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SCH 325 Biochemistry > Ch. 21: RNA Synthesis, Processing, and Gene Silencing > Flashcards

Ch. 21: RNA Synthesis, Processing, and Gene Silencing Flashcards

1
Q

RNA

A

A biochemical polymer that consists of 4 nucleotides: A, U, C, G

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2
Q

Which nucleotide is present in DNA and not RNA?

A

Thymine

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3
Q

What type of structure does RNA prefer?

A

Secondary structure

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4
Q

What kind of bonds can RNA make?

A
  1. RNA can bind to itself: RNA:RNA
  2. RNA can base pair with DNA to make RNA-DNA hybrids (Important in translation)
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5
Q

What are the three main types of RNA?

A
  1. mRNA
  2. tRNA
  3. rRNA
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6
Q

What is mRNA?

A

mRNA is messenger RNA (aka carrier RNA)

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7
Q

What is the role of mRNA?

A

To carry protein information from the DNA in a cell’s nucleus to the cell’s cytoplasm

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8
Q

What is rRNA?

A

rRNA is ribosomal RNA, and it is the major constituent of ribosomes

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9
Q

What is tRNA?

A

tRNA is transfer RNA, and it is the adaptor molecules that connects transcription to translation

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10
Q

What is the role of tRNA?

A

It serves as an adaptor between the genetic instructions written in nucleic acid sequences and the protein products encoded in genes.

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11
Q

What are the coding portions of DNA?

A

Exons

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12
Q

What are the NON-coding regions of DNA?

A

Introns

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13
Q

What are introns?

A

Sequences that interrupt RNA that must be removed from the precursor mRNA for transcription and translation to occur

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14
Q

Splicesomes

A

Huge, multimegadalton ribonucleoprotein (RNP) complexes found in eukaryotic nuclei

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15
Q

Where do splicesomes assemble?

A

On the RNA Pol III transcripts, where they excise introns and splice together exons

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16
Q

Is the coding sequencing continuous or discontinuous?

A

Discontinuous

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17
Q

In eukaryotic mRNA processing, what happens to the 5’ and 3’ ends?

A
  1. The 5’ end is capped with 7-methyl-guanylate (5’ cap)
  2. The 3’ end is extended by a poly A tail
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18
Q

What direction does mRNA synthesis occur?

A

5’ to 3’ direction

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19
Q

What does RNA polymerase do?

A

It unwinds DNA during the synthesis of RNA to create a transcription bubble that contains the enzyme and an RNA:DNA hybrid that is 8 base pairs long

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20
Q

What is used as a template for the synthesis of a complementary strand of DNA?

A

A single strand of DNA

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21
Q

Prokaryotic Transcription

A

Occurs in 3 phases:
1. Initiation
2. Elongation
3. Termination

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22
Q

Initiation (Prokaryotes)

A

Binding of the RNA polymerase to the sigma factor

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23
Q

Elongation (Prokaryotes)

A

Dissociation of the Rho factor from RNA polymerase complex; RNA-DNA helix separates; involves Mg ions

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24
Q

Termination (Prokaryotes)

A

Rho dependent or rho independent

25
Q

Rho Dependent Termination (Prokaryotes)

A

Requires both cis and trans factors

26
Q

Rho Independent Termination (Prokaryotes)

A

Does not require any trans- acting factors; depends only on the presence of certain sequences within the RNA

27
Q

What does the Rho protein do in termination?

A

It associates to a C-rich region in the newly synthesized RNA, destabilizing the RNA-DNA hybrid, releasing RNA Pol and terminating transcription

28
Q

Eukaryotic RNA synthesis

A

Requires multiple transcription factors

29
Q

TATA box

A

A DNA sequence that indicates where a genetic sequence can be read and decoded; a type of promoter sequence

30
Q

What is a promotor sequence?

A

DNA sequences that define where transcription of a gene by RNA polymerase begins

31
Q

Eukaryotic Transcription

A

Occurs in three phases:
1. Initiation
2. Elongation
3. Termination

32
Q

Initiation (Eukaryotes)

A

Multiple transcription factors are associated to the DNA template

33
Q

Elongation (Eukaryotes)

A

CTD region remains hyperphosphorylated

34
Q

Termination (Eukaryotes)

A

DNA template and trans-acting factors have signals; coupled with the processing of the 3’ end poly A tail of mRNA

35
Q

What does the CTD consist of?

