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Genetics - BI 312 > Chapter 12: Control of Gene Expression > Flashcards

Chapter 12: Control of Gene Expression Flashcards

1
Q

Define operon

A

a group of genes that share a common promoter and are transcribed as a unit, producing a single mRNA molecules that encodes several proteins

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2
Q

T/F: Operons control the expression of genes

A

True

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3
Q

True/False: Operons are common in bacteria, archaea, and eukaryotes.

A

False. Operons are common in bacteria and archaea but not as common in eukaryotes

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4
Q

Define gene regulation

A

Encompasses the mechanisms and system that control the expression of genes

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4
Q

How does gene regulation help bacteria?

A

By providing internal flexibility, turning genes on and off in response to environmental changes

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4
Q

Define central dogma

A

Genetic information flows from DNA to RNA to proteins.

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5
Q

How does gene regulation help multicellular eukaryotic organisms?

A

By bringing about cellular differentiation

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6
Q

Define structural genes

A

Encode proteins used in metabolism or biosynthesis or that play a structural role in the cell.

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7
Q

Define regulatory genes

A

Either RNA or proteins, interact with other DNA sequences and affect the transcription or translation of those sequences

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8
Q

The products are regulatory genes are often…

A

DNA-bonding proteins or RNA molecules that affect gene expression

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9
Q

Define constitutive genes

A

Structural genes that encode essential cellular functions and are expressed continually and are not regulated

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10
Q

Define regulatory element

A

DNA sequences that are not transcribe, bit still affect the expression of DNA sequences to which they are physically linked

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11
Q

Control is involved in gene expression. What are the two types of control?

A

Positive control and negative control

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12
Q

Define positive control

A

Processes that stimulate gene expression

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13
Q

Define negative control

A

Processes that inhibit gene expression

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14
Q

At what levels can gene expression be controlled?

A

Any number of levels.

DNA/chromatin structure, transcription, mRNA processing, mRNA stability, translation, posttranslational modification

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15
Q

Why is transcription a particularly important level of gene regulation in both bacteria and eukaryotes?

A

Transcription is the first step in the process of information transfer from DNA to protein. For cellular efficiency, gene expression is often regulated early in the process of protein production

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16
Q

What is the strucutre of an operon?

A

A promoter and a regulator which bind to an operator site connected to 3 structural genes

Promoter - regualtor/operator - gene a / gene b / gene c

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17
Q

Define regulator gene

A

helps control the expression of the structural genes of the operon by increasing or decreasing their transcription

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18
Q

Define regulator proteins

A

Can bind to a region of the operon called the operator and affect whether transcription can take place

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19
Q

Define operator

A

A region of the operon that regulator proteins can bind to

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20
Q

What is the difference between a structural gene and a regulator gene?

A. Structural genes are transcribe into mRNA; regulator genes aren’t

B. Structural genes have complex structure; regulator genes have simple structures

C. Structural genes encode proteins that function in the structure of the cell; regulator genes carry out metabolic reactions

D. Structural genes encode proteins used in metabolism or biosynthesis or cell structure; regulator genes control the transcription of structural genes

A

D

D. Structural genes encode proteins used in metabolism or biosynthesis or cell structure; regulator genes control the transcription of structural genes

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21
Q

What are the two types of transcriptional control?

A

Postitive control and negative control

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22
Q

What is negative control regarding transcriptional control

A

A regulator protein is a repressor, binding to DNA and inhibiting transcription.

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23
Q

What is positive control regarding transcriptional control?

A

A regulatory protein is an activator, stimulating transcription

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24
Q

Define inducible operons

A

Which transcription is normally off (not taking place), something must happen to induce transcription, or turn it on

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25
Q

Define repressisble operons

A

Which transcription is normally on (taking place); something must happen to repress transcription or turn if off

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26
Q

Define inducer

A

A small molecule that bins to the repressor protein and transcription of a negative inducible is turned on

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27
Q

What 2 binding sites do regulator proteins contain?

A
  1. One that bins to DNA
  2. Another that binds to small molecules such as the inducer
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28
Q

How do inducers affect proteins?

