Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

CMB2001: eukaryotic gene expression > control of transcription and chromatin > Flashcards

control of transcription and chromatin Flashcards

lectures 1-4

1
Q

What is the difference between the template and coding strands in transcription?

A

The template strand (3’-5’) is used by RNA polymerase to synthesize RNA, while the coding strand (5’-3’) has the same sequence as the mRNA (except T is replaced by U).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the key components involved in transcription?

A

RNA polymerase, ATP, UTP, CTP, GTP, and specific transcription factors like σ70 in prokaryotes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the role of the σ70 factor in prokaryotic transcription?

A

The σ70 factor is part of the RNA polymerase holoenzyme and helps recognize the promoter regions in bacterial DNA to initiate transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What are promoters in transcription?

A

Promoters are DNA sequences that initiate transcription, with key regions like the -35 and -10 sequences in prokaryotes or TATA boxes in eukaryotes.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are the consensus sequences in prokaryotic promoters?

A

The consensus sequences are the -35 and -10 regions (e.g., TTGACA and TATAAAT) that help in the binding of RNA polymerase for transcription initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the core promoter elements in eukaryotic transcription?

A

Core promoter elements in eukaryotes include the TATA box, initiator (Inr), motif ten element (MTE), and downstream promoter element (DPE).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are CpG islands and their role in transcription?

A

CpG islands are regions with a high frequency of CG sequences in the promoter region of genes, where methylation of cytosines typically silences gene expression.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What are UAS and Enhancers in eukaryotic transcription?

A

UAS (Upstream Activating Sequences) and enhancers are regulatory regions where activators bind to increase gene transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What are Silencers and URS in eukaryotic transcription?

A

Silencers and URS (Upstream Repressive Sequences) are DNA elements where repressors bind to decrease transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the role of RNA polymerase I, II, and III in eukaryotic cells?

A

RNA polymerase I transcribes rRNA, RNA polymerase II transcribes mRNA, and RNA polymerase III transcribes tRNA and other small RNAs.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

How does RNA polymerase II in eukaryotes differ from bacterial RNA polymerase?

A

RNA polymerase II requires general transcription factors (GTFs) to initiate transcription and lacks a sigma factor like bacterial RNA polymerase.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the General Transcription Factors (GTFs) in eukaryotic transcription?

A

GTFs are proteins like TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH that are involved in assembling the pre-initiation complex (PIC) at the promoter.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the role of TFIIH in transcription?

A

TFIIH has helicase activity to unwind DNA at the promoter, and its kinase activity phosphorylates the C-terminal domain (CTD) of RNA polymerase II.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does the C-terminal domain (CTD) of RNA polymerase II function during transcription initiation?

A

The CTD is phosphorylated during transcription initiation and helps recruit additional factors needed for elongation and processing of the nascent mRNA.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the function of TFIID in transcription?

A

TFIID binds to the TATA box and recruits other GTFs and RNA polymerase II to form the pre-initiation complex.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is promoter clearance in transcription initiation?

A

Promoter clearance occurs when RNA polymerase II starts transcribing the gene after the formation of the open complex and release of some general transcription factors.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the function of the helix-turn-helix structure in the TFIID complex?

A

The helix-turn-helix structure of the TATA binding protein (TBP) in TFIID helps it to recognize and bind to the TATA box, initiating transcription.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

How can reporter genes be used to study promoters?

A

Reporter genes like GFP, luciferase, and LacZ can be linked to a promoter to measure gene expression, location, and response to signals.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the Pre-Initiation Complex (PIC)?

A

The PIC is a large multi-protein complex formed by RNA polymerase II and general transcription factors at the promoter, required for transcription initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What are the major steps involved in transcription initiation by RNA polymerase II?

A

1) Formation of the pre-initiation complex (PIC),
2) DNA unwinding by TFIIH,
3) Phosphorylation of the CTD,
4) RNA polymerase II begins transcription and clears the promoter.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What does TFIIH contribute to in transcription?

A

TFIIH provides helicase activity to unwind the DNA and kinase activity to phosphorylate RNA polymerase II’s C-terminal domain (CTD), enabling transcription initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the role of UAS/Enhancer elements in transcription?

A

UAS (Upstream Activator Sequence) and enhancer elements bind activators that stimulate high levels of transcription by interacting with the core promoter and transcription machinery. They can be located close to the core promoter (promoter proximal) or far from the transcription start site (distal).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are some common types of UAS/Enhancer elements?

A

GC Box (GGGCGG) - Binds Sp1
Octamer (ATTTGCAT) - Binds Oct-1
**CAAT Box **(GGCCAATCT) - Binds NFY
**SRE **(TGACTCA) - Binds Serum Response Factor (SRF)
**HSE **(CTNGAATNTTCTAGA) - Binds Heat Shock Factor (HSF)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the function of activation domains in activators?

