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Cellular and Molecular Biology > Exam 2: Ch 7 Eukaryotic Gene Control > Flashcards

Exam 2: Ch 7 Eukaryotic Gene Control Flashcards

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1
Q

2 features of transcription control common to bacteria and eukaryotes

A

protein binding regulatory DNA sequences (control elements) associated with genes

specific proteins bind to a gene’s regulatory sequences to determine where transcription will start and either activate or repress transcription

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2
Q

what control do eukaryotes have but bacteria dont

A

chromatin structure regulation

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3
Q

promoter

A

DNA sequence that specifies where RNA polymerase binds and initiates transcription

controlled by DNA binding proteins

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4
Q

transcription factor

A

transcriptional regulatory proteins that either activate or repress transcription depending on association with other proteins

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5
Q

upstream

A

opposite the direction of transcription

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6
Q

downstream

A

in the same direction as transcription

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7
Q

TFs that regulate expression of protein binding genes can bind to control elements found…

A

very far away from the promoter they regulate

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8
Q

transcription of a single gene can be regulated by the binding of multiple different…

A

TFs to alternative control elements

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9
Q

reporter gene

A

analyze gene control regions by prepping recombinant DNA with a fragment to be tested containing a reporter gene

ex. luciferase (light generating) or GFP

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10
Q

enhancer

A

distant transcription control region

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11
Q

3 different …. catalyze formation of different RNAs

A

RNA polymerases I, II, III

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12
Q

RNA polymerase I

A

located in nucleolus

transcribed genes encoding precursor rRNA (pre-rRNA)

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13
Q

RNA polymerase II

A

transcribes all protein-coding genes

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14
Q

RNA polymerase III

A

transcribes genes encoding tRNAs

5SRNA

stable RNA

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15
Q

the largest subunit in RNA pol II has an essential carboxyl terminal repeat

A

carboxyl terminal domain (CTD), must have at least 10 copies in yeast to survive

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16
Q

RNA Pol II initiates transcription at DNA sequences corresponding to..

A

the 5’ cap of mRNA

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17
Q

3 DNA sequences can function as promoters for RNA Pol II

A

TATA boxes

initiators

CpG islands

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18
Q

TATA boxes

A

a conserved sequence upstream from the transcription site

required for efficient transcription in viral genes and cellular protein coding genes in cell cycle

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19
Q

initiator sequences

A

alternative promoter element with a cytosine at -1 and adenine at transcription start site (+1)

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20
Q

CpG island

A

relatively rare promoter sequence in mammals that contain high numbers of CG sequences

transcription initiated in both directions even though mRNA only made from sense strand (divergent transcription)

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21
Q

why are CpG islands rare in mammals

A

spontaneous deamination of C generates thymidine CG –> TG

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22
Q

initiation by RNA pol II requires…

A

several initiation factors called general transcription factors

position Pol II at transcription start sites and help separate DNA strands so template can enter active site

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23
Q

examples of general transcription factors

A

TFIIA TFIIB

contains TATA binding protein (TBP)

multimeric proteins

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24
Q

preinitiation complex

A

complex of Pol II and general transcription factors bound to a promoter and ready to initiate transcription

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25
Q

how does the preinitiation complex form with a TATA box

A

TBP binds to the TATA promoter and bends the DNA

TFIIB binds

Pol II-TFIIF binds

2 more general TF bind TFIIE and TFIIH

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26
Q

TFIIH exhibits _____ activity

A

helicase

uses energy from ATP to unwind DNA at start site to allow Pol II to begin transcription

also, DNA repair activity

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27
Q

in vivo transcription initiation by RNA Pol II requires…

A

TFIIA as well

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28
Q

_______ factors regulate the initial stages of transcription in the promoter-proximal region

A

elongation

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29
Q

in metazoans, at most promoters Pol II pauses after transcribing 20-50nt due to..

A

binding of negative elongation factor

DSIF binds and elongation continues

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30
Q

viral protein Tat allows

A

Pol II to read through transcription blocks

used in HIV

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31
Q

what are linker scanning mutations used for

A

pinpoint sequences in a regulatory region that control transcription

promoter-proximal elements were discovered this way

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32
Q

can enhancers be upstream or downstream from a promoter, within an intron, or downstream from the final exon of a gene?

A

yes

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33
Q

many enhancers are cell-type _____

A

specific

enhancer controlling Pax6 in retina is in intron between exons 4 & 5

enhancer controlling Pax6 in pancreas is located upstream of exon 0

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34
Q

do enhancers and promoters work when inverted?