A

When the protein binds with an inducer it’s shape changes and can no longer bind with DNA

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29
Q

Define allosteric proteins

A

Proteins that change shape upon binding to another molecule

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30
Q

What proteins do inducible operons usually control?

A

proteins that carry out degradative processes (proteins that break down molecules)

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31
Q

Define corepressor

A

A small molecule that binds to the repressor and makes it capable of binding to the operator

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32
Q

Is the lac operon a positive or negative control?

A

Positive.

The catabolite activator protein (CAP) binds to the promoter and increases the efficiency with which RNA polymerase can bind the promoter and transcribe the structural genes

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33
Q

The regulator protein that acts on a negative repressible operon is synthesized as
A: An active activator
B: an inactive activator
C: An active repressor
D: An inactive repressor

A

D

D: An inactive repressor

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34
Q

Define lactose

A

A major carbohydrate found in milk and can be metabolized by E. coli in the mammalian gut

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35
Q

What is the function of the protein lactose permease?

A

Permease helps lactose diffuse across the E. coli cell membrane

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36
Q

What is the function of B-Galactosidase?

A

Break down lactase into glucose and galactose. It also converts lactose into allolactose

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37
Q

Define allolactose

A

a compound that plays an important role in regulating lactose metabolism

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38
Q

Which lac gene encodes for permease?

A

lacY

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39
Q

Which lac gene encodes for B-galactosidase?

A

lacZ

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40
Q

Which lac gene encodes for thiogalactoside?

A

lacA

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41
Q

What is the function of thigalactoside?

A

Currently unknown

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42
Q

Define LacI

A

a regulator gene, transcribed into a short mRNA that is translated into a repressor

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43
Q

What role does lacP play in lactose regulation?

A

Promoter

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44
Q

What is lacO?

A

Operator for lactose regulation

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45
Q

How does the presence of lactose affect the lactose regulation?

A
  1. Lactose is converted into allolactose by B-Galactosidase
  2. The presence of allolactose keeps lacI from binding to lacO
  3. Transcription of lactose proteins (lacZ, lacY, and lacA) continues
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46
Q

How does the absence of lactose affect the lactose regulation?

A
  1. No lactose means no allolactose
  2. No allolactose means lacI binds to lacO
  3. The binding of lacO stops transcription for more lactose proteins (lacZ, lacY, and lacA)
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47
Q

In the presence of allolactose, the lac repressor
A: Binds to the operator
B: Binds to the promoter
C: Cannot bind to the operator
D: Binds to the regulator gene

A

C

C: Cannot bind to the operator

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48
Q

What does a partial-diploid do?

A

Helps define the roles of the different components of an operon

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49
Q

How do structural mutations affect the following:

lacZ
lacY

A

lacZ would not make B-galactosidase
lacY would not make permease

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50
Q

Are structural mutations linked or independent in lacZ and lacY genes?

A

Independent.

Meaning even if lacY was mutated and could not make permease lacZ could still make B-Galactosidase

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51
Q

How do regulator mutations (lacI) affect lacZ and lacY?

A

Both are affected. Even if both are present, mutations in lacI will keep either from forming their products

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52
Q

lacI+ is wild type where proteins function normally

lacI- is mutated type and proteins cannot function

Which type is dominant?

A

Wild type, lacI+

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53
Q

What is a superrepressor? (lacI^s)

A

Mutations that prevented transcription from taking place even in the presence of lactose

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54
Q

What is lacO^c vs. lacO+

A

lacO+ is wild type and can be turned on and off

lacO^c is the mutated type that cannot be turned off

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55
Q

Is lacO^c or lacO+ dominant?

A

lacO^c is dominant

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56
Q

Between lacI^s (superrepressor) and lacO^c (constitutive operator) which is dominant?

A

lacO^c is dominant, and even in the presence of lacI^s lac proteins will still be made

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57
Q

What happens if the promoter is mutated? (lacP is mutated into lacP-)

A

If the promoter cannot function no lac proteins will be made

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58
Q

Define catabolite repression:

A

When glucose is available, genes that participate in the metabolism of other sugars are turned off

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59
Q

Efficient transcription of the lac operon takes place only if _______ is present and _______ is absent

A. Glucose, Lactose
B. Lactose, Glucose

A

B. Lactose, Glucose

Efficient transcription of the lac operon takes places only if lactose is present and glucose is absent

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60
Q

Is catabolite repression a positive or negative control?