A

Activation domains in activators are regions that lack structural conservation and interact with components of the transcriptional machinery to increase transcription levels. They typically interact with TAFs, TFIID, TFIIB, and other transcription factors.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What are some examples of activation domains?

A

Acidic Patch - e.g., VP16
Glutamine-rich - e.g., SP1
Proline-rich - e.g., Jun

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

How do activators work to stimulate transcription?

A

**Promote binding of additional activators.
Stimulate complex assembly **by recruiting TFIID, TFIIB, and Mediator to the core promoter.
Release stalled RNA polymerase to initiate transcription.
Modulate chromatin structure to facilitate complex formation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is Mediator and what is its role in transcription?

A

Mediator is a large complex that bridges the interaction between activators and RNA polymerase II, aiding in the recruitment of RNA pol II to the promoter and enhancing the formation of the pre-initiation complex (PIC).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

What are the components of the Pre-Initiation Complex (PIC)?

A

The PIC consists of general transcription factors (GTFs) like TFIID, TFIIB, TFIIF, TFIIE, TFIIH, and RNA polymerase II. Activators interact with these factors to assemble the PIC.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What is the function of the Mediator complex?

A

Mediator helps to bring activators and RNA polymerase II together, facilitating transcription initiation. It is crucial for recruiting RNA pol II to the core promoter.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

What are some in vitro methods used to analyze activators?

A

DNA Footprinting
Electrophoretic Mobility Shift Assay (Gel Shift)
In vitro Transcription Assays to measure transcription activity.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

What is Chromatin Immunoprecipitation (ChIP) used for?

A

ChIP is used to identify the binding sites of activators on DNA. The method involves immunoprecipitating the protein-DNA complex and analyzing it using PCR or sequencing.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

How do activators modulate chromatin to facilitate transcription?

A

Activators can remodel chromatin to make it more accessible to the transcriptional machinery, aiding in the formation of the pre-initiation complex and facilitating transcription initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What is the purpose of Reporter Assays in studying activators?

A

Reporter assays use reporter genes (like GFP or luciferase) to measure the level of transcriptional activity, helping to assess how activators influence gene expression.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

How do activators interact with Mediator and TFIID to enhance transcription?

A

Activators interact with TAFs in TFIID and specific subunits of Mediator to recruit the transcriptional machinery, enhancing the formation of the pre-initiation complex and boosting transcription initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

How do activators influence RNA polymerase II activity?

A

Activators can help release stalled RNA polymerase II at the promoter, ensuring continued transcription elongation after initiation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are the primary mechanisms by which activators stimulate transcription?

A

Recruitment of transcription machinery.
Activation of chromatin remodeling.
Facilitation of RNA polymerase release from pausing.
Promoting the binding of additional activators.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What is the significance of “promoter proximal” enhancer elements?

A

Promoter proximal enhancer elements are located close to the core promoter and bind to activators that are constitutively active, helping regulate basal (low) transcription levels by interacting with the transcription machinery.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

What are the functions of response elements in enhancer/UAS elements?

A

Response elements are enhancer sequences that bind transcription factors whose activity is regulated by specific stimuli. These include factors such as serum response factors (SRF) for growth factors and heat shock factors (HSF) for heat shock.

39
Q

How do activators influence transcription levels under different conditions?

A

Activators interact with specific enhancer sequences, and their activity can be modulated by external signals, such as heat shock or growth factors, leading to an increase in transcription levels from basal to activated levels.

40
Q

What is combinatorial control of transcription?

A

Combinatorial control refers to the concept that different types and combinations of enhancer sequences and activators dictate the timing, location, and level of gene transcription, allowing fine-tuned regulation in response to various signals.

41
Q

What is the role of general transcription factors (GTFs) in transcription?

A

General transcription factors like TFIIB, TFIID, and TFIIH are essential for the assembly of the pre-initiation complex (PIC), and they interact with RNA polymerase II to facilitate the initiation of transcription.

42
Q

How do activators work to increase the rate of PIC formation?

A

Activators enhance PIC formation by increasing the binding of TFIID (via TAFs), the recruitment of TFIIB, and the assembly of the RNA polymerase II complex at the core promoter.

43
Q

How do activators influence the release of stalled RNA polymerase II?

A

Activators can release RNA polymerase II that is stalled after initiating transcription. This is crucial for genes that need rapid transcriptional activation, such as heat shock genes like hsp70, where RNA pol II stalls and requires activator-mediated release to continue.

44
Q

What role does chromatin remodeling play in transcription?

