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BMS > Transcription, RNA Processing, Gene Regulation, and Epigenetics > Flashcards

Transcription, RNA Processing, Gene Regulation, and Epigenetics Flashcards

1
Q

Besides the change between T and U, the RNA product should be identical to the

A

DNA Coding strand

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2
Q

The unit of prokaryotic RNA Polymerase that associates with the core enzyme to generate the holoenzyme

A

σ subunit

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3
Q

What are the three stages of transcription?

A
  1. ) Initiation
  2. ) Elongation
  3. ) Termination
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4
Q

Initiation is dependent on what two thing?

A
  1. ) σ subunit binding RNA polymerase (making holoenzyme)

2. ) Holo-RNA Polymerase binds promoter

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5
Q

What is the principal site for regulation of transcription?

A

Initiation

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6
Q

What initiates the elongation step?

A

σ dissociates from RNA polymerase and the promoter

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7
Q

Transcript is lengthened by the addition of nucleotides to the 3’ end of the RNA strand located in the active site of RNA Polymerase II

A

Elongation

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8
Q

What happens during termination?

A
  1. ) RNA synthesis stops
  2. ) RNA transcript is released
  3. ) Dissociation of RNA polymerase from DNA template
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9
Q

What are the two sequences within the prokaryotic promoter region that are recognized by the RNA polymerase holoenzyme?

A

-35 sequence (TTGACA) and Pribnow box (TATAAT)

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10
Q

Located ~7 base pairs upstream of the start of transcription

A

Pribnow box (TATAAT)

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11
Q

What is the distance between the -35 sequence and the Pribnow box?

A

19 bp

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12
Q

Can make DNA from RNA

A

Reverse transcriptase

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13
Q

Is translation reversible?

A

No

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14
Q

How many different RNA polymerases are there for

  1. ) Prokaryotic transcription
  2. ) Eukaryotic transcription
A
  1. ) One

2. ) Three (with a 4th that functions in mitochondrial transcription)

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15
Q

The structural and catalytic component of ribosomes

A

rRNA

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16
Q

rRNA comprises about

A

80% of cellular RNA

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17
Q

The ribosome includes four different rRNAs that are typically designated by their sedimentation coefficients. For example, in human cells, there is

A

5S, 5.8S, 18S, and 28S

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18
Q

Functions as an “adaptor” molecule that delivers amino acids to the ribosome

-about 15% of cellular RNA

A

t-RNA

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19
Q

The template for protein synthesis, and is heterogeneous in size, varying according to the length of the encoded protein

-typically represents less than 5% of total RNA content

A

mRNA

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20
Q

small nuclear RNAs (snRNAs) are involved in

A

DNA splicing

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21
Q

Small nucleolar RNAs (snoRNAs) function in

A

rRNA processing

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22
Q

microRNAs play important roles in

A

Regulation of gene expression

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23
Q

A cluster of genes encoding proteins involved in sugar utilization

A

lac operon

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24
Q

What type of reaction is the polymerization that forms RNA?

A

Nucleophilic attack by 3’ OH of growing strand on α-phosphate of incoming NTP (leaving group is pyrophosphate [PPi])

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25
Q

In contrast to DNA replication, RNA transcription does not require a

A

Primer

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26
Q

The core enzyme RNA polymerase is catalytically active but unable to recognize specific promoter DNA sequences until

A

σ subunit binds

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27
Q

Although they have only one core RNA polymerase, bacteria have several

A

σ subunits

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28
Q

What gets rid of the positive supercoils generated in the DNA by RNA polymerase during transcription?

A

DNA gyrase

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29
Q

What gets rid of the negative supercoils generated in DNA by RNA polymerase during transcription?

A

Topoisomerase I

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30
Q

What is the actual site of transcription initiation?

A

+1

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31
Q

Transcription is regulated primarily at the level of

A

Initiation

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32
Q

Either recruit RNA polymerase to the promoter, or stabilize its binding to promoter DNA

A

Transcriptional activators

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33
Q

Block RNA polymerases interaction with DNA

A

Transcriptional repressors

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34
Q

Transcription termination signals are present at the ends of genes, but function at the

A

RNA level

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35
Q

What are the two classes of bacterial terminators?

