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BIOCHEM 2 > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

1
Q

What does the unit symbol “S” represent?

A

Svedberg Unit (sedimentation coefficient) is a measure of how fast a particle of a certain mass, size, and density will sediment in a centrifuge.

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2
Q

Is there an absolute relationship between the mass of a particle and the value of “S” that is measured?

A

No, there are also factors such as shape and density of the particle that affect the sedimentation coefficient. For example, a large less dense particle may sediment slower than a small more dense particle.

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3
Q

Transcription

A

is the process where DNA is converted to RNA in order to be used for protein synthesis.

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4
Q

mRNA

A

carries the genetic information from DNA to the ribosomes for protein synthesis.

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5
Q

transfer RNA (tRNA)

A

delivers amino acid to the ribosome.

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6
Q

ribosomal RNA (rRNA)

A

forms the catalytic core of the ribosome.

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7
Q

small nuclear RNA (snRNAs)

A

RNA that are involved in splicing.

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8
Q

guide RNA

A

bind to specific ribonucleoprotein complexes and facilitate catalysis.

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9
Q

XIST

A

is a long non-coding RNA that resemble an mRNA but does not code for protein.

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10
Q

Barr Body

A

dense inactive X-chromosome found in nuclei of somatic cells in female mammals.

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11
Q

RNA vs. DNA sugar

A

DNA: deoxyribose
RNA: ribose

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12
Q

RNA vs. DNA sugar conformation

A

DNA: deoxyribose favors C2’ endo conformation.
RNA: ribose favors C3’ endo conformation due to extra hydroxyl group.

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13
Q

RNA vs. DNA preferred form in double stranded form

A

DNA: B-form
RNA: A-form

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14
Q

What are the major secondary structures of RNA?

A

stem, hairpin loop, pseudoknot, bulge, internal loop, and multiloop.

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15
Q

Housekeeping Genes

A

genes that are expressed at relatively constant levels throughout the cell cycle and play a critical role in cellular metabolism.

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16
Q

Constitutive Expression

A

genes that are transcribed at constant levels throughout the life of the cell.

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17
Q

Transcriptome

A

is the sum total of all RNA molecules made by an organism.

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18
Q

Promoter

A

is a DNA sequence located upstream of a gene and controls initiation of transcription.

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19
Q

Positive Control Elements

A

binding sites for activator proteins.

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20
Q

Transcription Ground State

A

is the activity of promoters in the absence of specific regulatory sequences.

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21
Q

Prokaryotic Transcription Ground State

A

promoters and associated proteins are generally active even in the absence of activator proteins.

Genomes are compact and lack the complex regulatory mechanisms.

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22
Q

Eukaryotic Transcription Ground State

A

promoters and associated proteins are generally inactive in the absence of regulatory proteins.

Access to promoters is restricted by chromatin.

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23
Q

Transcriptome vs. Genome

A

Transcriptome more selective.

Entire genome is copied exactly once, different variations in the composition of the transcriptome.

Genome long lived, transcriptome short life.

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24
Q

Chemical Mechanism of RNA Biosynthesis

A

IMAGE IN STUDY GUIDE LOOK

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25
Q

What is the nucleophile in the RNA biosynthesis?

A

3’-OH of the growing RNA chain

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26
Q

What is the electrophile in the RNA biosynthesis?

A

first phosphate of incoming nucleotide.

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27
Q

What is the leaving group in the RNA biosynthesis?

A

Inorganic pyrophosphate

28
Q

What is the energy that drives the reaction forward in RNA biosynthesis?

A

the hydrolysis of the high energy phosphate bonds on the incoming nucleotide.

29
Q

Initiation Step of Transcription

A
  1. RNA Polymerase binds to promoter, this leads to the closed complex.
  2. Partial unwinding of DNA leads to the open complex.
  3. Conformational change allows transcription to start.
30
Q

TATA BOX

A

regulates transcription of a nearby gene, is a conserved DNA sequence located at the promoter region of eukaryotic genes.

31
Q

What does the TATA box bind to?

A

The TATA box binds to the TATA box binding protein to form pre-initiation complex.

32
Q

What happens to genes that do not have a TATA box?

A

Uses a protein TAF to bring TBP to the DNA.

33
Q

What happens to the sigma subunit during initiation?

A

sigma dissociates from RNA polymerase before elongation happens.

NusA binds competitively to the polymerase and remains bound until transcription is complete.

34
Q

Elongation Step of Transcription

A

RNA polymerase moves away from the promoter and forms the elongation complex.

