chapter 13 part 1

Question 1

what do activator proteins bind & how do they affect transcription

Answer 1

bind regulatory sequences to stimulate transcription

Question 2

what do repressor proteins bind & how do they affect transcription

Answer 2

bind other (so not regulatory ones)
sequences to hinder transcription

Question 3

where are regulatory proteins often found?

Answer 3

in large complexes in eukaryotes
-unlike in bacteria, one transcription factor may regulate tens to hundreds of target genes

Question 4

what are the three regulatory DNA sequences

Answer 4

1. core promoter region
2. proximal elements
3. enhancer/silencer sequences

Question 5

about the core promoter region!

Answer 5

it contains the TATA Box & other sequences
it is immediately adjacent to the start of transcription
-binds RNA pol II & its associated general transcription factors (GTFs)

Question 6

tell me about proximal elements!

Answer 6

they are located upstream of the core promoter region & bind additional regulatory proteins

Question 7

tell me about enhancer/silencer sequences!

Answer 7

they act from greater distances from the core promoter
-the bind regulatory proteins that interact with proteins bound to one another
-enhancers/silencers can be located upstream, downstream, close to, or very far, or even within the genes they regulate

Question 8

where can enhancers/silencer sequences

Answer 8

can be located upstream, downstream, close to, or very far, or even within the genes they regulate

Question 9

all three regulatory regions contain ____-_______ regulatory sequences

Answer 9

cis acting
they regulate transcription of genes on the same chromosome as the sequence

Question 10

what binds the core promoter & are they cis or trans acting?

Answer 10

RNA pol II & various general transcription factors (GTFs)
-trans-acting regulatory proteins which can bind to their target sequence on any chromosome

Question 11

what are enhanceosomes

Answer 11

when there are aggregations of multiple proteins from large complexes at enhancers

Question 12

what does the enhanceosome direct

Answer 12

DNA bending/loop formation that allow enhanceosome proteins to interact with RNA pol & transcription factors at the core promoter & proximal promoter elements

Question 13

what does enhancer activity typically help control

Answer 13

the timing & location of gene transcription

Question 14

SV80 enhancer

Answer 14

consists of seven adjacent regions that are about 200 bp upstream of the transcription start point
each segment binds specific regulatory proteins

Question 15

Enhancers and silencers typically contain ___________ _____ (modules) for several transcription factors

Answer 15

binding sites

Question 16

what are modules

Answer 16

binding sites

Question 17

what do modules allow silencers/enhancers to do?

Answer 17

integrate activities of different transcription factors to produce different outputs

Question 18

what are pioneer factors?

Answer 18

are the first to bind regulatory molecules, facilitating the binding of additional transcription factors

Question 19

can the same sequence act as an enhancer or a silencer?

Answer 19

yes! depending on which regulatory proteins are present & bind to the sequence (often cell type specific)

Question 20

what is SHH

Answer 20

sonic hedgehog gene

Question 21

what does SHH gene do?

Answer 21

directs limb formage & is controlled by an enhancer 1 million base pairs away from SHH gene

Question 22

what type of fashion is SHH expressed in?

Answer 22

tissue-specific due to the action of two different enhancers

Question 23

what does LCR stand for?

Answer 23

locus control region

Question 24

what does LCR do?

Answer 24

it is a highly specialized enhancer that regulates transcription of multiple genes packaged into complexes of closely related genes

Question 25

how many sequences does the LCR regulating the beta-globin complex contain & what are they?

Answer 25

4 HS1, HS2, HS3, HS4

Question 26

what do the four distinct sequences regulating beta globin work together to do?

Answer 26

produce the correct expression of each type of beta-globin gene throughout development

Question 27

how does the LCR function

Answer 27

by recruiting the chromatin-modifying, coactivator, & transcription complexes

Question 28

what do HS1 & HS2 do?

Answer 28

they bind regulatory proteins that direct formation of small DNA loops & recruitment of additional factors

Question 29

muations in the sigma- & beta-globin genes produce hereditary anemias called what

Answer 29

thalassemia

Question 30

can some thalassemia patients have no discernible muations?

Answer 30

yes, some may have no discernible mutations in the protein-coding part of the globin genes, nor in their promoters

Question 31

what are some thalassemia cases due to?

Answer 31

deletions that alterd the LCR region, causing abnormal expression of the globin genes

Question 32

what is UAS

Answer 32

yeat upstream activator sequences

Question 33

in the yeast Saccharomyces cerevisiae, transcription of genes in what pathway are carefully refulated by enhancer-like sequences

Answer 33

galactose utilization pathway

Question 34

what happens in the UAS when galactose is the only sugar available?

