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Genetics > Exam 3 Chapter 12 > Flashcards

Exam 3 Chapter 12 Flashcards

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1
Q

regulatory transcription factors (RTFs)

A

proteins that affect whether RNAP can go forth with transcription of a certain gene/how fast it occurs

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2
Q

general transcription factors (GTFs)

A

required for RNAP to bind to core promoter and for elongation to occur
ex. TBP, TFIID

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3
Q

what do RTFs recognize

A

cis regulatory elements near the core promoter

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4
Q

other words for regulatory elements

A

control elements, regulatory sequences

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5
Q

activator

A

RTF that increases the rate of transcription

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6
Q

enhancer

A

sequences that activators bind to

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7
Q

repressor

A

RTF that decreases the rate of transcription

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8
Q

silencer

A

sequence that a repressor binds to

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9
Q

DNA methylation does what

A

can inhibit transcription
- prevent activator binding
- recruit proteins that compact the chromatin

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10
Q

possible functions of domains of transcription factors

A
  • DNA binding
  • binding site for effector molecules
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11
Q

up-regulation

A

increasing rate of transcription by binding to an enhancer
can be 10-fold to 1000-fold increase

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12
Q

down-regulation

A

decreasing rate of transcription by binding to a silencer

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13
Q

orientation independent/bidirectional

A

response elements that can function in forward or reverse orientation

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14
Q

where are response elements located

A

within a few hundred nucleotides upstream of the promoter (usually)
can be up to 100,000 nucleotides away
can be downstream of the promoter
can be within introns

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15
Q

TFIID can be used ______ or ______

A

directly or through cofactors

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16
Q

transcription enhanced via TFIID

A

activator binds to the enhancer
coactivator binds to activator and recruits TFIID to the core promotor
and/or activates its functions
transcription enhanced

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17
Q

transcription silenced via TFIID

A

repressor protein binds to the silencer, stops TFIID from binding to the core promoter

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18
Q

transcription activated via mediator

A

activator protein interacts with mediator ->
carboxy-terminal domain of RNAP is phosphorylated
GTFs are released
RNAP proceeds to elongation

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19
Q

transcription repressed via mediator

A

repressor protein interacts with mediator to prevent the phosphorylation of RNAP -> no elongation -> no transcription

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20
Q

small effector molecule i.e. hormone

A

binds to the transcription factor before it binds to the response element

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21
Q

protein-protein interactions

A

two transcription factors (proteins) bind and form a homodimer that attaches to the response element

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22
Q

covalent modification

A

groups are covalently bonded to he transcription factors, ex. phosphate groups (phosphorylation)