A

A tandem heptad repeat with the consensus sequence tyrosine-serine-proline-threonine-serine-proline-serine

36
Q

What does the CTD do?

A

Forms a flexible, tail-like extension from the catalytic core of Pol II with regions that are proximal and distal to the Pol II surface

37
Q

Group 1 and Group 2 Introns

A

Both are self splicing

38
Q

Group 1 Introns

A

Catalyze an intrastrand cleavage reaction that removes the intron and ligates the exonic sequences using exogenous guanosine cofactors

39
Q

Group 2 Introns

A

Do not require exogenous nucleosides to initiation cleavage reactions; forms a lariat structure

40
Q

Cis-acting Splicing

A

Intramolecular mechanism that removes introns and joins exons that are within the same RNA transcript

41
Q

Trans-acting Splicing

A

Intermolecular mechanism that removes introns or outrons and joins the exons that are not within the same RNA

42
Q

What does the spliceosome assembly pathway require?

A

snRNA (small nuclear RNA) nuclear export and snRNP nuclear import steps

43
Q

Spliceosome Assembly

A

Primary snRNA transcript is capped at the 5’ end, exported to the cytoplasm, assembled into a core snRNP complex containing 7 sm proteins, then imported back into the nucleus, where a functional splicesome complex is generated

44
Q

Spliceosome-Mediated Precursor mRNA Splicing

A

Consist of 2 esterification steps, which result in the release of an excised lariat intron and the correctly spliced exonic sequences

45
Q

What does the 5’ cap do?

A

Protects from 5’ to 3’ exonuclease

46
Q

Step 1 of the 5’ Capping Mechanism

A

The enzyme RTPase hydrolyzes the gamma phosphate on the 5’ terminal nucleotide to generate diphosphate RNA (ppN-RNA)

47
Q

Step 2 of the 5’ Capping Mechanism

A

GTase adds a GMP moiety to the ppN-RNA to form GppN-RNA

48
Q

Step 3 of the 5’ Capping Mechanism

A

Guanine-N7 methyltransferase (N7MTase) transfers a methyl group from 5-adenosyl-methionine (Adomet) to the guanine to form 7-methyl-GpppNRNA and release 5-adenosyl-1-homocysteine (AdoHcy)

49
Q

Polyadenylation of Eukaryotic mRNA

A

In a coupled process, the poly A signal AAUAAA is bound by the cleavage and polyadenylation specificity factor (CPSF); CStF, cleavage stimulation factor, cleavage factors: CFI and CFII
Binds to poly (A) polymerase (PAP), which synthesizes the poly A tail

50
Q

mRNA Decay

A

Regulated as a mechanism to control protein production

51
Q

When can mRNA decay occur?

A

1.During transcription
2.Post-transcriptionally

52
Q

Where does mRNA decay occur?

A

The cytoplasm

53
Q

Why does mRNA occur?

A

To decrease the expression of a toxic protein
To reduce the abundance of functional proteins by the half-life of their mRNA’s

54
Q

Alternative splicing

A

An alternative splicing process during gene expression that allows a single gene to code for multiple proteins

55
Q

Dicer (RNAi Pathway)

A

Cleaves any dsRNA RNA template regardless of the presence of non-canonical base pairing or minor deviations in duplex structure; proceeds siRNA assembled into RISC

56
Q

RISC - RNA-Induced Silencing Complexes (RNAi Pathway)

A

Mediates the interaction between siRNA and the target mRNA; composed of ribonucleoproteins that can be programmed to target almost any gene for silencing

57
Q

Micro RNA (miRNA)

A

Short ncRNAs that bind to mRNA and mediate gene silencing

58
Q

What does micro RNA do?

A

Regulates a variety of cellular processes, such as apoptosis, proliferation, development, and differentiation

59
Q

Prosha

A

An endoribonuclease that cleaves primary miRNA into precursor miRNA

SCH 325 Biochemistry (5 decks)

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