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Molekylær cellebiologi > Control of gene expression II > Flashcards

Control of gene expression II Flashcards

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1
Q

What is the role of DNA methylation in vertebrate cells?

A

DNA methylation allows gene expression patterns to be inherited by progeny cells

Methylation occurs mainly on cytosine (C) nucleotides in the sequence CG

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2
Q

What is 5-methylcytosine and how does it relate to cytosine?

A

5-methylcytosine (5-methyl C) is a modified form of cytosine that does not affect base-pairing

It has the same relation to cytosine as thymine has to uracil

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3
Q

How does maintenance methyl transferase function?

A

It methylates CG sequences that are base-paired with already methylated CG sequences

This allows the inherited pattern of DNA methylation to be maintained after DNA replication

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4
Q

What happens to DNA methylation patterns shortly after fertilization in mammals?

A

There is a genome-wide wave of demethylation, leading to the loss of most methyl groups

This can occur due to suppression of maintenance DNA methyl transferase activity or active removal by DNA demethylases

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5
Q

What is the significance of CG-rich islands in the human genome?

A

CG islands are regions with a high density of CG sequences, often associated with gene promoters

Approximately 60% of human protein-coding genes have promoters in CG islands

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6
Q

What is genomic imprinting?

A

Genomic imprinting is when the expression of certain genes depends on the parent from whom they are inherited

About 300 genes are imprinted in humans

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7
Q

How does DNA methylation contribute to gene repression?

A

Methyl groups on cytosines interfere with the binding of transcription regulators and general transcription factors

Dense methylation establishes a form of gene repression that is more efficient than in prokaryotes

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8
Q

What is the effect of unmethylated CG islands on gene expression?

A

They often allow RNA polymerase to bind to promoters, making them more accessible for transcription

This state is maintained by proteins that repel de novo methylases

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9
Q

What is a key outcome of the interaction between DNA methylation and histone modifications?

A

It leads to the establishment of a repressive chromatin state

This interaction can involve histone-modifying enzymes and DNA methyl-binding proteins

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10
Q

How does the process of deamination of cytosine differ from that of 5-methylcytosine?

A

Deamination of unmethylated C leads to U, which is easily repaired, while deamination of 5-methyl C leads to T, which is often not repaired

This contributes to the evolutionary loss of CG sequences

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11
Q

What is the role of ‘pioneer factors’ in gene activation during differentiation?

A

They are involved in the activation of tightly repressed genes in differentiated cells

Their action often requires multiple steps, including histone demethylases and DNA demethylases

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12
Q

What is the phenomenon called when only one copy of an imprinted gene is expressed?

A

Genomic imprinting

Imprinting can lead to the expression of harmful mutations if the functional copy is silenced.

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13
Q

What syndrome results from an imprinted gene deletion leading to silencing of the intact gene?

A

Angelman syndrome

This disorder affects the nervous system and causes reduced mental ability and severe speech impairment.

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14
Q

What marks genes subject to imprinting in early embryos?

A

Methylation

Methylation distinguishes gene copies derived from sperm or egg chromosomes.

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15
Q

What is the result of methylation of an insulator element on the paternal chromosome in the case of Igf2?

A

It blocks its function and allows distant cis-regulatory sequences to activate transcription

This demonstrates how methylation can influence gene expression.

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16
Q

What type of RNA is involved in some imprinting mechanisms?

A

Long noncoding RNAs (lncRNAs)

LncRNAs are RNA molecules longer than 200 nucleotides that do not code for proteins.

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17
Q

What process ensures that both male and female mammals produce the same amount of X-chromosome gene products?

A

Dosage compensation

This is achieved through the transcriptional inactivation of one of the two X chromosomes in females.

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18
Q

What is the process called that inactivates one of the two X chromosomes in female somatic cells?

A

X-inactivation

This process leads to a mosaic expression pattern in female mammals.

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19
Q

What is the significance of X-inactivation in female cats?

A

It creates the orange and black coat coloration

The random X-inactivation results in patches of different colors due to the genes on the X chromosomes.

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20
Q

What triggers the transcriptional inactivation of an entire X chromosome?

A

The synthesis of a long noncoding RNA called Xist

Xist RNA coats the chromosome that produces it and recruits proteins that carry out gene silencing.

