Chapter Nineteen: Gene Regulation in Eukaryotes Flashcards
(102 cards)
1
Q
what are at least five ways to regulate gene expression in a eukaryote
A
- transcription initiation
- transcription processing
- mRNA export from the nucleus
- translation of mRNA
- protein localization
- protein modification
2
Q
compared to prokaryotes, eukaryotes have additional levels of complexity for controlling ___
A
gene expression
3
Q
___ in eukaryotes often makes DNA unavailable to transcription machinery
A
chromatin structure
4
Q
additional ___ processing events occur in eukaryotes
A
RNA
5
Q
in eukaryotes, transcription occurs in the ___ and translation occurs in the ___
A
nucleus
cytoplasm
6
Q
gene regulation controls ___ into hundreds of specialized cell types
A
cell differentiation
7
Q
RNA pol I transcribes ___
RNA pol II transcribes ___
RNA pol III transcribes ___
A
rRNA genes
genes that encode proteins
tRNA genes and some small RNAs
8
Q
DNA sequence that is usually directly adjacent to the gene, where RNA polymerase binds
A
promoter
9
Q
promoters in eukaryotes often have a ___
A
TATA box
10
Q
genes that are expressed at low levels all the time
A
housekeeping genes
11
Q
genes that make cells unique, expression is cell or time specific
A
luxury genes
12
Q
there are ___ cell types in humans
A
200
13
Q
a regulatory site that can be far away from the gene
A
enhancer
14
Q
enhancers are binding sites for ___
A
transcription factors
15
Q
enhancers still function when moved to different positions relative to promoter because of ___
A
flexibility of DNA
16
Q
a ___ can tell you the location and time of gene expression
A
reporter gene
17
Q
three general reporter genes
A
- GFP
- LacZ
- luciferase
18
Q
GFP is ___ and has ___ sensitivity
A
fluorescent
high
19
Q
lacZ is ___ and has ___ sensitivity
A
chromatogenic
medium
20
Q
luciferase is ___ and has ___ sensitivity
A
luminescent
low
21
Q
transcription factors are ___ that act in ___ to control ___
A
proteins
trans
transcription initiation
22
Q
transcription factors bind to ___ and ___
A
promoters and enhancers
23
Q
transcription factors recruit ___ to influence transcription
A
other types of proteins
24
Q
three types of transcription factors
A
- basal factors
- activators
- repressors
25
basal factors bind to ___ of protein-encoding genes
promoters
26
a complex of more than 20 proteins needed most of the time for transcription of eukaryotic genes
mediator complex
27
mediator complex bridges ___ and ___
RNA pol II and enhancer
28
activators are responsible for much of the ___ in levels of transcription of different genes
variation
29
activators stimulate recruitment of ___ and ___ to promoters
basal factors and RNA pol II
30
activators recruit ___ to open chromatin structure
coactivators
31
activator proteins have at least ___ functional domains
two
32
most DNA binding proteins are dimers
true/false
true
33
domain that binds to a specific enhancer
DNA binding domain
34
domain that binds to other proteins
activation domain
35
domain that allows an activator to interact with other proteins
dimerization domain
36
two domains that every activator has
DNA binding domain
activation domain
37
two examples of a DNA binding domain
1. helix-turn-helix
2. zinc finger
38
DNA binding domains fit within the ___ of DNA
major groove
39
dimerization domains are specialized for ___ interactions
polypeptide-polypeptide
40
multimeric proteins made of identical subunits
homodimers
41
multimeric proteins made of nonidentical subunits
heterodimers
42
repressor proteins suppress transcription initiation by recruiting ___
corepressors
43
two alternate functions of corepressors
1. prevent RNA pol II complex from binding to promoter
2. modify histones to close chromatin structure
44
the same transcription factor can play ___ roles in different cells
different
45
repressor proteins can act through competition with an ___
activator protein
46
interferes with the function of an activator
indirect repressor
47
histone ___ affects transcription
modifications
48
___ acetylate histone tails
histone acetyl transferase (HAT)
49
many transcription factor ___ are HATs
coactivators
50
histone acetylation ___ chromatin, which ___ gene expression
opens
favors
51
___ methylate histone tails
histone methyltransferase (HMT)
52
HMT can ___ or ___ transcription, some are ___ some are ___
activate or repress
coactivators
corepressors
53
modifications made by HATs and HMTs can be taken off by ___ or ___
histone deacetylases ot histone demethylases
54
in humans, ___ genes code for transcriptional regulatory proteins
2000, 10%
55
each regulatory protein can act on ___
many genes
56
each enhancer has binding sites with ___ affinities for activators and repressors
