Chapter 9: Regulation of Transcription

Question 1

key to providing the cell with the correct amount of gene product at the correct time

Answer 1

transcriptional regulation

Question 2

transcriptional regulation underlies () and employs a wide range of mechanisms

Answer 2

cell differentiation and development

Question 3

one level of transcriptional regulation is (1), but most regulation comes from (2)

Answer 3

1. promoter strength
2. targeted gene regulation

Question 4

targeted gene regulation can happen at (3)

Answer 4

1. transcription initiation (most prevalent)
2. elongation or termination
3. regulation from transcribed RNA itself

Question 5

regulatory (1) regulate transcription by binding to regulatory (2)

Answer 5

1. proteins
2. sequences

Question 6

control relative amount of transcription from promoter

Answer 6

regulatory proteins

Question 7

2 types of regulatory proteins

Answer 7

1. repressors - decrease transcription level
2. activators - increase transcription level

Question 8

specific DNA regions to which regulatory proteins bind

Answer 8

regulatory sequences

Question 9

in bacteria, sequences recognized by regulatory proteins are called ()

Answer 9

operator sites

Question 10

bacterial operator sites are typically ()

Answer 10

close to or overlap promoter

Question 11

if operators or (and common for enhancers) are distal to the gene, DNA must loop around for the regulatory protein to interact with the polymerase, sometimes aided by ()

Answer 11

architectural DNA binding proteins

Question 12

eukaryotic analogs to bacterial operator sites; usual distal (1000s of bps away) from genes

Answer 12

enhancers

Question 13

to increase the sophistication and subtlety of regulation, eukaryotic regulatory sequences frequently bind ()

Answer 13

several regulatory proteins

Question 14

found in more complex eukaryotes; have a combination of enhancer and insulator elements

Answer 14

locus control regions (LCRs)

Question 15

blocks unwanted interaction between enhancers and certain genes

Answer 15

insulators

Question 16

role of LCRs in the expression of beta-globin genes

Answer 16

LCRs make sure that only fetal Hb is expressed while in the womb, and only adult Hb is expressed outside of the womb

Question 17

each regulatory protein has a () that recognizes a specific sequence

Answer 17

DNA binding domain

Question 18

regulatory proteins are often (), allowing them to have additional domains that give them additional functions

Answer 18

modular

Question 19

transcription level changes in response to (1); this can be done by changing the (2) of the regulatory proteins

Answer 19

1. changing conditions
2. activity

Question 20

small molecules that can bind directly to regulatory proteins and change their conformation upon binding

Answer 20

allosteric effectors

Question 21

() can also change how regulatory proteins interact

Answer 21

phosphorylation or other covalent modifications

Question 22

covalent modification, along with other factors such as () serve to fine-tune regulation of gene expression

Answer 22

regulator abundance and localization

Question 23

() chromatin tends to be actively transcribed

Answer 23

hyperacetylated

Question 24

hypoacetylated chromatin tends to have () levels of transcription

Answer 24

low

Question 25

other histone modifications like (4) also affect transcription, but the relationship is not yet clear

Answer 25

1. methylation
2. phosphorylation
3. ubiquitination
4. sumoylation

Question 26

a () has been proposed (and is being actively researched) in which certain combinations of modifications would lead to specific outcomes

Answer 26

histone code

Question 27

() are tailored to fit DNA; some are found throughout life, other are found just in eukaryotes or metazoans

Answer 27

DNA-binding motifs

Question 28

the () is a common DNA-binding motif and is found in many protein folds

Answer 28

helix-turn-helix

Question 29

the second helix in the helix-turn-helix motif is called the (), and fits into the major groove of DNA

Answer 29

recognition helix

Question 30

recognition helices in helix-turn-helix motifs read the DNA sequence through ()

Answer 30

interactions with the base pairs

Question 31

many helix-turn-helix DNA-binding motifs are dimers, with the recognition helices spaces () apart to fit in neighboring grooves

Answer 31

3.4 nm

Question 32

the () is a monomeric helix-turn-helix, commonly found in eukaryotes; its recognition helix is longer than its bacterial counterparts

