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MOLBIO OFFSEM MIDTERM > Eukaryotic RNA Polymerases and Their Promoters > Flashcards

Eukaryotic RNA Polymerases and Their Promoters Flashcards

1
Q

10.1 Multiple Forms of Eukaryotic RNA Polymerase

a. _______ of the Three Nuclear Polymerases
b. The ______ of the Three RNA Polymerases
c. _________ Subunit Structures

A

a. Separation
b. Roles
c. RNA Polymerase

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2
Q

10.2 Promoters

A

a. Class II Promoters
b. Class I Promoters
c. Class III Promoters

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3
Q

10.3 Enhancers and Silencers

A

a. Enhancers
b. Silencers

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4
Q

(MULTIPLE FORMS OF EUKARYOTIC RNA POLYMERASE)

Eukaryotic nuclei contain multiple RNA polymerases.

At least _____ RNA polymerases are identified in eukaryotic nuclei: one for transcribing _________ RNA genes (28S, 18S, and 5.8S rRNAs) and one or more for transcribing other _________.

A

two ; major ribosomal ; nuclear genes

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5
Q

(MULTIPLE FORMS OF EUKARYOTIC RNA POLYMERASE)

Ribosomal genes have distinct features:

  1. Different base composition (e.g., rat rRNA genes have ____ GC content, while other genes have ____ GC content)
  2. High repetitiveness (several hundred to over ______ copies per cell)
  3. Localized in the ______, a separate compartment within the nucleus.
A

60% ; 40% ; 20,000 ; nucleolus

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6
Q

(MULTIPLE FORMS OF EUKARYOTIC RNA POLYMERASE)

These differences imply the presence of specialized RNA polymerases in ____________

A

eukaryotic nuclei

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7
Q

(MULTIPLE FORMS OF EUKARYOTIC RNA POLYMERASE)

One RNA polymerase operates in the ______, synthesizing rRNA, while another operates in the _______, transcribing other types of RNA.

A

nucleolus ; nucleoplasm

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8
Q

(SEPARATION OF THE THREE NUCLEAR POLYMERASES)

Eukaryotes have three distinct RNA polymerases:

A

RNA polymerase I, RNA polymerase II, and RNA polymerase III.

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9
Q

(SEPARATION OF THE THREE NUCLEAR POLYMERASES)

These enzymes were separated and identified by ______ and ______ in 1969 using DEAE-Sephadex ion-exchange chromatography

A

Robert Roeder and William Rutter

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10
Q

(SEPARATION OF THE THREE NUCLEAR POLYMERASES)

The three polymerases have different properties and behaviors, such as responses to _________ and
__________

A

ionic strength and divalent metals.

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11
Q

(SEPARATION OF THE THREE NUCLEAR POLYMERASES)

Each polymerase has specific roles in transcription, synthesizing different kinds of RNA:

  1. ___________ is primarily responsible for synthesizing ribosomal RNA (rRNA) and is primarily located in the nucleolus.
  2. __________ and _________ are found in the nucleoplasm and are involved in the synthesis of other types of RNA.
A

RNA polymerase I ; RNA polymerase II and RNA polymerase III

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12
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

  • Synthesizes the large rRNA precursor.
  • In mammals, the precursor (45S) is processed into the mature rRNAs: 28S, 18S, and 5.8S.
A

RNA Polymerase I

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13
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

  • Produces heterogeneous nuclear RNA (hnRNA), precursor molecules for microRNAs (miRNAs), and most small nuclear RNAs (snRNAs).
  • hnRNAs act as precursors for messenger RNAs (mRNAs), while snRNAs are involved in the maturation of hnRNAs to mRNAs.
  • miRNAs regulate gene expression by causing mRNA degradation or limiting translation.
A

RNA Polymerase II

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14
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

Generates precursors for transfer RNAs (tRNAs), 5S rRNA, and some other small RNAs.

A

RNA Polymerase III

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15
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

___________ - a toxin found in certain mushrooms (Amanita species), was used in experiments to study the effects on RNA polymerases.