varying
57
call-type specific transcription is achieved by changes in ___
transcription factors
58
the function of trans acting proteins changes by ___, ___, or ___
allosteric interactions, modification of transcription factors, or transcription factor cascades
59
tool for finding all target gens of a particular transcription factor within the entire genome of a. particular cell
chromatin immunoprecipitation-sequencing (ChIP-Seq)
60
two methods to see if a protein binds to DNA
DNA foot printing
ChIP-Seq
61
sequences located between an enhancer and a promoter that block access to the promoter
insulators
62
insulators organize genomic DNA into ___
loops
63
human insulators bind ___ to form loops called ___
CTCF proteins
topologically associating domains (TADs)
64
enhancers activate promoters located in the ___ loop
same
65
scientists detect TADs through ___
chromatin conformation capture
66
correct enhancer promoter reactions require specific TAD ___
boundaries
67
mutations that disrupt TAD boundaries can alter ___
genes expression
68
one form of ___ is due to deletion of TAD boundary between EPH4A and IHH genes
polydactyly
69
post transcriptional regulation can occur at the level of ___ and ___
RNA and protein
70
three mechanisms of RNA regulation
splicing, stability, and localization
71
three mechanisms of protein regulation
synthesis, stability, modification, localization
72
sex-specific courting behavior is controlled by male-specific ___
Fru-M
73
Fru-M and Fru-F are produced by ___ of the ___ primary transcript
alternative splicing
same
74
___ and ___ are expressed in females and clock use of a splice acceptor site, so the use of different ___ leads different Fruits proteins in males and females
Tra and Tra2
exons
75
control of translation often occurs at ___
initiation
76
the small subunit of the ribosome recognizes a complex structure built around the ___ of the mRNA
5' cap
77
eIFG protein binds to ___ at the poly-A tail to circularize mRNA
poly-A binding protein (PABP)
78
mRNA translation can be regulated in response to ___ in the environment
nutrients
79
presence of nutrients and growth factors int he environment leads to ___ of 4E-NP1
phosphorylation
80
translation can also be controlled through ___ length
poly-A tail
81
longer poly-A tails bind PABP ___ efficiently than shorter tails, so the translation initiation complex forms ___ efficiently
more
more
82
upstream ORFs that begin with a decoy AUG and encode small peptides that have no function
decoy ORF
83
the decoy ORF mechanism is used in the drosophila ___ pathway
sex differentiation
84
ribosomal profiling measures translation ___
efficiency
85
the amount of gene product does not always correlate with the amount of ___
mRNA
86
ribosome profiling allows researchers to observe ___ of ribosomes on mRNA
positions
87
specialized RNAs that prevent expression of specific genes through complementary base pairing, 21-30 nt long
small RNAs
88
small RNAs regulate mRNA ___ and ___
stability and translation
89
three classes of small RNAs
1. micro-RNAs (miRNAs)
2. small interfering RNAs (siRNAs)
3. piwi-interacting RNAs (piRNAs)
90
miRNAs target ___; function to ___ translation and ___ mRNAs
mRNA
block
destabilize
91
siRNAs target ___ and ___; function to ___ translation/___ mRNA and recruit histone modifying enzymes to DNA resulting in ___
mRNA and nascent transcripts of chromosomal regions destined to become heterochromatin
block
destabilize
heterochromatin formation
92
piRNAs target ___; function to ___ TE mRNA and facilitate histone modifications that inhibit ___
transposable element transcripts and promoters
degrade
transposable element transcription
93
most miRNA are transcribed by ___
RNA pol II
94
two ways miRNAs can down regulate expression of target genes
1. when complementary is perfect, target mRNA is degraded
2. when complementary is imperfect, translation of mRNA target is repressed
95
siRNAs are useful experimental tools to selectively ___ of target genes through ___ interference
known down expression
RNA
96
piRNAs minimize ___
transposable element mobilization
97
the ___ of X chromosomes determines sex in drosophila
number
98
maleness is brought about by the present of ___ X chromosome
one
99
two X chromosomes are required to activate transcription of the ___ gene in early drosophila embryogenesis
Sxl
100
Sxl transcription influences sex through these three pathways
1. male vs. female appearance and behavior
2. development of germ cells as eggs or sperm
3. dosage compensation
101
sex lethal (Sxl) gene encodes an RNA binding protein that controls the ___ of RNA targets
alternative splicing
102
Sxl transcription is necessary for ___ development
female