Answer 32

homeodomain

Question 33

the sidechains of homeodomain motifs interact with (1), while its N-terminal arm makes contacts in the (2)

Answer 33

1. DNA base pairs
2. minor groove

Question 34

a prominent part of many DNA binding folds -> most common DNA-binding domain in the human genome; has a domain of ~30 amino acids

Answer 34

zinc finger

Question 35

structure of a zinc finger

Answer 35

alpha helix and 2 beta strands around a central zinc ion

Question 36

the zinc ion in zinc fingers interacts with (); these are always conserved in proteins with zinc fingers

Answer 36

2 cysteines and 2 histidines -> Cys2His2 zinc fingers

Question 37

each zinc finger inserts its alpha helix into the (1) of DNA and recognizes (2)

Answer 37

1. major groove
2. 2-3 base pairs

Question 38

how do proteins with zinc fingers enhance specificity when recognizing DNA sequences

Answer 38

proteins have multiple zinc fingers -> zinc fingers are multimerized

Question 39

alpha helices that wind around each other; form part of some DNA-binding domains

Answer 39

coiled-coils

Question 40

2 main examples of coiled-coil motifs in DNA-binding domains

Answer 40

1. basic region-leucine zipper (bZIP) proteins
2. basic region-helix-loop-helix (bHLH) proteins

Question 41

structure of bZIP proteins

Answer 41

• 2 alpha helices about 60 AAs long
• helices have hydrophobic leucine residues
• helices splay and sit in the DNA major groove at the N terminal end

Question 42

structure of bHLH proteins

Answer 42

• 4 helices joined by a loop (four-helix bundle)

Question 43

both bZIP and bHLH proteins become () when not bound to DNA

Answer 43

unstructured

Question 44

the () binds DNA with 2 beta strands

Answer 44

MetJ repressor

Question 45

(1), part of the mammalian transcriptional regulator nuclear factor (2), are largely beta sheets

Answer 45

1. p50 and p65
2. NF-kappa(B)

Question 46

() are entirely made up of beta sheets and connecting loops

Answer 46

immunoglobulins

Question 47

a simple way to regulate transcription is to ()

Answer 47

prevent RNA pol from accessing the promoter

Question 48

bacterial genes that are located, regulated, and transcribed together

Answer 48

operon

Question 49

the () is a protein with a helix-turn-helix DNA-binding motif that responds to the level of tryptophan in the cell

Answer 49

Trp repressor

Question 50

when tryptophan levels are high in the cell, Trp repressor binds to () and blocks RNA pol from binding

Answer 50

Trp operator

Question 51

Trp repressor can only bind to DNA when (1), which only happens when (2)

Answer 51

1. it is bound to Trp
2. Trp levels are high

Question 52

regulatory protein that enhances the binding of RNA pol to a promoter to increase transcription levels

Answer 52

activators

Question 53

() activates more than 100 E. coli promoters when carbon sources are low

Answer 53

catabolite activator protein (CAP)

Question 54

the catabolite activator protein (CAP) is also called

Answer 54

cAMP receptor protein (CRP)

Question 55

() leads to increase in cAMP levels -> cAMP binds to CAP and increases CAP’s binding to DNA

Answer 55

glucose depletion

Question 56

CAP enhances RNA pol binding to DNA by binding to the ()

Answer 56

CTD

Question 57

2 classes of promoters that interact with CAP

Answer 57

1. class I - CAP binds upstream of promoter
2. class II - CAP binding site overlaps the RNA pol binding site

Question 58

() responds to low glucose levels in the cell by allowing the cell to metabolize lactose instead (if lactose is present) -> contains genes that are needed for metabolizing lactose

Answer 58

lac operon

Question 59

(1) and (2) regulate the lac operon

Answer 59

1. CAP
2. LacI repressor

Question 60

how does the LacI repressor regulate the lac operon

Answer 60

1. when lactose is present, it binds to the LacI repressor and prevents it from binding to operator
2. when lactose is absent, LacI is able to bind to lac opertor to prevent transcription of lac operon

Question 61

how does CAP activator regulate the lac operon

Answer 61

1. glucose present: decreased cAMP levels -> cAMP doesn’t bind to CAP and CAP doesn’t bind to lac operator
2. glucose absent: increased cAMP levels -> cAMP binds CAP and CAP binds to lac operator to increase transcription of lac operon

Question 62

in () conditions, transcription for lac operon is strongly on

Answer 62

low glucose, available lactose

Question 63

in (1) conditions, there is weak transcription of lac operon; aka (2)

Answer 63

1. high glucose, available lactose
2. basal transcription

Question 64

if the spacing between -10 and -35 promoter elements is (), RNA pol binding is weakened -> another layer of regulation

Answer 64

very large

Question 65

() can change the way promoter elements are spatially related to each other, thereby enhancing transcription

Answer 65

MerR family regulators

Question 66

the MerR protein can bind to the DNA and change its conformation to ()

Answer 66

a spacing more favorable for RNA pol binding

Question 67

RNA pol holoenzyme that contains sigma 54 needs to be activated by () to drive promoter opening

Answer 67

ATP hydrolysis

Question 68

() is an example of an activator with sigma 54

Answer 68

NtrC

Question 69

NtrC binds at enhancer elements and activates transcription when ()

Answer 69

phosphorylated

Question 70

phosphorylation triggers () of NtrC, and promotes its interaction with the polymerase at the promoter

Answer 70

oligomerization

Question 71

in NtrC activation, oligomerization stimulates NtrC’s (), which helps promote the formation of the open complex

Answer 71

rate of ATP hydrolysis

Question 72

responses to external signals often involve () that leads to a signaling cascade

Answer 72

phosphorylation of a receptor protein

Question 73

a 2-component signal transduction pathway is an example of how phosphorylation of a receptor protein leads to a ()

Answer 73

signaling cascade

Question 74

2-component signal transduction pathway have a (1) and a (2)

Answer 74

1. sensor kinase
2. response regulator

Question 75

the sensor kinase in a 2 component transduction pathway has a () that becomes autophosphorylated on receipt of the signal

Answer 75

histidine (histidine kinases)

Question 76

in 2 component transduction pathways, the phosphoryl group on an autophosphorylated histidine is transferred to an (1) in a (2)

Answer 76

1. aspartic acid residue
2. response regulator protein

Question 77

Complex and differing signals regulate transcription. The outcome of the combination of signals, which can be (1), depends on the (2)

Answer 77

1. antagonistic
2. strength of the opposing regulators.

Question 78

() infects E. coli by injecting its chromosome into the
bacterium

Answer 78

Bacteriophage lambda

Question 79

after infecting E. coli, bacteriophage lambda enters either (1) or (2)

Answer 79

1. lytic growth
2. lysogeny

Question 80

when bacteriophage lambda infect E. coli, () produces lots of copies of the virus in the bacterial cell and eventually leads to cell lysis

Answer 80

lytic growth

Question 81

lytic growth allows a phage to () a cell that may not survive

Answer 81

escape

Question 82

when bacteriophage lambda infects E. coli, () happens when the virus integrates into the host genome and becomes dormant

Answer 82

lysogeny

Question 83

in lysogeny, the integrated virus is called a ()

Answer 83

prophage

Question 84

lysogeny allows bacteriophage lambda to multiply in conditions where ()

Answer 84

there might not be enough nearby cells to infect

Question 85

when E. coli containing prophage endures (1), the phage can be triggered to excise itself and (2)

Answer 85

1. difficult conditions (e.g. DNA damage)
2. undergo lytic growth

Question 86

lysis and lysogeny are regulated by levels of the DNA-binding proteins (3)

Answer 86

1. cI (lambda repressor)
2. cII
3. Cro

Question 87

cI, cII, and Cro bind to sites in the phage chromosome and control transcription at the ff 4 promoters:

Answer 87

1. P_R
2. P_L
3. P_RE
4. P_RM

Question 88

(2) are the early promoters involved in the choice between lysis and lysogeny -> host RNA pol initiates basal transcription