A

Positive

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61
Q

Define cAMP (cyclic AMP)

A

A modified nucleotide that is important in cellular signaling processes in both bacterial and eukaryotic cells

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62
Q

What is the relationships between cAMP and glucose?

A

High glucose = low cAMP
Results in little lac transcription

Low glucose = high cAMP
Results in lots of lac transcription

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63
Q

The lac operon is an…

A

inducible operon

Transcription does not normally take place and must be turned on

64
Q

Some operons are repressible; what does this mean?

A

Transcription is normally turned on and must be repressed / turned off when not needed

65
Q

Which kind of operon is the tryptophan (trp) operon?

A

Negative repressible operon

66
Q

What are the 5 structural genes for trp?

A

trpE, trpD, trpC, trpB, and trpA

67
Q

Define trpR

A

A regulator gene that encodes a repressor protein that is normally inactive. Regulates tryptophan.

68
Q

Is transcription on or off when trp is low?

A

On

69
Q

Is transcription on or off when trp is high?

A

Off

70
Q

In the trp operon, what happens to the trp repressor in the absence of tryptophan?

    A: It binds to the operator and represses transcription
B: It cannot bind to the operator, and transcription takes place 
C: It binds to the regulator gene and represses transcription
     D: It cannot bind to the regulator gene, and transcription takes place
A

B

B: It cannot bind to the operator, and transcription takes place

71
Q

How does chromatin structure repress gene expression?

A

The DNA is wrapped so tightly around the histone proteins that other transcription factors cannot reach the DNA

72
Q

Define chromatin-remodeling complexes:

A

Regulatory proteins and other transcription factors that alter the chromatin structure without altering the chemical structure of the histones directly

73
Q

Histones have 2 domains. What are they?

A
  1. A globular domain that associates with other histones and the DNA
  2. A positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA
74
Q

How are tails of histones often modified?

A

by the addition or removal of phosphate groups, methyl groups, or acetyl groups

75
Q

What is the ubiquitination modification to histones?

A

when a small molecule called ubiquitin is added or removed from the histones

76
Q

Define histone code

A

The collection of different mechanisms that affect chromatin structure

77
Q

How do histone codes affect gene expression?

A

by altering chromatin structure directly or sometimes by providing recognition sites for proteins that bind to DNA and regulate transcription

78
Q

Define methylation

A

The addition of a methyl group

79
Q

How does methylation affect histones?

A

the addition of methyl groups (CH3) to the tails of histone proteins can activate or repress transcription depending on the histone modified and which amino acids were affected

80
Q

Define histone methyltransferases

A

Enzymes that add methyl groups to specific amino acids

81
Q

Define demethylases

A

Enzymes that remove methyl groups from histones

82
Q

True/False: Enzymes and proteins that modify histones do not bind to specific DNA sequences and must be recruited to specific chromatin sites

A

True

83
Q

What 3 things serve to recruit histone-modifying enzymes to specific sites?

A

Sequence-specific binding proteins, preexisting histone modifications, and RNA molecules

84
Q

Define acetylation

A

A type of histone modification that affects the chromatin structure through the addition of acetyl groups (CH3CO)

85
Q

What effect does acetylation have?

A

Usually stimulates transcription by destabilizing chromatin structure

86
Q

Define Acetyltransferase enzymes

A

add acetyl groups (increase transcription)

87
Q

Define Deacetylases

A

remove acetyl groups (repress transcription)

88
Q

Which amino acid does methylation usually affect?

A

Cytosine

89
Q

How does methylation of cytosine affect the histone?

A

Methylation attracts deacetylases, deconstructing histones and allowing transcription

90
Q

Define cofactors

A

other proteins that can repress or activate transcription recruited by transcription factors

91
Q

Define general transcription factors

A

Bind to the promoter and are part of the basal transcript apparatus. These are the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription.