A

Alpha-amanitin

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16
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

RNA Polymerase Inhibition

  1. ____________: Highly sensitive to low concentrations of alpha- amanitin; completely inhibited even at low doses.
  2. ____________: Inhibited at higher concentrations, supporting its role in synthesizing small RNAs like 5S rRNA and tRNA precursors.
A

RNA Polymerase II ; RNA Polymerase III

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17
Q

(THE ROLES OF THE THREE RNA POLYMERASE)

Experimental Approach:
- __________nuclei were incubated with increasing concentrations of alpha-amanitin.

A

Mouse cell

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18
Q

(RNA POLYMERASE STRUCTURES)

Eukaryotic RNA polymerases are
_______, consisting of large and small subunits.

A

complex

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19
Q

(RNA POLYMERASE STRUCTURES)

Structures of RNA polymerases I, II, and III are complex, each comprising ___ large (greater than 100 kD) subunits and various smaller subunits.

A

two

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19
Q

(RNA POLYMERASE STRUCTURES)

Similarities exist between eukaryotic polymerases and prokaryotic core polymerases, indicating _____________

A

evolutionary relationships.

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19
Q

(RNA POLYMERASE STRUCTURES: Polymerase II Structure and Subunits)

__________: Scientists used epitope tagging to identify authentic polymerase II subunits in yeast cells.

A

Methodology

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19
Q

(RNA POLYMERASE STRUCTURES: Polymerase II Structure and Subunits)

________: Twelve subunits were identified for yeast polymerase II, named Rpb1 to Rpb12.

A

Subunits

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19
Q

(RNA POLYMERASE STRUCTURES: Polymerase II Structure and Subunits)

________: Rpb5, Rpb6, Rpb8, Rpb10, and Rpb12 are common subunits found in all three yeastnuclear polymerases, suggesting fundamental roles in transcription.

A

Commonality

19
Q

(RNA POLYMERASE STRUCTURES: Functional Relationships)

Rpb1 and Rpb2: ______ is homologous to the E. coli b9-subunit, binds DNA, and is at or near the active site. _____ shares functional similarities with the E. coli b-subunit.

A

Rpb1 ; Rpb2

20
Q

(RNA POLYMERASE STRUCTURES: Functional Relationships)

_____: Although not closely resembling E. coli a-subunit, ______ shares a 20-amino-acid region of similarity, has similar size and stoichiometry, and exhibits similar assembly defects, indicating homology

A

Rpb3 ; Rpb3

20
Q

(RNA POLYMERASE STRUCTURES: Common Subunits)

_____, ______, ______, _____, and _____: These subunits are present in all three yeast nuclear polymerases, indicating their fundamental roles in the transcription process. Their specific functions are not fully understood.

A

Rpb5, Rpb6, Rpb8, Rpb10, and Rpb12

20
Q

Promoters for RNA Polymerase II (Class II Promoters):

A

Core Promoter and Proximal Promoter

20
Q

Promoters for RNA Polymerase II (Class II Promoters):

Located within about 37 bp of the transcription start site, contains elements like TATA box, TFIIB recognition element (BRE), initiator (Inr), downstream promoter element (DPE), downstream core element (DCE), and motif ten element (MTE).

A

Core Promoter:

20
Q

Promoters for RNA Polymerase II (Class II Promoters):

Extends from about 37 bp up to 250 bp upstream of the transcription start site, includes elements like TATA box, Inr, DPE, etc.

A

Proximal Promoter

20
Q

(TATA Box)

Consensus Sequence: ______ (in the nontemplate strand).

______: Important for positioning the start of transcription. Some promoters require the TATA box for function, while others need it only to position the transription start site.

A

TATAAA ; Function

21
Q

(Initiators, Downstream Promoter Elements, and TFIIB Recognition Elements)

________: Conserved sequences around transcription start sites (e.g., PyPyAN(T/A)PyPy in mammals, TCA(G/T)T(T/C) in Drosophila).

Function: Essential for optimal transcription. Can constitute a functional promoter alone or work in conjunction with other elements.

A

Initiators

22
Q

(Initiators, Downstream Promoter Elements, and TFIIB Recognition Elements)

_______________: Common in Drosophila, located about 30 bp downstream of the transcription initiation site, includes the consensus sequence G(A/T)CG.

(Initiators, Downstream Promoter Elements, and TFIIB Recognition Elements)

Function: Can compensate for the lack of a TATA box in promoters, bind to TFIID, and participate in the formation of the preinitiation complex.

