Transcription, RNA Processing, Gene Regulation, and Epigenetics Flashcards Preview

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Flashcards in Transcription, RNA Processing, Gene Regulation, and Epigenetics Deck (155):
1

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

DNA Coding strand

2

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

σ subunit

3

What are the three stages of transcription?

1.) Initiation
2.) Elongation
3.) Termination

4

Initiation is dependent on what two thing?

1.) σ subunit binding RNA polymerase (making holoenzyme)
2.) Holo-RNA Polymerase binds promoter

5

What is the principal site for regulation of transcription?

Initiation

6

What initiates the elongation step?

σ dissociates from RNA polymerase and the promoter

7

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

Elongation

8

What happens during termination?

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

9

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

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

10

Located ~7 base pairs upstream of the start of transcription

Pribnow box (TATAAT)

11

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

19 bp

12

Can make DNA from RNA

Reverse transcriptase

13

Is translation reversible?

No

14

How many different RNA polymerases are there for
1.) Prokaryotic transcription
2.) Eukaryotic transcription

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

15

The structural and catalytic component of ribosomes

rRNA

16

rRNA comprises about

80% of cellular RNA

17

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

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

18

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

-about 15% of cellular RNA

t-RNA

19

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

mRNA

20

small nuclear RNAs (snRNAs) are involved in

DNA splicing

21

Small nucleolar RNAs (snoRNAs) function in

rRNA processing

22

microRNAs play important roles in

Regulation of gene expression

23

A cluster of genes encoding proteins involved in sugar utilization

lac operon

24

What type of reaction is the polymerization that forms RNA?

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

25

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

Primer

26

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

σ subunit binds

27

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

σ subunits

28

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

DNA gyrase

29

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

Topoisomerase I

30

What is the actual site of transcription initiation?

+1

31

Transcription is regulated primarily at the level of

Initiation

32

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

Transcriptional activators

33

Block RNA polymerases interaction with DNA

Transcriptional repressors

34

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

RNA level

35

What are the two classes of bacterial terminators?

1.) Rho-dependent
2.) Rho-independent

36

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

Rho

37

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

Rho independent terminator

38

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

Termination

39

Binds the β subunit of bacterial RNA polymerase and inhibits initiation

Rifampicin

40

Rifampicin is an effective antibiotic for treatment of certain

Bacterial infections (ex: tuberculosis)

41

Binds the DNA template, intercalating between neighboring base pairs

Actinomycin

42

Actinomycin blocks

Transcript elongation

43

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

Cancers

44

Actinomycin binds the

DNA phenoxazone ring

45

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)

TATA box

46

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.

TATA box

47

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

Promoter proximal elements and enhancer sequences

48

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

Ubiquitously expressed genes ("housekeeping genes")

49

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

SP1

50

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

Enhancers

51

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

Enhancers

52

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

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

53

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

General transcription factors (GTFs)

54

A general transcription factor which includes TATA binding protein

TFIID

55

Required to position RNA Polymerase II at the promoter

GTFs

56

Structurally similar to prokaryotic RNA polymerase

Eukaryotic RNA polymerase II

57

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

TATA binding protein (TBP)

58

Explain the process of RNA polymerase II binding

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

59

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

TFIIE and TFIIH

60

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

Transcriptional activators

61

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

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

62

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

Initiation

63

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

Protein Synthesis

64

Transcription termination by RNA polymerase II involves the addition of a

3'-pol(A) tail

65

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

1.) Endonucleolytic cleavage of nascent transcript
2.) Addition of poly(A) tail

66

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

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

67

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

Conservative

68

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

Adjacent

69

In prokaryotes, translation of the mRNA begins

Prior to transcription termination

70

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

Cytoplasm

71

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

N-terminus of the protein

72

In most eukaryotic genes, the coding information is

Discontinuous (introns and exons)

73

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

Exons

74

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

Introns

75

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

β-globin

76

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

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

77

When the intron sequences are removed, the adjacent exons are

Spliced together

78

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

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

79

The base sequence of an intron
1.) Begins with?
2.) Ends with?