A
  1. ) Rho-dependent

2. ) Rho-independent

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36
Q

Binds a specific RNA sequence as a hexameric protein and contacts RNA polymerase, signalling the polymerase to terminate transcription and dissociate from the DNA template

A

Rho

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37
Q

RNA hairpin structures generated by palindromic repeats followed by a U rich region

A

Rho independent terminator

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38
Q

In the case of rho-independent termination, a specific structure (stem and loop) forms in the RNA transcript, signalling

A

Termination

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39
Q

Binds the β subunit of bacterial RNA polymerase and inhibits initiation

A

Rifampicin

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40
Q

Rifampicin is an effective antibiotic for treatment of certain

A

Bacterial infections (ex: tuberculosis)

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41
Q

Binds the DNA template, intercalating between neighboring base pairs

A

Actinomycin

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42
Q

Actinomycin blocks

A

Transcript elongation

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43
Q

The DNA structure that binds actinomycin is conserved between prokaryotes and eukaryotes. As a result, actinomycin serves as an effective therapeutic for treatment of some

A

Cancers

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44
Q

Actinomycin binds the

A

DNA phenoxazone ring

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45
Q

The core promoter region of eukaryotic class II genes typically (but not always) contains a

-located about 25 bp upstream of the transcription start site (+1)

A

TATA box

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46
Q

The “nucleation site” for assembly of a transcription complex that includes a set of general transcription factors (GTFs) and RNA polymerase II and is functionally comparable to the –10 and –35 regions of a bacterial promoter.

A

TATA box

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47
Q

Transcriptional stimulatory sequences are generally located upstream of the core promoter in eukaryotes and include

A

Promoter proximal elements and enhancer sequences

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48
Q

Promoter proximal elements are usually located within 120 bp of the transcription start site and serve as binding sites for transcriptional activators of

-Ex: enzymes involved in metabolism

A

Ubiquitously expressed genes (“housekeeping genes”)

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49
Q

The most well characterized activator that functions at a proximal promoter is called

A

SP1

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50
Q

Found at variable distances from the core promoter and are DNA sequences that bind specific transcriptional activators

A

Enhancers

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51
Q

Binding sites for transcriptional activators that either make direct contact components of the RNA polymerase II transcriptional machinery, or recruit chromatin remodeling complexes to the regulatory promoter regions

A

Enhancers

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52
Q

What do RNA Polymerases I, II, and III transcribe?

A

RNA Polymerase I = rRNA
RNA Polymerase II = mRNA
RNA Polymerase III = 5s component of ribosome, tRNA, and certain snRNAs

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53
Q

Eukaryotic RNA polymerases do not recognize Specific DNA sequences on their own. Instead, promoter recognition requires

A

General transcription factors (GTFs)

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54
Q

A general transcription factor which includes TATA binding protein

A

TFIID

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55
Q

Required to position RNA Polymerase II at the promoter

A

GTFs

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56
Q

Structurally similar to prokaryotic RNA polymerase

A

Eukaryotic RNA polymerase II

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57
Q

As a subunit of the larger TFIID complex, binds the TATA element and confers a sharp bend in the promoter DNA.

A

TATA binding protein (TBP)

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58
Q

Explain the process of RNA polymerase II binding

A

TBP (as TFIID) binds the TATA box, enabling TFIIB to bind, which enables RNA polymerase II and TFIIF to bind

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59
Q

Once RNA polymerase II is bound to DNA, enable RNA polymerase to start transcription

A

TFIIE and TFIIH

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60
Q

Stimulate transcription by binding GTFs, either to recruit or stabilize their binding to the core promoter

A

Transcriptional activators

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61
Q

There are two notable features of eukaryotic RNA pol II transcription that do not occur either in bacteria or by RNA pol I or RNA pol III. These are

A

Addition of 5’ cap and 3’-poly(A) tail

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62
Q

A 7-methylguanosine “CAP” is covalently linked to the 5’-end of mRNA by a unique 5’ → 5’ triphosphate linkage. The CAP is not encoded by the DNA template. Instead, CAP is added to the mRNA shortly after

A

Initiation

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63
Q

Consistent with it being a unique feature of mRNA, the CAP is recognized by components of the translational machinery, thereby facilitating

A

Protein Synthesis

64
Q

Transcription termination by RNA polymerase II involves the addition of a

A

3’-pol(A) tail

65
Q

Termination is specified by distinct sequences in the DNA template and involves which two enzymatic reactions?