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23
Q

what carries out ATP-dependent chromatin remodeling

A

different kinds of multiprotein machines

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24
Q

closed conformation of chromatin

A

chromatin is tightly packed
transcription may be difficult/impossible

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25
open conformation of chromatin
chromatin is accessible to transcription factors transcription can take place
26
nucleosome positioning in B-globin
changes in the promotor region as part of gene activation
27
role of some transcriptional activators
induce changes in chromatin structure
28
what causes ATP-dependent chromatin remodeling
energy of ATP hydrolysis drives changes in nucleosome location/composition, making it easier or harder to transcribe
29
DNA translocase
catalytic ATPase subunit found in all remodeling complexes
30
eukaryotic families of chromatin remodelers
SWI/SNF ISWI INO80 Mi-2
31
3 ways chromatin remodeling complexes change chromatin structure
change in nucleosome position evicting histone octamers change in nucleosome composition
32
change in nucleosome position
making some relatively closer together or changing the spacing of all of them over a long distance
33
change in nucleosome composition
replacement of histones with histone variants
34
5 histone genes
H1, H2A, H2B, H3, H4
35
human genome contains _____ histone genes
over 70
36
most histone genes encode
standard histones
37
histone variants
caused by histone genes with mutations that alter the amino acid sequence
38
specialized chromatin
created when histone variants are incorporated into some nucleosomes
39
common types of histone modification
acetylation, methylation, phosphorylation
40
effects of histone modification
affect the level of transcription may affect interactions between nucleosomes
41
_____ enzymes in mammals that can modify histone amino terminal tails
over 50
42
histone code
pattern of modifications that provide binding sites for proteins that specify which changes will be made to chromatin structure
43
effect of acetylation
DNA is less tightly bound to histones histone acetyltransferase -> histone deacetylase
44
nucleosome-free region (NFR)
found at the beginning and end of genes
45
nucleosome positioning in a gene
precise near the beginning and end less regularly distributed in the middle
46
formation of the pre-initiation complex
GTFs and RNA poly II bind to the core promotor to form a pre-initiation complex
47
elongation
histones ahead of the open complex - covalently modified by acetylation and evicted histones behind the open complex - deacetylated and become tightly bound to the DNA
48
DNA methylation is carried out by
DNA methyltransferase
49
species with very little DNA methylation
yeast, drosophila
50
species with abundant DNA methylation
vertebrates and plants
51
mammals have _____ methylated DNA
2-7%
52
DNA methylation usually _______ transcription in eukaryotes
inhibits
53
CpG islands
1,000 to 2,000 nucleotides long high amount of CpG sites common in vertebrates and plants
54
CpG islands in housekeeping genes
unmethylated genes are expressed in most cell types
55
CpG islands in tissue-specific genes
expression of genes may be silenced by methylation of the islands methylation may influence the binding of transcription factors methyl-CpG-binding proteins may recruit factors that lead to the chromatin being compacted
56
enzyme adaptability
more substrate -> more enzymes
57
mediator
large co-activator/co-repressor molecule
58
3 ways to regulate eukaryotic gene expression
1. use of transcription factors (GTFs or RTFs) 2. chromatin remodeling complexes or histone modifying enzymes to change structure/composition of nucleosomes 3. DNA methylation
59
RNA editing
can delete codons to alter base sequence of mRNA
60
combinatorial control
most eukaryotic genes are regulated by many factors
61
common combos of factors
1 or more activator proteins may stimulate transcription 1 or more repressor proteins may inhibit transcription
62
number of bps in a nucleosome
~146-147
63
histones in a core/octamer
2 H2A 2 H2B 2 H3 2 H4
64
width of a DNA double helix
2 nm
65
width of "beads on a string" DNA wrapped around histones
11 nm
66
width of chromatin fiber of packed nucleosomes
30 nm
67
width of a section of the extended form of a chromosome
300 nm
68
69
width of a condensed section of a metaphase chromasome
700 nm
70
width of an entire metaphase chromosome
1400 nm
71
purpose of H1
linker - holds DNA in place on the histone
72
what AA gets acetylated
lysine (K)
73
process of acetylation
add acetyl group -> done by HAT histone acetyl transferase -> histones become less positive -> less attraction with DNA -> more open conformation -> transcription ON
74
process of deacetylation
remove acetyl group -> done by HDAC histone deacetylase -> histones become more positive -> closed conformation favored -> transcription OFF
75
phosphorylation most common on which AAs
tyrosine (Y) threonine (T) Serine (S)
76
process of phosphorylation
add phosphate group -> done by kinases -> histones are less positive -> DNA unwinds -> open conformation -> transcription ON
77
process of de-phosphorylation
remove phosphate group -> done by phosphotases -> histones are more positive -> DNA wraps tightly -> closed conformation -> transcription OFF
78
AAs that are methylated
lysine (k) histidine (H) arginine (R)
79
process of methylation
add methyl group -> carried out by histone methyl transferase can lead to EITHER turning transcription ON or OFF - not clear-cut - depends on # of times the AA is methylated
80
histone demethylase
removes methyl group from histones
81
lysine can be methylated ____
1x, 2x, or 3x
82
histidine can be methylated ____
only 1x
83
arginine can be methylated ______
1x or 2x
84
extent of ATP-dependent chromatin remodeling
can affect a few nucleosomes or a lot on a large scale

Genetics (8 decks)

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