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BIO230 Midterm > Week 3 > Flashcards

Week 3 Flashcards

1
Q

Why is transcriptome analyses powerful?

A
  • provides a “signature” of the cell state
  • response to extracellular stimuli
  • disease states
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2
Q

What happens during eukaryotic RNA processing?

A
  • it’s tightly coupled to transcription
    1. covalent modifications of RNA ends
    2. removal of intro sequences
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3
Q

What is RNA capping?

A

the addition of a modified guanine nucleotide to the 5’ end of pre-mRNA, which is one of the first modifications of eukaryotic pre-mRNAs.

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4
Q

What are the functions of the RNA cap?

A
  1. It aids in RNA processing and export from the nucleus.
  2. It plays a crucial role in the translation of mRNAs in the cytosol.
  3. It protects mRNA from degradation by exonucleases.
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5
Q

How does the cap-binding complex (CBC) relate to RNA capping?

A

The cap-binding complex (CBC) binds to the RNA cap and is important for the stability and processing of the mRNA, facilitating its export from the nucleus and translation.

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6
Q

What are exons and introns in eukaryotic genes?

A

Exons are the coding sequences that remain in the mature RNA after splicing, while introns are non-coding sequences that are removed during the splicing process.

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7
Q

What is RNA splicing?

A

RNA splicing is the process by which introns are removed from the pre-mRNA transcript and exons are joined together to form the final mRNA.

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8
Q

What must be present in a mature eukaryotic mRNA?

A
  • 5’ cap
  • 5’ uTR (untranslated area)
  • AUG (start)
  • Stop codon
  • 3’ uTR
  • poly-A tail
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9
Q

What is alternative splicing?

A

Alternative splicing is a process that allows different RNA transcripts to be produced from the same gene, leading to the generation of multiple protein isoforms.

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10
Q

How many human genes produce multiple proteins?

A

75% of human genes

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11
Q

What is the spliceosome?

A

The spliceosome is a complex made up of RNA and proteins that carries out the splicing of pre-mRNA.

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12
Q

What are exon junction complexes (EJCs)?

A

protein complexes that bind to the sites of properly spliced RNA, serving as markers for correctly processed RNA.

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13
Q

What role do splicing activators play in alternative splicing?

A

Splicing activators promote the inclusion of specific exons in the final mRNA transcript, enhancing the splicing process.

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14
Q

What is the function of splicing repressors?

A

Splicing repressors inhibit the inclusion of specific exons or promote the retention of introns, leading to the production of different mRNA isoforms.

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15
Q

What is the role of the Sex-lethal (Sxl) gene in Drosophila sex determination?

A

The Sxl gene acts as a splicing repressor in females, regulating the splicing of its own RNA and the RNA of other genes involved in sex determination.

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16
Q

How does the ratio of X chromosomes to autosomes (X:A ratio) influence sex determination in Drosophila?

A

An X:A ratio of 0.5 results in male development (default), while a ratio of 1.0 leads to female development.

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17
Q

What are the three key genes involved in Drosophila sex determination?

A

The three key genes are Sex-lethal (Sxl), Transformer (Tra), and Doublesex (Dsx).

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18
Q

What happens to Tra RNA in male Drosophila?

A

In males, Tra RNA is not spliced and produces a nonfunctional Tra protein.

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19
Q

What is the function of the Doublesex (Dsx) gene in Drosophila?

A

Dsx regulates the expression of sex-specific genes, leading to the development of male or female characteristics based on the splicing pattern influenced by Sxl and Tra.

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20
Q

How does the Sxl protein affect splicing in male Drosophila?

A

In males, Sxl protein is not produced due to the lack of splicing, leading to the production of nonfunctional Tra protein and no functional Dsx protein, which represses female gene expression.

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21
Q

What is the role of the Sxl gene in female Drosophila?

A

The Sxl (Sex-lethal) gene acts as a splicing repressor in females. It regulates the splicing of its own RNA and the RNA of the Tra (Transformer) gene, which is crucial for female sex determination.

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22
Q

What is the role of the Transformer (Tra) protein in females?

A

The Tra protein acts as a splicing activator, promoting the splicing of Dsx RNA to produce a functional Dsx protein that regulates female gene expression.

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23
Q

How does the absence of Sxl protein affect Drosophila development?

A

Without Sxl protein, Tra RNA is not spliced correctly, leading to the production of non-functional Tra protein. This results in the development of male characteristics due to the lack of female-specific splicing of Dsx.

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24
Q

What is 3’ polyadenylation?

