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genetics midterm 2 > lecture 24, 25 > Flashcards

lecture 24, 25 Flashcards

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1
Q

what does transcriptional regulation aim to regulate?

A

how much RNA is made

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2
Q

what does mRNA stability aim to regulate?

A

how quick RNA can degrade

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3
Q

what does protein stability aim to regulate?

A

how quick protein can degrade

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4
Q

what does translational regulation aim to regulate?

A

How much protein is made

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5
Q

promote-proximal elements

A

DNA sequences that precede the promoter of a eukaryotic gene & bind general transcription factors

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6
Q

enhancers

A

DNA sequences located far from the gene that bind transcription factors

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7
Q

what kinds of domains are found in eukaryotic transcription factors?

A

(1) DNA binding domain
(2) protein-protein interaction domain between TF-TF or TF-RNA pol
(3) domains that lead to histone modification
(4) domains that are a sensor of the physiological condition of the cell

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8
Q

what enhancer binds the transcription factor Gal4?

A

Upstream Activation Sequence (UAS)

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9
Q

what does UAS bind to?

A

the transcription factor Gal4

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10
Q

describe the pathway of galactose

A

Galactose (E) -> Galactose (I) -> Galactose-1-phosphate -> UDP galactose -> UDP-glucose -> Glucose-1-phosphate -> Glycolysis

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11
Q

what domains does Gal4 have?

A

DNA binding and activation domain

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12
Q

what does it mean for a transcriptional activator protein to be modular?

A

domains can be separated and still retain their basic activity

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13
Q

true or false: Gal4 is a modular activator

A

true

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14
Q

what does DNA binding domain do?

A

brings the activation domain to the enhancer

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15
Q

why is it important that the activation domain is brought to the enhancer?

A

so that it can help in binding to proteins associated with RNA pol

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16
Q

do DNA binding domains require the activation domain to bind DNA?

A

no; itll still bring the AD to the enhancer

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17
Q

does the activation domain need to have the DNA binding domain around to bind proteins associating with RNA pol?

A

no; itll still be able to try and bind proteins

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18
Q

reporter gene

A

a gene that is able to have its transcription state be monitored by an easily detectable phenotype associated with ON and OFF states

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19
Q

In cells with wild-type Gal4, what color will the colonies be in the presence of X-gal when lacZ is on?

A

blue

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20
Q

when the DNA binding domain and activation domain are separated within the Gal4 process, what happens with lacZ?

A

lacZ is unable to be produced and the colonies will be white in the presence of X-gal

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21
Q

what does Gal80 do?

A

binds the activation domain of Gal4

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22
Q

what happens when Gal80 binds with Gal4?

A

it prevents Gal4 from activating genes in the absence of galactose

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23
Q

what happens to Gal80 in the presence of galactose?

A

it disassociates from Gal4’s activation domain and allows it to activate genes

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24
Q

how does Gal80 disassociate from Gal4’s AD?