92
Q

Define coactivator

A

a protein that indirectly acts with the basal transcription apparatus at the core promoter to stimulate or stabilize transcription

basal transcription apparatus and core promoter are just part of the promoter in the operon

93
Q

Many transcription factors stimulate transcription by interacting with
A: introns
B: Basal transcription apparatus
C: DNA polymerase
D: Nucleosomes

A

B

B: Basal transcription apparatus

94
Q

Define enhancers

A

regulator elements that affects the transcription of distant genes

95
Q

True/False: Enhancers are very rare

A

False. They are very abundant

96
Q

Define silencers

A

A sequence that have an inhibitory effect on transcriptions of distance genes

97
Q

Define insulator

A

Also called boundary elements,which are DNA sequences that block the effects of enhancers in a position-dependent manner

Ex: an insulator is in-between an enhancer and a promoter; the enhancer is blocked

98
Q

How does the binding of transcription factors to enhancers affect transcription at genes that are thousands of base pairs away?

A

The DNA between the enhancers and the promoter loops out, so that transcription factors bound to the enhancer are able to interact directly with the basal transcription apparatus

99
Q

Define response elements

A

A common regulatory sequence that typically contain the same consensus sequences at varying distances from the genes being regulated

100
Q

How do transcription and translation differ time-wise in bacteria and eukaryotes?

A

Bacteria has transcription and translation simultaneously

Eukaryotes have transcription and the later translation

101
Q

How does alternative splicing affect pre-mRNA?

A

allows pre-mRNA to be spliced in multiple ways, generating different proteins in different tissues or at different times in development

102
Q

Are eukaryotic mRNAs or bacterial mRNAs more stable?

A

Eukaryotic

103
Q

How does the stability of mRNA affect the synthesis of proteins?

A

The longer it is stable the more proteins are made

104
Q

What 5 things affect the stability of mRNA?

A
  1. 5’ cap
  2. poly(A)tail
  3. 5’UTR
  4. Coding region
  5. Sequences in the 3’UTR
105
Q

How does the poly(A)tail affect mRNA stability?

A

The poly(A)tail stabilizes the 5’ cap, which must be removed before the mRNA molecule can be degraded from the 5’ end.

106
Q

What triggers RNA silencing?

A

Very small RNA molecules known as microRNA (miRNA) and small interfering RNAs (siRNA)

107
Q

Define Dicer

A

an enzyme that cleaves and processes double-stranded RNA to produce single-stranded siRNAs or miRNAs which combine with proteins to form an RNA-induced silencing complex

108
Q

Define RISC

A

A RNA-induced silencing complex formed by the Dicer enzyme

109
Q

What are the 3 ways siRNAs and miRNAs regulate gene expression?

A
  1. Cleavage of mRNA
  2. Inhibition of translation
  3. Inhibition of transcription
110
Q

How does cleavage of RNA take place?

A

mRNA is cleaved by a RISC containing siRNA or miRNA, after cleavage the mRNA degrades

111
Q

How do siRNAs and miRNAs affect translation?

A

The more miRNAs and siRNAs are around the less translation there is

112
Q

Transcriptional silencing which affects gene expression occurs in 3 steps involving siRNAs. What are these steps?

A
  1. siRNAs combine with RITS (RNA-induced transcriptional silencing)
  2. RITS attracts enzymes that methylate the tails of histone protein
  3. The addition of methyl groups to DNA keeps other proteins and enzymes from carrying out transcription since they can no longer bind to DNA
113
Q

In RNA silencing, siRNAs and miRNAs usually bind to which part of the mRNA molecules that they control?

A. 5’ UTR
B. 5’ cap
C. 3’ poly(A)tail - my guess
D. 3’UTR

A

D

D. 3’UTR

114
Q

Define epigenetics

A

The inheritance of variation above and beyond differences in DNA sequence

115
Q

True/False: Epigenetics are often unstable.

A

False, epigenetics are mostly stable

116
Q

How are epigentic effects brought about?

A

Through changes in chromatin strucutre

117
Q

What are 3 molecular mechanisms that change chromatin structure to bring about epigenetics?

A
  1. Changes in patterns of DNA methylation
  2. Chemical modification of histone proteins
  3. RNA molecules that affect chromatin structure and gene expression
118
Q

Where does changes in pattern of DNA methylation usually occur?