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21
Q

What role do insulator proteins, such as CTCF, play in gene expression on the inactive X chromosome?

A

They help hold DNA loops in place for transcriptionally active genes

These loops extend from the bulk of the tightly packaged chromosome.

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22
Q

What is the primary mechanism of dosage compensation in male flies?

A

The single X chromosome is upregulated approximately twofold to match the female dose

This differs from the mechanisms in mammals and nematodes.

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23
Q

What is epigenetic inheritance?

A

A heritable alteration in a cell or organism’s phenotype that does not result from changes in the nucleotide sequence of DNA

Examples include imprinting and X-inactivation.

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24
Q

What is the function of positive feedback loops in cell memory?

A

They help a cell remember its identity by activating the transcription of its own gene

This mechanism provides stability against fluctuations in transcription regulator levels.

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25
What is genomic imprinting?
A phenomenon where the expression of a gene depends on whether it was inherited from the mother or the father ## Footnote This is an example of monoallelic gene expression.
26
What is the role of Xist RNA in X-inactivation?
Xist RNA coats the inactive X chromosome and associates with proteins that modify histones and DNA ## Footnote This process is crucial for the silencing of the inactive X chromosome.
27
What is the significance of specialized biomolecular condensates in X-inactivation?
They help keep proteins and RNAs needed for gene repression at high local concentrations ## Footnote This model explains how active gene loops extend beyond the boundary of the condensate.
28
What are the two epigenetic mechanisms that act in cis?
Maintenance methylation and histone modification ## Footnote These mechanisms can propagate specific patterns of gene expression.
29
How can cells pass on gene expression patterns to their daughter cells?
Through epigenetic mechanisms that allow for the inheritance of gene expression patterns ## Footnote These mechanisms contribute to the complexity of multicellular life.
30
What are post-transcriptional controls?
Regulatory mechanisms that operate after RNA transcription has begun.
31
What is transcription attenuation?
A phenomenon where the expression of some genes is inhibited by premature termination of transcription.
32
What role do regulatory proteins play in transcription attenuation?
They bind to the nascent RNA chain to remove attenuation and allow complete RNA transcription.
33
Which virus is a well-studied example of transcription attenuation?
HIV (human immunodeficiency virus).
34
What is the function of the Tat protein in HIV?
It binds to a specific RNA structure to prevent premature termination of transcription.
35
What are riboswitches?
Short RNA sequences that change conformation when binding specific small molecules, regulating gene expression.
36
Where are riboswitches typically located?
Near the 5′ end of mRNAs.
37
What is alternative RNA splicing?
A process that allows a single gene to produce multiple protein variants by splicing RNA transcripts differently.
38
What is the impact of alternative RNA splicing on the complexity of an organism?
It allows for a greater protein complexity than the number of genes would suggest.
39
What is the significance of splicing site ambiguity?
It can lead to different splice site choices being made by chance, resulting in several protein versions.
40
How can alternative RNA splicing be regulated?
Negatively, by preventing access to a splice site, or positively, by directing the splicing machinery to a site.
41
What does the regulation of RNA splicing allow in different cell types?
The generation of different protein versions according to the specific needs of the cell.
42
How has the definition of a gene changed with the discovery of alternative RNA splicing?
It expanded from encoding a single polypeptide to encompassing regions that can produce multiple proteins through splicing.
43
What was the original definition of a gene based on early genetic studies?
A region of the genome that segregates as a single unit during meiosis and gives rise to a phenotypic trait.
44
What is the role of the spliceosome in RNA splicing?
It removes intron sequences from mRNA precursors.
45
What is the role of genes in relation to polypeptide chains?
Most genes correspond to a region of the genome that directs the synthesis of a single enzyme, leading to the view that each gene encodes one polypeptide chain.