A
  1. ) Endonucleolytic cleavage of nascent transcript

2. ) Addition of poly(A) tail

66
Q

The poly(A) tail is not encoded in the DNA template and is a unique feature of eukaryotic RNA pol II transcription. The poly(A) tail is involved in

A

mRNA stabilization, transport of mRNA from nucleus to cytoplasm, and efficient translation

67
Q

Unlike DNA replication, which is semi-conservative, trancription is

A

Conservative

68
Q

In eukaryotic transcription, the core and regulatory elements can be far apart, but in prokaryotes, they must be

A

Adjacent

69
Q

In prokaryotes, translation of the mRNA begins

A

Prior to transcription termination

70
Q

In ekaryotes, transcription takes place in the nucleus and translation in the

A

Cytoplasm

71
Q

In prokaryotes, The 5’ end in the DNA sequence of a gene is directly proportional to the

A

N-terminus of the protein

72
Q

In most eukaryotic genes, the coding information is

A

Discontinuous (introns and exons)

73
Q

Nucleic acid sequences that are transcribed and retained in the corresponding mature mRNA

A

Exons

74
Q

Nucleic acid sequences that are transcribed but spliced from the primary transcript to yield the mature mRNA

A

Introns

75
Q

A gene that is divided into 3 exons and 2 introns

  • The ATG start codon is found in exon 1
  • The TAA stop codon is contained in exon 3
A

β-globin

76
Q

Why must the translation start and stop codons be within exons?

A

Because introns are spliced out either co- or post-transcriptionally, but PRIOR to translation

77
Q

When the intron sequences are removed, the adjacent exons are

A

Spliced together

78
Q

pre-mRNA splicing is very important because a single nucleotide error in the splice point would have what consequence?

A

The reading frame would be shifted, resulting in an entirely different amino acid sequence

79
Q

The base sequence of an intron

  1. ) Begins with?
  2. ) Ends with?

-these sequences are invarient (never change)

A
  1. ) GU

2. ) AG

80
Q

A conserved sequence found 20-50 nucleotides from the 3’ end of the intron

A

The “branch” site

81
Q

Intron sequences other than the 5’ and 3’ splice sites, and the “branch site”, are unimportant in determining

A

Location of splicing

82
Q

The length of an intron varies from

A

Less than 100 nucleotides to several thousand nucleotides

83
Q

Intron splicing occurs by two

A

Transesterification reactions

84
Q

The first transesterification reaction involves

A

Cleaving the phosphodiester bond between exon 1 and intron 1, and using the 2’ OH of an adenylate residue at the branch site to form a phosphodiester bond with the 5’ end of the intron

85
Q

In the second transesterification, the 3’ OH of exon 1 cleaves the phosphodiester bond between the intron and exon 2. As a result,

A

Exon 1 and 2 are now bound together, and the intron is released as a “lariat” structure

86
Q

An assembly of ribonucleoprotein particles (SNURPs) that recognize the 5’ splice sit, the 3’ splice site, and the branch site

-Catalyzes the splicing reaction

A

Spliceosome

87
Q

The spliceosome assembles de novo from its constituent SNURPs on the precursor RNA in a process that requires

A

ATP

88
Q

Required for the spliceosome assembly, but not for either of the ensuing transesterification reactions

A

ATP hydrolysis

89
Q

Which spliceosome protein(s) bind the

  1. ) GU 5’ splice site
  2. ) Branch site A
A
  1. ) U1

2. ) U2

90
Q

Approximately 15% of mutations that cause genetic disease affect

A

pre-mRNA splicing

91
Q

A group of hereditary anemias characterized by defective synthesis of hemoglobin

A

Thalassemias

92
Q

One source of Thalassemias is due to point mutations that occur in either of the two β-globin gene

A

Introns

93
Q

Point mutations in β-globin gene introns create

-results in either shorter or longer forms of abnormal β-globin

A

Splicing defects

94
Q

What are three DNA sequence elements in eukaryotic transcription?

A
  1. ) Enhancers (>250)
  2. ) Proximal promoter (CpG: -120 to -60)
  3. ) Core promoter (TATA: -40 to +40)
95
Q

In eukaryotes, contains the transcription start site (+1), the TATA box (-25), and down stream promoter element (DPE: +30)

A

Core promoter

96
Q

The proximal promoter is the binding site for certain

A

Activator proteins

97
Q

What are the core promoter elements of RNA polymerase II?