A

Chromatin remodeling, facilitated by activators, involves changes to the structure of nucleosomes or histones that allow for better accessibility of the DNA to the transcription machinery, enabling efficient transcription initiation.

45
Q

What is the purpose of Electrophoretic Mobility Shift Assays (Gel Shift)?

A

Gel shift assays measure the binding of proteins, such as activators, to DNA by analyzing the change in mobility of the DNA-protein complex in a gel under non-denaturing conditions. This technique identifies specific protein-DNA interactions.

46
Q

How do activators enhance transcription initiation?

A

Activators enhance transcription initiation by facilitating the binding of transcription factors, including TFIID, TFIIB, and Mediator, to the core promoter. This accelerates the assembly of the pre-initiation complex and initiates transcription at higher levels.

47
Q

How do activators work through a modular structure?

A

Eukaryotic activators are modular, meaning they contain distinct functional domains, such as DNA binding domains (e.g., zinc fingers, leucine zippers) and activation domains (e.g., acidic patches), which work together to regulate gene expression effectively.

48
Q

What mechanisms contribute to the diversity of TCR genes?

A

Diversity is generated through multiple V, (D), and J gene segments, combinatorial diversity between these segments, and junctional diversity. Unlike BCR/Ig, no somatic hypermutation (SHM) occurs.

49
Q

How does TCR diversity differ from BCR/Ig diversity?

A

TCR diversity does not involve somatic hypermutation, and TCRs are never secreted as soluble molecules.

50
Q

Which TCR chain is similar to the Ig light chain, and which is similar to the Ig heavy chain?

A

The TCRα chain is similar to the Ig light chain, and the TCRβ chain is similar to the Ig heavy chain.

51
Q

What are the gene segments and chromosome locations for TCRα, TCRβ, TCRγ, and TCRδ?

A

TCRα: V, J, C (Chromosome 14)

TCRβ: V, D, J, C (Chromosome 7)

TCRγ: V, J, C (Chromosome 7)

TCRδ: V, D, J, C (Chromosome 14)

52
Q

How is the DNA rearrangement process in TCR generation similar to that in BCR/Ig generation?

A

Both involve rearrangement of V, (D), and J gene segments and imprecise joining for junctional diversity.

53
Q

Where are MHC molecule genes located in humans?

A

MHC molecule genes are located on chromosome 6 and are referred to as HLA (Human Leukocyte Antigen).

54
Q

What is unique about the expression of MHC genes?

A

MHC genes are co-dominantly expressed, meaning alleles from both parents are expressed simultaneously.

55
Q

What cells express MHC class I molecules?

A

All nucleated cells express MHC class I molecules.

56
Q

What cells express MHC class II molecules?

A

MHC class II molecules are expressed on antigen-presenting cells (APCs), such as B cells, macrophages, and dendritic cells, and can be upregulated by interferons during inflammation.

57
Q

What is the evolutionary advantage of MHC polymorphism?

A

High MHC polymorphism allows binding and presentation of a vast range of peptides, enabling the immune system to respond to a wide array of pathogens.

58
Q

What is the main source of peptides presented by MHC class I molecules?

A

Endogenous antigens, such as proteins synthesized within the cell (e.g., viral proteins), are presented by MHC class I molecules.

59
Q

What is the main source of peptides presented by MHC class II molecules?

A

Exogenous antigens, such as proteins from extracellular pathogens, are presented by MHC class II molecules.

60
Q

What accessory molecules are involved in antigen presentation via MHC class I molecules?

A

TAP (transporter associated with antigen processing), tapasin, and calreticulin are key accessory molecules.

61
Q

What is the role of the invariant chain in MHC class II antigen processing?

A

The invariant chain blocks the peptide-binding groove of MHC class II molecules in the ER, preventing premature peptide binding.

62
Q

What is the function of HLA-DM in MHC class II processing?

A

HLA-DM facilitates the removal of the CLIP peptide and the loading of antigenic peptides into the groove of MHC class II molecules.

63
Q

How are peptides processed for presentation by MHC class I molecules?

A

Proteins are degraded by the proteasome, transported to the ER by TAP, loaded onto MHC class I molecules, and then transported to the cell surface.

64
Q

How are peptides processed for presentation by MHC class II molecules?

A

Proteins are endocytosed, degraded into peptides by acid proteases, loaded onto MHC class II molecules in vesicles, and transported to the cell surface.

65
Q

What ensures that MHC class I molecules present endogenous antigens?

A

The proteasome and TAP ensure peptides from intracellular proteins are processed and loaded onto MHC class I molecules.

66
Q

What ensures that MHC class II molecules present exogenous antigens?