A

yes

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35
Q

two techniques for detecting cognate proteins that bind to a regulatory element

A

DNase I footprinting

electrophoretic mobility shift assay

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36
Q

activators are composed of distinct ______ _______

A

functional domains

DNA binding domain

activation domain

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37
Q

DNA binding domain

A

binds to specific DNA sequences

38
Q

activation domain

A

interacts with other proteins to simulate transcription from a nearby promoter

39
Q

constitutive expression

A

unregulated, abnormally high expression

results from inactivation of a repressor

40
Q

2 domains of repressors

A

DNA binding domain

repression domain

41
Q

recognition helix

A

alpha helix that binds major groove of DNA

42
Q

homeodomain

A

TF conserved DNA binding motif

43
Q

zinc finger

A

TF structural motif with regions that fold around zinc

C2H2 zinc finger

C4 zinc finger (nuclear receptor)

44
Q

leucine zipper proteins

A

TF binding domain made of leucine dimers

grip DNA like scissors

45
Q

a diverse group of _____ _____ sequences can function as activation domains

A

amino acid

46
Q

many TFs contain activation domains marked by an unusually high percentage of particular amino acids ____ ____ and most other yeast TFs ahve activation domains that are rich in _____ ____ ____

A

GAL4, CGN4

acidic amino acids (aspartic acid, glutamic acid)

47
Q

acidic activation domains

A

capable of stimulating transcription in almost all types of eukaryotic cells

must be bound to a protein co-activator

48
Q

example of TF with an acidic activation domain

A

mammalian CREB protein phosphorylated when there are high levels of cAMP

regulated phosphorylation required for binding of co-activator CBP, which results in transcription of genes whose control regions contain CREB binding site

49
Q

nuclear receptors may have ____-binding domains

A

ligand

binding of ligand activates domains by inducing conformational change

50
Q

combinatorial complexity of TFs

A

like a combination lock, some TFs bind in a certain order and must all be present for their effect to work

expands number of DNA sites these TFs can activate transcription and the numbed of ways they can be regulated

51
Q

enhanceosome

A

large DNA-protein complexes assembled from TFs binding multiple binding sites in an enhancer

52
Q

why is considerable leeway in spacing between regulatory elements in transcription control regions possible?

A

flexible regions connect DNA-binding domains and the activation/repression domains in TFs

ability of interacting proteins on distant sites to produce DNA loops

53
Q

there are _ general methods repressors and activators that bind to specific sites in DNA regulate expression of associated protein-coding genes

A

3

54
Q

1 way regulatory proteins regulate expression of genes by acting in concert

A

modulate chromatin structure to inhibit or stimulate ability of general TFs to bind to promoters

55
Q

mediator

A

mediator of transcription complex

regulatory proteins interact with this structure that binds to Pol II and directly regulates assembly of transcription preinitiation complexes

after chromatin in open form

56
Q

formation of heterochromatin silences gene expression in 3 regions

A

telomeres

centromeres

other

57
Q

heterochromatin

A

dark staining and highly condensed areas of chromatin

less accessible DNA for TFs

58
Q

central mating type locus of yeast, and 2 additional loci

A

MAT, actively transcribed and expresses TFs that control the mating type (alpha or a)

HML and HMR located near the right and left telomere, and are silent (nontranscribed copies of alpha/a genes)

the alpha/a genes are transferred from HML/HMR to MAT

59
Q

how is transcription of HML/HMR repressed?

A

silencer sequences located nearby

condensed chromatin sterically blocks TFs from interacting with DNA

60
Q

the telomeres of yeast chromosomes behave like…

A

silencer sequences

61
Q

repressors can direct histone _______ at specific genes

A

deacetylation

62
Q

histone deacetylation

A

unacetylated lysines pos charge interacts with phosphates on DNA, other histones, and other chromatin associated structures

causes condensation that TFs cant bind to

63
Q

how do activation domains of DNA-binding activators function

A

by binding co-activator complexes

activators can direct histone acetylation at specific genes

64
Q

what does activator directed hyperacetylation of nucleosomes near a promotor region do