A

3’ polyadenylation is the process of adding a poly-A tail, consisting of approximately 200 adenine nucleotides, to the 3’ end of a newly transcribed RNA molecule.

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25
Q

Why is 3’ polyadenylation important?

A

It plays a crucial role in RNA stability, export from the nucleus, and translation in the cytosol. The poly-A tail protects mRNA from degradation and aids in the initiation of translation.

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26
Q

What signals the start of polyadenylation?

A

The signals for polyadenylation are encoded in the genome, specifically in the RNA sequence that is transcribed.

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27
Q

Which protein complexes are involved in the polyadenylation process?

A

Cleavage Stimulation Factor (CstF) and Cleavage and Polyadenylation Specificity Factor (CPSF).

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28
Q

What happens during the polyadenylation process?

A

The RNA is cleaved, transcription terminates, and then poly-A polymerase (PAP) adds the adenine nucleotides to the 3’ end of the RNA.

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29
Q

Is the addition of the poly-A tail genome encoded?

A

No, the addition of the poly-A tail is not genome-encoded; it is performed by poly-A polymerase using ATP.

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30
Q

What is the role of poly-A binding proteins?

A

Poly-A binding proteins bind to the poly-A tail and help in RNA export, translation, and enhancing mRNA stability.

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31
Q

What is the significance of the AAUAA sequence in polyadenylation?

A

The AAUAA sequence is a signal that is transcribed but is not the actual poly-A tail; it indicates where the polyadenylation process should occur.

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32
Q

When is eukaryotic RNA processing initiated?

A

before transcription

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33
Q

What is transcription elongation in eukaryotes?

A

Transcription elongation is the process where RNA polymerase synthesizes RNA from the DNA template, adding nucleotides to the growing RNA strand. It is tightly coupled with RNA processing.

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34
Q

How does the C-terminus domain of RNA polymerase facilitate RNA processing?

A

The CTD binds to RNA processing proteins during transcription elongation, transferring them to the RNA at the appropriate time, thus coupling transcription with RNA processing.

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35
Q

How does phosphorylation of the CTD influence RNA processing?

A

Phosphorylation of the CTD regulates the binding of RNA processing proteins, ensuring that they associate with the RNA at the correct stages of transcription and processing.

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36
Q

What is the primary function of RNA transport out of the nucleus?

A

The primary function is to selectively transport mature mRNA from the nucleus to the cytosol, ensuring that only properly processed mRNA is exported.

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37
Q

What are the markers required for the export of mature mRNA?

A

The markers required for export include the cap binding complex (CBC), exon junction complexes (EJC), and poly-A-binding proteins.

38
Q

What must happen to immature mRNA before it can be exported from the nucleus?

A

Immature mRNA must lose proteins involved in RNA splicing (e.g., snRNPs) before it can be exported.

39
Q

What is the ratio of RNA that typically leaves the nucleus?

A

Only about 1 in 20 RNA molecules leaves the nucleus, indicating a selective export process.

40
Q

What happens to improperly processed mRNAs in the nucleus?

A

Improperly processed mRNAs are eventually degraded in the nucleus by the exosome.

41
Q

What is the primary function of ribosomes in translation?

A

Ribosomes decode the mRNA message and are composed of over 50 different proteins and several RNA molecules.

42
Q

In which direction are proteins synthesized during translation?

A

Proteins are synthesized from the N-terminus (amino end) to the C-terminus (carboxyl end).

43
Q

What are the key components recognized by the translation initiation machinery in eukaryotes?

A

The translation initiation machinery recognizes the 5’-cap and the poly-A tail of mRNA.

44
Q

Which eukaryotic initiation factors are involved in the translation initiation process?

A

eIF4E binds to the 5’ cap, and poly-A binding protein (eIF4G) binds to the poly-A tail.

45
Q

What role does the exon junction complex (EJC) play in translation?

A

The EJC stimulates translation and ensures proper splicing of mRNA.

46
Q

What is the role of the small ribosomal complex in translation?

A

The small ribosomal complex initiates translation by binding to the mRNA and scanning for the first AUG codon downstream of the 5’ cap.

47
Q

How does the 5’ cap influence the recruitment of the small ribosomal complex?

A

The 5’ cap is recognized by eIF4E, which is crucial for the recruitment of the small ribosomal complex and helps in stabilizing the mRNA for translation.

48
Q

What is the significance of the poly-A tail in the recruitment process?

A

The poly-A tail, bound by poly-A binding proteins (eIF4G), enhances the stability of the mRNA and aids in the recruitment of the ribosomal complex for translation initiation.