A

Acid proteases in endocytic vesicles and the invariant chain ensure peptides from extracellular proteins are processed and loaded onto MHC class II molecules.

67
Q

How many different MHC molecules can a heterozygous individual express?

A

Up to 12 MHC molecules: 6 class I (HLA-A, B, C) and 6 class II (HLA-DP, DQ, DR).

68
Q

How does MHC polymorphism benefit populations?

A

It provides a survival advantage by enabling responses to a wide range of pathogens.

69
Q

What is a downside of high MHC polymorphism?

A

It increases the risk of autoimmune diseases and reduces the compatibility pool for organ transplantation.

70
Q

List two similarities between TCR and BCR generation.

A

Both involve gene rearrangement of V, (D), and J segments and junctional diversity.

71
Q

List two differences between TCR and BCR generation.

A

TCRs do not undergo somatic hypermutation and are never secreted as soluble molecules.

72
Q

What are the main structural differences between MHC class I and II molecules?

A

MHC class I molecules have a single transmembrane chain (α) associated with β2-microglobulin, while MHC class II molecules have two transmembrane chains (α and β).

73
Q

How does MHC polymorphism affect peptide binding?

A

Polymorphic residues influence peptide-binding grooves, determining the range of peptides each MHC molecule can present.

74
Q

What role does the proteasome play in antigen presentation?

A

The proteasome degrades cytoplasmic proteins into peptides for loading onto MHC class I molecules.

75
Q

Do MHC class I molecules present peptides from exogenous sources?

A

No, MHC class I molecules primarily present peptides from endogenous sources.

76
Q

Can an individual express more than one type of MHC molecule on macrophages?

A

Yes, a single macrophage can express multiple MHC molecules due to co-dominant expression of HLA genes.

77
Q

What does the CLIP protein do?

A

CLIP occupies the peptide-binding groove of MHC class II molecules until antigenic peptides displace it.

78
Q

What is the function of TAP in antigen processing?

A

TAP transports peptides from the cytoplasm into the ER for loading onto MHC class I molecules.

79
Q

How do APCs activate CD4+ T cells?

A

APCs present extracellular antigens on MHC class II molecules, which are recognized by CD4+ T cells.

80
Q

What ensures MHC class II molecules present extracellular peptides?

A

Acid proteases degrade extracellular antigens, and the invariant chain ensures proper peptide loading in vesicles.

81
Q

Where do B cells develop, and which transcription factor do they express?

A

B cells develop from hematapoietic stem cells in the bone marrow and express the PAX5 transcription factor

82
Q

Approximately how many b cells are produced daily?

A

Around 3 ×10^10 B cells are produced daily.

83
Q

What processes are involved in B cell development?

A

Re-arrangement and expression of immunoglobulin (Ig) genes, and the expression of lymphocyte and B cell-specific markers. (e.g., CD45, then CD19).

84
Q

What is negative selection in B cell development?

A

It is the removal of self-reactive B cells to prevent autoimmunity.

85
Q

Which chain is rearranged first in pre-B cells, and what is formed?

A

The heavy (H) chain rearranged first, and it is expressed with surrogate light chains (VpreB and V preB and 𝜆5) to form the pre-B cell receptor (pBCR).

86
Q

What signal does the pre-B cell receptor (pBCR) deliver?

A

It signals that the heavy chain is functional, initiates light chain rearrangement, and halts surrogate light chain expression

87
Q

Which genes mediate gene rearrangement in B cells?

A

RAG-1 and RAG-2 genes are crucial for immunoglobulin gene rearrangement.

88
Q

What happens if a B cell fails to rearrange its heavy and light chains?

A

The B cell dies if it fails to rearrange both heavy and light chains productively.

89
Q

What are the possible outcomes for immature B cells binding multivalent self-antigen?

A

They may undergo:
1. Clonal deletion (apoptosis)
2. Receptor editing (further light chain rearrangement)

90
Q

What happens if an immature B cell binds soluble self-antigen?

A

The B cell becomes anergic (unresponsive)

91
Q

What Ig is expressed on immature B cells?

A

Immature B cells express membrane IgM

92
Q

What determines whether a B cell expresses 𝜅 or λ light chain?

A

K genes rearrange before λ genes, so more B cells express 𝜅 light chains.

93
Q

How many rearrangements can occur for the K light chain locus?

A

Up to 10 rearrangements are possible due to 5 𝐽𝜅 genes on each chromosome.

94
Q

What are the possible fates of a B cell that encounters self-antigen during cell development?

A

Depending on the nature of the self-antigen, the outcomes are:
- clonal deletion
- receptor editing
- anergy

CMB2001: eukaryotic gene expression (6 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions