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Biochemistry 2 > RNA Metabolism > Flashcards

RNA Metabolism Flashcards

1
Q

What has greater structural diversity: DNA or RNA?

A

RNA

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2
Q

What process makes RNA?

A

transcription of DNA

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3
Q

What are the 3 major types of RNA?

A

mRNA
rRNA
tRNA

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4
Q

mRNA

A

messenger RNA
carries info from DNA

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5
Q

rRNA

A

ribosomal RNA
makes ribosome that makes protein

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6
Q

tRNA

A

transfer RNA
translates mRNA into amino acids

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7
Q

siRNA

A

small interfering RNA
block gene expression by increasing mRNA breakdown and decrease in protein
made synthetically

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8
Q

miRNA

A

microRNA
regulate mRNA
suppress translation
come from other RNA

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9
Q

snRNA

A

small nuclear RNA
helps process mRNA

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10
Q

snoRNA

A

small nucleolar RNA
helps process rRNA

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11
Q

How is RNA synthesis similar to DNA synthesis?

A

same fundamental mechanism
same direction
uses a template

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12
Q

How is RNA synthesis different from DNA synthesis?

A

no primer required
only copies small sections at a time
only 1 strand is a template strand

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13
Q

RNA Polymerase

A

makes RNA and binds to promoter region in DNA

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14
Q

RNA synthesis makes more errors than DNA synthesis. Why is this not as detrimental?

A

more copies of RNA and higher turnover

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15
Q

What do the magnesium ions in RNA synthesis do?

A

one stabilizes the deprotonated 3’ OH
one coordinates incoming nucleotide

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16
Q

DNA bubble

A

about 17 base pairs of DNA where active replication is ongoing

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17
Q

What do promoters signal?

A

start point
level of expression
template strand

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18
Q

sigma factor

A

determines the promotor to bind to

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19
Q

sigma subunits

A

bind to different promoters
used under different conditions

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20
Q

In DNA dependent synthesis, RNA polymerase and sigma factor bind together and then to what?

A

The promotor

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21
Q

What opens the complex to start transcription in DNA dependent synthesis?

A

DNA bubble

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22
Q

In the elongation phase of DNA dependent synthesis, sigma factor dissociates. What binds in its place?

A

NusA

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23
Q

Can RNA polymerase be resused?

A

yes

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24
Q

cAMP receptor protein

A

activator; turns on genes that metabolize non-glucose sugars

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25
Q

Lac Repressor

A

shuts off genes that metabolize lactose

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26
Q

Protein regulation starts with?

A

RNA regulation

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27
Q

Rho independent termination

A

palindrome causes a hairpin to form
multi-A sequence causes RNA polymerase to pause
RNA breaks H bonds and leaves the polymerase

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28
Q

Rho dependent termination

A

rho helicase binds to rho utilization sequence and moves along the RNA strand
separates RNA from DNA to allow RNA to leave
requires ATP

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29
Q

RNA Polymerase 1 (eukaryotes)

A

makes pre-rRNA

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30
Q

RNA Polymerase 2 (eukaryotes)

A

makes pre-mRNA and some specialized
uses proteins, enzymes, and transcription factors
major promotor: TATA box
conserved and have well-defined function

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31
Q

RNA Polymerase 3 (eukaryotes)

A

makes pre-tRNA and some specialized

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32
Q

TF2F

A

gives specificity

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33
Q

TF2B

A

recruits TATA binding protein and TF2F

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34
Q

TF2E

A

helicase that opens the bubble

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35
Q

TF2H

A

kinase that phosphorylates the C terminal domain

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36
Q

Actinomycin D

A

targets RNA polymerase as a drug
antibiotic/anticancer

37
Q

Rifampicin

A

targets RNA polymerase as a drug
antibiotic used in TB treatment

38
Q

Amanitin

A

mushroom toxin selective for eukaryotes

39
Q

primary transcript

A

newly made RNA

40
Q

What does RNA Splicing remove?

A

introns

41
Q

During RNA processing, mRNA is given what two things?

A

a 5’ cap and a 3’ poly A tail

42
Q

What kind of bond is the 5’ cap ?

A

5’-5’ phosphodiester bond

43
Q

What is the purpose of the 5’ cap?