-these sequences are invarient (never change)

1.) GU
2.) AG

80

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

The "branch" site

81

Intron sequences other than the 5' and 3' splice sites, and the "branch site", are unimportant in determining

Location of splicing

82

The length of an intron varies from

Less than 100 nucleotides to several thousand nucleotides

83

Intron splicing occurs by two

Transesterification reactions

84

The first transesterification reaction involves

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

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

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

86

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

-Catalyzes the splicing reaction

Spliceosome

87

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

ATP

88

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

ATP hydrolysis

89

Which spliceosome protein(s) bind the
1.) GU 5' splice site
2.) Branch site A

1.) U1
2.) U2

90

Approximately 15% of mutations that cause genetic disease affect

pre-mRNA splicing

91

A group of hereditary anemias characterized by defective synthesis of hemoglobin

Thalassemias

92

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

Introns

93

Point mutations in β-globin gene introns create

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

Splicing defects

94

What are three DNA sequence elements in eukaryotic transcription?

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

95

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

Core promoter

96

The proximal promoter is the binding site for certain

Activator proteins

97

What are the core promoter elements of RNA polymerase II?

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

98

Nucleates the assembly of the transcription preinitiation complex

-TBP + 14 TBP-associated factors (TAFs)

TFIID

99

How does TFIID work?

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

100

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

-Eukaryotic version of Rifampicin

α-amanitin

101

Can produce multiple, related proteins from a single gene

Alternative splicing

102

What is the Donor splice site?

5' end of intron

103

What is the Acceptor splice site?

3' end of intron

104

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

Cell-surface receptors

105

Directly stimulate gene transcription as hormone-receptor complexes

Steroid hormones

106

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

Chromosome

107

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

Steroid hormone receptors

108

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

Promoter DNA (in a sequence specific manner)

109

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

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

110

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

RNA Polymerase II transcriptional machinery

111

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

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

112

Bind hormone receptors and stimulate receptor activity (gene expression)

Ex: Anabolic steroids

Agonists

113

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

Ex: tamoxifen

Antagonists

114

Recognizes specific enhancer elements

DNA binding domain

115

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

Binds a "coactivator" complex

116

These DNA sequences are enhancers for steroid responsive genes

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

Steroid response elements (SREs)

117

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

SRE's

118

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

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

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

Bridge the two components

120

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

Chromatin (either displacing or modifying nucleosomes)

121

Normally inhibit transcription

Nucleosomes

122

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

Coactivators

123

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

Chromatin

124

Steroid hormone receptors ultimately activate gene expression by altering

-Allows RNA polymerase II to bind the promoter

Chromatin Structure

125

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

Displace or disrupt nucleosomes

126

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

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

127

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

Histone acetyltransferases (HATs)

128

Histone modifications occur primarily at the

N-terminal tails of histones

129

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.

ATP-dependent chromatin remodeling complexes (coactivators)

130

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

Activate different sets of genes

131

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

Estogen

132

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

Glucocorticoids

133

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

Mouse mammary tumor virus (MMTV)

134

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

Uncontrolled cell proliferation

135

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

Tamoxifen

136

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

Coupling of transcription with DNA damage repair

137

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

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

138

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

RNA transcription

139

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

Sigma would bind too tightly

140

The σ subunit binds the -35 and TATAAT sequences

Simultaneously

141

Which sigma unit recognizes E coli promoters?

σ 70

142

A double stranded DNA sequence that the σ subunit binds to

Promoter

143

What are the 5 catalytic subunits of RNA polymerase II?

2α, β, β', and ω

144

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

Two magnesium ions

145

The core promoter spans about

80 base pairs

146

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)

Proximal Promoter

147

Core promoter, proximal promoter, and enhancers are all

Double-stranded DNA

148

Which GTF binds to -35?

TFIIB

149

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

-prevents degredation of mRNA and facilitates the initiation of translation

5' cap

150

The code to terminate transcription is in the
DNA template and has the consensus sequence

AAUAAA

151

Transcription factors that bind to double stranded DNA

Steroid receptors

152

What is a common structural motif in transcription factors?

Zinc finger

153

Has 1.74 turns of double stranded DNA and about 147 bps

-an impediment to RNA polymerase

Nucleosomes

154

Rely on estrogen-mediated pathways for cell proliferation

-Why tomoxifin is a good anti-cancer

Breast tumors

155

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

Bind DNA

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