Exam 2: Ch 7 Eukaryotic Gene Control Flashcards Preview

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

Flashcards in Exam 2: Ch 7 Eukaryotic Gene Control Deck (90):
1

2 features of transcription control common to bacteria and eukaryotes

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

2

what control do eukaryotes have but bacteria dont

chromatin structure regulation

3

promoter

DNA sequence that specifies where RNA polymerase binds and initiates transcription

controlled by DNA binding proteins

4

transcription factor

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

5

upstream

opposite the direction of transcription

6

downstream

in the same direction as transcription

7

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

very far away from the promoter they regulate

8

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

TFs to alternative control elements

9

reporter gene

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

ex. luciferase (light generating) or GFP

10

enhancer

distant transcription control region

11

3 different .... catalyze formation of different RNAs

RNA polymerases I, II, III

12

RNA polymerase I

located in nucleolus

transcribed genes encoding precursor rRNA (pre-rRNA)

13

RNA polymerase II

transcribes all protein-coding genes

14

RNA polymerase III

transcribes genes encoding tRNAs

5SRNA

stable RNA

15

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

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

16

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

the 5' cap of mRNA

17

3 DNA sequences can function as promoters for RNA Pol II

TATA boxes

initiators

CpG islands

18

TATA boxes

a conserved sequence upstream from the transcription site

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

19

initiator sequences

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

20

CpG island

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)

21

why are CpG islands rare in mammals

spontaneous deamination of C generates thymidine CG --> TG

22

initiation by RNA pol II requires...

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

23

examples of general transcription factors

TFIIA TFIIB

contains TATA binding protein (TBP)

multimeric proteins

24

preinitiation complex

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

25

how does the preinitiation complex form with a TATA box

TBP binds to the TATA promoter and bends the DNA

TFIIB binds

Pol II-TFIIF binds

2 more general TF bind TFIIE and TFIIH

26

TFIIH exhibits _____ activity

helicase

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

also, DNA repair activity

27

in vivo transcription initiation by RNA Pol II requires...

TFIIA as well

28

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

elongation

29

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

binding of negative elongation factor

DSIF binds and elongation continues

30

viral protein Tat allows

Pol II to read through transcription blocks

used in HIV

31

what are linker scanning mutations used for

pinpoint sequences in a regulatory region that control transcription

promoter-proximal elements were discovered this way

32

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

yes

33

many enhancers are cell-type _____

specific

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

enhancer controlling Pax6 in pancreas is located upstream of exon 0

34

do enhancers and promoters work when inverted?

yes

35

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

DNase I footprinting

electrophoretic mobility shift assay

36

activators are composed of distinct ______ _______

functional domains

DNA binding domain

activation domain

37

DNA binding domain

binds to specific DNA sequences

38

activation domain

interacts with other proteins to simulate transcription from a nearby promoter

39

constitutive expression

unregulated, abnormally high expression

results from inactivation of a repressor

40

2 domains of repressors

DNA binding domain

repression domain

41

recognition helix

alpha helix that binds major groove of DNA

42

homeodomain

TF conserved DNA binding motif

43

zinc finger

TF structural motif with regions that fold around zinc

C2H2 zinc finger

C4 zinc finger (nuclear receptor)

44

leucine zipper proteins

TF binding domain made of leucine dimers

grip DNA like scissors

45

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

amino acid

46

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 _____ ____ ____

GAL4, CGN4

acidic amino acids (aspartic acid, glutamic acid)

47

acidic activation domains

capable of stimulating transcription in almost all types of eukaryotic cells

must be bound to a protein co-activator

48

example of TF with an acidic activation domain

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

nuclear receptors may have ____-binding domains

ligand

binding of ligand activates domains by inducing conformational change

50

combinatorial complexity of TFs

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

enhanceosome

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

52

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

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

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

3

54

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

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

55

mediator

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

formation of heterochromatin silences gene expression in 3 regions

telomeres

centromeres

other

57

heterochromatin

dark staining and highly condensed areas of chromatin

less accessible DNA for TFs

58

central mating type locus of yeast, and 2 additional loci

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

how is transcription of HML/HMR repressed?

silencer sequences located nearby

condensed chromatin sterically blocks TFs from interacting with DNA

60

the telomeres of yeast chromosomes behave like...

silencer sequences

61

repressors can direct histone _______ at specific genes

deacetylation

62

histone deacetylation

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

causes condensation that TFs cant bind to

63

how do activation domains of DNA-binding activators function

by binding co-activator complexes

activators can direct histone acetylation at specific genes

64

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

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

generates binding sites for bromodomains

65

chromatin remodeling factors help...

activate or repress transcription

push DNA into nucleosomes to facilitate binding of TFs

66

chromatin remodeling factors required for many processes...

transcription control, DNA replication, recombination, and DNA repair

transcriptional repression

67

yeast two-hybrid system

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

how does yeast two-hybrid system work

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

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

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

extracellular signals

70

how do signals regulate TFs

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

transmits signal to nucleus where TFs are

71

2nd major group of extracellular signals

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

steroids, retinoids, thyroid hormones

72

nuclear receptor superfamily

intracellular receptor for most of the lipid hormone signal molecules

function as transcription activators when bound to ligand

73

all nuclear receptors have 3 common domains

N-terminal region: activation domain

zinc finger

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

74

response element

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

specificity of response elements afforded by

spacing between the repeats of the sequence

76

heterodimeric nuclear receptor functions when hormone binds/doesnt bind

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

homodimeric nuclear receptor

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

regulation of Pol II transition from initiation to elongation

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

epigenetic

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

epigenetics and CpG islands

active CpG island promoters have unmethylated C's

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

81

epigenetics and histone modification

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

are methylated histones passed down?

yes, to approximately half of daughter cells

maintains methylation of these histones in certain areas of chromosome

83

polycomb proteins

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

Hox genes

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

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

remain repressed throughout life

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

86

polycomb subunits

PRC1: ubiquitin ligase that prevents Pol II elongation

PRC2: histone deacetylase and histone methyl transferase

87

noncoding ___s can direct epigenetic repression in metazoans

RNAs

protein bound

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

88

regulation of flowering time

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

RNA Pol I

uses a core element and upstream control element for transcription

90

Pol III

internal promoter elements A box and B box

C box promoter

p53 represses Pol transcription