A

Downstream Promoter Elements (DPEs)

23
Q

(Initiators, Downstream Promoter Elements, and TFIIB Recognition Elements)

______________: DNA elements upstream of that TATA box that assist TFIIB binding to the DNA.

A

TFIIB Recognition Elements (BREs)

24
Q

IRNA Polymerase I Promoters (Class I Promoters)

________: Predominantly the rRNA precursor gene, with high copy numbers in each cell.

A

Target Gene

25
Q

Promoter Elements:

_____________: Located at the start of transcription, between positions 245 and 120.

______________: Positioned between positions 2156 and 2107.

A

Core Element (rINR/Initiator) ; Upstream Promoter Element (UPE)

26
Q

Importance of Spacing Between Elements:

  • Spacing Significance: The spacing between the core element and the upstream promoter element is crucial for promoter strength.
  • Effect of Deletions: Deletions between the elements significantly impact promoter strength, with shorter deletions having a more substantial effect. For example, a 16-bp deletion reduces promoter strength to 40% of wild-type, while a 44-bp deletion reduces it to 10%.
  • Effect of Insertions: Insertions between the elements also affect promoter strength, but the impact is less significant than deletions. For instance, adding 28 bp has no effect, while adding 49 bp reduces promoter strength by 70%.
A

IRNA Polymerase I Promoters (Class I Promoters)

27
Q

IRNA Polymerase I Promoters (Class I Promoters) - Importance of Spacing Between Elements:

____________: The spacing between the core element and the upstream promoter element is crucial for promoter strength

A

Spacing Significance

28
Q

IRNA Polymerase I Promoters (Class I Promoters) - Importance of Spacing Between Elements:

______________: Deletions between the elements significantly impact promoter strength, with shorter deletions having a more substantial effect. For example, a 16-bp deletion reduces promoter strength to 40% of wild-type, while a 44-bp deletion reduces it to 10%

A

Effect of Deletions

29
Q

IRNA Polymerase I Promoters (Class I Promoters) - Importance of Spacing Between Elements:

_____________: Insertions between the elements also affect promoter strength, but the impact is less significant than deletions. For instance, adding 28 bp has no effect, while adding 49 bp reduces promoter strength by 70%.

A

Effect of Insertions

30
Q

IRNA Polymerase III Promoters (Class III Promoters)

Target Genes:
1. _____________: Include the 5S rRNA and tRNA genes, as well as the adenovirus VA RNA genes.

  1. ____________: Include genes such as the U6 snRNA gene, the 7SL RNA gene, the 7SK RNA gene, and the Epstein–Barr virus EBER2 gene.
A

Classical Class III Genes ; Nonclassical Class III Genes

31
Q

IRNA Polymerase III Promoters (Class III Promoters)

Promoter Types:
______________: Promoters located entirely within the gene itself.

______________: Identified regions between bases 50 and 83 are crucial for promoter function.

______________: Box A, Intermediate Element, and Box C are essential components of the promoter.

A

Type I (5S rRNA Genes) ; Sensitive Regions ; Critical Elements

32
Q

________________: Promoters resembling tRNA and VA RNA promoters.

Components: Box A and Box B are key elements.

Spacing Sensitivity: Proper spacing between the boxes is crucial for efficient transcription.

A

Type II (Most Class III Genes)

33
Q

________________: Promoters with control elements restricted to the 5’-flanking region of the gene.

Examples: Human 7SK RNA promoter and human U6 RNA promoter.

A

Type III (Nonclassical Promoters)

34
Q

________________: Contain both internal and external elements necessary for promoter activity.

Example: Human 7SL RNA promoter.

A

Hybrid Promoters (Types II/III)

35
Q

_______________: Classical class III promoters, like the 5S rRNA promoter, are located within the genes they regulate, unlike class I and class II promoters.

A

Internal Promoter Location

36
Q

______________: Specific regions, such as Box A, Intermediate Element, and Box C, cannot be altered without significantly affecting promoter function.

A

Sensitivity to Sequence Changes

37
Q

__________: Some promoters exhibit characteristics of both type II and type III promoters, containing both internal and external elements essential for transcription initiation.