Answer 88

P_R and P_L

Question 89

P_R promoter encodes (1) regulators, while P_L encodes (2)

Answer 89

1. Cro and cII
2. N protein

Question 90

() prevents premature termination of the P_R transcript and thereby allows transcription of Cro and cII

Answer 90

N protein

Question 91

if sufficient cII accumulates, it stimulates transcription at (1), which produces (2)

Answer 91

1. P_RE
2. cI

Question 92

cI stimulates (), which makes more cI

Answer 92

P_RM

Question 93

high cI levels result in cI binding to P_R and P_L promoters -> repress (1) and activates transcription of (2)

Answer 93

1. lytic genes
2. integrase

Question 94

() promote and maintain lysogeny

Answer 94

high cI levels

Question 95

if not enough cII is produced, (1) binds to P_RM and represses (2)

Answer 95

1. Cro
2. cI production

Question 96

by preventing (), Cro ensures the expression of lytic genes from P_R and P_L

Answer 96

cI synthesis

Question 97

(1) regulate the levels of cII -> cII is sensitive to host cell (2)

Answer 97

1. environmental factors
2. proteases

Question 98

if proteases are (), cII is degraded -> cI cannot accumulate and virus enters (2)

Answer 98

1. highly active
2. lytic growth

Question 99

the () of cI and Cro at 6 DNA-binding sites determine the choice between lysogeny and lysis

Answer 99

binding affinities

Question 100

cI has 2 domains that can form (1) and (2)

Answer 100

1. tetramers
2. oligomers

Question 101

Cro has a single small domain that binds as a ()

Answer 101

dimer

Question 102

operators O_L and O_R (for promoters P_L and P_R, respectively) each have () that cI or Cro can bind to

Answer 102

3 sites

Question 103

cI binds first to operators (), where it has strongest affinity

Answer 103

OL1 and OR1

Question 104

binding of cI to OL1 and OR1 recruis another cI to weaker sites ()

Answer 104

OL2 and OR2

Question 105

the cI units bound to operators OL1-2, OR1-2 (1) to form a (2)

Answer 105

1. oligomerize
2. looped-out structure

Question 106

oligomerization of the cI units at operator sites stops (1) and promotes (2) -> increase in cI levels

Answer 106

1. RNA pol binding to PL and PR
2. transcription from PRM

Question 107

with increasing levels of cI, cI binds to (), stoping the activation of PRM -> suppressing cI synthesis

Answer 107

OL3 and OR3

Question 108

binding of cI to OL3 and OR3 serves as ()

Answer 108

autoregulation

Question 109

if there is insufficient cI, Cro accumulates and binds with the greatest affinity to (), blocking PRM and suppressing cI synthesis

Answer 109

OR3

Question 110

more Cro synthesis leads to binding at the other (1), autoregulating Cro by preventing RNA pol binding to (2)

Answer 110

1. OR and OL sites
2. PR promoter

Question 111

the prophage must be able to excise itself and switch from lysogeny to lytic growth if the host cell is ()

Answer 111

threatened

Question 112

excision of prophage is brought about by a response to () that disables cI

Answer 112

DNA damage

Question 113

DNA damage in a bacteriophage infected bacterium prompts a (1), activating (2)

Answer 113

1. host SOS response
2. RecA

Question 114

cleaves cI so it cannot dimerize or cooperate with other cI units

Answer 114

RecA

Question 115

after cI cleavage by RecA, cI dissociates from (), allowing transcription from PL and PR-> allowing lytic growth

Answer 115

operator sites

Question 116

regulation can also occur at the () steps of transcript synthesis

Answer 116

elongation and termination

Question 117

some phage lambda genes are transcribed only when transcription termination is actively prevented -> this is called ()

Answer 117

anti-termination

Question 118

() prevent stalling and termination by altering the properties of bacterial RNA pol

Answer 118

bacteriophage lambda N and Q proteins

Question 119

initially, transcription from PL and PR promoters successfully makes Cro and N protein until RNA pol encounters termination sites ()

Answer 119

tL and tR

Question 120

when N protein builds up, it stops ()