46
How is a gene defined in the context of gene expression?
A gene is identified as that stretch of DNA that is transcribed into RNA coding for either a single polypeptide chain or a single structural RNA such as tRNA or rRNA.
47
What is negative control in alternative RNA splicing?
In negative control, a repressor protein binds to a specific sequence in the pre-mRNA transcript and blocks access of the splicing machinery to a splice junction.
48
What is positive control in alternative RNA splicing?
In positive control, the splicing machinery is unable to remove a particular intron sequence efficiently without assistance from an activator protein.
49
What is back splicing?
Back splicing is when a 3′ splice site is joined to a downstream 5′ splice site, resulting in a covalently closed circular RNA molecule.
50
What is a characteristic of circular RNA molecules?
Circular RNAs are more stable than typical mRNAs and can accumulate to high concentrations in cells.
51
How does alternative cleavage and polyadenylation affect protein variants?
It can produce closely related proteins that differ only in the amino acid sequences at their C-terminal ends.
52
What are some types of covalent modifications found in mRNA?
Some types include: * N6-methyladenosine * 5-methyl cytidine * 1-methyladenosine * pseudouridine.
53
What is RNA editing?
RNA editing is a covalent modification that alters the nucleotide sequence of mRNA, changing the coded message.
54
What are the two principal types of RNA editing in animals?
A-to-I editing (deamination of adenine) and C-to-U editing (deamination of cytosine).
55
What is the role of ADAR enzymes in RNA editing?
ADAR enzymes perform A-to-I editing by recognizing double-strand RNA structures formed through base-pairing.
56
What is a consequence of A-to-I editing in mRNA?
It can change the amino acid sequence of the protein or produce a truncated protein by creating a premature stop codon.
57
What happens to mRNA modifications during transcription?
Methylases typically act on RNA as it is being transcribed, modifying adenosines adjacent to specific sequences.
58
What is the unique feature of circular RNAs compared to typical mRNAs?
Circular RNAs lack free ends, making them more stable and resistant to degradation.
59
What is the significance of A-to-I editing in mRNA?
A-to-I editing changes a glutamine to an arginine, altering Ca2+ permeability of the channel ## Footnote This editing is crucial for proper brain development, as shown by mutant mice prone to seizures.
60
What role does C-to-U editing play in mammals?
C-to-U editing creates a premature stop codon in apolipoprotein B mRNA, producing a shorter protein in the gut ## Footnote In the liver, the full-length apolipoprotein B is produced due to lack of the editing enzyme.
61
What are the possible evolutionary reasons for the existence of RNA editing?
* To correct genomic mistakes * To produce subtly different proteins from the same gene * As a defense mechanism against retroviruses ## Footnote RNA editing helps to hold many viruses in check, as seen with HIV.
62
What is the role of the Rev protein in HIV?
Rev protein binds to the Rev response element (RRE) and directs the export of unspliced viral RNAs from the nucleus ## Footnote This is crucial for the production of progeny virus.
63
What is the function of the Tat protein in HIV?
Tat counteracts premature transcription termination ## Footnote This regulation allows the virus to achieve latency in the host cell.
64
What is a notable example of mRNA localization in Drosophila?
The Bicoid transcription regulator mRNA is localized at the anterior tip of the developing egg ## Footnote This localization is essential for proper anterior development.
65
How do mRNAs typically exit the nucleus?
They exit through nuclear pores after undergoing extensive processing ## Footnote This includes modifications such as the 5′ cap and 3′ poly-A tail.
66
What happens to mRNAs that are not properly localized?
They may be degraded in the cytosol unless protected by anchor proteins ## Footnote This mechanism ensures that only correctly localized mRNAs are translated.
67
What is the role of the cytoskeleton in mRNA localization?
The cytoskeleton facilitates the directed transport of mRNAs to specific sites within the cell ## Footnote This transport is crucial for localized protein synthesis.
68
What is nonsense-mediated decay?
A quality-control mechanism that degrades mRNAs with premature stop codons ## Footnote This process helps prevent the translation of defective proteins.
69
What do untranslated regions (UTRs) of eukaryotic mRNAs resemble?
The untranslated regions of eukaryotic mRNAs resemble the transcriptional control regions of genes.
70