A

In cytosine, specifically CpG dinucleotides

119
Q

Define CpG

A

Cytosine nucleotides that are immediately adjacent to guanine nucleotides

P = phosphate groups that connects C and G nucleotides

120
Q

Define CpG Islands

A

DNa regions that have many CpG dinucleotides

121
Q

How does epigenetics transfer through DNA methylation?

A
  1. Before replication, DNA is fully methylated at CpG dinucleotides
  2. During replication, new DNA strands are synthesized without methyl groups
  3. After replication, each new DNA molecule will have methylation on one strand but not the other: the DNA is hemimethylated
  4. Methyl groups attract methyltransferase enzymes, which add methyl groups to the unmethylated strand
  5. Resulting in fully methylated DNA
122
Q

Define epigenetic marks

A

Types of modification that can alter chormatin structure and effect the transcription of genes

123
Q

Define Paramutation

A

An interaction between two alleles that leads to a gertibale change in the expression of one of the alleles

124
Q

What are 3 important features of paramutation?

A
  1. The newly established expression pattern of the converted allele is transmitted to future generation, even when the allele that brought about the alteration is no longer present
  2. The altered allele is now able to convert other alleles to the new phenotype
  3. There are no associated DNA sequence changes in the altered alleles
125
Q

Define epigenome

A

The overall pattern of chromatin modifications in a genome

126
Q

Gene regulation in bacteria cells:

a. Only occurs at the level of RNA processing

b. Is energy inefficient

c. Allows the bacteria to respond to environmental changes

d. Limits biochemical flexibility

A

c

c. Allows the bacteria to respond to environmental changes

127
Q

What percentage of human genes can be regulated through RNA splicing?

A

95%

128
Q

In vertebrates, the predominant DNA modification occurs at which base?

A

Cytosine

129
Q

Genes that encode protein which are used in metabolism or biosynthesis are called _____ genes

A

structural

130
Q

The DNA sequences that are capable of affecting transcription at distant promoters, sometimes tens of thousands of base pairs away, are referred to as…?

A

Enhancers

131
Q

What is a molecular mechanism that underlies epigenetic phenotypes?

A

Modification of histone proteins

132
Q

A mutations at the operator site prevents the regulator protein, which acts as a repressor, from binding. Constitutive expression results from the operon. This is an example of a(n) ___ operon.

A

Inducible

133
Q

Many transcription factors regulate transcription by recruiting other proteins, called…?

A

cofactors

134
Q

Unmethylated cytosines are usually near a DNA…?

A

promoter

135
Q

Which E. coli strains with the lac genotypes will synthesize B-galactosidase, in the absence of lactose?

A

lacI-lacP+ lacO+ lacZ+ lacY-

136
Q

What does the triple methylation of the fourth lysine in an H3 histone tail likely tell you about nearby genes?

A

That they are transcriptionally active

137
Q

A researcher is studying histones in mouse cells that have just been acetylated. Which of these statements is TRUE of these histones?

A

The chromatin formed with these histones will likely appear open

138
Q

A gene that encodes a protein which is continually expressed to help maintain essential cellular function would be considered…?

A

Constitutive

139
Q

How does the availability of molecules such as elongation and initiation factors affect gene expression?

A

affects the rate of mRNA translation

140
Q

_____ is initiated by double-stranded RNA molecules that are cleaved and processed

A

RNA interference

141
Q

What is a stably inherited phenotype resulting from changes in chromatin without alterations in the DNA sequence?

A

Epigenetic trait

142
Q

The observation that one histone mark may affect whether additional marks occur nearby is referred to as ______

A

crosstalk

143
Q

Which level of gene control is matched appropriately to a regulatory mechanism?

A

posttranslational modification-activation of a protein by cleaving it

144
Q

How would a scientist describe a double-stranded DNA molecule showing methylation on one strand but not the other?

A

hemi methylated

145
Q

Would epigenetic changes brought about by methylation be inherited if methyltransferases were NOT present?

A

No. DNA is replicated in a semiconservative fashion

146
Q

Enzymes called histone _____ add methyl groups to specific amino acids of histones. Other enzymes, called histone _____, remove methyl groups from histones

A

methyltransferases; demethylases

147
Q

What determines whether the addition of a methyl group to a histone tail activates or represses transcription?