Answer 120

termination of transcription from PL and PR promoters

Question 121

N proteins bind to (1) in the transcribed RNA in a (2)

Answer 121

1. nut sites
2. step-loop form

Question 122

when N protein binds to nut sites, it allows several proteins to be (), allowing RNA pol to transcribe through tL and tR

Answer 122

recruited and interact with RNA pol

Question 123

with termination at tL and tR suppressed (due to build up of N proteins), downstream genes can be transcribed, including ()

Answer 123

bacteriophage lambda protein Q

Question 124

() overrides termination at the PR promoter, allowing transcription of late lytic genes

Answer 124

Q protein

Question 125

in contrast to N protein, Q prevents termination by ()

Answer 125

binding directly to DNA

Question 126

the Q binding site (QBE) is between the () of the PR promoter

Answer 126

-35 and -10 elements

Question 127

without Q protein, transcription terminates very early, just downstream of ()

Answer 127

-10

Question 128

Q protein directly contacts the (1) and allows elongation to resume; Q remains associated with the (2)

Answer 128

1. sigma subunit (sigma70)
2. elongation complex

Question 129

() controls bacterial genes needed for amino acid biosynthesis

Answer 129

attenuation

Question 130

attenuation exploits ()

Answer 130

folding of RNA into alternative secondary structures

Question 131

the trp operon is controlled by Trp levels in the cells -> different levels cause the transcript to have ()

Answer 131

different secondary structures

Question 132

the genes for Trp synthesis are transcribed together -> a ()

Answer 132

polycistronic message

Question 133

the mRNA for Trp synthesis has a leader sequence near the start that has an (1) and 2 sequences that can form (2)

Answer 133

1. intrinsic terminator; an attenuator
2. stem-loops

Question 134

the leader sequence in mRNA for Trp synthesis has a () with lots of codons for Trp

Answer 134

small open reading frame

Question 135

the leader sequence in mRNA for Trp synthesis has 4 blocks that can form alternative pairing arrangements: 1 + 2

Answer 135

stem-loop

Question 136

the leader sequence in mRNA for Trp synthesis has 4 blocks that can form alternative pairing arrangements: 3 + 4

Answer 136

Rho-independent terminator

Question 137

the leader sequence in mRNA for Trp synthesis has 4 blocks that can form alternative pairing arrangements: 2 + 3 (1 and 4 are unpaired)

Answer 137

stem-loop

Question 138

in low Trp conditions, ribosome stalls while translating the peptide from leader sequence of mRNA (for Trp synthesis) -> region 1 is (a), region 2 and 3 (b), preventing 3 and 4 from (c), so transcription continues

Answer 138

a. blocked
b. form a stem-loop
c. binding and forming a terminator

Question 139

() are portions of a transcript that can directly bind a small molecule that controls the RNA secondary structure -> regulates transcription or translation

Answer 139

riboswitches

Question 140

riboswitches have 2 regions:

Answer 140

1. aptamer - binds to metabolite
2. expression platform - controls transcription or translation

Question 141

the () regulates adenine synthesis and transport -> gene expression depends on whether a terminator or anti-terminator forms

Answer 141

B. subtilis adenine riboswitch

Question 142

what happens to B. subtilis adenine riboswitch in low adenine conditions

Answer 142

regions 2 and 3 form anti-terminator -> transcription proceeds

Question 143

what happens to B. subtilis adenine riboswitch in high adenine conditions

Answer 143

regions 3 and 4 form a terminator

Question 144

Eukaryotes typically regulate transcription via DNA-binding proteins that recruit (1) or (2)

Answer 144

1. co-activators
2. co-repressors

Question 145

example of eukaryotic DNA-binding protein that recruits co-activator/co-repressor

Answer 145

ELK1, which recruits Mediator

Question 146

extracellular signals that promote entry into mitosis

Answer 146

mitogens

Question 147

in the absence of mitogens, ELK1 binds to () but doesn’t activate transcription

Answer 147

serum response factor (SRF)

Question 148

Mitogen binding at the cell surface activates kinases, which ()

Answer 148

phosphorylate ELK1

Question 149

phosphorylated ELK1 recruits (), promoting transcription

Answer 149

mediator

Question 150

() regulates genes that are responsible for galactose metabolism

Answer 150

Gal4

Question 151

Gal4 dimer activates transcription by binding to the ()

Answer 151

UASG sequence

Question 152

Gal4 activity is regulated by (), which respond to galactose in the cell

Answer 152

Gal80 and Gal3

Question 153

Unlike bacterial Trp repressor and CAP activator, the effector (galactose) for Gal80 and Gal3 doesn’t ()

Answer 153

bind directly to Gal4.

