answer

motif

Question 11

Many eukaryotic transcription factors
that function during development contain a conserved
60-residue DNA-binding motif, called a [blank_start]homeodomain[blank_end], that
is similar to the helix-turn-helix motif of bacterial repressors.

Accepted Answer

homeodomain

Question 12

The [blank_start]C2H2[blank_end] zinc finger is the most [blank_start]common[blank_end] DNA-binding
motif encoded in the human genome and the genomes of
other mammals.

Accepted Answer

C2H2

Accepted Answer

common

Question 13

A second type of zinc-finger structure, designated the
[blank_start]C4[blank_end] zinc finger (because it has four conserved cysteines
in contact with the Zn2+), is found in some 50 human transcription factors.

Accepted Answer

C4

Question 14

Another structural motif present
in the DNA-binding domains of a large class of transcription
factors contains the hydrophobic amino acid [blank_start]leucine[blank_end] at
every [blank_start]seventh[blank_end] position in the sequence. These proteins bind
to DNA as [blank_start]dimers[blank_end], and mutagenesis of the leucines showed
that they were required for [blank_start]dimerization[blank_end]. Consequently, the
name leucine [blank_start]zipper[blank_end] was coined to denote this structural
motif of a coiled coil of two α helixes.

Accepted Answer

leucine

Accepted Answer

seventh

Accepted Answer

dimers

Accepted Answer

dimerization

Accepted Answer

zipper

Question 15

The DNA-binding
domain of another class of dimeric transcription factors
contains a structural motif that is very similar to the basiczipper
motif except that a nonhelical loop of the polypeptide
chain separates two α-helical regions in each monomer
(Figure 9-30d). Termed a [blank_start]basic[blank_end] [blank_start]helix[blank_end]-[blank_start]loop[blank_end]-[blank_start]helix[blank_end] (bHLH), this
motif was predicted from the amino acid sequences of these
proteins, which contain an N-terminal α helix with basic
residues that interact with DNA, a middle loop region, and
a C-terminal region, with hydrophobic amino acids spaced
at intervals characteristic of an amphipathic α helix, that dimerizes
into a coiled coil. As with basic-zipper proteins, different
bHLH proteins can form heterodimers.

Accepted Answer

basic

Accepted Answer

helix

Accepted Answer

loop

Accepted Answer

helix

Question 16

Biophysical studies indicate that acidic activation domains
have an unstructured, random-coil, intrinsically disordered
conformation. These domains stimulate transcription
when they are bound to a protein [blank_start]co-activator[blank_end]

Accepted Answer

co-activator

Question 17

Multiple different transcription factors can interact with each other  to influence gene-control.

Answer

true

Question 18

Analysis of the roughly 50-bp enhancer
that regulates expression of β-interferon, an important protein
in defense against viral infections in vertebrates, provides
a good example of the structure of the DNA-binding
domains of several transcription factors bound to the several
transcription-factor-binding sites that constitute an enhancer
(Figure 9-34). The term [blank_start]enhanceosome[blank_end] has been coined to
describe such large DNA-protein complexes that assemble
from transcription factors as they bind to the multiple binding
sites in an enhancer.

Accepted Answer

enhanceosome

Question 19

This tolerance for variable spacing between binding
sites for specific transcription factors, and between promoter
binding sites for the general transcription factors and
for Pol II, probably contributed to rapid evolution of gene
control in eukaryotes.

Answer

true

Question 20

[blank_start]Promoters[blank_end] direct binding of RNA polymerase II to DNA,
determine the site of [blank_start]transcription[blank_end] initiation, and influence
the [blank_start]frequency[blank_end] of transcription initiation.

Accepted Answer

Promoters

Accepted Answer

transcription

Accepted Answer

frequency

Question 21

[blank_start]Promoter[blank_end]-[blank_start]proximal[blank_end] elements occur within about 200 bp
of a start site. Several such elements, containing 6–10 bp,
may help regulate a particular gene.

Accepted Answer

Promoter

Accepted Answer

proximal

Question 22

[blank_start]Enhancers[blank_end], which contain multiple short control elements,
may be located from 200 bp to tens of kilobases upstream
or downstream from a promoter, within an intron, or downstream
from the final exon of a gene.

Accepted Answer

Enhancers

Question 23

Promoter-proximal elements and enhancers are often celltype-
specific, functioning only in specific differentiated cell
types.

Answer

true

Question 24

[blank_start]Transcription factors[blank_end], which activate or repress transcription,
bind to promoter-proximal regulatory elements and
enhancers in eukaryotic DNA.

Accepted Answer

Transcription factors

Question 25

Transcription activators and repressors are generally
modular proteins containing a single DNA-binding domain
and one or a few activation domains (for activators) or repression
domains (for repressors). The different domains are
frequently linked by rigid, intrinsically ordered polypeptide
regions

Answer

true

Question 26

Activation and repression domains in transcription factors
exhibit a variety of amino acid sequences and threedimensional
structures. In general, these functional domains
interact with [blank_start]co-activators[blank_end] or [blank_start]co-repressors[blank_end], which are critical
to the ability of transcription factors to modulate gene
expression.

Accepted Answer

co-activators

Accepted Answer

co-repressors

Question 27

The transcription-control regions of most genes contain
binding sites for multiple transcription factors. Transcription
of such genes varies depending on the particular repertoire
of transcription factors that are expressed and activated in a
particular cell at a particular time.

Answer

true

Question 28

Binding of multiple transcription factors to multiple sites
in an enhancer forms a DNA-protein complex called an [blank_start]enhanceosome[blank_end]

Accepted Answer

enhanceosome

9.4

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