A

opens chromatin structure to facilitate binding of other proteins required for transcription initiation

generates binding sites for bromodomains

65
Q

chromatin remodeling factors help…

A

activate or repress transcription

push DNA into nucleosomes to facilitate binding of TFs

66
Q

chromatin remodeling factors required for many processes…

A

transcription control, DNA replication, recombination, and DNA repair

transcriptional repression

67
Q

yeast two-hybrid system

A

exploits flexibility in activator structures to identify genes whose products bind to a specific protein of interest

tests if 2 proteins bind to each other

use color assay to detect protein binding

68
Q

how does yeast two-hybrid system work

A

yeast vector expresses 2 hybrid proteins

DNA binding domain + linker + bait domain (protein of interest)

second hybrid protein: activator domain + linker + fish domain (proteins that may or may not interact with bait)

only transformed cells expressing the bait hybrid interacting with the fish hybrid can activate transcription (b/c activation domain on fish)

69
Q

which TFs are expressed in diff cell types and how much is determined by…

A

regulatory interactions btw TF genes that occur during development and differentiation of the cell type

extracellular signals

70
Q

how do signals regulate TFs

A

interactions between extracellular domains of transmembrane receptors and ligands activate intracellular domains

transmits signal to nucleus where TFs are

71
Q

2nd major group of extracellular signals

A

small, lipid soluble hormones that diffuse through plasma and nuclear membranes to interact w/ TFs they control

steroids, retinoids, thyroid hormones

72
Q

nuclear receptor superfamily

A

intracellular receptor for most of the lipid hormone signal molecules

function as transcription activators when bound to ligand

73
Q

all nuclear receptors have 3 common domains

A

N-terminal region: activation domain

zinc finger

C-terminal region: hormone binding domain (bound = activation, unbound may repress)

74
Q

response element

A

characteristic nt sequence of DNA sites that bind nuclear receptors

small repeat sequence like 6bp for estrogen are same for other receptors like thyroid hormone…differ by nt spacers

75
Q

specificity of response elements afforded by

A

spacing between the repeats of the sequence

76
Q

heterodimeric nuclear receptor functions when hormone binds/doesnt bind

A

located only in nucleus

with hormone, activate transcription by directing histone hyperacetylation

without hormone bound, repress transcription by directing histone deacetylation at nearby nucleosomes

77
Q

homodimeric nuclear receptor

A

found in cytoplasm when not bound to ligand (cant interact with response elements)

hormone binding directs transportation to nucleus, where it interacts with response elements, and activates transcription by interacting with chromatin-remodeling and histone acetylase complexes and mediator

78
Q

regulation of Pol II transition from initiation to elongation

A

Pol II paused around 200bp of transcription start site until TF binds

allows rapid response: genes are paused until an emergency where a TF binds and high expression occurs

ex. heat shock gene

79
Q

epigenetic

A

inherited changes in the phenotype of a cell that do not result from changes in DNA sequence

post translational modifications of histones and DNA

80
Q

epigenetics and CpG islands

A

active CpG island promoters have unmethylated C’s

in differentiated cells, a few CpG island promoters are methylated, which triggers chromatin condensation

81
Q

epigenetics and histone modification

A

acetylation/deacetylation is turned over quickly b/c held in equilibrium by acetylase enzymes

methylation turned over slowly and is good for propagating epigentic information

82
Q

are methylated histones passed down?

A

yes, to approximately half of daughter cells

maintains methylation of these histones in certain areas of chromosome

83
Q

polycomb proteins

A

epigenetic mark essential for repression of genes in specific cell types and all the subsequent cells that develop throughout life

repress Hox genes

opposite are Trithorax proteins (express Hox genes)

84
Q

Hox genes

A

direct development of tissues and organs in the embryo

important in cell growth and division (often mutated in cancer)

polycomb proteins repress these genes early in embryogenesis

trithorax proteins express these genes

85
Q

only Hox genes in cells where they were initially repressed by polycomb proteins…

A

remain repressed throughout life

same Hox genes in other cells remain active in the presence of same polycomb proteins

86
Q

polycomb subunits

A

PRC1: ubiquitin ligase that prevents Pol II elongation

PRC2: histone deacetylase and histone methyl transferase

87
Q

noncoding ___s can direct epigenetic repression in metazoans

A

RNAs

protein bound

ex. X-chromosome inactivation in females by Xist RNA-protein complex

88
Q

regulation of flowering time

A

FWA gene encodes a homeodomain TF that regulates flowering time in response to temp so plants don’t flower until the warm spring

repressed by CHH methylation

89
Q

RNA Pol I

A

uses a core element and upstream control element for transcription

90
Q

Pol III

A

internal promoter elements A box and B box

C box promoter

p53 represses Pol transcription

Cellular and Molecular Biology (34 decks)

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