Question 154

in the absence of galactose, () binds to activating domain of Gal4, preventing transcription

Answer 154

Gal80

Question 155

in the absence of galactose, Gal80 is found in (1), while Gal3 is found in (2)

Answer 155

1. nucleus and cytoplasm
2. cytoplasm only

Question 156

in presence of galactose, galactose binds to (1), which allows (1) to bind to (2)

Answer 156

1. Gal3
2. Gal80

Question 157

in presence of galactose, Gal3 sequesters Gal80 in the ()

Answer 157

cytoplasm

Question 158

with Gal80 sequestered in the cytoplasm, Gal4 is able to recruit () and Mediator, which activates transcription

Answer 158

SAGA (co-activator complex)

Question 159

() responds to nutritional cues in yeast and can activate or repress transcription

Answer 159

Ume6

Question 160

where there is enough (1) in the cell, Ume6 binds DNA and recruits co-repressors (2)

Answer 160

1. Nitrogen and Carbon
2. Sin3, Rpd3, Isw2

Question 161

(): a histone deacetylase – histone deacetylation promotes more compact chromatin, which represses transcription

Answer 161

Rpd3

Question 162

(): a nucleosome remodeling enzyme, which helps establish the altered chromatin pattern

Answer 162

Isw2

Question 163

Ume6 is (1) in the absence of N and C, (2) dissociate

Answer 163

1. phosphorylated
2. Sin3 and Rpd3

Question 164

additionally, in the absence of N and C, a co-activator, () is recruited

Answer 164

Ime1

Question 165

() is involved in protecting the cell during abnormally high temperatures (heat shock) -> particularly observed in Drosophila

Answer 165

Hsp70

Question 166

promoter proximal pausing is used to prime Hsp70 (heat shock protein 70) for rapid transcription in response to ()

Answer 166

heat shock

Question 167

without heat shock at 25C, () binds upstream of hsp70

Answer 167

GAGA factor

Question 168

without heat shock at 25C, GAGA factor recruits (), which keeps the promoter free of nucleosomes and allows polymerase binding

Answer 168

NURF

Question 169

But RNA Pol is paused by negative elongation factors () -> polymerase complex is not phosphorylated enough

Answer 169

NELF, DSIF

Question 170

in transcription of Hsp70, without heat shock, Hsf monomers are present in the cell but ()

Answer 170

cannot bind to DNA

Question 171

with heat shock at 37C, Heat-Shock Factor (Hsf) trimerizes and binds to ()

Answer 171

heat shock elements (HSEs)

Question 172

when bound to HSEs, Hsf recruits Mediator and ()

Answer 172

p-TEFb (kinase)

Question 173

recruitment of Mediator and p-TEFb by Hsf () Pol Rpb1, NELF, DSIF -> resumes elongation

Answer 173

phosphorylates

Question 174

() also depends on anti-termination (similar to phage lambda N protein)

Answer 174

HIV transcription

Question 175

in HIV transcription, the (1) forms a step-loop called the (2) -> leads to transcription termination

Answer 175

1. tar site
2. TAR element

Question 176

in HIV transcription, transcription termination occurs if () is absent

Answer 176

Tat protein

Question 177

() binds to tar site in HIV transcription along with a cellular kinase -> phosphoryltates RNA pol II CTD -> relieves pausing and precents premature transcript termination

Answer 177

Tat (viral protein)

Question 178

• regulation of a single gene with several different proteins, each of which is controlled by a different parameter

Answer 178

combinatorial control

Question 179

combinatorial control is the response of a gene to ()