35
Q

Does RNA Polymerase have high processivity?

A

Yes, a single RNA polymerase will transcribe an entire gene without dissociating.

36
Q

What are the two mechanisms that RNA Polymerases use for proofreading?

A

Kinetic Proofreading and Pyrophosphorolysis.

37
Q

What is kinetic proofreading?

A

The RNA polymerase moves much slower if wrong nucleotide has been incorporated into a base pair.
Nuc: water, Product: NMP

38
Q

What is pyrophosphorolysis?

A

cleavage of the nucleotide
Nuc: PPi, Product: NTP

39
Q

What are the two different types of termination in transcription?

A

Protein Independent Mechanism and Protein Dependent Mechanism

40
Q

What is the protein independent mechanism?

A

Termination sequence includes a segment of nucleotides that are self complementary and will fold into a hairpin structure.

HAIRPIN and Weak A/U base pairs in RNA cause the DNA and RNA to fully dissociate.

41
Q

What is the protein dependent mechanism?

A

involves the use of a rho protein.
A stem-loop causes RNA polymerase to pause. Rho protein catches up to the open complex and separates the RNA-DNA hybrid.

42
Q

Why do we need a rho protein in protein dependent mechanism?

A

Termination site lacks the AAA which causes the RNA-DNA hybrid to be more tightly associated which requires the rho protein.

43
Q

RNA Polymerase Enzyme: what is it composed of?

A

complex of proteins made of core enzyme and sigma factor.

44
Q

Alpha subunit of RNA Polymerase

A

promote assembly and binding to upstream elements.

45
Q

Beta subunit of RNA Polymerase

A

carries the active site of the enzyme.

46
Q

Beta Prime subunit of RNA Polymerase

A

binding to DNA.

47
Q

Sigma subunit of RNA Polymerase

A

binds to the promoter sequences

48
Q

What is the motif of the sigma subunit?

A

helix-turn-helix motif

49
Q

What is the difference between prokaryotic and eukaryotic RNA Polymerase?

A

Prokaryotes has a single RNA polymerase that transcribes all types of genes.

Eukaryotes have multiple RNA polymerases that are specialized for different types of genes.

50
Q

In the absence of proofreading, how will the correct nucleotide be incorporated?

A

Active site of the RNA polymerase plays a role in proofreading. The active site allows one nucleotide at a time.

Only the correct nucleotide fits well in the binding pocket.

51
Q

Conserved Sequences

A

sequences that are shared between many different transcripts.

52
Q

Inverted Repeat Sequences

A

when the nucleotide sequence on one strand is the reverse complement of the sequence on the other strand.

53
Q

What are transcription factors?

A

proteins that help to express a specific set of genes by assisting in the process of RNA polymerase binding to the DNA.

54
Q

How are transcription factors named?

A

named by the RNA polymerase they are associated with.

55
Q

What are activator proteins?

A

allow transcription to happen.

56
Q

What are some of the ways in which the activator protein allows transcription to happen?

A
  1. favor opening of DNA.
  2. Induce allosteric changes in the RNA polymerase that favor transition to the open state.
  3. Binds to the RNA polymerase and the DNA at a site next to the promoter, increases affinity of the polymerase for the promoter.
57
Q

What are repressor proteins?

A

prevent transcription from happening

58
Q

What are the mechanisms in which repressor protein prevents transcription from happening?

A
  1. Blocks promoter accessibility: bind to repressor sequence that overlap the promoter sequence. Create steric block that prevents RNA Polymerase from binding.
  2. Allosteric Mechanism: they bind to sequences that are close but not overlapping the promoter. Prevents opening of the DNA required for transcription.
59
Q

What are architectural regulator proteins?

A

proteins that bind to DNA and facilitate the process of looping.

60
Q

What are enhancers?

A

proteins that bind to distal regulatory sites.

61
Q

Insulators

A

limit the looping

62
Q

What is the CTC binding protein?

A

structurally bringing everything together for transcription to happen.

63
Q

RNA Polymerase II CTD

A

plays a crucial role in transcription, initiation, elongation, and mRNA processing.

64
Q

What are the post-translational modifications and structural alterations that are used to regulate RNA metabolism through the tail sequence of RNA Polymerase II?

A
  1. 2nd and 5th serine subject to phosphorylation
  2. phosphorylation of tyrosine
  3. Cis/Trans isomerization of two prolines.
65
Q

What is the mediator complex?

A

essential for transcriptional regulation in eukaryotic cells.

BIOCHEM 2 (17 decks)

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