Answer 34

wild-type yeast induce transcription of four enzyme-producing genes GAL1, GAL2, GAL7, GAL 10

Question 35

what are the four enzyme producing genes in UAS & what do they do?

Answer 35

GAL1, GAL2, GAL7, GAL10 they import and break down galactose

Question 36

do each of the GAL genes have their own promote and similar enhancer like sequencesr?

Answer 36

yes

Question 37

what are the GAL genes bound by?

Answer 37

Gal4

Question 38

what is Gal4 encodes by?

Answer 38

GAL4 gene

Question 39

is Gal4 sometime are always present in cells?

Answer 39

always it is continuously present in cells

Question 40

what is the enhancer like element

Answer 40

upstream activator sequence UAS of UASg

Question 41

what happens to Gal4 in the absence of Galactose

Answer 41

Gal4 is bound & inactivated by Gal80

Question 42

what is Gal4 like?

Answer 42

an enhancer like sequence

Question 43

things about UASG (how many, how many bp, binding site for what)

Answer 43

UASg element contains two 17 bp repeat sequences that are binding sites for Gal4

Question 44

what does Gal4 function as?

Answer 44

a homodimer

Question 45

what happens when Gal80 is bound to Gal4 (when galactose is absent)

Answer 45

the Gal4 DNA-binding domain is unable to bind to UASG

Question 46

what binds to Gal80 when galactose is present?

Answer 46

galactose & Gal3 bind to Gal80

Question 47

what is Gal3 encoded by?

Answer 47

the GAL3 gene

Question 48

what happens when galactose is present

Answer 48

-galactose & Gal3 bind to Gal80 -Gal80 releases Gal4- freeing the DNA-binding domain of Gal4 to recognize & bind to the UASG sites -the transcriptional activation domain of Gal4 homodimer then activates transcription of GAL genes

Question 49

what activates transcription of the GAL genes

Answer 49

transcriptional activation of the Gal4 homodimer when it binds to UASG sites

Question 50

what leads to formation of a mediator

Answer 50

when Gal4 binds UASG

Question 51

what is a mediator

Answer 51

a multiprotein complex an enhaceosome that induces formation of a DNA loop, contacting the general transcription apparatus at the GAL gene promoters

Question 52

what allows the transcription factors to bind?

Answer 52

physical changes in the DNA

Question 53

what does physical distortion of the DNA allow?

Answer 53

it allows UASG promoter to bring this sequence into contact with the promoter & RNA pol II to initiate transcription -UASG is NOT a proximal promoter; it is further upstream

Question 54

do eukaryotic repressors & bacteria repressors inhibit transcription through the same mechanisms?

Answer 54

no- eukaryotic repressors do it differently

Question 55

what is one mechanism of binding repressor proteins?

Answer 55

through silencer sequences that directly prevent enhancer-mediated transcription

Question 56

what do silencer sequences do

Answer 56

they directly prevent enhancer-mediated transcription

Question 57

are silencer sequences cis or trans acting?

Answer 57

they are cis-acting

Question 58

what genes utilize silencer sequences?

Answer 58

GAL genes

Question 59

what binds the silencer sequences upstream of the GAL genes?

Answer 59

protein Mig1 is produced in the presence of glucose & binds the silencer sequence

Question 60

is Mig1 produced in the presence or absence of glucose?

Answer 60

in the presence

Question 61

where are the silencer sequences of GAL genes located?

Answer 61

located between the UASG sequences & the promoters

Question 62

what protein does Mig1 attract?

Answer 62

Tup1 & the two together form a repressor complex that prevents UASG from initiating transcription

Question 63

what prevents UASG from initiating transcription?

Answer 63

when Mig1 attracts Tup1 & they form a repressor complex

Question 64

what are insulator sequences?

Answer 64

they are cis-acting sequences located between enhancers & the promoters of genes that need to be protected from the action of the enhancers

Question 65

what do insulators ensure?

Answer 65

there is only the target gene is regulated by the enhancer

Question 66

what may insulators allow?

Answer 66

DNA loops that contain the enhancers & their intended target promoters while excluding non-target genes

Question 67

what do DNA loops exclude?

Answer 67

non-target genes

Question 68

Some insulator sequences function by containing the spread of ________________.

Answer 68

heterochromatin

Question 69

what is constitutive heterochromatin

Answer 69

when regions of the genome are always heterochromatic

Question 70

facultative heterochromatin

Answer 70

regions that switch between euchromatin & heterochromatin often based on tissue type or cellular needs during certain times

Question 71

when does positron effect variegation occur?

Answer 71

(PEV) occurs when the euchromatin is placed (by mutation) neat heterochromtain, which can then spread converting some of the euchromatin or heterochromatin, this can silence genes

Question 72

when euchromatin is converted into heterochromatin, when can occur to genes?

Answer 72

it can silence them