Answer 179

multiple signals and regulatory proteins

Question 180

yeast cell type is controlled by () transcriptional factors

Answer 180

four

Question 181

yeast cell has 3 cell types:

Answer 181

1. a
2. alpha
3. a/alpha

Question 182

() yeast cell types are haploid

Answer 182

a and alpha

Question 183

(1) type yeast cells are diploid and result from mating of (2)

Answer 183

1. a/alpha
2. a and alpha

Question 184

a/alpha yeast cells cannot mate, but can () when starved

Answer 184

undergo meiosis

Question 185

a. alpha, and a/alpha yeast cells have distinctive gene expression patterns, regulated by 4 proteins:

Answer 185

a1, alpha1, alpha2, and MCM1

Question 186

regulatory proteins for yeast cells: repressors

Answer 186

a1 and alpha2

Question 187

regulatory proteins for yeast cells: activators

Answer 187

alpha1, MCM1

Question 188

in yeast cells, a1, alpha1, and alpha2 proteins are encoded at the (1) on (2)

Answer 188

1. MAT locus
2. chromosome III

Question 189

in yeast cells, the MAT loci are different in different cell types:
1. a cells encode: (a)
2. alpha cells encode (b)
3. all 3 types encode (c)

Answer 189

a. a1
b. alpha1/2
c. MCM1

Question 190

in a-type yeast cells, MCM1 activates (1), while (2) are off

Answer 190

1. a-specific genes
2. alpha-specific

Question 191

in alpha-type yeast cells, (1) activates alpha-specific genes; (2) represses a-specific genes

Answer 191

1. alpha1-MCM1
2. alpha2-MCM1

Question 192

in alpha yeast cells, MCM1 activates transcription when bound by (1), and represses transcription when bound to (2)

Answer 192

1. alpha1
2. alpha2

Question 193

in a/alpha yeast cells, (1) form a heterodimer and repress haploid-specific genes: (2)

Answer 193

1. a1-alpha2
2. alpha1 and RME1

Question 194

() represses meiosis genes in yeasts; if this is no longer expressed, meiosis can occur

Answer 194

RME1

Question 195

Several proteins regulate (). This is important in viral defense by inhibiting synthesis of viral genome and stimulating host immune response)

Answer 195

human interferon-β

Question 196

A number of proteins bind to the interferon-β enhancer to form an ()

Answer 196

enhanceosome

Question 197

() between neighboring proteins are required for stable complex assembly involving at the interferon-β enhancer

Answer 197

Cooperative interactions

Question 198

binding of proteins at the interferon-β enhancer are aided by an architectural DNA-binding protein – () -» induces DNA bending, which helps other factors bind

Answer 198

HMG-I(Y)

Question 199

Once the enhanceosome is complete, the interferon-β gene is activated -> requirement of using a large number of proteins to activate a single gene ensures that the gene is activated only under ().

Answer 199

a very precise set of conditions

Question 200

extracellular signals trigger biochemical events whose end result is a change in gene expression

Answer 200

signaling cascades

Question 201

() respond specifically to effectors (e.g. sex hormones) that diffuse through the membrane

Answer 201

nuclear receptor proteins

Question 202

nuclear receptor proteins have (1) and (2)

Answer 202

1. DNA-binding domain
2. ligand-binding domain

Question 203

The first step in response to extracellular signals is often (), which triggers downstream events that lead to transcriptional changes.

Answer 203

phosphorylation

Question 204

An example of a multi-step cascade involves (), which is important in mammalian inflammatory and immune responses.

