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Genetics (BIOL 4003) > Exam 2 pt2 > Flashcards

Exam 2 pt2 Flashcards

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1
Q

constitutive genes

A
  • unregulated
  • constant levels of expressionn
  • code proteins that are needed for survival
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2
Q

benefit of gene regulation is that

A

saving energy from only making proteins when they are needed

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3
Q

gene regulation is important to processes like

A
  • metabolism
  • response to stress
  • cell division
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4
Q

regulation can happen during

A

transcription or translation or posttranslation

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5
Q

attenuation

A

gene regulation during transcription where it is stoped right after beginning bc of protein binding

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6
Q

translational repressor proteins can

A

bind to the mRNA and prevent translation from starting

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7
Q

riboswitches can

A

produce an mRNA conformation that prevents translation from starting

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8
Q

antisense RNA can

A

bind to mRNA and prevent translation from starting

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9
Q

post translational modification examples

2

A
  • feedback inhibition
  • covalent modifications
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10
Q

3 examples of translation regulation of gene expression

A
  • translational repressor mproteins
  • riboswitches
  • antisense RNA
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11
Q

most common way of gene regulation

A

influencing rate of transcription (RNA synthesis)

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12
Q

repressors bind to DNA and

A

inhibit transcription

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13
Q

activators bind to _ and

A

DNA and increase transcription

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14
Q

negative control

A

transcriptional regulation by repressor proteins

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15
Q

positive control

A

regulation by activator proteins

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16
Q

small effector molecules bind to

A

regulatory proteins, not DNA

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17
Q

inducers

bind to and effect

A
  • small regulatory molecule
  • bind to activators and increase binding to DNA
  • bind to repressors and decrease binding of DNA
  • increase transcription
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18
Q

corepressors

bind to and effect

A
  • bind to repressors and cause DNA binding
  • decrease transcription
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19
Q

inhibitors

bind to and effect

A
  • bind to activators and prevent DNA binding
  • decrease transcription
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20
Q

repressible genes are regulated by

A
  • corepressors
  • inhibitors
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21
Q

inducers cause a _ in _ to prevent binding

A

conformational change in repressor proteins to prevent binding

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22
Q

corepressors cause a _ in _ to increase binding

A

conformational change in repressor proteins to increase binding

decrease transcription

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22
Q

corepressors cause a _ in _ to increase binding

A

conformational change in repressor proteins to increase binding

decrease transcription

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23
Q

enzyme adaptation

A

when an enzyme appears in the cell only after the cell is exposed to the enzyme substrate

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24
Q

operon is a

A

regulatory unit that consists of protein encoding genes under control of one promoter

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25
Q

polycistronic mRNA contains _ and is encoded by _

A

contains coding sequence for two or more protein genes and is encoded under control of operon

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26
Q

the lac operon consists of DNA regulatory elements…

list and what each binds

A
  • promoter (binds RNA polymerase)
  • operator (binds lac repressor protein)
  • CAP site (binds CAP)
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27
Q

lac operon has protein encoding genes for…

list

A
  • lac Z (beta galactogase)
  • lacY (permease)
  • lacA (transacetylase)
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28
Q

lacZ encodes _ , which _ function

A
  • encodes beta galactosidase
  • ^ cleaves lactose to allolactose
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29
Q

lacY encodes _ which _ function

A
  • encodes lactose permease
  • ^ required for transport of lactose
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30
Q

lacA encodes _ which _ function

A
  • encodes galactoside transacetylase
  • ^ covalently modifies lactose and analogs
  • prevents toxic buildup of lactose
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31
Q

What are the two conditions for the efficient utilization of lactose?

A

lactose is present

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32
Q

What is LacI? Is lacI included in the lac operon?

A

No, it is not included in the lac operon. LacI has its own promoter, is constantly expressed at low levels (10 proteins per cell) and encodes the lac repressor. Negatively regulates the lac operon.

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33
Q

Where does the lac repressor bind? How does this prevent transcription?

A

Lac operator. RNA polymerase cannot access the promoter when the repressor is bound.

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34
Q

Where does CAP bind? What is CAP’s coactivator?

