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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

(59 cards)

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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)

Study These Flashcards
A

Rho dependent or rho independent

25
Rho Dependent Termination (Prokaryotes)
Requires both cis and trans factors
26
Rho Independent Termination (Prokaryotes)
Does not require any trans- acting factors; depends only on the presence of certain sequences within the RNA
27
What does the Rho protein do in termination?
It associates to a C-rich region in the newly synthesized RNA, destabilizing the RNA-DNA hybrid, releasing RNA Pol and terminating transcription
28
Eukaryotic RNA synthesis
Requires multiple transcription factors
29
TATA box
A DNA sequence that indicates where a genetic sequence can be read and decoded; a type of promoter sequence
30
What is a promotor sequence?
DNA sequences that define where transcription of a gene by RNA polymerase begins
31
Eukaryotic Transcription
Occurs in three phases: 1. Initiation 2. Elongation 3. Termination
32
Initiation (Eukaryotes)
Multiple transcription factors are associated to the DNA template
33
Elongation (Eukaryotes)
CTD region remains hyperphosphorylated
34
Termination (Eukaryotes)
DNA template and trans-acting factors have signals; coupled with the processing of the 3' end poly A tail of mRNA
35
What does the CTD consist of?
A tandem heptad repeat with the consensus sequence tyrosine-serine-proline-threonine-serine-proline-serine
36
What does the CTD do?
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
Group 1 and Group 2 Introns
Both are self splicing
38
Group 1 Introns
Catalyze an intrastrand cleavage reaction that removes the intron and ligates the exonic sequences using exogenous guanosine cofactors
39
Group 2 Introns
Do not require exogenous nucleosides to initiation cleavage reactions; forms a lariat structure
40
Cis-acting Splicing
Intramolecular mechanism that removes introns and joins exons that are within the same RNA transcript
41
Trans-acting Splicing
Intermolecular mechanism that removes introns or outrons and joins the exons that are not within the same RNA
42
What does the spliceosome assembly pathway require?
snRNA (small nuclear RNA) nuclear export and snRNP nuclear import steps
43
Spliceosome Assembly
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
Spliceosome-Mediated Precursor mRNA Splicing
Consist of 2 esterification steps, which result in the release of an excised lariat intron and the correctly spliced exonic sequences
45
What does the 5' cap do?
Protects from 5' to 3' exonuclease
46
Step 1 of the 5' Capping Mechanism
The enzyme RTPase hydrolyzes the gamma phosphate on the 5' terminal nucleotide to generate diphosphate RNA (ppN-RNA)
47
Step 2 of the 5' Capping Mechanism
GTase adds a GMP moiety to the ppN-RNA to form GppN-RNA
48
Step 3 of the 5' Capping Mechanism
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
Polyadenylation of Eukaryotic mRNA
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
mRNA Decay
Regulated as a mechanism to control protein production
51
When can mRNA decay occur?
1.During transcription 2.Post-transcriptionally
52
Where does mRNA decay occur?
The cytoplasm
53
Why does mRNA occur?
To decrease the expression of a toxic protein To reduce the abundance of functional proteins by the half-life of their mRNA's
54
Alternative splicing
An alternative splicing process during gene expression that allows a single gene to code for multiple proteins
55
Dicer (RNAi Pathway)
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
RISC - RNA-Induced Silencing Complexes (RNAi Pathway)
Mediates the interaction between siRNA and the target mRNA; composed of ribonucleoproteins that can be programmed to target almost any gene for silencing
57
Micro RNA (miRNA)
Short ncRNAs that bind to mRNA and mediate gene silencing
58
What does micro RNA do?
Regulates a variety of cellular processes, such as apoptosis, proliferation, development, and differentiation
59
Prosha
An endoribonuclease that cleaves primary miRNA into precursor miRNA

SCH 325 Biochemistry (5 decks)

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