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MCB 450 > Class 9: RNA structure, Synthesis and Processing > Flashcards

Class 9: RNA structure, Synthesis and Processing Flashcards

1
Q

RNA synthesis differences from DNA synthesis

A

precursors are ribonuceloside tripjosphates

only one strand od DNA is used as template

RNA chains can be initiated de novo(no primer required)

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2
Q

antisense

A

RNA molecule will be complimentary to the DNA template

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3
Q

RNA polymerase

A

catalysts for RNA synthesis in the 5’ –> 3’ direction

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4
Q

uridine replaces ___in RNA synthesis

A

thymidine

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5
Q

Transfer RNA

A

15%

  • At least one specific type of tRNA for each of the 20 amino acids
  • adaptors between amino acids and the codons in mRNA
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6
Q

Ribosome RNA

A

80%

-structural and catalytic components of ribosomes.
-Facilitate the binding and positioning of the mRNA on the ribosomes

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7
Q

Messenger RNA

A

5%

  • Carry genetic information from DNA to cytosol
  • Template for protein synthesis
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8
Q

Requirements of RNA Polymerase

A
  1. Template
  2. Activated Precursors
  3. Divalent Metal Ions
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9
Q

3 steps in prokaryotic RNA synthesis

A
  1. Initiation
  2. Elongation
  3. Termination
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10
Q

Initiation

A

the recognition of a specific DNA sequence by RNA polymerase and the beginning of the bond formation

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11
Q

Elongation

A

RNA polymerase continues the binding, bond formation, and translocation cycle

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12
Q

Termination

A

The ends of the genes are recognized by the RNA polymerase complex (r-dependent and -independent)

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13
Q

Promoters

A

specific DNA sequences that direct RNA polymerase to the proper initiation site

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14
Q

sigma subunit of holoenzyme

A

helps the polymerase locate promoter sites

allows enzyme to rapidly scan DNA for promoter

once the promoter is found it disassociates from the enzyme to assist another polymerase in initiation

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15
Q

Elongation 2 features

A
  1. no primer required
  2. has helices activity (prokaryotic)
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16
Q

DNA topoisimerases 1 & 2

A

relax the supercoils

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17
Q

termination

A

The RNA polymerase stops moving on the DNA template. The RNA transcript falls off from the transcription complex

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18
Q

rho independent termination

A

intrinsic termination

  • RNA transcript forms a stable turn (semi-loop); RNA transcripts contain a string of U’s
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19
Q

rho dependent termination

A

factors bind to a C-rich region; contains helices activity (energy from ATP hydrolysis) unwind the 3’-end of the transcript from template; displace the DNA template strand

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20
Q

rifampin

A

inhibits intitiation, no effect on elongation

-blocks transcription initiation by biding to the polymerase on the DNA

21
Q

actinomycin D

A

intercalates between the bases of the DNA double helix, preventing the DNA from being used as a template

22
Q

@-amanitin

A

synthesized by the poisonous mushroom amanita phalloides. High specificity for eukaryotic RNA polymerase II

23
Q

intercalating agents

A

Several hydrophobic
molecules containing flat aromatic and fused
heterocyclic rings can insert between the stacked base pairs of DNA.

-Ethidium bromide,
Acridine orange,
Actinomycin D

24
Q

differences between prokaryotic and eukaryotic

A
  1. Chromatin remodeling
  2. Eukaryotic transcription factors bind to DNA and recruit RNA polymerase to the promoter
  3. Types of polymerase
  4. Transcription activators bind to the enhancer
  5. post-transcriptional modification of RNA
25
Q

RNA polymerase II

A

synthesis of the precursors of message RNAs and snRNA inhibited by @-amanitin

26
Q

TATA, CAAT, and GC boxes

A

boxes and other cis-acting elements in eukaryotic promoters are recognized by proteins other than RNA polymerase itself.

27
Q

enhancers

A

cis-acting elements that have no promoter activity of their own yet can exert their stimulatory actions over distances of several thousand base pairs.

are recognized by transcription activators or tissue specific transcription factors

28
Q

typical human protein-coding gene

A
29
Q

post transcriptional processing of rRNA

A

removal of external transcribed spacers and internal transcribed spacers

30
Q

posttransciptional modification of tRNA

A

cleavage, additions, modified nucleosides

31
Q

RNAse P

A

cleaves the 5’ end of pre-tRNAs

32
Q

ribozymes

A

catalytic RNA that function as enzymes and do not require proteins for catalysis

  • naturally occur with self-splicing introns and RNA encoded parasites
33
Q

possttranscriptional modification of mRNA

A
  1. 5’ Capping
  2. 3’ Addition of a poly-A tail (polyadenylation)
    3.REmoval of intron
34
Q

remove introns

A
  1. by precise endonucleolytic and cleavage and ligation reactions catalyzed by special splicing endonuclease and lieges activities (ribozyme)
  2. in two -step reactions carried out by spliceosomes
35
Q

splicing enzymes

A

small nuclear ribonucleoprotien particles (snRNPs), recognize the splice sequence

36
Q

splicing process

A
37
Q

systemic lupus erythematosus

A

autoimmune disease, producing antibodies targeting snRNPs

38
Q

Beta thalassemia

A

mutation at splicing sites (pGU –AGp) of the beta global mRNA resulting from single nucleotide substitution in an acceptor splice site

39
Q

non-coding RNA

A

an RNA molecule that functions without being translated into a protein

  • produce transcripts that. function directly as structural, catalytic, or regulatory RNA, rather than expressing mRNA that encode proteins
40
Q

housekeeping ncRNAs

A

are constitutively expressed and required for normal function and viability of cells

41
Q

regulatory ncRNAs

A

expressed only in certain stages of organism development or as a response to external stimuli. They can affect the expression of other genes at the level of transcription or translation

42
Q

siRNA

A

The precursor of siRNA is a perfectly complementary hairpin-shaped dsRNA originating from viral replication, from transcription of sense and antisense strands, and from the activity of RDR ssRNA. dsRNA is cleaved by DCL into siRNA duplexes. One strand, loaded into the RISC, guides RISC to target mRNA and directs its cleavage. siRNAs can also function to suppress gene expression through a transcription-mediated pathway: transcriptional gene silencing (TGS) acting on DNA methylatio

43
Q

primary-mRNA

A

pri-miRNA transcript contains imperfect foldbacks and is produced by RNA polymerase II from a miRNA gene. pri-miRNA is subsequently cleaved by DCL producing in succession a pre-miRNA and miRNA/miRNA*. The guide miRNA strand, incorporated into RISC complex, directs RISC to target mRNA, leading to mRNA degradation and/or its translation inhibition.

44
Q

siRNA

A

double strand RNA perfectly matched, only targets at mRNA (coding region)

a natural antiviral defense in plants, fungi, and invertebrates

45
Q

microRNA

A

single strand RNA some matched, more that one target non-coding region (3’UTR)

a mechanism for regulation of gene expression

46
Q

degradation of mRNA paathways

A
  1. mRNAs that are not engaged in translation are subject to degradation

2.is important in the regulation of gene expression

47
Q

nonsense mediated decay

A

detects and degrades
transcripts that contain premature termination codons.

48
Q

non stop decay

A

NSD targets mRNAs that lack a stop codon by facilitating the release of ribosome.

MCB 450 (11 decks)

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