A

Gal3, bound to galactose, binds to Gal80, which causes it to release from Gal4

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25
corepressor
a protein that represses transcription without directly binding to DNA
26
coactivator
a protein that activates transcription without directly binding to DNA
27
how does Gal4 help RNA pol II?
It binds basal transcription factors and the mediator complex for assistance
28
mediator complex
a co-activator that promotes RNA pol II activity but does not directly bind to DNA nor is it a part of RNA pol despite being required for transcription on most promoters
29
what types of mating type can yeast haploid cells have?
a or alpha
30
what type of genes do diploid cells need to suppress?
haploid, a, and alpha genes
31
what type of genes do a cells need to express/repress?
a and haploid genes, repress alpha genes
32
what type of genes do alpha cells need to express/repress?
alpha and haploid genes, repress a genes
33
what type of genes do diploid cells need to express/repress?
repress haploid, alpha and a genes
34
what proteins do diploid cells express/repress?
express a-1 and alpha-2, repress alpha-1
35
in a cells, what does MCM do?
acts as an activator of alpha genes
36
without help, what is MCM unable to do?
It cannot bind the alpha gene promoters
37
in alpha cells, what does MCM do?
act as an activator
38
are a1 proteins created in alpha cells?
no
39
what are the only proteins made in alpha cells?
alpha-1 and alpha-2
40
what does the alpha-2 protein do in alpha cells?
acts as a repressor of the MCM on the a promoter
41
what does the alpha-1 protein do in alpha cells?
acts as an activator on the alpha promoter
42
in diploid cells, what does MCM do?
acts an an activator
43
what type of proteins are made in diploid cells?
a1 and alpha-2
44
what does the alpha-2 protein do in diploid cells?
acts as a repressor and blocks MCM activity
45
how are haploid-specific genes and alpha-1 genes repressed in diploid cells?
by the combination of a1 and alpha-2 proteins working together
46
nucleosome
a protein complex; basic unit of chromatin
47
what are nucleosomes composed of?
8 subunits of histone (2 H2A, 2 H2B, 2 H3, 2 H4), and DNA
48
what are some histone variants?
CENP-A for H3 in centromeric DNA, H2A.Z to damaged DNA
49
histones
proteins that help package and organize DNA
50
what is needed for RNA pol to bind promoters securely?
the TATA box has to be free of nucleosomes
51
what presents a challenge for RNA pol when trying to bind promoters?
the TATA box is constantly being blocked by the nucleosome
52
chromatin remodeling
the process of changing histone position
53
what is the purpose of chromatin remodeling?
it removes histones from the promoter region which allows transcription factors and RNA pol to bind
54
what does H1 histone do?
stabilizes the structure of chromatin by binding to the DNA between nucleosomes, helping it pack tightly
55
what is acetylation
a histone modification that leads to activation of genes
56
what happens when lysine is acetylated?
it neutralizes the positive histone charge and reduces the interactions between histone and DNA, opening chromatin
57
what does HATs stand for?
histone acetyl transferases
58
what is HATs?
enzymes that add acetyl to histones
59
what does HDACs stand for?
histone deacetylases
60
what is HDACs?
enzymes that remove acetyl from histones
61
What are N-terminal tails?
the ends of histone proteins that stick out of the nucleosome
62
what is the purpose of post-translational histone modification?
regulates how tightly wrapped DNA is around histones which can make genes more/less accessible for transcription
63
what is Gal1 positively regulated by?
Gal4
64
what is Gal1 negatively regulated by?
Mig1-Tup1
65
where can Mig-1 be found?
in the nucleus when glucose is high
66
what is Tup1?
Tup1 is HDAC, and leads to the repression of Gal1 by creating repressive chromatin
67
methylation
histone post-translational modification on lysine or arginine
68
What does methylation of lysine do?
creates binding sites for other proteins that can activate/repress gene expression, but does not affect charge
69
what determines what kind of protein will bind to the methylated histone?
which histone residue is methylated and how much
70
even though methylation and acetylation can occur on the same amino acid, what is the restriction?
the modifications can not happen at the same time on the same amino acid
71
epigenetic inheritance
the passing of chromatin state from one generation to the other
72
what does epigenetic inheritance tell us?
during DNA replication, both the DNA sequence and the chromatin structure are passed onto the next cell generation
73
DNA methylation
the addition of methyl groups to DNA residues
74
in mammals, where is the methyl group usually added?
It is added to the cytosine in a CG dinucleotide
75
hemimethlyated DNA
DNA molecules methylated on only one strand
76
is DNA methylation or histone modifications more stable?
DNA methylation
77
where would you find DNA strands that have undergone methylation
in regions of the genome that are maintained in an inactive state for an organism's entire life