A

It binds to CAP site. cAMP is an inducer that allows LacI to bond. Binding of CAP is necessary for transcription to occur.

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35
Q

allolactose binds to _ and _

A

lac repressor and prevents the repressor from binding to DNA

operon is on

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36
Q

when there is no lactose in enviroments,

A

there is no allolactose so the repressor is binded and the lac operon is off

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37
Q

when lactose is present

A

beta galactosidase makes allolactose, which binds the repressor and prevents it from binding to DNA, which turns on lac operon

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38
Q

the lacI gene encodes _ and is _

A

lac repressor and is always on

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39
Q

the lacI- mutation

A

eliminates the function of the lac repressor

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40
Q

in the merozygote, in the absence of lactose

what does indicate

A
  • both lac operons are repressed by >1%
  • this inndicates that the repressor on the F factor can repress both operons
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41
Q

in the presence of lactose, in the merozygote

A
  • both lac operons are induced
  • lac operon activity is 220%
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42
Q

trans effect

A

genetic regulation between genes that are not physically next to each other
* mediated by genes that encode regalatory proteins

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43
Q

the lac repressor is a cis or trans effect

A

trans

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44
Q

cis effect

A
  • DNA sequence must be next to the gene it regulates
  • mediated by sequences that bind regulatory proteins
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45
Q

the lac operator is a cis or trans element

A

cis

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46
Q

a mutation in a trans element is _ by the introduction of a second normal gene

A

complemented
* the normal copy fixes the problem

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47
Q

a mutation in a cis acting element is _ by the introduction of another normal gene

A
  • is not affected
  • normal copy of the gene does not fix the problem since its not right next to the mutated copy
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48
Q

a mutated gene with a normal gene, an enzyme that has double expression in the presence of lactose but no expression without lactase is what type of effect

A

trans effect

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49
Q

the lac operon regulation by an activator is called

A

catabolite repression

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50
Q

when exposed to both lactose and glucose, e coli

A

uses the glucose first and lactose is catabolitely repressed
* lac operon not expressed until glucose is depleted

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51
Q

diauxic growth

A

sequential use of two sugars by a bacteria

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52
Q

the small effector molecule in catabolite repression of lac operon is

A

cAMP

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53
Q

in the lac operon, cAMP binds to

A

catabolite activator protein (CAP)

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54
Q

the cAMP-CAP complex is an example of transcritoinal regulation that is _ and under _ control

A

inducible and under positive control

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55
Q

the cAMP-CAP complex binds _ and _

A

binds CAP site and increases transcription

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56
Q

why does transcription of lac operon decrease in presence of glucose

A
  • Glucose inhibits adenylyl cyclase
  • cAMP levels go down
  • cAMP-CAP complex cannot bind to CAP site
  • transcription rate decreases
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57
Q

when there is no lactose or glucose but high cAMP, transcription is _

and why

A

low
* repressor bound bc no allolactose
* cAMP-CAP bound but repressor downstream

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58
Q

order of CAP site, promoter and operator on lac

A
  1. CAP site
  2. Promoter
  3. Operator (binds repressor)
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59
Q

lactose and glucose present, transcription is _

A

medium low
* no cAMP so no CAP binding
* but no repressor bound since allolactose present

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60
Q

glucose present but no lactose, transcription is

and why

A

transcription is very low
* no CAP binding bc glucose
* repressor bound bc no allolactose

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61
Q

the lac operon has _ operator sites for the lac repressor

A

3

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62
Q

where are the operator sites for the lac operon

A
  • O1 next to the promoter
  • O2 downstream of lacZ coding genes
  • O3 slightly upstream of promoter
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63
Q

the lac repressor must always have binding at operator _ and should _ for good repression

A

always binding at operator 1 and should have two repressors for good repression

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64
Q

why is binding of lac repressors to two sites required

A

so that the lac repressors can use its domains to bind both the operator sites and form a loop that inhibits transcription

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65
Q

lac repressor structure and why important

A

lac repressor is a tetramer that uses 2 domains each to bind different operator sites to form a loop that inhibits transcription

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66
Q

RNA exists _ and _ is due to the binding of a small molecule

A

RNA exists in 2 secondary conformations (active and inhibitory) and conversion is due to binding