What is the Shine–Dalgarno sequence?
A conserved stretch of nucleotides found in bacterial mRNAs required to start protein synthesis.
71
How do eukaryotic mRNAs initiate translation?
The selection of an AUG codon as a translation start site is largely determined by its proximity to the cap at the 5′ end of the mRNA.
72
What are microRNAs (miRNAs)?
Small RNAs that bind to mRNAs and reduce protein output.
73
What triggers eukaryotic cells to decrease their overall rate of protein synthesis?
Deprivation of growth factors or nutrients, infection by viruses, and sudden increases in temperature.
74
What is 'leaky scanning' in eukaryotic translation?
A phenomenon where scanning ribosomal subunits sometimes ignore the first AUG codon and skip to the second or third AUG codon.
75
What is the function of upstream open reading frames (uORFs)?
They serve a regulatory function, often decreasing translation of the downstream gene by trapping a scanning ribosome.
76
What is an internal ribosome entry site (IRES)?
A specialized RNA sequence that allows translation to initiate at positions distant from the 5′ end of the mRNA.
77
How do viruses utilize IRES sequences?
Viruses use IRESs to translate their own mRNA while blocking normal translation of host mRNAs.
78
Why can a bacterium adapt quickly to environmental changes?
Because its mRNAs are both rapidly synthesized and rapidly degraded.
79
What are the two general mechanisms for destroying a typical eukaryotic mRNA molecule?
* Decapping followed by rapid degradation from the 5′ end * 3′-to-5′ degradation
80
What begins the process of mRNA degradation in eukaryotic cells?
Gradual shortening of the poly-A tail by an exonuclease.
81
What happens when the poly-A tail of an mRNA is reduced to about 25 nucleotides?
The two destruction pathways converge.
82
What is the process called when the 5′ cap of an mRNA is removed?
Decapping.
83
Which part of the mRNA is especially important in controlling its lifetime?
3′ UTR sequences.
84
What are P-bodies?
Large aggregates of RNA and protein that can degrade or store mRNAs.
85
What happens to mRNAs in the cytosol that are no longer actively translated?
They often move to P-bodies.
86
What are stress granules?
Dynamic membraneless organelles that form when translation initiation is blocked.
87
What happens to ribosome-free mRNAs during stress conditions?
They accumulate in stress granules.
88
What role do P-bodies play in mRNA management?
* Degradation of mRNAs * Storage of translationally repressed mRNAs
89
What are the eight regulatory mechanisms that control gene expression from RNA to protein?
* Attenuation of RNA transcript * Alternative RNA splice-site selection * Control of 3′-end formation * RNA covalent modifications * Control of transport from the nucleus * Localization of mRNAs * Control of translation initiation * Regulated mRNA degradation
90
What do most control processes in gene expression require?
Recognition of specific sequences or structures in the RNA.
91
What is the central dogma of molecular biology?
The flow of genetic information proceeds from DNA through RNA to protein.
92
What are some critical tasks performed by RNA molecules besides serving as carriers of genetic information?
* Reading the genetic code * Synthesizing proteins * Serving as a template for chromosome replication * Modifying ribosomal RNA * Directing RNA splicing * Inactivating one copy of the X chromosome in females
93
What is RNA interference (RNAi)?
A process where short single-stranded RNAs bind to target RNAs to inhibit their translation or catalyze their destruction.
94
What are the three classes of small noncoding RNAs involved in RNA interference?
* microRNAs (miRNAs) * small interfering RNAs (siRNAs) * piwi-interacting RNAs (piRNAs)
95
What is the primary function of microRNAs (miRNAs)?
To regulate mRNA translation and stability.
96
What complex is formed when miRNAs are assembled with proteins?
RNA-induced silencing complex (RISC).
97
What happens when an miRNA binds extensively to its target mRNA?
The mRNA is cleaved (sliced) by the Argonaute protein.
98
What occurs if the base-pairing between miRNA and mRNA is less extensive?
Translation of the mRNA is repressed, leading to eventual degradation.
99
What allows a single miRNA to regulate multiple mRNAs?
The presence of short complementary sequences in the UTRs of different mRNAs.
100
How does RNA interference serve as a cell defense mechanism?
It orchestrates the degradation of foreign double-stranded RNA molecules from viruses and transposable elements.
101
What triggers RNA interference in the cell?
The presence of double-stranded RNA.
102
What are small interfering RNAs (siRNAs) derived from?
Double-stranded RNA that has been cleaved by the Dicer protein.
103