49
Q

What happens to the mRNA during the translation initiation process?

A

The mRNA is scanned by the small ribosomal complex until it finds the start codon (AUG), ensuring that both ends of the mRNA are intact for proper translation.

50
Q

What is nonsense-mediated mRNA decay (NMD)?

A

NMD is a prominent mRNA surveillance system that identifies and degrades mRNAs containing premature stop codons, which may indicate improper splicing or mutations.

51
Q

What role do exon junction complexes (EJCs) play in nonsense-mediated mRNA decay?

A

EJCs are markers for properly spliced mRNA and help ensure that translation is initiated correctly. They are displaced by the ribosome during translation, and their presence indicates whether an mRNA is likely to be degraded.

52
Q

How does nonsense-mediated mRNA decay function in normal splicing?

A

In normal splicing, the ribosome binds to the mRNA as it emerges from the nuclear pore, displacing EJCs by the moving ribosome, and when it reaches the stop codon in the last exon, no EJCs remain bound, allowing for the proper release of mRNA into cytosol.

53
Q

What happens during abnormal splicing in relation to nonsense-mediated mRNA decay?

A

the ribosome binds to the mRNA as it emerges from the nuclear pore, displacing EJCs by the moving ribosome. If the ribosome encounters a premature stop codon, EJCs remain on the mRNA when the ribosome reaches the stop codon, triggering degradation of the mRNA mediated by Upf proteins.

54
Q

Why is NMD considered important in eukaryotic evolution?

A

may have facilitated the evolution of eukaryotes by allowing the selection of DNA rearrangements or alternative splicing patterns that produce full-length proteins, enhancing genetic diversity.

55
Q

In what contexts is NMD particularly significant?

A

NMD plays a crucial role in the immune system, where extensive DNA rearrangements occur to produce antibodies, and in various human diseases caused by mutations that lead to aberrant proteins.

56
Q

Where does NMD primarily occur?

A

NMD occurs in the cytosol of eukaryotic cells during post-translational gene regulation

57
Q

What is the primary function of mRNA quality control in prokaryotes?

A

To prevent the production of aberrant proteins that can be toxic to cells by ensuring that only complete and correctly processed mRNAs are translated.

58
Q

What happens to ribosomes when they encounter broken or incomplete mRNAs in prokaryotes?

A

Ribosomes stall on broken or incomplete mRNAs and do not release them.

59
Q

What is tmRNA and what role does it play in prokaryotic mRNA quality control?

A

tmRNA is a special RNA that is recruited to the ribosome’s A site when it stalls on incomplete mRNA. It acts as both a tRNA and an mRNA, allowing the ribosome to continue translation.

60
Q

How does tmRNA facilitate the degradation of incomplete proteins?

A

tmRNA carries an alanine amino acid and allows the ribosome to translate a short sequence (10 codons) from the tmRNA, which includes a tag that signals proteases to degrade the entire protein.

61
Q

What is the significance of the 11th codon in the tmRNA sequence?

A

The 11th codon in the tmRNA sequence is a stop codon, which signals the ribosome to terminate translation, leading to the degradation of the incomplete protein.

62
Q

Why is it important for prokaryotes to have a quality control mechanism for mRNA?

A

Prokaryotes cannot afford to lose resources on making defective proteins, so quality control ensures that only functional mRNAs are translated, maintaining cellular efficiency and viability.

63
Q

How do prokaryotic cells ensure that they do not waste resources on faulty mRNA?

A

Through the use of tmRNA, which helps tag incomplete proteins for degradation and ensures that only properly processed mRNAs are translated.

64
Q

What is mRNA stability?

A

mRNA stability refers to the lifespan of mRNA molecules in the cell, which affects how much protein can be produced from them.

65
Q

What are the two main mechanisms of mRNA degradation in eukaryotes?

A

Both involve gradual poly-A-tail shortening
1. Deadenylation (shortening of the poly-A tail)
2. Decapping (removal of the 5’ cap)
both can occur on the same mRNA

66
Q

How does the poly-A tail affect mRNA stability?

A

The poly-A tail protects mRNA from degradation; when it shortens to a critical length (about 25 nucleotides), the mRNA becomes more susceptible to degradation.

67
Q

What role do deadenylases play in mRNA stability?

A

Deadenylases are enzymes that shorten the poly-A tail of mRNA, leading to its degradation.

68
Q

What is the significance of the 3’ UTR in mRNA stability?

A

The 3’ UTR contains regulatory elements that can influence mRNA stability and translation efficiency.