A

to protect mRNA from degradation and help it bind to the ribosome

44
Q

When does capping occur?

A

When RNA is being made

45
Q

S-adenosyl-methionine (SAM)

A

methylates the terminal G and first few ribonucleotides in mRNA capping

46
Q

How many adenosines does the poly A tail have?

A

80-250

47
Q

In eukaryotes why is the poly A tail good?

A

serves as a binding site for proteins; prevents degradation

48
Q

differential RNA processing allows a single gene to?

A

make multiple products

49
Q

Multiple processing sites allows the cell type and environmental factors to?

A

determine the product

50
Q

What does rRNA start as?

A

pre-rRNA

51
Q

Which contains the 16s rRNA? The 18s?

A

16- bacteria
18- eukaryotes

52
Q

Rnase D

A

removes from the 3’ end

53
Q

Rnase P

A

removes from the 5’ end

54
Q

All tRNA’s have 3’ terminal with the sequence?

A

CCA

55
Q

Where do snoRNAs come from?

A

introns of other RNAs

56
Q

Where do snRNAs come from?

A

larger pre-snRNAs

57
Q

pri-miRNA is cleaved to?

A

pre-miRNA

58
Q

pre-miRNA is cleaved to miRNA by what?

A

dicer and helicase

59
Q

4 classes of introns

A
  1. self-splicing, G nucleophile
  2. self-splicing, A nucleophile
  3. Spliceosome Catalyzed
  4. Endonuclease Catalyzed
60
Q

Self-splicing, G nucleophile

A

splicing occurs via 2 transesterifications
3’ OH of an external G acts as a nucleophile and breaks the strand
3’ OH of the new end attacks the 3’ end of the intron and removes it

61
Q

Self-Splicing, A nucleophile

A

splicing occurs via 2 transesterifications
2’ OH of an internal A acts as a nucleophile and attacks the 5’ end of the intron
3’ OH of the new terminus attacks the 3’ end of the intron cutting it out

62
Q

Spliceosome

A

has snRNPs
2’ OH attacks 5’ end
3’ OH attacks 3’ end

63
Q

In Group 3 RNA Processing what do the introns contain?

A

GU at 5’ end
AG at 3’ end

64
Q

Endonuclease

A

used mostly in tRNA
needs ATP
cleaves the backbone at both ends of the intron

65
Q

What is the main indicator of gene expression?

A

[mRNA]

66
Q

What is the degradation rate for vertebrates? Bacteria?

A

Vertebrates- 3hrs
bacteria- 1.5 min

67
Q

What is mRNA degraded by?

A

ribonucleases

68
Q

Reverse transcriptase makes DNA from?

A

RNA

69
Q

Retroviruses

A

incorporate their genome into the host
have a high error rate and high mutation rate

70
Q

gag

A

viral structural proteins

71
Q

pol

A

encodes reverse transcriptase, integrase, and protease

72
Q

env

A

envelope proteins

73
Q

What 3 reactions does reverse transcriptase catalyze?

A
  1. DNA synthesis from viral RNA
  2. Degradation of viral RNA
  3. Complimentary strand synthesis
74
Q

How does the double stranded DNA get inserted into the host?

A

with an integrase

75
Q

HIV

A

lentivirus
its reverse transcriptase has a high error rate and fast mutations
leads to drug resistances

76
Q

Why can’t we make a vaccine to HIV?

A

the envelope changes

77
Q

Dolutegravir

A

integrase inhibitor

78
Q

Zidovudine

A

nucleotide reverse transcriptase inhibitors

79
Q

Efavirenz

A

NNRTI

80
Q

Telomeres

A

made of TG repeats
protects ends of chromosomes
require a special enzyme to maintain their length

81
Q

Telomerase

A

acts as reverse transcriptase; carries its own template;

82
Q

T loop

A

TG strand inserts itself back into the double helix

83
Q

Telomerase activity can enhance?

A

the ability of cells to continue to divide

84
Q

Telomere length in fibroblast cells is inversely proportional to?

A

the age of the person they came from

85
Q

Do somatic cells have telomerase activity?

A

no

86
Q

Transcription

A

DNA -> RNA

87
Q

Translation

A

RNA->Protein

88
Q

Reverse Transcription

A

RNA -> DNA

Biochemistry 2 (11 decks)

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