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67
Q

the active form of thiamin is

A

thiamin pyrophosphate (TPP)

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68
Q

thiamin genes is found in

A

thi operon

69
Q

is TPP is _ transcription is _

A
  • low, transcription completed
  • high, terminantor stem loop forms and attenuation
70
Q

TPP causes a

A

conformational change from antiterminator stem loop to a terminator stem loop

causes transcription to end at U rich seq

71
Q

thiMD operon controls

A

translation of TPP

72
Q

low TPP means _ binds to mRNA and _

A

low TTP means ribsome binds and mRNA is translated

73
Q

high TPP means _ binds to mRNA and _

A

TPP binds to mRNA and a stem loop forms that prevents translation of mRNA

74
Q

when there is _ TPP, the _ in not accessible

A

high TPP, shine-dalgarno sequence not accessible

translation inhibited

75
Q

at different stages of development, there is variation

A

in gene expression in cell types

76
Q

transcription factors are proteins that

A

influence the ability of RNA polymerase to transcribe

77
Q

general transcription factors are

A

required for the bidning of RNA polymerase to the core promotor and progressing to elongation phase

78
Q

regulatory transcription factors function to

A

regulate the rate of transcription of genes by influencing the ability of RNA polymerase to begin transcription

79
Q

regulatory transcription factors recognize _ that are located _

A

recognize cis elements located near the promoter

80
Q

regulatory transcription factors vs effector molecules

A

regulatory TF bind to DNA while effectors molecules bind to a regulatory TF

81
Q

regulatory protein that increases transcription is a _ and binds to _ sequence

A

activator, enhancer sequence

82
Q

regulatory protein that decreases transcription is a _ and binds to _ sequence

A

repressor, silencer sequence

83
Q

common factors contributing to combinatorial control

A
  • one or more activators
  • one or more repressors
  • activators & repressors modulated by: effector proteins, protein interactions, covalent modifications
  • regulator proteins may alter nucleosomes near the promoter
  • DNA methylation
  • formation of hetrochromatin
84
Q

transcription factor proteins have regions called _ that have functions like

A

domains
* DNA binding
* binding siite for effector molecules
* dimerization

85
Q

motif

A

domain parts that have similar structures between proteins

86
Q

4 types of motifs

A
  • helix turn helix
  • helix loop helix
  • zinc finger motif
  • leurcine finger motif
87
Q

many response elements are _

A

orientation independent or bidirectional

88
Q

regulation via TFIID

described

A
  • activator/coactivator complex recruits TFIID to the core promoter: transcription is enhanced
  • repressor protein inhibits the binding of TFIID to the core promoter: transcription is silenced
89
Q

transcriptional activation via mediator

described

A
  • activator protein interacts with mediator
  • phosphorylates the carboxyl domain of RNA polymerase
  • general transcriptional factors are released
  • RNA pol proceeds to elongation phase
90
Q

transcriptional repression via mediator

A
  • repressor protein interaction prevents the phsophorylation of RNA polymerase
  • it cannot proceed to elongation
91
Q

activators & repressors modulated by:

A
  • effector proteins
  • protein interactions
  • covalent modifications
92
Q

glucocorticoids influence

A
  • nutrient metabolism in cells
  • glucose utilization, fat, protein breakdown
92
Q

glucocorticoids influence

A
  • nutrient metabolism in cells
  • glucose utilization, fat, protein breakdown
93
Q

gonadocorticoids include

A
  • estrogen and testosterone
94
Q

GRE function as

A

enhancers

95
Q

creb protein responses to

A

cAMP

96
Q

chromotin closed conformation

A
  • Chromatin is very tightly packed
  • Transcription may be difficult or impossible
97
Q

chromatin open conformation features

A
  • Chromatin is accessible to transcription factors
  • Transcription can take place
98
Q

ATP-dependent chromatin remodeling

A
  • Energy of ATP hydrolysis is used to drive changes in the locations and/or composition of nucleosomes
  • Makes the DNA more or less amenable to transcription
99
Q

Chromatin remodeling complexes change chromatin structure in one of 3 ways:

A
  • Change in the position of nucleosomes
  • Eviction of histone octamers
  • Change in the composition of nucleosomes
100
Q

histone variants

A

mutations in histones

101
Q

Histone variants are

A

incorporated into a subset of nucleosomes to create specialized chromatin

102
Q

changes in composition of histone variants can

A

regulate gene transcription

103
Q

enzymes that modify the tails of histones affect the level of transcription

2 ways

A
  • may influence interactions between DNA and proteins
  • occur in patterns, histone code
104
Q

histone code

A
  • The pattern of modifications provide binding sites for proteins that promote alterations in chromatin structure
  • These proteins bind to histones based on the code and affect transcription
105
Q

p

A

phosphate

106
Q

ac

A

acetyle group

107
Q

m

A

methyl group

108
Q

acetylation of _ eliminates _ and causes the DNA _

A

Acetylation of* positively charged lysines* eliminates the positive charge and causes the DNA to less tightly bound

109
Q

acetylation of lysines _ transcription

A

increases transcriptions

110
Q

ChIP Seq is used to

A

map the locations of specific nucleosomes within a genome

111
Q

ChIP sequencing allows determinations of

A
  • Where nucleosomes are located
  • Where histone variants are found
  • Where covalent modifications of histones occur
112
Q

_ is combined with ChIP Seq and performed in species where _

A

Chromatin immunoprecipitation is combined with ChIP Seq and performed in species where the entire genome has been sequenced

113
Q

A nucleosome-free region (NFR) is found…

A

at the beginning and end of many (most) eukaryotic genes.

114
Q

DNA methylation is…

A

the covalent attachment of methyl groups

115
Q

DNA methylation is carried out by

A

DNA methyltransferase

116
Q

DNA methylation usually _ transcription

A

inhibits

117
Q

In housekeeping genes, the CpG islands are _

A

unmethylated

118
Q

Methylation inhibits…

A

the binding of an activator protein

119
Q

Methyl-CpG-binding protein recruits…

A

other proteins that change the chromatin to a closed conformation.

120
Q

maintenance methylation

A

Pattern of one copy of the gene being methylated and the other not is maintained in the resulting offspring

121
Q

De novo methylation is an _ and _

A

infrequent and highly regulated event

122
Q

To be epigenetic, molecular changes must

A

be passed from cell to cell

123
Q

Genes or chromosomes can be targeted for epigenetic regulation in two ways:

A
  • Via transcription factors
  • Via noncoding RNA
124
Q

Cis-epigenetic changes are maintained

A

maintained at a specific site

125
Q

a cis-epigenetic change may affect…genes

A

only one copy of gene but not the other copy

126
Q

Trans-epigenetic changes are maintained

A

by diffusible factors, such as transcription factors

127
Q

a trans-epigenetic change affects…genes

A

both copies of a gene

128
Q

Cis- and trans-epigenetic mechanisms can be distinguished from each other by…

describe/define

A

cell fusion experiments
* One cell has gene B modified to be transcriptionally active; same gene in another cell is inactive

129
Q

Fuse cells: if a cis mechanism is involved _ will be modified.

A

only gene B that was originally modified

130
Q

Fuse cells: If trans mechanism, _ modified

A

both copies of the gene will be

131
Q

Euchromatin

4 things

A
  • not stained during interpahse
  • loop domains loose
  • transcriptionally active
  • central position in nucleus
132
Q

hetrochromatin

4 thin

A
  • stained during interphase
  • compact
  • inhibit gene expression
  • localized periphery of nucleus
133
Q

roles of heterochromatin formation

A
  • silencing viral genes
  • prevention of TE movement
  • gene silencing
134
Q

Constitutive heterochromatin –

A

regions that are heterochromatic at the same location in all cell types

135
Q

Facultative heterochromatin –

A

heterochromatin that varies in its location among different cell types

136
Q

facultative hertrochromatin allow for

A

silencing of genes in cell specfic manner

137
Q

facultative heterochromatin formation is _ and depends on _

A

reversible and depends on stage of develeopment or cell type

138
Q

DNA methylation in facultative heterochrom

A

methylation at CpG islands in gene regulatory regions

139
Q

reader domains

A

specific proteins bind to posttranslational modifications at these domains

140
Q

reader domains

A

specific proteins bind to posttranslational modifications at these domains

141
Q

Recruiter domains

A

recruit other proteins, such as chromatin remodelers or chromatin-modifying enzymes

142
Q

Eraser domains

A

remove PTMs

143
Q

writer domains

A

addition of PTMs

144
Q

heterochromatin with higher order structure features

A
  • Has closer, more stable contacts of nucleosomes with each other
  • Forms closer loop domains
  • Binds to the nuclear lamina
145
Q

Closer, more stable contacts of nucleosomes with each other

process

A
  • H3K9me3 recognized by HP1
  • HP1 bridges nucleosomes; makes them more compact
146
Q

Lamina-associated domains (LADS)

A
  • Organize chromosomes into chromatin territories
  • May be involved in gene repression
147
Q

HP1 binding to H3K9me3 modifications on AA tails causes

A

tighter compaction, no access to DNA

148
Q

H3K9me3

A

Histone 3 Lys at 9th position methylated 3x

149
Q

Initial formation of facultative and constitutive chromatin occurs in 3 phases:

describe each

A
  1. Nucleation – short chromosomal site bound by chromatin-modifying enzymes and chromatin-remodeling complexes
  2. Spreading – adjacent euchromatin is turned into heterochromatin
  3. Barrier – in interphase chromosomes, spreading stops when it reaches a barrier
150
Q

Mechanisms to Maintain Epigenetic Marks

A
  • maintainance DNA methylation
  • histone modifications
  • DNA polymerases recruit chromatin modifying complexes
  • higher order structure self maintains
151
Q

ICF can be due to

A

Can be due to a mutation in a DNA methyltransferase gene

152
Q

roberts syndrome caused by

A

mutations in a gene for acetyltransferase

153
Q

genomic imprinting occurs at two sites:

A
  • the imprinting control region (ICR)
  • differentially methylated region (DMR)
154
Q

genomic imprinting, methylation _ binding of _ so lgf2 gene is _

A

methulation prevents binding of CTCF and lgf2 gene is enhanced

155
Q

genomic imprinting, methylation _ binding of _ so lgf2 gene is _

A

methulation prevents binding of CTCF and lgf2 gene is enhanced

156
Q

The Xic encodes , _ which are _

A

Xist and Tsix, which are transcribed in opposite directions

157
Q

prior to X chromosome inactivation, _ is expressed in both chromosomes

A

Tsix

158
Q

mechanism of X chromosome inactivation

A
  • Tsix active in both bc pluripotency factors
  • CTCF bind to Xic, X chromosomes link and pass potency and CTCFs to one X that will stay active
  • on inactive X, Xist with bind to Xic
  • Xist RNA bind to each other in both directions
  • continues until spread along chromosome
  • Xist pull in and compact and barr body the inactive X
159
Q

Trx Group incolved in

A

gene activation in differentiation

160
Q

Pc group involved in

A

gene repression during differenciation

161
Q

PcG two types

A

PRC2 and PRC1

162
Q

how genes are silenced by Pc group

A

PRC2 binds to response element and trimythelates K27 on H3
* PRC1 compact chromosome
* PRC1 may modify H2A by attach Uq tags
* PRC1 may use direct inhibition

3 options

162
Q

how genes are silenced by Pc group

A

PRC2 binds to response element and trimythelates K27 on H3
* PRC1 compact chromosome
* PRC1 may modify H2A by attach Uq tags
* PRC1 may use direct inhibition

3 options

163
Q

_ inhibits the Agouti gene

A

DNA methylation

164
Q

the more methylated CpG islands, the _ the coat color

A

darker

165
Q

Vernalization

A

certain species of plants must be exposed to the cold before they can undergo flowering

166
Q

cold activates Vin3 and COLDAIR….

A

which activate VRN1 & 2
which activate PRC2
which inhibitsFLC
which disinhibits budding
so flowering happens

167
Q

cold activates Vin3 and COLDAIR….

A

which activate VRN1 & 2
which activate PRC2
which inhibitsFLC
which disinhibits budding
so flowering happens

Genetics (BIOL 4003) (7 decks)

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