A
  1. ) Initiator
  2. ) Down stream promoter element (DPE)
  3. ) TATA Box
  4. ) TFIIB Recognition element
98
Q

Nucleates the assembly of the transcription preinitiation complex

-TBP + 14 TBP-associated factors (TAFs)

A

TFIID

99
Q

How does TFIID work?

A

TBP binds TATA box, TAF1 and TAF2 bind initiator, and TAF 6 and TAF 9 bind the DPE

100
Q

Binds tightly to RNA Polymerase II and inhibits the elongation stage of transcription

-Eukaryotic version of Rifampicin

A

α-amanitin

101
Q

Can produce multiple, related proteins from a single gene

A

Alternative splicing

102
Q

What is the Donor splice site?

A

5’ end of intron

103
Q

What is the Acceptor splice site?

A

3’ end of intron

104
Q

Many hormones (e.g. epinephrine, insulin, epidermal growth factor) activate transcription by activating

A

Cell-surface receptors

105
Q

Directly stimulate gene transcription as hormone-receptor complexes

A

Steroid hormones

106
Q

Humans contain two copies (one from the mother and one from the father) of each

A

Chromosome

107
Q

Soluble proteins that function as transcriptional activators in response to hormone binding

A

Steroid hormone receptors

108
Q

In come cases, hormone binding exposes a nuclear localization signal, allowing the receptor-hormone complex to enter the nucleus, where it binds

A

Promoter DNA (in a sequence specific manner)

109
Q

In other cases, the hormone receptor is already located in the nucleus. In this case, hormone binding does one of what two things?

A
  1. ) Stimulates receptor-DNA binding

2. ) induces conformational change in the receptor-DNA complex

110
Q

Regardless of the specific mechanism, the DNA-hormone-receptor complex then interacts with a “coactivator” complex to stimulate

A

RNA Polymerase II transcriptional machinery

111
Q

Steroid hormones receptors, like other transcriptional activators, consist of discrete functional domains. What are they?

A

DNA-bining domain, hormone binding domain, dimerization domain, and activation domain

112
Q

Bind hormone receptors and stimulate receptor activity (gene expression)

Ex: Anabolic steroids

A

Agonists

113
Q

Bind hormone receptors and block receptor activity (repress gene expression)

Ex: tamoxifen

A

Antagonists

114
Q

Recognizes specific enhancer elements

A

DNA binding domain

115
Q

Upon hormone binding, Steroid receptors typically undergo a conformational change to create a transcriptional activation domain that

A

Binds a “coactivator” complex

116
Q

These DNA sequences are enhancers for steroid responsive genes

-bind hormone receptor complexes, resulting in stimulation of gene expression

A

Steroid response elements (SREs)

117
Q

Typically palindromic, and are related to one another by subtle, but important sequence differences

A

SRE’s

118
Q

Steroid hormone-receptor complexes are potent activators of transcription. The mechanism of activation involves

A

Binding of the hormone-receptor complex to the SRE (cognate regulatory element) and subsequent binding to a transcriptional coactivator that in turn stimulates transcription

119
Q

Some co-activators interact with both activators and the core transcriptional machinery (RNA Poly II and the GTFs), where they essentially

A

Bridge the two components

120
Q

Other coactivators do not interact with the core machinery, but instead target

A

Chromatin (either displacing or modifying nucleosomes)

121
Q

Normally inhibit transcription

A

Nucleosomes

122
Q

Some work by recruiting or stabilizing RNA polymerase II/GTP to the core promoter, and other “clear a path” for RNA polymerase II by altering the DNA template

A

Coactivators

123
Q

DNA in eukaryotic chromosomes is not naked, but is tightly associated with proteins to form

A

Chromatin

124
Q

Steroid hormone receptors ultimately activate gene expression by altering

-Allows RNA polymerase II to bind the promoter

A

Chromatin Structure

125
Q

In summary, a sequence specific enhancer element (DNA) binds the hormone receptor-hormone complex (transcriptional activator), which in turns binds a coactivator complex (chromatin modifier) to

A

Displace or disrupt nucleosomes

126
Q

Coactivators include two classes of chromatin modifiers. What are the two classes?