69
Q

What is the role of cytosolic aconitase in mRNA stability?

A

Aconitase binds to the 3’ UTR of transferrin receptor mRNA, stabilizing it when iron levels are low. When iron is abundant, aconitase undergoes a conformational change, leading mRNA being released, and the exposed 3’UTR endonucleolytic cleavage site which leads to the degradation of mRNA

70
Q

Describe the function of microRNAs (miRNAs) in post-transcriptional regulation.

A

miRNAs are small non-coding RNAs that bind to complementary sequences in mRNAs, leading to mRNA degradation or inhibition of translation, thus regulating gene expression.

71
Q

What is the RNA-induced silencing complex (RISC)?

A

RISC is a protein complex that incorporates miRNAs and is responsible for guiding them to their target mRNAs, leading to silencing or degradation of those mRNAs.

72
Q

What is the role of the Argonaute protein in the RISC complex?

A

Argonaute is a key protein in the RISC complex that facilitates the base-pairing of miRNAs with their target mRNAs and plays a critical role in the silencing mechanism.

73
Q

Define “extensive match” in the context of miRNA targeting.

A

An extensive match occurs when the miRNA has a perfect or near-perfect complementarity to its target mRNA, typically leading to mRNA degradation.

74
Q

What is a “less extensive match” in miRNA targeting?

A

A less extensive match occurs when the miRNA binds to its target mRNA with imperfect complementarity, often resulting in translational repression and eventually degradation of mRNA

75
Q

What is RNA interference (RNAi)?

A

RNA interference is a biological process in which double-stranded RNA leads to the suppression of gene expression by targeting specific mRNAs for degradation or inhibition.

76
Q

In what types of organisms is RNAi found?

A

RNAi is found in eukaryotes, including fungi, plants, and animals.

77
Q

What role does the Dicer protein complex play in RNAi?

A

The Dicer protein complex initiates RNAi by processing double-stranded RNA into small interfering RNAs (siRNAs).

78
Q

What is the function of Argonaute in the RNA-induced silencing complex (RISC)?

A

Argonaute is a protein in RISC that plays a critical role in base-pairing small RNAs (miRNAs or siRNAs) with their target mRNA.

79
Q

How do small interfering RNAs (siRNAs) interact with Argonaute and RISC?

A

siRNAs can bind to Argonaute and RISC to either degrade double-stranded RNA or regulate transcription through the RNA-induced transcriptional silencing (RITS) complex.

80
Q

What is the role of the RNA-induced transcriptional silencing (RITS) complex?

A

RITS interacts with newly transcribed RNA and recruits chromatin-modifying enzymes to silence transcription.

81
Q

How does RNAi serve as a defense mechanism?

A

RNAi helps protect cells from foreign RNA molecules, such as those from viruses and transposable elements, by degrading their RNA.

82
Q

What is the primary function of the CRISPR-Cas immune system?

A

To provide adaptive immunity against foreign RNA and DNA, such as viruses.

83
Q

How does the CRISPR-Cas system recognize foreign genetic material?

A

Short fragments of viral DNA integrate into the CRISPR region of the genome, serving as templates to produce crRNAs (CRISPR RNAs).

84
Q

What role do crRNAs play in CRISPR-Cas immunity?

A

crRNAs guide Cas (CRISPR-associated) proteins to degrade viral DNA that is complementary to the CRISPR regions.

85
Q

What is the function of Cas proteins in the CRISPR-Cas system?

A

Cas proteins utilize small single-stranded RNA to target and degrade foreign genetic material.

86
Q

How does the CRISPR-Cas system differ from RNA interference (RNAi)?

A

CRISPR-Cas primarily targets DNA (including viral DNA), while RNAi primarily targets RNA molecules.

87
Q

What is the significance of the integration of viral DNA into the CRISPR region?

A

It serves as a “memory” of past infections, allowing the organism to recognize and defend against future infections by the same virus.

88
Q

What is the process by which CRISPR-Cas provides immunity against previously encountered viruses?

A

The system uses crRNAs derived from the integrated viral DNA to guide Cas proteins to degrade matching viral RNA or DNA upon re-infection.

89
Q

In what types of organisms is the CRISPR-Cas system found?

A

It is primarily found in prokaryotes, including bacteria and archaea.

90
Q

What is a CM column?

A

Carboxymethyl - neg charge column (cation exchange resin) they bind pos. charged polypeptides

91
Q

What is a DEAE column?

A

Diethyl aminoethyl - pos charge column (anion exchange resin) bind neg charged polypeptides

BIO230 Midterm (3 decks)

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