78
synergistic effect
the effect of a combination of genes is greater than addicting the individual effects
79
enhanceosomes
a large protein complex and the enhancer it binds that work together to activate transcription
80
how are enhanceosomes formed?
by the binding of multiple regulatory proteins to the multiple binding sites in an enhancer
81
describe the process of enhanceosomes recruiting chromatin remodelers
(1) GCN5 binds the enhanceosome and acetylates the surrounding histone (2) acetylated histones recruit proteins that move away histones (3) histones move form the promoter and expose the promoter that can now bind RNA pol
82
what is GCN5?
a histone acetylate
83
insulator
a cis-acting element (DNA sequence) that limits chromatin state to a distinct DNA region
84
enhancer blocking insulator
DNA element that blocks the action of an enhancer
85
what does the action of an insulator involve?
DNA binding proteins that form complexes that can fold DNA and promote long range DNA interactions
86
hemetochromatin
condensed chromatin that is not favorable for transcription
87
euchromatin
open chromatin that is favorable for transcription
88
constitutive heterochromatin
permanently compact and inactive chromatin
89
where can you find constitutive heterochromatin?
in centromere and telomere regions
90
what can heterochromatin do?
change its position and spread to neighboring chromosomal regions
91
position effect variegation
expression of a gene depending on its position and silenced in some cells and active in others, despite being a part of the same issue as the other cells
92
when is position effect variegation most prevalent?
when a gene is placed in proximity to heterochromatin and caused by the spreading of repressive chromatin
93
what is HP1
a protein that is required for the repressed chromatin state and binds H3K9 methylated histones
94
what can some gene products do that effect the spread of heterochromatin?
it can bolster the spread and silence more of the gene in cells or suppress the spread and allow for more expression of previously silenced genes
95
barrier insulators
DNA element that blocks the spreading of heterochromatin
96
how do barrier insulators and HAT work together?
HAT adds another measure for euchromatin near the heterochromatin to be not as tightly packed to mitigate heterochromatin's effect
97
genomic imprinting
genomic region that are repressed depending on whether they were inherited from the mother or father
98
paternal imprinting
repression of an allele inherited from the male parent
99
maternal imprinting
repression of an allele inherited from the female parent
100
what does genomic imprinting require to work?
insulators
101
what genes require enhancer function for transcription?
H19 and lgf2
102
what is the limitation with the enhancer with regards to H19 and lgf2?
it can activate either one, but not both at the same time
103
what is CTCF
a DNA-binding protein that regulates chromatin structure and gene expression
104
what does CTCF do?
binds the imprinting control region sequence when the DNA is unmethylated
105
what happens when ICR (imprinting control region) is methylated?
CTCF does not bind the DNA at ICR and activates lgf2
106
what happens when CTCF binds the DNA at ICR?
lgf2 is blocked and H19 is activated
107
which allele is methylated?
the paternal allele
108
which allele is unmethylated?
the maternal allele
109
if an allele is methylated, which gene is expressed/repressed?
lgf2 is expressed, H19 is repressed
110
if an allele is unmethylated, which gene is expressed/repressed?
H19 is expressed, lgf2 is repressed
111
what is H19
a non-coding RNA gene expressed by the maternal gene, and plays a role in regulating growth suppression
112
what is lgf2
a protein-coding gene expressed by the paternal gene, and plays a role in regulating growth during development
113
if a recessive allele is inherited from a female and is imprinted in the female, what will the phenotype of the progeny be?
dominant
114
if a recessive allele is inherited from the female and it is imprinted in the male, what will the phenotype of the progeny be?
recessive
115
if a recessive allele is inherited from the male and it is imprinted in the female, what will the phenotype of the progeny be?
recessive
116
if a recessive allele is inherited from the male and it is imprinted in the male, what will the phenotype of the progeny be?
dominant
117
x-chromosome inactivation
one copy of the X becomes transcriptionally inactive
118
where is Xist transcribed from?
X-inactivation center
119
what will Xist do?
it coats the chromosomes it transcribed from and induces a silent chromatin state
120
HMTase
enzyme responsible for the methylation of histones
121
what does H2A do?
helps to package the DNA into a structure that is wrapped around histone proteins
122
what does H2B do?
helps in the structural integrity of the nucleosome
123
what does H3 do?
regulate gene expression
124
what does H4 do?
regulate gene expression

genetics midterm 2 (6 decks)

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