A
  1. ) Coactivators that catalyze covalent modifications to histones
  2. ) ATP-dependent remodeling complexes
127
Q

The most well characterized covalent histone modification is acetylation of histone lysine residues in the N-terminal tails of histones H3 and H4, catalyzed by

A

Histone acetyltransferases (HATs)

128
Q

Histone modifications occur primarily at the

A

N-terminal tails of histones

129
Q

These complexes do not catalyze covalent histone modification, but instead use the energy of ATP hydrolysis to remodel nucleosomes, thereby allowing other transcription factors to bind DNA and ultimately promote gene transcription.

A

ATP-dependent chromatin remodeling complexes (coactivators)

130
Q

Steroid hormones include estrogens, androgens, glucocorticoids and mineralocorticoids. These cholesterol derivatives, each slightly different in structure, bind specific hormone receptors to

A

Activate different sets of genes

131
Q

Target the oviduct to stimulate expression of genes whose encoded proteins participate in the ovarian cycle

A

Estogen

132
Q

Target the liver (and other tissues) to promote expression of genes required for gluconeogenesis, glycogen synthesis, degredation of fat, and inhibition of the inflammatory response

A

Glucocorticoids

133
Q

A DNA virus that causes breast epithelial cell carcinoma. It’s genome includes a DNA sequence that is identical to the estrogen enhancer

A

Mouse mammary tumor virus (MMTV)

134
Q

In MMTV, the estrogen/estrogen receptor complex binds the MMTV enhancer and stimulates wnt-1 gene expression, which results in

A

Uncontrolled cell proliferation

135
Q

Anti-cancer drug that binds the estrogen receptor and prevents coactivator binding

A

Tamoxifen

136
Q

Despite being a “general transcription factor” required for the expression of all protein genes, TFIIH also plys a very important role in the

A

Coupling of transcription with DNA damage repair

137
Q

Altered forms of TFIIH have been identified in what three diseases?

-These diseases are not due to defects in transcription initiation, but rather to defects in DNA repair

A
  1. ) Xeroderma pigmentosum (XP)
  2. ) Trichothio-dystrophy (TDD)
  3. ) Cockayne syndrome (CS)
138
Q

Will move 3’ to 5’ on the DNA template to generate a new 5’ to 3’ strand

A

RNA transcription

139
Q

The sequences indicating the -35 and TATAAT box are not exact, but rather consensus sequence. All six of the consensus nucleotides are never actually seen in the same gene because

A

Sigma would bind too tightly

140
Q

The σ subunit binds the -35 and TATAAT sequences

A

Simultaneously

141
Q

Which sigma unit recognizes E coli promoters?

A

σ 70

142
Q

A double stranded DNA sequence that the σ subunit binds to

A

Promoter

143
Q

What are the 5 catalytic subunits of RNA polymerase II?

A

2α, β, β’, and ω

144
Q

Found in the crab claw of RNA polymerase II and help make up the active site

A

Two magnesium ions

145
Q

The core promoter spans about

A

80 base pairs

146
Q

Not a promoter in the sense that it does not bind
RNA polymerase. Binds proteins that are regulatory proteins for “housekeeping” genes (genes encoding proteins that every cell needs to have)

A

Proximal Promoter

147
Q

Core promoter, proximal promoter, and enhancers are all

A

Double-stranded DNA

148
Q

Which GTF binds to -35?

A

TFIIB

149
Q

The only place a 5’ to 5’ triphosphate linkage occurs is on the

-prevents degredation of mRNA and facilitates the initiation of translation

A

5’ cap

150
Q

The code to terminate transcription is in the

DNA template and has the consensus sequence

A

AAUAAA

151
Q

Transcription factors that bind to double stranded DNA

A

Steroid receptors

152
Q

What is a common structural motif in transcription factors?

A

Zinc finger

153
Q

Has 1.74 turns of double stranded DNA and about 147 bps

-an impediment to RNA polymerase

A

Nucleosomes

154
Q

Rely on estrogen-mediated pathways for cell proliferation

-Why tomoxifin is a good anti-cancer

A

Breast tumors

155
Q

Zinc atoms associate with domains of steroid receptor protein domains to form zince fingers that

A

Bind DNA

BMS (62 decks)

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