Answer 204

NF-κB

Question 205

NF-κB is a heterodimer of () proteins

Answer 205

p50 and p65

Question 206

in unstimulated cells, NF-κB is held in the cytoplasm by () -> binds to nuclear localization signal of NF-κB

Answer 206

I-κB

Question 207

in the NF-κB signaling cascade, infection triggers activation of ()

Answer 207

I-κB kinase (IKK) -> I-κB is phosphorylated

Question 208

during infection, phosphorylated I-κB is ubiquitinated by (1), and is thus targeted for degradation by the (2)

Answer 208

1. E3 ubiquitin ligase
2. proteasome

Question 209

degradation of I-κB exposes () of NF-κB -> allows it to move into nucleus and activate transcription

Answer 209

nuclear localization signal (NLS)

Question 210

() is where large chromosomal regions (multiple genes) are suppressed for long periods of time

Answer 210

transcriptional silencing

Question 211

allows transcriptional silencing to persist for many cell divisions

Answer 211

epigenetic inheritance

Question 212

transcriptional silencing is due to changes in ()

Answer 212

chromatin structure

Question 213

chromatin structure: (1) is often transcriptionally active, while (2) is generally silent

Answer 213

1. euchromatin
2. heterochromatin

Question 214

yeast chromosome III has extra copies of a and alpha genes that are not expressed:
1. a silenced copy of a is found to the right of MAT locus: (a)
2. a silenced copy of alpha is found to the left of MAT locus: (b)

Answer 214

1. HMRa
2. HMLalpha

Question 215

silencing of HMRa and HMRalpha depends on () -> establish and maintain heterochromatin at HML and HMR

Answer 215

silencing information regulator (Sir) proteins

Question 216

in silencing of HML and HMR, the ff proteins bind to these regions and recruit other Sir proteins

Answer 216

Abf1, Rap1, Orc1

Question 217

after extra Sir proteins are recruited to HMR and HML, they spread along the chromatin and silence the genes via the ability of (1) to (2)

Answer 217

1. Sir2
2. deacetylate histones

Question 218

() plays a role in establishing silencing, although its precise function is not well understood.

Answer 218

Sir1

Question 219

Sir2 is also involved in repressing RNA pol II in the regions between the () -> helps establish heterochromatic state that prevents recombination between multiple copies of these genes

Answer 219

rDNA genes

Question 220

() can mediate transcriptional silencing, as in IGF2 and H19

Answer 220

DNA modifications

Question 221

IGF2 and H19 are () -> only 1 of the parental copies of a gene is expressed

Answer 221

imprinted genes

Question 222

imprinted gene that is expressed only on paternal chromosome -> produces a growth factor needed by a developing embryo

Answer 222

IGF2

Question 223

imprinted gene that is expressed only on maternal chromosome -> makes a non-coding RNA that may play a role in cancer.

Answer 223

H19

Question 224

both IGF2 and H19 are found on ()

Answer 224

chromosome 11

Question 225

regulation of IGF2 and H19 expression is due to methylation at the ()

Answer 225

insulator control region (ICR)

Question 226

protein () can only bind to ICR when ICR is not methylated

Answer 226

CTCF

Question 227

in the maternal chromosome, ICR is (methylated/not methylated) -> CTCF is bound to ICR and blocks enhancer to prevent transcription of ICF2 but allows transcription of H19

Answer 227

not methylated

Question 228

in paternal chromosome, ICR is (methylated/not methylated) -> CTCF is not bound to ICR and thus H19 promoter is methylated and inhibits its transcription

Answer 228

methylated

Question 229

Transcription is thought to be mediated by () of the DNA, and determined by access or blocking of enhancer-bound proteins.

Answer 229

looping

Question 230

Failure of correct imprinting can lead to () – children are larger than normal at birth and are prone to cancer

Answer 230

Beckwith-Wiedemann syndrome

Question 231

Methylated DNA can recruit specific proteins. Methyl-binding domains bind specifically to ()

Answer 231

methyl-cytosine

Question 232

binds to methylated DNA and recruits Sin3A

Answer 232

MeCP2

Question 233

transcriptional co-repressor that contains a histone deacetylase

Answer 233

Sin3A

Question 234

MeCP2 represses a number of human genes – mutations in this protein can cause ()

Answer 234

Rett Syndrome

Question 235

Rett syndrome is more common in (1) because MeCP2 is found on the (2) chromosome

Answer 235

1. girls
2. X chromosome

Question 236

defective X chromosome responsible for Rett chromosome can also appear in males, but ()

Answer 236

since there is no extra X chromosome to mask the mutation, male fetuses don’t survive to term