A

Hybrid Promoters:

38
Q

(KEY DIFFERENCE OF PROMOTERS)

Associated RNA Polymerase: RNA Polymerase I
Genes Transcribed: rRNA precursor genes
Promoter Location: Internal within genes
Promoter Elements: Core element (rINR) and Upstream Promoter Element (UPE)

A

Class I

39
Q

(KEY DIFFERENCE OF PROMOTERS)

Associated RNA Polymerase: RNA Polymerase II
Genes Transcribed: Protein-coding genes, some RNAs
Promoter Location: Upstream of genes
Promoter Elements: TATA box, Initiator (Inr), Downstream Promoter Elements

A

Class II

40
Q

(KEY DIFFERENCE OF PROMOTERS)

Associated RNA Polymerase: RNA Polymerase III
Genes Transcribed: tRNAs, 5S rRNA, small RNAs
Promoter Location: Internal within genes
Promoter Elements:
- Type I: Internal elements (e.g., Xenopus 5S rRNA promoter)
- Type II: Box A, Box B (e.g., tRNA promoters)
- Type III: External elements (e.g., human U6 RNA promoter)

A

Class III

41
Q

(10.3 ENHANCERS AND SILENCERS)

Discovery: The first enhancer was discovered in the ________ region of the SV40 early gene.

A

Enhancers ; 5’-flanking

42
Q

(10.3 ENHANCERS AND SILENCERS)

Characteristics:

________________: Enhancers stimulate transcription even when inverted or relocated far from the promoter, demonstrating their position and orientation independence.

______________: Enhancers act through proteins called transcription factors, enhancer-binding proteins, or activators, which interact with general transcription factors at the promoter

A

Position and Orientation Independence ; Proteins Involved

43
Q

(10.3 ENHANCERS AND SILENCERS)

Enhancers Within Genes:

Example: An enhancer was found within an intron of the g2b gene, encoding a mouse antibody subunit.

_____________: Deletions within the intron caused a decrease in gene product production, indicating the importance of the suspected enhancer region.

_____________: The enhancer functioned even when inverted or relocated upstream of the promoter, confirming its enhancer properties.

_____________: Gene expression was more active in plasmacytoma cells (antibody-producing cells) compared to fibroblasts, emphasizing the cell type-specificity of enhancer activity.

A

Effect of Deletions ; Position and Orientation Independence ; Cell Type-Specific Activity

44
Q

(10.3 ENHANCERS AND SILENCERS)

____________: Enhancers play a crucial role in regulating gene expression patterns in different cell types.

_____________: Different cell types express distinct activators that bind to enhancers, leading to the activation of specific genes and the production of cell type-specific proteins.

A

Differential Gene Expression ; Cell Type-Specificity

45
Q

(10.3 ENHANCERS AND SILENCERS)

Silencers:

Function: Silencers are DNA elements that inhibit transcription, acting at a distance to modulate gene expression negatively.

Example: Mating System in Yeast:
- _____: In yeast chromosome III, there are three loci—MAT, HML, and HMR—of very similar sequence.
- _____________: HML and HMR are not expressed, and silencers located at least 1 kb away are responsible for their genetic inactivity.
- _____________: Active yeast genes can be substituted for HML or HMR, but they become inactive, indicating a response to an external negative influence, namely, a silencer

A

Loci ; Inactivity of HML and HMR ; Response to External Influence

46
Q

(10.3 ENHANCERS AND SILENCERS)

Mechanism of Action:

_________________: Silencers cause chromatin to coil up into a condensed, inaccessible form, preventing transcription of nearby genes.

__________________: The process of silencing involves complex chromatin modifications and the recruitment of specific proteins, leading to the establishment of repressive chromatin states.

A

Chromatin Condensation ; Detailed Mechanism

47
Q

(10.3 ENHANCERS AND SILENCERS)

_________: Some DNA elements can exhibit both enhancer and silencer activity depending on the proteins bound to them. For example, the thyroid hormone response element can act as a silencer when bound by the thyroid hormone receptor without its ligand. However, it functions as an enhancer when the thyroid hormone receptor binds along with thyroid hormone.

A

Dual Activity

MOLBIO OFFSEM MIDTERM (9 decks)

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