Gene regulation in EUK

Question 0

two types of transcription factors

• ___________: required for binding RNA pol to core promoter
• ____________: affect rate of gene transcription, 2-3% of humans encode regulatory factors

Answer 0

general

regulatory

Question 1

transcription factors:

-proteins affecting _______ _________ (gene transcription)

Answer 1

RNA polymerase

Question 2

regulatory transcription factors:

typically recognize ___-_____ DNA elements, which are control/regulatory elements

Answer 2

cis-acting

Question 3

regulatory factors bind to regulatory elements
-___________: protein that enhances transcription
_____________: DNA seq. that activator binds
-__________: protein that inhibits transcription
__________: DNA seq. the repressor binds to

Answer 3

activator, enhancer

repressor, silencer

Question 4

most eukaryotic genes are regulated by several factors:

• ___________/___________ transcription initiation
• factors modulated (_________ molecules, protein-protein ____________, and __________ mods)

Answer 4

stimulate/inhibit

effector molecules, protein-protein interactions, and covalent mods

Question 5

alter composition of nucleosomes near promoter

Answer 5

combinational control

Question 6

most eukaryotic genes are regulated by several factors:
-______________ can inhibit transcription
prevent binding of __________
recruit proteins that compact __________

Answer 6

methylation
activator
chromatin

Question 7

structural features of regulatory transcription factors

-________: regions of protein with a function

Answer 7

domain

Question 8

dominant feature of regulatory factors

why? bc it fits into major groove of DNA helix, recognized base sequences, and hydrogen bonding occurs

Answer 8

alpha helix

Question 9

features such a Leucine Zipper Facilitate, the joining of two proteins

Answer 9

protein Dimerization (homo- and hetero-)

Question 10

transcription factors that recognize regulatory elements:
-_____&______ regulation of transcription
-location of regulatory elements ________ ________
up to 100,000 bp upstream of core _________
can be downstream of core _______ in introns

Answer 10

up and down
highly variable
promotor
promotor

Question 11

how do transcription factors affect RNA polymerase II?

• interact with proteins that interact with ____ ____________
• ________ & _________ (communicate effects of reg trans factors)
• TFIID (general transcription factor, binds to _______ box, required to recruit RNA pol II to the ____________)

Answer 11

• RNA polymerase II
• TFIID and mediator
• TATA, promotor

Question 12

protein complex that mediates RNA pol II and reg transcription factors

Answer 12

mediator

Question 13

_________ affect gene transcription

• synthesized by ___________ ______
• transported in ______ ________
• cells take up _________

Answer 13

steroids
endocrine glands
blood stream
steroids

Question 14

regulation transc factor that binds to steroids

Answer 14

steroid receptor

Question 15

-
-

Answer 15

• glucose sysnthesis
• breakdown of protines
• mobilization of fats

Question 16

unlike steroids, most signaling molecules bind to receptors in the plasma membrane
-triggers ____________ signal

Answer 16

covalent modification with CREB protein

intracellular

Question 17

covalent modification with CREB protein:

• cAMP response element-binding protein (CREB)
• reg transc factor
• signaling by _________ in cAMP (cyclic adenosine monophosphate)

Answer 17

increasing

Question 18

chromatin remodeling:
-changing the structure of chromatin can affect ___________
closed conformation= more compaction, transcription difficult
open conformation

Answer 18

transcription

Question 19

chromatin remodeling:
Chromatin remodeling complexes
-all have _________ ________(ATP dependent chromatin remodeling)
-similar to DNA _____________(motor proteins that move along DNA)

Answer 19

ATPase subunit

translocases

Question 20

__________ variants modify structure of chromatin

-affect transcription

Answer 20

histone

Question 21

• amino-terminal tail is variable, has different amino acids

- the charge of the tail can affect binding to proteins or DNA

Answer 21

histone code

Question 22

eukaryotic genes are flanked by ___________ free regions.

• NFR~ 150bp
• flanked by specific -1 & +1 ____________

Answer 22

nucleosome

nucleosomes

Question 23

activation of transcription requires modifications to _______________

Answer 23

nucleosomes

Question 24

many genes are flanked by nucleosome-free regions (NFR) and well-positioned nucleosomes.

Answer 24

silent

Question 25

activation of transcription: activator proteins bind to enhancer seq. the enhancers may be close to the transcriptional start site or they be far away

Answer 25

1. binding of activators

Question 26

activation of transcription: activator proteins recruit chromatin remodeling complexes such as SWI/SNF, and histone modifying enzymes. nucleosomes may be moved, and histones may be evicted. some histones are subjected to covalent modification, such as acetylation.

Answer 26

2. chromatin remodeling and histone modification

Question 27

activation of transcription: general transcription factors and RNA polymerase II are able to bind to the core promotor and form a pre-initiation complex.

Answer 27

3. formation of the pre initiation complex

Question 28

activation of transcription: during _________, histones ahead of the open complex are covalently modified by acetylation and evicted or partially displaced. behind the open complex, histones are deacetylated and become tightly bound to the DNA.

Answer 28

4. elongation

Question 29

__________ is rare in inverts, common in vetebrates. | -________% of mammalian DNA

Answer 29

methylation | 2-7

Question 30

CpG islands near promotor - C & G connected by Phosphodiester linkage - 1000-2000bp - methylation inhibits transcription

Answer 30

transcriptional regulation via DNA methylation | -inhibits transcription

Question 31

methylation affects transcription in __ ways: | -methylation of CpG islands may ________ or _______ binding or reg transcription factors

Answer 31

2 | enhance, suppress

Question 32

methylation affects transcription in 2 ways: | methyl-CpG-binding proteins bind to methylated CpG islands and recruit other _________ ________

Answer 32

inhibitor proteins

Question 33

methylation is inherited during ______ ________, de novo methylation

Answer 33

cell division

Question 34

- functions as a boundary btween two genes - acts as barrier to chromatin changes - blocks effects of neighboring enhancers

Answer 34

insulators

Question 35

insulators may promote the formation of ________

Answer 35

loops

Question 36

5 methods of gene regulation

Answer 36

``` control transcription processing of pre-mRNA RNA stability RNA interference control translation ```

Question 37

results in different polypeptide products from same gene

Answer 37

alternate splicing of pre-mRNA

Question 38

alternative splicing: - results in diff polypeptide products from _____ gene. - enables mRNA and ________ __________ - prominence varies by ________ (yeast:

Answer 38

same polypeptide variants species

Question 39

regulate alt splicing | -what is the factor?

Answer 39

splicing factors | -modulate the spliceosome (repression-exon skipping)

Question 40

regulate alt splicing | -whats the factor?

Answer 40

splicing factors | -modulate the spliceosome (enhancement)

Question 41

- minutes to months - stability can be regulated - poly A tails important to stability (avg 200 nucleosides long) - poly A binding protein enhancers stability (mRNA rapidly degrade after poly A tail ____________ to 10-30 nucleosides)

Answer 41

mRNA stability varies widely | decreases

Question 42

mRNA destabilizing agents: _______________ ( )- located in 3' untranslated region (3'-URT) -proteins bind, enhancing _____________

Answer 42

AU rich Element (ARE) | degredation

Question 43

RNA interference: - ___________ (______): 21-23 nucleosides, partially complimentary to mRNA, silence translocation, encoded by 200 genes in humans - ______-___________ _____ (_______): 21-23 nucleosides, perfect match to mRNA, silence translation due to mRNA degredation

Answer 43

microRNAs (miRNAs) | short-interfering RNAs (siRNAs)