A

which histone is modified and the amino acid in the tail that gets methylated

148
Q

In your experimental system, you notice that translation of the eukaryotic gene you are working with yields three different proteins. What might be the cause of this observation?

A

mRNA processing

149
Q

Where are CpG islands commonly located in mammalian DNA?

A

promoter regions

150
Q

What does the “p” stand for in “CpG”?

A

phosphate

151
Q

Which statement describes an operon?

A. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand

B. The processing of expos in mRNA that results in a single gene coding for multiple options

C. Protein modifications such as the addition of a function group, or alternate folding of the protein

D. mRNA modifications, such as the addition of a 5’-cap and 3’ poly-A tail and the removal on introns

E. Heritable changes in gene expression that occur without altering the DNA sequence

A

A

A. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand

152
Q

Which type of regulation doe the trp operon exhibit?

A. Positive regulation

B. Translational regulation

C. Protein modification

D. Negative regulation

A

D

D. Negative regulation

153
Q

A mutation at the operator sire of an operon prevents the repressor from binding.

What effect will this mutation have on transcription in a repressible operon?

A. There will be a significant decrease in the operon’s activity

B. It will be impossible to turn on transcription of the structural genes

C. The operon will always be transcriptionally active

D. There will be no change in the operon’s activity

A

C

C. The operon will always be transcriptionally active

154
Q

A mutation at the operator sire of an operon prevents the repressor from binding.

What effect will this, mutation have on transcription in an inducible operon?

A. There will be a significant decrease in the operon’s activity

B. The operon will always be transcriptionally active

C. It will be impossible to turn on transcription of the structural genes

D. There will be no chang in the operon’s activity

A

B

B. The operon will always be transcriptionally active

155
Q

A mutant strain of E. coli produces B-galactosidase in the presence and in the absence of lactose

Where in the operon might the mutation in this strain occur, why? (multiple answers)

A. In the lacI gene, which leads to an inactive lac repressor

B. In the promoter region of the operon, where the mutation leads to the failure of the RNA polymerase to bind to the promoter

C. In the operator region, where the mutation leads to the failure of the operator to normally bind the repressor

D. Near the lacI gene, where the mutation leads to increased levels of lac repressor being made

E. In the CAP binding site, where the mutation leads to the inefficiency of RNA polymerase activity

F. In the operator region, which leads to increased binding of the lac repressor to the operator

A

A and C

A. In the lacI gene, which leads to an inactive lac repressor

C. In the operator region, where the mutation leads to the failure of the operator to normally bind the repressor

156
Q

Which description applies to epigenetic gene regulation?

A. Heritable changes in gene expression that occur without altering the DNA sequences

B. Protein modification such as addition of a function group, or structural changes such as folding

C. A gene cluster controlled by a single promoter that transcribes to a single mRNA strand

D. Processing of exons in mRNA that results in a single gene coding for multiple proteins

E. mRNA modifications such as additions of a 5’ cap and 3’ poly-A tail and removal of introns

A

A

A. Heritable changes in gene expression that occur without altering the DNA sequences

157
Q

Choose all of the statements that describe the benefits of combinatorial control of transcription in a eukaryotic multi-cellular organism (multiple answers)

A. An operon is able to initiate transcription

B. RNA reverts to DNA prior to transcription

C. mRNA synthesis occurs at an accelerated rate

D. RNA polymerase has selective access to specific genes for tissues specific effects

A

C and D

C. mRNA synthesis occurs at an accelerated rate

D. RNA polymerase has selective access to specific genes for tissues specific effects

158
Q

Many molecules, including transcription factors, work together to transcribe genes and translate the information taken from the genes into proteins

What is a transcription factor?

A. A protein, such as RNA polymerase, that transcribes a specific DNA sequence

B. A nucleotide that binds to a specific DNA sequence to activate transcription

C. A protein that binds to a specific mRNA to prevent it from being translated

D. A protein that binds to a specific DNA sequence to regulate transcription

E. A nucleotide sequence that signals a ribosome to start protein translation

A

D

D. A protein that binds to a specific DNA sequence to regulate transcription

Genetics - BI 312 (11 decks)

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