What is the role of siRNAs in RNA interference?
They direct RISC to cleave complementary RNA molecules produced by viruses or transposable elements.
104
What is the RNA-induced transcriptional silencing (RITS) complex?
A complex that uses siRNAs to silence the transcription of target RNAs.
105
What is a unique feature of siRNA-mediated RNA interference?
It can amplify the RNAi response through RNA-dependent RNA polymerases.
106
What is the role of Dicer in the context of RNA interference?
To process double-stranded RNA into small interfering RNAs (siRNAs).
107
How does RNA interference contribute to the resistance of plants to viral infections?
By allowing the transfer of RNA fragments from cell to cell.
108
What is RNA interference (RNAi)?
A cellular mechanism that uses small RNA molecules to regulate gene expression by degrading mRNA or silencing transcription. ## Footnote RNAi plays a critical role in controlling transposable elements and viral infections.
109
What are piRNAs?
Piwi-interacting RNAs that protect the germ line from transposable elements by silencing their activity.
110
What is the significance of piRNA clusters?
They contain sequence fragments from transposons and help in targeting and silencing these elements during gametogenesis.
111
How are piRNAs synthesized?
From specialized piRNA clusters in the genome as long, single-strand RNA molecules that are processed into shorter fragments.
112
What happens when piRNAs cleave transposon-coded mRNA?
Additional piRNAs can be generated from nearby sequences in the transposon mRNA, amplifying the RNAi response.
113
How do cells defend against transposons and integrated viral genomes?
Through RNA-based strategies like siRNAs and piRNAs, and also via sequence-specific DNA-binding proteins.
114
What is CRISPR?
A defense mechanism in bacteria and archaea that uses small noncoding RNAs to destroy invading viruses.
115
Describe the three steps of the CRISPR mechanism.
1. Integration of viral DNA into CRISPR loci 2. Transcription and processing of crRNAs 3. Destruction of viral DNA by crRNA-Cas protein complexes.
116
What are crRNAs?
CRISPR RNAs that guide the destruction of viral genomes in bacteria and archaea.
117
What are long noncoding RNAs (lncRNAs)?
RNAs longer than 200 nucleotides that do not code for proteins and have various functions in the cell.
118
What is the primary transcription enzyme for most lncRNAs?
RNA polymerase II.
119
What is the function of CRISPR in bacteria and archaea?
CRISPR provides adaptive immunity by integrating short viral DNA sequences into its locus and using crRNAs to target and destroy viral sequences. ## Footnote This system allows surviving cells from a viral infection to 'remember' and defend against future infections.
120
What are the steps involved in CRISPR-mediated immunity?
1. Short viral DNA sequence is integrated into CRISPR locus 2. RNA is transcribed from CRISPR locus and bound to Cas protein 3. Small crRNA seeks out and destroys viral sequences.
121
What are PAMs in the context of CRISPR?
PAMs are protospacer adjacent motifs that must be present on the target molecule for crRNAs to effectively attack. ## Footnote These sequences lie outside the crRNA sequences, preventing destruction of the CRISPR locus itself.
122
Why is it difficult to accurately annotate lncRNAs?
Approximately 75% of the human genome produces low levels of RNA, often considered transcription noise, complicating functional annotation.
123
What are the three unifying features of lncRNAs?
1. They can function as scaffold RNA molecules 2. They can serve as guide sequences 3. They can organize biomolecular condensates.
124
How do lncRNAs serve as scaffold RNA molecules?
lncRNAs hold together groups of proteins to coordinate their functions, facilitating interactions and speeding reactions.
125
What role do lncRNAs play as guide sequences?
They bind to specific RNA or DNA target molecules through base-pairing, bringing proteins into proximity with these nucleic acid sequences.
126
What is one way lncRNAs can block translation?
Antisense lncRNAs can base-pair with mRNAs to inhibit their translation into protein.
127
What is the difference between lncRNAs that act in cis and those that act in trans?
Cis-acting lncRNAs affect only the chromosome from which they are transcribed, while trans-acting lncRNAs diffuse away and affect other chromosomes.
128
What are some examples of known lncRNAs mentioned?
1. RNA in telomerase 2. Xist RNA 3. RNA involved in imprinting.
129
What is one well-understood use of noncoding RNAs in the cell?
RNA interference, where guide RNAs base-pair with mRNAs to either destroy them or repress their translation.

Molekylær cellebiologi (11 decks)

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